C57BL/6, often referred to as "C57 black 6" or just "black 6" is a common inbred strain of lab mouse. It is probably the most widely used "genetic background" for genetically modifed mice for use as models of human disease. They are the most widely used lab mouse strain, due to the availability of congenic strains, easy breeding, robustness, and their relationship to GM models, making them ideal controls.
Dark brown, nearly black, coat. Easily irritable temperament. They have a tendency to bite, and cannot be handled like a typical pet mouse or even more docile laboratory strains such as BALB/c.
C57BL/6 mice which are group-housed also display barbering behavior, in which the dominant mouse in a cage selectively removes hair from its subordinate cage mates. Mice that have been barbered have large bald patches on their bodies, commonly around the head, snout, and shoulders, although barbering may appear anywhere on the body. Both hair and vibrissae may be removed. Barbering is more frequently seen in female mice; male mice are more likely to display dominance through fighting.[1]
C57BL/6 as a "Th1 responder"
C57BL/6 has certain immunophenotypes that distinguish it from other inbred strains like BALB/c. For example the immunological response to the same pathogen in C57BL/6 mice is often of an opposite spectrum compared to BALBb/c mice, namely C57BL/6 shows Th1 and BALB/c shows Th2 response in response to intracellular pathogen Leishmania major, where a Th1 response results in a resistant ie healer phenotype (since the pathogen is intracellular), whereas a Th2 response results in a susceptible (nonhealer) phenotype.[citation needed]
Though this trait had been observed in these two strains since 1988, in an article published in 2000 by Mills et al.[2] these observations were systematized and generalized to other strains of mice. Even without biasing towards Th1 or Th2 by priming through infection, the strains differ in their macrophages' ability to be activated, as measured from their arginine metabolic programs when stimulated by Interferon gamma or LPS or both:
* M-1 macrophages from typical Th1 responders: C57BL/6 or B10.D2 mice, preferentially produce NO by action of iNOS
* M-2 macrophages from typical Th2 responders: DBA or BALB/c mice, preferentially produce ornithine and urea by action of arginase.
Showing posts with label Laboratory medicine/Immunology. Show all posts
Showing posts with label Laboratory medicine/Immunology. Show all posts
Wednesday, December 10, 2008
Rules and Guidelines for Nomenclature of Mouse and Rat Strains
Revised: July 2007
International Committee on Standardized Genetic Nomenclature for Mice
Chairperson: Dr. Janan T. Eppig
(e-mail: jte@informatics.jax.org)
Rat Genome and Nomenclature Committee
Chairperson: Dr. Goran Levan
(e-mail: Goran.Levan@gen.gu.se)
In 2001, the International Committee on Standardized Nomenclature for Mice and the Rat Genome and Nomenclature Committee agreed to establish a joint set of rules for strain nomenclature, applicable to strains of both species. These rewritten guidelines reflect this collaboration, in addition to documenting new and revised rules for the naming of strains. This document is updated annually by the international nomenclature committees for mouse and rat.
Reference to former versions of the rules for mouse strain nomenclature can be found in Snell (1941), Committee for Standardized Genetic Nomenclature in Mice (1952, 1960, 1976, 1981, 1989, 1996), Festing (1979, 1993), Staats (1986), Maltais et al. (1997). The November 2006 revision is available here. Reference to former rules for rat strain nomenclature can be found in Committee on Rat Nomenclature (1992).
Current nomenclature rules for naming genes are available online at:
For mouse: http://www.informatics.jax.org/mgihome/nomen/gene.shtml#genenom
For rat: http://rgd.mcw.edu/nomen_rules.html
Table of Contents
1. Introduction
1.1 Mice
1.2 Rats
2. Laboratory codes
3. Inbred Strains and Hybrids
3.1 Definition
3.2 Nomenclature of Inbred Strains
3.3 Indication of Inbreeding
3.4 Substrains
3.5 Hybrids
4. Strains Made from Multiple Inbred Strains
4.1 Recombinant Inbred Strains
4.2 Mixed Inbred Strains
4.3 Recombinant Congenic Strains
4.4 Advanced Intercross Lines
5. Coisogenic, Congenic, and Segregating Inbred Strains
5.1 Coisogenic Strains
5.2 Congenic Strains
5.3 Consomic Strains
5.4 Segregating Inbred Strains
5.5 Conplastic Strains
6. Outbreds and Closed Colonies
6.1 Outbreds
6.2 Closed Colonies 7. References
1. Introduction
Mice and rats used in the laboratory derive from a variety of sources. Production of inbred strains means that these backgrounds can be defined and thus require nomenclature conventions. It should be borne in mind that genetic drift means that there may still be unknown genetic differences between individuals within strains.
1.1 Mice
Most laboratory mice have contributions from both Mus musculus musculus and Mus musculus domesticus. There is evidence that smaller contributions also may have come from Mus musculus molossinus and Mus musculus castaneus. Therefore, they should not be referred to by species name, but rather as laboratory mice or by use of a specific strain or stock name. (In addition, some recently developed laboratory mouse strains are derived wholly from other Mus species or other subspecies, such as M. spretus).
Mouse strain names should be registered through the Mouse Genome Database (MGD) at http://www.informatics.jax.org/mgihome/submissions/submissions_menu.shtml.
1.2 Rats
Laboratory rat strains derive from the Rattus norvegicus species. Another species, Rattus rattus, also is used as an experimental model, but has not contributed to the common laboratory rat strains.
Rat strain names should be registered through the Rat Genome Database (RGD) at http://rgd.mcw.edu.
2. Laboratory codes
A key feature of mouse and rat nomenclature is the Laboratory Registration Code or Laboratory code, which is a code of usually three to four letters (first letter uppercase, followed by all lowercase) that identifies a particular institute, laboratory, or investigator that produced, and may hold stocks of, a mouse or rat strain. Substrains should be identified by Laboratory codes, as should congenic and other strains where several different forms exist that are not otherwise distinguishable. Laboratory codes are assigned by the Institute of Laboratory Animal Research (ILAR) (http://dels.nas.edu/ilar_n/ilarhome/search_lc.shtml).
Examples of Laboratory codes are:
J The Jackson Laboratory
Rl W.L. and L.B. Russell
Jr John Rapp
Mcw Medical College of Wisconsin
Kyo Kyoto University
3. Inbred Strains and Hybrids
3.1 Definition
Strains can be termed inbred if they have been mated brother x sister for 20 or more consecutive generations, and individuals of the strain can be traced to a single ancestral pair at the 20th or subsequent generation. At this point the individuals' genomes will on average have only 0.01 residual heterozygosity (excluding any genetic drift) and can be regarded for most purposes as genetically identical. Inbred strains must be continuously mated brother x sister (or equivalent) thereafter
Other breeding schemes can be used to produce inbred strains; consecutive parent x offspring mating may be used, provided that the younger of the parents is always used (i.e., the offspring that is mated to parent is subsequently mated to its offspring). Other breeding schemes are acceptable provided that the inbreeding is equivalent to 20 successive generations of sib mating (Green 1981).
3.2 Nomenclature of Inbred Strains
An inbred strain should be designated by a unique brief symbol made up of uppercase, roman, letters, or a combination of letters and numbers beginning with a letter. (Note that some pre-existing strains do not follow this convention; e.g., mouse strain 129P1/J)
Care should be taken that mouse and rat strains do not overlap in strain designations. (Note: a few historical examples exist of similar mouse and rat strain designations and these are allowed to stand, with their substrain designations identifying them as unique).
Inbred strains that have a common origin, but are separated before F20 are related inbred strains, and symbols should reflect this relationship.
Examples:
Mouse strains: NZB, NZC, NZO
Rat strains: SR, SS
3.3 Indication of Inbreeding
The number of brother x sister inbreeding generations can be indicated, if necessary, by addition in parentheses of F followed by the number of generations.
Example:
Rat strain: ACI/N (F159)
If there is not information as to the total number of generations, but a minimum number of recent inbreeding generations is known, this can be shown by a question mark + the known number of subsequent generations of inbreeding.
Example:
Mouse strain: C3H/HeJ-ruf (F?+25)
3.4 Substrains
Established inbred strains may genetically diverge with time into substrains, due to a number of circumstances:
* If two branches are separated after 20 but before 40 generations of inbreeding there still will be enough residual heterozygosity that two genetically different substrains will result (Green 1981).
* If branches are separated for more than 20 generations from a common ancestor, it is likely that genetic variation between the branches will have occurred by mutation and genetic drift.
* If genetic differences are proven by genetic analysis to have occurred between branches.
Substrains are given the root symbol of the original strain, followed by a forward slash and a substrain designation. The designation is usually the Laboratory code of the individual or laboratory originating the strain.
Examples:
IS/Kyo Substrain of IS rat strain originating at Kyoto University.
A/He Substrain of A mouse strain originating from Walter Heston.
If a laboratory originates more than one substrain, serial numbers should be added to the Laboratory code.
Example:
Mouse strains: FL/1Re, FL/2Re
(Note that historical exceptions to this rule exist; for example, in mouse, BALB/c is not a substrain, DBA/1 and DBA/2 are separate strains and are not substrains.)
Substrains may give rise to further substrains by continued maintenance by a different investigator or through establishment of a new colony. In addition, substrains arise if demonstrable genetic differences from the original substrain are discovered. In either case, further substrain designations are added, without the addition of another slash.
Examples:
C3H/HeH Mouse substrain derived at Harwell (H) from the Heston (He) substrain of C3H.
SR/JrIpcv Rat substrain derived at Institute of Physiology, Czech Academy of Sciences (Ipcv) from the John Rapp (Jr) substrain of SR
Laboratory codes should be accumulated because genetic differences will accumulate with time, the rate depending to some extent on varying levels of quality control at the facilities that have housed and bred the strain or substrain. Organizations distributing mice and rats should include the number of generations the strain has been separated from the parent strain in the information they provide regarding the strain. Strain names can be abbreviated in publications after the first mention of the full proper designation.
3.5 Hybrids
Mice or rats that are the progeny of two inbred strains, crossed in the same direction, are genetically identical, and can be designated using uppercase abbreviations of the two parents (maternal strain listed first), followed by F1. Note that reciprocal F1 hybrids are not genetically identical, and their designations are, therefore, different.
Examples:
D2B6F1 Mouse that is the offspring of a DBA/2 mother and C57BL6/J father. A full F1 designation is (DBA/2N x C57BL/6J)F1.
B6D2F1 Mouse that is the offspring of the reciprocal cross. A full F1 designation is (C57BL/6J x DBA/2N)F1.
CB1BD22F1 Mouse that is the offspring of two recombinant inbred strains, a CXB1 mother and BXD22 father; full F1 designation is (CXB1/ByJ x BXD22/TyJ)F1.
Further crosses produce offspring that are no longer genetically identical, but it may still be appropriate to give them designations reflecting their parentage, similar to those for F1 hybrids.
Examples:
D2B6F2 are offspring of a D2B6F1 intercross.
B6(D2AKRF1) are offspring of a (DBA/2 x AKR/J)F1 male backcrossed to a C57BL/6J female.
In all the above cases, for clarity, the full strain symbols should be given in any publication when the hybrids or crosses are first referred to. If a hybrid is constructed using a substrain known to differ from the "standard" strain genetically and/or phenotypically, the substrain should be indicated in the hybrid symbol; e.g., BALB/cBy = CBy, C3H/HeSn = C3Sn.
Approved abbreviations for common mouse strains are listed below:
129 129 strains (may include subtype, e.g., 129S6 for strain 129S6/SvEvTac)
A A strains
AK AKR strains
B C57BL
B6 C57BL/6 strains
B10 C57BL/10 strains
BR C57BR/CD
C BALB/c strains
C3 C3H strains
CB CBA
D1 DBA/1 strains
D2 DBA/2 strains
HR HRS/J
L C57L/J
R3 RIIIS/J
J SJL
SW SWR
4. Strains Made from Multiple Inbred Strains
Mice or rats can be produced that have a defined genetic background, derived from two or more inbred strains, and that may or may not be genetically identical. Such animals should be designated appropriately, according to the breeding scheme that produced them.
4.1 Recombinant Inbred Strains
Recombinant inbred (RI) strains contain unique, approximately equal proportions of genetic contributions from two original progenitor inbred strains. Traditionally, recombinant inbred (RI) strains are formed by crossing animals of two inbred strains, followed by 20 or more consecutive generations of brother x sister matings (Bailey 1971, Taylor 1978). Alternate breeding schemes can be used, such as creating RI strain sets from Advanced Intercross Lines, where F2 animals are nonsib mated for several generations, followed ultimately by 20 or more consecutive generations of brother x sister matings. Note that if backcrossing to one of the parental strains is involved, this will create recombinant congenic strains and should be named accordingly. RI strains should be designated by uppercase one- or two-letter abbreviations of both parental strain names, with the female strain written first, and separated by an uppercase letter X with no intervening spaces. All members of RI sets involving the same two strains will be serially numbered regardless of whether they were created in one or more laboratories. Sequential numbers may be obtained from MGD (email to: nomen@informatics.jax.org).
Examples:
CXB Recombinant inbred mouse strain derived from a cross of BALB/c x C57BL/6J.
Multiple RI are given serial numbers.
Examples:
BXD1, BXD2, BXD3 Members of the BXD set of mouse RI strains derived from a cross of C57BL/6 x DBA/2.
HXB1, HXB2, HXB3 Members of the HXB set of rat RI strains derived from a cross of SHR/OlaIpcv x BN-Lx/Cub.
If the second strain abbreviation ends in a number (e.g., CX8 RI strains), a hyphen should be used to separate it from the serial number (e.g., CX8-1).
Recombinant inbred strains may be intercrossed for mapping complex traits. Such F1s are called recombinant inbred intercrosses (RIX) and are symbolized the same as F1s between other inbred strains
Example:
(BXD1/Ty X AXB19/Pgn)F1 An F1 between a female BXD1/Ty and a male AXB19/Pgn.
4.2 Mixed Inbred Strains
Incipient inbred stocks or inbred strains that are derived from only two parental strains (one of which could be a gene-targeted ES cell line) can be designated using uppercase abbreviations for the two strains, separated by a semicolon. The strain designation preceding the semicolon should be the host and the strain following the semicolon the donor, specifically for targeted mutations where the donor is the ES cell line. When the two progenitor strains do not have a donor/host relationship, the convention followed is the same as when constructing a F1 hybrid designation; that is, the abbreviation of the strain from which the female originated in the first cross is given before the semicolon. Laboratory codes and serial numbers should be used to distinguish strains produced in different laboratories, or multiple strains from the same laboratory. Because these designations may be used for a mixed stock before it is fully inbred, these stocks should not be assumed to be inbred unless accompanied by an inbreeding generation number (e.g., > F20).
Example:
B6;129-Acvr2tm1Zuk A mixed strain derived from C57BL/6J and a 129 ES cell line carrying a targeted knockout of the Acvr2 gene.
A mutant strain, incipient or inbred, derived from more than two progenitor strains or having genetic contribution from an unknown source is considered a "mixed" inbred and may be designated as STOCK followed by a space (i.e., no hyphen) and the mutation(s) or chromosome anomaly it carries.
Example:
STOCK Rb(16.17)5Bnr An inbred strain of unknown or complex background carrying the Robertsonian translocation Rb(16.17)5Bnr.
Once such a mutant stock achieves inbred status, it should be given the appropriate strain designation. It may be designated using the symbols for the genetic mutations it carries in all uppercase, provided the symbols are short. Because the change in strain name is optional, though strongly recommended, some strains designated as STOCK may be inbred.
Example:
JIGR/Dn An inbred strain developed from a mixed background stock carrying the mutations gr(grizzled) and ji (jittery).
When a mutant allele or chromosomal aberration is maintained by crossing animals bearing the mutation to an F1 hybrid at every generation or at alternate generation(s), the stock is designated by the symbol that would be used for that F1, but without the "F1" suffix, and followed by the appropriate allele or chromosome anomaly symbol.
Examples:
B6C3Fe a/a-Dh The Dh (dominant hemimelia) mutation is maintained by crossing to a (B6C3Fe a/a)F1 at each generation, but the stock itself is not an F1.
4.3 Recombinant Congenic Strains
Recombinant Congenic (RC) Strains are formed by crossing two inbred strains, followed by a few (usually two) backcrosses of the hybrids to one of the parental strains (the "recipient" strain), with subsequent inbreeding without selection for any specific markers (Demant and Hart, 1986). Such inbred strains will consist of the background recipient strain genome interspersed with homozygous segments of the donor (the amount of donor strain genome depending on the number of original backcrosses, 2 backcrosses will give on average 12.5%).
