AUTHOR=Doria Priscila Galvão , Rocha Gisele Vieira , Bertoni Vanessa Dybal , Santos Roberto de Souza Batista dos , Araújo-Pereira Mariana , Gurgel Clarissa 

TITLE=Gene expression profile in colon cancer therapeutic resistance and its relationship with the tumor microenvironment

JOURNAL=Frontiers in Bioinformatics

VOLUME=Volume 5 - 2025

YEAR=2025

URL=https://www.frontiersin.org/journals/bioinformatics/articles/10.3389/fbinf.2025.1674179

DOI=10.3389/fbinf.2025.1674179

ISSN=2673-7647

ABSTRACT=IntroductionColon cancer is a common disease, treated with few chemotherapeutic agents with similar treatment sequencing despite its heterogeneity. A significant proportion of patients are diagnosed with metastasis, and resistance to antineoplastic drugs is associated with disease progression and therapeutic failure. It is known that the tumor microenvironment plays an essential role in cancer progression, contributing to processes that may be associated with therapeutic resistance mechanisms in colon cancer. In this study, we aim to identify a gene expression signature and its relationship with immune cell infiltration in colon cancer, contributing to the identification of potential resistance biomarkers.MethodsAn in silico study was conducted using RNA-seq data from The Cancer Genome Atlas Program (TCGA) samples, subdivided into two groups (treatment-resistant and non-resistant), taking into account the molecular subgroups (CMS1, CMS2, CMS3, and CMS4). The following algorithms were used: i. Limma was applied to identify differentially expressed genes; ii. WGCNA was applied to construct co-expression networks; iii. CIBERSORT was applied to estimate the proportion of infiltrating immune cells; and iv. TIMER was applied to explore the relationship between core genes and immune cell content.ResultsTwenty differentially expressed genes (DEGs) were found, with 18 related to the group considered resistant to oncologic treatment and presenting poorer overall survival. T CD4 memory resting cells and M0 and M2 macrophages were found in more significant proportions in the analyzed samples and more infiltrated in the tumor microenvironment, the higher the expression of some of these resistance DEGs. Additionally, these genes correlate with biological aspects of neuronal differentiation, axogenesis, and synaptic transmission.ConclusionThe gene expression signature suggests the presence of differentially expressed synaptic membrane genes, which may be involved in neuronal pathways that influence the tumor microenvironment, potentially serving as future biomarkers. Furthermore, the presence of M0 and M2 macrophages and T CD4 memory resting cells suggests a potential interaction that may play a role in therapeutic resistance.