HLA Haplotypes Research Articles

An Optimal Multi-Locus HLA-Typing in Potential Donors of Allogeneic Hematopoietic Stem Cells

Background. HLA-typing and matched donor selection as well as the detection of donor-specific anti-HLA antibodies are essential for allogeneic hematopoietic cell transplantation (allo-HSCT). In accordance with the guidelines of the Center for International Blood and Marrow Transplant Research (CIBMTR) optimal HLA-typing is performed on 11 HLA genes (-A, ‐B, ‐C, ‐DRB1, ‐DRB3/4/5, ‐DQA1, ‐DQB1, ‐DPA1, and ‐DPB1) with an adequate coverage aiming to obtain the values at the two-field level.
 Aim. To assess the results of multi-locus HLA-typing in bone marrow/hematopoietic cell donors from the database at the National Research Center for Hematology in terms of their conformance with the CIBMTR guidelines for allo-HSCT and to analyze the frequency and distribution of HLA alleles and multi-locus HLA haplotypes.
 Materials & Methods. The study enrolled 3485 donors who were HLA-typed by next-generation sequencing.
 Results. In all donors, the alleles of HLA class I genes were identified at the fourth-field level (nucleotide sequence). When the results were reduced to the second-field level (amino acid sequence), 61 HLA-A, 92 HLA-B, and 49 HLA-C alleles were detected. The alleles of class II genes were discovered either at the two-field or high-resolution levels. Among the HLA-DRB locus genes, 57 DRB1, 11 DRB3, 6 DRB4, and 5 DRB5 alleles were identified. Also, 23 HLA-DQA1, 30 HLA-DQB1, 14 HLA-DPA1, and 33 HLA-DPB1 alleles were detected. There were reported 3289 different HLA haplotypes of A-B-C-DRB1-DQA1-DQB1-DPA1-DPB1 genes.
 Conclusion. The database created at the National Research Center for Hematology includes potential bone marrow/hematopoietic stem cell donors typed for 11 classical polymorphic genes HLA-A, ‐B, ‐C, ‐DRB1, ‐DRB3/4/5, ‐DQA1, ‐DQB1, ‐DPA1, and -DPB1, which is in line with the guidelines of CIBMTR. The frequency and distribution of HLA alleles and multi-locus HLA haplotypes in our donors correspond to those in populations of European origin. HLA-typing and donor selection with regard to 11 HLA genes will contribute to improving the outcomes of both unrelated and haploidentical HSCTs.

Genetic and Epigenetic Aspects of Type 1 Diabetes Mellitus: Modern View on the Problem.

Omics technologies accumulated an enormous amount of data that advanced knowledge about the molecular pathogenesis of type 1 diabetes mellitus and identified a number of fundamental problems focused on the transition to personalized diabetology in the future. Among them, the most significant are the following: (1) clinical and genetic heterogeneity of type 1 diabetes mellitus; (2) the prognostic significance of DNA markers beyond the HLA genes; (3) assessment of the contribution of a large number of DNA markers to the polygenic risk of disease progress; (4) the existence of ethnic population differences in the distribution of frequencies of risk alleles and genotypes; (5) the infancy of epigenetic research into type 1 diabetes mellitus. Disclosure of these issues is one of the priorities of fundamental diabetology and practical healthcare. The purpose of this review is the systemization of the results of modern molecular genetic, transcriptomic, and epigenetic investigations of type 1 diabetes mellitus in general, as well as its individual forms. The paper summarizes data on the role of risk HLA haplotypes and a number of other candidate genes and loci, identified through genome-wide association studies, in the development of this disease and in alterations in T cell signaling. In addition, this review assesses the contribution of differential DNA methylation and the role of microRNAs in the formation of the molecular pathogenesis of type 1 diabetes mellitus, as well as discusses the most currently central trends in the context of early diagnosis of type 1 diabetes mellitus.

Recognition of HLA-DPB1 alleles and their associated HLA haplotypes in 55 randomized unrelated Taiwanese individuals.

Here, we report the distribution of HLA-DPB1 alleles studied in a cohort of 55 randomly collected blood samples from unrelated Taiwanese individuals and the deduced most likely HLA haplotypes associated with the defined DPB1 alleles in the cohort. Our aim is to reveal the unprecedented data on the distribution of HLA-DPB1 alleles in the Taiwanese population and to find out the most probable HLA haplotypes associated with the HLA-DPB1 alleles detected. The material for this study was blood samples, preserved in K2EDTA and/or acid citrate dextrose anticoagulants. The blood donors were voluntary individuals of Tzu Chi Bone Marrow Donor Registry, Tzu Chi Stem Cells Center, Hualien Tzu Chi Hospital. Sequence-based typing of the Sanger's sequencing method was performed for the HLA allelic typing. To discern the HLA-DPB1 alleles, exons 2 and 3 of the HLA-DPB1 locus were sequenced. Target exon sequence amplifications were achieved by polymerase chain reaction, and the resulting amplicons were sequenced by BigDye Terminator Cycle Sequencing Ready Reaction Kit according to the manufacturer's protocols. In the total number of 55 randomized unrelated Taiwanese individuals studied, we detected 11 different HLA-DPB1 alleles. DPB1*05:01 (44.54%) was the allele with the highest frequency observed and the next highest frequency allele found was DPB1*02:01 (17.27%), while DPB1*38:01 (0.90%) and DPB1*700:01N (0.90%) ranked the least observed DPB1 alleles. Our findings in this study may be useful in researches reinforcing the comprehensive understanding on the distribution of DPB1 alleles and their associated HLA haplotypes and their clinical applications in Taiwanese.

An Insulin-Chromogranin A Hybrid Peptide Activates DR11-Restricted T Cells in Human Type 1 Diabetes.

