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Nishide M, Shimagami H, Kumanogoh A. Single-cell analysis in rheumatic and allergic diseases: insights for clinical practice. Nat Rev Immunol 2024:10.1038/s41577-024-01043-3. [PMID: 38914790 DOI: 10.1038/s41577-024-01043-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/08/2024] [Indexed: 06/26/2024]
Abstract
Since the advent of single-cell RNA sequencing (scRNA-seq) methodology, single-cell analysis has become a powerful tool for exploration of cellular networks and dysregulated immune responses in disease pathogenesis. Advanced bioinformatics tools have enabled the combined analysis of scRNA-seq data and information on various cell properties, such as cell surface molecular profiles, chromatin accessibility and spatial information, leading to a deeper understanding of pathology. This Review provides an overview of the achievements in single-cell analysis applied to clinical samples of rheumatic and allergic diseases, including rheumatoid arthritis, systemic lupus erythematosus, systemic sclerosis, allergic airway diseases and atopic dermatitis, with an expanded scope beyond peripheral blood cells to include local diseased tissues. Despite the valuable insights that single-cell analysis has provided into disease pathogenesis, challenges remain in translating single-cell findings into clinical practice and developing personalized treatment strategies. Beyond understanding the atlas of cellular diversity, we discuss the application of data obtained in each study to clinical practice, with a focus on identifying biomarkers and therapeutic targets.
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Affiliation(s)
- Masayuki Nishide
- Department of Respiratory Medicine and Clinical Immunology, Graduate School of Medicine, Osaka University, Suita, Osaka, Japan.
- Department of Immunopathology, World Premier International Research Center Initiative (WPI), Immunology Frontier Research Center (IFReC), Osaka University, Suita, Osaka, Japan.
- Department of Advanced Clinical and Translational Immunology, Graduate School of Medicine, Osaka University, Suita, Osaka, Japan.
| | - Hiroshi Shimagami
- Department of Respiratory Medicine and Clinical Immunology, Graduate School of Medicine, Osaka University, Suita, Osaka, Japan
- Department of Immunopathology, World Premier International Research Center Initiative (WPI), Immunology Frontier Research Center (IFReC), Osaka University, Suita, Osaka, Japan
- Department of Advanced Clinical and Translational Immunology, Graduate School of Medicine, Osaka University, Suita, Osaka, Japan
| | - Atsushi Kumanogoh
- Department of Respiratory Medicine and Clinical Immunology, Graduate School of Medicine, Osaka University, Suita, Osaka, Japan.
- Department of Immunopathology, World Premier International Research Center Initiative (WPI), Immunology Frontier Research Center (IFReC), Osaka University, Suita, Osaka, Japan.
- Integrated Frontier Research for Medical Science Division, Institute for Open and Transdisciplinary Research Initiatives (OTRI), Osaka University, Suita, Osaka, Japan.
- Center for Infectious Diseases for Education and Research (CiDER), Osaka University, Suita, Osaka, Japan.
- Center for Advanced Modalities and DDS (CAMaD), Osaka University, Suita, Osaka, Japan.
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2
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Ritchie C, Li L. PELI2 is a negative regulator of STING signaling that is dynamically repressed during viral infection. Mol Cell 2024:S1097-2765(24)00479-9. [PMID: 38917796 DOI: 10.1016/j.molcel.2024.06.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2023] [Revised: 03/12/2024] [Accepted: 06/01/2024] [Indexed: 06/27/2024]
Abstract
The innate immune cGAS-STING pathway is activated by cytosolic double-stranded DNA (dsDNA), a ubiquitous danger signal, to produce interferon, a potent anti-viral and anti-cancer cytokine. However, STING activation must be tightly controlled because aberrant interferon production leads to debilitating interferonopathies. Here, we discover PELI2 as a crucial negative regulator of STING. Mechanistically, PELI2 inhibits the transcription factor IRF3 by binding to phosphorylated Thr354 and Thr356 on the C-terminal tail of STING, leading to ubiquitination and inhibition of the kinase TBK1. PELI2 sets a threshold for STING activation that tolerates low levels of cytosolic dsDNA, such as that caused by silenced TREX1, RNASEH2B, BRCA1, or SETX. When this threshold is reached, such as during viral infection, STING-induced interferon production temporarily downregulates PELI2, creating a positive feedback loop allowing a robust immune response. Lupus patients have insufficient PELI2 levels and high basal interferon production, suggesting that PELI2 dysregulation may drive the onset of lupus and other interferonopathies.
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Affiliation(s)
- Christopher Ritchie
- Department of Biochemistry, Stanford University, Stanford, CA 94305, USA; Sarafan ChEM-H Institute, Stanford University, Stanford, CA 94305, USA; Arc Institute, Palo Alto, CA 94304, USA.
| | - Lingyin Li
- Department of Biochemistry, Stanford University, Stanford, CA 94305, USA; Sarafan ChEM-H Institute, Stanford University, Stanford, CA 94305, USA; Arc Institute, Palo Alto, CA 94304, USA.
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3
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Chen M, Dahl A. A robust model for cell type-specific interindividual variation in single-cell RNA sequencing data. Nat Commun 2024; 15:5229. [PMID: 38898015 PMCID: PMC11186839 DOI: 10.1038/s41467-024-49242-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2023] [Accepted: 05/28/2024] [Indexed: 06/21/2024] Open
Abstract
Single-cell RNA sequencing (scRNA-seq) has been widely used to characterize cell types based on their average gene expression profiles. However, most studies do not consider cell type-specific variation across donors. Modelling this cell type-specific inter-individual variation could help elucidate cell type-specific biology and inform genes and cell types underlying complex traits. We therefore develop a new model to detect and quantify cell type-specific variation across individuals called CTMM (Cell Type-specific linear Mixed Model). We use extensive simulations to show that CTMM is powerful and unbiased in realistic settings. We also derive calibrated tests for cell type-specific interindividual variation, which is challenging given the modest sample sizes in scRNA-seq. We apply CTMM to scRNA-seq data from human induced pluripotent stem cells to characterize the transcriptomic variation across donors as cells differentiate into endoderm. We find that almost 100% of transcriptome-wide variability between donors is differentiation stage-specific. CTMM also identifies individual genes with statistically significant stage-specific variability across samples, including 85 genes that do not have significant stage-specific mean expression. Finally, we extend CTMM to partition interindividual covariance between stages, which recapitulates the overall differentiation trajectory. Overall, CTMM is a powerful tool to illuminate cell type-specific biology in scRNA-seq.
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Affiliation(s)
- Minhui Chen
- Section of Genetic Medicine, University of Chicago, Chicago, IL, 60637, USA.
| | - Andy Dahl
- Section of Genetic Medicine, University of Chicago, Chicago, IL, 60637, USA.
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Strober BJ, Zhang MJ, Amariuta T, Rossen J, Price AL. Fine-mapping causal tissues and genes at disease-associated loci. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2024:2023.11.01.23297909. [PMID: 37961337 PMCID: PMC10635248 DOI: 10.1101/2023.11.01.23297909] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/15/2023]
Abstract
Heritable diseases often manifest in a highly tissue-specific manner, with different disease loci mediated by genes in distinct tissues or cell types. We propose Tissue-Gene Fine-Mapping (TGFM), a fine-mapping method that infers the posterior probability (PIP) for each gene-tissue pair to mediate a disease locus by analyzing GWAS summary statistics (and in-sample LD) and leveraging eQTL data from diverse tissues to build cis-predicted expression models; TGFM also assigns PIPs to causal variants that are not mediated by gene expression in assayed genes and tissues. TGFM accounts for both co-regulation across genes and tissues and LD between SNPs (generalizing existing fine-mapping methods), and incorporates genome-wide estimates of each tissue's contribution to disease as tissue-level priors. TGFM was well-calibrated and moderately well-powered in simulations; unlike previous methods, TGFM was able to attain correct calibration by modeling uncertainty in cis-predicted expression models. We applied TGFM to 45 UK Biobank diseases/traits (average N = 316K) using eQTL data from 38 GTEx tissues. TGFM identified an average of 147 PIP > 0.5 causal genetic elements per disease/trait, of which 11% were gene-tissue pairs. Implicated gene-tissue pairs were concentrated in known disease-critical tissues, and causal genes were strongly enriched in disease-relevant gene sets. Causal gene-tissue pairs identified by TGFM recapitulated known biology (e.g., TPO -thyroid for Hypothyroidism), but also included biologically plausible novel findings (e.g., SLC20A2 -artery aorta for Diastolic blood pressure). Further application of TGFM to single-cell eQTL data from 9 cell types in peripheral blood mononuclear cells (PBMC), analyzed jointly with GTEx tissues, identified 30 additional causal gene-PBMC cell type pairs at PIP > 0.5-primarily for autoimmune disease and blood cell traits, including the biologically plausible example of CD52 in classical monocyte cells for Monocyte count. In conclusion, TGFM is a robust and powerful method for fine-mapping causal tissues and genes at disease-associated loci.
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Ferreté-Bonastre AG, Martínez-Gallo M, Morante-Palacios O, Calvillo CL, Calafell-Segura J, Rodríguez-Ubreva J, Esteller M, Cortés-Hernández J, Ballestar E. Disease activity drives divergent epigenetic and transcriptomic reprogramming of monocyte subpopulations in systemic lupus erythematosus. Ann Rheum Dis 2024; 83:865-878. [PMID: 38413168 DOI: 10.1136/ard-2023-225433] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2023] [Accepted: 02/15/2024] [Indexed: 02/29/2024]
Abstract
OBJECTIVES Systemic lupus erythematosus (SLE) is characterised by systemic inflammation involving various immune cell types. Monocytes, pivotal in promoting and regulating inflammation in SLE, differentiate from classic monocytes into intermediate and non-classic monocytes, assuming diverse roles and changing their proportions in inflammation. In this study, we investigated the epigenetic and transcriptomic profiles of these and novel monocyte subsets in SLE in relation to activity and progression. METHODS We obtained the DNA methylomes and transcriptomes of classic, intermediate, non-classic monocytes in patients with SLE (at first and follow-up visits) and healthy donors. We integrated these data with single-cell transcriptomics of SLE and healthy donors and interrogated their relationships with activity and progression. RESULTS In addition to shared DNA methylation and transcriptomic alterations associated with a strong interferon signature, we identified monocyte subset-specific alterations, especially in DNA methylation, which reflect an impact of SLE on monocyte differentiation. SLE classic monocytes exhibited a proinflammatory profile and were primed for macrophage differentiation. SLE non-classic monocytes displayed a T cell differentiation-related phenotype, with Th17-regulating features. Changes in monocyte proportions, DNA methylation and expression occurred in relation to disease activity and involved the STAT pathway. Integration of bulk with single-cell RNA sequencing datasets revealed disease activity-dependent expansion of SLE-specific monocyte subsets, further supported the interferon signature for classic monocytes, and associated intermediate and non-classic populations with exacerbated complement activation. CONCLUSIONS Disease activity in SLE drives a subversion of the epigenome and transcriptome programme in monocyte differentiation, impacting the function of different subsets and allowing to generate predictive methods for activity and progression.
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Affiliation(s)
| | - Mónica Martínez-Gallo
- Immunology Division, Vall d'Hebron University Hospital and Diagnostic Immunology Research Group, Vall d'Hebron Research Institute (VHIR), Barcelona, Spain
| | | | - Celia Lourdes Calvillo
- Epigenetics and Immune Disease Group, Josep Carreras Leukaemia Research Institute (IJC), Badalona, Barcelona, Spain
| | - Josep Calafell-Segura
- Epigenetics and Immune Disease Group, Josep Carreras Leukaemia Research Institute (IJC), Badalona, Barcelona, Spain
| | - Javier Rodríguez-Ubreva
- Epigenetics and Immune Disease Group, Josep Carreras Leukaemia Research Institute (IJC), Badalona, Barcelona, Spain
| | - Manel Esteller
- Cancer Epigenetics Group, Josep Carreras Leukaemia Research Institute (IJC), Badalona, Barcelona, Spain
- Centro de Investigación Biomédica en Red Cancer (CIBERONC), Madrid, Spain
- Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain
- Physiological Sciences Department, School of Medicine and Health Sciences, University of Barcelona (UB), Barcelona, Spain
| | - Josefina Cortés-Hernández
- Rheumatology Department, Hospital Vall d'Hebron and Vall d'Hebron Research Institute (VHIR), Barcelona, Spain
| | - Esteban Ballestar
- Epigenetics and Immune Disease Group, Josep Carreras Leukaemia Research Institute (IJC), Badalona, Barcelona, Spain
- Epigenetics in Inflammatory and Metabolic Diseases Laboratory, Health Science Center (HSC), East China Normal University (ECNU), Shanghai, China
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Curion F, Theis FJ. Machine learning integrative approaches to advance computational immunology. Genome Med 2024; 16:80. [PMID: 38862979 PMCID: PMC11165829 DOI: 10.1186/s13073-024-01350-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2023] [Accepted: 05/23/2024] [Indexed: 06/13/2024] Open
Abstract
The study of immunology, traditionally reliant on proteomics to evaluate individual immune cells, has been revolutionized by single-cell RNA sequencing. Computational immunologists play a crucial role in analysing these datasets, moving beyond traditional protein marker identification to encompass a more detailed view of cellular phenotypes and their functional roles. Recent technological advancements allow the simultaneous measurements of multiple cellular components-transcriptome, proteome, chromatin, epigenetic modifications and metabolites-within single cells, including in spatial contexts within tissues. This has led to the generation of complex multiscale datasets that can include multimodal measurements from the same cells or a mix of paired and unpaired modalities. Modern machine learning (ML) techniques allow for the integration of multiple "omics" data without the need for extensive independent modelling of each modality. This review focuses on recent advancements in ML integrative approaches applied to immunological studies. We highlight the importance of these methods in creating a unified representation of multiscale data collections, particularly for single-cell and spatial profiling technologies. Finally, we discuss the challenges of these holistic approaches and how they will be instrumental in the development of a common coordinate framework for multiscale studies, thereby accelerating research and enabling discoveries in the computational immunology field.
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Affiliation(s)
- Fabiola Curion
- Institute of Computational Biology, Helmholtz Center Munich, Munich, Germany
- Department of Mathematics, School of Computation, Information and Technology, Technical University of Munich, Munich, Germany
| | - Fabian J Theis
- Institute of Computational Biology, Helmholtz Center Munich, Munich, Germany.
- Department of Mathematics, School of Computation, Information and Technology, Technical University of Munich, Munich, Germany.
- School of Life Sciences Weihenstephan, Technical University of Munich, Munich, Germany.
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Hu Z, Zheng M, Guo Z, Zhou W, Zhou W, Yao N, Zhang G, Lu Q, Zhao M. Single-cell sequencing reveals distinct immune cell features in cutaneous lesions of pemphigus vulgaris and bullous pemphigoid. Clin Immunol 2024; 263:110219. [PMID: 38631594 DOI: 10.1016/j.clim.2024.110219] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2024] [Revised: 03/27/2024] [Accepted: 04/09/2024] [Indexed: 04/19/2024]
Abstract
Bullous pemphigoid (BP) and pemphigus vulgaris (PV) are two common subtypes of autoimmune bullous disease (AIBD). The key role of circulating autoreactive immune cells contributing to skin damage of AIBD has been widely recognized. Nevertheless, the immune characteristics in cutaneous lesions remain unclear. Here, we performed single-cell RNA sequencing (scRNA-seq) and single-cell VDJ sequencing (scRNA-seq) to generate transcriptional profiles for cells and T/B cell clonetype in skin lesions of BP and PV. We found that the proportions of NK&T, macrophages/ dendritic cells, B cells, and mast cells increased in BP and PV lesions. Then, BP and PV cells constituted over 75% of all myeloid cell subtypes, CD4+ T cell subtypes and CD8+ T cell subtypes. Strikingly, CD8+ Trm was identified to be expanded in PV, and located in the intermediate state of the pseudotime trajectory from CD8+ Tm to CD8+ Tem. Interestingly, CD8+ Tem and CD4+ Treg highly expressed exhaustion-related genes, especially in BP lesions. Moreover, the enhanced cell communication between stromal cells and immune cells like B cells and macrophages/ dendritic cells was also identified in BP and PV lesions. Finally, clone expansion was observed in T cells of BP and PV compared with HC, while CD8+ Trm represented the highest ratio of hyperexpanded TCR clones among all T cell subtypes. Our study generally depicts a large and comprehensive single-cell landscape of cutaneous lesions and highlights immune cell features in BP and PV. This offers potential research targets for further investigation.
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Affiliation(s)
- Zhi Hu
- Hospital for Skin Diseases, Institute of Dermatology, Chinese Academy of Medical Sciences and Peking Union Medical College, Nanjing 210042, China; Key Laboratory of Basic and Translational Research on Immune-Mediated Skin Diseases, Chinese Academy of Medical Sciences, Nanjing 210042, China; Department of Dermatology, Hunan Key Laboratory of Medical Epigenomics, Second Xiangya Hospital of Central South University, Changsha 410011, China
| | - Meiling Zheng
- Hospital for Skin Diseases, Institute of Dermatology, Chinese Academy of Medical Sciences and Peking Union Medical College, Nanjing 210042, China; Key Laboratory of Basic and Translational Research on Immune-Mediated Skin Diseases, Chinese Academy of Medical Sciences, Nanjing 210042, China; Department of Dermatology, Hunan Key Laboratory of Medical Epigenomics, Second Xiangya Hospital of Central South University, Changsha 410011, China
| | - Ziyu Guo
- Department of Dermatology, Hunan Key Laboratory of Medical Epigenomics, Second Xiangya Hospital of Central South University, Changsha 410011, China
| | - Wenhui Zhou
- Department of Dermatology, Hunan Key Laboratory of Medical Epigenomics, Second Xiangya Hospital of Central South University, Changsha 410011, China
| | - Wenyu Zhou
- Department of Dermatology, Hunan Key Laboratory of Medical Epigenomics, Second Xiangya Hospital of Central South University, Changsha 410011, China
| | - Nan Yao
- Department of Dermatology, Hunan Key Laboratory of Medical Epigenomics, Second Xiangya Hospital of Central South University, Changsha 410011, China
| | - Guiying Zhang
- Department of Dermatology, Hunan Key Laboratory of Medical Epigenomics, Second Xiangya Hospital of Central South University, Changsha 410011, China.
| | - Qianjin Lu
- Hospital for Skin Diseases, Institute of Dermatology, Chinese Academy of Medical Sciences and Peking Union Medical College, Nanjing 210042, China; Key Laboratory of Basic and Translational Research on Immune-Mediated Skin Diseases, Chinese Academy of Medical Sciences, Nanjing 210042, China.
| | - Ming Zhao
- Hospital for Skin Diseases, Institute of Dermatology, Chinese Academy of Medical Sciences and Peking Union Medical College, Nanjing 210042, China; Key Laboratory of Basic and Translational Research on Immune-Mediated Skin Diseases, Chinese Academy of Medical Sciences, Nanjing 210042, China; Department of Dermatology, Hunan Key Laboratory of Medical Epigenomics, Second Xiangya Hospital of Central South University, Changsha 410011, China.
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8
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Aubert A, Jung K, Hiroyasu S, Pardo J, Granville DJ. Granzyme serine proteases in inflammation and rheumatic diseases. Nat Rev Rheumatol 2024; 20:361-376. [PMID: 38689140 DOI: 10.1038/s41584-024-01109-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/15/2024] [Indexed: 05/02/2024]
Abstract
Granzymes (granule-secreted enzymes) are a family of serine proteases that have been viewed as redundant cytotoxic enzymes since their discovery more than 30 years ago. Predominantly produced by cytotoxic lymphocytes and natural killer cells, granzymes are delivered into the cytoplasm of target cells through immunological synapses in cooperation with the pore-forming protein perforin. After internalization, granzymes can initiate cell death through the cleavage of intracellular substrates. However, evidence now also demonstrates the existence of non-cytotoxic, pro-inflammatory, intracellular and extracellular functions that are granzyme specific. Under pathological conditions, granzymes can be produced and secreted extracellularly by immune cells as well as by non-immune cells. Depending on the granzyme, accumulation in the extracellular milieu might contribute to inflammation, tissue injury, impaired wound healing, barrier dysfunction, osteoclastogenesis and/or autoantigen generation.
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Affiliation(s)
- Alexandre Aubert
- International Collaboration on Repair Discoveries (ICORD) Centre; British Columbia Professional Firefighters' Burn and Wound Healing Group, Vancouver Coastal Health Research Institute; Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, British Columbia, Canada
| | - Karen Jung
- International Collaboration on Repair Discoveries (ICORD) Centre; British Columbia Professional Firefighters' Burn and Wound Healing Group, Vancouver Coastal Health Research Institute; Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, British Columbia, Canada
| | - Sho Hiroyasu
- Department of Dermatology, Osaka Metropolitan University Graduate School of Medicine, Osaka, Japan
| | - Julian Pardo
- Fundación Instituto de Investigación Sanitaria Aragón (IIS Aragón), Biomedical Research Centre of Aragon (CIBA); Department of Microbiology, Radiology, Paediatrics and Public Health, University of Zaragoza, Zaragoza, Spain
- CIBER de Enfermedades Infecciosas, Instituto de Salud Carlos III, Madrid, Spain
| | - David J Granville
- International Collaboration on Repair Discoveries (ICORD) Centre; British Columbia Professional Firefighters' Burn and Wound Healing Group, Vancouver Coastal Health Research Institute; Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, British Columbia, Canada.
- Centre for Heart Lung Innovation, Providence Research, University of British Columbia, Vancouver, British Columbia, Canada.
