Human Major Histocompatibility Complex Research Articles

How the Soluble Human Leukocyte Antigen-G levels in Amniotic Fluid and Maternal Serum Correlate with the Feto-Placental Growth in Uncomplicated Pregnancies.

Introduction: Trophoblast-derived angiogenic factors are considered to play an important role in the pathophysiology of various complications of pregnancy. Human Leukocyte Antigen-G (HLA-G) belongs to the non-classical human major histocompatibility complex (MHC-I) molecule and has membrane-bound and soluble forms. HLA-G is primarily expressed by extravillous cytotrophoblasts located in the placenta between the maternal and fetal compartments and plays a pivotal role in providing immune tolerance. The aim of this study was to establish a relationship between concentrations of soluble HLA-G (sHLA-G) in maternal serum and amniotic fluid at 16-22 weeks of gestation and the sonographic measurements of fetal and placental growth. Materials and methods: sHLA-G in serum and amniotic fluid, as well as fetal biometric data and placental volume and perfusion indices, were determined in 41 singleton pregnancies with no complications. The level of sHLA-G (U/mL) was tested with a sandwich enzyme-linked immunosorbent assay (ELISA) kit. Results: The sHLA-G levels were unchanged both in amniotic fluid and serum during mid-pregnancy. The sHLA-G level in serum correlated positively with amniotic sHLA-G level (β = 0.63, p < 0.01). Serum sHLA-G level was significantly correlated with abdominal measurements (β = 0.41, p < 0.05) and estimated fetal weight (β = 0.41, p < 0.05). Conversely, amniotic sHLA-G level and placental perfusion (VI: β = -0.34, p < 0.01 and VFI: β = -0.44, p < 0.01, respectively) were negatively correlated. A low amniotic sHLA-G level was significantly associated with nuchal translucency (r = -0.102, p < 0.05). Conclusions: sHLA-G assayed in amniotic fluid might be a potential indicator of placental function, whereas the sHLA-G level in serum can be a prognostic factor for feto-placental insufficiency.

Haplotype-resolved assembly of diploid and polyploid genomes using quantum computing

Precision medicine's emphasis on individual genetic variants highlights the importance of haplotype-resolved assembly, a computational challenge in bioinformatics given its combinatorial nature. While classical algorithms have made strides in addressing this issue, the potential of quantum computing remains largely untapped. Here, we present the vehicle routing problem (VRP) assembler: an approach that transforms this task into a vehicle routing problem, an optimization formulation solvable on a quantum computer. We demonstrate its potential and feasibility through a proof of concept on short synthetic diploid and triploid genomes using a D-Wave quantum annealer. To tackle larger-scale assembly problems, we integrate the VRP assembler with Google's OR-Tools, achieving a haplotype-resolved local assembly across the human major histocompatibility complex (MHC) region. Our results show encouraging performance compared to Hifiasm with phasing accuracy approaching the theoretical limit, underscoring the promising future of quantum computing in bioinformatics.

Human MHC Class II and Invariant Chain Knock-in Mice Mimic Rheumatoid Arthritis with Allele Restriction in Immune Response and Arthritis Association.

Transgenic mice expressing human major histocompatibility complex class II (MHCII) risk alleles are widely used in autoimmune disease research, but limitations arise due to non-physiologic expression. To address this, physiologically relevant mouse models are established via knock-in technology to explore the role of MHCII in diseases like rheumatoid arthritis. The gene sequences encoding the ectodomains are replaced with the human DRB1*04:01 and 04:02 alleles, DRA, and CD74 (invariant chain) in C57BL/6N mice. The collagen type II (Col2a1) gene is modified to mimic human COL2. Importantly, DRB1*04:01 knock-in mice display physiologic expression of human MHCII also on thymic epithelial cells, in contrast to DRB1*04:01 transgenic mice. Humanization of the invariant chain enhances MHCII expression on thymic epithelial cells, increases mature B cell numbers in spleen, and improves antigen presentation. To validate its functionality, the collagen-induced arthritis (CIA) model is used, where DRB1*04:01 expression led to a higher susceptibility to arthritis, as compared with mice expressing DRB1*04:02. In addition, the humanized T cell epitope on COL2 allows autoreactive T cell-mediated arthritis development. In conclusion, the humanized knock-in mouse faithfully expresses MHCII, confirming the DRB1*04:01 alleles role in rheumatoid arthritis and being also useful for studying MHCII-associated diseases.

