Reference component analysis of single-cell transcriptomes elucidates cellular heterogeneity in human colorectal tumors.
Intratumoral heterogeneity is a major obstacle to cancer treatment and a significant confounding factor in bulk-tumor profiling. We performed an unbiased analysis of transcriptional heterogeneity in colorectal tumors and their microenvironments using single-cell RNA-seq from 11 primary colorectal tumors and matched normal mucosa. To robustly cluster single-cell transcriptomes, we developed reference component analysis (RCA), an algorithm that substantially improves clustering accuracy. Using RCA, we identified two distinct subtypes of cancer-associated fibroblasts (CAFs). Additionally, epithelial-mesenchymal transition (EMT)-related genes were found to be upregulated only in the CAF subpopulation of tumor samples. Notably, colorectal tumors previously assigned to a single subtype on the basis of bulk transcriptomics could be divided into subgroups with divergent survival probability by using single-cell signatures, thus underscoring the prognostic value of our approach. Overall, our results demonstrate that unbiased single-cell RNA-seq profiling of tumor and matched normal samples provides a unique opportunity to characterize aberrant cell states within a tumor.
Computational and Systems Biology, Genome Institute of Singapore, Singapore.
Huipeng
H
Li
Computational and Systems Biology, Genome Institute of Singapore, Singapore.|Developmental Cellomics Laboratory, Genome Institute of Singapore, Singapore.
Elise T
http://orcid.org/0000-0002-8749-2719
ET
Courtois
Computational and Systems Biology, Genome Institute of Singapore, Singapore.|Department of Computer Science and Engineering and Center for Computational Biology, Indraprastha Institute of Information Technology, Delhi, India.
Debarka
D
Sengupta
Computational and Systems Biology, Genome Institute of Singapore, Singapore.|Developmental Cellomics Laboratory, Genome Institute of Singapore, Singapore.
Yuliana
Y
Tan
Synthetic Biology, Genome Institute of Singapore, Singapore.
Kok Hao
KH
Chen
Synthetic Biology, Genome Institute of Singapore, Singapore.
Jolene Jie Lin
JJL
Goh
Cancer Therapeutics and Stratified Oncology, Genome Institute of Singapore, Singapore.
Say Li
SL
Kong
Department of Medical Oncology, National Cancer Centre Singapore, Singapore.
Clarinda
C
Chua
Department of Pathology, Singapore General Hospital, Singapore.
Lim Kiat
LK
Hon
Department of Colorectal Surgery, Singapore General Hospital, Singapore.
Wah Siew
WS
Tan
Department of Colorectal Surgery, Singapore General Hospital, Singapore.
Mark
M
Wong
Synthetic Biology, Genome Institute of Singapore, Singapore.
Paul Jongjoon
PJ
Choi
Data Analytics Department, Institute for Infocomm Research, Singapore.
Lawrence J K
LJK
Wee
Cancer Therapeutics and Stratified Oncology, Genome Institute of Singapore, Singapore.
Axel M
http://orcid.org/0000-0002-3381-7266
AM
Hillmer
Cancer Therapeutics and Stratified Oncology, Genome Institute of Singapore, Singapore.|Department of Medical Oncology, National Cancer Centre Singapore, Singapore.|Program in Cancer and Stem Cell Biology, Duke-NUS Medical School, Singapore.
Iain Beehuat
IB
Tan
Developmental Cellomics Laboratory, Genome Institute of Singapore, Singapore.|The Jackson Laboratory for Genomic Medicine, Farmington, Connecticut, USA.|Department of Genetics and Genome Sciences, Institute for Systems Genomics, University of Connecticut, Farmington, Connecticut, USA.|Department of Biological Sciences, National University of Singapore, Singapore.
Paul
http://orcid.org/0000-0002-0191-3958
P
Robson
Computational and Systems Biology, Genome Institute of Singapore, Singapore.
Shyam
S
Prabhakar
D000072283:A549 Cells; D000465:Algorithms; D002460:Cell Line; D045744:Cell Line, Tumor; D016000:Cluster Analysis; D015179:Colorectal Neoplasms / Q000235:genetics* / Q000473:pathology; D058750:Epithelial-Mesenchymal Transition / Q000235:genetics; D005347:Fibroblasts / Q000378:metabolism; D020869:Gene Expression Profiling / Q000379:methods*; D015972:Gene Expression Regulation, Neoplastic; D018740:Genetic Heterogeneity; D006801:Humans; D007150:Immunohistochemistry; D017404:In Situ Hybridization, Fluorescence; D020014:K562 Cells; D025341:Principal Component Analysis; D011379:Prognosis; D017423:Sequence Analysis, RNA / Q000379:methods; D059010:Single-Cell Analysis / Q000379:methods*; D016019:Survival Analysis; D059467:Transcriptome