Polymorphisms in genes in the human leukocyte antigen (HLA) class II region comprise the most important inherited risk factors for many autoimmune diseases, including type 1 diabetes (T1D) and celiac disease (CD): both diseases are positively associated with the HLA-DR3 haplotype ( DRB1*03:01-DQA1*05:01-DQB1*02:01 ). Studies of two different populations have recently documented that T1D susceptibility in HLA-DR3 homozygous individuals is stratified by a haplotype consisting of three single nucleotide polymorphisms (‘tri-SNP’) in intron 1 of the HLA-DRA gene. In this study, we use a large cohort from the longitudinal ‘The Environmental Determinants of Diabetes in the Young’ (TEDDY) study to further refine the tri-SNP association with T1D and with autoantibody-defined T1D endotypes. We found that the tri-SNP association is primarily in subjects whose first-appearing T1D autoantibody is to insulin. In addition, we discovered that the tri-SNP is also associated with CD, and that the particular tri-SNP haplotype (‘101’) that is negatively associated with T1D risk is positively associated with risk for CD. The opposite effect of the tri-SNP haplotype on two DR3-associated diseases can enhance and refine current models of disease prediction based on genetic risk. Finally, we investigated possible functional differences between the individuals carrying high and low-risk tri-SNP haplotypes and found that differences in complement system genes C4A and C4B may underlie the observed divergence in disease risk.

Polymorphisms in genes in the human leukocyte antigen (HLA) class II region comprise the most important inherited risk factors for many autoimmune diseases, including type 1 diabetes (T1D) and celiac disease (CD): both diseases are positively associated with the HLA-DR3 haplotype (DRB1*03:01-DQA1*05:01-DQB1*02:01). Studies of two different populations have recently documented that T1D susceptibility in HLA-DR3 homozygous individuals is stratified by a haplotype consisting of three single nucleotide polymorphisms ('tri-SNP') in intron 1 of the HLA-DRA gene. In this study, we use a large cohort from the longitudinal 'The Environmental Determinants of Diabetes in the Young' (TEDDY) study to further refine the tri-SNP association with T1D and with autoantibody-defined T1D endotypes. We found that the tri-SNP association is primarily in subjects whose first-appearing T1D autoantibody is to insulin. In addition, we discovered that the tri-SNP is also associated with CD, and that the particular tri-SNP haplotype ('101') that is negatively associated with T1D risk is positively associated with risk for CD. The opposite effect of the tri-SNP haplotype on two DR3-associated diseases can enhance and refine current models of disease prediction based on genetic risk. Finally, we investigated possible functional differences between the individuals carrying high and low-risk tri-SNP haplotypes and found that differences in complement system genes C4A and C4B may underlie the observed divergence in disease risk.

Multiple sclerosis (MS), which can lead to severe physical or cognitive disability and neurological deficits, is a chronic autoimmune disease affecting the central nervous system (CNS). The etiology and pathogenesis of MS remain unclear; nonetheless, it is asserted that its cause is complex, with genetic predisposition playing a significant role. In this study, our aim was to analyze the relationship between MS and HLA-DRA (rs3135388 and rs3135391), HLA-DQA1 (rs9272346) and IL-6 (rs1800795 and rs1900796) gene polymorphisms, which play an important role in inflammation and immune response. The study included 100 healthy controls and 98 MS patients. Real-time polymerase chain reaction (RT-PCR) was used to analyze variations in rs3135388 and rs3135391 in the HLA-DRA gene, rs9272346 in the HLA-DQA1 gene, and rs1800795 and rs1900796 in the IL-6 gene following DNA isolation from peripheral blood. Statistical techniques were applied to assess the outcomes. The results showed a significant difference in IL-6 (rs1800796) G/C (p = 0.024) between the patient and control groups when genotypes and allele distributions were analyzed. HLA-DQA1 (rs9272346) and HLA-DRA (rs3135388 and rs3135391) variations did not substantially differ between the two groups. Similarly, no significant difference was found between the two groups in VitD, B12 and folic acid parameters, and there was no relationship between these parameters and genotypes. There is evidence suggesting a significant association between IL-6 (rs1800796) polymorphisms and MS. IL-6 (rs1800796) GC genotype may be associated with disease susceptibility or risk. This should be taken into account in association and intervention studies on MS.

