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Balachandran S, Prada-Medina CA, Mensah MA, Kakar N, Nagel I, Pozojevic J, Audain E, Hitz MP, Kircher M, Sreenivasan VKA, Spielmann M. STIGMA: Single-cell tissue-specific gene prioritization using machine learning. Am J Hum Genet 2024; 111:338-349. [PMID: 38228144 PMCID: PMC10870135 DOI: 10.1016/j.ajhg.2023.12.011] [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: 08/04/2023] [Revised: 12/01/2023] [Accepted: 12/07/2023] [Indexed: 01/18/2024] Open
Abstract
Clinical exome and genome sequencing have revolutionized the understanding of human disease genetics. Yet many genes remain functionally uncharacterized, complicating the establishment of causal disease links for genetic variants. While several scoring methods have been devised to prioritize these candidate genes, these methods fall short of capturing the expression heterogeneity across cell subpopulations within tissues. Here, we introduce single-cell tissue-specific gene prioritization using machine learning (STIGMA), an approach that leverages single-cell RNA-seq (scRNA-seq) data to prioritize candidate genes associated with rare congenital diseases. STIGMA prioritizes genes by learning the temporal dynamics of gene expression across cell types during healthy organogenesis. To assess the efficacy of our framework, we applied STIGMA to mouse limb and human fetal heart scRNA-seq datasets. In a cohort of individuals with congenital limb malformation, STIGMA prioritized 469 variants in 345 genes, with UBA2 as a notable example. For congenital heart defects, we detected 34 genes harboring nonsynonymous de novo variants (nsDNVs) in two or more individuals from a set of 7,958 individuals, including the ortholog of Prdm1, which is associated with hypoplastic left ventricle and hypoplastic aortic arch. Overall, our findings demonstrate that STIGMA effectively prioritizes tissue-specific candidate genes by utilizing single-cell transcriptome data. The ability to capture the heterogeneity of gene expression across cell populations makes STIGMA a powerful tool for the discovery of disease-associated genes and facilitates the identification of causal variants underlying human genetic disorders.
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Affiliation(s)
- Saranya Balachandran
- Institute of Human Genetics, University Hospital Schleswig-Holstein, University of Lübeck and Kiel University, Lübeck, Germany
| | - Cesar A Prada-Medina
- Human Molecular Genetics Group, Max Planck Institute for Molecular Genetics, 14195 Berlin, Germany
| | - Martin A Mensah
- Institut für Medizinische Genetik und Humangenetik, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Augustenburger Platz 1, 13353 Berlin, Germany; BIH Charité Digital Clinician Scientist Program, BIH Biomedical Innovation Academy, Anna-Louisa-Karsch-Strasse 2, 10178 Berlin, Germany; RG Development & Disease, Max Planck Institute for Molecular Genetics, 14195 Berlin, Germany
| | - Naseebullah Kakar
- Institute of Human Genetics, University Hospital Schleswig-Holstein, University of Lübeck and Kiel University, Lübeck, Germany; Department of Biotechnology, BUITEMS, Quetta, Pakistan
| | - Inga Nagel
- Institute of Human Genetics, University Hospital Schleswig-Holstein, University of Lübeck and Kiel University, Lübeck, Germany
| | - Jelena Pozojevic
- Institute of Human Genetics, University Hospital Schleswig-Holstein, University of Lübeck and Kiel University, Lübeck, Germany
| | - Enrique Audain
- Institute of Medical Genetics, Carl von Ossietzky University, 26129 Oldenburg, Germany; DZHK e.V. (German Center for Cardiovascular Research), Partner Site Hamburg/Kiel/Lübeck; Department of Congenital Heart Disease and Pediatric Cardiology, University Hospital of Schleswig-Holstein, 24105 Kiel, Germany
| | - Marc-Phillip Hitz
- Institute of Medical Genetics, Carl von Ossietzky University, 26129 Oldenburg, Germany; DZHK e.V. (German Center for Cardiovascular Research), Partner Site Hamburg/Kiel/Lübeck; Department of Congenital Heart Disease and Pediatric Cardiology, University Hospital of Schleswig-Holstein, 24105 Kiel, Germany
| | - Martin Kircher
- Institute of Human Genetics, University Hospital Schleswig-Holstein, University of Lübeck and Kiel University, Lübeck, Germany
| | - Varun K A Sreenivasan
- Institute of Human Genetics, University Hospital Schleswig-Holstein, University of Lübeck and Kiel University, Lübeck, Germany.
| | - Malte Spielmann
- Institute of Human Genetics, University Hospital Schleswig-Holstein, University of Lübeck and Kiel University, Lübeck, Germany; Human Molecular Genetics Group, Max Planck Institute for Molecular Genetics, 14195 Berlin, Germany; DZHK e.V. (German Center for Cardiovascular Research), Partner Site Hamburg/Kiel/Lübeck.
