Live Chat Support Software

HLA DNA typing – Disease Association

HLA DNA typing – Disease Association

HLA or “human leukocyte antigen” system is the major histocompatibility complex (MHC) in humans, which includes several hundreds of genes located in a highly polymorphic region of chromosome 6 that encode for proteins critical for the immune system [1]. Historically, these proteins are called antigens because of their discovery as crucial factors in tissue rejection by the host, a critical matter of in organ transplantations. Thus, typing of the HLAs from donor and recipient, allows matching those with the highest similarities between their HLA genes or alleles to minimize the chances of rejection; an application that is still the most important for HLA typing. In fact, the HLA profile defines the cells from an individual or “self”, distinguishing them from those from other individuals showing a different HLA profile, “non-self”. As indicated, HLAs play a critical role in the immune system, particularly in antigen presentation, the process by which macrophages and dendritic cells or antigen presenting cells, process antigens for recognition by T cells. The two main HLA groups involved in antigen presentation are the Class I and Class II antigens that have different immunological roles.

HLA Class I antigens (A, B and C) transport and present Peptides Synthesis produced by degradation of proteins inside the cell, i.e. endogenous antigens such as viral antigens, to CD8+ T cells (killer T cells) that seek and destroy only those cells that in addition to the HLA Class I, carry also foreign or not-self antigens (T cell immunity). Under normal conditions, these killer T cells recognize but do not destroy those cells with the right “self” tag, i.e. HLA-I, unless they also carry a non-self antigen. Yet, under pathological conditions, like in certain autoimmune conditions, killer T cells can destroy cells carrying self-antigens, causing damage to the body.

In contrast to HLA-Class I, the role of HLA Class II antigens (DRB1, DRB3,4,5, DQA1/DQB1, DPB1) is to present the peptides from processed proteins that are produced outside the cell, exogenous antigens derived from sources like bacteria and protozoa, to helper T-cells to stimulate their multiplication. These helper T cells then stimulate B-cells to produce antibodies against the foreign antigens (humoral immunity) [2].

Although HLA typing is largely use to match organ donors and recipients, advances in the biomedical field have allowed the typing techniques to become more accurate and yield more detail information. Studies using this new information have made obvious the fact that there are significant correlations between certain HLA types and specific diseases. Consequently, HLA typing is becoming a tool to screen susceptibility to certain autoimmune diseases, as a factor affecting the prognosis of certain autoimmune and infectious diseases. However, the association between HLA type and most infectious diseases is not very clear because of the multiplicity of factors that can affect their outcome. Nevertheless, in some cases such a relation is obvious, a situation that may be helpful in establishing either the resistance or susceptibility to certain infectious diseases and even a prognosis of the disease progression [3]. Another area in which HLA typing is becoming quite important is cancer, a class of diseases where HLAs can play a role in increasing susceptibility and resistance, as well as in tumor cells evading immune surveillance. Moreover, in some cases, the HLA type shows a good correlation with the prognosis of the disease upon treatment. Here, we would discuss the different applications of HLA DNA-typing to autoimmune, infectious diseases and cancer.

Autoimmune diseases

As previously indicated, the immune system under normal conditions is usually tolerant to cells carrying “self” HLAs, i.e. it does not mount an immune response against them. Yet, in many cases, there is a mild low level of autoimmunity that presumably allows immune surveillance by the immune system and the destruction of newly formed cancer cells. Although apparently there are several genes suspected to be involved in autoimmunity, there is strong evidence that certain inherited HLAs are involved in certain specific autoimmune diseases. Because of their important role in the presentation of processed antigens to T cells, HLAs are in a unique position to modify the immune response and cause autoimmunity. HLAs can determine which antigenic peptides are bound for presentation to the immune system, thus it can present “self” peptides auto reactive T cells. In other cases, certain HLAs may bind peptides from infectious agents that share some similarities to the self-antigens to generate an immune response against self-antigens; this molecular mimicry often leads to autoimmunity. In fact, several HLAs, like HLA-B27, are associated with various autoimmune inflammatory diseases. Some of these autoimmune diseases, their association to specific HLAs, and the relative risk of acquiring the disease as a function of specific HLAs are briefly discuss here.

Rheumatoid Arthritis. An inflammatory disease that is the result of a complex immune cascade and that its susceptibility is dependent on the presence of HLA-DR4 and HLA-DRB1 [4]. Presence of these HLA types increases the risk factor of contracting the disease 7-fold when compared to that population not carrying these HLA genes. In Peruvian mestizo patients the HLA allele DRB1*1402 is associated with a significant risk of contracting the disease.

