Distribution Of HLA Alleles Research Articles

Distribution of HLA Alleles and Haplotypes in Tamil-Speaking South Indian Populations: Affinities with Spanish and Austronesian

The present study was aimed to study HLA-DRB1, -DQB1 alleles and haplotypes of two endogamous groups of South India. PCR-SSP typing of HLA-DRB1, -DQB1 alleles were performed on 63 Mukkuvar, primarily a coastal population and 101 Valayar, a population primarily living on the fringes of forest areas. Genetic distances, neighbor-joining dendrograms and correspondence analysis have been performed. The HLA class II alleles, DRB1*07 (32.5%), DRB1*15 (23.0%), DRB1*13 (11.1%) and DRB1*12 (10.3%) were more frequent among Mukkuvar. Among Valayar, DRB1*12 (18.8%), DRB1*15 (17.3%), DRB1*04 (15.4%), DRB1*07 (13.4%) and DRB1*10 (10.9%) were more frequent. Similarly, DQB1*06 (38.1%), DQB1*02 (26.2%) and DQB1*05 (20.5%) alleles among Mukkuvar and DQB1*06 (40.2%) and DQB1*05 (28.9%) among Valayar were more frequent. We genotyped the two most common South Indian two-locus haplotypes, such as DRB1*15-DQB1*06 and DRB1*07-DQB1*02 for HLA-A, -B and -C alleles to identify the 5-locus extended haplotypes. We identified the presence of a highly unique extended haplotype A*03-B*35-C*12-DRB1*07-DQB1*02 in Valayar (HF: 0.2777) and Mukkuvar (HF: 0.1666) hitherto not reported in any of the world populations. The HLA-DRB1 allele based phylogenetic analysis have demonstrated the unique and distinct phylogenetic relatedness of Mukkuvar and Valayar with other ethnic populations. The coastal population Mukkuvar is more closely related to Hispanic and Guanche populations. However, the Valayar revealed phylogenetic relatedness with Austronesian and Micronesian populations supporting the theory of coastal migrations of Out-of-Africa ancestral founding populations.

DO THE BLOOD GROUPS AND HLA TYPES HAVE A ROLE IN END STAGE CHRONIC RENAL FAILURE PATHOGENESIS? A COMPARATIVE RETROSPECTIVE SINGLE-CENTER STUDY

Objective: The aim of this study was to investigate the distribution of blood groups and HLA types in patients with end stage chronic renal failure (ESCRF) following in our transplant center and their living donor candidates. Materials and Methods: We performed a retrospective analysis based on 2698 cases’ results registered in our center between July 01, 2011 and February 15, 2020. The study groups were composed of 1798 kidney recipients and 900 living donors. HLA typing for -A, -B, -C, -DQ and -DR loci were done by using polymerase chain reaction with sequence specific primers (PCR-SSP) low-resolution methods. SPSS (SPSS 11.5, SPSS Inc., Chicago, IL, USA) statistical package was used for statistical analyses. Results: Male gender dominance was determined in the recipient group and female gender dominance was found in the donor group (p<0.01).While “A” blood group was statistically more frequent in recipients than those of donor candidates, “0” blood group frequency was significantly higher in donor candidates than those of recipients (p<0.001). Similarly, significant “ARh+” dominance was observed in recipients but “0Rh+” dominance in donor candidates (p<0.001). According to frequencies, first six HLA alleles at Class-I “A” locus and Class-I “B” locus were same and ordered as HLA-A*02>-A*24>-A*03>-A*01>-A*11>-A*26; HLA-B*35>-B*51>-B*44>-B*18>B*38>B*07 in both recipients and donor candidates, respectively. The most frequent HLA allele at Class-I “C” locus was -C*07 in recipients, but -C*04 in donor candidates. There was an exact opposite situation in these alleles for the second alleles at the same locus. The other four alleles were respectively ordered as HLA-C *12>-C*06>-C*15>-C*03 in both recipients and donor candidates. While first six HLA allele at Class II “DR” locus was same as HLA-DRB1*11>-DRB1*04>-DRB1*13>-DRB1*15>-DRB1*03>-DRB1*07 and first five HLA allele at Class II “DQ” locus was same as HLA-DQB1*03>-DQB1*05>-DQB1*06>-DQB1*02>-DQB1*04 in both groups. In both study groups, most frequent genotype was same in all HLA loci, except “C” locus. In addition, first six HLA genotypes at Class-I “B” locus were same and ordered as HLA-B*35:51>-B*35:35>-B*51:51>-B*35:44>-B*18:35>-B*18:51. Although there are some subtle differences between distribution of HLA alleles, genotypes, and haplotypes detected in recipients and donor candidates, these are not significantly different from each other. Conclusion: The insignificant differences observed in distribution of HLA types between recipients and donor candidates support that there is not a considerable relationship between HLA types and ESCRF. However, significant differences shown in distribution of blood groups between recipients and donor candidates evidence the role of ABO system in pathogenesis of ESCRF.

