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Mou W, Zhu L, Yang T, Lin A, Lyu Q, Guo L, Liu Z, Cheng Q, Zhang J, Luo P. Relationship between ATOH1 and tumor microenvironment in colon adenocarcinoma patients with different microsatellite instability status. Cancer Cell Int 2022; 22:229. [PMID: 35836254 PMCID: PMC9281179 DOI: 10.1186/s12935-022-02651-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2022] [Accepted: 07/05/2022] [Indexed: 11/19/2022] Open
Abstract
Background Colon adenocarcinoma (COAD) is one of the major varieties of malignant tumors threatening human health today. Immune checkpoint inhibitors (ICIs) have recently begun to emerge as an effective option for the treatment of COAD patients, but not all patients can benefit from ICI treatment. Previous studies have suggested that ICIs boast significant clinical effects on patients with microsatellite instability-high (MSI-H), while conversely patients with microsatellite-stable/microsatellite instability-low (MSS/MSI-L) have shown limited response. Methods We used ATAC-seq, RNA-seq, and mutation data from The Cancer Genome Atlas Colon adenocarcinoma (TCGA-COAD) cohort to perform multi-omics differential analysis on COAD samples with different MSI statuses, then further screened genes by additionally combining these results with survival analysis. We analyzed the effects of the screened genes on the tumor microenvironment and immunogenicity of COAD patients, and subsequently determined their influence on the efficacy of ICIs in COAD patients using a series of predictive indexes. Results Twelve genes were screened in the TCGA-COAD cohort, and after the combined survival analysis, we identified ATOH1 as having significant effects. ATOH1 is characterized by high chromatin accessibility, high expression, and high mutation in COAD patients in the MSI-H group. COAD patients with high ATOH1 expression are associated with a better prognosis, unique immune microenvironment, and higher efficacy in ICI treatment. Enrichment analysis showed that COAD patients with high ATOH1 expression displayed significant upregulation in their humoral immunity and other related pathways. Conclusions We speculate that ATOH1 may influence the efficacy of ICIs therapy in patients with COAD by affecting the immune microenvironment and immunogenicity of the tumor. Supplementary Information The online version contains supplementary material available at 10.1186/s12935-022-02651-6.
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Affiliation(s)
- Weiming Mou
- Department of Oncology, Zhujiang Hospital, Southern Medical University, 253 Industrial Avenue, Guangzhou, 510282, Guangdong, China.,The First Clinical Medical School, Southern Medical University, 1023 Shatai South Road, Guangzhou, 510515, Guangdong, China
| | - Lingxuan Zhu
- Department of Oncology, Zhujiang Hospital, Southern Medical University, 253 Industrial Avenue, Guangzhou, 510282, Guangdong, China.,The First Clinical Medical School, Southern Medical University, 1023 Shatai South Road, Guangzhou, 510515, Guangdong, China
| | - Tao Yang
- Department of Oncology, Zhujiang Hospital, Southern Medical University, 253 Industrial Avenue, Guangzhou, 510282, Guangdong, China.,The First Clinical Medical School, Southern Medical University, 1023 Shatai South Road, Guangzhou, 510515, Guangdong, China
| | - Anqi Lin
- Department of Oncology, Zhujiang Hospital, Southern Medical University, 253 Industrial Avenue, Guangzhou, 510282, Guangdong, China
| | - Qiong Lyu
- Department of Oncology, Zhujiang Hospital, Southern Medical University, 253 Industrial Avenue, Guangzhou, 510282, Guangdong, China
| | - Linlang Guo
- Department of Pathology, Zhujiang Hospital, Southern Medical University, Guangzhou, 510282, Guangdong, China
| | - Zaoqu Liu
- Department of Interventional Radiology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China
| | - Quan Cheng
- Department of Neurosurgery, Xiangya Hospital, Central South University, Changsha, 410008, Hunan, China.,National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, China
| | - Jian Zhang
- Department of Oncology, Zhujiang Hospital, Southern Medical University, 253 Industrial Avenue, Guangzhou, 510282, Guangdong, China.
| | - Peng Luo
- Department of Oncology, Zhujiang Hospital, Southern Medical University, 253 Industrial Avenue, Guangzhou, 510282, Guangdong, China.
