Specific HLA Alleles Research Articles

Genetic alteration of class I HLA in cutaneous T-cell lymphoma

AbstractAbnormalities involving class I HLA are frequent in many lymphoma subtypes but have not yet been extensively studied in cutaneous T-cell lymphomas (CTCLs). We characterized the occurrence of class I HLA abnormalities in 65 patients with advanced mycosis fungoides or Sézary syndrome. Targeted DNA sequencing, including coverage of HLA loci, revealed at least 1 HLA abnormality in 26 of 65 patients (40%). Twelve unique somatic HLA mutations were identified across 9 patients, and loss of heterozygosity or biallelic loss of HLA was found to affect 24 patients. Although specific HLA alleles were commonly disrupted, these events did not associate with a decrease in the total class I HLA expression. Genetic events preferentially disrupted HLA alleles capable of presenting greater numbers of putative neoantigens. HLA abnormalities co-occurred with other genetic immune evasion events and were associated with worse progression-free survival. Single-cell analyses demonstrated that HLA abnormalities were frequently subclonal. Through analysis of serial samples, we observed that disrupting class I HLA events change dynamically over the disease course. The dynamics of HLA disruption are highlighted in a patient who received pembrolizumab and in whom resistance to pembrolizumab was associated with the elimination of an HLA mutation. Overall, our findings show that genomic class I HLA abnormalities are common in advanced CTCL and may be an important consideration in understanding the effects of immunotherapy in CTCL.

The Putative Role of TIM-3 Variants in Polyendocrine Autoimmunity: Insights from a WES Investigation.

Autoimmune polyglandular syndrome (APS) comprises a complex association of autoimmune pathological conditions. APS Type 1 originates from loss-of-function mutations in the autoimmune regulator (AIRE) gene. APS2, APS3 and APS4 are linked to specific HLA alleles within the major histocompatibility complex, with single-nucleotide polymorphisms (SNPs) in non-HLA genes also contributing to disease. In general, variability in the AIRE locus and the presence of heterozygous loss-of-function mutations can impact self-antigen presentation in the thymus. In this study, whole-exome sequencing (WES) was performed on a sixteen-year-old female APS3A/B patient to investigate the genetic basis of her complex phenotype. The analysis identified two variants (p.Arg111Trp and p.Thr101Ile) of the hepatitis A virus cell receptor 2 gene (HAVCR2) encoding for the TIM-3 (T cell immunoglobulin and mucin domain 3) protein. These variants were predicted, through in silico analysis, to impact protein structure and stability, potentially influencing the patient's autoimmune phenotype. While confocal microscopy analysis revealed no alteration in TIM-3 fluorescence intensity between the PBMCs isolated from the patient and those of a healthy donor, RT-qPCR showed reduced TIM-3 expression in the patient's unfractionated PBMCs. A screening conducted on a cohort of thirty APS patients indicated that the p.Thr101Ile and p.Arg111Trp mutations were unique to the proband. This study opens the pathway for the search of TIM-3 variants possibly linked to complex autoimmune phenotypes, highlighting the potential of novel variant discovery in contributing to APS classification and diagnosis.

12622 Molecular Physiology And Compensatory Response In Maladapted Pancreatic Islets Of Humanized Mice Model For Type 1 Diabetes

Abstract Disclosure: A. Hussain: None. A. Aldasouqi: None. S. Rafiqi: None. S.S. Khan: None. R. Paparodis: None. J.C. Jaume: None. S. Imam: None. Genetic predisposition linked with specific HLA (DR and DQ) alleles, environmental factors, and other uncharacterized physiological aberrations triggers an autoimmune attack and depletion of β cells in pancreatic islets, leading to decreased insulin secretion and diabetes. Our laboratory has generated humanized mice carrying the antigen-presenting HLA-DQ8 diabetes-linked haplotype and expressing the human autoantigen GAD65 in pancreatic beta cells. These humanized mice spontaneously develop type 1 diabetes (T1D) and represent the full spectrum of pathophysiological conditions experienced in T1D. Using humanized mice as a model of study, we studied the molecular physiology and compensatory response in maladapted pancreas under normal physiological conditions and hyperglycemic stress of T1D. We studied the differential expression of some important genes by quantitative PCR in maladapted islets to identify the physiological processes affected during the initial oxidative stress exerted by autoimmune conditions. Our results confirmed that levels of cyclin B, cMyc, Cyc D, Cyc E, PDGFRA, and NOTCH are reduced during autoimmune insult, reflecting the poor regenerative capacity of islet cells. However, Cyc A has an elevated expression, reflecting that islet cells, particularly the β cells of Type 1 diabetic mice, may have regenerative potential that may be explored. The genes for Desmin and Survivin showed decreased expression, whereas genes for Smad and Synuclein displayed increased expression. The genes for insulin and somatostatin showed elevated expression, whereas the gene for glucagon displayed reduced expression. The results suggest that during autoimmune insults, the β cells moderately whip up the synthesis of insulin-specific RNA to maintain the requirements. Among the endoplasmic reticulum-specific molecular chaperones, Calnexin showed an elevated expression, whereas calreticulin displayed a reduced expression. Among the genes involved with the architecture of the islet, Lamin and Integrin both display increased expression, reflecting the dynamic change in islet architecture during the autoimmune depletion of β cells. We also investigated the expression of ER-specific stress genes both at RNA and protein levels. Our preliminary results have confirmed that ER-specific stress genes showed an elevated expression during oxidative stress mediated by autoimmune T1D conditions. Presentation: 6/3/2024

