Opportunities and challenges of single-cell and spatially resolved genomics methods for neuroscience discovery

被引：2

作者：

Bonev, Boyan ^{[1
,2
]}

Goncalo, Castelo-Branco ^{[3
]}

Chen, Fei ^{[4
]}

Codeluppi, Simone ^{[5
]}

Corces, M. Ryan ^{[6
,7
,8
]}

Fan, Jean ^{[9
]}

Heiman, Myriam ^{[10
,11
]}

Harris, Kenneth ^{[12
]}

Inoue, Fumitaka ^{[13
]}

Kellis, Manolis ^{[4
,14
]}

Levine, Ariel ^{[15
]}

Lotfollahi, Mo ^{[16
,17
]}

Luo, Chongyuan ^{[18
]}

Maynard, Kristen R. ^{[19
,20
,21
]}

Nitzan, Mor ^{[22
,23
,24
]}

Ramani, Vijay ^{[7
,25
,26
]}

Satijia, Rahul ^{[27
,28
]}

Schirmer, Lucas ^{[29
]}

Shen, Yin ^{[8
,30
,31
]}

Sun, Na ^{[4
,14
]}

Green, Gilad S. ^{[32
]}

Theis, Fabian ^{[17
,18
]}

Wang, Xiao ^{[4
,33
,34
]}

Welch, Joshua D. ^{[35
]}

Gokce, Ozgun ^{[36
,37
]}

Konopka, Genevieve ^{[38
,39
]}

Liddelow, Shane ^{[40
,41
,42
,43
]}

Macosko, Evan ^{[4
,34
,44
,45
]}

Bayraktar, Omer ^{[46
]}

Habib, Naomi ^{[32
]}

Nowakowski, Tomasz J. ^{[31
,47
,48
,49
,50
]}

机构：

[1] Helmholtz Zent Munchen, Helmholtz Pioneer Campus, Neuherberg, Germany

[2] Ludwig Maximilians Univ Munchen, Biomed Ctr, Physiol Genom, Munich, Germany

[3] Karolinska Inst, Dept Med Biochem & Biophys, Lab Mol Neurobiol, Stockholm, Sweden

[4] Broad Inst MIT & Harvard, Cambridge, MA 02142 USA

[5] Moleculent, Stockholm, Sweden

[6] Gladstone Inst Neurol Dis, San Francisco, CA USA

[7] Gladstone Inst Data Sci & Biotechnol, San Francisco, CA USA

[8] Univ Calif San Francisco, Dept Neurol, San Francisco, CA USA

[9] Johns Hopkins Univ, Dept Biomed Engn, Baltimore, MD USA

[10] MIT, Dept Brain & Cognit Sci, Cambridge, MA USA

[11] MIT, Picower Inst Learning & Memory, Cambridge, MA USA

[12] UCL, UCL Queen Sq Inst Neurol, London, England

[13] Kyoto Univ, Inst Adv Study Human Biol WPI ASHBi, Kyoto, Japan

[14] MIT, Comp Sci & Artificial Intelligence Lab, Cambridge, MA USA

[15] NINDS, Spinal Circuits & Plast Unit, Bethesda, MD USA

[16] German Res Ctr Environm Hlth, Helmholtz Ctr Munich, Inst Computat Biol, Neuherberg, Germany

[17] Wellcome Genome Campus, Wellcome Sanger Inst, Cambridge, England

[18] Univ Calif Los Angeles, Dept Human Genet, Los Angeles, CA USA

[19] Lieber Inst Brain Dev, Baltimore, MD USA

[20] Johns Hopkins Sch Med, Dept Psychiat, Baltimore, MD USA

[21] Johns Hopkins Sch Med, Dept Neurosci, Baltimore, MD USA

[22] Hebrew Univ Jerusalem, Sch Comp Sci & Engn, Jerusalem, Israel

[23] Hebrew Univ Jerusalem, Racah Inst Phys, Jerusalem, Israel

[24] Hebrew Univ Jerusalem, Fac Med, Jerusalem, Israel

[25] Univ Calif San Francisco, Dept Biochem & Biophys, San Francisco, CA USA

[26] Bakar Computat Hlth Sci Inst, San Francisco, CA USA

[27] New York Genome Ctr, New York, NY USA

[28] NYU, Ctr Genom & Syst Biol, New York, NY USA

[29] Heidelberg Univ, Med Fac Mannheim, Mannheim Ctr Translat Neurosci, Dept Neurol, Mannheim, Germany

