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Wang L, Chen X, Zhang H, Hong L, Wang J, Shao L, Chen G, Wu J. Comprehensive analysis of transient receptor potential channels-related signature for prognosis, tumor immune microenvironment, and treatment response of colorectal cancer. Front Immunol 2022; 13:1014834. [PMID: 36389750 PMCID: PMC9642045 DOI: 10.3389/fimmu.2022.1014834] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2022] [Accepted: 09/23/2022] [Indexed: 08/13/2023] Open
Abstract
BACKGROUND Transient receptor potential channels (TRPC) play critical regulatory functions in cancer occurrence and progression. However, knowledge on its role in colorectal cancer (CRC) is limited. In addition, neoadjuvant treatment and immune checkpoint inhibitors (ICIs) have increasing roles in CRC management, but not all patients benefit from them. In this study, a TRPC related signature (TRPCRS) was constructed for prognosis, tumor immune microenvironment (TIME), and treatment response of CRC. METHODS Data on CRC gene expression and clinical features were retrospectively collected from TCGA and GEO databases. Twenty-eight TRPC regulators (TRPCR) were retrieved using gene set enrichment analysis. Different TRPCR expression patterns were identified using non-negative matrix factorization for consensus clustering, and a TRPCRS was established using LASSO. The potential value of TRPCRS was assessed using functional enrichment analysis, tumor immune analysis, tumor somatic mutation analysis, and response to preoperative chemoradiotherapy or ICIs. Moreover, an external validation was conducted using rectal cancer samples that received preoperative chemoradiotherapy at Fujian Cancer Hospital (FJCH) via qRT-PCR. RESULTS Among 834 CRC samples in the TCGA and meta-GEO cohorts, two TRPCR expression patterns were identified, which were associated with various immune infiltrations. In addition, 266 intersected genes from 5564 differentially expressed genes (DEGs) between two TRPC subtypes, 4605 DEGs between tumor tissue and adjacent non-tumor tissue (all FDR< 0.05, adjusted P< 0.001), and 1329 prognostic related genes (P< 0.05) were identified to establish the TRPCRS, which was confirmed in the TCGA cohort, two cohorts from GEO, and one qRT-PCR cohort from FJCH. According to the current signature, the high-TRPC score group had higher expressions of PD-1, PD-L1, and CTLA4, lower TIDE score, and improved response to anti-PD-1 treatment with better predictive ability. Compared to the high-TRPC score group, the low-TRPC score group comprised an immunosuppressive phenotype with increased infiltration of neutrophils and activated MAPK signaling pathway, but was more sensitive to preoperative chemoradiotherapy and associated with improved prognosis. CONCLUSIONS The current TRPCRS predicted the prognosis of CRC, evaluated the TIME in CRC, and anticipated the response to immune therapy and neoadjuvant treatment.
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Affiliation(s)
- Lei Wang
- Department of Radiation Oncology, Clinical Oncology School of Fujian Medical University, Fujian Cancer Hospital, Fuzhou, China
| | - Xingte Chen
- Department of Radiation Oncology, Clinical Oncology School of Fujian Medical University, Fujian Cancer Hospital, Fuzhou, China
| | - Hejun Zhang
- Department of Pathology, Clinical Oncology School of Fujian Medical University, Fujian Cancer Hospital, Fuzhou, China
| | - Liang Hong
- Department of Radiation Oncology, Clinical Oncology School of Fujian Medical University, Fujian Cancer Hospital, Fuzhou, China
| | - Jianchao Wang
- Department of Pathology, Clinical Oncology School of Fujian Medical University, Fujian Cancer Hospital, Fuzhou, China
| | - Lingdong Shao
- Department of Radiation Oncology, Clinical Oncology School of Fujian Medical University, Fujian Cancer Hospital, Fuzhou, China
| | - Gang Chen
- Department of Pathology, Clinical Oncology School of Fujian Medical University, Fujian Cancer Hospital, Fuzhou, China
| | - Junxin Wu
- Department of Radiation Oncology, Clinical Oncology School of Fujian Medical University, Fujian Cancer Hospital, Fuzhou, China
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Kapoor S, Damiani E, Wang S, Dharmanand R, Tripathi C, Tovar Perez JE, Dashwood WM, Rajendran P, Dashwood RH. BRD9 Inhibition by Natural Polyphenols Targets DNA Damage/Repair and Apoptosis in Human Colon Cancer Cells. Nutrients 2022; 14:nu14204317. [PMID: 36297001 PMCID: PMC9610492 DOI: 10.3390/nu14204317] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2022] [Revised: 10/07/2022] [Accepted: 10/14/2022] [Indexed: 11/07/2022] Open
Abstract
Epigenetic mechanisms play an important role in the etiology of colorectal cancer (CRC) and other malignancies due, in part, to deregulated bromodomain (BRD) functions. Inhibitors of the bromodomain and extraterminal (BET) family have entered into clinical trials as anticancer agents, and interest has grown in other acetyl 'reader' proteins as therapeutic targets, including non-BET member bromodomain-containing protein 9 (BRD9). We report here that overexpression of BRD9 is associated with poor prognosis in CRC patients, and that siRNA-mediated knockdown of BRD9 decreased cell viability and activated apoptosis in human colon cancer cells, coincident with increased DNA damage. Seeking natural compounds as BRD9 antagonists, molecular docking in silico identified several polyphenols such as Epigallocatechin-3-gallate (EGCG), Equol, Quercetin, and Aspalathin, with favorable binding energies, supported by BROMOscan® (DiscoverX) and isothermal titration calorimetry experiments. Polyphenols mimicked BRD9 knockdown and iBRD9 treatment in reducing colon cancer cell viability, inhibiting colony formation, and enhancing DNA damage and apoptosis. Normal colonic epithelial cells were unaffected, signifying cancer-specific effects. These findings suggest that natural polyphenols recognize and target BRD9 for inhibition, and might serve as useful lead compounds for bromodomain therapeutics in the clinical setting.
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Affiliation(s)
- Sabeeta Kapoor
- Center for Epigenetics & Disease Prevention, Texas A&M Health, Houston, TX 77030, USA
| | - Elisabetta Damiani
- Department of Life and Environmental Sciences, Università Politecnica delle Marche, 60121 Ancona, Italy
| | - Shan Wang
- Stomatology Hospital, School of Stomatology, Zhejiang University School of Medicine, Hangzhou 310030, China
| | - Ravirajan Dharmanand
- Center for Infectious & Inflammatory Diseases, Texas A&M Health, Houston, TX 77030, USA
| | - Chakrapani Tripathi
- Center for Epigenetics & Disease Prevention, Texas A&M Health, Houston, TX 77030, USA
| | | | - Wan Mohaiza Dashwood
- Center for Epigenetics & Disease Prevention, Texas A&M Health, Houston, TX 77030, USA
| | - Praveen Rajendran
- Center for Epigenetics & Disease Prevention, Texas A&M Health, Houston, TX 77030, USA
- Department of Translational Medical Sciences, Texas A&M College of Medicine, Houston, TX 77030, USA
- Correspondence: (P.R.); (R.H.D.); Tel.: +1-713-677-7803 (P.R.); +1-713-677-7806 (R.H.D.)
| | - Roderick Hugh Dashwood
- Center for Epigenetics & Disease Prevention, Texas A&M Health, Houston, TX 77030, USA
- Department of Translational Medical Sciences, Texas A&M College of Medicine, Houston, TX 77030, USA
- Correspondence: (P.R.); (R.H.D.); Tel.: +1-713-677-7803 (P.R.); +1-713-677-7806 (R.H.D.)
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203
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Zhang R, Zhang G, Li B, Wang J, Wang J, Che J, Wang X, Zhang Z. Analysis of LINC01314 and miR-96 Expression in Colorectal Cancer Patients via Tissue Microarray-Based Fluorescence In Situ Hybridization. DISEASE MARKERS 2022; 2022:5378963. [PMID: 36246563 PMCID: PMC9568347 DOI: 10.1155/2022/5378963] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/19/2022] [Accepted: 09/27/2022] [Indexed: 11/23/2022]
Abstract
Methods A tissue microarray (TMA) containing 76 individual colorectal tumor samples and 28 adjacent normal samples was constructed, and the expression levels of LINC01314 and miR-96 were detected by fluorescence in situ hybridization. Results The expression levels of both LINC01314 and miR-96 were upregulated in CRC tissues and were associated with vascular metastasis (p < 0.05). A significantly positive correlation was observed between LINC01314 and miR-96 expression in tumor tissues (p < 0.001, r = 0.870). Dominant expression of LINC01314 was a risk factor for both blood vessel invasion (p < 0.05) and poor 5-year survival (p = 0.001, hazard ratio = 4.144). The Kaplan-Meier analysis indicated that patients with LINC01314-dominant expression exhibited worse 5-year survival rates than those with miR-96-dominant expression (p < 0.05). Conclusion The expression patterns of both LINC01314 and miR-96 may be diagnostic of, and prognostic for, CRC. These findings will facilitate further exploration of the molecular mechanism of lncRNAs in CRC.
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Affiliation(s)
- Runan Zhang
- Department of Clinical Laboratory, Tongde Hospital of Zhejiang Province, Hangzhou, Zhejiang, China
| | - Genhua Zhang
- Department of Pathology, Tongde Hospital of Zhejiang Province, Hangzhou, Zhejiang, China
| | - Baohua Li
- Department of Clinical Laboratory, Tongde Hospital of Zhejiang Province, Hangzhou, Zhejiang, China
| | - Juan Wang
- Department of Clinical Laboratory, Tongde Hospital of Zhejiang Province, Hangzhou, Zhejiang, China
| | - Jvfang Wang
- Department of Clinical Laboratory, Tongde Hospital of Zhejiang Province, Hangzhou, Zhejiang, China
| | - Jia Che
- Department of Clinical Laboratory, Tongde Hospital of Zhejiang Province, Hangzhou, Zhejiang, China
| | - Xiaojun Wang
- Department of Clinical Laboratory, Tongde Hospital of Zhejiang Province, Hangzhou, Zhejiang, China
| | - Zhen Zhang
- Department of Clinical Laboratory, Tongde Hospital of Zhejiang Province, Hangzhou, Zhejiang, China
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Volovat SR, Augustin I, Zob D, Boboc D, Amurariti F, Volovat C, Stefanescu C, Stolniceanu CR, Ciocoiu M, Dumitras EA, Danciu M, Apostol DGC, Drug V, Shurbaji SA, Coca LG, Leon F, Iftene A, Herghelegiu PC. Use of Personalized Biomarkers in Metastatic Colorectal Cancer and the Impact of AI. Cancers (Basel) 2022; 14:cancers14194834. [PMID: 36230757 PMCID: PMC9562853 DOI: 10.3390/cancers14194834] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2022] [Revised: 09/18/2022] [Accepted: 09/29/2022] [Indexed: 12/09/2022] Open
Abstract
Colorectal cancer is a major cause of cancer-related death worldwide and is correlated with genetic and epigenetic alterations in the colonic epithelium. Genetic changes play a major role in the pathophysiology of colorectal cancer through the development of gene mutations, but recent research has shown an important role for epigenetic alterations. In this review, we try to describe the current knowledge about epigenetic alterations, including DNA methylation and histone modifications, as well as the role of non-coding RNAs as epigenetic regulators and the prognostic and predictive biomarkers in metastatic colorectal disease that can allow increases in the effectiveness of treatments. Additionally, the intestinal microbiota’s composition can be an important biomarker for the response to strategies based on the immunotherapy of CRC. The identification of biomarkers in mCRC can be enhanced by developing artificial intelligence programs. We present the actual models that implement AI technology as a bridge connecting ncRNAs with tumors and conducted some experiments to improve the quality of the model used as well as the speed of the model that provides answers to users. In order to carry out this task, we implemented six algorithms: the naive Bayes classifier, the random forest classifier, the decision tree classifier, gradient boosted trees, logistic regression and SVM.
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Affiliation(s)
- Simona-Ruxandra Volovat
- Department of Medical Oncology-Radiotherapy, “Grigore T. Popa” University of Medicine and Pharmacy, 16 University Str., 700115 Iasi, Romania
| | - Iolanda Augustin
- Department of Medical Oncology, AI.Trestioreanu Institute of Oncology, 022328 Bucharest, Romania
| | - Daniela Zob
- Department of Medical Oncology, AI.Trestioreanu Institute of Oncology, 022328 Bucharest, Romania
| | - Diana Boboc
- Department of Medical Oncology-Radiotherapy, “Grigore T. Popa” University of Medicine and Pharmacy, 16 University Str., 700115 Iasi, Romania
| | - Florin Amurariti
- Department of Medical Oncology-Radiotherapy, “Grigore T. Popa” University of Medicine and Pharmacy, 16 University Str., 700115 Iasi, Romania
| | - Constantin Volovat
- Department of Medical Oncology, “Euroclinic” Center of Oncology, 2 Vasile Conta Str., 700106 Iasi, Romania
- Correspondence: (C.V.); (C.S.)
| | - Cipriana Stefanescu
- Department of Biophysics and Medical Physics-Nuclear Medicine, “Grigore T. Popa” University of Medicine and Pharmacy, 16 University Str., 700115 Iasi, Romania
- Correspondence: (C.V.); (C.S.)
| | - Cati Raluca Stolniceanu
- Department of Biophysics and Medical Physics-Nuclear Medicine, “Grigore T. Popa” University of Medicine and Pharmacy, 16 University Str., 700115 Iasi, Romania
| | - Manuela Ciocoiu
- Department of Pathophysiology, “Grigore T. Popa” University of Medicine and Pharmacy, 700115 Iasi, Romania
| | - Eduard Alexandru Dumitras
- Department of Pathophysiology, “Grigore T. Popa” University of Medicine and Pharmacy, 700115 Iasi, Romania
- Department of Anesthesiology and Intensive Care, Regional Institute of Oncology, 700115 Iasi, Romania
| | - Mihai Danciu
- Pathology Department, “Grigore T. Popa” University of Medicine and Pharmacy, 700115 Iasi, Romania
| | | | - Vasile Drug
- Department of Gastroenterology, “Grigore T. Popa” University of Medicine and Pharmacy, 16 University Str., 700115 Iasi, Romania
- Gastroenterology Clinic, Institute of Gastroenterology and Hepatology, ‘St. Spiridon’ Clinical Hospital, 700115 Iasi, Romania
| | - Sinziana Al Shurbaji
- Gastroenterology Clinic, Institute of Gastroenterology and Hepatology, ‘St. Spiridon’ Clinical Hospital, 700115 Iasi, Romania
| | - Lucia-Georgiana Coca
- Faculty of Computer Science, Alexandru Ioan Cuza University, 700115 Iasi, Romania
| | - Florin Leon
- Faculty of Automatic Control and Computer Engineering, Gheorghe Asachi Technical University, 700115 Iasi, Romania
| | - Adrian Iftene
- Faculty of Computer Science, Alexandru Ioan Cuza University, 700115 Iasi, Romania
| | - Paul-Corneliu Herghelegiu
- Faculty of Automatic Control and Computer Engineering, Gheorghe Asachi Technical University, 700115 Iasi, Romania
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205
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Cheng X, Li Y, Liu F. Prognostic impact of mitofusin 2 expression in colon cancer. Transl Cancer Res 2022; 11:3610-3619. [PMID: 36388028 PMCID: PMC9641083 DOI: 10.21037/tcr-22-589] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2022] [Accepted: 06/24/2022] [Indexed: 08/12/2024]
Abstract
BACKGROUND Mitofusin 2 (MFN2) is involved in several biological processes, including cancer. MFN2 is downregulated in some types of cancer and inhibits cancer cell proliferation, migration, and invasion. However, the relationship between MFN2 and colon cancer remains unknown. METHODS In this study, MFN2 expression was investigated using The Cancer Genome Atlas (TCGA) and the Human Protein Atlas (HPA), and the associations between prognostic factors and survival outcomes were assessed via univariate and multivariate analyses. Functional enrichment analyses based on Kyoto Encyclopedia of Genes and Genomes (KEGG) resource and Gene Set Enrichment Analysis (GSEA) were carried out. RESULTS MFN2 was downregulated in colon cancer tissues compared with paracancerous colon tissues (P<0.001), and low MFN2 expression was associated with an advanced tumor stage (stage IV vs. stage I, P=0.03; stage I-III vs. stage IV, P=0.003). MFN2 immunohistochemistry (IHC) staining was medium to high in colon normal tissues, but MFN2 IHC staining was faint or not identified in colorectal cancer (CRC) tumor tissues. MFN2 expression was either low or non-existent in colon cancer distinct cell clusters, according to differential gene analysis. Univariate analysis revealed that MFN2 expression in colon cancer patients was significantly associated with the stage [odds ratio (OR) =0.29 for stage IV vs. stage I, P=0.001], T-stage (OR =0.20 for T4 vs. T1, P=0.033), and distant metastasis (OR =0.31 for M1 vs. M0, P=0.000). Furthermore, Kaplan-Meier survival analysis revealed that patients with colon cancer and high MFN2 expression have a better prognosis than those with low MFN2 expression (P=0.002). MFN2 (hazard ratio =0.95, 95% confidence interval: 0.92-0.99, P=0.007) was an independent predictor of colon cancer according to univariate and multivariate Cox models. Finally, GSEA results showed that the KEGG GALACTOSE METABOLISM, APOPTOSIS, and VEGF SIGNALING pathways were activated in the high MFN2 mRNA expression group, whereas the KEGG RIBOSOME pathway was inhibited in the low MFN2 expression group. CONCLUSIONS Our research revealed MFN2 to be a promising predictive biomarker and therapeutic target for colon cancer.
