Mineto Ota

All Publications

• Base-editing mutagenesis maps alleles to tune human T cell functions. Nature Schmidt, R., Ward, C. C., Dajani, R., Armour-Garb, Z., Ota, M., Allain, V., Hernandez, R., Layeghi, M., Xing, G., Goudy, L., Dorovskyi, D., Wang, C., Chen, Y. Y., Ye, C. J., Shy, B. R., Gilbert, L. A., Eyquem, J., Pritchard, J. K., Dodgson, S. E., Marson, A. 2023

  Abstract

  CRISPR-enabled screening is a powerful tool for the discovery of genes that control T cell function and has nominated candidate targets for immunotherapies1-6. However, new approaches are required to probe specific nucleotide sequences within key genes. Systematic mutagenesis in primary human T cells could reveal alleles that tune specific phenotypes. DNA base editors are powerful tools for introducing targeted mutations with high efficiency7,8. Here we develop a large-scale base-editing mutagenesis platform with the goal of pinpointing nucleotides that encode amino acid residues that tune primary human T cell activation responses. We generated a library of around 117,000 single guide RNA molecules targeting base editors to protein-coding sites across 385 genes implicated in T cell function and systematically identified protein domains and specific amino acid residues that regulate T cell activation and cytokine production. We found a broad spectrum of alleles with variants encoding critical residues in proteins including PIK3CD, VAV1, LCP2, PLCG1 and DGKZ, including both gain-of-function and loss-of-function mutations. We validated the functional effects of many alleles and further demonstrated that base-editing hits could positively and negatively tune T cell cytotoxic function. Finally, higher-resolution screening using a base editor with relaxed protospacer-adjacent motif requirements9 (NG versus NGG) revealed specific structural domains and protein-protein interaction sites that can be targeted to tune T cell functions. Base-editing screens in primary immune cells thus provide biochemical insights with the potential to accelerate immunotherapy design.

  View details for DOI 10.1038/s41586-023-06835-6

  View details for PubMedID 38093011

  View details for PubMedCentralID 6689405

• CRISPR screens decode cancer cell pathways that trigger γδ T cell detection. Nature Mamedov, M. R., Vedova, S., Freimer, J. W., Sahu, A. D., Ramesh, A., Arce, M. M., Meringa, A. D., Ota, M., Chen, P. A., Hanspers, K., Nguyen, V. Q., Takeshima, K. A., Rios, A. C., Pritchard, J. K., Kuball, J., Sebestyen, Z., Adams, E. J., Marson, A. 2023

  Abstract

  γδ T cells are potent anticancer effectors with the potential to target tumours broadly, independent of patient-specific neoantigens or human leukocyte antigen background1-5. γδ T cells can sense conserved cell stress signals prevalent in transformed cells2,3, although the mechanisms behind the targeting of stressed target cells remain poorly characterized. Vγ9Vδ2 T cells-the most abundant subset of human γδ T cells4-recognize a protein complex containing butyrophilin 2A1 (BTN2A1) and BTN3A1 (refs. 6-8), a widely expressed cell surface protein that is activated by phosphoantigens abundantly produced by tumour cells. Here we combined genome-wide CRISPR screens in target cancer cells to identify pathways that regulate γδ T cell killing and BTN3A cell surface expression. The screens showed previously unappreciated multilayered regulation of BTN3A abundance on the cell surface and triggering of γδ T cells through transcription, post-translational modifications and membrane trafficking. In addition, diverse genetic perturbations and inhibitors disrupting metabolic pathways in the cancer cells, particularly ATP-producing processes, were found to alter BTN3A levels. This induction of both BTN3A and BTN2A1 during metabolic crises is dependent on AMP-activated protein kinase (AMPK). Finally, small-molecule activation of AMPK in a cell line model and in patient-derived tumour organoids led to increased expression of the BTN2A1-BTN3A complex and increased Vγ9Vδ2 T cell receptor-mediated killing. This AMPK-dependent mechanism of metabolic stress-induced ligand upregulation deepens our understanding of γδ T cell stress surveillance and suggests new avenues available to enhance γδ T cell anticancer activity.