Generation of antigen-specific mature T cells from RAG1−/−RAG2−/−B2M−/− stem cells by engineering their microenvironment

Pluripotent stem cells (PSCs) are a promising source of allogeneic T cells for off-the-shelf immunotherapies. However, the process of differentiating genetically engineered PSCs to generate mature T cells requires that the same molecular elements that are crucial for the selection of these cells be removed to prevent alloreactivity. Here we show that antigen-restricted mature T cells can be generated in vitro from PSCs edited via CRISPR to lack endogenous T cell receptors (TCRs) and class I major histocompatibility complexes. Specifically, we used T cell precursors from RAG1−/−RAG2−/−B2M−/− human PSCs expressing a single TCR, and a murine stromal cell line providing the cognate human major histocompatibility complex molecule and other critical signals for T cell maturation. Possibly owing to the absence of TCR mispairing, the generated T cells showed substantially better tumour control in mice than T cells with an intact endogenous TCR. Introducing the T cell selection components into the stromal microenvironment of the PSCs overcomes inherent biological challenges associated with the development of T cell immunotherapies from allogeneic PSCs.

Vector-Mediated Delivery of Human Major Histocompatibility Complex-I into Hepatocytes Enables Investigation of T Cell Receptor-Redirected Hepatitis B Virus-Specific T Cells in Mice, and in Macaque Cell Cultures.

Adoptive T cell therapy using natural T cell receptor (TCR) redirection is a promising approach to fight solid cancers and viral infections in liver and other organs. However, clinical efficacy of such TCR+-T cells has been limited so far. One reason is that syngeneic preclinical models to evaluate safety and efficacy of TCR+-T cells are missing. We, therefore, developed an efficient viral vector strategy mediating expression of human major histocompatibility complex (MHC)-I in hepatocytes, which allows evaluation of TCR-T cell therapies targeting diseased liver cells. We designed adeno-associated virus (AAV) and adenoviral vectors encoding either the human-mouse chimeric HLA-A*02-like molecule, or fully human HLA-A*02 and human β2 microglobulin (hβ2m). Upon transduction of murine hepatocytes, the HLA-A*02 construct proved superior in terms of expression levels, presentation of endogenously processed peptides and activation of murine TCR+-T cells grafted with HLA-A*02-restricted, hepatitis B virus (HBV)-specific TCRs. In vivo, these T cells elicited effector function, controlled HBV replication, and reduced HBV viral load and antigen expression in livers of those mice that had received AAV-HBV and AAV-HLA-A*02. We then demonstrated the broad utility of this approach by grafting macaque T cells with the HBV-specific TCRs and enabling them to recognize HBV-infected primary macaque hepatocytes expressing HLA-A*02 upon adenoviral transduction. In conclusion, AAV and adenovirus vectors are suitable for delivery of HLA-A*02 and hβ2m into mouse and macaque hepatocytes. When recognizing their cognate antigen in HLA-A*02-transduced mouse livers or on isolated macaque hepatocytes, HLA-A*02-restricted, HBV-specific TCR+-T cells become activated and exert antiviral effector functions. This approach is applicable to any MHC restriction and target disease, paving the way for safety and efficacy studies of human TCR-based therapies in physiologically relevant preclinical animal models.