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Affiliation(s)
- Xiaofei Cheng
- Department of Colorectal Surgery, the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Yanqing Li
- Department of Pathology, the Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Fanlong Liu
- Department of Colorectal Surgery, the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
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206
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Kaplun DS, Kaluzhny DN, Prokhortchouk EB, Zhenilo SV. DNA Methylation: Genomewide Distribution, Regulatory Mechanism and Therapy Target. Acta Naturae 2022; 14:4-19. [PMID: 36694897 PMCID: PMC9844086 DOI: 10.32607/actanaturae.11822] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2022] [Accepted: 11/29/2022] [Indexed: 01/22/2023] Open
Abstract
DNA methylation is the most important epigenetic modification involved in the regulation of transcription, imprinting, establishment of X-inactivation, and the formation of a chromatin structure. DNA methylation in the genome is often associated with transcriptional repression and the formation of closed heterochromatin. However, the results of genome-wide studies of the DNA methylation pattern and transcriptional activity of genes have nudged us toward reconsidering this paradigm, since the promoters of many genes remain active despite their methylation. The differences in the DNA methylation distribution in normal and pathological conditions allow us to consider methylation as a diagnostic marker or a therapy target. In this regard, the need to investigate the factors affecting DNA methylation and those involved in its interpretation becomes pressing. Recently, a large number of protein factors have been uncovered, whose ability to bind to DNA depends on their methylation. Many of these proteins act not only as transcriptional activators or repressors, but also affect the level of DNA methylation. These factors are considered potential therapeutic targets for the treatment of diseases resulting from either a change in DNA methylation or a change in the interpretation of its methylation level. In addition to protein factors, a secondary DNA structure can also affect its methylation and can be considered as a therapy target. In this review, the latest research into the DNA methylation landscape in the genome has been summarized to discuss why some DNA regions avoid methylation and what factors can affect its level or interpretation and, therefore, can be considered a therapy target.
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Affiliation(s)
- D. S. Kaplun
- Institute of Bioengineering, Research Center of Biotechnology, Russian Academy of Sciences, Moscow, 119071 Russia
- Institute of Gene Biology, Russian Academy of Sciences, Moscow, 119071 Russia
| | - D. N. Kaluzhny
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, 119991 Russia
| | - E. B. Prokhortchouk
- Institute of Bioengineering, Research Center of Biotechnology, Russian Academy of Sciences, Moscow, 119071 Russia
- Institute of Gene Biology, Russian Academy of Sciences, Moscow, 119071 Russia
| | - S. V. Zhenilo
- Institute of Bioengineering, Research Center of Biotechnology, Russian Academy of Sciences, Moscow, 119071 Russia
- Institute of Gene Biology, Russian Academy of Sciences, Moscow, 119071 Russia
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207
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Khayami R, Goltzman D, Rabbani SA, Kerachian MA. Epigenomic effects of vitamin D in colorectal cancer. Epigenomics 2022; 14:1213-1228. [PMID: 36325830 DOI: 10.2217/epi-2022-0288] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Vitamin D regulates a plethora of physiological processes in the human body and has been proposed to exert several anticancer effects. Epigenetics plays an important role in regulating vitamin D actions. In this review, we highlight the recent advances in the understanding of different epigenetic factors such as lncRNAs, miRNAs, methylation and acetylation influenced by vitamin D and its downstream targets in colorectal cancer to find more potential therapeutic targets. We discuss how vitamin D exerts anticancer properties through interactions between the vitamin D receptor and genes (e.g., SLC30A10), the microenvironment, microbiota and other factors in colorectal cancer. Developing therapeutic approaches targeting the vitamin D signaling system will be aided by a better knowledge of the epigenetic impact of vitamin D.
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Affiliation(s)
- Reza Khayami
- Medical Genetics Research Center, Mashhad University of Medical Sciences, Mashhad, Iran
- Department of Medical Genetics, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - David Goltzman
- Department of Medicine, McGill University Health Center, Montreal, QC, H3G 1A4, Canada
| | - Shafaat A Rabbani
- Department of Medicine, McGill University Health Center, Montreal, QC, H3G 1A4, Canada
| | - Mohammad Amin Kerachian
- Medical Genetics Research Center, Mashhad University of Medical Sciences, Mashhad, Iran
- Department of Medical Genetics, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
- Department of Chemistry and Biology, Toronto Metropolitan University, Toronto, On, H3A 1A4, Canada
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208
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Kim K, Ryu TY, Lee J, Son MY, Kim DS, Kim SK, Cho HS. Epigenetic Silencing of CHOP Expression by the Histone Methyltransferase EHMT1 Regulates Apoptosis in Colorectal Cancer Cells. Mol Cells 2022; 45:622-630. [PMID: 35748228 PMCID: PMC9448644 DOI: 10.14348/molcells.2022.0014] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2022] [Revised: 04/26/2022] [Accepted: 04/26/2022] [Indexed: 11/27/2022] Open
Abstract
Colorectal cancer (CRC) has a high mortality rate among cancers worldwide. To reduce this mortality rate, chemotherapy (5-fluorouracil, oxaliplatin, and irinotecan) or targeted therapy (bevacizumab, cetuximab, and panitumumab) has been used to treat CRC. However, due to various side effects and poor responses to CRC treatment, novel therapeutic targets for drug development are needed. In this study, we identified the overexpression of EHMT1 in CRC using RNA sequencing (RNA-seq) data derived from TCGA, and we observed that knocking down EHMT1 expression suppressed cell growth by inducing cell apoptosis in CRC cell lines. In Gene Ontology (GO) term analysis using RNA-seq data, apoptosis-related terms were enriched after EHMT1 knockdown. Moreover, we identified the CHOP gene as a direct target of EHMT1 using a ChIP (chromatin immunoprecipitation) assay with an anti-histone 3 lysine 9 dimethylation (H3K9me2) antibody. Finally, after cotransfection with siEHMT1 and siCHOP, we again confirmed that CHOP-mediated cell apoptosis was induced by EHMT1 knockdown. Our findings reveal that EHMT1 plays a key role in regulating CRC cell apoptosis, suggesting that EHMT1 may be a therapeutic target for the development of cancer inhibitors.
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Affiliation(s)
- Kwangho Kim
- Korea Research Institute of Bioscience and Biotechnology, Daejeon 34141, Korea
- College of Pharmacy, Chungnam National University, Daejeon 34134, Korea
| | - Tae Young Ryu
- Korea Research Institute of Bioscience and Biotechnology, Daejeon 34141, Korea
| | - Jinkwon Lee
- Korea Research Institute of Bioscience and Biotechnology, Daejeon 34141, Korea
- Department of Functional Genomics, Korea University of Science and Technology, Daejeon 34113, Korea
| | - Mi-Young Son
- Korea Research Institute of Bioscience and Biotechnology, Daejeon 34141, Korea
- Department of Functional Genomics, Korea University of Science and Technology, Daejeon 34113, Korea
| | - Dae-Soo Kim
- Korea Research Institute of Bioscience and Biotechnology, Daejeon 34141, Korea
- Department of Functional Genomics, Korea University of Science and Technology, Daejeon 34113, Korea
| | - Sang Kyum Kim
- College of Pharmacy, Chungnam National University, Daejeon 34134, Korea
| | - Hyun-Soo Cho
- Korea Research Institute of Bioscience and Biotechnology, Daejeon 34141, Korea
- Department of Functional Genomics, Korea University of Science and Technology, Daejeon 34113, Korea
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209
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Li Z, Liu Y, Yi H, Cai T, Wei Y. Identification of N6-methylandenosine related lncRNA signatures for predicting the prognosis and therapy response in colorectal cancer patients. Front Genet 2022; 13:947747. [PMID: 36246627 PMCID: PMC9561883 DOI: 10.3389/fgene.2022.947747] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2022] [Accepted: 09/06/2022] [Indexed: 11/18/2022] Open
Abstract
Despite recent advances in surgical and multimodal therapies, the overall survival (OS) of advanced colorectal cancer (CRC) patients remains low. Thus, discerning sensitive prognostic biomarkers to give the optimistic treatment for CRC patients is extremely critical. N6-methyladenosine (m6A) and long noncoding RNAs (lncRNAs) play an important role in CRC progression. Nonetheless, few studies have focused on the impact of m6A-related lncRNAs on the prognosis, tumor microenvironment (TME) and treatment of CRC. In this study, 1707 m6A-related lncRNAs were identified through Pearson correlation analysis and Weighted co-expression network analysis (WGCNA) using The Cancer Genome Atlas (TCGA) cohort. Then, 28 m6A-related prognostic lncRNAs were screened by univariate Cox regression analysis, followed by identifying two clusters by consensus clustering analysis. A prognostic model consisted of 8 lncRNA signatures was constructed by the least absolute shrinkage and selection operator (LASSO). Kaplan–Meier curve analysis and a nomogram were performed to investigate the prognostic ability of this model. The risk score of prognostic model act as an independent risk factor for OS rate. Functional enrichment analysis indicated that lncRNA signatures related tumor immunity. The low-risk group characterized by increased microsatellite instability-high (MSI-H), mutation burden, and immunity activation, indicated favorable odds of OS. Moreover, the lncRNA signatures were significantly associated with the cancer stem cell (CSC) index and drug sensitivity. In addition, 3 common immune genes shared by the lncRNA signatures were screened out. We found that these immune genes were widely distributed in 2 cell types of TME. Finally, a ceRNA network was constructed to identify ZEB1-AS1 regulatory axis in CRC. We found that ZEB1-AS1 was significantly overexpressed in tumor tissues, and was related to the metastasis of EMT and the chemoresistance of 5-Fu in CRC. Therefore, our study demonstrated the important role of m6A-related lncRNAs in TME remodeling. Moreover, these results illustrated the levels of ZEB1-AS1 might be valuable for predicting the progression and prognosis of CRC, and further provided a new target for the diagnosis and treatment of CRC patients.
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Affiliation(s)
- Zhiyong Li
- Department of Oncological and Endoscopic Surgery, The First Affiliated Hospital of Harbin Medical University, Harbin, China
- Pancreatic and Gastrointestinal Surgery Division, HwaMei Hospital, University of Chinese Academy of Science, Ningbo, China
- Translational Medicine Research and Cooperation Center of Northern China, Heilongjiang Academy of Medical Sciences, Harbin, China
| | - Yang Liu
- Pancreatic and Gastrointestinal Surgery Division, HwaMei Hospital, University of Chinese Academy of Science, Ningbo, China
| | - Huijie Yi
- Peking University School of Nursing, Beijing, China
- Respiratory and Critical Care Medicine, Peking University People’s Hospital, Beijing, China
| | - Ting Cai
- Department of Experimental Medical Science, HwaMei Hospital,University of Chinese Academy of Sciences, Ningbo, China
- Key Laboratory of Diagnosis and Treatment of Digestive System Tumors, Ningbo, Zhejiang, China
- *Correspondence: Ting Cai, ; Yunwei Wei,
| | - Yunwei Wei
- Department of Oncological and Endoscopic Surgery, The First Affiliated Hospital of Harbin Medical University, Harbin, China
- Pancreatic and Gastrointestinal Surgery Division, HwaMei Hospital, University of Chinese Academy of Science, Ningbo, China
- *Correspondence: Ting Cai, ; Yunwei Wei,
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Wang S, Xiao F, Li J, Fan X, He Z, Yan T, Yang M, Yang D. Circular RNAs Involved in the Regulation of the Age-Related Pathways. Int J Mol Sci 2022; 23:ijms231810443. [PMID: 36142352 PMCID: PMC9500598 DOI: 10.3390/ijms231810443] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2022] [Revised: 08/31/2022] [Accepted: 09/03/2022] [Indexed: 12/04/2022] Open
Abstract
Circular RNAs (circRNAs) are a class of covalently circular noncoding RNAs that have been extensively studied in recent years. Aging is a process related to functional decline that is regulated by signal transduction. An increasing number of studies suggest that circRNAs can regulate aging and multiple age-related diseases through their involvement in age-related signaling pathways. CircRNAs perform several biological functions, such as acting as miRNA sponges, directly interacting with proteins, and regulating transcription and translation to proteins or peptides. Herein, we summarize research progress on the biological functions of circRNAs in seven main age-related signaling pathways, namely, the insulin-insulin-like, PI3K-AKT, mTOR, AMPK, FOXO, p53, and NF-κB signaling pathways. In these pathways, circRNAs mainly function as miRNA sponges. In this review, we suggest that circRNAs are widely involved in the regulation of the main age-related pathways and are potential biomarkers for aging and age-related diseases.
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Affiliation(s)
- Siqi Wang
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, China
| | - Feng Xiao
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, China
| | - Jiamei Li
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, China
| | - Xiaolan Fan
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, China
| | - Zhi He
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China
| | - Taiming Yan
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China
| | - Mingyao Yang
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, China
- Correspondence: (M.Y.); (D.Y.); Tel.: +86-28-86290991 (M.Y.)
| | - Deying Yang
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, China
- Correspondence: (M.Y.); (D.Y.); Tel.: +86-28-86290991 (M.Y.)
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Peripheral Blood DNA Methylation Profiles Do Not Predict Endoscopic Post-Operative Recurrence in Crohn's Disease Patients. Int J Mol Sci 2022; 23:ijms231810467. [PMID: 36142381 PMCID: PMC9503775 DOI: 10.3390/ijms231810467] [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: 08/01/2022] [Revised: 08/30/2022] [Accepted: 09/04/2022] [Indexed: 11/30/2022] Open
Abstract
Prediction of endoscopic post-operative recurrence (POR) in Crohn’s disease (CD) patients following ileocolonic resection (ICR) using clinical risk factors alone has thus far been inadequate. While peripheral blood leukocyte (PBL) DNA methylation has shown promise as a tool for predicting recurrence in cancer, no data in CD patients exists. Therefore, this study explored the association and predictive value of PBL DNA methylation in CD patients following ICR. From a cohort of 117 CD patients undergoing ICR, epigenome-wide PBL methylation profiles from 25 carefully selected patients presenting either clear endoscopic remission (n = 12) or severe recurrence (n = 13) were assessed using the Illumina MethylationEPIC (850K) array. No statistically significant differentially methylated positions (DMPs) or regions (DMRs) associated with endoscopic POR were identified (FDR p ≤ 0.05), further evidenced by the low accuracy (0.625) following elastic net classification analysis. Nonetheless, interrogating the most significant differences in methylation suggested POR-associated hypermethylation in the MBNL1, RAB29 and LEPR genes, respectively, which are involved in intestinal fibrosis, inflammation and wound healing. Notably, we observed a higher estimated proportion of monocytes in endoscopic POR compared to remission. Altogether, we observed limited differences in the genome-wide DNA methylome among CD patients with and without endoscopic POR. We therefore conclude that PBL DNA methylation is not a feasible predictive tool in post-operative CD.
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212
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Maslankova J, Vecurkovska I, Rabajdova M, Katuchova J, Kicka M, Gayova M, Katuch V. Regulation of transforming growth factor-β signaling as a therapeutic approach to treating colorectal cancer. World J Gastroenterol 2022. [PMID: 36156927 DOI: 10.3748/wjg.v28.i33.4744.pmid:36156927;pmcid:pmc9476856] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 05/09/2023] Open
Abstract
According to data from 2020, Slovakia has long been among the top five countries with the highest incidence rate of colorectal cancer (CRC) worldwide, and the rate is continuing to rise every year. In approximately 80% of CRC cases, allelic loss (loss of heterozygosity, LOH) occurs in the long arm of chromosome 18q. The most important genes that can be silenced by 18q LOH or mutations are small mothers against decapentaplegic homolog (SMAD) 2 and SMAD4, which are intracellular mediators of transforming growth factor (TGF)-β superfamily signals. TGF-β plays an important role in the pro-oncogenic processes, including such properties as invasion, epithelial-mesenchymal transition (commonly known as EMT), promotion of angiogenesis, and immunomodulatory effects. Several recent studies have reported that activation of TGF-β signaling is related to drug resistance in CRC. Because the mechanisms of drug resistance are different between patients in different stages of CRC, personalized treatment is more effective. Therefore, knowledge of the activation and inhibition of factors that affect the TGF-β signaling pathway is very important.