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Pekayvaz K, Losert C, Knottenberg V, Gold C, van Blokland IV, Oelen R, Groot HE, Benjamins JW, Brambs S, Kaiser R, Gottschlich A, Hoffmann GV, Eivers L, Martinez-Navarro A, Bruns N, Stiller S, Akgöl S, Yue K, Polewka V, Escaig R, Joppich M, Janjic A, Popp O, Kobold S, Petzold T, Zimmer R, Enard W, Saar K, Mertins P, Huebner N, van der Harst P, Franke LH, van der Wijst MGP, Massberg S, Heinig M, Nicolai L, Stark K. Multiomic analyses uncover immunological signatures in acute and chronic coronary syndromes. Nat Med 2024; 30:1696-1710. [PMID: 38773340 PMCID: PMC11186793 DOI: 10.1038/s41591-024-02953-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2023] [Accepted: 03/26/2024] [Indexed: 05/23/2024]
Abstract
Acute and chronic coronary syndromes (ACS and CCS) are leading causes of mortality. Inflammation is considered a key pathogenic driver of these diseases, but the underlying immune states and their clinical implications remain poorly understood. Multiomic factor analysis (MOFA) allows unsupervised data exploration across multiple data types, identifying major axes of variation and associating these with underlying molecular processes. We hypothesized that applying MOFA to multiomic data obtained from blood might uncover hidden sources of variance and provide pathophysiological insights linked to clinical needs. Here we compile a longitudinal multiomic dataset of the systemic immune landscape in both ACS and CCS (n = 62 patients in total, n = 15 women and n = 47 men) and validate this in an external cohort (n = 55 patients in total, n = 11 women and n = 44 men). MOFA reveals multicellular immune signatures characterized by distinct monocyte, natural killer and T cell substates and immune-communication pathways that explain a large proportion of inter-patient variance. We also identify specific factors that reflect disease state or associate with treatment outcome in ACS as measured using left ventricular ejection fraction. Hence, this study provides proof-of-concept evidence for the ability of MOFA to uncover multicellular immune programs in cardiovascular disease, opening new directions for mechanistic, biomarker and therapeutic studies.
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Grants
- Deutsche Forschungsgemeinschaft (German Research Foundation)
- Deutsches Zentrum fr Herz-Kreislaufforschung (Deutsches Zentrum fr Herz-Kreislaufforschung e.V.)
- Deutsche Herzstiftung e.V., Frankfurt a.M. Institutional Strategy LMUexcellent of LMU Munich Else-Krner-Fresenius Stiftung DFG Clinician Scientist Programme PRIME DZHK Sule B Antrag DZHK B 21-014 SE
- Was supported by the Helmholtz Association under the joint research school ;Munich School for Data Science MUDS
- DFG GO 3823/1-1, grant number: 510821390 Frderprogramm fr Forschung und Lehre der Medizinischen Fakultt der LMU the Bavarian Cancer Research Center (BZKF) Else Kroner-Fresenius-Stiftung
- Was supported by a grant from the Frderprogramm fur Forschung und Lehre (FFoLe) of the Ludwig Maximilian University (LMU) of Munich.
- DFG SFB 1123, Z02
- DFG EN 1093/2-1
- DFG KO5055-2-1 and KO5055/3-1 the Bavarian Cancer Research Center (BZKF) the international doctoral program i-Target: immunotargeting of cancer the Melanoma Research Alliance (grant number 409510), Marie Sklodowska-Curie Training Network for Optimizing Adoptive T Cell Therapy of Cancer (funded by the Horizon 2020 programme of the European Union; grant 955575), Else Kroner-Fresenius-Stiftung (IOLIN), German Cancer Aid (AvantCAR.de), the Wilhelm-Sander-Stiftung, Ernst Jung Stiftung, Institutional Strategy LMUexcellent of LMU Munich (within the framework of the German Excellence Initiative), the Go-Bio-Initiative, the m4-Award of the Bavarian Ministry for Economical Affairs, Bundesministerium fur Bildung und Forschung, European Research Council (Starting Grant 756017 and PoC Grant 101100460, by the SFB-TRR 338/1 2021452881907, Fritz-Bender Foundation, Deutsche Jose#x0301; Carreras Leuk#x00E4;mie Stiftung, Hector Foundation, the Bavarian Research Foundation, the Bruno and Helene J#x00F6;ster Foundation (360#x00B0; CAR)
- T.P. from the DFG (PE 2704/3-1)
- DFG SFB1243, A14 DFG EN 1093/2-1,
- DZHK Säule B Antrag DZHK B 21-014 SE
- DZHK Säule B Antrag DZHK B 21-014 SE DFG SFB-1470-B03 the Chan Zuckerberg Foundation ERC Advanced Grant under the European Union Horizon 2020 Research and Innovation Program (AdG788970)
- Deutsche Forschungsgemeinschaft (DFG) SFB 914, B02 and Z01 DFG SFB 1123, B06 DFG SFB1321, P10 DFG FOR 2033 ERC-2018-ADG German Centre for Cardiovascular Research (DZHK) MHA 1.4VD
- DZHK project 81Z0600106 Supported by the Chan Zuckerberg Foundation
- DZHK S#x00E4;ule B Antrag DZHK B 21-014 SE Deutsche Herzstiftung e.V., Frankfurt a.M. DFG SFB 1123, B06 DFG NI 2219/2-1 Corona Foundation German Centre for Cardiovascular Research (DZHK) Clinician Scientist Programme the Ernst und Berta Grimmke Stiftung the GTH Junior research grant
- DZHK partner site project Deutsche Forschungsgemeinschaft (DFG) SFB 914, B02 DFG SFB 1123, A07 DFG SFB 359, A03 ERC grant 947611
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Affiliation(s)
- Kami Pekayvaz
- Medizinische Klinik und Poliklinik I, LMU University Hospital, Munich, Germany.
- DZHK (German Centre for Cardiovascular Research), Partner Site Munich Heart Alliance, Munich, Germany.
| | - Corinna Losert
- Institute of Computational Biology, German Research Center for Environmental Health, Helmholtz Zentrum München, Neuherberg, Germany
- Department of Computer Science, TUM School of Computation, Information and Technology, Technical University of Munich, Garching, Germany
| | | | - Christoph Gold
- Medizinische Klinik und Poliklinik I, LMU University Hospital, Munich, Germany
- DZHK (German Centre for Cardiovascular Research), Partner Site Munich Heart Alliance, Munich, Germany
| | - Irene V van Blokland
- Department of Cardiology, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
- Department of Genetics, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Roy Oelen
- Department of Genetics, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Hilde E Groot
- Department of Cardiology, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Jan Walter Benjamins
- Department of Cardiology, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Sophia Brambs
- Medizinische Klinik und Poliklinik I, LMU University Hospital, Munich, Germany
| | - Rainer Kaiser
- Medizinische Klinik und Poliklinik I, LMU University Hospital, Munich, Germany
- DZHK (German Centre for Cardiovascular Research), Partner Site Munich Heart Alliance, Munich, Germany
| | - Adrian Gottschlich
- Department of Medicine III, LMU University Hospital, Munich, Germany
- Division of Clinical Pharmacology, LMU University Hospital, Member of the German Center for Lung Research (DZL), Munich, Germany
| | - Gordon Victor Hoffmann
- Division of Clinical Pharmacology, LMU University Hospital, Member of the German Center for Lung Research (DZL), Munich, Germany
| | - Luke Eivers
- Medizinische Klinik und Poliklinik I, LMU University Hospital, Munich, Germany
| | | | - Nils Bruns
- Medizinische Klinik und Poliklinik I, LMU University Hospital, Munich, Germany
| | - Susanne Stiller
- Medizinische Klinik und Poliklinik I, LMU University Hospital, Munich, Germany
| | - Sezer Akgöl
- Medizinische Klinik und Poliklinik I, LMU University Hospital, Munich, Germany
| | - Keyang Yue
- Medizinische Klinik und Poliklinik I, LMU University Hospital, Munich, Germany
| | - Vivien Polewka
- Medizinische Klinik und Poliklinik I, LMU University Hospital, Munich, Germany
| | - Raphael Escaig
- Medizinische Klinik und Poliklinik I, LMU University Hospital, Munich, Germany
| | - Markus Joppich
- Department of Informatics, Ludwig-Maximilian University, Munich, Germany
| | - Aleksandar Janjic
- Anthropology and Human Genomics, Faculty of Biology, Ludwig-Maximilian University, Munich, Germany
| | - Oliver Popp
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin, Germany
| | - Sebastian Kobold
- Division of Clinical Pharmacology, LMU University Hospital, Member of the German Center for Lung Research (DZL), Munich, Germany
- German Cancer Consortium (DKTK), a partnership between DKFZ and LMU University Hospital, Partner Site Munich, Munich, Germany
- Einheit für Klinische Pharmakologie (EKLiP), Helmholtz Zentrum München-German Research Center for Environmental Health, Neuherberg, Germany
| | - Tobias Petzold
- Medizinische Klinik und Poliklinik I, LMU University Hospital, Munich, Germany
- DZHK (German Centre for Cardiovascular Research), Partner Site Munich Heart Alliance, Munich, Germany
- Department of Cardiology, Angiology and Intensive Care Medicine, Deutsches Herzzentrum der Charité (DHZC), Berlin, Germany
- German Center for Cardiovascular Research (DZHK), Partner Site Berlin, Berlin, Germany
- Charite-Universitätsmedizin Berlin, Berlin, Germany
| | - Ralf Zimmer
- Department of Informatics, Ludwig-Maximilian University, Munich, Germany
| | - Wolfgang Enard
- Anthropology and Human Genomics, Faculty of Biology, Ludwig-Maximilian University, Munich, Germany
| | - Kathrin Saar
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin, Germany
- German Center for Cardiovascular Research (DZHK), Partner Site Berlin, Berlin, Germany
| | - Philipp Mertins
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin, Germany
| | - Norbert Huebner
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin, Germany
- German Center for Cardiovascular Research (DZHK), Partner Site Berlin, Berlin, Germany
- Charite-Universitätsmedizin Berlin, Berlin, Germany
| | - Pim van der Harst
- Department of Cardiology, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Lude H Franke
- Department of Genetics, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Monique G P van der Wijst
- Department of Genetics, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Steffen Massberg
- Medizinische Klinik und Poliklinik I, LMU University Hospital, Munich, Germany
- DZHK (German Centre for Cardiovascular Research), Partner Site Munich Heart Alliance, Munich, Germany
| | - Matthias Heinig
- DZHK (German Centre for Cardiovascular Research), Partner Site Munich Heart Alliance, Munich, Germany.
- Institute of Computational Biology, German Research Center for Environmental Health, Helmholtz Zentrum München, Neuherberg, Germany.
- Department of Computer Science, TUM School of Computation, Information and Technology, Technical University of Munich, Garching, Germany.
| | - Leo Nicolai
- Medizinische Klinik und Poliklinik I, LMU University Hospital, Munich, Germany.
- DZHK (German Centre for Cardiovascular Research), Partner Site Munich Heart Alliance, Munich, Germany.
| | - Konstantin Stark
- Medizinische Klinik und Poliklinik I, LMU University Hospital, Munich, Germany.
- DZHK (German Centre for Cardiovascular Research), Partner Site Munich Heart Alliance, Munich, Germany.
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10
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Mowery CT, Freimer JW, Chen Z, Casaní-Galdón S, Umhoefer JM, Arce MM, Gjoni K, Daniel B, Sandor K, Gowen BG, Nguyen V, Simeonov DR, Garrido CM, Curie GL, Schmidt R, Steinhart Z, Satpathy AT, Pollard KS, Corn JE, Bernstein BE, Ye CJ, Marson A. Systematic decoding of cis gene regulation defines context-dependent control of the multi-gene costimulatory receptor locus in human T cells. Nat Genet 2024; 56:1156-1167. [PMID: 38811842 PMCID: PMC11176074 DOI: 10.1038/s41588-024-01743-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2022] [Accepted: 04/04/2024] [Indexed: 05/31/2024]
Abstract
Cis-regulatory elements (CREs) interact with trans regulators to orchestrate gene expression, but how transcriptional regulation is coordinated in multi-gene loci has not been experimentally defined. We sought to characterize the CREs controlling dynamic expression of the adjacent costimulatory genes CD28, CTLA4 and ICOS, encoding regulators of T cell-mediated immunity. Tiling CRISPR interference (CRISPRi) screens in primary human T cells, both conventional and regulatory subsets, uncovered gene-, cell subset- and stimulation-specific CREs. Integration with CRISPR knockout screens and assay for transposase-accessible chromatin with sequencing (ATAC-seq) profiling identified trans regulators influencing chromatin states at specific CRISPRi-responsive elements to control costimulatory gene expression. We then discovered a critical CCCTC-binding factor (CTCF) boundary that reinforces CRE interaction with CTLA4 while also preventing promiscuous activation of CD28. By systematically mapping CREs and associated trans regulators directly in primary human T cell subsets, this work overcomes longstanding experimental limitations to decode context-dependent gene regulatory programs in a complex, multi-gene locus critical to immune homeostasis.
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Grants
- P30 DK063720 NIDDK NIH HHS
- R01 HG008140 NHGRI NIH HHS
- T32 GM007618 NIGMS NIH HHS
- S10 OD028511 NIH HHS
- F99 CA234842 NCI NIH HHS
- S10 OD021822 NIH HHS
- K00 CA234842 NCI NIH HHS
- P01 AI138962 NIAID NIH HHS
- U01 HL157989 NHLBI NIH HHS
- R01 DK129364 NIDDK NIH HHS
- T32 DK007418 NIDDK NIH HHS
- R01 AI136972 NIAID NIH HHS
- F30 AI157167 NIAID NIH HHS
- R01 HG011239 NHGRI NIH HHS
- NIH grants 1R01DK129364-01A1, P01AI138962, and R01HG008140; the Larry L. Hillblom Foundation (grant no. 2020-D-002-NET); and Northern California JDRF Center of Excellence. A.M. is a member of the Parker Institute for Cancer Immunotherapy (PICI), and has received funding from the Arc Institute, Chan Zuckerberg Biohub, Innovative Genomics Institute (IGI), Cancer Research Institute (CRI) Lloyd J. Old STAR award, a gift from the Jordan Family, a gift from the Byers family and a gift from B. Bakar.
- UCSF ImmunoX Computational Immunology Fellow, is supported by NIH grant F30AI157167, and has received support from NIH grants T32DK007418 and T32GM007618
- NIH grant R01HG008140
- Career Award for Medical Scientists from the Burroughs Wellcome Fund, a Lloyd J. Old STAR Award from the Cancer Research Institute, and the Parker Institute for Cancer Immunotherapy
- NIH grant U01HL157989
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Affiliation(s)
- Cody T Mowery
- Medical Scientist Training Program, University of California, San Francisco, San Francisco, CA, USA
- Biomedical Sciences Graduate Program, University of California, San Francisco, San Francisco, CA, USA
- Gladstone-UCSF Institute of Genomic Immunology, San Francisco, CA, USA
- Department of Medicine, University of California, San Francisco, San Francisco, CA, USA
- Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA, USA
| | - Jacob W Freimer
- Gladstone-UCSF Institute of Genomic Immunology, San Francisco, CA, USA
- Department of Medicine, University of California, San Francisco, San Francisco, CA, USA
- Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA, USA
- Department of Genetics, Stanford University, Stanford, CA, USA
| | - Zeyu Chen
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Departments of Cell Biology and Pathology, Harvard Medical School, Boston, MA, USA
| | - Salvador Casaní-Galdón
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Departments of Cell Biology and Pathology, Harvard Medical School, Boston, MA, USA
| | - Jennifer M Umhoefer
- Biomedical Sciences Graduate Program, University of California, San Francisco, San Francisco, CA, USA
- Gladstone-UCSF Institute of Genomic Immunology, San Francisco, CA, USA
- Department of Medicine, University of California, San Francisco, San Francisco, CA, USA
- Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA, USA
| | - Maya M Arce
- Biomedical Sciences Graduate Program, University of California, San Francisco, San Francisco, CA, USA
- Gladstone-UCSF Institute of Genomic Immunology, San Francisco, CA, USA
- Department of Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Ketrin Gjoni
- Gladstone Institute of Data Science and Biotechnology, San Francisco, CA, USA
- Department of Epidemiology and Biostatistics, University of California, San Francisco, San Francisco, CA, USA
| | - Bence Daniel
- Gladstone-UCSF Institute of Genomic Immunology, San Francisco, CA, USA
- Department of Pathology, Stanford University, Stanford, CA, USA
- Center for Personal Dynamic Regulomes, Stanford University, Stanford, CA, USA
- Department of Microchemistry, Proteomics, Lipidomics and Next Generation Sequencing, Genentech, South San Francisco, CA, USA
| | - Katalin Sandor
- Gladstone-UCSF Institute of Genomic Immunology, San Francisco, CA, USA
- Department of Pathology, Stanford University, Stanford, CA, USA
| | - Benjamin G Gowen
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, USA
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, USA
| | - Vinh Nguyen
- Gladstone-UCSF Institute of Genomic Immunology, San Francisco, CA, USA
- Department of Medicine, University of California, San Francisco, San Francisco, CA, USA
- Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA, USA
- Diabetes Center, University of California, San Francisco, San Francisco, CA, USA
- Department of Surgery, University of California, San Francisco, San Francisco, CA, USA
- UCSF CoLabs, University of California, San Francisco, San Francisco, CA, USA
| | - Dimitre R Simeonov
- Biomedical Sciences Graduate Program, University of California, San Francisco, San Francisco, CA, USA
- Department of Medicine, University of California, San Francisco, San Francisco, CA, USA
- Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA, USA
| | - Christian M Garrido
- Gladstone-UCSF Institute of Genomic Immunology, San Francisco, CA, USA
- Department of Medicine, University of California, San Francisco, San Francisco, CA, USA
- Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA, USA
| | - Gemma L Curie
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, USA
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, USA
| | - Ralf Schmidt
- Gladstone-UCSF Institute of Genomic Immunology, San Francisco, CA, USA
- Department of Medicine, University of California, San Francisco, San Francisco, CA, USA
- Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA, USA
- Department of Laboratory Medicine, Medical University of Vienna, Vienna, Austria
| | - Zachary Steinhart
- Gladstone-UCSF Institute of Genomic Immunology, San Francisco, CA, USA
- Department of Medicine, University of California, San Francisco, San Francisco, CA, USA
- Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA, USA
| | - Ansuman T Satpathy
- Gladstone-UCSF Institute of Genomic Immunology, San Francisco, CA, USA
- Department of Pathology, Stanford University, Stanford, CA, USA
- Parker Institute for Cancer Immunotherapy, San Francisco, CA, USA
- Program in Immunology, Stanford University, Stanford, CA, USA
| | - Katherine S Pollard
- Gladstone Institute of Data Science and Biotechnology, San Francisco, CA, USA
- Department of Epidemiology and Biostatistics, University of California, San Francisco, San Francisco, CA, USA
- Chan Zuckerberg Biohub SF, San Francisco, CA, USA
| | - Jacob E Corn
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, USA
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, USA
- Department of Biology, ETH Zürich, Zürich, Switzerland
| | - Bradley E Bernstein
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Departments of Cell Biology and Pathology, Harvard Medical School, Boston, MA, USA
| | - Chun Jimmie Ye
- Gladstone-UCSF Institute of Genomic Immunology, San Francisco, CA, USA.
- Department of Epidemiology and Biostatistics, University of California, San Francisco, San Francisco, CA, USA.
- Parker Institute for Cancer Immunotherapy, San Francisco, CA, USA.
- Chan Zuckerberg Biohub SF, San Francisco, CA, USA.
- Rosalind Russell/Ephraim P. Engleman Rheumatology Research Center, University of California, San Francisco, San Francisco, CA, USA.
- Bakar Computational Health Sciences Institute, University of California, San Francisco, San Francisco, CA, USA.
- Institute for Human Genetics, University of California, San Francisco, San Francisco, CA, USA.
| | - Alexander Marson
- Gladstone-UCSF Institute of Genomic Immunology, San Francisco, CA, USA.
- Department of Medicine, University of California, San Francisco, San Francisco, CA, USA.
- Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA, USA.
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, USA.
- Parker Institute for Cancer Immunotherapy, San Francisco, CA, USA.
- Institute for Human Genetics, University of California, San Francisco, San Francisco, CA, USA.
- UCSF Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA, USA.
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11
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Tang C, Sun Q, Zeng X, Yang X, Liu F, Zhao J, Shen Y, Liu B, Wen J, Li Y. Cell-type specific inference from bulk RNA-sequencing data by integrating single cell reference profiles via EPIC-unmix. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.23.595514. [PMID: 38826297 PMCID: PMC11142188 DOI: 10.1101/2024.05.23.595514] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2024]
Abstract
Cell type specific (CTS) analysis is essential to reveal biological insights obscured in bulk tissue data. However, single-cell (sc) or single-nuclei (sn) resolution data are still cost-prohibitive for large-scale samples. Thus, computational methods to perform deconvolution from bulk tissue data are highly valuable. We here present EPIC-unmix, a novel two-step empirical Bayesian method integrating reference sc/sn RNA-seq data and bulk RNA-seq data from target samples to enhance the accuracy of CTS inference. We demonstrate through comprehensive simulations across three tissues that EPIC-unmix achieved 4.6% - 109.8% higher accuracy compared to alternative methods. By applying EPIC-unmix to human bulk brain RNA-seq data from the ROSMAP and MSBB cohorts, we identified multiple genes differentially expressed between Alzheimer's disease (AD) cases versus controls in a CTS manner, including 57.4% novel genes not identified using similar sample size sc/snRNA-seq data, indicating the power of our in-silico approach. Among the 6-69% overlapping, 83%-100% are in consistent direction with those from sc/snRNA-seq data, supporting the reliability of our findings. EPIC-unmix inferred CTS expression profiles similarly empowers CTS eQTL analysis. Among the novel eQTLs, we highlight a microglia eQTL for AD risk gene AP3B2, obscured in bulk and missed by sc/snRNA-seq based eQTL analysis. The variant resides in a microglia-specific cCRE, forming chromatin loop with AP3B2 promoter region in microglia. Taken together, we believe EPIC-unmix will be a valuable tool to enable more powerful CTS analysis.
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Affiliation(s)
- Chenwei Tang
- Department of Biostatistics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Quan Sun
- Department of Biostatistics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Xinyue Zeng
- Department of Biostatistics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Xiaoyu Yang
- Institute for Human Genetics, University of California, San Francisco, San Francisco, CA, USA
| | - Fei Liu
- Department of Pharmacy and Pharmaceutical Sciences, Faculty of Science, National University of Singapore, Singapore
| | - Jinying Zhao
- Department of Epidemiology, College of Public Health & Health Professions and College of Medicine, University of Florida, Gainesville, FL, USA; Center for Genetic Epidemiology and Bioinformatics, University of Florida, Gainesville, FL, USA
| | - Yin Shen
- Institute for Human Genetics, University of California, San Francisco, San Francisco, CA, USA
| | - Bixiang Liu
- Department of Pharmacy and Pharmaceutical Sciences, Faculty of Science, National University of Singapore, Singapore
- Department of Biomedical Informatics, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Jia Wen
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC
| | - Yun Li
- Department of Biostatistics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC
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12
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Nguyen H, Nguyen H, Tran D, Draghici S, Nguyen T. Fourteen years of cellular deconvolution: methodology, applications, technical evaluation and outstanding challenges. Nucleic Acids Res 2024; 52:4761-4783. [PMID: 38619038 PMCID: PMC11109966 DOI: 10.1093/nar/gkae267] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2023] [Revised: 03/01/2024] [Accepted: 04/02/2024] [Indexed: 04/16/2024] Open
Abstract
Single-cell RNA sequencing (scRNA-Seq) is a recent technology that allows for the measurement of the expression of all genes in each individual cell contained in a sample. Information at the single-cell level has been shown to be extremely useful in many areas. However, performing single-cell experiments is expensive. Although cellular deconvolution cannot provide the same comprehensive information as single-cell experiments, it can extract cell-type information from bulk RNA data, and therefore it allows researchers to conduct studies at cell-type resolution from existing bulk datasets. For these reasons, a great effort has been made to develop such methods for cellular deconvolution. The large number of methods available, the requirement of coding skills, inadequate documentation, and lack of performance assessment all make it extremely difficult for life scientists to choose a suitable method for their experiment. This paper aims to fill this gap by providing a comprehensive review of 53 deconvolution methods regarding their methodology, applications, performance, and outstanding challenges. More importantly, the article presents a benchmarking of all these 53 methods using 283 cell types from 30 tissues of 63 individuals. We also provide an R package named DeconBenchmark that allows readers to execute and benchmark the reviewed methods (https://github.com/tinnlab/DeconBenchmark).