Associations of classical HLA alleles with sleep behaviours.

Immune dysregulation has been observed in individuals with sleep disturbance, with HLA molecules play a crucial role in the immune response. This study aimed to investigate the associations between HLA alleles and sleep behaviours, considering several environmental factors. Data were sourced from the UK Biobank. Logistic regression analyses were performed to explore the associations between 359 HLA alleles and 4 sleep behaviours, including chronotype (n = 204,636), insomnia (n = 227,553), snoring (n = 214,350) and daytime dozing (n = 227,197). Furthermore, gene-environmental interaction studies (GEIS) were conducted to evaluate the interactions of HLA alleles with environmental factors on sleep behaviours. This study analysed a total sample and subgroups stratified by sex to elucidate the impact of HLA alleles on sleep behaviours. Our findings revealed several associations between specific HLA alleles and sleep behaviours. Notably, HLA-A*23:01 was associated with evening chronotype in the total sample (OR = 0.918, 95%CI: 0.872-0.965), while HLA-A*32:01 was associated with evening chronotype in males (OR = 1.089, 95%CI: 1.037-1.144). Furthermore, GEIS identified multiple sets of interactions associated with sleep behaviours. For example, the interaction of HLA-DPA1*01:04 with alcohol consumption was associated with daytime dozing in the total sample (OR = 1.993, 95%CI: 1.351-2.941), while the interaction of HLA-DQB1*05:04 with ever suffered mental distress preventing usual activities was associated with insomnia in males (OR = 0.409, 95%CI: 0.254-0.658). Our findings highlight the involvement of HLA in sleep regulation and underscore the potential interactions between HLA alleles and environmental factors in modulating susceptibility to sleep behaviours.

Abstract P181: Class 1 human leukocyte antigens exhibit marked variability in capacity to present isolevuglandin adducts

Introduction: Isolevuglandins (isoLGs) are lipid peroxidation products that covalently modify lysine residues on self-proteins. These modified self-proteins are processed to peptides that are presented in the context of class I major histocompatibility complexes (MHC-I). In hypertension, this modification enhances CD8 + T cell activation, contributing to inflammation and elevated blood pressure. In mice we found that IsoLG-adduct presentation is highly dependent on class I MHC structure. We sought to determine if human class I MHC (HLAs) exhibit similar variability in their ability to present these adducts by screening alleles representing 90% of the population. Hypothesis: We hypothesize that HLA subtypes exhibit variable capacity for isoLG presentation. Methods: HLA alleles representing 90% demographic frequency were identified from the US National Merit Donor Program Allele Frequency Database. HLA-null human K562 cells were transduced with these alleles, expanded, and enriched for HLA expression by flow cytometry to produce single HLA allele lines. To induce isoLG adduct presentation, cells were treated with 1mM tert-Butyl hydroperoxide (tBHP). After 24 hours, we employed Forster resonance energy transfer (FRET) between HLAs and isoLG-adducts using antibodies specific for both, which we have shown is indicative of IsoLG-adduct presentation (Fig 1A-C). Results: Substantial variability for isoLG-adduct presentation was observed between HLA subtypes A, B and C (Figure 1A-1C). Scikit-learn’s KMeans clustering revealed four patterns of isoLG-adduct presentation among HLAs: Low baseline/low activation, low baseline/high activation, intermediate baseline/intermediate activation, and high baseline/high activation alleles (Fig 1D). Conclusions: These findings identify specific HLA alleles as high isoLG presenters, potentially associated with increased immune activation risk. Combining these findings, HLA alleles, and diagnosis code databases could aid in identifying high-risk haplotypes for immune activation in human hypertension.

