COMMENTARY HLA on Chromosome 6: The Story Gets Longer and Longer Leslie J. Raffel,1 Janelle A. Noble,2 and Jerome I. Rotter1

within the MHC has played a substantial role in allowing disease linkages and associations to be detected. The early ver the past three decades, substantial progress studies that reported associations with HLA-B8 and -B15 has been made in understanding the genetic used remarkably small numbers of cases and controls basis for diabetes. One of the important first relative to the hundreds to thousands considered neces- Osteps that allowed this progress to occur was sary in current studies (4–6). Had it not been for the realizing that diabetes is heterogeneous, and, therefore, strong LD, those initial studies would have been unlikely separation of clinically distinct forms of the disorder (i.e., to yield positive results. Yet, at the same time, this LD has type 1 vs. type 2 diabetes) improves the ability to detect also created challenges in accomplishing the next step, genetic associations. The key points that allowed type 1 that of identification of the specific genes that are respon- diabetes to be separated from type 2 diabetes included sible for disease susceptibility. The fact that researchers realization of the clinical differences (typically childhood have spent Ͼ30 years trying to elucidate all of the loci onset, thin, ketosis-prone versus adult onset, obese, non- responsible for type 1 diabetes susceptibility in the HLA ketosis prone); family and twin studies that demonstrated region underscores the complexity of the task. While that the two forms of diabetes usually segregate separately researchers attempting to localize the gene responsible for and, while both demonstrate substantial monozygotic twin a linkage signal or association detected in other genomic concordance, the concordance rate in type 2 diabetes is at segments have often struggled with the lack of an obvious least double that in type 1 diabetes; and appreciation that candidate gene within the region, type 1 diabetes investi- ␤ there is automimmune -cell destruction in type 1 diabetes gators have had the converse problem with HLA, i.e., too that does not occur in type 2 diabetes (rev. in 1). The many candidate genes, all plausibly involved in autoim- confirmation that these clinical observations truly repre- mune regulation/disregulation. When the initial HLA-B8 sented genetic differences came from the early studies of and -B15 associations were followed rapidly by identifica- the human leukocyte antigen (HLA) region, which we now tion of associations with HLA-DR3 and -DR4, interest in know plays an important role in type 1 but not in type 2 the class I HLA region was replaced by enthusiasm for the diabetes susceptibility. class II genes (7,8). Interest in the DR locus was then HLA, the human form of the major histocompatibility superceded by excitement over DQ and so forth (9). While complex (MHC), has indeed long been recognized as the the exact loci (and polymorphisms within loci) that ac- major genetic region influencing risk for type 1 diabetes. count for HLA-linked susceptibility are still not clearly The fact that it was the first genetic susceptibility region defined, the results of many reports show that multiple identified was, in part, serendipitous, as the emerging loci, including, at a minimum, DRB1, DQB1, DP, as well as ability to distinguish a variety of HLA-A and -B serotypes HLA-A and HLA-B, all contribute (10–16). made HLA one of the first highly polymorphic genetic Understanding the mechanisms by which loci in the regions that could be used in linkage and association HLA region result in diabetes susceptibility is made diffi- studies. In retrospect, the autoimmune basis of type 1 cult by the tremendous genetic heterogeneity within this diabetes made it a logical disorder to be linked to genes in region. When initial HLA associations with type 1 diabetes the MHC, but, given the dearth of genetic markers avail- were reported, each of the HLA loci had a handful of able back in the 1970s, diabetes researchers would likely reported alleles. Current totals are approaching 1,000 for have tested the region, regardless of whether anything was some of the most polymorphic HLA loci, such as HLA-B known about its role in the immune system. Remember and -DRB1 (see http://www.anthonynolan.org.uk/HIG/ ABO and Kidd blood group testing (2,3)? Back in those index.html). Additional complexity is generated by the fact days, we were desperate to test any polymorphic marker that for some loci (such as DQB1) polypeptide products that we could lay our hands on. from both