Human Leukocyte Antigen Complex Research Articles

Long Non-Coding RNA HCP5 Affects Ferroptosis in Lung Adenocarcinoma through miR-17-5p/HOXA7 Axis.

Ferroptosis, a regulated cell death initiated by Fe-dependent lipoperoxidation, is closely linked to the development of lung adenocarcinoma (LUAD). LncRNA human leukocyte antigen complex P5 (HCP5) has been confirmed as oncogenic in LUAD, but its function in ferroptosis is unknown. Based on the previous bioinformatics mining of the ceRNA (competitive endogenous RNA) network HCP5/miR-17-5p/ Homeobox A7 (HOXA7) related to ferroptosis in LUAD, in this study, we characterized the cell-based experiments to validate the binding between the HCP5/miR-17-5p/HOXA7 axis and ferroptosis. The HCP5/miR-17-5p/HOXA7 linkage was identified by a two-luciferase reporter. Cell Counting Kit-8 (CCK-8) and Transwell assay were employed for the detection of viability, invasion, and migration of A549 cells, respectively. ACSL4 and SLC7A11 were associated with ferroptosis, MMP 9, vimentin, and E-cadherin, which were associated with migration and invasion and were assessed by WB and qRT-PCR. Fe2+ and malondialdehyde (MDA) were analyzed using kits. Over-expression of HCP5 enhances the growth, invasion, and migration of A549 cells by adjusting miR-17-5P to increase the expression of HOXA7. In addition, the knock-down of HCP5 elevated miR-17-5p, which inhibited HOXA7 expression and suppressed ferroptosis and EMT in A549 cells. HCP5/miR-17-5p/HOXA7 can affect ferroptosis as well as the biological behavior of A549 cells.

Computational insights in design of Crimean-Congo hemorrhagic fever virus conserved immunogenic nucleoprotein peptides containing multiple epitopes.

Crimean-Congo hemorrhagic fever virus (CCHFV) belongs to Nairoviridae family and has tripartite RNA genome. It is endemic in various countries of Asia, Africa, and Europe and is primarily transmitted by Hyalomma ticks but nosocomial transmission also been reported. Vaccines for CCHF are in early phase of clinical trial; therefore, this work is centered on identification of potential immunogenic peptide as vaccine candidates with application of different immunoinformatics approaches. Eleven conserved (>90%) peptides of CCHFV nucleoprotein were selected for CD8+ T-cell (NetMHCpan 4.1b and NetCTLpan 1.1 server) and CD4+ T-cell (NetMHCIIpan-4.0 server and Tepitool) epitope prediction. Three peptides containing multiple CD8+ and CD4+ T-cell and B-cell epitopes were identified on basis of consensus prediction approach. Peptides displayed good antigenicity score of 0.45-0.68 and predicted to bind with diverse human leukocyte antigen (HLA) alleles. Molecular docking was performed with epitopes to HLA and HLA-epitopes complex to T-cell receptor (TCR). In most of the cases, docked complex of HLA-epitope and HLA-epitopes-TCR have the binding energy close to respective natural bound peptide complex with HLA and TCR. Molecular dynamic simulation also revealed that HLA-peptide complexes have minimum fluctuation and deviation than HLA-peptide-TCR docked over 50ns simulation run. Considering these findings, identified peptides can serve as potential vaccine candidates for CCHFV disease.

The clinical value of serum long non-coding RNA human leukocyte antigen complex group 11/microRNA-532-3p in the diagnosis and prognosis of patients with acute myocardial infarction undergoing percutaneous coronary intervention

BackgroundAcute myocardial infarction (AMI) is a cardiovascular disease with the highest morbidity and mortality rate in the world. Several studies have suggested that abnormal regulation of non-coding RNAs (ncRNAs) may play a vital role in the occurrence and progress of AMI.ObjectiveThe purpose of this study was to investigate the clinical values of human leukocyte antigen complex group 11 (HCG11) or miR-532-3p in the diagnosis and prognosis of patients with AMI after percutaneous coronary intervention (PCI).MethodsThe clinical data of 100 AMI patients who underwent PCI were analyzed retrospectively. According to whether major adverse cardiovascular events (MACE) occurred after PCI, they were divided into MACE group (n = 38) and non-MACE group (n = 62). Basic clinical data and serum HCG11 and miR-532-3p levels were analyzed. Multivariate Cox regression analysis was performed to evaluate the risk factors for MACE, and the receiver operator characteristic (ROC) curve was constructed to assess the clinical predictive value of HCG11 and miR-532-3p for MACE.ResultsCompared with the control group, the serum HCG11 level and miR-532-3p in AMI patients were significantly increased or decreased, and the serum levels of HCG11 and miR-532-3p in the MACE group were significantly increased and decreased, compared with those in non-MACE group. Multivariate Cox regression showed that HCG11 and miR-532-3p were risk factors for MACE occurrence. ROC curve investigated that HCG11 combined with miR-532-3p has accurate predictive value for MACE.ConclusionThis study showed that serum HCG11 and miR-532-3p have certain predictive value for MACE after PCI in patients with AMI.

