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Dissecting The Multicellular Ecosystem Of Metastatic Melanoma By Single-cell RNA-seq

I. Tirosh, Benjamin Izar, S. Prakadan, Marc H. Wadsworth, D. Treacy, John J. Trombetta, A. Rotem, C. Rodman, C. Lian, G. Murphy, M. Fallahi-Sichani, K. Dutton-Regester, Jia-Ren Lin, O. Cohen, Parin Shah, D. Lu, Alex S Genshaft, Travis K. Hughes, C. K. Ziegler, S. Kazer, Aleth Gaillard, Kellie E Kolb, A. Villani, Cory M. Johannessen, A. Andreev, E. V. Van Allen, M. Bertagnolli, P. Sorger, R. Sullivan, K. Flaherty, D. Frederick, Judit Jané-Valbuena, C. Yoon, O. Rozenblatt-Rosen, A. Shalek, A. Regev, L. Garraway
Published 2016 · Biology, Medicine

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Single-cell expression profiles of melanoma Tumors harbor multiple cell types that are thought to play a role in the development of resistance to drug treatments. Tirosh et al. used single-cell sequencing to investigate the distribution of these differing genetic profiles within melanomas. Many cells harbored heterogeneous genetic programs that reflected two different states of genetic expression, one of which was linked to resistance development. Following drug treatment, the resistance-linked expression state was found at a much higher level. Furthermore, the environment of the melanoma cells affected their gene expression programs. Science, this issue p. 189 Melanoma cells show transcriptional heterogeneity. 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.
This paper references
10.1056/NEJMoa1200694
Safety and activity of anti-PD-L1 antibody in patients with advanced cancer.
J. Brahmer (2012)
10.1136/jcp.2007.046763
Comparing subjective and digital image analysis HER2/neu expression scores with conventional and modified FISH scores in breast cancer
I. Skaland (2007)
10.1016/j.cell.2010.04.020
A Temporarily Distinct Subpopulation of Slow-Cycling Melanoma Cells Is Required for Continuous Tumor Growth
A. Rösch (2010)
10.1016/j.ejca.2008.10.026
New response evaluation criteria in solid tumours: revised RECIST guideline (version 1.1).
E. Eisenhauer (2009)
10.1038/nature12688
A melanocyte lineage program confers resistance to MAP kinase pathway inhibition
C. Johannessen (2013)
10.1016/j.cell.2011.02.013
Hallmarks of Cancer: The Next Generation
D. Hanahan (2011)
10.1038/ni.2035
T cell exhaustion
E. Wherry (2011)
10.1101/gr.107524.110
The Genome Analysis Toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data.
A. McKenna (2010)
10.1200/JCO.2013.51.4802
Safety, efficacy, and biomarkers of nivolumab with vaccine in ipilimumab-refractory or -naive melanoma.
J. Weber (2013)
10.1038/nature09744
The genomic complexity of primary human prostate cancer
M. Berger (2011)
10.3389/fimmu.2015.00310
Inhibitory Receptors Beyond T Cell Exhaustion
Silvia A Fuertes Marraco (2015)
10.3389/fonc.2015.00031
Phenotype Switching in Melanoma: Implications for Progression and Therapy
F. Li (2015)
10.1016/j.immuni.2015.01.006
The transcription factor NFAT promotes exhaustion of activated CD8⁺ T cells.
Gustavo J Martinez (2015)
10.1016/j.cell.2015.05.002
Highly Parallel Genome-wide Expression Profiling of Individual Cells Using Nanoliter Droplets
Evan Z. Macosko (2015)
10.1038/nature12172
Single-cell transcriptomics reveals bimodality in expression and splicing in immune cells
A. Shalek (2013)
10.1101/gr.192237.115
Single-cell RNA-seq reveals changes in cell cycle and differentiation programs upon aging of hematopoietic stem cells.
Monika S. Kowalczyk (2015)
10.1200/JCO.2009.26.7609
Phase I study of single-agent anti-programmed death-1 (MDX-1106) in refractory solid tumors: safety, clinical activity, pharmacodynamics, and immunologic correlates.
