Multiplexed, targeted profiling of single-cell proteomes and transcriptomes in a single reaction

被引：126

作者：

Genshaft, Alex S. ^{[1
,2
,3
,4
,5
]}

Li, Shuqiang ^{[3
]}

Gallant, Caroline J. ^{[7
,8
]}

Darmanis, Spyros ^{[7
,8
,9
,10
,11
]}

Prakadan, Sanjay M. ^{[1
,2
,3
,4
,5
]}

Ziegler, Carly G. K. ^{[1
,3
,4
,5
,12
,13
]}

Lundberg, Martin ^{[14
]}

Fredriksson, Simon ^{[14
]}

Hong, Joyce ^{[15
]}

Regev, Aviv ^{[3
,16
,17
,18
]}

Livak, Kenneth J. ^{[6
]}

Landegren, Ulf ^{[7
,8
]}

Shalek, Alex K. ^{[1
,2
,3
,4
,5
,12
,13
]}

机构：

[1] MIT, Inst Med Engn & Sci, 77 Massachusetts Ave, Cambridge, MA 02139 USA

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

[3] Broad Inst MIT & Harvard, Cambridge, MA USA

[4] MIT, Ragon Inst Massachusetts Gen Hosp, 77 Massachusetts Ave, Cambridge, MA 02139 USA

[5] Harvard Univ, Cambridge, MA 02138 USA

[6] Fluidigm Corp, San Francisco, CA 94080 USA

[7] Uppsala Univ, Dept Immunol Genet & Pathol, Uppsala, Sweden

[8] Uppsala Univ, Sci Life Lab, Uppsala, Sweden

[9] Stanford Univ, Dept Bioengn, Stanford, CA 94305 USA

[10] Stanford Univ, Dept Appl Phys, Stanford, CA 94305 USA

[11] Howard Hughes Med Inst, Stanford, CA USA

[12] Harvard Univ, Div Hlth Sci & Technol, Cambridge, MA 02138 USA

[13] MIT, 77 Massachusetts Ave, Cambridge, MA 02139 USA

[14] Olink Prote, Uppsala, Sweden

[15] MIT, Dept Elect Engn & Comp Sci, Cambridge, MA 02139 USA

[16] MIT, Dept Biol, Boston, MA 02142 USA

[17] MIT, Koch Inst, Boston, MA 02142 USA

[18] Howard Hughes Med Inst, Chevy Chase, MD 20815 USA

来源：

GENOME BIOLOGY | 2016年 / 17卷

基金：

瑞典研究理事会; 欧洲研究理事会;

关键词：

Single-cell transcriptomics; Single-cell proteomics; Single-cell multi-omics; Proximity extension assay; Metadata; RNA-SEQ; REGULATORY VARIATION; IMMUNE-RESPONSES; MESSENGER-RNA; DNA LIGATION; EXPRESSION; HETEROGENEITY; PROTEINS; GENE; DRUG;

D O I：

10.1186/s13059-016-1045-6

中图分类号：

Q81 [生物工程学（生物技术）]; Q93 [微生物学];

学科分类号：

071005 ; 0836 ; 090102 ; 100705 ;

摘要：

We present a scalable, integrated strategy for coupled protein and RNA detection from single cells. Our approach leverages the DNA polymerase activity of reverse transcriptase to simultaneously perform proximity extension assays and complementary DNA synthesis in the same reaction. Using the Fluidigm C1 (TM) system, we profile the transcriptomic and proteomic response of a human breast adenocarcinoma cell line to a chemical perturbation, benchmarking against in situ hybridizations and immunofluorescence staining, as well as recombinant proteins, ERCC Spike-Ins, and population lysate dilutions. Through supervised and unsupervised analyses, we demonstrate synergies enabled by simultaneous measurement of single-cell protein and RNA abundances. Collectively, our generalizable approach highlights the potential for molecular metadata to inform highly-multiplexed single-cell analyses.

引用

页数：15

共 53 条

[1] Digital Quantification of Proteins and mRNA in Single Mammalian Cells [J].

Albayrak, Cem ;

Jordi, Christian A. ;

Zechner, Christoph ;

Lin, Jing ;

Bichsel, Colette A. ;

Khammash, Mustafa ;

Tay, Savas .

