Although human tumours are shaped by the genetic evolution of cancer cells, evidence also suggests that they display hierarchies related to developmental pathways and epigenetic programs in which cancer stem cells (CSCs) can drive tumour growth and give rise to differentiated progeny1. Yet, unbiased evidence for CSCs in solid human malignancies remains elusive. Here we profile 4,347 single cells from six IDH1 or IDH2 mutant human oligodendrogliomas by RNA sequencing (RNA-seq) and reconstruct their developmental programs from genome-wide expression signatures. We infer that most cancer cells are differentiated along two specialized glial programs, whereas a rare subpopulation of cells is undifferentiated and associated with a neural stem cell expression program. Cells with expression signatures for proliferation are highly enriched in this rare subpopulation, consistent with a model in which CSCs are primarily responsible for fuelling the growth of oligodendroglioma in humans. Analysis of copy number variation (CNV) shows that distinct CNV sub-clones within tumours display similar cellular hierarchies, suggesting that the architecture of oligodendroglioma is primarily dictated by developmental programs. Subclonal point mutation analysis supports a similar model, although a full phylogenetic tree would be required to definitively determine the effect of genetic evolution on the inferred hierarchies. Our single-cell analyses provide insight into the cellular architecture of oligodendrogliomas at single-cell resolution and support the cancer stem cell model, with substantial implications for disease management.
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Gene Expression Omnibus
We thank L. Gaffney for graphic support. This work was supported by grants from the National Brain Tumor Society (to M.L.S. and D.N.L.), the Smith Family Foundation (to M.L.S.), NIH-NCI SPORE on brain cancer Career Enhancement Project and Developmental Research Project (to M.L.S.), the Broad Institute Broadnext10 program (to M.L.S. and O.R.R.), the American Cancer Society (to M.L.S.) and start-up funds from the MGH department of Pathology. A.S.V. was supported by the NIH R25 fellowship (NS065743) and research grants from the American Brain Tumor Association and Neurosurgery Research and Education Foundation. I.T. was supported by a Human Frontier Science Program fellowship and a Rothschild fellowship. A.R. was supported by funds from the Howard Hughes Medicine Institute, the Klarman Cell Observatory, STARR cancer consortium, NCI grant 1U24CA180922, by the Koch Institute Support (core) grant P30-CA14051 from the National Cancer Institute, the Ludwig Center and the Broad Institute. A.R. is a scientific advisory board member for ThermoFisher Scientific and Syros Pharmaceuticals and a consultant for Driver Group. Flow cytometry and sorting services were supported by shared instrumentation grant 1S10RR023440-01A1. M.M. was supported by the California Institute of Regenerative Medicine (CIRM) grants RB4-06093 and RN3-06510 and the Virginia and D.K. Ludwig Fund for Cancer Research.
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Genome Biology (2018)