scholarly journals LINC02257, an Enhancer RNA of Prognostic Value in Colon Adenocarcinoma, Correlates With Multi-Omics Immunotherapy-Related Analysis in 33 Cancers

2021 ◽  
Vol 8 ◽  
Author(s):  
Junbo Xiao ◽  
Yajun Liu ◽  
Jun Yi ◽  
Xiaowei Liu
Keyword(s):  
Survival Analysis ◽  
Signaling Pathway ◽  
Large Scale ◽  
Immune Cell ◽  
Colon Adenocarcinoma ◽  
Akt Signaling ◽  
The Cancer Genome Atlas ◽  
Akt Signaling Pathway ◽  
Free Interval ◽  
Cancer Types

Accumulated evidence supports that long non-coding RNAs (lncRNAs) are involved significantly in the development of human cancers. Enhancer RNAs (eRNAs), a subtype of lncRNAs, have recently attracted much attention about their roles in carcinogenesis. Colon adenocarcinoma is one of the most commonly diagnosed tumors with unfavorable prognosis. It highlights the great significance of screening and identifying novel biomarkers. More importantly, it remains to be elucidated with respect to the function of eRNAs in colon adenocarcinoma, as is in pan-cancers. The expression of LINC02257 was determined based on the data obtained from The Cancer Genome Atlas (TCGA). Further evaluation was performed on the basis of the following analyses: clinicopathology and survival analysis, gene ontology (GO) terms, and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis, as well as multi-omics immunotherapy-related analysis and co-expression analysis. The statistical analysis was conducted in R software, and immune cell infiltration of LINC02257 expression in cancers was investigated by using the CIBERSORT algorithm. By large-scale data mining, our study highlighted that a total of 39 eRNA genes were associated with colon adenocarcinoma prognosis, among which 25 eRNAs showed significant associations with their predicted target genes. LINC02257 was identified as the most significant survival-associated eRNA, with DUSP10 as its target gene. Besides, the high expression of LINC02257 in colon adenocarcinoma was more vulnerable to unfavorable prognosis and correlated with various clinical characteristics. GO and KEGG analyses revealed that LINC02257 was closely correlated with extracellular matrix organization via the PI3K-Akt signaling pathway. Besides, LINC02257 expression correlated with a multi-omics analysis of 33 cancer types, such as survival analysis [overall survival (OS), disease-specific survival (DSS), disease-free interval (DFI), and progression-free interval (PFI)] and immunotherapy-related analysis [tumor microenvironment (TME), tumor mutational burden (TMB), and microsatellite instability (MSI)]. Finally, we investigated the co-expression genes of LINC02257 and its potential signaling pathways across different cancer types. LINC02257 is screened and can function as an independent prognostic biomarker through the PI3K-Akt signaling pathway for colon adenocarcinoma. Simultaneously, LINC02257 may be a multifaceted and significant immunotherapy-related eRNA in different cancers.

scholarly journals Pan-Cancer Analysis of PIMREG as a Biomarker for the Prognostic and Immunological Role

2021 ◽  
Vol 12 ◽  
Author(s):  
Hua Zhu ◽  
Xinyao Hu ◽  
Yingze Ye ◽  
Zhihong Jian ◽  
Yi Zhong ◽  
...  
Keyword(s):  
Signaling Pathway ◽  
Chemokine Receptors ◽  
Antigen Processing ◽  
Immune Cell ◽  
Nk Cell ◽  
Cell Lineage ◽  
Cell Receptor ◽  
The Cancer Genome Atlas ◽  
Cancer Types ◽  
Pan Cancer