Hybrid insulin peptides (HIPs) formed through covalent cross-linking of proinsulin fragments to secretory granule peptides are detectable within murine and human islets. The 2.5HIP (C-peptide-Chromogranin A (CgA) HIP), recognized by the diabetogenic BDC-2.5 clone, is a major autoantigen in the NOD mouse. However, the relevance of this epitope in human disease is currently unclear. A recent study probed T-cell reactivity toward HIPs in patients with type 1 diabetes, documenting responses in one third of the subjects and isolating several HIP-reactive T-cell clones. In this study, we isolated a novel T cell clone and showed that it responds vigorously to the human equivalent of the 2.5HIP. Although the responding subject carried the risk-associated DRB1*04:01/DQ8 haplotype, the response was restricted by DRB1*11:03 (DR11). HLA class II tetramer staining revealed higher frequencies of HIP9-reactive T cells in individuals with diabetes than in controls. Furthermore, in DR11+ subjects carrying the DRB4 allele, HIP9-reactive T-cell frequencies were higher than observed frequencies for the immunodominant proinsulin 9-28 epitope. Finally, there was a negative correlation between HIP9-reactive T-cell frequency and age at diagnosis. These results provide direct evidence that this C-peptide-CgA HIP is relevant in human type 1 diabetes and suggest a mechanism by which non-risk HLA haplotypes may contribute to the development of β-cell autoimmunity.

P918 Can we rely on HLA to predict resistance to biological therapy in Inflammatory Bowel Disease patients?

Abstract Background Monoclonal antibodies revolutionized IBD therapy, although some patients do not respond or progressively loose response due to antidrug antibodies. Immunogenicity seems to be related with HLA haplotypes, namely HLA-DQA1*05 allele associated with an increased risk of immunogenicity to anti-TNF therapy in CD. There are no data regarding the association between HLA-DQA1*05 positivity in UC patients and other biological drugs. Objectives We aim to determine HLA-DQA1*05 prevalence in IBD patients and evaluate its association with loss of response to biological therapy. As a secondary endpoint we aim to evaluate the effect of HLA-DQA1*05 genotype in a composite outcome that encompasses clinical, biochemical, and endoscopic remission at week 54. Methods Single center prospective cohort study, including consecutive adult bio-naïve IBD patients followed at IBD consultation, that initiated biological therapy. Data was collected regarding demographic, disease characterization and disease activity at baseline. All patients were screened for HLA-DQA1*05. Pharmacokinetic data was collected, and biological therapy was adjusted based on standardized protocols. Patients were classified as primary non-responders or as secondary non-responders. Response assessment was carried out at week 54 with a composite outcome that encompasses clinical, biochemical, and endoscopic remission. Statistical analysis: Chi-square test; Student’s t-test; Mann Whitney test; Kaplan-Meier survival analysis. Results We included 100 patients (67 CD, 33 UC), of whom 33 primary non-responders, 12 secondary non-responders and 55 achieved w54 of treatment. Patients started anti-TNF (72 patients, 51 Infliximab and 21 Adalimumab), Vedolizumab (18 patients) or Ustekinumab (10 patients), and 26 were on combined therapy. 43 (43%) patients were HLA-DQA1*05 positive. Kaplan-Meier survival analysis revealed no statistically significant differences in therapy persistence between HLA groups in all patients. However, a Kaplan-Meier survival sub analysis revealed patients under Vedolizumab had significant lower therapy persistence if HLA-DQA1*05 positive (p<0.001). UC´s patients revealed tendency to lower therapy persistence if HLA-DQA1*05 positive, although not statistically significant (p=0.051). HLA-DQA1*05 negative patients under Vedolizumab achieved our composite outcome (p<0,001) and patients under anti-TNF revealed a higher response to the composite outcome but without statistical significance. Conclusion HLA-DQA1*05 genotyping demonstrated no impact in therapy persistence, except in the subgroup of patients treated with Vedolizumab. HLA-DQA1*05 negative patients had a higher response to the composite outcome, but with statistical significance only in Vedolizumab subgroup.

HLA haploidentical stem cell transplantation from HLA homozygous donors to HLA heterozygous donors may have lower survival rates than haploidentical transplantation from HLA heterozygous donors to HLA heterozygous donors: a retrospective nationwide analysis.

In HLA haploidentical stem cell transplantation, patients and donors usually share one HLA haplotype and have one different HLA haplotype (hetero-to-hetero). However, there are rare cases of transplantation from HLA homozygous donors to heterozygous recipients (homo-to-hetero), resulting in mismatches only in the graft-versus-host direction. We previously reported that homo-to-hetero transplants have a lower survival rate in a mouse model than hetero-to-hetero transplants due to stronger graft-versus-host disease (GVHD) but inferior graft-versus-leukemia effect. To examine whether homo-to-hetero transplant effects also occur in humans, we retrospectively compared the results of 59 homo-to-hetero and 4,539 hetero-to-hetero cases in the Japanese transplant registry data. The results showed no statistical difference between the homo-to-hetero and hetero-to-hetero groups in the cumulative incidences of neutrophil engraftment (83.1% vs 89.0%), acute GVHD II-IV (36.8% vs 38.8%), III-IV (16.8% vs 17.4%), chronic GVHD (32.7% vs 30.7%), relapse (52.9% vs 49.0%), and non-relapse mortality (31.6% vs 28.2%). In contrast, overall survival was significantly lower in the homo-to-hetero group than in the hetero-to-hetero group (12.6% vs 26.2%, p = 0.0308). The inferior effect of homo-to-hetero transplantation on overall survival remained significant in multivariate analyses.

An intermediate-sized donor registry experience: HLA barriers in matching procedures.

The data enabling the estimation of the possibility of finding a matched unrelated donor (MUD) within a relatively short time is important for the success of hematopoietic stem cell transplantation (HSCT). In the present study, 738 unrelated Croatian patients in the program of unrelated HSCT were retrospectively analyzed for gender matching, donor origin (national or international), the distribution of HLA alleles and haplotypes, as well as for the probability of finding a 9-10/10 MUD. Almost 70% of the patients in our study group had a 10/10 MUD, while among the patients with a 9/10 MUD, a 1st field resolution level mismatched donor was selected for 55.0% of patients. The majority of pairs were HLA-A mismatched (33.8%). A comparison of HLA allele frequencies between two subgroups of patients revealed significant differences for 13 alleles. However, after p value correction, the difference in frequency remained significant only for four alleles; three HLA alleles (B*08:01, C*07:01, and DRB1*03:01) demonstrated a significantly higher frequency among patients with a 10/10 MUD (Pcorr < 0.0001, Pcorr = 0.0096, and Pcorr < 0.0001, respectively), while the B*35:08 allele was significantly more present among patients with a 9/10 MUD (Pcorr = 0.0328). The comparison of the distribution of HLA haplotypes between patients with a 10/10 MUD and patients with a 9/10 MUD showed significant differences for a number of two-locus and three-locus haplotypes, as well as for one five-locus haplotype (HLA-A*01:01~B*08:01~C*07:01~DRB1*03:01~DQB1*02:01), which was significantly more present in the group of patients with a 10/10 MUD. At least one HLA haplotype from the group of non-frequent HLA haplotypes (positions >1000) was carried by patients with a 9/10 MUD. The data obtained by the present study will contribute to a better estimation of the probability of finding a suitable 9-10/10 MUD for Croatian patients in need of HSCT.