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Guo B, Zhao F, Zhang S. CILP is a potential pan-cancer marker: combined silico study and in vitro analyses. Cancer Gene Ther 2024; 31:119-130. [PMID: 37968343 DOI: 10.1038/s41417-023-00688-x] [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: 07/11/2023] [Revised: 10/11/2023] [Accepted: 11/02/2023] [Indexed: 11/17/2023]
Abstract
CILP (Cartilage intermediate layer protein), an ECM (extracellular matrix) glycoprotein, is found to be associated with intervertebral disc degeneration, chronic heart failure, obese and cardiac fibrosis. However, there are few reports on the role of CILP in tumors. Thus, in this study, we mainly explored the function of CILP in the occurrence and development of tumors and whether it could be a potential pan-cancer marker. Pan-cancer data in this study were obtained from UCSC Xena. Single-cell data were obtained from GSE152938. ROC (Receiver operating characteristic) curves were used to evaluate the accuracy of CILP in predicting the occurrence of different tumor types. The Kaplan-Meier plots were used to assess the relationship between CILP expression and survival prognosis in different tumor types by COX regression analysis. Pseudotime analysis and cell communication analysis were used to further explore the function of CILP at Single cell level. The human RCC (renal cell carcinoma) cell lines ACHN and 786-O were used for further experimental verification. Bulk RNA-seq showed differences in CILP expression in several tumors. ROC curves showed that 14 tumors have AUC > 0.7. Kaplan-Meier plots indicated that CILP is a risk factor for patients in 3 kinds of tumors. ScRNA-seq (Single cell RNA sequencing) suggested that CILP might influence tumors through fibroblasts and cell-cell communication. Finally, we verified the function of CILP at the cellular level by using RCC cell lines ACHN and 786-O and found that knockdown of CILP could significantly inhibit migration and invasion. This finding supports that CILP could be a risk factor as well as a pan-cancer predictor for patients.
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Affiliation(s)
- Bingjie Guo
- Yueyang Hospital of Integrated Traditional Chinese and Western Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Feiran Zhao
- Yueyang Hospital of Integrated Traditional Chinese and Western Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Sailong Zhang
- Department of Pharmacology, Second Military Medical University/Naval Medical University, Shanghai, China.
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Lang NJ, Gote-Schniering J, Porras-Gonzalez D, Yang L, De Sadeleer LJ, Jentzsch RC, Shitov VA, Zhou S, Ansari M, Agami A, Mayr CH, Hooshiar Kashani B, Chen Y, Heumos L, Pestoni JC, Molnar ES, Geeraerts E, Anquetil V, Saniere L, Wögrath M, Gerckens M, Lehmann M, Yildirim AÖ, Hatz R, Kneidinger N, Behr J, Wuyts WA, Stoleriu MG, Luecken MD, Theis FJ, Burgstaller G, Schiller HB. Ex vivo tissue perturbations coupled to single-cell RNA-seq reveal multilineage cell circuit dynamics in human lung fibrogenesis. Sci Transl Med 2023; 15:eadh0908. [PMID: 38055803 DOI: 10.1126/scitranslmed.adh0908] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2023] [Accepted: 11/16/2023] [Indexed: 12/08/2023]
Abstract
Pulmonary fibrosis develops as a consequence of failed regeneration after injury. Analyzing mechanisms of regeneration and fibrogenesis directly in human tissue has been hampered by the lack of organotypic models and analytical techniques. In this work, we coupled ex vivo cytokine and drug perturbations of human precision-cut lung slices (hPCLS) with single-cell RNA sequencing and induced a multilineage circuit of fibrogenic cell states in hPCLS. We showed that these cell states were highly similar to the in vivo cell circuit in a multicohort lung cell atlas from patients with pulmonary fibrosis. Using micro-CT-staged patient tissues, we characterized the appearance and interaction of myofibroblasts, an ectopic endothelial cell state, and basaloid epithelial cells in the thickened alveolar septum of early-stage lung fibrosis. Induction of these states in the hPCLS model provided evidence that the basaloid cell state was derived from alveolar type 2 cells, whereas the ectopic endothelial cell state emerged from capillary cell plasticity. Cell-cell communication routes in patients were largely conserved in hPCLS, and antifibrotic drug treatments showed highly cell type-specific effects. Our work provides an experimental framework for perturbational single-cell genomics directly in human lung tissue that enables analysis of tissue homeostasis, regeneration, and pathology. We further demonstrate that hPCLS offer an avenue for scalable, high-resolution drug testing to accelerate antifibrotic drug development and translation.