The exact pathogenesis of Kawasaki disease (KD) is unknown despite extensive research in the area. Several studies have also implicated CD8+ T lymphocytes in the pathogenesis of KD. However, studies on the activation status of T lymphocytes have shown conflicting results. In this prospective study, early (CD69) and late activation (HLA-DR) markers were assessed in T lymphocytes by flow cytometry. We assessed serum levels of soluble CD25 (sCD25) by enzyme-linked immunosorbent assay. We compared these activation markers between children with KD (n = 10), febrile controls (n = 9), and healthy controls (n = 10). Furthermore, we studied the HLA-DRA and HLA-DRB gene expression in subgroups of KD with or without coronary artery aneurysms (CAAs). A significantly higher percentage of CD69 in CD3+ and CD3 + CD4+ T lymphocytes was noted in KD and febrile controls compared with healthy controls. We found no significant increase in late activation marker HLA-DR in CD3, CD3 + CD4+, and CD3 + CD8+ lymphocytes between KD, febrile, and healthy controls. We observed higher levels of sCD25 in KD and febrile controls than in healthy controls. Longitudinal follow-up in KD showed a decreasing trend of CD69 expression in CD3 + CD8+ lymphocytes and sCD25 levels over time. HLA-DRA and HLABRB expression was comparable between children with CAAs and those without CAAs. Our study showed early but not late activation of T lymphocytes in children with KD. Markers of lymphocyte activation do fall with subsidence of systemic inflammation following intravenous immunoglobulin therapy in KD.

Multiple sclerosis (MS) is among the most common autoimmune disorders and is characterized by inflammation and degeneration affecting the central nervous system. Glatiramer acetate (GA) is an immunomodulatory drug utilized for treating relapsing-remitting MS. However, a considerable number of patients do not exhibit an appropriate response to this drug. This condition is known as GA resistance. This study aimed to investigate the relationship between nucleotide variations in the HLA-DRA, HLA-DQA1 and IL-6 genes and GA resistance. Additionally, the relationship of environmental factors with MS was investigated. One hundred thirty-nine MS patients were enrolled in this study. Patients were divided into two groups: non-responders (n = 58) and responders (n = 81). After DNA was isolated from peripheral blood, the rs3135388 and rs3135391 variations in HLA-DRA, the rs9272346 variation in HLA-DQA1, and the rs1800795 and rs1900796 variations in IL-6 were analyzed by Real-Time Polymerase Chain Reaction (RT-PCR). At the end of the study, it was found that the number of females was approximately 3 times greater in responders and 4 times greater in non-responders than in males. When nucleotide variations and allele distributions were compared between the groups, no significant relationships were found. Similarly, no significant relationship was found between risk factors and nucleotide variations. However, in non-responders, the expanded disability status scale and lesion load were found to be significantly high. In conclusion, by increasing the number of patients, more meaningful results can be achieved in future studies. Elucidating the pharmacogenetic characteristics (the drug-gene relationship) of MS patients using GA could lead to the development of personalized treatment strategies.

Hypoimmunogenic universal induced pluripotent stemn (iPS) cells were generated through the targeted disruption of key genes, including human leukocyte antigen (HLA)-A, HLA-B and HLA-DR alpha (DRA), using the CRISPR–Cas9 system. This approach aimed to minimize immune recognition and enhance the potential of iPS cells for allogeneic therapy. Heterozygous iPS cells were used for guide RNA design and validation to facilitate the knockout (KO) of the HLA-A, HLA-B and HLA-DRA genes. The electroporation of iPS cells using the selected guide RNAs enabled the generation of triple-KO iPS cells, followed by single-cell cloning for clone selection. Clone A7, an iPS cell with targeted KOs of the HLA-A, HLA-B and HLA-DRA genes, was identified as the final candidate. Messenger RNA analysis revealed robust expression of pluripotency markers, such as octamer-binding transcription factor 4, sex-determining region Y box 2, Krüppel-like factor 4, Lin-28 homolog A and Nanog homeobox, while protein expression assays confirmed the presence of octamer-binding transcription factor 4, stage-specific embryonic antigen 4, Nanog homeobox and tumor rejection antigen 1–60. A karyotype examination revealed no anomalies, and three-germ layer differentiation assays confirmed the differentiation potential. After interferon gamma stimulation, the gene-corrected clone A7 lacked HLA-A, HLA-B and HLA-DR protein expression. Immunogenicity testing further confirmed the hypoimmunogenicity of clone A7, which was evidenced by the absence of proliferation in central memory T cells and effector memory T cells. In conclusion, clone A7, a triple-KO iPS cell clone that demonstrates immune evasion properties, retained its intrinsic iPS cell characteristics and exhibited no immunogenicity.