Phosphatidylinositol binding clathrin assembly protein interacting mitotic regulator (PIMREG) localizes to the nucleus and can significantly elevate the nuclear localization of clathrin assembly lymphomedullary leukocythemia gene. Although there is some evidence to support an important action for PIMREG in the occurrence and development of certain cancers, currently no pan-cancer analysis of PIMREG is available. Therefore, we intended to estimate the prognostic predictive value of PIMREG and to explore its potential immune function in 33 cancer types. By using a series of bioinformatics approaches, we extracted and analyzed datasets from Oncomine, The Cancer Genome Atlas, Cancer Cell Lineage Encyclopedia (CCLE) and the Human Protein Atlas (HPA), to explore the underlying carcinogenesis of PIMREG, including relevance of PIMREG to prognosis, microsatellite instability (MSI), tumor mutation burden (TMB), tumor microenvironment (TME) and infiltration of immune cells in various types of cancer. Our findings indicate that PIMREG is highly expressed in at least 24 types of cancer, and is negatively correlated with prognosis in major cancer types. In addition, PIMREG expression was correlated with TMB in 24 cancers and with MSI in 10 cancers. We revealed that PIMREG is co-expressed with genes encoding major histocompatibility complex, immune activation, immune suppression, chemokine and chemokine receptors. We also found that the different roles of PIMREG in the infiltration of different immune cell types in different tumors. PIMREG can potentially influence the etiology or pathogenesis of cancer by acting on immune-related pathways, chemokine signaling pathway, regulation of autophagy, RIG-I like receptor signaling pathway, antigen processing and presentation, FC epsilon RI pathway, complement and coagulation cascades, T cell receptor pathway, NK cell mediated cytotoxicity and other immune-related pathways. Our study suggests that PIMREG can be applied as a prognostic marker in a variety of malignancies because of its role in tumorigenesis and immune infiltration.

TRPV4 is a Prognostic Biomarker That Correlates With the Immunosuppressive Microenvironment and Chemoresistance of Anti-Cancer Drugs

2021 ◽  
Author(s):  
kai wang ◽  
Jun xing Feng ◽  
Zhi ling Zheng ◽  
Ying ze Chai ◽  
Hui jun Yu ◽  
...  
Keyword(s):  
Ovarian Cancer ◽  
Transient Receptor Potential ◽  
Immune Cell ◽  
Colon Adenocarcinoma ◽  
Enrichment Analysis ◽  
Receptor Potential ◽  
Gene Set Enrichment Analysis ◽  
The Cancer Genome Atlas ◽  
Free Interval ◽  
Pan Cancer

Abstract Background: Transient receptor potential cation channel subfamily V member 4 (TRPV4) has been reported to regulate tumor progression in many tumor types. However, its association with the tumor immune microenvironment remains unclear.Methods: TRPV4 expression was assessed using data from The Cancer Genome Atlas (TCGA) and the Genotype-Tissue Expression (GTEx) database. The clinical features and prognostic roles of TRPV4 were assessed using TCGA cohort. Gene set enrichment analysis (GSEA) of TRPV4 was conducted using the R package clusterProfiler. We analyzed the association between TRPV4 and immune cell infiltration scores of TCGA samples downloaded from published articles and the TIMER2 database.Results: TRPV4 was highly expressed and associated with worse overall survival (OS), disease-specific survival (DSS), disease-free interval (DFI), and progression-free interval (PFI) in colon adenocarcinoma (COAD) and ovarian cancer. Furthermore, TRPV4 expression was closely associated with immune regulation-related pathways. Moreover, tumor-associated macrophage (TAM) infiltration levels were positively correlated with TRPV4 expression in TCGA pan-cancer samples. Immunosuppressive genes such as PD-L1, PD-1, CTLA4, LAG3, TIGIT, TGFB1, and TGFBR1 were positively correlated with TRPV4 expression in most tumors.Conclusions: Our results suggest that TRPV4 is an oncogene and a prognostic marker in COAD and ovarian cancer. High TRPV4 expression is associated with tumor immunosuppressive status and may contribute to TAM infiltration based on TCGA data from pan-cancer samples.

scholarly journals ClpP regulates breast cancer cell proliferation, invasion and apoptosis by modulating the Src/PI3K/Akt signaling pathway

PeerJ ◽  
2020 ◽  
Vol 8 ◽  
pp. e8754
Author(s):  
Juan Luo ◽  
Beilei Zeng ◽  
Chunfang Tao ◽  
Mengqi Lu ◽  
Guosheng Ren
Keyword(s):  
Breast Cancer ◽  
Western Blot ◽  
Signaling Pathway ◽  
Flow Cytometric Analysis ◽  
Akt Signaling ◽  
The Cancer Genome Atlas ◽  
Akt Signaling Pathway ◽  
Inner Mitochondrial Membrane ◽  
Kaplan Meier ◽  
Kaplan Meier Plotter