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Affiliation(s)
- Niklas J Lang
- Comprehensive Pneumology Center (CPC) with the CPC-M bioArchive/Institute of Lung Health and Immunity (LHI), Helmholtz Munich, Member of the German Center for Lung Research (DZL), 81377 Munich, Germany
| | - Janine Gote-Schniering
- Comprehensive Pneumology Center (CPC) with the CPC-M bioArchive/Institute of Lung Health and Immunity (LHI), Helmholtz Munich, Member of the German Center for Lung Research (DZL), 81377 Munich, Germany
- Department of Rheumatology and Immunology, Department of Pulmonary Medicine, Inselspital, Bern University Hospital, University of Bern, 3010 Bern, Switzerland
- Lung Precision Medicine Program, Department for BioMedical Research, University of Bern, 3008 Bern, Switzerland
| | - Diana Porras-Gonzalez
- Comprehensive Pneumology Center (CPC) with the CPC-M bioArchive/Institute of Lung Health and Immunity (LHI), Helmholtz Munich, Member of the German Center for Lung Research (DZL), 81377 Munich, Germany
| | - Lin Yang
- Comprehensive Pneumology Center (CPC) with the CPC-M bioArchive/Institute of Lung Health and Immunity (LHI), Helmholtz Munich, Member of the German Center for Lung Research (DZL), 81377 Munich, Germany
| | - Laurens J De Sadeleer
- Comprehensive Pneumology Center (CPC) with the CPC-M bioArchive/Institute of Lung Health and Immunity (LHI), Helmholtz Munich, Member of the German Center for Lung Research (DZL), 81377 Munich, Germany
- Laboratory of Respiratory Diseases and Thoracic Surgery (BREATHE), Department CHROMETA, KU Leuven, 3000 Leuven, Belgium
| | - R Christoph Jentzsch
- Comprehensive Pneumology Center (CPC) with the CPC-M bioArchive/Institute of Lung Health and Immunity (LHI), Helmholtz Munich, Member of the German Center for Lung Research (DZL), 81377 Munich, Germany
| | - Vladimir A Shitov
- Comprehensive Pneumology Center (CPC) with the CPC-M bioArchive/Institute of Lung Health and Immunity (LHI), Helmholtz Munich, Member of the German Center for Lung Research (DZL), 81377 Munich, Germany
- Institute of Computational Biology, Helmholtz Munich, Member of the German Center for Lung Research (DZL), 85764 Munich, Germany
| | - Shuhong Zhou
- Comprehensive Pneumology Center (CPC) with the CPC-M bioArchive/Institute of Lung Health and Immunity (LHI), Helmholtz Munich, Member of the German Center for Lung Research (DZL), 81377 Munich, Germany
| | - Meshal Ansari
- Comprehensive Pneumology Center (CPC) with the CPC-M bioArchive/Institute of Lung Health and Immunity (LHI), Helmholtz Munich, Member of the German Center for Lung Research (DZL), 81377 Munich, Germany
- Institute of Computational Biology, Helmholtz Munich, Member of the German Center for Lung Research (DZL), 85764 Munich, Germany
| | - Ahmed Agami
- Comprehensive Pneumology Center (CPC) with the CPC-M bioArchive/Institute of Lung Health and Immunity (LHI), Helmholtz Munich, Member of the German Center for Lung Research (DZL), 81377 Munich, Germany
| | - Christoph H Mayr
- Comprehensive Pneumology Center (CPC) with the CPC-M bioArchive/Institute of Lung Health and Immunity (LHI), Helmholtz Munich, Member of the German Center for Lung Research (DZL), 81377 Munich, Germany
| | - Baharak Hooshiar Kashani
- Comprehensive Pneumology Center (CPC) with the CPC-M bioArchive/Institute of Lung Health and Immunity (LHI), Helmholtz Munich, Member of the German Center for Lung Research (DZL), 81377 Munich, Germany
| | - Yuexin Chen
- Comprehensive Pneumology Center (CPC) with the CPC-M bioArchive/Institute of Lung Health and Immunity (LHI), Helmholtz Munich, Member of the German Center for Lung Research (DZL), 81377 Munich, Germany
| | - Lukas Heumos
- Comprehensive Pneumology Center (CPC) with the CPC-M bioArchive/Institute of Lung Health and Immunity (LHI), Helmholtz Munich, Member of the German Center for Lung Research (DZL), 81377 Munich, Germany
- Institute of Computational Biology, Helmholtz Munich, Member of the German Center for Lung Research (DZL), 85764 Munich, Germany
| | - Jeanine C Pestoni
- Comprehensive Pneumology Center (CPC) with the CPC-M bioArchive/Institute of Lung Health and Immunity (LHI), Helmholtz Munich, Member of the German Center for Lung Research (DZL), 81377 Munich, Germany
| | - Eszter Sarolta Molnar
- Comprehensive Pneumology Center (CPC) with the CPC-M bioArchive/Institute of Lung Health and Immunity (LHI), Helmholtz Munich, Member of the German Center for Lung Research (DZL), 81377 Munich, Germany
| | | | | | | | - Melanie Wögrath
- Comprehensive Pneumology Center (CPC) with the CPC-M bioArchive/Institute of Lung Health and Immunity (LHI), Helmholtz Munich, Member of the German Center for Lung Research (DZL), 81377 Munich, Germany
| | - Michael Gerckens
- Comprehensive Pneumology Center (CPC) with the CPC-M bioArchive/Institute of Lung Health and Immunity (LHI), Helmholtz Munich, Member of the German Center for Lung Research (DZL), 81377 Munich, Germany
- Department of Medicine V, LMU University Hospital, LMU Munich, Comprehensive Pneumology Center Munich (CPC-M), Member of the German Center for Lung Research (DZL), 81377 Munich, Germany
| | - Mareike Lehmann
