Molecular and cellular changes during development of cardiac fibrosis in cardiomyopathy
Final Report Abstract
Single cell RNA sequencing (scRNAseq) has helped to gain deeper insights into the cellular compositions of organs by specific cell type and cell state (cell sub-types) characterization. Single nuclei RNA sequencing (snRNAseq) demonstrates several advantages over scRNAseq: frozen tissues can be used for nuclei isolation, snRNAseq is more robust in terms of technical artefacts and – most importantly - snRNAseq allows to analyze cardiomyocytes since the average nuclei diameter of 7-12µm makes them suitable for droplet-based single cells/nuclei machines. During my stay in the lab of Christine and Jonathan Seidman, snRNAseq was used to re-map the healthy human heart cell-by-cell. Approximately 500K nuclei and cells were isolated from transmural heart biopsies of 14 healthy donor hearts (7 female, 7 male) for snRNAseq and scRNAseq. Six regions covering left and right ventricular free wall, septum, apex, left and right atrium were included and helped to identify gene expression patterns of 11 major cell types and 65 cell states. These results highlight the heterogeneity of cardiomyocytes, fibroblasts, and others cell types in terms of their regional distribution, distinct gene expressions and functional states. To confirm specific findings and investigate gene expression patterns across the tissues, multiplex fluorescent RNA in-situ hybridizations were performed. This atlas at single cell level of the healthy human heart lays the ground for additional studies involving diseased tissues or perturbation models and will further add to the knowledge of pathologic molecular mechanisms.
Publications
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Cells of the adult human heart. Nature. 2020 Dec;588(7838):466-472
Litviňuková M, Talavera-López C, Maatz H, Reichart D, Worth CL, Lindberg EL, Kanda M, Polanski K, Heinig M, Lee M, Nadelmann ER, Roberts K, Tuck L, Fasouli ES, DeLaughter DM, McDonough B, Wakimoto H, Gorham JM, Samari S, Mahbubani KT, Saeb-Parsy K, Patone G, Boyle JJ, Zhang H, Zhang H, Viveiros A, Oudit GY, Bayraktar OA, Seidman JG, Seidman CE, Noseda M, Hubner N, Teichmann SA
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SARS-CoV-2 entry factors are highly expressed in nasal epithelial cells together with innate immune genes. Nat Med. 2020 May;26(5):681-687
Sungnak W, Huang N, Bécavin C, Berg M, Queen R, Litvinukova M, Talavera-López C, Maatz H, Reichart D, Sampaziotis F, Worlock KB, Yoshida M, Barnes JL; HCA Lung Biological Network
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Isolation of Nuclei from Mammalian Cells and Tissues for Single-Nucleus Molecular Profiling. Curr Protoc. 2021 May;1(5):e132
Nadelmann ER, Gorham JM, Reichart D, Delaughter DM, Wakimoto H, Lindberg EL, Litviňukova M, Maatz H, Curran JJ, Ischiu Gutierrez D, Hübner N, Seidman CE, Seidman JG
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Single-cell meta-analysis of SARS-CoV-2 entry genes across tissues and demographics. Nature medicine 27 (3), 546-559
Christoph Muus, ..., Daniel Reichart, ..., Carly GK Ziegler
