Gradient of Developmental and Injury Response transcriptional states define functional vulnerabilities underpinning glioblastoma heterogeneity

Laura M. Richards, Owen K. N. Whitley, Graham MacLeod, Florence M. G. Cavalli, Fiona J. Coutinho, Julia E. Jaramillo, Nataliia Svergun, Mazdak Riverin, Danielle C. Croucher, Michelle Kushida, Kenny Yu, Paul Guilhamon, Naghmeh Rastegar, Moloud Ahmadi, Jasmine K. Bhatti, Danielle A. Bozek, Naijin Li, Lilian Lee, Clare Che, Erika Luis, Nicole I. Park, Zhiyu Xu, Troy Ketela, Richard A. Moore, Marco A. Marra, Julian Spears, Michael D. Cusimano, Sunit Das, Mark Bernstein, Benjamin Haibe-Kains, Mathieu Lupien, H. Artee Luchman, Samuel Weiss, Stephane Angers, Peter B. Dirks, Gary D. Bader & Trevor J. Pugh

DOI: https://doi.org/10.1038/s43018-020-00154-9

Glioblastomas harbor diverse cell populations, including rare glioblastoma stem cells (GSCs) that drive tumorigenesis. To characterize functional diversity within this population, we performed single-cell RNA sequencing on >69,000 GSCs cultured from the tumors of 26 patients. We observed a high degree of inter- and intra-GSC transcriptional heterogeneity that could not be fully explained by DNA somatic alterations. Instead, we found that GSCs mapped along a transcriptional gradient spanning two cellular states reminiscent of normal neural development and inflammatory wound response. Genome-wide CRISPR–Cas9 dropout screens independently recapitulated this observation, with each state characterized by unique essential genes. Further single-cell RNA sequencing of >56,000 malignant cells from primary tumors found that the majority organize along an orthogonal astrocyte maturation gradient yet retain expression of founder GSC transcriptional programs. We propose that glioblastomas grow out of a fundamental GSC-based neural wound response transcriptional program, which is a promising target for new therapy development.

Visualized Dataset: 65,655 GSCs (28 samples); 14,207 malignant tumour cells (7 patients). Corresponds to Figure 7 in manuscript. Other datasets, including primary tumor data, can be accessed under the ‘Download’ tab.

Study Contact: trevor.pugh@utoronto.ca