- Comprehensive Pneumology Center (CPC) with the CPC-M bioArchive/Institute of Lung Health and Immunity (LHI), Helmholtz Munich, Member of the German Center for Lung Research (DZL), 81377 Munich, Germany
- Institute for Lung Research, Philipps-University Marburg, Universities of Giessen and Marburg Lung Center, Member of the German Center for Lung Research (DZL), 35043 Marburg, Germany
| | - Ali Önder Yildirim
- Comprehensive Pneumology Center (CPC) with the CPC-M bioArchive/Institute of Lung Health and Immunity (LHI), Helmholtz Munich, Member of the German Center for Lung Research (DZL), 81377 Munich, Germany
- Institute of Experimental Pneumology, LMU University Hospital, Ludwig-Maximilians University, 81377 Munich, Germany
| | - Rudolf Hatz
- Center for Thoracic Surgery Munich, Ludwig-Maximilians-University of Munich (LMU) and Asklepios Medical Center, Munich-Gauting, 82131 Gauting, Germany
| | - Nikolaus Kneidinger
- Comprehensive Pneumology Center (CPC) with the CPC-M bioArchive/Institute of Lung Health and Immunity (LHI), Helmholtz Munich, Member of the German Center for Lung Research (DZL), 81377 Munich, Germany
- Department of Medicine V, LMU University Hospital, LMU Munich, Comprehensive Pneumology Center Munich (CPC-M), Member of the German Center for Lung Research (DZL), 81377 Munich, Germany
| | - Jürgen Behr
- Comprehensive Pneumology Center (CPC) with the CPC-M bioArchive/Institute of Lung Health and Immunity (LHI), Helmholtz Munich, Member of the German Center for Lung Research (DZL), 81377 Munich, Germany
- Department of Medicine V, LMU University Hospital, LMU Munich, Comprehensive Pneumology Center Munich (CPC-M), Member of the German Center for Lung Research (DZL), 81377 Munich, Germany
| | - Wim A Wuyts
- Laboratory of Respiratory Diseases and Thoracic Surgery (BREATHE), Department CHROMETA, KU Leuven, 3000 Leuven, Belgium
| | - Mircea-Gabriel Stoleriu
- Comprehensive Pneumology Center (CPC) with the CPC-M bioArchive/Institute of Lung Health and Immunity (LHI), Helmholtz Munich, Member of the German Center for Lung Research (DZL), 81377 Munich, Germany
- Center for Thoracic Surgery Munich, Ludwig-Maximilians-University of Munich (LMU) and Asklepios Medical Center, Munich-Gauting, 82131 Gauting, Germany
| | - Malte D Luecken
- Comprehensive Pneumology Center (CPC) with the CPC-M bioArchive/Institute of Lung Health and Immunity (LHI), Helmholtz Munich, Member of the German Center for Lung Research (DZL), 81377 Munich, Germany
- Institute of Computational Biology, Helmholtz Munich, Member of the German Center for Lung Research (DZL), 85764 Munich, Germany
| | - Fabian J Theis
- Institute of Computational Biology, Helmholtz Munich, Member of the German Center for Lung Research (DZL), 85764 Munich, Germany
- Department of Mathematics, Technische Universität München, 85748 Garching bei München, Germany
| | - Gerald Burgstaller
- Comprehensive Pneumology Center (CPC) with the CPC-M bioArchive/Institute of Lung Health and Immunity (LHI), Helmholtz Munich, Member of the German Center for Lung Research (DZL), 81377 Munich, Germany
| | - Herbert B Schiller
- Comprehensive Pneumology Center (CPC) with the CPC-M bioArchive/Institute of Lung Health and Immunity (LHI), Helmholtz Munich, Member of the German Center for Lung Research (DZL), 81377 Munich, Germany
- Institute of Experimental Pneumology, LMU University Hospital, Ludwig-Maximilians University, 81377 Munich, Germany
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Carraro C, Bonaguro L, Srinivasa R, van Uelft M, Isakzai V, Schulte-Schrepping J, Gambhir P, Elmzzahi T, Montgomery JV, Hayer H, Li Y, Theis H, Kraut M, Mahbubani KT, Aschenbrenner AC, König I, Fava E, Fried HU, De Domenico E, Beyer M, Saglam A, Schultze JL. Chromatin accessibility profiling of targeted cell populations with laser capture microdissection coupled to ATAC-seq. CELL REPORTS METHODS 2023; 3:100598. [PMID: 37776856 PMCID: PMC10626193 DOI: 10.1016/j.crmeth.2023.100598] [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: 03/27/2023] [Revised: 08/04/2023] [Accepted: 09/05/2023] [Indexed: 10/02/2023]
Abstract
Spatially resolved omics technologies reveal context-dependent cellular regulatory networks in tissues of interest. Beyond transcriptome analysis, information on epigenetic traits and chromatin accessibility can provide further insights on gene regulation in health and disease. Nevertheless, compared to the enormous advancements in spatial transcriptomics technologies, the field of spatial epigenomics is much younger and still underexplored. In this study, we report laser capture microdissection coupled to ATAC-seq (LCM-ATAC-seq) applied to fresh frozen samples for the spatial characterization of chromatin accessibility. We first demonstrate the efficient use of LCM coupled to in situ tagmentation and evaluate its performance as a function of cell number, microdissected areas, and tissue type. Further, we demonstrate its use for the targeted chromatin accessibility analysis of discrete contiguous or scattered cell populations in tissues via single-nuclei capture based on immunostaining for specific cellular markers.