Identification of gene signature markers in gestational hypertension and early-onset pre-eclampsia

Sarcoidosis is a complex systemic disease. Our study aimed to (1) identify novel alleles associated with sarcoidosis susceptibility; (2) provide an in-depth evaluation of HLA alleles and sarcoidosis susceptibility and (3) integrate genetic and transcription data to identify risk loci that may more directly impact disease pathogenesis. We report a genome-wide association study of 1335 sarcoidosis cases and 1264 controls of European descent (EA) and investigate associated alleles in a study of African Americans (AA: 1487 cases and 1504 controls). The EA and AA cohort was recruited from multiple United States sites. HLA alleles were imputed and tested for association with sarcoidosis susceptibility. Expression quantitative locus and colocalization analysis were performed using a subset of subjects with transcriptome data. Forty-nine SNPs in the HLA region in HLA-DRA, -DRB9, -DRB5, -DQA1 and BRD2 genes were significantly associated with sarcoidosis susceptibility in EA, rs3129888 was also a risk variant for sarcoidosis in AA. Classical HLA alleles DRB1*0101, DQA1*0101 and DQB1*0501, which are highly correlated, were also associated with sarcoidosis. rs3135287 near HLA-DRA was associated with HLA-DRA expression in peripheral blood mononuclear cells and bronchoalveolar lavage from subjects and lung tissue and whole blood from GTEx. We identified six novel SNPs (out of the seven SNPs representing the 49 significant SNPs) and nine HLA alleles associated with sarcoidosis susceptibility in the largest EA population. We also replicated our findings in an AA population. Our study reiterates the potential role of antigen recognition and/or presentation HLA class II genes in sarcoidosis pathogenesis.

Polymorphisms in genes in the human leukocyte antigen (HLA) class II region comprise the most important inherited risk factors for many autoimmune diseases, including type 1 diabetes (T1D) and celiac disease (CD): both diseases are positively associated with the HLA-DR3 haplotype (DRB1*03:01-DQA1*05:01-DQB1*02:01). Studies of two different populations have recently documented that T1D susceptibility in HLA-DR3 homozygous individuals is stratified by a haplotype consisting of three single nucleotide polymorphisms (‘tri-SNP’) in intron 1 of the HLA-DRA gene. In this study, we use a large cohort from the longitudinal ‘The Environmental Determinants of Diabetes in the Young’ (TEDDY) study to further refine the tri-SNP association with T1D and with autoantibody-defined T1D endotypes. We found that the tri-SNP association is primarily in subjects whose first-appearing T1D autoantibody is to insulin. In addition, we discovered that the tri-SNP is also associated with CD, and that the particular tri-SNP haplotype (‘101’) that is negatively associated with T1D risk is positively associated with risk for CD. The opposite effect of the tri-SNP haplotype on two DR3-associated diseases can enhance and refine current models of disease prediction based on genetic risk. Finally, we investigated possible functional differences between the individuals carrying high and low-risk tri-SNP haplotypes and found that differences in complement system genes C4A and C4B may underlie the observed divergence in disease risk.