Association between human leukocyte antigen class II-DR-DQ and narcolepsy: a case control study.

Narcolepsy is a neurologic disorder characterized by irresistible sleep attacks. Although its etiology is unknown, it is strongly associated with genetic variances in the human leukocyte antigen (HLA) complex. We investigated the association of HLA class II-DR-DQ alleles in a sample of patients with narcolepsy-cataplexy (narcolepsy type 1; NT1) and patients with narcolepsy without cataplexy (narcolepsy type 2; NT2) with a control group. Additionally, we compared demographic, clinical, and laboratory characteristics of patients with narcolepsy with or without the DQB1*06:02 allele. This case control study included 21 patients with NT1 (56.8%), 16 patients with NT2 (43.2%), and 100 controls. Sequence-based typing identified HLA-DRB1 alleles, and HLA-DQB1 typing was done using PCR-Sequence-Specific Oligonucleotide. Allele and haplotype frequencies were calculated by direct counting. Nocturnal polysomnography and Multiple Sleep Latency Test were performed in all participants. In the NT1 group, only one allele had a significantly higher frequency than in the NT2 group: DQB1*06:02 (61.9% vs. 18.8%;). Compared to controls, DQB1*06:02 (61.9% vs. 18.0% in controls) and DRB1*15:01(47.6% vs. 8.0%), had higher frequencies in patients with NT1. Multiple analyses showed that patients with NT1 had an increased chance of being HLA-DQB1*06:02 positive. HLA-DRB1*15:01-DQA1*01:02-DQB1*06:02 haplotype is associated with NT1 in our Brazilian patients. PSG was identified in DQB1*06:02 positive subgroup REM sleep latency (REML) ≤ 15 minutes, and all patients had two or more sleep-onset REM periods (SOREMPs) at MSLT. This study showed a strong association between HLA DQB1*06:02 and the haplotype HLA-DRB1*15:01-DQA1*01:02-DQB1*06:02 in patients with NT1. Patients with DQB1*0602 allele showed shorter REMLs at PSG. These results reinforce the suggestion of DQB1 genotyping as relevant to narcolepsy screening.

Preimplantation Genetic Testing for HLA Matching (PGT-HLA) When Only Partial Embryo Matches are Identified

Introduction: Preimplantation Genetic Testing (PGT) is an option for couples to select embryos that have a matching Human Leukocyte Antigen (HLA) type to a child that is in need of hematopoietic stem cell transplant (HSCT). Families in search of HLA-matched donors for HSCT may have a difficult time finding publicly available optimal donors or donors within their families. The likelihood of a family finding an optimal donor can vary from 16% to 75%, depending on ethnic and racial groups. Previously, PGT-HLA has been used to identify potential future siblings who would be an HLA match to an affected child through embryo testing as early as 2001 for conditions like Fanconi Anemia. PGT-HLA can be complicated by the presence of recombination within the HLA complex on chromosome 6 in the affected individual. If an affected child is found to be recombinant within the HLA complex (6-7% of PGT-HLA cases), the chances of finding a full sibling-matched donor can be extremely low. PGT for partial HLA matching can be used when the affected child is found to be recombinant or if a full parental match is not possible. When a child is identified as recombinant in the HLA region, consultation with their transplant team can determine whether a partial sibling match would be a good therapeutic candidate. PGT-HLA is performed by linkage analysis which requires DNA samples from the oocyte source, sperm source, and the affected child. These results will determine shared parental regions of the HLA complex genes so that partial matches can be identified. Case Reviews: We present two cases of PGT-HLA where only partial matches were identified during embryo testing. Of these 2 cases, both families completed one testing cycle for PGT-M and PGT-HLA and both had partial matches that were recommended for transfer per patient consent. One family had 3 partial match embryos, but they did not have a successful pregnancy following frozen embryo transfer. However, during the period of their transfers, they were able to find an adequate publicly-matched donor for HSCT therapy for their child. In one family, only a paternal HLA match was sought due to advanced maternal age of the mother. Consultation with the family’s transplant team indicated that a paternal-only match would be sufficient for a therapeutic effect. Conclusions: Despite the complexity of testing for PGT-HLA matching for a child where a full sibling match is not available embryo testing can still provide a therapeutic benefit. Interdisciplinary consultation in these cases would optimally include the couple, the affected child’s transplant team, the couple’s reproductive endocrinologist, and genetic counseling available at the PGT laboratory or the REI office. As accessibility to PGT continues to grow and as guidelines for PGT acceptability continue to be written, PGT-HLA should similarly find more usage. Inevitably, partial embryo matches will be seen and we will continue to learn how these can be used in clinical practice.