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Affiliation(s)
- Hung Nguyen
- Department of Computer Science and Software Engineering, Auburn University, Auburn, AL, USA
| | - Ha Nguyen
- Department of Computer Science and Software Engineering, Auburn University, Auburn, AL, USA
| | - Duc Tran
- Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA
| | - Sorin Draghici
- Department of Computer Science, Wayne State University, Detroit, MI, USA
- Advaita Bioinformatics, Ann Arbor, MI, USA
| | - Tin Nguyen
- Department of Computer Science and Software Engineering, Auburn University, Auburn, AL, USA
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13
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Gómez-Bañuelos E, Goldman DW, Andrade V, Darrah E, Petri M, Andrade F. Uncoupling interferons and the interferon signature explains clinical and transcriptional subsets in SLE. Cell Rep Med 2024; 5:101569. [PMID: 38744279 PMCID: PMC11148857 DOI: 10.1016/j.xcrm.2024.101569] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2023] [Revised: 02/06/2024] [Accepted: 04/22/2024] [Indexed: 05/16/2024]
Abstract
Systemic lupus erythematosus (SLE) displays a hallmark interferon (IFN) signature. Yet, clinical trials targeting type I IFN (IFN-I) have shown variable efficacy, and blocking IFN-II failed to treat SLE. Here, we show that IFN type levels in SLE vary significantly across clinical and transcriptional endotypes. Whereas skin involvement correlated with IFN-I alone, systemic features like nephritis associated with co-elevation of IFN-I, IFN-II, and IFN-III, indicating additive IFN effects in severe SLE. Notably, while high IFN-II/-III levels without IFN-I had a limited effect on disease activity, IFN-II was linked to IFN-I-independent transcriptional profiles (e.g., OXPHOS and CD8+GZMH+ cells), and IFN-III enhanced IFN-induced gene expression when co-elevated with IFN-I. Moreover, dysregulated IFNs do not explain the IFN signature in 64% of patients or clinical manifestations including cytopenia, serositis, and anti-phospholipid syndrome, implying IFN-independent endotypes in SLE. This study sheds light on mechanisms underlying SLE heterogeneity and the variable response to IFN-targeted therapies in clinical trials.
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Affiliation(s)
| | - Daniel W Goldman
- Division of Rheumatology, The Johns Hopkins School of Medicine, Baltimore, MD 21224
| | - Victoria Andrade
- Division of Rheumatology, The Johns Hopkins School of Medicine, Baltimore, MD 21224
| | - Erika Darrah
- Division of Rheumatology, The Johns Hopkins School of Medicine, Baltimore, MD 21224
| | - Michelle Petri
- Division of Rheumatology, The Johns Hopkins School of Medicine, Baltimore, MD 21224
| | - Felipe Andrade
- Division of Rheumatology, The Johns Hopkins School of Medicine, Baltimore, MD 21224.
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14
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Wang L, Khunsriraksakul C, Markus H, Chen D, Zhang F, Chen F, Zhan X, Carrel L, Liu DJ, Jiang B. Integrating single cell expression quantitative trait loci summary statistics to understand complex trait risk genes. Nat Commun 2024; 15:4260. [PMID: 38769300 DOI: 10.1038/s41467-024-48143-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2023] [Accepted: 04/22/2024] [Indexed: 05/22/2024] Open
Abstract
Transcriptome-wide association study (TWAS) is a popular approach to dissect the functional consequence of disease associated non-coding variants. Most existing TWAS use bulk tissues and may not have the resolution to reveal cell-type specific target genes. Single-cell expression quantitative trait loci (sc-eQTL) datasets are emerging. The largest bulk- and sc-eQTL datasets are most conveniently available as summary statistics, but have not been broadly utilized in TWAS. Here, we present a new method EXPRESSO (EXpression PREdiction with Summary Statistics Only), to analyze sc-eQTL summary statistics, which also integrates 3D genomic data and epigenomic annotation to prioritize causal variants. EXPRESSO substantially improves existing methods. We apply EXPRESSO to analyze multi-ancestry GWAS datasets for 14 autoimmune diseases. EXPRESSO uniquely identifies 958 novel gene x trait associations, which is 26% more than the second-best method. Among them, 492 are unique to cell type level analysis and missed by TWAS using whole blood. We also develop a cell type aware drug repurposing pipeline, which leverages EXPRESSO results to identify drug compounds that can reverse disease gene expressions in relevant cell types. Our results point to multiple drugs with therapeutic potentials, including metformin for type 1 diabetes, and vitamin K for ulcerative colitis.
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Affiliation(s)
- Lida Wang
- Department of Public Health Sciences; Pennsylvania State University College of Medicine, Hershey, Pennsylvania, USA
| | - Chachrit Khunsriraksakul
- Bioinformatics and Genomics PhD Program; Pennsylvania State University College of Medicine, Hershey, Pennsylvania, USA
- Institute for Personalized Medicine; Pennsylvania State University College of Medicine, Hershey, Pennsylvania, USA
| | - Havell Markus
- Bioinformatics and Genomics PhD Program; Pennsylvania State University College of Medicine, Hershey, Pennsylvania, USA
- Institute for Personalized Medicine; Pennsylvania State University College of Medicine, Hershey, Pennsylvania, USA
| | - Dieyi Chen
- Department of Public Health Sciences; Pennsylvania State University College of Medicine, Hershey, Pennsylvania, USA
| | - Fan Zhang
- Bioinformatics and Genomics PhD Program; Pennsylvania State University College of Medicine, Hershey, Pennsylvania, USA
| | - Fang Chen
- Department of Public Health Sciences; Pennsylvania State University College of Medicine, Hershey, Pennsylvania, USA
| | - Xiaowei Zhan
- Department of Statistical Science, Southern Methodist University, Dallas, TX, US
- Quantitative Biomedical Research Center, Department of Population and Data Sciences, University of Texas Southwestern Medical Center, Dallas, TX, US
- Center for Genetics of Host Defense, University of Texas Southwestern Medical Center, Dallas, TX, US
| | - Laura Carrel
- Department of Biochemistry and Molecular Biology; Pennsylvania State University College of Medicine, Hershey, Pennsylvania, USA.
| | - Dajiang J Liu
- Department of Public Health Sciences; Pennsylvania State University College of Medicine, Hershey, Pennsylvania, USA.
- Bioinformatics and Genomics PhD Program; Pennsylvania State University College of Medicine, Hershey, Pennsylvania, USA.
- Department of Statistical Science, Southern Methodist University, Dallas, TX, US.
| | - Bibo Jiang
- Department of Public Health Sciences; Pennsylvania State University College of Medicine, Hershey, Pennsylvania, USA.
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15
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Wen X, Chang X, He X, Cai Q, Wang G, Liu J. Increased Thyroid DPP4 Expression Is Associated With Inflammatory Process in Patients With Hashimoto Thyroiditis. J Clin Endocrinol Metab 2024; 109:1517-1525. [PMID: 38127960 PMCID: PMC11099486 DOI: 10.1210/clinem/dgad723] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/18/2023] [Revised: 11/10/2023] [Accepted: 12/07/2023] [Indexed: 12/23/2023]
Abstract
CONTEXT Dipeptidyl peptidase-4 (DPP4) is originally described as a surface protein in lymphocytes. Lymphocyte infiltration and subsequent destruction of thyroid tissue have been considered as the central pathological mechanism in Hashimoto thyroiditis (HT). OBJECTIVE The present study aimed to investigate DPP4 expression in peripheral blood and thyroid tissue in HT patients, and explore the role of DPP4 in the pathophysiological process of HT. METHODS This case-control study recruited 40 drug-naive HT patients and 81 control individuals. Peripheral blood and thyroid specimens were collected for assessing the expression and activity of DPP4. Moreover, single-cell RNA sequencing (scRNA-seq) analysis of 6 "para-tumor tissues" samples from scRNA-seq data set GSE184362 and in vitro cell experiments were also conducted. RESULTS The HT patients had similar DPP4 serum concentration and activity as the controls. However, the expression and activity of DPP4 was significantly increased in the thyroid of the HT group than in the control group. The scRNA-seq analysis showed that DPP4 expression was significantly increased in the HT group, and mainly expressed in T cells. Further in vitro studies showed that inhibition of lymphocyte DPP4 activity with sitagliptin downregulated the production of inflammatory factors in co-cultured thyroid cells. CONCLUSION DPP4 expression was significantly increased in the thyroid of the HT group compared with the control group, and was mainly localized in the lymphocytes. Inhibition of lymphocyte DPP4 activity reduced the production of inflammatory factors in co-cultured thyroid cells. Therefore, inhibition of DPP4 may have a beneficial effect by alleviating inflammatory reactions in HT patients.
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Affiliation(s)
- Xiaohui Wen
- Department of Otolaryngology, Beijing Chao-Yang Hospital, Capital Medical University, Beijing 100020, China
| | - Xiaona Chang
- Department of Endocrinology, Beijing Chao-Yang Hospital, Capital Medical University, Beijing 100020, China
| | - Xueqing He
- Department of Endocrinology, Beijing Chao-Yang Hospital, Capital Medical University, Beijing 100020, China
| | - Qingyun Cai
- Department of Endocrinology, Beijing Chao-Yang Hospital, Capital Medical University, Beijing 100020, China
| | - Guang Wang
- Department of Endocrinology, Beijing Chao-Yang Hospital, Capital Medical University, Beijing 100020, China
| | - Jia Liu
- Department of Endocrinology, Beijing Chao-Yang Hospital, Capital Medical University, Beijing 100020, China
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16
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Zhou W, Cuomo ASE, Xue A, Kanai M, Chau G, Krishna C, Xavier RJ, MacArthur DG, Powell JE, Daly MJ, Neale BM. Efficient and accurate mixed model association tool for single-cell eQTL analysis. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2024:2024.05.15.24307317. [PMID: 38798318 PMCID: PMC11118640 DOI: 10.1101/2024.05.15.24307317] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2024]
Abstract
Understanding the genetic basis of gene expression can help us understand the molecular underpinnings of human traits and disease. Expression quantitative trait locus (eQTL) mapping can help in studying this relationship but have been shown to be very cell-type specific, motivating the use of single-cell RNA sequencing and single-cell eQTLs to obtain a more granular view of genetic regulation. Current methods for single-cell eQTL mapping either rely on the "pseudobulk" approach and traditional pipelines for bulk transcriptomics or do not scale well to large datasets. Here, we propose SAIGE-QTL, a robust and scalable tool that can directly map eQTLs using single-cell profiles without needing aggregation at the pseudobulk level. Additionally, SAIGE-QTL allows for testing the effects of less frequent/rare genetic variation through set-based tests, which is traditionally excluded from eQTL mapping studies. We evaluate the performance of SAIGE-QTL on both real and simulated data and demonstrate the improved power for eQTL mapping over existing pipelines.
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Wang FQ, Shao L, Dang X, Wang YF, Chen S, Liu Z, Mao Y, Jiang Y, Hou F, Guo X, Li J, Zhang L, Sang Y, Zhao X, Ma R, Zhang K, Zhang Y, Yang J, Wen X, Liu J, Wei W, Zhang C, Li W, Qin X, Lei Y, Feng H, Yang X, She CH, Zhang C, Su H, Chen X, Yang J, Lau YL, Wu Q, Ban B, Song Q, Yang W. Unraveling transcriptomic signatures and dysregulated pathways in systemic lupus erythematosus across disease states. Arthritis Res Ther 2024; 26:99. [PMID: 38741185 DOI: 10.1186/s13075-024-03327-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2024] [Accepted: 04/21/2024] [Indexed: 05/16/2024] Open
Abstract
OBJECTIVES This study aims to elucidate the transcriptomic signatures and dysregulated pathways in patients with Systemic Lupus Erythematosus (SLE), with a particular focus on those persisting during disease remission. METHODS We conducted bulk RNA-sequencing of peripheral blood mononuclear cells (PBMCs) from a well-defined cohort comprising 26 remission patients meeting the Low Lupus Disease Activity State (LLDAS) criteria, 76 patients experiencing disease flares, and 15 healthy controls. To elucidate immune signature changes associated with varying disease states, we performed extensive analyses, including the identification of differentially expressed genes and pathways, as well as the construction of protein-protein interaction networks. RESULTS Several transcriptomic features recovered during remission compared to the active disease state, including down-regulation of plasma and cell cycle signatures, as well as up-regulation of lymphocytes. However, specific innate immune response signatures, such as the interferon (IFN) signature, and gene modules involved in chromatin structure modification, persisted across different disease states. Drug repurposing analysis revealed certain drug classes that can target these persistent signatures, potentially preventing disease relapse. CONCLUSION Our comprehensive transcriptomic study revealed gene expression signatures for SLE in both active and remission states. The discovery of gene expression modules persisting in the remission stage may shed light on the underlying mechanisms of vulnerability to relapse in these patients, providing valuable insights for their treatment.
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Affiliation(s)
- Frank Qingyun Wang
- Department of Paediatrics and Adolescent Medicine, The University of Hong Kong, Hong Kong, China
| | - Li Shao
- Department of Rheumatology and Lupus Research Institute, Affiliated Hospital of Jining Medical University, Jining, Shandong, China
| | - Xiao Dang
- Department of Paediatrics and Adolescent Medicine, The University of Hong Kong, Hong Kong, China
| | - Yong-Fei Wang
- School of Life and Health Sciences, School of Medicine, and Warshel Institute for Computational Biology, The Chinese University of Hong Kong - Shenzhen, Shenzhen, Guangdong, China
| | - Shuxiong Chen
- Medical Research Center, Affiliated Hospital of Jining Medical University, Jining, Shandong, China
- Department of Endocrinology, Affiliated Hospital of Jining Medical University, Jining, Shandong, China
| | - Zhongyi Liu
- Department of Paediatrics, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong, China
| | - Yujing Mao
- Department of Rheumatology and Lupus Research Institute, Affiliated Hospital of Jining Medical University, Jining, Shandong, China
| | - Yuping Jiang
- Department of Rheumatology and Lupus Research Institute, Affiliated Hospital of Jining Medical University, Jining, Shandong, China
| | - Fei Hou
- Department of Rheumatology and Lupus Research Institute, Affiliated Hospital of Jining Medical University, Jining, Shandong, China
| | - Xianghua Guo
- Department of Rheumatology and Lupus Research Institute, Affiliated Hospital of Jining Medical University, Jining, Shandong, China
| | - Jian Li
- Department of Rheumatology and Lupus Research Institute, Affiliated Hospital of Jining Medical University, Jining, Shandong, China
| | - Lili Zhang
- Department of Rheumatology and Lupus Research Institute, Affiliated Hospital of Jining Medical University, Jining, Shandong, China
| | - Yuting Sang
- Department of Rheumatology and Lupus Research Institute, Affiliated Hospital of Jining Medical University, Jining, Shandong, China
| | - Xuan Zhao
- Department of Rheumatology and Lupus Research Institute, Affiliated Hospital of Jining Medical University, Jining, Shandong, China
| | - Ruirui Ma
- Department of Rheumatology and Lupus Research Institute, Affiliated Hospital of Jining Medical University, Jining, Shandong, China
| | - Kai Zhang
- Department of Rheumatology and Lupus Research Institute, Affiliated Hospital of Jining Medical University, Jining, Shandong, China
| | - Yanfang Zhang
- Department of Rheumatology and Lupus Research Institute, Affiliated Hospital of Jining Medical University, Jining, Shandong, China
| | - Jing Yang
- Department of Rheumatology and Lupus Research Institute, Affiliated Hospital of Jining Medical University, Jining, Shandong, China
| | - Xiwu Wen
- Medical Research Center, Affiliated Hospital of Jining Medical University, Jining, Shandong, China
| | - Jiong Liu
- Medical Research Center, Affiliated Hospital of Jining Medical University, Jining, Shandong, China
| | - Wei Wei
- Medical Laboratory of Jining Medical University, Jining Medical University, Jining, Shandong, China
| | - Chuanpeng Zhang
- Medical Laboratory of Jining Medical University, Jining Medical University, Jining, Shandong, China
| | - Weiyang Li
- Department of Rheumatology and Lupus Research Institute, Affiliated Hospital of Jining Medical University, Jining, Shandong, China
| | - Xiao Qin
- Department of Rheumatology and Lupus Research Institute, Affiliated Hospital of Jining Medical University, Jining, Shandong, China
| | - Yao Lei
- Department of Paediatrics and Adolescent Medicine, The University of Hong Kong, Hong Kong, China
| | - Hong Feng
- Department of Paediatrics and Adolescent Medicine, The University of Hong Kong, Hong Kong, China
| | - Xingtian Yang
- Department of Paediatrics and Adolescent Medicine, The University of Hong Kong, Hong Kong, China
| | - Chun Hing She
- Department of Paediatrics and Adolescent Medicine, The University of Hong Kong, Hong Kong, China
| | - Caicai Zhang
- Department of Paediatrics and Adolescent Medicine, The University of Hong Kong, Hong Kong, China
| | - Huidong Su
- Department of Paediatrics and Adolescent Medicine, The University of Hong Kong, Hong Kong, China
| | - Xinxin Chen
- Department of Paediatrics and Adolescent Medicine, The University of Hong Kong, Hong Kong, China
| | - Jing Yang
- Department of Paediatrics and Adolescent Medicine, The University of Hong Kong, Hong Kong, China
| | - Yu Lung Lau
- Department of Paediatrics and Adolescent Medicine, The University of Hong Kong, Hong Kong, China
| | - Qingjun Wu
- Department of Rheumatology and Clinical Immunology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Bo Ban
- Department of Endocrinology, Affiliated Hospital of Jining Medical University, Jining, Shandong, China
| | - Qin Song
- Department of Rheumatology and Lupus Research Institute, Affiliated Hospital of Jining Medical University, Jining, Shandong, China.
| | - Wanling Yang
- Department of Paediatrics and Adolescent Medicine, The University of Hong Kong, Hong Kong, China.
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Li X, Sun W, Huang M, Gong L, Zhang X, Zhong L, Calderon V, Bian Z, He Y, Suh WK, Li Y, Song T, Zou Y, Lian ZX, Gu H. Deficiency of CBL and CBLB ubiquitin ligases leads to hyper T follicular helper cell responses and lupus by reducing BCL6 degradation. Immunity 2024:S1074-7613(24)00228-0. [PMID: 38761804 DOI: 10.1016/j.immuni.2024.04.023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2023] [Revised: 02/01/2024] [Accepted: 04/24/2024] [Indexed: 05/20/2024]
Abstract
Recent evidence reveals hyper T follicular helper (Tfh) cell responses in systemic lupus erythematosus (SLE); however, molecular mechanisms responsible for hyper Tfh cell responses and whether they cause SLE are unclear. We found that SLE patients downregulated both ubiquitin ligases, casitas B-lineage lymphoma (CBL) and CBLB (CBLs), in CD4+ T cells. T cell-specific CBLs-deficient mice developed hyper Tfh cell responses and SLE, whereas blockade of Tfh cell development in the mutant mice was sufficient to prevent SLE. ICOS was upregulated in SLE Tfh cells, whose signaling increased BCL6 by attenuating BCL6 degradation via chaperone-mediated autophagy (CMA). Conversely, CBLs restrained BCL6 expression by ubiquitinating ICOS. Blockade of BCL6 degradation was sufficient to enhance Tfh cell responses. Thus, the compromised expression of CBLs is a prevalent risk trait shared by SLE patients and causative to hyper Tfh cell responses and SLE. The ICOS-CBLs axis may be a target to treat SLE.
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Affiliation(s)
- Xin Li
- Medical Research Institute, Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou, Guangdong 510080, China; Montreal Clinical Research Institute, Montreal, QC H2W 1R7, Canada; Division of Experimental Medicine, McGill University, Montreal, QC H3A 0G4, Canada.
| | - Weili Sun
- Montreal Clinical Research Institute, Montreal, QC H2W 1R7, Canada; Division of Experimental Medicine, McGill University, Montreal, QC H3A 0G4, Canada
| | - Mengxing Huang
- Medical Research Institute, Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou, Guangdong 510080, China
| | - Liying Gong
- Montreal Clinical Research Institute, Montreal, QC H2W 1R7, Canada; Division of Experimental Medicine, McGill University, Montreal, QC H3A 0G4, Canada
| | - Xiaochen Zhang
- Montreal Clinical Research Institute, Montreal, QC H2W 1R7, Canada; Department of Microbiology, Infectiology, and Immunology, University of Montreal, Montreal, QC H3T 1J4, Canada
| | - Li Zhong
- Montreal Clinical Research Institute, Montreal, QC H2W 1R7, Canada; Division of Experimental Medicine, McGill University, Montreal, QC H3A 0G4, Canada
| | | | - Zhenhua Bian
- School of Biomedical Sciences and Engineering, South China University of Technology, Guangzhou International Campus, Guangzhou, Guangdong 511442, China
| | - Yi He
- Department of Rheumatology and Immunology, The Third Affiliated Hospital, Southern Medical University, Guangzhou 510630, China
| | - Woong-Kyung Suh
- Montreal Clinical Research Institute, Montreal, QC H2W 1R7, Canada; Division of Experimental Medicine, McGill University, Montreal, QC H3A 0G4, Canada
| | - Yang Li
- Department of Rheumatology and Immunology, Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou, Guangdong 510080, China
| | - Tengfei Song
- The Feinstein Institute for Medical Research, Manhasset, NY 11030, USA
| | - Yongrui Zou
- The Feinstein Institute for Medical Research, Manhasset, NY 11030, USA
| | - Zhe-Xiong Lian
- Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou, Guangdong 510080, China.
| | - Hua Gu
- Montreal Clinical Research Institute, Montreal, QC H2W 1R7, Canada; Division of Experimental Medicine, McGill University, Montreal, QC H3A 0G4, Canada; Department of Microbiology, Infectiology, and Immunology, University of Montreal, Montreal, QC H3T 1J4, Canada.