Genetic association of antinuclear antibodies with HLA in JIA patients: a Swedish cohort study

BackgroundJuvenile Idiopathic Arthritis (JIA) is a complex autoimmune disease and the most common chronic rheumatological disease affecting children under the age of 16. The etiology of JIA remains poorly understood, but evidence suggests a significant genetic predisposition.MethodsWe analyzed a Swedish cohort of 329 JIA patients and 728 healthy adult controls using the Illumina OmniExpress array for genotyping. HLA alleles were imputed from GWAS data using the SNP2HLA algorithm.ResultsCase–control analysis yielded 12 SNPs with genome-wide significant association to JIA, all located on chromosome 6 within the MHC class II gene region. Notably, the top SNP (rs28421666) was located adjacent to HLA-DQA1 and HLA-DRB1. HLA-DRB1*08:01, HLA-DQA1*04:01, and HLA-DQB1*04:02 were the haplotypes most strongly associated with an increased risk of JIA in the overall cohort. When analyzing disease specific subtypes, these alleles were associated with oligoarthritis and RF-negative polyarthritis. Within the complex linkage disequilibrium of the HLA-DRB1-DQA1-DQB1 haplotype, our analysis suggests that HLA-DRB1*08 might be the primary allele linked to JIA susceptibility. The HLA-DRB1*11 allele group was also independently associated with JIA and specifically enriched in the oligoarthritis patient group. Additionally, our study revealed a significant correlation between antinuclear antibody (ANA) positivity and specific HLA alleles. The ANA-positive JIA group showed stronger associations with the HLA-DRB1-DQA1-DQB1 haplotype, HLA-DRB1*11, and HLA-DPB1*02, suggesting a potential connection between genetic factors and ANA production in JIA. Furthermore, logistic regression analysis reaffirmed the effects of HLA alleles, female sex, and lower age at onset on ANA positivity.ConclusionsThis study identified distinct genetic associations between HLA alleles and JIA subtypes, particularly in ANA-positive patients. These findings contribute to a better understanding of the genetic basis of JIA and provide insights into the genetic control of autoantibody production in ANA-positive JIA patients. This may inform future classification and personalized treatment approaches for JIA, ultimately improving patient outcomes and management of this disease.

Model for the Study of Drug Hypersensitivity Based on Bucilamine and the HLA-DRB1*08:02 Allele in Colombian Amerindian Populations

Backgrounds: Allergic diseases and hypersensitivity reactions are common disorders that in turn consist of an extensive genetic component in which the molecules of the Major Histocompatibility Complex (MHC) are included, which have certain alleles associated with the development of hypersensitivity to certain drugs, among which is the allele HLA-DRB1 * 08: 02 as a predisposing factor of hypersensitivity to Bucillamine; this drug is the starting point for the study of the relationship between hypersensitivity reactions to medications and the expression of certain alleles of MHC. Objective: Find the relationship between hypersensitivity to the drug and the expression of the specific allele in Amerindian populations of the Sierra Nevada de Santa Marta and in turn suggest the application of the methodological model proposed in similar studies that seek to relate drug allergies with specific HLA alleles. Methods: A systematic search of information was carried out in the Sience, ScienceDirect, Elsevier and Pubmed databases, the frequencies obtained were tabulated and organized according to their expression to be analyzed with the MEGA7 software. Results: A significant frequency of the HLA-DRB1 * 08: 02 allele was found in the Ijka (61.7%), Arhuaco (41.5%), Kogi (17.9%) and Arsario (15%). Conclusion: A cautious use of Bucillamine and structurally similar drugs it’s recommended in susceptible Amerindian populations, at the same time the application of the proposed model it’s recommended for the study of different drugs that could trigger an allergic reaction based on HLA’s allele expression.

In silico analysis of the protein-protein interaction of the SARS-CoV-2 spike protein

The pandemic caused by the SARS-CoV-2 virus has represented a global challenge with a significant impact on public health since its emergence in 2019. Understanding the interactions between this virus and the human immune system is essential for the development of new strategies more effective therapies and diagnoses. This study aimed to predict epitopes for SARS-CoV-2 T and B cells, as well as evaluate the interaction of the spike protein with other viral proteins, using bioinformatics methods. SARS-CoV-2 protein sequences were collected from UniProt. Epitopes for T cells were predicted in silico using specific HLA alleles from the Bahia population. Epitopes for B cells were predicted using the IEDB server with multiple methods based on amino acid features. Protein-protein interaction was analyzed using the STRING database. The result is 10,671 peptides related to various SARS-CoV-2 viral proteins, including the spike, essential for the infection and pathogenesis of COVID-19. In addition to spike, proteins such as ORF3a, ORF7a, and ORF8 showed significant immunogenic potential. Protein-protein interaction analysis revealed that proteases such as TMPRSS2 and TMPRSS11D are crucial for viral entry and are potential therapeutic targets. This study expands the understanding of the molecular interactions of SARS-CoV-2, highlighting new therapeutic targets and clinical complications associated with COVID-19. The results provide valuable insights for the development of targeted therapeutic strategies and improved diagnostics, contributing to the mitigation of the global pandemic.