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Affiliation(s)
- Jana Maslankova
- Department of Medical and Clinical Biochemistry, Faculty of Medicine, Pavol Jozef Safarik University in Kosice, Kosice 04011, Slovakia
| | - Ivana Vecurkovska
- Department of Medical and Clinical Biochemistry, Faculty of Medicine, Pavol Jozef Safarik University in Kosice, Kosice 04011, Slovakia
| | - Miroslava Rabajdova
- Department of Medical and Clinical Biochemistry, Faculty of Medicine, Pavol Jozef Safarik University in Kosice, Kosice 04011, Slovakia
| | - Jana Katuchova
- First Department of Surgery, Medical Faculty of Safarik University, Kosice 04011, Kosicky kraj, Slovakia.
| | - Milos Kicka
- First Department of Surgery, Medical Faculty of Safarik University, Kosice 04011, Kosicky kraj, Slovakia
| | - Michala Gayova
- Department of Burns and Reconstructive Surgery, Medical Faculty at Safarik University and University Hospital, Kosice 04011, Slovakia
| | - Vladimir Katuch
- Department of Neurosurgery, Medical Faculty at Safarik University and University Hospital, Kosice 04011, Slovakia
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213
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Maslankova J, Vecurkovska I, Rabajdova M, Katuchova J, Kicka M, Gayova M, Katuch V. Regulation of transforming growth factor-β signaling as a therapeutic approach to treating colorectal cancer. World J Gastroenterol 2022; 28:4744-4761. [PMID: 36156927 PMCID: PMC9476856 DOI: 10.3748/wjg.v28.i33.4744] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/12/2022] [Revised: 07/06/2022] [Accepted: 08/16/2022] [Indexed: 02/06/2023] Open
Abstract
According to data from 2020, Slovakia has long been among the top five countries with the highest incidence rate of colorectal cancer (CRC) worldwide, and the rate is continuing to rise every year. In approximately 80% of CRC cases, allelic loss (loss of heterozygosity, LOH) occurs in the long arm of chromosome 18q. The most important genes that can be silenced by 18q LOH or mutations are small mothers against decapentaplegic homolog (SMAD) 2 and SMAD4, which are intracellular mediators of transforming growth factor (TGF)-β superfamily signals. TGF-β plays an important role in the pro-oncogenic processes, including such properties as invasion, epithelial-mesenchymal transition (commonly known as EMT), promotion of angiogenesis, and immunomodulatory effects. Several recent studies have reported that activation of TGF-β signaling is related to drug resistance in CRC. Because the mechanisms of drug resistance are different between patients in different stages of CRC, personalized treatment is more effective. Therefore, knowledge of the activation and inhibition of factors that affect the TGF-β signaling pathway is very important.
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Affiliation(s)
- Jana Maslankova
- Department of Medical and Clinical Biochemistry, Faculty of Medicine, Pavol Jozef Safarik University in Kosice, Kosice 04011, Slovakia
| | - Ivana Vecurkovska
- Department of Medical and Clinical Biochemistry, Faculty of Medicine, Pavol Jozef Safarik University in Kosice, Kosice 04011, Slovakia
| | - Miroslava Rabajdova
- Department of Medical and Clinical Biochemistry, Faculty of Medicine, Pavol Jozef Safarik University in Kosice, Kosice 04011, Slovakia
| | - Jana Katuchova
- First Department of Surgery, Medical Faculty of Safarik University, Kosice 04011, Kosicky kraj, Slovakia
| | - Milos Kicka
- First Department of Surgery, Medical Faculty of Safarik University, Kosice 04011, Kosicky kraj, Slovakia
| | - Michala Gayova
- Department of Burns and Reconstructive Surgery, Medical Faculty at Safarik University and University Hospital, Kosice 04011, Slovakia
| | - Vladimir Katuch
- Department of Neurosurgery, Medical Faculty at Safarik University and University Hospital, Kosice 04011, Slovakia
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214
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Chen CY, Wu JJ, Lin YJ, Hsu CH, Hu JM, Chang PK, Sun CA, Yang T, Su JQ, Chou YC. Significance of Hypermethylation of Tumor-Suppressor Genes PTGER4 and ZNF43 at CpG Sites in the Prognosis of Colorectal Cancer. Int J Mol Sci 2022; 23:ijms231810225. [PMID: 36142151 PMCID: PMC9499344 DOI: 10.3390/ijms231810225] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2022] [Revised: 08/29/2022] [Accepted: 08/30/2022] [Indexed: 11/26/2022] Open
Abstract
The status of DNA methylation in primary tumor tissue and adjacent tumor-free tissue is associated with the occurrence of aggressive colorectal cancer (CRC) and can aid personalized cancer treatments at early stages. Tumor tissue and matched adjacent nontumorous tissue were extracted from 208 patients with CRC, and the correlation between the methylation levels of PTGER4 and ZNF43 at certain CpG loci and the prognostic factors of CRC was determined using the MassARRAY System testing platform. The Wilcoxon signed-rank test, a Chi-square test, and McNemar’s test were used for group comparisons, and Kaplan–Meier curves and a log-rank test were used for prediction. The hypermethylation of PTGER4 at the CpG_4, CpG_5, CpG_15, and CpG_17 tumor tissue sites was strongly correlated with shorter recurrence-free survival (RFS), progression-free survival (PFS), and overall survival (OS) [hazard ratio (HR) = 3.26, 95% confidence interval (CI) = 1.38–7.73 for RFS, HR = 2.35 and 95% CI = 1.17–4.71 for PFS, HR = 4.32 and 95% CI = 1.8–10.5 for OS]. By contrast, RFS and PFS were significantly longer in the case of increased methylation of ZNF43 at the CpG_5 site of normal tissue [HR = 2.33, 95% CI = 1.07–5.08 for RFS, HR = 2.42 and 95% CI = 1.19–4.91 for PFS]. Aberrant methylation at specific CpG sites indicates tissue with aggressive behavior. Therefore, the differential methylation of PTGER4 and ZNF43 at specific loci can be employed for the prognosis of patients with CRC.
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Affiliation(s)
- Chao-Yang Chen
- Division of Colorectal Surgery, Department of Surgery, Tri-Service General Hospital, National Defense Medical Center, Taipei 114, Taiwan
| | - Jia-Jheng Wu
- School of Public Health, National Defense Medical Center, Taipei 114, Taiwan
| | - Yu-Jyun Lin
- School of Public Health, National Defense Medical Center, Taipei 114, Taiwan
| | - Chih-Hsiung Hsu
- School of Public Health, National Defense Medical Center, Taipei 114, Taiwan
| | - Je-Ming Hu
- Division of Colorectal Surgery, Department of Surgery, Tri-Service General Hospital, National Defense Medical Center, Taipei 114, Taiwan
- Graduate Institute of Medical Sciences, National Defense Medical Center, Taipei 114, Taiwan
| | - Pi-Kai Chang
- Division of Colorectal Surgery, Department of Surgery, Tri-Service General Hospital, National Defense Medical Center, Taipei 114, Taiwan
- Graduate Institute of Medical Sciences, National Defense Medical Center, Taipei 114, Taiwan
| | - Chien-An Sun
- Department of Public Health, College of Medicine, Fu-Jen Catholic University, New Taipei City 242, Taiwan
- Data Science Center, College of Medicine, Fu-Jen Catholic University, New Taipei City 242, Taiwan
| | - Tsan Yang
- Department of Health Business Administration, Meiho University, Pingtung 912, Taiwan
| | - Jing-Quan Su
- Department of Medical Education and Research, Kaohsiung Veterans General Hospital, Kaohsiung 813, Taiwan
- Correspondence: (J.-Q.S.); (Y.-C.C.); Tel.: +886-7-3422121 (ext. 78058) (J.-Q.S.); +886-2-87923100 (ext. 18437) (Y.-C.C.); Fax: +886-7-3468056 (J.-Q.S.); +886-2-87923147 (Y.-C.C.)
| | - Yu-Ching Chou
- School of Public Health, National Defense Medical Center, Taipei 114, Taiwan
- Correspondence: (J.-Q.S.); (Y.-C.C.); Tel.: +886-7-3422121 (ext. 78058) (J.-Q.S.); +886-2-87923100 (ext. 18437) (Y.-C.C.); Fax: +886-7-3468056 (J.-Q.S.); +886-2-87923147 (Y.-C.C.)
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215
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An electrochemical biosensor for exosome detection based on covalent organic frameworks conjugated with DNA and horseradish peroxidase. J Electroanal Chem (Lausanne) 2022. [DOI: 10.1016/j.jelechem.2022.116576] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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216
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Krieg C, Weber LM, Fosso B, Marzano M, Hardiman G, Olcina MM, Domingo E, El Aidy S, Mallah K, Robinson MD, Guglietta S. Complement downregulation promotes an inflammatory signature that renders colorectal cancer susceptible to immunotherapy. J Immunother Cancer 2022; 10:e004717. [PMID: 36137652 PMCID: PMC9511657 DOI: 10.1136/jitc-2022-004717] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/29/2022] [Indexed: 11/25/2022] Open
Abstract
BACKGROUND AND AIMS The role of inflammatory immune responses in colorectal cancer (CRC) development and response to therapy is a matter of intense debate. While inflammation is a known driver of CRC, inflammatory immune infiltrates are a positive prognostic factor in CRC and predispose to response to immune checkpoint blockade (ICB) therapy. Unfortunately, over 85% of CRC cases are primarily unresponsive to ICB due to the absence of an immune infiltrate, and even the cases that show an initial immune infiltration can become refractory to ICB. The identification of therapy supportive immune responses in the field has been partially hindered by the sparsity of suitable mouse models to recapitulate the human disease. In this study, we aimed to understand how the dysregulation of the complement anaphylatoxin C3a receptor (C3aR), observed in subsets of patients with CRC, affects the immune responses, the development of CRC, and response to ICB therapy. METHODS We use a comprehensive approach encompassing analysis of publicly available human CRC datasets, inflammation-driven and newly generated spontaneous mouse models of CRC, and multiplatform high-dimensional analysis of immune responses using microbiota sequencing, RNA sequencing, and mass cytometry. RESULTS We found that patients' regulation of the complement C3aR is associated with epigenetic modifications. Specifically, downregulation of C3ar1 in human CRC promotes a tumor microenvironment characterized by the accumulation of innate and adaptive immune cells that support antitumor immunity. In addition, in vivo studies in our newly generated mouse model revealed that the lack of C3a in the colon activates a microbiota-mediated proinflammatory program which promotes the development of tumors with an immune signature that renders them responsive to the ICB therapy. CONCLUSIONS Our findings reveal that C3aR may act as a previously unrecognized checkpoint to enhance antitumor immunity in CRC. C3aR can thus be exploited to overcome ICB resistance in a larger group of patients with CRC.
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Affiliation(s)
- Carsten Krieg
- Department of Pathology and Laboratory Medicine, Medical University of South Carolina, Charleston, South Carolina, USA
- Hollings Cancer Center Charleston, Medical University of South Carolina, Charleston, South Carolina, USA
| | - Lukas M Weber
- Institute of Molecular Life Sciences, University of Zurich, Zurich, Switzerland
- SIB Swiss Institute of Bioinformatics, University of Zurich, Zurich, Switzerland
| | - Bruno Fosso
- Institute of Biomembranes, Bioenergetics and Molecular Biotechnologies, Consiglio Nazionale delle Ricerche, Bari, Italy
| | - Marinella Marzano
- Institute of Biomembranes, Bioenergetics and Molecular Biotechnologies, Consiglio Nazionale delle Ricerche, Bari, Italy
| | - Gary Hardiman
- School of Biological Sciences and Institute for Global Food Security, Queens University of Belfast, Belfast, UK
| | - Monica M Olcina
- Institute of Radiation Oncology, Medical Research Council Oxford Institute for Radiation Oncology, Oxford, UK
| | - Enric Domingo
- Institute of Radiation Oncology, Medical Research Council Oxford Institute for Radiation Oncology, Oxford, UK
| | - Sahar El Aidy
- Host-microbe Metabolic Interactions, Microbiology, University of Groningen, Groningen, The Netherlands
| | - Khalil Mallah
- Department of Microbiology and Immunology, Medical University of South Carolina, Charleston, South Carolina, USA
| | - Mark D Robinson
- Institute of Molecular Life Sciences, University of Zurich, Zurich, Switzerland
- SIB Swiss Institute of Bioinformatics, University of Zurich, Zurich, Switzerland
| | - Silvia Guglietta
- Hollings Cancer Center Charleston, Medical University of South Carolina, Charleston, South Carolina, USA
- Regenerative Medicine and Cell Biology, Medical University of South Carolina, Charleston, South Carolina, USA
- Department of Experimental Oncology, IEO European Institute of Oncology IRCCS, Milan, Italy
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217
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Zhang X, Hong R, Bei L, Hu Z, Yang X, Song T, Chen L, Meng H, Niu G, Ke C. SELENBP1 inhibits progression of colorectal cancer by suppressing epithelial–mesenchymal transition. Open Med (Wars) 2022; 17:1390-1404. [PMID: 36117772 PMCID: PMC9438969 DOI: 10.1515/med-2022-0532] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2021] [Revised: 06/19/2022] [Accepted: 07/11/2022] [Indexed: 01/13/2023] Open
Abstract
Selenium-binding protein 1 (SELENBP1) is frequently dysregulated in various malignancies including colorectal cancer (CRC); however, its roles in progression of CRCs and the underlying mechanism remain to be elucidated. In this study, we compared the expression of SELENBP1 between CRCs and colorectal normal tissues (NTs), as well as between primary and metastatic CRCs; we determined the association between SELENBP1 expression and CRC patient prognoses; we conducted both in vitro and in vivo experiments to explore the functional roles of SELENBP1 in CRC progression; and we characterized the potential underlying mechanisms associated with SELENBP1 activities. We found that the expression of SELENBP1 was significantly and consistently decreased in CRCs than that in adjacent NTs, while significantly and frequently decreased in metastatic than primary CRCs. High expression of SELENBP1 was an independent predictor of favorable prognoses in CRC patients. Overexpression of SELENBP1 suppressed, while silencing of SELENBP1 promoted cell proliferation, migration and invasion, and in vivo tumorigenesis of CRC. Mechanically, SELENBP1 may suppress CRC progression by inhibiting the epithelial–mesenchymal transition.
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Affiliation(s)
- Xiaotian Zhang
- Department of General Surgery, Shanghai Fifth People’s Hospital, Fudan University, Shanghai, 200240, P.R. China
| | - Runqi Hong
- Department of General Surgery, Shanghai Fifth People’s Hospital, Fudan University, Shanghai, 200240, P.R. China
| | - Lanxin Bei
- Department of Animal Science, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Zhiqing Hu
- Department of General Surgery, Shanghai Fifth People’s Hospital, Fudan University, Shanghai, 200240, P.R. China
| | - Ximin Yang
- Department of Radiology, Dongying New District Hospital, Dongying, Shandong Province, 257000, P.R. China
| | - Tao Song
- Department of General Surgery, Shanghai Fifth People’s Hospital, Fudan University, 801 Heqing Road, Minhang District, Shanghai, 200240, P.R. China
| | - Liang Chen
- Department of General Surgery, Shanghai Fifth People’s Hospital, Fudan University, Shanghai, 200240, P.R. China
| | - He Meng
- Department of Animal Science, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Gengming Niu
- Department of General Surgery, Shanghai Fifth People’s Hospital, Fudan University, 801 Heqing Road, Minhang District, Shanghai, 200240, P.R. China
| | - Chongwei Ke
- Department of General Surgery, Shanghai Fifth People’s Hospital, Fudan University, 801 Heqing Road, Minhang District, Shanghai, 200240, P.R. China
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218
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Durmus S, Gelisgen R, Uzun H. DNA Methylation Biomarkers in Cancer: Current Clinical Utility and Future Perspectives. Biomark Med 2022. [DOI: 10.2174/9789815040463122010007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
Epigenetic alterations are related to inherited but reversible changes in
modifications that regulate gene activity beyond the DNA sequence. DNA methylation
is the best characterized epigenetic modification, controlling DNA stability, DNA
structure, transcription, and regulation, contributing to normal development and
differentiation. In this section, we first discuss the cellular functions of DNA
methylation and focus on how this fundamental biological process is impaired in
cancer. Changes in DNA methylation status in cancer have been heralded as promising
targets for the development of diagnostic, prognostic, and predictive biomarkers due to
their noninvasive accessibility in bodily fluids (such as blood, urine, stool),
reversibility, stability, and frequency. The absence of markers for definitive diagnosis
of most types of cancer and, in some cases, DNA methylation biomarkers being more
specific and sensitive than commonly used protein biomarkers indicate a strong need
for continued research to expand DNA methylation markers. Although the information
on changes in DNA methylation status in cancer and research on its clinical relevance
is rapidly increasing, the number of DNA methylation biomarkers currently available
as commercial tests is very small. Here, we focus on the importance of DNA
methylation location and target genes likely to be developed in the future for the
development of biomarkers in addition to existing commercial tests. Following a
detailed study of possible target genes, we summarize the current clinical application
status of the most studied and validated DNA methylation biomarkers, including
SEPT9, SDC2, BMP3, NDRG4, SFRP2, TFPI2, VIM and MGMT.