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19
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Qi T, Song L, Guo Y, Chen C, Yang J. From genetic associations to genes: methods, applications, and challenges. Trends Genet 2024:S0168-9525(24)00095-7. [PMID: 38734482 DOI: 10.1016/j.tig.2024.04.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2023] [Revised: 04/15/2024] [Accepted: 04/16/2024] [Indexed: 05/13/2024]
Abstract
Genome-wide association studies (GWASs) have identified numerous genetic loci associated with human traits and diseases. However, pinpointing the causal genes remains a challenge, which impedes the translation of GWAS findings into biological insights and medical applications. In this review, we provide an in-depth overview of the methods and technologies used for prioritizing genes from GWAS loci, including gene-based association tests, integrative analysis of GWAS and molecular quantitative trait loci (xQTL) data, linking GWAS variants to target genes through enhancer-gene connection maps, and network-based prioritization. We also outline strategies for generating context-dependent xQTL data and their applications in gene prioritization. We further highlight the potential of gene prioritization in drug repurposing. Lastly, we discuss future challenges and opportunities in this field.
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Affiliation(s)
- Ting Qi
- Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou 310024, China; School of Life Sciences, Westlake University, Hangzhou 310024, China.
| | - Liyang Song
- Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou 310024, China; School of Life Sciences, Westlake University, Hangzhou 310024, China
| | - Yazhou Guo
- Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou 310024, China; School of Life Sciences, Westlake University, Hangzhou 310024, China
| | - Chang Chen
- Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou 310024, China; School of Life Sciences, Westlake University, Hangzhou 310024, China
| | - Jian Yang
- Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou 310024, China; School of Life Sciences, Westlake University, Hangzhou 310024, China.
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20
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Alserawan L, Mulet M, Anguera G, Riudavets M, Zamora C, Osuna-Gómez R, Serra-López J, Barba Joaquín A, Sullivan I, Majem M, Vidal S. Kinetics of IFNγ-Induced Cytokines and Development of Immune-Related Adverse Events in Patients Receiving PD-(L)1 Inhibitors. Cancers (Basel) 2024; 16:1759. [PMID: 38730712 PMCID: PMC11083441 DOI: 10.3390/cancers16091759] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2024] [Revised: 04/25/2024] [Accepted: 04/27/2024] [Indexed: 05/13/2024] Open
Abstract
Immune checkpoint inhibitors (ICI) have the potential to trigger unpredictable immune-related adverse events (irAEs), which can be severe. The underlying mechanisms of these events are not fully understood. As PD-L1 is upregulated by IFN, the heightened immune activation resulting from PD-1/PD-L1 inhibition may enhance the IFN response, triggering the expression of IFN-inducible genes and contributing to irAE development and its severity. In this study, we investigated the interplay between irAEs and the expression of IFN-inducible chemokines and cytokines in 134 consecutive patients with solid tumours treated with PD-(L)1 inhibitors as monotherapy or in combination with chemotherapy or other immunotherapy agents. We compared the plasma levels of IFN-associated cytokines (CXCL9/10/11, IL-18, IL-10, IL-6 and TGFβ) at various time points (at baseline, at the onset of irAE and previous to irAE onset) in three patient groups categorized by irAE development and severity: patients with serious irAEs, mild irAEs and without irAEs after PD-(L)1 inhibitors. No differences were observed between groups at baseline. However, patients with serious irAEs exhibited significant increases in CXCL9/10/11, IL-18 and IL-10 levels at the onset of the irAE compared to baseline. A network analysis and correlation patterns highlighted a robust relationship among these chemokines and cytokines at serious-irAE onset. Combining all of the analysed proteins in a cluster analysis, we identified a subgroup of patients with a higher incidence of serious irAEs affecting different organs or systems. Finally, an ROC analysis and a decision tree model proposed IL-18 levels ≥ 807 pg/mL and TGFβ levels ≤ 114 pg/mL as predictors for serious irAEs in 90% of cases. In conclusion, our study elucidates the dynamic changes in cytokine profiles associated with serious irAE development during treatment with PD-(L)1 inhibitors. The study's findings offer valuable insights into the intricate IFN-induced immune responses associated with irAEs and propose potential predictive markers for their severity.
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Affiliation(s)
- Leticia Alserawan
- Immunology-Inflammatory Diseases, Biomedical Research Institute Sant Pau (IIB Sant Pau), 08025 Barcelona, Spain; (L.A.); (M.M.); (C.Z.); (R.O.-G.)
- Department of Immunology, Hospital Clínic Barcelona, 08036 Barcelona, Spain
| | - Maria Mulet
- Immunology-Inflammatory Diseases, Biomedical Research Institute Sant Pau (IIB Sant Pau), 08025 Barcelona, Spain; (L.A.); (M.M.); (C.Z.); (R.O.-G.)
| | - Geòrgia Anguera
- Department of Medical Oncology, Hospital de la Santa Creu i Sant Pau, 08025 Barcelona, Spain; (G.A.); (M.R.); (J.S.-L.); (A.B.J.); (I.S.); (M.M.)
| | - Mariona Riudavets
- Department of Medical Oncology, Hospital de la Santa Creu i Sant Pau, 08025 Barcelona, Spain; (G.A.); (M.R.); (J.S.-L.); (A.B.J.); (I.S.); (M.M.)
- Department of Pneumologie, Hôpital Cochin—APHP Centre, 75014 Paris, France
| | - Carlos Zamora
- Immunology-Inflammatory Diseases, Biomedical Research Institute Sant Pau (IIB Sant Pau), 08025 Barcelona, Spain; (L.A.); (M.M.); (C.Z.); (R.O.-G.)
| | - Rubén Osuna-Gómez
- Immunology-Inflammatory Diseases, Biomedical Research Institute Sant Pau (IIB Sant Pau), 08025 Barcelona, Spain; (L.A.); (M.M.); (C.Z.); (R.O.-G.)
| | - Jorgina Serra-López
- Department of Medical Oncology, Hospital de la Santa Creu i Sant Pau, 08025 Barcelona, Spain; (G.A.); (M.R.); (J.S.-L.); (A.B.J.); (I.S.); (M.M.)
| | - Andrés Barba Joaquín
- Department of Medical Oncology, Hospital de la Santa Creu i Sant Pau, 08025 Barcelona, Spain; (G.A.); (M.R.); (J.S.-L.); (A.B.J.); (I.S.); (M.M.)
| | - Ivana Sullivan
- Department of Medical Oncology, Hospital de la Santa Creu i Sant Pau, 08025 Barcelona, Spain; (G.A.); (M.R.); (J.S.-L.); (A.B.J.); (I.S.); (M.M.)
| | - Margarita Majem
- Department of Medical Oncology, Hospital de la Santa Creu i Sant Pau, 08025 Barcelona, Spain; (G.A.); (M.R.); (J.S.-L.); (A.B.J.); (I.S.); (M.M.)
| | - Silvia Vidal
- Immunology-Inflammatory Diseases, Biomedical Research Institute Sant Pau (IIB Sant Pau), 08025 Barcelona, Spain; (L.A.); (M.M.); (C.Z.); (R.O.-G.)
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Dou J, Tan Y, Kock KH, Wang J, Cheng X, Tan LM, Han KY, Hon CC, Park WY, Shin JW, Jin H, Wang Y, Chen H, Ding L, Prabhakar S, Navin N, Chen R, Chen K. Single-nucleotide variant calling in single-cell sequencing data with Monopogen. Nat Biotechnol 2024; 42:803-812. [PMID: 37592035 PMCID: PMC11098741 DOI: 10.1038/s41587-023-01873-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2022] [Accepted: 06/21/2023] [Indexed: 08/19/2023]
Abstract
Single-cell omics technologies enable molecular characterization of diverse cell types and states, but how the resulting transcriptional and epigenetic profiles depend on the cell's genetic background remains understudied. We describe Monopogen, a computational tool to detect single-nucleotide variants (SNVs) from single-cell sequencing data. Monopogen leverages linkage disequilibrium from external reference panels to identify germline SNVs and detects putative somatic SNVs using allele cosegregating patterns at the cell population level. It can identify 100 K to 3 M germline SNVs achieving a genotyping accuracy of 95%, together with hundreds of putative somatic SNVs. Monopogen-derived genotypes enable global and local ancestry inference and identification of admixed samples. It identifies variants associated with cardiomyocyte metabolic levels and epigenomic programs. It also improves putative somatic SNV detection that enables clonal lineage tracing in primary human clonal hematopoiesis. Monopogen brings together population genetics, cell lineage tracing and single-cell omics to uncover genetic determinants of cellular processes.
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Affiliation(s)
- Jinzhuang Dou
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Yukun Tan
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Kian Hong Kock
- Genome Institute of Singapore (GIS), Agency for Science, Technology and Research (A*STAR), Singapore, Republic of Singapore
| | - Jun Wang
- Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Xuesen Cheng
- Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Le Min Tan
- Genome Institute of Singapore (GIS), Agency for Science, Technology and Research (A*STAR), Singapore, Republic of Singapore
| | - Kyung Yeon Han
- Samsung Genome Institute, Samsung Medical Center, Seoul, South Korea
| | - Chung-Chau Hon
- Laboratory for Genome Information Analysis, RIKEN center for Integrative Medical Sciences, Graduate School of Integrated Sciences for Life, Hiroshima University, Higashi-Hiroshima, Japan
| | - Woong-Yang Park
- Samsung Genome Institute, Samsung Medical Center, Seoul, South Korea
| | - Jay W Shin
- Genome Institute of Singapore (GIS), Agency for Science, Technology and Research (A*STAR), Singapore, Republic of Singapore
- Laboratory for Advanced Genomics Circuit, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Haijing Jin
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Yujia Wang
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Han Chen
- Human Genetics Center, Department of Epidemiology, Human Genetics and Environmental Sciences, School of Public Health, The University of Texas Health Science Center, Houston, TX, USA
- Center for Precision Health, McWilliams School of Biomedical Informatics, The University of Texas Health Science Center, Houston, TX, USA
| | - Li Ding
- McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO, USA
- Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA
- Department of Genetics, Washington University School of Medicine, St. Louis, MO, USA
- Siteman Cancer Institute, Washington University School of Medicine, St. Louis, MO, USA
| | - Shyam Prabhakar
- Genome Institute of Singapore (GIS), Agency for Science, Technology and Research (A*STAR), Singapore, Republic of Singapore
| | - Nicholas Navin
- Department of Systems Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Rui Chen
- Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Ken Chen
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.
- Department of Systems Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.
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22
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Mangiola S, Milton M, Ranathunga N, Li-Wai-Suen C, Odainic A, Yang E, Hutchison W, Garnham A, Iskander J, Pal B, Yadav V, Rossello J, Carey VJ, Morgan M, Bedoui S, Kallies A, Papenfuss AT. A multi-organ map of the human immune system across age, sex and ethnicity. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.06.08.542671. [PMID: 38746418 PMCID: PMC11092463 DOI: 10.1101/2023.06.08.542671] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2024]
Abstract
Understanding tissue biology's heterogeneity is crucial for advancing precision medicine. Despite the centrality of the immune system in tissue homeostasis, a detailed and comprehensive map of immune cell distribution and interactions across human tissues and demographics remains elusive. To fill this gap, we harmonised data from 12,981 single-cell RNA sequencing samples and curated 29 million cells from 45 anatomical sites to create a comprehensive compositional and transcriptional healthy map of the healthy immune system. We used this resource and a novel multilevel modelling approach to track immune ageing and test differences across sex and ethnicity. We uncovered conserved and tissue-specific immune-ageing programs, resolved sex-dependent differential ageing and identified ethnic diversity in clinically critical immune checkpoints. This study provides a quantitative baseline of the immune system, facilitating advances in precision medicine. By sharing our immune map, we hope to catalyse further breakthroughs in cancer, infectious disease, immunology and precision medicine.
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Affiliation(s)
- S Mangiola
- Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia
- Department of Medical Biology, University of Melbourne, Melbourne, Victoria, Australia
| | - M Milton
- Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia
| | - N Ranathunga
- Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia
- Department of Medical Biology, University of Melbourne, Melbourne, Victoria, Australia
| | - Csn Li-Wai-Suen
- Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia
- Department of Medical Biology, University of Melbourne, Melbourne, Victoria, Australia
| | - A Odainic
- The Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
- Institute of Clinical Chemistry and Clinical Pharmacology, University Hospital Bonn, 53127 Bonn, Germany
| | - E Yang
- Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia
| | - W Hutchison
- Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia
- Department of Medical Biology, University of Melbourne, Melbourne, Victoria, Australia
| | - A Garnham
- Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia
- Department of Medical Biology, University of Melbourne, Melbourne, Victoria, Australia
| | - J Iskander
- Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia
| | - B Pal
- Olivia Newton-John Cancer Research Institute, Heidelberg, Victoria, Australia
| | - V Yadav
- Systems Biology of Aging Laboratory, Columbia University; New York, USA
| | - Jfj Rossello
- Murdoch Children's Research Institute, The Royal Children's Hospital, Melbourne, VIC 3052, Australia
- Novo Nordisk Foundation Center for Stem Cell Medicine, Murdoch Children's Research Institute, Melbourne, VIC 3052, Australia
- Department of Clinical Pathology, University of Melbourne, Melbourne, VIC, Australia
- Australian Regenerative Medicine Institute, Monash University, Victoria, Australia
| | - V J Carey
- Channing Division of Network Medicine, Mass General Brigham, Harvard Medical School, Harvard University, Boston, USA
| | - M Morgan
- Department of Biostatistics and Bioinformatics, Roswell Park Comprehensive Cancer Center, NY, USA
| | - S Bedoui
- The Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
| | - A Kallies
- The Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
| | - A T Papenfuss
- Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia
- Department of Medical Biology, University of Melbourne, Melbourne, Victoria, Australia
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23
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Curion F, Wu X, Heumos L, André MMG, Halle L, Ozols M, Grant-Peters M, Rich-Griffin C, Yeung HY, Dendrou CA, Schiller HB, Theis FJ. hadge: a comprehensive pipeline for donor deconvolution in single-cell studies. Genome Biol 2024; 25:109. [PMID: 38671451 PMCID: PMC11055383 DOI: 10.1186/s13059-024-03249-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2023] [Accepted: 04/16/2024] [Indexed: 04/28/2024] Open
Abstract
Single-cell multiplexing techniques (cell hashing and genetic multiplexing) combine multiple samples, optimizing sample processing and reducing costs. Cell hashing conjugates antibody-tags or chemical-oligonucleotides to cell membranes, while genetic multiplexing allows to mix genetically diverse samples and relies on aggregation of RNA reads at known genomic coordinates. We develop hadge (hashing deconvolution combined with genotype information), a Nextflow pipeline that combines 12 methods to perform both hashing- and genotype-based deconvolution. We propose a joint deconvolution strategy combining best-performing methods and demonstrate how this approach leads to the recovery of previously discarded cells in a nuclei hashing of fresh-frozen brain tissue.
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Affiliation(s)
- Fabiola Curion
- Institute of Computational Biology, Computational Health Center, Helmholtz Munich, Neuherberg, Germany
- Department of Mathematics, School of Computation, Information and Technology, Technical University of Munich, Garching, Germany
| | - Xichen Wu
- Institute of Computational Biology, Computational Health Center, Helmholtz Munich, Neuherberg, Germany
- Department of Mathematics, School of Computation, Information and Technology, Technical University of Munich, Garching, Germany
| | - Lukas Heumos
- Institute of Computational Biology, Computational Health Center, Helmholtz Munich, Neuherberg, Germany
- Comprehensive Pneumology Center, German Center for Lung Research (DZL), Munich, Germany
- TUM School of Life Sciences Weihenstephan, Technical University of Munich, Freising, Germany
| | - Mylene Mariana Gonzales André
- Institute of Computational Biology, Computational Health Center, Helmholtz Munich, Neuherberg, Germany
- Department of Mathematics, School of Computation, Information and Technology, Technical University of Munich, Garching, Germany
| | - Lennard Halle
- Institute of Computational Biology, Computational Health Center, Helmholtz Munich, Neuherberg, Germany
| | - Matiss Ozols
- Wellcome Sanger Institute, Hinxton, UK
- School of Cell Matrix and Regenerative Medicine, The University of Manchester, Manchester, UK
| | - Melissa Grant-Peters
- Nuffield Department of Medicine, Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Charlotte Rich-Griffin
- Nuffield Department of Medicine, Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Hing-Yuen Yeung
- Nuffield Department of Medicine, Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Calliope A Dendrou
- Nuffield Department of Medicine, Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
- Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, The Kennedy Institute of Rheumatology, University of Oxford, Oxford, UK
| | - Herbert B Schiller
- Comprehensive Pneumology Center, German Center for Lung Research (DZL), Munich, Germany
- Research Unit Precision Regenerative Medicine, Helmholtz Munich, Neuherberg, Germany
- Institute of Experimental Pneumology, LMU University Hospital, Ludwig-Maximilians University, Munich, Germany
| | - Fabian J Theis
- Institute of Computational Biology, Computational Health Center, Helmholtz Munich, Neuherberg, Germany.
- Department of Mathematics, School of Computation, Information and Technology, Technical University of Munich, Garching, Germany.
- TUM School of Life Sciences Weihenstephan, Technical University of Munich, Freising, Germany.
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24
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Schepps S, Xu J, Yang H, Mandel J, Mehta J, Tolotta J, Baker N, Tekmen V, Nikbakht N, Fortina P, Fuentes I, LaFleur B, Cho RJ, South AP. Skin in the game: a review of single-cell and spatial transcriptomics in dermatological research. Clin Chem Lab Med 2024; 0:cclm-2023-1245. [PMID: 38656304 DOI: 10.1515/cclm-2023-1245] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2023] [Accepted: 02/29/2024] [Indexed: 04/26/2024]
Abstract
Single-cell RNA sequencing (scRNA-seq) and spatial transcriptomics (ST) are two emerging research technologies that uniquely characterize gene expression microenvironments on a cellular or subcellular level. The skin, a clinically accessible tissue composed of diverse, essential cell populations, serves as an ideal target for these high-resolution investigative approaches. Using these tools, researchers are assembling a compendium of data and discoveries in healthy skin as well as a range of dermatologic pathophysiologies, including atopic dermatitis, psoriasis, and cutaneous malignancies. The ongoing advancement of single-cell approaches, coupled with anticipated decreases in cost with increased adoption, will reshape dermatologic research, profoundly influencing disease characterization, prognosis, and ultimately clinical practice.
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Affiliation(s)
- Samuel Schepps
- Department of Dermatology and Cutaneous Biology, 6559 Thomas Jefferson University , Philadelphia, PA, USA
| | - Jonathan Xu
- Department of Dermatology and Cutaneous Biology, 6559 Thomas Jefferson University , Philadelphia, PA, USA
| | - Henry Yang
- Department of Dermatology and Cutaneous Biology, 6559 Thomas Jefferson University , Philadelphia, PA, USA
| | - Jenna Mandel
- Department of Dermatology and Cutaneous Biology, 6559 Thomas Jefferson University , Philadelphia, PA, USA
| | - Jaanvi Mehta
- Department of Dermatology and Cutaneous Biology, 6559 Thomas Jefferson University , Philadelphia, PA, USA
| | - Julianna Tolotta
- Department of Dermatology and Cutaneous Biology, 6559 Thomas Jefferson University , Philadelphia, PA, USA
| | - Nicole Baker
- Department of Dermatology and Cutaneous Biology, 6559 Thomas Jefferson University , Philadelphia, PA, USA
| | - Volkan Tekmen
- Department of Dermatology and Cutaneous Biology, 6559 Thomas Jefferson University , Philadelphia, PA, USA
| | - Neda Nikbakht
- Department of Dermatology and Cutaneous Biology, 6559 Thomas Jefferson University , Philadelphia, PA, USA
- Department of Pharmacology, Physiology and Cancer Biology, 6559 Thomas Jefferson University , Philadelphia, PA, USA
| | - Paolo Fortina
- Department of Pharmacology, Physiology and Cancer Biology, 6559 Thomas Jefferson University , Philadelphia, PA, USA
- International Federation of Clinical Chemistry Working Group on Single Cell and Spatial Transcriptomics, Milan, Italy
| | - Ignacia Fuentes
- International Federation of Clinical Chemistry Working Group on Single Cell and Spatial Transcriptomics, Milan, Italy
- Departamento de Biología Celular y Molecular, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Directora de Investigación Fundación DEBRA Chile, Santiago, Chile
| | - Bonnie LaFleur
- International Federation of Clinical Chemistry Working Group on Single Cell and Spatial Transcriptomics, Milan, Italy
- R. Ken Coit College of Pharmacy, University of Arizona, University of Arizona Cancer Center, Tucson, AZ, USA
| | - Raymond J Cho
- International Federation of Clinical Chemistry Working Group on Single Cell and Spatial Transcriptomics, Milan, Italy
- Department of Dermatology, University of San Francisco, San Francisco, CA, USA
| | - Andrew P South
- Department of Pharmacology, Physiology and Cancer Biology, 6559 Thomas Jefferson University , Philadelphia, PA, USA
- International Federation of Clinical Chemistry Working Group on Single Cell and Spatial Transcriptomics, Milan, Italy
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25
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Okuzono Y, Miyakawa S, Itou T, Sagara M, Iwata M, Ishizuchi K, Sekiguchi K, Motegi H, Oyama M, Warude D, Kikukawa Y, Suzuki S. B-cell immune dysregulation with low soluble CD22 levels in refractory seronegative myasthenia gravis. Front Immunol 2024; 15:1382320. [PMID: 38711503 PMCID: PMC11071663 DOI: 10.3389/fimmu.2024.1382320] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2024] [Accepted: 04/01/2024] [Indexed: 05/08/2024] Open
Abstract
Myasthenia gravis (MG), primarily caused by acetylcholine receptor (AChR) autoantibodies, is a chronic autoimmune disorder causing severe muscle weakness and fatigability. In particular, seronegative MG constitutes 10%-15% of MG cases and presents diagnostic challenges especially in early-onset female patients who often show severe disease and resistance to immunosuppressive therapy. Furthermore, the immunopathology of seronegative MG remains unclear. Thus, in this study, we aimed to elucidate the pathogenic mechanism of seronegative MG using scRNA-seq analysis and plasma proteome analysis; in particular, we investigated the relationship between immune dysregulation status and disease severity in refractory seronegative MG. Employing single-cell RNA-sequencing and plasma proteome analyses, we analyzed peripheral blood samples from 30 women divided into three groups: 10 healthy controls, 10 early-onset AChR-positive MG, and 10 refractory early-onset seronegative MG patients, both before and after intravenous immunoglobulin treatment. The disease severity was evaluated using the MG-Activities of Daily Living (ADL), MG composite (MGC), and revised 15-item MG-Quality of Life (QOL) scales. We observed numerical abnormalities in multiple immune cells, particularly B cells, in patients with refractory seronegative MG, correlating with disease activity. Notably, severe MG cases had fewer regulatory T cells without functional abnormalities. Memory B cells were found to be enriched in peripheral blood cells compared with naïve B cells. Moreover, plasma proteome analysis indicated significantly lower plasma protein levels of soluble CD22, expressed in the lineage of B-cell maturation (including mature B cells and memory B cells), in refractory seronegative MG patients than in healthy donors or patients with AChR-positive MG. Soluble CD22 levels were correlated with disease severity, B-cell frequency, and RNA expression levels of CD22. In summary, this study elucidates the immunopathology of refractory seronegative MG, highlighting immune disorders centered on B cells and diminished soluble CD22 levels. These insights pave the way for novel MG treatment strategies focused on B-cell biology.