HLA variants and their association with IgE-Mediated banana allergy: A cross-sectional study

BackgroundBanana allergy is on the rise in tropical regions. Advances in genomics and candidate gene identification have increased interest in genetic factors in food allergies. However, the genetic basis of IgE-mediated banana allergy is underexplored. ObjectiveTo characterize HLA variants and their association with IgE-mediated banana allergy. MethodsThis cross-sectional study recruited banana-allergic adults, confirmed by allergology tests, with non-allergic individuals as controls. Genomic DNA extraction and sequencing BAM files for HLA typing were conducted. Allele frequency was calculated using the direct counting method, and odds ratio (OR) with 95 % confidence interval (CI) were determined. Fisher's exact or chi-square tests were used to assess associations with Bonferroni's correction for multiple tests. The allele frequency of the Thai population from The Allele Frequency Net Database was used to compute the allele enrichment ratio (ER). ResultsA total of 59 cases and 64 controls were recruited. HLA genotyping indicated potential associations of HLA-B*15:25 (OR 11.872; p-value 0.027), HLA-C*04:03 (OR 7.636; p-value 0.033), and HLA-DQB1*06:09 (OR 11.558; p-value 0.039) with banana allergy. However, after Bonferroni correction, none of these associations reached statistical significance. Comparing allele frequency with the general population from The Allele Frequency Net Database, our ER analysis revealed a higher prevalence in the banana allergy group for B*15:25 (ER 1.849), C*04:03 (ER 1.332), and DQB1*06:09 (ER 6.602) alleles. ConclusionsThis study provides initial genetic insights into banana allergy, suggesting potential links with specific HLA alleles. Despite 12 initially identifying alleles, none were statistically significant after multiple testing correction. Larger studies are needed to detect possible significant correlations.

A multi-ethnic reference panel to impute HLA classical and non-classical class I alleles in admixed samples: Testing imputation accuracy in an admixed sample from Brazil.

The MHC class I region contains crucial genes for the innate and adaptive immune response, playing a key role in susceptibility to many autoimmune and infectious diseases. Genome-wide association studies have identified numerous disease-associated SNPs within this region. However, these associations do not fully capture the immune-biological relevance of specific HLA alleles. HLA imputation techniques may leverage available SNP arrays by predicting allele genotypes based on the linkage disequilibrium between SNPs and specific HLA alleles. Successful imputation requires diverse and large reference panels, especially for admixed populations. This study employed a bioinformatics approach to call SNPs and HLA alleles in multi-ethnic samples from the 1000 genomes (1KG) dataset and admixed individuals from Brazil (SABE), utilising 30X whole-genome sequencing data. Using HIBAG, we created three reference panels: 1KG (n = 2504), SABE (n = 1171), and the full model (n = 3675) encompassing all samples. In extensive cross-validation of these reference panels, the multi-ethnic 1KG reference exhibited overall superior performance than the reference with only Brazilian samples. However, the best results were achieved with the full model. Additionally, we expanded the scope of imputation by developing reference panels for non-classical, MICA, MICB and HLA-H genes, previously unavailable for multi-ethnic populations. Validation in an independent Brazilian dataset showcased the superiority of our reference panels over the Michigan Imputation Server, particularly in predicting HLA-B alleles among Brazilians. Our investigations underscored the need to enhance or adapt reference panels to encompass the target population's genetic diversity, emphasising the significance of multiethnic references for accurate imputation across different populations.

