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DQ1 binding pocket with ligand
major histocompatibility complex, class II, DQ
Type Cell surface receptor
Quartenary αβ-heterodimer, ligand
Ligand polypeptides, >9 residues DQ type restricted
MMDB 17145
Symbol(s) HLA-DQA1 CELIAC1
Entrez 3117
OMIM 146880
EBI-HLA DQA1*010101
beta 1
Symbol(s) HLA-DQB1, IDDM1, CELIAC1
Entrez 3119
OMIM 604305
EBI-HLA DQB1*050501
Shared data
Locus chr.6 6p21.31
EBI-HLA *Allele Alignments*

HLA-DQ (DQ) is a cell surface type protein found on antigen presenting cells.

DQ functions: (See MHC Class II):

  • Generally found on antigen presenting cells, is an antigen presenting molecule.
  • Binds peptides, potential antigens (11 amino acids or greater)
  • Presents peptides to T-cells, where T-cells become stimulated to help other cells make antibodies.

DQ Structure:

  • protein (cell surface receptor)
  • αβ heterodimer
  • transmembrane protein
  • 2 genes x 2 alleles of each gene per person allows 4 variant isoforms/person

DQ Involvements:

  • Defense of body against disease - presents foreign peptides to T-cells, which in turn help to make antibodies
  • Present self-peptides to the immune system, generally suppressed - occasionally cause autoimmune disease
  • Are responsible for recognizing non-self proteins, causing graft versus host disease (organ transplant rejection)

DQ Genetics:

  • DQ α and β are encoded by two adjacent loci
  • These loci are found on chromosome 6 region 6p21.3
  • DQ loci are in the "D" region, which encodes DR, DP, and DQ proteins.
  • HLA-DQA1 encodes DQ α
  • HLA-DQB1 encodes DQ β
  • DQ α & DQ β combine to form DQαβ which is the DQ receptor
  • 2 genes x 2 alleles of each gene per person allows 4 variant isoforms/person

DQ Determination:

  • 9 Serotypes: HLA-DQ1, DQ2, DQ3, DQ4, DQ5,DQ6, DQ7, DQ8, DQ9
  • >100 alleles sequenced with SSP-PCR typing capability.
    • >33 DQA1* Alleles ~15 commonly found in 6 groups: HLA-DQA1*01, *02, *03, *04, *05, and *06
    • >78 DQB1* Alleles ~15 commonly found in 5 groups: HLA-DQB1*02, *03, *04, *05, *06


Structure, Functions, Genetics



The name 'HLA DQ' originally describes a transplantation antigen of MHC class II category of the major histocompatibility complex of humans; however, this status is an artifact of the early era of organ transplantation.

HLA DQ functions as a cell surface receptor for foreign or self antigens. The immune system surveys antigens for foreign pathogens when presented by MHC receptors (like HLA DQ). The MHC Class II antigens are found on antigen presenting cells (APC) (macrophages, dendritic cells, and B-lymphocytes). Normally, these APC 'present' class II receptor/antigens to a great many T-cells, each with unique T-cell receptor (TCR) variants. A few TCR variants that recognize these DQ/antigen complexes are on CD4 positive (CD4+) T-cells. These T-cells, called T-helper cells, can promote the amplification of B-cells which, in turn recognize a different portion of the same antigen. Alternatively, macrophages and other megalocytes consume cells by apoptotic signaling and present self-antigens. Self antigens, in the right context, form a suppressor T-cell population that protects self tissues from immune attack or autoimmunity.



HLA-DQ (DQ) is encoded on the HLA region of chromosome 6, in what was classically known as the "D" antigen region. This region encoded the subunits for DP,-Q and -R which are the major MHC class II antigens in humans. Each of these proteins have slightly different functions and are regulated in slightly different ways.

DQ is made up of two different subunits to form an αβ-heterodimer. each subunit is encoded by its own "gene" (a coding locus). The DQα subunit is encoded by the HLA-DQA1 gene and the DQβ subunit is encoded by the HLA-DQB1 gene. Both loci are variable in the human population (see regional evolution).

