Identification of COL1A1 and COL1A2 as candidate prognostic factors in gastric cancer

Li, Jun; Ding, Yuemin; Li, Aiqing

doi:10.1186/s12957-016-1056-5

Cited by 148 publications

(131 citation statements)

References 23 publications

(25 reference statements)

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“…Disruption in collagen metabolism causes progression of osteoarthritis, osteoporosis, and oncogenesis . Interestingly, the genes involved in this study were the key structural components of ECM . ECM contains multiple proteins including collagens, laminin, fibronectin, hyaluronan and proteoglycan .…”

Section: Discussionmentioning

confidence: 78%

“…Collagen is the dominant structural component of connective tissue, which maintains the stability of organs and supports structural integrity . These collagens are the key structural components of ECM . We then validated the RNA expression of these four candidate genes in our dataset.…”

Section: Resultsmentioning

confidence: 99%

“…29 Interestingly, the genes involved in this study were the key structural components of ECM. 30 ECM contains multiple proteins including collagens, laminin, fibronectin, hyaluronan and proteoglycan. 36 ECM composition is changed typically by the deposition of collagen I, III and other proteins, leading to pathological changes in the hepatic architecture.…”

Section: Discussionmentioning

confidence: 99%

“…29 These collagens are the key structural components of ECM. 30 We then validated the RNA expression of these four candidate genes in our dataset. As can be seen in…”

Section: Col1a1 Col1a2 Col3a1 and Col6a3 Were Identified By Humanmentioning

confidence: 99%

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(‐)‐Epigallocatechin‐3‐gallate and atorvastatin treatment down‐regulates liver fibrosis‐related genes in non‐alcoholic fatty liver disease

Ying

Yan

Zhao

et al. 2017

Clin Exp Pharma Physio

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Non-alcoholic fatty liver disease (NAFLD) and associated advanced liver diseases have become prevalent conditions in many countries and are associated with increased mortality. Gene expression profiles in NAFLD have been examined recently but changes in expression elicited by chemical compound treatments have not been investigated. Since (-)-Epigallocatechin-3-gallate (EGCG) and atorvastatin (ATST) exhibit similar efficacy in NAFLD models, we reasoned that some common key genes might alter after treatment of EGCG and ATST. Accordingly, we applied integrated bioinformatics analyses of RNA microarray data from EGCG and ATST treatment groups compared to controls in a NAFLD phenotypic mouse model. Using differential expression (DE) analysis, Kyoto Encyclopaedia of Genes and Genomes (KEGG) pathway analysis, Gene Set Enrichment Analysis (GSEA) and ClueGO enrichment, shared EGCG and ATST down-regulated pathways were identified which included extracellular matrix (ECM)-receptor interaction and protein processing in endoplasmic reticulum (ER). To refine key genes associated with liver fibrosis, a human NAFLD signature derived from patients of different fibrosis stages was analyzed. The results showed that fibrosis-related genes Col1a1, Col1a2, Col3a1 and Col6a3 were significantly down-regulated. These four genes were further validated as down-regulated in an independent mouse NAFLD dataset. We conclude that EGCG and ATST treatment results in the significant down-regulation of genes related to liver fibrosis.

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Section: Discussionmentioning

confidence: 78%

Section: Resultsmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

“…29 These collagens are the key structural components of ECM. 30 We then validated the RNA expression of these four candidate genes in our dataset. As can be seen in…”

Section: Col1a1 Col1a2 Col3a1 and Col6a3 Were Identified By Humanmentioning

confidence: 99%

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(‐)‐Epigallocatechin‐3‐gallate and atorvastatin treatment down‐regulates liver fibrosis‐related genes in non‐alcoholic fatty liver disease

Ying

Yan

Zhao

et al. 2017

Clin Exp Pharma Physio

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“…COL1A1 encodes the subunit of type I collagen, which is preferentially synthesized in the bone, dermis, and tendons [24], and is recognized as a tumor-related gene. Previous studies reported that COL1A1 is upregulated in the tumor tissues in breast, gastric and liver cancers, and most likely participates in tumorigenesis [25][26][27]. Thus, the mis-splicing of COL1A1 may play a potential role in LSCC tumorigenesis.…”

Section: Evaluation Of the Target Mirnas Of Hsa_circ_0044520 And Hsa_mentioning

confidence: 96%

Circular RNA Expression Profile in Laryngeal Squamous Cell Carcinoma Revealed by Microarray