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Affiliation(s)
- Sinem Durmus
- Cerrahpasa Faculty of Medicine, Istanbul University,Department of Biochemistry,Department of Biochemistry, Cerrahpasa Faculty of Medicine, Istanbul University-Cerrahpasa, Istanbul,Turkey
| | - Remise Gelisgen
- Cerrahpasa Faculty of Medicine, Istanbul University,Department of Biochemistry,Department of Biochemistry, Cerrahpasa Faculty of Medicine, Istanbul University-Cerrahpasa, Istanbul,Turkey
| | - Hafize Uzun
- Department of Biochemistry, Faculty of Medicine, Istanbul Atlas University, Istanbul,Turkey
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219
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Xie H, Wu Z, Li Z, Huang Y, Zou J, Zhou H. Significance of ZEB2 in the immune microenvironment of colon cancer. Front Genet 2022; 13:995333. [PMID: 36072677 PMCID: PMC9442042 DOI: 10.3389/fgene.2022.995333] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2022] [Accepted: 07/28/2022] [Indexed: 11/30/2022] Open
Abstract
Background: ZEB2 is a protein-coding gene that is differentially expressed in tumors and can regulate the growth of tumor cells. This study investigated the specific regulatory mechanism of ZEB2 in COAD, a common cancer with high rates of morbidity and mortality. Methods: Multi-omics panoramic display of expression and function of ZEB2 in colon cancer. R software was used to study the expression of ZEB2 in 33 types of cancer. Furthermore, RT-PCR was used to detect the expression of ZEB2 in colon cancers and para-cancer tissues, as well as in colon cancer cells and normal cells. The ssGSEA was then used to explore the relationship between ZEB2 and immune cells, with UALCAN, EWAS and MEXPRESS applied to explore the methylation of ZEB2. The relationship between immunomodulators and chemokines (or receptors) based on expression data, copy number data, methylation data, and mutation data of ZEB2 was investigated using TISIDB. Finally, a protein interaction network of ZEB2 was constructed, and GO and KEGG analyses were performed on the differentially expressed genes. Results: ZEB2 is downregulated in most cancers, including COAD. The infiltration of the immune cells NK CD56 and Th17 cells was negatively correlated with ZEB2 expression, while the other 22 cells were positively correlated with ZEB2 expression. The DNA methylation of ZEB2 and the methylation of the ZEB2 protein on the EWAS website increased significantly. Analysis of the methylation levels and ZEB2 expression revealed that only the DNA methylation level and the expression of ZEB2 were significantly negatively correlated. The tumor-infiltrating lymphocytes positively correlated with the expression of ZEB2 but negatively correlated with the methylation of ZEB2. The same trend was observed for immunomodulators, chemokines, and receptors. The network showed that the protein performed certain biological functions, thereby affecting disease symptoms. Conclusion: These findings provide evidence that ZEB2-based therapy may represent a powerful treatment strategy for COAD.
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Affiliation(s)
- Hao Xie
- Department of Gastrointestinal Surgery, The Second Affiliated Hospital of Wannan Medical College, Wuhu, China
| | - Zhaoying Wu
- Department of Gastrointestinal Surgery, The Second Affiliated Hospital of Wannan Medical College, Wuhu, China
| | - Zhenhan Li
- School of Clinical Medicine, Wannan Medical College, Wuhu, China
| | - Yong Huang
- Department of Gastrointestinal Surgery, The Second Affiliated Hospital of Wannan Medical College, Wuhu, China
| | - Junwei Zou
- Department of Gastrointestinal Surgery, The Second Affiliated Hospital of Wannan Medical College, Wuhu, China
- *Correspondence: Hailang Zhou, ; Junwei Zou,
| | - Hailang Zhou
- Department of Gastroenterology, Lianshui People’s Hospital Affiliated to Kangda College of Nanjing Medical University, Huai’an, Jiangsu, China
- *Correspondence: Hailang Zhou, ; Junwei Zou,
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220
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Li J, Li H, Run ZC, Wang ZL, Jiang T, An Y, Li Z. RASSF1A methylation as a biomarker for detection of colorectal cancer and hepatocellular carcinoma. World J Gastrointest Oncol 2022; 14:1574-1584. [PMID: 36160746 PMCID: PMC9412931 DOI: 10.4251/wjgo.v14.i8.1574] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/26/2022] [Revised: 07/02/2022] [Accepted: 07/22/2022] [Indexed: 02/05/2023] Open
Abstract
BACKGROUND Studies have validated the potential of methylated cell-free DNA as a biomarker in various tumors, and methylated DNA in plasma may be a potential biomarker for cancer.
AIM To evaluate the diagnostic value of RASSF1A methylation in plasma for colorectal cancer (CRC) and hepatocellular carcinoma (HCC).
METHODS A total of 92 CRC patients, 67 colorectal polyp (CRP) patients, 63 HCC patients, and 66 liver cirrhosis (LC) patients were enrolled. The plasma DNA was subjected to DNA extraction, double-strand DNA concentration determination, bisulfite conversion, purification, single-strand DNA concentration determination, and digital polymerase chain reaction (PCR) detection. The methylation rate was calculated. The diagnostic value was evaluated by the area under the curve (AUC).
RESULTS The age and sex in the CRC and CRP groups and the HCC and LC groups were also matched. The DNA methylation rate of RASSF1A in plasma in the CRC group was 2.87 ± 1.80, and that in the CRP group was 1.50 ± 0.64. DNA methylation of RASSF1A in plasma showed a significant difference between the CRC and CRP groups. The AUC of RASSF1A methylation for discriminating the CRC and CRP groups was 0.82 (0.76-0.88). The AUCs of T1, T2, T3 and T4 CRC and CRP were 0.83 (0.72-0.95), 0.87 (0.78-0.95), 0.86 (0.77-0.95), and 0.75 (0.64-0.85), respectively. The DNA methylation rate of RASSF1A in plasma in the HCC group was 4.45 ± 2.93, and that in the LC group was 2.46 ± 2.07. DNA methylation of RASSF1A in plasma for the HCC and LC groups showed a significant difference. The AUC of RASSF1A methylation for discriminating the HCC and LC groups was 0.70 (0.60-0.79). The AUCs of T1, T2, T3 and T4 HCC and LC were 0.80 (0.61, 1.00), 0.74 (0.59-0.88), 0.60 (0.42-0.79), and 0.68 (0.53-0.82), respectively.
CONCLUSION RASSF1A methylation in plasma detected by digital PCR may be a potential biomarker for CRC and HCC.
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Affiliation(s)
- Jian Li
- Department of General Surgery, Affiliated Tumor Hospital of Zhengzhou University, Henan Tumor Hospital, Zhengzhou 450000, Henan Province, China
| | - Huan Li
- Department of Gastroenterology, Sixth Medical Center of Chinese PLA General Hospital, Beijing 100048, China
| | - Zeng-Ci Run
- Department of General Surgery, Affiliated Tumor Hospital of Zhengzhou University, Henan Tumor Hospital, Zhengzhou 450000, Henan Province, China
| | - Zhen-Lei Wang
- Department of General Surgery, Affiliated Tumor Hospital of Zhengzhou University, Henan Tumor Hospital, Zhengzhou 450000, Henan Province, China
| | - Tao Jiang
- Medicine Innovation Research Division of Chinese PLA General Hospital, Beijing 100853, China
| | - Yang An
- Faculty of Hepato-Pancreato-Biliary Surgery, Sixth Medical Center of Chinese PLA General Hospital, Beijing 100048, China
| | - Zhi Li
- Department of General Surgery, Affiliated Tumor Hospital of Zhengzhou University, Henan Tumor Hospital, Zhengzhou 450000, Henan Province, China
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Yoshikawa T, Fukuda A, Omatsu M, Namikawa M, Sono M, Yuichi F, Masuda T, Araki O, Nagao M, Ogawa S, Masuo K, Goto N, Hiramatsu Y, Muta Y, Tsuda M, Maruno T, Nakanishi Y, Kawada K, Takaishi S, Seno H. JNK pathway plays a critical role for expansion of human colorectal cancer in the context of BRG1 suppression. Cancer Sci 2022; 113:3417-3427. [PMID: 35924439 PMCID: PMC9530857 DOI: 10.1111/cas.15520] [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: 01/26/2022] [Revised: 07/14/2022] [Accepted: 07/26/2022] [Indexed: 12/09/2022] Open
Abstract
Tumor stem cells (TSCs), capable of self‐renewal and continuous production of progeny cells, could be potential therapeutic targets. We have recently reported that chromatin remodeling regulator Brg1 is required for maintenance of murine intestinal TSCs and stemness feature of human colorectal cancer (CRC) cells by inhibiting apoptosis. However, it is still unclear how BRG1 suppression changes the underlying intracellular mechanisms of human CRC cells. We found that Brg1 suppression resulted in upregulation of the JNK signaling pathway in human CRC cells and murine intestinal TSCs. Simultaneous suppression of BRG1 and the JNK pathway, either by pharmacological inhibition or silencing of c‐JUN, resulted in even stronger inhibition of the expansion of human CRC cells compared to Brg1 suppression alone. Consistently, high c‐JUN expression correlated with worse prognosis for survival in human CRC patients with low BRG1 expression. Therefore, the JNK pathway plays a critical role for expansion and stemness of human CRC cells in the context of BRG1 suppression, and thus a combined blockade of BRG1 and the JNK pathway could be a novel therapeutic approach against human CRC.
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Affiliation(s)
- Takaaki Yoshikawa
- Department of Gastroenterology and Hepatology, Kyoto University Graduate School of Medicine, Kyoto, Japan.,Department of Gastroenterology and Hepatology, Kitano Hospital, Tazuke Kofukai Medical Research Institute, Osaka, Japan
| | - Akihisa Fukuda
- Department of Gastroenterology and Hepatology, Kyoto University Graduate School of Medicine, Kyoto, Japan
| | - Mayuki Omatsu
- Department of Gastroenterology and Hepatology, Kyoto University Graduate School of Medicine, Kyoto, Japan
| | - Mio Namikawa
- Department of Gastroenterology and Hepatology, Kyoto University Graduate School of Medicine, Kyoto, Japan
| | - Makoto Sono
- Department of Gastroenterology and Hepatology, Kyoto University Graduate School of Medicine, Kyoto, Japan
| | - Fukunaga Yuichi
- Department of Gastroenterology and Hepatology, Kyoto University Graduate School of Medicine, Kyoto, Japan.,Department of Drug Discovery Medicine, Medical Innovation Center, Kyoto University Graduate School of Medicine, Kyoto, Japan
| | - Tomonori Masuda
- Department of Gastroenterology and Hepatology, Kyoto University Graduate School of Medicine, Kyoto, Japan
| | - Osamu Araki
- Department of Gastroenterology and Hepatology, Kyoto University Graduate School of Medicine, Kyoto, Japan
| | - Munemasa Nagao
- Department of Gastroenterology and Hepatology, Kyoto University Graduate School of Medicine, Kyoto, Japan
| | - Satoshi Ogawa
- Department of Gastroenterology and Hepatology, Kyoto University Graduate School of Medicine, Kyoto, Japan
| | - Kenji Masuo
- Department of Gastroenterology and Hepatology, Kyoto University Graduate School of Medicine, Kyoto, Japan.,Laboratory for Malignancy Control Research (DSK project), Medical Innovation Center, Kyoto University Graduate School of Medicine, Kyoto, Japan
| | - Norihiro Goto
- Department of Gastroenterology and Hepatology, Kyoto University Graduate School of Medicine, Kyoto, Japan
| | - Yukiko Hiramatsu
- Department of Gastroenterology and Hepatology, Kyoto University Graduate School of Medicine, Kyoto, Japan
| | - Yu Muta
- Department of Gastroenterology and Hepatology, Kyoto University Graduate School of Medicine, Kyoto, Japan
| | - Motoyuki Tsuda
- Department of Gastroenterology and Hepatology, Kyoto University Graduate School of Medicine, Kyoto, Japan
| | - Takahisa Maruno
- Department of Gastroenterology and Hepatology, Kyoto University Graduate School of Medicine, Kyoto, Japan
| | - Yuki Nakanishi
- Department of Gastroenterology and Hepatology, Kyoto University Graduate School of Medicine, Kyoto, Japan
| | - Kenji Kawada
- Department of Surgery, Kyoto University Graduate School of Medicine, Kyoto, Japan
| | - Shigeo Takaishi
- Laboratory for Malignancy Control Research (DSK project), Medical Innovation Center, Kyoto University Graduate School of Medicine, Kyoto, Japan
| | - Hiroshi Seno
- Department of Gastroenterology and Hepatology, Kyoto University Graduate School of Medicine, Kyoto, Japan
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Hussain S, Tulsyan S, Dar SA, Sisodiya S, Abiha U, Kumar R, Mishra BN, Haque S. Role of epigenetics in carcinogenesis: Recent advancements in anticancer therapy. Semin Cancer Biol 2022; 83:441-451. [PMID: 34182144 DOI: 10.1016/j.semcancer.2021.06.023] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2020] [Revised: 04/29/2021] [Accepted: 06/23/2021] [Indexed: 02/08/2023]
Abstract
The role of epigenetics in the etiology of cancer progression is being emphasized for the past two decades to check the impact of chromatin modifiers and remodelers. Histone modifications, DNA methylation, chromatin remodeling, nucleosome positioning, regulation by non-coding RNAs and precisely microRNAs are influential epigenetic marks in the field of progressive cancer sub-types. Furthermore, constant epigenetic changes due to hyper or hypomethylation could efficiently serve as effective biomarkers of cancer diagnosis and therapeutic development. Ongoing research in the field of epigenetics has resulted in the resolutory role of various epigenetic markers and their inhibition using specific inhibitors to arrest their key cellular functions in in-vitro and pre-clinical studies. Although, the mechanism of epigenetics in cancer largely remains unexplored. Nevertheless, various advancements in the field of epigenetics have been made through transcriptome analysis and in-vitro genome targeting technologies to unravel the applicability of epigenetic markers for future cancer therapeutics and management. Therefore, this review emphasizes on recent advances in epigenetic landscapes that could be targeted/explored using novel approaches as personalized treatment modalities for cancer containment.
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Affiliation(s)
- Showket Hussain
- Division of Molecular Oncology & Molecular Diagnostics, ICMR-National Institute of Cancer Prevention and Research, Noida, India
| | - Sonam Tulsyan
- Division of Molecular Oncology & Molecular Diagnostics, ICMR-National Institute of Cancer Prevention and Research, Noida, India
| | - Sajad Ahmad Dar
- Research and Scientific Studies Unit, College of Nursing and Allied Health Sciences, Jazan University, Jazan, Saudi Arabia
| | - Sandeep Sisodiya
- Division of Molecular Oncology & Molecular Diagnostics, ICMR-National Institute of Cancer Prevention and Research, Noida, India; Symbiosis School of Biological Sciences, Symbiosis International (Deemed University), Pune, India
| | - Umme Abiha
- Centre for Medical Biotechnology, Amity Institute of Biotechnology, Amity University, Noida, India
| | - Rakesh Kumar
- Dr. B.R.A. Institute Rotary Cancer Hospital, All India Institute of Medical Sciences, New Delhi, India
| | - Bhartendu Nath Mishra
- Department of Biotechnology, Institute of Engineering and Technology, Lucknow, India
| | - Shafiul Haque
- Research and Scientific Studies Unit, College of Nursing and Allied Health Sciences, Jazan University, Jazan, Saudi Arabia; Bursa Uludağ University Faculty of Medicine, Görükle Campus, Nilüfer, Bursa, Turkey.
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223
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Martelli V, Pastorino A, Sobrero AF. Prognostic and predictive molecular biomarkers in advanced colorectal cancer. Pharmacol Ther 2022; 236:108239. [PMID: 35780916 DOI: 10.1016/j.pharmthera.2022.108239] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Revised: 06/21/2022] [Accepted: 06/27/2022] [Indexed: 10/17/2022]
Abstract
The revolution of precision medicine has produced unprecedented seismic shifts in the treatment paradigm of advanced cancers. Among the major killers, colorectal cancer (CRC) is far behind the others. In fact, the great successes obtained in breast, NSCLC, melanoma, and genitourinary tract tumors have been observed only in fewer than 5 % metastatic colorectal cancer (mCRC): those with the mismatch repair deficiency (dMMR), a well-known predictive factor for to the outstanding efficacy of checkpoint inhibitors (CPI). The treatment of the remaining vast majority mCRC patients is still based upon only two molecular determinants: the RAS and BRAF mutational status. New promising biomarkers include HER2, tumor mutational burden (TMB) for its possible implications on CPI efficacy, and the extremely rare NTRK fusions. The Consensus Molecular Subtypes classification (CMS) is a good example of the efforts to combine different molecular features of this disease, although its relevance in clinical practice is still under investigation. In this Review, we focus on all these prognostic and predictive biomarkers, analyzing data from the most important clinical trials of the last years. We also try to rank them according to their prognostic and predictive power.
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Affiliation(s)
- Valentino Martelli
- Medical Oncology Unit 1, Ospedale Policlinico San Martino - IRCCS, Largo Rosanna Benzi 10, 16132 Genoa, Italy
| | - Alessandro Pastorino
- Medical Oncology Unit 1, Ospedale Policlinico San Martino - IRCCS, Largo Rosanna Benzi 10, 16132 Genoa, Italy
| | - Alberto F Sobrero
- Medical Oncology Unit 1, Ospedale Policlinico San Martino - IRCCS, Largo Rosanna Benzi 10, 16132 Genoa, Italy.