Association of HLA-C*07:359 with HLA-A, -B, and -DRB1 alleles in Taiwanese.

It is thought that Taiwanese indigenous people were the "first people" to populate Taiwan (Formosa) having been there for over 5000 years, preceding the Dutch colonization (from 1624 to 1662) and Spanish colonization (from 1626 to 1642). Taiwan's indigenes, represented by Austronesian language speakers, currently constitute approximately 2% of the total population in Taiwan. It is unknown whether they evolved from Taiwan's Paleolithic or Neolithic cultures, arrived during or after the Neolithic period from China or Southeast Asia or both. HLA studies on the Taiwanese indigenous population have found several intriguing genetic information showing one or two relatively frequently observed alleles and a small number of relatively less frequently observed ones. We report here a relatively frequently observed HLA-C*07:359 allele in the Taiwanese indigenous population, its linkage with HLA-B*39:01, and its probable associated HLA haplotype in two Taiwanese indigenous families. HLA-C*07:359 is a rarely observed allele in the HLA-C locus in the world populations. The objective of this study is to report the allele HLA-C*07:359 that is more frequently found in the Taiwanese population, especially in the Taiwanese indigenous people, to demonstrate that it has a close linkage with HLA-B*39:01 allele in the HLA-B locus and to show the plausible deduced HLA-A-C-B-DRB1-DQB1 haplotypes in association with HLA-C*07:359 in two families of Taiwanese indigenous unrelated individuals. The samples were peripheral whole blood, with dipotassium ethylenediaminetetraacetic acid and/or acid citrate dextrose anticoagulation additives. The sequence-based typing method was employed to confirm the low incidence of the allele of HLA-C*07:359 observed in Taiwanese. Polymerase chain reaction was carried out to amplify exons 2, 3, and 4 of the HLA-A,-B,-C,-DRB1 and-DQB1 loci with group-specific primer sets. Amplicons were sequenced using the BigDye Terminator Cycle Sequencing Ready Reaction Kit in both directions according to the manufacturer's protocol. C*07:359 is an uncommon allele in the HLA-C locus in the world general population, according to our literature review. However, in this study, it is observed in the general Taiwanese population (frequency 0.41%), especially in the Taiwanese indigenous people at a frequency of 0.23%. In addition, we deduced two probable HLA haplotypes in association with C*07:359 in two indigenous families: A*24:02-C*07:359-B*39:01-DRB1*04:36 and A*24:02-C*07:359-B*39:01-DRB1*04:04. The two deduced HLA haplotypes associated with the uncommon C*07:359 allele that we report here are valuable for HLA tissue typing laboratories for reference purposes and for stem cell transplantation donor search coordinators to determine the likelihood of finding compatible donors in unrelated bone marrow donor registries for patients bearing the uncommon HLA allele. Since C*07:359 was found mostly in the Taiwanese indigenous population, we think the allele and its haplotypes we report here are important in population and anthropological studies.

Next-generation sequencing reveals additional HLA class I and class II alleles associated with type 1 diabetes and age at onset.

Type 1 diabetes is an autoimmune disease with an significant genetic component, played mainly by the HLA class II genes. Although evidence on the role of HLA class I genes in developing type 1 diabetes and its onset have emerged, current HLA screening is limited to determining DR3 and DR4 haplotypes. This study aimed to investigate the role of HLA genes on type 1 diabetes risk and age of onset by extensive typing. This study included 115 children and young adults with type 1 diabetes for whom typing of HLA-A, -B, -C, -DRB1, -DRB3/4/5, -DQA1, -DQB1, -DPA1 and -DPB1 genes was conducted using Next Generation Sequencing. We observed that 13% of type 1 diabetes subjects had non-classical HLA haplotypes that predispose to diabetes. We also found that compared to type 1 diabetes subjects with classical HLA haplotypes, non-classical HLA subjects had a significantly higher frequency of HLA-B*39:06:02 (p-value=0.01) and HLA-C*07:02:01 (p-value=0.03) alleles, known to be involved in activating the immune response. Non-classical HLA subjects also presented peculiar clinical features compared to classical HLA subjects, such as multiple diabetic antibodies and the absence of other autoimmune diseases (i.e., coeliac disease and thyroiditis). We also observed that subjects with early onset had a higher frequency of DQ2/DQ8 genotype than late-onset individuals. Moreover, subjects with late-onset had a higher frequency of alleles HLA-B*27 (p-value=0.003), HLA-C*01:02:01 (p-value=0.027) and C*02:02:02 (p-value=0.01), known to be associated with increased protection against viral infections. This study reveals a broader involvement of the HLA locus in the development and onset of type 1 diabetes, providing insights into new possible disease prevention and management strategies.

Graph-Based Imputation Methods and Their Applications to Single Donors and Families.

The outcome of Hematopoietic Stem Cell (HSCT) and organ transplant is strongly affected by the matching of the HLA alleles of the donor and the recipient. However, donors and sometimes recipients are often typed at low resolution, with some alleles either missing or ambiguous. Thus, imputation methods are required to detect the most probably high-resolution HLA haplotypes consistent with a typing. Such imputation algorithms require predefined haplotype frequencies. As such, the phasing of the typing is required for both imputation and frequency generation.We have developed a new approach to HLA haplotype and genotype imputation, where first all candidate phases of a typing are explicated, and then the ambiguity within each phase is solved. This ambiguity is solved through a graph structure of all partial haplotypes and the haplotypes consistent with them.This phasing approach was used to produce an imputation algorithm (GRIMM-Graph Imputation and Matching). GRIMM was then combined with the possibility of combining information from multiple races to produce MR-GRIMM (Multi-Race GRIMM). When family information is available, the phasing of each family member can be restricted by the others. We propose GRAMM (GRaph-bAsed faMily iMputation) to phase alleles in family pedigree HLA typing data and in mother-cord blood unit pairs. Finally, we combined MR-GRIMM with an expectation-maximization (EM) algorithm to estimate haplotype frequencies sharing information between races to produce MR-GRIMME (MR-GRIMM EM).We have shown that these algorithms naturally combine information between races and family members. The accuracy of each of these algorithms is significantly better than its current parallel methods. MR-GRIMM leads to high accuracy in matching predictions. GRAMM better imputes family members than either MR-GRIMM or any existing algorithm and has practically no phasing errors. MR-GRIMME obtains a higher likelihood than existing algorithms.MR-GRIMM, MR-GRIMME, and GRAMM are available as servers or through stand-alone versions in GITHUB and PyPi, as detailed in the appropriate sections.