J. Brahmer (2010)
10.1038/nrc1802
Common markers of proliferation
M. Whitfield (2006)
10.1186/s12885-015-1383-x
High-recovery visual identification and single-cell retrieval of circulating tumor cells for genomic analysis using a dual-technology platform integrated with automated immunofluorescence staining
Daniel E Campton (2015)
10.1093/bioinformatics/bts271
Strelka: accurate somatic small-variant calling from sequenced tumor-normal sample pairs
C. T. Saunders (2012)
10.1038/ncomms6712
Low MITF/AXL ratio predicts early resistance to multiple targeted drugs in melanoma.
J. Müller (2014)
10.1158/0008-5472.CAN-07-2491
In vivo switching of human melanoma cells between proliferative and invasive states.
K. Hoek (2008)
10.1200/jco.2013.31.15_suppl.2500
A first-in-human phase I study of the CDK4/6 inhibitor, LY2835219, for patients with advanced cancer.
G. Shapiro (2013)
10.1038/ni.1655
Modulation of the anti-tumor immune response by complement
M. Markiewski (2008)
10.1038/nbt.2203
Absolute quantification of somatic DNA alterations in human cancer
S. Carter (2012)
Aguirre for fruitful discussions
M We Thank
The Cancer Genome Atlas Network
(2015)
Prognostic and predictive markers for the new immunotherapies.
K. Mahoney (2014)
10.1002/humu.22771
Oncotator: Cancer Variant Annotation Tool
A. Ramos (2015)
10.1056/NEJMoa1510665
Nivolumab versus Everolimus in Advanced Renal-Cell Carcinoma.
R. Motzer (2015)
10.1186/1472-6890-11-3
Development and evaluation of a virtual microscopy application for automated assessment of Ki-67 expression in breast cancer
J. Konsti (2011)
10.1038/nature11003
The Cancer Cell Line Encyclopedia enables predictive modeling of anticancer drug sensitivity
J. Barretina (2012)
10.1056/NEJMoa1504030
Combined Nivolumab and Ipilimumab or Monotherapy in Untreated Melanoma.
J. Larkin (2015)
10.1038/nmeth.2639
Smart-seq2 for sensitive full-length transcriptome profiling in single cells
S. Picelli (2013)
Cancer immunology Mutational landscape determines sensitivity to PD-1 blockade in non-small cell lung cancer
NA Rizvi (2015)
10.1038/nri3405
Molecular mechanisms of T cell co-stimulation and co-inhibition
L. Chen (2013)
10.1073/pnas.0801497105
Selective expansion of a subset of exhausted CD8 T cells by αPD-L1 blockade
S. D. Blackburn (2008)
10.1186/gb-2009-10-3-r25
Ultrafast and memory-efficient alignment of short DNA sequences to the human genome
B. Langmead (2008)
A Density-Based Algorithm for Discovering Clusters in Large Spatial Databases with Noise
M. Ester (1996)
10.1038/nature13437
Single cell RNA Seq reveals dynamic paracrine control of cellular variation
A. Shalek (2014)
Oncotator: cancer variant annotation
AH Ramos (2015)
The Cancer Genome Atlas Network
L. K. George (2010)
10.1038/nature03664
Integrative genomic analyses identify MITF as a lineage survival oncogene amplified in malignant melanoma
Levi A. Garraway (2005)
10.1172/JCI46102
Exhaustion of tumor-specific CD8⁺ T cells in metastases from melanoma patients.
Lukas Baitsch (2011)
10.1186/1471-2105-12-323
RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome
Bo Li (2011)
10.1093/bioinformatics/btp324
Fast and accurate short read alignment with Burrows–Wheeler transform
Heng Li (2009)
10.1126/science.aaa1348
Mutational landscape determines sensitivity to PD-1 blockade in non–small cell lung cancer
N. Rizvi (2015)
10.1200/JCO.2010.33.2312
Dissecting therapeutic resistance to RAF inhibition in melanoma by tumor genomic profiling.
N. Wagle (2011)
10.18632/ONCOTARGET.2542
AXL kinase as a novel target for cancer therapy
Xiaoliang Wu (2014)
10.1158/2159-8290.CD-13-0617
The genetic landscape of clinical resistance to RAF inhibition in metastatic melanoma.