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224
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Yan S, Wang S, Wang X, Dai W, Chu J, Cheng M, Guo Z, Xu D. Emerging role of non-coding RNAs in glucose metabolic reprogramming and chemoresistance in colorectal cancer. Front Oncol 2022; 12:954329. [PMID: 35978828 PMCID: PMC9376248 DOI: 10.3389/fonc.2022.954329] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2022] [Accepted: 07/11/2022] [Indexed: 11/28/2022] Open
Abstract
Metabolic reprogramming plays a critical role in colorectal cancer (CRC). It contributes to CRC by shaping metabolic phenotypes and causing uncontrolled proliferation of CRC cells. Glucose metabolic reprogramming is common in carcinogenesis and cancer progression. Growing evidence has implicated the modifying effects of non-coding RNAs (ncRNAs) in glucose metabolic reprogramming and chemoresistance in CRC. In this review, we have summarized currently published studies investigating the role of ncRNAs in glucose metabolic alterations and chemoresistance in CRC. Elucidating the interplay between ncRNAs and glucose metabolic reprogramming provides insight into exploring novel biomarkers for the diagnosis and prognosis prediction of CRC.
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Affiliation(s)
- Shushan Yan
- Department of Gastrointestinal and Anal Diseases Surgery of the Affiliated Hospital, Weifang Medical University, Weifang, China
| | - Shufeng Wang
- Medical Experimental Training Center, Weifang Medical University, Weifang, China
| | - Xinyi Wang
- Clinical Medicine of Basic Medical School, Shandong First Medical University, Jinan, China
| | - Wenqing Dai
- Central Laboratory of the First Affiliated Hospital, Weifang Medical University, Weifang, China
| | - Jinjin Chu
- Central Laboratory of the First Affiliated Hospital, Weifang Medical University, Weifang, China
| | - Min Cheng
- Department of Physiology, Weifang Medical University, Weifang, China
| | - Zhiliang Guo
- Department of Spine Surgery, The 80th Group Army Hospital of Chinese People’s Liberation Army (PLA), Weifang, China
- *Correspondence: Zhiliang Guo, ; Donghua Xu,
| | - Donghua Xu
- Central Laboratory of the First Affiliated Hospital, Weifang Medical University, Weifang, China
- Department of Rheumatology of the First Affiliated Hospital, Weifang Medical University, Weifang, China
- *Correspondence: Zhiliang Guo, ; Donghua Xu,
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225
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Sattar RSA, Verma R, Nimisha, Kumar A, Dar GM, Apurva, Sharma AK, Kumari I, Ahmad E, Ali A, Mahajan B, Saluja SS. Diagnostic and prognostic biomarkers in colorectal cancer and the potential role of exosomes in drug delivery. Cell Signal 2022; 99:110413. [PMID: 35907519 DOI: 10.1016/j.cellsig.2022.110413] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2022] [Revised: 07/13/2022] [Accepted: 07/15/2022] [Indexed: 11/03/2022]
Abstract
Colorectal cancer (CRC) is third most common cancer with second most common cause of death worldwide. One fourth to one fifth of the CRC cases are detected at advance stage. Early detection of colorectal cancer might help in decreasing mortality and morbidity worldwide. CRC being a heterogeneous disease, new non-invasive approaches are needed to complement and improve the screening and management of CRC. Reliable and early detectable biomarkers would improve diagnosis, prognosis, therapeutic responses, and will enable the prediction of drug response and recurrence risk. Over the past decades molecular research has demonstrated the potentials of CTCs, ctDNAs, circulating mRNA, ncRNAs, and exosomes as tumor biomarkers. Non-invasive screening approaches using fecal samples for identification of altered gut microbes in CRC is also gaining attention. Exosomes can be potential candidates that can be employed in the drug delivery system. Further, the integration of in vitro, in vivo and in silico models that involve CRC biomarkers will help to understand the interactions occurring at the cellular level. This review summarizes recent update on CRC biomarkers and their application along with the nanoparticles followed by the application of organoid culture in CRC.
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Affiliation(s)
- Real Sumayya Abdul Sattar
- Central Molecular Laboratory, Govind Ballabh Pant Institute of Postgraduate Medical Education and Research (GIPMER), New Delhi, India
| | - Renu Verma
- Central Molecular Laboratory, Govind Ballabh Pant Institute of Postgraduate Medical Education and Research (GIPMER), New Delhi, India
| | - Nimisha
- Central Molecular Laboratory, Govind Ballabh Pant Institute of Postgraduate Medical Education and Research (GIPMER), New Delhi, India
| | - Arun Kumar
- Central Molecular Laboratory, Govind Ballabh Pant Institute of Postgraduate Medical Education and Research (GIPMER), New Delhi, India
| | - Ghulam Mehdi Dar
- Central Molecular Laboratory, Govind Ballabh Pant Institute of Postgraduate Medical Education and Research (GIPMER), New Delhi, India
| | - Apurva
- Central Molecular Laboratory, Govind Ballabh Pant Institute of Postgraduate Medical Education and Research (GIPMER), New Delhi, India
| | - Abhay Kumar Sharma
- Central Molecular Laboratory, Govind Ballabh Pant Institute of Postgraduate Medical Education and Research (GIPMER), New Delhi, India
| | - Indu Kumari
- Central Molecular Laboratory, Govind Ballabh Pant Institute of Postgraduate Medical Education and Research (GIPMER), New Delhi, India
| | - Ejaj Ahmad
- Central Molecular Laboratory, Govind Ballabh Pant Institute of Postgraduate Medical Education and Research (GIPMER), New Delhi, India
| | - Asgar Ali
- Central Molecular Laboratory, Govind Ballabh Pant Institute of Postgraduate Medical Education and Research (GIPMER), New Delhi, India
| | - Bhawna Mahajan
- Central Molecular Laboratory, Govind Ballabh Pant Institute of Postgraduate Medical Education and Research (GIPMER), New Delhi, India; Department of Biochemistry, Govind Ballabh Pant Institute of Postgraduate Medical Education and Research (GIPMER), New Delhi, India
| | - Sundeep Singh Saluja
- Central Molecular Laboratory, Govind Ballabh Pant Institute of Postgraduate Medical Education and Research (GIPMER), New Delhi, India; Department of GI Surgery, Govind Ballabh Pant Institute of Postgraduate Medical Education and Research (GIPMER), New Delhi, India.
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226
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Sahoo OS, Pethusamy K, Srivastava TP, Talukdar J, Alqahtani MS, Abbas M, Dhar R, Karmakar S. The metabolic addiction of cancer stem cells. Front Oncol 2022; 12:955892. [PMID: 35957877 PMCID: PMC9357939 DOI: 10.3389/fonc.2022.955892] [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: 05/29/2022] [Accepted: 06/28/2022] [Indexed: 11/13/2022] Open
Abstract
Cancer stem cells (CSC) are the minor population of cancer originating cells that have the capacity of self-renewal, differentiation, and tumorigenicity (when transplanted into an immunocompromised animal). These low-copy number cell populations are believed to be resistant to conventional chemo and radiotherapy. It was reported that metabolic adaptation of these elusive cell populations is to a large extent responsible for their survival and distant metastasis. Warburg effect is a hallmark of most cancer in which the cancer cells prefer to metabolize glucose anaerobically, even under normoxic conditions. Warburg's aerobic glycolysis produces ATP efficiently promoting cell proliferation by reprogramming metabolism to increase glucose uptake and stimulating lactate production. This metabolic adaptation also seems to contribute to chemoresistance and immune evasion, a prerequisite for cancer cell survival and proliferation. Though we know a lot about metabolic fine-tuning in cancer, what is still in shadow is the identity of upstream regulators that orchestrates this process. Epigenetic modification of key metabolic enzymes seems to play a decisive role in this. By altering the metabolic flux, cancer cells polarize the biochemical reactions to selectively generate "onco-metabolites" that provide an added advantage for cell proliferation and survival. In this review, we explored the metabolic-epigenetic circuity in relation to cancer growth and proliferation and establish the fact how cancer cells may be addicted to specific metabolic pathways to meet their needs. Interestingly, even the immune system is re-calibrated to adapt to this altered scenario. Knowing the details is crucial for selective targeting of cancer stem cells by choking the rate-limiting stems and crucial branch points, preventing the formation of onco-metabolites.
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Affiliation(s)
- Om Saswat Sahoo
- Department of Biotechnology, National Institute of technology, Durgapur, India
| | - Karthikeyan Pethusamy
- Department of Biochemistry, All India Institute of Medical Sciences, New Delhi, India
| | | | - Joyeeta Talukdar
- Department of Biochemistry, All India Institute of Medical Sciences, New Delhi, India
| | - Mohammed S. Alqahtani
- Radiological Sciences Department, College of Applied Medical Sciences, King Khalid University, Abha, Saudi Arabia
- BioImaging Unit, Space Research Centre, Michael Atiyah Building, University of Leicester, Leicester, United Kingdom
| | - Mohamed Abbas
- Electrical Engineering Department, College of Engineering, King Khalid University, Abha, Saudi Arabia
- Computers and communications Department, College of Engineering, Delta University for Science and Technology, Gamasa, Egypt
| | - Ruby Dhar
- Department of Biochemistry, All India Institute of Medical Sciences, New Delhi, India
| | - Subhradip Karmakar
- Department of Biochemistry, All India Institute of Medical Sciences, New Delhi, India
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227
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Lamichhane S, Mo JS, Sharma G, Joung SM, Chae SC. MIR133A regulates cell proliferation, migration, and apoptosis by targeting SOX9 in human colorectal cancer cells. Am J Cancer Res 2022; 12:3223-3241. [PMID: 35968353 PMCID: PMC9360235] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2022] [Accepted: 06/18/2022] [Indexed: 06/15/2023] Open
Abstract
The human microRNA 133A (MIR133A) was identified as a CRC-associated miRNA. It was down-regulated in human CRC tissues. We identified the putative MIR133A1 and A2 target genes by comparing the transcriptome analysis data of MIR133A1 and A2 knock-in cells with the candidate MIR133A target genes predicted by bioinformatics tools. We identified 29 and 33 putative MIR133A and A2 direct target genes, respectively. Among them, we focused on the master transcription regulator gene SRY-box transcription factor 9 (SOX9), which exhibits a pleiotropic role in cancer. We confirmed that SOX9 is a direct target gene of MIR133A by luciferase reporter assay, quantitative RT-PCR, and western blot analysis. Overexpression of MIR133A in CRC cell lines significantly decreased SOX9 and its downstream PIK3CA-AKT1-GSK3B-CTNNB1 and KRAS-BRAF-MAP2K1-MAPK1/3 pathways and increased apoptosis. Furthermore, functional studies reveal that cell proliferation, colony formation, and migration ability were significantly decreased by MIR133A-overexpressed CRC cell lines. Knockdown of SOX9 in CRC cell lines by SOX9 gene silencing showed similar results. We also used a xenograft model to show that MIR133A overexpression suppresses tumor growth and proliferation. Our results suggest that MIR133A regulates cell proliferation, migration, and apoptosis by targeting SOX9 in human colorectal cancer.
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Affiliation(s)
- Santosh Lamichhane
- Department of Pathology, School of Medicine, Wonkwang UniversityIksan, Chonbuk 54538, Korea
| | - Ji-Su Mo
- Digestive Disease Research Institute, Wonkwang UniversityIksan, Chonbuk 54538, Korea
| | - Grinsun Sharma
- Department of Pathology, School of Medicine, Wonkwang UniversityIksan, Chonbuk 54538, Korea
| | - Sun-Myoung Joung
- Department of Pathology, School of Medicine, Wonkwang UniversityIksan, Chonbuk 54538, Korea
| | - Soo-Cheon Chae
- Department of Pathology, School of Medicine, Wonkwang UniversityIksan, Chonbuk 54538, Korea
- Digestive Disease Research Institute, Wonkwang UniversityIksan, Chonbuk 54538, Korea
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228
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Yuan RQ, Zhao H, Wang Y, Song K, Yang J, He W, Miao DZ, Wang Q, Jia YH. SEPTIN9-SDC2-VIM methylation signature as a biomarker for the early diagnosis of colorectal cancer. Am J Cancer Res 2022; 12:3128-3140. [PMID: 35968354 PMCID: PMC9360219] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2022] [Accepted: 06/13/2022] [Indexed: 06/15/2023] Open
Abstract
The accurate detection of colorectal cancer (CRC) at its initial stage can reduce mortality. However, the broad application of endoscopy has been limited due to the invasive procedure and patient noncompliance. Liquid biopsy with subsequent mapping of methylation in specific cell-free DNA (cfDNA) may represent an alternative approach for early diagnosis. In this study, we have developed a minimal-invasive blood-based test for detection of precancerous lesions and early-stage CRC. Using TCGA M450K methylation data, we identified candidate methylation sites with the highest Fold Change (FC) for three genes (SEPTIN9, SDC2 and VIM), which were selected from previous studies. Based on logistic regression models, we developed a 3-gene methylation signature for CRC diagnosis with high accuracy (Sensitivity =0.959, Specificity =1, AUC =0.997). Using independent public databases and data from blood samples, this model has demonstrated superior performance. The AUC was 0.919-1 and 0.905-0.916 in public tissue database for CRC and blood sample data, respectively. Thus, our proposed 3-gene methylation signature has a more reliable performance than other methods. Furthermore, signal enhancement effect of 3-gene methylation signature can improve the accuracy of early diagnosis for CRC, which demonstrates the potential for clinical application.
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Affiliation(s)
- Rong-Qiang Yuan
- Department of Systems Biology, College of Bioinformatics Science and Technology, Harbin Medical UniversityHarbin 150086, Heilongjiang, China
| | - Hui Zhao
- The First Affiliated Hospital, Harbin Medical UniversityHarbin 150001, Heilongjiang, China
| | - Yan Wang
- Harbin Medical University Cancer Hospital Colorectal Cancer CenterHarbin 150086, Heilongjiang, China
| | - Kai Song
- Zhuhai Interventional Medical Center, Zhuhai Precision Medical Center, Zhuhai People’s Hospital, Zhuhai Hospital Affiliated with Jinan University, Jinan UniversityZhuhai 519000, Guangdong, China
| | - Jia Yang
- Department of Systems Biology, College of Bioinformatics Science and Technology, Harbin Medical UniversityHarbin 150086, Heilongjiang, China
| | - Wei He
- Harbin Medical University Cancer Hospital Colorectal Cancer CenterHarbin 150086, Heilongjiang, China
| | - Da-Zhuang Miao
- Harbin Medical University Cancer Hospital Colorectal Cancer CenterHarbin 150086, Heilongjiang, China
| | - Qi Wang
- Harbin Medical University Cancer Hospital Colorectal Cancer CenterHarbin 150086, Heilongjiang, China
| | - Yun-He Jia
- Harbin Medical University Cancer Hospital Colorectal Cancer CenterHarbin 150086, Heilongjiang, China
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Wang T, Yao Y, Hu X, Zhao Y. Message in hand: the application of CRISPRi, RNAi, and LncRNA in adenocarcinoma. Med Oncol 2022; 39:148. [PMID: 35834017 DOI: 10.1007/s12032-022-01727-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2021] [Accepted: 04/05/2022] [Indexed: 06/15/2023]
Abstract
Gene editing interference technology has been flourishing for more than 30 years. It has always been a common means to interfere with the expression of particular genes. Today it has shown a broad application prospect in clinical treatment, especially in adenocarcinoma treatment. In just a few years, the CRISPRi technology has attracted much z attention with its precise targeting and convenient operability significantly promoted the transformation from bench to bedside, and won the Nobel Prize in Chemistry 2020. In recent years, the importance of non-coding RNA has led LncRNA research to the center. At the same time, it also recalls the surprises obtained in laboratory and clinic research by RNAi technologies such as microRNA, siRNA, and shRNA at the beginning of the century. Therefore, this article focuses on CRISPRi, RNAi, and LncRNA to review their gene interference mechanisms currently expected to be translational research. Their applications and differences in adenocarcinoma research will also be described powerfully. It will provide a helpful reference for scientists to understand better and apply several RNA interference technologies.
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Affiliation(s)
- Ting Wang
- Cancer Research Institute, Guangdong Medical University, Dongguan, 523808, China
- Pathology Department, Guangdong Medical University, Dongguan, 523808, China
| | - Yunhong Yao
- Pathology Department, Guangdong Medical University, Dongguan, 523808, China
| | - Xinrong Hu
- Cancer Research Institute, Guangdong Medical University, Dongguan, 523808, China.
- Pathology Department, Guangdong Medical University, Dongguan, 523808, China.
| | - Yi Zhao
- Cancer Research Institute, Guangdong Medical University, Dongguan, 523808, China.
- Microbiology and Immunology Department, Guangdong Medical University, Dongguan, 523808, China.
- Department of Traditional Chinese Medicine, The First Dongguan Affiliated Hospital of Guangdong Medical University, Dongguan, 523713, China.
