Papers - Ishigaki, Kazuyoshi

Host Genetic Architecture between Epstein-Barr Virus Activity and Multiple Sclerosis Reveals Shared Pathways.

Yasumizu Y, Kim N, Rivier CA, Moon J, Kojima S, Chen HL, Buitrago-Pocasangre N, Quinn E, Vaughn S, Morgan A, Huo S, Silberfeld A, Sumida TS, Ishigaki K, Longbrake EE, Falcone GJ, Hafler DA

medRxiv : the preprint server for health sciences  2025.12

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The dynamic role of HLA proteins on compositional alterations of T-cell repertoires in inflammatory bowel disease

 2025.10

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Nonrandomized Allocation of Steroid Therapy in Patients With Fukuyama Congenital Muscular Dystrophy: Study Protocol for a Phase II Clinical Trial.

Murakami T, Sato T, Ishizuka T, Nakamura H, Tachimori H, Harada H, Oi H, Hatano K, Oba MS, Ishiguro K, Shichiji M, Kihara Y, Takeshima Y, Taniguchi-Ikeda M, Hattori A, Shimizu-Motohashi Y, Awano H, Bo R, Nagata S, Ishigaki K

Neuropsychopharmacology reports 45 ( 3 ) e70043 2025.09

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Tracking clonal dynamics of CD8 T cells and immune dysregulation in progression of systemic lupus erythematosus with nephritis

Paek S.J., Lee H.S., Lee Y.J., Bang S.Y., Kim D., Kang B.K., Park D.J., Joo Y.B., Kim M., Kim H., Park S.Y., Park W.Y., Abe T., Itamiya T., Nagafuchi Y., Ishigaki K., Fujio K., Kim K.T., Bae S.C.

Experimental and Molecular Medicine 57 ( 8 ) 1700 - 1710 2025.08

ISSN  12263613

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The fluctuating nature of disease activity in systemic lupus erythematosus (SLE), alternating between flares and remissions, poses substantial challenges for its effective management. The use of current biomarkers for monitoring SLE is limited in clinical settings owing to insufficient comprehension of the complex immune involvement underlying the disease course. Here, therefore, we profiled peripheral blood mononuclear cells at both stable and exacerbation states (total of n = 19) from six patients with SLE and 32 healthy donors using integrated single-cell RNA and T cell receptor (TCR) sequencing. To validate our findings, we analyzed two independent external datasets: bulk RNA sequencing and TCR data from 79 controls and 62 patients with SLE and single-cell RNA sequencing data from 99 healthy controls and 162 patients with SLE. Our analysis revealed cell type-specific activation of interferon-related genes in SLE grouped into four clusters, with elevated activity in disease-associated immune cells. Among these, atypical B cells associated with autoantibody production exhibited distinct differentiation patterns compared with conventional memory B cells, driven by heightened interferon signaling in SLE. Notably, clonal expansion of effector CD8 T cells emerged as a key driver of disease exacerbation, as indicated by reduced TCR diversity. Specific CD8 T cell clonotypes expanded during flare states, transitioning to effector phenotypes that exhibited heightened cytotoxicity and amplified interferon signaling, strongly correlating with tissue damage and flare severity. Our findings establish a critical link between interferon-driven mechanisms and cytotoxic T cell dysfunction in SLE flares, offering potential targets for therapeutic intervention and predictive biomarkers.

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Accurate, sensitive, and efficient chromatin accessibility quantification at target loci using UNIChro-seq

 2025.07

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<jats:title>Abstract</jats:title>
<jats:p>Recent progress in statistical and experimental fine mapping of disease risk variants prompts us to focus on specific target loci for functional investigation. However, current genetics is hindered by a limited toolbox for target-loci analysis. To address this, we developed UNIChro-seq, a method that digitally counts accessible chromatin molecules at target loci. UNIChro-seq allows for accurate, sensitive, and efficient quantification of allelic effects compared to conventional methods. Using UNIChro-seq, we investigated the effects of 57 autoimmunity risk alleles on chromatin accessibility and estimated the causal effects of 20 artificial variants generated through genome editing. As a caveat, non-negligible fraction of the edited allele exhibited a falsely positive effect on chromatin accessibility, which can be effectively distinguished from the true causal effect through bi-directional genome editing. Finally, functional dissection of a fine-mapped risk variant at the <jats:italic>LEF1</jats:italic> locus illuminated its impact on T cell pathology in rheumatoid arthritis. Together, these findings underscore the utility of combining UNIChro-seq with genome editing technology to enable precise and scalable functional analysis of disease-associated loci.</jats:p>

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Granzyme K activates the entire complement cascade

Donado C.A., Theisen E., Zhang F., Nathan A., Fairfield M.L., Rupani K.V., Jones D., Johannes K.P., Wyse A., Cordle A., Li Z.J., Zhu Z., Xiao Q., Weisman M.H., Weisenfeld D., Weinand K., Utz P.J., Tabechian D., Smith M., Slowikowski K., Singaraju A., Scheel-Toellner D., Seifert J.A., Sakaue S., Sahbudin I., Rumker L., Robinson W.H., Rivellese F., Ritchlin C., Reshef Y., Raza K., Rangel-Moreno J., Pitzalis C., Perlman H., Orange D.E., Nerviani A., Nayar S., Moreland L., Millard N., Meednu N., Mears J.R., McGeachy M.J., McDavid A., Maybury M., Marks K.E., Mantel I., Mandelin A.M., Liao K., Li Y., Lewis M.J., Lederer J.A., Lakhanpal A., Keras G., Kang J.B., James J.A., Ishigaki K., Ivashkiv L.B., Hughes L.B., Horowitz D., Holers V.M., Gutierrez-Arcelus M., Guthridge J.M., Gregersen P.K., Rao D., Gravallese E.M., Goodman S.M., Geraldino-Pardilla L., Forbess L., Firestein G.S., Carr H., Filer A., Dunn P., Donlin L.T., DiCarlo E., Deane K.D., Curtis M., Chicoine A., Ceponis A., Campbell D., Bykerk V.P., Bridges S.L., Boyle D.L., Boyce B.F., Ben-Artzi A., Bathon J.M., Barnas J.L., Apruzzese W., Anolik J.H., Albrecht J., Raychaudhuri S., Dwyer D.F., Jonsson A.H., Brenner M.B.

Nature 641 ( 8061 ) 211 - 221 2025.05

ISSN  00280836

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Granzymes are a family of serine proteases that are mainly expressed by CD8⁺ T cells, natural killer cells and innate-like lymphocytes¹. Although their primary function is thought to be the induction of cell death in virally infected cells and tumours, accumulating evidence indicates that some granzymes can elicit inflammation by acting on extracellular substrates¹. We previously found that most tissue CD8⁺ T cells in rheumatoid arthritis synovium, and in inflamed organs for some other diseases, express granzyme K (GZMK)², a tryptase-like protease with poorly defined function. Here, we show that GZMK can activate the complement cascade by cleaving the C2 and C4 proteins. The nascent C4b and C2b fragments form a C3 convertase that cleaves C3, enabling the assembly of a C5 convertase that cleaves C5. The resulting convertases generate all the effector molecules of the complement cascade: the anaphylatoxins C3a and C5a, the opsonins C4b and C3b, and the membrane attack complex. In rheumatoid arthritis synovium, GZMK is enriched in regions with abundant complement activation, and fibroblasts are the main producers of complement proteins that serve as substrates for GZMK-mediated complement activation. Furthermore, Gzmk-deficient mice are significantly protected from inflammatory disease, exhibiting reduced arthritis and dermatitis, with concomitant decreases in complement activation. Our findings describe the discovery of a previously unidentified mechanism of complement activation that is driven entirely by lymphocyte-derived GZMK. Given the widespread abundance of GZMK-expressing T cells in tissues in chronic inflammatory diseases, GZMK-mediated complement activation is likely to be an important contributor to tissue inflammation in multiple disease contexts.

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Asian diversity in human immune cells

Kock K.H., Tan L.M., Han K.Y., Ando Y., Jevapatarakul D., Chatterjee A., Lin Q.X.X., Buyamin E.V., Sonthalia R., Rajagopalan D., Tomofuji Y., Sankaran S., Park M.S., Abe M., Chantaraamporn J., Furukawa S., Ghosh S., Inoue G., Kojima M., Kouno T., Lim J., Myouzen K., Nguantad S., Oh J.M., Rayan N.A., Sarkar S., Suzuki A., Thungsatianpun N., Venkatesh P.N., Moody J., Nakano M., Chen Z., Tian C., Zhang Y., Tong Y., Tan C.T.Y., Tizazu A.M., Loh M., Hwang Y.Y., Ho R.C., Larbi A., Ng T.P., Won H.H., Wright F.A., Villani A.C., Park J.E., Choi M., Liu B., Maitra A., Pithukpakorn M., Suktitipat B., Ishigaki K., Okada Y., Yamamoto K., Carninci P., Chambers J.C., Hon C.C., Matangkasombut P., Charoensawan V., Majumder P.P., Shin J.W., Park W.Y., Prabhakar S.

Cell 188 ( 8 ) 2288 - 2306.e24 2025.04

ISSN  00928674

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The relationships of human diversity with biomedical phenotypes are pervasive yet remain understudied, particularly in a single-cell genomics context. Here, we present the Asian Immune Diversity Atlas (AIDA), a multi-national single-cell RNA sequencing (scRNA-seq) healthy reference atlas of human immune cells. AIDA comprises 1,265,624 circulating immune cells from 619 donors, spanning 7 population groups across 5 Asian countries, and 6 controls. Though population groups are frequently compared at the continental level, we found that sub-continental diversity, age, and sex pervasively impacted cellular and molecular properties of immune cells. These included differential abundance of cell neighborhoods as well as cell populations and genes relevant to disease risk, pathogenesis, and diagnostics. We discovered functional genetic variants influencing cell-type-specific gene expression, which were under-represented in non-Asian populations, and helped contextualize disease-associated variants. AIDA enables analyses of multi-ancestry disease datasets and facilitates the development of precision medicine efforts in Asia and beyond.

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Unveiling the dynamics of B lymphocytes in systemic lupus erythematosus patients treated with belimumab through longitudinal single-cell RNA sequencing

Bang S.Y., Joh C.S.Y., Itamiya T., Jeong S., Lee J.H., Kwon H., Jin H., Jung J., Chung H., Lee B.H., Gong J.R., Ishigaki K., Fujio K., Bae S.C., Kim H.J., Lee H.S.

Rheumatology 64 ( 4 ) 2220 - 2226 2025.04

ISSN  14620324

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Objectives: Unravelling the mechanisms underlying treatment response for targeted therapeutics in systemic lupus erythematosus (SLE) patients is challenging due to the limited understanding of diverse responses of circulating immune cells, particularly B cells. We investigated B lymphocyte dynamics during anti-BAFF treatment, utilizing longitudinal single-cell transcriptome data. Methods: We conducted single-cell RNA sequencing on peripheral blood mononuclear cells (PBMCs) in four Korean SLE patients before and after belimumab treatment at the following time points: 2 weeks, 1, 3, 6 and 12 months. Results: Analysing over 73 000 PBMCs, we identified eight distinct subsets of B cells and plasmablasts and analysed dynamic changes within these cell subsets: initial declines in naïve and transitional B cells followed by an increase at 3 months, contrasted by an initial increase and subsequent decrease in memory B cells by the third month. Meanwhile, plasmablasts exhibited a consistent decline throughout the treatment. B cell activation pathways, specifically in naïve and memory B cells, were downregulated during the third and sixth months. These findings were validated at the protein level throughout the first 4 weeks of treatment using flow cytometry. Comparative analysis with bulk transcriptome data from 22 Japanese SLE patients showed increased NR4A1 expression 6 months post-belimumab treatment, indicating its role in restricting self-reactive B cells, thereby contributing to the biological responses of anti-BAFF treatment. Conclusion: The observed B cell dynamics provided insights into the immunological mechanisms underlying the therapeutic effects of anti-BAFF in SLE patients. Furthermore, it underscores the need for research in predicting drug responses based on immune profiling.

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Peripheral blood immunophenotypic diversity in patients with rheumatoid arthritis and its impact on therapeutic responsiveness

Kubo S., Miyazaki Y., Nishino T., Fujita Y., Kono M., Kawashima T., Ishigaki K., Kusaka K., Tanaka H., Ueno M., Satoh-Kanda Y., Inoue Y., Todoroki Y., Miyagawa I., Hanami K., Nakayamada S., Tanaka Y.

Annals of the Rheumatic Diseases 84 ( 2 ) 210 - 220 2025.02

ISSN  00034967

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Objective: Considering the diverse aetiologies and immunodysregulatory statuses observed in each patient with rheumatoid arthritis (RA), stratification based on peripheral blood immunophenotyping holds the potential to enhance therapeutic responses to molecular targeted therapies, biological/targeted synthetic disease-modifying antirheumatic drugs (b/tsDMARDs). Methods: Immunophenotype analysis was conducted on a cohort of over 500 b/tsDMARDs-naïve patients using flow cytometry. Patients with RA were stratified based on their immunophenotypes, and the treatment response to each targeted therapy was evaluated. Validation was performed using an additional cohort of 183 b/tsDMARDs-naïve patients with RA. Results: Patients with RA were stratified into five clusters, two of which exhibited distinct RA phenotypes compared with controls, characterised by significant increases in CD4⁺ effector memory T cells re-expressing CD45RA. Notably, the effectiveness of different b/tsDMARDs varied across clusters. The group using promising b/tsDMARDs was labelled as ‘expected’ whereas the ‘non-expected’ group comprised those using others. The expected group outperformed the non-expected group with higher 26-week remission rates (39.9% vs 24.6%, p=0.0004) and low disease activity achievement (80.8% vs 60.2%, p<0.0001). Trajectory analysis showed the non-expected group's 26-week disease activity was influenced by Clinical Disease Activity Index at baseline unlike the expected group. Additionally, different molecular targeted therapies influenced the proportions of each immune cell subset variably. To validate, immunophenotyping was performed on a validation cohort. When 183 cases were grouped based on their b/tsDMARDs usage into expected/non-expected groups, the expected group had a higher remission rate (p=0.0021), further confirming the observed trend. Conclusion: Our findings offer valuable insights into the diversity of RA and potential therapeutic strategies grounded in the molecular underpinnings.