SummaryBackgroundMass vaccination has dramatically reduced the incidence of severe COVID-19, with most cases now presenting as self-limiting upper respiratory tract infections. However, those with co-morbidities, the elderly and immunocompromised, as well as the unvaccinated, remain disproportionately vulnerable to severe COVID-19 and its sequelae. Furthermore, as the effectiveness of vaccination wanes with time, immune escape SARS-CoV-2 variants could emerge to cause severe COVID-19. Reliable prognostic biomarkers for severe disease could be used as early indicator of re-emergence of severe COVID-19 as well as for triaging of patients for antiviral therapy.MethodsWe performed a systematic review and re-analysis of 7 publicly available datasets, analysing a total of 140 severe and 181 mild COVID-19 patients, to determine the most consistent differentially regulated genes in peripheral blood of severe COVID-19 patients. In addition, we included an independent cohort where blood transcriptomics of COVID-19 patients were prospectively and longitudinally monitored previously, to track the time in which these gene expression changes occur before nadir of respiratory function. Single cell RNA-sequencing of peripheral blood mononuclear cells from publicly available datasets was then used to determine the immune cell subsets involved.FindingsThe most consistent differentially regulated genes in peripheral blood of severe COVID-19 patients were MCEMP1, HLA-DRA and ETS1 across the 7 transcriptomics datasets. Moreover, we found significantly heightened MCEMP1 and reduced HLA-DRA expression as early as four days before the nadir of respiratory function, and the differential expression of MCEMP1 and HLA-DRA occurred predominantly in CD14+ cells. The online platform which we developed is publicly available at https://kuanrongchan-covid19-severity-app-t7l38g.streamlitapp.com/, for users to query gene expression differences between severe and mild COVID-19 patients in these datasets.InterpretationElevated MCEMP1 and reduced HLA-DRA gene expression in CD14+ cells during the early phase of disease are prognostic of severe COVID-19.FundingK.R.C is funded by the 10.13039/501100001349National Medical Research Council (NMRC) of Singapore under the Open Fund Individual Research Grant (MOH-000610). E.E.O. is funded by the 10.13039/501100001349NMRC Senior Clinician-Scientist Award (MOH-000135-00). J.G.H.L. is funded by the 10.13039/501100001349NMRC under the Clinician-Scientist Award (NMRC/CSAINV/013/2016-01). S.K. is funded by the 10.13039/501100001349NMRC under the Transition Award. This study was sponsored in part by a generous gift from The Hour Glass.

Human leucocyte antigen DRβ3 is associated with specific autoimmune thyroid disease and plays a vital role in the progression of Grave’s disease. The available crystallographic structure of the HLA DRA, DRβ3*0101, was selected and used to generate mutation at position 57 from valine amino acid to Aspartic acid (D), Glutamic acid (E), Alanine (A), and Serine (S) amino acids by computational modeling approach. Mutant models were minimized, and stable conformation was chosen based on the lowest root mean square deviation value. Molecular docking assessed the best binding affinity of ligands C1, C2, C3, and C4 with wild-type and mutant HLA-DRβ3 models. Molecular dynamics simulation studies were executed to evaluate the stability of selected hits with wild-type and mutant dock complexes. The C3 has shown good binding affinity with wild-type and selected mutants; V57A, V57E, and V57D. Structural and molecular dynamics insights reveal the differences between wild-type and mutant-type HLA-DRβ3, which could help design novel antagonist molecules against autoimmune thyroid disorder. Communicated by Ramaswamy H. Sarma

