Abstract 480P
Background
NANOG is a pluripotency transcription factor that serves as a signaling hub in cancer stemness pathways while also mediating immune evasion. This study aimed to clarify molecular characters relating to gene expression levels of NANOG and NANOGP8 (P8), both of which encode full-length NANOG protein, in patients with colorectal cancer (CRC).
Methods
Next-generation sequencing and whole transcriptome sequencing (WTS) were performed on 7,604 CRC tumors submitted to Caris Life Sciences (Phoenix, AZ). Top quartile transcripts per million (TPM) for NANOG and P8 expression were considered high (Q4); while bottom quartile was classified as low (Q1). Consensus molecular subtypes (CMS) were identified using WTS data. Microsatellite instability (MSI) status, tumor mutational burden (TMB) and PD-L1 expression were tested. Cell infiltration in the tumor microenvironment (TME) was assessed using QuantiSEQ and MCP counter. Molecular profiles were compared between Q4 and Q1. Comparisons were done using Chi-squaredor Fisher-Exact tests and significance was determined by p<0.05 after adjusting for multiple comparison.
Results
CMS1, CMS2, and CMS3 were negatively associated with NANOG TPM (Q1 > Q4, p < 0.001) while CMS4 had a positive association (Q4 > Q1: 33% vs. 19%, p < 0.001). Similarly, CMS1 and CMS3 were negatively associated with P8 while CMS4 showed a positive association (33% vs. 17%). APC (NANOG Q4 vs. Q1: 79% vs. 74%; P8: 82% vs. 72%) mutations and CDX2 amplifications (15% vs. 7.5%; 15% vs. 8.8%) were more frequently observed in Q4 than Q1 of NANOG and P8. Positivity rates of MSI-high (7.9 vs. 5.1%; 9 vs. 5%), TMB-high (11 vs. 7%; 12 vs. 7%), and PD-L1 expression (5 vs 2%; 6 vs 2%) were all negatively associated with both genes’ TPM. In the TME, abundance of macrophage M1 was significantly lower in Q4 while that of neutrophils, NK cells, B cells, T cells, endothelial cells, and fibroblasts was higher in Q4 compared to Q1 of NANOG and P8. (all adjusted p<0.05)
Conclusions
CRC harboring high expression levels of NANOG and P8 genes was enriched in CMS4 and had a possible association with alterations in the WNT pathway. These tumors had an inflammatory TME which may lead to resistance to immunotherapy. Further investigations including clinical outcome data are warranted to reveal the clinical implications of NANOG.
Clinical trial identification
Editorial acknowledgement
Legal entity responsible for the study
Caris Life Sciences.
Funding
This work was supported by the National Cancer Institute [P30CA 014089 to H-J.Lenz], Gloria Borges WunderGlo Foundation, Dhont Family Foundation, Victoria and Philip Wilson Research Fund, San Pedro Peninsula Cancer Guild, and Daniel Butler Research Fund.
Disclosure
All authors have declared no conflicts of interest.