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Proximity-dependent biotinylation reveals an interaction between ubiquitin-specific peptidase 46 and centrosome-related proteins.

Yoshioka K, Nakagawa R, Nguyen CLK, Suzuki H, Ishigaki K, Mizuno S, Okiyoneda T, Ebihara S, Murata K

FEBS open bio 15 ( 1 ) 151 - 164 2025.01

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Naturally arising memory-phenotype CD4+ T lymphocytes contain an undifferentiated population that can generate TH1, TH17, and Treg cells

Kawajiri A., Li J., Koinuma K., Yang Z., Yoon H.J., Yi J., Nagashima H., Ishii M., Gao F., Sato K., Tayama S., Harigae H., Iwakura Y., Ishii N., Sher A., Ishigaki K., Zhu J., Kim K.S., Kawabe T.

Science Advances 10 ( 49 ) eadq6618 2024.12

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Memory-phenotype (MP) CD4⁺ T lymphocytes develop from naïve cells via self-recognition at homeostasis. While previous studies defined MP cells as a heterogeneous population that comprises T helper 1 (T<inf>H</inf>1)/17–like subsets, functional significance of the T-bet⁻ Rorγt⁻ subpopulation remains unknown. Here we show that MP lymphocytes as a whole population can differentiate into T<inf>H</inf>1/17/regulatory T (T<inf>reg</inf>) cells to mediate mild and persistent inflammation in lymphopenic environments, whereas naïve cells exhibit strong, T<inf>H</inf>1-dominated responses. Moreover, we demonstrate that MP lymphocytes comprise not only T<inf>H</inf>1/17-differentiated subsets but a polyclonal, transcriptomically immature “undifferentiated” subpopulation at homeostasis. Furthermore, our data argue that while the T-bet⁺ Rorγt⁻ MP subset is terminally T<inf>H</inf>1-differentiated, its undifferentiated counterpart retains the capacity to rapidly proliferate to differentiate into T<inf>H</inf>1/17/T<inf>reg</inf> cells, with the latter response tonically constrained by preexisting T<inf>reg</inf> cells. Together, our results identify undifferentiated MP CD4⁺ T lymphocytes as a unique precursor that has a diverse differentiation potential to generate T<inf>H</inf>1/17/T<inf>reg</inf> cells to contribute to pathogenesis of inflammation.

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The genetic basis of autoimmunity seen through the lens of T cell functional traits

Lagattuta K.A., Park H.L., Rumker L., Ishigaki K., Nathan A., Raychaudhuri S.

Nature Communications 15 ( 1 ) 1204 2024.12

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Autoimmune disease heritability is enriched in T cell-specific regulatory regions of the genome. Modern-day T cell datasets now enable association studies between single nucleotide polymorphisms (SNPs) and a myriad of molecular phenotypes, including chromatin accessibility, gene expression, transcriptional programs, T cell antigen receptor (TCR) amino acid usage, and cell state abundances. Such studies have identified hundreds of quantitative trait loci (QTLs) in T cells that colocalize with genetic risk for autoimmune disease. The key challenge facing immunologists today lies in synthesizing these results toward a unified understanding of the autoimmune T cell: which genes, cell states, and antigens drive tissue destruction?

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Single-cell RNA sequencing of peripheral blood links cell-type-specific regulation of splicing to autoimmune and inflammatory diseases

Tian C., Zhang Y., Tong Y., Kock K.H., Sim D.Y., Liu F., Dong J., Jing Z., Wang W., Gao J., Tan L.M., Han K.Y., Tomofuji Y., Nakano M., Buyamin E.V., Sonthalia R., Ando Y., Hatano H., Sonehara K., Moody J., Lin Q.X.X., Venkatesh P.N., Maitra A., Lim J., Kouno T., Kojima M., Suzuki A., Oh J.M., Myouzen K., Inoue G., Furukawa S., Abe M., Thungsatianpun N., Sarkar S., Nguantad S., Jevapatarakul D., Ghosh S., Chatterjee A., Chantaraamporn J., Sankaran S., Rayan N.A., Rajagopalan D., Yamamoto K., Suktitipat B., Pithukpakorn M., Chambers J.C., Carninci P., Matangkasombut P., Majumder P.P., Charoensawan V., Jin X., Loh M., Hon C.C., Choi M., Park J.E., Ishigaki K., Okamura T., Fujio K., Okada Y., Park W.Y., Shin J.W., Roca X., Prabhakar S., Liu B.

Nature Genetics 56 ( 12 ) 2739 - 2752 2024.12

ISSN  10614036

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Alternative splicing contributes to complex traits, but whether this differs in trait-relevant cell types across diverse genetic ancestries is unclear. Here we describe cell-type-specific, sex-biased and ancestry-biased alternative splicing in ~1 M peripheral blood mononuclear cells from 474 healthy donors from the Asian Immune Diversity Atlas. We identify widespread sex-biased and ancestry-biased differential splicing, most of which is cell-type-specific. We identify 11,577 independent cis-splicing quantitative trait loci (sQTLs), 607 trans-sGenes and 107 dynamic sQTLs. Colocalization between cis-eQTLs and trans-sQTLs revealed a cell-type-specific regulatory relationship between HNRNPLL and PTPRC. We observed an enrichment of cis-sQTL effects in autoimmune and inflammatory disease heritability. Specifically, we functionally validated an Asian-specific sQTL disrupting the 5′ splice site of TCHP exon 4 that putatively modulates the risk of Graves’ disease in East Asian populations. Our work highlights the impact of ancestral diversity on splicing and provides a roadmap to dissect its role in complex diseases at single-cell resolution.

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The chromatin landscape of pathogenic transcriptional cell states in rheumatoid arthritis

Weinand K., Sakaue S., Nathan A., Jonsson A.H., Zhang F., Watts G.F.M., Al Suqri M., Zhu Z., Rao D.A., Anolik J.H., Brenner M.B., Donlin L.T., Wei K., Raychaudhuri S., Albrecht J., Apruzzese W., Banda N., Barnas J.L., Bathon J.M., Ben-Artzi A., Boyce B.F., Boyle D.L., Bridges S.L., Bykerk V.P., Campbell D., Carr H.L., Ceponis A., Chicoine A., Cordle A., Curtis M., Deane K.D., DiCarlo E., Dunn P., Filer A., Firestein G.S., Forbess L., Geraldino-Pardilla L., Goodman S.M., Gravallese E.M., Gregersen P.K., Guthridge J.M., Gutierrez-Arcelus M., Gurajala S., Holers V.M., Horowitz D., Hughes L.B., Ishigaki K., Ivashkiv L.B., James J.A., Kang J.B., Keras G., Korsunsky I., Lakhanpal A., Lederer J.A., Li Z.J., Li Y., Liao K.P., Mandelin A.M., Mantel I., Maybury M., McDavid A., Mears J., Meednu N., Millard N., Moreland L.W., Nerviani A., Orange D.E., Perlman H., Pitzalis C., Rangel-Moreno J., Raza K., Reshef Y., Ritchlin C., Rivellese F., Robinson W.H., Rumker L., Sahbudin I., Scheel-Toellner D., Seifert J.A., Slowikowski K., Smith M.H., Tabechian D., Utz P.J., Weisenfeld D., Weisman M.H., Xiao Q.

Nature Communications 15 ( 1 )  2024.12

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Synovial tissue inflammation is a hallmark of rheumatoid arthritis (RA). Recent work has identified prominent pathogenic cell states in inflamed RA synovial tissue, such as T peripheral helper cells; however, the epigenetic regulation of these states has yet to be defined. Here, we examine genome-wide open chromatin at single-cell resolution in 30 synovial tissue samples, including 12 samples with transcriptional data in multimodal experiments. We identify 24 chromatin classes and predict their associated transcription factors, including a CD8 + GZMK+ class associated with EOMES and a lining fibroblast class associated with AP-1. By integrating with an RA tissue transcriptional atlas, we propose that these chromatin classes represent ‘superstates’ corresponding to multiple transcriptional cell states. Finally, we demonstrate the utility of this RA tissue chromatin atlas through the associations between disease phenotypes and chromatin class abundance, as well as the nomination of classes mediating the effects of putatively causal RA genetic variants.

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Population-specific reference panel improves imputation quality for genome-wide association studies conducted on the Japanese population

Flanagan J., Liu X., Ortega-Reyes D., Tomizuka K., Matoba N., Akiyama M., Koido M., Ishigaki K., Ashikawa K., Takata S., Shi M.Y., Aoi T., Momozawa Y., Ito K., Murakami Y., Matsuda K., Koretsune Y., Masumoto A., Higashiyama M., Obata D., Nagayama S., Yoshimori K., Murayama S., Minami S., Yamaguchi H., Sinozaki N., Suzuki T., Takahashi Y., Asai S., Takahashi K., Yamaji K., Obara W., Nagai A., Muto K., Kamatani Y., Morisaki T., Furukawa Y., Yamanashi Y., Morris A.P., Horikoshi M., Terao C.

Communications Biology 7 ( 1 ) 1665 2024.12

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To improve imputation quality for genome-wide association studies (GWAS) conducted on the Japanese population, we developed and evaluated four Japanese population-specific reference panels. These panels were constructed through the augmentation of the 1000 Genomes Project (1KG) panel using Japanese whole genome sequencing (WGS) data, with sample sizes ranging from 1 K to 7 K individuals enrolled through the Biobank Japan (BBJ) project, and sequencing depths ranging from 3× to 30×. Among these panels, an augmented reference panel comprising 7472 WGS samples of mixed depth (1KG+7K) exhibit the greatest improvement in imputation quality relative to the Trans-Omics for Precision Medicine (TOPMed) reference panel. Notably, we observe these improvements primarily for rare variants with a minor allele frequency (MAF) <5%. To demonstrate the benefits of improved imputation quality in association analyses of complex traits, we conducted GWAS for serum uric acid and total cholesterol levels following imputation up to the 1KG+7K panel. The analysis reveals several loci reaching genome-wide significance (P < 5 × 10^–8) in the 1KG+7K imputation output yet remaining undetected when the same sample set is imputed up to the TOPMed reference panel. In summary, the 1KG+7K panel demonstrates significant advantages in the discovery of trait-associated loci, particularly those influenced by low-frequency association signals.

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Long-read sequencing for 29 immune cell subsets reveals disease-linked isoforms

Inamo J., Suzuki A., Ueda M.T., Yamaguchi K., Nishida H., Suzuki K., Kaneko Y., Takeuchi T., Hatano H., Ishigaki K., Ishihama Y., Yamamoto K., Kochi Y.

Nature Communications 15 ( 1 ) 4285 2024.12

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Alternative splicing events are a major causal mechanism for complex traits, but they have been understudied due to the limitation of short-read sequencing. Here, we generate a full-length isoform annotation of human immune cells from an individual by long-read sequencing for 29 cell subsets. This contains a number of unannotated transcripts and isoforms such as a read-through transcript of TOMM40-APOE in the Alzheimer’s disease locus. We profile characteristics of isoforms and show that repetitive elements significantly explain the diversity of unannotated isoforms, providing insight into the human genome evolution. In addition, some of the isoforms are expressed in a cell-type specific manner, whose alternative 3’-UTRs usage contributes to their specificity. Further, we identify disease-associated isoforms by isoform switch analysis and by integration of several quantitative trait loci analyses with genome-wide association study data. Our findings will promote the elucidation of the mechanism of complex diseases via alternative splicing.

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Clonal associations between lymphocyte subsets and functional states in rheumatoid arthritis synovium

Dunlap G., Wagner A., Meednu N., Wang R., Zhang F., Ekabe J.C., Jonsson A.H., Wei K., Sakaue S., Nathan A., Bykerk V.P., Donlin L.T., Goodman S.M., Firestein G.S., Boyle D.L., Holers V.M., Moreland L.W., Tabechian D., Pitzalis C., Filer A., Raychaudhuri S., Brenner M.B., Thakar J., McDavid A., Rao D.A., Anolik J.H., Albrecht J., Apruzzese W., Barnas J.L., Bathon J.M., Ben-Artzi A., Boyce B.F., Bridges S.L., Campbell D., Carr H.L., Ceponis A., Chicoine A., Cordle A., Curtis M., Deane K.D., DiCarlo E., Dunn P., Forbess L., Geraldino-Pardilla L., Gravallese E.M., Gregersen P.K., Guthridge J.M., Horowitz D., Hughes L.B., Ishigaki K., Ivashkiv L.B., James J.A., Kang J.B., Keras G., Korsunsky I., Lakhanpal A., Lederer J.A., Li Y., Li Z.J., Liao K.P., Maecker H., Mandelin A.M., Mantel I., Maybury M., McGeachy M.J., Mears J., Nerviani A., Orange D.E., Perlman H., Rangel-Moreno J., Raza K., Reshef Y., Ritchlin C., Rivellese F., Robinson W.H., Rumker L., Sahbudin I., Salomon-Escoto K., Scheel-Toellner D., Seifert J.A., Singaraju A., Smith M.H., Utz P.J., Weinand K., Weisenfeld D., Weisman M.H., Xiao Q., Zhu Z.