Ancient genomes reveal insights into ritual life at Chichén Itzá

The ancient city of Chichén Itzá in Yucatán, Mexico, was one of the largest and most influential Maya settlements during the Late and Terminal Classic periods (ad 600–1000) and it remains one of the most intensively studied archaeological sites in Mesoamerica1–4. However, many questions about the social and cultural use of its ceremonial spaces, as well as its population’s genetic ties to other Mesoamerican groups, remain unanswered2. Here we present genome-wide data obtained from 64 subadult individuals dating to around ad 500–900 that were found in a subterranean mass burial near the Sacred Cenote (sinkhole) in the ceremonial centre of Chichén Itzá. Genetic analyses showed that all analysed individuals were male and several individuals were closely related, including two pairs of monozygotic twins. Twins feature prominently in Mayan and broader Mesoamerican mythology, where they embody qualities of duality among deities and heroes5, but until now they had not been identified in ancient Mayan mortuary contexts. Genetic comparison to present-day people in the region shows genetic continuity with the ancient inhabitants of Chichén Itzá, except at certain genetic loci related to human immunity, including the human leukocyte antigen complex, suggesting signals of adaptation due to infectious diseases introduced to the region during the colonial period.

A phase 1 dose-escalation and expansion study of CUE-101, given as monotherapy and in combination with pembrolizumab, in patients with recurrent/metastatic HPV16+ head and neck squamous cell cancer (R/M HNSCC).

6004 Background: Immuno-STATs are modular T cell engagers engineered to selectively activate tumor-antigen specific CD8+ T cells via targeted delivery of cytokines. CUE-101, the first Immuno-STAT in clinical trials, is composed of a human leukocyte antigen (HLA) complex, HLA-A*0201, a peptide epitope derived from the HPV16 E7 protein and 4 molecules of attenuated human interleukin-2 (IL-2), to bind, expand, and activate HPV16-specific CD8+ T cells for the treatment of HPV16+ HNSCC. Methods: CUE-101-01 is an ongoing first-in-human study in HLA-A*0201 patients with HPV16+ R/M HNSCC. Escalating doses of CUE-101 monotherapy (0.06 mg/kg to 8 mg/kg) were evaluated in R/M HNSCC refractory to ≥ 1 platinum or checkpoint inhibitor (CPI) based therapy, alone or combined with pembrolizumab (1 mg/kg to 4 mg/kg + 200 mg pembrolizumab) in the first line treatment of PD-L1+ R/M HNSCCs. Enrollment at the recommended phase 2 dose (RP2D) was expanded. Therapy was administered every 3 weeks (Q3W) until disease progression or intolerable toxicity. Safety, PK/PD, and antitumor activity were assessed. Results: Enrollment in both monotherapy and combination cohorts is now completed (N=80 patients, 49 in monotherapy and 31 CUE-101 plus pembrolizumab). Following dose escalation, 4 mg/kg Q3W of CUE-101 was selected for RP2D for both monotherapy and pembrolizumab combination cohorts. At data cut-off, adverse events (AEs) have been manageable and 92% grade ≤2. The most frequent grade 3 AEs reported include lymphocyte count decreased (7.6%), anemia (6.3%), decreased appetite (5.1%) and infusion-related reactions (5.1%). In combination with pembrolizumab no unanticipated significant safety concerns have emerged. Exposure-dependent PD effects of CUE-101 are consistent with IL-2 pharmacology and indicate preferential expansion of CUE-101 on E7-specific T cells. Among the 19 evaluable patients treated with the RP2D of CUE-101 plus pembrolizumab, an ORR of 47% (1 CR, 8 PRs), a Disease Control Rate (ORR + durable SDs) of 74%, and mPFS of 5.8 months [95% CI 2.56; NA] were observed. A median OS has not been reached. Of the 9 patients with confirmed objective responses, all achieved >99% reduction in HPV16 cfDNA in plasma during their treatment course. Among the 19 evaluable monotherapy RP2D patients, 1 PR and 6 durable SD (SD ≥ 12 weeks) and mOS of 20.8 months [95% CI 11.0; NA] were observed. Conclusions: An ORR of 47% and a mPFS of 5.8 months were observed in R/M HNSCC patients treated with CUE-101 4 mg/kg + pembrolizumab as 1L therapy. A median OS of 20.8 was observed in patients treated with CUE-101 monotherapy as post-platinum/CPI therapy. CUE-101 continues to demonstrate safety, tolerability and meaningful clinical benefit in patients with HPV16+ R/M HNSCC. Clinical trial information: NCT03978689 .

A phase 1, open-label, dose escalation, and expansion study of CUE-102, a novel WT1-pHLA-IL2-Fc fusion protein, in patients with HLA-A*0201-positive disease and WT1-positive recurrent/metastatic cancers.