Abstract 571: The shared mutation and neoantigen landscape of MMR-deficient colorectal cancers suggests immunoediting during tumor evolution

Abstract The immune system can recognize and attack cancer cells and their precursors, especially those with a high load of mutation-induced neoantigens. Such neoantigens are particularly abundant in DNA mismatch repair (MMR)-deficient cancers. MMR deficiency results in microsatellite instability (MSI), which leads to multiple insertion/deletion mutations at coding microsatellites and to neoantigen-inducing translational frameshifts. The significance of immune selection and immunoediting potentially shaping the neoantigen landscape during the progression from premalignant MMR-deficient lesions into cancers has not yet been analyzed. We hypothesized that the neoantigen landscape of MSI cancers may reflect the impact of immunoediting. We developed a novel tool for quantitative analysis of microsatellite mutations to explore the neoantigen landscape of MSI colorectal (CRC, n=139) cancers. Frameshift mutations were examined in 41 coding microsatellite (cMS) regions using our new algorithm. We predicted the resulting frameshift neoantigen sequences and used the publicly available prediction tool NetMHCpan 4.0 for prediction of MHC binding sequences. Immunological scores were generated to quantify the likelihood of defined cMS mutations to generate immunogenic neoantigens in different populations with defined HLA allele distributions. Across the 41 cMS analyzed, 77% of all mutations were in the reading frame of 1 nucleotide deletions (m1). The cMS mutation frequency and FSP epitope distribution across HLA genotypes (described by a general epitope likelihood score, GELS) showed a significant negative correlation (Pearson’s r=-0.42, p=0.0149). Some cMS presented with high mutation frequencies despite a high GELS (i.e. TGFBR2: pmut = 88%, GELS = 78.9%), suggesting mutation-induced driver effects, which may outweigh the increased immunogenicity. Our results show that MSI cancers share several highly immunogenic neoantigens. Importantly, a negative correlation between the antigenic strength of neoepitopes and their mutation frequency in MMR-deficient cancers points towards continuous immunoediting during their evolution. These findings will have substantial impact on the optimization of vaccines designed to potentially prevent or treat MSI-driven cancers. Citation Format: Matthias Kloor, Alexej Ballhausen, Moritz Przybilla, Michael Jendrusch, Elisabeth Pfaffendorf, Markus Draxlbauer, Florian Seidler, Sonja Krausert, Aysel Ahadova, Simon Kalteis, Daniel Heid, Johannes Gebert, Maria Bonsack, Sarah Schott, Hendrik Bläker, Toni Seppälä, Jukka-Pekka Mecklin, Sanne Ten Broeke, Maartje Nielsen, Julia Krzykalla, Axel Benner, Angelika Riemer, Magnus von Knebel Doeberitz. The shared mutation and neoantigen landscape of MMR-deficient colorectal cancers suggests immunoediting during tumor evolution [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 571.

Genotypic Analysis Revealed Association of HLA Alleles with Clinical Parameters in Bangladeshi Patients with Rheumatoid Arthritis

This study investigated distribution of HLA alleles (HLADRB1*01, *03, *04, *07, HLA-DQB1*0201, *0301/4) in 34 healthy controls and 57 rheumatoid arthritis (RA) patients in a Bangladeshi population and correlated the genotypic frequencies with clinical parameters. Frequency distribution of HLA-DRB1*04 (34%) and HLA-DRB1*01 (32%) were the highest followed by HLA-DQB1*0301/4 (29%) and HLA-DQB1*0201 (26%) in RA patients while HLA-DRB1*03 (12%) had lowest frequency. Plasma level of anti-CCP and rheumatoid factor antibodies confirmed diagnosis of RA patients that varied significantly between patients and healthy controls. Likewise, plasma levels of C-reactive protein, triglycerides, cholesterol, HDL-cholesterol and activities of AST and ALT exhibited significant variation between the two groups. In contrast, the levels of glucose, total protein, uric acid, LDL-cholesterol and plasma activity of ALP in RA patients had no significant deviations from healthy controls. Relationship between HLA genotype frequency and clinical parameters revealed that the mean levels of anti-CCP and rheumatoid factor antibodies were highest in the patients harboring HLA-DRB1*04 allele. These findings underpin the correlation between HLA genotype with clinical markers of RA which are indicative of disease severity. The positive correlation of these markers with certain HLA genes may be used to identify susceptible individuals who are likely to have RA in Bangladeshi population.

HLA common and well-documented alleles in China.

The American Society for Histocompatibility and Immunogenetics HLA common and well-documented (CWD) catalog, CWD 2.0.0 catalog and European Federation for Immunogenetics (EFI) CWD catalog have been published, which are useful for improving the accuracy of HLA genotyping in laboratories. Here, we studied the Chinese HLA CWD catalog. A total of 812 211 unrelated volunteer donors from the China Marrow Donor Program (CMDP) were analyzed. Six hundred seventy-six alleles at the HLA-A, -B, -C, -DRB1, and -DQB1 loci were defined as CWD alleles in the Chinese population, including 159 common and 517 well-documented alleles. The distribution of HLA alleles in the Chinese CWD catalog is different from that in the EFI CWD catalog. Thirty-two percent (215/676) of CWD alleles in the Chinese CWD catalog are shared with those in the EFI CWD catalog. Fifty-six percent (380/676) of alleles in the Chinese CWD catalog are not found in the EFI CWD catalog, while 655 alleles in the EFI CWD catalog are neither common nor well-documented alleles in the Chinese CWD catalog. The Chinese CWD catalog described in this study may help to improve high-resolution histocompatibility testing for CMDP-accredited laboratories in China. However, to accommodate an increasing number of HLA alleles, this Chinese CWD catalog should be regularly updated.