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Affiliation(s)
- Yuumi Okuzono
- Oncology Drug Discovery Unit Japan, Research, Takeda Pharmaceutical Company Limited, Kanagawa, Japan
| | - Shuuichi Miyakawa
- Oncology Drug Discovery Unit Japan, Research, Takeda Pharmaceutical Company Limited, Kanagawa, Japan
| | - Tatsuo Itou
- Oncology Drug Discovery Unit Japan, Research, Takeda Pharmaceutical Company Limited, Kanagawa, Japan
| | - Masaki Sagara
- Oncology Drug Discovery Unit Japan, Research, Takeda Pharmaceutical Company Limited, Kanagawa, Japan
| | - Masashi Iwata
- Oncology Drug Discovery Unit Japan, Research, Takeda Pharmaceutical Company Limited, Kanagawa, Japan
| | - Kei Ishizuchi
- Department of Neurology, Keio University School of Medicine, Tokyo, Japan
| | - Koji Sekiguchi
- Department of Neurology, Keio University School of Medicine, Tokyo, Japan
| | - Haruhiko Motegi
- Department of Neurology, Keio University School of Medicine, Tokyo, Japan
- Department of Neurology, The Jikei University School of Medicine, Tokyo, Japan
| | - Munenori Oyama
- Department of Neurology, Keio University School of Medicine, Tokyo, Japan
| | - Dnyaneshwar Warude
- Oncology Drug Discovery Unit Japan, Research, Takeda Pharmaceutical Company Limited, Kanagawa, Japan
| | - Yusuke Kikukawa
- Oncology Drug Discovery Unit Japan, Research, Takeda Pharmaceutical Company Limited, Kanagawa, Japan
| | - Shigeaki Suzuki
- Department of Neurology, Keio University School of Medicine, Tokyo, Japan
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26
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Yu X, Chen Y, Chen J, Fan Y, Lu H, Wu D, Xu Y. Shared genetic architecture between autoimmune disorders and B-cell acute lymphoblastic leukemia: insights from large-scale genome-wide cross-trait analysis. BMC Med 2024; 22:161. [PMID: 38616254 PMCID: PMC11017616 DOI: 10.1186/s12916-024-03385-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/08/2024] [Accepted: 04/08/2024] [Indexed: 04/16/2024] Open
Abstract
BACKGROUND To study the shared genetic structure between autoimmune diseases and B-cell acute lymphoblastic leukemia (B-ALL) and identify the shared risk loci and genes and genetic mechanisms involved. METHODS Based on large-scale genome-wide association study (GWAS) summary-level data sets, we observed genetic overlaps between autoimmune diseases and B-ALL, and cross-trait pleiotropic analysis was performed to detect shared pleiotropic loci and genes. A series of functional annotation and tissue-specific analysis were performed to determine the influence of pleiotropic genes. The heritability enrichment analysis was used to detect crucial immune cells and tissues. Finally, bidirectional Mendelian randomization (MR) methods were utilized to investigate the casual associations. RESULTS Our research highlighted shared genetic mechanisms between seven autoimmune disorders and B-ALL. A total of 73 pleiotropic loci were identified at the genome-wide significance level (P < 5 × 10-8), 16 of which had strong evidence of colocalization. We demonstrated that several loci have been previously reported (e.g., 17q21) and discovered some novel loci (e.g., 10p12, 5p13). Further gene-level identified 194 unique pleiotropic genes, for example IKZF1, GATA3, IKZF3, GSDMB, and ORMDL3. Pathway analysis determined the key role of cellular response to cytokine stimulus, B cell activation, and JAK-STAT signaling pathways. SNP-level and gene-level tissue enrichment suggested that crucial role pleiotropic mechanisms involved in the spleen, whole blood, and EBV-transformed lymphocytes. Also, hyprcoloc and stratified LD score regression analyses revealed that B cells at different developmental stages may be involved in mechanisms shared between two different diseases. Finally, two-sample MR analysis determined causal effects of asthma and rheumatoid arthritis on B-ALL. CONCLUSIONS Our research proved shared genetic architecture between autoimmune disorders and B-ALL and shed light on the potential mechanism that might involve in.
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Affiliation(s)
- Xinghao Yu
- National Clinical Research Center for Hematologic Diseases, Jiangsu Institute of Hematology, The First Affiliated Hospital of Soochow University, Suzhou, China
- Collaborative Innovation Center of Hematology, Institute of Blood and Marrow Transplantation, Soochow University, Suzhou, China
| | - Yiyin Chen
- National Clinical Research Center for Hematologic Diseases, Jiangsu Institute of Hematology, The First Affiliated Hospital of Soochow University, Suzhou, China
- Collaborative Innovation Center of Hematology, Institute of Blood and Marrow Transplantation, Soochow University, Suzhou, China
| | - Jia Chen
- National Clinical Research Center for Hematologic Diseases, Jiangsu Institute of Hematology, The First Affiliated Hospital of Soochow University, Suzhou, China
| | - Yi Fan
- National Clinical Research Center for Hematologic Diseases, Jiangsu Institute of Hematology, The First Affiliated Hospital of Soochow University, Suzhou, China
| | - Huimin Lu
- Department of Outpatient and Emergency, The First Affiliated Hospital of Soochow University, Suzhou, China
| | - Depei Wu
- National Clinical Research Center for Hematologic Diseases, Jiangsu Institute of Hematology, The First Affiliated Hospital of Soochow University, Suzhou, China.
- Collaborative Innovation Center of Hematology, Institute of Blood and Marrow Transplantation, Soochow University, Suzhou, China.
| | - Yang Xu
- National Clinical Research Center for Hematologic Diseases, Jiangsu Institute of Hematology, The First Affiliated Hospital of Soochow University, Suzhou, China.
- Collaborative Innovation Center of Hematology, Institute of Blood and Marrow Transplantation, Soochow University, Suzhou, China.
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27
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Fan Y, Li L, Sun S. Powerful and accurate detection of temporal gene expression patterns from multi-sample multi-stage single-cell transcriptomics data with TDEseq. Genome Biol 2024; 25:96. [PMID: 38622747 PMCID: PMC11020788 DOI: 10.1186/s13059-024-03237-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2023] [Accepted: 04/03/2024] [Indexed: 04/17/2024] Open
Abstract
We present a non-parametric statistical method called TDEseq that takes full advantage of smoothing splines basis functions to account for the dependence of multiple time points in scRNA-seq studies, and uses hierarchical structure linear additive mixed models to model the correlated cells within an individual. As a result, TDEseq demonstrates powerful performance in identifying four potential temporal expression patterns within a specific cell type. Extensive simulation studies and the analysis of four published scRNA-seq datasets show that TDEseq can produce well-calibrated p-values and up to 20% power gain over the existing methods for detecting temporal gene expression patterns.
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Affiliation(s)
- Yue Fan
- Center for Single-Cell Omics and Health, School of Public Health, Xi'an Jiaotong University, Xi'an, Shaanxi, 710061, People's Republic of China
- Collaborative Innovation Center of Endemic Diseases and Health Promotion in Silk Road Region; NHC Key Laboratory of Environment and Endemic Diseases, Xi'an Jiaotong University, Xi'an, Shaanxi, 710061, People's Republic of China
- Key Laboratory of Environment and Genes Related to Diseases (Xi'an Jiaotong University), Ministry of Education, Xi'an, Shaanxi, 710061, People's Republic of China
| | - Lei Li
- Center for Single-Cell Omics and Health, School of Public Health, Xi'an Jiaotong University, Xi'an, Shaanxi, 710061, People's Republic of China
- Collaborative Innovation Center of Endemic Diseases and Health Promotion in Silk Road Region; NHC Key Laboratory of Environment and Endemic Diseases, Xi'an Jiaotong University, Xi'an, Shaanxi, 710061, People's Republic of China
| | - Shiquan Sun
- Center for Single-Cell Omics and Health, School of Public Health, Xi'an Jiaotong University, Xi'an, Shaanxi, 710061, People's Republic of China.
- Collaborative Innovation Center of Endemic Diseases and Health Promotion in Silk Road Region; NHC Key Laboratory of Environment and Endemic Diseases, Xi'an Jiaotong University, Xi'an, Shaanxi, 710061, People's Republic of China.
- Key Laboratory of Environment and Genes Related to Diseases (Xi'an Jiaotong University), Ministry of Education, Xi'an, Shaanxi, 710061, People's Republic of China.
- Key Laboratory for Disease Prevention and Control and Health Promotion of Shaanxi Province, Xi'an, Shaanxi, 710061, People's Republic of China.
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28
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Nigrovic PA, Wang Q, Kim T, Martinez-Bonet M, Aguiar VRC, Sim S, Cui J, Sparks JA, Chen X, Todd M, Wauford B, Marion MC, Langefeld CD, Weirauch MT, Gutierrez-Arcelus M. High-throughput identification of functional regulatory SNPs in systemic lupus erythematosus. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.08.16.553538. [PMID: 37645953 PMCID: PMC10462027 DOI: 10.1101/2023.08.16.553538] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/31/2023]
Abstract
Genome-wide association studies implicate multiple loci in risk for systemic lupus erythematosus (SLE), but few contain exonic variants, rendering systematic identification of non-coding variants essential to decoding SLE genetics. We utilized SNP-seq and bioinformatic enrichment to interrogate 2180 single-nucleotide polymorphisms (SNPs) from 87 SLE risk loci for potential binding of transcription factors and related proteins from B cells. 52 SNPs that passed initial screening were tested by electrophoretic mobility shift and luciferase reporter assays. To validate the approach, we studied rs2297550 in detail, finding that the risk allele enhanced binding to the transcription factor Ikaros (IKZF1), thereby modulating expression of IKBKE. Correspondingly, primary cells from genotyped healthy donors bearing the risk allele expressed higher levels of the interferon / NF-κB regulator IKKϵ. Together, these findings define a set of likely functional non-coding lupus risk variants and identify a new regulatory pathway involving rs2297550, Ikaros, and IKKϵ implicated by human genetics in risk for SLE.
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29
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Chen W, Jin B, Cheng C, Peng H, Zhang X, Tan W, Tang R, Lian X, Diao H, Luo N, Li X, Fan J, Shi J, Yin C, Wang J, Peng S, Yu L, Li J, Wu RQ, Kuang DM, Shi GP, Zhou Y, Wang F, Jiang X. Single-cell profiling reveals kidney CD163 + dendritic cell participation in human lupus nephritis. Ann Rheum Dis 2024; 83:608-623. [PMID: 38290829 DOI: 10.1136/ard-2023-224788] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2023] [Accepted: 01/12/2024] [Indexed: 02/01/2024]
Abstract
OBJECTIVES The current work aimed to provide a comprehensive single-cell landscape of lupus nephritis (LN) kidneys, including immune and non-immune cells, identify disease-associated cell populations and unravel their participation within the kidney microenvironment. METHODS Single-cell RNA and T cell receptor sequencing were performed on renal biopsy tissues from 40 patients with LN and 6 healthy donors as controls. Matched peripheral blood samples from seven LN patients were also sequenced. Multiplex immunohistochemical analysis was performed on an independent cohort of 60 patients and validated using flow cytometric characterisation of human kidney tissues and in vitro assays. RESULTS We uncovered a notable enrichment of CD163+ dendritic cells (DC3s) in LN kidneys, which exhibited a positive correlation with the severity of LN. In contrast to their counterparts in blood, DC3s in LN kidney displayed activated and highly proinflammatory phenotype. DC3s showed strong interactions with CD4+ T cells, contributing to intrarenal T cell clonal expansion, activation of CD4+ effector T cell and polarisation towards Th1/Th17. Injured proximal tubular epithelial cells (iPTECs) may orchestrate DC3 activation, adhesion and recruitment within the LN kidneys. In cultures, blood DC3s treated with iPTECs acquired distinct capabilities to polarise Th1/Th17 cells. Remarkably, the enumeration of kidney DC3s might be a potential biomarker for induction treatment response in LN patients. CONCLUSION The intricate interplay involving DC3s, T cells and tubular epithelial cells within kidneys may substantially contribute to LN pathogenesis. The enumeration of renal DC3 holds potential as a valuable stratification feature for guiding LN patient treatment decisions in clinical practice.
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Affiliation(s)
- Wei Chen
- Department of Nephrology, Sun Yat-sen University First Affiliated Hospital, Guangzhou, Guangdong, China
- National Health Commission (NHC), Key Laboratory of Clinical Nephrology (SunYat-Sen University) and Guangdong Provincial Key Laboratory of Nephrology, Guangzhou, Guangdong, China
| | - Bei Jin
- Department of Pediatric Rheumatology and Nephrology, Sun Yat-sen University First Affiliated Hospital, Guangzhou, Guangdong, China
| | - Cheng Cheng
- Department of Pediatric Rheumatology and Nephrology, Sun Yat-sen University First Affiliated Hospital, Guangzhou, Guangdong, China
| | - Huajing Peng
- Department of Nephrology, Sun Yat-sen University First Affiliated Hospital, Guangzhou, Guangdong, China
- National Health Commission (NHC), Key Laboratory of Clinical Nephrology (SunYat-Sen University) and Guangdong Provincial Key Laboratory of Nephrology, Guangzhou, Guangdong, China
| | - Xinxin Zhang
- Department of Nephrology, Sun Yat-sen University First Affiliated Hospital, Guangzhou, Guangdong, China
- National Health Commission (NHC), Key Laboratory of Clinical Nephrology (SunYat-Sen University) and Guangdong Provincial Key Laboratory of Nephrology, Guangzhou, Guangdong, China
| | - Weiping Tan
- Department of Pediatrics, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, China
| | - Ruihan Tang
- Department of Nephrology, Sun Yat-sen University First Affiliated Hospital, Guangzhou, Guangdong, China
- National Health Commission (NHC), Key Laboratory of Clinical Nephrology (SunYat-Sen University) and Guangdong Provincial Key Laboratory of Nephrology, Guangzhou, Guangdong, China
| | - Xingji Lian
- Department of Nephrology, Sun Yat-sen University First Affiliated Hospital, Guangzhou, Guangdong, China
- National Health Commission (NHC), Key Laboratory of Clinical Nephrology (SunYat-Sen University) and Guangdong Provincial Key Laboratory of Nephrology, Guangzhou, Guangdong, China
| | - Hui Diao
- Department of Nephrology, Sun Yat-sen University First Affiliated Hospital, Guangzhou, Guangdong, China
- National Health Commission (NHC), Key Laboratory of Clinical Nephrology (SunYat-Sen University) and Guangdong Provincial Key Laboratory of Nephrology, Guangzhou, Guangdong, China
| | - Ning Luo
- Department of Nephrology, Sun Yat-sen University First Affiliated Hospital, Guangzhou, Guangdong, China
- National Health Commission (NHC), Key Laboratory of Clinical Nephrology (SunYat-Sen University) and Guangdong Provincial Key Laboratory of Nephrology, Guangzhou, Guangdong, China
| | - Xiaoyan Li
- Department of Nephrology, Sun Yat-sen University First Affiliated Hospital, Guangzhou, Guangdong, China
- National Health Commission (NHC), Key Laboratory of Clinical Nephrology (SunYat-Sen University) and Guangdong Provincial Key Laboratory of Nephrology, Guangzhou, Guangdong, China
| | - Jinjin Fan
- Department of Nephrology, Sun Yat-sen University First Affiliated Hospital, Guangzhou, Guangdong, China
- National Health Commission (NHC), Key Laboratory of Clinical Nephrology (SunYat-Sen University) and Guangdong Provincial Key Laboratory of Nephrology, Guangzhou, Guangdong, China
| | - Jian Shi
- Institute of Precision Medicine, Sun Yat-sen University First Affiliated Hospital, Guangzhou, Guangdong, China
| | - Changjun Yin
- Institute of Precision Medicine, Sun Yat-sen University First Affiliated Hospital, Guangzhou, Guangdong, China
- Institute for Cardiovascular Prevention (IPEK), Ludwig-Maximilians-University, Munich, Germany
| | - Ji Wang
- Institute of Precision Medicine, Sun Yat-sen University First Affiliated Hospital, Guangzhou, Guangdong, China
| | - Sui Peng
- Institute of Precision Medicine, Sun Yat-sen University First Affiliated Hospital, Guangzhou, Guangdong, China
- Clinical Trials Unit, Sun Yat-sen University First Affiliated Hospital, Guangzhou, Guangdong, China
- Department of Gastroenterology and Hepatology, Sun Yat-sen University First Affiliated Hospital, Guangzhou, Guangdong, China
| | - Li Yu
- Department of Pediatrics, Guangzhou First People's Hospital, Guangzhou Medical University, Guangzhou, China
| | - Jun Li
- Organ Transplant Center, Sun Yat-sen University First Affiliated Hospital, Guangzhou, Guangdong, China
| | - Rui-Qi Wu
- Guangdong Province Key Laboratory of Pharmaceutical Functional Genes, MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, and Sun Yat-sen University Cancer Center, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Dong-Ming Kuang
- Guangdong Province Key Laboratory of Pharmaceutical Functional Genes, MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, and Sun Yat-sen University Cancer Center, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Guo-Ping Shi
- Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts, USA
| | - Yi Zhou
- Department of Nephrology, Sun Yat-sen University First Affiliated Hospital, Guangzhou, Guangdong, China
- National Health Commission (NHC), Key Laboratory of Clinical Nephrology (SunYat-Sen University) and Guangdong Provincial Key Laboratory of Nephrology, Guangzhou, Guangdong, China
| | - Fang Wang
- Institute of Precision Medicine, Sun Yat-sen University First Affiliated Hospital, Guangzhou, Guangdong, China
| | - Xiaoyun Jiang
- Department of Pediatric Rheumatology and Nephrology, Sun Yat-sen University First Affiliated Hospital, Guangzhou, Guangdong, China
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30
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Guo M, Guo H, Zhu J, Wang F, Chen J, Wan C, Deng Y, Wang F, Xu L, Chen Y, Li R, Liu S, Zhang L, Wang Y, Zhou J, Li S. A novel subpopulation of monocytes with a strong interferon signature indicated by SIGLEC-1 is present in patients with in recent-onset type 1 diabetes. Diabetologia 2024; 67:623-640. [PMID: 38349399 DOI: 10.1007/s00125-024-06098-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/06/2023] [Accepted: 12/08/2023] [Indexed: 03/01/2024]
Abstract
AIMS/HYPOTHESIS Type 1 diabetes is a T cell-mediated autoimmune disease characterised by pancreatic beta cell destruction. In this study, we explored the pathogenic immune responses in initiation of type 1 diabetes and new immunological targets for type 1 diabetes prevention and treatment. METHODS We obtained peripheral blood samples from four individuals with newly diagnosed latent autoimmune diabetes in adults (LADA) and from four healthy control participants. Single-cell RNA-sequencing (scRNA-seq) was performed on peripheral blood mononuclear cells to uncover transcriptomic profiles of early LADA. Validation was performed through flow cytometry in a cohort comprising 54 LADA, 17 adult-onset type 2 diabetes, and 26 healthy adults, matched using propensity score matching (PSM) based on age and sex. A similar PSM method matched 15 paediatric type 1 diabetes patients with 15 healthy children. Further flow cytometry analysis was performed in both peripheral blood and pancreatic tissues of non-obese diabetic (NOD) mice. Additionally, cell adoptive transfer and clearance assays were performed in NOD mice to explore the role of this monocyte subset in islet inflammation and onset of type 1 diabetes. RESULTS The scRNA-seq data showed that upregulated genes in peripheral T cells and monocytes from early-onset LADA patients were primarily enriched in the IFN signalling pathway. A new cluster of classical monocytes (cluster 4) was identified, and the proportion of this cluster was significantly increased in individuals with LADA compared with healthy control individuals (11.93% vs 5.93%, p=0.017) and that exhibited a strong IFN signature marked by SIGLEC-1 (encoding sialoadhesin). These SIGLEC-1+ monocytes expressed high levels of genes encoding C-C chemokine receptors 1 or 2, as well as genes for chemoattractants for T cells and natural killer cells. They also showed relatively low levels of genes for co-stimulatory and HLA molecules. Flow cytometry analysis verified the elevated levels of SIGLEC-1+ monocytes in the peripheral blood of participants with LADA and paediatric type 1 diabetes compared with healthy control participants and those with type 2 diabetes. Interestingly, the proportion of SIGLEC-1+ monocytes positively correlated with disease activity and negatively with disease duration in the LADA patients. In NOD mice, the proportion of SIGLEC-1+ monocytes in the peripheral blood was highest at the age of 6 weeks (16.88%), while the peak occurred at 12 weeks in pancreatic tissues (23.65%). Adoptive transfer experiments revealed a significant acceleration in diabetes onset in the SIGLEC-1+ group compared with the SIGLEC-1- or saline control group. CONCLUSIONS/INTERPRETATION Our study identified a novel group of SIGLEC-1+ monocytes that may serve as an important indicator for early diagnosis, activity assessment and monitoring of therapeutic efficacy in type 1 diabetes, and may also be a novel target for preventing and treating type 1 diabetes. DATA AVAILABILITY RNA-seq data have been deposited in the GSA human database ( https://ngdc.cncb.ac.cn/gsa-human/ ) under accession number HRA003649.