Detecting DQ isoforms

In the human population DQ is highly variable, the β subunit more so than the alpha chain. The variants are encoded by the HLA DQ genes and are the result of single nucleotide polymorphisms (SNP). Some SNP result in no change in amino-acid sequence. Others result in changes in regions that are removed when the proteins is processed to the cell surface, still others result in change in the non-functional regions of the protein, and some changes result in a change of function of the DQ isoform that is produced. The isoforms generally change in the peptides they bind and present to T-cells. Much of the isoform variation in DQ is within these 'functional' regions.

Seroyping. Antibodies raised against DQ tend to recognize these functional regions, in most cases the β-subunit. As a result these antibodies can discriminate different classes of DQ based on the recognition similar DQβ proteins known as serotypes.

An example of a serotype is DQ2.

  • Recognize HLA-DQB1*02 gene products which include gene products of the following alleles:
    • HLA-DQB1*0201
    • HLA-DQB1*0202
    • HLA-DQB1*0203

Sometimes DQ2 antibodies recognize other gene products, such as DQB1*0303, resulting serotyping errors. Because of this mistyping serotyping is not as reliable as gene sequencing or SSP-PCR.

While the DQ2 isoforms are recognized by the same antibodies, and all DQB1*02 are functionally similar, they can bind different α subunit and these αβ isoform variants can bind different sets of peptides. This difference in binding is an important feature that helps to understand autoimmune disease.

There are 9 DQ serotypes:HLA-DQ1, HLA-DQ2, HLA-DQ3, HLA-DQ4, HLA-DQ5, HLA-DQ6, HLA-DQ7, HLA-DQ8, HLA-DQ9. The first identified were DQw1 to DQw3. DQw1 (DQ1) recognized the alpha chain of DQA1*01 alleles. This group was later split by beta chain recognition to DQ5 and DQ6. DQ3 is known as broad antigen serotypes, because they recognize a broad group of antigens. However, because of this broad antigen recognition their specificity and usefulness is somewhat less than desirable.

For most modern typing the DQ2, DQ4 - DQ9 set is used.

Some common haplotypes and their cis-isoforms
Haplotype DQA1 DQB1 haplotype
DQ2.5 *0501 *0201 α5β2
DQ2.2 *0201 *0202 α2β2
DQ7.3 *03 *0301 α3β301
DQ7.4 *0401 *0301 α401β301
DQ7.5 *0505 *0301 α5β301
DQ7.6 *0601 *0301 α601β301
DQ4.3 *0303 *0402 α3β402
DQ4.4 *0401 *0402 α4β402
DQ5.1 *0101 *0501 α101β501
DQ5.2 *0102 *0502 α102β502
DQ6.2 *0102 *0602 α102β602
DQ6.4 *0102 *0604 α102β604
DQ8.1 *0301 *0302 α3β302

Genetic Typing. With the exception of DQ2 (*0201) which has a 98% detection capability, serotyping has drawbacks in relative accuracy. In addition, for many HLA studies genetic typing does not offer that much greater advantage over serotyping, but in the case of DQ there is a need for precise identification of HLA-DQB1 and HLA-DQA1 which cannot be provided by serotyping.

Isoform functionality is dependent on αβ composition. Most studies indicate a chromosomal linkage between disease causing DQA1 and DQB1 genes. Therefore the DQA1, α, component is as important as DQB1. An example of this is DQ2, DQ2 mediates Coeliac disease and Type 1 diabetes but only if the α5 subunit is present. This subunit can be encoded by either DQA1*0501 or DQA1*0505. When the DQ2 encoding β-chain gene is on the same chromosome as the α5 subunit isoform, then individuals who have this chromosome have a much higher risk of these two disease. When DQA1 and DQB1 alleles are linked in this way they form a haplotype. The DQA1*0501-DQB1*0201 haplotype is called the DQ2.5 haplotype, and the DQ that results α5β² is the "cis-haplotype" or "cis-chromosomal" isoform of DQ2.5

To detect these potential combinations one uses a technique called SSP-PCR (Sequence specific primer polymerase chain reaction). This techniques works because, outside of a few areas of Africa, we know the overwhelming majority of all DQ alleles in the world. The primers are specific for known DQ and thus, if a product is seen it means that gene motif is present. This results in nearly 100% accurate typing of DQA1 and DQB1 alleles.