E. V. Van Allen (2014)
10.1126/science.1254257
Single-cell RNA-seq highlights intratumoral heterogeneity in primary glioblastoma
Anoop P. Patel (2014)
10.1126/science.aad0095
Genomic correlates of response to CTLA-4 blockade in metastatic melanoma
E. V. Van Allen (2015)
10.1038/nature12624
Tumour heterogeneity and cancer cell plasticity
Corbin E. Meacham (2013)
10.1038/nature09626
Melanomas acquire resistance to B-RAF(V600E) inhibition by RTK or N-RAS upregulation
R. Nazarian (2010)
10.1016/j.cell.2015.07.061
Non-genomic and Immune Evolution of Melanoma Acquiring MAPKi Resistance
W. Hugo (2015)
10.1056/NEJMoa1406498
Genetic basis for clinical response to CTLA-4 blockade in melanoma.
A. Snyder (2014)
10.1056/NEJMoa1507643
Nivolumab versus Docetaxel in Advanced Nonsquamous Non-Small-Cell Lung Cancer.
H. Borghaei (2015)
Materials and methods are available as supplementary materials on Science Online
10.1016/J.IMMUNI.2007.09.006
Molecular signature of CD8+ T cell exhaustion during chronic viral infection.
E. Wherry (2007)
10.1056/NEJMoa1003466
Improved survival with ipilimumab in patients with metastatic melanoma.
F. S. Hodi (2010)
10.1158/2159-8290.CD-13-0424
A melanoma cell state distinction influences sensitivity to MAPK pathway inhibitors.
D. Konieczkowski (2014)
10.1093/bioinformatics/btl646
A faster circular binary segmentation algorithm for the analysis of array CGH data
E. S. Venkatraman (2007)
10.1002/0471142727.mb0422s107
Preparation of Single‐Cell RNA‐Seq Libraries for Next Generation Sequencing
John J. Trombetta (2014)
10.1038/nature14248
Integrative analysis of 111 reference human epigenomes
R. Consortium (2015)
10.1091/MBC.02-02-0030
Identification of genes periodically expressed in the human cell cycle and their expression in tumors.
M. Whitfield (2002)
10.1038/ng.2330
Activation of the AXL Kinase Causes Resistance to EGFR-Targeted Therapy in Lung Cancer
Z. Zhang (2012)
10.1038/nature09161
Human Melanoma Initiating Cells Express Neural Crest Nerve Growth Factor Receptor CD271
A. D. Boiko (2010)
10.1056/NEJMoa1305133
Safety and tumor responses with lambrolizumab (anti-PD-1) in melanoma.
O. Hamid (2013)
Visualizing Data using t-SNE
L. V. D. Maaten (2008)
10.1038/nrc3245
The immune contexture in human tumours: impact on clinical outcome
W. Fridman (2012)
10.1016/j.cell.2015.05.044
Genomic Classification of Cutaneous Melanoma
Rehan Akbani (2015)
10.1038/nbt.2514
Sensitive detection of somatic point mutations in impure and heterogeneous cancer samples
K. Cibulskis (2013)
10.1056/NEJMoa1200690
Safety, activity, and immune correlates of anti-PD-1 antibody in cancer.
S. Topalian (2012)



This paper is referenced by
10.1016/J.ADENGL.2019.02.018
Telomerase Expression in a Series of Melanocytic Neoplasms.
B. deUnamunoBustos (2019)
10.1038/s41467-019-11738-0
Metabolic landscape of the tumor microenvironment at single cell resolution
Zhengtao Xiao (2019)
10.1101/2020.08.25.267336
Single-nucleus and spatial transcriptomics of archival pancreatic cancer reveals multi-compartment reprogramming after neoadjuvant treatment
William L. Hwang (2020)
10.1038/s41592-019-0689-z
Uncovering axes of variation among single-cell cancer specimens
W. S. Chen (2020)
10.1101/2020.07.23.217703
Single-cell landscape of immunological responses in COVID-19 patients
J. Zhang (2020)
10.1016/j.ctrv.2020.101997
Targeting complex, adaptive responses in melanoma therapy.