Mining local exome and HLA data to characterize pharmacogenetic variants in Saudi Arabia.

Pharmacogenomics (PGx) is a promising field of precision medicine where efficacy of drugs is maximized while side effects are minimized for individual patients. Knowledge of the frequency of PGx-relevant variants (pharmacovariants) in the local population is a pre-requisite to informed policy making. Unfortunately, such knowledge is largely lacking from the Middle East. Here, we describe the use of a large clinical exome database (n = 13,473) and HLA haplotypes (n = 64,737) from Saudi Arabia, one of the largest countries in the Middle East, along with previously published datafrom the local population to ascertain allele frequencies of known pharmacovariants. In addition, we queried another exome database (n = 816) of well-phenotyped research subjects from Saudi Arabia to discover novel candidate variants in known PGx genes (pharmacogenes). Although our results show that only 26% (63/242) of class 1A/1B PharmGKB variants were identified, we estimate that 99.57% of the local population have at least one such variant. This translates to a minimum estimated impact of 9% of medications dispensed by our medical center annually. We also highlight the contribution of rare variants where 71% of the pharmacogenes devoid of common pharmacovariants had at least one potentially deleterious rare variant. Thus, we show that approaches that go beyond the use of commercial PGx kits that have been optimized for other populations should be implemented to ensure universal and equitable access of all members of the local population to personalized prescription practices.

HLA-based banking of induced pluripotent stem cells in Saudi Arabia

BackgroundHuman iPSCs' derivation and use in clinical studies are transforming medicine. Yet, there is a high cost and long waiting time associated with autologous iPS-based cellular therapy, and the genetic engineering of hypo-immunogenic iPS cell lines is hampered with numerous hurdles. Therefore, it is increasingly interesting to create cell stocks based on HLA haplotype distribution in a given population. This study aimed to assess the potential of HLA-based iPS banking for the Saudi population.MethodsIn this study, we interrogated the HLA database of the Saudi Stem Cell Donor Registry (SSCDR), containing high-resolution HLA genotype data from 64,315 registered Saudi donors at the time of analysis. This database was considered to be a representative sample of the Saudi population. The most frequent HLA haplotypes in the Saudi population were determined, and an in-house developed iterative algorithm was used to identify their HLA matching percentages in the SSCDR database and cumulative coverage. Subsequently, to develop a clinically relevant protocol for iPSCs generation, and to illustrate the applicability of the concept of HLA-based banking for cell therapy purposes, the first HLA-based iPS cell line in Saudi Arabia was generated. Clinically relevant methods were employed to generate the two iPS clones from a homozygous donor for the most prevalent HLA haplotype in the Saudi population. The generated lines were then assessed for pluripotency markers, and their ability to differentiate into all three germ layers, beating cardiomyocytes, and neural progenitors was examined. Additionally, the genetic stability of the HLA-iPS cell lines was verified by comparing the mutational burden in the clones and the original blood sample, using whole-genome sequencing. The standards set by the American College of Medical Genetics and Genomics (ACMG) were used to determine the clinical significance of identified variants.ResultsThe analysis revealed that the establishment of only 13 iPSC lines would match 30% of the Saudi population, 39 lines would attain 50% coverage, and 596 lines would be necessary for over 90% coverage. The proof-of-concept HLA-iPSCs, which cover 6.1% of the Saudi population, successfully demonstrated pluripotency and the ability to differentiate into various cell types including beating cardiomyocytes and neuronal progenitors. The comprehensive genetic analysis corroborated that all identified variants in the derived iPSCs were inherently present in the original donor sample and were classified as benign according to the standards set by the ACMG.ConclusionsOur study sets a road map for introducing iPS-based cell therapy in the Kingdom of Saudi Arabia. It underscores the pragmatic approach of HLA-based iPSC banking which circumvents the limitations of autologous iPS-based cellular therapies. The successful generation and validation of iPSC lines based on the most prevalent HLA haplotype in the Saudi population signify a promising step toward broadening the accessibility and applicability of stem cell therapies and regenerative medicine in Saudi Arabia.

HLA frequency distribution of the Portuguese bone marrow donor registry.

The Portuguese donor Registry of CEDACE was the fifth largest per capita bone marrow donor Registry of the WMDA as of 2019 and has yet to be thoroughly analyzed. We aimed to characterize its various aspects, including demographics and HLA allele and haplotype frequencies, to evaluate the genetic matching propensity score and ultimately further develop it. We described and compared characteristics of the donor population with census data and used an Expectation-Maximization algorithm and analyses of molecular variance to assess haplotype frequencies and establish phylogenetic distances between regions and districts within the country. We identified 396545 donors, corresponding to 3.85% of the Portuguese population; the median donor age was 39 years, with 60.4% of female donors. Most donors were Portuguese nationals, although 40 other nationalities were present, with a significant proportion of donors from Brazil and Portuguese-speaking African Countries; almost all donors self-reported as Western, with the second largest group reporting African ancestry. There was an asymmetric contribution of donors from different districts and regions, with most coming from coastal districts and few from the southern districts and autonomous regions; foreign and self-declared non-Western donors were mainly located in the Metropolitan Area of Lisbon and the South. Although most donors were typed in three loci (HLA-A, HLA-B and HLA-DRB1), only 44% were also typed in HLA-C, 1.28% in HLA-DQB1 and only 0.77% in all five loci and in high-resolution. There were varying allele and haplotype frequencies across districts and regions, with the most common three loci, low-resolution haplotypes, being HLA-A*01~B*08~DRB1*03, A*29~B*44~DRB1*07 and HLA-A*02~B*44~DRB1*04; some haplotypes were more prevalent in the South, others in the North and a few in the autonomous regions; African and foreign donors presented relevant differences in haplotype frequency distributions, including rare haplotypes of potential interest. We also report on four loci, low-resolution frequency distributions. Using AMOVA, we compared genetic distances between districts and regions, which recapitulated the country's geography. Our analysis showed potential paths to optimization of the Registry, including increasing the male donor pool and focusing on underrepresented districts and particular populations of interest, such as donors from Portuguese-speaking African countries.