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Affiliation(s)
- Mengqi Guo
- Department of Endocrinology and Metabolism, The Affiliated Hospital of Qingdao University, Qingdao, Shandong, China
- Department of Cardiology, The Affiliated Hospital of Qingdao University, Qingdao, Shandong, China
| | - Han Guo
- Department of Endocrinology and Metabolism, The Affiliated Hospital of Qingdao University, Qingdao, Shandong, China
| | - Jingjing Zhu
- Department of Endocrinology and Metabolism, The Affiliated Hospital of Qingdao University, Qingdao, Shandong, China
| | - Fei Wang
- Department of Endocrinology and Metabolism, The Affiliated Hospital of Qingdao University, Qingdao, Shandong, China
| | - Jianni Chen
- Department of Endocrinology and Metabolism, The Affiliated Hospital of Qingdao University, Qingdao, Shandong, China
| | - Chuan Wan
- Department of Endocrinology and Metabolism, The Affiliated Hospital of Qingdao University, Qingdao, Shandong, China
| | - Yujie Deng
- Department of Endocrinology and Metabolism, The Affiliated Hospital of Qingdao University, Qingdao, Shandong, China
| | - Fang Wang
- Department of Endocrinology and Metabolism, The Affiliated Hospital of Qingdao University, Qingdao, Shandong, China
| | - Lili Xu
- Department of Endocrinology and Metabolism, The Affiliated Hospital of Qingdao University, Qingdao, Shandong, China
| | - Ying Chen
- Department of Endocrinology and Metabolism, The Affiliated Hospital of Qingdao University, Qingdao, Shandong, China
| | - Ran Li
- Department of Endocrinology and Metabolism, The Affiliated Hospital of Qingdao University, Qingdao, Shandong, China
| | - Shikai Liu
- Key Laboratory of Mariculture, Ministry of Education College of Fisheries, Ocean University of China, Qingdao, China
| | - Lin Zhang
- Department of Pharmacy, Shaoxing People's Hospital, Shaoxing, Zhejiang Province, China
| | - Yangang Wang
- Department of Endocrinology and Metabolism, The Affiliated Hospital of Qingdao University, Qingdao, Shandong, China.
| | - Jing Zhou
- Institute of Immunology, Third Military Medical University, Chongqing, China.
| | - Shufa Li
- Department of Endocrinology and Metabolism, The Affiliated Hospital of Qingdao University, Qingdao, Shandong, China.
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31
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Ambler WG, Kaplan MJ. Vascular damage in systemic lupus erythematosus. Nat Rev Nephrol 2024; 20:251-265. [PMID: 38172627 DOI: 10.1038/s41581-023-00797-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/29/2023] [Indexed: 01/05/2024]
Abstract
Vascular disease is a major cause of morbidity and mortality in patients with systemic autoimmune diseases, particularly systemic lupus erythematosus (SLE). Although comorbid cardiovascular risk factors are frequently present in patients with SLE, they do not explain the high burden of premature vascular disease. Profound innate and adaptive immune dysregulation seems to be the primary driver of accelerated vascular damage in SLE. In particular, evidence suggests that dysregulation of type 1 interferon (IFN-I) and aberrant neutrophils have key roles in the pathogenesis of vascular damage. IFN-I promotes endothelial dysfunction directly via effects on endothelial cells and indirectly via priming of immune cells that contribute to vascular damage. SLE neutrophils are vasculopathic in part because of their increased ability to form immunostimulatory neutrophil extracellular traps. Despite improvements in clinical care, cardiovascular disease remains the leading cause of mortality among patients with SLE, and treatments that improve vascular outcomes are urgently needed. Improved understanding of the mechanisms of vascular injury in inflammatory conditions such as SLE could also have implications for common cardiovascular diseases, such as atherosclerosis and hypertension, and may ultimately lead to personalized therapeutic approaches to the prevention and treatment of this potentially fatal complication.
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Affiliation(s)
- William G Ambler
- Systemic Autoimmunity Branch, National Institute of Arthritis and Musculoskeletal and Skin Diseases, National Institutes of Health, Bethesda, Maryland, USA
| | - Mariana J Kaplan
- Systemic Autoimmunity Branch, National Institute of Arthritis and Musculoskeletal and Skin Diseases, National Institutes of Health, Bethesda, Maryland, USA.
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32
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Zhang S, Wang P, Shi L, Wang C, Zhu Z, Qi C, Xie Y, Yuan S, Cheng L, Yin X, Zhang X. Exploring COVID-19 causal genes through disease-specific Cis-eQTLs. Virus Res 2024; 342:199341. [PMID: 38403000 PMCID: PMC10904281 DOI: 10.1016/j.virusres.2024.199341] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2024] [Revised: 02/20/2024] [Accepted: 02/22/2024] [Indexed: 02/27/2024]
Abstract
Genome-wide association study (GWAS) analysis has exposed that genetic factors play important roles in COVID-19. Whereas a deeper understanding of the underlying mechanism of COVID-19 was hindered by the lack of expression of quantitative trait loci (eQTL) data specific for disease. To this end, we identified COVID-19-specific cis-eQTLs by integrating nucleotide sequence variations and RNA-Seq data from COVID-19 samples. These identified eQTLs have different regulatory effect on genes between patients and controls, indicating that SARS-CoV-2 infection may cause alterations in the human body's internal environment. Individuals with the TT genotype in the rs1128320 region seemed more susceptible to SARS-CoV-2 infection and developed into severe COVID-19 due to the abnormal expression of IFITM1. We subsequently discovered potential causal genes, of the result, a total of 48 genes from six tissues were identified. siRNA-mediated depletion assays in SARS-CoV-2 infection proved that 14 causal genes were directly associated with SARS-CoV-2 infection. These results enriched existing research on COVID-19 causal genes and provided a new sight in the mechanism exploration for COVID-19.
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Affiliation(s)
- Sainan Zhang
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, Heilongjiang 150081, China
| | - Ping Wang
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, Heilongjiang 150081, China
| | - Lei Shi
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, Heilongjiang 150081, China
| | - Chao Wang
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, Heilongjiang 150081, China
| | - Zijun Zhu
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, Heilongjiang 150081, China
| | - Changlu Qi
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, Heilongjiang 150081, China
| | - Yubin Xie
- Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam 999077, Hong Kong Special Administrative Region of China; State Key Laboratory of Emerging Infectious Diseases, Li Ka Shing Faculty of Medicine, the University of Hong Kong, Pokfulam 999077, Hong Kong Special Administrative Region of China
| | - Shuofeng Yuan
- Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam 999077, Hong Kong Special Administrative Region of China; State Key Laboratory of Emerging Infectious Diseases, Li Ka Shing Faculty of Medicine, the University of Hong Kong, Pokfulam 999077, Hong Kong Special Administrative Region of China
| | - Liang Cheng
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, Heilongjiang 150081, China; NHC Key Laboratory of Molecular Probes and Targeted Diagnosis and Therapy, Harbin Medical University, Harbin, Heilongjiang 150028, China.
| | - Xin Yin
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin 150040, China
| | - Xue Zhang
- NHC Key Laboratory of Molecular Probes and Targeted Diagnosis and Therapy, Harbin Medical University, Harbin, Heilongjiang 150028, China; McKusick-Zhang Center for Genetic Medicine, State Key Laboratory of Medical Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100005, China
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33
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Chen DG, Xie J, Choi J, Ng RH, Zhang R, Li S, Edmark R, Zheng H, Solomon B, Campbell KM, Medina E, Ribas A, Khatri P, Lanier LL, Mease PJ, Goldman JD, Su Y, Heath JR. Integrative systems biology reveals NKG2A-biased immune responses correlate with protection in infectious disease, autoimmune disease, and cancer. Cell Rep 2024; 43:113872. [PMID: 38427562 PMCID: PMC10995767 DOI: 10.1016/j.celrep.2024.113872] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2023] [Revised: 01/19/2024] [Accepted: 02/09/2024] [Indexed: 03/03/2024] Open
Abstract
Infection, autoimmunity, and cancer are principal human health challenges of the 21st century. Often regarded as distinct ends of the immunological spectrum, recent studies hint at potential overlap between these diseases. For example, inflammation can be pathogenic in infection and autoimmunity. T resident memory (TRM) cells can be beneficial in infection and cancer. However, these findings are limited by size and scope; exact immunological factors shared across diseases remain elusive. Here, we integrate large-scale deeply clinically and biologically phenotyped human cohorts of 526 patients with infection, 162 with lupus, and 11,180 with cancer. We identify an NKG2A+ immune bias as associative with protection against disease severity, mortality, and autoimmune/post-acute chronic disease. We reveal that NKG2A+ CD8+ T cells correlate with reduced inflammation and increased humoral immunity and that they resemble TRM cells. Our results suggest NKG2A+ biases as a cross-disease factor of protection, supporting suggestions of immunological overlap between infection, autoimmunity, and cancer.
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Affiliation(s)
- Daniel G Chen
- Institute of Systems Biology, Seattle, WA, USA; Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA; Clinical Research Division, Program in Immunology, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Jingyi Xie
- Institute of Systems Biology, Seattle, WA, USA; Molecular Engineering & Sciences Institute, University of Washington, Seattle, WA, USA
| | | | - Rachel H Ng
- Institute of Systems Biology, Seattle, WA, USA; Department of Bioengineering, University of Washington, Seattle, WA, USA
| | - Rongyu Zhang
- Institute of Systems Biology, Seattle, WA, USA; Department of Bioengineering, University of Washington, Seattle, WA, USA
| | - Sarah Li
- Institute of Systems Biology, Seattle, WA, USA
| | - Rick Edmark
- Institute of Systems Biology, Seattle, WA, USA
| | - Hong Zheng
- Institute for Immunity, Transplantation and Infection, School of Medicine, Stanford University, Stanford, CA, USA; Center for Biomedical Informatics Research, Department of Medicine, School of Medicine, Stanford University, Stanford, CA, USA
| | - Ben Solomon
- Department of Pediatrics, Division of Allergy and Immunology, Stanford School of Medicine, Stanford, CA, USA
| | - Katie M Campbell
- Department of Medicine, Division of Hematology-Oncology, University of California, Los Angeles, Los Angeles, CA, USA; Parker Institute for Cancer Immunotherapy, San Francisco, CA, USA
| | - Egmidio Medina
- Department of Medicine, Division of Hematology-Oncology, University of California, Los Angeles, Los Angeles, CA, USA
| | - Antoni Ribas
- Department of Medicine, Division of Hematology-Oncology, University of California, Los Angeles, Los Angeles, CA, USA; Jonsson Comprehensive Cancer Center at the University of California, Los Angeles, CA, USA; Parker Institute for Cancer Immunotherapy, San Francisco, CA, USA
| | - Purvesh Khatri
- Institute for Immunity, Transplantation and Infection, School of Medicine, Stanford University, Stanford, CA, USA; Center for Biomedical Informatics Research, Department of Medicine, School of Medicine, Stanford University, Stanford, CA, USA
| | - Lewis L Lanier
- Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA, USA; Parker Institute for Cancer Immunotherapy, San Francisco, CA, USA
| | - Philip J Mease
- Swedish Center for Research and Innovation, Swedish Medical Center, Seattle, WA, USA; Providence St. Joseph Health, Renton, WA, USA
| | - Jason D Goldman
- Swedish Center for Research and Innovation, Swedish Medical Center, Seattle, WA, USA; Providence St. Joseph Health, Renton, WA, USA; Division of Allergy and Infectious Diseases, University of Washington, Seattle, WA, USA
| | - Yapeng Su
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA; Clinical Research Division, Program in Immunology, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - James R Heath
- Institute of Systems Biology, Seattle, WA, USA; Department of Bioengineering, University of Washington, Seattle, WA, USA; Parker Institute for Cancer Immunotherapy, San Francisco, CA, USA.
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34
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Lin KZ, Qiu Y, Roeder K. eSVD-DE: cohort-wide differential expression in single-cell RNA-seq data using exponential-family embeddings. BMC Bioinformatics 2024; 25:113. [PMID: 38486150 PMCID: PMC10941434 DOI: 10.1186/s12859-024-05724-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2023] [Accepted: 02/28/2024] [Indexed: 03/17/2024] Open
Abstract
BACKGROUND Single-cell RNA-sequencing (scRNA) datasets are becoming increasingly popular in clinical and cohort studies, but there is a lack of methods to investigate differentially expressed (DE) genes among such datasets with numerous individuals. While numerous methods exist to find DE genes for scRNA data from limited individuals, differential-expression testing for large cohorts of case and control individuals using scRNA data poses unique challenges due to substantial effects of human variation, i.e., individual-level confounding covariates that are difficult to account for in the presence of sparsely-observed genes. RESULTS We develop the eSVD-DE, a matrix factorization that pools information across genes and removes confounding covariate effects, followed by a novel two-sample test in mean expression between case and control individuals. In general, differential testing after dimension reduction yields an inflation of Type-1 errors. However, we overcome this by testing for differences between the case and control individuals' posterior mean distributions via a hierarchical model. In previously published datasets of various biological systems, eSVD-DE has more accuracy and power compared to other DE methods typically repurposed for analyzing cohort-wide differential expression. CONCLUSIONS eSVD-DE proposes a novel and powerful way to test for DE genes among cohorts after performing a dimension reduction. Accurate identification of differential expression on the individual level, instead of the cell level, is important for linking scRNA-seq studies to our understanding of the human population.
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Affiliation(s)
- Kevin Z Lin
- Department of Biostatistics, University of Washington, Seattle, WA, USA.
| | - Yixuan Qiu
- School of Statistics and Management, Shanghai University of Finance and Economics, Shanghai, People's Republic of China
| | - Kathryn Roeder
- Department of Statistics and Data Science, Carnegie Mellon University, Pittsburgh, PA, USA
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35
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Torell A, Stockfelt M, Blennow K, Zetterberg H, Akhter T, Leonard D, Rönnblom L, Pihl S, Saleh M, Sjöwall C, Strevens H, Jönsen A, Bengtsson AA, Trysberg E, Majczuk Sennström M, Zickert A, Svenungsson E, Gunnarsson I, Bylund J, Jacobsson B, Rudin A, Lundell AC. Low CD4 + T cell count is related to specific anti-nuclear antibodies, IFNα protein positivity and disease activity in systemic lupus erythematosus pregnancy. Arthritis Res Ther 2024; 26:65. [PMID: 38459582 PMCID: PMC10924387 DOI: 10.1186/s13075-024-03301-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Accepted: 03/01/2024] [Indexed: 03/10/2024] Open
Abstract
BACKGROUND Lymphopenia, autoantibodies and activation of the type I interferon (IFN) system are common features in systemic lupus erythematosus (SLE). We speculate whether lymphocyte subset counts are affected by pregnancy and if they relate to autoantibody profiles and/or IFNα protein in SLE pregnancy. METHODS Repeated blood samples were collected during pregnancy from 80 women with SLE and 51 healthy controls (HC). Late postpartum samples were obtained from 19 of the women with SLE. Counts of CD4 + and CD8 + T cells, B cells and NK cells were measured by flow cytometry. Positivity for anti-nuclear antibodies (ANA) fine specificities (double-stranded DNA [dsDNA], Smith [Sm], ribonucleoprotein [RNP], chromatin, Sjögren's syndrome antigen A [SSA] and B [SSB]) and anti-phospholipid antibodies (cardiolipin [CL] and β2 glycoprotein I [β2GPI]) was assessed with multiplexed bead assay. IFNα protein concentration was quantified with Single molecule array (Simoa) immune assay. Clinical data were retrieved from medical records. RESULTS Women with SLE had lower counts of all lymphocyte subsets compared to HC throughout pregnancy, but counts did not differ during pregnancy compared to postpartum. Principal component analysis revealed that low lymphocyte subset counts differentially related to autoantibody profiles, cluster one (anti-dsDNA/anti-Sm/anti-RNP/anti-Sm/RNP/anti-chromatin), cluster two (anti-SSA/anti-SSB) and cluster three (anti-CL/anti-β2GPI), IFNα protein levels and disease activity. CD4 + T cell counts were lower in women positive to all ANA fine specificities in cluster one compared to those who were negative, and B cell numbers were lower in women positive for anti-dsDNA and anti-Sm compared to negative women. Moreover, CD4 + T cell and B cell counts were lower in women with moderate/high compared to no/low disease activity, and CD4 + T cell count was lower in IFNα protein positive relative to negative women. Finally, CD4 + T cell count was unrelated to treatment. CONCLUSION Lymphocyte subset counts are lower in SLE compared to healthy pregnancies, which seems to be a feature of the disease per se and not affected by pregnancy. Our results also indicate that low lymphocyte subset counts relate differentially to autoantibody profiles, IFNα protein levels and disease activity, which could be due to divergent disease pathways.
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Affiliation(s)
- Agnes Torell
- Department of Rheumatology and Inflammation Research, Institute of Medicine, Sahlgrenska Academy at the University of Gothenburg, Guldhedsgatan 10A, 405 30, Gothenburg, Sweden.
| | - Marit Stockfelt
- Department of Rheumatology and Inflammation Research, Institute of Medicine, Sahlgrenska Academy at the University of Gothenburg, Guldhedsgatan 10A, 405 30, Gothenburg, Sweden
- Rheumatology, Sahlgrenska University Hospital, Gothenburg, Sweden
| | - Kaj Blennow
- Department of Psychiatry and Neurochemistry, Institute of Neuroscience and Physiology, Sahlgrenska Academy at the University of Gothenburg, Mölndal, Sweden
- Clinical Neurochemistry Laboratory, Sahlgrenska University Hospital, Mölndal, Sweden
- Paris Brain Institute, ICM, Pitié-Salpêtrière Hospital, Sorbonne University, Paris, France
- Neurodegenerative Disorder Research Center, Division of Life Sciences and Medicine and Department of Neurology, Institute On Aging and Brain Disorders, University of Science and Technology of China and First Affiliated Hospital of USTC, Hefei, People's Republic of China
| | - Henrik Zetterberg
- Department of Psychiatry and Neurochemistry, Institute of Neuroscience and Physiology, Sahlgrenska Academy at the University of Gothenburg, Mölndal, Sweden
- Clinical Neurochemistry Laboratory, Sahlgrenska University Hospital, Mölndal, Sweden
- Department of Neurodegenerative Disease, UCL Institute of Neurology, Queen Square, London, UK
- UK Dementia Research Institute at UCL, London, UK
- Hong Kong Center for Neurodegenerative Diseases, Clear Water Bay, Hong Kong, China
- Winsconsin Alzheimer's Disease Research Center, School of Medicine and Public Health, University of Wisconsin, University of Wisconsin-Madison, Madison, WI, USA
| | - Tansim Akhter
- Department of Women's and Children's Health, Section of Obstetrics and Gynecology, Uppsala University, Uppsala, Sweden
| | - Dag Leonard
- Department of Medical Sciences, Rheumatology, Uppsala University, Uppsala, Sweden
| | - Lars Rönnblom
- Department of Medical Sciences, Rheumatology, Uppsala University, Uppsala, Sweden
| | - Sofia Pihl
- Department of Obstetrics and Gynecology, Linköping University Hospital, Linköping, Sweden
- Department of Biomedical and Clinical Sciences, Division of Children's and Women's Health, Linköping University, Linköping, Sweden
| | - Muna Saleh
- Division of Inflammation and Infection, Department of Biomedical and Clinical Sciences, Linköping University, Linköping, Sweden
| | - Christopher Sjöwall
- Division of Inflammation and Infection, Department of Biomedical and Clinical Sciences, Linköping University, Linköping, Sweden
| | - Helena Strevens
- Department of Obstetrics and Gynecology, Institute of Clinical Sciences, Skåne University Hospital, Lund, Sweden
| | - Andreas Jönsen
- Department of Clinical Sciences Lund, Rheumatology, Lund University, Skåne University Hospital, Lund, Sweden
| | - Anders A Bengtsson
- Department of Clinical Sciences Lund, Rheumatology, Lund University, Skåne University Hospital, Lund, Sweden
| | - Estelle Trysberg
- Rheumatology, Sahlgrenska University Hospital, Gothenburg, Sweden
| | - Maria Majczuk Sennström
- Department of Womens and Childrens Health, Division for Obstetrics and Gynecology, Karolinska University Hospital, Karolinska Institute, Stockholm, Sweden
| | - Agneta Zickert
- Division of Rheumatology, Department of Medicine Solna, Karolinska Institute, Karolinska University Hospital, Stockholm, Sweden
| | - Elisabet Svenungsson
- Division of Rheumatology, Department of Medicine Solna, Karolinska Institute, Karolinska University Hospital, Stockholm, Sweden
| | - Iva Gunnarsson
- Division of Rheumatology, Department of Medicine Solna, Karolinska Institute, Karolinska University Hospital, Stockholm, Sweden
| | - Johan Bylund
- Department of Oral Microbiology and Immunology, Institute of Odontology, Sahlgrenska Academy at the University of Gothenburg, Gothenburg, Sweden
| | - Bo Jacobsson
- Department of Obstetrics and Gynecology, Sahlgrenska University Hospital, Gothenburg, Sweden
- Department of Obstetrics and Gynecology, Sahlgrenska Academy at the University of Gothenburg, Gothenburg, Sweden
- Department of Genetics and Bioinformatics, Division of Health Data and Digitalisation, Institute of Public Health, Oslo, Norway
| | - Anna Rudin
- Department of Rheumatology and Inflammation Research, Institute of Medicine, Sahlgrenska Academy at the University of Gothenburg, Guldhedsgatan 10A, 405 30, Gothenburg, Sweden
| | - Anna-Carin Lundell
- Department of Rheumatology and Inflammation Research, Institute of Medicine, Sahlgrenska Academy at the University of Gothenburg, Guldhedsgatan 10A, 405 30, Gothenburg, Sweden
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36
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Zhou Z, Du J, Wang J, Liu L, Gordon MG, Ye CJ, Powell JE, Li MJ, Rao S. SingleQ: a comprehensive database of single-cell expression quantitative trait loci (sc-eQTLs) cross human tissues. Database (Oxford) 2024; 2024:baae010. [PMID: 38459946 PMCID: PMC10924434 DOI: 10.1093/database/baae010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2023] [Revised: 01/09/2024] [Accepted: 02/11/2024] [Indexed: 03/11/2024]
Abstract
Mapping of expression quantitative trait loci (eQTLs) and other molecular QTLs can help characterize the modes of action of disease-associated genetic variants. However, current eQTL databases present data from bulk RNA-seq approaches, which cannot shed light on the cell type- and environment-specific regulation of disease-associated genetic variants. Here, we introduce our Single-cell eQTL Interactive Database which collects single-cell eQTL (sc-eQTL) datasets and provides online visualization of sc-eQTLs across different cell types in a user-friendly manner. Although sc-eQTL mapping is still in its early stage, our database curates the most comprehensive summary statistics of sc-eQTLs published to date. sc-eQTL studies have revolutionized our understanding of gene regulation in specific cellular contexts, and we anticipate that our database will further accelerate the research of functional genomics. Database URL: http://www.sqraolab.com/scqtl.