  View details for DOI 10.1038/s41586-023-06482-x

  View details for PubMedID 37648854

  View details for PubMedCentralID 7614706

• Multimodal repertoire analysis unveils B cell biology in immune-mediated diseases. Annals of the rheumatic diseases Ota, M., Nakano, M., Nagafuchi, Y., Kobayashi, S., Hatano, H., Yoshida, R., Akutsu, Y., Itamiya, T., Ban, N., Tsuchida, Y., Shoda, H., Yamamoto, K., Ishigaki, K., Okamura, T., Fujio, K. 2023

  Abstract

  OBJECTIVES: Despite the involvement of B cells in the pathogenesis of immune-mediated diseases (IMDs), biological mechanisms underlying their function are scarcely understood. To overcome this gap, here we constructed and investigated a large-scale repertoire catalogue of five B cell subsets of patients with IMDs.METHODS: We mapped B cell receptor regions from RNA sequencing data of sorted B cell subsets. Our dataset consisted of 595 donors under IMDs and health. We characterised the repertoire features from various aspects, including their association with immune cell transcriptomes and clinical features and their response to belimumab treatment.RESULTS: Heavy-chain complementarity-determining region 3 (CDR-H3) length among naive B cells was shortened among autoimmune diseases. Strong negative correlation between interferon signature strength and CDR-H3 length was observed in naive B cells and suggested the role for interferon in premature B cell development. VDJ gene usage was skewed especially in plasmablasts and unswitched-memory B cells of patients with systemic lupus erythematosus (SLE). We developed a scoring system to quantify this skewing, and it positively correlated with peripheral helper T cell transcriptomic signatures and negatively correlated with the amount of somatic hyper mutations in plasmablasts, suggesting the association of extrafollicular pathway. Further, this skewing led to high usage of IGHV4-34 gene with 9G4 idiotypes in unswitched-memory B cells, which showed a prominent positive correlation with disease activity in SLE. Gene usage skewing in unswitched-memory B cells was ameliorated after belimumab treatment.CONCLUSIONS: Our multimodal repertoire analysis enabled us the system-level understanding of B cell abnormality in diseases.

  View details for DOI 10.1136/ard-2023-224421

  View details for PubMedID 37468219

• Dynamic landscape of immune cell-specific gene regulation in immune-mediated diseases. Cell Ota, M., Nagafuchi, Y., Hatano, H., Ishigaki, K., Terao, C., Takeshima, Y., Yanaoka, H., Kobayashi, S., Okubo, M., Shirai, H., Sugimori, Y., Maeda, J., Nakano, M., Yamada, S., Yoshida, R., Tsuchiya, H., Tsuchida, Y., Akizuki, S., Yoshifuji, H., Ohmura, K., Mimori, T., Yoshida, K., Kurosaka, D., Okada, M., Setoguchi, K., Kaneko, H., Ban, N., Yabuki, N., Matsuki, K., Mutoh, H., Oyama, S., Okazaki, M., Tsunoda, H., Iwasaki, Y., Sumitomo, S., Shoda, H., Kochi, Y., Okada, Y., Yamamoto, K., Okamura, T., Fujio, K. 2021; 184 (11): 3006-3021.e17

  Abstract

  Genetic studies have revealed many variant loci that are associated with immune-mediated diseases. To elucidate the disease pathogenesis, it is essential to understand the function of these variants, especially under disease-associated conditions. Here, we performed a large-scale immune cell gene-expression analysis, together with whole-genome sequence analysis. Our dataset consists of 28 distinct immune cell subsets from 337 patients diagnosed with 10 categories of immune-mediated diseases and 79 healthy volunteers. Our dataset captured distinctive gene-expression profiles across immune cell types and diseases. Expression quantitative trait loci (eQTL) analysis revealed dynamic variations of eQTL effects in the context of immunological conditions, as well as cell types. These cell-type-specific and context-dependent eQTLs showed significant enrichment in immune disease-associated genetic variants, and they implicated the disease-relevant cell types, genes, and environment. This atlas deepens our understanding of the immunogenetic functions of disease-associated variants under in vivo disease conditions.