RC Strains should be regarded as fully inbred when the theoretical coefficient of inbreeding approximates that of a standard inbred strain. For this purpose, one generation of backcrossing will be regarded as being equivalent to two generations of brother x sister mating. Thus, a strain produced by two backcrosses (N3, equivalent to F6) followed by 14 generations of brother x sister mating (F14) would be fully inbred.
RC strains should be designated by an uppercase abbreviation of the two strains, recipient strain listed first, separated by lowercase "c."
Example:
CcS Recombinant congenic strain between BALB/c recipient and STS donor.
Multiple RC are given serial numbers.
Example:
CcS1, CcS2, CcS3, etc.
If the second strain abbreviation ends in a number (e.g., 129P2), a hyphen should be used to separate it from the serial number.
4.4 Advanced Intercross Lines
Advanced intercross lines (AIL) are made by producing an F2 generation between two inbred strains and then intercrossing in each subsequent generation, but avoiding sibling matings (Darvasi and Soller, 1995). The purpose is to increase the possibility of tightly linked genes recombining.
The symbols should contain the Laboratory code of the laboratory that has produced the line, followed by a colon, the two inbred strain abbreviations, separated by a comma, with the generation number included in the symbol following a hyphen. Generations are designated G3, G4, etc. beginning with the first non-sib cross after the F2 generation.
Example:
Pri:B6,D2-G# This is an AIL stock created at Princeton from the inbred strains C57BL/6 x DBA/2. The G number will increase with each generation.
5 Coisogenic, Congenic, and Segregating Inbred Strains
There are several ways in which inbred strains may differ at only a small part of the genome.
5.1 Coisogenic Strains
Coisogenic strains are inbred strains that differ at only a single locus through mutation occurring in that strain. Strains containing targeted mutations in ES cells that are then crossed to, and maintained, on the same inbred substrain from which the ES cells were derived can be regarded as coisogenic, but the possibility of mutations elsewhere should be considered. Similarly, chemically or radiation induced mutants on an inbred background can be considered coisogenic, although other genomic alterations could be present. A coisogenic strain may accumulate genetic differences over time by genetic drift unless periodically backcrossed to the parental strain.
Coisogenic strains should be designated by the strain symbol (and where appropriate the substrain symbol) followed by a hyphen and the gene symbol of the differential allele, in italics.
Example:
129S7/SvEvBrd-Fyntm1Sor A targeted mutation of the Fyn gene was produced using the AB1 ES cell line derived from 129S7/SvEvBrd. Chimeric animals were mated to 129S7/SvEvBrd and the allele subsequently maintained on this coisogenic strain.
Example:
C57BL/6JEi-tth The tumor with tilted head mutation in the C57BL/6JEi strain.
In some cases, such mutations will be maintained in heterozygous condition. It should be noted that this means that the strain designation does not reflect the breeding system, nor indicate the specific genotype of a given mouse or rat.
Example:
C57BL/6J-cph The congenital progressive hydronephrosis mutation arose on the C57BL/6J strain. It is a coisogenic strain, but because homozygotes are generally juvenile lethal, the strain is maintained by breeding heterozygotes +/cph x +/cph.
If the number of generations of inbreeding since the mutation arose in a coisogenic strain is to be shown, it can be indicated by adding the number of generations since the mutation to the number before:
Example:
F110 + F23 indicates 23 generations of brother x sister matings since the occurrence of a mutation at F110 in an inbred strain.
5.2 Congenic Strains
Congenic strains are produced by repeated backcrosses to an inbred (background) strain, with selection for a particular marker from the donor strain (Snell 1978, Flaherty 1981). Congenic lines that differ at a histocompatibility locus and therefore resist each other's grafts are called congenic resistant (CR) lines.
A strain developed by this method is regarded as congenic when a minimum of 10 backcross generations to the background strain have been made, counting the first hybrid or F1 generation as generation 1. At this point the residual amount of unlinked donor genome in the strain is likely to be less than 0.01. (Note that the amount of donor genome linked to the selected gene or marker is reduced at a much slower rate, approximately equivalent to 200/N, where N is the number of backcross generations for N>5 (Flaherty 1981; Silver 1995).
Marker assisted breeding or marker assisted selection breeding, also known as "speed congenics" permits the production of congenic strains equivalent to 10 backcross generations in as few as 5 generations. (Markel et al., 1997; Wakeland et al., 1997). Provided that the appropriate marker selection has been used, these are termed congenic strains if the donor strain contribution unlinked to the selected locus or chromosomal region is less than 0.01. Ideally, descriptions of speed congenic strains in first publications thereof should include the number and genomic spacing of markers used to define the congenicity of the strain. Because speed congenics depend upon thorough marker analysis and can vary by particular experimental protocol, the inbred status of speed congenics should be regarded with caution.
Congenic strains are designated by a symbol consisting of three parts. The full or abbreviated symbol of the recipient strain is separated by a period from an abbreviated symbol of the donor strain, this being the strain in which the allele or mutation originated, which may or may not be its immediate source in constructing the congenic strain. (In cases where the chromosome on which the mutation arose is unknown, e.g., the donor is not inbred or is complex or an F1 hybrid, the symbol Cg should be used to denote congenic. The use of the donor strain symbol or Cg is essential to distinguish congenic from coisogenic strains. Cg is also used to designate a strain constructed by crossing together two congenic strains that have been backcrossed separately to the same host background, but where their respective donor strains differ. Cg is also applied where alleles originate from a single donor strain, but the congenic strain also carries other coisogenic alleles. In each case, the use of Cg indicates that alleles in the strain name came from more than one source). A hyphen then separates the strain name from the symbol (in italics) of the differential allele(s) introgressed from the donor strain.
Examples:
B6.AKR-H2k A mouse strain with the genetic background of C57BL/6 but which differs from that strain by the introduction of a differential allele (H2k) derived from strain AKR/J.
LEW.BN-RT1n A rat strain with the genetic background of LEW but which differs from that strain by the introduction of a differential segment (RT1n) derived from strain BN.
DA.F344-Cia5 A rat strain with the genetic background of DA onto which a segment from the F344 strain containing the Cia5 QTL has been transferred.
B6.Cg- KitW-44J Gpi1a A mouse strain with the genetic background of C57BL/6, but where the donor strain is mixed, the Kit allele originating from C3H/HeJ and the Gpi1 allele originating from CAST/Ei.
If several lines derived from the same host background and donor strains and carrying the same differential allele(s) are available, the individual lines should be distinguished by adding a forward slash followed by serial numbers and Laboratory codes.
Examples:
C.B10-H2b/1Sn
C.B10-H2b/2Sn
Parentheses may be used to show that an inbred, incipient congenic or congenic inbred strain may have a minor contribution from one other strain.
Examples:
B6(C)-mut A mutation originates on an inbred (e.g., C57BL/6J), is crossed out to or onto another background (e.g., BALB/c) and then is crossed back onto the original background.
C.129P(B6)-Il2tm1Hor A targeted mutation created in a 129 ES cell line and transferred from a B6;129P mixed background to BALB/c.
B6(C)-mut A mutation arises on a congenic strain carrying another mutation (e.g., B6.C-m) and the original mutation is bred out of the new strain. Note if the original mutation is not proved to be removed from the strain, the symbol would be B6.C m-mut.
B6(C)-mut A mutation arises on a hybrid or mixed background stock (e.g., B6CF1) and is backcrossed onto one of the original inbred strains (e.g., C57BL/6J).
B6.C(Cg)-mut A mutation has been backcrossed from one strain (e.g., BALB/c) onto another (e.g., C57BL/6J) but arose on a mixed background or has had a varied history and the origin of the chromosomal segment is unknown.
If the chromosomal segment that has been transferred is defined by several genes or multiple DNA loci, the segment can be defined in the symbol by listing the most proximal and the most distal markers demonstrated to be in the segment in parentheses, separated by a hyphen.
Examples:
B6.Cg-(D4Mit25-D4Mit80)/Lt A congenic strain made by introducing into C57BL/6J a segment of chromosome 4 from an outbred or mixed strain (=Cg), extending between the two defined markers.
B6.CBA-(D4Mit25-D4Mit80)/Lt A similar congenic strain in which the donor chromosomal segment comes from the CBA/J strain.
Note that the markers defining the segment only describe the most proximal and distal markers tested, and this does not imply that there are not other untested markers further proximal or distal. If several lines are made, in the same or different labs that contain the same segment and would be otherwise indistinguishable, then a forward slash, serial number and Laboratory code should be appended.
If necessary, the number of backcross generations should be indicated by N and the number in parentheses following the strain name; generations should not be incorporated into the strain name. Incipient congenics may be given congenic nomenclature at N5, as long as the number of generations of backcrossing is clearly documented in information accompanying the strain. In cases where it is necessary to use more complex mating systems, the generations should be expressed as N equivalents (NE) and the strain regarded as congenic at a minimum of NE10. For example, when backcrossing a recessive gene onto an inbred background, after 10 rounds of backcrossing and intercrossing to recover a homozygote for the next backcross (20 generations), the strain would be at NE10. When a congenic strain is maintained by brother x sister matings after backcrossing, the number of brother x sister generations follows the number of backcross generations, e.g., (N10F6), 10 generations of backcrossing followed by 6 generations of brother x sister inbreeding; (NE12F17), a complex system of backcrosses and intercrosses genetically equivalent to 12 backcrosses, followed by 17 generations of brother x sister matings.
When generating speed congenics N will be less than 10 initially, nevertheless the actual number should be given in parentheses following the N, e.g., N(6), and the details of breeding system and markers used detailed elsewhere in a publication or database.
5.3 Consomic Strains
Consomic strains (also called chromosome substitution strains, Nadeau et al., 2000) are produced by repeated backcrossing of a whole chromosome onto an inbred strain. As with congenic strains, a minimum of 10 backcross generations is required, counting the F1 generation as generation 1. For autosomes it is necessary to genotype progeny to ensure that the selected donor chromosome has not recombined with the corresponding recipient chromosome. The generic designation for consomic strains is HOST STRAIN-Chr #DONOR STRAIN.
Examples:
SHR-Chr YBN In this consomic rat strain, the Y chromosome from BN has been backcrossed onto SHR.
C56BL/6J-Chr 19SPR In this consomic mouse strain, a M.spretus Chromosome 19 has been backcrossed onto C57BL/6J.
C56BL/6J-Chr 1A/J Chr 3DBA/2J In this consomic mouse strain, Chromosome 1 from the A/J strain and Chromosome 3 from the DBA/2J strain have been backcrossed onto C57BL/6J.
Experience shows that on occasion it is impossible to transfer an entire chromosome from one strain to another due to lethal effects on a particular chromosome. For example, a consomic set on which PWD/Ph individual chromosomes were transferred to C57BL/6J revealed that Chr 11 and Chr X cannot be transferred intact. To designate "sections" of transferred chromosomes that contribute to a consomic set, regions can be indicated as a decimal 1, 2, 3, etc.
Thus, a part of Chr 11 of this consomic set would be: C57BL/6J-Chr 11.1PWD/Ph/ForeJ
Although consomic strains are similar in concept and development to congenic strains, in consomic nomenclature the name of the host strain is not abbreviated, and no period followed by the donor strain is required because the strain of origin is shown in the superscript. Capitalization of all letters in the superscript and non-italicization of the chromosome letter/number and of the superscript distinguish a chromosome identifier from an allele symbol.
5.4 Segregating Inbred Strains
Segregating inbred strains are inbred stains in which a particular allele or mutation is maintained in heterozygous state. They are developed by inbreeding (usually brother x sister mating) but with heterozygosity selected at each generation. They are designated like other inbred strains since the segregating locus is part of the standard genotype of the strain (see Section 5.1 Coisogenic Strains). When segregating coat color alleles are part of the inbred strain's normal phenotype, they need not be included in the strain name (see examples below). Details of inbred strain genotypes are available in publications and databases.
Examples:
129P3/J This mouse strain segregates for the tyrosinase alleles albino (Tyrc) and chinchilla (Tyr c-ch)
WB/Re This mouse strain segregates for the dominant white spotting allele of the kit oncogene (KitW).
Strains that carry linked alleles in coupling or repulsion should be designated so that it is clear that the alleles are linked and the phase of the linked genes is specified.
Examples:
B6.Cg-m Leprdb/+ + In this strain the m andLeprdb alleles are carried on one chromosome (in coupling) and the wild type alleles on the other.
B6.Cg-m +/+ Leprdb In this strain the m and Leprdb alleles are carried on different homologs of the chromosome (in repulsion); this is also called a balanced strain.
5.5 Conplastic Strains
Conplastic strains are strains in which the nuclear genome from one strain has been crossed onto the cytoplasm of another, i.e., the mitochondrial donor is always the female parent during the backcrossing program. The designation is NUCLEAR GENOME-mtCYTOPLASMIC GENOME.
Example:
C57BL/6J-mt BALB/c A strain with the nuclear genome of C57BL/6J and the cytoplasmic (mitochondrial) genome of BALB/c.
Such a strain is developed by crossing male C57BL/6J mice with BALB/c females, followed by repeated backcrossing of female offspring to male C57BL/6J. As with congenic strains, a minimum of 10 backcross generations is required, counting the F1 generation as generation 1.
6. Outbreds and Closed Colonies
6.1 Outbreds
Outbred stocks are genetically undefined; that is, no two individuals from an outbred stock are the same. Outbreds are intentionally not bred with siblings or close relatives, as the purpose of an outbred stock is to maintain maximum heterozygosity. One advantage of using outbred stocks is lower cost, because outbreds have relatively long lifespan, are resistant to disease, and have high fecundity. They are useful for experimentation where genotype is unimportant and where a random genetic population is desired. For outbreds, the common strain root is preceded by the Laboratory Code of the institution holding the stock.
Examples:
Tac:ICR The ICR outbred stock maintained by Taconic Farms, Inc.
Hsd:NIH Swiss The NIH Swiss outbred stock maintained by Harlan Sprague Dawley, Inc.
6.2 Closed Colonies
A closed colony contains limited genetic diversity, and is maintained neither by sib-mating (inbred), nor by selective mating to maximize heterozygosity (outbred). All matings occur within the colony members, but breeders need not be selected from specific parentage. No animals are introduced into the colony from outside the stock from generation to generation.
Closed colonies may be established as a way to more readily maintain a difficult mutation, where the desire is to maintain a reasonably uniform background, but poor mating performance prohibits use of sib-mating schemes. Note that closed colonies describe a permanent mating system and this does not apply, for example, if an inbred strain is out-crossed to a near relative in a single generation because of a temporary breeding crisis.
Closed colony designations consist of the strain of origin and appropriately designated mutations (if applicable), followed by [cc] to indicate closed colony.
Example:
C57BL/6Tac-Bmp4tm1Blh[cc] A closed colony of mice originating from the C57BL/6Tac inbred strain and carrying the Bmp4tm1Blh targeted mutation.
7. References
Bailey, D.W. 1971. Recombinant inbred strains, an aid to finding identity, linkage, and function of histocompatibility and other genes. Transplantation 11:325-327
Committee on Rat Nomenclature. 1992. Definition, nomenclature, and conservation of rat strains. ILAR News 34: S1-S26
Committee on Standardized Genetic Nomenclature for Mice. 1952. Standardized nomenclature for inbred strains of mice. Cancer Res. 12:602-613.
Committee on Standardized Genetic Nomenclature for Mice. 1960. Standardized nomenclature for inbred strains of mice, second listing. Cancer Res. 20:145-169.
Committee on Standardized Genetic Nomenclature for Mice. 1976. Nomenclature for inbred strains of mice preserved by freezing. Mouse News Lett 54:2-3.
Committee on Standardized Genetic Nomenclature for Mice, Chair: Lyon, M.F. Rules for nomenclature of inbred strains, pp. 368-372. In: Genetic Variants and Strains of the Laboratory Mouse, Green, M.C. (ed.), First Edition, Gustav Fischer Verlag, Stuttgart, 1981.
Committee on Standardized Genetic Nomenclature for Mice, Chair: Lyon, M.F. Rules for nomenclature of inbred strains, pp. 632-635. In: Genetic Variants and Strains of the Laboratory Mouse, Lyon, M.F., A.G. Searle (eds.), Second Edition, Oxford University Press, Oxford, 1989.
Committee on Standardized Genetic Nomenclature for Mice, Chair: Davisson, M.T. Rules for nomenclature of inbred strains, pp. 1532-1536. In: Genetic Variants and Strains of the Laboratory Mouse, Lyon MF, Rastan S, Brown SDM (eds.), Third Edition, Oxford University Press, Oxford, 1996
Darvasi A, Soller M. 1995. Advanced intercross lines, an experimental population for fine genetic mapping. Genetics 141: 1199-1207
Demant, P. and Hart, A.A.M. 1986. Recombinant congenic strains- a new tool for analyzing genetic traits determined by more than one gene. Immunogenetics 24:416-422.
