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Sekita A, Kawasaki H, Fukushima-Nomura A, Yashiro K, Tanese K, Toshima S, Ashizaki K, Miyai T, Yazaki J, Kobayashi A, Namba S, Naito T, Wang QS, Kawakami E, Seita J, Ohara O, Sakurada K, Okada Y, Amagai M, Koseki H. Multifaceted analysis of cross-tissue transcriptomes reveals phenotype-endotype associations in atopic dermatitis. Nat Commun 2023; 14:6133. [PMID: 37783685 PMCID: PMC10545679 DOI: 10.1038/s41467-023-41857-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2022] [Accepted: 09/19/2023] [Indexed: 10/04/2023] Open
Abstract
Atopic dermatitis (AD) is a skin disease that is heterogeneous both in terms of clinical manifestations and molecular profiles. It is increasingly recognized that AD is a systemic rather than a local disease and should be assessed in the context of whole-body pathophysiology. Here we show, via integrated RNA-sequencing of skin tissue and peripheral blood mononuclear cell (PBMC) samples along with clinical data from 115 AD patients and 14 matched healthy controls, that specific clinical presentations associate with matching differential molecular signatures. We establish a regression model based on transcriptome modules identified in weighted gene co-expression network analysis to extract molecular features associated with detailed clinical phenotypes of AD. The two main, qualitatively differential skin manifestations of AD, erythema and papulation are distinguished by differential immunological signatures. We further apply the regression model to a longitudinal dataset of 30 AD patients for personalized monitoring, highlighting patient heterogeneity in disease trajectories. The longitudinal features of blood tests and PBMC transcriptome modules identify three patient clusters which are aligned with clinical severity and reflect treatment history. Our approach thus serves as a framework for effective clinical investigation to gain a holistic view on the pathophysiology of complex human diseases.
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Affiliation(s)
- Aiko Sekita
- RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
- Department of Dermatology, Keio University School of Medicine, Tokyo, Japan
| | - Hiroshi Kawasaki
- RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
- Department of Dermatology, Keio University School of Medicine, Tokyo, Japan
| | | | - Kiyoshi Yashiro
- Department of Dermatology, Keio University School of Medicine, Tokyo, Japan
| | - Keiji Tanese
- Department of Dermatology, Keio University School of Medicine, Tokyo, Japan
| | - Susumu Toshima
- RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
- Department of Dermatology, Keio University School of Medicine, Tokyo, Japan
| | - Koichi Ashizaki
- RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
- Department of Dermatology, Keio University School of Medicine, Tokyo, Japan
- Advanced Data Science Project, RIKEN Information R&D and Strategy Headquarters, Tokyo, Japan
| | - Tomohiro Miyai
- RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
- Department of Dermatology, Keio University School of Medicine, Tokyo, Japan
| | - Junshi Yazaki
- RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Atsuo Kobayashi
- RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Shinichi Namba
- Department of Statistical Genetics, Osaka University Graduate School of Medicine, Osaka, Japan
- Department of Genome Informatics, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Tatsuhiko Naito
- Department of Statistical Genetics, Osaka University Graduate School of Medicine, Osaka, Japan
| | - Qingbo S Wang
- RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
- Department of Statistical Genetics, Osaka University Graduate School of Medicine, Osaka, Japan
- Department of Genome Informatics, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Eiryo Kawakami
- Advanced Data Science Project, RIKEN Information R&D and Strategy Headquarters, Tokyo, Japan
- Artificial Intelligence Medicine, Graduate School of Medicine, Chiba University, Chiba, Japan
| | - Jun Seita
- RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
- Advanced Data Science Project, RIKEN Information R&D and Strategy Headquarters, Tokyo, Japan
| | | | - Kazuhiro Sakurada
- Advanced Data Science Project, RIKEN Information R&D and Strategy Headquarters, Tokyo, Japan
- Department of Extended Intelligence for Medicine, Keio University School of Medicine, Tokyo, Japan
| | - Yukinori Okada
- RIKEN Center for Integrative Medical Sciences, Yokohama, Japan.
- Department of Statistical Genetics, Osaka University Graduate School of Medicine, Osaka, Japan.
- Department of Genome Informatics, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan.
| | - Masayuki Amagai
- RIKEN Center for Integrative Medical Sciences, Yokohama, Japan.
- Department of Dermatology, Keio University School of Medicine, Tokyo, Japan.
| | - Haruhiko Koseki
- RIKEN Center for Integrative Medical Sciences, Yokohama, Japan.
- Cellular and Molecular Medicine, Advanced Research Departments, Graduate School of Medicine, Chiba University, Chiba, Japan.
