TY - JOUR
T1 - Dissecting the multicellular ecosystem of metastatic melanoma by single-cell RNA-seq
AU - Tirosh, Itay
AU - Izar, Benjamin
AU - Prakadan, Sanjay M.
AU - Wadsworth, Marc H.
AU - Treacy, Daniel
AU - Trombetta, John J.
AU - Rotem, Asaf
AU - Rodman, Christopher
AU - Lian, Christine
AU - Murphy, George
AU - Fallahi-Sichani, Mohammad
AU - Dutton-Regester, Ken
AU - Lin, Jia Ren
AU - Cohen, Ofir
AU - Shah, Parin
AU - Lu, Diana
AU - Genshaft, Alex S.
AU - Hughes, Travis K.
AU - Ziegler, Carly G.K.
AU - Kazer, Samuel W.
AU - Gaillard, Aleth
AU - Kolb, Kellie E.
AU - Villani, Alexandra Chloé
AU - Johannessen, Cory M.
AU - Andreev, Aleksandr Y.
AU - Van Allen, Eliezer M.
AU - Bertagnolli, Monica
AU - Sorger, Peter K.
AU - Sullivan, Ryan J.
AU - Flaherty, Keith T.
AU - Frederick, Dennie T.
AU - Jané-Valbuena, Judit
AU - Yoon, Charles H.
AU - Rozenblatt-Rosen, Orit
AU - Shalek, Alex K.
AU - Regev, Aviv
AU - Garraway, Levi A.
N1 - Funding Information:
We thank M. Singer, A. Anderson, V. K. Kuchroo, and A. Aguirre for fruitful discussions; S. Barthel and T. Schatton for providing the Tim-3 antibody; Q. Zhan for preparing IF staining; and J. Thurman for guidance on complement biology. L.A.G., B.I., S.M.P., A. Re., O.R.-R., A.K.S., I.T., M.H.W.II, The Broad Institute, Brigham and Women's Hospital, Dana-Farber Cancer Institute, MIT, and the president and fellows of Harvard College have filed a patent application (BI-2015/077) that relates to tumor and microenvironment gene expression, compositions of matter, and methods of use thereof. L.A.G., B.I., A. Ro., and the Dana-Farber Cancer Institute have filed a patent application (DFCI 2105.001) that relates to cancer-patient-derived tumor dissociation for biological analysis. L.A.G was supported by National Cancer Institute (NCI) grants P01CA163222 and R35CA197737, the Dr. Miriam and Sheldon Adelson Medical Research Foundation, the Melanoma Research Alliance, and the Ludwig Center at Harvard Medical School. L.A.G. is a member of the scientific advisory board for Warp Drive; a consultant for Novartis, Bayer Oncology, and Foundation Medicine, and an equity holder in Foundation Medicine. A. Re. was supported by funds from the Howard Hughes Medicine Institute, the Klarman Cell Observatory, STARR Cancer Consortium, NCI grant 1U24CA180922, Koch Institute support (core) grant P30-CA14051 from NCI, and the Broad Institute. A. Re. is a scientific advisory board member for ThermoFisher Scientific and Syros Pharmaceuticals and a consultant for Driver Group. E.M.V.A. is a consultant for Roche Ventana, Takeda, and Third Rock Ventures. A.K.S. was supported by the Searle Scholars Program, the Beckman Young Investigator Program, and the NIH New Innovator Award (DP2 OD020839). B.I. was supported by the Wong Family Award for Translational Oncology of the Dana-Farber Cancer Institute. I.T. was supported by a Human Frontier Science Program long-term fellowship, a Rothschild fellowship, STARR Cancer Consortium, and an Integrative Cancer Biology Program grant (U54CA112962). I.T., A.K.S., and O.R.-R. were supported by the Broad Institute. O.R.-R. was supported by a grant from the Next Generation Fund at the Broad Institute of MIT and Harvard. S.W.K. was supported by a fellowship from the NSF Graduate Research Fellowships Program. M.F.-S. was supported by the NCI (grant K99CA194163), and P.K.S. was supported by the NIH (grant P50GM107618) and the Ludwig Center at Harvard. Processed single-cell and bulk RNA-seq data are available through the Gene Expression Omnibus (accession numbers GSE72056 and GSE77940). Raw RNA-seq and WES data will be available through dbGAP (the database of Genotypes and Phenotypes).
PY - 2016/4/8
Y1 - 2016/4/8
N2 - To explore the distinct genotypic and phenotypic states of melanoma tumors, we applied single-cell RNA sequencing (RNA-seq) to 4645 single cells isolated from 19 patients, profiling malignant, immune, stromal, and endothelial cells. Malignant cells within the same tumor displayed transcriptional heterogeneity associated with the cell cycle, spatial context, and a drug-resistance program. In particular, all tumors harbored malignant cells from two distinct transcriptional cell states, such that tumors characterized by high levels of the MITF transcription factor also contained cells with low MITF and elevated levels of the AXL kinase. Single-cell analyses suggested distinct tumor microenvironmental patterns, including cell-to-cell interactions. Analysis of tumor-infiltrating T cells revealed exhaustion programs, their connection to Tcell activation and clonal expansion, and their variability across patients. Overall, we begin to unravel the cellular ecosystem of tumors and how single-cell genomics offers insights with implications for both targeted and immune therapies.
AB - To explore the distinct genotypic and phenotypic states of melanoma tumors, we applied single-cell RNA sequencing (RNA-seq) to 4645 single cells isolated from 19 patients, profiling malignant, immune, stromal, and endothelial cells. Malignant cells within the same tumor displayed transcriptional heterogeneity associated with the cell cycle, spatial context, and a drug-resistance program. In particular, all tumors harbored malignant cells from two distinct transcriptional cell states, such that tumors characterized by high levels of the MITF transcription factor also contained cells with low MITF and elevated levels of the AXL kinase. Single-cell analyses suggested distinct tumor microenvironmental patterns, including cell-to-cell interactions. Analysis of tumor-infiltrating T cells revealed exhaustion programs, their connection to Tcell activation and clonal expansion, and their variability across patients. Overall, we begin to unravel the cellular ecosystem of tumors and how single-cell genomics offers insights with implications for both targeted and immune therapies.
UR - http://www.scopus.com/inward/record.url?scp=84963614956&partnerID=8YFLogxK
U2 - 10.1126/science.aad0501
DO - 10.1126/science.aad0501
M3 - Article
C2 - 27124452
AN - SCOPUS:84963614956
SN - 0036-8075
VL - 352
SP - 189
EP - 196
JO - Science
JF - Science
IS - 6282
ER -