Nature Communications 15 ( 1 )  2024.12

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Rheumatoid arthritis (RA) is an autoimmune disease involving antigen-specific T and B cells. Here, we perform single-cell RNA and repertoire sequencing on paired synovial tissue and blood samples from 12 seropositive RA patients. We identify clonally expanded CD4 + T cells, including CCL5+ cells and T peripheral helper (Tph) cells, which show a prominent transcriptomic signature of recent activation and effector function. CD8 + T cells show higher oligoclonality than CD4 + T cells, with the largest synovial clones enriched in GZMK+ cells. CD8 + T cells with possibly virus-reactive TCRs are distributed across transcriptomic clusters. In the B cell compartment, NR4A1+ activated B cells, and plasma cells are enriched in the synovium and demonstrate substantial clonal expansion. We identify synovial plasma cells that share BCRs with synovial ABC, memory, and activated B cells. Receptor-ligand analysis predicted IFNG and TNFRSF members as mediators of synovial Tph-B cell interactions. Together, these results reveal clonal relationships between functionally distinct lymphocyte populations that infiltrate the synovium of patients with RA.

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Adipocyte associated glucocorticoid signaling regulates normal fibroblast function which is lost in inflammatory arthritis

Faust H.J., Cheng T.Y., Korsunsky I., Watts G.F.M., Gal-Oz S.T., Trim W.V., Kongthong S., Jonsson A.H., Simmons D.P., Zhang F., Padera R., Chubinskaya S., Wyse A., Cordle A., Li Z.J., Zhu Z., Xiao Q., Weisman M.H., Weisenfeld D., Weinand K., Utz P.J., Tabechian D., Smith M., Slowikowski K., Singaraju A., Scheel-Toellner D., Seifert J.A., Sakaue S., Sahbudin I., Rumker L., Robinson W.H., Rivellese F., Ritchlin C., Reshef Y., Raza K., Rangel-Moreno J., Pitzalis C., Perlman H., Orange D.E., Nerviani A., Nayar S., Moreland L., Millard N., Meednu N., Mears J.R., McGeachy M.J., McDavid A., Maybury M., Marks K.E., Mantel I., Mandelin A.M., Liao K., Li Y., Lewis M.J., Lederer J.A., Lakhanpal A., Keras G., Kang J.B., James J.A., Ishigaki K., Ivashkiv L.B., Hughes L.B., Horowitz D., Holers V.M., Gutierrez-Arcelus M., Guthridge J.M., Gregersen P.K., Rao D., Gravallese E.M., Goodman S.M., Geraldino-Pardilla L., Forbess L., Firestein G.S., Carr H., Filer A., Dunn P., Donlin L.T., DiCarlo E., Deane K.D., Curtis M., Chicoine A., Ceponis A., Campbell D., Bykerk V.P., Bridges S.L., Boyle D.L., Boyce B.F., Ben-Artzi A., Bathon J.M., Barnas J.L., Apruzzese W., Anolik J.H., Albrecht J., Wei K., Raychaudhuri S., Lynch L., Moody D.B., Brenner M.B.

Nature Communications 15 ( 1 )  2024.12

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Fibroblasts play critical roles in tissue homeostasis, but in pathologic states they can drive fibrosis, inflammation, and tissue destruction. Little is known about what regulates the homeostatic functions of fibroblasts. Here, we perform RNA sequencing and identify a gene expression program in healthy synovial fibroblasts characterized by enhanced fatty acid metabolism and lipid transport. We identify cortisol as the key driver of the healthy fibroblast phenotype and that depletion of adipocytes, which express high levels of Hsd11b1, results in loss of the healthy fibroblast phenotype in mouse synovium. Additionally, fibroblast-specific glucocorticoid receptor Nr3c1 deletion in vivo leads to worsened arthritis. Cortisol signaling in fibroblasts mitigates matrix remodeling induced by TNF and TGF-β1 in vitro, while stimulation with these cytokines represses cortisol signaling and adipogenesis. Together, these findings demonstrate the importance of adipocytes and cortisol signaling in driving the healthy synovial fibroblast state that is lost in disease.

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Paired analysis of host and pathogen genomes identifies determinants of human tuberculosis

Luo Y., Huang C.C., Howard N.C., Wang X., Liu Q., Li X., Zhu J., Amariuta T., Asgari S., Ishigaki K., Calderon R., Raman S., Ramnarine A.K., Mayfield J.A., Moody D.B., Lecca L., Fortune S.M., Murray M.B., Raychaudhuri S.

Nature Communications 15 ( 1 ) 10393 2024.12

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Infectious disease is the result of interactions between host and pathogen and can depend on genetic variations in both. We conduct a genome-to-genome study of paired human and Mycobacterium tuberculosis genomes from a cohort of 1556 tuberculosis patients in Lima, Peru. We identify an association between a human intronic variant (rs3130660, OR = 10.06, 95%CI: 4.87 − 20.77, P = 7.92 × 10⁻⁸) in the FLOT1 gene and a subclavaluee of Mtb Lineage 2. In a human macrophage infection model, we observe hosts with the rs3130660-A allele exhibited stronger interferon gene signatures. The interacting strains have altered redox states due to a thioredoxin reductase mutation. We investigate this association in a 2020 cohort of 699 patients recruited during the COVID-19 pandemic. While the prevalence of the interacting strain almost doubled between 2010 and 2020, its infection is not associated with rs3130660 in this recent cohort. These findings suggest a complex interplay among host, pathogen, and environmental factors in tuberculosis dynamics.

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A genome-wide association study identified PTPN2 as a population-specific susceptibility gene locus for primary biliary cholangitis

Hitomi Y., Ueno K., Aiba Y., Nishida N., Kono M., Sugihara M., Kawai Y., Kawashima M., Khor S.S., Sugi K., Kouno H., Kohno H., Naganuma A., Iwamoto S., Katsushima S., Furuta K., Nikami T., Mannami T., Yamashita T., Ario K., Komatsu T., Makita F., Shimada M., Hirashima N., Yokohama S., Nishimura H., Sugimoto R., Komura T., Ota H., Kojima M., Nakamuta M., Fujimori N., Yoshizawa K., Mano Y., Takahashi H., Hirooka K., Tsuruta S., Sato T., Yamasaki K., Kugiyama Y., Motoyoshi Y., Suehiro T., Saeki A., Matsumoto K., Nagaoka S., Abiru S., Yatsuhashi H., Ito M., Kawata K., Takaki A., Arai K., Arinaga-Hino T., Abe M., Harada M., Taniai M., Zeniya M., Ohira H., Shimoda S., Komori A., Tanaka A., Ishigaki K., Nagasaki M., Tokunaga K., Nakamura M.

Hepatology 80 ( 4 ) 776 - 790 2024.10

ISSN  02709139

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Background and Aims: Previous genome-wide association studies (GWAS) have indicated the involvement of shared (population-nonspecific) and nonshared (population-specific) susceptibility genes in the pathogenesis of primary biliary cholangitis (PBC) among European and East-Asian populations. Although a meta-Analysis of these distinct populations has recently identified more than 20 novel PBC susceptibility loci, analyses of population-specific genetic architecture are still needed for a more comprehensive search for genetic factors in PBC. Approach and Results: Protein tyrosine phosphatase nonreceptor type 2 (PTPN2) was identified as a novel PBC susceptibility gene locus through GWAS and subsequent genome-wide meta-Analysis involving 2181 cases and 2699 controls from the Japanese population (GWAS-lead variant: rs8098858, p = 2.6 × 10-8). In silico and in vitro functional analyses indicated that the risk allele of rs2292758, which is a primary functional variant, decreases PTPN2 expression by disrupting Sp1 binding to the PTPN2 promoter in T follicular helper cells and plasmacytoid dendritic cells. Infiltration of PTPN2-positive T-cells and plasmacytoid dendritic cells was confirmed in the portal area of the PBC liver by immunohistochemistry. Furthermore, transcriptomic analysis of PBC-liver samples indicated the presence of a compromised negative feedback loop in vivo between PTPN2 and IFNG in patients carrying the risk allele of rs2292758. Conclusions: PTPN2, a novel susceptibility gene for PBC in the Japanese population, may be involved in the pathogenesis of PBC through an insufficient negative feedback loop caused by the risk allele of rs2292758 in IFN-γ signaling. This suggests that PTPN2 could be a potential molecular target for PBC treatment.

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Interferon subverts an AHR–JUN axis to promote CXCL13+ T cells in lupus

Law C., Wacleche V.S., Cao Y., Pillai A., Sowerby J., Hancock B., Horisberger A., Bracero S., Skidanova V., Li Z., Adejoorin I., Dillon E., Benque I.J., Nunez D.P., Simmons D.P., Keegan J., Chen L., Baker T., Brohawn P.Z., Al-Mossawi H., Hao L.Y., Jones B., Rao N., Qu Y., Alves S.E., Albrecht J., Anolik J.H., Apruzzese W., Barnas J.L., Bathon J.M., Ben-Artzi A., Boyce B.F., Boyle D.L., Bridges S.L., Bykerk V.P., Campbell D., Ceponis A., Chicoine A., Curtis M., Deane K.D., DiCarlo E., Donlin L.T., Dunn P., Filer A., Carr H., Firestein G.S., Forbess L., Geraldino-Pardilla L., Goodman S.M., Gravallese E.M., Gregersen P.K., Guthridge J.M., Gutierrez-Arcelus M., Holers V.M., Horowitz D., Hughes L.B., Ivashkiv L.B., Ishigaki K., James J.A., Jonsson A.H., Kang J.B., Keras G., Korsunsky I., Lakhanpal A., Lederer J.A., Lewis M.J., Li Y., Liao K., Mandelin A.M., Mantel I., Marks K.E., Maybury M., McDavid A., McGeachy M.J., Mears J.R., Meednu N., Millard N., Moreland L., Nayar S., Nerviani A., Orange D.E., Perlman H., Pitzalis C., Rangel-Moreno J., Raychaudhuri S., Raza K., Reshef Y., Ritchlin C., Rivellese F., Robinson W.H., Rumker L., Sahbudin I., Sakaue S., Seifert J.A., Scheel-Toellner D., Singaraju A., Slowikowski K., Smith M., Tabechian D., Utz P.J.

Nature 631 ( 8022 ) 857 - 866 2024.07

ISSN  00280836

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Systemic lupus erythematosus (SLE) is prototypical autoimmune disease driven by pathological T cell–B cell interactions^1,2. Expansion of T follicular helper (T<inf>FH</inf>) and T peripheral helper (T<inf>PH</inf>) cells, two T cell populations that provide help to B cells, is a prominent feature of SLE^3,4. Human T<inf>FH</inf> and T<inf>PH</inf> cells characteristically produce high levels of the B cell chemoattractant CXCL13 (refs. ^5,6), yet regulation of T cell CXCL13 production and the relationship between CXCL13⁺ T cells and other T cell states remains unclear. Here, we identify an imbalance in CD4⁺ T cell phenotypes in patients with SLE, with expansion of PD-1⁺/ICOS⁺ CXCL13⁺ T cells and reduction of CD96^hi IL-22⁺ T cells. Using CRISPR screens, we identify the aryl hydrocarbon receptor (AHR) as a potent negative regulator of CXCL13 production by human CD4⁺ T cells. Transcriptomic, epigenetic and functional studies demonstrate that AHR coordinates with AP-1 family member JUN to prevent CXCL13⁺ T<inf>PH</inf>/T<inf>FH</inf> cell differentiation and promote an IL-22⁺ phenotype. Type I interferon, a pathogenic driver of SLE⁷, opposes AHR and JUN to promote T cell production of CXCL13. These results place CXCL13⁺ T<inf>PH</inf>/T<inf>FH</inf> cells on a polarization axis opposite from T helper 22 (T<inf>H</inf>22) cells and reveal AHR, JUN and interferon as key regulators of these divergent T cell states.

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An atlas of transcribed enhancers across helper T cell diversity for decoding human diseases

Oguchi A., Suzuki A., Komatsu S., Yoshitomi H., Bhagat S., Son R., Bonnal R.J.P., Kojima S., Koido M., Takeuchi K., Myouzen K., Inoue G., Hirai T., Sano H., Takegami Y., Kanemaru A., Yamaguchi I., Ishikawa Y., Tanaka N., Hirabayashi S., Konishi R., Sekito S., Inoue T., Kere J., Takeda S., Takaori-Kondo A., Endo I., Kawaoka S., Kawaji H., Ishigaki K., Ueno H., Hayashizaki Y., Pagani M., Carninci P., Yanagita M., Parrish N., Terao C., Yamamoto K., Murakawa Y.

Science 385 ( 6704 ) eadd8394 2024.07

ISSN  00368075

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Transcribed enhancer maps can reveal nuclear interactions underpinning each cell type and connect specific cell types to diseases. Using a 5′ single-cell RNA sequencing approach, we defined transcription start sites of enhancer RNAs and other classes of coding and noncoding RNAs in human CD4⁺ T cells, revealing cellular heterogeneity and differentiation trajectories. Integration of these datasets with single-cell chromatin profiles showed that active enhancers with bidirectional RNA transcription are highly cell type–specific and that disease heritability is strongly enriched in these enhancers. The resulting cell type–resolved multimodal atlas of bidirectionally transcribed enhancers, which we linked with promoters using fine-scale chromatin contact maps, enabled us to systematically interpret genetic variants associated with a range of immune-mediated diseases.