3553 Background: Immuno-STATs are modular fusion proteins designed for the selective activation of tumor antigen specific CD8+ T cells. CUE-102, the second Immuno-STAT in clinical trials, is composed of a human leukocyte antigen (HLA) complex, HLA-A*0201, a peptide epitope derived from the Wilms Tumor 1 (WT1) protein, and 4 molecules of reduced affinity human interleukin-2 (IL-2). In preclinical studies CUE-102 binds, activates and expands WT1-specific CD8+ T cells with the potential to enhance anti-tumor immunity in patients with WT1+ cancers. Here we present the results of the dose-finding portion (Part A) of the CUE-102-01 study. Methods: CUE-102-01 is a 2 part phase 1 study. HLA-A*02:01 positive patients with WT1+ advanced colorectal (CRC), gastric (GA) and gastroesophageal junction (GEJ), pancreatic (PDAC) or ovarian (OvCa) tumors refractory to standard therapies were eligible for participation. WT1 status is determined by IHC via central testing. CUE-102 monotherapy was administered intravenously every three weeks in doses ranging from 1 mg/kg to 8 mg/kg following 3+3 design rules with a Bayesian Logistic Regression Model overlay. Dose levels that exhibit an immune or tumor response may be expanded to further characterize activity and toxicity as allowed by safety rules. Results: Dose escalation was successfully completed in 28 patients with CRC (17), PDAC (6), GA/GEJ (3) and OvCa (2). No DLTs were observed. Three dose levels (2, 4 and 8 mg/kg) exhibited evidence of immune activity and were expanded up to 9 patients each for further evaluation. CUE-102 was well-tolerated with > 96% of treatment-related adverse events (TRAEs) grade ≤2. The most common TRAEs, were fatigue, infusion reactions, nausea and vomiting. There were no cases of CRS Grade ≥ 2. Preliminary PK data demonstrate dose dependent increases in exposure across the dose range assessed. Preliminary analysis of patient samples demonstrates selective expansion of WT1-specific CD8+ T cells. Stable disease of ≥ 6 weeks (range 6-36 weeks), as determined by RECIST 1.1, has been observed in 10 of 23 patients (DCR 43.5%). Conclusions: CUE-102 is a novel T cell engager that demonstrates acceptable tolerability, favorable PK, and supportive preliminary PD readouts. No DLTs or drug-related SAEs have been observed in doses up to 8 mg/kg as of the data cut-off. Adverse events have been manageable and consistent with the CUE-102 mechanism of action and underlying disease. Early signs of disease stabilization and anti-tumor activity in late-stage patients are encouraging. Part B is a dose expansion that further evaluates safety, PK/PD, recommended phase 2 dose (RP2D), antitumor efficacy and is currently enrolling patients. Clinical trial information: NCT05360680 .

Construction and analysis of competitive endogenous RNA networks and prognostic models associated with ovarian cancer based on the exoRBase database.

To construct a competitive endogenous RNA (ceRNA) regulatory network in blood exosomes of patients with ovarian cancer (OC) using bioinformatics and explore its pathogenesis. The exoRbase2.0 database was used to download blood exosome gene sequencing data from patients OC and normal controls and the expression profiles of exosomal mRNA, long non-coding RNA (lncRNA), and circular RNA (circRNA) were detected independently using R language for differential expression analysis. TargetScan and miRanda databases were combined for the prediction and differential expression of mRNA-binding microRNAs (miRNA). The miRcode and starBase databases were used to predict miRNAs that bind to differentially expressed lncRNAs and circRNAs repectively. The relevant mRNA, circRNA, lncRNA and their corresponding miRNA prediction data were imported into Cytoscape software for visualization of the ceRNA network. The R language and KEGG Orthology-based Annotation System (KOBAS) were used to execute and illustrate the Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses. Hub genes were identified using The CytoHubba plugin. Thirty-one differentially expressed mRNAs, 17 differentially expressed lncRNAs, and 24 differentially expressed circRNAs were screened. Cytoscape software was used to construct the ceRNA network with nine mRNA nodes, two lncRNA nodes, eight circRNA nodes, and 51 miRNA nodes. Both GO and KEGG were focused on the Spliceosome pathway, indicating that spliceosomes are closely linked with the development of OC, while heterogenous nuclear ribonucleoprotein K and RNA binding motif protein X-linked genes were the top 10 score Hub genes screened by Cytoscape software, including two lncRNAs, four mRNAs, and four circRNAs. In patients with OC, the expression of eukaryotic translation initiation factor 4 gamma 2 (EIF4G2), SERPINE 1 mRNA binding protein 1 (SERBP1), ribosomal protein L15 (RPL15) and human leukocyte antigen complex P5 (HCP5) was significantly higher whereas that of testis expressed transcript, Y-linked 15 and DEAD-box helicase 3 Y-linked genes was lower compared to normal controls Immunocorrelation scores revealed that SERBP1 was significantly and negatively correlated with endothelial cells and CD4+ T cells and positively correlated with natural killer (NK) cells and macrophages, respectively; RPL15 was significantly positively correlated with macrophages and endothelial cells and negatively correlated with CD8+ T cells and uncharacterized cells, respectively. EIF4G2 was significantly and negatively correlated with endothelial cells and CD4+ T cells, and positively correlated with uncharacterized cells, respectively. Based on the survival data and the significant correlation characteristics derived from the multifactorial Cox analysis (P < 0.05), the survival prediction curves demonstrated that the prognostic factors associated with 3-year survival in patients with OC were The prognostic factors associated with survival were Macrophage, RPL15. This study successfully constructs a ceRNA regulatory network in blood exosomes of OV patients, which provides the specific targets for diagnosis and treatment of OC.