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Alizadeh-Sedigh M, Fazeli MS, Mahmoodzadeh H, Sharif SB, Teimoori-Toolabi L. Methylation of FBN1, SPG20, ITF2, RUNX3, SNCA, MLH1, and SEPT9 genes in circulating cell-free DNA as biomarkers of colorectal cancer. Cancer Biomark 2021; 34:221-250. [PMID: 34957998 DOI: 10.3233/cbm-210315] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
BACKGROUND Investigating aberrant tumor-specific methylation in plasma cell-free DNA provides a promising and noninvasive biomarker for cancer detection. OBJECTIVE We aimed to investigate methylation status of some promoter regions in the plasma and tumor tissues to find biomarkers for early detection of colorectal cancer. METHODS This case-control study on seventy colorectal cancer patients and fifty matched healthy controls used Methylation-Specific High-Resolution Melting Curve analysis to evaluate the methylation of the selected promoter regions in converted genomic tissue DNA and plasma cfDNA. RESULTS The methylation levels in selected regions of SPG20 (+24375 to +24680, +24209 to +24399, and +23625 to +23883), SNCA (+807 to +1013, +7 to +162, and -180 to +7), FBN1 (+223 to +429, +1 to +245, and -18 to -175), ITF2 (+296 to +436 and -180 to +55), SEPT9 (-914412 to -91590 and -99083 to -92264), and MLH1 (-13 to +22) were significantly higher in tumor tissues compared with normal adjacent tissues. The methylation levels of FBN1, ITF2, SNCA, and SPG20 promoters were significantly higher in the patient's plasma compared to patient's normal tissue and plasma of healthy control subjects. FBN1, SPG20, and SEPT9 promoter methylation had a good diagnostic performance for discriminating CRC tissues from normal adjacent tissues (AUC > 0.8). A panel of SPG20, FBN1, and SEPT9 methylation had a higher diagnostic value than that of any single biomarker and other panels in tissue-based assay (AUC > 0.9). The methylation of FBN1(a) and SPG20(a) regions, as the closest region to the first coding sequence (CDS), had a good diagnostic performance in plasma cfDNA (AUC > 0.8) while a panel consisted of FBN1(a) and SPG20(a) regions showed excellent diagnostic performance for CRC detection in plasma cfDNA (AUC > 0.9). CONCLUSION Methylation of FBN1(a) and SPG20(a) promoter regions in the plasma cfDNA can be an excellent simple, non-invasive blood-based test for early detection of CRC.
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Affiliation(s)
- Maryam Alizadeh-Sedigh
- Molecular Medicine Department, Biotechnology Research Center, Pasteur Institute of Iran, Tehran, Iran
| | - Mohammad Sadegh Fazeli
- Department of Surgery, Division of Colorectal Surgery, Imam Khomeini Medical Complex, Tehran University of Medical Sciences, Tehran, Iran
| | - Habibollah Mahmoodzadeh
- Cancer Institute of Iran, Imam Khomeini Medical Complex, Tehran University of Medical Sciences, Tehran, Iran
| | - Shahin Behrouz Sharif
- Molecular Medicine Department, Biotechnology Research Center, Pasteur Institute of Iran, Tehran, Iran
| | - Ladan Teimoori-Toolabi
- Molecular Medicine Department, Biotechnology Research Center, Pasteur Institute of Iran, Tehran, Iran
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Ma X, Liu J, Li J, Li Y, Le VM, Li S, Liang X, Liu L, Liu J. miR-139-5p reverses stemness maintenance and metastasis of colon cancer stem-like cells by targeting E2-2. J Cell Physiol 2019; 234:22703-22718. [PMID: 31120140 DOI: 10.1002/jcp.28836] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2019] [Revised: 04/30/2019] [Accepted: 05/01/2019] [Indexed: 12/20/2022]
Abstract
Colon cancer stem cells (CCSCs) stand for a critical subpopulation of colon cancer cells that possess self-renewal and multilineage differentiation potentials and drive tumorigenicity. Due to their impact on treatment tolerance, CCSCs have been a hot research topic in the past few years. We have previously reported that miR-139-5p is a vital tumor repressive noncoding RNA whose level decreases in the clinical colon cancer samples with the increase of tumor malignancy. This research discovered that miR-139-5p targets the Wnt/β-catenin/TCF7L2 downstream effector E2-2 in CCSCs. E2-2 is a pivot molecule in the negative feedback loop of miR-139-5p/Wnt/β-catenin/TCF7L2. Its small interfering RNA reverses the stemness maintenance and epithelial-mesenchymal transition of colon cancer CSCs. This study provides a theoretical foundation for the clinical diagnosis and medical treatment of recurrent or metastatic colon cancer with miR-139-5p and its target E2-2.