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Affiliation(s)
- Caterina Carraro
- Systems Medicine, Deutsches Zentrum für Neurodegenerative Erkrankungen (DZNE) e.V., Bonn, Germany; Genomics and Immunoregulation, Life & Medical Sciences (LIMES) Institute, University of Bonn, Bonn, Germany.
| | - Lorenzo Bonaguro
- Systems Medicine, Deutsches Zentrum für Neurodegenerative Erkrankungen (DZNE) e.V., Bonn, Germany; Genomics and Immunoregulation, Life & Medical Sciences (LIMES) Institute, University of Bonn, Bonn, Germany; PRECISE Platform for Genomics and Epigenomics, Deutsches Zentrum für Neurodegenerative Erkrankungen (DZNE) e.V. and University of Bonn, Bonn, Germany
| | - Rachana Srinivasa
- Systems Medicine, Deutsches Zentrum für Neurodegenerative Erkrankungen (DZNE) e.V., Bonn, Germany; Genomics and Immunoregulation, Life & Medical Sciences (LIMES) Institute, University of Bonn, Bonn, Germany
| | - Martina van Uelft
- Systems Medicine, Deutsches Zentrum für Neurodegenerative Erkrankungen (DZNE) e.V., Bonn, Germany; Genomics and Immunoregulation, Life & Medical Sciences (LIMES) Institute, University of Bonn, Bonn, Germany
| | - Victoria Isakzai
- Systems Medicine, Deutsches Zentrum für Neurodegenerative Erkrankungen (DZNE) e.V., Bonn, Germany; Genomics and Immunoregulation, Life & Medical Sciences (LIMES) Institute, University of Bonn, Bonn, Germany
| | - Jonas Schulte-Schrepping
- Systems Medicine, Deutsches Zentrum für Neurodegenerative Erkrankungen (DZNE) e.V., Bonn, Germany; Genomics and Immunoregulation, Life & Medical Sciences (LIMES) Institute, University of Bonn, Bonn, Germany; PRECISE Platform for Genomics and Epigenomics, Deutsches Zentrum für Neurodegenerative Erkrankungen (DZNE) e.V. and University of Bonn, Bonn, Germany
| | - Prerna Gambhir
- Systems Medicine, Deutsches Zentrum für Neurodegenerative Erkrankungen (DZNE) e.V., Bonn, Germany; Genomics and Immunoregulation, Life & Medical Sciences (LIMES) Institute, University of Bonn, Bonn, Germany
| | - Tarek Elmzzahi
- Systems Medicine, Deutsches Zentrum für Neurodegenerative Erkrankungen (DZNE) e.V., Bonn, Germany; Immunogenomics & Neurodegeneration, Deutsches Zentrum für Neurodegenerative Erkrankungen (DZNE) e.V., Bonn, Germany
| | - Jessica V Montgomery
- Systems Medicine, Deutsches Zentrum für Neurodegenerative Erkrankungen (DZNE) e.V., Bonn, Germany
| | - Hannah Hayer
- Systems Medicine, Deutsches Zentrum für Neurodegenerative Erkrankungen (DZNE) e.V., Bonn, Germany; Genomics and Immunoregulation, Life & Medical Sciences (LIMES) Institute, University of Bonn, Bonn, Germany
| | - Yuanfang Li
- Systems Medicine, Deutsches Zentrum für Neurodegenerative Erkrankungen (DZNE) e.V., Bonn, Germany; Immunogenomics & Neurodegeneration, Deutsches Zentrum für Neurodegenerative Erkrankungen (DZNE) e.V., Bonn, Germany
| | - Heidi Theis
- PRECISE Platform for Genomics and Epigenomics, Deutsches Zentrum für Neurodegenerative Erkrankungen (DZNE) e.V. and University of Bonn, Bonn, Germany
| | - Michael Kraut
- PRECISE Platform for Genomics and Epigenomics, Deutsches Zentrum für Neurodegenerative Erkrankungen (DZNE) e.V. and University of Bonn, Bonn, Germany
| | - Krishnaa T Mahbubani
- Department of Surgery, University of Cambridge, and Cambridge NIHR Biomedical Research Centre, Cambridge, UK
| | - Anna C Aschenbrenner
- Systems Medicine, Deutsches Zentrum für Neurodegenerative Erkrankungen (DZNE) e.V., Bonn, Germany
| | - Ireen König