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Affiliation(s)
- Zhiwei Zhou
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, 288 Nanjing Road, Tianjin 300020, China
- Tianjin Institutes of Health Science, 28 Tuanbo Avenue, Tianjin 301600, China
| | - Jingyi Du
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, 288 Nanjing Road, Tianjin 300020, China
- Tianjin Institutes of Health Science, 28 Tuanbo Avenue, Tianjin 301600, China
| | - Jianhua Wang
- Department of Pharmacology, Tianjin Key Laboratory of Inflammation Biology, School of Basic Medical Sciences, National Clinical Research Center for Cancer, Tianjin Medical University Cancer Institute and Hospital, Tianjin Medical University, 22 Qixiangtai Road, Tianjin 300070, China
| | - Liangyi Liu
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, 288 Nanjing Road, Tianjin 300020, China
| | - M Gracie Gordon
- Biological and Medical Informatics Graduate Program, University of California, 500 Parnassus Avenue, San Francisco, CA 94143, USA
- Division of Rheumatology, Department of Medicine, University of California, 500 Parnassus Avenue, San Francisco, CA 94143, USA
- Institute for Human Genetics, University of California, 500 Parnassus Avenue, San Francisco, CA 94143, USA
- Department of Bioengineering and Therapeutic Sciences, University of California, 500 Parnassus Avenue, San Francisco, CA 94143, USA
| | - Chun Jimmie Ye
- Division of Rheumatology, Department of Medicine, University of California, 500 Parnassus Avenue, San Francisco, CA 94143, USA
- Institute for Human Genetics, University of California, 500 Parnassus Avenue, San Francisco, CA 94143, USA
- Rosalind Russell/Ephraim P. Engleman Rheumatology Research Center, University of California, 500 Parnassus Avenue, San Francisco, CA 94143, USA
- Department of Epidemiology and Biostatistics, University of California, 500 Parnassus Avenue, San Francisco, CA 94143, USA
- Parker Institute for Cancer Immunotherapy, University of California, 500 Parnassus Avenue, San Francisco, CA 94143, USA
- Chan Zuckerberg Biohub, 499 Illinois Street, San Francisco, CA 94158, USA
- Bakar Computational Health Sciences Institute, University of California, 500 Parnassus Avenue, San Francisco, CA 94143, USA
| | - Joseph E Powell
- Garvan-Weizmann Centre for Cellular Genomics, Garvan Institute of Medical Research, 384 Victoria Street, Sydney, NSW 2010, Australia
- UNSW Cellular Genomics Futures Institute, University of New South Wales, UNSW Sydney, Sydney, NSW 2052, Australia
| | - Mulin Jun Li
- Department of Pharmacology, Tianjin Key Laboratory of Inflammation Biology, School of Basic Medical Sciences, National Clinical Research Center for Cancer, Tianjin Medical University Cancer Institute and Hospital, Tianjin Medical University, 22 Qixiangtai Road, Tianjin 300070, China
| | - Shuquan Rao
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, 288 Nanjing Road, Tianjin 300020, China
- Tianjin Institutes of Health Science, 28 Tuanbo Avenue, Tianjin 301600, China
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37
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Lin KZ, Qiu Y, Roeder K. eSVD-DE: Cohort-wide differential expression in single-cell RNA-seq data using exponential-family embeddings. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.11.22.568369. [PMID: 38045428 PMCID: PMC10690270 DOI: 10.1101/2023.11.22.568369] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/05/2023]
Abstract
Background Single-cell RNA-sequencing (scRNA) datasets are becoming increasingly popular in clinical and cohort studies, but there is a lack of methods to investigate differentially expressed (DE) genes among such datasets with numerous individuals. While numerous methods exist to find DE genes for scRNA data from limited individuals, differential-expression testing for large cohorts of case and control individuals using scRNA data poses unique challenges due to substantial effects of human variation, i.e., individual-level confounding covariates that are difficult to account for in the presence of sparsely-observed genes. Results We develop the eSVD-DE, a matrix factorization that pools information across genes and removes confounding covariate effects, followed by a novel two-sample test in mean expression between case and control individuals. In general, differential testing after dimension reduction yields an inflation of Type-1 errors. However, we overcome this by testing for differences between the case and control individuals' posterior mean distributions via a hierarchical model. In previously published datasets of various biological systems, eSVD-DE has more accuracy and power compared to other DE methods typically repurposed for analyzing cohort-wide differential expression. Conclusions eSVD-DE proposes a novel and powerful way to test for DE genes among cohorts after performing a dimension reduction. Accurate identification of differential expression on the individual level, instead of the cell level, is important for linking scRNA-seq studies to our understanding of the human population.
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Affiliation(s)
- Kevin Z Lin
- Department of Biostatistics, University of Washington, Seattle, Washington, United States of America
| | - Yixuan Qiu
- School of Statistics & Management, Shanghai University of Finance and Economics, Shanghai,People's Republic of China
| | - Kathryn Roeder
- Department of Statistics & Data Science, Carnegie Mellon University, Pittsburgh, Pennsylvania, United States of America
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38
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Hurabielle C, LaFlam TN, Gearing M, Ye CJ. Functional genomics in inborn errors of immunity. Immunol Rev 2024; 322:53-70. [PMID: 38329267 PMCID: PMC10950534 DOI: 10.1111/imr.13309] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/09/2024]
Abstract
Inborn errors of immunity (IEI) comprise a diverse spectrum of 485 disorders as recognized by the International Union of Immunological Societies Committee on Inborn Error of Immunity in 2022. While IEI are monogenic by definition, they illuminate various pathways involved in the pathogenesis of polygenic immune dysregulation as in autoimmune or autoinflammatory syndromes, or in more common infectious diseases that may not have a significant genetic basis. Rapid improvement in genomic technologies has been the main driver of the accelerated rate of discovery of IEI and has led to the development of innovative treatment strategies. In this review, we will explore various facets of IEI, delving into the distinctions between PIDD and PIRD. We will examine how Mendelian inheritance patterns contribute to these disorders and discuss advancements in functional genomics that aid in characterizing new IEI. Additionally, we will explore how emerging genomic tools help to characterize new IEI as well as how they are paving the way for innovative treatment approaches for managing and potentially curing these complex immune conditions.
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Affiliation(s)
- Charlotte Hurabielle
- Division of Rheumatology, Department of Medicine, UCSF, San Francisco, California, USA
| | - Taylor N LaFlam
- Division of Pediatric Rheumatology, Department of Pediatrics, UCSF, San Francisco, California, USA
| | - Melissa Gearing
- Division of Rheumatology, Department of Medicine, UCSF, San Francisco, California, USA
| | - Chun Jimmie Ye
- Institute for Human Genetics, UCSF, San Francisco, California, USA
- Institute of Computational Health Sciences, UCSF, San Francisco, California, USA
- Gladstone Genomic Immunology Institute, San Francisco, California, USA
- Parker Institute for Cancer Immunotherapy, UCSF, San Francisco, California, USA
- Department of Epidemiology and Biostatistics, UCSF, San Francisco, California, USA
- Department of Microbiology and Immunology, UCSF, San Francisco, California, USA
- Department of Bioengineering and Therapeutic Sciences, UCSF, San Francisco, California, USA
- Arc Institute, Palo Alto, California, USA
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39
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Liu Y, Zhang L. Integrated bioinformatics analysis reveals vital genes and immune infiltration for the co-occurrence of Epstein-Barr virus-related infectious mononucleosis and systemic lupus erythematosus. Int J Rheum Dis 2024; 27:e15017. [PMID: 38443758 DOI: 10.1111/1756-185x.15017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2023] [Revised: 11/20/2023] [Accepted: 12/12/2023] [Indexed: 03/07/2024]
Affiliation(s)
- Yuchen Liu
- Division of Infectious Diseases, Department of Internal Medicine, State Key Laboratory of Complex Severe and Rare Disease, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
- Clinical Epidemiology Unit, Peking Union Medical College, International Clinical Epidemiology Network, Beijing, China
- Center for Tuberculosis Research, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
- Peking Union Medical College, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Lifan Zhang
- Division of Infectious Diseases, Department of Internal Medicine, State Key Laboratory of Complex Severe and Rare Disease, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
- Clinical Epidemiology Unit, Peking Union Medical College, International Clinical Epidemiology Network, Beijing, China
- Center for Tuberculosis Research, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
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40
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Wolf C, Lim EL, Mokhtari M, Kind B, Odainic A, Lara-Villacanas E, Koss S, Mages S, Menzel K, Engel K, Dückers G, Bernbeck B, Schneider DT, Siepermann K, Niehues T, Goetzke CC, Durek P, Minden K, Dörner T, Stittrich A, Szelinski F, Guerra GM, Massoud M, Bieringer M, de Oliveira Mann CC, Beltrán E, Kallinich T, Mashreghi MF, Schmidt SV, Latz E, Klughammer J, Majer O, Lee-Kirsch MA. UNC93B1 variants underlie TLR7-dependent autoimmunity. Sci Immunol 2024; 9:eadi9769. [PMID: 38207055 DOI: 10.1126/sciimmunol.adi9769] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2023] [Accepted: 12/22/2023] [Indexed: 01/13/2024]
Abstract
UNC93B1 is critical for trafficking and function of nucleic acid-sensing Toll-like receptors (TLRs) TLR3, TLR7, TLR8, and TLR9, which are essential for antiviral immunity. Overactive TLR7 signaling induced by recognition of self-nucleic acids has been implicated in systemic lupus erythematosus (SLE). Here, we report UNC93B1 variants (E92G and R336L) in four patients with early-onset SLE. Patient cells or mouse macrophages carrying the UNC93B1 variants produced high amounts of TNF-α and IL-6 and upon stimulation with TLR7/TLR8 agonist, but not with TLR3 or TLR9 agonists. E92G causes UNC93B1 protein instability and reduced interaction with TLR7, leading to selective TLR7 hyperactivation with constitutive type I IFN signaling. Thus, UNC93B1 regulates TLR subtype-specific mechanisms of ligand recognition. Our findings establish a pivotal role for UNC93B1 in TLR7-dependent autoimmunity and highlight the therapeutic potential of targeting TLR7 in SLE.
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Affiliation(s)
- Christine Wolf
- Department of Pediatrics, Medizinische Fakultät Carl Gustav Carus, Technische Universität Dresden, Dresden 01307, Germany
| | - Ee Lyn Lim
- Max Planck Institute for Infection Biology, Berlin 10117, Germany
| | - Mohammad Mokhtari
- Gene Center, Systems Immunology, Ludwig-Maximilians-Universität Munich, Munich 81377, Germany
| | - Barbara Kind
- Department of Pediatrics, Medizinische Fakultät Carl Gustav Carus, Technische Universität Dresden, Dresden 01307, Germany
| | - Alexandru Odainic
- Institute of Innate Immunity, University of Bonn, Bonn 53127, Germany
- Department of Microbiology and Immunology, Peter Doherty Institute for Infection & Immunity, University of Melbourne, Melbourne, VIC 3010, Australia
| | - Eusebia Lara-Villacanas
- Department of Pediatrics, Klinikum Dortmund, University Witten/Herdecke, Dortmund 44145, Germany
| | - Sarah Koss
- Department of Pediatrics, Medizinische Fakultät Carl Gustav Carus, Technische Universität Dresden, Dresden 01307, Germany
| | - Simon Mages
- Gene Center, Systems Immunology, Ludwig-Maximilians-Universität Munich, Munich 81377, Germany
| | - Katharina Menzel
- Department of Pediatrics, Medizinische Fakultät Carl Gustav Carus, Technische Universität Dresden, Dresden 01307, Germany
| | - Kerstin Engel
- Department of Pediatrics, Medizinische Fakultät Carl Gustav Carus, Technische Universität Dresden, Dresden 01307, Germany
| | - Gregor Dückers
- Department of Pediatrics, Helios Klinik Krefeld, Krefeld 47805, Germany
| | - Benedikt Bernbeck
- Department of Pediatrics, Klinikum Dortmund, University Witten/Herdecke, Dortmund 44145, Germany
| | - Dominik T Schneider
- Department of Pediatrics, Klinikum Dortmund, University Witten/Herdecke, Dortmund 44145, Germany
| | | | - Tim Niehues
- Department of Pediatrics, Helios Klinik Krefeld, Krefeld 47805, Germany
| | - Carl Christoph Goetzke
- Department of Pediatric Respiratory Medicine, Immunology and Critical Care Medicine, Charité-Universitätsmedizin Berlin, Berlin 10117, Germany
- Deutsches Rheuma-Forschungszentrum (DRFZ), an institute of the Leibniz Association, Berlin 10117, Germany
- Berlin Institute of Health at Charité-Universitätsmedizin Berlin, Berlin 10178, Germany
| | - Pawel Durek
- Deutsches Rheuma-Forschungszentrum (DRFZ), an institute of the Leibniz Association, Berlin 10117, Germany
| | - Kirsten Minden
- Department of Pediatric Respiratory Medicine, Immunology and Critical Care Medicine, Charité-Universitätsmedizin Berlin, Berlin 10117, Germany
- Deutsches Rheuma-Forschungszentrum (DRFZ), an institute of the Leibniz Association, Berlin 10117, Germany
| | - Thomas Dörner
- Deutsches Rheuma-Forschungszentrum (DRFZ), an institute of the Leibniz Association, Berlin 10117, Germany
- Department of Medicine, Rheumatology and Clinical Immunology, Charite-Universitätsmedizin Berlin, Berlin 10117, Germany
| | - Anna Stittrich
- Labor Berlin Charité-Vivantes GmbH, Department of Human Genetics, Berlin 13353, Germany
| | - Franziska Szelinski
- Deutsches Rheuma-Forschungszentrum (DRFZ), an institute of the Leibniz Association, Berlin 10117, Germany
- Department of Medicine, Rheumatology and Clinical Immunology, Charite-Universitätsmedizin Berlin, Berlin 10117, Germany
| | - Gabriela Maria Guerra
- Deutsches Rheuma-Forschungszentrum (DRFZ), an institute of the Leibniz Association, Berlin 10117, Germany
| | - Mona Massoud
- Deutsches Rheuma-Forschungszentrum (DRFZ), an institute of the Leibniz Association, Berlin 10117, Germany
| | - Markus Bieringer
- Department of Cardiology and Nephrology, HELIOS Klinikum Berlin-Buch, Berlin 13125, Germany
| | | | - Eduardo Beltrán
- Institute for Clinical Neuroimmunology, BioMedizinisches Zentrum, Ludwig-Maximilians-Universität Munich, Munich 82152, Germany
| | - Tilmann Kallinich
- Department of Pediatric Respiratory Medicine, Immunology and Critical Care Medicine, Charité-Universitätsmedizin Berlin, Berlin 10117, Germany
- Deutsches Rheuma-Forschungszentrum (DRFZ), an institute of the Leibniz Association, Berlin 10117, Germany
- Berlin Institute of Health at Charité-Universitätsmedizin Berlin, Berlin 10178, Germany
| | - Mir-Farzin Mashreghi
- Deutsches Rheuma-Forschungszentrum (DRFZ), an institute of the Leibniz Association, Berlin 10117, Germany
| | - Susanne V Schmidt
- Institute of Innate Immunity, University of Bonn, Bonn 53127, Germany
| | - Eicke Latz
- Institute of Innate Immunity, University of Bonn, Bonn 53127, Germany
- German Center for Neurodegenerative Diseases (DZNE), Bonn 53175, Germany
| | - Johanna Klughammer
- Gene Center, Systems Immunology, Ludwig-Maximilians-Universität Munich, Munich 81377, Germany
| | - Olivia Majer
- Max Planck Institute for Infection Biology, Berlin 10117, Germany
| | - Min Ae Lee-Kirsch
- Department of Pediatrics, Medizinische Fakultät Carl Gustav Carus, Technische Universität Dresden, Dresden 01307, Germany
- University Center for Rare Diseases, Medizinische Fakultät Carl Gustav Carus, Technische Universität Dresden, Dresden 01307, Germany
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41
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Yasumizu Y, Takeuchi D, Morimoto R, Takeshima Y, Okuno T, Kinoshita M, Morita T, Kato Y, Wang M, Motooka D, Okuzaki D, Nakamura Y, Mikami N, Arai M, Zhang X, Kumanogoh A, Mochizuki H, Ohkura N, Sakaguchi S. Single-cell transcriptome landscape of circulating CD4 + T cell populations in autoimmune diseases. CELL GENOMICS 2024; 4:100473. [PMID: 38359792 PMCID: PMC10879034 DOI: 10.1016/j.xgen.2023.100473] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/09/2023] [Revised: 09/07/2023] [Accepted: 12/05/2023] [Indexed: 02/17/2024]
Abstract
CD4+ T cells are key mediators of various autoimmune diseases; however, their role in disease progression remains unclear due to cellular heterogeneity. Here, we evaluated CD4+ T cell subpopulations using decomposition-based transcriptome characterization and canonical clustering strategies. This approach identified 12 independent gene programs governing whole CD4+ T cell heterogeneity, which can explain the ambiguity of canonical clustering. In addition, we performed a meta-analysis using public single-cell datasets of over 1.8 million peripheral CD4+ T cells from 953 individuals by projecting cells onto the reference and cataloging cell frequency and qualitative alterations of the populations in 20 diseases. The analyses revealed that the 12 transcriptional programs were useful in characterizing each autoimmune disease and predicting its clinical status. Moreover, genetic variants associated with autoimmune diseases showed disease-specific enrichment within the 12 gene programs. The results collectively provide a landscape of single-cell transcriptomes of CD4+ T cell subpopulations involved in autoimmune disease.
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Affiliation(s)
- Yoshiaki Yasumizu
- Department of Experimental Immunology, Immunology Frontier Research Center, Osaka University, Osaka, Japan; Department of Neurology, Graduate School of Medicine, Osaka University, Osaka, Japan; Integrated Frontier Research for Medical Science Division, Institute for Open and Transdisciplinary Research Initiatives (OTRI), Osaka University, Osaka, Japan
| | - Daiki Takeuchi
- Department of Experimental Immunology, Immunology Frontier Research Center, Osaka University, Osaka, Japan; Faculty of Medicine, Osaka University, Osaka, Japan
| | - Reo Morimoto
- Department of Experimental Immunology, Immunology Frontier Research Center, Osaka University, Osaka, Japan
| | - Yusuke Takeshima
- Department of Experimental Immunology, Immunology Frontier Research Center, Osaka University, Osaka, Japan
| | - Tatsusada Okuno
- Department of Neurology, Graduate School of Medicine, Osaka University, Osaka, Japan
| | - Makoto Kinoshita
- Department of Neurology, Graduate School of Medicine, Osaka University, Osaka, Japan
| | - Takayoshi Morita
- Department of Respiratory Medicine and Clinical Immunology, Osaka University Graduate School of Medicine, Osaka, Japan
| | - Yasuhiro Kato
- Department of Respiratory Medicine and Clinical Immunology, Osaka University Graduate School of Medicine, Osaka, Japan; Department of Immunopathology, Immunology Frontier Research Center, Osaka University, Osaka, Japan
| | - Min Wang
- Clinical Immunology Center, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China; Department of Rheumatology, Beijing Hospital, National Center of Gerontology, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing, China
| | - Daisuke Motooka
- Integrated Frontier Research for Medical Science Division, Institute for Open and Transdisciplinary Research Initiatives (OTRI), Osaka University, Osaka, Japan; Genome Information Research Center, Research Institute for Microbial Diseases, Osaka University, Osaka, Japan
| | - Daisuke Okuzaki
- Integrated Frontier Research for Medical Science Division, Institute for Open and Transdisciplinary Research Initiatives (OTRI), Osaka University, Osaka, Japan; Genome Information Research Center, Research Institute for Microbial Diseases, Osaka University, Osaka, Japan
| | - Yamami Nakamura
- Department of Experimental Immunology, Immunology Frontier Research Center, Osaka University, Osaka, Japan
| | - Norihisa Mikami
- Department of Experimental Immunology, Immunology Frontier Research Center, Osaka University, Osaka, Japan
| | - Masaya Arai
- Department of Experimental Immunology, Immunology Frontier Research Center, Osaka University, Osaka, Japan
| | - Xuan Zhang
- Department of Rheumatology, Beijing Hospital, National Center of Gerontology, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing, China
| | - Atsushi Kumanogoh
- Integrated Frontier Research for Medical Science Division, Institute for Open and Transdisciplinary Research Initiatives (OTRI), Osaka University, Osaka, Japan; Department of Respiratory Medicine and Clinical Immunology, Osaka University Graduate School of Medicine, Osaka, Japan; Department of Immunopathology, Immunology Frontier Research Center, Osaka University, Osaka, Japan; Center for Infectious Diseases for Education and Research, Osaka University, Osaka, Japan
| | - Hideki Mochizuki
- Department of Neurology, Graduate School of Medicine, Osaka University, Osaka, Japan; Integrated Frontier Research for Medical Science Division, Institute for Open and Transdisciplinary Research Initiatives (OTRI), Osaka University, Osaka, Japan
| | - Naganari Ohkura
- Department of Experimental Immunology, Immunology Frontier Research Center, Osaka University, Osaka, Japan; Department of Frontier Research in Tumor Immunology, Graduate School of Medicine, Osaka University, Osaka, Japan.
| | - Shimon Sakaguchi
- Department of Experimental Immunology, Immunology Frontier Research Center, Osaka University, Osaka, Japan; Department of Experimental Immunology, Institute for Life and Medical Sciences, Kyoto University, Kyoto, Japan.