Eppig JT. 2006. Mouse Strain and Genetic Nomenclature: an Abbreviated Guide. In: The Mouse in Biomedical Research, Volume 1, Second Edition. Fox J, Barthold S, Davisson M, Newcomer C, Quimby F, Smith A, eds. Academic Press. pp 79-98.
Festing, M.F.W. 1979. Inbred strains in biomedical research, Macmillan Press, London: Oxford University Press, New York.
Festing, M.F.W. 1993. Origins and characteristics of inbred strains of mice, 11th listing. Mouse Genome 91:393-550.
Flaherty L. 1981. Congenic strains. In The Mouse in Biomedical Research, Vol. 1, Foster HL, Small JD, Fox JG (eds.), Academic Press, New York, pp. 215-222.
Green EL. 1981. Genetics and Probability in Animal Breeding Experiments. Oxford University Press, New York
Maltais LJ, Blake JA, Eppig JT, Davisson MT 1997. Rules and guidelines for mouse gene nomenclature: a condensed version. International Committee on Standardized Genetic Nomenclature for Mice. Genomics 45: 471-476
Markel P, Shu P, Ebeling C, Carlson GA, Nagle DL, Smutko JS, Moore KJ. 1997. Theoretical and empirical issues for marker-assisted breeding of congenic mouse strains. Nat Genet. 17:280-284.
Nadeau JH, Singer JB, Matin A, Lander ES. 2000. Analyzing complex genetic traits with chromosome substitution strains. Nat Genet. 24: 221-225.
Silver LM. 1995. Mouse Genetics: Concepts and Applications. Oxford University Press, Oxford.
Snell GD. 1941. Biology of the Laboratory Mouse, 1st Edition, McGraw-Hill, New York
Snell GD. 1978. Congenic resistant strains of mice. In Origins of Inbred Mice, Morse HC (ed.), Academic Press, New York, pp. 1-31.
Staats J. 1985. Standardized Nomenclature for Inbred Strains of Mice: eighth listing. Cancer Res. 45: 945-977
Taylor B.A. 1978. Recombinant inbred strains: use in gene mapping. In Origins of Inbred Mice, Morse, HC. (eds.), Academic Press, New York, pp. 423-438.
Wakeland E, Morel L, Achey K, Yui M, Longmate J. 1997. Speed congenics: a classic technique in the fast lane (relatively speaking). Immunol Today 18: 472-477.
International Committee on Standardized Genetic Nomenclature for Mice
Chairperson: Dr. Janan T. Eppig
(e-mail: jte@informatics.jax.org)
Rat Genome and Nomenclature Committee
Chairperson: Dr. Goran Levan
(e-mail: Goran.Levan@gen.gu.se)
In 2001, the International Committee on Standardized Nomenclature for Mice and the Rat Genome and Nomenclature Committee agreed to establish a joint set of rules for strain nomenclature, applicable to strains of both species. These rewritten guidelines reflect this collaboration, in addition to documenting new and revised rules for the naming of strains. This document is updated annually by the international nomenclature committees for mouse and rat.
Reference to former versions of the rules for mouse strain nomenclature can be found in Snell (1941), Committee for Standardized Genetic Nomenclature in Mice (1952, 1960, 1976, 1981, 1989, 1996), Festing (1979, 1993), Staats (1986), Maltais et al. (1997). The November 2006 revision is available here. Reference to former rules for rat strain nomenclature can be found in Committee on Rat Nomenclature (1992).
Current nomenclature rules for naming genes are available online at:
For mouse: http://www.informatics.jax.org/mgihome/nomen/gene.shtml#genenom
For rat: http://rgd.mcw.edu/nomen_rules.html
Table of Contents
1. Introduction
1.1 Mice
1.2 Rats
2. Laboratory codes
3. Inbred Strains and Hybrids
3.1 Definition
3.2 Nomenclature of Inbred Strains
3.3 Indication of Inbreeding
3.4 Substrains
3.5 Hybrids
4. Strains Made from Multiple Inbred Strains
4.1 Recombinant Inbred Strains
4.2 Mixed Inbred Strains
4.3 Recombinant Congenic Strains
4.4 Advanced Intercross Lines
5. Coisogenic, Congenic, and Segregating Inbred Strains
5.1 Coisogenic Strains
5.2 Congenic Strains
5.3 Consomic Strains
5.4 Segregating Inbred Strains
5.5 Conplastic Strains
6. Outbreds and Closed Colonies
6.1 Outbreds
6.2 Closed Colonies 7. References
1. Introduction
Mice and rats used in the laboratory derive from a variety of sources. Production of inbred strains means that these backgrounds can be defined and thus require nomenclature conventions. It should be borne in mind that genetic drift means that there may still be unknown genetic differences between individuals within strains.
1.1 Mice
Most laboratory mice have contributions from both Mus musculus musculus and Mus musculus domesticus. There is evidence that smaller contributions also may have come from Mus musculus molossinus and Mus musculus castaneus. Therefore, they should not be referred to by species name, but rather as laboratory mice or by use of a specific strain or stock name. (In addition, some recently developed laboratory mouse strains are derived wholly from other Mus species or other subspecies, such as M. spretus).
Mouse strain names should be registered through the Mouse Genome Database (MGD) at http://www.informatics.jax.org/mgihome/submissions/submissions_menu.shtml.
1.2 Rats
Laboratory rat strains derive from the Rattus norvegicus species. Another species, Rattus rattus, also is used as an experimental model, but has not contributed to the common laboratory rat strains.
Rat strain names should be registered through the Rat Genome Database (RGD) at http://rgd.mcw.edu.
2. Laboratory codes
A key feature of mouse and rat nomenclature is the Laboratory Registration Code or Laboratory code, which is a code of usually three to four letters (first letter uppercase, followed by all lowercase) that identifies a particular institute, laboratory, or investigator that produced, and may hold stocks of, a mouse or rat strain. Substrains should be identified by Laboratory codes, as should congenic and other strains where several different forms exist that are not otherwise distinguishable. Laboratory codes are assigned by the Institute of Laboratory Animal Research (ILAR) (http://dels.nas.edu/ilar_n/ilarhome/search_lc.shtml).
Examples of Laboratory codes are:
J The Jackson Laboratory
Rl W.L. and L.B. Russell
Jr John Rapp
Mcw Medical College of Wisconsin
Kyo Kyoto University
3. Inbred Strains and Hybrids
3.1 Definition
Strains can be termed inbred if they have been mated brother x sister for 20 or more consecutive generations, and individuals of the strain can be traced to a single ancestral pair at the 20th or subsequent generation. At this point the individuals' genomes will on average have only 0.01 residual heterozygosity (excluding any genetic drift) and can be regarded for most purposes as genetically identical. Inbred strains must be continuously mated brother x sister (or equivalent) thereafter
Other breeding schemes can be used to produce inbred strains; consecutive parent x offspring mating may be used, provided that the younger of the parents is always used (i.e., the offspring that is mated to parent is subsequently mated to its offspring). Other breeding schemes are acceptable provided that the inbreeding is equivalent to 20 successive generations of sib mating (Green 1981).
3.2 Nomenclature of Inbred Strains
An inbred strain should be designated by a unique brief symbol made up of uppercase, roman, letters, or a combination of letters and numbers beginning with a letter. (Note that some pre-existing strains do not follow this convention; e.g., mouse strain 129P1/J)
Care should be taken that mouse and rat strains do not overlap in strain designations. (Note: a few historical examples exist of similar mouse and rat strain designations and these are allowed to stand, with their substrain designations identifying them as unique).
Inbred strains that have a common origin, but are separated before F20 are related inbred strains, and symbols should reflect this relationship.
Examples:
Mouse strains: NZB, NZC, NZO
Rat strains: SR, SS
3.3 Indication of Inbreeding
The number of brother x sister inbreeding generations can be indicated, if necessary, by addition in parentheses of F followed by the number of generations.
Example:
Rat strain: ACI/N (F159)
If there is not information as to the total number of generations, but a minimum number of recent inbreeding generations is known, this can be shown by a question mark + the known number of subsequent generations of inbreeding.
Example:
Mouse strain: C3H/HeJ-ruf (F?+25)
3.4 Substrains
Established inbred strains may genetically diverge with time into substrains, due to a number of circumstances:
* If two branches are separated after 20 but before 40 generations of inbreeding there still will be enough residual heterozygosity that two genetically different substrains will result (Green 1981).
* If branches are separated for more than 20 generations from a common ancestor, it is likely that genetic variation between the branches will have occurred by mutation and genetic drift.
* If genetic differences are proven by genetic analysis to have occurred between branches.
Substrains are given the root symbol of the original strain, followed by a forward slash and a substrain designation. The designation is usually the Laboratory code of the individual or laboratory originating the strain.
Examples:
IS/Kyo Substrain of IS rat strain originating at Kyoto University.
A/He Substrain of A mouse strain originating from Walter Heston.
If a laboratory originates more than one substrain, serial numbers should be added to the Laboratory code.
Example:
Mouse strains: FL/1Re, FL/2Re
(Note that historical exceptions to this rule exist; for example, in mouse, BALB/c is not a substrain, DBA/1 and DBA/2 are separate strains and are not substrains.)
Substrains may give rise to further substrains by continued maintenance by a different investigator or through establishment of a new colony. In addition, substrains arise if demonstrable genetic differences from the original substrain are discovered. In either case, further substrain designations are added, without the addition of another slash.
Examples:
C3H/HeH Mouse substrain derived at Harwell (H) from the Heston (He) substrain of C3H.
SR/JrIpcv Rat substrain derived at Institute of Physiology, Czech Academy of Sciences (Ipcv) from the John Rapp (Jr) substrain of SR
Laboratory codes should be accumulated because genetic differences will accumulate with time, the rate depending to some extent on varying levels of quality control at the facilities that have housed and bred the strain or substrain. Organizations distributing mice and rats should include the number of generations the strain has been separated from the parent strain in the information they provide regarding the strain. Strain names can be abbreviated in publications after the first mention of the full proper designation.
3.5 Hybrids
Mice or rats that are the progeny of two inbred strains, crossed in the same direction, are genetically identical, and can be designated using uppercase abbreviations of the two parents (maternal strain listed first), followed by F1. Note that reciprocal F1 hybrids are not genetically identical, and their designations are, therefore, different.
Examples:
D2B6F1 Mouse that is the offspring of a DBA/2 mother and C57BL6/J father. A full F1 designation is (DBA/2N x C57BL/6J)F1.
B6D2F1 Mouse that is the offspring of the reciprocal cross. A full F1 designation is (C57BL/6J x DBA/2N)F1.
CB1BD22F1 Mouse that is the offspring of two recombinant inbred strains, a CXB1 mother and BXD22 father; full F1 designation is (CXB1/ByJ x BXD22/TyJ)F1.
Further crosses produce offspring that are no longer genetically identical, but it may still be appropriate to give them designations reflecting their parentage, similar to those for F1 hybrids.
Examples:
D2B6F2 are offspring of a D2B6F1 intercross.
B6(D2AKRF1) are offspring of a (DBA/2 x AKR/J)F1 male backcrossed to a C57BL/6J female.
In all the above cases, for clarity, the full strain symbols should be given in any publication when the hybrids or crosses are first referred to. If a hybrid is constructed using a substrain known to differ from the "standard" strain genetically and/or phenotypically, the substrain should be indicated in the hybrid symbol; e.g., BALB/cBy = CBy, C3H/HeSn = C3Sn.
Approved abbreviations for common mouse strains are listed below:
129 129 strains (may include subtype, e.g., 129S6 for strain 129S6/SvEvTac)
A A strains
AK AKR strains
B C57BL
B6 C57BL/6 strains
B10 C57BL/10 strains
BR C57BR/CD
C BALB/c strains
C3 C3H strains
CB CBA
D1 DBA/1 strains
D2 DBA/2 strains
HR HRS/J
L C57L/J
R3 RIIIS/J
J SJL
SW SWR
4. Strains Made from Multiple Inbred Strains
Mice or rats can be produced that have a defined genetic background, derived from two or more inbred strains, and that may or may not be genetically identical. Such animals should be designated appropriately, according to the breeding scheme that produced them.
4.1 Recombinant Inbred Strains
Recombinant inbred (RI) strains contain unique, approximately equal proportions of genetic contributions from two original progenitor inbred strains. Traditionally, recombinant inbred (RI) strains are formed by crossing animals of two inbred strains, followed by 20 or more consecutive generations of brother x sister matings (Bailey 1971, Taylor 1978). Alternate breeding schemes can be used, such as creating RI strain sets from Advanced Intercross Lines, where F2 animals are nonsib mated for several generations, followed ultimately by 20 or more consecutive generations of brother x sister matings. Note that if backcrossing to one of the parental strains is involved, this will create recombinant congenic strains and should be named accordingly. RI strains should be designated by uppercase one- or two-letter abbreviations of both parental strain names, with the female strain written first, and separated by an uppercase letter X with no intervening spaces. All members of RI sets involving the same two strains will be serially numbered regardless of whether they were created in one or more laboratories. Sequential numbers may be obtained from MGD (email to: nomen@informatics.jax.org).
Examples:
CXB Recombinant inbred mouse strain derived from a cross of BALB/c x C57BL/6J.
Multiple RI are given serial numbers.
Examples:
BXD1, BXD2, BXD3 Members of the BXD set of mouse RI strains derived from a cross of C57BL/6 x DBA/2.
HXB1, HXB2, HXB3 Members of the HXB set of rat RI strains derived from a cross of SHR/OlaIpcv x BN-Lx/Cub.
If the second strain abbreviation ends in a number (e.g., CX8 RI strains), a hyphen should be used to separate it from the serial number (e.g., CX8-1).
Recombinant inbred strains may be intercrossed for mapping complex traits. Such F1s are called recombinant inbred intercrosses (RIX) and are symbolized the same as F1s between other inbred strains
Example:
(BXD1/Ty X AXB19/Pgn)F1 An F1 between a female BXD1/Ty and a male AXB19/Pgn.
4.2 Mixed Inbred Strains
Incipient inbred stocks or inbred strains that are derived from only two parental strains (one of which could be a gene-targeted ES cell line) can be designated using uppercase abbreviations for the two strains, separated by a semicolon. The strain designation preceding the semicolon should be the host and the strain following the semicolon the donor, specifically for targeted mutations where the donor is the ES cell line. When the two progenitor strains do not have a donor/host relationship, the convention followed is the same as when constructing a F1 hybrid designation; that is, the abbreviation of the strain from which the female originated in the first cross is given before the semicolon. Laboratory codes and serial numbers should be used to distinguish strains produced in different laboratories, or multiple strains from the same laboratory. Because these designations may be used for a mixed stock before it is fully inbred, these stocks should not be assumed to be inbred unless accompanied by an inbreeding generation number (e.g., > F20).
Example:
B6;129-Acvr2tm1Zuk A mixed strain derived from C57BL/6J and a 129 ES cell line carrying a targeted knockout of the Acvr2 gene.
A mutant strain, incipient or inbred, derived from more than two progenitor strains or having genetic contribution from an unknown source is considered a "mixed" inbred and may be designated as STOCK followed by a space (i.e., no hyphen) and the mutation(s) or chromosome anomaly it carries.
Example:
STOCK Rb(16.17)5Bnr An inbred strain of unknown or complex background carrying the Robertsonian translocation Rb(16.17)5Bnr.
Once such a mutant stock achieves inbred status, it should be given the appropriate strain designation. It may be designated using the symbols for the genetic mutations it carries in all uppercase, provided the symbols are short. Because the change in strain name is optional, though strongly recommended, some strains designated as STOCK may be inbred.
Example:
JIGR/Dn An inbred strain developed from a mixed background stock carrying the mutations gr(grizzled) and ji (jittery).
When a mutant allele or chromosomal aberration is maintained by crossing animals bearing the mutation to an F1 hybrid at every generation or at alternate generation(s), the stock is designated by the symbol that would be used for that F1, but without the "F1" suffix, and followed by the appropriate allele or chromosome anomaly symbol.
Examples:
B6C3Fe a/a-Dh The Dh (dominant hemimelia) mutation is maintained by crossing to a (B6C3Fe a/a)F1 at each generation, but the stock itself is not an F1.
4.3 Recombinant Congenic Strains
Recombinant Congenic (RC) Strains are formed by crossing two inbred strains, followed by a few (usually two) backcrosses of the hybrids to one of the parental strains (the "recipient" strain), with subsequent inbreeding without selection for any specific markers (Demant and Hart, 1986). Such inbred strains will consist of the background recipient strain genome interspersed with homozygous segments of the donor (the amount of donor strain genome depending on the number of original backcrosses, 2 backcrosses will give on average 12.5%).