  View details for DOI 10.1016/j.cell.2021.03.056

  View details for PubMedID 33930287

• Gene regulatory network inference from CRISPR perturbations in primary CD4+ T cells elucidates the genomic basis of immune disease. Cell genomics Weinstock, J. S., Arce, M. M., Freimer, J. W., Ota, M., Marson, A., Battle, A., Pritchard, J. K. 2024: 100671

  Abstract

  The effects of genetic variation on complex traits act mainly through changes in gene regulation. Although many genetic variants have been linked to target genes in cis, the trans-regulatory cascade mediating their effects remains largely uncharacterized. Mapping trans-regulators based on natural genetic variation has been challenging due to small effects, but experimental perturbations offer a complementary approach. Using CRISPR, we knocked out 84 genes in primary CD4+ T cells, targeting inborn error of immunity (IEI) disease transcription factors (TFs) and TFs without immune disease association. We developed a novel gene network inference method called linear latent causal Bayes (LLCB) to estimate the network from perturbation data and observed 211 regulatory connections between genes. We characterized programs affected by the TFs, which we associated with immune genome-wide association study (GWAS) genes, finding that JAK-STAT family members are regulated by KMT2A, an epigenetic regulator. These analyses reveal the trans-regulatory cascades linking GWAS genes to signaling pathways.

  View details for DOI 10.1016/j.xgen.2024.100671

  View details for PubMedID 39395408

• An autoimmune transcriptional circuit drives FOXP3<SUP>+</SUP> regulatory T cell dysfunction SCIENCE TRANSLATIONAL MEDICINE Sumida, T. S., Lincoln, M. R., He, L., Park, Y., Ota, M., Oguchi, A., Son, R., Alice, Y., Stillwell, H. A., Leissa, G. A., Fujio, K., Murakawa, Y., Kulminski, A. M., Epstein, C. B., Bernstein, B. E., Kellis, M., Hafler, D. A. 2024; 16 (762): eadp1720

  Abstract

  Autoimmune diseases, among the most common disorders of young adults, are mediated by genetic and environmental factors. Although CD4+FOXP3+ regulatory T cells (Tregs) play a central role in preventing autoimmunity, the molecular mechanism underlying their dysfunction is unknown. Here, we performed comprehensive transcriptomic and epigenomic profiling of Tregs in the autoimmune disease multiple sclerosis (MS) to identify critical transcriptional programs regulating human autoimmunity. We found that up-regulation of a primate-specific short isoform of PR domain zinc finger protein 1 (PRDM1-S) induces expression of serum and glucocorticoid-regulated kinase 1 (SGK1) independent from the evolutionarily conserved long PRDM1, which led to destabilization of forkhead box P3 (FOXP3) and Treg dysfunction. This aberrant PRDM1-S/SGK1 axis is shared among other autoimmune diseases. Furthermore, the chromatin landscape profiling in Tregs from individuals with MS revealed enriched activating protein-1 (AP-1)/interferon regulatory factor (IRF) transcription factor binding as candidate upstream regulators of PRDM1-S expression and Treg dysfunction. Our study uncovers a mechanistic model where the evolutionary emergence of PRDM1-S and epigenetic priming of AP-1/IRF may be key drivers of dysfunctional Tregs in autoimmune diseases.

  View details for DOI 10.1126/scitranslmed.adp1720

  View details for Web of Science ID 001305380400001

  View details for PubMedID 39196959

• Age-associated CD4<SUP>+</SUP> T cells with B cell-promoting functions are regulated by ZEB2 in autoimmunity SCIENCE IMMUNOLOGY Goto, M., Takahashi, H., Yoshida, R., Itamiya, T., Nakano, M., Nagafuchi, Y., Harada, H., Shimizu, T., Maeda, M., Kubota, A., Toda, T., Hatano, H., Sugimori, Y., Kawahata, K., Yamamoto, K., Shoda, H., Ishigaki, K., Ota, M., Okamura, T., Fujio, K. 2024; 9 (93): eadk1643

