Landscape of Genome-Wide DNA Methylation of Colorectal Cancer Metastasis

Colorectal cancer is a heterogeneous disease caused by both genetic and epigenetics factors. Analysing DNA methylation changes occurring during colorectal cancer progression and metastasis formation is crucial for the identification of novel epigenetic markers of patient prognosis. Genome-wide methylation sequencing of paired samples of colon (normal adjacent, primary tumour and lymph node metastasis) showed global hypomethylation and CpG island (CGI) hypermethylation of primary tumours compared to normal. In metastasis we observed high global and non-CGI regions methylation, but lower CGI methylation, compared to primary tumours. Gene ontology analysis showed shared biological processes between hypermethylated CGIs in metastasis and primary tumours. After complementary analysis with The Cancer Genome Atlas (TCGA) cohort, FIGN, HTRA3, BDNF, HCN4 and STAC2 genes were found associated with poor survival. We mapped the methylation landscape of colon normal tissues, primary tumours and lymph node metastasis, being capable of identified methylation changes throughout the genome. Furthermore, we found five genes with potential for methylation biomarkers of poor prognosis in colorectal cancer patients.

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Proteomic analysis shows down-regulations of cytoplasmic carbonic anhydrases, CAI and CAII, are early events of colorectal carcinogenesis but are not correlated with lymph node metastasis

Tumori Journal ◽

10.1177/030089161209800617 ◽

2012 ◽

Vol 98 (6) ◽

pp. 783-791 ◽

Cited By ~ 4

Author(s):

Ning Wang ◽

Yang Chen ◽

Yuchen Han ◽

Yue Zhao ◽

Yu Liu ◽

...

Keyword(s):

Colorectal Cancer ◽

Lymph Node ◽

Lymph Node Metastasis ◽

Cancer Progression ◽

Normal Mucosa ◽

Laser Desorption Ionization ◽

Ionization Time ◽

Node Metastasis ◽

Flight Mass Spectrometry ◽

Differential Gel Electrophoresis

Aim The aim of the study was to screen the markedly down-regulated proteins in colorectal cancer and analyze their relationship to carcinogenesis, cancer progression and pathological aspects. Methods Proteomic analysis was preformed on six fresh colorectal cancer tissues and paired normal colorectal mucosa by two-dimensional differential gel electrophoresis and matrix-assisted laser desorption/ionization-time of flight mass spectrometry. Two markedly down-regulated proteins among the proteins, of which the expressions were significantly decreased in colorectal cancer compared to normal mucosa, were confirmed by Western Blot in 12 colorectal cancers. Their relationship to carcinogenesis, cancer progression and pathological aspects of colorectal cancer were analyzed in 64 colorectal cancer and paired normal mucosa, 27 benign polyps, and 20 lymph node metastases by immunohistochemistry. Results Two-dimensional differential gel electrophoresis analysis showed there were 2 protein spots, of which the average abundances decreased 3.62 and 3.76 fold in colorectal cancer compared to normal mucosa, respectively. They were identified by matrix-assisted laser desorption/ionization-time of flight mass spectrometry as carbonic anhydrase I and II (CAI and CAII). Validation by Western Blot in 12 colorectal cancers showed there were significantly different expressions of CAI and CAII between colorectal cancer and normal mucosa (P = 0.002 and 0.027, respectively). Immunohistochemistry analysis indicated the expression of CAI and CAII was decreased from normal mucosa to benign polyps, and to colorectal cancer stepwise significantly (P <0.05). However, there were no differences in their expressions between lymph node metastasis and colorectal cancer (P >0.05). There were decreasing trends of CAI and CAII expressions from well to poor differentiation and from stage I or II to stage III or IV, but they were not statistically significant (P >0.05). Conclusions CAI and CAII are necessary enzymes of the colorectum for their normal function. Down-regulations of CAI and CAII are early events of colorectum carcinogenesis. They have no correlations with lymph node metastasis.