HLA Pharmacogenetic Markers of Drug Hypersensitivity in a Thai Population.

Severe cutaneous adverse drug reactions (SCARs) including Stevens-Johnson syndrome (SJS), toxic epidermal necrolysis (TEN), and drug reactions with eosinophilia and systemic symptoms (DRESS) are potentially life-threatening cutaneous reactions caused by several drugs. Recently, a number of genes encoding for human antigen presenting proteins, HLA alleles, have been discovered as valid pharmacogenetic markers for prediction of these life-threatening reactions. This study was aimed to determine the distribution of HLA alleles including the HLA class I and class II genes in 183 unrelated individuals of a Thai population using high resolution HLA genotyping in order to obtain 2-field data (4-digit resolution) and compare the frequencies of the HLA alleles that have been proposed as markers of SCARs with other ethnics. Results revealed a high prevalence of pharmacogenetic markers of drug-induced SCARs e.g., B*13:01 for dapsone; B*15:02 for carbamazepine and oxcarbazepine; B*58:01, A*33:03 and C*03:02 for allopurinol; C*08:01, C*14:02 and DRB1*12:02 for co-trimoxazole. Whereas, low prevalence of pharmacogenetic markers of SCARs induced by abacavir, B*57:01 and phenytoin, B*56:02/B*56:04 were noticed. The allele frequencies of B*13:01, B*15:02, and B*58:01 observed in a Thai population were significantly higher than those reported in Japanese and Caucasian populations. Similar to those observed in other Southeast Asian populations, low frequencies of A*31:01 and B*57:01 alleles were noted in the study population. Based on the frequencies of HLA pharmacogenetic markers, Thai and other Southeast Asian populations may at higher risk of drug-induced SCARs compared with Caucasian population.

Genotyping in patients affected by HLA-related diseases. App development for diagnostic support.

HLA typing requests for association studies of immune-mediated diseases are often redundant and inadequate. We designed a series of meta-analyses to evaluate the accuracy of typing and distribution of HLA alleles predisposing to diseases, aiming at developing an app that can help doctors in choosing the most suitable molecular analysis. The first study was on celiac disease (CD) and HLA-DQ in children. We searched all english articles published in the main bibliographic databases up to May 2016. The search strategy has been developed using controlled terms (e.g. MeSH) and free terms. We identified 1885 articles. 1334 abstracts were examined. 46 manuscripts were evaluated, and 13 studies were included in the meta-analysis (740 CD and 943 controls). The risk of developing CD in children with allelic variants encoding the HLA-DQ2.5 and/or HLA-DQ8 molecules has been confirmed. The greatest CD risk resides in carriers of two DQ2.5 molecules, i.e. subjects homozygous for the DQB1*02:01 and DQA1*05 alleles (OR=5.4, 95 % CI=4.1-6.8) compared to any other DQ genotype. Carriers of two DQB1*02:01 (chain β2) alleles and one DQA1*05 (chain α5) allele have the same risk (p=0.8089) of DQ2.5 homozygotes (OR=5.3%, 95 CI=4,1 to 6.5). We found no differences between DQ8/β2 and DQ2.5/DQ8, nor between β2/DQX and DQ2.5/X. We suggest a two-step process: first typing the DQB1*02:01 allele and, in case of a negative result, full typing of HLA-DQ.

P265 HLA haplotype structure in a Chinese population

Aim In order to study the gene structure of HLA haplotypes, these haplotypes must be determined in a large sample from a given population. Diploid combinations of alleles from different loci must be placed in phase with each other. In this study, this accomplished by family segregation analysis. Methods Samples come from a Chinese population in Taiwan collected for disease association. 490 mother-father-child trios were used in this study. HLA typing is based on Mia Fora next-generation sequencing by Immucor. The following loci are included: A, B, C, DRB1, DRB345, DQA1, DQB1, DPA1 and DPB1. A simple propositional-logic algorithm based on basic Mendelian genetics principles was used to do family segregation analysis and determine the haplotypes in each family. Results Full 2 × 2 contingency tables, for each pair of variables, with their corresponding chi-square, p value and other measures of correlation are presented for the following pairs of HLA loci or groups of loci: 1) B vs C, 2) DRB1 vs DRB345, 3) DQA1 vs DQB1, 4) DPA1 vs DPB1, 5) A vs B-C, 6) DRB1-DRB345 vs DQA1-DQB1, 7) DPA1-DPB1 vs DRB1-DRB345-DQA1-DQB1, and 8) A vs DRB1-DRB345-DQA1-DQB1. Conclusions Results may be biased by the disease association in this project. (The disease in question cannot be disclosed at this time.) Nevertheless, the bias effect will hardly diminish the value of the linkage disequilibrium data presented here. It is possible that haplotype frequencies are over-represented or under-represented, but the identity of the haplotype itself will not be affected by this bias. One of the main finding in this study is that, contrary to what is generally believed, NGS does not disclose a hidden abundance of HLA alleles, it rather helps us characterise in full detail alleles we were already familiar with. This study shows the distribution of HLA alleles in a given population, but their inter-loci structure, their association with alleles in other loci. The second main finding in this study is that in those cases where more than one genetic variant is represented by a single previously known protein allele, the linkage disequilibrium measures increase significantly when this genetic variants are taken into account individually.

