An integrative analysis of transcriptome, methylome and single-cell RNA sequencing data identifies UBE2H as a marker of oxaliplatin resistance in colorectal cancer

Cancer Cell International Fang et al. Cancer Cell International (2025) 25:383 https://doi.org/10.1186/s12935-025-03996-4 Open Access RESEARCH An integrative analysis of transcriptome, methylome and single-cell RNA sequencing data identifies UBE2H as a marker of oxaliplatin resistance in colorectal cancer Jinman Fang1,2, Qizhi Zhu1,2,3, Bo Hong1,2, Xueling Li1,2* and Hongzhi Wang1,2 Abstract Metastatic colorectal cancer is commonly treated with oxaliplatin. However, patients may develop resistance to treatment over time, and currently, there are no validated predictive biomarkers for this resistance. A differential analysis of the transcriptome and DNA methylome of colorectal cancer cell lines, classified by their varying IC50 values for oxaliplatin, revealed that genes associated with resistance were enriched for interferon regulatory factor pathways. In contrast, sensitive genes showed enrichment for transcription, amino acid metabolism, development, and binding motifs of c-MyC:Max, AP1 and others. In univariate Cox’s proportional hazard model analysis, it was found that UBE2H expression is linked to shorter survival time in the TCGA dataset and was further validated across five GEO datasets of colorectal cancer. The transcription of UBE2H, along with its gene body methylation, and copy number variation was found to be higher in resistant cell lines compared to sensitive ones. Additionally, UBE2H levels were higher in cancer samples than in control samples, while the promoter methylation is lower in cancer samples than in control samples. In groups with high UBE2H, there was an increased infiltration of eight cell types, including CD8+ T cells and type 2 T helper cells. Conversely, only T helper 17 cells showed reduced infiltration. Moreover, UBE2H expression was positively correlated with checkpoint inhibitors, CTLA4 and PDCD1, along with immune regulatory genes, such as FOXP3, IL10, IGFB1, CD274, and LAG3, etc. Analysis of single cell RNA-sequencing data revealed that UBE2H expression is elevated in undifferentiated and proliferative cells located at the base of intestinal crypts in normal colon tissue. Our findings suggest that UBE2H could serve as a resistance marker to oxaliplatin, as it is associated with methylation, the presence of proliferative and undifferentiated cancer cells, and immune exhaustion. The proposed analytical pipeline may also be applicable to other cancers and diseases. Keywords Oxaliplatin resistance, UBE2H, ScRNA-Seq data, Methylome, Survival analysis, Colorectal cancer *Correspondence: Xueling Li 1 Science Island Branch of Graduate School, University of Science and Technology of China, Hefei, P. R. China 2 Hefei Cancer Hospital of CAS, Anhui Province Key Laboratory of Medical Physics and Technology; Institute of Health and Medical Technology, HFIPS, Chinese Academy of Sciences (CAS), 350 Shushanhu Road, Hefei 230031, China 3 Institute of Intelligent Machines Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei, China © The Author(s) 2025. Open Access This article is licensed under a Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International License, which permits any non-commercial use, sharing, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if you modified the licensed material. You do not have permission under this licence to share adapted material derived from this article or parts of it. The images or other third party material in this article are included in the article’s Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creati vecommons.org/licenses/by-nc-nd/4.0/. Fang et al. Cancer Cell International (2025) 25:383 Introduction Colorectal cancer (CRC) ranks third in mortality worldwide and accounted for 9.6% of the estimated 20 million new colorectal cancer cases in 2022, with a 2nd mortality rate of 9.3% among approximately 9.7 million new cancer deaths [1]. Oxaliplatin, used in combination with infusional 5-fluorouracil and leucovorin (FOLFOX), is commonly prescribed for treating metastatic colorectal cancer, as well as for adjuvant treatment of CRC.However, as treatment duration increases, drug resistance develops [2, 3]. Furthermore, myelosuppression [4, 5] and other toxicity associated with various administration methods and schedules of oxaliplatin [6] represent significant doselimiting factors for its treatment. Approximately 15% of early-stage and 5% advanced advanced colorectal cancers (CRCs) are characterized as deficient in mismatch repair or exhibit microsatellite instability (dMMR/MSI) [7]. The status of microsatellite instability has been shown to correlate with resistance to 5-fluorouracil (5-FU) when combined with oxaliplatin [8]. Patients with stage III mismatch repair deficient colon are reported to benefit significantly from initiating oxaliplatin treatment earlier [9]. Furthermore, colorectal cancer organoid models have identified genes associated with oxaliplatin resistance, such as STMN, VEGFA and NDRG1, as well as transcription factors including E2F1, BRCA1, MYBL2, CDX2 and CDX1 [10].The activation of ABCG2, which alleviates endoplasmic reticulum (ER) stress-induced apoptosis, has been implicated in mediating oxaliplatin resistance in colorectal cancer cells [11]. While the mechanisms of oxaliplatin-resistance have been documented, the role of the epigenetic factors, particularly DNA methylation, which can be more easily modified than DNA mutations, remains underexplored. Additionally, multi-omics approaches hold promise for identifying more reproducible and reliable markers. Studies indicate that treatment resistance is influenced not only by intrinsic factors, such as the tumor cells themselves, but also by extrinsic factors within the tumor microenvironment [12]. Nevertheless, the effects of the cellular heterogeneity in the tumor microenvironment on oxaliplatin resistance are still not fully understood. In this study, we integrated transcriptome and DNA methylome data from the Genomics of Drug Sensitivity in Cancer (GDSC) database [13], TCGA and scRNA-Seq data from colorectal cancers. By performing differential analysis between resistant and sensitive cell lines and examining their association with overall patient survival across multiple independent datasets, we identified differentially expressed genes linked to the response to oxaliplatin treatment. From this analysis, we discovered the predictive marker UBE2H, which may serve as a prognostic indicator for colorectal cancer. Page 2 of 18 Addition (...truncated)