Correlation of allele-specific HLA loss of heterozygosity in patients with cancer with driver mutations.

e14658 Background: While immunotherapies have revolutionized cancer treatment, the limited predictability of response and resistance mechanisms present challenges to the development of novel therapeutics for solid tumors. Many of these use a sensitive and specific T cell receptor (TCR)-HLA:peptide interaction as a mechanism of action and can be impacted by HLA loss of heterozygosity (LOH). Allele-agnostic HLA LOH analyses assessing loss of any MHC class I allele are relevant for HLA-agnostic approaches such as immune checkpoint inhibitors; however, context-specific studies remain limited. For example, adoptive TCR T cell therapies and bi-specific TCR T cell engagers target neoantigen peptides derived from oncogenic driver mutations, such as those of KRAS and TP53, presented by a specific HLA allele. Thus, allele-agnostic analyses may overestimate the frequency and relevance of HLA LOH for allele-specific modalities. Methods: A real-world comprehensive genomic profiling dataset consisting of 78,418 cases (1), germline heterozygous for one or more HLA class I locus, was analyzed for HLA LOH in the context of frequent driver mutations (KRAS G12C, G12D, G12V and TP53 R175H), the corresponding HLA alleles (A*02:01, A*03:01, and A*11:01), and within tumor subtypes. Results: Allele-agnostic HLA LOH was observed in 16.6% of all samples and varied between indications. Notably, allele-specific loss of HLAs A*02:01, A*03:01, and A*11:01 across all samples was much lower than allele-agnostic loss (6.3%, 6.6%, and 6.3% cases, respectively). Although, a trend for increased allele-specific HLA LOH was observed when analyzed by driver mutation, the frequency remained low. Specifically, across all cases, A*02:01, A*03:01, and A*11:01 allele-specific LOH ranged between 5.9% - 9.7% in relation to KRAS G12C, G12D, and G12V compared to 5.9% - 6.2% for wild-type (WT). Moreover, it did not achieve statistical significance for any HLA-KRAS mutation pairs in colorectal (CRC), non-small cell lung (NSCLC), and pancreatic (PDAC) cancers, except for A*11:01 and KRAS G12C in NSCLC, which was lower in mutated cases (5.3% for G12C vs 10.1% for WT KRAS, p=0.045). Both allele-agnostic and A*02:01-specific HLA LOH in TP53 WT samples were lower than average. The TP53 R175H mutation was associated with limited increase in HLA-A*02:01 LOH (from 4.4% for WT to 8.1% for TP53 R175H) and varied between indications, e.g. no significant increase was observed in R175H-positive breast cancer and NSCLC cases contrary to CRC and PDAC. Conclusions: Based on this real-world dataset, over 90% of cases retain the TCR-targeted allele and, therefore, preserve the molecular complex necessary for HLA/driver mutation-based therapies. Notably, the database is enriched for advanced cancer patients. Further studies should test correlations with treatments and whether tumors in earlier lines of treatment have an even lower rate of HLA LOH. 1. Montesion et al., PMID: 33127846.

HLA-DR and HLA-DQ Polymorphism Correlation with Sexually Transmitted Infection Caused by Chlamydia trachomatis.

Background and Objectives: Chlamydia trachomatis (C. trachomatis) represents one of the most prevalent bacterial sexually transmitted diseases. This study aims to explore the relationship between HLA alleles/genotypes/haplotypes and C. trachomatis infection to better understand high-risk individuals and potential complications. Materials and Methods: This prospective study recruited participants from Transylvania, Romania. Patients with positive NAAT tests for C. trachomatis from cervical/urethral secretion or urine were compared with controls regarding HLA-DR and -DQ alleles. DNA extraction for HLA typing was performed using venous blood samples. Results: Our analysis revealed that the presence of the DRB1*13 allele significantly heightened the likelihood of C. trachomatis infection (p = 0.017). Additionally, we observed that individuals carrying the DRB1*01/DRB1*13 and DQB1*03/DQB1*06 genotype had increased odds of C. trachomatis infection. Upon adjustment, the association between the DRB1*01/DRB1*13 genotype and C. trachomatis remained statistically significant. Conclusions: Our findings underscore the importance of specific HLA alleles and genotypes in influencing susceptibility to C. trachomatis infection. These results highlight the intricate relationship between host genetics and disease susceptibility, offering valuable insights for targeted prevention efforts and personalized healthcare strategies.

Low C4A copy numbers and higher HERV gene insertion contributes to increased risk of SLE, with absence of association with disease phenotype and disease activity.