Evaluation of GenDx Protocol for HLA NGS Genotyping Using the Ion Torrent Sequencing Platform

Abstract Background: The Human Major Histocompatibility Complex (HLA) is the most polymorphic region of the human genome and encodes molecules with a central role in antigen-specific immune responses. Class I and class II HLA genes have an important role in bone marrow and solid organ transplantations. HLA typing by Next Generation Sequencing (NGS) provides unambiguous second field or allelic level resolution and, therefore, better matching of donor and recipient and a higher chance of survival for transplanted patients. The aim of this study was to validate GenDx NGS HLA typing protocol for 6 HLA loci (HLA-A, -B, -C, DRB1, -DQB1 and DPB1). Materials and methods: 240 samples of both bone marrow healthy donors from the Bulgarian Bone Marrow Donors Registry (BBMDR) and bone marrow recipients were sequenced on the Ion Torrent System using the GenDx NGS HLA typing kit, compared to 65 samples from the BBMDR analyzed by Holotype HLA kit (Omixon) and sequenced on the Illumina platform MiniSeq. A number of metrics including allele balance, read length, mappability, coverage and ambiguity were assessed in order to evaluate the GenDx NGS HLA typing protocol. We also investigated haplotype and allele frequencies of class I (HLA-A, -B, -C) and class II (HLA-DRB1, -DQB1 and -DPB1) alleles. Results: The results demonstrate the accuracy of this protocol, eliminating almost all ambiguities, providing a reasonable read length of 180, 76% mappability and 1267 depth of coverage on average for all 6 HLA loci. We found that the most frequent alleles for class I are HLA-A*02:01:01 (27,5%), B*51:01:01 (16,5%), C*07:01:01 (16,5%) and class II – DRB1*11:04:01 (14,5%), DQB1*03:01:01 (26,9%) and DPB1*04:01:01 (33,2%) which corresponds with other investigations of the research team on HLA diversity in the Bulgarian population. Conclusion: The main advantages of GenDx NGS HLA typing protocol are the shorter time for DNA library preparation and the shorter sequencing time. Phasing ambiguities are also liminated, which is a significant advantage in the clinical environment. The presented data show the suitability of this NGS protocol for clinical practice, especially in HLA typing of donors from Bone Marrow Donors registries.

HLA-OLI: A new MHC class I pseudogene and HLA-Y are located on a 60 kb indel in the human MHC between HLA-W and HLA-J.

Analysis of publicly available whole-genome sequence data from the Human Pangenome Project and the 1000 Genomes Project has identified a DNA segment of approximately 60 kb in the major histocompatibility complex (MHC) between HLA-W and HLA-J that is present in some MHC haplotypes but not others. This DNA segment is largely repeat element-rich but includes the pseudogene HLA-Y, thus pinpointing the location of this pseudogene, and a new HLA class I sequence we have called HLA-OLI. HLA-OLI clusters phylogenetically with the HLA class I pseudogenes, HLA-P and HLA-W, and appears to have a similar genetic structure. The availability of whole-genome sequence data from diverse populations enables a detailed characterization of the MHC at the population level and will have implications for understanding MHC disease associations and the non-HLA MHC factors that impact unrelated hematopoietic cell transplant outcomes.

The Molecular Mechanisms of HLA-G Regulatory Function on Immune Cells during Early Pregnancy.

Human leukocyte antigen-G (HLA-G) is a non-classical human major histocompatibility complex (MHC-I) molecule with the membrane-bound and soluble types. HLA-G is primarily expressed by extravillous cytotrophoblast cells located at the maternal-fetal interface during pregnancy and is essential in establishing immune tolerance. This review provides a comprehensive understanding of the multiple molecular mechanisms by which HLA-G regulates the immune function of NK cells. It highlights that HLA-G binds to microRNA to suppress NK cell cytotoxicity and stimulate the secretion of growth factors to support fetal growth. The interactions between HLA-G and NK cells also activate senescence signaling, promoting spiral artery remodeling and maintaining the balance of maternal-fetal immune responses. In addition, HLA-G can inhibit the function of decidual T cells, dendritic cells, and macrophages. Overall, the interaction between trophoblast cells and immune cells mediated by HLA-G plays a crucial role in understanding immune regulation at the maternal-fetal interface and offers insights into potential treatments for pregnancy-related diseases.