'How does one know which isoforms are functionally unique and which isoforms are functionally synonymous with other isoforms'?. The IMGT/HLA database also provides alignments for various alleles, these alignments show the variable regions and conserved regions. By examining the structure of these variable regions with different ligands bound (such as the MMDB) one can see which residues come into close contact with peptides and those the have side chains that are distal. Those changes more than 10 Angstoms away generally do not affect binding of peptides. The structure of HLA-DQ8/insulin peptide at NCBI can be view with Cn3D or Rasmol. In Cn3D one can highlight the peptide and then select for amino acids within 3 or more Angstroms of the peptide. Side chains that come close to the peptide can be identified and then examined on the sequence alignments at IMGT/HLA database. Anyone can download software and sequence. Have fun!

Effects of heterogeneity of isoform pairing

As an MHC class II antigen-presenting receptor, DQ functions as a dimer containing two protein subunits, alpha (DQA1 gene product) and beta (DQB1 gene product), a DQ heterodimer. These receptors can be made from alpha+beta sets of two different DQ haplotypes, one set from the maternal and paternal chromosome. If one carries haplotype -A-B- from one parent and -a-b- from the other, that person makes 2 alpha isoforms (A and a) and 2 beta isoforms (B and b). This can produce 4 slightly different receptor heterodimers (or more simply, DQ isoforms). Two isoforms are in the cis-haplotype pairing (AB and ab) and 2 are in the trans-haplotype pairing (Ab and aB). Such a person is a double heterozygote for these genes, for DQ the most popular situation. If a person carries haplotypes -A-B- and -A-b- then they can only make 2 DQ (AB and Ab), but if a person carries haplotypes -A-B- and -A-B- then they can only make DQ isoform AB, called a double homozygote. In coeliac disease, certain homozygotes and are at higher risk for disease and some specific complications of coeliac disease such as Gluten-sensitive enteropathy associated T-cell lymphoma

homozygotes and double homozygotes. Homozygotes at DQ loci can change risk for disease. In mice for instance, mice with 2 copies of the DQ-like Iab haplotype are more likely to progress toward fatal disease compared to mice that are heterozygotes only for the beta allele (MHC IAαb / IAαb, IAβb / IAβbm12). In humans, celiac disease DQ2.5/DQ2 homozygotes are several times more likely to have celiac disease versus DQ2.5/DQX individuals[1]. DQ2/DQ2 homozygotes are at elevated risk for severe complications of disease.[2]. For an explanation of the risk association see:Talk:HLA-DQ#Effects of heterogeneity of isoform pairing-Expanded

Involvement of transhaplotypes in disease
There is some controversy in the literature whether trans-isoforms are relevant. Recent genetic studies into coeliac disease have revealed that that the DQA1*0505:X/Y:DQB1*0202 gene products explain disease not linked to the haplotype that produces DQ8 and DQ2.5, strongly suggesting the trans-isoforms can be involved in disease. But, in this example, it is known that the transproduct is almost identical to a know cis-'isoform' produced by DQ2.5. There is other evidence that some haplotypes are linked to disease but show neutral linkage with other particular haplotypes are present. At present, the bias of relative isoform frequency toward cis pairing is unknown, it is known that some trans-isoforms occur. see:Talk:HLA-DQ#Effects of heterogeneity of isoform pairing-Expanded

DQ Function in Autoimmunity

HLA D (-P,-Q,-R) genes are members of the Major Histocompatibility Complex (MHC) gene family and have analogs in other mammalian species. In mice the MHC locus known as IA is homologous to human HLA DQ. Several autoimmune diseases that occur in humans that are mediated by DQ also can be induced in mice and are mediated through IA. Myasthenia Gravis is an example of one such disease[3]. Linking specific sites on autoantigens is more difficult in humans due to the complex variation of heterologous humans, but subtle differences in T-cell stimulation associated with DQ-types has been observed[4]. These studies indicate that potentially a small change or increase in the presentation of a potential self-antigen can result in autoimmunity. This may explain why there is often linkage to DR or DQ, but the linkage is often weak.

DQ Selection and Evolution

The table below represents the most frequent 3 loci DR-DQ haplotypes in European Americans[5]. The top 25 of these cover the vast majority of haplotypes encountered in Europe and North America but also are highly represented in Asia, the Indigeonous American and African populations, where there are gaps they will be mentioned. The table illustrates that there is considerable [linkage disequilbrium] in Caucasian.