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Editorial introductions

HLA-B*60 and HLA-DR*14 Alleles might be associated with the Hyperuricemic and Possibly Metabolic Syndrome Status in Renal Transplant

Background: Hyperuricemia is frequent among renal transplant recipients. The role of the HLA system in the susceptibility of hyperuricemia is unknown. Methods: We evaluated the HLA-B and HLA-DRB1 distribution among 160 renal recipients: 132 with hyperuricemia (Group 1) and 28 free of it (Group 2) as well as 381 ethnic-specific Mexicanmestizo population historic controls. The HLA alleles were assessed by PCR-SSP and the HLA allele gene frequencies were obtained by direct gene counting and compared by X 2 test. P values were adjusted by Bonferroni. Results: The median post-transplant follow-up was 3.9 years. The prevalence of diabetes, hypertension and use of calcineurin inhibitors was similar among groups; however dyslipidemia predominated in Group 1. HLA-B*35 and B*39 alleles were more frequent in Group 2 vs. controls (OR 2.17 95% CI 1.1-4.0; p = 0.01 and OR = 2.17, CI 95% 1.07-4.34; p = 0.04, respectively). Compared to controls, Group 1 had a higher prevalence of the allele HLA-B*60 (OR 3.5 95% CI 1.52-8.3; p = 0.004). The allele HLA-DRB1*14 predominated in Group 2 when compared with Group 1(OR 3.12 95% CI 1.06-9.9, p = 0.03) and controls (OR 2.50 95% CI 1.13-5, p = 0.007). Conclusion: The HLA allele distribution differed among groups, suggesting that hyperuricemia in the renal transplant setting might be influenced by ethnicity. Prospective studies using predicting HLA models in different ethnic populations are needed.

HLA-DRB1, DQA1 and DQB1 diversity in a mixed population of paraná, Southern Brazil

Aim The purpose of this study was to determine the allelic and haplotype frequencies of HLA-DRB1, -DQA1 and -DQB1 in a mixed population from Parana, Brazil. Methods Samples of 733 donors registered in the National Registry of Bone Marrow Donors (REDOME) from the northern/northwestern Parana, Southern Brazil were analyzed. Genotyping of HLA-DRB1 was performed by PCR-SSOP HD (High Definition) with Luminex method (One Lambda®, CA, USA), and of HLA-DQA1 and DQB1 by PCR-SSO (One Lambda ®, CA, USA) medium/high resolution. To resolve ambiguities in HLA-DRB1 and -DQB1, PCR-SSP (One Lambda ®, CA, USA) was used. Allele and haplotype frequencies, Hardy-Weinberg equilibrium (HWE) and linkage disequilibrium (LD) among different loci were determined by software version 3.11 ARLEQUIN. Results The analysis of the total sample 53, 14 and 23 alleles HLA-DRB1, -DQA1 and DQB1 were identified, respectively. For HLA-DRB1 locus, the most frequent were HLA-DRB1∗07:01 (13.16%), ∗03:01 (8.86%), ∗11:01 (8.59%), ∗15:01 (6.07%), ∗13:01 (5.93%) and ∗01:01 (5.86%). For the loci HLA-DQA1 and HLA-DQB1, alleles with the following frequencies were found: HLA-DQA1∗01:02 (16.85%), ∗05:05 (16.10%), ∗01:01 (14.80%), ∗02:01 (13.16%), ∗05:01 (10.77%) and ∗03:01 (10.64%); HLA-DQB1∗03:01 (20.19%), ∗05:01 (13.98%), ∗02:02 (11.93%), ∗03:02 and ∗02:01 (9.55%) and ∗06:01 (8.59%). One hundred seventy-three HLA-DQA1/DQB1 possible haplotypes, with HLA-DQA1∗05:05/DQB1∗03:01 (15.11%), DQA1∗01:01/DQB1∗05:01 (12.89%) and DQA1∗02:01/DQB∗02:02 (11.05%) were the most frequent. We observed 1275 HLA-DRB1/DQA1/DQB1 possible haplotypes and the most common were HLA-DRB1∗07:01/DQA1∗02:01/DQB1∗02:02 (10.30%), DRB1∗03:01/DQA1∗05:01/DQB1∗02:01 (8.39%) and DRB1∗11:01/DQA1∗05:05/DQB1∗03:01 (5.91%). The distribution of HLA alleles was in HWE. For LD analysis, the strength of the associations between the pair wises HLA DRB1-DQA1, DRB1-DQB1, and DQA1-DQB1 was observed, and all of them were statistically significant (P 0.05). The HLA diversity measured by the estimated heterozygosity was very high, 0.948-0.945 for HLA-DRB1, 0.806-0.876 for HLA-DQA1 and 0.888-0.890 for HLA-DQB1. Conclusion The results obtained in this study underscore the importance of using HLA genes as a tool of research of the ethnic composition of populations.