The role of lncRNA HCG18 in human diseases.

A substantial number of long noncoding RNAs (lncRNAs) have been identified as potent regulators of human disease. Human leukocyte antigen complex group 18 (HCG18) is a new type of lncRNA that has recently been proven to play an important role in the occurrence and development of various diseases. Studies have found that abnormal expression of HCG18 is closely related to the clinicopathological characteristics of many diseases. More importantly, HCG18 was also found to promote disease progression by affecting a series of cell biological processes. This article mainly discusses the expression characteristics, clinical characteristics, biological effects and related regulatory mechanisms of HCG18 in different human diseases, providing a scientific theoretical basis for its early clinical application.

Multi-omics analysis of overexpressed tumor-associated proteins: gene expression, immunopeptide presentation, and antibody response in oropharyngeal squamous cell carcinoma, with a focus on cancer-testis antigens.

The human leukocyte antigen complex (HLA) is essential for inducing specific immune responses to cancer by presenting tumor-associated peptides (TAP) to T cells. Overexpressed tumor associated antigens, mainly cancer-testis antigens (CTA), are outlined as essential targets for immunotherapy in oropharyngeal squamous cell carcinoma (OPSCC). This study assessed the degree to which presentation, gene expression, and antibody response (AR) of TAP, mainly CTA, are correlated in OPSCC patients to evaluate their potential as immunotherapy targets. Snap-frozen tumor (NLigand/RNA=40), healthy mucosa (NRNA=6), and healthy tonsils (NLigand=5) samples were obtained. RNA-Seq was performed using Illumina HiSeq 2500/NovaSeq 6000 and whole exome sequencing (WES) utilizing NextSeq500. HLA ligands were isolated from tumor tissue using immunoaffinity purification, UHPLC, and analyzed by tandem MS. Antibodies were measured in serum (NAb=27) utilizing the KREX™ CT262 protein array. Data analysis focused on 312 proteins (KREX™ CT262 panel + overexpressed self-proteins). 183 and 94 of HLA class I and II TAP were identified by comparative profiling with healthy tonsils. Genes from 26 TAP were overexpressed in tumors compared to healthy mucosa (LFC>1; FDR<0.05). Low concordance (r=0.25; p<0.0001) was found between upregulated mRNA and class I TAP. The specific mode of correlation of TAP was found to be dependent on clinical parameters. A lack of correlation was observed both between mRNA and class II TAP, as well as between class II tumor-unique TAP (TAP-U) presentation and antibody response (AR) levels. This study demonstrates that focusing exclusively on gene transcript levels fails to capture the full extent of TAP presentation in OPSCC. Furthermore, our findings reveal that although CTA are presented at relatively low levels, a few CTA TAP-U show potential as targets for immunotherapy.

Associação dos alelos de risco HLA-DQ2 e HLA-DQ8 à lesão intestinal e sorologia em pacientes com doença celíaca

ABSTRACT Objective This study aims to describe the distribution of main celiac disease risk alleles related to human leucocyte antigen complex and their association to the severity of intestinal injury, serological test results, CD-associated diseases and symptomatology. Methods The DNA of 140 celiac disease patients was analyzed, and the distribution of the three most important risk alleles to the celiac disease development was identified (DQA1*05:01, DQB1*02:01 and DRB1*04, the last one as a DQB1*03:02/DQA1*03/DRB1*04 haplotype marker). Data on serological tests, biopsy results, symptomatology and incidence of CD-associated diseases were collected by using a previously validated questionnaire. Results It was found that 98% of patients presented at least one copy of the studied alleles. Patients carrying simultaneously both HLA-DQ2 risk alleles were highly prevalent (75%), and 20.7% patients carried the HLA-DQ8 haplotype. Positive patients for both HLA-DQ2 risk alleles presented positive association to anti-gliadin (p=0.037), anti-endomysium (p=0.001) and anti-transglutaminase (p=0.032) serological tests, and a higher prevalence of osteoporosis and hypothyroidism. Patients carrying one or none of those alleles often presented negative serological results. In addition, it was found an association between intestinal injury severity and genetic profile (No-BreakpNo-Break&lt;0.001). Conclusion Results suggest that the HLA-DQ genotyping are associated to serological tests and the severity of intestinal damage in celiac disease patients.

Insights to HIV-1 coreceptor usage by estimating HLA adaptation with Bayesian generalized linear mixed models.