- Core Research Facilities and Services, Light Microscope Facility (LMF), Deutsches Zentrum für Neurodegenerative Erkrankungen (DZNE) e.V., Bonn, Germany
| | - Eugenio Fava
- Core Research Facilities and Services, Deutsches Zentrum für Neurodegenerative Erkrankungen (DZNE) e.V., Bonn, Germany
| | - Hans-Ulrich Fried
- Core Research Facilities and Services, Light Microscope Facility (LMF), Deutsches Zentrum für Neurodegenerative Erkrankungen (DZNE) e.V., Bonn, Germany
| | - Elena De Domenico
- Systems Medicine, Deutsches Zentrum für Neurodegenerative Erkrankungen (DZNE) e.V., Bonn, Germany; Genomics and Immunoregulation, Life & Medical Sciences (LIMES) Institute, University of Bonn, Bonn, Germany; PRECISE Platform for Genomics and Epigenomics, Deutsches Zentrum für Neurodegenerative Erkrankungen (DZNE) e.V. and University of Bonn, Bonn, Germany
| | - Marc Beyer
- Systems Medicine, Deutsches Zentrum für Neurodegenerative Erkrankungen (DZNE) e.V., Bonn, Germany; PRECISE Platform for Genomics and Epigenomics, Deutsches Zentrum für Neurodegenerative Erkrankungen (DZNE) e.V. and University of Bonn, Bonn, Germany; Immunogenomics & Neurodegeneration, Deutsches Zentrum für Neurodegenerative Erkrankungen (DZNE) e.V., Bonn, Germany
| | - Adem Saglam
- Systems Medicine, Deutsches Zentrum für Neurodegenerative Erkrankungen (DZNE) e.V., Bonn, Germany; PRECISE Platform for Genomics and Epigenomics, Deutsches Zentrum für Neurodegenerative Erkrankungen (DZNE) e.V. and University of Bonn, Bonn, Germany.
| | - Joachim L Schultze
- Systems Medicine, Deutsches Zentrum für Neurodegenerative Erkrankungen (DZNE) e.V., Bonn, Germany; Genomics and Immunoregulation, Life & Medical Sciences (LIMES) Institute, University of Bonn, Bonn, Germany; PRECISE Platform for Genomics and Epigenomics, Deutsches Zentrum für Neurodegenerative Erkrankungen (DZNE) e.V. and University of Bonn, Bonn, Germany
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Stabile AM, Pistilli A, Mariangela R, Rende M, Bartolini D, Di Sante G. New Challenges for Anatomists in the Era of Omics. Diagnostics (Basel) 2023; 13:2963. [PMID: 37761332 PMCID: PMC10529314 DOI: 10.3390/diagnostics13182963] [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: 07/31/2023] [Revised: 09/08/2023] [Accepted: 09/10/2023] [Indexed: 09/29/2023] Open
Abstract
Anatomic studies have traditionally relied on macroscopic, microscopic, and histological techniques to investigate the structure of tissues and organs. Anatomic studies are essential in many fields, including medicine, biology, and veterinary science. Advances in technology, such as imaging techniques and molecular biology, continue to provide new insights into the anatomy of living organisms. Therefore, anatomy remains an active and important area in the scientific field. The consolidation in recent years of some omics technologies such as genomics, transcriptomics, proteomics, and metabolomics allows for a more complete and detailed understanding of the structure and function of cells, tissues, and organs. These have been joined more recently by "omics" such as radiomics, pathomics, and connectomics, supported by computer-assisted technologies such as neural networks, 3D bioprinting, and artificial intelligence. All these new tools, although some are still in the early stages of development, have the potential to strongly contribute to the macroscopic and microscopic characterization in medicine. For anatomists, it is time to hitch a ride and get on board omics technologies to sail to new frontiers and to explore novel scenarios in anatomy.
