Development and validation of a novel ubiquitination-related gene prognostic signature based on tumor microenvironment for colon cancer

Huang, Baoyi; Deng, Wei‐Ping; Chen, Pengfei; Mao, Qiuxian; Chen, Hao; Zhuo, Zewei; Huang, Zhemin; Chen, Kequan; Huang, Jiayu; Luo, Yujun

doi:10.21037/tcr-22-607

Cited by 3 publications

(1 citation statement)

References 88 publications

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“…Lung cancer is the most frequently diagnosed cancer in 36 countries, accounting for 18% of cancer deaths, and it comprises a variety of histological subtypes, of which lung adenocarcinoma (LUAD) is the most common type ( 2 ). Despite the great advances in therapeutic methods for lung cancer, the prognosis of some patients remains poor and there is an urgent requirement to identify new therapeutic targets and biomarkers in LUAD ( 3 , 4 ).…”

Section: Introductionmentioning

confidence: 99%

Comprehensive pan-cancer analysis identifies FHL2 associated with poor prognosis in lung adenocarcinoma

Pan¹,

Wan²,

Yu³

et al. 2023

Transl Cancer Res

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Background The FHL family (four-and-a-half-LIM-only protein family) contains five multifunctional proteins (FHL1-5) that are involved in cell survival, transcriptional regulation, and signal transduction. Among these proteins, FHL2 is one of the most reported members in tumors, which is differentially expressed in numerous tumors. However, no systematic pan-cancer analysis of FHL2 has been performed so far. Methods We obtained The Cancer Genome Atlas (TCGA) expression profiles and clinical data from Xena database and the Tumor Immune Estimation Resource (TIMER) database. Gene expression, prognosis, mRNA modification, and immune infiltration of FHL2 in pan-cancer were analyzed. Functional analysis validated the potential mechanism of FHL2 in lung adenocarcinoma (LUAD). Results FHL2 is differentially expressed in a wide range of tumors and has prognostic value. Digging into the immune landscape of FHL2, we found that FHL2 is significantly associated with tumor-associated fibroblasts. Furthermore, Gene Ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG), and Gene Set Enrichment Analysis (GSEA) suggested that FHL2 may be involved in epithelial-mesenchymal transition (EMT)-associated pathways such as NF-KB and TGF-β in LUAD. Conclusions Our comprehensive bioinformatics analysis identified mRNA level expression of FHL2 correlates with prognosis in different cancers. This study may help to more fully explore the role of FHL2 in tumor progression and metastasis.

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Section: Introductionmentioning

confidence: 99%

Comprehensive pan-cancer analysis identifies FHL2 associated with poor prognosis in lung adenocarcinoma

Pan¹,

Wan²,

Yu³

et al. 2023

Transl Cancer Res

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Isoform alterations in the ubiquitination machinery impacting gastrointestinal malignancies

Kasturirangan,

Nancarrow,

Shah

et al. 2024

Cell Death Dis

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The advancement of RNAseq and isoform-specific expression platforms has led to the understanding that isoform changes can alter molecular signaling to promote tumorigenesis. An active area in cancer research is uncovering the roles of ubiquitination on spliceosome assembly contributing to transcript diversity and expression of alternative isoforms. However, the effects of isoform changes on functionality of ubiquitination machineries (E1, E2, E3, E4, and deubiquitinating (DUB) enzymes) influencing onco- and tumor suppressor protein stabilities is currently understudied. Characterizing these changes could be instrumental in improving cancer outcomes via the identification of novel biomarkers and targetable signaling pathways. In this review, we focus on highlighting reported examples of direct, protein-coded isoform variation of ubiquitination enzymes influencing cancer development and progression in gastrointestinal (GI) malignancies. We have used a semi-automated system for identifying relevant literature and applied established systems for isoform categorization and functional classification to help structure literature findings. The results are a comprehensive snapshot of known isoform changes that are significant to GI cancers, and a framework for readers to use to address isoform variation in their own research. One of the key findings is the potential influence that isoforms of the ubiquitination machinery have on oncoprotein stability.

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Ubiquitination-Related Gene Signature, Nomogram and Immune Features for Prognostic Prediction in Patients with Head and Neck Squamous Cell Carcinoma

Yang,

Zhou,

Shi

et al. 2024

Genes

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The objective of this research was to create a prognostic model focused on genes related to ubiquitination (UbRGs) for evaluating their clinical significance in head and neck squamous cell carcinoma (HNSCC) patients. The transcriptome expression data of UbRGs were obtained from The Cancer Genome Atlas (TCGA) database, and weighted gene co-expression network analysis (WGCNA) was used to identify specific UbRGs within survival-related hub modules. A multi-gene signature was formulated using LASSO Cox regression analysis. Furthermore, various analyses, including time-related receiver operating characteristics (ROCs), Kaplan–Meier, Cox regression, nomogram prediction, gene set enrichment, co-expression, immune, tumor mutation burden (TMB), and drug sensitivity, were conducted. Ultimately, a prognostic signature consisting of 11 gene pairs for HNSCC was established. The Kaplan–Meier curves indicated significantly improved overall survival (OS) in the low-risk group compared to the high-risk group (p < 0.001), suggesting its potential as an independent and dependable prognostic factor. Additionally, a nomogram with AUC values of 0.744, 0.852, and 0.861 at 1-, 3-, and 5-year intervals was developed. Infiltration of M2 macrophages was higher in the high-risk group, and the TMB was notably elevated compared to the low-risk group. Several chemotherapy drugs targeting UbRGs were recommended for low-risk and high-risk patients, respectively. The prognostic signature derived from UbRGs can effectively predict prognosis and provide new personalized therapeutic targets for HNSCC.

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Development and validation of a novel ubiquitination-related gene prognostic signature based on tumor microenvironment for colon cancer

Cited by 3 publications

References 88 publications

Comprehensive pan-cancer analysis identifies FHL2 associated with poor prognosis in lung adenocarcinoma

Comprehensive pan-cancer analysis identifies FHL2 associated with poor prognosis in lung adenocarcinoma

Isoform alterations in the ubiquitination machinery impacting gastrointestinal malignancies

Ubiquitination-Related Gene Signature, Nomogram and Immune Features for Prognostic Prediction in Patients with Head and Neck Squamous Cell Carcinoma

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