RC Strains should be regarded as fully inbred when the theoretical coefficient of inbreeding approximates that of a standard inbred strain. For this purpose, one generation of backcrossing will be regarded as being equivalent to two generations of brother x sister mating. Thus, a strain produced by two backcrosses (N3, equivalent to F6) followed by 14 generations of brother x sister mating (F14) would be fully inbred.
RC strains should be designated by an uppercase abbreviation of the two strains, recipient strain listed first, separated by lowercase "c."
Example:
CcS Recombinant congenic strain between BALB/c recipient and STS donor.
Multiple RC are given serial numbers.
Example:
CcS1, CcS2, CcS3, etc.
If the second strain abbreviation ends in a number (e.g., 129P2), a hyphen should be used to separate it from the serial number.
4.4 Advanced Intercross Lines
Advanced intercross lines (AIL) are made by producing an F2 generation between two inbred strains and then intercrossing in each subsequent generation, but avoiding sibling matings (Darvasi and Soller, 1995). The purpose is to increase the possibility of tightly linked genes recombining.
The symbols should contain the Laboratory code of the laboratory that has produced the line, followed by a colon, the two inbred strain abbreviations, separated by a comma, with the generation number included in the symbol following a hyphen. Generations are designated G3, G4, etc. beginning with the first non-sib cross after the F2 generation.
Example:
Pri:B6,D2-G# This is an AIL stock created at Princeton from the inbred strains C57BL/6 x DBA/2. The G number will increase with each generation.
5 Coisogenic, Congenic, and Segregating Inbred Strains
There are several ways in which inbred strains may differ at only a small part of the genome.
5.1 Coisogenic Strains
Coisogenic strains are inbred strains that differ at only a single locus through mutation occurring in that strain. Strains containing targeted mutations in ES cells that are then crossed to, and maintained, on the same inbred substrain from which the ES cells were derived can be regarded as coisogenic, but the possibility of mutations elsewhere should be considered. Similarly, chemically or radiation induced mutants on an inbred background can be considered coisogenic, although other genomic alterations could be present. A coisogenic strain may accumulate genetic differences over time by genetic drift unless periodically backcrossed to the parental strain.
Coisogenic strains should be designated by the strain symbol (and where appropriate the substrain symbol) followed by a hyphen and the gene symbol of the differential allele, in italics.
Example:
129S7/SvEvBrd-Fyntm1Sor A targeted mutation of the Fyn gene was produced using the AB1 ES cell line derived from 129S7/SvEvBrd. Chimeric animals were mated to 129S7/SvEvBrd and the allele subsequently maintained on this coisogenic strain.
Example:
C57BL/6JEi-tth The tumor with tilted head mutation in the C57BL/6JEi strain.
In some cases, such mutations will be maintained in heterozygous condition. It should be noted that this means that the strain designation does not reflect the breeding system, nor indicate the specific genotype of a given mouse or rat.
Example:
C57BL/6J-cph The congenital progressive hydronephrosis mutation arose on the C57BL/6J strain. It is a coisogenic strain, but because homozygotes are generally juvenile lethal, the strain is maintained by breeding heterozygotes +/cph x +/cph.
If the number of generations of inbreeding since the mutation arose in a coisogenic strain is to be shown, it can be indicated by adding the number of generations since the mutation to the number before:
Example:
F110 + F23 indicates 23 generations of brother x sister matings since the occurrence of a mutation at F110 in an inbred strain.
5.2 Congenic Strains
Congenic strains are produced by repeated backcrosses to an inbred (background) strain, with selection for a particular marker from the donor strain (Snell 1978, Flaherty 1981). Congenic lines that differ at a histocompatibility locus and therefore resist each other's grafts are called congenic resistant (CR) lines.
A strain developed by this method is regarded as congenic when a minimum of 10 backcross generations to the background strain have been made, counting the first hybrid or F1 generation as generation 1. At this point the residual amount of unlinked donor genome in the strain is likely to be less than 0.01. (Note that the amount of donor genome linked to the selected gene or marker is reduced at a much slower rate, approximately equivalent to 200/N, where N is the number of backcross generations for N>5 (Flaherty 1981; Silver 1995).
Marker assisted breeding or marker assisted selection breeding, also known as "speed congenics" permits the production of congenic strains equivalent to 10 backcross generations in as few as 5 generations. (Markel et al., 1997; Wakeland et al., 1997). Provided that the appropriate marker selection has been used, these are termed congenic strains if the donor strain contribution unlinked to the selected locus or chromosomal region is less than 0.01. Ideally, descriptions of speed congenic strains in first publications thereof should include the number and genomic spacing of markers used to define the congenicity of the strain. Because speed congenics depend upon thorough marker analysis and can vary by particular experimental protocol, the inbred status of speed congenics should be regarded with caution.
Congenic strains are designated by a symbol consisting of three parts. The full or abbreviated symbol of the recipient strain is separated by a period from an abbreviated symbol of the donor strain, this being the strain in which the allele or mutation originated, which may or may not be its immediate source in constructing the congenic strain. (In cases where the chromosome on which the mutation arose is unknown, e.g., the donor is not inbred or is complex or an F1 hybrid, the symbol Cg should be used to denote congenic. The use of the donor strain symbol or Cg is essential to distinguish congenic from coisogenic strains. Cg is also used to designate a strain constructed by crossing together two congenic strains that have been backcrossed separately to the same host background, but where their respective donor strains differ. Cg is also applied where alleles originate from a single donor strain, but the congenic strain also carries other coisogenic alleles. In each case, the use of Cg indicates that alleles in the strain name came from more than one source). A hyphen then separates the strain name from the symbol (in italics) of the differential allele(s) introgressed from the donor strain.
Examples:
B6.AKR-H2k A mouse strain with the genetic background of C57BL/6 but which differs from that strain by the introduction of a differential allele (H2k) derived from strain AKR/J.
LEW.BN-RT1n A rat strain with the genetic background of LEW but which differs from that strain by the introduction of a differential segment (RT1n) derived from strain BN.
DA.F344-Cia5 A rat strain with the genetic background of DA onto which a segment from the F344 strain containing the Cia5 QTL has been transferred.
B6.Cg- KitW-44J Gpi1a A mouse strain with the genetic background of C57BL/6, but where the donor strain is mixed, the Kit allele originating from C3H/HeJ and the Gpi1 allele originating from CAST/Ei.
If several lines derived from the same host background and donor strains and carrying the same differential allele(s) are available, the individual lines should be distinguished by adding a forward slash followed by serial numbers and Laboratory codes.
Examples:
C.B10-H2b/1Sn
C.B10-H2b/2Sn
Parentheses may be used to show that an inbred, incipient congenic or congenic inbred strain may have a minor contribution from one other strain.
Examples:
B6(C)-mut A mutation originates on an inbred (e.g., C57BL/6J), is crossed out to or onto another background (e.g., BALB/c) and then is crossed back onto the original background.
C.129P(B6)-Il2tm1Hor A targeted mutation created in a 129 ES cell line and transferred from a B6;129P mixed background to BALB/c.
B6(C)-mut A mutation arises on a congenic strain carrying another mutation (e.g., B6.C-m) and the original mutation is bred out of the new strain. Note if the original mutation is not proved to be removed from the strain, the symbol would be B6.C m-mut.
B6(C)-mut A mutation arises on a hybrid or mixed background stock (e.g., B6CF1) and is backcrossed onto one of the original inbred strains (e.g., C57BL/6J).
B6.C(Cg)-mut A mutation has been backcrossed from one strain (e.g., BALB/c) onto another (e.g., C57BL/6J) but arose on a mixed background or has had a varied history and the origin of the chromosomal segment is unknown.
If the chromosomal segment that has been transferred is defined by several genes or multiple DNA loci, the segment can be defined in the symbol by listing the most proximal and the most distal markers demonstrated to be in the segment in parentheses, separated by a hyphen.
Examples:
B6.Cg-(D4Mit25-D4Mit80)/Lt A congenic strain made by introducing into C57BL/6J a segment of chromosome 4 from an outbred or mixed strain (=Cg), extending between the two defined markers.
B6.CBA-(D4Mit25-D4Mit80)/Lt A similar congenic strain in which the donor chromosomal segment comes from the CBA/J strain.
Note that the markers defining the segment only describe the most proximal and distal markers tested, and this does not imply that there are not other untested markers further proximal or distal. If several lines are made, in the same or different labs that contain the same segment and would be otherwise indistinguishable, then a forward slash, serial number and Laboratory code should be appended.
If necessary, the number of backcross generations should be indicated by N and the number in parentheses following the strain name; generations should not be incorporated into the strain name. Incipient congenics may be given congenic nomenclature at N5, as long as the number of generations of backcrossing is clearly documented in information accompanying the strain. In cases where it is necessary to use more complex mating systems, the generations should be expressed as N equivalents (NE) and the strain regarded as congenic at a minimum of NE10. For example, when backcrossing a recessive gene onto an inbred background, after 10 rounds of backcrossing and intercrossing to recover a homozygote for the next backcross (20 generations), the strain would be at NE10. When a congenic strain is maintained by brother x sister matings after backcrossing, the number of brother x sister generations follows the number of backcross generations, e.g., (N10F6), 10 generations of backcrossing followed by 6 generations of brother x sister inbreeding; (NE12F17), a complex system of backcrosses and intercrosses genetically equivalent to 12 backcrosses, followed by 17 generations of brother x sister matings.
When generating speed congenics N will be less than 10 initially, nevertheless the actual number should be given in parentheses following the N, e.g., N(6), and the details of breeding system and markers used detailed elsewhere in a publication or database.
5.3 Consomic Strains
Consomic strains (also called chromosome substitution strains, Nadeau et al., 2000) are produced by repeated backcrossing of a whole chromosome onto an inbred strain. As with congenic strains, a minimum of 10 backcross generations is required, counting the F1 generation as generation 1. For autosomes it is necessary to genotype progeny to ensure that the selected donor chromosome has not recombined with the corresponding recipient chromosome. The generic designation for consomic strains is HOST STRAIN-Chr #DONOR STRAIN.
Examples:
SHR-Chr YBN In this consomic rat strain, the Y chromosome from BN has been backcrossed onto SHR.
C56BL/6J-Chr 19SPR In this consomic mouse strain, a M.spretus Chromosome 19 has been backcrossed onto C57BL/6J.
C56BL/6J-Chr 1A/J Chr 3DBA/2J In this consomic mouse strain, Chromosome 1 from the A/J strain and Chromosome 3 from the DBA/2J strain have been backcrossed onto C57BL/6J.
Experience shows that on occasion it is impossible to transfer an entire chromosome from one strain to another due to lethal effects on a particular chromosome. For example, a consomic set on which PWD/Ph individual chromosomes were transferred to C57BL/6J revealed that Chr 11 and Chr X cannot be transferred intact. To designate "sections" of transferred chromosomes that contribute to a consomic set, regions can be indicated as a decimal 1, 2, 3, etc.
Thus, a part of Chr 11 of this consomic set would be: C57BL/6J-Chr 11.1PWD/Ph/ForeJ
Although consomic strains are similar in concept and development to congenic strains, in consomic nomenclature the name of the host strain is not abbreviated, and no period followed by the donor strain is required because the strain of origin is shown in the superscript. Capitalization of all letters in the superscript and non-italicization of the chromosome letter/number and of the superscript distinguish a chromosome identifier from an allele symbol.
5.4 Segregating Inbred Strains
Segregating inbred strains are inbred stains in which a particular allele or mutation is maintained in heterozygous state. They are developed by inbreeding (usually brother x sister mating) but with heterozygosity selected at each generation. They are designated like other inbred strains since the segregating locus is part of the standard genotype of the strain (see Section 5.1 Coisogenic Strains). When segregating coat color alleles are part of the inbred strain's normal phenotype, they need not be included in the strain name (see examples below). Details of inbred strain genotypes are available in publications and databases.
Examples:
129P3/J This mouse strain segregates for the tyrosinase alleles albino (Tyrc) and chinchilla (Tyr c-ch)
WB/Re This mouse strain segregates for the dominant white spotting allele of the kit oncogene (KitW).
Strains that carry linked alleles in coupling or repulsion should be designated so that it is clear that the alleles are linked and the phase of the linked genes is specified.
Examples:
B6.Cg-m Leprdb/+ + In this strain the m andLeprdb alleles are carried on one chromosome (in coupling) and the wild type alleles on the other.
B6.Cg-m +/+ Leprdb In this strain the m and Leprdb alleles are carried on different homologs of the chromosome (in repulsion); this is also called a balanced strain.
5.5 Conplastic Strains
Conplastic strains are strains in which the nuclear genome from one strain has been crossed onto the cytoplasm of another, i.e., the mitochondrial donor is always the female parent during the backcrossing program. The designation is NUCLEAR GENOME-mtCYTOPLASMIC GENOME.
Example:
C57BL/6J-mt BALB/c A strain with the nuclear genome of C57BL/6J and the cytoplasmic (mitochondrial) genome of BALB/c.
Such a strain is developed by crossing male C57BL/6J mice with BALB/c females, followed by repeated backcrossing of female offspring to male C57BL/6J. As with congenic strains, a minimum of 10 backcross generations is required, counting the F1 generation as generation 1.
6. Outbreds and Closed Colonies
6.1 Outbreds
Outbred stocks are genetically undefined; that is, no two individuals from an outbred stock are the same. Outbreds are intentionally not bred with siblings or close relatives, as the purpose of an outbred stock is to maintain maximum heterozygosity. One advantage of using outbred stocks is lower cost, because outbreds have relatively long lifespan, are resistant to disease, and have high fecundity. They are useful for experimentation where genotype is unimportant and where a random genetic population is desired. For outbreds, the common strain root is preceded by the Laboratory Code of the institution holding the stock.
Examples:
Tac:ICR The ICR outbred stock maintained by Taconic Farms, Inc.
Hsd:NIH Swiss The NIH Swiss outbred stock maintained by Harlan Sprague Dawley, Inc.
6.2 Closed Colonies
A closed colony contains limited genetic diversity, and is maintained neither by sib-mating (inbred), nor by selective mating to maximize heterozygosity (outbred). All matings occur within the colony members, but breeders need not be selected from specific parentage. No animals are introduced into the colony from outside the stock from generation to generation.
Closed colonies may be established as a way to more readily maintain a difficult mutation, where the desire is to maintain a reasonably uniform background, but poor mating performance prohibits use of sib-mating schemes. Note that closed colonies describe a permanent mating system and this does not apply, for example, if an inbred strain is out-crossed to a near relative in a single generation because of a temporary breeding crisis.
Closed colony designations consist of the strain of origin and appropriately designated mutations (if applicable), followed by [cc] to indicate closed colony.
Example:
C57BL/6Tac-Bmp4tm1Blh[cc] A closed colony of mice originating from the C57BL/6Tac inbred strain and carrying the Bmp4tm1Blh targeted mutation.
7. References
Bailey, D.W. 1971. Recombinant inbred strains, an aid to finding identity, linkage, and function of histocompatibility and other genes. Transplantation 11:325-327
Committee on Rat Nomenclature. 1992. Definition, nomenclature, and conservation of rat strains. ILAR News 34: S1-S26
Committee on Standardized Genetic Nomenclature for Mice. 1952. Standardized nomenclature for inbred strains of mice. Cancer Res. 12:602-613.
Committee on Standardized Genetic Nomenclature for Mice. 1960. Standardized nomenclature for inbred strains of mice, second listing. Cancer Res. 20:145-169.
Committee on Standardized Genetic Nomenclature for Mice. 1976. Nomenclature for inbred strains of mice preserved by freezing. Mouse News Lett 54:2-3.
Committee on Standardized Genetic Nomenclature for Mice, Chair: Lyon, M.F. Rules for nomenclature of inbred strains, pp. 368-372. In: Genetic Variants and Strains of the Laboratory Mouse, Green, M.C. (ed.), First Edition, Gustav Fischer Verlag, Stuttgart, 1981.
Committee on Standardized Genetic Nomenclature for Mice, Chair: Lyon, M.F. Rules for nomenclature of inbred strains, pp. 632-635. In: Genetic Variants and Strains of the Laboratory Mouse, Lyon, M.F., A.G. Searle (eds.), Second Edition, Oxford University Press, Oxford, 1989.
Committee on Standardized Genetic Nomenclature for Mice, Chair: Davisson, M.T. Rules for nomenclature of inbred strains, pp. 1532-1536. In: Genetic Variants and Strains of the Laboratory Mouse, Lyon MF, Rastan S, Brown SDM (eds.), Third Edition, Oxford University Press, Oxford, 1996
Darvasi A, Soller M. 1995. Advanced intercross lines, an experimental population for fine genetic mapping. Genetics 141: 1199-1207
Demant, P. and Hart, A.A.M. 1986. Recombinant congenic strains- a new tool for analyzing genetic traits determined by more than one gene. Immunogenetics 24:416-422.