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Tissue-specific enhancer–gene maps from multimodal single-cell data identify causal disease alleles

Sakaue S., Weinand K., Isaac S., Dey K.K., Jagadeesh K., Kanai M., Watts G.F.M., Zhu Z., Brenner M.B., McDavid A., Donlin L.T., Wei K., Price A.L., Raychaudhuri S., Albrecht J., Anolik J.H., Apruzzese W., Banda N., Barnas J.L., Bathon J.M., Ben-Artzi A., Boyce B.F., Boyle D.L., Bridges S.L., Bykerk V.P., Campbell D., Carr H.L., Ceponis A., Chicoine A., Cordle A., Curtis M., Deane K.D., DiCarlo E., Dunn P., Filer A., Firestein G.S., Forbess L., Geraldino-Pardilla L., Goodman S.M., Gravallese E.M., Gregersen P.K., Guthridge J.M., Gutierrez-Arcelus M., Gurajala S., Michael Holers V., Horowitz D., Hughes L.B., Ishigaki K., Ivashkiv L.B., James J.A., Jonsson A.H., Kang J.B., Keras G., Korsunsky I., Lakhanpal A., Lederer J.A., Li Z.J., Li Y., Liao K.P., Mandelin A.M., Mantel I., Maybury M., Mears J., Meednu N., Millard N., Moreland L.W., Nathan A., Nerviani A., Orange D.E., Perlman H., Pitzalis C., Rangel-Moreno J., Rao D.A., Raza K., Reshef Y., Ritchlin C., Rivellese F., Robinson W.H., Rumker L., Sahbudin I., Seifert J.A., Slowikowski K., Smith M.H., Tabechian D., Scheel-Toellner D., Utz P.J., Weisenfeld D., Weisman M.H., Xiao Q., Zhang F.

Nature Genetics 56 ( 4 ) 615 - 626 2024.04

ISSN  10614036

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Translating genome-wide association study (GWAS) loci into causal variants and genes requires accurate cell-type-specific enhancer–gene maps from disease-relevant tissues. Building enhancer–gene maps is essential but challenging with current experimental methods in primary human tissues. Here we developed a nonparametric statistical method, SCENT (single-cell enhancer target gene mapping), that models association between enhancer chromatin accessibility and gene expression in single-cell or nucleus multimodal RNA sequencing and ATAC sequencing data. We applied SCENT to 9 multimodal datasets including >120,000 single cells or nuclei and created 23 cell-type-specific enhancer–gene maps. These maps were highly enriched for causal variants in expression quantitative loci and GWAS for 1,143 diseases and traits. We identified likely causal genes for both common and rare diseases and linked somatic mutation hotspots to target genes. We demonstrate that application of SCENT to multimodal data from disease-relevant human tissue enables the scalable construction of accurate cell-type-specific enhancer–gene maps, essential for defining noncoding variant function.

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Age-associated CD4+ T cells with B cell–promoting functions are regulated by ZEB2 in autoimmunity

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.

Science Immunology 9 ( 93 ) eadk1643 2024.03

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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 CXCR3^midCD4⁺ effector memory T cell subset that expands with age, which we designated “age-associated T helper (T<inf>H</inf>A) cells.” T<inf>H</inf>A 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 T<inf>H</inf>A cells, gene expression in T<inf>H</inf>A 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 T<inf>H</inf>A cells infiltrate damaged organs in patients with autoimmune diseases. Together, our characterization of T<inf>H</inf>A cells may facilitate improved understanding of the relationship between aging and autoimmune diseases.

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Associations Between Rheumatoid Arthritis Clinical Factors and Synovial Cell Types and States

Weisenfeld D., Zhang F., Donlin L., Jonsson A.H., Apruzzese W., Campbell D., Albrecht J., Barnas J.L., Bathon J.M., Ben-Artzi A., Boyce B.F., Boyle D.L., Louis Bridges S., Carr H.L., Ceponis A., Chicoine A., Cordle A., Curtis M., Deane K.D., DiCarlo E., Dunn P., Firestein G.S., Forbess L., Geraldino-Pardilla L., Gregersen P.K., Guthridge J.M., Gutierrez-Arcelus M., Gurajala S., Horowitz V.D., Hughes L.B., Ishigaki K., Ivashkiv L.B., James J.A., Kang J.B., Keras G., Korsunsky I., Lakhanpal A., Lederer J.A., Lewis M., Li Z.J., Li Y., Mandelin A.M., Mantel I., Marks K., Maybury M., McDavid A., McGeachy M.J., Mears J., Meednu N., Millard N., Nathan A., Nayar S., Nerviani A., Orange D.E., Perlman H., Pitzalis C., Rangel-Moreno J., Raza K., Reshef Y., Ritchlin C., Rivellese F., Robinson W.H., Rumker L., Sahbudin I., Sakaue S., Scheel-Toellner D., Seifert J.A., Singaraju A., Slowikowski K., Smith M.H., Tabechian D., Utz P.J., Watts G.F.M., Weinand K., Weisman M.H., Wyse A., Xiao Q., Zhu Z., Rao D.A., Wei K., Holers V.M., Gravallese E., Moreland L., Goodman S., Brenner M., Raychaudhuri S., Filer A., Anolik J., Bykerk V., Liao K.P.

Arthritis and Rheumatology 76 ( 3 ) 356 - 362 2024.03

ISSN  23265191

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Objective: Recent studies have uncovered diverse cell types and states in the rheumatoid arthritis (RA) synovium; however, limited data exist correlating these findings with patient-level clinical information. Using the largest cohort to date with clinical and multicell data, we determined associations between RA clinical factors with cell types and states in the RA synovium. Methods: The Accelerated Medicines Partnership Rheumatoid Arthritis study recruited patients with active RA who were not receiving disease-modifying antirheumatic drugs (DMARDs) or who had an inadequate response to methotrexate (MTX) or tumor necrosis factor inhibitors. RA clinical factors were systematically collected. Biopsies were performed on an inflamed joint, and tissue were disaggregated and processed with a cellular indexing of transcriptomes and epitopes sequencing pipeline from which the following cell type percentages and cell type abundance phenotypes (CTAPs) were derived: endothelial, fibroblast, and myeloid (EFM); fibroblasts; myeloid; T and B cells; T cells and fibroblasts (TF); and T and myeloid cells. Correlations were measured between RA clinical factors, cell type percentage, and CTAPs. Results: We studied 72 patients (mean age 57 years, 75% women, 83% seropositive, mean RA duration 6.6 years, mean Disease Activity Score-28 C-reactive Protein 3 [DAS28-CRP3] score 4.8). Higher DAS28-CRP3 correlated with a higher T cell percentage (P < 0.01). Those receiving MTX and not a biologic DMARD (bDMARD) had a higher percentage of B cells versus those receiving no DMARDs (P < 0.01). Most of those receiving bDMARDs were categorized as EFM (57%), whereas none were TF. No significant difference was observed across CTAPs for age, sex, RA disease duration, or DAS28-CRP3. Conclusion: In this comprehensive screen of clinical factors, we observed differential associations between DMARDs and cell phenotypes, suggesting that RA therapies, more than other clinical factors, may impact cell type/state in the synovium and ultimately influence response to subsequent therapies.

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How can genetics analysis allow for early detection of rheumatoid arthritis

Yamamoto K., Ishigaki K., Okada Y.

Seminars in Arthritis and Rheumatism 64   152323 2024.02

ISSN  00490172

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Early detection and diagnosis of rheumatoid arthritis (RA) is crucial for initiating appropriate therapy promptly, thereby leading to increase the likelihood of achieving remission and eventual cure. In this article, we will discuss the contribution of genetic information in predicting and detecting RA.

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Natural history of Becker muscular dystrophy: a multicenter study of 225 patients.

Nakamura A, Matsumura T, Ogata K, Mori-Yoshimura M, Takeshita E, Kimura K, Kawashima T, Tomo Y, Arahata H, Miyazaki D, Takeshima Y, Takahashi T, Ishigaki K, Kuru S, Wakisaka A, Awano H, Funato M, Sato T, Saito Y, Takada H, Sugie K, Kobayashi M, Ozasa S, Fujii T, Maegaki Y, Oi H, Tachimori H, Komaki H

Annals of clinical and translational neurology 10 ( 12 ) 2360 - 2372 2023.12

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Mapping the dynamic genetic regulatory architecture of HLA genes at single-cell resolution

Kang J.B., Shen A.Z., Gurajala S., Nathan A., Rumker L., Aguiar V.R.C., Valencia C., Lagattuta K.A., Zhang F., Jonsson A.H., Yazar S., Alquicira-Hernandez J., Khalili H., Ananthakrishnan A.N., Jagadeesh K., Dey K., Albrecht J., Apruzzese W., Banda N., Barnas J.L., Bathon J.M., Ben-Artzi A., Boyce B.F., Boyle D.L., Bridges S.L., Bykerk V.P., Campbell D., Carr H.L., Ceponis A., Chicoine A., Cordle A., Curtis M., Deane K.D., DiCarlo E., Dunn P., Filer A., Firestein G.S., Forbess L., Geraldino-Pardilla L., Goodman S.M., Gravallese E.M., Gregersen P.K., Guthridge J.M., Holers V.M., Horowitz D., Hughes L.B., Ishigaki K., Ivashkiv L.B., James J.A., Keras G., Korsunsky I., Lakhanpal A., Lederer J.A., Lewis M., Li Z.J., Li Y., Liao K.P., Mandelin A.M., Mantel I., Marks K.E., Maybury M., McDavid A., McGeachy M.J., Mears J., Meednu N., Millard N., Moreland L.W., Nayar S., Nerviani A., Orange D.E., Perlman H., Pitzalis C., Rangel-Moreno J., Raza K., Reshef Y., Ritchlin C., Rivellese F., Robinson W.H., Sahbudin I., Singaraju A., Seifert J.A., Slowikowski K., Smith M.H., Tabechian D., Scheel-Toellner D., Utz P.J., Watts G.F.M., Wei K., Weinand K., Weisenfeld D., Weisman M.H., Wyse A., Xiao Q., Zhu Z., Daly M.J., Xavier R.J., Donlin L.T., Anolik J.H., Powell J.E., Rao D.A.

Nature Genetics 55 ( 12 ) 2255 - 2268 2023.12

ISSN  10614036

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The human leukocyte antigen (HLA) locus plays a critical role in complex traits spanning autoimmune and infectious diseases, transplantation and cancer. While coding variation in HLA genes has been extensively documented, regulatory genetic variation modulating HLA expression levels has not been comprehensively investigated. Here we mapped expression quantitative trait loci (eQTLs) for classical HLA genes across 1,073 individuals and 1,131,414 single cells from three tissues. To mitigate technical confounding, we developed scHLApers, a pipeline to accurately quantify single-cell HLA expression using personalized reference genomes. We identified cell-type-specific cis-eQTLs for every classical HLA gene. Modeling eQTLs at single-cell resolution revealed that many eQTL effects are dynamic across cell states even within a cell type. HLA-DQ genes exhibit particularly cell-state-dependent effects within myeloid, B and T cells. For example, a T cell HLA-DQA1 eQTL (rs3104371) is strongest in cytotoxic cells. Dynamic HLA regulation may underlie important interindividual variability in immune responses.

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Immunosuppression causes dynamic changes in expression QTLs in psoriatic skin

Xiao Q., Mears J., Nathan A., Ishigaki K., Baglaenko Y., Lim N., Cooney L.A., Harris K.M., Anderson M.S., Fox D.A., Smilek D.E., Krueger J.G., Raychaudhuri S.

Nature Communications 14 ( 1 )  2023.12

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Psoriasis is a chronic, systemic inflammatory condition primarily affecting skin. While the role of the immune compartment (e.g., T cells) is well established, the changes in the skin compartment are more poorly understood. Using longitudinal skin biopsies (n = 375) from the “Psoriasis Treatment with Abatacept and Ustekinumab: A Study of Efficacy”(PAUSE) clinical trial (n = 101), we report 953 expression quantitative trait loci (eQTLs). Of those, 116 eQTLs have effect sizes that were modulated by local skin inflammation (eQTL interactions). By examining these eQTL genes (eGenes), we find that most are expressed in the skin tissue compartment, and a subset overlap with the NRF2 pathway. Indeed, the strongest eQTL interaction signal – rs1491377616-LCE3C – links a psoriasis risk locus with a gene specifically expressed in the epidermis. This eQTL study highlights the potential to use biospecimens from clinical trials to discover in vivo eQTL interactions with therapeutically relevant environmental variables.

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Genome-wide association study reveals BET1L associated with survival time in the 137,693 Japanese individuals

Akiyama M., Sakaue S., Takahashi A., Ishigaki K., Hirata M., Matsuda K., Momozawa Y., Okada Y., Ninomiya T., Koido M., Morisaki T., Nagai A., Sagiya Y., Terao C., Murakami Y., Kubo M., Kamatani Y.

Communications Biology 6 ( 1 ) 143 2023.12

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Human lifespan is reported to be heritable. Although previous genome-wide association studies (GWASs) have identified several loci, a limited number of studies have assessed the genetic associations with the real survival information on the participants. We conducted a GWAS to identify loci associated with survival time in the Japanese individuals participated in the BioBank Japan Project by carrying out sex-stratified GWASs involving 78,029 males and 59,664 females. Of them, 31,324 (22.7%) died during the mean follow-up period of 7.44 years. We found a novel locus associated with survival (BET1L; P = 5.89 × 10⁻⁹). By integrating with eQTL data, we detected a significant overlap with eQTL of BET1L in skeletal muscle. A gene-set enrichment analysis showed that genes related to the BCAR1 protein–protein interaction subnetwork influence survival time (P = 1.54 × 10⁻⁷). These findings offer the candidate genes and biological mechanisms associated with human lifespan.