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Identification of the miRNA signature and key genes in colorectal cancer lymph node metastasis

Cancer Cell International ◽

10.1186/s12935-021-02058-9 ◽

2021 ◽

Vol 21 (1) ◽

Author(s):

Xi Wang ◽

Guangyu Gao ◽

Zhengrong Chen ◽

Zhihao Chen ◽

Mingxiao Han ◽

...

Keyword(s):

Gene Expression ◽

Colorectal Cancer ◽

Lymph Node ◽

Lymph Node Metastasis ◽

Expression Profiles ◽

Bioinformatic Analysis ◽

The Cancer Genome Atlas ◽

Node Metastasis ◽

Novel Mirna ◽

Potential Biomarker

Abstract Background Because its metastasis to the lymph nodes are closely related to poor prognosis, miRNAs and mRNAs can serve as biomarkers for the diagnosis, prognosis, and therapy of colorectal cancer (CRC). This study aimed to identify novel gene signatures in the lymph node metastasis of CRC. Methods GSE56350, GSE70574, and GSE95109 datasets were downloaded from the Gene Expression Omnibus (GEO) database, while data from 569 colorectal cancer cases were also downloaded from The Cancer Genome Atlas (TCGA) database. Differentially expressed miRNAs (DE-miRNAs) were calculated using R programming language (Version 3.6.3), while gene ontology and enrichment analysis of target mRNAs were performed using FunRich (http://www.funrich.org). Furthermore, the mRNA–miRNA network was constructed using Cytoscape software (Version 3.8.0). Gene expression levels were verified using the GEO datasets. Similarly, quantitative real-time PCR (qPCR) was used to examine expression profiles from 20 paired non-metastatic and metastatic lymph node tissue samples obtained from patients with CRC. Results In total, five DE-miRNAs were selected, and 34 mRNAs were identified after filtering the results. Moreover, two key miRNAs (hsa-miR-99a, hsa-miR-100) and one gene (heparan sulfate-glucosamine 3-sulfotransferase 2 [HS3ST2]) were identified. The GEO datasets analysis and qPCR results showed that the expression of key miRNA and genes were consistent with that obtained from the bioinformatic analysis. A novel miRNA–mRNA network capable of predicting the prognosis and confirmed experimentally, hsa-miR-99a-HS3ST2-hsa-miR-100, was found after expression analysis in metastasized lymph node tissue from CRC samples. Conclusion In summary, miRNAs and genes with potential as biomarkers were found and a novel miRNA–mRNA network was established for CRC lymph node metastasis by systematic bioinformatic analysis and experimental validation. This network may be used as a potential biomarker in the development of lymph node metastatic CRC.

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Genome-wide screening of DNA methylation associated with lymph node metastasis in esophageal squamous cell carcinoma

Oncotarget ◽

10.18632/oncotarget.17147 ◽

2017 ◽

Vol 8 (23) ◽

pp. 37740-37750 ◽

Cited By ~ 10

Author(s):

Hiroaki Nagata ◽

Ken-Ichi Kozaki ◽

Tomoki Muramatsu ◽

Hidekazu Hiramoto ◽

Kousuke Tanimoto ◽

...

Keyword(s):

Dna Methylation ◽

Squamous Cell Carcinoma ◽

Lymph Node ◽

Lymph Node Metastasis ◽

Esophageal Squamous Cell Carcinoma ◽

Cell Carcinoma ◽

Squamous Cell ◽

Node Metastasis ◽

Genome Wide

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Effect of brain-derived neurotrophic factor/TrkB axis on cancer progression in colorectal cancer.

Journal of Clinical Oncology ◽

10.1200/jco.2012.30.15_suppl.e14039 ◽

2012 ◽

Vol 30 (15_suppl) ◽

pp. e14039-e14039

Author(s):

Yasuhiro Inoue ◽

Yoshinaga Okugawa ◽

Susumu Saigusa ◽

Junichiro Hiro ◽

Yuji Toiyama ◽

...