[30] Univ Calif San Francisco, Inst Human Genet, San Francisco, CA USA

[31] Univ Calif San Francisco, Weill Inst Neurosci, San Francisco, CA 94143 USA

[32] Hebrew Univ Jerusalem, Edmond & Lily Safra Ctr Brain Sci, Jerusalem, Israel

[33] MIT, Dept Chem, Cambridge, MA 02139 USA

[34] Broad Inst MIT & Harvard, Stanley Ctr Psychiat Res, Cambridge, MA 02142 USA

[35] Univ Michigan, Dept Computat Med & Bioinformat, Ann Arbor, MI USA

[36] German Ctr Neurodegenerat Dis DZNE, Bonn, Germany

[37] Univ Hosp Bonn, Dept Neurodegenerat Dis & Geriatr Psychiat, Bonn, Germany

[38] UT Southwestern Med Ctr, Dept Neurosci, Dallas, TX 75390 USA

[39] UT Southwestern Med Ctr, Peter ODonnell Jr Brain Inst, Dallas, TX 75390 USA

[40] NYU Grossman Sch Med, Neurosci Inst, New York, NY 10016 USA

[41] NYU Grossman Sch Med, Dept Neurosci & Physiol, New York, NY 10016 USA

[42] NYU Grossman Sch Med, Parekh Ctr Interdisciplinary Neurol, New York, NY 10016 USA

[43] NYU Grossman Sch Med, Dept Ophthalmol, New York, NY 10016 USA

[44] Harvard Med Sch, Dept Neurobiol, Boston, MA 02115 USA

[45] Massachusetts Gen Hosp, Dept Psychiat, Boston, MA 02114 USA

[46] Wellcome Sanger Inst, Hinxton, England

[47] Univ Calif San Francisco, Dept Neurol Surg, San Francisco, CA 94143 USA

[48] Univ Calif San Francisco, Dept Anat, San Francisco, CA 94143 USA

[49] Univ Calif San Francisco, Dept Psychiat & Behav Sci, San Francisco, CA 94143 USA

[50] Univ Calif San Francisco, Eli & Edythe Broad Ctr Regenerat Med & Stem Cell R, San Francisco, CA 94143 USA

来源：

NATURE NEUROSCIENCE | 2024年 / 27卷 / 12期

基金：

欧洲研究理事会; 以色列科学基金会; 美国国家卫生研究院; 瑞典研究理事会;

关键词：

REGULATORY NETWORK INFERENCE; CHROMATIN ACCESSIBILITY; GENE-EXPRESSION; MOUSE CORTEX; RNA-ANALYSIS; DYNAMICS; SEQ; TRANSCRIPTION; ORGANIZATION; METHYLATION;

D O I：

10.1038/s41593-024-01806-0

中图分类号：

Q189 [神经科学];

学科分类号：

071006 ;

摘要：

Over the past decade, single-cell genomics technologies have allowed scalable profiling of cell-type-specific features, which has substantially increased our ability to study cellular diversity and transcriptional programs in heterogeneous tissues. Yet our understanding of mechanisms of gene regulation or the rules that govern interactions between cell types is still limited. The advent of new computational pipelines and technologies, such as single-cell epigenomics and spatially resolved transcriptomics, has created opportunities to explore two new axes of biological variation: cell-intrinsic regulation of cell states and expression programs and interactions between cells. Here, we summarize the most promising and robust technologies in these areas, discuss their strengths and limitations and discuss key computational approaches for analysis of these complex datasets. We highlight how data sharing and integration, documentation, visualization and benchmarking of results contribute to transparency, reproducibility, collaboration and democratization in neuroscience, and discuss needs and opportunities for future technology development and analysis.