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Deconstruction of rheumatoid arthritis synovium defines inflammatory subtypes

Zhang F., Jonsson A.H., Nathan A., Millard N., Curtis M., Xiao Q., Gutierrez-Arcelus M., Apruzzese W., Watts G.F.M., Weisenfeld D., Nayar S., Rangel-Moreno J., Meednu N., Marks K.E., Mantel I., Kang J.B., Rumker L., Mears J., Slowikowski K., Weinand K., Orange D.E., Geraldino-Pardilla L., Deane K.D., Tabechian D., Ceponis A., Firestein G.S., Maybury M., Sahbudin I., Ben-Artzi A., Mandelin A.M., Nerviani A., Lewis M.J., Rivellese F., Pitzalis C., Hughes L.B., Horowitz D., DiCarlo E., Gravallese E.M., Boyce B.F., Albrecht J., Barnas J.L., Bathon J.M., Boyle D.L., Bridges S.L., Campbell D., Carr H.L., Chicoine A., Cordle A., Dunn P., Forbess L., Gregersen P.K., Guthridge J.M., Ivashkiv L.B., Ishigaki K., James J.A., Keras G., Korsunsky I., Lakhanpal A., Lederer J.A., Li Z.J., Li Y., McDavid A., McGeachy M.J., Raza K., Reshef Y., Ritchlin C., Robinson W.H., Sakaue S., Seifert J.A., Singaraju A., Smith M.H., Scheel-Toellner D., Utz P.J., Weisman M.H., Wyse A., Zhu Z., Moreland L.W., Goodman S.M., Perlman H., Holers V.M., Liao K.P., Filer A., Bykerk V.P., Wei K., Rao D.A., Donlin L.T., Anolik J.H., Brenner M.B., Raychaudhuri S.

Nature 623 ( 7987 ) 616 - 624 2023.11

ISSN  00280836

　View Summary

Rheumatoid arthritis is a prototypical autoimmune disease that causes joint inflammation and destruction¹. There is currently no cure for rheumatoid arthritis, and the effectiveness of treatments varies across patients, suggesting an undefined pathogenic diversity^1,2. Here, to deconstruct the cell states and pathways that characterize this pathogenic heterogeneity, we profiled the full spectrum of cells in inflamed synovium from patients with rheumatoid arthritis. We used multi-modal single-cell RNA-sequencing and surface protein data coupled with histology of synovial tissue from 79 donors to build single-cell atlas of rheumatoid arthritis synovial tissue that includes more than 314,000 cells. We stratified tissues into six groups, referred to as cell-type abundance phenotypes (CTAPs), each characterized by selectively enriched cell states. These CTAPs demonstrate the diversity of synovial inflammation in rheumatoid arthritis, ranging from samples enriched for T and B cells to those largely lacking lymphocytes. Disease-relevant cell states, cytokines, risk genes, histology and serology metrics are associated with particular CTAPs. CTAPs are dynamic and can predict treatment response, highlighting the clinical utility of classifying rheumatoid arthritis synovial phenotypes. This comprehensive atlas and molecular, tissue-based stratification of rheumatoid arthritis synovial tissue reveal new insights into rheumatoid arthritis pathology and heterogeneity that could inform novel targeted treatments.

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Identification of a regulatory pathway governing TRAF1 via an arthritis-associated non-coding variant

Wang Q., Martínez-Bonet M., Kim T., Sparks J.A., Ishigaki K., Chen X., Sudman M., Aguiar V., Sim S., Hernandez M.C., Chiu D.J., Wactor A., Wauford B., Marion M.C., Gutierrez-Arcelus M., Bowes J., Eyre S., Nordal E., Prahalad S., Rygg M., Videm V., Raychaudhuri S., Weirauch M.T., Langefeld C.D., Thompson S.D., Nigrovic P.A.

Cell Genomics 3 ( 11 )  2023.11

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TRAF1/C5 was among the first loci shown to confer risk for inflammatory arthritis in the absence of an associated coding variant, but its genetic mechanism remains undefined. Using Immunochip data from 3,939 patients with juvenile idiopathic arthritis (JIA) and 14,412 control individuals, we identified 132 plausible common non-coding variants, reduced serially by single-nucleotide polymorphism sequencing (SNP-seq), electrophoretic mobility shift, and luciferase studies to the single variant rs7034653 in the third intron of TRAF1. Genetically manipulated experimental cells and primary monocytes from genotyped donors establish that the risk G allele reduces binding of Fos-related antigen 2 (FRA2), encoded by FOSL2, resulting in reduced TRAF1 expression and enhanced tumor necrosis factor (TNF) production. Conditioning on this JIA variant eliminated attributable risk for rheumatoid arthritis, implicating a mechanism shared across the arthritis spectrum. These findings reveal that rs7034653, FRA2, and TRAF1 mediate a pathway through which a non-coding functional variant drives risk of inflammatory arthritis in children and adults.

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Multimodal repertoire analysis unveils B cell biology in immune-mediated 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.

Annals of the Rheumatic Diseases 82 ( 11 ) 1455 - 1463 2023.11

ISSN  00034967

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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 naïve B cells was shortened among autoimmune diseases. Strong negative correlation between interferon signature strength and CDR-H3 length was observed in naïve 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.

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Multimodal repertoire analysis unveils B cell biology in immune-mediated 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

Annals of the rheumatic diseases 82 ( 11 ) 1455 - 1463 2023.11

ISSN  0003-4967

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Immunosuppression causes dynamic changes in expression QTLs in psoriatic skin.

Xiao Q, Mears J, Nathan A, Ishigaki K, Baglaenko Y, Lim N, Cooney LA, Harris KM, Anderson MS, Fox DA, Smilek DE, Krueger JG, Raychaudhuri S

Nature communications 14 ( 1 ) 6268 2023.10

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Tutorial: a statistical genetics guide to identifying HLA alleles driving complex disease

Sakaue S., Gurajala S., Curtis M., Luo Y., Choi W., Ishigaki K., Kang J.B., Rumker L., Deutsch A.J., Schönherr S., Forer L., LeFaive J., Fuchsberger C., Han B., Lenz T.L., de Bakker P.I.W., Okada Y., Smith A.V., Raychaudhuri S.

Nature Protocols 18 ( 9 ) 2625 - 2641 2023.09

ISSN  17542189

　View Summary

The human leukocyte antigen (HLA) locus is associated with more complex diseases than any other locus in the human genome. In many diseases, HLA explains more heritability than all other known loci combined. In silico HLA imputation methods enable rapid and accurate estimation of HLA alleles in the millions of individuals that are already genotyped on microarrays. HLA imputation has been used to define causal variation in autoimmune diseases, such as type I diabetes, and in human immunodeficiency virus infection control. However, there are few guidelines on performing HLA imputation, association testing, and fine mapping. Here, we present a comprehensive tutorial to impute HLA alleles from genotype data. We provide detailed guidance on performing standard quality control measures for input genotyping data and describe options to impute HLA alleles and amino acids either locally or using the web-based Michigan Imputation Server, which hosts a multi-ancestry HLA imputation reference panel. We also offer best practice recommendations to conduct association tests to define the alleles, amino acids, and haplotypes that affect human traits. Along with the pipeline, we provide a step-by-step online guide with scripts and available software (https://github.com/immunogenomics/HLA_analyses_tutorial). This tutorial will be broadly applicable to large-scale genotyping data and will contribute to defining the role of HLA in human diseases across global populations.

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Population-specific reference panel improves imputation quality and enhances locus discovery and fine-mapping

 2023.08

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Immunomics analysis of rheumatoid arthritis identified precursor dendritic cells as a key cell subset of treatment resistance

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.

Annals of the Rheumatic Diseases 82 ( 6 ) 809 - 819 2023.06

ISSN  00034967

　View Summary

Objectives 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. Methods 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. Results 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. Conclusions An increase in pre-DC in peripheral blood predicted RA treatment resistance. Pre-DC could have pathophysiological relevance to RA treatment response.

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Prediction of the cell-type-specific transcription of non-coding RNAs from genome sequences via machine learning

Koido M., Hon C.C., Koyama S., Kawaji H., Murakawa Y., Ishigaki K., Ito K., Sese J., Parrish N.F., Kamatani Y., Carninci P., Terao C.

Nature Biomedical Engineering 7 ( 6 ) 830 - 844 2023.06

　View Summary

Gene transcription is regulated through complex mechanisms involving non-coding RNAs (ncRNAs). As the transcription of ncRNAs, especially of enhancer RNAs, is often low and cell type specific, how the levels of RNA transcription depend on genotype remains largely unexplored. Here we report the development and utility of a machine-learning model (MENTR) that reliably links genome sequence and ncRNA expression at the cell type level. Effects on ncRNA transcription predicted by the model were concordant with estimates from published studies in a cell-type-dependent manner, regardless of allele frequency and genetic linkage. Among 41,223 variants from genome-wide association studies, the model identified 7,775 enhancer RNAs and 3,548 long ncRNAs causally associated with complex traits across 348 major human primary cells and tissues, such as rare variants plausibly altering the transcription of enhancer RNAs to influence the risks of Crohn’s disease and asthma. The model may aid the discovery of causal variants and the generation of testable hypotheses for biological mechanisms driving complex traits.

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Mobile element variation contributes to population-specific genome diversification, gene regulation and disease risk

Kojima S., Koyama S., Ka M., Saito Y., Parrish E.H., Endo M., Takata S., Mizukoshi M., Hikino K., Takeda A., Gelinas A.F., Heaton S.M., Koide R., Kamada A.J., Noguchi M., Hamada M., Matsuda K., Yamanashi Y., Furukawa Y., Morisaki T., Murakami Y., Muto K., Nagai A., Obara W., Yamaji K., Takahashi K., Asai S., Takahashi Y., Suzuki T., Sinozaki N., Yamaguchi H., Minami S., Murayama S., Yoshimori K., Nagayama S., Obata D., Higashiyama M., Masumoto A., Koretsune Y., Kamatani Y., Murakawa Y., Ishigaki K., Nakamura Y., Ito K., Terao C., Momozawa Y., Parrish N.F.

Nature Genetics 55 ( 6 ) 939 - 951 2023.06

ISSN  10614036

　View Summary

Mobile genetic elements (MEs) are heritable mutagens that recursively generate structural variants (SVs). ME variants (MEVs) are difficult to genotype and integrate in statistical genetics, obscuring their impact on genome diversification and traits. We developed a tool that accurately genotypes MEVs using short-read whole-genome sequencing (WGS) and applied it to global human populations. We find unexpected population-specific MEV differences, including an Alu insertion distribution distinguishing Japanese from other populations. Integrating MEVs with expression quantitative trait loci (eQTL) maps shows that MEV classes regulate tissue-specific gene expression by shared mechanisms, including creating or attenuating enhancers and recruiting post-transcriptional regulators, supporting class-wide interpretability. MEVs more often associate with gene expression changes than SNVs, thus plausibly impacting traits. Performing genome-wide association study (GWAS) with MEVs pinpoints potential causes of disease risk, including a LINE-1 insertion associated with keloid and fasciitis. This work implicates MEVs as drivers of human divergence and disease risk.

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Genome-Wide Association Study of Age-Related Macular Degeneration Reveals 2 New Loci Implying Shared Genetic Components with Central Serous Chorioretinopathy

Akiyama M., Miyake M., Momozawa Y., Arakawa S., Maruyama-Inoue M., Endo M., Iwasaki Y., Ishigaki K., Matoba N., Okada Y., Yasuda M., Oshima Y., Yoshida S., Nakao S.y., Morino K., Mori Y., Kido A., Kato A., Yasukawa T., Obata R., Nagai Y., Takahashi K., Fujisawa K., Miki A., Nakamura M., Honda S., Ushida H., Yasuma T., Nishiguchi K.M., Mori R., Tanaka K., Wakatsuki Y., Yamashiro K., Kadonosono K., Terao C., Ishibashi T., Tsujikawa A., Sonoda K.H., Kubo M., Kamatani Y.

Ophthalmology 130 ( 4 ) 361 - 372 2023.04

ISSN  01616420

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Purpose: To investigate the genetic architecture of age-related macular degeneration (AMD) in a Japanese population. Design: Genome-wide association study (GWAS). Participants: Three thousand seven hundred seventy-two patients with AMD and 16 770 control participants from the Japanese population were enrolled in the association analyses. Methods: We conducted a meta-analysis of 2 independent GWASs that included a total of 2663 patients with AMD and 9471 control participants using the imputation reference panel for genotype imputation specified for the Japanese population (n = 3541). A replication study was performed using an independent set of 1109 patients with AMD and 7299 control participants. Main Outcome Measures: Associations of genetic variants with AMD. Results: A meta-analysis of the 2 GWASs identified 6 loci significantly associated with AMD (P < 5.0 × 10^–8). Of these loci, 4 were known to be associated with AMD (CFH, C2/FB, TNFRSF10A, and ARMS2), and 2 were novel (rs4147157 near WBP1L and rs76228488 near GATA5). The newly identified associations were confirmed in a replication study (P < 0.01). After the meta-analysis of all datasets, we observed strong associations in these loci (P = 1.88 × 10^–12 and P = 1.35 × 10^–9 for meta-analysis for rs4147157 and rs76228488, respectively). When we looked up the associations in the reported central serous chorioretinopathy (CSC) GWAS conducted in the Japanese population, both loci were associated significantly with CSC (P = 4.86 × 10^–3 and P = 4.28 × 10^–3 for rs4147157 and rs76228488, respectively). We performed a genetic colocalization analysis for these loci and estimated that the posterior probabilities of shared causal variants between AMD and CSC were 0.39 and 0.60 for WBP1L and GATA5, respectively. Genetic correlation analysis focusing on the epidemiologically suggested clinical risk factors implicated shared polygenic architecture between AMD and smoking cessation (r<inf>g</inf> [the measure of genetic correlation] = –0.33; P = 0.01; false discovery rate, 0.099). Conclusions: Our findings imply shared genetic components conferring the risk of both AMD and CSC. Financial Disclosure(s): Proprietary or commercial disclosure may be found after the references.