Keyword(s):

Colorectal Cancer ◽

Lymph Node ◽

Lymph Node Metastasis ◽

Cancer Cells ◽

Cancer Progression ◽

Hepatic Metastasis ◽

Neurotrophic Factor ◽

Brain Derived Neurotrophic Factor ◽

Mrna Levels ◽

Node Metastasis

e14039 Background: Brain-derived neurotrophic factor (BDNF) is one of the member of the neurotropin family known to activate the high affinity tyrosine kinase B (TrkB) receptor together with the pan-neurotropin low-affinity coreceptor p75 (p75NTR). TrkB activation by BDNF has been shown to facilitate the progression of several cancers, however, no reports have shown the clinical and biological effects of BDNF/TrkB axis expression in colorectal cancer(CRC). Methods: A total of 223 consecutive patients undergoing surgery for CRC were enrolled. We analyzed BDNF/TrkB mRNA levels by real-time reverse transcription PCR in CRC tissues, and their relationships with clinicopathological findings including survival were investigated. BDNF and TrkB expression were also evaluated by immunohistochemistry. To investigate the biological role of the BDNF/TrkB axis, recombinant human BDNF and Trk antagonist K252a were used for proliferation, migration, and anoikis assays in CRC cell lines. Results: The mean BDNF level in CRC tissue was 94.3 (0-1326.8). One hundred five of 223 patients (47.1%) showed detectable BDNF levels, whereas the remainder had no detectable. BDNF positive expression was significantly associated with undifferenciated histological type, lymph node metastasis, and hepatic metastasis. In addition, increased BDNF/TrkB axis expression associated with lymph node metastasis, hepatic metastasis, and peritoneal disseamination. Immunohistochemical analysis indicated intense BDNF expression in the cytoplasm of cancer cells, and intense TrkB expression in the nuclei of cancer cells, respectively. In vitro, administration of recombinant human BDNF promoted proliferation, anoikis resistance, and partial migration. These effects were generally inhibited by Trk antagonist K252a. Conclusions: We demonstrated the clinical and biological function of BDNF/TrkB axis in CRC. BDNF/TrkB axis appears to play an important role in cancer progression, and blocking this pathway might be clinically useful in developing therapies for patients with CRC.

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Genome-Wide Analysis Revealed a Robust Gene Expression Signature to Identify Lymph Node Metastasis in Submucosal Colorectal Cancer

Gastroenterology ◽

10.1016/s0016-5085(17)33450-9 ◽

2017 ◽

Vol 152 (5) ◽

pp. S1018

Author(s):

Raju Kandimalla ◽

Tsuyoshi Ozawa ◽

Feng Gao ◽

Keisuke Hata ◽

Hiroaki Nozawa ◽

...

Keyword(s):

Gene Expression ◽

Colorectal Cancer ◽

Lymph Node ◽

Lymph Node Metastasis ◽

Gene Expression Signature ◽

Genome Wide Analysis ◽

Expression Signature ◽

Node Metastasis ◽

Genome Wide ◽

Submucosal Colorectal Cancer

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Identification of Mirna Signature and Key Genes in Colorectal Cancer Lymph Node Metastasis

10.21203/rs.3.rs-385507/v1 ◽

2021 ◽

Author(s):

Xi Wang ◽

Guangyu Gao ◽

Zhengrong Chen ◽

Zhihao Chen ◽

Mingxiao Han ◽

...

Keyword(s):