Fan¹,

Xia²,

Zhu³

et al. 2018

Cell Physiol Biochem

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Background/Aims: A growing body of evidence has suggested that circular RNAs (circRNAs) have crucial functions in the regulation of gene expression, and their dysregulation has been implicated in various types of cancers. However, the roles of circRNAs in laryngeal cancer remain largely unknown. This study investigated the global changes in the expression pattern of circRNAs in laryngeal squamous cell carcinoma (LSCC) to identify potential differentially expressed circRNAs. Methods: Microarray-based circRNA expression was determined in LSCC and paired normal laryngeal tissues. Pathway analyses of the genes producing differentially expressed circRNAs were performed to predict the function of circRNAs using standard enrichment computational methods. Expression levels of candidate circRNAs and microRNAs (miRNAs) were detected by quantitative real-time PCR. The circRNA/ miRNA interactions were constructed using bioinformatics methods to predict the binding of miRNA with circRNA. Results: We identified 506 differentially expressed circRNAs from human LSCC and normal laryngeal mucosa tissues. We confirmed that hsa_circ_0044520 and hsa_circ_0044529 were significantly upregulated in LSCC tissues. The most likely potential target miRNAs for hsa_ circ_0044520 and hsa_circ_0044529 were hsa-miR-4726-5p and hsa-miR-4640-5p, respectively. Functional analysis showed that hsa_circ_0044520 and hsa_circ_0044529 were involved in the process of collagen synthesis. Conclusion: Competitive endogenous RNA network prediction and bioinformatics functional analysis revealed that hsa_circ_0044520 and hsa_circ_0044529 play important regulatory roles by sponging hsa-miR-4726-5p and hsa-miR-4640-5p, thereby providing novel insights into the tumorigenesis of LSCC.

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A construction and comprehensive analysis of ceRNA networks and infiltrating immune cells in papillary renal cell carcinoma

et al. 2021

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Background As the second most common malignancy in adults, papillary renal cell carcinoma (PRCC) has shown an increasing trend in both incidence and mortality. Effective treatment for advanced metastatic PRCC is still lacking. In this study, we aimed to establish competitive endogenous RNA (ceRNA) networks related to PRCC tumorigenesis, and analyze the specific role of differentially expressed ceRNA components and infiltrating immune cells in tumorigenesis. Methods CeRNA networks were established to identify the key ceRNAs related to PRCC tumorigenesis based on the 318 samples from The Cancer Genome Atlas database (TCGA), including 285 PRCC and 33 normal control samples. The R package, “CIBERSORT,” was used to evaluate the infiltration of 22 types of immune cells. Then we identified the significant ceRNAs and immune cells, based on which two nomograms were obtained for predicting the prognosis in PRCC patients. Finally, we investigated the co‐expression of PRCC‐specific immune cells and core ceRNAs via Pearson correlation test. Results COL1A1, H19, ITPKB, LDLR, TCF4, and WNK3 were identified as hub genes in ceRNA networks. Four prognostic‐related tumor‐infiltrating immune cells, including T cells CD4 memory resting, Macrophages M1, and Macrophages M2 were revealed. Pearson correlation test indicated that Macrophage M1 was negatively related with COL1A1 (p < 0.01) and LDLR (p < 0.01), while Macrophage M2 was positively related with COL1A1 (p < 0.01), TCF4 (p < 0.01), and H19 (p = 0.032). Two nomograms were conducted with favorable accuracies (area under curve of 1‐year survival: 0.935 and 0.877; 3‐year survival: 0.849 and 0.841; and 5‐year survival: 0.818 and 0.775, respectively). Conclusion The study constructed two nomograms suited for PRCC prognosis predicting. Moreover, we concluded that H19‐miR‐29c‐3p‐COL1A1 axis might promote the polarization of M2 macrophages and inhibit M1 macrophage activation through Wnt signaling pathway, collaborating to promote PRCC tumorigenesis and lead to poor overall survival of PRCC patients.

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Identification of COL1A1 and COL1A2 as candidate prognostic factors in gastric cancer

Cited by 148 publications

References 23 publications

(‐)‐Epigallocatechin‐3‐gallate and atorvastatin treatment down‐regulates liver fibrosis‐related genes in non‐alcoholic fatty liver disease

(‐)‐Epigallocatechin‐3‐gallate and atorvastatin treatment down‐regulates liver fibrosis‐related genes in non‐alcoholic fatty liver disease

Circular RNA Expression Profile in Laryngeal Squamous Cell Carcinoma Revealed by Microarray

A construction and comprehensive analysis of ceRNA networks and infiltrating immune cells in papillary renal cell carcinoma

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