DNA methylation-based signature of CD8+ tumor-infiltrating lymphocytes enables evaluation of immune response and prognosis in colorectal cancer

Abstract

BackgroundTumor-infiltrating lymphocytes (TILs), especially CD8+ TILs, can be used for predicting immunotherapy responsiveness and survival outcome. However, the evaluation of CD8+ TILs currently relies on histopathological methodology with high variability. We therefore aimed to develop a DNA methylation signature for CD8+ TILs (CD8+ MeTIL) that could evaluate immune response and prognosis in colorectal cancer (CRC).MethodsA CD8+ MeTIL signature score was constructed by using CD8+ T cell-specific differentially methylated positions (DMPs) that were identified from Illumina EPIC methylation arrays. Immune cells, colon epithelial cells, and two CRC cohorts (n=282 and 335) were used to develop a PCR-based assay for quantitative analysis of DNA methylation at single-base resolution (QASM) to determine CD8 + MeTIL signature score.ResultsThree CD8+ T cell-specific DMPs were identified to construct the CD8+ MeTIL signature score, which showed a dramatic discriminability between CD8+ T cells and other cells. The QASM assay we developed for CD8+ MeTIL markers could measure CD8+ TILs distributions in a fully quantitative, accurate, and simple manner. The CD8+ MeTIL score determined by QASM assay showed a strong association with histopathology-based CD8+ TIL counts and a gene expression-based immune marker. Furthermore, the low CD8+ MeTIL score (enriched CD8+ TILs) was associated with MSI-H tumors and predicted better survival in CRC cohorts.ConclusionsThis study developed a quantitative DNA methylation-based signature that was reliable to evaluate CD8+ TILs and prognosis in CRC. This approach has the potential to be a tool for investigations on CD8+ TILs and a biomarker for therapeutic approaches, including immunotherapy.

NTRK fusion positive colorectal cancer is a unique subset of CRC with high TMB and microsatellite instability

“…Thus, not only will most patients with this subset NTRK+ CRC benefit from the current approved NTRK TKIs, but may also potentially benefit from ICIs. Notably, a prior study by Zou et al 20 reported that enriched CD8+ tumor‐infiltration T cells, quantified by using a DNA methylation‐based method, was associated with MSI‐H tumors in CRC cohorts and predicted better survival. However, it will require further investigation as to whether two molecular signatures (TMB and MSI) being positive, the response to pembrolizumab will be higher (additive or synergistic effect) than just having one molecular signature.…”

Identification and validation of immunotherapy for four novel clusters of colorectal cancer based on the tumor microenvironment

“…Among the ESTIMATE scores of the four ImmClusts, the highest immune ( Figure 2A ) and stromal scores ( Figure 2B ) were observed in CS2, in contrast to the lowest scores in CS4 ( Figures 2A, B ) . A study has shown that the MeTIL score system may assess immune and immunotherapy responses in CRC ( 54 ). Interestingly, our data suggested that CS2 had the highest MeTIL score ( Figure 2C ), while CS4 had the lowest MeTIL score, which further suggested the differences in immunotherapy responses among the four ImmClusts.…”

Methylation statuses of NCOR2, PARK2, and ZSCAN12 signify densities of tumor-infiltrating lymphocytes in gastric carcinoma

“…The five markers comprise single CpG sites of five individual genes, including INA , KLHL6 , PTPRCAP , RASSF1 , and SEMA3B , which are different from the three methylation markers in the present study 10 . During the submission of our manuscript, it was reported that Zou et al developed DNA methylation signature for CD8+ TILs that could assess CD8+ TILs in colorectal cancers, using three individual CpG sites that are located in the low-CpG density regions and highly differentially methylated between CD8+ T cells and other cells 20 . The selected CpG sites are not located within CpG island loci, so that classical MethyLight assay could not assess methylation levels of these single CpG sites.…”