&lt;p&gt;Gene Expression Along with Genomic Copy Number Variation and Mutational Analysis Were Used to Develop a 9-Gene Signature for Estimating Prognosis of COAD&lt;/p&gt;

Lu, Yiping; Wu, Shu Fen; Cui, Changwan; Yu, Miao; Wang, Shuang; Yue, Yuanyi; Liu, Miao; Sun, Zhengrong

doi:10.2147/ott.s255590

Cited by 5 publications

(4 citation statements)

References 43 publications

(43 reference statements)

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“…The mechanism may be that ONECUT1 promotes the proliferation and tumor growth of colorectal cancer cells and promotes liver metastasis by endogenic resistance to anoikis [24]. The high expression of DNAJB13 in colon cancer tissues also con rmed that DNAJB13 is an independent prognostic risk factor for colon cancer patients [25]. The results of the above three genes are consistent with our experiments.…”

Section: Discussionsupporting

confidence: 89%

Construction of a prognostic model for gastric cancer patients based on NAD+ metabolism-related genes and tumor microenvironment analysis

Xing

Zhang

Gao

et al. 2023

Preprint

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Background Nicotinamide adenine dinucleotide (NAD+) metabolism is important in the regulation of tumor immune escape. This study endeavored to develop a NAD + metabolism-related signature in gastric cancer (GC), which could provide a theoretical foundation for prognosis and therapy of GC patients. Methods First, differentially expressed genes (DEGs) between GC and paraneoplastic tissues were intersected with NAD + metabolism-related genes (NMRGs) to obtain differentially expressed NMRGs (DE NMRGs). Then, based on the transcript levels of NMRGs, GC patients were classified into high and low scoring groups using the Gene set variation analysis (GSVA) algorithm. Next, the DEGs between the high and low scoring groups were intersected with DEGs between GC and paraneoplastic tissues to obtain the GC-NM DEGs. Additionally, univariate Cox analysis and Least absolute shrinkage and selection operator (LASSO) regression analysis of GC-NM DEGs were performed to obtain prognostic biomarkers, which were used to construct a risk model. In addition, independent prognostic factors were obtained by Cox analysis based on risk scores and clinicopathological factors. Gene set enrichment analysis (GSEA) enrichment analysis and immune infiltration analysis were performed for the high- and low-risk groups. Finally, the mRNA expression of prognostic related genes was verified by experiment. Results 10 DE NMRGs were obtained and they were involved in the biological process of NAD biosynthetic process, nicotinamide nucleotide, and biosynthetic process. Further 7 biomarkers, including DNAJB13, CST2, THPO, CIDEA, ONECUT1, UPK1B, and SNCG, were obtained through univariate Cox and LASSO analyses of 1001 GC-NM DEGs. In addition, risk score and gender were demonstrated as credible independent prognostic factors for GC. Moreover, GSEA showed that the high-risk group was associated with bile secretion, intrinsic component of synaptic membrane and other pathways, while the low-risk group was associated with CMG complex. In addition, T cells, B cells, and natural killer cells were positively correlated with risk scores, and plasmacytoid dendritic cells were negatively correlated with risk scores. By QRT-PCR, the expression of prognostic genes in GC tissues was significantly up-regulated compared with paraneoplastic tissues. Conclusion This study established a NAD + metabolism-related signature based on DNAJB13, CST2, THPO, CIDEA, ONECUT1, UPK1B, and SNCG, which is of great significance in developing prognostic molecular biomarkers, clinical prognosis prediction, and treatment strategy decision for GC patients.

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Section: Discussionsupporting

confidence: 89%

Construction of a prognostic model for gastric cancer patients based on NAD+ metabolism-related genes and tumor microenvironment analysis

Xing

Zhang

Gao

et al. 2023

Preprint

View full text Add to dashboard Cite

show abstract

“…The mechanism may be that ONECUT1 promotes the proliferation and tumor growth of colorectal cancer cells and promotes liver metastasis by endogenic resistance to anoikis ( Jiang et al, 2019 ). The high expression of DNAJB13 in colon cancer tissues also confirmed that DNAJB13 is an independent prognostic risk factor for colon cancer patients ( Lu et al, 2020 ). The results of the above three genes are consistent with our experiments.…”

