Identification of the collagen family as prognostic biomarkers and immune-associated targets in gastric cancer

Chen, Yihuan; Chen, Wei; Dai, Xiaoshuo; Zhang, Chengjuan; Zhang, Qiushuang; Lü, Jing

doi:10.1016/j.intimp.2020.106798

Cited by 18 publications

(13 citation statements)

References 69 publications

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“…In recent years, several bioinformatics studies have emerged emphasizing the importance of the collagen family in solid cancer development. Thus, Chen Y et al identified COL1A1, COL1A2, and COL12A1 as prognostic biomarkers and immune-associated targets in GC using two GEO OMBIBUS data files with 25 pairs of gastric tumor and adjacent non-tumor mucosa tissues [ 25 ]. Moreover, Zhaoxing Li et al extended the list including other family members such as COL1A1, COL1A2, COL3A1, COL5A2, COL4A1, FN1, COL5A1, COL4A2, and COL6A3, where COL1A1 and COL1A2 were proposed as poor prognostic biomarkers for GC [ 26 ].…”

Section: Discussionmentioning

confidence: 99%

Collagen Family and Other Matrix Remodeling Proteins Identified by Bioinformatics Analysis as Hub Genes Involved in Gastric Cancer Progression and Prognosis

Chivu‐Economescu¹,

Necula

Matei³

et al. 2022

IJMS

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Gastric cancer has remained in the top five cancers for over ten years, both in terms of incidence and mortality due to the shortage of biomarkers for disease follow-up and effective therapies. Aiming to fill this gap, we performed a bioinformatics assessment on our data and two additional GEO microarray profiles, followed by a deep analysis of the 40 differentially expressed genes identified. PPI network analysis and MCODE plug-in pointed out nine upregulated hub genes coding for proteins from the collagen family (COL12A1, COL5A2, and COL10A1) or involved in the assembly (BGN) or degradation of collagens (CTHRC1), and also associated with cell adhesion (THBS2 and SPP1) and extracellular matrix degradation (FAP, SULF1). Those genes were highly upregulated at the mRNA and protein level, the increase being correlated with pathological T stages. The high expression of BGN (p = 8 × 1012), THBS2 (p = 1.2 × 106), CTHRC1 (p = 1.1 × 104), SULF1 (p = 3.8 × 104), COL5A1 (p = 1.3 × 104), COL10A1 (p = 5.7 × 104), COL12A1 (p = 2 × 103) correlated with poor overall survival and an immune infiltrate based especially on immunosuppressive M2 macrophages (p-value range 4.82 × 107–1.63 × 1013). Our results emphasize that these genes could be candidate biomarkers for GC progression and prognosis and new therapeutic targets.

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Section: Discussionmentioning

confidence: 99%

Collagen Family and Other Matrix Remodeling Proteins Identified by Bioinformatics Analysis as Hub Genes Involved in Gastric Cancer Progression and Prognosis

Chivu‐Economescu¹,

Necula

Matei³

et al. 2022

IJMS

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“…There were several literatures using the same dataset in this study ( Chen et al, 2020 ; Chi et al, 2020 ; Li Z. et al, 2020 ; Tian et al, 2020 ; Wang F. et al, 2020 ; Wu et al, 2020 ). However, most of them selected multiple genes for GC by some routine methods and did not concentrate on one gene/biomarker.…”

Section: Discussionmentioning

confidence: 99%

Analysis of Cyclin-Dependent Kinase 1 as an Independent Prognostic Factor for Gastric Cancer Based on Statistical Methods

Zhang

Zou

et al. 2020

Front. Cell Dev. Biol.

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ObjectiveThe aim of this study was to investigate the expression of cyclin-dependent kinase 1 (CDK1) in gastric cancer (GC), evaluate its relationship with the clinicopathological features and prognosis of GC, and analyze the advantage of CDK1 as a potential independent prognostic factor for GC.MethodsThe Cancer Genome Atlas (TCGA) data and corresponding clinical features of GC were collected. First, the aim gene was selected by combining five topological analysis methods, where the gene expression in paracancerous and GC tissues was analyzed by Limma package and Wilcox test. Second, the correlation between gene expression and clinical features was analyzed by logistic regression. Finally, the survival analysis was carried out by using the Kaplan–Meier. The gene prognostic value was evaluated by univariate and multivariate Cox analyses, and the gene potential biological function was explored by gene set enrichment analysis (GSEA).ResultsCDK1 was selected as one of the most important genes associated with GC. The expression level of CDK1 in GC tissues was significantly higher than that in paracancerous tissues, which was significantly correlated with pathological stage and grade. The survival rate of the CDK1 high expression group was significantly lower than that of the low expression group. CDK1 expression was significantly correlated with overall survival (OS). CDK1 expression was mainly involved in prostate cancer, small cell lung cancer, and GC and was enriched in the WNT signaling pathway and T cell receptor signaling pathway.ConclusionCDK1 may serve as an independent prognostic factor for GC. It is also expected to be a new target for molecular targeted therapy of GC.

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“…It has been well known that the molecules of the collagen family play important functions in the progression of many diseases. Collagen families, especially COL1A1, COL1A2, may be potential prognostic biomarkers of gastric cancer and its immune-related therapeutic targets (25). They were found to be positively correlated with macrophage in ltration and M2 macrophage marker expression, meanwhile, the expression of collagen was related to the sensitivity and drug resistance of gastric cancer cells to therapeutic drugs.…”

Section: Discussionmentioning

confidence: 97%

Identification of Potential Crucial Immune-related Genes and Key Pathways in Oral Lichen Planus

Geng¹,

Zhang²,

Tang³

et al. 2021

Preprint

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Oral lichen planus (OLP) is a chronic autoimmune oral mucosal disease which seriously affect the life quality of the patients. But till now, the exact etiology and pathogenesis of OLP still remains unclear. The aim of our study was to find the key molecules and pathway involved in the pathogenesis mechanisms of OLP, therefore, provide reference for identifying more effective therapeutic strategies for OLP. Data from GSE52130 were downloaded from GEO data sets for analysis, and a total of 255 differentially expressed genes were selected out. Then by means of a series of gene enrichment analysis, we illustrated that most of these important genes were enriched in the focal adhesion pathway and metabolism pathways. In addition, we also constructed a protein-protein interaction (PPI) network and identified 8 hub genes which may play the important role in the development of OLP, including THBS2, COL3A1, IGFBP3, COL1A2, COL1A1, PTGS2, IL1B, ARG1. Lastly, we also predicted transcription factors of these hub genes, then constructed the corresponding transcription regulatory network. Taken together, our data indicated that the focal adhesion pathway and metabolism pathways, as well as 8 crucial immune-related genes might be most likely involved in the development of OLP, which would provide important information and objective basis for elucidating the pathogenesis of OLP and providing more effective targeted immunotherapy strategies for OLP.

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Identification of the collagen family as prognostic biomarkers and immune-associated targets in gastric cancer

Cited by 18 publications

References 69 publications

Collagen Family and Other Matrix Remodeling Proteins Identified by Bioinformatics Analysis as Hub Genes Involved in Gastric Cancer Progression and Prognosis

Collagen Family and Other Matrix Remodeling Proteins Identified by Bioinformatics Analysis as Hub Genes Involved in Gastric Cancer Progression and Prognosis

Analysis of Cyclin-Dependent Kinase 1 as an Independent Prognostic Factor for Gastric Cancer Based on Statistical Methods

Identification of Potential Crucial Immune-related Genes and Key Pathways in Oral Lichen Planus

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