Eppig JT. 2006. Mouse Strain and Genetic Nomenclature: an Abbreviated Guide. In: The Mouse in Biomedical Research, Volume 1, Second Edition. Fox J, Barthold S, Davisson M, Newcomer C, Quimby F, Smith A, eds. Academic Press. pp 79-98.
Festing, M.F.W. 1979. Inbred strains in biomedical research, Macmillan Press, London: Oxford University Press, New York.
Festing, M.F.W. 1993. Origins and characteristics of inbred strains of mice, 11th listing. Mouse Genome 91:393-550.
Flaherty L. 1981. Congenic strains. In The Mouse in Biomedical Research, Vol. 1, Foster HL, Small JD, Fox JG (eds.), Academic Press, New York, pp. 215-222.
Green EL. 1981. Genetics and Probability in Animal Breeding Experiments. Oxford University Press, New York
Maltais LJ, Blake JA, Eppig JT, Davisson MT 1997. Rules and guidelines for mouse gene nomenclature: a condensed version. International Committee on Standardized Genetic Nomenclature for Mice. Genomics 45: 471-476
Markel P, Shu P, Ebeling C, Carlson GA, Nagle DL, Smutko JS, Moore KJ. 1997. Theoretical and empirical issues for marker-assisted breeding of congenic mouse strains. Nat Genet. 17:280-284.
Nadeau JH, Singer JB, Matin A, Lander ES. 2000. Analyzing complex genetic traits with chromosome substitution strains. Nat Genet. 24: 221-225.
Silver LM. 1995. Mouse Genetics: Concepts and Applications. Oxford University Press, Oxford.
Snell GD. 1941. Biology of the Laboratory Mouse, 1st Edition, McGraw-Hill, New York
Snell GD. 1978. Congenic resistant strains of mice. In Origins of Inbred Mice, Morse HC (ed.), Academic Press, New York, pp. 1-31.
Staats J. 1985. Standardized Nomenclature for Inbred Strains of Mice: eighth listing. Cancer Res. 45: 945-977
Taylor B.A. 1978. Recombinant inbred strains: use in gene mapping. In Origins of Inbred Mice, Morse, HC. (eds.), Academic Press, New York, pp. 423-438.
Wakeland E, Morel L, Achey K, Yui M, Longmate J. 1997. Speed congenics: a classic technique in the fast lane (relatively speaking). Immunol Today 18: 472-477.
Monday, December 1, 2008
CD 27, CD28
CD27
Also called tumor necrosis factor receptor superfamily member 7
Binds to CD70
Marker of T cell activation; also regulates B cell activation and immunoglobulin synthesis
Uses: help differentiate memory-type CD8+ T cells (CD27+) from effector-type CD8+ T cells (important against pathogens, CD27-); memory B cells (CD27+) from naïve B cells (CD27-)
Positive staining (normal): T cells, memory B cells, NK cells, plasma cells, medullary thymocytes
Positive staining (disease): myelomas (64%, Br J Haematol 2006;132:168)
Negative staining: hairy cell leukemia (Haematologica 2005;90:266)
References: OMIM 186711
CD28
T cells require 2 signals for full activation - the first by binding of the antigen/MHC complex on antigen presenting cell to the T cell receptor; the second is delivered by the interaction of CD28 with its ligands CD80 (B7-1) or CD86 (B7-2), found on activated B cells, and is called a costimulation signal (diagram of 2 signals)
However, “superantagonistic” anti-CD28 antibodies, awaiting clinical trials for autoimmune diseases, activate mature T cells with only one signal (Ann Rheum Dis 2005;64 Suppl 4:iv91)
The costimulatory signal induces T cell activation and survival, interleukin-2 production, T-helper type 2 development and clonal expansion
CD28 is a constitutive, high abundance, low affinity receptor; its binding also increases expression of CTLA4 (CD152), a structurally related cell surface receptor on T cells which has the same ligands but opposite effects (J Clin Immunol 2002;22:1, Curr Pharm Des 2006;12:149); CTLA4 competes with CD28 for the same ligands (diagram)
Imbalance in CTLA-4/CD28 expression at the maternal-fetal interface may confer susceptibility to unexplained pregnancy loss (Int J Gynaecol Obstet 2006;93:123)
CD8+, CD28+ T cells: antigen specific cytotoxic T cells (class I restricted) (90% of CD8+ T cells)
CD8+, CD28- T cells: suppressor T cells; increased in various infectious diseases and autoimmune diseases and associated with aging Loss of T cell CD28 expression is associated with aging, and frequency of CD28(null) T cells predicts immune incompetence in elderly; these T cells are functionally active and long-lived, but have no/limited proliferative capacity (Immunol Rev 2005;205:158)
Uses: no significant clinical use by pathologists
Positive staining (normal): CD4+ T cells (95%), CD8+ T cells (50%); activated B cells, plasma cells (some)
Positive staining (disease): myeloma (95%)
References: OMIM 186760, Blood 2005;105:13
Also called tumor necrosis factor receptor superfamily member 7
Binds to CD70
Marker of T cell activation; also regulates B cell activation and immunoglobulin synthesis
Uses: help differentiate memory-type CD8+ T cells (CD27+) from effector-type CD8+ T cells (important against pathogens, CD27-); memory B cells (CD27+) from naïve B cells (CD27-)
Positive staining (normal): T cells, memory B cells, NK cells, plasma cells, medullary thymocytes
Positive staining (disease): myelomas (64%, Br J Haematol 2006;132:168)
Negative staining: hairy cell leukemia (Haematologica 2005;90:266)
References: OMIM 186711
CD28
T cells require 2 signals for full activation - the first by binding of the antigen/MHC complex on antigen presenting cell to the T cell receptor; the second is delivered by the interaction of CD28 with its ligands CD80 (B7-1) or CD86 (B7-2), found on activated B cells, and is called a costimulation signal (diagram of 2 signals)
However, “superantagonistic” anti-CD28 antibodies, awaiting clinical trials for autoimmune diseases, activate mature T cells with only one signal (Ann Rheum Dis 2005;64 Suppl 4:iv91)
The costimulatory signal induces T cell activation and survival, interleukin-2 production, T-helper type 2 development and clonal expansion
CD28 is a constitutive, high abundance, low affinity receptor; its binding also increases expression of CTLA4 (CD152), a structurally related cell surface receptor on T cells which has the same ligands but opposite effects (J Clin Immunol 2002;22:1, Curr Pharm Des 2006;12:149); CTLA4 competes with CD28 for the same ligands (diagram)
Imbalance in CTLA-4/CD28 expression at the maternal-fetal interface may confer susceptibility to unexplained pregnancy loss (Int J Gynaecol Obstet 2006;93:123)
CD8+, CD28+ T cells: antigen specific cytotoxic T cells (class I restricted) (90% of CD8+ T cells)
CD8+, CD28- T cells: suppressor T cells; increased in various infectious diseases and autoimmune diseases and associated with aging Loss of T cell CD28 expression is associated with aging, and frequency of CD28(null) T cells predicts immune incompetence in elderly; these T cells are functionally active and long-lived, but have no/limited proliferative capacity (Immunol Rev 2005;205:158)
Uses: no significant clinical use by pathologists
Positive staining (normal): CD4+ T cells (95%), CD8+ T cells (50%); activated B cells, plasma cells (some)
Positive staining (disease): myeloma (95%)
References: OMIM 186760, Blood 2005;105:13
Saturday, November 29, 2008
Anti-inflammatory cytokines
A general term for those immunoregulatory cytokines that counteract various aspects of inflammation, for example cell activation or the production of pro-inflammatory cytokines, and thus contribute to the control of the magnitude of the inflammatory responses in vivo.
These mediators act mainly by the inhibition of the production of pro-inflammatory cytokines or by counteracting many biological effects of pro-inflammatory mediators in different ways.
The major anti-inflammatory cytokines are:-
IL4,
IL10, and
IL13.
Other anti-inflammatory mediators include
IL16,
IFN-alpha,
TGF-beta,
IL1ra,
G-CSF,
soluble receptors for TNF or IL6.
These mediators act mainly by the inhibition of the production of pro-inflammatory cytokines or by counteracting many biological effects of pro-inflammatory mediators in different ways.
The major anti-inflammatory cytokines are:-
IL4,
IL10, and
IL13.
Other anti-inflammatory mediators include
IL16,
IFN-alpha,
TGF-beta,
IL1ra,
G-CSF,
soluble receptors for TNF or IL6.
Proinflammatory Cytokines
A general term for those immunoregulatory cytokines that favour inflammation.
The major pro-inflammatory cytokines that are responsible for early responses are:-
IL1-alpha, IL1-beta,
IL6, and
TNF-alpha.
Other pro-inflammatory mediators include:-
LIF,
IFN-gamma,
OSM,
CNTF,
TGF-beta,
GM-CSF,
IL11,
IL12,
IL17,
IL18,
IL8 and a variety of other chemokines that chemoattract inflammatory cells.
These cytokines either act as endogenous pyrogens (IL1, IL6, TNF-alpha), up-regulate the synthesis of secondary mediators and pro-inflammatory cytokines by both macrophages and mesenchymal cells (including fibroblasts, epithelial and endothelial cells), stimulate the production of acute phase proteins, or attract inflammatory cells.
The net effect of an inflammatory response is determined by the balance between pro-inflammatory and anti-inflammatory cytokines. It should be noted that the common and clear-cut classification of cytokines as either pro anti-inflammatory or pro-inflammatory may be misleading. The type, duration, and also the extent of cellular activities induced by one particular cytokine can be influenced considerably by the nature of the target cells, the micro-environment of a cell, depending, for example, on the growth and activation state of the cells, the type of neighboring cells, cytokine concentrations, the presence of other cytokines, and even on the temporal sequence of several cytokines acting on the same cell.
The major pro-inflammatory cytokines that are responsible for early responses are:-
IL1-alpha, IL1-beta,
IL6, and
TNF-alpha.
Other pro-inflammatory mediators include:-
LIF,
IFN-gamma,
OSM,
CNTF,
TGF-beta,
GM-CSF,
IL11,
IL12,
IL17,
IL18,
IL8 and a variety of other chemokines that chemoattract inflammatory cells.
These cytokines either act as endogenous pyrogens (IL1, IL6, TNF-alpha), up-regulate the synthesis of secondary mediators and pro-inflammatory cytokines by both macrophages and mesenchymal cells (including fibroblasts, epithelial and endothelial cells), stimulate the production of acute phase proteins, or attract inflammatory cells.
The net effect of an inflammatory response is determined by the balance between pro-inflammatory and anti-inflammatory cytokines. It should be noted that the common and clear-cut classification of cytokines as either pro anti-inflammatory or pro-inflammatory may be misleading. The type, duration, and also the extent of cellular activities induced by one particular cytokine can be influenced considerably by the nature of the target cells, the micro-environment of a cell, depending, for example, on the growth and activation state of the cells, the type of neighboring cells, cytokine concentrations, the presence of other cytokines, and even on the temporal sequence of several cytokines acting on the same cell.
Elispot
The Enzyme-linked immunosorbent spot (ELISPOT) assay is a common method for monitoring immune responses in humans and animals. It was developed by Cecil Czerkinsky in 1983.[1]
The ELISPOT assay is based on, and was developed from a modified version of the ELISA immunoassay. ELISPOT assays were originally developed to enumerate B cells secreting antigen-specific antibodies, and have subsequently been adapted for various tasks, especially the identification and enumeration of cytokine-producing cells at the single cell level. Simply put, at appropriate conditions the ELISPOT assay allows visualization of the secretory product of individual activated or responding cells. Each spot that develops in the assay represents a single reactive cell. Thus, the ELISPOT assay provides both qualitative (type of immune protein) and quantitative (number of responding cells) information.
By virtue of exquisite sensitivity of the ELISPOT assay, frequency analysis of rare cell populations (e.g., antigen-specific responses) which were not possible before are now relatively easy. This exceptional sensitivity is in part because the product is rapidly captured around the secreting cell: before it is either diluted in the supernatant, captured by receptors of adjacent cells, or degraded. This makes ELISPOT assays much more sensitive than conventional ELISA measurements. Limits of detection are below 1/100,000 rendering the assay uniquely useful for monitoring antigen-specific responses, applicable to a wide range of areas of immunology research, including cancer, transplantation, infectious disease, and vaccine development. The assay has gained a recent increase in popularity, especially as a surrogate measure for CTL responses, in large part because it is both reliable and highly sensitive.
While ELISPOT assay techniques have existed for more than two decades now advancements are still being made in the assay. Modern ELISPOT analysis is typically performed using ELISPOT readers, which employ computer vision techniques to enumerate the actively producing cells. This allows much of the analysis process to be automated, and permits a greater level of accuracy than what can be achieved using manual inspection.