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Li N, Zeng A, Wang Q, Chen M, Zhu S, Song L. Regulatory function of DNA methylation mediated lncRNAs in gastric cancer. Cancer Cell Int 2022; 22:227. [PMID: 35810299 PMCID: PMC9270757 DOI: 10.1186/s12935-022-02648-1] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2022] [Accepted: 06/28/2022] [Indexed: 12/31/2022] Open
Abstract
As one of the most common malignancies worldwide, gastric cancer contributes to cancer death with a high mortality rate partly responsible for its out-of-control progression as well as limited diagnosis. DNA methylation, one of the epigenetic events, plays an essential role in the carcinogenesis of many cancers, including gastric cancer. Long non-coding RNAs have emerged as the significant factors in the cancer progression functioned as the oncogene genes, the suppressor genes and regulators of signaling pathways over the decade. Intriguingly, increasing reports, recently, have claimed that abnormal DNA methylation regulates the expression of lncRNAs as tumor suppressor genes in gastric cancer and lncRNAs as regulators could exert the critical influence on tumor progression through acting on DNA methylation of other cancer-related genes. In this review, we summarized the DNA methylation-associated lncRNAs in gastric cancer which play a large impact on tumor progression, such as proliferation, invasion, metastasis and so on. Furthermore, the underlying molecular mechanism and signaling pathway might be developed as key points of gastric cancer range from diagnosis to prognosis and treatment in the future.
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Affiliation(s)
- Nan Li
- School of Medical and Life Sciences, Chengdu University of Traditional Chinese Medicine, Chengdu, Sichuan, 611137, People's Republic of China
| | - Anqi Zeng
- Institute of Translational Pharmacology and Clinical Application, Sichuan Academy of Chinese Medical Science, Chengdu, Sichuan, 610041, People's Republic of China
| | - Qian Wang
- School of Medical and Life Sciences, Chengdu University of Traditional Chinese Medicine, Chengdu, Sichuan, 611137, People's Republic of China
| | - Maohua Chen
- School of Medical and Life Sciences, Chengdu University of Traditional Chinese Medicine, Chengdu, Sichuan, 611137, People's Republic of China
| | - Shaomi Zhu
- School of Medical and Life Sciences, Chengdu University of Traditional Chinese Medicine, Chengdu, Sichuan, 611137, People's Republic of China.
| | - Linjiang Song
- School of Medical and Life Sciences, Chengdu University of Traditional Chinese Medicine, Chengdu, Sichuan, 611137, People's Republic of China.
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231
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Kim HJ, Moon SJ, Hong S, Won HH, Kim JH. DBC1 is a key positive regulator of enhancer epigenomic writers KMT2D and p300. Nucleic Acids Res 2022; 50:7873-7888. [PMID: 35801925 PMCID: PMC9371912 DOI: 10.1093/nar/gkac585] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2022] [Revised: 06/14/2022] [Accepted: 06/24/2022] [Indexed: 11/13/2022] Open
Abstract
Histone modification is a key epigenetic mechanism for regulation of chromatin dynamics and gene expression. Deleted in breast cancer 1 (DBC1) has been shown to act as a negative regulator of epigenetic modifiers and as a co-activator for nuclear receptors and other transcription factors. However, little is known about the role of DBC1 in the regulation of histone modifications and chromatin landscapes. Here, we analyzed genome-wide profiles of active enhancer and promoter marks in colorectal cancer cells and report DBC1 as a critical positive regulator of histone epigenetic writers KMT2D (H3K4 methyltransferase) and p300 (histone acetyltransferase). DBC1 is required for establishing the landscape of active enhancers, for genome-wide chromatin binding and enhancer recruitment of KMT2D and p300, and for gene activation involved in colorectal cancer progression. DBC1 interacts directly with KMT2D and p300, and enhances KMT2D-mediated histone H3K4 methylation (H3K4me1/2/3) and p300-mediated H3 acetylation. Importantly, DBC1 contributes to super-enhancer formation and function by facilitating the recruitment of KMT2D and p300 and by enhancing their functional interaction and cooperative cross-talk. Our results highlight the critical role of DBC1 as a key positive regulator of KMT2D and p300, and provide insights into regulatory mechanisms underlying the interplay between the enhancer epigenomic writers in enhancer activation.
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Affiliation(s)
- Hwa Jin Kim
- Department of Health Sciences and Technology, Samsung Advanced Institute for Health Sciences and Technology, Sungkyunkwan University, Seoul, 06351, South Korea.,Research Institute for Future Medicine, Samsung Medical Center, Seoul, 06351, South Korea
| | - Sue Jin Moon
- Department of Health Sciences and Technology, Samsung Advanced Institute for Health Sciences and Technology, Sungkyunkwan University, Seoul, 06351, South Korea.,Research Institute for Future Medicine, Samsung Medical Center, Seoul, 06351, South Korea
| | - Sanghoon Hong
- Department of Digital Health, Samsung Advanced Institute for Health Sciences and Technology, Sungkyunkwan University, Seoul, 06351, South Korea
| | - Hong-Hee Won
- Research Institute for Future Medicine, Samsung Medical Center, Seoul, 06351, South Korea.,Department of Digital Health, Samsung Advanced Institute for Health Sciences and Technology, Sungkyunkwan University, Seoul, 06351, South Korea
| | - Jeong Hoon Kim
- Department of Health Sciences and Technology, Samsung Advanced Institute for Health Sciences and Technology, Sungkyunkwan University, Seoul, 06351, South Korea.,Research Institute for Future Medicine, Samsung Medical Center, Seoul, 06351, South Korea
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232
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Zhu Q, Gu X, Wei W, Wu Z, Gong F, Dong X. BRD9 is an essential regulator of glycolysis that creates an epigenetic vulnerability in colon adenocarcinoma. Cancer Med 2022; 12:1572-1587. [PMID: 35778964 PMCID: PMC9883419 DOI: 10.1002/cam4.4954] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2021] [Revised: 05/28/2022] [Accepted: 06/07/2022] [Indexed: 02/01/2023] Open
Abstract
BACKGROUND The intensive interplay between aberrant epigenetic events and metabolic remodeling represents one of the hallmarks of tumors, including colon cancer. The functions of Bromodomain Containing Protein BRD-9 in colon cancer remains indefinite. We aimed to identify the biological roles and clinical significance of BRD9 in colon cancer. METHODS The univariate- and multi-variate Cox regression models were used to screen risk epigenetic regulators. Kaplan-Meier analysis and Pearson correlation analysis were used to assess clinical significance of BRD9. CCK-8 assays, colony formation assay, Transwell, and soft-agar assay were performed to determine the in vitro roles of BRD9. The oxygen consumption rate (OCR) and extracellular acidification rate (ECAR) of colon cancer cells were evaluated by a Seahorse XF Extracellular Flux Analyzer. In vivo models and RT-qPCR, western blotting, and Chromatin Immunoprecipitation (ChIP) assay were conducted to explore the functional roles of BRD9 in COAD. RESULTS In the study, we detected the expressions of 662 epigenetic regulators in COAD and identified a series of 42 hazard epigenetic factors with p < 0.05. Low-throughput MTT assays highlighted that BRD9 is an essential target, and targeting BRD9 could reduce significant decreases of cell growth. BRD9 overexpression could notably elevate proliferation and migration potentialities, whereas, BRD9 ablation abolished these effects. Mechanistically, functional enrichment analysis indicated the potential associations between BRD9 and glycolysis metabolism. In addition, BRD9 epigenetically coordinates the H3K27ac modifications on the promoter regions of ENO2 and ALDOC, inducing enhanced glycolysis activity. Lastly, I-BRD9 could significantly suppress the growth of colon cancer cells in vitro and in vivo. CONCLUSIONS Together, our study revealed previously unidentified roles of BRD9 in colon cancer metabolism and tumor progression, indicating that BRD9 could be a valuable therapeutic target for COAD patients.
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Affiliation(s)
- Qunshan Zhu
- Department of General SurgeryThe First Affiliated Hospital of Soochow UniversitySuzhouChina,Department of General SurgeryJiangdu People's Hospital Affiliated to Medical College of Yangzhou UniversityYangzhouChina
| | - Xiang Gu
- Department of RadiotherapyJiangdu People's Hospital Affiliated to Medical College of Yangzhou UniversityYangzhouChina
| | - Wei Wei
- Department of General SurgeryJiangdu People's Hospital Affiliated to Medical College of Yangzhou UniversityYangzhouChina
| | - Zheng Wu
- Department of General SurgeryJiangdu People's Hospital Affiliated to Medical College of Yangzhou UniversityYangzhouChina
| | - Fengqin Gong
- Department of General SurgeryJiangdu People's Hospital Affiliated to Medical College of Yangzhou UniversityYangzhouChina
| | - Xiaoqiang Dong
- Department of General SurgeryThe First Affiliated Hospital of Soochow UniversitySuzhouChina
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233
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RGS10 suppression by DNA methylation is associated with low survival rates in colorectal carcinoma. Pathol Res Pract 2022; 236:154007. [DOI: 10.1016/j.prp.2022.154007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/15/2022] [Revised: 06/27/2022] [Accepted: 06/29/2022] [Indexed: 01/12/2023]
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234
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Zhao Z, Wang S, Zucknick M, Aittokallio T. Tissue-specific identification of multi-omics features for pan-cancer drug response prediction. iScience 2022; 25:104767. [PMID: 35992090 PMCID: PMC9385562 DOI: 10.1016/j.isci.2022.104767] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2022] [Revised: 06/28/2022] [Accepted: 07/11/2022] [Indexed: 11/29/2022] Open
Abstract
Current statistical models for drug response prediction and biomarker identification fall short in leveraging the shared and unique information from various cancer tissues and multi-omics profiles. We developed mix-lasso model that introduces an additional sample group penalty term to capture tissue-specific effects of features on pan-cancer response prediction. The mix-lasso model takes into account both the similarity between drug responses (i.e., multi-task learning), and the heterogeneity between multi-omics data (multi-modal learning). When applied to large-scale pharmacogenomics dataset from Cancer Therapeutics Response Portal, mix-lasso enabled accurate drug response predictions and identification of tissue-specific predictive features in the presence of various degrees of missing data, drug-drug correlations, and high-dimensional and correlated genomic and molecular features that often hinder the use of statistical approaches in drug response modeling. Compared to tree lasso model, mix-lasso identified a smaller number of tissue-specific features, hence making the model more interpretable and stable for drug discovery applications. Pan-cancer cell lines provide a test bench for exploring gene-drug relationships Multi-omics data were integrated with pharmacological profiles for joint modeling Mix-lasso identifies tissue-specific biomarkers predictive of multi-drug responses Mix-lasso provides small number of stable features for drug discovery applications
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Affiliation(s)
- Zhi Zhao
- Institute for Cancer Research, Department of Cancer Genetics, Oslo University Hospital, Norway
- Centre for Biostatistics and Epidemiology (OCBE), Faculty of Medicine, University of Oslo, Norway
| | - Shixiong Wang
- Institute for Cancer Research, Department of Cancer Genetics, Oslo University Hospital, Norway
| | - Manuela Zucknick
- Centre for Biostatistics and Epidemiology (OCBE), Faculty of Medicine, University of Oslo, Norway
- Corresponding author
| | - Tero Aittokallio
- Institute for Cancer Research, Department of Cancer Genetics, Oslo University Hospital, Norway
- Centre for Biostatistics and Epidemiology (OCBE), Faculty of Medicine, University of Oslo, Norway
- Institute for Molecular Medicine Finland (FIMM), HiLIFE, University of Helsinki, Finland
- Corresponding author
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235
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Wang J, Liu B, Cao J, Zhao L, Wang G. MIR31HG Expression Predicts Poor Prognosis and Promotes Colorectal Cancer Progression. Cancer Manag Res 2022; 14:1973-1986. [PMID: 35733512 PMCID: PMC9208482 DOI: 10.2147/cmar.s351928] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Accepted: 05/28/2022] [Indexed: 11/23/2022] Open
Abstract
Purpose Long noncoding RNAs (lncRNAs) are correlated with cancer pathogenesis and prognosis. Many studies have shown that aberrant expression of MIR31HG is implicated in the cancer progression and patient prognosis. However, the biological function and predictive value of MIR31HG in colorectal cancer is unclear. Methods The correlation between MIR31HG expression and clinicopathological characteristics of colorectal cancer patients was analyzed by collating the information from The Cancer Genome Atlas (TCGA) database. Kaplan–Meier analysis, univariable and multivariable Cox regression analysis were performed to evaluate the prognostic value of MIR31HG. Gene set enrichment analysis (GSEA) was conducted to identify the potential carcinogenic mechanisms implicated in MIR31HG. Moreover, MIR31HG was knocked down using siRNA in colorectal cancer cells, and cell migration, invasion, growth and colony formation assays were performed. The expression of MIR31HG influenced gene markers was quantified by qRT-PCR in MIR31HG-silenced colorectal cancer cells. Results In TCGA database, we found that MIR31HG was elevated in colorectal cancer patients. The patients with high MIR31HG expression had poor overall survival and disease-specific survival. Univariable and multivariable analyses showed that MIR31HG expression was an independent prognostic predictor in colorectal cancer patients. GSEA revealed that MIR31HG mainly modulated focal adhesion, extracellular matrix organization, integrin cell surface interactions and focal adhesion-PI3K-Akt-mTOR-signaling pathway. Besides, MIR31HG knockdown significantly impaired colorectal cancer cell migration, invasion, growth and colony formation. Further qRT-PCR data confirmed that alteration of MIR31HG expression notably affected the tumorigenesis-related key gene expression in the cells. Conclusion Our findings provide evidence that MIR31HG is a key factor in maintaining the malignant phenotype of colorectal cancer and may act as an independent predictor for patients with colorectal cancer.
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Affiliation(s)
- Jianlong Wang
- Department of General surgery, the Second Hospital of Hebei Medical University, Shijiazhuang, People's Republic of China.,Department of General Surgery, the Fourth Hospital of Hebei Medical University, Shijiazhuang, People's Republic of China
| | - Bin Liu
- Central Laboratory, the Second Hospital of Hebei Medical University, Shijiazhuang, People's Republic of China
| | - Jiewei Cao
- Central Laboratory, the Second Hospital of Hebei Medical University, Shijiazhuang, People's Republic of China
| | - Lianmei Zhao
- Department of Research Center, the Fourth Hospital of Hebei Medical University, Shijiazhuang, People's Republic of China
| | - Guiying Wang
- Department of General Surgery, the Fourth Hospital of Hebei Medical University, Shijiazhuang, People's Republic of China.,Department of General Surgery, the Third Hospital of Hebei Medical University, Shijiazhuang, People's Republic of China
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236
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Zhang Y, Chen Y, Huang J, Wu X, Tang R, Huang Q, Xu Y, Peng X, Fu K, Xiao S. Mucinous histology is associated with poor prognosis in locally advanced colorectal adenocarcinoma treated with postoperative first-line adjuvant chemotherapy: A systematic review and meta-analysis. EUROPEAN JOURNAL OF SURGICAL ONCOLOGY 2022; 48:2075-2081. [PMID: 35768312 DOI: 10.1016/j.ejso.2022.06.024] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2022] [Revised: 06/04/2022] [Accepted: 06/19/2022] [Indexed: 12/27/2022]
Abstract
PURPOSE Postoperative adjuvant chemotherapy followed surgery is the standard management for localized advanced colorectal carcinoma (CRC). Mucinous adenocarcinoma (MAC) is a peculiar histological subtype of CRC, but the prognosis of MAC patients is controversial. The objective of this study is to assess the implication of MAC in survival of patients treated with surgery and firs-line adjuvant chemotherapy. METHODS Studies describing outcomes for advanced MAC and non-specific adenocarcinoma (AC) of CRC patients treated with first-line postoperative adjuvant chemotherapy followed surgery were searched in PubMed, Embase, Medline, EBSCO, Wiley, and Cochrane Library (January 1963-August 2021). Hazard ratios (HRs) of overall survival (OS), disease-free survival (DFS) and cancer-specific survival (CSS) for MAC to AC were extracted. Random-effects model was used for calculating the pooled HRs and 95% confidence interval (CI). RESULTS This meta-analysis is comprised of 8 studies involving a total of 124,303 CRC patients treated with first-line adjuvant chemotherapy followed surgery. The pooled HR for MAC was 1.23 (95% CI, 1.07-1.41, p < 0.01, I2 = 80%), and the DFS (HR, 2.95, 95% CI, 1.22-7.14) of MAC patients were significantly poorer than AC patients. Similar results were also observed in stage III and FOLFOX regimen subgroups. CONCLUSION MAC was a risk factor for prognosis of localized advanced CRC patients treated with postoperative first-line adjuvant chemotherapy. Thus, the role of first-line adjuvant chemotherapy regimens should be further studied in these MAC patients.