SARS-CoV-2 immune response and reinfection in vaccinated Maya and mestizo in Southeast of Mexico.

Immune response to pathogens, including coronaviruses, is influenced by HLA haplotypes. 1,2. Maya ethnic group is predominant in Yucatan peninsula, this Amerindian group present allele frequency HLA-G*01:01:02, HLA-G*01:01:01, HLA-G*01:04:01, HLA-A*68 not found in another Amerindians.3-5 Immune response to SARS-CoV-2 vaccination and reinfection particularly after Omicron variant appeared was explored in 118 vaccinated subjects with complete two shots immunization in Maya ascendant and mestizo no-Maya. 1172 epidemiological survey applied to university staff in Campeche, Mexico to evaluate reinfection, co-morbidities, variant virus, disease severity, aftermaths, clinical outcomes, age, sex, ethnicity, and vaccination shots. Multiple logistic regression, correspondence analysis, and association tests were used to analysis data. Sixteen percent of vaccinated subjects became seronegative after 11 months. We found that vaccinated Maya subjects respond with higher IgG immune response compared to no-Maya subjects, similarly women respond with higher IgG response than men (p<0.05). During an eleven-month period and after two vaccination shots, 7% of the vaccinated subjects reported a confirmed positive infection, and after the third vaccine shot a higher IgG immune response than two vaccination shots or natural infection was detected. However, we observed 23.7% reinfection in people after the third shot. This data represents almost three times the reinfection rate reported when compared to previous third vaccine shots. The increase of reinfection in vaccinated subjects was associated with circulation of Omicron variant by 71.5%. Others have reported reinfection of 40% and vaccine effectiveness of 60% during Omicron dominance.6 To understand COVID-19 severity after reinfection in vaccinated subjects and the associated variables, we carried out a multiple logistic regression, and found a strong association between less severe symptoms with Alfa and Omicron variants (B 5.3; Error 0.39; Wald 0.00; Significance 0.00; OR201). However, subjects with severe symptoms and or hospitalization correspondent to individuals with multiplex comorbidities and Gamma SARS-CoV-2 variants (B 5.06; Error 0.97; Wald 26.8; Significance 0.00; OR 158). A follow-up survey of COVID-19 recovered patients experienced diverse digestive, respiratory, cardiac, neurological, or joints involvement sequelae. We looked for SARS-CoV-2 variant and COVID-19 sequelae in a correspondence analysis. Our data suggest that Beta and Delta variants are associated with respiratory and digestive symptoms, whereas Omicron was more closely associated with joints and digestive symptoms, and finally the Gamma variant displayed wider and more diverse symptoms. Our results suggest that genetic background and gender influence IgG response to SARS-CoV-2 vaccine, and Maya ascendant has higher immune IgG response to vaccine than mestizos. Reinfection in our population studied fluctuate from 7% to 23.7% nevertheless is higher if Omicron variant is involved, but symptoms are less severe and more closely associated with joints and digestive symptoms.

Post-COVID-19 and Post-COVID-19 Vaccine Arthritis, Polymyalgia Rheumatica and Horton's Arteritis: A Single-Center Assessment of Clinical, Serological, Genetic, and Ultrasonographic Biomarkers.

The potential role of the COVID-19 vaccine and infection to induce autoimmunity is currently underestimated despite the literature emphasizing arthralgia as a common adverse event. We aimed to study the impact of rheumatological complications post-COVID-19 (PC) and post-COVID-19 vaccine (PCV), comparing undifferentiated arthritis (UA) to Polymyalgia Rheumatica, Horton's Arteritis (PMR-HA) and isolated arthritis to UA with "connective-like" accompanying symptoms. We retrospectively included 109 patients with at least 6 months of follow-up, analyzing serum biomarkers, joint ultrasound (US), lung HRCT, DLCO, and HLA haplotypes. There were 87 UA patients showing increased gastrointestinal and lung involvement (p = 0.021 and p = 0.012), higher anti-spike protein IgG levels (p = 0.003), and anti-SARS-CoV-2 IgG positivity (p = 0.003). Among them, 66 cases progressed to ACR-EULAR 2010 early arthritis after 3 months, whereas PMR-HA patients were more commonly PCV (81.8%, p = 0.008), demonstrating higher CRP (p = 0.007) and ESR (p = 0.006) levels, a lower rate of ANA positivity (p = 0.005), and a higher remission rate after six months (p = 0.050). In UA patients, the prevalent HLA was DRB1*11 and C*07 (36.8% and 42.1%). Serum calprotectin, interleukin-6, and C*07 (p = 0.021, 0.041, 0.018) seemed more specific for isolated UA. Conversely, "connective-like" arthritis showed poorer DLCO (p = 0.041) and more frequent US synovitis (p = 0.041). In conclusion, UA is a frequent common PC and PCV complication and may persist over time when compared to PMR-HA.