  Abstract

  Aging is a significant risk factor for autoimmunity, and many autoimmune diseases tend to onset during adulthood. We conducted an extensive analysis of CD4+ T cell subsets from 354 patients with autoimmune disease and healthy controls via flow cytometry and bulk RNA sequencing. As a result, we identified a distinct CXCR3midCD4+ effector memory T cell subset that expands with age, which we designated "age-associated T helper (THA) cells." THA cells exhibited both a cytotoxic phenotype and B cell helper functions, and these features were regulated by the transcription factor ZEB2. Consistent with the highly skewed T cell receptor usage of THA cells, gene expression in THA cells from patients with systemic lupus erythematosus reflected disease activity and was affected by treatment with a calcineurin inhibitor. Moreover, analysis of single-cell RNA sequencing data revealed that THA cells infiltrate damaged organs in patients with autoimmune diseases. Together, our characterization of THA cells may facilitate improved understanding of the relationship between aging and autoimmune diseases.

  View details for DOI 10.1126/sciimmunol.adk1643

  View details for Web of Science ID 001194834100003

  View details for PubMedID 38330141

• Synovial Tissue Heterogeneity in Japanese Patients With Rheumatoid Arthritis Elucidated Using a Cell-Type Deconvolution Approach ARTHRITIS & RHEUMATOLOGY Nakajima, S., Tsuchiya, H., Ota, M., Ogawa, M., Yamada, S., Yoshida, R., Maeda, J., Shirai, H., Kasai, T., Hirose, J., Ninagawa, K., Fujieda, Y., Iwasaki, T., Aizaki, Y., Kajiyama, H., Matsushita, M., Kawakami, E., Tamura, N., Mimura, T., Ohmura, K., Morinobu, A., Atsumi, T., Tanaka, Y., Takeuchi, T., Tanaka, S., Okamura, T., Fujio, K. 2023

  Abstract

  Recent advances in single-cell RNA sequencing technology have improved our understanding of the immunological landscape of rheumatoid arthritis (RA). We aimed to stratify the synovium from East Asian patients with RA by immune cell compositions and gain insight into the inflammatory drivers of each synovial phenotype.Synovial tissues were obtained from East Asian patients in Japan with RA (n = 41) undergoing articular surgery. The cellular composition was quantified by a deconvolution approach using a public single-cell-based reference. Inflammatory pathway activity was calculated by gene set variation analysis, and chromatin accessibility was evaluated using assay of transposase accessible chromatin-sequencing.We stratified RA synovium into three distinct subtypes based on the hierarchical clustering of cellular composition data. One subtype was characterized by abundant HLA-DRAhigh synovial fibroblasts, autoimmune-associated B cells, GZMK+ GZMB+ CD8+ T cells, interleukin (IL)1-β+ monocytes, and plasmablasts. In addition, tumor necrosis factor (TNF)-α, interferons (IFNs), and IL-6 signaling were highly activated in this subtype, and the expression of various chemokines was significantly enhanced. Moreover, we found an open chromatin region overlapping with RA risk locus rs9405192 near the IRF4 gene, suggesting the genetic background influences the development of this inflammatory synovial state. The other two subtypes were characterized by increased IFNs and IL-6 signaling, and expression of molecules associated with degeneration, respectively.This study adds insights into the synovial heterogeneity in East Asian patients and shows a promising link with predominant inflammatory signals. Evaluating the site of inflammation has the potential to lead to appropriate drug selection that matches the individual pathology.

