Unveiling mitophagy-mediated molecular heterogeneity and development of a risk signature model for colorectal cancer by integrated scRNA-seq and bulk RNA-seq analysis

Abstract

Background Accumulating researchers have recognized mitophagy as a key player in tumors, but few studies have investigated its role in the tumor microenvironment (TME). Advances in the technology of single-cell RNA sequencing (scRNA-seq) have allowed unveiling the concealed features of the TME at cellular resolution. This study aimed to elucidate the role of mitophagy within the TME of colorectal cancer (CRC) and to establish a mitophagy-mediated risk model. Methods We assessed mitophagy-related pathway activities at both single-cell and tissue levels. Subsequently, an unsupervised clustering algorithm was employed to identify mitophagy-mediated subtypes. Furthermore, we developed a mitophagy-mediated risk signature (MMRS) using least absolute shrinkage and selection operator (LASSO) Cox analysis and constructed a MMRS model incorporating the risk score and clinical variables. Subsequently, we used quantitative reverse transcription polymerase chain reaction analysis to verify the expression of the screened genes. Results We retrieved and annotated a total of 14,719 cells from eight samples in the scRNA-seq GSE132465 data set. The activities of mitophagy-related pathways were uniformly upregulated in cancer cells. Integrating with bulk RNA-seq data, we identified two mitophagy-mediated clusters (C1 and C2) with distinct characteristics and prognoses. C2 was identified as a mitophagy-high cluster. Then, we developed a five-gene MMRS via LASSO Cox analysis in The Cancer Genome Atlas (TCGA) cohort. We utilized the GSE39582 cohort to validate the efficacy of our model. The expression of CX3CL1 and INHBB was upregulated in CRC tissues. Conclusions The present study identified two mitophagy-mediated CRC subtypes with distinct features. Our MMRS may provide potential therapeutic strategies for CRC. The findings of our work offer novel insights into the involvement of mitophagy in CRC.

Integrated analysis of tumor-associated macrophages and M2 macrophages in CRC: unraveling molecular heterogeneity and developing a novel risk signature

“…CRC exhibits significant heterogeneity in clinicopathological and molecular profiles, influencing tumor progression and treatment responses [ 21 ]. TME interactions facilitate CRC progression via multiple pathways.…”

Single‐cell analysis revealed a potential role of T‐cell exhaustion in colorectal cancer with liver metastasis

“…Applying advanced next‐generation sequencing techniques, single‐cell RNA sequencing (scRNA‐Seq) enables the exploration of gene expression patterns in individual cells, unveiling the diversity within cell populations 15 . ScRNA‐seq has been used to characterize CRC heterogeneity to develop a risk model for cancer based on mitochondrial autophagy‐mediated profiling 16 . Also, Xu et al.…”

“…15 ScRNA-seq has been used to characterize CRC heterogeneity to develop a risk model for cancer based on mitochondrial autophagymediated profiling. 16 Also, Xu et al used scRNA-seq and observed a marked decrease in activated B cells in CRC with LM. 17…”