Abstract B011: Dynamics of predicted tumor neoepitope burden in a pan-cancer solid tumor pediatric cohort

Abstract Human leukocyte antigen (HLA) binding of tumor neoepitopes confers clinical value in certain adult malignancies. However, the prevalence of tumors that result in HLA binding of neoepitopes in pediatric malignancies is not as well-characterized. We set out to establish the feasibility of predicting neoepitope burden and the prevalence of predicted neoepitope across a previously established cohort of pediatric oncology patients. Additionally, because this analysis requires knowledge of each patient’s HLA haplotype for predicting binding of tumor peptides, we also set out to develop a novel algorithm to profile HLA haplotypes within the context of a larger whole genome (WGS) and RNAseq analysis pipeline. Finally, in this high-risk pediatric oncology cohort, we sought to determine the dynamics of predicted neoepitope burden at multiple time points in disease progression, including relapsed/refractory disease and metastatic disease. A previously established cohort of 147 high-risk pediatric oncology patients, including solid tumors CNS tumors, and leukemias/lymphomas was used for this analysis. This comprised patients with relapsed/refractory disease (66), and rare diagnoses (14). For these 147 patients, tumor/normal WGS (tumor ~60X; germline ~30X), as well as tumor RNAseq (polyA selected, ≥20 million reads) was performed. In addition to the initial timepoints, additional tumor samples were profiled for 27 patients, resulting in 179 total samples. A special focus on longitudinal analysis is devoted to osteosarcoma patients (12 with multiple timepoints). WGS and RNAseq were analyzed using a previously established pipeline. Somatic variants (SNVs), mutational burden, structural rearrangements (SVs), mutational signatures, and copy-number alterations (CNAs) were identified using WGS. As part of this new analysis, HLA class I haplotypes were identified from WGS integrated with RNAseq expression. Putative neoepitopes were predicted from expressed protein altering somatic variants using MHCFlurry. Importantly, HLA and neoepitope analysis was able to use intermediate data from the existing WGS/RNAseq analysis pipeline, resulting in significantly faster turnaround times. Our results demonstrate that our algorithm for determining HLA haplotypes by sampling already-mapped WGS and RNASeq performs with comparable accuracy to similar previously published methods that rely on unmapped data. In terms of predicted of tumor neoepitope burden, of the 171 samples with at least one protein altering variant, 166 are predicted to have at least one bound neoantigen (median=6). Of these, 133 samples are predicted to have at least one bound neoantigen that is clonal and expressed in RNA (median=3). Further characterization of the neoepitope burden of these tumors and the evolution of predicted neoepitope burden across multiple time points will be shared at the meeting. Citation Format: Charles W Macaulay, Marcus R Breese, E. Alejandro Sweet-Cordero. Dynamics of predicted tumor neoepitope burden in a pan-cancer solid tumor pediatric cohort [abstract]. In: Proceedings of the AACR Special Conference in Cancer Research: Tumor Immunology and Immunotherapy; 2023 Oct 1-4; Toronto, Ontario, Canada. Philadelphia (PA): AACR; Cancer Immunol Res 2023;11(12 Suppl):Abstract nr B011.

Endogenous Retroviral Elements Constitute a Promising Vaccine Antigen Source for Haematological Malignancies

Introduction Immunotherapy has revolutionized modern cancer treatment, both within the fields of solid and haematology malignancies. The recent success of checkpoint inhibitor (CPI) therapies (e.g., aPD-1, aCTLA-4) in so called “high” tumour mutational burden (TMB) cancers, such as melanoma and lung cancer (Alexandrov et al. Nature 2013), have found only limited transferability to the haematological setting outside classical Hodgkins lymphoma (Pianko et al. Cancer J. 2018). Recently, the effect of CPIs in high TMB cancers has been further augmented by the combination of CPIs with personalized cancer vaccines (PCVs) in patients with resectable melanoma (NCT03897881). However, recent progress in the identification of novel alternative antigen targets, besides classical missense mutations targeted by PCVs, provides hope for the targeting of haematological cancers with low TMB by immunotherapy-based treatments such as PCVs or even precision-based cancer vaccines. Such sources include endogenous retroviral elements (ERVs) (Saini et al. Nat Commun. 2020), structural rearrangements (Robbe et al. Nat Gen 2022), or activation of transposon elements (Wolf et al. Nat Rev Nephrol. 2023). To investigate the applicability of such approaches in a haematological setting, prospective datasets curated from the database of Genotypes and Phenotypes (dbGaP) and in-house developed antigen prediction platforms, were employed. Methods Data was downloaded from dbGAP and missense mutations (SNVs, INDELs) were determined either from datasets (firehose, TCGA), when available, or through GATK-Mutect2. ERVs were identified using an in-house developed platform (ObsERV), as previously described (Garde et al. BioRxiv 2023). Simulated PCVs were designed for seven selected patients covering high/low TMB and ERV burdens from datasets pertaining to Acute Myeloid Leukaemia (AML), Acute Lymphoblastic Leukaemia (ALL), Multiple Myeloma (MM), Diffuse Large B Cell Lymphoma (DLBCL) and Chronic Lymphocytic Leukaemia (CLL) using in-house platforms PIONEER (neo-epitope identification and ranking for PCV design) and/or ObsERV. PIONEER ranking was based on MHC class I and II ligand propensity, epitope expression level, clonality and tumour specificity Cut-off for inclusion of “efficacious” neoepitopes were based on PIONEER ranking from a recent Phase 1 clinical trial (Mørk et al. ASCO 2023-9551). Due to the high degree of ERV conservation amongst patients within each haematological indications, a precision-based approach was attempted relying on MHC I/II ligand propensity prediction and epitope combination for optimal patient coverage (HLA haplotype) - a similar machine learning approach was proven useful for viral vaccine design (Persson et al Front. Immunol. 2023). Shared vaccines were designed based on HLA frequencies in the human population, which was then applied to the dataset of each patient. The resulting patient specific coverage was then used to compute the total coverage for a given indication. Results and Discussion We found a high presence of ERVs in several haematological malignancies suggesting the potential application of PCVs in these indications, relying on this antigen source (Fig 1A). The combination of missense mutations and ERV sources allowed PCVs to be designed for six of seven patients on average for AML, CLL, and MM compared to only three of seven on average with missense mutations alone. The high level of ERV expression in AML, CLL, and ALL allowed for the generation of vaccines based on shared antigens within each indication. The resulting vaccines had an average coverage, with at least three epitopes, for 84% of AML, 45% of ALL and 35% of CLL patients. In comparison, a missense mutation approach, for the highest TMB cancer (melanoma) would result in only 2.6 % patient coverage with three epitopes. We believe that these findings suggest a novel approach to the treatment of haematological malignancies, either through a PCVs approach, combining multiple sources of antigens, or a precision-based approach with “warehouse” HLA haplotype-specific vaccines for a given indication. This may allow for treatment regimens with greater treatment effect, more durable response, and improved quality of life in indications with a high unmet medical need such as AML and CLL.