Gene Expression ◽

Colorectal Cancer ◽

Lymph Node ◽

Lymph Node Metastasis ◽

Bioinformatic Analysis ◽

Gene Expression Omnibus ◽

The Cancer Genome Atlas ◽

Cancer Statistics ◽

Node Metastasis ◽

Novel Mirna

Abstract Background: miRNAs and mRNAs can serve as biomarkers for the diagnosis, prognosis and therapy of colorectal cancer (CRC), whose metastasis to lymph node is closely related to the poor prognosis. The current study aimed to identify the novel gene signatures in the lymph node metastasis of CRC.Methods: GSE56350, GSE70574 and GSE95109 were downloaded from the Gene Expression Omnibus (GEO) database and 569 colorectal cancer statistics were also downloaded from the The Cancer Genome Atlas (TCGA) database. Differentially expressed miRNAs (DE-miRNAs) were calculated by using R software. Besides, gene ontology and Enriched pathway analysis of target mRNAs were analyzed by using FunRich. Furthermore, the mRNA-miRNA network was constructed using Cytoscape software. Gene expression level was verified by GEO datasets and forty paired lymph node non-metastasis CRC tissues and lymph node metastatic CRC tissues obtained from patients with CRC using quantitative real-time PCR (qPCR) .Results: In total, five DE-miRNAs were selected, and 34 mRNAs were identified after filtering. Moreover, 2 key miRNAs and one gene were identified including hsa-miR-99a, has-miR-100 and heparan sulfate-glucosamine 3-sulfotransferase 2 (HS3ST2). The GEO datasets analysis and qPCR results showed the expression of key miRNA and genes were consistent with that in the bioinformatic analysis. A novel miRNA-mRNA network, hsa-miR-99a-HS3ST2-has-miR-100 was found in lymph node metastasis of CRC after expression analysis, prognostic prediction and experiments confirmation.Conclusions: In summary, the potential miRNAs and genes were found and a novel miRNA-mRNA network was established in CRC lymph node metastasis by systematic bioinformatic analysis and experiments validation, which may be used as potential biomarkers in the development of lymph node metastatic CRC.

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Follistatin-Like 3 Correlates With Lymph Node Metastasis and Serves as a Biomarker of Extracellular Matrix Remodeling in Colorectal Cancer

Frontiers in Immunology ◽

10.3389/fimmu.2021.717505 ◽

2021 ◽

Vol 12 ◽

Author(s):

Chao Yang ◽

Fengyu Cao ◽

Shuoyang Huang ◽

Yongbin Zheng

Keyword(s):

Colorectal Cancer ◽

Extracellular Matrix ◽

Lymph Node ◽

Lymph Node Metastasis ◽

Protein Level ◽

Cox Regression ◽

External Validation ◽

The Cancer Genome Atlas ◽

Cox Regression Analysis ◽

Node Metastasis

BackgroundAs a heterogeneous disease, colorectal cancer (CRC) presents a great challenge to individualized treatment due to its lymph node metastasis (LNM). Existing studies have shown that immune and stromal components in extracellular matrix (ECM) act as important part in tumorigenicity and progression, while their roles in LNM have not been fully elucidated. Here, crucial ECM-related genes responsible for LNM in CRC were selected by multi-omics analysis.MethodsFirstly, we characterized the immune infiltration landscape of CRC samples from The Cancer Genome Atlas (TCGA) and the Gene Expression Omnibus (GEO) databases by using ssGSEA algorithm. The CRC patients were divided into several immune subgroups by hierarchical clustering analyses. Then, differential genes were identified among immune subgroups and CRC vs. normal tissues in TCGA and GEO GSE39582 cohorts, respectively. Next, weighted correlation network analysis (WGCNA) was employed to construct a co-expression network to find LNM-related modules and hub genes. Subsequently, we evaluated the clinical value of hub gene in prognostic prediction and chemotherapy/immunotherapy. Besides, the protein level of key gene was verified in an external cohort from our center. Finally, we explored the underlying mechanism of FSTL3-mediated LNM by Gene function annotation and correlation analysis.ResultsTwo immune subgroups, namely Immunity_High and Immunity_Low, were defined among the two CRC cohorts using ssGSEA algorithm, respectively. Based on the two immune subgroups, 2,635 overlapping differentially expressed genes were obtained from two cohorts, which were sequentially subjected to WGCNA and univariate Cox regression analysis. Ultimately, FSTL3 was selected as the key gene. Here, we first confirmed that overexpression of FSTL3 correlated with LNM and worse prognosis in CRC and was verified at the protein level in the external validation cohort. Moreover, FSTL3 expression showed strongly positive correlation with immune and stromal components in ECM. We furthermore found that FSTL3 may accelerate LNM through the formation of inhibitory immune microenvironment via promoting macrophage and fibroblast polarization and T cell exhaustion. Interestingly, high FSTL3 expression is linked to chemoresistance, but immunotherapy-sensitive.ConclusionFSTL3 is identified as a biomarker for ECM remodeling and worse clinical outcomes for the first time in CRC and is also a potential immunotherapeutic target to block LNM for CRC.

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