GIMAP7 as a Potential Predictive Marker for Pan-Cancer Prognosis and Immunotherapy Efficacy

Qin, Yan; Li, He; Huang, Xiaoliang; Huang, Lihaoyun; Liao, Lixian; Li, Jiasheng; Zhang, Lihua; Li, Wei; Yang, Jianrong

doi:10.2147/jir.s342503

Cited by 19 publications

(18 citation statements)

References 34 publications

(39 reference statements)

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“…These prior studies support our finding that GIMAP7 could be important in severity given its presence on the surface of T-lymphocytes [51]. In the time since GIMAP7 was initially identified [52], it has subsequently been shown to be a potential marker for various cancer types, which further supports its immune-related role [53][54][55][56]. Although the underlying mechanism for this protein is yet to be characterized, we are not surprised by its role in other immune-related diseases or in SARS-CoV-2 disease severity.…”

Section: Discussionsupporting

confidence: 87%

Transcriptomics Meta-Analysis Predicts Two Robust Human Biomarkers for Severe Infection with SARS-CoV-2

Clancy

Hoffmann

Pickett

2022

Preprint

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Defining the human factors associated with severe vs mild SARS-CoV-2 infection has become of increasing interest. Mining large numbers of public gene expression datasets is an effective way to identify genes that contribute to a given phenotype. Combining RNA-sequencing data with the associated clinical metadata describing disease severity can enable earlier identification of patients who are at higher risk of developing severe COVID-19 disease. We consequently identified 356 public RNA-seq human transcriptome samples from the Gene Expression Omnibus database that had disease severity metadata. We then subjected these samples to a robust RNA-seq data processing workflow to quantify gene expression in each patient. This process involved using Salmon to map the reads to the reference transcriptomes, edgeR to calculate significant differential expression levels, and gene ontology enrichment using Camera. We then applied a machine learning algorithm to the read counts data to identify features that best differentiated samples based on COVID-19 severity phenotype. Ultimately, we produced a ranked list of genes based on their Gini importance values that includes GIMAP7 and S1PR2, which are associated with immunity and inflammation (respectively). Our results show that these two genes can potentially predict people with severe COVID-19 at up to ~90% accuracy. We expect that our findings can help contribute to the development of improved prognostics for severe COVID-19.

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Section: Discussionsupporting

confidence: 87%

Transcriptomics Meta-Analysis Predicts Two Robust Human Biomarkers for Severe Infection with SARS-CoV-2

Clancy

Hoffmann

Pickett

2022

Preprint

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“…The immune system is essential in control of tumors, and effective immunotherapy could be achieved through preexisting adaptive immune responses within tumors, such as checkpoint inhibitors (Bruni et al, 2020a). In view of the prevalence of tumors and the convoluted process of tumorigenesis, it is of great significance to explore in-depth the expression of relevant genes in pan-cancer and to assess their levels for clinical treatment and prognostic prediction (Qin et al, 2022).…”

Section: Introductionmentioning

confidence: 99%

Pan-cancer analyses confirmed the cuproptosis-related gene FDX1 as an immunotherapy predictor and prognostic biomarker

Zhang

Zeng²,

Guo³

et al. 2022

Front. Genet.

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Background: The latest research identified cuproptosis as an entirely new mechanism of cell death. However, as a key regulator in copper-induced cell death, the prognostic and immunotherapeutic value of FDX1 in pan-cancer remains unclear.Methods: Data from the UCSC Xena, GEPIA, and CPTAC were analyzed to conduct an inquiry into the overall differential expression of FDX1 across multiple cancer types. The expression of FDX1 in GBM, LUAD and HCC cell lines as well as their control cell lines was verified by RT-QPCR. The survival prognosis, clinical features, and genetic changes of FDX1 were also evaluated. Finally, the relationship between FDX1 and immunotherapy response was further explored through Gene Set Enrichment Analysis enrichment analysis, tumor microenvironment, immune cell infiltration, immune gene co-expression and drug sensitivity analysis.Results: The transcription and protein expression of FDX1 were significantly reduced in most cancer types and had prognostic value for the survival of certain cancer patients such as ACC, KIRC, HNSC, THCA and LGG. In some cancer types, FDX1 expression was also markedly correlated with the clinical characteristics, TMB, MSI, and antitumor drug susceptibility or resistance of different tumors. Gene set enrichment analysis showed that FDX1 was significantly associated with immune-related pathways. Moreover, the expression level of FDX1 was confirmed to be strongly correlated with immune cell infiltration, immune checkpoint genes, and immune regulatory genes to a certain extent.Conclusion: This study comprehensively explored the potential value of FDX1 as a prognostic and immunotherapeutic marker for pan-cancer, providing new direction and evidence for cancer therapy.