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Affiliation(s)
- Xiaoying Ma
- State Key Laboratory of Bioreactor Engineering & Shanghai Key Laboratory of New Drug Design, School of Pharmacy, East China University of Science and Technology, Shanghai, People's Republic of China
| | - Jiajun Liu
- State Key Laboratory of Bioreactor Engineering & Shanghai Key Laboratory of New Drug Design, School of Pharmacy, East China University of Science and Technology, Shanghai, People's Republic of China
| | - Jiyu Li
- Department of General Surgery, Shanghai Tenth People's Hospital, Tongji University School of Medicine, Shanghai, People's Republic of China
| | - Yueqi Li
- State Key Laboratory of Bioreactor Engineering & Shanghai Key Laboratory of New Drug Design, School of Pharmacy, East China University of Science and Technology, Shanghai, People's Republic of China
| | - Van Minh Le
- Research Center of Ginseng and Medicinal Materials, National Institute of Medicinal Materials, Ho Chi Minh City, Vietnam
| | - Shaoyu Li
- Department of Clinical Laboratory, The Third Affiliated Hospital of Xinjiang Medical University, Urumqi, Xinjiang, People's Republic of China
| | - Xin Liang
- State Key Laboratory of Bioreactor Engineering & Shanghai Key Laboratory of New Drug Design, School of Pharmacy, East China University of Science and Technology, Shanghai, People's Republic of China
| | - Lingshuang Liu
- Department of Oncology, Longhua Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai, People's Republic of China
| | - Jianwen Liu
- State Key Laboratory of Bioreactor Engineering & Shanghai Key Laboratory of New Drug Design, School of Pharmacy, East China University of Science and Technology, Shanghai, People's Republic of China
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Qian Z, Zhang G, Song G, Shi J, Gong L, Mou Y, Han Y. Integrated analysis of genes associated with poor prognosis of patients with colorectal cancer liver metastasis. Oncotarget 2018; 8:25500-25512. [PMID: 28424419 PMCID: PMC5421946 DOI: 10.18632/oncotarget.16064] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2016] [Accepted: 02/07/2017] [Indexed: 12/12/2022] Open
Abstract
Colorectal cancer (CRC) is one of the most common malignances in the gut. Liver is the most common metastasis site of CRC. This study focuses on the primary CRC and its liver metastasis, aiming to discover several liver metastasis related genes and provide therapeutic candidates. We compared gene expression patterns among the groups of normal colorectal mucosa, primary tumor and the liver metastasis using a CRC gene expression dataset. 84 genes were found to be upregulated in both primary tumor and liver metastases. Function enrichment analysis indicated that these genes are enriched in pathways such as chemotaxis, coagulation and lipid metabolism which are crucial in multi-step cancer metastasis. Gene network analysis identified several important hub genes that may be involved in carcinogenesis and liver metastasis. Then we used a validation dataset containing 562 CRC samples with detailed clinical information, to screen prognostic biomarkers for overall survival (OS) and relapse free survival (RFS). Finally, overexpression of THBS2 (thrombospondin 2), INHBB (inhibin, beta B) and BGN (biglycan) were proved to be correlated with poor OS and RFS. In conclusion, this study indicated that chemotaxis, coagulation and lipid metabolism might play critical roles in the processes of carcinogenesis and liver metastasis. THBS2, INHBB and BGN are prognostic markers and potential therapeutic targets for CRC.