chromosomes can form “trans-encoded” het- The strong linkage disequilibrium (LD) that exists erodimeric proteins that are thought to be major contrib- utors to disease risk. Simply put, HLA region susceptibility From the 1Medical Genetics Institute, Cedars-Sinai Medical Center, Los to type 1 diabetes is extremely complicated. Thus, while Angeles, California; and 2Children’s Hospital Oakland Research Institute, great advances have occurred in the field over the past 30 Oakland, Calrifornia. years, much more remains to be learned. The article by Aly Address correspondence and reprint requests to Jerome Rotter, Medical Genetics Institute, Cedars-Sinai Medical Center, Los Angeles, California. et al. (17) in this issue of Diabetes represents one more E-mail: [email protected]. significant step toward unraveling the mysteries of the DOI: 10.2337/db07-1756 HLA region. HLA, human leukocyte antigen; LD, linkage disequilibrium; MHC, major histocompatibility complex. The research reported by Aly et al. (17) provides not © 2008 by the American Diabetes Association. only additional support for contributions by classical The costs of publication of this article were defrayed in part by the payment of page HLA loci, but also convincing evidence that at least one charges. This article must therefore be hereby marked “advertisement” in accordance with 18 U.S.C. Section 1734 solely to indicate this fact. additional locus, in the vicinity of UBD/MASIL, is also See accompanying Original Article, p. 770. involved. Thus, the stretch of chromosome 6p that

DIABETES, VOL. 57, MARCH 2008 527 HLA ON CHROMOSOME 6 contributes to type 1 diabetes susceptibility appears to antigens in genetic analysis of insulin dependent diabetes mellitus. Dia- be at least 4 Mb in length, twice as long as previously betologia 21:108–115, 1981 thought. 9. Todd JA, Bell JI, McDevitt HO: HLA-DQ beta gene contributes to suscep- tibility and resistance to insulin-dependent diabetes mellitus. Nature Aly et al. (17) state that “[t]here has been a renewed 329:599–604, 1987 interest in” finding additional type 1 diabetes susceptibility 10. Erlich H, Rotter JI, Chang J, Shaw S, Raffel LJ, Klitz W, Beshkov Y, Costin loci within the HLA region. In fact, this interest has R, Pressman S, Bugawan TL, Zeidler A: HLA class II alleles and suscepti- persisted for 30 years, as illustrated by the numerous type bility and resistance to insulin dependent diabetes mellitus in Mexican- 1 diabetes association and linkage studies of other genes American families. Nat Genet 3:358–364, 1993 within the HLA region, including (among others) TNF, 11. Fennessy M, Metcalfe K, Hitman GA, Niven M, Biro PA, Tuomilehto J, MICA, and TAP (18–23). As molecular technology has Tuomilehto-Wolf E. A gene in the HLA class I region contributes to susceptibility to IDDM in the Finnish population: Childhood Diabetes in advanced, so has our ability to delve more deeply into the Finland (DiMe) Study Group. Diabetologia 37:937–944, 1994 intricacies of the HLA region. 12. Zavattari P, Lampis R, Motzo C, Loddo M, Mulargia A, Whalen M, Maioli M, The work reported by Aly et al. (17) demonstrates Angius E, Todd JA, Cucca F: Conditional linkage disequilibrium analysis of several important points. First, the use of intensive single a complex disease superlocus, IDDM1 in the HLA region, reveals the nucleotide polymorphism (SNP) genotyping across a re- presence of independent modifying gene effects influencing the type 1 gion, even one demonstrating as much LD as the MHC, can diabetes risk encoded by the major HLA-DQB1, -DRB1 disease loci. help distinguish discrete loci that may each be contribut- Human Mol Gen 10:881–889, 2001 ing to overall disease susceptibility. Second, just because 13. Noble JA, Valdes AM, Bugawan TL, Apple RJ, Thomson G, Erlich HA: The HLA class I A locus affects susceptibility to type 1 diabetes. Hum Immunol one or more putative causative genes have been identified 63:657–664, 2002 within a region, one should not assume that all of the 14. Cruz TD, Valdes AM, Santiago A, Frazer de Llado T, Raffel LJ, Zeidler A, genes important in disease susceptibility in that region Rotter JI, Erlich HA, Rewers M, Bugawan T, Noble JA: DPB1 alleles are have been found. In fact, the magnitude of the evidence for associated with type 1 diabetes susceptibility in multiple ethnic groups. linkage between this chromosome 6 region and type 1 Diabetes 53:2158–2163, 2004 diabetes, when contrasted to the more modest predispo- 15. Valdes AM, Erlich HA, Noble JA: Human leukocyte antigen class I B and C sition that can be accounted for by any specific gene loci contribute to