Abstract The genetic etiology for Hodgkin lymphoma (HL) has been investigated with findings reported in both human leukocyte antigens (HLA) and non-HLA genomic regions. However, results of genetic association studies that focus on HL developed among children and adolescent individuals are limited. Given the historically high survival rate, it is reasonable to leverage available genetic data for survivors of childhood/adolescent HL for this investigation. Utilizing existing data from the St. Jude Lifetime Cohort, the Childhood Cancer Survivor Study (CCSS) original cohort and CCSS expansion cohort, we performed a fixed-effects meta-analysis of three genome-wide association studies for a total of 1,286 HL cases, 6,824 other childhood cancer cases and 373 non-cancer controls, all of whom are of European ancestry. Three independent SNPs in the HLA locus (rs28383311, Odds Ratio [OR] = 1.80, P = 2.14×10-21; rs3129198, OR = 1.52, P = 2.05×10-14; rs3129890, OR = 1.51, P = 6.21×10-13) were identified using step-wise conditional logistic regression. HLA SNP rs28383311 had a moderate correlation (r2 = 0.46) with rs2858870 reported previously by Cozen et al. (Blood, 2012) in the HLA-DRA gene region in adolescent/young adults onset HL. HLA SNP rs3129198 had a perfect correlation (r2 = 1.0) with rs2281389 (HLA-DPB1) reported previously by Moutsianas et al. (Blood, 2011) in mostly adults-onset HL. In contrast, SNP rs3129890 had a low correlation (r2 = 0.15) with rs2395185 (HLA-DRA) reported previously by Urayama et al. (JNCI, 2012) in HL cases diagnosed across a wide age range between 16 and 80 years old. Our analysis also identified additional SNPs for non-HLA loci at genome-wide significance level including: 1) rs1432297 (OR = 1.30, P = 2.5×10-8), which is in moderate correlation (r2=0.52) with previously reported rs1432295 (REL); 2) rs13279159 (OR = 1.32, P = 1.7×10-8), which is in high correlation (r2=0.75) with previously reported rs2019960 (PVT1); and 3) rs3824662 (OR = 1.52, P = 3.9×10-10), which had a high correlation (r2 = 0.91) with previously reported rs3781093 (GATA3). In addition, a novel uncommon SNP with a large effect size (rs117361561, OR = 1.95, P = 2.50×10-8, minor allele frequency = 0.02) was identified and mapped to PDGFD, a plausible gene for HL susceptibility. Twelve out 18 (67%) previously reported genome-wide significant non-HLA SNPs were replicated with P < 0.05 based on our meta-analysis. By analyzing early onset HL within pediatric and adolescent age range, we further dissected the associations in HLA locus by replicating three independent SNPs. We also found a novel non-HLA locus and replicated the majority of previous findings in the non-HLA region, suggesting mostly overlapping as well as potentially unique genetic etiology for HL risk across different ages of onset. Citation Format: Cheng Chen, Nan Song, Xiaojun Sun, Qian Dong, Zhenghong Li, Hui Wang, Smita Bhatia, Heather Mulder, John Easton, Jinghui Zhang, Yutaka Yasui, Gregory T. Armstrong, Kirsten K. Ness, Melissa M. Hudson, Leslie L. Robison, Zhaoming Wang. HLA and non-HLA associations with childhood and adolescent Hodgkin lymphoma risk [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 6344.

The Major Histocompatibility Complex (MHC) locus regulates the adaptive immune response and self-recognition and is the largest contributor to genetic risk of type 1 diabetes (T1D) . Protein-coding alleles in MHC class II and class I genes have long been known to contribute substantial T1D risk, yet whether additional variants affect T1D risk at this locus particularly in the non-coding genome has not been exhaustively evaluated. We therefore performed high-resolution fine-mapping of the MHC locus to identify additional coding and non-coding variants that contribute to T1D risk. We imputed genotypes for 39,270 samples from six European or American cohorts of T1D cases and controls into the T1DGC reference panel using SNP2HLA. We then performed two analyses to fine-map causal variants, first, stepwise conditional analysis using Firth bias-corrected logistic likelihood ratio test and second, iterative Bayesian stepwise selection analysis using the Sum of Single Effects (SuSiE) method. We identified 33 signals in stepwise conditional analysis with p<1×10-6 and 30 signals in SuSiE, where the results were highly concordant between methods. Both methods identified the known high-risk amino acid residue 57 of HLA-DQB1 as the top signal, as well as most known and several novel protein-coding risk and protective alleles in MHC class I and II genes. In addition, we identified multiple signals where the likely causal variant was non-coding and not linked to a protein-coding variant, including those that mapped to the LST1, HLA-DRA and NOTCH4 genes. We further annotated these non-coding signals using accessible chromatin, and several likely causal variants mapped in immune cell and/or pancreatic islet accessible chromatin. In ongoing analyses, we are replicating these signals in independent cohorts and performing molecular validation studies of their regulatory effects in relevant cell types. In total, high-resolution fine-mapping of the MHC locus identified additional T1D risk including in the non-coding genome. Disclosure C.Mcgrail: None. J.Chiou: Employee; Pfizer Inc. P.Benaglio: None. K.J.Gaulton: Consultant; Genentech, Inc., Stock/Shareholder; Neurocrine Biosciences, Inc., Vertex Pharmaceuticals Incorporated. Funding National Institutes of Health (DK120429) National Institutes of Health (DK122607)