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Functional Genetics to Understand the Etiology of Autoimmunity

Hatano H., Ishigaki K.

Genes 14 ( 3 )  2023.03

　View Summary

Common variants strongly influence the risk of human autoimmunity. Two categories of variants contribute substantially to the risk: (i) coding variants of HLA genes and (ii) non-coding variants at the non-HLA loci. We recently developed a novel analytic pipeline of T cell receptor (TCR) repertoire to understand how HLA coding variants influence the risk. We identified that the risk variants increase the frequency of auto-reactive T cells. In addition, to understand how non-coding variants contribute to the risk, the researchers conducted integrative analyses using expression quantitative trait loci (eQTL) and splicing quantitative trait loci (sQTL) and demonstrated that the risk non-coding variants dysregulate specific genes’ expression and splicing. These studies provided novel insight into the immunological consequences of two major genetic risks, and we will introduce these research achievements in detail in this review.

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T CELL RECEPTOR-MEDIATED REGULATION OF IMMUNE SYSTEM

Ishigaki K.

Japanese Journal of Allergology 72 ( 8 ) 1021 - 1025 2023

ISSN  00214884

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Splicing QTL analysis focusing on coding sequences reveals mechanisms for disease susceptibility loci

Yamaguchi K., Ishigaki K., Suzuki A., Tsuchida Y., Tsuchiya H., Sumitomo S., Nagafuchi Y., Miya F., Tsunoda T., Shoda H., Fujio K., Yamamoto K., Kochi Y.

Nature Communications 13 ( 1 ) 4659 2022.12

　View Summary

Splicing quantitative trait loci (sQTLs) are one of the major causal mechanisms in genome-wide association study (GWAS) loci, but their role in disease pathogenesis is poorly understood. One reason is the complexity of alternative splicing events producing many unknown isoforms. Here, we propose two approaches, namely integration and selection, for this complexity by focusing on protein-structure of isoforms. First, we integrate isoforms with the same coding sequence (CDS) and identify 369-601 integrated-isoform ratio QTLs (i²-rQTLs), which altered protein-structure, in six immune subsets. Second, we select CDS incomplete isoforms annotated in GENCODE and identify 175-337 isoform-ratio QTL (i-rQTL). By comprehensive long-read capture RNA-sequencing among these incomplete isoforms, we reveal 29 full-length isoforms with unannotated CDSs associated with GWAS traits. Furthermore, we show that disease-causal sQTL genes can be identified by evaluating their trans-eQTL effects. Our approaches highlight the understudied role of protein-altering sQTLs and are broadly applicable to other tissues and diseases.

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Control of naive and effector CD4 T cell receptor repertoires by rheumatoid-arthritis-risk HLA alleles

Nagafuchi Y., Ota M., Hatano H., Inoue M., Kobayashi S., Okubo M., Sugimori Y., Nakano M., Yamada S., Yoshida R., Tsuchida Y., Iwasaki Y., Shoda H., Okada Y., Yamamoto K., Ishigaki K., Okamura T., Fujio K.

Journal of Autoimmunity 133   102907 2022.12

ISSN  08968411

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Objective: Human Leukocyte Antigen (HLA) alleles regulate susceptibility to rheumatoid arthritis (RA) and immune-mediated diseases. This study aims to elucidate the impact of HLA alleles to T cell subsets. Methods: We performed genome-wide and HLA allele association analysis for T cell receptor (TCR) beta chain repertoire in 13 purified T cell subsets from the ImmuNexUT database, consisting of 407 donors with ten immune-mediated diseases and healthy controls. Results: HLA class II alleles were associated with TRBV gene usage and the public clones of CD4 T cells, while HLA class I alleles were associated with CD8 T cells. RA-risk and immune-mediated diseases-risk HLA alleles were associated with TRBV gene usage of naive and effector CD4 T cell subsets and public clones accumulating in Th17. Clonal diversity was independent of HLA alleles and was correlated with transcriptome changes that reflect TCR signaling. Conclusion: This study revealed in vivo evidence that both HLA alleles and environmental factors shape naive and effector TCR repertoires in RA and immune-mediated diseases patients.

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Genetic and clinical landscape of childhood cerebellar hypoplasia and atrophy.

Sakamoto M, Iwama K, Sasaki M, Ishiyama A, Komaki H, Saito T, Takeshita E, Shimizu-Motohashi Y, Haginoya K, Kobayashi T, Goto T, Tsuyusaki Y, Iai M, Kurosawa K, Osaka H, Tohyama J, Kobayashi Y, Okamoto N, Suzuki Y, Kumada S, Inoue K, Mashimo H, Arisaka A, Kuki I, Saijo H, Yokochi K, Kato M, Inaba Y, Gomi Y, Saitoh S, Shirai K, Morimoto M, Izumi Y, Watanabe Y, Nagamitsu SI, Sakai Y, Fukumura S, Muramatsu K, Ogata T, Yamada K, Ishigaki K, Hirasawa K, Shimoda K, Akasaka M, Kohashi K, Sakakibara T, Ikuno M, Sugino N, Yonekawa T, Gürsoy S, Cinleti T, Kim CA, Teik KW, Yan CM, Haniffa M, Ohba C, Ito S, Saitsu H, Saida K, Tsuchida N, Uchiyama Y, Koshimizu E, Fujita A, Hamanaka K, Misawa K, Miyatake S, Mizuguchi T, Miyake N, Matsumoto N

Genetics in medicine : official journal of the American College of Medical Genetics 24 ( 12 ) 2453 - 2463 2022.12

ISSN  1098-3600

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Discovery and systematic characterization of risk variants and genes for coronary artery disease in over a million participants

Aragam K.G., Jiang T., Goel A., Kanoni S., Wolford B.N., Atri D.S., Weeks E.M., Wang M., Hindy G., Zhou W., Grace C., Roselli C., Marston N.A., Kamanu F.K., Surakka I., Venegas L.M., Sherliker P., Koyama S., Ishigaki K., Åsvold B.O., Brown M.R., Brumpton B., de Vries P.S., Giannakopoulou O., Giardoglou P., Gudbjartsson D.F., Güldener U., Haider S.M.I., Helgadottir A., Ibrahim M., Kastrati A., Kessler T., Kyriakou T., Konopka T., Li L., Ma L., Meitinger T., Mucha S., Munz M., Murgia F., Nielsen J.B., Nöthen M.M., Pang S., Reinberger T., Schnitzler G., Smedley D., Thorleifsson G., von Scheidt M., Ulirsch J.C., Danesh J., Arnar D.O., Burtt N.P., Costanzo M.C., Flannick J., Ito K., Jang D.K., Kamatani Y., Khera A.V., Komuro I., Kullo I.J., Lotta L.A., Nelson C.P., Roberts R., Thorgeirsson G., Thorsteinsdottir U., Webb T.R., Baras A., Björkegren J.L.M., Boerwinkle E., Dedoussis G., Holm H., Hveem K., Melander O., Morrison A.C., Orho-Melander M., Rallidis L.S., Ruusalepp A., Sabatine M.S., Stefansson K., Zalloua P., Ellinor P.T., Farrall M., Ruff C.T., Finucane H.K., Hopewell J.C., Clarke R., Gupta R.M., Erdmann J., Samani N.J., Schunkert H., Watkins H., Willer C.J., Deloukas P., Kathiresan S., Butterworth A.S., de Vries P.S.

Nature Genetics 54 ( 12 ) 1803 - 1815 2022.12

ISSN  10614036

　View Summary

The discovery of genetic loci associated with complex diseases has outpaced the elucidation of mechanisms of disease pathogenesis. Here we conducted a genome-wide association study (GWAS) for coronary artery disease (CAD) comprising 181,522 cases among 1,165,690 participants of predominantly European ancestry. We detected 241 associations, including 30 new loci. Cross-ancestry meta-analysis with a Japanese GWAS yielded 38 additional new loci. We prioritized likely causal variants using functionally informed fine-mapping, yielding 42 associations with less than five variants in the 95% credible set. Similarity-based clustering suggested roles for early developmental processes, cell cycle signaling and vascular cell migration and proliferation in the pathogenesis of CAD. We prioritized 220 candidate causal genes, combining eight complementary approaches, including 123 supported by three or more approaches. Using CRISPR–Cas9, we experimentally validated the effect of an enhancer in MYO9B, which appears to mediate CAD risk by regulating vascular cell motility. Our analysis identifies and systematically characterizes >250 risk loci for CAD to inform experimental interrogation of putative causal mechanisms for CAD.

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High incidence of proliferative and membranous nephritis in SLE patients with low proteinuria in the Accelerating Medicines Partnership

Carlucci P.M., Li J., Fava A., Deonaraine K.K., Wofsy D., James J.A., Putterman C., Diamond B., Davidson A., Fine D.M., Monroy-Trujillo J., Atta M.G., Dejager W., Guthridge J.M., Haag K., Rao D.A., Brenner M.B., Lederer J.A., Apruzzese W., Belmont H.M., Izmirly P.M., Zaminski D., Wu M., Connery S., Payan-Schober F., Furie R., Dall'era M., Cho K., Kamen D., Kalunian K., Anolik J., Barnas J., Ishimori M., Weisman M.H., Goff J., Dunn P.J., Raychaudhuri S., Zhang F., Korsunsky I., Nathan A., Mears J., Ishigaki K., Xiao Q., Millard N., Weinand K., Sakaue S., Utz P.J., Mao R., Robinson B., Maecker H., MacWana S., Bridges S.L., Bykerk V., Donlin L., Goodman S., Dicarlo E., Smith M., Lakhanpal A., Sherman H., Singaraju A., Shakib L., Ritchlin C., Boyce B., Tabechian D., McDavid A., Rangel-Moreno J., Meednu N., Albrecht J., Wei K., Helena Jonsson A., Simmons D., Keras G., Keegan J., Watts G., Li Zhu Y., Chicoine A., Jian Li Z., Gravallese E.M., Howard K., McGeachy M., Firestein G.S., Boyle D.L., Ceponis A., Gregersen P.K., Horowitz D., Perlman H., Dominguez S., Cuda C.M., Mandolin A.M., Thakrar A., Bathon J.M., Hughes L., Michael Holers V., Seifert J., Deane K., Moreland L.W., Filer A., Raza K., Sahbudin I., Pitzalis C.

Rheumatology United Kingdom 61 ( 11 ) 4335 - 4343 2022.11

ISSN  14620324

　View Summary

Objective: Delayed detection of LN associates with worse outcomes. There are conflicting recommendations regarding a threshold level of proteinuria at which biopsy will likely yield actionable management. This study addressed the association of urine protein:creatinine ratios (UPCR) with clinical characteristics and investigated the incidence of proliferative and membranous histology in patients with a UPCR between 0.5 and 1. Methods: A total of 275 SLE patients (113 first biopsy, 162 repeat) were enrolled in the multicentre multi-ethnic/racial Accelerating Medicines Partnership across 15 US sites at the time of a clinically indicated renal biopsy. Patients were followed for 1 year. Results: At biopsy, 54 patients had UPCR <1 and 221 had UPCR ≥1. Independent of UPCR or biopsy number, a majority (92%) of patients had class III, IV, V or mixed histology. Moreover, patients with UPCR <1 and class III, IV, V, or mixed had a median activity index of 4.5 and chronicity index of 3, yet 39% of these patients had an inactive sediment. Neither anti-dsDNA nor low complement distinguished class I or II from III, IV, V or mixed in patients with UPCR <1. Of 29 patients with baseline UPCR <1 and class III, IV, V or mixed, 23 (79%) had a UPCR <0.5 at 1 year. Conclusion: In this prospective study, three-quarters of patients with UPCR <1 had histology showing class III, IV, V or mixed with accompanying activity and chronicity despite an inactive sediment or normal serologies. These data support renal biopsy at thresholds lower than a UPCR of 1.

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Multi-ancestry genome-wide association analyses identify novel genetic mechanisms in rheumatoid arthritis

Ishigaki K., Sakaue S., Terao C., Luo Y., Sonehara K., Yamaguchi K., Amariuta T., Too C.L., Laufer V.A., Scott I.C., Viatte S., Takahashi M., Ohmura K., Murasawa A., Hashimoto M., Ito H., Hammoudeh M., Emadi S.A., Masri B.K., Halabi H., Badsha H., Uthman I.W., Wu X., Lin L., Li T., Plant D., Barton A., Orozco G., Verstappen S.M.M., Bowes J., MacGregor A.J., Honda S., Koido M., Tomizuka K., Kamatani Y., Tanaka H., Tanaka E., Suzuki A., Maeda Y., Yamamoto K., Miyawaki S., Xie G., Zhang J., Amos C.I., Keystone E., Wolbink G., van der Horst-Bruinsma I., Cui J., Liao K.P., Carroll R.J., Lee H.S., Bang S.Y., Siminovitch K.A., de Vries N., Alfredsson L., Rantapää-Dahlqvist S., Karlson E.W., Bae S.C., Kimberly R.P., Edberg J.C., Mariette X., Huizinga T., Dieudé P., Schneider M., Kerick M., Denny J.C., Matsuda K., Matsuo K., Mimori T., Matsuda F., Fujio K., Tanaka Y., Kumanogoh A., Traylor M., Lewis C.M., Eyre S., Xu H., Saxena R., Arayssi T., Kochi Y., Ikari K., Harigai M., Gregersen P.K., Yamamoto K., Louis Bridges S., Padyukov L., Martin J., Klareskog L., Okada Y., Raychaudhuri S.