25 (of 75) Most common DR-DQ haplotypes in Caucasian Americans
Serotype haplotype B1 A1 B1 %[5] rank
DQ2 DR17-DQ2 0301 0501 0201 13. 1 ²
DR7-DQ2 0701 0201 0202 11. 1 ³
DQ4 DR8-DQ4 0801 0401 0402 2. 2 12
DQ5 DR1-DQ5 0101 0101 0501 9. 1 4
0102 0101 0501 1. 4 14
0103 0101 0501 0. 5 25
DR10-DQ5 1001 0104 0501 0. 7 21
DR16-DQ5 1601 0102 0502 1. 0 17
DR14-DQ5 1401 0104 0503 2. 0 13
DQ6 DR15-DQ6 1502 0103 0601 0. 7 23
1501 0102 0602 14. 2 1
DR13-DQ6 1301 0103 0603 5. 6 6
1302 0102 0604 0. 7 10
1302 0102 0609 3. 4 22
DQ7 DR11-DQ7 1101 0505 0301 5. 6 5
1104 0505 0301 2. 7 11
DR12-DQ7 1201 0505 0301 1. 1 15
DR13-DQ7 1303 0505 0301 0. 7 20
DR4-DQ7 0401 0303 0301 5. 3 7
0407 0303 0301 0. 9 18
DQ8 DR4-DQ8 0402 0301 0302 1. 0 16
0404 0301 0302 4. 2 8
0401 0302 0302 0. 7 24
DQ9 DR7-DQ9 0701 0201 0303 3. 7 9
DR9-DQ9 0901 0302 0303 0. 8 19

A common question asked by many patients affected by autoimmunity, after being typed for various HLA or cytokines, is the meaning of the genetic typing. This page is designed to help understand the nature of the MHC Class II types including their distribution and linked diseases. The HLA-DR and DQ loci are associated with probably the greatest number of different diseases relative to any other loci. This is due to the complex nature of immunity and the great variation at these loci. Most of these diseases are low in frequency, some, like Type 1 diabetes and Celiac Disease are uncommon but not rare.

One common belief about 'gene tests' is that because a gene is linked to a disease it is therefore a mutation or genetic abnormality. With DQ this is not typically true, there can frequently be a suspect environmental causes. As human culture has evolved and people have moved around their DQ haplotypes evolve to become optimal for foods, diseases or lifestyles.

Gluten-sensitive enteropathy is an example. In the case of Coeliac disease, wheat is a factor that changed for some groups 25000 years ago and for other groups, 7500 to 5500 years ago as Near Eastern/Danubian Neolithic culture spread from SE Anatolia into susceptible populations of NW Europe. There are other factors, shortening of the period of breast feeding, the child's age when wheat is first introduced, whether or not one is exposed to a chronic upper GI infection, whether or not one eats wheat during the infection, etc. Molecular genetics and archaeology has offered a window into the past. For example the molecular genetics tells us that Homo sapiens redistributed about >95,000 years ago[6] and at that time, current population genetics suggests that most of the common DR-DQ types had already formed. The archaeology reveals that hunter/gatherers, early on, primarily were coastal foragers that moved inland. As they moved inland they became more effective seed gatherers and eventually seed cultivators. Before the neolithization in many parts of the world, human activities were frequently associated with shell middens, nut harvesting, or, alternatively, hunting camps. The seeds that archaeologist have found from the last Ice Age tend to be more diverse, but in places like the Levant, seed utilization had already increased. Of the seeds used from the tribe Triticeae the greatest diversity used was in the region from Anatolia to Iran to Arabia, these seeds were small and difficult to harvest and were probably only eaten periodically. Another suspected environmental trigger for autoimmune disease is bovid milk consumption, particular consumption in children who would normally be of breast feeding age. These environmental changes require periods of selection to optimize immune behavior in a circumstance of evolving diet. Currently Autoimmune diseases are on the rise as human culture is changing rapidly and food cultures are changing around the world. Therefore DQ associated diseases may not manifest the deficiency of the genes so much as humans are outpacing their immune systems ability to undergo adaptive evolution over time.