type 1 diabetes (T1D) susceptibility and age at T1D onset. Hum Immunol 66:301–313, 2005 association within the region, is one of the compelling 16. Nejentsev S, Howson JM, Walker NM, et al.. Localization of type 1 diabetes arguments favoring the existence of at least two, and most susceptibility to the MHC class I genes HLA-B and HLA-A. Nature likely several, genes that contribute to diabetes suscepti- 450:887–892, 2007 bility in the region (24). Much about the human genome 17. Aly TA, Baschal EE, Jahromi MM, Fernando MS, Babu SR, Fingerlin TE, remains to be understood, and while in some cases two or Kretowski A, Erlich HA, Fain PR, Rewers MJ, Eisenbarth GS. Analysis of more susceptibility genes may lie in close proximity by SNPs identifies major type 1A diabetes locus telomeric of the MHC. chance alone, in other cases an extended gene region may Diabetes 57:770–776, 2008 contain a cluster of interacting genes. This is not a new 18. Ma L, Penfornis A, Wang X, Schoenfeld D, Tuomilehto-Wolf E, Metcalfe K, Hitman G, Faustman D: Evaluation of TAP1 polymorphisms with insulin concept. Walter Bodmer eloquently discussed such clus- dependent diabetes mellitus in Finnish diabetic patients: the Childhood ters, using HLA as the emblematic example, in his 1980 Diabetes in Finland (DiMe) Study Group. Hum Immunol 53:159–166, 1997 Allen Award address (25). How and why such clusters of 19. Noble JA, Valdes AM, Lane JA, Green AE, Erlich HA: Linkage disequilib- physically and pathophysiologically related genes devel- rium with predisposing DR3 haplotypes accounts for apparent effects of oped, as well as what mechanisms have acted to perpetu- tumor necrosis factor and lymphotoxin-alpha polymorphisms on type 1 ate their persistence, however, will need to be the topic of diabetes susceptibility. Hum Immunol 67:999–1004, 2006 ongoing investigations. 20. Aminkeng F, Van Autreve JE, Koeleman BP, Quartier E, Van Schravendijk C, Gorus FK, Van der Auwera BJ; Belgian Diabetes Registry: TNFa microsatellite polymorphism modulates the risk of type 1 diabetes in the REFERENCES Belgian population, independent of HLA-DQ. Hum Immunol 68:690–697, 1. Raffel LJ, Goodarzi MO, Rotter JI: Diabetes mellitus. In Principles and 2007 Practice of Medical Genetics. 5th ed. Rimoin DL, Connor JM, Pyeritz RY, 21. Kumar R, Goswami R, Agarwal S, Israni N, Singh SK, Rani R: Association Eds. London, Churchill Livingstone, 2007, p. 1980–2022 and interaction of the TNF-alpha gene with other pro- and anti-inflamma- 2. McConnell RB, Pyke DA, Roberts JA: Blood groups in diabetes mellitus. Br tory cytokine genes and HLA genes in patients with type 1 diabetes from Med J 1:772–776, 1956 North India. Tissue Antigens 69:557–567, 2007 3. Hodge SE, Anderson CE, Neiswanger K, Field LL, Spence MA, Sparkes RS, 22. Alizadeh BZ, Eerligh P, van der Slik AR, Shastry A, Zhernakova A, Valdigem Sparkes MC, Crist M, Terasaki PI, Rimoin DL, Rotter JI: Close genetic G, Bruining JG, Sanjeevi CB, Wijmenga C, Roep BO, Koeleman BP: MICA linkage between diabetes mellitus and Kidd blood group. Lancet 2:893– marks additional risk factors for Type 1 diabetes on extended HLA 895, 1981 haplotypes: an association and meta-analysis. Mol Immunol 44:2806–2812, 4. Nerup J, Platz P, Andersen OO, Christy M, Lyngsoe J, Poulsen JE, Ryder 2007 LP, Nielsen LS, Thomsen M, Svejgaard A: HL-A antigens and diabetes 23. Qu HQ, Lu Y, Marchand L, Bacot F, Fre´chette R, Tessier MC, Montpetit A, mellitus. Lancet 2:864–866, 1974 Polychronakos C: Genetic control of alternative splicing in the TAP2 gene: 5. Cudworth AG, Woodrow JC: HL-A system and diabetes mellitus. Diabetes possible implication in the genetics of type 1 diabetes. Diabetes 56:270– 24:345–349, 1975 275, 2007 6. Cudworth AG, Woodrow JC. Evidence for HL-A-linked genes in “juvenile” 24. Concannon P, Erlich HA, Julier C, Morahan G, Nerup J, Pociot F, Todd JA, diabetes mellitus. Br Med J 3:133–135, 1975 Rich SS; Type 1 Diabetes Genetics Consortium: Type 1 diabetes: evidence 7. Nerup J, Christy M, Kromann H, Platz P, Ryder LP, Thomsen M, Svejgaard for susceptibility loci from four genome-wide linkage scans in 1,435 A: HLA and insulin-dependent diabetes mellitus. Postgrad Med J 55 (Suppl. multiplex families. Diabetes 54:2995–3001, 2005 2):8–13, 1979 25. Bodmer WF: The William Allan Memorial Award Address: Gene clusters, 8. Platz P, Jakobsen BK, Morling N, Ryder LP, Svejgaard A, Thomsen M, genome organization, and complex phenotypes: when the sequence is Christy M, Kromann H, Benn J, Nerup J, Green A, Hauge M: HLA-D and -DR known, what will it mean? Am J Hum Genet 33:664–682, 1981

528 DIABETES, VOL. 57, MARCH 2008