Current and future perspectives of single-cell multi-omics technologies in cardiovascular research

被引：3

作者：

Tan, Wilson Lek Wen ^{[1
]}

Seow, Wei Qiang ^{[1
]}

Zhang, Angela ^{[1
,2
]}

Rhee, Siyeon ^{[1
,2
]}

Wong, Wing H. ^{[3
,4
]}

Greenleaf, William J. ^{[5
]}

Wu, Joseph C. ^{[1
,2
,6
]}

机构：

[1] Stanford Cardiovasc Inst, Stanford, CA 94305 USA

[2] Greenstone Biosci, Palo Alto, CA 94304 USA

[3] Stanford Univ, Sch Med, Dept Stat, Stanford, CA USA

[4] Stanford Univ, Sch Med, Dept Biomed Data Sci, Stanford, CA USA

[5] Stanford Univ, Sch Med, Dept Genet, Stanford, CA USA

[6] Stanford Univ, Sch Med, Dept Med, Div Cardiovasc Med, Stanford, CA 94305 USA

来源：

NATURE CARDIOVASCULAR RESEARCH | 2023年 / 2卷 / 01期

基金：

美国国家卫生研究院;

关键词：

TRANSCRIPTOME ANALYSIS; GENE-EXPRESSION; RNA-SEQ; CHROMATIN ACCESSIBILITY; HUMAN HEART; REVEALS; PROTEINS; HETEROGENEITY; THOUSANDS; PLATFORM;

D O I：

10.1038/s44161-022-00205-7

中图分类号：

R5 [内科学];

学科分类号：

1002 ; 100201 ;

摘要：

Single-cell technology has become an indispensable tool in cardiovascular research since its first introduction in 2009. Here, we highlight the recent remarkable progress in using single-cell technology to study transcriptomic and epigenetic heterogeneity in cardiac disease and development. We then introduce the key concepts in single-cell multi-omics modalities that apply to cardiovascular research. Lastly, we discuss some of the trending concepts in single-cell technology that are expected to propel cardiovascular research to the next phase of single-cell research. Wen Tan et al. review the current technologies available for single-cell transcriptomics, epigenomics and multi-omics analyses, their impact on the cardiovascular research and possible future applications.

引用

页码：20 / 34

页数：15

共 118 条

[31] Microanatomy of the Human Atherosclerotic Plaque by Single-Cell Transcriptomics [J].

Depuydt, Marie A. C. ;

Prange, Koen H. M. ;

Slenders, Lotte ;

Ord, Tiit ;

Elbersen, Danny ;

Boltjes, Arjan ;

de Jager, Saskia C. A. ;

Asselbergs, Folkert W. ;

de Borst, Gert J. ;

Aavik, Einari ;

Lonnberg, Tapio ;

Lutgens, Esther ;

Glass, Christopher K. ;

den Ruijter, Hester M. ;

Kaikkonen, Minna U. ;

Bot, Ilze ;

Slutter, Bram ;

van der Laan, Sander W. ;

Yla-Herttuala, Seppo ;

Mokry, Michal ;

Kuiper, Johan ;

de Winther, Menno P. J. ;

Pasterkamp, Gerard .

CIRCULATION RESEARCH, 2020, 127 (11) :1437-1455

[32] Interpretable dimensionality reduction of single cell transcriptome data with deep generative models [J].

Ding, Jiarui ;

Condon, Anne ;

Shah, Sohrab P. .

NATURE COMMUNICATIONS, 2018, 9

[33] Perturb-Seq: Dissecting Molecular Circuits with Scalable Single-Cell RNA Profiling of Pooled Genetic Screens [J].

Dixit, Atray ;

Pamas, Oren ;

Li, Biyu ;

Chen, Jenny ;

Fulco, Charles P. ;

Jerby-Amon, Livnat ;

Marjanovic, Nemanja D. ;

Dionne, Danielle ;

Burks, Tyler ;

Raychowdhury, Raktima ;

Adamson, Britt ;

Norman, Thomas M. ;

Lander, Eric S. ;

Weissman, Jonathan S. ;

Friedman, Nir ;

Regev, Aviv .

CELL, 2016, 167 (07) :1853-+

[34] A human cell atlas of fetal chromatin accessibility [J].

Domcke, Silvia ;

Hill, Andrew J. ;

Daza, Riza M. ;

Cao, Junyue ;

O'Day, Diana R. ;

Pliner, Hannah A. ;

Aldinger, Kimberly A. ;

Pokholok, Dmitry ;

Zhang, Fan ;

Milbank, Jennifer H. ;

Zager, Michael A. ;

Glass, Ian A. ;

Steemers, Frank J. ;

Doherty, Dan ;

Trapnell, Cole ;

Cusanovich, Darren A. ;

Shendure, Jay .

SCIENCE, 2020, 370 (6518) :809-+

[35] A Review of the Autoencoder and Its Variants A comparative perspective from target recognition in synthetic-aperture radar images [J].

Dong, Ganggang ;

Liao, Guisheng ;

Liu, Hongwei ;

Kuang, Gangyao .

IEEE GEOSCIENCE AND REMOTE SENSING MAGAZINE, 2018, 6 (03) :44-68

[36] CellPhoneDB: inferring cell-cell communication from combined expression of multi-subunit ligand-receptor complexes [J].

Efremova, Mirjana ;

Vento-Tormo, Miquel ;

Teichmann, Sarah A. ;

Vento-Tormo, Roser .

NATURE PROTOCOLS, 2020, 15 (04) :1484-1506

[37] Single-cell sequencing reveals lineage-specific dynamic genetic regulation of gene expression during human cardiomyocyte differentiation [J].

Elorbany, Reem ;

Popp, Joshua M. ;

Rhodes, Katherine ;

Strober, Benjamin J. ;

Barr, Kenneth ;

Qi, Guanghao ;

Gilad, Yoav ;

Battle, Alexis .

PLOS GENETICS, 2022, 18 (01)

[38] Improving target assessment in biomedical research: the GOT-IT recommendations [J].

Emmerich, Christoph H. ;

Gamboa, Lorena Martinez ;

Hofmann, Martine C. J. ;

Bonin-Andresen, Marc ;

Arbach, Olga ;

Schendel, Pascal ;

Gerlach, Bjoern ;

Hempel, Katja ;

Bespalov, Anton ;

Dirnagl, Ulrich ;

Parnham, Michael J. .

NATURE REVIEWS DRUG DISCOVERY, 2021, 20 (01) :64-81

[39] Transcriptome-scale super-resolved imaging in tissues by RNA seqFISH [J].

Eng, Chee-Huat Linus ;

Lawson, Michael ;

Zhu, Qian ;

Dries, Ruben ;

Koulena, Noushin ;

Takei, Yodai ;

Yun, Jina ;

Cronin, Christopher ;

Karp, Christoph ;

Yuan, Guo-Cheng ;

Cai, Long .

NATURE, 2019, 568 (7751) :235-+

[40] Single-cell RNA-seq denoising using a deep count autoencoder [J].

Eraslan, Goekcen ;

Simon, Lukas M. ;

Mircea, Maria ;

Mueller, Nikola S. ;

Theis, Fabian J. .

NATURE COMMUNICATIONS, 2019, 10 (1)

← 1 2 3 4 5 6 7 8 9 10 →