Abstract 2258: Starvation response to chemotherapy induces MHC class 1 upregulation in cancer cells

Abstract In tumor Major Histocompatibility Complex (MHC) class 1 expression pathway, antigen presenting peptides get hijacked and thus cancer cells escape immune recognition and promote immunosuppressive microenvironment. The restoration of altered MHC 1 expression is important for the treatment of cancer. Inhibition of amino acid uptake or tRNA synthase which mediates amino acid incorporation into protein, mimics starvation. The cancer cell responds to starvation by upregulating proteases to mobilize fatty acids and cellular surface molecules to scavenge exogenous molecules. EPRS (Glutamyl prolyl tRNA synthetase) catalyzes the aminoacylation of glutamic acid and proline to cognate tRNAs. Apart from that, the overexpression of EPRS1 gene is related to tumor angiogenesis, but the mechanism is not clear. Research showed that inhibition of EPRS is effective for the inhibition of triple negative breast cancer (TNBC) and colon cancer. Camptothecin (CPT) is a kind of chemotherapy drug that causes DNA damage by binding topoisomerase enzyme and DNA complex and arrest cells cycle in the S and G2 phases resulting in apoptosis. The knockdown (KD) of EPRS in TNBCs and the use of CPT for the treatment of colon cancer are both likely to have an impact on the accumulation of self epitopes, PTMs, and the creation of neoepitopes within tumors as a result. In this study, we examined the effects of EPRS and CPT treatment on the stimulation of MHC 1 in TNBC and colon cancer cells, as well as the diversity of peptide repertoires in EPRS KD breast cancer cells and CPT treated colon cancer cells. We conducted flow cytometer to detect the HLA specific antibodies on CPT treated RKO and SW620 colon cancer as well as EPRS KD MDA MB 231 triple negative breast cancer cells in our laboratory. In addition, we also performed immunopeptidomes on these cell lines to gain a deeper understanding of the biochemistry and immune pathway. Furthermore, we conducted cell cycle assays in both CRISPR and lentiviral mediated EPRS KD MDA MB 231 cells after CPT treatment. The human MHC class 1 expression were higher in both CPT treated RKO and SW620 colon cancer and EPRS KD MDA MB 231 TNBC cells as compared to the control in both our laboratory and Cayman Immunopeptidome analysis tests. In addition, the cell cycle result showed increment in S phase and reduction in G1 phase in some of the CPT treated EPRS KD ShRNA samples as compared to the control. These results showed that CPT as well as EPRS may play some role in the MHC Class 1 presentation in cancer cells. There were no significant changes observed in the total peptide content of TNBC cells after EPRS knockdown and colon cancer cells after CPT treatment. However, the knockdown of EPRS gene and the CPT treatment resulted in a novel peptide repertoire presented by the cells, which could have relevant to antigen presentation. Further studies are needed for detailed understanding of the biochemistry and immune pathway. Citation Format: Reshma Gurung, Alehegne Yirsaw, Mohammad Hassan, Temesgen Samuel, Clayton Yates, Deepa Bedi. Starvation response to chemotherapy induces MHC class 1 upregulation in cancer cells [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 2258.

A New Strategy for Mapping Epitopes of LACK and PEPCK Proteins of Leishmania amazonensis Specific for Major Histocompatibility Complex Class I.

Leishmaniasis represents a complex of diseases with a broad clinical spectrum and epidemiological diversity, considered a major public health problem. Although there is treatment, there are still no vaccines for cutaneous leishmaniasis. Because Leishmania spp. is an intracellular protozoan with several escape mechanisms, a vaccine must provoke cellular and humoral immune responses. Previously, we identified the Leishmania homolog of receptors for activated C kinase (LACK) and phosphoenolpyruvate carboxykinase (PEPCK) proteins as strong immunogens and candidates for the development of a vaccine strategy. The present work focuses on the in silico prediction and characterization of antigenic epitopes that might interact with mice or human major histocompatibility complex class I. After immunogenicity prediction on the Immune Epitope Database (IEDB) and the Database of MHC Ligands and Peptide Motifs (SYFPEITHI), 26 peptides were selected for interaction assays with infected mouse lymphocytes by flow cytometry and ELISpot. This strategy identified nine antigenic peptides (pL1-H2, pPL3-H2, pL10-HLA, pP13-H2, pP14-H2, pP15-H2, pP16-H2, pP17-H2, pP18-H2, pP26-HLA), which are strong candidates for developing a peptide vaccine against leishmaniasis.

