Autophagy, an integral process of cellular self-consumption, plays a contradictory role in tumor genesis and dissemination (Levine & Kroemer, 2008). It serves as a crucial monitoring system that oversees the transformation of normal cells into cancerous ones. Concurrently, autophagy helps in averting cell death, supplying necessary nutrients, and cultivating drug resistance, thereby facilitating tumor initiation and development (Burada et al., 2015). The complex molecular interplay of autophagy is recognized for its significant role in modulating chemoresistance in CRC, viewed through clinical, biological, and mechanistic lenses (Yu et al., 2017). Therefore, developing a comprehensive autophagy-related signature is critical for a deeper understanding and effective management of CRC's malignant progression.
In this research, we pinpointed eleven key prognostic signature DAGs (CANX, NRG1, WIPI1, EIF2AK3, WDR45, PELP1, ULK1, WIPI2, DAPK1, ULK3 and MAP1LC3C) and developed a prognostic signature centered on these genes for autophagy-related processes. External validation of our findings indicates that this signature robustly and independently stratifies the risk for CRC patients. Among these genes, CANX (calnexin) is notable as a critical regulator of the leucine-stimulated mechanistic target of rapamycin kinase complex 1 (Yan et al., 2022), and it has been observed to significantly enhance CD8 + T-cell-mediated immune responses in CRC both in vitro and in vivo (Zheng et al., 2021). WIPI1 and WIPI2 are key in autophagy, localizing to autophagic membranes (Polson et al., 2010; Proikas-Cezanne et al., 2004), with WIPI1 knockdown impacting virus-induced autophagy, highlighting its role in the phagophore formation process (Liao et al., 2013). EIF2AK3, also known as PERK, is integral in managing intracellular proteostasis through unfolded protein response and integrated stress response (Park et al., 2023) and is recognized as an important gene linked to lung cancer risk due to its association with endoplasmic reticulum (ER) stress (Liu et al., 2022). WDR45, a mammalian homolog of yeast Atg18, is crucial in autophagosome formation (Bakula et al., 2017). While these studies underscore the importance of these DAGs in autophagy, their specific biological functions in CRC warrant further exploration.
The intricate tumor microenvironment (TME) of CRC significantly impacts patient prognoses, which encompasses not only the tumor cells but also includes tumor-associated fibroblasts, endothelial cells, and various infiltrating immune cells (Chen et al., 2022). Recognizing the critical role of immune cell infiltration in solid tumors, our study delved into the influence of prognostic signature DAGs on the infiltration levels of diverse immune cells. We noted a higher infiltration ratio of T cells CD8+, regulatory T cells (Tregs), and Mast cells in autophagy high-risk group. Conversely, there was a greater abundance of B cell plasma, activated memory T cell CD4+, T cell gamma delta, activated myeloid dendritic cells, resting Mast cells, and Eosinophils in the autophagy low-risk group. Previous studies have linked increased infiltration by cytotoxic T cells, memory T cells, and T helper cells with improved survival prospects (Bremnes et al., 2016). Antigen-specific B and T lymphocytes collaboratively orchestrate the immune response against tumor growth and progression (N et al., 2021). Additionally, pancreatic cancer research indicates that patients with a higher percentage of myeloid dendritic cells in cancer tissue have a longer survival compared to those with lower percentages or numbers in the peripheral blood (Yamamoto et al., 2012). Thus, our analysis of tumor-infiltrating immune cells suggests that a potent immunosuppressive microenvironment, marked by immune checkpoint inhibitors, in high-risk patients might result in a diminished response to immunotherapies.
Importantly, we focused on validating the expression levels of six pivotal prognostic signature DAGs (NRG1, PELP1, ULK1, WIPI2, DAPK1 and MAP1LC3C). Notably, DAPK1 and MAP1LC3C, which were shown to be downregulated in CRC in our bioinformatics analysis, presented a contrasting trend to the findings from tissue microarray. To our knowledge, death-associated protein kinase (DAPK1) has been identified as a facilitator of gastric cancer cell migration and invasion, leading to the establishment of four DAPK1-related signature genes that independently predict survival in gastric cancer patients (Wang et al., 2022). In prostate cancer, however, DAPK1 functions as a tumor suppressor, attributed to its roles in inhibiting cellular transformation and metastasis (Nong et al., 2021). A recent study by Wang et al. (Wang et al., 2021) corroborated this by demonstrating DAPK1's downregulation in colon cancer tissues through immunohistochemistry. This variability in DAPK1 expression can be attributed to differences in tumor types, tissue sources, and even subtypes within the same tumor. Regarding MAP1LC3C (LC3C), a vital protein in autophagosome formation, it is one of the two paralogs, LC3B and LC3C, with contrasting activities in renal cancer (Bischoff et al., 2021). Given the dual nature of autophagy in organisms, it's understandable that MAP1LC3C expression may vary in tumor tissues.
To conclude, our research effectively pinpointed 11 crucial prognostic signature DAGs (CANX, NRG1, WIPI1, EIF2AK3, WDR45, PELP1, ULK1, WIPI2, DAPK1, ULK3 and MAP1LC3C) to formulate a novel autophagy-related signature. This signature not only facilitates the prognostic assessment of CRC patients but also holds promise in differentiating responses to targeted therapies in specific cancer types. Nevertheless, the deeper molecular mechanisms underlying these findings warrant additional experimental exploration.