Background Caseinolytic protease P (ClpP), which is located on the inner mitochondrial membrane, degrades mitochondrial proteins damaged by oxidative stress. The role of ClpP varies among tumor types. However, the expression pattern and biological functions of ClpP in breast cancer (BC) have not yet been investigated. Methods The Cancer Genome Atlas (TCGA) and Kaplan Meier-plotter database were used to analyze the expression level of ClpP in BC tissues, relationships with clinicopathological characteristics, and the influence on the prognosis of BC. Protein and mRNA expression levels of ClpP in BC cell lines and tissues were detected by quantitative real-time PCR, western blot and immunohistochemical (IHC) analyses. The colony formation assay, transwell assay and flow cytometric analysis were performed to assess various functions of ClpP. Western blot analysis was also conducted to determine the mechanism of ClpP. Results ClpP expression was markedly increased in BC cells and tissues. High expression of ClpP was significantly correlated with the T stage, estrogen receptor (ER) expression, and poor recurrence-free survival (RFS) in TCGA and Kaplan Meier-plotter database. ClpP silencing significantly inhibited proliferation, migration, invasion, and promoted apoptosis of BC cells, which resulted in suppression of the Src/PI3K/Akt signaling pathway. The gain-of-function assay confirmed partial these results.

scholarly journals Quantitative proteomic profiling of tumor-associated vascular endothelial cells in colorectal cancer

2019 ◽  
Author(s):  
Guoqiang Wang ◽  
Qiongzhi Yang ◽  
Maoyu Li ◽  
Ye Zhang ◽  
Yu-xiang Cai ◽  
...  
Keyword(s):  
Colorectal Cancer ◽  
Endothelial Cells ◽  
Signaling Pathway ◽  
Large Scale ◽  
Vascular Endothelial Cells ◽  
Quantitative Information ◽  
Akt Signaling ◽  
Vascular Endothelial ◽  
Proteomic Profiling ◽  
Akt Signaling Pathway

SummeryTo investigate the global proteomic profiles of vascular endothelial cells (VECs) in the tumor microenvironment and antiangiogenic therapy for colorectal cancer (CRC), matched pairs of normal (NVECs) and tumor-associated VECs (TVECs) were purified from CRC tissues by laser capture microdissection and subjected to iTRAQ based quantitative proteomics analysis. Here, 216 differentially expressed proteins (DEPs) were identified and performed bioinformatics analysis. Interestingly, these proteins were implicated in epithelial mesenchymal transition (EMT), ECM-receptor interaction, focal adhesion, PI3K-Akt signaling pathway, angiogenesis and HIF-1 signaling pathway, which may play important roles in CRC angiogenesis. Among these DEPs, Tenascin-C (TNC) was found to upregulated in the TVECs of CRC and be correlate with CRC multistage carcinogenesis and metastasis. Furthermore, the reduction of tumor-derived TNC could attenuate human umbilical vein endothelial cell (HUVEC) proliferation, migration and tube formation through ITGB3/FAK/Akt signaling pathway. Based on the present work, we provided a large-scale proteomic profiling of VECs in CRC with quantitative information, a certain number of potential antiangiogenic targets and a novel vision in the angiogenesis bio-mechanism of CRC.Summery statementWe provided large-scale proteomic profiling of vascular endothelial cells in colorectal cancer with quantitative information, a number of potential antiangiogenic targets and a novel vision in the angiogenesis bio-mechanism of CRC.

scholarly journals Comprehensive Combined Proteomics and Genomics Analysis Identifies Prognostic Related Transcription Factors in Breast Cancer and Explores the Role of DMAP1 in Breast Cancer

2021 ◽  
Vol 11 (11) ◽  
pp. 1068
Author(s):  
Xuan Li ◽  
Hefen Sun ◽  
Yifeng Hou ◽  
Wei Jin
Keyword(s):  
Breast Cancer ◽  
Transcription Factors ◽  
Signaling Pathway ◽  
Cancer Progression ◽  
Immune Cell ◽  
Akt Signaling ◽  
High Expression ◽  
Akt Signaling Pathway ◽  
Normal Tissues