  View details for DOI 10.1002/art.42642

  View details for Web of Science ID 001099808100001

  View details for PubMedID 37390361

• Gene regulatory network inference from CRISPR perturbations in primary CD4+ T cells elucidates the genomic basis of immune disease. bioRxiv : the preprint server for biology Weinstock, J. S., Arce, M. M., Freimer, J. W., Ota, M., Marson, A., Battle, A., Pritchard, J. K. 2023

  Abstract

  The effects of genetic variation on complex traits act mainly through changes in gene regulation. Although many genetic variants have been linked to target genes in cis, the trans-regulatory cascade mediating their effects remains largely uncharacterized. Mapping trans-regulators based on natural genetic variation, including eQTL mapping, has been challenging due to small effects. Experimental perturbation approaches offer a complementary and powerful approach to mapping trans-regulators. We used CRISPR knockouts of 84 genes in primary CD4+ T cells to perturb an immune cell gene network, targeting both inborn error of immunity (IEI) disease transcription factors (TFs) and background TFs matched in constraint and expression level, but without a known immune disease association. We developed a novel Bayesian structure learning method called Linear Latent Causal Bayes (LLCB) to estimate the gene regulatory network from perturbation data and observed 211 directed edges among the genes which could not be detected in existing CD4+ trans-eQTL data. We used LLCB to characterize the differences between the IEI and background TFs, finding that the gene groups were highly interconnected, but that IEI TFs were much more likely to regulate immune cell specific pathways and immune GWAS genes. We further characterized nine coherent gene programs based on downstream effects of the TFs and linked these modules to regulation of GWAS genes, finding that canonical JAK-STAT family members are regulated by KMT2A, a global epigenetic regulator. These analyses reveal the trans-regulatory cascade from upstream epigenetic regulator to intermediate TFs to downstream effector cytokines and elucidate the logic linking immune GWAS genes to key signaling pathways.

  View details for DOI 10.1101/2023.09.17.557749

  View details for PubMedID 37745614

  View details for PubMedCentralID PMC10516010

• Functional evaluation of rare OASL variants by analysis of SLE patient-derived iPSCs JOURNAL OF AUTOIMMUNITY Natsumoto, B., Shoda, H., Nagafuchi, Y., Ota, M., Okumura, T., Horie, Y., Okamura, T., Yamamoto, K., Tsuji, M., Otsu, M., Taniguchi, H., Fujio, K. 2023; 139: 103085

  Abstract

  Systemic lupus erythematosus (SLE) is a chronic systemic autoimmune disease characterized by genetic heterogeneity and an interferon (IFN) signature. The overall landscapes of the heritability of SLE remains unclear.To identify and elucidate the biological functions of rare variants underlying SLE, we conducted analyses of patient-derived induced pluripotent stem cells (iPSCs) in combination with genetic analysis.Two familial SLE patient- and two healthy donor (HD)-derived iPSCs were established. Type 1 IFN-secreting dendritic cells (DCs) were differentiated from iPSCs. Genetic analyses of SLE-iPSCs, and 117 SLE patients and 107 HDs in the ImmuNexUT database were performed independently. Genome editing of the variants on iPSCs was performed with the CRISPR/Cas9 system.Type 1 IFN secretion was significantly increased in DCs differentiated from SLE-iPSCs compared to HD-iPSCs. Genetic analyses revealed a rare variant in the 2'-5'-Oligoadenylate Synthetase Like (OASL) shared between SLE-iPSCs and another independent SLE patient, and significant accumulation of OASL variants among SLE patients (HD 0.93%, SLE 6.84%, OR 8.387) in the database. Genome editing of mutated OASL 202Q to wild-type 202 R or wild-type OASL 202 R to mutated 202Q resulted in reduced or enhanced Type 1 IFN secretion of DCs. Three other OASL variants (R60W, T261S and A447V) accumulated in SLE patients had also capacities to enhance Type 1 IFN secretion in response to dsRNA.We established a patient-derived iPSC-based strategy to investigate the linkage of genotype and phenotype in autoimmune diseases. Detailed case-based investigations using patient-derived iPSCs provide information to unveil the heritability of the pathogenesis of autoimmune diseases.