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“…In addition, GABRD gene may be a prognostic marker in gliomas with low expression, and it is associated with poor prognosis [ 10 , 11 ]. In another study, GABRD expression was found to be significantly lower in IDH wild-type diffuse gliomas compared to IDH mutant tumors [ 12 ], and patients with high GABRD expression had a better prognosis than those with low GABRD expression [ 13 ]. Taken together, it is suggested that the functional mechanism of GABRD in cancer needs to be investigated on specific cancer types.…”

Section: Introductionmentioning

confidence: 99%

Clinical Data and Biocalculation Methods of GABRD Determine the Clinical Characteristics and Immune Relevance of Colorectal Cancer

Liu

et al. 2022

Evidence-Based Complementary and Alternative Medicine

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Background. The aim of this study was to clarify the expression of gamma-aminobutyric acid type A receptor delta subunit (GABRD) gene in pan-cancer and its correlation with patient prognosis, and to investigate the function and possible mechanism of GABRD in colorectal cancer (CRC). Methods. The Cancer Genome Atlas (TCGA) data were used to analyze the expression differences of GABRD in pan-cancer, and the correlation between GABRD and clinical prognosis of various tumors was analyzed by Cox regression method. According to the expression level of GABRD, Gene Function Annotation (GO) and Kyoto Encyclopedia of Genomes (KEGG) functional enrichment analysis were performed on the differentially expressed genes. Expression of GABRD gene and 44 marker genes of three types of RNA modification (m1A (10), m5C (13), m6A (21)) genes in different tumors was observed. Pearson correlation of GABRD gene and marker genes of five immune pathways was measured. Results: TCGA data analysis showed that GABRD was significantly upregulated in various tumor tissues, especially COAD and READCOAD. Survival analysis showed that GABRD was a prognostic protective factor in CRC ( p < 0.001 ). The results of survival nomogram showed that GABRD, age, and tumor (T) lymph node (N) distant metastasis (M) stage were independent prognostic factors, and the survival model C-index was 0.724 (0.644-1). Gene enrichment and functional analysis showed that GABRD may be related to protein digestion and absorption, ECM-receptor interaction, extracellular structure organization, extracellular matrix organization, pancreatic secretion, and antimicrobial humoral response. The expression of GABRD was positively correlated in m1A-, m5C-, and m6A-related genes. The GABRD gene was found in B cell, T cell CD4, T cell CD8, neutrophil, macrophage in TCGA-COAD (N = 282), and TCGA-COADREAD (N = 373). The infiltration level and DC was significantly positively correlated ( p < 0.05 ). Also, the Pearson correlation coefficient is the largest. Conclusion. The involvement of GABRD in the occurrence and development of CRC may be related to protein digestion and absorption, ECM-receptor interaction, extracellular structure organization, extracellular matrix organization, pancreatic secretion, and antimicrobial humoral response. GABRD can be used as a molecular marker for the prognosis of CRC.

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GIMAP7 as a Potential Predictive Marker for Pan-Cancer Prognosis and Immunotherapy Efficacy

Cited by 19 publications

References 34 publications

Transcriptomics Meta-Analysis Predicts Two Robust Human Biomarkers for Severe Infection with SARS-CoV-2

Transcriptomics Meta-Analysis Predicts Two Robust Human Biomarkers for Severe Infection with SARS-CoV-2

Pan-cancer analyses confirmed the cuproptosis-related gene FDX1 as an immunotherapy predictor and prognostic biomarker

Clinical Data and Biocalculation Methods of GABRD Determine the Clinical Characteristics and Immune Relevance of Colorectal Cancer

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