A Phase I Trial of Activated Donor-Derived Marrow Infiltrating Lymphocytes to Treat Relapsed Hematologic Malignancies after Allogeneic Transplantation with Post-Transplantation Cyclophosphamide As Graft-Versus-Host Disease Prophylaxis

Background: Donor lymphocyte infusion (DLI) or a second allogeneic transplant (HCT) are the only curative treatments for hematologic malignancies relapsing after initial HCT. Both approaches lack significant efficacy and may cause considerable toxicity. Post-transplant cyclophosphamide (PTCy) used as graft-versus-host disease (GVHD) prophylaxis eliminates alloreactive T cells and enriches for tumor-specific T cells in the bone marrow. We hypothesized that expanded, donor-derived marrow infiltrating lymphocytes (alloMILs) collected post-HCT could restore antitumor immunity in relapsed recipients without the additional GVHD and toxicity seen with DLI or second HCT. Methods: We conducted a phase I dose-escalation trial (NCT02342613) of expanded alloMILs to treat bone marrow infiltrating hematologic malignancies relapsing after HCT with PTCy. Key inclusion criteria were age ≥ 18 years; relapsed hematologic malignancy ≥ 6 months after HLA matched or mismatched HCT with PTCy; donor CD3 + chimerism ≥ 30% in the peripheral blood; and lack of immunosuppressant use for 2 weeks prior to alloMILs harvest. Enrolled patients underwent salvage chemotherapy prior to or after alloMILs harvest to control the disease during the expansion process. Harvested bone marrow mononuclear cells were co-incubated with anti-CD3/CD28 beads and IL-2 for 7 to 14 days until the target CD3 + dose was reached. Given the differential risk of GVHD with matched versus mismatched DLI, dosing progressed from 1 x 10 7 to 5 x10 7 CD3 + cells/kg for matched HCT recipients and 1 x 10 6 to 5 x10 7 CD3 + cells/kg for mismatched HCT recipients. The primary endpoint was the feasibility of the product, defined as: successful harvest; expansion; infusion; and absence of grade III-IV acute GVHD for 90 days after infusion. Evaluation for HLA loss was performed using next-generation sequencing (NGS) of HLA loci. Single cell RNA sequencing (scRNAseq) was performed using 10x Genomics technology, Cell Ranger (v6.0.2), and Seurat (v4.3.0). Results: Thirty-two patients enrolled and underwent bone marrow harvest. Two patients were inaspirable, and five patients were not expanded due to low cell counts or high tumor volume. Twenty-five patients underwent alloMILs expansion, of which five failed to expand. Twenty patients received an infusion and six received a second infusion. Of the twenty patients receiving an infusion, eleven had multiple myeloma (MM) or plasma cell leukemia; five had acute myeloid leukemia (AML); one had chronic myeloid leukemia in blast phase; and three had chronic lymphocytic leukemia. Harvest, expansion, and infusion were well tolerated with minimal adverse events. No patient developed acute or chronic GVHD after infusion. Dosing advanced to the highest level of 5 x10 7 CD3 + cells/kg in both the mismatched and matched HCT cohorts. At day 60, the overall response rate (composite of complete (CR) and partial responses) was 40 percent (8/20) in the entire cohort; 33.3 percent (2/6) in the myeloid cohort (Figure 1A); 30 percent (3/10 evaluable patients) in the MM cohort; and 66.7 percent (2/3) in the lymphoid cohort. One MM patient achieved sustained &amp;gt; 2 years long CR and one AML patient is in ongoing CR, both of whom received alloMILs with no or minimal disease followed by maintenance therapy. HLA loss analysis was performed on pre-expansion samples from three AML patients receiving a mismatched HCT and alloMILs. Both non-responders in this cohort had loss of the host mismatched HLA haplotype. ScRNAseq on pre-expansion samples from ten AML patients, eleven MM patients, and four AML patients in remission after HCT (control) yielded 197 522 total cells and 32 587 CD8 + T cells. CD8 + T cells expressing a senescent-like gene signature previously associated with dysfunctional tumor killing in AML patients (Mazziotta et al ASH 2022) were associated with non-response primarily in AML patients (observed log2 fold change -2.48 compared with responders; FDR = 0.0017) (Figure 1B). Conclusions: AlloMILs demonstrated feasibility, a favorable safety profile, and early evidence of clinical activity in patients with measurable residual disease. The maximum dose of 5 x10 7 CD3 + cells/kg was reached, and no patient developed acute or chronic GVHD. HLA loss and CD8 + T cell senescence may be associated with non-response in AML patients. A clinical trial utilizing alloMILs as maintenance therapy for patients with measurable residual disease is in development.

Inflammation Shapes the Transcriptional Landscape of the Bone Marrow Microenvironment in Post-Transplantation Leukemia Relapses