Low copy numbers (CNs) of C4 genes are associated with systemic autoimmune disorders and affects autoantibody diversity and disease subgroups. The primary objective of this study was to characterize diversity of complement (C4) and C4-Human Endogenous Retrovirus (HERV) gene copy numbers in SLE. We also sought to assess the association of C4 and C4-HERV CNs with serum complement levels, autoantibodies, disease phenotypes and activity. Finally, we checked the association of C4 and HERV CNs with specific HLA alleles. Genomic DNA from 70 SLE and 90 healthy controls of south Indian Tamil origin were included. Demographic, clinical and serological data was collected in a predetermined proforma. CNs of C4A and C4B genes and the frequency of insertion of 6.4kb HERV within C4 gene (C4AL, C4BL) was determined using droplet digital polymerase chain reaction (ddPCR). A four digit high resolution HLA genotyping was done using next generation sequencing. In our cohort, the total C4 gene copies ranged from 2 to 6. Compared to controls, presence of two or less copies of C4A gene was associated with SLE risk (p = 0.005; OR = 2.79; 95% CI = 1.29-6.22). Higher frequency of HERV insertion in C4A than in C4B increases such risk (p = 0.000; OR = 12.67; 95% CI = 2.80-115.3). AL-AL-AL-BS genotype was significantly higher in controls than SLE (9%vs1%, p = 0.04; OR = 0.15, 95% CI = 0.00-0.16). Distribution of HLA alleles was not different in SLE compared to controls as well as in SLE subjects with ≤ 2 copies and > 2 copies of C4A, but HLA allele distribution was diverse in subjects with C4B ≤ 2 copies and > 2 copies. Finally, there was no correlation between the C4 and the C4-HERV diversity and complement levels, autoantibodies, disease phenotypes and activity. In conclusion, our data show that, low C4A copy number and higher insertion of HERV-K in C4A increases the risk for SLE. C4 and C4-HERV CNs did not correlate with serum complements, autoantibodies, disease phenotypes and activity in SLE. Further validation in a larger homogenous SLE cohort is needed.

Abstract 1204: Neoantigen MHC presentability ratios influence the tumor microenvironment and response to immunotherapy

Abstract Introduction: Recent literature suggests that neoantigens presented via MHC-II induce a CD4+ T Cell mediated immune response, and MHC-I presented neoantigens expand CD8+ cytotoxic T Cells populations. We developed an algorithm to stratify patients into MHC-I Reliant and MHC-II Reliant immune checkpoint blockade (ICB) responders. Experimental Procedures: Our algorithm generates patient mean harmonic best rank scores (PHBR) of each neoantigen in a tumor to estimate the proportion of neoantigens that are likely well presented by each MHC complex, given a patient’s specific HLA alleles. From there, the ratio of neoantigens presented by each MHC (class-I and class-II) can be used to stratify patients into MHC-I or MHC-II Reliant groupings. The primary goals of our study were to investigate tumor immune microenvironment and survival differences between these groups. First, we used CIBERSORTx infiltration estimates of the ratio of these CD4/CD8 T cell populations across our MHC Reliance categories and by response vs nonresponse in two separate cohorts: Discovery (110) and Validation (77). Results: We first observed that the CD4/CD8 ratio is higher in MHC-II responders than in MHC-I responders (Fig 6. A, P=~0.0057 Discovery; P=0.025 Validation), but no such a difference was found in nonresponders. Using an alternate digital cytometry tool (xCell) we obtained similar results (MHC-II vs MHC-I responders discovery P=0.44; validation P=0.0015) (Fig. S7). We applied an identical methodology to immune-hot ICB-naive cancer samples from TCGA and found that there was a powerful protective effect of the CD4/CD8 ratio in TCGA MHC-II Reliant patients (Fig S6. HR=-0.76, P=0.0092), there was a significantly harmful effect of that same ratio in TCGA MHC-I Reliant patients (Fig S6 HR=0.59, P=0.0352). These data demonstrate a benefit to having some level of concordance between CD4/CD8+ T cell infiltration and MHC-II/MHC-I neoantigen presentability ratios. Since CD4 memory based immune responses have a longer duration of action over more transient CD8 cytotoxic immune responses (cite), we compared the survival of responders in MHC-II vs MHC-I Reliance groups. MHC-II Reliant responders had a significantly longer overall survival in both discovery and validation cohorts (Fig 6. B-C, discovery P=0.0073; validation P=0.0398). Conclusions: While neoantigens are already used in ICB stratification in the context of tumor mutational burden, we demonstrate that the balance of which MHC is presenting a set of neoantigens is relevant to immune infiltration and treatment outcome. Citation Format: Timothy J. Sears, Ko-Han Lee, Meghana Pagadala, Andrea Castro, Maurizio Zanetti, Hannah Carter. Neoantigen MHC presentability ratios influence the tumor microenvironment and response to immunotherapy [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 1204.

The Influence of HLA Polymorphisms on the Severity of COVID-19 in the Romanian Population.