Friday, November 28, 2008
CD86
Also called B7-2
T cells need two signals for activation - the first signal is antigen peptide presented on MHC class II through the T cell receptor
The second (costimulatory) signal is delivered by CD80 or CD86, expressed on surface of antigen presenting cells, which interact with either CD28 or CD152 (CTLA-4)
CD80 and CD86 appear to have opposing functions on regulatory T cells (J Immunol 2004;172:2778)
Polymorphisms are associated with liver transplant acceptance (Transpl Immunol 2005;15:69) and systemic sclerosis (Int J Immunogenet 2006;33:155)
Increased expression may cause excessive antigen presentation in fulminant hepatic failure as an early step in its pathogenesis before the onset of tissue damage (Am J Pathol 1999;154:1711)
High circulating soluble levels are poor prognostic factor in myeloma (Br J Haematol 2006;133:165); are associated with severe asthma (Thorax 2004;59:870)
Receptor for some adenovirus species (Virus Res 2006;122:144)
Associated with H. pylori dependent early stage high grade MALT lymphoma of stomach (World J Gastroenterol 2005;11:4357)
Uses: no significant clinical use by pathologists
Diagram: costimulatory signal
Micro images: inflamed skin; fulminant hepatic failure; chronic HBV infection of liver; liver sinusoidal endothelial cells; thyroid carcinoma (E-H); normal esophagus; esophageal carcinoma
early stage high grade gastric MALT lymphoma - H. pylori dependent case (CD86+); H. pylori independent case (CD86-)
Positive staining (normal): interdigitating dendritic cells in T zones of secondary lymphoid organs, Langerhans cells, peripheral blood dendritic cells, memory B cells, germinal center B cells, monocytes, endothelial cells, activated T cells
Positive staining (disease): AML (29%, Clin Cancer Res 2005;11:5708), ulcerative colitis (100%, Dig Dis Sci 2004;49:1738)
Negative staining: immature dendritic cells
References: OMIM 601020
T cells need two signals for activation - the first signal is antigen peptide presented on MHC class II through the T cell receptor
The second (costimulatory) signal is delivered by CD80 or CD86, expressed on surface of antigen presenting cells, which interact with either CD28 or CD152 (CTLA-4)
CD80 and CD86 appear to have opposing functions on regulatory T cells (J Immunol 2004;172:2778)
Polymorphisms are associated with liver transplant acceptance (Transpl Immunol 2005;15:69) and systemic sclerosis (Int J Immunogenet 2006;33:155)
Increased expression may cause excessive antigen presentation in fulminant hepatic failure as an early step in its pathogenesis before the onset of tissue damage (Am J Pathol 1999;154:1711)
High circulating soluble levels are poor prognostic factor in myeloma (Br J Haematol 2006;133:165); are associated with severe asthma (Thorax 2004;59:870)
Receptor for some adenovirus species (Virus Res 2006;122:144)
Associated with H. pylori dependent early stage high grade MALT lymphoma of stomach (World J Gastroenterol 2005;11:4357)
Uses: no significant clinical use by pathologists
Diagram: costimulatory signal
Micro images: inflamed skin; fulminant hepatic failure; chronic HBV infection of liver; liver sinusoidal endothelial cells; thyroid carcinoma (E-H); normal esophagus; esophageal carcinoma
early stage high grade gastric MALT lymphoma - H. pylori dependent case (CD86+); H. pylori independent case (CD86-)
Positive staining (normal): interdigitating dendritic cells in T zones of secondary lymphoid organs, Langerhans cells, peripheral blood dendritic cells, memory B cells, germinal center B cells, monocytes, endothelial cells, activated T cells
Positive staining (disease): AML (29%, Clin Cancer Res 2005;11:5708), ulcerative colitis (100%, Dig Dis Sci 2004;49:1738)
Negative staining: immature dendritic cells
References: OMIM 601020
CD43
Also called leukosialin, sialophorin
Appears to be important for immune function and may be part of a physiologic ligand-receptor complex involved in T-cell activation
Serves as a ligand for E-selectin on T cells and may regulate T cell trafficking (Blood 2006;107:1421, J Immunol 2005;175:8042)
Defective expression in T cells of males with Wiskott-Aldrich syndrome (OMIM 301000)
Uses: pan T cell marker, diagnosis of granulocytic sarcoma (J Clin Pathol 2005;58:211), classify T cell and low grade B cell lymphoma subtype, differentiate pulmonary MALT lymphoma (CD20+ CD43+) from lymphoid hyperplasia (CD43 neg, AJSP 2002;26:76)
Micro images: anaplastic large B cell lymphoma #1 of breast (figure c); #2-post transplant tumor of stomach (figure D); #3-AIDS associated; blastic NK lymphoma; #1 of breast (figure 6); atypical SLL/CLL
Positive staining (normal): most T cells, activated B cells, B cells in terminal ileum (Appl Immunohistochem Mol Morphol 2005;13:138), plasma cells (Scand J Immunol. 1991 Feb;33(2):211-8.), NK cells, granulocytes, monocytes, megakaryocytes, erythroid cells, hematogones (Br J Haematol 2005;128:820), Langerhans cells, brain, thymocytes, some macrophages, platelets (weak)
Positive staining (disease): T/NK cell lymphomas - anaplastic large cell (variable), blastic NK, hepatosplenic gamma-delta T cell, lymphoplasmacytic (variable), NK/T cell-nasal type (96%, Hum Path 2004;35:86), peripheral T cell, subcutaneous panniculitis-like, CD4+ CD56+ lineage negative malignancies (AJSP 2005;29:1274)
B cell lymphomas - ALL (most), Burkitt’s (almost all), Burkitt’s-like (almost all, AJSP 2005;29:1652), lymphoblastic (variable), mantle cell (100%, AJCP 2003;119:218), marginal zone (variable), nodal marginal zone (variable, AJSP 2003;27:762), plasmablastic, SLL/CLL (AJCP 1999;112:319)
other - AML, granulocytic sarcoma, hemangioma, Langerhans cell histiocytosis, mast cell disease (AJSP 2000;24:703), plasmacytoma; early colonic adenoma (Oncol Rep 2004;11:327)
Negative staining: colonic epithelium, follicular lymphoma, Hodgkin’s lymphoma, lymphoepithelioma-like thymic carcinoma, primary effusion lymphoma, splenic marginal zone lymphoma
References: OMIM 182160
Appears to be important for immune function and may be part of a physiologic ligand-receptor complex involved in T-cell activation
Serves as a ligand for E-selectin on T cells and may regulate T cell trafficking (Blood 2006;107:1421, J Immunol 2005;175:8042)
Defective expression in T cells of males with Wiskott-Aldrich syndrome (OMIM 301000)
Uses: pan T cell marker, diagnosis of granulocytic sarcoma (J Clin Pathol 2005;58:211), classify T cell and low grade B cell lymphoma subtype, differentiate pulmonary MALT lymphoma (CD20+ CD43+) from lymphoid hyperplasia (CD43 neg, AJSP 2002;26:76)
Micro images: anaplastic large B cell lymphoma #1 of breast (figure c); #2-post transplant tumor of stomach (figure D); #3-AIDS associated; blastic NK lymphoma; #1 of breast (figure 6); atypical SLL/CLL
Positive staining (normal): most T cells, activated B cells, B cells in terminal ileum (Appl Immunohistochem Mol Morphol 2005;13:138), plasma cells (Scand J Immunol. 1991 Feb;33(2):211-8.), NK cells, granulocytes, monocytes, megakaryocytes, erythroid cells, hematogones (Br J Haematol 2005;128:820), Langerhans cells, brain, thymocytes, some macrophages, platelets (weak)
Positive staining (disease): T/NK cell lymphomas - anaplastic large cell (variable), blastic NK, hepatosplenic gamma-delta T cell, lymphoplasmacytic (variable), NK/T cell-nasal type (96%, Hum Path 2004;35:86), peripheral T cell, subcutaneous panniculitis-like, CD4+ CD56+ lineage negative malignancies (AJSP 2005;29:1274)
B cell lymphomas - ALL (most), Burkitt’s (almost all), Burkitt’s-like (almost all, AJSP 2005;29:1652), lymphoblastic (variable), mantle cell (100%, AJCP 2003;119:218), marginal zone (variable), nodal marginal zone (variable, AJSP 2003;27:762), plasmablastic, SLL/CLL (AJCP 1999;112:319)
other - AML, granulocytic sarcoma, hemangioma, Langerhans cell histiocytosis, mast cell disease (AJSP 2000;24:703), plasmacytoma; early colonic adenoma (Oncol Rep 2004;11:327)
Negative staining: colonic epithelium, follicular lymphoma, Hodgkin’s lymphoma, lymphoepithelioma-like thymic carcinoma, primary effusion lymphoma, splenic marginal zone lymphoma
References: OMIM 182160
CD23
Also known as low affinity IgE receptor, Fc fragment of IgE receptor, FCER
A type C lectin that can be secreted
After physiologic germinal cell development, the follicular dendritic cell meshwork expands and follicular dendritic cells in the light zone of the germinal center become CD23 positive
CD23 acts as a B cell growth and activation factor, promoting differentiation into plasma cells
Regulates IgE synthesis through CD21 and IgE binding (J Exp Med 2005;202:751), and mediates IgE related immune responses (Clin Rev Allergy Immunol 2005;29:61)
Shows variability in flow cytometry expression between specimens from same patient (AJCP 2002;117:615)
CD21, CD23 and CD35 are dendritic cell markers
High expression on B cells in peripheral blood is associated with bullous pemphigoid (J Dermatol Sci 2004;35:53)
CD23 antibodies may decrease adherence of Plasmodium falciparum-infected erythrocytes (Cell Microbiol 2004;6:839)
Mantle cell lymphoma: usually CD23 negative, but rarely/often has CD23 present with dim intensity by flow cytometry, AJCP 2003;120:760 / AJCP 2001;116:893; CD23+ mantle cell cases have high cyclin D1 levels, AJCP 2002;117:237); rarely has CD23+ cells in peripheral blood (AJCP 2002;118:758)
Uses: differentiate SLL/CLL (CD23+) vs. mantle cell lymphoma or MALT lymphoma (CD23-); B cell marker, particularly for SLL/CLL, mediastinal large B cell lymphoma and lymphoplasmacytic lymphoma; distinguish nodal mantle cell lymphoma from follicular lymphoma by identifying a disrupted follicular dendritic cell pattern (Int J Surg Pathol 2005;13:73), may identify prognostically favorable cases of diffuse large B cell lymphoma (Clin Cancer Res 2003;9:722), high soluble CD23 is associated with aggressive disease and poorer prognosis in CLL (Leuk Lymphoma 2002;43:549, Clin Lab Haematol 2006;28:30)
Micro images: angioimmunoblastic T cell lymphoma (figure F: CD23 highlights extrafollicular meshworks of follicular dendritic cells); CD23 negative MALT lymphoma with CD23+ follicular centers; CD23 negative mantle cell lymphoma with CD23+ follicular center
contributed by Leica Microsystems, Biosystems Division: normal tonsil; follicular lymphoma
Positive staining (normal): activated mature B cells expressing IgM or IgD (particularly mantle cells), activated monocytes / macrophages, T cell subsets, platelets, eosinophils, Langerhans cells, follicular dendritic cells, intestinal epithelium (encodes IgE receptor, Gastroenterology 2005;129:928)
Positive staining (disease): B-cell CLL/SLL (almost all cases; high levels, Leuk Res 2002;26:809; atypical cases may have higher levels, AJCP 2001;116:655); follicular dendritic cell tumors (including inflammatory pseudotumor type- AJSP 2001;25:721), mediastinal large B cell lymphoma (70%, Histopathology 2004;45:619), lymphoplasmacytic lymphoma (61%, usually dim intensity by flow cytometry, AJCP 2005;124:414, Clin Lymphoma 2005;5:246), hairy cell leukemia (17%, AJCP 2006;125:251), diffuse large B cell lymphoma (16%),
Negative staining: other B cell lymphomas including Burkitt’s lymphoma, Burkitt-like lymphoma (AJSP 2005;29:1652), follicular lymphoma, mantle cell lymphoma, marginal zone lymphoma (AJSP 1999;23:59, Mod Path 1998;11:967); also most T cell lymphomas, inflammatory fibroid polyps of the gastrointestinal tract (although of dendritic cell origin, AJSP 2004;28:107), follicular dendritic cell tumor, interdigitating dendritic cell tumor
References: OMIM 151445, Hum Path 1999;30:648 (early study)
A type C lectin that can be secreted
After physiologic germinal cell development, the follicular dendritic cell meshwork expands and follicular dendritic cells in the light zone of the germinal center become CD23 positive
CD23 acts as a B cell growth and activation factor, promoting differentiation into plasma cells
Regulates IgE synthesis through CD21 and IgE binding (J Exp Med 2005;202:751), and mediates IgE related immune responses (Clin Rev Allergy Immunol 2005;29:61)
Shows variability in flow cytometry expression between specimens from same patient (AJCP 2002;117:615)
CD21, CD23 and CD35 are dendritic cell markers
High expression on B cells in peripheral blood is associated with bullous pemphigoid (J Dermatol Sci 2004;35:53)
CD23 antibodies may decrease adherence of Plasmodium falciparum-infected erythrocytes (Cell Microbiol 2004;6:839)
Mantle cell lymphoma: usually CD23 negative, but rarely/often has CD23 present with dim intensity by flow cytometry, AJCP 2003;120:760 / AJCP 2001;116:893; CD23+ mantle cell cases have high cyclin D1 levels, AJCP 2002;117:237); rarely has CD23+ cells in peripheral blood (AJCP 2002;118:758)
Uses: differentiate SLL/CLL (CD23+) vs. mantle cell lymphoma or MALT lymphoma (CD23-); B cell marker, particularly for SLL/CLL, mediastinal large B cell lymphoma and lymphoplasmacytic lymphoma; distinguish nodal mantle cell lymphoma from follicular lymphoma by identifying a disrupted follicular dendritic cell pattern (Int J Surg Pathol 2005;13:73), may identify prognostically favorable cases of diffuse large B cell lymphoma (Clin Cancer Res 2003;9:722), high soluble CD23 is associated with aggressive disease and poorer prognosis in CLL (Leuk Lymphoma 2002;43:549, Clin Lab Haematol 2006;28:30)
Micro images: angioimmunoblastic T cell lymphoma (figure F: CD23 highlights extrafollicular meshworks of follicular dendritic cells); CD23 negative MALT lymphoma with CD23+ follicular centers; CD23 negative mantle cell lymphoma with CD23+ follicular center
contributed by Leica Microsystems, Biosystems Division: normal tonsil; follicular lymphoma
Positive staining (normal): activated mature B cells expressing IgM or IgD (particularly mantle cells), activated monocytes / macrophages, T cell subsets, platelets, eosinophils, Langerhans cells, follicular dendritic cells, intestinal epithelium (encodes IgE receptor, Gastroenterology 2005;129:928)
Positive staining (disease): B-cell CLL/SLL (almost all cases; high levels, Leuk Res 2002;26:809; atypical cases may have higher levels, AJCP 2001;116:655); follicular dendritic cell tumors (including inflammatory pseudotumor type- AJSP 2001;25:721), mediastinal large B cell lymphoma (70%, Histopathology 2004;45:619), lymphoplasmacytic lymphoma (61%, usually dim intensity by flow cytometry, AJCP 2005;124:414, Clin Lymphoma 2005;5:246), hairy cell leukemia (17%, AJCP 2006;125:251), diffuse large B cell lymphoma (16%),
Negative staining: other B cell lymphomas including Burkitt’s lymphoma, Burkitt-like lymphoma (AJSP 2005;29:1652), follicular lymphoma, mantle cell lymphoma, marginal zone lymphoma (AJSP 1999;23:59, Mod Path 1998;11:967); also most T cell lymphomas, inflammatory fibroid polyps of the gastrointestinal tract (although of dendritic cell origin, AJSP 2004;28:107), follicular dendritic cell tumor, interdigitating dendritic cell tumor
References: OMIM 151445, Hum Path 1999;30:648 (early study)
CD21
Also called CR2, C3d receptor, EBV receptor
Binds to Epstein Barr virus (EBV) and HHV8 (J Virol 2005;79:4651), breakdown products of complement component C3 (C3d), CD23 (plays a role in IgE synthesis) and possibly gamma interferon
Follicular dendritic cells produce a different isoform of CD21 than B cells (J Exp Med 1997;185:165)
CD21, CD23 and CD35 are dendritic cell markers
Hodgkin’s lymphoma demonstrates disruption of follicular dendritic cell-germinal cell clusters (evaluated by CD21 and CD23)
Note: although CD21 is the receptor for EBV, it is not necessarily expressed in EBV+ tumors
Shows variability in flow cytometry expression between specimens from same patient (AJCP 2002;117:615)
Uses: diagnose follicular dendritic cell sarcomas (AJSP 1996;20:944); assess follicular dendritic cell meshwork infrastructure (AJCP 2005;124:182, AJSP 2001;25:388), distinguish cutaneous or nodal mantle cell lymphoma from follicular lymphoma (AJSP 2001;25:732, Int J Surg Pathol 2005;13:73), distinguish splenic littoral cell angioma (CD21+ lining cells) from splenic hamartomas (CD21-, AJSP 1997;21:827), confirm that atypical cells have follicular dendritic origin in fine needle aspirates of hyaline-vascular Castleman’s disease (Diagn Cytopathol 2000;22:230)
Micro images: normal germinal center
follicular dendritic cell sarcoma - (1) liver (figure 2B); (2) figure 1: liver tumor (inset: splenic tumor); 2a/b: H&E; 2c: CD21; 2d: CD35; (3) stomach (figure 4 is CD21/CD35 cocktail)
follicular lymphoma - well organized clusters of dendritic cells in follicular lymphoma #1 (testicular)); #2 (head and neck); #3 (head and neck); peripheral T cell lymphoma resembling follicular lymphoma
Positive staining (normal): mature B cells (particularly marginal and mantle cells), follicular dendritic cells, pharyngeal and cervical epithelial cells, some thymocytes, some T cells
Positive staining (tumors): follicular dendritic cell sarcoma (AJSP 2004;28:988, AJSP 2001;25:721), hairy cell leukemia, B cell lymphomas (particularly mantle and marginal zone), hyaline vascular variant of Castleman's disease (AJSP 2002;26:662), splenic littoral cell angiomas (lining cells are CD21+, AJSP 1997;21:827), some T-ALL
