Background: Previous studies have traditionally attributed the initiation of cancer cells to genetic mutations, considering them as the fundamental drivers of carcinogenesis. However, recent research has shed light on the crucial role of epigenomic alterations in various cell types present within the tumor microenvironment, suggesting their potential contribution to tumor formation and progression. Despite these significant findings, the progress in understanding the epigenetic mechanisms regulating tumor heterogeneity has been impeded over the past few years due to the lack of appropriate technical tools and methodologies. Results: The emergence of single-cell sequencing has enhanced our understanding of the epigenetic mechanisms governing tumor heterogeneity by revealing the distinct epigenetic layers of individual cells (chromatin accessibility, DNA/RNA methylation, histone modifications, nucleosome localization) and the diverse omics (transcriptomics, genomics, multi-omics) at the single-cell level. These technologies provide us with new insights into the molecular basis of intratumoral heterogeneity and help uncover key molecular events and driving mechanisms in tumor development. Conclusion: This paper provides a comprehensive review of the emerging analytical and experimental approaches of single-cell sequencing in various omics, focusing specifically on epigenomics. These approaches have the potential to capture and integrate multiple dimensions of individual cancer cells, thereby revealing tumor heterogeneity and epigenetic features. Additionally, this paper outlines the future trends of these technologies and their current technical limitations.

The C-X-C motif (CXC) chemokines are a family of chemotactic molecules that have been identified as potential prognostic markers and prospective therapeutic targets for many kinds of cancer types. Increasing evidence shows that CXC chemokines are associated with the progression of colorectal cancer (CRC); however, the correlations of CXC chemokines with prognostic and immune infiltrates in CRC remain to be clarified. In this study, we analyzed the mRNA expression level, prognostic data and immune infiltrates of CXC chemokines in CRC patients from the Gene Expression Profiling Interactive Analysis, Oncomine, cBioPortal and databases using GeneMANIA, STRING, DAVID 6.8, and TIMER. Our results showed that CXCL1/2/3/4/5/8/9/10/11/13/14/16 were significantly overexpressed in CRC tissues. Furthermore, expression of CXCL1/2/3/9/10/11 was associated with tumor stage in CRC. A significant association was also identified between the co-expression of CXCL16 with EGFR, KRAS and NRAS. In addition, the survival analysis suggested that high CXCL2/3/8/9/10/11/14 expression is correlated with clinical outcomes of CRC patients. Moreover, a significant association was observed between the CXCL8/9/10/11 expression and immune infiltration in colonic and rectal adenocarcinoma. Overall, CXC chemokines are not only implicated as prognostic biomarkers for CRC patients, but may also influence the immune status of CRC tissues.

Lymph node metastasis is a common metastatic route of gastric cancer. However, the heterogeneity of tumor cells and tumor microenvironment between primary gastric cancer and metastatic lymph nodes, as well as the driving mechanisms of metastasis, remain not fully understood. In this study, single-cell RNA sequencing and spatial transcriptomics analysis were performed on 4 gastric cancer patients (four primary tumors and two paired metastatic lymph nodes). Additionally, the TCGA database was used as an external validation dataset to validate the unfavorable clinical outcomes of necroptosis genes and the correlation between MDK-NCL and immune infiltration. Our single-cell analysis revealed significant heterogeneity in the tumor microenvironment between primary and metastatic lymph nodes of gastric cancer. Pseudotime analysis indicated that gastric cancer cells may follow two potential differentiation trajectories during lymph node metastasis. One type of cells possess the ability to migrate to lymph nodes, while the other type remain in the primary site during tumor progression. We observed that the expression of necroptosis-related gene CHMP3 was significantly associated with lymph node metastasis. Immunofluorescence further suggested upregulated CHMP3 protein expression in metastatic lymph node. Furthermore, we found that MDK-NCL interaction was active in metastatic lymph nodes. External validation using the TCGA cohort indicated that high MDK-NCL expression correlated with an immunosuppressive microenvironment. Finally, through integrated single-cell and spatial analysis, we observed that gastric cancer cells may remodel the tumor microenvironment via the MDK-NCL signaling pathway. In summary, our study revealed the dynamics of tumor cells in lymph node metastasis in GC and identified a subtype of GC cells with potential metastatic capability. Our data suggest that necroptosis and the MDK-NCL signaling pathway may be involved in facilitating lymph node metastasis, providing new insights into the mechanisms of GC progression and potential therapeutic targets.

The morbidity and mortality of esophageal carcinoma (ESCA) patients is high in China for which radical radiotherapy remains the frontline treatment. Radio-resistant patients show high rates of relapse and poor overall survival (OS). In this study, we report high YTHDF1 expression in ESCA patients that is associated with radio-resistance and poor OS. Accordingly, YTHDF1 silencing improved the radio-sensitivity of ESCC cells. Bioinformatics, m6A sequencing, KEGG and GO analysis, and m6A-IP-qPCR validations revealed a positive correlation between AURKA and YTHDF1. AURKA was subsequently found to positively regulate NHEJ promoting radio-resistance. From these data, we speculate that YTHDF1 binds to AURKA to upregulate NHEJ, promoting radio-resistance. Clinical specimens were collected and the role of YTHDF1 and AURKA during radio-resistance in vivo were investigated. These data reveal new predictors of radiotherapy efficacy and highlight novel and effective interventions to reverse radio-resistance.

Paranitrophenol, a metabolite of organophosphate insecticides, was associated with various adverse health outcomes. However, the association of Paranitrophenol with all-cause and cancer mortality in adults remains unclear. A total of 3,362 participants (1680 male) were included from the National Health and Nutrition Examination Surveys (NHANES). Urinary Paranitrophenol was measured using ultra-high-performance LC-MS/MS. Mortality status and causes were obtained from National Death Index. Cox proportional hazards regression analysis was performed to explore the associations between Paranitrophenol and all-cause and cancer mortality, respectively. After a follow-up of 22.75 thousand person-years, there were 297 deaths from all causes and 69 deaths from cancer. Comparing with the lowest quartile, the highest quartile was not associated with all-cause mortality in the neither univariate model nor adjusted model. In terms of cancer mortality, the hazard ratios and 95% confidence interval of the highest quartile is 0.44 (0.21–0.93) in the univariate model, 0.40 (0.18–0.86) in the partly-adjusted model, and 0.40 (0.18–0.88) in the fully-adjusted model. Higher urinary Paranitrophenol levels were associated with a decreased risk of cancer mortality. This association remained independent of demographics, lifestyle factors, and comorbidities.