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Affiliation(s)
- Yiwei Zhang
- The First Affiliated Hospital, Cancer Research Institute, Hengyang Medical School, University of South China, Hengyang, Hunan, 421001, China
| | - Yuqiao Chen
- Institute of Molecular Precision Medicine and Hunan Key Laboratory of Molecular Precision Medicine, Department of General Surgery, Xiangya Hospital, Central South University, Changsha, Hunan, 410008, China
| | - Jia Huang
- The First Affiliated Hospital, Cancer Research Institute, Hengyang Medical School, University of South China, Hengyang, Hunan, 421001, China
| | - Xiaofeng Wu
- The First Affiliated Hospital, Department of Gastrointestinal Surgery, Hengyang Medical School, University of South China, Hengyang, Hunan, 421001, China
| | - Rong Tang
- The First Affiliated Hospital, Department of Gastrointestinal Surgery, Hengyang Medical School, University of South China, Hengyang, Hunan, 421001, China
| | - Qiulin Huang
- The First Affiliated Hospital, Department of Gastrointestinal Surgery, Hengyang Medical School, University of South China, Hengyang, Hunan, 421001, China
| | - Yunhua Xu
- The First Affiliated Hospital, Cancer Research Institute, Hengyang Medical School, University of South China, Hengyang, Hunan, 421001, China
| | - Xiuda Peng
- The First Affiliated Hospital, Cancer Research Institute, Hengyang Medical School, University of South China, Hengyang, Hunan, 421001, China.
| | - Kai Fu
- Institute of Molecular Precision Medicine and Hunan Key Laboratory of Molecular Precision Medicine, Department of General Surgery, Xiangya Hospital, Central South University, Changsha, Hunan, 410008, China.
| | - Shuai Xiao
- The First Affiliated Hospital, Cancer Research Institute, Hengyang Medical School, University of South China, Hengyang, Hunan, 421001, China; The First Affiliated Hospital, Department of Gastrointestinal Surgery, Hengyang Medical School, University of South China, Hengyang, Hunan, 421001, China.
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237
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Fatemi N, Tierling S, Es HA, Varkiani M, Nazemalhosseini Mojarad E, Asadzadeh Aghdaei H, Walter J, Totonchi M. DNA Methylation Biomarkers in Colorectal Cancer: Clinical Applications for Precision Medicine. Int J Cancer 2022; 151:2068-2081. [PMID: 35730647 DOI: 10.1002/ijc.34186] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2022] [Revised: 04/29/2022] [Accepted: 06/08/2022] [Indexed: 11/06/2022]
Abstract
Colorectal cancer (CRC) is the second leading cause of cancer death worldwide that is attributed to gradual long-term accumulation of both genetic and epigenetic changes. To reduce the mortality rate of CRC and to improve treatment efficacy, it will be important to develop accurate noninvasive diagnostic tests for screening, acute, and personalized diagnosis. Epigenetic changes such as DNA methylation play an important role in the development and progression of CRC. Over the last decade, a panel of DNA methylation markers has been reported showing a high accuracy and reproducibility in various semi-invasive or noninvasive biosamples. Research to obtain comprehensive panels of markers allowing a highly sensitive and differentiating diagnosis of CRC is ongoing. Moreover, the epigenetic alterations for cancer therapy, as a precision medicine strategy will increase their therapeutic potential over time. Here, we discuss the current state of DNA methylation-based biomarkers and their impact on CRC diagnosis. We emphasize the need to further identify and stratify methylation-biomarkers and to develop robust and effective detection methods that are applicable for a routine clinical setting of CRC diagnostics particularly at the early stage of the disease.
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Affiliation(s)
- Nayeralsadat Fatemi
- Basic & Molecular Epidemiology of Gastrointestinal Disorders Research Center, Research Institute for Gastroenterology & Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Sascha Tierling
- Department of Genetics/Epigenetics, Faculty NT, Life Sciences, Saarland University, Saarbrücken, Germany
| | | | - Maryam Varkiani
- Department of Molecular Genetics, Faculty of Basic Sciences and Advanced Technologies in Biology, University of Science and Culture, Tehran, Iran
| | - Ehsan Nazemalhosseini Mojarad
- Gastroenterology and Liver Diseases Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Hamid Asadzadeh Aghdaei
- Basic & Molecular Epidemiology of Gastrointestinal Disorders Research Center, Research Institute for Gastroenterology & Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Jörn Walter
- Department of Genetics/Epigenetics, Faculty NT, Life Sciences, Saarland University, Saarbrücken, Germany
| | - Mehdi Totonchi
- Basic & Molecular Epidemiology of Gastrointestinal Disorders Research Center, Research Institute for Gastroenterology & Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran.,Department of Genetics, Reproductive Biomedicine Research Center, Royan Institute for Reproductive Biomedicine, ACECR, Tehran, Iran
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238
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Guo X, Yue L, Li M, Dai A, Sun J, Fang L, Zhao H, Sun Q. Nuclear receptor estrogen-related receptor gamma suppresses colorectal cancer aggressiveness by regulating Wnt/β-catenin signalling. Carcinogenesis 2022; 43:865-873. [PMID: 35728800 DOI: 10.1093/carcin/bgac054] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2022] [Revised: 05/22/2022] [Accepted: 06/21/2022] [Indexed: 12/09/2022] Open
Abstract
Colorectal cancer is the predominant cause of cancer-related death worldwide, because of lack of effective therapeutic targets. Estrogen-related receptor gamma (ESRRG), which belongs to the family of nuclear receptors, functions as an important element regulating gene transcription. In our report, we identified ESRRG as a potential tumor suppressor. The decreased level of ESRRG was initially observed in CRC and was highly associated with poor prognosis. ESRRG overexpression abrogated cell growth and metastasis in vitro and in vivo. Mechanistically, ESRRG repressed the epithelial-to-mesenchymal transition (EMT) process and antagonized Wnt signaling by regulating β-catenin degradation. In addition, significant ESRRG hypermethylation was found in CRC and inversely correlated with its expression. Consistently, the expression of ESRRG was induced after treatment with DNA demethylating agent 5-AZA. Taken together, these findings define a tumor-suppressive role of ESRRG in CRC, providing a potential novel therapeutic approach for this cancer.
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Affiliation(s)
- Xiaohong Guo
- Department of Pathology, The First Affiliated Hospital, Shandong First Medical University& Shandong Qianfoshan Hospital, Jinan, Shandong, China
| | - Longtao Yue
- Department of Pathology, The First Affiliated Hospital, Shandong First Medical University& Shandong Qianfoshan Hospital, Jinan, Shandong, China
| | - Min Li
- Department of Pathology, The First Affiliated Hospital, Shandong First Medical University& Shandong Qianfoshan Hospital, Jinan, Shandong, China
| | - Ang Dai
- Department of Pathology and Pathophysiology, Weifang Medical University, Weifang, Shandong, China
| | - Junying Sun
- Department of Pathology, The First Affiliated Hospital, Shandong First Medical University& Shandong Qianfoshan Hospital, Jinan, Shandong, China
| | - Lei Fang
- Department of Pathology, The First Affiliated Hospital, Shandong First Medical University& Shandong Qianfoshan Hospital, Jinan, Shandong, China
| | - Hai Zhao
- Department of Pathology, The First Affiliated Hospital, Shandong First Medical University& Shandong Qianfoshan Hospital, Jinan, Shandong, China
| | - Qing Sun
- Department of Pathology, The First Affiliated Hospital, Shandong First Medical University& Shandong Qianfoshan Hospital, Jinan, Shandong, China
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Xu S, Zhou Y, Luo J, Chen S, Xie J, Liu H, Wang Y, Li Z. Integrated Analysis of a Ferroptosis-Related LncRNA Signature for Evaluating the Prognosis of Patients with Colorectal Cancer. Genes (Basel) 2022; 13:1094. [PMID: 35741856 PMCID: PMC9223081 DOI: 10.3390/genes13061094] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2022] [Revised: 06/15/2022] [Accepted: 06/15/2022] [Indexed: 12/18/2022] Open
Abstract
LncRNAs have been well known for their multiple functions in the tumorigenesis, development, and relapse of colorectal cancer (CRC). Accumulating studies demonstrated that the expression of lncRNAs can be regulated by ferroptosis, a biological process that has been revealed to suppress CRC progression. However, the functions and clinical implications of ferroptosis-associated lncRNAs in CRC remain largely unknown. We, herein, aim to construct a prognostic signature with ferroptosis-related lncRNAs for the prognostic estimation of CRC patients. Firstly, we identified the lncRNAs related to ferroptosis based on the RNA-Seq data of CRC from the TCGA database. The univariate and multivariate Cox analyses were then performed to establish a prognostic signature composed of eight ferroptosis-related lncRNAs (AL161729.4, AC010973.2, CCDC144NL-AS1, AC009549.1, LINC01857, AP003555.1, AC099850.3, and AC008494.3). Furthermore, we divided the CRC patients into high- and low-risk groups based on the signature and found the overall survival (OS) of patients in the high-risk group was significantly shorter than that in the low-risk group (p = 3.31 × 10-11). Moreover, the patients in the high-risk groups had shorter recurrence-free survival (RFS) (p = 6.5 × 10-3) and disease-free survival (DFS) (p = 4.27 × 10-4), as well as higher tumor recurrence rate. Additionally, we found that the oncogenic pathways were enriched in the high-risk group, whereas the ferroptosis pathway that probably repressed CRC development was enriched in the low-risk group. In summary, our signature may provide a theoretical foundation for not only accurate judgment for prognosis but also evaluation for recurrence and metastasis in CRC patients.
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Affiliation(s)
- Shaohua Xu
- Research Institute of Hunan University in Chongqing, Chongqing 401120, China; (S.X.); (Y.Z.)
- Hunan Provincial Key Laboratory of Medical Virology, Institute of Pathogen Biology and Immunology of College of Biology, Hunan University, Changsha 410082, China; (J.L.); (S.C.); (J.X.); (H.L.)
| | - Yanjie Zhou
- Research Institute of Hunan University in Chongqing, Chongqing 401120, China; (S.X.); (Y.Z.)
- Hunan Provincial Key Laboratory of Medical Virology, Institute of Pathogen Biology and Immunology of College of Biology, Hunan University, Changsha 410082, China; (J.L.); (S.C.); (J.X.); (H.L.)
| | - Junyun Luo
- Hunan Provincial Key Laboratory of Medical Virology, Institute of Pathogen Biology and Immunology of College of Biology, Hunan University, Changsha 410082, China; (J.L.); (S.C.); (J.X.); (H.L.)
| | - Su Chen
- Hunan Provincial Key Laboratory of Medical Virology, Institute of Pathogen Biology and Immunology of College of Biology, Hunan University, Changsha 410082, China; (J.L.); (S.C.); (J.X.); (H.L.)
| | - Jiahui Xie
- Hunan Provincial Key Laboratory of Medical Virology, Institute of Pathogen Biology and Immunology of College of Biology, Hunan University, Changsha 410082, China; (J.L.); (S.C.); (J.X.); (H.L.)
| | - Hui Liu
- Hunan Provincial Key Laboratory of Medical Virology, Institute of Pathogen Biology and Immunology of College of Biology, Hunan University, Changsha 410082, China; (J.L.); (S.C.); (J.X.); (H.L.)
| | - Yirong Wang
- Bioinformatics Center, College of Biology, Hunan University, Changsha 410082, China
| | - Zhaoyong Li
- Research Institute of Hunan University in Chongqing, Chongqing 401120, China; (S.X.); (Y.Z.)
- Hunan Provincial Key Laboratory of Medical Virology, Institute of Pathogen Biology and Immunology of College of Biology, Hunan University, Changsha 410082, China; (J.L.); (S.C.); (J.X.); (H.L.)
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Chen L, Luo Z, Zhao C, Li Q, Geng Y, Xiao Y, Chen MK, Li L, Chen ZX, Wu M. Dynamic Chromatin States Coupling with Key Transcription Factors in Colitis-Associated Colorectal Cancer. ADVANCED SCIENCE 2022; 9:e2200536. [PMID: 35712778 PMCID: PMC9376751 DOI: 10.1002/advs.202200536] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/27/2022] [Revised: 05/14/2022] [Indexed: 12/13/2022]
Abstract
Inflammation is one of the critical risk factors for colorectal cancer (CRC). However, the mechanisms for transition from colitis to CRC remain elusive. Recently, epigenetic changes have emerged as important regulatory factors for colitis-associated cancer. Here, a systematic epigenomic study of histone modifications is performed, including H3K4me1, H3K4me3, H3K27ac, H3K27me3 and H3K9me3, in an AOM-DSS-induced CRC mouse model. In combination with transcriptomic data, the authors generate a dataset of 105 deep sequencing files and illustrate the dynamic landscape of chromatin states at five time points during inflammation-cancer transition. Functional gene clusters are identified based on dynamic transcriptomic and epigenomic information, and key signaling pathways in the process are illustrated. This study's results reveal that enhancer state regions play important roles during inflammation-cancer transition. It predicts novel transcription factors based on enhancer information, and experimentally proves OTX2 as a critical tumor suppressive transcription factor. Taken together, this study provides comprehensive epigenomic data and reveals novel molecular mechanisms for colitis-associated cancer.
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Affiliation(s)
- Lin Chen
- Frontier Science Center for Immunology and Metabolism, Hubei Key Laboratory of Cell Homeostasis, Hubei Key Laboratory of Developmentally Originated Disease, Hubei Key Laboratory of Enteropathy, College of Life Sciences, Renmin Hospital of Wuhan University, Wuhan University, Wuhan, Hubei, 430072, China
| | - Zhihui Luo
- Hubei Hongshan Laboratory, Hubei Key Laboratory of Agricultural Bioinformatics, College of Life Science and Technology, College of Biomedicine and Health, Interdisciplinary Sciences Institute, Huazhong Agricultural University, Wuhan, 430070, China
| | - Chen Zhao
- Frontier Science Center for Immunology and Metabolism, Hubei Key Laboratory of Cell Homeostasis, Hubei Key Laboratory of Developmentally Originated Disease, Hubei Key Laboratory of Enteropathy, College of Life Sciences, Renmin Hospital of Wuhan University, Wuhan University, Wuhan, Hubei, 430072, China
| | - Qinglan Li
- Frontier Science Center for Immunology and Metabolism, Hubei Key Laboratory of Cell Homeostasis, Hubei Key Laboratory of Developmentally Originated Disease, Hubei Key Laboratory of Enteropathy, College of Life Sciences, Renmin Hospital of Wuhan University, Wuhan University, Wuhan, Hubei, 430072, China
| | - Yingjie Geng
- Hubei Hongshan Laboratory, Hubei Key Laboratory of Agricultural Bioinformatics, College of Life Science and Technology, College of Biomedicine and Health, Interdisciplinary Sciences Institute, Huazhong Agricultural University, Wuhan, 430070, China
| | - Yong Xiao
- Frontier Science Center for Immunology and Metabolism, Hubei Key Laboratory of Cell Homeostasis, Hubei Key Laboratory of Developmentally Originated Disease, Hubei Key Laboratory of Enteropathy, College of Life Sciences, Renmin Hospital of Wuhan University, Wuhan University, Wuhan, Hubei, 430072, China
| | - Ming-Kai Chen
- Frontier Science Center for Immunology and Metabolism, Hubei Key Laboratory of Cell Homeostasis, Hubei Key Laboratory of Developmentally Originated Disease, Hubei Key Laboratory of Enteropathy, College of Life Sciences, Renmin Hospital of Wuhan University, Wuhan University, Wuhan, Hubei, 430072, China
| | - Lianyun Li
- Frontier Science Center for Immunology and Metabolism, Hubei Key Laboratory of Cell Homeostasis, Hubei Key Laboratory of Developmentally Originated Disease, Hubei Key Laboratory of Enteropathy, College of Life Sciences, Renmin Hospital of Wuhan University, Wuhan University, Wuhan, Hubei, 430072, China
| | - Zhen-Xia Chen
- Hubei Hongshan Laboratory, Hubei Key Laboratory of Agricultural Bioinformatics, College of Life Science and Technology, College of Biomedicine and Health, Interdisciplinary Sciences Institute, Huazhong Agricultural University, Wuhan, 430070, China.,Shenzhen Institute of Nutrition and Health, Huazhong Agricultural University, Shenzhen, 518000, China.,Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518000, China
| | - Min Wu
- Frontier Science Center for Immunology and Metabolism, Hubei Key Laboratory of Cell Homeostasis, Hubei Key Laboratory of Developmentally Originated Disease, Hubei Key Laboratory of Enteropathy, College of Life Sciences, Renmin Hospital of Wuhan University, Wuhan University, Wuhan, Hubei, 430072, China
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Bamberg LV, Heigwer F, Wandmacher AM, Singh A, Betge J, Rindtorff N, Werner J, Josten J, Skabkina OV, Hinsenkamp I, Erdmann G, Röcken C, Ebert MP, Burgermeister E, Zhan T, Boutros M. Targeting euchromatic histone lysine methyltransferases sensitizes colorectal cancer to histone deacetylase inhibitors. Int J Cancer 2022; 151:1586-1601. [PMID: 35666536 DOI: 10.1002/ijc.34155] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2021] [Revised: 05/09/2022] [Accepted: 05/17/2022] [Indexed: 11/10/2022]
Abstract
Epigenetic dysregulation is an important feature of colorectal cancer (CRC). Combining epigenetic drugs with other antineoplastic agents is a promising treatment strategy for advanced cancers. Here, we exploited the concept of synthetic lethality to identify epigenetic targets that act synergistically with histone deacetylase (HDAC) inhibitors to reduce the growth of CRC. We applied a pooled CRISPR-Cas9 screen using a custom sgRNA library directed against 614 epigenetic regulators and discovered that knockout of the euchromatic histone-lysine N-methyltransferases 1 and 2 (EHMT1/2) strongly enhanced the antiproliferative effect of clinically used HDAC inhibitors. Using tissue microarrays from 1066 CRC samples with different tumor stages, we showed that low EHMT2 protein expression is predominantly found in advanced CRC and associated with poor clinical outcome. Co-targeting of HDAC and EHMT1/2 with specific small molecule inhibitors synergistically reduced proliferation of CRC cell lines. Mechanistically, we used a high-throughput Western blot assay to demonstrate that both inhibitors elicited distinct cellular mechanisms to reduce tumor growth, including cell cycle arrest and modulation of autophagy. On the epigenetic level, the compounds increased H3K9 acetylation and reduced H3K9 dimethylation. Finally, we used a panel of patient-derived CRC organoids to show that HDAC and EHMT1/2 inhibition synergistically reduced tumor viability in advanced models of CRC.