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Affiliation(s)
- Zhenyuan Qian
- Department of Gastrointestinal Surgery, Zhejiang Provincial People's Hospital, Hangzhou, Zhejiang 310014, P.R. China
| | - Guobing Zhang
- Department of Pharmacy, Zhejiang Provincial People's Hospital, Hangzhou, Zhejiang 310014, P.R. China
| | - Guangyuan Song
- Zhejiang Chinese Medical University, Hangzhou, Zhejiang 310053, P.R. China
| | - Ji Shi
- Zhejiang Chinese Medical University, Hangzhou, Zhejiang 310053, P.R. China
| | - Lijie Gong
- Zhejiang Chinese Medical University, Hangzhou, Zhejiang 310053, P.R. China
| | - Yiping Mou
- Department of Gastrointestinal Surgery, Zhejiang Provincial People's Hospital, Hangzhou, Zhejiang 310014, P.R. China.,Key Laboratory of Gastroenterology of Zhejiang Province, Zhejiang Provincial People's Hospital, Hangzhou, Zhejiang 310014, P.R. China
| | - Yong Han
- Clinical Research Institute, Zhejiang Provincial People's Hospital, Hangzhou, Zhejiang 310014, P.R. China
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Wils LJ, Bijlsma MF. Epigenetic regulation of the Hedgehog and Wnt pathways in cancer. Crit Rev Oncol Hematol 2018; 121:23-44. [DOI: 10.1016/j.critrevonc.2017.11.013] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2017] [Revised: 11/17/2017] [Accepted: 11/17/2017] [Indexed: 12/14/2022] Open
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Zhao Z, Liu W, Liu J, Wang J, Luo B. The effect of EBV on WIF1, NLK, and APC gene methylation and expression in gastric carcinoma and nasopharyngeal cancer. J Med Virol 2017; 89:1844-1851. [PMID: 28543390 DOI: 10.1002/jmv.24863] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2016] [Accepted: 05/07/2017] [Indexed: 12/27/2022]
Abstract
Epstein-Barr virus (EBV) is an important DNA tumor virus that is associated with approximately 10% of gastric carcinomas and 99% of nasopharyngeal cancers (NPC). DNA methylation and microRNAs (miRNAs) are the most studied epigenetic mechanisms that can prompt disease susceptibility. This study aimed to detect the effect of EBV on Wnt inhibitory factor 1 (WIF1), Nemo-like kinase (NLK), and adenomatous polyposis coli (APC) gene methylation, and expression in gastric carcinoma and NPC. The WIF1, NLK, and APC gene mRNA expression levels were measured by real-time quantitative RT-PCR in four EBV-positive cell lines and four EBV-negative cell lines. Bisulfite genomic sequencing or methylation-specific PCR was used to detect the methylation status of the WIF1, NLK, and APC promoters. All cell lines were treated with 5-azacytidine (5-aza-dC), miR-BART19-3p mimics or an inhibitor, and analyzed by flow cytometry and MTT cell proliferation assays. The WIF1, NLK, and APC promoters were hypermethylated in all eight cell lines. 5-Aza-dC displayed a growth inhibitory effect on cells . After transfection with miR-BART19-3p mimics, the expression of WIF1, and APC decreased, and the cellular proliferation rate increased. After transfection with the miR-BART19-3p inhibitor, the expression levels were higher, and the cell growth was inhibited. In the NPC and GC cell lines, the promoters of WIF1, NLK, and APC are highly methylated, and the expression of these three genes is regulated by miR-BART19-3p. The activity of the Wnt pathway in EBV-associated tumors may be enhanced by miR-BART19-3p.
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Affiliation(s)
- Zhenzhen Zhao
- Department of Medical Microbiology, Qingdao University Medical College, Qingdao, China
| | - Wen Liu
- Department of Medical Microbiology, Qingdao University Medical College, Qingdao, China
| | - Jincheng Liu
- Department of Medical Microbiology, Qingdao University Medical College, Qingdao, China
| | - Jiayi Wang
- Department of Medical Microbiology, Qingdao University Medical College, Qingdao, China
| | - Bing Luo
- Department of Medical Microbiology, Qingdao University Medical College, Qingdao, China
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