Dissecting the multicellular ecosystem of metastatic melanoma by single-cell RNA-seq

Itay Tirosh; Benjamin Izar; Sanjay M Prakadan; Marc H Wadsworth 2nd; Daniel Treacy; John J Trombetta; Asaf Rotem; Christopher Rodman; Christine Lian; George Murphy; Mohammad Fallahi-Sichani; Ken Dutton-Regester; Jia-Ren Lin; Ofir Cohen; Parin Shah; Diana Lu; Alex S Genshaft; Travis K Hughes; Carly G K Ziegler; Samuel W Kazer; Aleth Gaillard; Kellie E Kolb; Alexandra-Chloé Villani; Cory M Johannessen; Aleksandr Y Andreev; Eliezer M Van Allen; Monica Bertagnolli; Peter K Sorger; Ryan J Sullivan; Keith T Flaherty; Dennie T Frederick; Judit Jané-Valbuena; Charles H Yoon; Orit Rozenblatt-Rosen; Alex K Shalek; Aviv Regev; Levi A Garraway

doi:10.1126/science.aad0501

Dissecting the multicellular ecosystem of metastatic melanoma by single-cell RNA-seq

Science. 2016 Apr 8;352(6282):189-96. doi: 10.1126/science.aad0501.

Authors

Itay Tirosh¹, Benjamin Izar², Sanjay M Prakadan³, Marc H Wadsworth 2nd³, Daniel Treacy¹, John J Trombetta¹, Asaf Rotem⁴, Christopher Rodman¹, Christine Lian⁵, George Murphy⁵, Mohammad Fallahi-Sichani⁶, Ken Dutton-Regester⁷, Jia-Ren Lin⁸, Ofir Cohen¹, Parin Shah⁹, Diana Lu¹, Alex S Genshaft³, Travis K Hughes¹⁰, Carly G K Ziegler¹⁰, Samuel W Kazer³, Aleth Gaillard³, Kellie E Kolb³, Alexandra-Chloé Villani¹, Cory M Johannessen¹, Aleksandr Y Andreev¹, Eliezer M Van Allen⁴, Monica Bertagnolli¹¹, Peter K Sorger¹², Ryan J Sullivan¹³, Keith T Flaherty¹³, Dennie T Frederick¹³, Judit Jané-Valbuena¹, Charles H Yoon¹¹, Orit Rozenblatt-Rosen¹, Alex K Shalek¹⁴, Aviv Regev¹⁵, Levi A Garraway¹⁶

Affiliations

¹ Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.
² Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA. Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02215, USA. Center for Cancer Precision Medicine, Dana-Farber Cancer Institute, Boston, MA 02215, USA. bizar@partners.org aregev@broadinstitute.org levi_garraway@dfci.harvard.edu.
³ Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA. Institute for Medical Engineering and Science, Massachusetts Institute of Technology (MIT), Cambridge, MA 02139, USA. Department of Chemistry, MIT, Cambridge, MA 02142, USA. Ragon Institute of Massachusetts General Hospital, MIT and Harvard University, Cambridge, MA 02139, USA.
⁴ Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA. Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02215, USA. Center for Cancer Precision Medicine, Dana-Farber Cancer Institute, Boston, MA 02215, USA.
⁵ Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA.
⁶ Program in Therapeutic Sciences, Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA.
⁷ Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA. Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02215, USA. Department of Genetics and Computational Biology, QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia.
⁸ HMS LINCS Center and Laboratory of Systems Pharmacology, Harvard Medical School, Boston, MA 02115, USA.
⁹ Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02215, USA.
¹⁰ Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA. Institute for Medical Engineering and Science, Massachusetts Institute of Technology (MIT), Cambridge, MA 02139, USA. Ragon Institute of Massachusetts General Hospital, MIT and Harvard University, Cambridge, MA 02139, USA. Division of Health Sciences and Technology, Harvard Medical School, Boston, MA 02115, USA.
¹¹ Department of Surgical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02215, USA. Department of Surgical Oncology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA.
¹² Program in Therapeutic Sciences, Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA. HMS LINCS Center and Laboratory of Systems Pharmacology, Harvard Medical School, Boston, MA 02115, USA. Ludwig Center at Harvard, Boston, MA 02215, USA.
¹³ Division of Medical Oncology, Massachusetts General Hospital Cancer Center, Boston, MA 02114, USA.
¹⁴ Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA. Institute for Medical Engineering and Science, Massachusetts Institute of Technology (MIT), Cambridge, MA 02139, USA. Department of Chemistry, MIT, Cambridge, MA 02142, USA. Ragon Institute of Massachusetts General Hospital, MIT and Harvard University, Cambridge, MA 02139, USA. Division of Health Sciences and Technology, Harvard Medical School, Boston, MA 02115, USA. Department of Immunology, Massachusetts General Hospital, Boston, MA 02114, USA.
¹⁵ Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA. Department of Biology and Koch Institute, MIT, Boston, MA 02142, USA. Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA. bizar@partners.org aregev@broadinstitute.org levi_garraway@dfci.harvard.edu.
¹⁶ Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA. bizar@partners.org aregev@broadinstitute.org levi_garraway@dfci.harvard.edu.

Abstract

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 T cell 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.

Publication types

Research Support, N.I.H., Extramural
Research Support, Non-U.S. Gov't
Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

Base Sequence
Cell Communication
Cell Cycle
Drug Resistance, Neoplasm / genetics
Endothelial Cells / pathology
Genomics
Humans
Immunotherapy
Lymphocyte Activation
Melanoma / genetics*
Melanoma / secondary*
Melanoma / therapy
Microphthalmia-Associated Transcription Factor / metabolism
Neoplasm Metastasis
RNA / genetics
Sequence Analysis, RNA
Single-Cell Analysis
Skin Neoplasms / pathology*
Stromal Cells / pathology
T-Lymphocytes / immunology
T-Lymphocytes / pathology
Transcriptome
Tumor Microenvironment*

Substances

Microphthalmia-Associated Transcription Factor
RNA

Abstract

Publication types

MeSH terms

Substances

Grants and funding