Network-based identification of biomarkers for colon adenocarcinoma

Abstract

Background: As one of the most common cancers with high mortality in the world, we are still facing a huge challenge in the prevention and treatment of colon cancer. With the rapid development of high throughput technologies, new biomarkers identification for colon cancer has been confronted with the new opportunities and challenges. Methods: We firstly constructed functional networks for each sample of colon adenocarcinoma (COAD) by using a sample-specific network (SSN) method which can construct individual-specific networks based on gene expression profiles of a single sample. The functional genes and interactions were identified from the functional networks, respectively. Results: Classification and subtyping were used to test the function of the functional genes and interactions. The results of classification showed that the functional genes could be used as diagnostic biomarkers. The subtypes displayed different mechanisms, which were shown by the functional and pathway enrichment analysis for the representative genes of each subtype. Besides, subtype-specific molecular patterns were also detected, such as subtype-specific clinical and mutation features. Finally, 12 functional genes and 13 functional edges could serve as prognosis biomarkers since they were associated with the survival rate of COAD. Conclusions: In conclusion, the functional genes and interactions in the constructed functional network could be used as new biomarkers for COAD.

Action of m6A-related gene signatures on the prognosis and immune microenvironment of colonic adenocarcinoma

“…The global estimate suggests a yearly increase of 4.2 % in CRC incidence, with over 1.4 million new cases identified in 2020 alone [ 2 ]. Among the diverse pathological forms of CRC, colonic adenocarcinoma (COAD) predominates, often arising from dysregulated hyperplasia in the colonic mucosal epithelium that evolves into malignancy through invasive progression [ 3 , 4 ]. Enhanced insights into the pathophysiology of COAD have broadened therapeutic avenues, contributing to a twofold increase in the overall survival rate of advanced-stage patients [ 5 ].…”

Establishment and evaluation of module-based immune-associated gene signature to predict overall survival in patients of colon adenocarcinoma

“…Colorectal cancer (CRC) is the second leading cause of cancer death worldwide [1]. Colon adenocarcinoma (COAD) is the most common subtype of CRC [2]. Despite the advancements in earlier diagnosis and treatment over the past decades, the 5-year survival rate of CRC patients remains unsatisfactory [3].…”

Focus on pattern recognition receptors to identify prognosis and immune microenvironment in colon cancer

“…The colon adenocarcinoma (COAD) is the representative subtype regarding colon cancer, which takes up 98% of new colon cancer cases, with the 5-year survival rate of 40 -60% (3). The early diagnosis rate of COAD was low, and most patients were in the middle and late stages when they were found (4). With the development of diagnostic techniques and optimization of treatment technologies, the mortality rate of COAD has decreased by 20% in the last 10 years (5).…”