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Affiliation(s)
- Anna Maria Stabile
- Department of Medicine and Surgery, Section of Human, Clinical and Forensic Anatomy, University of Perugia, 60132 Perugia, Italy; (A.M.S.); (A.P.); (R.M.); (M.R.)
| | - Alessandra Pistilli
- Department of Medicine and Surgery, Section of Human, Clinical and Forensic Anatomy, University of Perugia, 60132 Perugia, Italy; (A.M.S.); (A.P.); (R.M.); (M.R.)
| | - Ruggirello Mariangela
- Department of Medicine and Surgery, Section of Human, Clinical and Forensic Anatomy, University of Perugia, 60132 Perugia, Italy; (A.M.S.); (A.P.); (R.M.); (M.R.)
| | - Mario Rende
- Department of Medicine and Surgery, Section of Human, Clinical and Forensic Anatomy, University of Perugia, 60132 Perugia, Italy; (A.M.S.); (A.P.); (R.M.); (M.R.)
| | - Desirée Bartolini
- Department of Medicine and Surgery, Section of Human, Clinical and Forensic Anatomy, University of Perugia, 60132 Perugia, Italy; (A.M.S.); (A.P.); (R.M.); (M.R.)
- Department of Pharmaceutical Sciences, University of Perugia, 06126 Perugia, Italy
| | - Gabriele Di Sante
- Department of Medicine and Surgery, Section of Human, Clinical and Forensic Anatomy, University of Perugia, 60132 Perugia, Italy; (A.M.S.); (A.P.); (R.M.); (M.R.)
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Wang WJ, Chu LX, He LY, Zhang MJ, Dang KT, Gao C, Ge QY, Wang ZG, Zhao XW. Spatial transcriptomics: recent developments and insights in respiratory research. Mil Med Res 2023; 10:38. [PMID: 37592342 PMCID: PMC10433685 DOI: 10.1186/s40779-023-00471-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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/28/2023] [Accepted: 07/24/2023] [Indexed: 08/19/2023] Open
Abstract
The respiratory system's complex cellular heterogeneity presents unique challenges to researchers in this field. Although bulk RNA sequencing and single-cell RNA sequencing (scRNA-seq) have provided insights into cell types and heterogeneity in the respiratory system, the relevant specific spatial localization and cellular interactions have not been clearly elucidated. Spatial transcriptomics (ST) has filled this gap and has been widely used in respiratory studies. This review focuses on the latest iterative technology of ST in recent years, summarizing how ST can be applied to the physiological and pathological processes of the respiratory system, with emphasis on the lungs. Finally, the current challenges and potential development directions are proposed, including high-throughput full-length transcriptome, integration of multi-omics, temporal and spatial omics, bioinformatics analysis, etc. These viewpoints are expected to advance the study of systematic mechanisms, including respiratory studies.
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Affiliation(s)
- Wen-Jia Wang
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing, 210096, China
| | - Liu-Xi Chu
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing, 210096, China
- Oujiang Laboratory (Zhejiang Lab for Regenerative Medicine, Vision and Brain Health), School of Pharmaceutical Sciences, Wenzhou Medical University, Wenzhou, 325035, Zhejiang, China
| | - Li-Yong He
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing, 210096, China
| | - Ming-Jing Zhang
- Orthopaedic Bioengineering Research Group, Division of Surgery and Interventional Science, University College London, London, HA7 4LP, UK
| | - Kai-Tong Dang
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing, 210096, China
| | - Chen Gao
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing, 210096, China
| | - Qin-Yu Ge
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing, 210096, China
| | - Zhou-Guang Wang
- Oujiang Laboratory (Zhejiang Lab for Regenerative Medicine, Vision and Brain Health), School of Pharmaceutical Sciences, Wenzhou Medical University, Wenzhou, 325035, Zhejiang, China.
| | - Xiang-Wei Zhao
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing, 210096, China.
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Dudchenko O, Ordovas-Montanes J, Bingle CD. Respiratory epithelial cell types, states and fates in the era of single-cell RNA-sequencing. Biochem J 2023; 480:921-939. [PMID: 37410389 PMCID: PMC10422933 DOI: 10.1042/bcj20220572] [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: 11/19/2022] [Revised: 06/19/2023] [Accepted: 06/20/2023] [Indexed: 07/07/2023]
Abstract
Standalone and consortia-led single-cell atlases of healthy and diseased human airways generated with single-cell RNA-sequencing (scRNA-seq) have ushered in a new era in respiratory research. Numerous discoveries, including the pulmonary ionocyte, potentially novel cell fates, and a diversity of cell states among common and rare epithelial cell types have highlighted the extent of cellular heterogeneity and plasticity in the respiratory tract. scRNA-seq has also played a pivotal role in our understanding of host-virus interactions in coronavirus disease 2019 (COVID-19). However, as our ability to generate large quantities of scRNA-seq data increases, along with a growing number of scRNA-seq protocols and data analysis methods, new challenges related to the contextualisation and downstream applications of insights are arising. Here, we review the fundamental concept of cellular identity from the perspective of single-cell transcriptomics in the respiratory context, drawing attention to the need to generate reference annotations and to standardise the terminology used in literature. Findings about airway epithelial cell types, states and fates obtained from scRNA-seq experiments are compared and contrasted with information accumulated through the use of conventional methods. This review attempts to discuss major opportunities and to outline some of the key limitations of the modern-day scRNA-seq that need to be addressed to enable efficient and meaningful integration of scRNA-seq data from different platforms and studies, with each other as well as with data from other high-throughput sequencing-based genomic, transcriptomic and epigenetic analyses.