Background Autoimmune thyroid disease (AITD), one of the most prevalent organ-specific autoimmune diseases, mainly includes Graves' disease (GD) and Hashimoto's thyroiditis (HT). This study was aimed at researching the association between AITD and single nucleotide polymorphisms (SNPs) of the HLA-DRA gene. Methods Using Hi-SNP high-throughput sequencing technology, we detected the distribution of three SNPs (rs3177928, rs7197, and rs3129878) of HLA-DRA genotypes in 1033 AITD patients (634 GD and 399 HT ones) and 791 healthy volunteers in Chinese Han Population. Chi-square test, multivariate logistic regression, and haplotype analysis were performed by SPSS and Haploview software to analyze the relationship between HLA-DRA gene polymorphisms and AITD. Results The results show that allele frequency and genotype distribution of rs3177928 and rs7197 were correlated with AITD and GD compared with the healthy control group, but not with HT. Rs3177928 and rs7197 were correlated with AITD and HT in the allele model, dominant model, and overdominant model before and after gender and age adjustment, but not with HT. In addition, we found that two loci (rs3177928 and rs7197) constituted a linkage disequilibrium (LD) region, and haplotype AA was associated with AITD and GD. However, we found no association between rs3129878 and AITD. Conclusion Our study is the first to find that rs3177928 and rs7197 of HLA-DRA are significantly correlated with AITD and GD in the Chinese Han population. This will help further reveal the pathogenesis of AITD and provide new candidate genes for the prediction or treatment of AITD.

Juvenile localized scleroderma (LS) is an autoimmune disease of the skin whose pathogenesis is not well understood due to the rarity of the disease. This study was undertaken to determine the skin transcriptome in skin biopsy tissue from children with juvenile LS compared to pediatric healthy controls, with identification of significant molecular targets using RNA sequencing (RNA-Seq). In this study, differentially expressed genes (DEGs) were assessed for correlations with histopathologic and clinical features in children with juvenile LS, and were used to group the children into distinct genetic clusters based on immunophenotype. RNA-Seq was performed on sections of paraffin-embedded skin tissue obtained from 28 children with juvenile LS and 10 pediatric healthy controls. RNA-Seq was carried out using an Illumina HTS TruSeq RNA Access library prep kit, with data aligned using STAR and data analysis using a DESeq2 platform. A standardized histologic scoring system was used to score skin sections for the severity of inflammation and levels of collagen deposition. Histologic scoring was completed by 2 pathologists who were blinded with regard to the status of each sample. Spearman's rank correlation coefficients were used to assess significant correlations between DEG expression profiles and skin histologic findings in patients with juvenile LS. We identified 589 significant DEGs in children with juvenile LS as compared to healthy controls. Hierarchical clustering was used to demonstrate 3 distinct juvenile LS immunophenotype clusters. The histologic scores of skin inflammation (based on numbers and categories of inflammatory cell infiltrates) were significantly correlated with the expression levels of HLA-DPB1, HLA-DQA2, HLA-DRA, and STAT1 genes (rs > 0.5, P < 0.01). Collagen thickness correlated with the expression levels of collagen organization genes as well as with genes found to be correlated with the severity of inflammation, including genes for major histocompatibility complex (MHC) class I, MHC class II, and interferon-γ signaling. Among children with juvenile LS, 3 distinct genetic signatures, or clusters, were identified. In one cluster, inflammation-related pathways were up-regulated, corresponding to the histologic skin inflammation score. In the second cluster, fibrosis-related pathways were up-regulated. In the third cluster, gene expression in the skin corresponded to the patterns seen in healthy controls. Up-regulation of HLA class II genes was observed within the first cluster (characterized by predominant inflammation), a feature that has also been observed in the peripheral blood of patients with morphea and in the skin of patients with systemic sclerosis.