Regional Evolution

HLA DQ- subunit alleles, mature chains, contact variants
Known HLA-DQ Potential
Locus: A1 B1 Combinations
Alleles 33 78 2475
Subunit: α β isoforms
Mature Chains 24 58 1392
Contact Variants* ~9 40 360
Caucasian (USA)
Contact Variants (CV) 7 12 84
CV-haplotypes 30
*Subunits vary within 9Â of peptide in DQ2.5 or DQ8

Many HLA DQ were under positive selection of 10,000s potentially 100,000s of years in some regions. As people moved they have tend to loose haplotypes and in the process loose allelic diversity. On the other hand, on arrival at new distal locations, selection would offer unknown selective forces that would have initially favored diversity in arrivals. By an unknown process, rapid evolution occurs, as has been seen in South Americas indigeonous population (Parham and Ohta, 1996, Watkins 1995), and new alleles rapidly appear. This process may be of immediate benefit of being positively selective in that new environment, but these new alleles might also be 'sloppy' in a selective perspective, having side effects if selection changed. The table to the left demonstrates how absolute diversity at the global level translates into relative diversity at the regional level.


Heterozygous DQ Combinations and Disease

DQ2.5 DQ8 DQ2.5/8
Sweden 15.9 18.7 5.9
Jalisco 11.4 22.8 5.2
England 12.4 16.8 4.2
Kazahk 13.1 11 2.9
Uygur 12.6 11.4 2.9
Finland 9 15.7 2.8
Poland 10.7 9.9 2.1

DQ2.5/DQ8 Heterozygotes

The distribution of this phenotype is largely the result of admixtures between peoples of eastern or central Asian origin and peoples of western or central Asian origin. The highest frequencies, by random mating, are expected in Sweden, but pockets of high levels also occur in Mexico, and a larger range risk exists in Central Asia.

Diseases that appear to be increased in Heterozygotes are Type 1 Diabetes. New evidence is showing an increased risk for late onset Type 1 diabetes in Heterozygotes (which includes ambiguous Type I/Type II diabetes. Celiac Disease may have a slightly increased risk with a more severe course of disease.


  1. ^ Jores RD, Frau F, Cucca F, et al (2007). "HLA-DQB1*0201 homozygosis predisposes to severe intestinal damage in celiac disease". Scand. J. Gastroenterol. 42 (1): 48-53. doi:10.1080/00365520600789859. PMID 17190762.
  2. ^ Al-Toma A, Verbeek WH, Hadithi M, von Blomberg BM, Mulder CJ (2007). "Survival in Refractory Coeliac Disease and Enteropathy associated T cell Lymphoma: Retrospective evaluation of single centre experience". doi:10.1136/gut.2006.114512. PMID 17470479.
  3. ^ Atassi MZ, Oshima M, and Deitiker P (2001). "n the initial trigger of myasthenia gravis and suppression of the disease by antibodies against the MHC peptide region involved in the presentation of a pathogenic T-cell epitope.". Crit Rev Immunol. 21 (1-3): 1-27. PMID 11642597.
  4. ^ Deitiker PR, Oshima M, Smith RG, Mosier DR, and Atassi MZ (2006). "Subtle differences in HLA DQ haplotype-associated presentation of AChR alpha-chain peptides may suffice to mediate myasthenia gravis.". Autoimmunity 39 (4): 277-288. PMID 16891216.
  5. ^ a b Klitz W, Maiers M, Spellman S, Baxter-Lowe LA, Schmeckpeper B, Williams TM, and Fernandez-Vina M (2003). "New HLA haplotype frequency reference standards: high-resolution and large sample typing of HLA DR-DQ haplotypes in a sample of European Americans.". Tissue Antigens 62 (4): 296-307. PMID 12974796.
  6. ^ Vigilant L, Stoneking M, Harpending H, Hawkes K, Wilson A (1991). "African populations and the evolution of human mitochondrial DNA.". Science 253 (5027): 1503-7. PMID 1840702.

External links

  • Molecular Anthropology Yahoo Group
  • HLA Allele and Haplotype Frequency Database
  • IMGT-HLA Database
This article is licensed under the GNU Free Documentation License. It uses material from the Wikipedia article "HLA-DQ". A list of authors is available in Wikipedia.
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