The mechanisms triggering the human immunodeficiency virus type I (HIV-1) to switch the coreceptor usage from CCR5 to CXCR4 during the course of infection are not entirely understood. While low CD4+ T cell counts are associated with CXCR4 usage, a predominance of CXCR4 usage with still high CD4+ T cell counts remains puzzling. Here, we explore the hypothesis that viral adaptation to the human leukocyte antigen (HLA) complex, especially to the HLA class II alleles, contributes to the coreceptor switch. To this end, we sequence the viral gag and env protein with corresponding HLA class I and II alleles of a new cohort of 312 treatment-naive, subtype C, chronically-infected HIV-1 patients from South Africa. To estimate HLA adaptation, we develop a novel computational approach using Bayesian generalized linear mixed models (GLMMs). Our model allows to consider the entire HLA repertoire without restricting the model to pre-learned HLA-polymorphisms. In addition, we correct for phylogenetic relatedness of the viruses within the model itself to account for founder effects. Using our model, we observe that CXCR4-using variants are more adapted than CCR5-using variants (p-value = 1.34e-2). Additionally, adapted CCR5-using variants have a significantly lower predicted false positive rate (FPR) by the geno2pheno[coreceptor] tool compared to the non-adapted CCR5-using variants (p-value = 2.21e-2), where a low FPR is associated with CXCR4 usage. Consequently, estimating HLA adaptation can be an asset in predicting not only coreceptor usage, but also an approaching coreceptor switch in CCR5-using variants. We propose the usage of Bayesian GLMMs for modeling virus-host adaptation in general.

Systematic discovery of neoepitope–HLA pairs for neoantigens shared among patients and tumor types

The broad application of precision cancer immunotherapies is limited by the number of validated neoepitopes that are common among patients or tumor types. To expand the known repertoire of shared neoantigen–human leukocyte antigen (HLA) complexes, we developed a high-throughput platform that coupled an in vitro peptide–HLA binding assay with engineered cellular models expressing individual HLA alleles in combination with a concatenated transgene harboring 47 common cancer neoantigens. From more than 24,000 possible neoepitope–HLA combinations, biochemical and computational assessment yielded 844 unique candidates, of which 86 were verified after immunoprecipitation mass spectrometry analyses of engineered, monoallelic cell lines. To evaluate the potential for immunogenicity, we identified T cell receptors that recognized select neoepitope–HLA pairs and elicited a response after introduction into human T cells. These cellular systems and our data on therapeutically relevant neoepitopes in their HLA contexts will aid researchers studying antigen processing as well as neoepitope targeting therapies.

Thalassemia, biobanking infrastructures, and personalized stem cell therapies in Chennai.

Thalassemia and leukemia and related blood disorders are approved for blood stem cell transplants in India, for a stem cell transplant to be successful, the human leukocyte antigen (HLA) complex located on the arm of chromosome six must be a match between the cord blood donor and the recipient. In the quest to find an exact blood stem cell match for an individual, the HLA becomes the node at the center of community genetics where the HLA match is sought (not necessarily successful) in the extended family, the same caste, language, and ethnic (both national and the diaspora) groups. By considering thalassemia as a case study, how do we understand personalized stem cell therapies within biobanking infrastructures in Chennai? How do social categories get entwined with biological materials like cord blood?

A phase 1 dose-escalation and expansion study of CUE-101, a novel HPV16 E7-pHLA-IL2-Fc fusion protein, given as monotherapy and in combination with pembrolizumab in patients with recurrent/metastatic HPV16+ head and neck cancer.

6013 Background: Immuno-STATs are modular T cell engagers engineered to selectively activate tumor-antigen specific CD8+ T cells via targeted delivery of cytokines. CUE-101, the first Immuno-STAT in clinical trials, is composed of a human leukocyte antigen (HLA) complex, HLA-A*0201, a peptide epitope derived from the HPV16 E7 protein, and 4 molecules of attenuated human interleukin-2 (IL-2) designed to bind, expand, and activate HPV16-specific CD8+ T cells for the treatment of HPV16+ cancers. Methods: CUE-101-01 is an ongoing first-in-human study in HLA-A*0201 patients with HPV16+ recurrent/metastatic head and neck squamous cell carcinoma (R/M HNSCC). Escalating doses of CUE-101 monotherapy (0.06 mg/kg to 8 mg/kg) and in combination with pembrolizumab (1 mg/kg to 4 mg/kg + 200 mg pembrolizumab) were evaluated, followed by expanded enrollment at the recommended phase 2 dose (RP2D). Patients with R/M HNSCC refractory to ≥ 1 platinum-based or checkpoint inhibitor therapy received CUE-101 monotherapy. Patients with previously untreated PD-L1+ R/M HNSCC received CUE-101 + pembrolizumab as first-line treatment. Therapy was administered every 3 weeks until disease progression or intolerable toxicity. Safety, pharmacokinetics (PK), pharmacodynamics (PD), and antitumor activity were assessed. Results: As of January 12, 2023, 67 patients were enrolled. A MTD was not established in monotherapy or combination-treated patients; 4 mg/kg of CUE-101, alone or in combination with pembrolizumab, was chosen as the RP2D dose in both cohorts. Monotherapy RP2D enrollment is complete and combination RP2D enrollment is ongoing. Frequent adverse events include fatigue (45%), anemia (34%), chills (27%), infusion related reactions (25%), constipation (22%), lymphopenia (22%) and nausea (22%). CUE-101 PK data demonstrate dose-dependent increases in drug exposure sustained with repeat dosing. PD data demonstrate selective expansion of HPV-16 E711-20-specific CD8+ T cells, sustained increase in NK cells and transient increase in Treg cells. Among 19 evaluable monotherapy RP2D patients, 1 PR and 6 durable SD (SD ≥ 12 weeks) were observed, with mOS of 24.4 months (9.1, NA). Among 12 evaluable RP2D combination patients to date, 5 PRs, and 2 durable SDs have been observed, with 71% (5/7) of patients expressing PD-L1 CPS ≤ 20. Conclusions: CUE-101 facilitates the targeted delivery of high concentrations of IL-2 to relevant tumor-specific CD8+ T cells. We demonstrate safety and tolerability with encouraging PD signals and antitumor activity with monotherapy and in combination with pembrolizumab in HPV+ R/M HNSCC patients. Enrollment continues in the CUE-101 and pembrolizumab combination cohort. Clinical trial information: Clinical trial information: NCT03978689 .