Abstract The mechanistic investigations have defined that AXL inhibition reprograms the immunological microenvironment leading to increased T cells and antigen-presenting cells. However, previous reports did not clearly demonstrate the linchpin mechanism of anti-tumor effects with AXL inhibitors. It may be possible to elucidate the immunological mechanism of AXL inhibitor based on a comprehensive analysis of cell type-specific transcriptomic changes using scRNA-seq. The human CD34-NSG mice were engrafted LUSC tumor. These mice were divided into four dose groups: Vehicle, SKI-G-801, pembrolizumab, and combination groups. The tumor-associated cells were collected for flow cytometry and scRNA-seq analysis, and FFPE sample of tumor tissue was analyzed by a multispectral imager. The combination group demonstrated the superior anti-cancer efficacy to vehicle, pembrolizumab, and SKI-G-801 groups (all p&amp;lt;0.05). The scRNA-seq was performed with Seurat 4.0. The cells were separated into total 9 clusters. Following SKI-G-801 treatment, the T cells showed higher expressions of CD2, CCL5, CCL4, GZMA, and GZMB compared to both pembrolizumab and vehicle groups (both p&amp;lt;0.05). The gene expressions of CD2 and GZMA were higher than pembrolizumab and vehicle groups (both p&amp;lt;0.05). The CDR3 length differences of TCRs and diversity of T cell clones were higher increased in SKI-G-801, pembrolizumab and combination groups than vehicle group (p&amp;lt;0.05). In the macrophage cluster, the HLA-A, HLA-DRA, HLA-DRB1, and IL-1B genes were commonly expressed in SKI-G-801 and combination group (p&amp;lt;0.05). Mostly, the professional antigen-presenting macrophages (MHC class 2 protein complex high, p&amp;lt;0.05) were increased in the combination group. The combination effects between pembrolizumab and SKI-G-801 can be addressed by enhanced antigen presenting machinery, T cell activation and unique T cell clones. These transcriptomic results were highly correlated with the results of multispectral imaging and flow cytometry. Tumor infiltrations of helper T cells and cytotoxic T cells significantly increased in combination and SKI-G-801 groups (p &amp;lt; 0.01, p &amp;lt; 0.001 respectively). In multiplex IHC analysis, the proportion of CD4+ and CD8+ T cells were significantly increased in the tumor nest (both p&amp;lt;0.05), but the Tregs were not changed in the tumor nest which observations were validated by further flow cytometry analysis. A novel AXL inhibitor, SKI-G-801 drives priming of professional antigen-presenting cells and tumor-infiltrating T cells, leading to immunological synapsis for tumor killing, which is significantly enhanced by the combination with pembrolizumab. These results suggest the inhibition of AXL signal pathway by SKI-G-801 could confer a solid rationale for clinical investigation of lung cancer cells. Citation Format: Kyung-Ho Pyo, Hee Kyu Lee, Ha Ni Jo, Wongeun Lee, Seong Gu Heo, Sang Bin Lim, Dong Kwon Kim, Chun-Bong Synn, Youngseon Byeon, Young Seob Kim, Beung-Chul Ahn, Min Hee Hong, Sun Min Lim, Hye Ryun Kim, Byoung Chul Cho. Single-cell RNA sequencing reveals priming professional antigen-presenting macrophages and chemokine expressing T cells in tumor microenvironment by AXL inhibitor, SKI-G-801 [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2021; 2021 Apr 10-15 and May 17-21. Philadelphia (PA): AACR; Cancer Res 2021;81(13_Suppl):Abstract nr 2755.