Negative staining: dendritic cell neurofibroma with pseudorosettes (AJSP 2001;25:587), interdigitating dendritic cell sarcoma (AJCP 2001;115:589), histiocytic sarcoma (AJSP 2004;28:1133), inflammatory fibroid polyps of GI tract (AJSP 2004;28:107), splenic hamartomas, plasma cells
References: AJSP 2001;25:721, Mod Path 2002;15:50, OMIM 120650
Binds to Epstein Barr virus (EBV) and HHV8 (J Virol 2005;79:4651), breakdown products of complement component C3 (C3d), CD23 (plays a role in IgE synthesis) and possibly gamma interferon
Follicular dendritic cells produce a different isoform of CD21 than B cells (J Exp Med 1997;185:165)
CD21, CD23 and CD35 are dendritic cell markers
Hodgkin’s lymphoma demonstrates disruption of follicular dendritic cell-germinal cell clusters (evaluated by CD21 and CD23)
Note: although CD21 is the receptor for EBV, it is not necessarily expressed in EBV+ tumors
Shows variability in flow cytometry expression between specimens from same patient (AJCP 2002;117:615)
Uses: diagnose follicular dendritic cell sarcomas (AJSP 1996;20:944); assess follicular dendritic cell meshwork infrastructure (AJCP 2005;124:182, AJSP 2001;25:388), distinguish cutaneous or nodal mantle cell lymphoma from follicular lymphoma (AJSP 2001;25:732, Int J Surg Pathol 2005;13:73), distinguish splenic littoral cell angioma (CD21+ lining cells) from splenic hamartomas (CD21-, AJSP 1997;21:827), confirm that atypical cells have follicular dendritic origin in fine needle aspirates of hyaline-vascular Castleman’s disease (Diagn Cytopathol 2000;22:230)
Micro images: normal germinal center
follicular dendritic cell sarcoma - (1) liver (figure 2B); (2) figure 1: liver tumor (inset: splenic tumor); 2a/b: H&E; 2c: CD21; 2d: CD35; (3) stomach (figure 4 is CD21/CD35 cocktail)
follicular lymphoma - well organized clusters of dendritic cells in follicular lymphoma #1 (testicular)); #2 (head and neck); #3 (head and neck); peripheral T cell lymphoma resembling follicular lymphoma
Positive staining (normal): mature B cells (particularly marginal and mantle cells), follicular dendritic cells, pharyngeal and cervical epithelial cells, some thymocytes, some T cells
Positive staining (tumors): follicular dendritic cell sarcoma (AJSP 2004;28:988, AJSP 2001;25:721), hairy cell leukemia, B cell lymphomas (particularly mantle and marginal zone), hyaline vascular variant of Castleman's disease (AJSP 2002;26:662), splenic littoral cell angiomas (lining cells are CD21+, AJSP 1997;21:827), some T-ALL
Negative staining: dendritic cell neurofibroma with pseudorosettes (AJSP 2001;25:587), interdigitating dendritic cell sarcoma (AJCP 2001;115:589), histiocytic sarcoma (AJSP 2004;28:1133), inflammatory fibroid polyps of GI tract (AJSP 2004;28:107), splenic hamartomas, plasma cells
References: AJSP 2001;25:721, Mod Path 2002;15:50, OMIM 120650
CD19, CD20
CD19
Coreceptor with CD21
Earliest B cell antigen in fetal tissue
Regulates B cell development, activation and differentiation (J Immunol 2003;171:5921)
May define intrinsic and antigen receptor-induced signaling thresholds critical for clonal expansion of the B cell pool and humoral immunity (Curr Dir Autoimmun 2005;8:55)
More common in plasma cells in steroid resistant ulcerative colitis than Crohn’s disease (Virchows Arch 2006;448:412); presence of CD19+ cells in intestinal mucosa may predict long remission after infliximab (anti-TNF alpha) therapy in Crohn’s disease (Hepatogastroenterology 2005;52:1128)
Uses: diagnosis of B cells and B cell disorders; may be more sensitive than CD20 to detect B cell acute leukemias (Zhongguo Shi Yan Xue Ye Xue Za Zhi 2005;13:943), to differentiate follicular lymphoma (dimmer CD19 in CD10+ B cells by flow cytometry) from reactive hyperplasia (AJCP 2005;124:576)
Flow cytometry images: follicular lymphoma with IgG light chain restriction; biphenotypic acute leukemia with CD19 and myeloperoxidase coexpression (figure B); hairy cell leukemia variant: A-CD20 (bright) and CD22+; B-CD11c+ and CD22+; C-CD103+ and CD25 negative; D-CD19+ and FMC7+; E-kappa+; F-lambda negative
Positive staining (normal): Pre B cells, B cells (considered a pan B cell antigen); first B cell antigen after HLA-DR, follicular dendritic cells
Positive staining (disease): B cell lymphomas and leukemias but often weak/negative in follicular lymphoma or diffuse large B cell lymphoma (Histopathology 2006;48:239, Cytometry B Clin Cytom 2005;63:28), occasional myeloid leukemias (AML-AJCP 1998;109:211; AML-M0-AJCP 2001;115:876; CML blast phase-AJCP 2004;121:836), occasional anaplastic large cell lymphoma by flow cytometry (AJCP 2003;119:205)
Negative staining: plasma cells, myeloma (AJCP 2004;121:482), most T cell lymphomas, often L&H cells in lymphocyte predominant Hodgkin’s lymphoma, often post-transplant B cell lymphoproliferative disorder
References: OMIM 107265
CD20
Also called L26, membrane spanning 4 domains (MS4A1)
33kd phosphoprotein with 3 hydrophobic regions that traverse the cell membrane, creating a structure similar to an ion channel that allows for the influx of calcium required for cell activation
Initially expressed on B cells after CD19/CD10 expression and before CD21/CD22 and surface immunoglobulin expression; retained on mature B cells until plasma cell development
Delivers early signal in B cell activation, allowing resting B cells to respond to later antigens
Closely related to FMC7, which recognizes a CD20 epitope (Leukemia 2003;17:1384), particularly if there is strong CD20 expression (AJCP 2003;120:754)
Rituximab is a chimeric murine-human anti-CD20 antibody used to treat B cell lymphomas; treatment may cause selection of CD20 negative (but CD79a+) tumor subclones (AJSP 2005;29:1399)
Rituximab is also used to treat autoimmune disorders (Clin Immunol 2005;117:207), TTP/HUS (Acta Cytol 2005;19:423), ABO incompatible transplantation (Transplant Proc 2005;37:1205) and transplant rejection (Clin Transplant 2005;19:137)
Anti CD20-antibody attached to radioisotopes is also used to treat B cell lymphomas (Clin Exp Med 2006;6:1)
Case reports: CD20+ T cell lymphomas (Am J Hematol 2002;71:331, AJCP 1994;102:483, Mod Path 2001;14:105, Mod Path 2000;13:1244); rarely stains nucleoli of malignant T cells (Acta Cytol 2005;49:365), but see J Clin Pathol 2004;57:442
Uses: commonly used marker for B cells
Micro images: normal lymph node #1; #2
angioimmunoblastic T cell lymphoma (figure d)
diffuse large B cell lymphoma - bone; brain-#1; #4 (figure A); #5 (intravascular); #6 (intravascular); liver; nasal cavity (figure 3A); ovary CD20 (fig 3), CD3 (fig 4); sclerosing; skin (figure 1D); small intestine; unknown site #1-intravascular; #2-sclerosing subtype
other leukemia/lymphoma - follicular lymphoma #1; #2 (childhood); hairy cell leukemia #1; #2-variant type (figure D); Hodgkin’s lymphoma #1-lymphocyte predominant (figures C&D); #2 (figure C); #3-mostly negative Reed-Sternberg cells); lymphoplasmacytic lymphoma/ Waldenström macroglobulinemia #1 (brain-figure D); MALT lymphoma #1 of bladder; #2 of liver; #3 of lung;
SLL of colon (figure C)
post-transplantation lymphoproliferative disorder - #1; #2 (polymorphic subtype-figure C); #3 of liver: H&E, CD20, EBV
other - ectopic hamartomatous thymoma (figure C); lymphocytic mastitis: CD20+/CD3- lymphocytes (B, not T cells); immunoblastic myofibroblastic tumor (figure 2d-reactive B cells)
Additional images: intravascular large cell lymphoma (figure 2a); post-transplant lymphoproliferative disorder
Virtual slides: diffuse large B cell lymphoma
Flow cytometry images: hairy cell leukemia variant - A-CD20 (bright) and CD22+; B-CD11c+ and CD22+; C-CD103+ and CD25 negative; D-CD19+ and FMC7+; E-kappa+; F-lambda negative
Positive staining (normal): most B cells (considered a pan B cell antigen), also follicular dendritic cells
Positive staining (disease): 90% of B cell lymphomas; also B-CLL, hairy cell leukemia, spindle cell thymomas (AJSP 1992;16:988), 40% of pre B ALL/LBL; 80% of nodular lymphocyte predominant Hodgkin’s lymphoma, 20% of classic Hodgkin’s lymphoma (may be an adverse prognostic factor, Br J Haematol 2004;125:701); dimly expressed in T cells (benign and neoplastic, particularly in bone marrow, AJCP 1996;106:78, AJCP 1994;102:483), some myelomas (Mod Path 2004;17:1217, Blood 2003;102:1070)
Negative staining: non-hematopoietic cells, most T cells, plasma cells, mastocytosis
Note: staining does not work well with Bouin’s fixative
Flow cytometry: brighter expression in follicular lymphomas than normal B cells (AJCP 2005;124:576)
References: OMIM 112210, J Biol Chem 2004;279:19893 (presence in lipid rafts)
Coreceptor with CD21
Earliest B cell antigen in fetal tissue
Regulates B cell development, activation and differentiation (J Immunol 2003;171:5921)
May define intrinsic and antigen receptor-induced signaling thresholds critical for clonal expansion of the B cell pool and humoral immunity (Curr Dir Autoimmun 2005;8:55)
More common in plasma cells in steroid resistant ulcerative colitis than Crohn’s disease (Virchows Arch 2006;448:412); presence of CD19+ cells in intestinal mucosa may predict long remission after infliximab (anti-TNF alpha) therapy in Crohn’s disease (Hepatogastroenterology 2005;52:1128)
Uses: diagnosis of B cells and B cell disorders; may be more sensitive than CD20 to detect B cell acute leukemias (Zhongguo Shi Yan Xue Ye Xue Za Zhi 2005;13:943), to differentiate follicular lymphoma (dimmer CD19 in CD10+ B cells by flow cytometry) from reactive hyperplasia (AJCP 2005;124:576)
Flow cytometry images: follicular lymphoma with IgG light chain restriction; biphenotypic acute leukemia with CD19 and myeloperoxidase coexpression (figure B); hairy cell leukemia variant: A-CD20 (bright) and CD22+; B-CD11c+ and CD22+; C-CD103+ and CD25 negative; D-CD19+ and FMC7+; E-kappa+; F-lambda negative
Positive staining (normal): Pre B cells, B cells (considered a pan B cell antigen); first B cell antigen after HLA-DR, follicular dendritic cells
Positive staining (disease): B cell lymphomas and leukemias but often weak/negative in follicular lymphoma or diffuse large B cell lymphoma (Histopathology 2006;48:239, Cytometry B Clin Cytom 2005;63:28), occasional myeloid leukemias (AML-AJCP 1998;109:211; AML-M0-AJCP 2001;115:876; CML blast phase-AJCP 2004;121:836), occasional anaplastic large cell lymphoma by flow cytometry (AJCP 2003;119:205)
Negative staining: plasma cells, myeloma (AJCP 2004;121:482), most T cell lymphomas, often L&H cells in lymphocyte predominant Hodgkin’s lymphoma, often post-transplant B cell lymphoproliferative disorder
References: OMIM 107265
CD20
Also called L26, membrane spanning 4 domains (MS4A1)
33kd phosphoprotein with 3 hydrophobic regions that traverse the cell membrane, creating a structure similar to an ion channel that allows for the influx of calcium required for cell activation
Initially expressed on B cells after CD19/CD10 expression and before CD21/CD22 and surface immunoglobulin expression; retained on mature B cells until plasma cell development
Delivers early signal in B cell activation, allowing resting B cells to respond to later antigens
Closely related to FMC7, which recognizes a CD20 epitope (Leukemia 2003;17:1384), particularly if there is strong CD20 expression (AJCP 2003;120:754)
Rituximab is a chimeric murine-human anti-CD20 antibody used to treat B cell lymphomas; treatment may cause selection of CD20 negative (but CD79a+) tumor subclones (AJSP 2005;29:1399)
Rituximab is also used to treat autoimmune disorders (Clin Immunol 2005;117:207), TTP/HUS (Acta Cytol 2005;19:423), ABO incompatible transplantation (Transplant Proc 2005;37:1205) and transplant rejection (Clin Transplant 2005;19:137)
Anti CD20-antibody attached to radioisotopes is also used to treat B cell lymphomas (Clin Exp Med 2006;6:1)
Case reports: CD20+ T cell lymphomas (Am J Hematol 2002;71:331, AJCP 1994;102:483, Mod Path 2001;14:105, Mod Path 2000;13:1244); rarely stains nucleoli of malignant T cells (Acta Cytol 2005;49:365), but see J Clin Pathol 2004;57:442
Uses: commonly used marker for B cells
Micro images: normal lymph node #1; #2
angioimmunoblastic T cell lymphoma (figure d)
diffuse large B cell lymphoma - bone; brain-#1; #4 (figure A); #5 (intravascular); #6 (intravascular); liver; nasal cavity (figure 3A); ovary CD20 (fig 3), CD3 (fig 4); sclerosing; skin (figure 1D); small intestine; unknown site #1-intravascular; #2-sclerosing subtype
other leukemia/lymphoma - follicular lymphoma #1; #2 (childhood); hairy cell leukemia #1; #2-variant type (figure D); Hodgkin’s lymphoma #1-lymphocyte predominant (figures C&D); #2 (figure C); #3-mostly negative Reed-Sternberg cells); lymphoplasmacytic lymphoma/ Waldenström macroglobulinemia #1 (brain-figure D); MALT lymphoma #1 of bladder; #2 of liver; #3 of lung;
SLL of colon (figure C)
post-transplantation lymphoproliferative disorder - #1; #2 (polymorphic subtype-figure C); #3 of liver: H&E, CD20, EBV
other - ectopic hamartomatous thymoma (figure C); lymphocytic mastitis: CD20+/CD3- lymphocytes (B, not T cells); immunoblastic myofibroblastic tumor (figure 2d-reactive B cells)
Additional images: intravascular large cell lymphoma (figure 2a); post-transplant lymphoproliferative disorder
Virtual slides: diffuse large B cell lymphoma
Flow cytometry images: hairy cell leukemia variant - A-CD20 (bright) and CD22+; B-CD11c+ and CD22+; C-CD103+ and CD25 negative; D-CD19+ and FMC7+; E-kappa+; F-lambda negative
Positive staining (normal): most B cells (considered a pan B cell antigen), also follicular dendritic cells
Positive staining (disease): 90% of B cell lymphomas; also B-CLL, hairy cell leukemia, spindle cell thymomas (AJSP 1992;16:988), 40% of pre B ALL/LBL; 80% of nodular lymphocyte predominant Hodgkin’s lymphoma, 20% of classic Hodgkin’s lymphoma (may be an adverse prognostic factor, Br J Haematol 2004;125:701); dimly expressed in T cells (benign and neoplastic, particularly in bone marrow, AJCP 1996;106:78, AJCP 1994;102:483), some myelomas (Mod Path 2004;17:1217, Blood 2003;102:1070)
Negative staining: non-hematopoietic cells, most T cells, plasma cells, mastocytosis
Note: staining does not work well with Bouin’s fixative
Flow cytometry: brighter expression in follicular lymphomas than normal B cells (AJCP 2005;124:576)
References: OMIM 112210, J Biol Chem 2004;279:19893 (presence in lipid rafts)
CD16
CD16a
Also known as Fc gamma receptor III A, low affinity immunoglobulin gamma Fc region receptor III-A
Receptor for the Fc portion of IgG; binds various IgG molecules, including rheumatoid factor
Mediates antibody dependent cytotoxicity of foreign cells, phagocytosis and other antibody-dependent responses; also platelet satellitism (AJCP 1995;103:740)
Affinity to ligand is regulated by glycosylation (Immunology 2003;110:335)
CD14+ CD16+ monocytes have increased capacity to produce proinflammatory cytokines such as TNF-alpha, and are elevated in various inflammatory diseases, including coronary artery disease (Thromb Haemost 2004;92:419)
Polymorphisms influence: (a) the severity but not the incidence of IgA nephropathy in Japanese patients (Nephrol Dial Transplant 2005;20:2439); (b) pathogenesis of coronary artery disease (Atherosclerosis 2005;180:277), (c) clinical response to rituximab (Cancer Res 2004;64:4664)
If target cell has class I MHC, then NK cell's killer cell inhibitory receptor (KIR) inhibits cytolysis
Note: preincubation with CD16/CD32 antibodies is commonly used to prevent nonspecific binding
Uses: NK cell and macrophage marker; to subtype leukemia/lymphoma
Diagrams: NK cell mediated cytotoxicity [CD16 / FcgammaRIII is activating receptor on NK cell]
Positive staining (normal): NK cells (10-20%), granulocytes, macrophages, T cells (reactive), immature thymocytes, placental trophoblast
Positive staining (disease): NK proliferative disorders, T cell large granular lymphocyte leukemia, hepatosplenic gamma-delta T cell lymphoma
References: OMIM 146740
CD16b
Also known as Fc gamma receptor III B, low affinity immunoglobulin gamma Fc region receptor III-B
Highly homologous to CD16a
The most common receptor for the Fc domain of IgG on leukocytes
The only Fc receptor linked to the plasma membrane by a GPI (glycosylphosphatidylinositol) anchor
Bears allotypes that define the human neutrophil antigen-1 (HNA-1 and NA) system involved in major post-transfusional reactions (Tissue Antigens 2004;64:119)
Low copy number is associated with glomerulonephritis in systemic lupus erythematosus (Nature 2006;439:851)
CD16+ eosinophils are upregulated in allergic conditions (J Allergy Clin Immunol 2002;109:463)
Affinity to ligand is regulated by glycosylation (Immunology 2003;110:335)
Uses: no significant clinical use by pathologists
Positive staining: neutrophils
Also known as Fc gamma receptor III A, low affinity immunoglobulin gamma Fc region receptor III-A
Receptor for the Fc portion of IgG; binds various IgG molecules, including rheumatoid factor
Mediates antibody dependent cytotoxicity of foreign cells, phagocytosis and other antibody-dependent responses; also platelet satellitism (AJCP 1995;103:740)
Affinity to ligand is regulated by glycosylation (Immunology 2003;110:335)
CD14+ CD16+ monocytes have increased capacity to produce proinflammatory cytokines such as TNF-alpha, and are elevated in various inflammatory diseases, including coronary artery disease (Thromb Haemost 2004;92:419)
