Identification of hub genes associated with prognosis, diagnosis, immune infiltration and therapeutic drug in liver cancer by integrated analysis

Lei, Xinyi; Zhang, Miao; Guan, Bingsheng; Chen, Qiang; Dong, Zhiyong; Wang, Cunchuan

doi:10.1186/s40246-021-00341-4

Cited by 21 publications

(13 citation statements)

References 89 publications

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“…Users can fully explore the clinical and genomic characteristics of tumors with TIMER's ( https://cistrome.shinyapps.io/timer/ ) comprehensive analysis of immune infiltrates of different cancer types [ 31 ]. We examined the correlation of hub genes in CRA and CRC with six immune cells: B cells, CD8+ T cells, CD4+ T cells, macrophages, neutrophils, and dendritic cells [ 32 ].…”

Section: Methodsmentioning

confidence: 99%

Identification of Key MicroRNAs and Genes between Colorectal Adenoma and Colorectal Cancer via Deep Learning on GEO Databases and Bioinformatics

Zhang

Jin

Liu

et al. 2023

Contrast Media & Molecular Imaging

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Background. Deep learning techniques are gaining momentum in medical research. Colorectal adenoma (CRA) is a precancerous lesion that may develop into colorectal cancer (CRC) and its etiology and pathogenesis are unclear. This study aims to identify transcriptome differences between CRA and CRC via deep learning on Gene Expression Omnibus (GEO) databases and bioinformatics in the Chinese population. Methods. In this study, three microarray datasets from the GEO database were used to identify the differentially expressed genes (DEGs) and differentially expressed miRNAs (DEMs) in CRA and CRC. The FunRich software was performed to predict the targeted mRNAs of DEMs. The targeted mRNAs were overlapped with DEGs to determine the key DEGs. Molecular mechanisms of CRA and CRC were evaluated using enrichment analysis. Cytoscape was used to construct protein–protein interaction (PPI) and miRNA–mRNA regulatory networks. We analyzed the expression of key DEMs and DEGs, their prognosis, and correlation with immune infiltration based on the Kaplan–Meier plotter, UALCAN, and TIMER databases. Results. A total of 38 DEGs are obtained after the intersection, including 11 upregulated genes and 27 downregulated genes. The DEGs were involved in the pathways, including epithelial-to-mesenchymal transition, sphingolipid metabolism, and intrinsic pathway for apoptosis. The expression of has-miR-34c ( P = 0.036 ), hsa-miR-320a ( P = 0.045 ), and has-miR-338 ( P = 0.0063 ) was correlated with the prognosis of CRC patients. The expression levels of BCL2, PPM1L, ARHGAP44, and PRKACB in CRC tissues were significantly lower than normal tissues ( P < 0.001 ), while the expression levels of TPD52L2 and WNK4 in CRC tissues were significantly higher than normal tissues ( P < 0.01 ). These key genes are significantly associated with the immune infiltration of CRC. Conclusion. This preliminary study will help identify patients with CRA and early CRC and establish prevention and monitoring strategies to reduce the incidence of CRC.

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Section: Methodsmentioning

confidence: 99%

Identification of Key MicroRNAs and Genes between Colorectal Adenoma and Colorectal Cancer via Deep Learning on GEO Databases and Bioinformatics

Zhang

Jin

Liu

et al. 2023

Contrast Media & Molecular Imaging

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“…Coincidently, previous studies have reported a close relationship between increased expression of ANXA2 , 31 EGLN3 , 32 GAS2L3 , 33 MKI67 , 31 MMP12 , 34 NQO1 35 and PTTG1 36 genes and poor survival in HCC tumors, while variants of PPP1RB gene have been associated with liver steatosis and increased risk of developing liver cancer 37 . Since our comparison revealed INMT as the most downregulated gene (Supplementary Table S5), we analyzed its expression among the 371 cases from the TCGA database.…”

Section: Resultsmentioning

confidence: 56%

Downregulation of indolethylamine N‐methyltransferase is an early event in the rat hepatocarcinogenesis and is associated with poor prognosis in hepatocellular carcinoma patients

López-Torres

Torres-Mena

Castro-Gil

et al. 2022

The Journal of Gene Medicine

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Hepatocellular carcinoma (HCC) is one of the deadliest cancers worldwide, often preceded by cirrhosis and usually diagnosed at advanced stages; therefore, identifying molecular changes at early stages is an attractive strategy for detection and timely treatment. Here, we investigated the progressive transcriptomic changes during experimental hepatocarcinogenesis to identify novel early tumor markers in an HCC model induced by chronic administration of sublethal doses of diethylnitrosamine. An

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“…Numerous studies demonstrated that tumor microenvironment in uences BC development, invasion, and metastasis. In addition, previous study indicated that MDSCs [37], cancer associated broblasts (CAFs) and the extra cellular matrix (ECM) changes are crucial for BC from happens to metastasis [38]. Those supported that CDK1 possibly plays an important role in immune in ltration and even metastasis.…”

Section: Discussionmentioning

confidence: 95%

Bioinformatics analysis reveling prognostic roles of CDK1 in breast cancer

Zhao

Zhang

Wang

et al. 2022

Preprint

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Background The current treatment of breast cancer (BC) commonly adopts endocrine therapy and immunotherapy. And the acquired resistance to those therapies remains a major challenge. Recent evidences indicate that the alternation in tumor microenvironment is a critical factor for cancer therapeutic resistance. Thus, identification of genes that impact tumor micro-environment could contribute to early diagnosis of BC and development of potential therapeutic options. Methods In this study, 3 datasets were acquired from the GEO database to identify the differentially expressed genes (DEGs) between BC tissues and normal tissues. The GO functional and KEGG pathway enrichment of the DEGs were analyzed by using the DAVID database, followed by the construction of a protein-protein interaction (PPI) network. CytoHubba and MCODE were used to select hub genes. GEPIA, Kaplan-Meier Plotter, and UALCAN were used for key gene screening and investigating its effect on patients’ outcome. Results In total, 183 up-regulated and 85 down-regulated DEGs were identified. We identified 10 key genes, including CDK1, CEP55, CENPF, PRC1, TOP2A, NCAPG, KIF4A, CCNB1, ASPM, and KIF20A, and the expression of those genes was correlated well with overall survival of BC patients. Further, the expression level of CDK1 was positively correlated with macrophages, CD4 + T cells, CD8 + T cells and special MDSCs, and negatively correlated with CAFs cells. Conclusions Results of this study may reveal that CDK1 could influence clinicopathological parameters and immune micro-environment, especial immune cell infiltration including myeloid derived suppressor cells (MDSCs), which could serve as a prognostic biomarker in BC patients.

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Identification of hub genes associated with prognosis, diagnosis, immune infiltration and therapeutic drug in liver cancer by integrated analysis

Cited by 21 publications

References 89 publications

Identification of Key MicroRNAs and Genes between Colorectal Adenoma and Colorectal Cancer via Deep Learning on GEO Databases and Bioinformatics

Identification of Key MicroRNAs and Genes between Colorectal Adenoma and Colorectal Cancer via Deep Learning on GEO Databases and Bioinformatics

Downregulation of indolethylamine N‐methyltransferase is an early event in the rat hepatocarcinogenesis and is associated with poor prognosis in hepatocellular carcinoma patients

Bioinformatics analysis reveling prognostic roles of CDK1 in breast cancer

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