Development of mouse models with restricted HLA-B∗57:01 presentation for the study of flucloxacillin-driven T-cell activation and tolerance in liver injury

Flucloxacillin (FLX)-induced liver injury is immune-mediated and highly associated to HLA-B∗57:01 expression. Host factors leading to drug-induced liver injury are not yet well understood. Characterize invivo immune mechanisms determining the development of CD8+ T cells reactive to FLX in animals expressing the risk human leukocyte antigen (HLA) allotype. HLA-B∗57:01 transgenic mice (Tg) or Tg strains with H2-KbDb knockout (Tg/KO) or H2-KbDb/PD-1 double knockout (Tg/DKO) were treated with drug and/or anti-CD4 antibody. Drug-induced liver injury was evaluated on the basis of liver enzyme and histologic changes at day 10 of treatment. FLX-reactive CD8+ T cells were characterized invitro by release of effector molecules on drug restimulation, gene expression, and flow cytometry analysis, and functionality tested for hepatic cytotoxicity. CD8+ T-cell responses to FLX in Tg were dependent on both HLA and mouse major histocompatibility complex I presentation and invivo priming. Eliminating H2-KbDb in Tg/KO to allow exclusive presentation of FLX by HLA resulted in a less robust drug-specific CD8+T-cell response unless CD4+ cells, including regulatory T cells, were depleted. Treatment of Tg/KO with anti-CD4 antibody and FLX led to subclinical liver inflammation associated with an increase in PD1+CD8+ T cells in the lymphoid organs and liver. Impaired PD-1 expression in Tg/DKO led to liver histopathologic and transcriptional alterations but without hepatic enzyme elevations. Moreover, effector lymphocytes accumulated in the liver and showed FLX-dependent hepatic cytotoxicity invitro when tolerogenic liver cells were depleted. In our invivo models, FLX primes CD8+ T cells to recognize drug presented by HLA-B∗57:01 and murine major histocompatibility complex I. HLA-B∗57:01-dependent CD8+ T-cell reaction to FLX is limited by the presence of CD4+ cells, presumably regulatory T cells, and PD-1 expression. Tolerogenic hepatic cells limit clinical disease through PD-L1 or additional unexplored mechanisms.

Abstract 3013: The immunogenetic basis of hepatitis B virus-related hepatocellular carcinoma