The Raikas – A unique combination of high prevalence of type 1 diabetes susceptibility genes and near zero incidence of the disease

The Raikas, a camel rearing tribal group living in the Thar desert of Rajasthan has been reported with a very low incidence of diabetes. We analysed the frequency distribution of HLA alleles in this community and compared the same with the non-Raika group living in the same geographic location and also that of the healthy North Indian (NI) population. The data revealed an exceptionally high phenotype frequency of HLA-DRB1*03 in this community (53%) as compared to the non-Raika group (27.73%, p=7.9E-05) and the NI population (14.6%, p=7.65E06). Further analysis revealed the occurrence of four major DRB1*03 haplotypes in the Raikas: (i) A*26-B*08-DRB1*03 (AH8.2, 11.76%); (ii) A*24-B*08-DRB1*03 (AH8.3, 8.82%); (iii) A*02-B*08-DRB1*03 (3.78%); (iv) A*01-B*08-DRB1*03 (AH8.1v, 0.84%); all of which occurred with a several fold higher frequency in the Raikas than the other two groups. These haplotypes have been reported to be positively associated with T1D in the NI population. The apparent lack of T1D and/or other autoimmune diseases in the Raikas despite the higher occurrence of known disease associated HLA alleles/haplotypes is intriguing and highlights the quintessential role of the environmental factors, food habits and level of physical activity in the manifestation of T1D. Possible influence of other protection conferring genes located on, as yet undefined chromosomal locations cannot be ruled out.

P111 : DISTRIBUTION OF CLASS I AND II HLA HAPLOTYPES IN A MIXED POPULATION FROM SOUTHERN BRAZIL

The aim of this study was evaluate of allele and haplotype frequencies of HLA-A, -B, -DRB1, -DQA1 and -DQB1 in a mixed population from Southern Brazil. Sample donors registered in the National Registry of Bone Marrow Donors (REDOME) were analyzed. Four hundred and seventy-three (67%) subjects were female while 231 (33%) were male. The average age was 33.63 years (SD = 9.37). Genotyping allelic groups of HLA-A , -B-DQA1 and DQB1 was performed by PCR-SSO with Luminex method (One Lambda®, CA, USA) and the HLA-DRB1 alleles was performed by PCR-SSOP HD (High Definition) methodology with Luminex (One Lambda®, CA , USA) in 704 individuals. The distribution of HLA alleles was in Hardy-Weinberg equilibrium. Twenty-two allelic groups were observed for HLA-A locus, the most frequent HLA-A ∗ 02 (27.1%), ∗ 03 (10.7%), ∗ 24 (9.6%), ∗ 01 (9.5%), ∗ 68 (6.3%) and ∗ 11 (5.4%), while for HLA-B locus with 34 allelic groups were the most frequent HLA-B ∗ 35 (12.1 %), ∗ 44 (10.2%), ∗ 51 (8.5%), ∗ 15 (7.5%), ∗ 7 (7.3%) and ∗ 18 (6.5%). The most common DRB1 alleles were: HLA-DRB1 ∗ 07:01 (13.2%), ∗ 03:01 (9.1%), ∗ 11:01 (8.4%), ∗ 15:01 (6.1%) ∗ 1:01 (5.92%) and ∗ 13:01 (5.9%). For the loci HLA-DQA1 and HLA-DQB1: HLA-DQA1 ∗ 01:02 (16.8%), ∗ 05:05 (15.8%) ∗ 02:01 (13.1%), 05:01 (9.8%), ∗ 01:01/04/05 (9.1%); HLA-DQB1 ∗ 03:01 (20.1%), ∗ 05:01 (14.1%), ∗ 02:02 (11.9%), ∗ 02:01 and ∗ 03:02 (9.74%). Four hundred HLA-A/B found possible haplotype, with HLA-A ∗ 02/B ∗ 51 (4.3%), A ∗ 02/B ∗ 15 (2.9%) and A ∗ 01/B ∗ 08 (2.9%) were the most frequent. We observed 2839 HLA-A/B/DRB1 possible haplotypes and the most common were HLA-A ∗ 01/B ∗ 08/DRB1 ∗ 03:01 (2.7%) and A ∗ 29/B ∗ 44/DRB1 ∗ 07:01 (1.9%). For HLA-DRB1/DQA1/DQB1 observed in 1369 possible haplotypes, the most frequent were HLA-DRB1 ∗ 03:01/DQA1 ∗ 05:01/DQB1 ∗ 02:01 (8.4%) and HLA-DRB1 ∗ 11:01/DQA1 ∗ 05:05/DQB1 ∗ 03:01 (5.7%), and the HLA-DQA1 ∗ 05:05/DQB1 ∗ 03:01 (14.9%) and HLA-DQA1 ∗ 02:01/DQB1 ∗ 02:02 (10.9%) were the most frequent. The results obtained for the haplotype extended HLA-A/B/DRB1/DQA1/DQB1 is given below: 15,006 possible haplotypes and HLA-A ∗ 01/B ∗ 08/DRB1 ∗ 03:01/DQA1 ∗ 05:01/DQB1 ∗ 02:01 (2.7%); HLA-A ∗ 29/B ∗ 44/DRB1 ∗ 07:01/DQA1 ∗ 02:01/DQB1 ∗ 02:02 (1.8%), the most frequent haplotypes.