Phil F. Cheng (2020)
10.1038/s41586-019-1914-8
Tertiary lymphoid structures improve immunotherapy and survival in melanoma
Rita Cabrita (2020)
10.1007/978-3-030-35805-1_5
Advances in the Characterization of Circulating Tumor Cells in Metastatic Breast Cancer: Single Cell Analyses and Interactions, and Patient-Derived Models for Drug Testing.
P. Kujur (2020)
10.1016/j.immuni.2020.09.003
T Cell Receptor Is Required for Differentiation, but Not Maintenance, of Intestinal CD4+ Intraepithelial Lymphocytes.
Angelina M. Bilate (2020)
10.1016/j.gene.2020.145347
Single-cell profiles of human bone marrow-derived mesenchymal stromal cells after IFN-γ and TNF-α licensing.
Shuanglong Lu (2020)
10.1101/2020.12.09.417626
High-throughput Single-cell CNV Detection Reveals Clonal Evolution During Hepatocellular Carcinoma Recurrence
Liang Wu (2020)
10.1038/s41423-020-0488-6
The history and advances in cancer immunotherapy: understanding the characteristics of tumor-infiltrating immune cells and their therapeutic implications
Y. Zhang (2020)
10.1101/127761
Challenges and emerging directions in single-cell analysis
Guo-Cheng Yuan (2017)
10.1084/jem.20200785
Anti-human TREM2 induces microglia proliferation and reduces pathology in an Alzheimer's disease model.
Shoutang Wang (2020)
10.1038/s41590-020-0772-8
Dynamic regulation of hypoxia-inducible factor-1α activity is essential for normal B cell development
N. Burrows (2020)
10.1093/nar/gkaa838
SC2disease: a manually curated database of single-cell transcriptome for human diseases
Tianyi Zhao (2020)
10.1101/455121
A comprehensive analysis of single-cell transcriptome network underlying gastric premalignant lesions and early gastric cancer
P. Zhang (2018)
Molecular signatures linked to stemness and tumorigenesis in tumorspheres from in vitro transformed cells
Bartolo Bono (2017)
Application of multi-omics in single cells 1
Xiaolong Kang (2018)
10.3390/genes8110308
Gene Regulatory Network Rewiring in the Immune Cells Associated with Cancer
Pengyong Han (2017)
10.1101/761981
Expressed barcodes enable clonal characterization of chemotherapeutic responses in chronic lymphocytic leukemia
A. Al'Khafaji (2019)
10.1101/481317
Defining developmental diversification of diencephalon neurons through single-cell gene expression profiling
Q. Guo (2018)
10.1073/pnas.1620498114
Exhaustion-associated regulatory regions in CD8+ tumor-infiltrating T cells
G. Mognol (2017)
10.1038/ng.3899
Neuroblastoma is composed of two super-enhancer-associated differentiation states
Tim van Groningen (2017)
10.1038/s41467-018-06461-1
Biosynthetic energy cost for amino acids decreases in cancer evolution
H. Zhang (2018)
10.3166/onco-2019-0036
AACR 2019 — Congrès de l’association américaine de recherche contre le cancer
T. Pudlarz (2019)
10.18632/oncotarget.13666
Mapping heterogeneity in patient-derived melanoma cultures by single-cell RNA-seq
T. Gerber (2017)
10.1093/jnci/djx131
Targeted Therapy for Cancer-Associated Fibroblasts: Are We There Yet?
R. M. Barnett (2018)
10.20517/cdr.2020.41
Decoding cancer’s camouflage: epithelial-mesenchymal plasticity in resistance to immune checkpoint blockade
Maria L. Lotsberg (2020)
An Ovol2-Zeb1 EMT-Regulatory Circuit Governs Mammary Basal-Luminal Binary Differentiation
Villarreal Ponce (2017)
10.1093/hmg/ddy400
Single‐cell RNA sequencing in facioscapulohumeral muscular dystrophy disease etiology and development
Anita van den Heuvel (2019)
10.1016/j.jid.2019.08.451
Inhibition of p38/MK2 signaling prevents vascular invasion of melanoma.
J. Wenzina (2019)
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