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42
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Lagattuta KA, Park HL, Rumker L, Ishigaki K, Nathan A, Raychaudhuri S. The genetic basis of autoimmunity seen through the lens of T cell functional traits. Nat Commun 2024; 15:1204. [PMID: 38331990 PMCID: PMC10853555 DOI: 10.1038/s41467-024-45170-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2023] [Accepted: 01/15/2024] [Indexed: 02/10/2024] Open
Abstract
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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Affiliation(s)
- Kaitlyn A Lagattuta
- Center for Data Sciences, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
- Division of Rheumatology, Inflammation, and Immunity, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
| | - Hannah L Park
- Center for Data Sciences, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
- Division of Rheumatology, Inflammation, and Immunity, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
| | - Laurie Rumker
- Center for Data Sciences, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
- Division of Rheumatology, Inflammation, and Immunity, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
| | - Kazuyoshi Ishigaki
- Center for Data Sciences, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
- Division of Rheumatology, Inflammation, and Immunity, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Laboratory for Human Immunogenetics, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Aparna Nathan
- Center for Data Sciences, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA.
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA.
- Division of Rheumatology, Inflammation, and Immunity, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA.
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA.
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA.
| | - Soumya Raychaudhuri
- Center for Data Sciences, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA.
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA.
- Division of Rheumatology, Inflammation, and Immunity, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA.
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA.
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA.
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43
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Joodaki M, Shaigan M, Parra V, Bülow RD, Kuppe C, Hölscher DL, Cheng M, Nagai JS, Goedertier M, Bouteldja N, Tesar V, Barratt J, Roberts IS, Coppo R, Kramann R, Boor P, Costa IG. Detection of PatIent-Level distances from single cell genomics and pathomics data with Optimal Transport (PILOT). Mol Syst Biol 2024; 20:57-74. [PMID: 38177382 PMCID: PMC10883279 DOI: 10.1038/s44320-023-00003-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2023] [Revised: 11/20/2023] [Accepted: 11/24/2023] [Indexed: 01/06/2024] Open
Abstract
Although clinical applications represent the next challenge in single-cell genomics and digital pathology, we still lack computational methods to analyze single-cell or pathomics data to find sample-level trajectories or clusters associated with diseases. This remains challenging as single-cell/pathomics data are multi-scale, i.e., a sample is represented by clusters of cells/structures, and samples cannot be easily compared with each other. Here we propose PatIent Level analysis with Optimal Transport (PILOT). PILOT uses optimal transport to compute the Wasserstein distance between two individual single-cell samples. This allows us to perform unsupervised analysis at the sample level and uncover trajectories or cellular clusters associated with disease progression. We evaluate PILOT and competing approaches in single-cell genomics or pathomics studies involving various human diseases with up to 600 samples/patients and millions of cells or tissue structures. Our results demonstrate that PILOT detects disease-associated samples from large and complex single-cell or pathomics data. Moreover, PILOT provides a statistical approach to find changes in cell populations, gene expression, and tissue structures related to the trajectories or clusters supporting interpretation of predictions.
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Affiliation(s)
- Mehdi Joodaki
- Institute for Computational Genomics, Joint Research Center for Computational Biomedicine, RWTH Aachen University Medical School, Aachen, Germany
| | - Mina Shaigan
- Institute for Computational Genomics, Joint Research Center for Computational Biomedicine, RWTH Aachen University Medical School, Aachen, Germany
| | - Victor Parra
- Institute for Computational Genomics, Joint Research Center for Computational Biomedicine, RWTH Aachen University Medical School, Aachen, Germany
| | - Roman D Bülow
- Institute of Pathology, RWTH Aachen University Medical School, Aachen, Germany
| | - Christoph Kuppe
- Institute of Experimental Medicine and Systems Biology, RWTH Aachen University, Aachen, Germany
| | - David L Hölscher
- Institute of Pathology, RWTH Aachen University Medical School, Aachen, Germany
| | - Mingbo Cheng
- Institute for Computational Genomics, Joint Research Center for Computational Biomedicine, RWTH Aachen University Medical School, Aachen, Germany
| | - James S Nagai
- Institute for Computational Genomics, Joint Research Center for Computational Biomedicine, RWTH Aachen University Medical School, Aachen, Germany
| | - Michaël Goedertier
- Institute for Computational Genomics, Joint Research Center for Computational Biomedicine, RWTH Aachen University Medical School, Aachen, Germany
- Institute of Pathology, RWTH Aachen University Medical School, Aachen, Germany
| | - Nassim Bouteldja
- Institute of Pathology, RWTH Aachen University Medical School, Aachen, Germany
| | - Vladimir Tesar
- Department of Nephrology, 1st Faculty of Medicine and General University Hospital, Charles University, Prague, Czech Republic
| | - Jonathan Barratt
- John Walls Renal Unit, University Hospital of Leicester National Health Service Trust, Leicester, UK
- Department of Cardiovascular Sciences, University of Leicester, Leicester, UK
| | - Ian Sd Roberts
- Department of Cellular Pathology, Oxford University Hospitals National Health Services Foundation Trust, Oxford, UK
| | - Rosanna Coppo
- Fondazione Ricerca Molinette, Regina Margherita Children's University Hospital, Torino, Italy
| | - Rafael Kramann
- Institute of Experimental Medicine and Systems Biology, RWTH Aachen University, Aachen, Germany
- Department of Internal Medicine, Nephrology and Transplantation, Erasmus Medical Center, Rotterdam, Netherlands
| | - Peter Boor
- Institute of Pathology, RWTH Aachen University Medical School, Aachen, Germany.
| | - Ivan G Costa
- Institute for Computational Genomics, Joint Research Center for Computational Biomedicine, RWTH Aachen University Medical School, Aachen, Germany.
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44
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Evans P, Nagai T, Konkashbaev A, Zhou D, Knapik EW, Gamazon ER. Transcriptome-Wide Association Studies (TWAS): Methodologies, Applications, and Challenges. Curr Protoc 2024; 4:e981. [PMID: 38314955 PMCID: PMC10846672 DOI: 10.1002/cpz1.981] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2024]
Abstract
Transcriptome-wide association study (TWAS) methodologies aim to identify genetic effects on phenotypes through the mediation of gene transcription. In TWAS, in silico models of gene expression are trained as functions of genetic variants and then applied to genome-wide association study (GWAS) data. This post-GWAS analysis identifies gene-trait associations with high interpretability, enabling follow-up functional genomics studies and the development of genetics-anchored resources. We provide an overview of commonly used TWAS approaches, their advantages and limitations, and some widely used applications. © 2024 Wiley Periodicals LLC.
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Affiliation(s)
- Patrick Evans
- Division of Genetic Medicine and Vanderbilt Genetics Institute, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Taylor Nagai
- Division of Genetic Medicine and Vanderbilt Genetics Institute, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Anuar Konkashbaev
- Division of Genetic Medicine and Vanderbilt Genetics Institute, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Dan Zhou
- Division of Genetic Medicine and Vanderbilt Genetics Institute, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Ela W Knapik
- Division of Genetic Medicine and Vanderbilt Genetics Institute, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Eric R Gamazon
- Division of Genetic Medicine and Vanderbilt Genetics Institute, Vanderbilt University Medical Center, Nashville, Tennessee
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Strober BJ, Tayeb K, Popp J, Qi G, Gordon MG, Perez R, Ye CJ, Battle A. SURGE: uncovering context-specific genetic-regulation of gene expression from single-cell RNA sequencing using latent-factor models. Genome Biol 2024; 25:28. [PMID: 38254214 PMCID: PMC10801966 DOI: 10.1186/s13059-023-03152-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2022] [Accepted: 12/20/2023] [Indexed: 01/24/2024] Open
Abstract
Genetic regulation of gene expression is a complex process, with genetic effects known to vary across cellular contexts such as cell types and environmental conditions. We developed SURGE, a method for unsupervised discovery of context-specific expression quantitative trait loci (eQTLs) from single-cell transcriptomic data. This allows discovery of the contexts or cell types modulating genetic regulation without prior knowledge. Applied to peripheral blood single-cell eQTL data, SURGE contexts capture continuous representations of distinct cell types and groupings of biologically related cell types. We demonstrate the disease-relevance of SURGE context-specific eQTLs using colocalization analysis and stratified LD-score regression.
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Affiliation(s)
- Benjamin J Strober
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Karl Tayeb
- Department of Human Genetics, University of Chicago, Chicago, IL, USA
| | - Joshua Popp
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD, USA
| | - Guanghao Qi
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD, USA
| | - M Grace Gordon
- Biological and Medical Informatics Graduate Program, University of California, San Francisco, CA, USA
- Division of Rheumatology, Department of Medicine, University of California, San Francisco, CA, USA
- Institute for Human Genetics, University of California, San Francisco, CA, USA
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, CA, USA
| | - Richard Perez
- Institute for Human Genetics, University of California, San Francisco, CA, USA
| | - Chun Jimmie Ye
- Division of Rheumatology, Department of Medicine, University of California, San Francisco, CA, USA
- Institute for Human Genetics, University of California, San Francisco, CA, USA
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, CA, USA
- Institute for Computational Health Sciences, University of California, San Francisco, San Francisco, CA, USA
- Chan-Zuckerberg Biohub, San Francisco, CA, USA
| | - Alexis Battle
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD, USA.
- Department of Computer Science, Johns Hopkins University, Baltimore, MD, USA.
- Department of Genetic Medicine, Johns Hopkins University, Baltimore, MD, USA.
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Venema WJ, Hiddingh S, van Loosdregt J, Bowes J, Balliu B, de Boer JH, Ossewaarde-van Norel J, Thompson SD, Langefeld CD, de Ligt A, van der Veken LT, Krijger PHL, de Laat W, Kuiper JJW. A cis-regulatory element regulates ERAP2 expression through autoimmune disease risk SNPs. CELL GENOMICS 2024; 4:100460. [PMID: 38190099 PMCID: PMC10794781 DOI: 10.1016/j.xgen.2023.100460] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/16/2023] [Revised: 10/04/2023] [Accepted: 11/09/2023] [Indexed: 01/09/2024]
Abstract
Single-nucleotide polymorphisms (SNPs) near the ERAP2 gene are associated with various autoimmune conditions, as well as protection against lethal infections. Due to high linkage disequilibrium, numerous trait-associated SNPs are correlated with ERAP2 expression; however, their functional mechanisms remain unidentified. We show by reciprocal allelic replacement that ERAP2 expression is directly controlled by the splice region variant rs2248374. However, disease-associated variants in the downstream LNPEP gene promoter are independently associated with ERAP2 expression. Allele-specific conformation capture assays revealed long-range chromatin contacts between the gene promoters of LNPEP and ERAP2 and showed that interactions were stronger in patients carrying the alleles that increase susceptibility to autoimmune diseases. Replacing the SNPs in the LNPEP promoter by reference sequences lowered ERAP2 expression. These findings show that multiple SNPs act in concert to regulate ERAP2 expression and that disease-associated variants can convert a gene promoter region into a potent enhancer of a distal gene.
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Affiliation(s)
- Wouter J Venema
- Department of Ophthalmology, University Medical Center Utrecht, Utrecht University, Utrecht, the Netherlands; Center for Translational Immunology, University Medical Center Utrecht, Utrecht University, Utrecht, the Netherlands
| | - Sanne Hiddingh
- Department of Ophthalmology, University Medical Center Utrecht, Utrecht University, Utrecht, the Netherlands; Center for Translational Immunology, University Medical Center Utrecht, Utrecht University, Utrecht, the Netherlands
| | - Jorg van Loosdregt
- Center for Translational Immunology, University Medical Center Utrecht, Utrecht University, Utrecht, the Netherlands
| | - John Bowes
- Centre for Genetics and Genomics Versus Arthritis, Centre for Musculoskeletal Research, Manchester Academic Health Science Centre, The University of Manchester, Manchester, UK
| | - Brunilda Balliu
- Department of Computational Medicine, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
| | - Joke H de Boer
- Department of Ophthalmology, University Medical Center Utrecht, Utrecht University, Utrecht, the Netherlands
| | | | - Susan D Thompson
- Department of Pediatrics, University of Cincinnati College of Medicine, Division of Human Genetics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Carl D Langefeld
- Department of Biostatistics and Data Science, and Center for Precision Medicine, Wake Forest University School of Medicine, Winston-Salem, NC, USA
| | - Aafke de Ligt
- Department of Ophthalmology, University Medical Center Utrecht, Utrecht University, Utrecht, the Netherlands; Center for Translational Immunology, University Medical Center Utrecht, Utrecht University, Utrecht, the Netherlands
| | - Lars T van der Veken
- Department of Genetics, Division Laboratories, Pharmacy and Biomedical Genetics, University Medical Center Utrecht, Utrecht University, Utrecht, the Netherlands
| | - Peter H L Krijger
- Oncode Institute, Hubrecht Institute-KNAW and University Medical Center Utrecht, 3584 CT Utrecht, the Netherlands
| | - Wouter de Laat
- Oncode Institute, Hubrecht Institute-KNAW and University Medical Center Utrecht, 3584 CT Utrecht, the Netherlands
| | - Jonas J W Kuiper
- Department of Ophthalmology, University Medical Center Utrecht, Utrecht University, Utrecht, the Netherlands; Center for Translational Immunology, University Medical Center Utrecht, Utrecht University, Utrecht, the Netherlands.
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Kang H, Pan S, Lin S, Wang YY, Yuan N, Jia P. PharmGWAS: a GWAS-based knowledgebase for drug repurposing. Nucleic Acids Res 2024; 52:D972-D979. [PMID: 37831083 PMCID: PMC10767932 DOI: 10.1093/nar/gkad832] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2023] [Revised: 09/12/2023] [Accepted: 09/21/2023] [Indexed: 10/14/2023] Open
Abstract
Leveraging genetics insights to promote drug repurposing has become a promising and active strategy in pharmacology. Indeed, among the 50 drugs approved by FDA in 2021, two-thirds have genetically supported evidence. In this regard, the increasing amount of widely available genome-wide association studies (GWAS) datasets have provided substantial opportunities for drug repurposing based on genetics discoveries. Here, we developed PharmGWAS, a comprehensive knowledgebase designed to identify candidate drugs through the integration of GWAS data. PharmGWAS focuses on novel connections between diseases and small-molecule compounds derived using a reverse relationship between the genetically-regulated expression signature and the drug-induced signature. Specifically, we collected and processed 1929 GWAS datasets across a diverse spectrum of diseases and 724 485 perturbation signatures pertaining to a substantial 33609 molecular compounds. To obtain reliable and robust predictions for the reverse connections, we implemented six distinct connectivity methods. In the current version, PharmGWAS deposits a total of 740 227 genetically-informed disease-drug pairs derived from drug-perturbation signatures, presenting a valuable and comprehensive catalog. Further equipped with its user-friendly web design, PharmGWAS is expected to greatly aid the discovery of novel drugs, the exploration of drug combination therapies and the identification of drug resistance or side effects. PharmGWAS is available at https://ngdc.cncb.ac.cn/pharmgwas.
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Affiliation(s)
- Hongen Kang
- CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Siyu Pan
- CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Shiqi Lin
- CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yin-Ying Wang
- CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China
| | - Na Yuan
- CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China
| | - Peilin Jia
- CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
- National Genomics Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China
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Wu Y, Weng C, Zhou Y, Zhu Q, Liu Y, Zheng J, Yang B, Cao W, Yuan L, Yang M, Deng D. A comprehensive exploration of the heterogeneity of immune cells in Han and Zang systemic lupus erythematosus patients via single-cell RNA sequencing. Genomics 2024; 116:110770. [PMID: 38128704 DOI: 10.1016/j.ygeno.2023.110770] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2023] [Revised: 11/16/2023] [Accepted: 12/18/2023] [Indexed: 12/23/2023]
Abstract
Systemic Lupus Erythematosus (SLE) is an autoimmune sickness with unclear pathogenesis. The goal of this research was to reveal the heterogeneity of immune cells in SLE patients of Han and Zang nationality by single-cell RNA sequencing (scRNA-seq) and bioinformatics profiling. METHODS A total of 94,102 peripheral blood mononuclear cells (PBMCs) from six volunteers with SLE (3 Zang, 3 Han) and six healthy controls were first conducted through scRNA-seq analysis. The immune cell subsets in the pathogenesis of SLE were analyzed as well. Real-time quantitative PCR (RT-qPCR) was applied to confirm the results of sc-RNA seq analysis. RESULTS For the Tibetan samples, the ratios of Naïve CD4 RPS4Y1 cells, Naïve CD4 cells, Memory BC CD24 and Memory BC differed significantly between the SLE and control samples, while that of CD8 CTL MAL cells was significantly different between the two groups in Han nationality samples. Variable differentiation states of CD8 CTL MAL cells, CD8 CTL GZMK cells, and Naïve CD4 cells were detected through pseudotime analysis. Moreover, T-cell receptor (TCR) abundance was notably higher in Tibetan SLE specimens than that in controls, while B-cell receptor (BCR) abundance in Tibetan and Han samples was higher than in control groups. CONCLUSIONS In summary, the immune cellular heterogeneity of SLE patients both Han and Zang nationality was explored based on various bioinformatics approaches, providing new perspectives for immunological characteristics of SLE among different ethnic groups.
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Affiliation(s)
- Yongzhuo Wu
- Department of Dermatology, The Second Affiliated Hospital of Kunming Medical University, Kunming 650101, PR China
| | - Chongjun Weng
- State Key Laboratory of Genetic Resources and Evolution, Key Laboratory of Healthy Aging Research of Yunnan Province, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650201, PR China
| | - Yali Zhou
- Department of Dermatology, The Second Affiliated Hospital of Kunming Medical University, Kunming 650101, PR China
| | - Qinghuan Zhu
- Department of Dermatology, The Second Affiliated Hospital of Kunming Medical University, Kunming 650101, PR China
| | - Yingying Liu
- Department of Dermatology, The Second Affiliated Hospital of Kunming Medical University, Kunming 650101, PR China
| | - Junjuan Zheng
- State Key Laboratory of Genetic Resources and Evolution, Key Laboratory of Healthy Aging Research of Yunnan Province, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650201, PR China
| | - Binbin Yang
- Department of Dermatology, The Second Affiliated Hospital of Kunming Medical University, Kunming 650101, PR China
| | - Wenting Cao
- Department of Dermatology, The Second Affiliated Hospital of Kunming Medical University, Kunming 650101, PR China
| | - Limei Yuan
- Department of Dermatology, The Second Affiliated Hospital of Kunming Medical University, Kunming 650101, PR China
| | - Meng Yang
- Department of Dermatology, The Second Affiliated Hospital of Kunming Medical University, Kunming 650101, PR China; Department of Dermatology, The Third Affiliated Hospital of Guangxi Medical University, Nanning 530031, PR China
| | - Danqi Deng
- Department of Dermatology, The Second Affiliated Hospital of Kunming Medical University, Kunming 650101, PR China.
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Gilis J, Perin L, Malfait M, Van den Berge K, Takele Assefa A, Verbist B, Risso D, Clement L. Differential detection workflows for multi-sample single-cell RNA-seq data. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.12.17.572043. [PMID: 38187695 PMCID: PMC10769270 DOI: 10.1101/2023.12.17.572043] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/09/2024]
Abstract
In single-cell transcriptomics, differential gene expression (DE) analyses typically focus on testing differences in the average expression of genes between cell types or conditions of interest. Single-cell transcriptomics, however, also has the promise to prioritise genes for which the expression differ in other aspects of the distribution. Here we develop a workflow for assessing differential detection (DD), which tests for differences in the average fraction of samples or cells in which a gene is detected. After benchmarking eight different DD data analysis strategies, we provide a unified workflow for jointly assessing DE and DD. Using simulations and two case studies, we show that DE and DD analysis provide complementary information, both in terms of the individual genes they report and in the functional interpretation of those genes.
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Affiliation(s)
- Jeroen Gilis
- These authors contributed equally
- Applied Mathematics, Computer science and Statistics, Ghent University, Ghent, 9000, Belgium
- Bioinformatics Institute, Ghent University, Ghent, 9000, Belgium
- Data Mining and Modeling for Biomedicine, VIB Flemish Institute for Biotechnology, Ghent, 9000, Belgium
| | - Laura Perin
- These authors contributed equally
- Department of Statistical Sciences, University of Padova, Padova, Italy
| | - Milan Malfait
- Applied Mathematics, Computer science and Statistics, Ghent University, Ghent, 9000, Belgium
| | - Koen Van den Berge
- Statistics and Decision Sciences, Johnson and Johnson Innovative Medicine, Beerse, Belgium
| | - Alemu Takele Assefa
- Statistics and Decision Sciences, Johnson and Johnson Innovative Medicine, Beerse, Belgium
| | - Bie Verbist
- Statistics and Decision Sciences, Johnson and Johnson Innovative Medicine, Beerse, Belgium
| | - Davide Risso
- Department of Statistical Sciences, University of Padova, Padova, Italy
- Padua Center for Network Medicine, University of Padova, Padova, Italy
| | - Lieven Clement
- Applied Mathematics, Computer science and Statistics, Ghent University, Ghent, 9000, Belgium
- Bioinformatics Institute, Ghent University, Ghent, 9000, Belgium
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50
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Dai Q, Epstein MP, Yang J. STACCato: Supervised Tensor Analysis tool for studying Cell-cell Communication using scRNA-seq data across multiple samples and conditions. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.12.15.571918. [PMID: 38168391 PMCID: PMC10760171 DOI: 10.1101/2023.12.15.571918] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/05/2024]
Abstract
Research on cell-cell communication (CCC) is crucial for understanding biology and diseases. Many existing CCC inference tools neglect potential confounders, such as batch and demographic variables, when analyzing multi-sample, multi-condition scRNA-seq datasets. To address this significant gap, we introduce STACCato, a Supervised Tensor Analysis tool for studying Cell-cell Communication, that identifies CCC events and estimates the effects of biological conditions (e.g., disease status, tissue types) on such events, while adjusting for potential confounders. Application of STACCato to both simulated data and real scRNA-seq data of lupus and autism studies demonstrate that incorporating sample-level variables into CCC inference consistently provides more accurate estimations of disease effects and cell type activity patterns than existing methods that ignore sample-level variables. A computational tool implementing the STACCato framework is available on GitHub.
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Affiliation(s)
- Qile Dai
- Department of Biostatistics and Bioinformatics, Emory University School of Public Health, Atlanta, Georgia 30322, United States of America
- Center for Computational and Quantitative Genetics, Department of Human Genetics, Emory University School of Medicine, Atlanta, Georgia 30322, United States of America
| | - Michael P. Epstein
- Center for Computational and Quantitative Genetics, Department of Human Genetics, Emory University School of Medicine, Atlanta, Georgia 30322, United States of America
| | - Jingjing Yang
- Center for Computational and Quantitative Genetics, Department of Human Genetics, Emory University School of Medicine, Atlanta, Georgia 30322, United States of America
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