Generation of TGFβR2(-1) neoantigen-specific HLA-DR4-restricted T cell receptors for cancer therapy

BackgroundAdoptive transfer of patient’s T cells, engineered to express a T cell receptor (TCR) with defined novel antigen specificity, is a convenient form of cancer therapy. In most cases, major...

The genetic polymorphisms at the promoter region of HLA-DQB1 gene, creating responsive elements for NF1/CTF and converting the TFII-D binding site to GR-alpha.

Human leukocyte antigen-DQB1 (HLA-DQB1, OMIM: 604305) is the human major histocompatibility complex (MHC) system. HLA genes are classified into three classes (I, II, and III). The HLA-DQB1 belongs to class II, is mainly involved in the actions of the human immune system and plays a fundamental role in donor-recipient matching in transplantation and can be associated with most autoimmune diseases. In this study, the potential influence(s) of the G-71C (rs71542466) and T-80C (rs9274529) genetic polymorphisms were investigated. These polymorphisms, located in the HLA-DQB1 promoter region, have a significant frequency in the world population. The online software ALGGEN-PROMO.v8.3 was used in this work. The results indicate that the C allele at the -71 position actually creates a new potential binding site for NF1/CTF and the C allele at the -80 position changes the TFII-D binding site into a GR-alpha response element. The NF1/CTF plays the role of activator and the GR-alpha is the inhibitor; thus, according to the roles of these transcription factors, it is suggested that the above-mentioned polymorphisms alter the expression levels of HLA-DQB1. Therefore, this genetic variation is associated with autoimmune diseases; however, this cannot be generalized because this is the first report and more studies are needed in the future.

Connection between MHC class II binding and aggregation propensity: The antigenic peptide 10 of Paracoccidioides brasiliensis as a benchmark study

The aggregation of epitopes that are also able to bind major histocompatibility complex (MHC) alleles raises questions around the potential connection between the formation of epitope aggregates and their affinities to MHC receptors. We first performed a general bioinformatic assessment over a public dataset of MHC class II epitopes, finding that higher experimental binding correlates with higher aggregation-propensity predictors. We then focused on the case of P10, an epitope used as a vaccine candidate against Paracoccidioides brasiliensis that aggregates into amyloid fibrils. We used a computational protocol to design variants of the P10 epitope to study the connection between the binding stabilities towards human MHC class II alleles and their aggregation propensities. The binding of the designed variants was tested experimentally, as well as their aggregation capacity. High-affinity MHC class II binders in vitro were more disposed to aggregate forming amyloid fibrils capable of binding Thioflavin T and congo red, while low affinity MHC class II binders remained soluble or formed rare amorphous aggregates. This study shows a possible connection between the aggregation propensity of an epitope and its affinity for the MHC class II cleft.

The structure of songbird MHC class I reveals antigen binding that is flexible at the N-terminus and static at the C-terminus.

Long-distance migratory animals such as birds and bats have evolved to withstand selection imposed by pathogens across the globe, and pathogen richness is known to be particularly high in tropical regions. Immune genes, so-called Major Histocompatibility Complex (MHC) genes, are highly duplicated in songbirds compared to other vertebrates, and this high MHC diversity has been hypothesised to result in a unique adaptive immunity. To understand the rationale behind the evolution of the high MHC genetic diversity in songbirds, we determined the structural properties of an MHC class I protein, Acar3, from a long-distance migratory songbird, the great reed warbler Acrocephalus arundinaceus (in short: Acar). The structure of Acar3 was studied in complex with pathogen-derived antigens and shows an overall antigen presentation similar to human MHC class I. However, the peptides bound to Acar3 display an unusual conformation: Whereas the N-terminal ends of the peptides display enhanced flexibility, the conformation of their C-terminal halves is rather static. This uncommon peptide-binding mode in Acar3 is facilitated by a central Arg residue within the peptide-binding groove that fixes the backbone of the peptide at its central position, and potentially permits successful interactions between MHC class I and innate immune receptors. Our study highlights the importance of investigating the immune system of wild animals, such as birds and bats, to uncover unique immune mechanisms which may neither exist in humans nor in model organisms.