In this study, we aimed to investigate whether specific HLA alleles found in patients from Romania and the Republic of Moldova were associated with the severity of COVID-19 infection and its associated mortality. We analyzed the HLA alleles at the -A, -B, -C, -DRB1, and -DQB1 loci in a cohort of 130 individuals with severe and extremely severe forms of COVID-19, including 44 individuals who died. We compared these findings to a control group consisting of individuals who had either not been diagnosed with COVID-19 or had experienced mild forms of the disease. Using multivariate logistic regression models, we discovered that the B*27 and B*50 alleles were associated with an increased susceptibility to developing a severe form of COVID-19. The A*33 and C*15 alleles showed potential for offering protection against the disease. Furthermore, we identified two protective alleles (A*03 and DQB1*02) against the development of extremely severe forms of COVID-19. By utilizing score statistics, we established a statistically significant association between haplotypes and disease severity (p = 0.021). In summary, this study provides evidence that HLA genotype plays a role in influencing the clinical outcome of COVID-19 infection.

Abstract B036: Exploration of the human leukocyte antigen immunopeptidome in pancreatic adenocarcinoma

Abstract Pancreatic adenocarcinoma (PDAC) is a lethal disease with an 11% five-year survival rate and frequent distant metastasis at diagnosis. The immune escape mechanisms driving this unchecked proliferation in PDAC remain unclear. The HLA system plays a crucial role in immune-mediated recognition of neoplasms. HLA class I presents endogenously processed peptides to circulating CD8+ T-cells, while HLA class II presents exogenous peptides to CD4+ T-cells, with the collective sum of these peptides known as the immunopeptidome. Most immunopeptidome studies rely on peptides derived solely from cell lines, with few peptides directly reported from patients. Characterization of the immunopeptidome in cancer patients is critical for understanding peptide presentation and neoantigen recognition in PDAC. We hypothesize that isolating HLA class I and II peptides directly from PDAC donors will identify novel neoantigen-derived peptides presented to the immune system with high fidelity for specific HLA alleles. Whole Exome Sequencing (WES) was performed on nine PDAC donors from the UNMC Rapid Autopsy Program. Somatic mutations were identified using best practices published by the BROAD Institute. HLA alleles were identified with the HLA-HD algorithm. Large-scale immunopurification of HLA class I complexes and associated peptides was performed on PDAC liver metastases. Data-Dependent-Acquisition MS/MS with PEAKS analysis identified individual peptide sequences. Similar strategies are being employed for HLA class II peptide isolation from matched donor spleens. To date 39,639 HLA class I peptides and 2,995 HLA class II peptides have been identified from nine donors. Of HLA class I isolated peptides, 9,987 unique sequences have been traced and mapped to the human reference genome. Of the remaining 29,652 unmapped peptides, we have manual confirmation of the presence of neoantigen-derived peptides within that pool, with a pipeline for large scale alignment of these peptides to the annotated mutated genome pending. The gold standard HLA-peptide predictive binding algorithm, netMHC, confirms that 24.2% of our isolated HLA class I peptides are predicted binders for their patient-specific HLA alleles. A notable finding is that 9% of identified HLA class II peptide sequences contained sequences identical to those isolated during independent HLA class I isolations from the same donor. These data establish the high-fidelity of our pipeline for identification of peptides presented by the HLA system directly from PDAC donors. The quantity of HLA-associated peptides discovered sets this study on track to surpass all previously reported patient-derived immunopeptidome studies. The observed conservation of HLA class I and II sequences from independent isolations within the same donor implicates a novel mechanism by which specific combinations of HLA class I and II alleles shape the immunopeptidome. Further work identifying neoantigens in our unmatched isolated HLA class I and II peptides will be continued to uncover potential novel targets for future immunotherapies. Citation Format: William R. Miklavcic, Paul Grandgenett, Michael A. Hollingsworth. Exploration of the human leukocyte antigen immunopeptidome in pancreatic adenocarcinoma [abstract]. In: Proceedings of the AACR Special Conference in Cancer Research: Pancreatic Cancer; 2023 Sep 27-30; Boston, Massachusetts. Philadelphia (PA): AACR; Cancer Res 2024;84(2 Suppl):Abstract nr B036.

Role of Human Leukocyte Antigen Class II in Antibody-Mediated Skin Disorders.