Polymorphisms influence: (a) the severity but not the incidence of IgA nephropathy in Japanese patients (Nephrol Dial Transplant 2005;20:2439); (b) pathogenesis of coronary artery disease (Atherosclerosis 2005;180:277), (c) clinical response to rituximab (Cancer Res 2004;64:4664)
If target cell has class I MHC, then NK cell's killer cell inhibitory receptor (KIR) inhibits cytolysis
Note: preincubation with CD16/CD32 antibodies is commonly used to prevent nonspecific binding
Uses: NK cell and macrophage marker; to subtype leukemia/lymphoma
Diagrams: NK cell mediated cytotoxicity [CD16 / FcgammaRIII is activating receptor on NK cell]
Positive staining (normal): NK cells (10-20%), granulocytes, macrophages, T cells (reactive), immature thymocytes, placental trophoblast
Positive staining (disease): NK proliferative disorders, T cell large granular lymphocyte leukemia, hepatosplenic gamma-delta T cell lymphoma
References: OMIM 146740
CD16b
Also known as Fc gamma receptor III B, low affinity immunoglobulin gamma Fc region receptor III-B
Highly homologous to CD16a
The most common receptor for the Fc domain of IgG on leukocytes
The only Fc receptor linked to the plasma membrane by a GPI (glycosylphosphatidylinositol) anchor
Bears allotypes that define the human neutrophil antigen-1 (HNA-1 and NA) system involved in major post-transfusional reactions (Tissue Antigens 2004;64:119)
Low copy number is associated with glomerulonephritis in systemic lupus erythematosus (Nature 2006;439:851)
CD16+ eosinophils are upregulated in allergic conditions (J Allergy Clin Immunol 2002;109:463)
Affinity to ligand is regulated by glycosylation (Immunology 2003;110:335)
Uses: no significant clinical use by pathologists
Positive staining: neutrophils
CD8
Also called T cell suppressor/cytotoxic cells, OKT8
Cell surface glycoprotein, member of immunoglobulin superfamily; at 2p12
Heterodimer of an alpha and a beta chain linked by two disulfide bonds; heterodimer on thymocytes and homodimer on peripheral blood T cells
MHC class I restricted receptor; binds to nonpolymorphic region of class I molecules; may increase avidity of interactions between cytotoxic T cell and target cell during antigen-specific activation
Can kill target cells by recognizing peptide-MHC complexes on them or by secreting cytokines capable of signaling through death receptors on target cell surface
CD8 alpha cells promote survival and differentiation of activated T cells into memory CD8+ T cells, which may become clonal (but not malignant) in the elderly (Immunol Rev 2005;205:170)
Contribute to initiation, progression and regulation of autoimmune responses (Curr Opin Immunol 2005;17:624)
Associated with lymphoepithelioma-like carcinoma of lung (AJSP 2002;26:715); low CD8:CD3 ratio in epidermotrophic component of lymphoid infiltrate is suggestive of mycosis fungoides (Mod Path 2003;16:857)
Uses: cytotoxic T cell marker
Drawings: (1) CD8+ T cell interaction with antigen presenting cell #1; #2; (3) destruction of viral infected cell
Micro images: (4) infiltrating lymphocytes in lymphoepithelioma-like carcinoma of cervix-figure 3; (5) T cell lymphoma (type not specified); (6) sinus lining cells in splenic hamartomas #1 are CD8+; #2 (figure 3A); (8) nodal cytotoxic T cell lymphoma; (9) mycosis fungoides; (10) intraepithelial lymphocytes in duodenum (figure 1c); (11) increased intraepithelial lymphocytes at villous tip (figure 2e)
Positive staining (normal): cortical thymocytes (70-80%), T cells (25-35% of mature peripheral T cells, mostly cytotoxic T cells); NK cells (30%, which are also CD3 negative)
Positive staining (disease): epidermotrophic lymphocytes in mycosis fungoides (AJSP 2002;26:450), subcutaneous panniculitis-like T cell lymphoma, indolent T cell lymphoblastic proliferation, sinus lining cells in splenic hemartoma, heterotopic ovarian splenoma, NK/T cell lymphoma (variable), some post-thymic T cell lymphomas, rarely mantle cell lymphoma (AJCP 1998;109:689), rarely CLL (AJCP 1994;102:212, Archives 2000;124:1361), T cell infiltrate in 30% of cases of nodular regenerative hyperplasia of liver (Hum Path 2004;35:1241)
Negative stains: adult T cell leukemia/lymphoma, littoral cell hemangioma of spleen
References: Mod Path 2002;15:1131; OMIM 186910 (alpha chain), OMIM 186730 (beta chain)
Cell surface glycoprotein, member of immunoglobulin superfamily; at 2p12
Heterodimer of an alpha and a beta chain linked by two disulfide bonds; heterodimer on thymocytes and homodimer on peripheral blood T cells
MHC class I restricted receptor; binds to nonpolymorphic region of class I molecules; may increase avidity of interactions between cytotoxic T cell and target cell during antigen-specific activation
Can kill target cells by recognizing peptide-MHC complexes on them or by secreting cytokines capable of signaling through death receptors on target cell surface
CD8 alpha cells promote survival and differentiation of activated T cells into memory CD8+ T cells, which may become clonal (but not malignant) in the elderly (Immunol Rev 2005;205:170)
Contribute to initiation, progression and regulation of autoimmune responses (Curr Opin Immunol 2005;17:624)
Associated with lymphoepithelioma-like carcinoma of lung (AJSP 2002;26:715); low CD8:CD3 ratio in epidermotrophic component of lymphoid infiltrate is suggestive of mycosis fungoides (Mod Path 2003;16:857)
Uses: cytotoxic T cell marker
Drawings: (1) CD8+ T cell interaction with antigen presenting cell #1; #2; (3) destruction of viral infected cell
Micro images: (4) infiltrating lymphocytes in lymphoepithelioma-like carcinoma of cervix-figure 3; (5) T cell lymphoma (type not specified); (6) sinus lining cells in splenic hamartomas #1 are CD8+; #2 (figure 3A); (8) nodal cytotoxic T cell lymphoma; (9) mycosis fungoides; (10) intraepithelial lymphocytes in duodenum (figure 1c); (11) increased intraepithelial lymphocytes at villous tip (figure 2e)
Positive staining (normal): cortical thymocytes (70-80%), T cells (25-35% of mature peripheral T cells, mostly cytotoxic T cells); NK cells (30%, which are also CD3 negative)
Positive staining (disease): epidermotrophic lymphocytes in mycosis fungoides (AJSP 2002;26:450), subcutaneous panniculitis-like T cell lymphoma, indolent T cell lymphoblastic proliferation, sinus lining cells in splenic hemartoma, heterotopic ovarian splenoma, NK/T cell lymphoma (variable), some post-thymic T cell lymphomas, rarely mantle cell lymphoma (AJCP 1998;109:689), rarely CLL (AJCP 1994;102:212, Archives 2000;124:1361), T cell infiltrate in 30% of cases of nodular regenerative hyperplasia of liver (Hum Path 2004;35:1241)
Negative stains: adult T cell leukemia/lymphoma, littoral cell hemangioma of spleen
References: Mod Path 2002;15:1131; OMIM 186910 (alpha chain), OMIM 186730 (beta chain)
CD4
Also called OKT4
Nonpolymorphous glycoproteins belonging to immunoglobulin superfamily
Expressed on surface of T helper cells; serves as coreceptor in MHC class II-restricted antigen induced T cell activation
CD4+ CD25+ T cells maintain peripheral tolerance and prevent autoimmunity (Curr Top Microbiol Immunol 2005;293:115)
Serves as HIV receptor on T cells, macrophages, brain
Downregulated by HIV Nef protein during AIDS progression (J Virol 2003;77:11536, J Biol Chem 2003;278:33912)
Normally CD4 > CD8; in HIV patients, CD4/CD8 ratio is inverted (i.e. CD4 < CD8) and patients are at risk for opportunistic infections
Homologous to CD223
Uses: classify lymphomas and inflammatory conditions; serum levels are marker of HIV disease progression and response to therapy (CD4+ cells are killed by HIV); serum levels also increased by transient stress (AJCP 2002;117:819)
Drawings: (1) CD4+ T cell and antigen presenting cell; (2) HIV entry into T cells
Positive staining (normal): thymocytes (80-90%), T helper cells, macrophages, Langerhans cells, dendritic cells, granulocytes
Positive staining (disease): many post-thymic T cell leukemia/lymphomas, indolent T cell lymphoblastic proliferation, pityriasis lichenoides, CD4+ CD56+ hematodermic malignancies (blastic NK lymphoma), histiocytic lymphoma / sarcoma, acute myeloid leukemia (AJCP 1995;104:204), some pyothorax associated lymphomas, cutaneous lymphomatoid granulomatosis (AJSP 2001;25:1111), lymphomatoid papulosis (variable), florid antiviral inflammatory response (Mod Path 2003;16:166)
Negative staining: NK cells, T cell lymphoma with cytotoxic phenotype, hepatosplenic alpha/beta and gamma/delta lymphoma, enteropathy associated T cell lymphoma, B cell lymphoma (usually), Hodgkin’s lymphoma (usually), nonhematopoietic neoplasms
References: Cell 1985;42:93 (early article), OMIM 186940
Nonpolymorphous glycoproteins belonging to immunoglobulin superfamily
Expressed on surface of T helper cells; serves as coreceptor in MHC class II-restricted antigen induced T cell activation
CD4+ CD25+ T cells maintain peripheral tolerance and prevent autoimmunity (Curr Top Microbiol Immunol 2005;293:115)
Serves as HIV receptor on T cells, macrophages, brain
Downregulated by HIV Nef protein during AIDS progression (J Virol 2003;77:11536, J Biol Chem 2003;278:33912)
Normally CD4 > CD8; in HIV patients, CD4/CD8 ratio is inverted (i.e. CD4 < CD8) and patients are at risk for opportunistic infections
Homologous to CD223
Uses: classify lymphomas and inflammatory conditions; serum levels are marker of HIV disease progression and response to therapy (CD4+ cells are killed by HIV); serum levels also increased by transient stress (AJCP 2002;117:819)
Drawings: (1) CD4+ T cell and antigen presenting cell; (2) HIV entry into T cells
Positive staining (normal): thymocytes (80-90%), T helper cells, macrophages, Langerhans cells, dendritic cells, granulocytes
Positive staining (disease): many post-thymic T cell leukemia/lymphomas, indolent T cell lymphoblastic proliferation, pityriasis lichenoides, CD4+ CD56+ hematodermic malignancies (blastic NK lymphoma), histiocytic lymphoma / sarcoma, acute myeloid leukemia (AJCP 1995;104:204), some pyothorax associated lymphomas, cutaneous lymphomatoid granulomatosis (AJSP 2001;25:1111), lymphomatoid papulosis (variable), florid antiviral inflammatory response (Mod Path 2003;16:166)
Negative staining: NK cells, T cell lymphoma with cytotoxic phenotype, hepatosplenic alpha/beta and gamma/delta lymphoma, enteropathy associated T cell lymphoma, B cell lymphoma (usually), Hodgkin’s lymphoma (usually), nonhematopoietic neoplasms
References: Cell 1985;42:93 (early article), OMIM 186940
Gating in FACS
Gating will allow you to view cells of interest by any combination of criteria that you choose. Gating does not change the intensity value assigned to an event as is the case for changes in voltage or compensation.
It simply lets you decide which data to view and which data to ignore or discard.
It is important to check that small changes in your gates don't have significant effects on your results or else your data will be prone to artifact.
When you create or format a data plot (i.e. on the Data menu select "Format Histogram" or "Format Dot Plot") you can select any of the gates that you have created.
This will filter the data and plot will only display those events which meet the gate criteria.
Gating will not discard data unless you have requested this under "Acquisiton and Storage". Gating can subsequently be changed when you analyze your data without any loss of information.
To set up a gate you first draw a "Region" using one of the tools on the tool palette (there are four geometric shapes to choose from outlined with dotted lines). Note that the "Marker bar" (designated with an M) and the quadrant maker tool next do not define regions. They are used for statistical analysis only and can't be used to filter data like the regions/gates.
Regions which are commonly employed include: PI for DNA content: FL2 area vs FL2 width. This window is useful for gaiting out apoptotic cells (lower left quadrant) and doublets (a separate cloud with increased FL2 width). FSC vs SSC: This is useful for gating out RBC, myeloid cells etc, from blood or marrow. Each region that is setup automatically defines a gate (e.g. G1 = R1). To delete regions select "Region List" under the Gates menu. To combine regions into more complex gating criteria use the "Gate List" under the Gates menu. (e.g. G5 = (R1 or R2) and R3).
It simply lets you decide which data to view and which data to ignore or discard.
It is important to check that small changes in your gates don't have significant effects on your results or else your data will be prone to artifact.
When you create or format a data plot (i.e. on the Data menu select "Format Histogram" or "Format Dot Plot") you can select any of the gates that you have created.
This will filter the data and plot will only display those events which meet the gate criteria.
Gating will not discard data unless you have requested this under "Acquisiton and Storage". Gating can subsequently be changed when you analyze your data without any loss of information.
To set up a gate you first draw a "Region" using one of the tools on the tool palette (there are four geometric shapes to choose from outlined with dotted lines). Note that the "Marker bar" (designated with an M) and the quadrant maker tool next do not define regions. They are used for statistical analysis only and can't be used to filter data like the regions/gates.
Regions which are commonly employed include: PI for DNA content: FL2 area vs FL2 width. This window is useful for gaiting out apoptotic cells (lower left quadrant) and doublets (a separate cloud with increased FL2 width). FSC vs SSC: This is useful for gating out RBC, myeloid cells etc, from blood or marrow. Each region that is setup automatically defines a gate (e.g. G1 = R1). To delete regions select "Region List" under the Gates menu. To combine regions into more complex gating criteria use the "Gate List" under the Gates menu. (e.g. G5 = (R1 or R2) and R3).
What are Northern, Southern, Western, Southwestern Blots?
Southern blotting was the original of the four.
It got its name from the developer, Edwin Southern.
Western blotting was named as a sort of joke. (North, South, East, West).
The rest arose based on these first two.
Southern blotting uses gel electrophoresis for the detection of a specific DNA sequence in a sample of DNA.
Western blotting also uses gel electrophoresis but it is to detect proteins and separate them based on size and shape.
Northern blotting is for the detection of RNA sequences, and so is geared towards detecting gene expression (the technique is very similar to Southern blotting only formaldehyde is used to denature the RNA).
There is no Eastern blot, but there is a southwestern one. It is used to find where proteins (DNA binding proteins) bind to specific sequences of DNA.
Far-western blotting is a molecular biological method which is based on the technique of western blotting. While usual western blotting uses an antibody to detect a protein of interest, far-western blotting uses a non-antibody protein, which can bind the protein of interest. Thus, whereas western blotting is used for the detection of certain proteins, far-western blotting is rather employed to detect protein:protein interactions.
By the way, they all use gel electrophoresis.
Far-Eastern blotting is different from the above. It is a technique developed in the 1990s by T. Taki and colleagues at the Cellular Technology Institute of Otsuka Pharmaceutical Co., Japan for the analysis of lipids separated by high-performance thin layer chromatography (HPTLC). The lipids are transferred from the HPTLC plate to a PVDF membrane for further analysis, for example by enzymatic or ligand binding assays[1] or mass spectrometry[2].
Cholesterol, glycerophospholipids and sphingolipids are major constituents of the cell membrane and in certain cases function as second messengers in cell proliferation, apoptosis and cell adhesion in inflammation and tumor metastasis. Far-eastern blotting was established as a method for transferring lipids from an HPTLC plate to a polyvinyledene difluoride (PVDF) membrane within a minute. Applications of this with other methods have been studied. Far-eastern blotting allows for the following techniques:
* Purification of glycosphingolipids and phospholipids.
* Structural analysis of lipids in conjunction with direct mass spectrometry.
* Binding study using various ligands such as antibodies, lectins, bacterium, viruses, and toxins, and
* Enzyme reaction on membranes.
Not only analysis of lipids but also metabolites of drugs and natural compounds from plants, and environmental hormones are possible by this method.
Alum
Alum, (IPA: /ˈæləm/) refers to a specific chemical compound and a class of chemical compounds. The specific compound is the hydrated aluminum potassium sulfate with the formula KAl(SO4)2.12H2O. The wider class of compounds known as alums have the related stoichiometry, AB(SO4)2.12H2O.
Alum is used in vaccines as an adjuvant to enhance the body's response to immunogens.
Alum is used in vaccines as an adjuvant to enhance the body's response to immunogens.
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