Single-cell transcriptomics reveals stage- and side-specificity of gene modules in colorectal cancer.

BACKGROUND: An understanding of mechanisms underlying colorectal cancer (CRC) development and progression is yet to be fully elucidated. This study aims to employ network theoretic approaches to analyse single cell transcriptomic data from CRC to better characterize its progression and sided-ness. METHODS: We utilized a recently published single-cell RNA sequencing data (GEO-GSE178341) and parsed the cell X gene data by stage and side (right and left colon). Using Weighted Gene Co-expression Network Analysis (WGCNA), we identified gene modules with varying preservation levels (weak or strong) of network topology between early (pT1) and late stages (pT234), and between right and left colons. Spearman's rank correlation (ρ) was used to assess the similarity or dissimilarity in gene connectivity. RESULTS: Equalizing cell counts across different stages, we detected 13 modules for the early stage, two of which were non-preserved in late stages. Both non-preserved modules displayed distinct gene connectivity patterns between the early and late stages, characterized by low ρ values. One module predominately dealt with myeloid cells, with genes mostly enriched for cytokine-cytokine receptor interaction potentiallystimulating myeloid cells to participate in angiogenesis. The second module, representing a subset of epithelial cells, was mainly enriched for carbohydrate digestion and absorption, influencing the gut microenvironment through the breakdown of carbohydrates. In the comparison of left vs. right colons, two of 12 modules identified in the right colon were non-preserved in the left colon. One captured a small fraction of epithelial cells and was enriched for transcriptional misregulation in cancer, potentially impacting communication between epithelial cells and the tumor microenvironment. The other predominantly contained B cells with a crucial role in maintaining human gastrointestinal health and was enriched for B-cell receptor signalling pathway. CONCLUSIONS: We identified modules with topological and functional differences specific to cell types between the early and late stages, and between the right and left colons. This study enhances the understanding of roles played by different cell types at different stages and sides, providing valuable insights for future studies focused on the diagnosis and treatment of CRC.

Prediction of Postoperative Clinical Outcomes in Resected Stage I Non-Small Cell Lung Cancer Focusing on the Preoperative Glasgow Prognostic Score.

Background: The Glasgow Prognostic Score (GPS), which consists of albumin and C-reactive protein (CRP), may predict overall survival (OS) in cancer patients. The aim of this retrospective analysis was to evaluate the clinical impact of the preoperative GPS on patients with resected early stage non-small cell lung cancer (NSCLC). Methods: 300 patients with curatively resected stage I NSCLC were followed-up for OS, recurrence-free survival (RFS), cancer-specific survival (CSS), and death from other causes. Results: 229 patients (76%) had a preoperative GPS of 0, and 71 (24%) a GPS ≥ 1. The three-year probabilities of RFS, OS, CSS, and death from other causes were 81%, 84%, 88%, and 96% in patients with GPS = 0, and 79%, 74%, 91%, and 82% in patients with a GPS ≥ 1, respectively. GPS ≥ 1 was significantly associated with a higher risk of death from other causes (p = 0.022), serving as an independent predictor of death from other causes (p = 0.034). Pathologically elevated CRP levels (CRP > 5 mg/L) were found in 91 patients (30%). The mean CRP level was 7.88 ± 15.80 mg/L (0.5-135.6 mg/L). Pre-treatment CRP level was significantly associated with coronary heart disease (p < 0.0001), histology (p = 0.013), tumor size (p = 0.018), tumor stage (p = 0.002), and vascular invasion (p = 0.017). Conclusion: The preoperative GPS predicts adverse survival outcomes in patients with resected stage I NSCLC.

Epigenetic modification of SALL1 as a novel biomarker for the prognosis of early stage head and neck cancer.

This study examined Sal-like protein (SALL)1 methylation profiles in head and neck squamous-cell carcinoma (HNSCC) patients at diagnosis and follow-up, and evaluated their prognostic significance and value as a biomarker. SALL1 expression was examined in a panel of cell lines by quantitative reverse transcription PCR (qRT-PCR). Promoter methylation was determined by quantitative methylation-specific polymerase chain reaction (qMSP) and was compared to the clinical characteristics of 205 samples. SALL1 promoter methylation was associated with transcriptional inhibition and was correlated with disease recurrence in 31.7% of cases, with an odds ratio of 1.694 (95% confidence interval: 1.093-2.626; P = 0.018) by multivariate Cox proportional hazard regression analysis. SALL1 promoter hypermethylation showed highly discriminatory receiver operator characteristic curve profiles that clearly distinguished HNSCC from adjacent normal mucosal tissue, and was correlated with reduced disease-free survival in early stage T1 and T2 patients (log-rank test, P < 0.001). SALL1 methylation was significantly correlated with the methylation status of both SALL3 and CDH1. This study suggests that CpG hypermethylation is a likely mechanism of SALL1 gene inactivation, supporting the hypothesis that SALL1 might play a role in HNSCC tumorigenesis and could serve as an important biomarker.