Neural cell diversity in the light of single-cell transcriptomics

被引：3

作者：

Fernandez-Moya, Sandra Maria ^{[1
,2
,4
]}

Ganesh, Akshay Jaya ^{[1
,2
]}

Plass, Mireya ^{[1
,2
,3
,4
]}

机构：

[1] Bellvitge Inst Biomed Res IDIBELL, Regenerat Med Program, Gene Regulat Cell Ident, Barcelona, Spain

[2] Program Adv Clin Translat Regenerat Med Catalonia, Barcelona, Spain

[3] Ctr Networked Biomed Res Bioengn Biomat & Nanomed, Madrid, Spain

[4] Bellvitge Inst Biomed Res IDIBELL, Regenerat Med Program, Gene Regulat Cell Ident, Barcelona 08908, Spain

来源：

TRANSCRIPTION-AUSTIN | 2023年 / 14卷 / 3-5期

关键词：

Cell diversity; single-cell transcriptomics; neural cells; brain; gene regulatory networks; RNA-SEQ; CHROMATIN; ATLAS; NEURONS; PROTEINS; SUBTYPES; DORSAL; MOUSE;

D O I：

10.1080/21541264.2023.2295044

中图分类号：

Q5 [生物化学]; Q7 [分子生物学];

学科分类号：

071010 ; 081704 ;

摘要：

The development of highly parallel and affordable high-throughput single-cell transcriptomics technologies has revolutionized our understanding of brain complexity. These methods have been used to build cellular maps of the brain, its different regions, and catalog the diversity of cells in each of them during development, aging and even in disease. Now we know that cellular diversity is way beyond what was previously thought. Single-cell transcriptomics analyses have revealed that cell types previously considered homogeneous based on imaging techniques differ depending on several factors including sex, age and location within the brain. The expression profiles of these cells have also been exploited to understand which are the regulatory programs behind cellular diversity and decipher the transcriptional pathways driving them. In this review, we summarize how single-cell transcriptomics have changed our view on the cellular diversity in the human brain, and how it could impact the way we study neurodegenerative diseases. Moreover, we describe the new computational approaches that can be used to study cellular differentiation and gain insight into the functions of individual cell populations under different conditions and their alterations in disease.

引用

页码：158 / 176

页数：19

共 143 条

[1]

Aibar S, 2017, NAT METHODS, V14, P1083, DOI [10.1038/NMETH.4463, 10.1038/nmeth.4463]

[2] Astrocyte Regulation of Synaptic Behavior [J].

Allen, Nicola J. .

ANNUAL REVIEW OF CELL AND DEVELOPMENTAL BIOLOGY, VOL 30, 2014, 30 :439-463

[3] Resolving cellular and molecular diversity along the hippocampal anterior-to-posterior axis in humans [J].

Ayhan, Fatma ;

Kulkarni, Ashwinikumar ;

Berto, Stefano ;

Sivaprakasam, Karthigayini ;

Douglas, Connor ;

Lega, Bradley C. ;

Konopka, Genevieve .

NEURON, 2021, 109 (13) :2091-+

[4] Comparative cellular analysis of motor cortex in human, marmoset and mouse [J].

Bakken, Trygve E. ;

Jorstad, Nikolas L. ;

Hu, Qiwen ;

Lake, Blue B. ;

Tian, Wei ;

Kalmbach, Brian E. ;

Crow, Megan ;

Hodge, Rebecca D. ;

Krienen, Fenna M. ;

Sorensen, Staci A. ;

Eggermont, Jeroen ;

Yao, Zizhen ;

Aevermann, Brian D. ;

Aldridge, Andrew I. ;

Bartlett, Anna ;

Bertagnolli, Darren ;

Casper, Tamara ;

Castanon, Rosa G. ;

Crichton, Kirsten ;

Daigle, Tanya L. ;

Dalley, Rachel ;

Dee, Nick ;

Dembrow, Nikolai ;

Diep, Dinh ;

Ding, Song-Lin ;

Dong, Weixiu ;

Fang, Rongxin ;

Fischer, Stephan ;

Goldman, Melissa ;

Goldy, Jeff ;

Graybuck, Lucas T. ;

Herb, Brian R. ;

Hou, Xiaomeng ;

Kancherla, Jayaram ;

Kroll, Matthew ;

Lathia, Kanan ;

van Lew, Baldur ;

Li, Yang Eric ;

Liu, Christine S. ;

Liu, Hanqing ;

Lucero, Jacinta D. ;

Mahurkar, Anup ;

McMillen, Delissa ;

Miller, Jeremy A. ;

Moussa, Marmar ;

Nery, Joseph R. ;

Nicovich, Philip R. ;

Niu, Sheng-Yong ;

Orvis, Joshua ;

Osteen, Julia K. .