引用

页码：2292 / 2309

页数：18

共 192 条

[1] Nucleosome density shapes kilobase-scale regulation by a mammalian chromatin remodeler
Abdulhay, Nour J.
Hsieh, Laura J.
Mcnally, Colin P.
Ostrowski, Megan S.
Moore, Camille M.
Ketavarapu, Mythili
Kasinathan, Sivakanthan
Nanda, Arjun S.
Wu, Ke
Chio, Un Seng
Zhou, Ziling
Goodarzi, Hani
Narlikar, Geeta J.
Ramani, Vijay
[J]. NATURE STRUCTURAL & MOLECULAR BIOLOGY, 2023, 30 (10) : 1571 - +
[2] Massively multiplex single-molecule oligonucleosome footprinting
Abdulhay, Nour J.
McNally, Colin P.
Hsieh, Laura J.
Kasinathan, Sivakanthan
Keith, Aidan
Estes, Laurel S.
Karimzadeh, Mehran
Underwood, Jason G.
Goodarzi, Hani
Narlikar, Geeta J.
Ramani, Vijay
[J]. ELIFE, 2020, 9
[3] Applying single-cell and single-nucleus genomics to studies of cellular heterogeneity and cell fate transitions in the nervous system
Adameyko, Igor
Bakken, Trygve
Bhaduri, Aparna
Chhatbar, Chintan
Filbin, Mariella G.
Gate, David
Hochgerner, Hannah
Kim, Chang Nam
Krull, Jordan
La Manno, Gioele
Li, Qingyun
Linnarsson, Sten
Ma, Qin
Mayer, Christian
Menon, Vilas
Nano, Patricia
Prinz, Marco
Quake, Steve
Walsh, Christopher A.
Yang, Jin
Bayraktar, Omer Ali
Gokce, Ozgun
Habib, Naomi
Konopka, Genevieve
Liddelow, Shane A.
Nowakowski, Tomasz J.
[J]. NATURE NEUROSCIENCE, 2024, 27 (12) : 2278 - 2291
[4] Aibar S, 2017, NAT METHODS, V14, P1083, DOI [10.1038/NMETH.4463, 10.1038/nmeth.4463]
[5] Gene regulation inference from single-cell RNA-seq data with linear differential equations and velocity inference
Aubin-Frankowski, Pierre-Cyril
Vert, Jean-Philippe
[J]. BIOINFORMATICS, 2020, 36 (18) : 4774 - 4780
[6] scds: computational annotation of doublets in single-cell RNA sequencing data
Bais, Abha S.
Kostka, Dennis
[J]. BIOINFORMATICS, 2020, 36 (04) : 1150 - 1158
[7] Dividing out quantification uncertainty allows efficient assessment of differential transcript expression with edgeR
Baldoni, Pedro L.
Chen, Yunshun
Hediyeh-zadeh, Soroor
Liao, Yang
Dong, Xueyi
Ritchie, Matthew E.
Shi, Wei
Smyth, Gordon K.
[J]. NUCLEIC ACIDS RESEARCH, 2024, 52 (03) : E13
[8] Multimodal chromatin profiling using nanobody-based single-cell CUT&Tag
Bartosovic, Marek
Castelo-Branco, Goncalo
[J]. NATURE BIOTECHNOLOGY, 2023, 41 (06) : 794 - +
[9] Single-cell CUT&Tag profiles histone modifications and transcription factors in complex tissues
Bartosovic, Marek
Kabbe, Mukund
Castelo-Branco, Goncalo
[J]. NATURE BIOTECHNOLOGY, 2021, 39 (07) : 825 - 835
[10] Astrocyte layers in the mammalian cerebral cortex revealed by a single-cell in situ transcriptomic map
Bayraktar, Omer Ali
Bartels, Theresa
Holmqvist, Staffan
Kleshchevnikov, Vitalii
Martirosyan, Araks
Polioudakis, Damon
Ben Haim, Lucile
Young, Adam M. H.
Batiuk, Mykhailo Y.
Prakash, Kirti
Brown, Alexander
Roberts, Kenny
Paredes, Mercedes F.
Kawaguchi, Riki
Stockley, John H.
Sabeur, Khalida
Chang, Sandra M.
Huang, Eric
Hutchinson, Peter
Ullian, Erik M.
Hemberg, Martin
Coppola, Giovanni
Holt, Matthew G.
Geschwind, Daniel H.
Rowitch, David H.
[J]. NATURE NEUROSCIENCE, 2020, 23 (04) : 500 - +

← 1 2 3 4 5 6 7 8 9 10 →