Post-infectious Arthritis. An inflammatory condition of the joints, triggered by gastrointestinal or genitourinary bacterial infections or by a viral infection. Although it is assumed that the synovial fluid is sterile, studies using PCR had detected bacterial DNA in the fluid. It has been found that individuals that suffer of this disease carry the gene for HLA-B27 and that the risk factor increases 10 to 20-fold [5]. Diagnosis is usually made by examining the synovial fluid for the presence of pathogenic antigens or DNA. However¸ detection of the HLA-B27 gene should be an effective confirmatory test.

Type I Diabetes. A disease strongly linked to HLA genes, however, the relative importance of the different HLA genes involve is quite complex and changing with new discoveries in the area. Moreover, in addition to the HLA genes there are other unrelated genes that play a role in the susceptibility to contract the disease. The HLA-DR3 and DR4 genes have been identified as playing important roles and that the presence of any of these two genes increases the risk of contracting the disease 5-6-fold, while the presence of both genes increases the risk factor to 15 [6]. Yet, new research indicates that some HLA-DQ genes play a role in susceptibility to the disease that is even higher than that of the DR genes.

Autoimmune Hepatitis. An inflammation of the liver due to unknown causes that raises the possibility that the chronic hepatitis observed in many patients may be in many cases due to an autoimmune reaction. The incidence of autoimmune hepatitis in South America although not well established it is apparently significant. Like other autoimmune diseases, there are genetic factors that affect its occurrence, e.g. HLAs; however, different ethnic groups have different susceptibility alleles. For instance, in South America is HLA DRB1*1301 while in Europe is HLA DR3. These HLAs have significant differences in their sequences within the antigen binding grove of the HLA DR molecule [7]. This fact strongly suggests that perhaps an unidentified indigenous etiologic agent must be the cause of autoimmune hepatitis in South America.

Celiac Disease. This autoimmune disorder of the small intestine is triggered by gluten proteins that occur in genetically predisposed people. The condition causes chronic diarrhea, fatigue and other problems, with the only effective therapy being a gluten-free diet. Although for some time it was assumed that the disease was limited to Europeans, recently it has been established that this condition is worldwide spread. For instance, the prevalence of this condition in Peru is estimated to around 0.40% or 1 of every 250 people, a prevalence quite similar to that of the US and many European countries. Over 95% of the celiac patients have some isoform of HLA-DQ2 or DQ8, however, their frequency varies geographically around the world. In effect, in South America where DQ8 accounts for 90% of the phenotype, the dominant HLA associated with celiac disease is DQ8 [8].

There are other autoimmune conditions with a strong association with HLAs, such as: Ankylosing Spondylitis associated to HLA B27; Narcolepsy a neurological disease closely associated with the HLA-DQB1*0602, i.e. over 90% of the patients carry this gene, but 20% of the population carry this gene, a situation that indicates the role of other factors in triggering this disease; Primary Sjögren Syndrome, in South America the HLA-DRB1*0301-DQB1*0201 haplotype is associated with the disease and apparently plays a role in the production of autoantibodies [9].

Infectious diseases

HLAs’ crucial role in mounting an immune response is show by the fact, that in many vaccines the nature of an individual’s HLA profile decides the production of an effective or ineffective immune response. In many cases, the susceptibility, resistance and progression of an infectious disease show an association with the individual’s genetic HLA profile. Perhaps the best study diseases are those caused by Mycobacteria, i.e. M. tuberculosis and M. leprae, in both cases the form of disease is link to the HLA profile. In tuberculosis the severity of the disease is associated with HLA DR2, i.e. the DR2 patients have a strong antibody response but a low T cell immunity, the later being the protective response against tuberculosis [10]. Consequently, the HLA DR2 does not only increase the susceptibility to the disease, but it also affects its progression. Yet, it is apparent that besides the HLA component, there are also other factors deciding TB susceptibility. A brief review of some infections associated with certain HLAs is given here.

Malaria. The association between HLA class I-B53 and protection from severe malaria is well established. In fact, a nonapeptide from P. falciparum hepatic phase that is HLA-B53 restricted and recognized by cytotoxic T lymphocytes (CTL) has been identify, which provides the bases to explain the killing of infected cells by (CTLs) [11]. This finding supports the approach of using the hepatic phase of the parasite to develop an effective vaccine.