Nature Genetics 54 ( 11 ) 1640 - 1651 2022.11

ISSN  10614036

　View Summary

Rheumatoid arthritis (RA) is a highly heritable complex disease with unknown etiology. Multi-ancestry genetic research of RA promises to improve power to detect genetic signals, fine-mapping resolution and performances of polygenic risk scores (PRS). Here, we present a large-scale genome-wide association study (GWAS) of RA, which includes 276,020 samples from five ancestral groups. We conducted a multi-ancestry meta-analysis and identified 124 loci (P < 5 × 10⁻⁸), of which 34 are novel. Candidate genes at the novel loci suggest essential roles of the immune system (for example, TNIP2 and TNFRSF11A) and joint tissues (for example, WISP1) in RA etiology. Multi-ancestry fine-mapping identified putatively causal variants with biological insights (for example, LEF1). Moreover, PRS based on multi-ancestry GWAS outperformed PRS based on single-ancestry GWAS and had comparable performance between populations of European and East Asian ancestries. Our study provides several insights into the etiology of RA and improves the genetic predictability of RA.

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Immunosuppression causes dynamic changes in expression QTLs in psoriatic skin

 2022.10

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Biological insights into systemic lupus erythematosus through an immune cell-specific transcriptome-wide association study

Yin X., Kim K., Suetsugu H., Bang S.Y., Wen L., Koido M., Ha E., Liu L., Sakamoto Y., Jo S., Leng R.X., Otomo N., Kwon Y.C., Sheng Y., Sugano N., Hwang M.Y., Li W., Mukai M., Yoon K., Cai M., Ishigaki K., Chung W.T., Huang H., Takahashi D., Lee S.S., Wang M., Karino K., Shim S.C., Zheng X., Miyamura T., Kang Y.M., Ye D., Nakamura J., Suh C.H., Tang Y., Motomura G., Park Y.B., Ding H., Kuroda T., Choe J.Y., Li C., Niiro H., Park Y., Shen C., Miyamoto T., Ahn G.Y., Fei W., Takeuchi T., Shin J.M., Li K., Kawaguchi Y., Lee Y.K., Wang Y.F., Amano K., Park D.J., Yang W., Tada Y., Lau Y.L., Yamaji K., Zhu Z., Shimizu M., Atsumi T., Suzuki A., Sumida T., Okada Y., Matsuda K., Matsuo K., Kochi Y., Yamamoto K., Ohmura K., Kim T.H., Yang S., Yamamoto T., Kim B.J., Shen N., Ikegawa S., Lee H.S., Zhang X., Terao C., Cui Y., Bae S.C.

Annals of the Rheumatic Diseases 81 ( 9 ) 1273 - 1280 2022.09

ISSN  00034967

　View Summary

Objective Genome-wide association studies (GWAS) have identified >100 risk loci for systemic lupus erythematosus (SLE), but the disease genes at most loci remain unclear, hampering translation of these genetic discoveries. We aimed to prioritise genes underlying the 110 SLE loci that were identified in the latest East Asian GWAS meta-analysis. Methods We built gene expression predictive models in blood B cells, CD4 + and CD8 + T cells, monocytes, natural killer cells and peripheral blood cells of 105 Japanese individuals. We performed a transcriptome-wide association study (TWAS) using data from the latest genome-wide association meta-analysis of 208 370 East Asians and searched for candidate genes using TWAS and three data-driven computational approaches. Results TWAS identified 171 genes for SLE (p<1.0×10 -5); 114 (66.7%) showed significance only in a single cell type; 127 (74.3%) were in SLE GWAS loci. TWAS identified a strong association between CD83 and SLE (p<7.7×10 -8). Meta-analysis of genetic associations in the existing 208 370 East Asian and additional 1498 cases and 3330 controls found a novel single-variant association at rs72836542 (OR=1.11, p=4.5×10 -9) around CD83. For the 110 SLE loci, we identified 276 gene candidates, including 104 genes at recently-identified SLE novel loci. We demonstrated in vitro that putative causal variant rs61759532 exhibited an allele-specific regulatory effect on ACAP1, and that presence of the SLE risk allele decreased ACAP1 expression. Conclusions Cell-level TWAS in six types of immune cells complemented SLE gene discovery and guided the identification of novel genetic associations. The gene findings shed biological insights into SLE genetic associations.

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Distinct transcriptome architectures underlying lupus establishment and exacerbation

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.

Cell 185 ( 18 ) 3375 - 3389.e21 2022.09

ISSN  00928674

　View Summary

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.

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Large-scale genome-wide association study of coronary artery disease in genetically diverse populations

Tcheandjieu C., Zhu X., Hilliard A.T., Clarke S.L., Napolioni V., Ma S., Lee K.M., Fang H., Chen F., Lu Y., Tsao N.L., Raghavan S., Koyama S., Gorman B.R., Vujkovic M., Klarin D., Levin M.G., Sinnott-Armstrong N., Wojcik G.L., Plomondon M.E., Maddox T.M., Waldo S.W., Bick A.G., Pyarajan S., Huang J., Song R., Ho Y.L., Buyske S., Kooperberg C., Haessler J., Loos R.J.F., Do R., Verbanck M., Chaudhary K., North K.E., Avery C.L., Graff M., Haiman C.A., Le Marchand L., Wilkens L.R., Bis J.C., Leonard H., Shen B., Lange L.A., Giri A., Dikilitas O., Kullo I.J., Stanaway I.B., Jarvik G.P., Gordon A.S., Hebbring S., Namjou B., Kaufman K.M., Ito K., Ishigaki K., Kamatani Y., Verma S.S., Ritchie M.D., Kember R.L., Baras A., Lotta L.A., Kathiresan S., Hauser E.R., Miller D.R., Lee J.S., Saleheen D., Reaven P.D., Cho K., Gaziano J.M., Natarajan P., Huffman J.E., Voight B.F., Rader D.J., Chang K.M., Lynch J.A., Damrauer S.M., Wilson P.W.F., Tang H., Sun Y.V., Tsao P.S., O’Donnell C.J., Assimes T.L.

Nature Medicine 28 ( 8 ) 1679 - 1692 2022.08

ISSN  10788956

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We report a genome-wide association study (GWAS) of coronary artery disease (CAD) incorporating nearly a quarter of a million cases, in which existing studies are integrated with data from cohorts of white, Black and Hispanic individuals from the Million Veteran Program. We document near equivalent heritability of CAD across multiple ancestral groups, identify 95 novel loci, including nine on the X chromosome, detect eight loci of genome-wide significance in Black and Hispanic individuals, and demonstrate that two common haplotypes at the 9p21 locus are responsible for risk stratification in all populations except those of African origin, in which these haplotypes are virtually absent. Moreover, in the largest GWAS for angiographically derived coronary atherosclerosis performed to date, we find 15 loci of genome-wide significance that robustly overlap with established loci for clinical CAD. Phenome-wide association analyses of novel loci and polygenic risk scores (PRSs) augment signals related to insulin resistance, extend pleiotropic associations of these loci to include smoking and family history, and precisely document the markedly reduced transferability of existing PRSs to Black individuals. Downstream integrative analyses reinforce the critical roles of vascular endothelial, fibroblast, and smooth muscle cells in CAD susceptibility, but also point to a shared biology between atherosclerosis and oncogenesis. This study highlights the value of diverse populations in further characterizing the genetic architecture of CAD.

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Single-cell eQTL models reveal dynamic T cell state dependence of disease loci

Nathan A., Asgari S., Ishigaki K., Valencia C., Amariuta T., Luo Y., Beynor J.I., Baglaenko Y., Suliman S., Price A.L., Lecca L., Murray M.B., Moody D.B., Raychaudhuri S.

Nature 606 ( 7912 ) 120 - 128 2022.06

ISSN  00280836

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Non-coding genetic variants may cause disease by modulating gene expression. However, identifying these expression quantitative trait loci (eQTLs) is complicated by differences in gene regulation across fluid functional cell states within cell types. These states—for example, neurotransmitter-driven programs in astrocytes or perivascular fibroblast differentiation—are obscured in eQTL studies that aggregate cells^1,2. Here we modelled eQTLs at single-cell resolution in one complex cell type: memory T cells. Using more than 500,000 unstimulated memory T cells from 259 Peruvian individuals, we show that around one-third of 6,511 cis-eQTLs had effects that were mediated by continuous multimodally defined cell states, such as cytotoxicity and regulatory capacity. In some loci, independent eQTL variants had opposing cell-state relationships. Autoimmune variants were enriched in cell-state-dependent eQTLs, including risk variants for rheumatoid arthritis near ORMDL3 and CTLA4; this indicates that cell-state context is crucial to understanding potential eQTL pathogenicity. Moreover, continuous cell states explained more variation in eQTLs than did conventional discrete categories, such as CD4⁺ versus CD8⁺, suggesting that modelling eQTLs and cell states at single-cell resolution can expand insight into gene regulation in functionally heterogeneous cell types.

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Immune cell multiomics analysis reveals contribution of oxidative phosphorylation to B-cell functions and organ damage of lupus

Takeshima Y., Iwasaki Y., Nakano M., Narushima Y., Ota M., Nagafuchi Y., Sumitomo S., Okamura T., Elkon K., Ishigaki K., Suzuki A., Kochi Y., Yamamoto K., Fujio K.

Annals of the Rheumatic Diseases 81 ( 6 ) 845 - 853 2022.06

ISSN  00034967

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Objective Systemic lupus erythematosus (SLE) is the prototypical systemic autoimmune disease. While the long-term prognosis has greatly improved, better long-term survival is still necessary. The type I interferon (IFN) signature, a prominent feature of SLE, is not an ideal therapeutic target or outcome predictor. To explore immunological pathways in SLE more precisely, we performed transcriptomic, epigenomic and genomic analyses using 19 immune cell subsets from peripheral blood. Methods We sorted 19 immune cell subsets and identified the mRNA expression profiles and genetic polymorphisms in 107 patients with SLE and 92 healthy controls. Combined differentially expressed genes and expression quantitative trait loci analysis was conducted to find key driver genes in SLE pathogenesis. Results We found transcriptomic, epigenetic and genetic importance of oxidative phosphorylation (OXPHOS)/mitochondrial dysfunction in SLE memory B cells. Particularly, we identified an OXPHOS-regulating gene, PRDX6 (peroxiredoxin 6), as a key driver in SLE B cells. Prdx6-deficient B cells showed upregulated mitochondrial respiration as well as antibody production. We revealed OXPHOS signature was associated with type I IFN signalling-related genes (ISRGs) signature in SLE memory B cells. Furthermore, the gene sets related to innate immune signalling among ISRGs presented correlation with OXPHOS and these two signatures showed associations with SLE organ damage as well as specific clinical phenotypes. Conclusion This work elucidated the potential prognostic marker for SLE. Since OXPHOS consists of the electron transport chain, a functional unit in mitochondria, these findings suggest the importance of mitochondrial dysfunction as a key immunological pathway involved in SLE.

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HLA autoimmune risk alleles restrict the hypervariable region of T cell receptors

Ishigaki K., Lagattuta K.A., Luo Y., James E.A., Buckner J.H., Raychaudhuri S.

Nature Genetics (Springer Science and Business Media {LLC})  54 ( 4 ) 393 - 402 2022.04

ISSN  10614036

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Polymorphisms in the human leukocyte antigen (HLA) genes strongly influence autoimmune disease risk. HLA risk alleles may influence thymic selection to increase the frequency of T cell receptors (TCRs) reactive to autoantigens (central hypothesis). However, research in human autoimmunity has provided little evidence supporting the central hypothesis. Here we investigated the influence of HLA alleles on TCR composition at the highly diverse complementarity determining region 3 (CDR3), which confers antigen recognition. We observed unexpectedly strong HLA–CDR3 associations. The strongest association was found at HLA-DRB1 amino acid position 13, the position that mediates genetic risk for multiple autoimmune diseases. We identified multiple CDR3 amino acid features enriched by HLA risk alleles. Moreover, the CDR3 features promoted by the HLA risk alleles are more enriched in candidate pathogenic TCRs than control TCRs (for example, citrullinated epitope-specific TCRs in patients with rheumatoid arthritis). Together, these results provide genetic evidence supporting the central hypothesis.

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Repertoire analyses reveal T cell antigen receptor sequence features that influence T cell fate

Lagattuta K.A., Kang J.B., Nathan A., Pauken K.E., Jonsson A.H., Rao D.A., Sharpe A.H., Ishigaki K., Raychaudhuri S.

Nature Immunology 23 ( 3 ) 446 - 457 2022.03

ISSN  15292908

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T cells acquire a regulatory phenotype when their T cell antigen receptors (TCRs) experience an intermediate- to high-affinity interaction with a self-peptide presented via the major histocompatibility complex (MHC). Using TCRβ sequences from flow-sorted human cells, we identified TCR features that promote regulatory T cell (T<inf>reg</inf>) fate. From these results, we developed a scoring system to quantify TCR-intrinsic regulatory potential (TiRP). When applied to the tumor microenvironment, TiRP scoring helped to explain why only some T cell clones maintained the conventional T cell (T<inf>conv</inf>) phenotype through expansion. To elucidate drivers of these predictive TCR features, we then examined the two elements of the T<inf>reg</inf> TCR ligand separately: the self-peptide and the human MHC class II molecule. These analyses revealed that hydrophobicity in the third complementarity-determining region (CDR3β) of the TCR promotes reactivity to self-peptides, while TCR variable gene (TRBV gene) usage shapes the TCR’s general propensity for human MHC class II-restricted activation.