  View details for DOI 10.1016/j.jaut.2023.103085

  View details for Web of Science ID 001031657200001

  View details for PubMedID 37354689

• Immunomics analysis of rheumatoid arthritis identified precursor dendritic cells as a key cell subset of treatment resistance ANNALS OF THE RHEUMATIC DISEASES Yamada, S., Nagafuchi, Y., Wang, M., Ota, M., Hatano, H., Takeshima, Y., Okubo, M., Kobayashi, S., Sugimori, Y., Masahiro, N., Yoshida, R., Hanata, N., Suwa, Y., Tsuchida, Y., Iwasaki, Y., Sumitomo, S., Kubo, K., Shimane, K., Setoguchi, K., Azuma, T., Kanda, H., Shoda, H., Zhang, X., Yamamoto, K., Ishigaki, K., Okamura, T., Fujio, K. 2023; 82 (6): 809-819

  Abstract

  Little is known about the immunology underlying variable treatment response in rheumatoid arthritis (RA). We performed large-scale transcriptome analyses of peripheral blood immune cell subsets to identify immune cells that predict treatment resistance.We isolated 18 peripheral blood immune cell subsets of 55 patients with RA requiring addition of new treatment and 39 healthy controls, and performed RNA sequencing. Transcriptome changes in RA and treatment effects were systematically characterised. Association between immune cell gene modules and treatment resistance was evaluated. We validated predictive value of identified parameters for treatment resistance using quantitative PCR (qPCR) and mass cytometric analysis cohorts. We also characterised the identified population by synovial single cell RNA-sequencing analysis.Immune cells of patients with RA were characterised by enhanced interferon and IL6-JAK-STAT3 signalling that demonstrate partial normalisation after treatment. A gene expression module of plasmacytoid dendritic cells (pDC) reflecting the expansion of dendritic cell precursors (pre-DC) exhibited strongest association with treatment resistance. Type I interferon signalling was negatively correlated to pre-DC gene expression. qPCR and mass cytometric analysis in independent cohorts validated that the pre-DC associated gene expression and the proportion of pre-DC were significantly higher before treatment in treatment-resistant patients. A cluster of synovial DCs showed both features of pre-DC and pro-inflammatory conventional DC2s.An increase in pre-DC in peripheral blood predicted RA treatment resistance. Pre-DC could have pathophysiological relevance to RA treatment response.

  View details for DOI 10.1136/ard-2022-223645

  View details for Web of Science ID 000968517000001

  View details for PubMedID 36918189

  View details for PubMedCentralID PMC10314026

• Distinct transcriptome architectures underlying lupus establishment and exacerbation. Cell Nakano, M., Ota, M., Takeshima, Y., Iwasaki, Y., Hatano, H., Nagafuchi, Y., Itamiya, T., Maeda, J., Yoshida, R., Yamada, S., Nishiwaki, A., Takahashi, H., Takahashi, H., Akutsu, Y., Kusuda, T., Suetsugu, H., Liu, L., Kim, K., Yin, X., Bang, S. Y., Cui, Y., Lee, H. S., Shoda, H., Zhang, X., Bae, S. C., Terao, C., Yamamoto, K., Okamura, T., Ishigaki, K., Fujio, K. 2022; 185 (18): 3375-3389.e21

  Abstract

  Systemic lupus erythematosus (SLE) is a complex autoimmune disease involving multiple immune cells. To elucidate SLE pathogenesis, it is essential to understand the dysregulated gene expression pattern linked to various clinical statuses with a high cellular resolution. Here, we conducted a large-scale transcriptome study with 6,386 RNA sequencing data covering 27 immune cell types from 136 SLE and 89 healthy donors. We profiled two distinct cell-type-specific transcriptomic signatures: disease-state and disease-activity signatures, reflecting disease establishment and exacerbation, respectively. We then identified candidate biological processes unique to each signature. This study suggested the clinical value of disease-activity signatures, which were associated with organ involvement and therapeutic responses. However, disease-activity signatures were less enriched around SLE risk variants than disease-state signatures, suggesting that current genetic studies may not well capture clinically vital biology. Together, we identified comprehensive gene signatures of SLE, which will provide essential foundations for future genomic and genetic studies.

