TY - JOUR
T1 - 1 Identification of colorectal cancer cell stemness from single-cell RNA sequencing
AU - Lin, Kangyu
AU - Chowdhury, Saikat
AU - Zeineddine, Mohammad A.
AU - Zeineddine, Fadl A.
AU - Hornstein, Nicholas J.
AU - Villarreal, Oscar E.
AU - Maru, Dipen M.
AU - Haymaker, Cara L.
AU - Vauthey, Jean Nicolas
AU - Chang, George J.
AU - Bogatenkova, Elena
AU - Menter, David
AU - Kopetz, Scott
AU - Shen, John Paul
N1 - Publisher Copyright:
© 2024 American Association for Cancer Research Inc.. All rights reserved.
PY - 2024/4
Y1 - 2024/4
N2 - Cancer stem cells (CSCs) play a critical role in metastasis, relapse, and therapy resistance in colorectal cancer. While characterization of the normal lineage of cell development in the intestine has led to the identification of many genes involved in the induction and maintenance of pluripotency, recent studies suggest significant heterogeneity in CSC populations. Moreover, while many canonical colorectal cancer CSC marker genes have been identified, the ability to use these classical markers to annotate stemness at the single-cell level is limited. In this study, we performed single-cell RNA sequencing on a cohort of 6 primary colon, 9 liver metastatic tumors, and 11 normal (non-tumor) controls to identify colorectal CSCs at the single-cell level. Finding poor alignment of the 11 genes most used to identify colorectal CSC, we instead extracted a single-cell stemness signature (SCS_sig) that robustly identified ‘gold-standard’ colorectal CSCs that expressed all marker genes. Using this SCS_sig to quantify stemness, we found that while normal epithelial cells show a bimodal distribution, indicating distinct stem and differentiated states, in tumor epithelial cells stemness is a continuum, suggesting greater plasticity in these cells. The SCS_sig score was quite variable between different tumors, reflective of the known transcriptomic heterogeneity of CRC. Notably, patients with higher SCS_sig scores had significantly shorter disease-free survival time after curative intent surgical resection, suggesting stemness is associated with relapse.
AB - Cancer stem cells (CSCs) play a critical role in metastasis, relapse, and therapy resistance in colorectal cancer. While characterization of the normal lineage of cell development in the intestine has led to the identification of many genes involved in the induction and maintenance of pluripotency, recent studies suggest significant heterogeneity in CSC populations. Moreover, while many canonical colorectal cancer CSC marker genes have been identified, the ability to use these classical markers to annotate stemness at the single-cell level is limited. In this study, we performed single-cell RNA sequencing on a cohort of 6 primary colon, 9 liver metastatic tumors, and 11 normal (non-tumor) controls to identify colorectal CSCs at the single-cell level. Finding poor alignment of the 11 genes most used to identify colorectal CSC, we instead extracted a single-cell stemness signature (SCS_sig) that robustly identified ‘gold-standard’ colorectal CSCs that expressed all marker genes. Using this SCS_sig to quantify stemness, we found that while normal epithelial cells show a bimodal distribution, indicating distinct stem and differentiated states, in tumor epithelial cells stemness is a continuum, suggesting greater plasticity in these cells. The SCS_sig score was quite variable between different tumors, reflective of the known transcriptomic heterogeneity of CRC. Notably, patients with higher SCS_sig scores had significantly shorter disease-free survival time after curative intent surgical resection, suggesting stemness is associated with relapse.
KW - Cancer stem cells
KW - Colorectal cancer
KW - Plasticity
KW - scRNA-seq
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U2 - 10.1158/1541-7786.MCR-23-0468
DO - 10.1158/1541-7786.MCR-23-0468
M3 - Article
C2 - 38156967
AN - SCOPUS:85189748503
SN - 1541-7786
VL - 22
JO - Molecular Cancer Research
JF - Molecular Cancer Research
IS - 4
ER -