Transcription factors (TFs) are important for regulating gene transcription and are the hallmark of many cancers. The identification of breast cancer TFs will help in developing new diagnostic and individualized cancer treatment tools. In this study, we used quantitative proteomic analyses of nuclear proteins and massive transcriptome data to identify enriched potential TFs and explore the possible role of the transcription factor DMAP1 in breast cancer. We identified 13 prognostic-related TFs and constructed their regulated genes, alternative splicing (AS) events, and splicing factor (SF) regulation networks. DMAP1 was reported less in breast cancer. The expression of DMAP1 decreased in breast cancer tumors compared with normal tissues. The poor prognosis of patients with low DMAP1 expression may relate to the activated PI3K/Akt signaling pathway, as well as other cancer-relevant pathways. This may be due to the low methylation and high expression of these pathway genes and the fact that such patients show more sensitivity to some PI3K/Akt signaling pathway inhibitors. The high expression of DMAP1 was correlated with low immune cell infiltration, and the response to immune checkpoint inhibitor treatment in patients with high DMAP1 expression was low. Our study identifies some transcription factors that are significant for breast cancer progression, which can be used as potential personalized prognostic markers in the future.

scholarly journals Kinesin Family Member C1 (KIFC1) Accelerates Proliferation and Invasion of Endometrial Cancer Cells Through Modulating the PI3K/AKT Signaling Pathway

2020 ◽  
Vol 19 ◽  
pp. 153303382096421
Author(s):  
Kening Zhou ◽  
Jian Zhao ◽  
Lifang Qi ◽  
Yingying He ◽  
Jingui Xu ◽  
...  
Keyword(s):  
Endometrial Cancer ◽  
Family Member ◽  
Signaling Pathway ◽  
Akt Signaling ◽  
The Cancer Genome Atlas ◽  
Migration And Invasion ◽  
Akt Signaling Pathway ◽  
Ec Cells ◽  
Kinesin Family ◽  
Proliferation And Invasion

Endometrial cancer (EC) is one of the most common cancers among women worldwide. Kinesin family member C1 (KIFC1) has been demonstrated to play crucial roles in various tumors. However, the function of KIFC1 in EC remains to be revealed. In this study, upregulation of KIFC1 expression in human EC tissues was found from analysis on data from The Cancer Genome Atlas (TCGA), and positively correlated with short survival outcome of EC patients. In addition, the mRNA and protein levels of KIFC1 were confirmed to be up-regulated in EC cells (Ishikawa, HEC-1B, HEC-1A and KLE) compared to human normal endometrial stromal cells (hESCs) by quantitative real time PCR and western blot. In vitro functional experiments showed that overexpression of KIFC1 promoted proliferation, migration and invasion of EC cells, while KIFC1 depletion showed the opposite results. Moreover, KIFC1 knockdown suppressed tumor growth in mice. Further mechanism analysis showed that KIFC1 participated in the regulation of EC progression through regulating the PI3K/AKT signaling pathway. Collectively, KIFC1 promoted proliferation and invasion through modulating PI3K/AKT signaling pathway in EC, implying that KIFC1 might provide a promising therapeutic target for the therapy of EC.

scholarly journals Potential prognostic value of hsa-miR-18a in hepatocellular carcinoma and the underlying key down-stream gene CHRM2: a comprehensive bioinformatic analysis*

2021 ◽  
Author(s):  
Zile Fu ◽  
Shuzhan Wen ◽  
Tianchang Wei ◽  
Ruiqi Gu ◽  
Shuying Chen
Keyword(s):  
Hepatocellular Carcinoma ◽  
Cell Cycle ◽  
Survival Analysis ◽  
Signaling Pathway ◽  
Target Genes ◽  
Differential Expression Analysis ◽  
Bioinformatic Analysis ◽  
Akt Signaling ◽  
Akt Signaling Pathway ◽  
Pubmed Database

