Analysis of the molecular nature associated with microsatellite status in colon cancer identifies clinical implications for immunotherapy

Abstract

BackgroundMicrosatellite instability in colon cancer implies favorable therapeutic outcomes after checkpoint blockade immunotherapy. However, the molecular nature of microsatellite instability is not well elucidated.MethodsWe examined the immune microenvironment of colon cancer using assessments of the bulk transcriptome and the single-cell transcriptome focusing on molecular nature of microsatellite stability (MSS) and microsatellite instability (MSI) in colorectal cancer from a public database. The association of the mutation pattern and microsatellite status was analyzed by a random forest algorithm in The Cancer Genome Atlas (TCGA) and validated by our in-house dataset (39 tumor mutational burden (TMB)-low MSS colon cancer, 10 TMB-high MSS colon cancer, 15 MSI colon cancer). A prognostic model was constructed to predict the survival potential and stratify microsatellite status by a neural network.ResultsDespite the hostile CD8+ cytotoxic T lymphocyte (CTL)/Th1 microenvironment in MSI colon cancer, a high percentage of exhausted CD8+ T cells and upregulated expression of immune checkpoints were identified in MSI colon cancer at the single-cell level, indicating the potential neutralizing effect of cytotoxic T-cell activity by exhausted T-cell status. A more homogeneous highly expressed pattern of PD1 was observed in CD8+ T cells from MSI colon cancer; however, a small subgroup of CD8+ T cells with high expression of checkpoint molecules was identified in MSS patients. A random forest algorithm predicted important mutations that were associated with MSI status in the TCGA colon cancer cohort, and our in-house cohort validated higher frequencies of BRAF, ARID1A, RNF43, and KM2B mutations in MSI colon cancer. A robust microsatellite status–related gene signature was built to predict the prognosis and differentiate between MSI and MSS tumors. A neural network using the expression profile of the microsatellite status–related gene signature was constructed. A receiver operating characteristic curve was used to evaluate the accuracy rate of neural network, reaching 100%.ConclusionOur analysis unraveled the difference in the molecular nature and genomic variance in MSI and MSS colon cancer. The microsatellite status–related gene signature is better at predicting the prognosis of patients with colon cancer and response to the combination of immune checkpoint inhibitor–based immunotherapy and anti-VEGF therapy.

Cytogenomic Changes in Sporadic Colorectal Cancer and Surrounding Nonneoplastic Tissues: The Relevance of Subtelomeric Copy Number Variations

“…Short-arm loss of chromosome 18 and long-arm duplications of chromosome 20 are commonly associated with CIN in preliminary genomic events in CRC [4,6,8,10], and our results showed both types of genomic alterations: deletions in 18p11.3 involving the THOC1 gene, and duplications in 20q13 involving the UCKL1 gene. Previous studies have also associated deletions near the terminal regions located at 18p and 18q with the malignant progression of adenomas to adenocarcinomas [15][16][17][18], suggesting that subtelomeric genomic changes may be closely involved in the CRC process.…”

“…Furthermore, subtelomeric regions are more susceptible to rearrangement and have recently been implicated in a genomic rearrangement event known as chromothripsis, which has been reported in some types of cancer [41][42][43][44]. The aberrant chromosomal architecture -i.e., the variation of small insertions or deletions leading to major chromosomal changes such as premitotic defects, stress in replication and telomeric fusionshas an important role in CIN and is usually found in cancer genomes [6,41,[45][46][47][48]. Studies have reported aneuploidies of whole chromosomes in 70% of colorectal tumors [45,46].…”

“…The study of genomic variations related to hereditary colorectal cancer (CRC) can provide strong clues to individual's sporadic CRC development predisposition [5,6]. The presence of pathogenic CNVs may also disturb gene dosage and be a relevant source of cytogenomic instability in human cancers [1].…”

“…CIN can result from defects in chromosomal segregation, telomere instability, or the response to DNA damage [2]. Approximately 85% of CRC cases have accumulated chromosomal imbalances and runs of homozygosity (ROH), which lead to altered expression of tumor suppressor genes and oncogenes [2][3][4][5][6][7]. MSI is a hypermutable event caused by the loss of DNA mismatch repair activity, whereas a CIMP is produced by hypermethylation of promoter CpG island sites [7,8].…”

Radiogenomics in Colorectal Cancer

“…MSI-H non-metastatic CRC patients have improved survival and receive no benefit from fluorouracil (FU)-based adjuvant therapy [ 56 ]. Therapy with programmed cell death 1 (PD1)-blocking antibodies, pembrolizumab, and nivolumab have shown efficacy in patients with MSI metastatic CRC [ 57 ]. Other pathways implicated in initiation, progression, activation, and migration of CRC, such as Wnt/β-catenin, Notch, Hedgehog, and TGF-β/SMAD, (PI3K)/AKT could be potential sites for targeted therapy [ 58 ].…”