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Affiliation(s)
- Oleksandr Dudchenko
- Department of Infection, Immunity and Cardiovascular Disease, The Medical School, University of Sheffield, Sheffield, South Yorkshire, U.K
| | - Jose Ordovas-Montanes
- Division of Gastroenterology, Hepatology and Nutrition, Boston Children's Hospital, Boston, MA, U.S.A
- Programme in Immunology, Harvard Medical School, Boston, MA, U.S.A
| | - Colin D. Bingle
- Department of Infection, Immunity and Cardiovascular Disease, The Medical School, University of Sheffield, Sheffield, South Yorkshire, U.K
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Kermani NZ, Adcock IM, Djukanović R, Chung F, Schofield JPR. Systems Biology in Asthma. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2023; 1426:215-235. [PMID: 37464123 DOI: 10.1007/978-3-031-32259-4_10] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/20/2023]
Abstract
The application of mathematical and computational analysis, together with the modelling of biological and physiological processes, is transforming our understanding of the pathophysiology of complex diseases. This systems biology approach incorporates large amounts of genomic, transcriptomic, proteomic, metabolomic, breathomic, metagenomic and imaging data from disease sites together with deep clinical phenotyping, including patient-reported outcomes. Integration of these datasets will provide a greater understanding of the molecular pathways associated with severe asthma in each individual patient and determine their personalised treatment regime. This chapter describes some of the data integration methods used to combine data sets and gives examples of the results obtained using single datasets and merging of multiple datasets (data fusion and data combination) from several consortia including the severe asthma research programme (SARP) and the Unbiased Biomarkers Predictive of Respiratory Disease Outcomes (U-BIOPRED) consortia. These results highlight the involvement of several different immune and inflammatory pathways and factors in distinct subsets of patients with severe asthma. These pathways often overlap in patients with distinct clinical features of asthma, which may explain the incomplete or no response in patients undergoing specific targeted therapy. Collaboration between groups will improve the predictions obtained using a systems medicine approach in severe asthma.
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Affiliation(s)
- Nazanin Zounemat Kermani
- Data Science Institute, Imperial College London, London, UK
- National Heart & Lung Institute, Imperial College London, London, UK
| | - Ian M Adcock
- National Heart & Lung Institute, Imperial College London, London, UK
| | - Ratko Djukanović
- NIHR Southampton Biomedical Research Centre, Clinical and Experimental Sciences, Faculty of Medicine, University of Southampton, Southampton, UK.
| | - Fan Chung
- National Heart & Lung Institute, Imperial College London, London, UK
- Biomedical Research Unit, Royal Brompton & Harefield NHS Trust, London, UK
| | - James P R Schofield
- Centre for Proteomic Research, Institute for Life Sciences, University of Southampton, Southampton, UK
- TopMD Precision Medicine Ltd, Southampton, UK
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Role of Respiratory Epithelial Cells in Allergic Diseases. Cells 2022; 11:cells11091387. [PMID: 35563693 PMCID: PMC9105716 DOI: 10.3390/cells11091387] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2022] [Revised: 04/11/2022] [Accepted: 04/19/2022] [Indexed: 02/07/2023] Open
Abstract
The airway epithelium provides the first line of defense to the surrounding environment. However, dysfunctions of this physical barrier are frequently observed in allergic diseases, which are tightly connected with pro- or anti-inflammatory processes. When the epithelial cells are confronted with allergens or pathogens, specific response mechanisms are set in motion, which in homeostasis, lead to the elimination of the invaders and leave permanent traces on the respiratory epithelium. However, allergens can also cause damage in the sensitized organism, which can be ascribed to the excessive immune reactions. The tight interaction of epithelial cells of the upper and lower airways with local and systemic immune cells can leave an imprint that may mirror the pathophysiology. The interaction with effector T cells, along with the macrophages, play an important role in this response, as reflected in the gene expression profiles (transcriptomes) of the epithelial cells, as well as in the secretory pattern (secretomes). Further, the storage of information from past exposures as memories within discrete cell types may allow a tissue to inform and fundamentally alter its future responses. Recently, several lines of evidence have highlighted the contributions from myeloid cells, lymphoid cells, stromal cells, mast cells, and epithelial cells to the emerging concepts of inflammatory memory and trained immunity.
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