HLA class II molecules are key factors determining susceptibility to autoimmune disorders, and their role in immune-mediated skin conditions such as psoriasis has been extensively investigated. However, there is currently little understanding of their role in antibody-mediated skin diseases such as autoimmune blistering disorders. We researched the available literature using PubMed to narratively review the current knowledge on HLA associations in antibody-mediated blistering skin pathologies. Our results summarized the risk alleles that are identified in the literature, together with certain known protective alleles: in the pemphigus group, alleles HLA-DQB1*0503 and HLA-DRB1*0402 are most commonly associated with disease; in the pemphigoid group, the most studied allele is HLA-DQB1*0301; in epidermolysis bullosa acquisita, few genetic studies are available; in dermatitis herpetiformis, the association with haplotypes HLA-DQ2 and HLA-DQ8 is strongly established; finally, in linear IgA bullous disease, specific HLA alleles may be responsible for pediatric presentations. Our current pathogenic understanding of this group of disorders assigns a key role to predisposing HLA class II alleles that are able to bind disease autoantigens and therefore stimulate antigen-specific autoreactive T cells. The latter engage B lymphocytes that will produce pathogenic autoantibodies. The distribution of HLA alleles and their disease associations are variable across demographics, and an in-depth pathogenetic understanding is needed to support associations between HLA alleles and disease phenotypes. Additionally, in a personalized medicine approach, the identification of HLA alleles associated with the risk of disease may become clinically relevant in identifying susceptible subjects that should avoid exposure to known triggers, such as medication, when possible.

Rare peptide anchors of HLA class I alleles contribute to the COVID-19 disease severity and T cell memory

Understanding how human leukocyte antigen (HLA) polymorphism affects both the susceptibility and severity of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection will help to identify individuals at higher risk to better manage and prioritize vaccination at the clinical level and explain the differences in epidemic trends in different regions at the epidemiological level. This study compared the frequencies of HLA class I alleles (HLA-A, B) in 214 coronavirus disease 2019 (COVID-19) patients with different disease severity and 35 healthy controls and analyzed the correlations between specific HLA alleles and disease severity and T cell memory. The results showed no significant difference in HLA allele frequencies between COVID-19 patients and healthy controls (P > 0.05). The allele HLA-B*13:02 was significantly correlated with the disease severity of COVID-19 patients (P = 0.006). After adjustment for age and disease severity, the T cell responses of COVID-19 convalescents with the allele HLA-B*40:01 may be lower at six months (P = 0.044) and 12 months (P = 0.069). Moreover, these results may be due to their rare peptide anchors by analyzing the binding peptide motifs of these HLA alleles. The study may be valuable for investigating the potential association of specific HLA alleles with SARS-CoV-2 infection.

The influence of HLA A, B, C, DR alleles and HLA haplotypes on cytomegalovirus-specific cell mediated immunity in seropositive Korean kidney transplant candidates.

We evaluated the effect of specific HLA alleles and haplotypes on cytomegalovirus (CMV)-specific cell mediated immunity (CMI) in kidney transplant (KT) candidates. CMV-specific ELISPOT against pp65 and IE-1 antigens (hereafter referred to as pp65 and IE-1, respectively) was performed in 229 seropositive KT candidates. We analyzed the results related to 44 selected HLA alleles (9 HLA-A, 15 HLA-B, 9 HLA-C, and 11 HLA-DR) and 13 HLA haplotypes commonly found in study participants. The pp65 and IE-1 results in 229 seropositive candidates were 227.5 (114.5-471.5) and 41.0 (8.8-185.8) (median [interquartile range]) spots/2 × 105 PBMCs, respectively. The pp65 and IE-1 results showed significant differences between candidates with different HLA alleles (A*02 vs. A*26 [p = 0.016], A*24 vs. A*30 [p = 0.031], B*07 vs. B*46 [p = 0.005], B*54 vs. B*35 [p = 0.041], B*54 vs. B*44 [p = 0.018], B*54 vs. B*51 [p = 0.025], and C*06 vs. C*14 [p = 0.034]). HLA-A*02 and B*54 were associated with increased pp65 and IE-1 results, respectively (p = 0.005 and p < 0.001, respectively). In contrast, the HLA-A*26 and B*46 alleles were associated with a decreased pp65 response, whereas the A*30 allele was associated with a decreased IE-1 response (p < 0.05). The pp65 results correlated with the HLA-A allele frequencies (R = 0.7546, p = 0.019) and the IE-1 results correlated with the HLA-C allele frequencies of the study participants (R = 0.7882, p = 0.012). Among 13 haplotypes, HLA-A*30 ~ B*13 ~ C*06 ~ DRB1*07 showed decreased CMV-CMIs compared to the other HLA haplotypes, probably due to a combination of HLA alleles associated with lower CMV-CMIs. Our results demonstrated that CMV-specific CMIs may be influenced by the HLA allele as well as the HLA haplotype. To better predict CMV reactivation, it is important to estimate risk in the context of HLA allele and haplotype information.

Dapsone hypersensitivity syndrome.

Dapsone hypersensitivity syndrome.