Host-Specific Adaptation of HIV-1 Subtype B in the Japanese Population

The extent to which HIV-1 clade B strains exhibit population-specific adaptations to host HLA alleles remains incompletely known, in part due to incomplete characterization of HLA-associated HIV-1 polymorphisms (HLA-APs) in different global populations. Moreover, it remains unknown to what extent the same HLA alleles may drive significantly different escape pathways across populations. As the Japanese population exhibits distinctive HLA class I allele distributions, comparative analysis of HLA-APs between HIV-1 clade B-infected Japanese and non-Asian cohorts could shed light on these questions. However, HLA-APs remain incompletely mapped in Japan. In a cohort of 430 treatment-naive Japanese with chronic HIV-1 clade B infection, we identified 284 HLA-APs in Gag, Pol, and Nef using phylogenetically corrected methods. The number of HLA-associated substitutions in Pol, notably those restricted by HLA-B*52:01, was weakly inversely correlated with the plasma viral load (pVL), suggesting that the transmission and persistence of B*52:01-driven Pol mutations could modulate the pVL. Differential selection of HLA-APs between HLA subtype members, including those differing only with respect to substitutions outside the peptide-binding groove, was observed, meriting further investigation as to their mechanisms of selection. Notably, two-thirds of HLA-APs identified in Japan had not been reported in previous studies of predominantly Caucasian cohorts and were attributable to HLA alleles unique to, or enriched in, Japan. We also identified 71 cases where the same HLA allele drove significantly different escape pathways in Japan versus predominantly Caucasian cohorts. Our results underscore the distinct global evolution of HIV-1 clade B as a result of host population-specific cellular immune pressures. Cytotoxic T lymphocyte (CTL) escape mutations in HIV-1 are broadly predictable based on the HLA class I alleles expressed by the host. Because HLA allele distributions differ among worldwide populations, the pattern and diversity of HLA-associated escape mutations are likely to be somewhat distinct to each race and region. HLA-associated polymorphisms (HLA-APs) in HIV-1 have previously been identified at the population level in European, North American, Australian, and African cohorts; however, large-scale analyses of HIV-1 clade B-specific HLA-APs in Asians are lacking. Differential intraclade HIV-1 adaptation to global populations can be investigated via comparative analyses of HLA-associated polymorphisms across ethnic groups, but such studies are rare. Here, we identify HLA-APs in a large Japanese HIV-1 clade B cohort using phylogenetically informed methods and observe that the majority of them had not been previously characterized in predominantly Caucasian populations. The results highlight HIV's unique adaptation to cellular immune pressures imposed by different global populations.

Generation and Characterization of a Third Party GMP Grade Bank of CMV Specific T-Cells for Adoptive Immunotherapy of CMV Infections in Recipients of HSCT from Cord Blood or Seronegative Donors

