RNA sequencing of long-term label-retaining colon cancer stem cells identifies novel regulators of quiescence

Joseph L Regan; Dirk Schumacher; Stephanie Staudte; Andreas Steffen; Ralf Lesche; Joern Toedling; Thibaud Jourdan; Johannes Haybaeck; Dominik Mumberg; David Henderson; Balázs Győrffy; Christian R A Regenbrecht; Ulrich Keilholz; Reinhold Schäfer; Martin Lange

doi:10.1016/j.isci.2021.102618

RNA sequencing of long-term label-retaining colon cancer stem cells identifies novel regulators of quiescence

iScience. 2021 May 24;24(6):102618. doi: 10.1016/j.isci.2021.102618. eCollection 2021 Jun 25.

Authors

Joseph L Regan^{1

2}, Dirk Schumacher^{3

4}, Stephanie Staudte^{1

4

5}, Andreas Steffen¹, Ralf Lesche^{1

6}, Joern Toedling^{1

6}, Thibaud Jourdan¹, Johannes Haybaeck^{7

8}, Dominik Mumberg¹, David Henderson¹, Balázs Győrffy^{9

10}, Christian R A Regenbrecht^{3

11

12}, Ulrich Keilholz², Reinhold Schäfer^{2

3

4}, Martin Lange^{1

6}

Affiliations

¹ Bayer AG, Research & Development, Pharmaceuticals, 13342 Berlin, Germany.
² Charité Comprehensive Cancer Center, Charité - Universitätsmedizin Berlin, 10117 Berlin, Germany.
³ Laboratory of Molecular Tumor Pathology, Charité Universitätsmedizin Berlin, 10117 Berlin, Germany.
⁴ German Cancer Consortium (DKTK), DKFZ, 69120 Heidelberg, Germany.
⁵ Department of Radiation Oncology and Radiotherapy, Charité Universitätsmedizin Berlin, 10117 Berlin, Germany.
⁶ Nuvisan ICB GmbH, 13353 Berlin, Germany.
⁷ Institute of Pathology, Neuropathology and Molecular Pathology, Medical University of Innsbruck, A-6020 Innsbruck, Austria.
⁸ Diagnostic & Research Center for Molecular Biomedicine, Institute of Pathology, Medical University of Graz, 8036 Graz, Austria.
⁹ Department of Bioinformatics, Semmelweis University, 1094 Budapest, Hungary.
¹⁰ TTK Cancer Biomarker Research Group, Institute of Enzymology, 1117 Budapest, Hungary.
¹¹ CELLphenomics GmbH, 13125 Berlin, Germany.
¹² Institute of Pathology, University Medical Center Göttingen, 37075 Göttingen, Germany.

Abstract

Recent data suggest that therapy-resistant quiescent cancer stem cells (qCSCs) are the source of relapse in colon cancer. Here, using colon cancer patient-derived organoids and xenografts, we identify rare long-term label-retaining qCSCs that can re-enter the cell cycle to generate new tumors. RNA sequencing analyses demonstrated that these cells display the molecular hallmarks of quiescent tissue stem cells, including expression of p53 signaling genes, and are enriched for transcripts common to damage-induced quiescent revival stem cells of the regenerating intestine. In addition, we identify negative regulators of cell cycle, downstream of p53, that we show are indicators of poor prognosis and may be targeted for qCSC abolition in both p53 wild-type and mutant tumors. These data support the temporal inhibition of downstream targets of p53 signaling, in combination with standard-of-care treatments, for the elimination of qCSCs and prevention of relapse in colon cancer.

Keywords: Cancer stem cells; Colon cancer; Organoids; Quiescence; Transcriptomics; p53 signaling.