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A FLOT1 host regulatory allele is associated with a recently expanded Mtb clade in patients with tuberculosis

Yang Luo and Chuan-Chin Huang and Qingyun Liu and Nicole Howard and Xinyi Li and Junhao Zhu and Tiffany Amariuta and Samira Asgari and Kazuyoshi Ishigaki and Roger Calderon and D. Branch Moody and Leonid Lecca and Sarah M Fortune and Megan B Murray and Soumya Raychaudhuri

(Cold Spring Harbor Laboratory)   2022.02

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Splicing QTL analysis focusing on coding sequences reveals pathogenicity of disease susceptibility loci

 2022.01

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Beyond GWAS: from simple associations to functional insights

Ishigaki K.

Seminars in Immunopathology (Springer Science and Business Media {LLC})  44 ( 1 ) 3 - 14 2022.01

ISSN  18632297

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Each human, when born, has slightly different DNA sequences, which make each of us unique. The variations in DNA sequences are called genetic variants. The primary aim of genome-wide association study (GWAS) is to detect associations between genetic variants and human phenotypes. Since GWAS focuses on germ-line variants, there is no reverse causation. Therefore, GWAS is one of the few tools that can assess the causality of human diseases. In the past 10 years, many large-scale GWAS have been conducted. Although the primary outputs of GWAS are just a series of statistics, its downstream analyses provided many insights beyond simple associations: the causal mechanisms for autoimmune diseases and shared etiology between diseases. Moreover, GWAS downstream analyses generated scores potentially helpful in predicting clinical outcomes of each patient. This review focuses on GWAS for autoimmune diseases and introduces significant achievements of its downstream analyses. We also provide future directions that potentially overcome current limitations. We restrict our discussion to common autoimmune diseases (e.g., rheumatoid arthritis) since rare Mendelian diseases possess distinct genetic etiologies and are not tested by GWAS.

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Trans-ancestry genome-wide association study identifies novel genetic mechanisms in rheumatoid arthritis

 2021.12

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Restoration of the defect in radial glial fiber migration and cortical plate organization in a brain organoid model of Fukuyama muscular dystrophy.

Taniguchi-Ikeda M, Koyanagi-Aoi M, Maruyama T, Takaori T, Hosoya A, Tezuka H, Nagase S, Ishihara T, Kadoshima T, Muguruma K, Ishigaki K, Sakurai H, Mizoguchi A, Novitch BG, Toda T, Watanabe M, Aoi T

iScience 24 ( 10 ) 103140 2021.10

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A cross-population atlas of genetic associations for 220 human phenotypes

Sakaue S., Kanai M., Tanigawa Y., Karjalainen J., Kurki M., Koshiba S., Narita A., Konuma T., Yamamoto K., Akiyama M., Ishigaki K., Suzuki A., Suzuki K., Obara W., Yamaji K., Takahashi K., Asai S., Takahashi Y., Suzuki T., Shinozaki N., Yamaguchi H., Minami S., Murayama S., Yoshimori K., Nagayama S., Obata D., Higashiyama M., Masumoto A., Koretsune Y., Ito K., Terao C., Yamauchi T., Komuro I., Kadowaki T., Tamiya G., Yamamoto M., Nakamura Y., Kubo M., Murakami Y., Yamamoto K., Kamatani Y., Palotie A., Rivas M.A., Daly M.J., Matsuda K., Okada Y.

Nature Genetics 53 ( 10 ) 1415 - 1424 2021.10

ISSN  10614036

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Current genome-wide association studies do not yet capture sufficient diversity in populations and scope of phenotypes. To expand an atlas of genetic associations in non-European populations, we conducted 220 deep-phenotype genome-wide association studies (diseases, biomarkers and medication usage) in BioBank Japan (n = 179,000), by incorporating past medical history and text-mining of electronic medical records. Meta-analyses with the UK Biobank and FinnGen (n<inf>total</inf> = 628,000) identified ~5,000 new loci, which improved the resolution of the genomic map of human traits. This atlas elucidated the landscape of pleiotropy as represented by the major histocompatibility complex locus, where we conducted HLA fine-mapping. Finally, we performed statistical decomposition of matrices of phenome-wide summary statistics, and identified latent genetic components, which pinpointed responsible variants and biological mechanisms underlying current disease classifications across populations. The decomposed components enabled genetically informed subtyping of similar diseases (for example, allergic diseases). Our study suggests a potential avenue for hypothesis-free re-investigation of human diseases through genetics.

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Blocking VCAM-1 inhibits pancreatic tumour progression and cancer-associated thrombosis/thromboembolism.

Sano M, Takahashi R, Ijichi H, Ishigaki K, Yamada T, Miyabayashi K, Kimura G, Mizuno S, Kato H, Fujiwara H, Nakatsuka T, Tanaka Y, Kim J, Masugi Y, Morishita Y, Tanaka M, Ushiku T, Nakai Y, Tateishi K, Ishii Y, Isayama H, Moses HL, Koike K

Gut 70 ( 9 ) 1713 - 1723 2021.09

ISSN  0017-5749

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Modeling memory T cell states at single-cell resolution identifies in vivo state-dependence of eQTLs influencing disease

Aparna Nathan and Samira Asgari and Kazuyoshi Ishigaki and Tiffany Amariuta and Yang Luo and Jessica I Beynor and Yuriy Baglaenko and Sara Suliman and Alkes Price and Leonid Lecca and Megan B Murray and D. Branch Moody and Soumya Raychaudhuri

(Cold Spring Harbor Laboratory)   2021.07

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Contribution of a European-Prevalent Variant near CD83 and an East Asian–Prevalent Variant near IL17RB to Herpes Zoster Risk in Tofacitinib Treatment: Results of Genome-Wide Association Study Meta-Analyses

Bing N., Zhou H., Chen X., Hirose T., Kochi Y., Tsuchida Y., Ishigaki K., Sumitomo S., Fujio K., Zhang B., Valdez H., Vincent M.S., Martin D., Clark J.D.

Arthritis and Rheumatology 73 ( 7 ) 1155 - 1166 2021.07

ISSN  23265191

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Objective: Tofacitinib is an oral JAK inhibitor for the treatment of rheumatoid arthritis (RA), psoriatic arthritis, and ulcerative colitis, and has been previously investigated for psoriasis (PsO). This meta-analysis of genome-wide association studies (GWAS) was performed to identify genetic factors associated with increased risk/faster onset of herpes zoster (HZ) in subjects with RA or PsO receiving tofacitinib treatment, and to determine potential mechanisms that could be attributed to the varying rates of HZ across ethnicities. Methods: In an ethnicity/indication-specific, trans-ethnic, trans-population meta-analysis of GWAS in subjects with RA or PsO from phase II, phase III, and long-term extension studies of tofacitinib, 8 million genetic variants were evaluated for their potential association with time to an HZ event and incidence of an HZ event (case versus control) with tofacitinib treatment, using Cox proportional hazard and logistic regression analyses, respectively. Results: In total, 5,246 subjects were included (3,168 with RA and 2,078 with PsO). After adjustment for age, baseline absolute lymphocyte count, genetically defined ethnicity, and concomitant methotrexate use (in RA subjects only), 4 loci were significantly associated with faster onset of HZ in European subjects (P < 5 × 10⁻⁸), including a single-nucleotide polymorphism (SNP) near CD83 (frequency of risk allele ~2% in European subjects versus ~0.1% in East Asian subjects). In the trans-ethnic, trans-population meta-analysis, the CD83 SNP remained significant. Four additional significant loci were identified in the meta-analysis, among which a SNP near IL17RB was associated with faster onset of HZ (meta-analysis hazard ratio 3.6 [95% confidence interval 2.40–5.44], P = 7.6 × 10⁻¹⁰; frequency of risk allele ~12% in East Asian subjects versus <0.2% in European subjects). Conclusion: Genetic analysis of tofacitinib-treated subjects with RA or PsO identified multiple loci associated with increased HZ risk. Prevalent variants near the immune-relevant genes CD83 and IL17RB in European and East Asian populations, respectively, may contribute to risk of HZ in tofacitinib-treated subjects.

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Repertoire analyses reveal TCR sequence features that influence T cell fate

Kaitlyn A. Lagattuta and Joyce B. Kang and Aparna Nathan and Kristen E. Pauken and Anna Helena Jonsson and Deepak A. Rao and Kazuyoshi Ishigaki and Soumya Raychaudhuri

(Cold Spring Harbor Laboratory)   2021.06

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Multimodally profiling memory T cells from a tuberculosis cohort identifies cell state associations with demographics, environment and disease

Nathan A., Beynor J.I., Baglaenko Y., Suliman S., Ishigaki K., Asgari S., Huang C.C., Luo Y., Zhang Z., Lopez K., Lindestam Arlehamn C.S., Ernst J.D., Jimenez J., Calderón R.I., Lecca L., Van Rhijn I., Moody D.B., Murray M.B., Raychaudhuri S.

Nature Immunology (Springer Science and Business Media {LLC})  22 ( 6 ) 781 - 793 2021.06

ISSN  15292908

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Multimodal T cell profiling can enable more precise characterization of elusive cell states underlying disease. Here, we integrated single-cell RNA and surface protein data from 500,089 memory T cells to define 31 cell states from 259 individuals in a Peruvian tuberculosis (TB) progression cohort. At immune steady state >4 years after infection and disease resolution, we found that, after accounting for significant effects of age, sex, season and genetic ancestry on T cell composition, a polyfunctional type 17 helper T (T<inf>H</inf>17) cell–like effector state was reduced in abundance and function in individuals who previously progressed from Mycobacterium tuberculosis (M.tb) infection to active TB disease. These cells are capable of responding to M.tb peptides. Deconvoluting this state—uniquely identifiable with multimodal analysis—from public data demonstrated that its depletion may precede and persist beyond active disease. Our study demonstrates the power of integrative multimodal single-cell profiling to define cell states relevant to disease and other traits.

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Dynamic landscape of immune cell-specific gene regulation in immune-mediated diseases

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.

Cell 184 ( 11 ) 3006 - 3021.e17 2021.05

ISSN  00928674

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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.

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Meta-analysis of 208370 East Asians identifies 113 susceptibility loci for systemic lupus erythematosus

Yin X., Kim K., Suetsugu H., Bang S.Y., Wen L., Koido M., Ha E., Liu L., Sakamoto Y., Jo S., Leng R.X., Otomo N., Laurynenka V., Kwon Y.C., Sheng Y., Sugano N., Hwang M.Y., Li W., Mukai M., Yoon K., Cai M., Ishigaki K., Chung W.T., Huang H., Takahashi D., Lee S.S., Wang M., Karino K., Shim S.C., Zheng X., Miyamura T., Kang Y.M., Ye D., Nakamura J., Suh C.H., Tang Y., Motomura G., Park Y.B., Ding H., Kuroda T., Choe J.Y., Li C., Niiro H., Park Y., Shen C., Miyamoto T., Ahn G.Y., Fei W., Takeuchi T., Shin J.M., Li K., Kawaguchi Y., Lee Y.K., Wang Y., Amano K., Park D.J., Yang W., Tada Y., Yamaji K., Shimizu M., Atsumi T., Suzuki A., Sumida T., Okada Y., Matsuda K., Matsuo K., Kochi Y., Kottyan L.C., Weirauch M.T., Parameswaran S., Eswar S., Salim H., Chen X., Yamamoto K., Harley J.B., Ohmura K., Kim T.H., Yang S., Yamamoto T., Kim B.J., Shen N., Ikegawa S., Lee H.S., Zhang X., Terao C., Cui Y., Bae S.C.

Annals of the Rheumatic Diseases 80 ( 5 ) 632 - 640 2021.05

ISSN  00034967

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Objective Systemic lupus erythematosus (SLE), an autoimmune disorder, has been associated withnearly 100 susceptibility loci. Nevertheless, these loci only partially explain SLE heritability and their putative causal variants are rarely prioritised, which make challenging to elucidate disease biology. To detect new SLE loci and causal variants, we performed the largest genome-wide meta-analysis for SLE in East Asian populations. Methods We newly genotyped 10 029 SLE cases and 180 167 controls and subsequently meta-analysed them jointly with 3348 SLE cases and 14 826 controls from published studies in East Asians. We further applied a Bayesian statistical approach to localise the putative causal variants for SLE associations. Results We identified 113 genetic regions including 46 novel loci at genome-wide significance (p<5×10 -8). Conditional analysis detected 233 association signals within these loci, which suggest widespread allelic heterogeneity. We detected genome-wide associations at six new missense variants. Bayesian statistical fine-mapping analysis prioritised the putative causal variants to a small set of variants (95% credible set size ≤10) for 28 association signals. We identified 110 putative causal variants with posterior probabilities ≥0.1 for 57 SLE loci, among which we prioritised 10 most likely putative causal variants (posterior probability ≥0.8). Linkage disequilibrium score regression detected genetic correlations for SLE with albumin/globulin ratio (r g =-0.242) and non-albumin protein (r g =0.238). Conclusion Thisstudy reiterates the power of large-scale genome-wide meta-analysis for novel genetic discovery. These findings shed light on genetic and biological understandings of SLE.

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Parsing multiomics landscape of activated synovial fibroblasts highlights drug targets linked to genetic risk of rheumatoid arthritis

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.

Annals of the Rheumatic Diseases 80 ( 4 ) 440 - 450 2021.04

ISSN  00034967

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Objectives 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. Methods 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. Results 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-γwas 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. Conclusions Our findings established the dynamic landscape of activated SFs and yielded potential therapeutic targets associated with genetic risk of RA.

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