Adoptive transfer of virus-specific T-cells (CTLs) derived from allogeneic HLA partially matched third party donors can also be effective in a proportion of patients developing EBV lymphomas, or infections due to CMV or adenovirus following transplants from seronegative donors. Such third party donor derived CTLs offer an off the shelf reagent for treatment of viral infections developing after transplant. However, the immunodominant cytotoxic activity exhibited by the CTLs is directed against specific epitopes of the viral protein and restricted by 1-2 HLA alleles. Therefore, it is critical that the T-cells administered from third party donors can recognize viral epitopes presented on shared HLA alleles. We have established a bank of 119 CMV specific T-cell lines (CMV CTLs) generated using autologous APCs loaded with a pool of overlapping peptides spanning the sequence of the dominant immunogenic protein CMVpp65. Each of these 119 CMV CTL lines has been characterized as to the epitope inducing T-cell response as well as the HLA allele restricting the epitope specific T-cell response. Epitopes were identified using an overlapping grid of peptide pools and the HLA restriction by cytotoxic activity against peptide loaded EBVBLCLs matched at a single HLA allele with the T-cell donor. The distribution of the common HLA alleles among the donors for these CTL lines was predominantly within the distribution of HLA allele frequencies represented in the caucasian and black populations, except for HLA A0201 and B0702, which were over represented ( 33% vs 25% and 21% vs 8.7% respectively). In 54% of the CTL lines, the immunodominant T-cell responses were restricted by HLA A0201 (25%), B0702 (21%) and B 3501-11(8%), and in the remaining 50%, the responses were restricted by other HLA class-I alleles, while only 16/119 lines (13%) were restricted by HLA class-II alleles. All 25 donors inheriting HLA B0702 (25/25) demonstrated HLA B0702 restricted CMV CTL responses, while 30/39 (77%) donors inheriting HLA A0201 and 9/19 (47%) donors inheriting HLA B3501-11 demonstrated HLA A0201 and B3501-11 restricted CMV CTL responses. Among all 9 donors co-inheriting HLA A0201 and B 0702, the immunodominant T-cell response was restricted by B0702. Among 12 donors co-inheriting A0201 and B 4401-04, 11/12 (91.6%) demonstrated immunodominant CMV CTL responses restricted by A0201; 1 donor also co-inherited HLA B0702 whose response was restricted by B0702. Therefore, an immunodominance hierarchy for HLA class-I alleles presenting the dominant CMVpp65 epitope was evident through this analysis among these 119 donors and was as follows: B 0702, A0201, B3501-11, A2601, B44, B40, B4201, A0101, B 1801. Strikingly, only 1 of 119 donors demonstrated T-cell responses restricted by A1101; a commonly inherited HLA class –I allele. In a series of 239 consecutive HLA matched related or unrelated transplants (MUD) and 137 HLA mismatched unrelated (MMUD) transplants, and 100 cord blood transplants conducted at our center, in 86%, 89% and 80% of the cases respectively, we could identify a CMV CTL line restricted by a shared HLA allele and matched at 2-3 alleles within this GMP grade CTL bank that would be immediately available for treatment of CMV infection. Appropriately restricted CMV CTLs would only be available in 60-70% of MMUD transplant and none of the cord blood transplants without this approach. This CMV CTL bank therefore represents a readily available clinical reagent for the treatment of resistant CMV infections developing in post transplant patients. The characterization of the CTLs has also enabled the further elucidation of immunodominant CMVpp65 epitopes and hierarchies. Since we have previously shown that CMV CTLs can be generated against subdominant epitopes presented by both common HLA alleles as well as less prevalent HLA alleles using a panel of artificial antigen presenting cells (AAPCs), expansion of this bank using T-cell sensitized against CMVpp65 presented on such AAPCs should broaden the applicability of this bank to all HSCT recipients. Disclosures: No relevant conflicts of interest to declare.

HLA variation reveals genetic continuity rather than population group structure in East Asia

Genetic differences between Northeast Asian (NEA) and Southeast Asian (SEA) populations have been observed in numerous studies. At the among-population level, despite a clear north-south differentiation observed for many genetic markers, debates were led between abrupt differences and a continuous pattern. At the within-population level, whether NEA or SEA populations have higher genetic diversity is also highly controversial. In this study, we analyzed a large set of HLA data from East Asia in order to map the genetic variation among and within populations in this continent and to clarify the distribution pattern of HLA lineages and alleles. We observed a genetic differentiation between NEA and SEA populations following a continuous pattern from north to south, and we show a significant and continuous decrease of HLA diversity by the same direction. This continuity is shaped by clinal distributions of many HLA lineages and alleles with increasing or decreasing frequencies along the latitude. These results bring new evidence in favor of the "overlapping model" proposed previously for East Asian peopling history, whereby modern humans migrated eastward from western Eurasia via two independent routes along each side of the Himalayas and, later, overlapped in East Asia across open land areas. Our study strongly suggests that intensive gene flow between NEA and SEA populations occurred and shaped the latitude-related continuous pattern of genetic variation and the peculiar HLA lineage and allele distributions observed in this continent. Probably for a very long period, the exact duration of these events remains to be estimated.

Generation and Characterization Of a Third Party GMP Grade Bank Of CMV Specific T-Cells For Adoptive Immunotherapy Of CMV Infections In Recipients Of HSCT From Cord Blood Or Seronegative Donors

