Application of Single-Cell Genomics in Cardiovascular Research

Cardiology and Therapy - Tập 12 - Trang 101-125 - 2023
Xuejing Yu1, Xianggui Yang2, Jinjin Cao3
1Department of Internal Medicine, Division of Cardiology, University of Texas Southwestern Medical Center, Dallas, USA
2Department of Laboratory Medicine, Clinical Medical College and the First Affiliated Hospital of Chengdu Medical College, Chengdu, People’s Republic of China
3Department of Radiology, Division of Abdominal Imaging, Massachusetts General Hospital, Boston, USA

Tóm tắt

Cardiovascular diseases (CVDs) are the leading cause of death in the global world. The emergence of single-cell technologies has greatly facilitated the research on CVDs. Currently, those single-cell technologies have been widely applied in atherosclerosis, myocardial infarction, cardiac ischemia–reperfusion injury, arrhythmia, hypertrophy cardiomyopathy, and heart failure, which are extremely helpful in elucidating the underlying mechanisms of CVDs from physiological and pathological perspectives at DNA, RNA, protein, post-transcriptional, post-translational, and metabolite levels. In this review, we would like to briefly introduce the current single-cell technologies, and will focus on the utilization of single-cell genomics in various heart diseases. Single-cell technologies have great potential in exploration of CVDs, and widespread application of single-cell genomics will promote the understanding and therapeutic treatments for CVDs.