MOLECULAR CELL, 2016, 61 (06) :914-924

[2] Homogenous 96-Plex PEA Immunoassay Exhibiting High Sensitivity, Specificity, and Excellent Scalability [J].

Assarsson, Erika ;

Lundberg, Martin ;

Holmquist, Goeran ;

Bjoerkesten, Johan ;

Thorsen, Stine Bucht ;

Ekman, Daniel ;

Eriksson, Anna ;

Dickens, Emma Rennel ;

Ohlsson, Sandra ;

Edfeldt, Gabriella ;

Andersson, Ann-Catrin ;

Lindstedt, Patrik ;

Stenvang, Jan ;

Gullberg, Mats ;

Fredriksson, Simon .

PLOS ONE, 2014, 9 (04)

[3] Pathogen Cell-to-Cell Variability Drives Heterogeneity in Host Immune Responses [J].

Avraham, Roi ;

Haseley, Nathan ;

Brown, Douglas ;

Penaranda, Cristina ;

Jijon, Humberto B. ;

Trombetta, John J. ;

Satija, Rahul ;

Shalek, Alex K. ;

Xavier, Ramnik J. ;

Regev, Aviv ;

Hung, Deborah T. .

CELL, 2015, 162 (06) :1309-1321

[4] Impact of regulatory variation from RNA to protein [J].

Battle, Alexis ;

Khan, Zia ;

Wang, Sidney H. ;

Mitrano, Amy ;

Ford, Michael J. ;

Pritchard, Jonathan K. ;

Gilad, Yoav .

SCIENCE, 2015, 347 (6222) :664-667

[5] Single-Cell Mass Cytometry of Differential Immune and Drug Responses Across a Human Hematopoietic Continuum [J].

Bendall, Sean C. ;

Simonds, Erin F. ;

Qiu, Peng ;

Amir, El-ad D. ;

Krutzik, Peter O. ;

Finck, Rachel ;

Bruggner, Robert V. ;

Melamed, Rachel ;

Trejo, Angelica ;

Ornatsky, Olga I. ;

Balderas, Robert S. ;

Plevritis, Sylvia K. ;

Sachs, Karen ;

Pe'er, Dana ;

Tanner, Scott D. ;

Nolan, Garry P. .

SCIENCE, 2011, 332 (6030) :687-696

[6] Flow Cytometry, Amped Up [J].

Benoist, Christophe ;

Hacohen, Nir .

SCIENCE, 2011, 332 (6030) :677-678

[7] The heterogeneity of human CD127+ innate lymphoid cells revealed by single-cell RNA sequencing [J].

Bjorklund, Asa K. ;

Forkel, Marianne ;

Picelli, Simone ;

Konya, Viktoria ;

Theorell, Jakob ;

Friberg, Danielle ;

Sandberg, Rickard ;

Mjosberg, Jenny .

NATURE IMMUNOLOGY, 2016, 17 (04) :451-+

[8] Scalable microfluidics for single-cell RNA printing and sequencing [J].

Bose, Sayantan ;

Wan, Zhenmao ;

Carr, Ambrose ;

Rizvi, Abbas H. ;

Vieira, Gregory ;

Pe'er, Dana ;

Sims, Peter A. .

GENOME BIOLOGY, 2015, 16

[9] Single-cell chromatin accessibility reveals principles of regulatory variation [J].

Buenostro, Jason D. ;

Wu, Beijing ;

Litzenburger, Ulrike M. ;

Ruff, Dave ;

Gonzales, Michael L. ;

Snyder, Michael P. ;

Chang, Howard Y. ;

Greenleaf, William J. .

NATURE, 2015, 523 (7561) :486-U264

[10] Dynamic Proteomics of Individual Cancer Cells in Response to a Drug [J].

Cohen, A. A. ;

Geva-Zatorsky, N. ;

Eden, E. ;

Frenkel-Morgenstern, M. ;

Issaeva, I. ;

Sigal, A. ;

Milo, R. ;

Cohen-Saidon, C. ;

Liron, Y. ;

Kam, Z. ;

Cohen, L. ;

Danon, T. ;

Perzov, N. ;

Alon, U. .

SCIENCE, 2008, 322 (5907) :1511-1516

← 1 2 3 4 5 6 →