Perspective of Human Leukocyte Antigen testing

Most of the cells in the body have proteins or markers called human leukocyte antigens (HLA). To determine which cells, belong in the body and which do not, the immune system uses HLA. Human leukocyte antigen (HLA) typing is used to match recipients and donors for bone marrow or cord blood transplants. The human major histocompatibility complex (HLA) is located on the short arm of chromosome 6, and it is a complex of genes that encode cell-surface proteins necessary for immune system regulation. It is well known that this human genetic system is the most polymorphic. HLA class I and class II molecules' biological function is to present antigens that have been processed into peptides. HLA was initially just a list of antigens discovered as a result of transplant rejection. HLAs are alloantigen’s that range from person to person due to genetic variance. In essence, every person's immune system is tailored to the distinct HLA and self-proteins produced by that person; when tissues are transferred to another person, however, things go wrong. Individuals almost always have different "banks" of HLAs, which causes transplant rejection because the recipient's immune system mistakes the transplanted tissue for non-self and kills the foreign tissue. HLAs were found as a result of this realization.

The IPD-IMGT/HLA Database.

It is 24 years since the IPD-IMGT/HLA Database, http://www.ebi.ac.uk/ipd/imgt/hla/, was first released, providing the HLA community with a searchable repository of highly curated HLA sequences. The database now contains over 35 000 alleles of the human Major Histocompatibility Complex (MHC) named by the WHO Nomenclature Committee for Factors of the HLA System. This complex contains the most polymorphic genes in the human genome and is now considered hyperpolymorphic. The IPD-IMGT/HLA Database provides a stable and user-friendly repository for this information. Uptake of Next Generation Sequencing technology in recent years has driven an increase in the number of alleles and the length of sequences submitted. As the size of the database has grown the traditional methods of accessing and presenting this data have been challenged, in response, we have developed a suite of tools providing an enhanced user experience to our traditional web-based users while creating new programmatic access for our bioinformatics user base. This suite of tools is powered by the IPD-API, an Application Programming Interface (API), providing scalable and flexible access to the database. The IPD-API provides a stable platform for our future development allowing us to meet the future challenges of the HLA field and needs of the community.

Abstract LB099: Direct identification of MHC class I and class II epitopes for TCR-based T cell therapy for pancreatic cancer

Abstract Background: Tumor-associated antigens and neoantigens serve as primary targets for cancer immunotherapies such as vaccines and T-cell based therapy. However, identifying pancreatic ductal adenocarcinoma (PDAC) associated T-cell epitopes have been challenging due to its low genomic mutational burden. In this study, we attempted to directly identify PDAC T-cell epitopes by using mass spectrometry. Methods: The protein lysate from PDAC specimens and cell lines were subjected to the antibody affinity purification of human major histocompatibility complexes (MHC) including both HLA Class I and Class II complexes. Peptides bound to the MHC were eluted and identified through LC-MS/MS. Peptide sequences were analyzed with MAXQUANT and Novor Denovo. HLA-binding affinity of peptides were predicted using NetMHC4.0 and validated by in vitro T2 binding assays. Their ability to induce T cell response were measured in a cytokine-Flurospot assay. TCRs specific for selected peptides were cloned by single-cell TCR sequencing and their anti-PDAC activity were tested in vivo on the patient-derived xenograft(PDX) models. Results: We identified 6553 unique HLA-I bound 9-mer peptides from eight PDAC specimens and two PDAC cell lines (Panc10.05 and Pan06.03). Among them, 1163 peptides and 1354 proteins were found in two or more PDAC specimens. We identified 8 potentially immunogenic peptides that bind strongly to matched and nonmatched HLA molecules and induced T cell response in peripheral T cells from both HLA-type matched and non-matched patients. We also identified HLA-II bound peptides in six PDAC tissues and found that the HLA-I and HLA-II peptides isolated from the same patient are highly overlapped. These overlapped peptides were able to induce polyfunctional cytokine response (IFN-γ, TNF-α, and IL-2) in peripheral T cells from patient PBMC. We further investigated the anti-tumor capability of T cell receptors (TCR) for an LAMC-2 derived HLA-class I epitope and a TMSB10 derived peptide eluted from both HLA-Class I and Class II affinity purification. Immunohistochemistry revealed both proteins to be more highly expressed in PDAC tissue compared to paranormal normal tissue. We stimulated HLA-type matched patient’s PBMC with LAMC-2 and TMSB10 peptides to induce clonal expansion of epitope-specific CD8+ and CD4+ T-cells, respectively. We subsequently performed single-cell TCR sequencing of these expanded T cells and infected Jurkat cells with the lentivirus expressing TCR of interest. Mice with orthotopically implanted PDAC tumors that were treated with Jurkat cells expressing LAMC-2 specific cells showed significant slowdown tumor growth. We are currently in the processing of testing TMSB10 peptide targeting TCRs. Conclusion: This study provides a novel venue for identifying T cell epitopes in a nonimmunogenic tumor such as PDAC for the design and development of cancer vaccine and T cell therapy. Citation Format: Tengyi Zhang, Jianxin Wang, Yingkuan Shao, Pan Li, Nan Niu, Brian Herbst, Jessica Gai, Juan Fu, Pingbo Zhang, Jun Yu, Kenji Fujiwara, Lei Zheng. Direct identification of MHC class I and class II epitopes for TCR-based T cell therapy for pancreatic cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr LB099.