Tài liệu tham khảo

Cardiovascular Disease Statistics. AHA. 2008. WHO Cardiovascular Diseases. 2007. Davis N. What is single cell genomics? December 16, 2015 Updated June 23, 2021. Simeon M, Dangwal S, Sachinidis A, Doss MX. Application of the pluripotent stem cells and genomics in cardiovascular research-what we have learnt and not learnt until now. Cells. 2021;10. Williams JW, Winkels H, Durant CP, Zaitsev K, Ghosheh Y, Ley K. Single cell RNA sequencing in atherosclerosis research. Circ Res. 2020;126:1112–26. Yusuke YASC, Takahiro O. Chapter 22, Single Cell Genomics. HANDBOOK OF SINGLE-CELL TECHNOLOGIES. 2021:521–538. Ingela Lanekoff VVS, Cátia Ma. Single-cell metabolomics: where are we and where are we going? Curr Opin Biotechnol. 2022;75. Li G, Tian L, Goodyer W, Kort EJ, Buikema JW, Xu A, Wu JC, Jovinge S and Wu SM. Single cell expression analysis reveals anatomical and cell cycle-dependent transcriptional shifts during heart development. Development. 2019;146. Cui Y, Zheng Y, Liu X, Yan L, Fan X, Yong J, Hu Y, Dong J, Li Q, Wu X, Gao S, Li J, Wen L, Qiao J, Tang F. Single-cell transcriptome analysis maps the developmental track of the human heart. Cell Rep. 2019;26(1934–1950): e5. DeLaughter DM, Bick AG, Wakimoto H, McKean D, Gorham JM, Kathiriya IS, Hinson JT, Homsy J, Gray J, Pu W, Bruneau BG, Seidman JG, Seidman CE. Single-cell resolution of temporal gene expression during heart development. Dev Cell. 2016;39:480–90. Tombor LS, John D, Glaser SF, Luxan G, Forte E, Furtado M, Rosenthal N, Baumgarten N, Schulz MH, Wittig J, Rogg EM, Manavski Y, Fischer A, Muhly-Reinholz M, Klee K, Looso M, Selignow C, Acker T, Bibli SI, Fleming I, Patrick R, Harvey RP, Abplanalp WT, Dimmeler S. Single cell sequencing reveals endothelial plasticity with transient mesenchymal activation after myocardial infarction. Nat Commun. 2021;12:681. Ruiz-Villalba A, Romero JP, Hernandez SC, Vilas-Zornoza A, Fortelny N, Castro-Labrador L, San Martin-Uriz P, Lorenzo-Vivas E, Garcia-Olloqui P, Palacio M, Gavira JJ, Bastarrika G, Janssens S, Wu M, Iglesias E, Abizanda G, de Morentin XM, Lasaga M, Planell N, Bock C, Alignani D, Medal G, Prudovsky I, Jin YR, Ryzhov S, Yin H, Pelacho B, Gomez-Cabrero D, Lindner V, Lara-Astiaso D, Prosper F. Single-cell RNA sequencing analysis reveals a crucial role for CTHRC1 (Collagen Triple Helix Repeat Containing 1) cardiac fibroblasts after myocardial infarction. Circulation. 2020;142:1831–47. Wang N, Wang W, Wang X, Mang G, Chen J, Yan X, Tong Z, Yang Q, Wang M, Chen L, Sun P, Yang Y, Cui J, Yang M, Zhang Y, Wang D, Wu J, Zhang M, Yu B. Histone lactylation boosts reparative gene activation post-myocardial infarction. Circ Res. 2022;131:893–908. Thankam FG, Agrawal DK. Single cell genomics identifies unique cardioprotective phenotype of stem cells derived from epicardial adipose tissue under ischemia. Stem Cell Rev Rep. 2022;18:294–335. Gladka MM, Molenaar B, de Ruiter H, van der Elst S, Tsui H, Versteeg D, Lacraz GPA, Huibers MMH, van Oudenaarden A, van Rooij E. Single-cell sequencing of the healthy and diseased heart reveals cytoskeleton-associated protein 4 as a new modulator of fibroblasts activation. Circulation. 2018;138:166–80. Molenaar B, Timmer LT, Droog M, Perini I, Versteeg D, Kooijman L, Monshouwer-Kloots J, de Ruiter H, Gladka MM, van Rooij E. Single-cell transcriptomics following ischemic injury identifies a role for B2M in cardiac repair. Commun Biol. 2021;4:146. Willemsen L, de Winther MP. Macrophage subsets in atherosclerosis as defined by single-cell technologies. J Pathol. 2020;250:705–14. Kim K, Shim D, Lee JS, Zaitsev K, Williams JW, Kim KW, Jang MY, Seok Jang H, Yun TJ, Lee SH, Yoon WK, Prat A, Seidah NG, Choi J, Lee SP, Yoon SH, Nam JW, Seong JK, Oh GT, Randolph GJ, Artyomov MN, Cheong C, Choi JH. Transcriptome analysis reveals nonfoamy rather than foamy plaque macrophages are proinflammatory in atherosclerotic murine models. Circ Res. 2018;123:1127–42. Beckers CML, Simpson KR, Griffin KJ, Brown JM, Cheah LT, Smith KA, Vacher J, Cordell PA, Kearney MT, Grant PJ, Pease RJ. Cre/lox studies identify resident macrophages as the major source of circulating coagulation factor XIII-A. Arterioscler Thromb Vasc Biol. 2017;37:1494–502. Winkels H, Ehinger E, Vassallo M, Buscher K, Dinh HQ, Kobiyama K, Hamers AAJ, Cochain C, Vafadarnejad E, Saliba AE, Zernecke A, Pramod AB, Ghosh AK, Anto Michel N, Hoppe N, Hilgendorf I, Zirlik A, Hedrick CC, Ley K, Wolf D. Atlas of the immune cell repertoire in mouse atherosclerosis defined by single-cell RNA-sequencing and mass cytometry. Circ Res. 2018;122:1675–88. Albrecht C, Preusch MR, Hofmann G, Morris-Rosenfeld S, Blessing E, Rosenfeld ME, Katus HA, Bea F. Egr-1 deficiency in bone marrow-derived cells reduces atherosclerotic lesion formation in a hyperlipidaemic mouse model. Cardiovasc Res. 2010;86:321–9. Pan H, Xue C, Auerbach BJ, Fan J, Bashore AC, Cui J, Yang DY, Trignano SB, Liu W, Shi J, Ihuegbu CO, Bush EC, Worley J, Vlahos L, Laise P, Solomon RA, Connolly ES, Califano A, Sims PA, Zhang H, Li M, Reilly MP. Single-cell genomics reveals a novel cell state during smooth muscle cell phenotypic switching and potential therapeutic targets for atherosclerosis in mouse and human. Circulation. 2020;142:2060–75. Winkels H, Ehinger E, Ghosheh Y, Wolf D, Ley K. Atherosclerosis in the single-cell era. Curr Opin Lipidol. 2018;29:389–96. Alan SKL, Michael W, Linsin S, Chenwei T, Heather E, Ivan M, Anindita B, Xin H, Sebastian P. Single-cell genomics improves the discovery of risk variants and genes of cardiac traits. medRxiv. 2022. Martijn WAEdL, Maya WC, Joep ECE, Cornelis JB, Bas M, Petra H van der Kraak, Diederik W D Kuster, Jolanda van der Velden, Michelle Michels, Aryan Vink, Eva van Rooij. Single-cell transcriptomics provides insights into hypertrophic cardiomyopathy. Cell Rep. 2022;39. Chaffin M, Papangeli I, Simonson B, Akkad AD, Hill MC, Arduini A, Fleming SJ, Melanson M, Hayat S, Kost-Alimova M, Atwa O, Ye J, Bedi KC Jr, Nahrendorf M, Kaushik VK, Stegmann CM, Margulies KB, Tucker NR, Ellinor PT. Single-nucleus profiling of human dilated and hypertrophic cardiomyopathy. Nature. 2022;608:174–80. Andrew LKIS, Junedh A, Prabhakar SA, Konstantin Z, Lulu L, Geetika B, Andrea B, Gabriella S, Cameran J, Emily T, Stacey LR, Maxim NA, Kory JL. Single-cell transcriptomics reveals cell-type specific diversification in human heart failure. Nat Cardiovasc Res. 2022;1:263–80. Wang L, Yu P, Zhou B, Song J, Li Z, Zhang M, Guo G, Wang Y, Chen X, Han L, Hu S. Single-cell reconstruction of the adult human heart during heart failure and recovery reveals the cellular landscape underlying cardiac function. Nat Cell Biol. 2020;22:108–19. Reichart D, Lindberg EL, Maatz H, Miranda AMA, Viveiros A, Shvetsov N, Gartner A, Nadelmann ER, Lee M, Kanemaru K, Ruiz-Orera J, Strohmenger V, DeLaughter DM, Patone G, Zhang H, Woehler A, Lippert C, Kim Y, Adami E, Gorham JM, Barnett SN, Brown K, Buchan RJ, Chowdhury RA, Constantinou C, Cranley J, Felkin LE, Fox H, Ghauri A, Gummert J, Kanda M, Li R, Mach L, McDonough B, Samari S, Shahriaran F, Yapp C, Stanasiuk C, Theotokis PI, Theis FJ, van den Bogaerdt A, Wakimoto H, Ware JS, Worth CL, Barton PJR, Lee YA, Teichmann SA, Milting H, Noseda M, Oudit GY, Heinig M, Seidman JG, Hubner N, Seidman CE. Pathogenic variants damage cell composition and single cell transcription in cardiomyopathies. Science. 2022;377:1984. Linnarsson S, Teichmann SA. Single-cell genomics: coming of age. Genome Biol. 2016;17:97. Gawad C, Koh W, Quake SR. Single-cell genome sequencing: current state of the science. Nat Rev Genet. 2016;17:175–88.