  View details for DOI 10.1016/j.cell.2022.07.021

  View details for PubMedID 35998627

• AFF3, a susceptibility factor for autoimmune diseases, is a molecular facilitator of immunoglobulin class switch recombination. Science advances Tsukumo, S. I., Subramani, P. G., Seija, N., Tabata, M., Maekawa, Y., Mori, Y., Ishifune, C., Itoh, Y., Ota, M., Fujio, K., Di Noia, J. M., Yasutomo, K. 2022; 8 (34): eabq0008

  Abstract

  Immunoglobulin class switch recombination (CSR) plays critical roles in controlling infections and inflammatory tissue injuries. Here, we show that AFF3, a candidate gene for both rheumatoid arthritis and type 1 diabetes, is a molecular facilitator of CSR with an isotype preference. Aff3-deficient mice exhibit low serum levels of immunoglobulins, predominantly immunoglobulin G2c (IgG2c) followed by IgG1 and IgG3 but not IgM. Furthermore, Aff3-deficient mice show weak resistance to Plasmodium yoelii infection, confirming that Aff3 modulates immunity to this pathogen. Mechanistically, the AFF3 protein binds to the IgM and IgG1 switch regions via a C-terminal domain, and Aff3 deficiency reduces the binding of AID to the switch regions less efficiently. One AFF3 risk allele for rheumatoid arthritis is associated with high mRNA expression of AFF3, IGHG2, and IGHA2 in human B cells. These findings demonstrate that AFF3 directly regulates CSR by facilitating the recruitment of AID to the switch regions.

  View details for DOI 10.1126/sciadv.abq0008

  View details for PubMedID 36001653

  View details for PubMedCentralID PMC9401627

• Parsing multiomics landscape of activated synovial fibroblasts highlights drug targets linked to genetic risk of rheumatoid arthritis. Annals of the rheumatic diseases Tsuchiya, H., Ota, M., Sumitomo, S., Ishigaki, K., Suzuki, A., Sakata, T., Tsuchida, Y., Inui, H., Hirose, J., Kochi, Y., Kadono, Y., Shirahige, K., Tanaka, S., Yamamoto, K., Fujio, K. 2021; 80 (4): 440-450

  Abstract

  Synovial fibroblasts (SFs) are one of the major components of the inflamed synovium in rheumatoid arthritis (RA). We aimed to gain insight into the pathogenic mechanisms of SFs through elucidating the genetic contribution to molecular regulatory networks under inflammatory condition.SFs from RA and osteoarthritis (OA) patients (n=30 each) were stimulated with eight different cytokines (interferon (IFN)-α, IFN-γ, tumour necrosis factor-α, interleukin (IL)-1β, IL-6/sIL-6R, IL-17, transforming growth factor-β1, IL-18) or a combination of all 8 (8-mix). Peripheral blood mononuclear cells were fractioned into five immune cell subsets (CD4+ T cells, CD8+ T cells, B cells, natural killer (NK) cells, monocytes). Integrative analyses including mRNA expression, histone modifications (H3K27ac, H3K4me1, H3K4me3), three-dimensional (3D) genome architecture and genetic variations of single nucleotide polymorphisms (SNPs) were performed.Unstimulated RASFs differed markedly from OASFs in the transcriptome and epigenome. Meanwhile, most of the responses to stimulations were shared between the diseases. Activated SFs expressed pathogenic genes, including CD40 whose induction by IFN-γ was significantly affected by an RA risk SNP (rs6074022). On chromatin remodelling in activated SFs, RA risk loci were enriched in clusters of enhancers (super-enhancers; SEs) induced by synergistic proinflammatory cytokines. An RA risk SNP (rs28411362), located in an SE under synergistically acting cytokines, formed 3D contact with the promoter of metal-regulatory transcription factor-1 (MTF1) gene, whose binding motif showed significant enrichment in stimulation specific-SEs. Consistently, inhibition of MTF1 suppressed cytokine and chemokine production from SFs and ameliorated mice model of arthritis.Our findings established the dynamic landscape of activated SFs and yielded potential therapeutic targets associated with genetic risk of RA.

  View details for DOI 10.1136/annrheumdis-2020-218189

  View details for PubMedID 33139312