Section: Discussionmentioning

confidence: 54%

Immune infiltration and prognosis in gastric cancer: role of NAD+ metabolism-related markers

Xing,

Zhang,

Gao

et al. 2024

PeerJ

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Background This study endeavored to develop a nicotinamide adenine dinucleotide (NAD+) metabolism-related biomarkers in gastric cancer (GC), which could provide a theoretical foundation for prognosis and therapy of GC patients. Methods In this study, differentially expressed genes (DEGs1) between GC and paraneoplastic tissues were overlapped with NAD+ metabolism-related genes (NMRGs) to identify differentially expressed NMRGs (DE-NMRGs). Then, GC patients were divided into high and low score groups by gene set variation analysis (GSVA) algorithm for differential expression analysis to obtain DEGs2, which was overlapped with DEGs1 for identification of intersection genes. These genes were further analyzed using univariate Cox and least absolute shrinkage and selection operator (LASSO) regression analyses to obtain prognostic genes for constructing a risk model. Enrichment and immune infiltration analyses further investigated investigate the different risk groups, and qRT-PCR validated the prognostic genes. Results Initially, we identified DE-NMRGs involved in NAD biosynthesis, with seven (DNAJB13, CST2, THPO, CIDEA, ONECUT1, UPK1B and SNCG) showing prognostic significance in GC. Subsequent, a prognostic model was constructed in which the risk score, derived from the expression profiles of these genes, along with gender, emerged as robust independent predictors of patient outcomes in GC. Enrichment analysis linked high-risk patients to synaptic membrane pathways and low-risk to the CMG complex pathway. Tumor immune infiltration analysis revealed correlations between risk scores and immune cell abundance, suggesting a relationship between NAD+ metabolism and immune response in GC. The prognostic significance of our identified genes was validated by qRT-PCR, which confirmed their upregulated expression in GC tissue samples. Conclusion In this study, seven NAD+ metabolism-related markers were established, which is of great significance for the development of prognostic molecular biomarkers and clinical prognosis prediction for gastric cancer patients.

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“…TNM staging of COAD, reflected poor prognosis in COAD ( 26 ). Hence, the remarkable predictive ability of SNHG7 expression suggests its potential as a prognostic biomarker of poor survival in COAD.…”

Section: Discussionmentioning

confidence: 99%

Long Noncoding RNA SNHG7 Is a Diagnostic and Prognostic Marker for Colon Adenocarcinoma

Jiang

et al. 2022

Front. Oncol.

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Numerous studies have shown that long noncoding RNAs (lncRNAs) play a critical role in the malignant progression of cancer. However, the potential involvement of lncRNAs in colon adenocarcinoma (COAD) remains unexplored. In this study, the expression of lncRNA SNHG7 in colon cancer tissues and its correlation with clinical characteristics were analyzed based on data from The Cancer Genome Atlas (TCGA) database. SNHG7 was found to be highly expressed in 17 types of cancer, including COAD. Next, TCGA data were further investigated to identify differentially expressed genes, and Gene Ontology and Kyoto Encyclopedia of Genes and Genomes analyses were performed. In addition, the relationship between SNHG7 expression and clinical features were analyzed. SNHG7 expression was found to be a potentially valuable indicator for COAD diagnosis and prognosis. Finally, gene set enrichment analysis showed that SNHG7 may affect lupus erythematosus and reactome cellular senescence, possibly influencing the prognosis of patients with COAD. Altogether, these results suggest that SNHG7 may be associated with the occurrence and development of COAD, having potential diagnostic and prognostic value.

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<p>Gene Expression Along with Genomic Copy Number Variation and Mutational Analysis Were Used to Develop a 9-Gene Signature for Estimating Prognosis of COAD</p>

Cited by 5 publications

References 43 publications

Construction of a prognostic model for gastric cancer patients based on NAD+ metabolism-related genes and tumor microenvironment analysis

Construction of a prognostic model for gastric cancer patients based on NAD+ metabolism-related genes and tumor microenvironment analysis

Immune infiltration and prognosis in gastric cancer: role of NAD+ metabolism-related markers

Long Noncoding RNA SNHG7 Is a Diagnostic and Prognostic Marker for Colon Adenocarcinoma

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