Abstract 6258: Development of humanized patient-derived xenograft models for triple negative breast cancer

Abstract As a new promising in vivo platform for personalized treatment in the field of cancer research, the most improved way has been adopted by far is grafting patient-derived xenograft (PDX) to humanized mouse models which represent the unique features of interaction with human immune system and tumor microenvironment (TME). Here, we engineered triple negative breast cancer (TNBC) humanized PDX mouse (Hu-PDX) model to observe human immune system and tumor growth in TME. In addition, we analyzed gene ontology of PDX isolated from hu or non-humanized mouse model. Method: Human CD34+hematopoietic stem cells (HSCs) derived from cord blood is reconstructed into mature human leukocytes (hCD45+) in NOD.Cg-PrkdcscidIL2γgtm1 Sug (NOG) mice. TNBC PDX tumors are established it with unmatched human leukocyte antigen (HLA) genotypes, confirmed by that hCD45+ engraftment levels did not exceed 20-30% in the peripheral blood of mice. To be repopulated functional human T cells in xenograft models with severely depleted thymus, hCD34-PBMC cells are directly intravenously injected into tail vein of humanized mice followed by hCD34+cells injected without the onset of graft-versus-host disease (GVHD). The growth and gene expression of TNBC PDX tumors, as well as engrafted human immune population including T, B, natural killer (NK) cells and myeloid cells in TME, are monitored and investigated in both hu and non-hu-mice model. Results: Human immune reconstruction of cells, of the lymphoid as well as myeloid lineages, has been successfully accomplished in peripheral blood, spleen, and bone marrow over time in TME. Although the number of human mature leukocytes was gradually decreased in mice by 17 weeks, humanized mice have enabled studies of human immunity and TME in limitation period. Also, one of remaining limitations is unable to positive and negative selection of human T cells in the humanized mouse thymus and required to human major histocompatibility complex (MHC) molecules in humanized mice. To overcome this barrier, additional stimulation factor for generating functional T cells have successfully engrafted by transferring hCD34-PBMC cells. Moreover, tumor infiltrating human lymphocytes (TILs) have obviously detected in Hu-PDX model, although the differences tumor growth rate was not significantly monitored, compared with non-humanized mice. Interestingly, the analysis of gene ontology; biological process, cellular component and molecular function, ribosomal relevant proteins, not immune related genes, were highly up-regulated in TNBC PDX humanized in comparison to non-humanized mouse model. Conclusion: Humanized PDX model will contribute to studies more efficiently for the machinery underlying immunological response in breast tumor microenvironment. Furthermore, it might be an important unknown mechanism that the effect of elevated cancer-related ribosomal proteins expression within hu immune-TME. Citation Format: Yujeong Her, Hye Yeon Son, Ju Hee Kim, Woo Hang Heo, Mingji Quan, Songbin Li, Hyeong Gon Moon. Development of humanized patient-derived xenograft models for triple negative breast cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 6258.