Abstract Background Hepatocellular carcinoma (HCC) is still the fourth leading cause of cancer-related death. Better prognosticators are warranted for HCC. Hsa-miR-18a has been considered implicated in the pathogenesis of several tumors including HCC. Methods Bioinformatic analyses were conducted to predict target genes and carry out enrichment analysis. Validated downstream genes of hsa-miR-18a were obtained from PubMed database. Differential expression analysis was conducted within the “edgeR” R package based on the TCGA datasets. Survival analysis was performed by Kaplan-Meier survival analysis. All the visualizations were implemented by R. Results Bioinformatic analysis obtained a total of 90 target genes of hsa-miR-18a and revealed that target genes were involved in pathways essential for cancer onset and development such as cell cycle and PI3K/AKT signaling pathway. A review of literatures found target genes of miR-18a indeed participating in the biological processes of HCC. CHRM2 was identified as a special gene after the intersection analysis of TCGA differentially expressed genes (DEGs) and predicted target genes. Survival analysis validated that hsa-miR-18a and CHRM2 significantly affected the prognosis of HCC patients. Conclusion There is a strong association between hsa-miR-18a with tumors including HCC via participating essential tumor-promoting pathways including cell cycle, PI3K/AKT signaling pathway, etc. Furthermore, high miR-18a expression and low CHRM2 expression could lead to a poor prognosis in HCC. In conclusion, miR-18a could serve as an expectational prognostic biomarker in HCC.

scholarly journals Sulfatase 2-Induced Cancer-Associated Fibroblasts Promote Hepatocellular Carcinoma Progression via Inhibition of Apoptosis and Induction of Epithelial-to-Mesenchymal Transition

2021 ◽  
Vol 9 ◽  
Author(s):  
Cong Wang ◽  
Chuzhi Shang ◽  
Xiaohong Gai ◽  
Tao Song ◽  
Shaoshan Han ◽  
...  
Keyword(s):  
Hepatocellular Carcinoma ◽  
Signaling Pathway ◽  
Epithelial To Mesenchymal Transition ◽  
Akt Signaling ◽  
The Cancer Genome Atlas ◽  
Luciferase Reporter ◽  
Akt Signaling Pathway ◽  
Mesenchymal Transition ◽  
Hcc Cells

BackgroundSulfatase 2 (SULF2) removes the 6-O-sulfate groups from heparan sulfate proteoglycans (HSPG) and consequently alters the binding sites for various signaling molecules. Here, we elucidated the role of SULF2 in the differentiation of hepatic stellate cells (HSCs) into carcinoma-associated fibroblasts (CAFs) in the hepatocellular carcinoma (HCC) microenvironment and the mechanism underlying CAF-mediated HCC growth.MethodsThe clinical relevance of SULF2 and CAFs was examined using in silico and immunohistochemical (IHC) analyses. Functional studies were performed to evaluate the role of SULF2 in the differentiation of HSCs into CAFs and elucidate the mechanism underlying CAF-mediated HCC growth. Mechanistic studies were performed using the chromatin immunoprecipitation, luciferase reporter, and RNA immunoprecipitation assays. The in vitro findings were verified using the nude HCC xenograft mouse model.ResultsThe Cancer Genome Atlas (TCGA) database and IHC analyses revealed that the expression of CAF markers, which was positively correlated with that of SULF2 in the HCC tissues, predicted unfavorable postsurgical outcomes. Co-culturing HSCs with HCC cells expressing SULF2 promoted CAF differentiation. Additionally, CAFs repressed HCC cell apoptosis by activating the SDF-1/CXCR4/PI3K/AKT signaling pathway. Meanwhile, SULF2-induced CAFs promoted epithelial-to-mesenchymal transition (EMT) of HCC cells by modulating the SDF-1/CXCR4/OIP5-AS1/miR-153-3p/SNAI1 axis. Studies using HCC xenograft mouse models demonstrated that OIP5-AS1 induced EMT by upregulating SNAI1 and promoted HCC growth in vivo.ConclusionThese data indicated that SULF2 secreted by the HCC cells induced the differentiation of HSCs into CAFs through the TGFβ1/SMAD3 signaling pathway. SULF2-induced CAFs attenuated HCC apoptosis by activating the SDF-1/CXCR4/PI3K/AKT signaling pathway and induced EMT through the SDF-1/CXCR4/OIP5-AS1/miR-153-3p/SNAI1 axis. This study revealed a novel mechanism involved in the crosstalk between HCC cells and CAFs in the tumor microenvironment, which can aid in the development of novel and efficient therapeutic strategies for primary liver cancer.

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