Adoptive transfer of virus-specific T-cells (CTLs) derived from allogeneic HLA partially matched third party donors can also be effective in a proportion of patients developing EBV lymphomas, or infections due to CMV or adenovirus following transplants from seronegative donors. Such third party donor derived CTLs offer an off the shelf reagent for treatment of viral infections developing after transplant. However, the immunodominant cytotoxic activity exhibited by the CTLs is directed against specific epitopes of the viral protein and restricted by 1-2 HLA alleles. Therefore, it is critical that the T-cells administered from third party donors can recognize viral epitopes presented on shared HLA alleles. We have established a bank of 119 CMV specific T-cell lines (CMV CTLs) generated using autologous APCs loaded with a pool of overlapping peptides spanning the sequence of the dominant immunogenic protein CMVpp65. Each of these 119 CMV CTL lines has been characterized as to the epitope inducing T-cell response as well as the HLA allele restricting the epitope specific T-cell response. Epitopes were identified using an overlapping grid of peptide pools and the HLA restriction by cytotoxic activity against peptide loaded EBVBLCLs matched at a single HLA allele with the T-cell donor.The distribution of the common HLA alleles among the donors for these CTL lines was predominantly within the distribution of HLA allele frequencies represented in the caucasian and black populations, except for HLA A0201 and B0702, which were over represented ( 33% vs 25% and 21% vs 8.7% respectively). In 54% of the CTL lines, the immunodominant T-cell responses were restricted by HLA A0201 (25%), B0702 (21%) and B 3501-11(8%), and in the remaining 50%, the responses were restricted by other HLA class-I alleles, while only 16/119 lines (13%) were restricted by HLA class-II alleles.All 25 donors inheriting HLA B0702 (25/25) demonstrated HLA B0702 restricted CMV CTL responses, while 30/39 (77%) donors inheriting HLA A0201 and 9/19 (47%) donors inheriting HLA B3501-11 demonstrated HLA A0201 and B3501-11 restricted CMV CTL responses. Among all 9 donors co-inheriting HLA A0201 and B 0702, the immunodominant T-cell response was restricted by B0702. Among 12 donors co-inheriting A0201 and B 4401-04, 11/12 (91.6%) demonstrated immunodominant CMV CTL responses restricted by A0201; 1 donor also co-inherited HLA B0702 whose response was restricted by B0702. Therefore, an immunodominance hierarchy for HLA class-I alleles presenting the dominant CMVpp65 epitope was evident through this analysis among these 119 donors and was as follows: B 0702, A0201, B3501-11, A2601, B44, B40, B4201, A0101, B 1801. Strikingly, only 1 of 119 donors demonstrated T-cell responses restricted by A1101; a commonly inherited HLA class –I allele.In a series of 239 consecutive HLA matched related or unrelated transplants (MUD) and 137 HLA mismatched unrelated (MMUD) transplants, and 100 cord blood transplants conducted at our center, in 86%, 89% and 80% of the cases respectively, we could identify a CMV CTL line restricted by a shared HLA allele and matched at 2-3 alleles within this GMP grade CTL bank that would be immediately available for treatment of CMV infection. Appropriately restricted CMV CTLs would only be available in 60-70% of MMUD transplant and none of the cord blood transplants without this approach. This CMV CTL bank therefore represents a readily available clinical reagent for the treatment of resistant CMV infections developing in post transplant patients. The characterization of the CTLs has also enabled the further elucidation of immunodominant CMVpp65 epitopes and hierarchies. Since we have previously shown that CMV CTLs can be generated against subdominant epitopes presented by both common HLA alleles as well as less prevalent HLA alleles using a panel of artificial antigen presenting cells (AAPCs), expansion of this bank using T-cell sensitized against CMVpp65 presented on such AAPCs should broaden the applicability of this bank to all HSCT recipients. Disclosures:No relevant conflicts of interest to declare.

THU0223 Genetics of behçet’s disease in sardinia: two distinct extended hla haplotypes harbor the B*51 allele in normal population and in patients

BackgroundSeveral observations suggest that genes other than HLA-B*51 might be implicated in BD susceptibility and pathogenesis. In particular, as a consequence of the strong linkage disequilibrium characterizing the MHC region,...

Distribution of Human Leukocyte Antigen alleles in Systemic Lupus Erythematosus patients with Angiotensin Converting Enzyme Insertion/Deletion Polymorphism

Systemic Lupus Erythematosus is one of the classic examples of autoimmune diseases among human beings and is a rare disease in Pakistani population. Clinically it is a quite diverse and complicated autoimmune disease in a sense that it involves multiple organs of the body and mimics with other diseases as well. This study focused on the distribution of HLA alleles in SLE patients with ACE I/D Polymorphism. A total of 122 individuals were enrolled in this study, 61 were the SLE patients who fulfilled revised ACR criteria and 61 were the healthy controls. Mean age of SLE patients at diagnosis was 30.35 ± 1.687 years (Range: 12-68 years). ACE gene I/D polymorphism was performed by nested PCR and DNA based HLA typing technique was used. ACE gene I/D polymorphism of Intron16 was studied and found to be involved in the activity of SLE. There is high frequency of HLA-A*01, HLA-B*40, HLA-DRB1*01 alleles in SLE patients with ACE DD genotype. The distribution of HLA-A, -B, -DRB1 alleles was analyzed in SLE patients with various disease phenotypes. HLA-A*01 and HLA-B*40 was the most common allele found in SLE patients with the involvement of skin. HLA-A*01, -A*03, HLA-B*13 and -B*46 were common in SLE patients with arthritis while HLA-A*26 and -A*69 were commonly found in Lupus nephritis cases. SLE patients involving both skin and kidney had an allele HLA-DRB1*01 common in them.

The frequency of HLA alleles in a population of Inuit women of northern Quebec

BackgroundHuman leukocyte antigen (HLA) alleles code for proteins that are involved in the recognition of foreign antigens and activation of the immune system. The frequency of HLA alleles varies across different populations.ObjectiveTo describe the frequency of HLA alleles in a population of Inuit women of Nunavik, Quebec, Canada.DesignA cohort of women was recruited from 4 different communities between January 2002 and December 2007. HLA-B*07, HLA-DQB1*03, DQB1*06:02, DRB1*13 and DRB1*15:01 alleles were typed by PCR sequence-specific primers (PCR-SSP) and HLA-E and G alleles were type by DNA-sequencing procedures.ResultsWe obtained data on 524 participants. The most frequent HLA alleles in this population were HLA-E*01:03, HLA-G*01:04:01 and HLA-DQB1*03, and they were found in 89, 75 and 94% of the population, respectively.ConclusionsThe distribution of HLA alleles in Nunavik, Quebec is unique when compared to other populations in Canada or around the world.