Characterizing the diversity of MHC conserved extended haplotypes using families from the United Arab Emirates

Aside from its anthropological relevance, the characterization of the allele frequencies of genes in the human Major Histocompatibility Complex (MHC) and the combination of these alleles that make up MHC conserved extended haplotypes (CEHs) is necessary for histocompatibility matching in transplantation as well as mapping disease association loci. The structure and content of the MHC region in Middle Eastern populations remain poorly characterized, posing challenges when establishing disease association studies in ethnic groups that inhabit the region and reducing the capacity to translate genetic research into clinical practice. This study was conceived to address a gap of knowledge, aiming to characterize CEHs in the United Arab Emirates (UAE) population through segregation analysis of high-resolution, pedigree-phased, MHC haplotypes derived from 41 families. Twenty per cent (20.5%) of the total haplotype pool derived from this study cohort were identified as putative CEHs in the UAE population. These consisted of CEHs that have been previously detected in other ethnic groups, including the South Asian CEH 8.2 [HLA- C*07:02-B*08:01-DRB1*03:01-DQA1*05:01-DQB1*02:01 (H.F. 0.094)] and the common East Asian CEH 58.1 [HLA- C*03:02-B*58:01-DRB1*03:01- DQA1*05:01-DQB1*02:01 (H.F. 0.024)]. Additionally, three novel CEHs were identified in the current cohort, including HLA- C*15:02-B*40:06-DRB1*16:02-DQB1*05:02 (H.F. 0.035), HLA- C*16:02-B*51:01-DRB1*16:01-DQA1*01:02-DQB1*05:02 (H.F. 0.029), and HLA- C*03:02-B*58:01-DRB1*16:01-DQA1*01:02-DQB1*05:02 (H.F. 0.024). Overall, the results indicate a substantial gene flow with neighbouring ethnic groups in the contemporary UAE population including South Asian, East Asian, African, and European populations. Importantly, alleles and haplotypes that have been previously associated with autoimmune diseases (e.g., Type 1 Diabetes) were also present. In this regard, this study emphasizes that an appreciation for ethnic differences can provide insights into subpopulation-specific disease-related polymorphisms, which has remained a difficult endeavour.

Identification of Potential Vaccine Candidates Against SARS-CoV-2 to Fight COVID-19: Reverse Vaccinology Approach.

BackgroundThe recent emergence of COVID-19 has caused an immense global public health crisis. The etiological agent of COVID-19 is the novel coronavirus SARS-CoV-2. More research in the field of developing effective vaccines against this emergent viral disease is indeed a need of the hour.ObjectiveThe aim of this study was to identify effective vaccine candidates that can offer a new milestone in the battle against COVID-19.MethodsWe used a reverse vaccinology approach to explore the SARS-CoV-2 genome among strains prominent in India. Epitopes were predicted and then molecular docking and simulation were used to verify the molecular interaction of the candidate antigenic peptide with corresponding amino acid residues of the host protein.ResultsA promising antigenic peptide, GVYFASTEK, from the surface glycoprotein of SARS-CoV-2 (protein accession number QIA98583.1) was predicted to interact with the human major histocompatibility complex (MHC) class I human leukocyte antigen (HLA)-A*11-01 allele, showing up to 90% conservancy and a high antigenicity value. After vigorous analysis, this peptide was predicted to be a suitable epitope capable of inducing a strong cell-mediated immune response against SARS-CoV-2.ConclusionsThese results could facilitate selecting SARS-CoV-2 epitopes for vaccine production pipelines in the immediate future. This novel research will certainly pave the way for a fast, reliable, and effective platform to provide a timely countermeasure against this dangerous virus responsible for the COVID-19 pandemic.