Hepatitis B and C. The hepatitis B virus (HBV) is worldwide the major cause of chronic hepatitis and hepatocellular carcinoma. HLA-Class II DR1*1301-02 has been identified as being associated with resistance to infection by HBV and protection against chronic hepatitis [12]. The same allele has been associated with protection against chronic hepatitis due to hepatitis C virus (HCV).

Epstein-Barr Virus (EBV). The etiological agent of infectious mononucleosis that infects B cells, in addition to CD21 needs HLA Class II-DR, to enter the cell. It has been shown that HLA-DR can be substituted by HLA-DP or a subset of HLA-DQ as co-receptors for EBV. These findings raise the possibility that individuals expressing HLA-DR, -DP or –DQ, are susceptible to EBV infection [13].


Like in the case of autoimmune diseases, there are clear associations between some cancer’s resistance or susceptibility and the classic HLA profile of an individual. Like in autoimmunity, the HLA profile is largely dependent on the ethnic group, particularly in the cases where cancer is trigger by an infectious agent, e.g. virus and bacteria. The role of HLA in resistance or susceptibility to cancer is not well understood, but it is possible that because of their role in immunity they influence the immune surveillance process. Nevertheless, independent of their role, it has been shown that HLAs are associated with either susceptibility or resistance to certain cancers. In addition to the classical HLAs, a non-classic HLA, HLA-G, is becoming relevant to cancer development, as well as a new biomarker for tumor cells [14]. Following is a brief discussion of two cancers quite common in Peru where HLA can affect their development.

Breast cancer. There are many genes unrelated to HLAs that affect the susceptibility to breast cancer. However, in the US two HLA Class II genes, HLA DQB*03032 and HLA DRB1*11, have been identified that may have a protective role in human breast cancer in Caucasians [15].

Cervical cancer. This cancer is caused by infection with several strains of human papilloma virus (HPV) with HPV16 being one of the most oncogenic. HLA typing have shown that two alleles, DQB1*0602 and DRB1*1501, are associated with the presence of cancer in Hispanic patients [16]. Apparently, these two alleles also contribute to the inability to clear HPV infection. However, there are also HLA alleles, DRB1*1301 and *1302, that protect against cancer induced by HPV infection.


The expression of this non-classic HLA Class I is under epigenetic control, i.e. when the DNA is methylated the expression of HLA-G is suppressed [17]. There is evidence that HLA-G promotes tolerance during pregnancy, however, this protein is also produced by many types of cancer cells. This situation suggests that HLA-G may play some role in tumor cells evading immune surveillance by inducing tolerance of the immune system. In addition to the cell-associated HLA-G, there is a secreted, circulating form, sHLA-G, that may suppress the immune regulation of cancer cells [18]. The production of HLA-G can be a good indicator for the clinical prognosis of different cancers. As a rule, HLA-G is always associated with malignant tumor cells and it never has been found in normal cells. Thus, HLA-G appears to be a promising biomarker to predict the clinical progression of different cancers.


1. Gerlach John. Arch Pathol Lab Med, 2002, 126:281-284.

2. Mingari MC et al. Hum Immunnol. 2000;61:44-50

3. Klein J et al. N. Engl. J. Med. 2000, 343:782-786

4. Weyand CN et al. Arthritis Res. 2000, 2:212-214.

5. Amital H et al. Clin Exp Rheumatol. 2008, 26:S27-32.

6. Chiu FK et al. J Endocrinol Invest. 2004, 27:480-484.

7. De Silva S et al. Liver Int. 2006, 26:509-511.

8. Green PH et al. Lancet, 2003, 362:383-391.

9. Quelvenecc E et al. Clin Exp Rheumatol. 1998, 16:725-728

10. Selvaraj P. Ind J Tub. 2000; 47:133-138.

11. Sing N. et al. Emerging Infect Dis. 1997; 3:41-49

12. Ramezani A et al. J Gastroenterol Hepatol. 2008; 23:1716-1721

13. Haan KM et al. J Virol. 2000; 74:2451-2454

14. Ie-Ming S. Hum Immunol. 2007; 68:272-276

15. Chaudhuri S et al. Proc Nat Acad Sci USA 2000; 97:11451-11454

16. Garcia Corona C. et al. Arch Dermatol. 2004; 140: 1227-1231

17. Menendez L et al. Molecular Cancer 2008; 7:43

18. Rouas-Freiss N et al. Cancer Res. 2005; 65:10139-10144