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Yaung KN, Yeo JG, Kumar P, Wasser M, Chew M, Ravelli A, Law AHN, Arkachaisri T, Martini A, Pisetsky DS, Albani S. Artificial intelligence and high-dimensional technologies in the theragnosis of systemic lupus erythematosus. THE LANCET. RHEUMATOLOGY 2023; 5:e151-e165. [PMID: 38251610 DOI: 10.1016/s2665-9913(23)00010-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/30/2022] [Revised: 12/14/2022] [Accepted: 01/04/2023] [Indexed: 02/22/2023]
Abstract
Systemic lupus erythematosus is a complex, systemic autoimmune disease characterised by immune dysregulation. Pathogenesis is multifactorial, contributing to clinical heterogeneity and posing challenges for diagnosis and treatment. Although strides in treatment options have been made in the past 15 years, with the US Food and Drug Administration approval of belimumab in 2011, there are still many patients who have inadequate responses to therapy. A better understanding of underlying disease mechanisms with a holistic and multiparametric approach is required to improve clinical assessment and treatment. This Review discusses the evolution of genomics, epigenomics, transcriptomics, and proteomics in the study of systemic lupus erythematosus and ways to amalgamate these silos of data with a systems-based approach while also discussing ways to strengthen the overall process. These mechanistic insights will facilitate the discovery of functionally relevant biomarkers to guide rational therapeutic selection to improve patient outcomes.
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Affiliation(s)
- Katherine Nay Yaung
- Translational Immunology Institute, SingHealth Duke-NUS Academic Medical Centre, Singapore; Duke-NUS Medical School, Singapore.
| | - Joo Guan Yeo
- Translational Immunology Institute, SingHealth Duke-NUS Academic Medical Centre, Singapore; Duke-NUS Medical School, Singapore; Rheumatology and Immunology Service, KK Women's and Children's Hospital, Singapore
| | - Pavanish Kumar
- Translational Immunology Institute, SingHealth Duke-NUS Academic Medical Centre, Singapore
| | - Martin Wasser
- Translational Immunology Institute, SingHealth Duke-NUS Academic Medical Centre, Singapore
| | - Marvin Chew
- Translational Immunology Institute, SingHealth Duke-NUS Academic Medical Centre, Singapore
| | - Angelo Ravelli
- Direzione Scientifica, IRCCS Istituto Giannina Gaslini, Genoa, Italy; Dipartimento di Neuroscienze, Riabilitazione, Oftalmologia, Genetica e Scienze Materno-Infantili, Università degli Studi di Genova, Genoa, Italy
| | - Annie Hui Nee Law
- Duke-NUS Medical School, Singapore; Department of Rheumatology and Immunology, Singapore General Hospital, Singapore
| | - Thaschawee Arkachaisri
- Duke-NUS Medical School, Singapore; Rheumatology and Immunology Service, KK Women's and Children's Hospital, Singapore
| | | | - David S Pisetsky
- Department of Medicine and Department of Immunology, Duke University Medical Center, Durham, NC, USA; Medical Research Service, Veterans Administration Medical Center, Durham, NC, USA
| | - Salvatore Albani
- Translational Immunology Institute, SingHealth Duke-NUS Academic Medical Centre, Singapore; Duke-NUS Medical School, Singapore; Rheumatology and Immunology Service, KK Women's and Children's Hospital, Singapore
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3
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Ghafouri-Fard S, Shahir M, Taheri M, Salimi A. A review on the role of chemokines in the pathogenesis of systemic lupus erythematosus. Cytokine 2021; 146:155640. [PMID: 34252872 DOI: 10.1016/j.cyto.2021.155640] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2021] [Revised: 07/01/2021] [Accepted: 07/01/2021] [Indexed: 12/14/2022]
Abstract
Chemokines are a group of cytokines with low molecular weight that principally direct chemotaxis of target cells. They have prominent roles in the pathogenesis systemic lupus erythematosus (SLE) and related complications particularly lupus nephritis. These molecules not only induce autoimmune responses in the organs of patients, but also can amplify the induced inflammatory responses. Although chemokine family has at least 46 identified members, the role of a number of these molecules have been more clarified in SLE patients or animal models of this disorder. In the current paper, we review the role of CCL2, CCL3, CCL4, CCL11, CCL20, CXCL1, CXCL2, CXCL8, CXCL10, CXCL12 and CXCL13 in the pathogenesis of SLE.
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Affiliation(s)
- Soudeh Ghafouri-Fard
- Department of Medical Genetics, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Mehri Shahir
- Department of Immunology, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Mohammad Taheri
- Skull Base Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran.
| | - Alireza Salimi
- Critical Care Quality Improvement Research Center, Loghman Hakim Hospital, Shahid Beheshti University of Medical Sciences, Tehran, Iran.
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