Stem cells from fetal tissue protect against aging and possess greater proliferative capacity than their adult counterparts. These cells can more readily expand in vitro and senesce later in culture. However, the underlying molecular mechanisms for these differences are still not fully understood. In this study, we used a robust rank aggregation (RRA) method to discover robust differentially expressed genes (DEGs) between fetal bone marrow mesenchymal stem cells (fMSCs) and aged adult bone marrow mesenchymal stem cells (aMSCs). Multiple methods, including gene set enrichment analysis (GSEA), Gene Ontology (GO) analysis, and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis were performed for functional annotation of the robust DEGs, and the results were visualized using the R software. The hub genes and other genes with which they interacted directly were detected by protein–protein interaction (PPI) network analysis. Correlation of gene expression was measured by Pearson correlation coefficient. A total of 388 up-regulated and 289 down-regulated DEGs were identified between aMSCs and fMSCs. We found that the down-regulated genes were mainly involved in the cell cycle, telomerase activity, and stem cell proliferation. The up-regulated DEGs were associated with cell adhesion molecules, extracellular matrix (ECM)–receptor interactions, and the immune response. We screened out four hub genes, MYC, KIF20A, HLA-DRA, and HLA-DPA1, through PPI-network analysis. The MYC gene was negatively correlated with TXNIP, an age-related gene, and KIF20A was extensively involved in the cell cycle. The results suggested that MSCs derived from the bone marrow of an elderly donor present a pro-inflammatory phenotype compared with that of fMSCs, and the HLA-DRA and HLA-DPA1 genes are related to the immune response. These findings provide new insights into the differences between aMSCs and fMSCs and may suggest novel strategies for ex vivo expansion and application of adult MSCs.

Class II human leucocyte antigen (HLA) proteins are involved in the immune response by presenting pathogen-derived peptides to CD4+ T lymphocytes. At the molecular level, they are constituted by α/β-heterodimers on the surface of professional antigen-presenting cells. Here, we report that the acceptor variant (rs8084) in the HLA-DRA gene mediates the transcription of an alternative version of the α-chain lacking 25 amino acids in its extracellular domain. Molecular dynamics simulations suggest this isoform undergoes structural refolding which in turn affects its stability and cellular trafficking. The short HLA-DRA isoform cannot reach the cell surface, although it is still able to bind the corresponding β-chain. Conversely, it remains entrapped within the endoplasmic reticulum where it is targeted for degradation. Furthermore, we demonstrate that the short isoform can be transported to the cell membrane via interactions with the peptide-binding site of canonical HLA heterodimers. Altogether, our findings indicate that short HLA-DRA functions as a novel intact antigen for class II HLA molecules.

Multiple sclerosis (MS) is a common demyelinating neurodegenerative disorder with significant heritability. Previous studies have associated genetic variants in human leukocyte antigen (HLA) complex, IL2RA , and HMGB1 genes with the pathophysiology of MS. In order to investigate the gene association in the Iranian population, we performed a genotyping study of 36 variants in the mentioned genes using Sanger sequencing in 102 MS patients and 113 healthy controls. Our results identified significant associations as well as significant allele frequency differences in some of the studied single-nucleotide polymorphisms including rs4935356, rs3177928, and rs7197 from HLA-DRA gene, and rs12722489 and rs12722490 variants from IL2RA gene (p< 0.05). Moreover, the strong linkage disequilibrium of two common haplotypes was estimated from the HLA-DRA gene. This association study may suggest the role of these polymorphisms in the genetic susceptibility of MS in the Iranian population and would facilitate the recognition of causative variants in this disease.

Background Parkinson’s disease (PD) is a common progressive neurodegenerative disorder. Up to now, several single-nucleotide polymorphisms (SNPs) located in virulence gene sites have been reported linked to PD. Candidate gene association studies and genome-wide association studies have identified rs3129882, rs4248166 in HLA-DRA and rs34372695 in SYT11 as risk factors for familial or sporadic PD. However, the association between variants of HLA-DRA, SYT11 and PD are still controversial, especially in the Central Chinese population. We here performed a case-control study to investigate whether HLA-DRA and SYT11 genes could predispose to sporadic PD in the Chinese population. Methods We investigate 486 PD patients and 457 age- and sex-matched controls from Central China to assess this association. Results In the allele model, the odds ratio (OR) result of rs3129882 was 0.905 (p = 0.287). Moreover, no significant difference was observed in the association between rs424816 (OR = 0.864, p = 0.106) and rs34372695 (p = 1.0) with PD risk. Genotypic analysis in SNP rs3129882, rs4248166 and rs34372695 indicated no significant association with PD. Subgroup analysis of our data showed age-onset and gender were not associated with either genotype or minor allele frequencies of rs3129882 and rs4248166. Moreover, the negative results were also observed in a meta-analysis of studies of rs3129882 from mainland China and Taiwanese population. Conclusions Our results reveal that rs3129882, rs4248166 and rs34372695 do not confer significant risks for sporadic PD in the Central Chinese population.