Abstract Background: The reported associations of genetic variants within the human leukocyte antigen (HLA) region with hepatis B virus (HBV)-related hepatocellular carcinoma (HCC) are not consistent, and the structure-function patterns involved in this disease remain unclear. Methods: Utilizing genotype data from 706 HBV-related HCC cases and 6197 chronic HBV carriers without HCC collected from three resources in Taiwan, we imputed the classical HLA alleles at 2-field resolution and analyzed the molecular landscape of HLA complexes by deeply dissecting their genotypic configurations, functional divergence, and HBV-antigen binding capabilities in associations with the HCC risk. Logistic regression models were used, and all models were adjusted for sex, age, and population structure using the top 10 principal components. We also tested the underlying biological implications of our findings by investigating the HLA binding affinities and HLA effect on control of viral replication (i.e, HBV DNA load), viral population diversity (i.e, quasispecies), and inflammation (i.e, chemokines, cytokines, and soluble programmed cell death 1 [sPD-1]-associated T cell exhaustion). Results: We found high accuracy (≥95% concordance) of HLA imputation at all HLA class I and class II alleles. The strongest evidence for an association with HCC was observed for HLA-DQB1*03:01 (adjusted OR= 1.35 in an additive genetic model, P=1.3×10-6). Three amino acids at specific positions within or near the peptide-binding groove of DQB1 molecules might explain the observed allele association, which leads to loss of binding HBV nucleocapsid protein (i.e., low binding affinity predicted by NetMHCIIpan 4.0 for HLA-DQB1*03:01). HLA-DQB1*03:01 was significantly associated with a higher HBV DNA load (P= 4.3×10-4) and an increased level of serum sPD-1 (P=6.8×10-4), but not with increased levels of chemokines, cytokines, and viral complexity (i.e., Shannon entropy for HBV quasispecies, all P values&amp;gt;0.05). Analysis of HLA zygosity confirmed that HLA-DQB1 heterozygosity was associated with a decreased risk of HCC (adjusted OR=0.77, P= 0.015). Analysis of HLA evolutionary divergence (HED) showed that high HED at HLA-DRB1 loci was marginally associated with a decreased risk of HCC among HLA-DQB1*03:01 non-carriers (P=0.05). Conclusion: Our data shed light on the immunogenetic risk associated with HBV-related HCC. The effect of HLA-DQB1*03:01 could be partly explained by its low binding affinity with HBV nucleocapsid antigen, and/or its effect on viral load control and sPD-1, but not by its control on other inflammation markers (chemokines and cytokines) and viral population diversity. The association between HLA-DQB1 heterozygosity and HCC risk could be independent of the HLA-DQB1*03:01 effect, which indicates underlying mechanisms related to increased immunosurveillance in clearing potential viral antigens or neoantigens. Citation Format: Zhiwei Liu, Chih-Jen Huang, Yu-Han Huang, Mei-Hung Pan, Mei-Hsuan Lee, Mathias Viard, Allan Hildesheim, Ruth M. Pfeiffer, Mary Carrington, Chien-Jen Chen, Tobias L. Lenz, Hwai-I Yang. The immunogenetic basis of hepatitis B virus-related hepatocellular carcinoma [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 3013.

Relationship between cerebrovascular diseases and human leukocyte antigen subgroups

Purpose: Ischemic stroke is classified as large artery atherosclerosis, small vessel occlusion (lacunar infarcts), ischemic stroke due to other identified causes, and cryptogenic. The human leukocyte antigen (HLA) complex is a group of genes on chromosome six in humans responsible for encoding cell-surface proteins that regulate the immune system. In this study, HLA’s roles in the pathophysiology of ischemic stroke, especially the lacunar subgroup, are investigated, and their potential mechanisms are presented.&#x0D; Materials and methods: This study consisted of 49 patients with ischemic stroke and 50 healthy participants. HLA-A, HLA-B, HLA-C, HLA-DQB, and HLA-DRB subgroup genomes were assessed.&#x0D; Results: A statistically significant difference in the presence of HLA-A, HLA-B, HLA-C, HLA-DQB, and HLA-DRB subgroups was found between the control and patient groups. The presence of HLA-A*02, HLA-A*30, HLA-B*08, HLA-B*15, and HLA-DQB*06 genomes was higher in the patient group than in the control group (p≤0.05). Nevertheless, HLA-DQB*03 and HLA-DRB*11 genomes were found more in the control group than the patient group (p≤0.05)&#x0D; Conclusion: The results of this study pioneered in scrutinizing HLA alleles in small vascular disease (SVD). HLA-A*01, HLA-A*30, HLA-B*08, HLA-B*15, HLA-DQB*06, HLA-DQB*03 and HLA-DRB*11 are associated with HLA alleles of stroke patients with small vessel occlusion. We attempted to provide objective evidence for whether HLA genomes could act as a discriminative factor between SVD patients and control groups, which might hold considerable promise for future therapies.

Genome-wide association study of the age of onset of type 1 diabetes reveals HTATIP2 as a novel T cell regulator.

Type 1 diabetes, a disorder caused by autoimmune destruction of pancreatic insulin-producing cells, is more difficult to manage when it presents at a younger age. We sought to identify genetic correlates of the age of onset by conducting the first genome-wide association study (GWAS) treating the age of first diagnosis as a quantitative trait. We performed GWAS with a discovery cohort of 4,014 cases and a replication cohort of 493 independent cases. Genome-wide significant SNPs were mapped to a causal variant by Bayesian conditional analysis and gel shift assay. The causal protein-coding gene was identified and characterized by RNA interference treatment of primary human pan-CD4+ T cells with RNA-seq of the transcriptome. The candidate gene was evaluated functionally in primary cells by CD69 staining and proliferation assays. Our GWAS replicated the known association of the age of diagnosis with the human leukocyte antigen complex (HLA-DQB1). The second signal identified was in an intron of the NELL1 gene on chromosome 11 and fine-mapped to variant rs10833518 (P < 1.54 × 10-9). Homozygosity for the risk allele leads to average age of onset one year earlier. Knock-down of HIV TAT-interacting protein 2 (HTATIP2), but not other genes in the locus, resulted in alterations to gene expression in signal transduction pathways including MAP kinases and PI3-kinase. Higher levels of HTATIP2 expression are associated with increased viability, proliferation, and activation of T cells in the presence of signals from antigen and cytokine receptors. This study implicates HTATIP2 as a new type 1 diabetes gene acting via T cell regulation. Larger population sample sizes are expected to reveal additional loci.