Allogeneic Hematopoietic Cell Transplantation (allo-HCT) represents the most successful therapeutic option for many patients suffering from Acute Myeloid Leukemia (AML). Nevertheless, leukemic cells often find means to evade control from the donor-derived immune system and re-emerge. To date, three alternative and frequent mechanisms by which AML cells modify their features and escape immune control have been described: genetic loss of the mismatched HLA haplotype (HLA loss), downregulation of HLA class II molecules and upregulation of inhibitory ligands, all ultimately leading to abolished leukemia recognition by T lymphocytes. However, increasing evidence suggests that leukemic cells weave a much broader net of interactions, involving several other immune cell types within the bone marrow microenvironment. Still, how this complex crosstalk between malignant cells and the bone marrow niche may shape the features of leukemia post-transplant relapse remains unknown. By exploiting the high resolution provided by single-cell RNA-sequencing (scRNA-seq), we provide a detailed insight of the human bone marrow immune microenvironment and the changes that occur following allo-HCT, both when disease reemergence is prevented, and when it occurs. Using cryopreserved BM aspirates, we profiled a total of 145,420 mononuclear cells from 25 adult AML patients at the time of disease relapse; 56,831 cells from 5 post-transplant patients in complete remission (CR), each tested at two different timepoints (+90 and +365 days) and 45,279 cells from 6 healthy controls (HC). First, scRNA-seq allowed us to recapitulate known leukemia-intrinsic features of each relapse modality, such as HLA loss, down-regulation of HLA class II molecules and upregulation of inhibitory T cell ligands. Moreover, combining genotype and Copy Number Variation (CNV) inference algorithms, we were able to separate malignant cells from their healthy counterparts. Interestingly, HLA loss relapses exhibited a more immature profile, with a significantly higher leukemia stem cell signature (LSC17) (p-value &amp;lt; 0.0001, Wilcoxon rank-sum test) (Ng SW et al., Nature 2016), hinting that the hematopoietic cell of origin impacts on the mechanism of post-transplantation relapse. Leukemic cells also featured a high inflammation-associated gene score (iScore) (Lasry A et al., Nat Cancer 2023), as also evident in non-malignant HSPCs from relapsed patients, which showed an increased IFN-α signature compared to HC and CR. However, AML samples that couldn't be categorized by a known mechanism of relapse displayed a significantly lower iScore, suggesting that leukemia escape in these patients might not have had an immune-related driver (Figure 1a). We next sought to characterize specific BM immune compartments. We overall detected a lower frequency of CD4 T cells in relapsed patients as compared to HC and CR patients (p-value = 0.04, Wilcoxon rank-sum test). We annotated 5 major Natural Killer (NK) cell clusters (immature CD56 dim, mature CD56 dim, CD56 bright, proliferating NK, NKT cells) and a smaller subset of immature CD56 bright NK cells characterized by higher expression of IFN-related genes and NK exhaustion markers, which was defined as inflamed NK cluster. Inflamed NK cells were more represented in patients with upregulation of T cell inhibitory ligands compared to other relapsed patients (5.42% of total NK vs. 0.74%, respectively. p-value = 0.03, Wilcoxon rank-sum test), thus suggesting a shared mechanism of dysfunction signature between T and NK cell that may favor leukemia immune evasion (Figure 1b). In conclusion, we generated a comprehensive atlas of the BM immune microenvironment in AML post-transplantation relapses, showing that inflammation shapes immune subset composition and transcriptional profile in the BM, and that leukemia mechanisms of immune evasion are influenced by the surrounding milieu. Overall, while an in depth understanding of whether leukemia relapse is caused by an inflamed microenvironment, or vice versa, might only be achieved through longitudinal sampling from patients before and after transplant, our results here exemplify how the BM niche could be exploited to find novel vulnerabilities in AML relapses, to be specifically targeted by personalized therapeutic approaches.

Reverse Engineering of Antigenic Peptides in LGL to Decipher Disease Triggers

One of the hypotheses as to the pathogenesis of T-cell large granular lymphocytic leukemia (LGL) posits its origin from the initially polyclonal stimulation by unknown antigens, e.g., viral, autoimmune or tumor antigens. LGL evolves then via oligoclonal and ultimately monoclonal cytotoxic T-cell expansion. This process may be accompanied by acquisition of STAT3 (or rarely STAT5) mutations in 40% of cases. Identification of driver antigens is a key research question in LGL as it could both clarify its triggers as well as the mechanisms of cytopenias. We investigated a cohort of patients with this disease (n=195) by combining HLA allotypes and NGS-based TCR analysis to identify marker TCR Vβ clonotypes with the goal to reverse engineer or deduce peptides and therefore antigenic targets. For this purpose we used in silico and machine-learning modelling to capture structural features predictive of CDR3 Vβ epitope interactions in specific HLA allotype context. To focus on specific HLA/TCR interactions we have analyzed HLA for the presence of common haplotypes. First, we generated HLA haplotype calls using whole-exome sequencing data. We have found that HLA-A*02 was the most common class I allele, but not overrepresented in LGL vs controls. We have also identified HLA-B*44 as a risk allele present in 36% LGL with STAT3 mutation which was further enriched when considering HLA-A*02/HLA-B*44 together (Fig.1A). After TCR NGS we selected a threshold of 5.0% (based on study of 900 controls) to define an expanded (co)dominant clonotypes: 145 expanded clones were identified, of which 143 were unique/private. To identify possible consensus sequence across the CDR3 profile, we clustered the CDR3 AA sequences based on global alignment scores (Needleman-Wunsch) using BLOSUM62 substitution matrix and identified 9 clusters. However, multiple-sequence alignment within each CDR3 cluster did not show any distinct consensus sequence patterns overall and within cases sharing HLA-A*02. Cross-referencing with CDR3 databases of known conditions yielded 87 CDR3β (co)dominant LGL clonotypes. About 50% of those LGL clonotypes were shared in 2 common disease: type I diabetes, Celiac disease We also mined the VDJdb[2] for known CDR3-pHLA associations. Filtering to include high quality annotations, matches and HLA-A*02 restriction; LGL-derived TCR were found to recognize multiple epitopes. Prominent examples include CMV and EBV derived peptidic antigens from pp65, BRLF1, and BMLF1 (NLVPMVATV, RPPIFIRRL) present in 44% LGL expanded clonotypes (Fig.1B). In order to reverse engineer the identity of antigenic peptides based on the CDR3β sequence and HLA type (high affinity peptides restricted to HLA A2, a machine-learning method was developed as predictive modelling tool that quantifies CDR3β/peptide binding. The previously developed LLM trained on AA sequences was used for that purpose[3] whereby LLM embeddings serve as input to a deep CNN-based model, which is trained on IEDB pos/neg datasets[4]. This method was augmented with control CDR3 sequences as negative data points. As a result, our model showed an AUC of 0.94 in cross-validation. As a proof of concept of the proposed model in epitope discovery, CMV pp65-derived peptides were fitted into specific LGL CDR3 and CMV specific CDR3 clonotypes were found to match e.g., pp65 epitope NLVPMVATV among several others overlapping with the above-described findings. In conclusion, our analysis shows that a significant number of expanded clonotypes may be derived from known epitopes e.g., in autoimmune disease and viral infection pointing towards molecular mimicry. However, the specificity of a large fraction of the LGL spectrum remains unknown. For the discovery of corresponding peptides we generated ML-based antigen simulation method allowing to identify the best fitting peptides into the corresponding HLA allele and CDRVβ clonotype. Fig. Global map of co-occurrence of HLA allotypes showing the delta frequency compared to healthy controls and Sankey plot of identified CDR3β - Epitope associations (a) Using the whole-exome sequencing based HLA genotype calls, we calculated the frequency of co-occurrence of different HLA loci and investigated the differences in regards to controls (b) Using the VDJdb, we conducted sequence similarity based search and extracted the CDR3-pHLA annotations.