NATURE, 2021, 598 (7879) :111-+

[5] Single-nucleus and single-cell transcriptomes compared in matched cortical cell types [J].

Bakken, Trygve E. ;

Hodge, Rebecca D. ;

Miller, Jeremy A. ;

Yao, Zizhen ;

Thuc Nghi Nguyen ;

Aevermann, Brian ;

Barkan, Eliza ;

Bertagnolli, Darren ;

Casper, Tamara ;

Dee, Nick ;

Garren, Emma ;

Goldy, Jeff ;

Graybuck, Lucas T. ;

Kroll, Matthew ;

Lasken, Roger S. ;

Lathia, Kanan ;

Parry, Sheana ;

Rimorin, Christine ;

Scheuermann, Richard H. ;

Schork, Nicholas J. ;

Shehata, Soraya I. ;

Tieu, Michael ;

Phillips, John W. ;

Bernard, Amy ;

Smith, Kimberly A. ;

Zeng, Hongkui ;

Lein, Ed S. ;

Tasic, Bosiljka .

PLOS ONE, 2018, 13 (12)

[6] Single-Cell Trajectory Detection Uncovers Progression and Regulatory Coordination in Human B Cell Development [J].

Bendall, Sean C. ;

Davis, Kara L. ;

Amir, El-ad David ;

Tadmor, Michelle D. ;

Simonds, Erin F. ;

Chen, Tiffany J. ;

Shenfeld, Daniel K. ;

Nolan, Garry P. ;

Pe'er, Dana .

CELL, 2014, 157 (03) :714-725

[7] Generalizing RNA velocity to transient cell states through dynamical modeling [J].

Bergen, Volker ;

Lange, Marius ;

Peidli, Stefan ;

Wolf, F. Alexander ;

Theis, Fabian J. .

NATURE BIOTECHNOLOGY, 2020, 38 (12) :1408-1414

[8] Transcriptomic and morphophysiological evidence for a specialized human cortical GABAergic cell type [J].

Boldog, Eszter ;

Bakken, Trygve E. ;

Hodge, Rebecca D. ;

Novotny, Mark ;

Aevermann, Brian D. ;

Baka, Judith ;

Borde, Sandor ;

Close, Jennie L. ;

Diez-Fuertes, Francisco ;

Ding, Song-Lin ;

Farago, Nora ;

Kocsis, Agnes K. ;

Kovacs, Balazs ;

Maltzer, Zoe ;

McCorrison, Jamison M. ;

Miller, Jeremy A. ;

Molnar, Gabor ;

Olah, Gaspar ;

Ozsvar, Attila ;

Rozsa, Marton ;

Shehata, Soraya I. ;

Smith, Kimberly A. ;

Sunkin, Susan M. ;

Tran, Danny N. ;

Venepally, Pratap ;

Wall, Abby ;

Puskas, Laszlo G. ;

Barzo, Pal ;

Steemers, Frank J. ;

Schork, Nicholas J. ;

Scheuermann, Richard H. ;

Lasken, Roger S. ;

Lein, Ed S. ;

Tamas, Gabor .

NATURE NEUROSCIENCE, 2018, 21 (09) :1185-+

[9] SCENIC plus : single-cell multiomic inference of enhancers and gene regulatory networks [J].

Gonzalez-Blas, Carmen Bravo ;

De Winter, Seppe ;

Hulselmans, Gert ;

Hecker, Nikolai ;

Matetovici, Irina ;

Christiaens, Valerie ;

Poovathingal, Suresh ;

Wouters, Jasper ;

Aibar, Sara ;

Aerts, Stein .

NATURE METHODS, 2023, 20 (09) :1355-+

[10]

Buenrostro Jason D, 2015, Curr Protoc Mol Biol, V109, DOI 10.1002/0471142727.mb2129s109

← 1 2 3 4 5 6 7 8 9 10 →