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Affiliation(s)
- Leonhard Valentin Bamberg
- German Cancer Research Center (DKFZ), Div. Signaling and Functional Genomics and Heidelberg University, Dept. Cell and Molecular Biology, Faculty of Medicine Mannheim, Heidelberg, Germany.,Heidelberg University, Medical Faculty Mannheim, Department of Internal Medicine II, Mannheim, Germany
| | - Florian Heigwer
- German Cancer Research Center (DKFZ), Div. Signaling and Functional Genomics and Heidelberg University, Dept. Cell and Molecular Biology, Faculty of Medicine Mannheim, Heidelberg, Germany
| | - Anna Maxi Wandmacher
- German Cancer Research Center (DKFZ), Div. Signaling and Functional Genomics and Heidelberg University, Dept. Cell and Molecular Biology, Faculty of Medicine Mannheim, Heidelberg, Germany
| | - Ambika Singh
- German Cancer Research Center (DKFZ), Div. Signaling and Functional Genomics and Heidelberg University, Dept. Cell and Molecular Biology, Faculty of Medicine Mannheim, Heidelberg, Germany
| | - Johannes Betge
- German Cancer Research Center (DKFZ), Div. Signaling and Functional Genomics and Heidelberg University, Dept. Cell and Molecular Biology, Faculty of Medicine Mannheim, Heidelberg, Germany.,Heidelberg University, Medical Faculty Mannheim, Department of Internal Medicine II, Mannheim, Germany.,German Cancer Research Center (DKFZ), Junior Clinical Cooperation Unit Translational Gastrointestinal Oncology and Preclinical Models, Heidelberg, Germany.,DKFZ-Hector Cancer Institute at the University Medical Center, Mannheim, Germany
| | - Niklas Rindtorff
- German Cancer Research Center (DKFZ), Div. Signaling and Functional Genomics and Heidelberg University, Dept. Cell and Molecular Biology, Faculty of Medicine Mannheim, Heidelberg, Germany
| | - Johannes Werner
- German Cancer Research Center (DKFZ), Div. Signaling and Functional Genomics and Heidelberg University, Dept. Cell and Molecular Biology, Faculty of Medicine Mannheim, Heidelberg, Germany
| | - Julia Josten
- German Cancer Research Center (DKFZ), Div. Signaling and Functional Genomics and Heidelberg University, Dept. Cell and Molecular Biology, Faculty of Medicine Mannheim, Heidelberg, Germany
| | - Olga Valerievna Skabkina
- Heidelberg University, Medical Faculty Mannheim, Department of Internal Medicine II, Mannheim, Germany
| | - Isabel Hinsenkamp
- Heidelberg University, Medical Faculty Mannheim, Department of Internal Medicine II, Mannheim, Germany
| | | | - Christoph Röcken
- Christian-Albrechts University, Department of Pathology, Schleswig-Holstein University Hospital, Kiel, Germany
| | - Matthias P Ebert
- Heidelberg University, Medical Faculty Mannheim, Department of Internal Medicine II, Mannheim, Germany.,DKFZ-Hector Cancer Institute at the University Medical Center, Mannheim, Germany
| | - Elke Burgermeister
- Heidelberg University, Medical Faculty Mannheim, Department of Internal Medicine II, Mannheim, Germany
| | - Tianzuo Zhan
- German Cancer Research Center (DKFZ), Div. Signaling and Functional Genomics and Heidelberg University, Dept. Cell and Molecular Biology, Faculty of Medicine Mannheim, Heidelberg, Germany.,Heidelberg University, Medical Faculty Mannheim, Department of Internal Medicine II, Mannheim, Germany
| | - Michael Boutros
- German Cancer Research Center (DKFZ), Div. Signaling and Functional Genomics and Heidelberg University, Dept. Cell and Molecular Biology, Faculty of Medicine Mannheim, Heidelberg, Germany.,German Cancer Consortium (DKTK), Heidelberg, Germany
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Overexpression of long non-coding RNA ACTA2-AS1 inhibits the viability, proliferation, migration and invasion of colorectal cancer cells. Tissue Cell 2022; 76:101769. [DOI: 10.1016/j.tice.2022.101769] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2021] [Revised: 02/25/2022] [Accepted: 02/25/2022] [Indexed: 11/21/2022]
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Jung G, Hernández-Illán E, Lozano JJ, Sidorova J, Muñoz J, Okada Y, Quintero E, Hernandez G, Jover R, Carballal S, Cuatrecasas M, Moreno L, Diaz M, Ocaña T, Sánchez A, Rivero L, Ortiz O, Llach J, Castells A, Pellisé M, Goel A, Batlle E, Balaguer F. Epigenome-Wide DNA Methylation Profiling of Normal Mucosa Reveals HLA-F Hypermethylation as a Biomarker Candidate for Serrated Polyposis Syndrome. J Mol Diagn 2022; 24:674-686. [PMID: 35447336 DOI: 10.1016/j.jmoldx.2022.03.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2021] [Revised: 01/08/2022] [Accepted: 03/04/2022] [Indexed: 11/16/2022] Open
Abstract
Serrated polyposis syndrome (SPS) is associated with a high risk for colorectal cancer. Intense promoter hypermethylation is a frequent molecular finding in the serrated pathway and may be present in normal mucosa, predisposing to the formation of serrated lesions. To identify novel biomarkers for SPS, fresh-frozen samples of normal mucosa from 50 patients with SPS and 19 healthy individuals were analyzed by using the 850K BeadChip Technology (Infinium). Aberrant methylation levels were correlated with gene expression using a next-generation transcriptome profiling tool. Two validation steps were performed on independent cohorts: first, on formalin-fixed, paraffin-embedded tissue of the normal mucosa; and second, on 24 serrated lesions. The most frequently hypermethylated genes were HLA-F, SLFN12, HLA-DMA, and RARRES3; and the most frequently hypomethylated genes were PIWIL1 and ANK3 (Δβ = 10%; P < 0.05). Expression levels of HLA-F, SLFN12, and HLA-DMA were significantly different between SPS patients and healthy individuals and correlated well with the methylation status of the corresponding differentially methylated region (fold change, >20%; r > 0.55; P < 0.001). Significant hypermethylation of CpGs in the gene body of HLA-F was also found in serrated lesions (Δβ = 23%; false discovery rate = 0.01). Epigenome-wide methylation profiling has revealed numerous differentially methylated CpGs in normal mucosa from SPS patients. Significant hypermethylation of HLA-F is a novel biomarker candidate for SPS.
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Affiliation(s)
- Gerhard Jung
- Gastroenterology Department, Hospital Clínic de Barcelona, Barcelona, Spain; Institut d'Investigacions Biomèdiques August Pi i Sunyer, Barcelona, Spain; Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBEREHD), Barcelona, Spain; Faculty of Medicine, University of Barcelona, Barcelona, Spain
| | | | - Juan J Lozano
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBEREHD), Barcelona, Spain; Bioinformatics Platform, CIBEREHD, Barcelona, Spain
| | - Julia Sidorova
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBEREHD), Barcelona, Spain; Bioinformatics Platform, CIBEREHD, Barcelona, Spain
| | - Jenifer Muñoz
- Institut d'Investigacions Biomèdiques August Pi i Sunyer, Barcelona, Spain; Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBEREHD), Barcelona, Spain
| | - Yasuyuki Okada
- Department of Molecular Diagnostics and Experimental Therapeutics, Beckman Research Institute, Biomedical Research Center, Monrovia, California; Department of Gastroenterology and Oncology, Tokushima University Graduate School, Tokushima, Japan
| | - Enrique Quintero
- Department of Gastroenterology, University Hospital of the Canary Islands, Santa Cruz de Tenerife, Spain
| | - Goretti Hernandez
- Department of Gastroenterology, University Hospital of the Canary Islands, Santa Cruz de Tenerife, Spain
| | - Rodrigo Jover
- Servicio de Medicina Digestiva, Hospital General Universitario de Alicante, Instituto de Investigación Sanitaria y Biomédica de Alicante (ISABIAL), Alicante, Spain
| | - Sabela Carballal
- Gastroenterology Department, Hospital Clínic de Barcelona, Barcelona, Spain; Institut d'Investigacions Biomèdiques August Pi i Sunyer, Barcelona, Spain; Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBEREHD), Barcelona, Spain; Faculty of Medicine, University of Barcelona, Barcelona, Spain
| | - Miriam Cuatrecasas
- Institut d'Investigacions Biomèdiques August Pi i Sunyer, Barcelona, Spain; Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBEREHD), Barcelona, Spain; Faculty of Medicine, University of Barcelona, Barcelona, Spain; Pathology Department, Hospital Clínic de Barcelona, Barcelona, Spain
| | - Lorena Moreno
- Gastroenterology Department, Hospital Clínic de Barcelona, Barcelona, Spain; Institut d'Investigacions Biomèdiques August Pi i Sunyer, Barcelona, Spain; Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBEREHD), Barcelona, Spain; Faculty of Medicine, University of Barcelona, Barcelona, Spain
| | - Mireia Diaz
- Gastroenterology Department, Hospital Clínic de Barcelona, Barcelona, Spain; Institut d'Investigacions Biomèdiques August Pi i Sunyer, Barcelona, Spain; Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBEREHD), Barcelona, Spain; Faculty of Medicine, University of Barcelona, Barcelona, Spain
| | - Teresa Ocaña
- Gastroenterology Department, Hospital Clínic de Barcelona, Barcelona, Spain; Institut d'Investigacions Biomèdiques August Pi i Sunyer, Barcelona, Spain; Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBEREHD), Barcelona, Spain; Faculty of Medicine, University of Barcelona, Barcelona, Spain
| | - Ariadna Sánchez
- Gastroenterology Department, Hospital Clínic de Barcelona, Barcelona, Spain; Institut d'Investigacions Biomèdiques August Pi i Sunyer, Barcelona, Spain; Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBEREHD), Barcelona, Spain; Faculty of Medicine, University of Barcelona, Barcelona, Spain
| | - Liseth Rivero
- Gastroenterology Department, Hospital Clínic de Barcelona, Barcelona, Spain; Institut d'Investigacions Biomèdiques August Pi i Sunyer, Barcelona, Spain; Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBEREHD), Barcelona, Spain; Faculty of Medicine, University of Barcelona, Barcelona, Spain
| | - Oswaldo Ortiz
- Gastroenterology Department, Hospital Clínic de Barcelona, Barcelona, Spain; Institut d'Investigacions Biomèdiques August Pi i Sunyer, Barcelona, Spain; Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBEREHD), Barcelona, Spain; Faculty of Medicine, University of Barcelona, Barcelona, Spain
| | - Joan Llach
- Gastroenterology Department, Hospital Clínic de Barcelona, Barcelona, Spain; Institut d'Investigacions Biomèdiques August Pi i Sunyer, Barcelona, Spain; Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBEREHD), Barcelona, Spain; Faculty of Medicine, University of Barcelona, Barcelona, Spain
| | - Antoni Castells
- Gastroenterology Department, Hospital Clínic de Barcelona, Barcelona, Spain; Institut d'Investigacions Biomèdiques August Pi i Sunyer, Barcelona, Spain; Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBEREHD), Barcelona, Spain; Faculty of Medicine, University of Barcelona, Barcelona, Spain
| | - Maria Pellisé
- Gastroenterology Department, Hospital Clínic de Barcelona, Barcelona, Spain; Institut d'Investigacions Biomèdiques August Pi i Sunyer, Barcelona, Spain; Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBEREHD), Barcelona, Spain; Faculty of Medicine, University of Barcelona, Barcelona, Spain
| | - Ajay Goel
- Department of Molecular Diagnostics and Experimental Therapeutics, Beckman Research Institute, Biomedical Research Center, Monrovia, California; City of Hope Comprehensive Cancer Center, Duarte, California
| | - Eduard Batlle
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Francesc Balaguer
- Gastroenterology Department, Hospital Clínic de Barcelona, Barcelona, Spain; Institut d'Investigacions Biomèdiques August Pi i Sunyer, Barcelona, Spain; Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBEREHD), Barcelona, Spain; Faculty of Medicine, University of Barcelona, Barcelona, Spain.
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244
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Liu Z, Gu Y, Li X, Zhou L, Cheng X, Jiang H, Huang Y, Zhang Y, Xu T, Yang W, Huang Q. Mucin 16 Promotes Colorectal Cancer Development and Progression Through Activation of Janus Kinase 2. Dig Dis Sci 2022; 67:2195-2208. [PMID: 33982216 DOI: 10.1007/s10620-021-07004-3] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/03/2021] [Accepted: 04/14/2021] [Indexed: 01/24/2023]
Abstract
BACKGROUND Mucin 16 (MUC16), a cell surface-associated mucin, has been implicated to be upregulated in a large repertoire of malignances. However, its function in the pathogenesis of colorectal cancer (CRC) is unknown. AIMS Here, we explored the regulatory role of MUC16 in CRC. METHODS First, tumor and paracancerous tissues, and serum samples from 162 CRC patients, peripheral blood samples from 48 healthy volunteers and 72 benign colorectal patients were collected. The correlation between the MUC16 expression and the clinical phenotypes of the patients was analyzed. Subsequently, HCT116 and SW480 cells with deletion of MUC16 were established to detect changes in the growth and metastatic capacities of CRC cells. The genes with the highest correlation with MUC16 were predicted by bioinformatics, and their binding relationships were detected by Co-IP and double-labeled immunofluorescence, followed by functional rescue experiments. RESULTS Overexpression of MUC16 in CRC patients was positively correlated with serum biomarkers and poor prognosis of patients. It was demonstrated by in vitro and in vivo experiments that knocking-down the expression of MUC16 could significantly inhibit the growth and metastasis of CRC cells. MUC16 activated janus kinase 2 (JAK2)/signal transducer and activator of transcription 3 (STAT3) by interacting with JAK2. Further overexpression of JAK2 in cells with poor expression of MUC16 revealed a significant increase in the proliferative and metastatic capacities of CRC cells. CONCLUSIONS MUC16 contributes to the development and progression of CRC by binding to JAK2, thereby promoting phosphorylation of JAK2 and further activating STAT3 phosphorylation.
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Affiliation(s)
- Zhining Liu
- Department of General Surgery, Anhui Provincial Hospital, Cheeloo College of Medicine, Shandong University, No. 27, Shanda South Road, Jinan, 250012, Shandong, People's Republic of China.,Department of General Surgery, The Second Hospital of Anhui Medical University, Hefei, 230601, Anhui, People's Republic of China
| | - Yimei Gu
- Department of Emergency ICU, The First Affiliated Hospital of Anhui Medical University, Hefei, 230000, Anhui, People's Republic of China
| | - Xianghua Li
- Department of Molecular Pathology, Guangzhou Daan Clinical Testing Center Co., Ltd, Guangzhou, 510000, Guangdong, People's Republic of China
| | - Lianbang Zhou
- Department of General Surgery, The Second Hospital of Anhui Medical University, Hefei, 230601, Anhui, People's Republic of China
| | - Xiaohu Cheng
- Department of General Surgery, The Second Hospital of Anhui Medical University, Hefei, 230601, Anhui, People's Republic of China
| | - Heng Jiang
- Department of General Surgery, The Second Hospital of Anhui Medical University, Hefei, 230601, Anhui, People's Republic of China
| | - Yang Huang
- Department of General Surgery, The Second Hospital of Anhui Medical University, Hefei, 230601, Anhui, People's Republic of China
| | - Yingfeng Zhang
- Department of General Surgery, The Second Hospital of Anhui Medical University, Hefei, 230601, Anhui, People's Republic of China
| | - Tongtong Xu
- Department of General Surgery, The Second Hospital of Anhui Medical University, Hefei, 230601, Anhui, People's Republic of China
| | - Wanshui Yang
- Department of Nutrition, School of Public Health, Anhui Medical University, Hefei, 230032, Anhui, People's Republic of China
| | - Qiang Huang
- Department of General Surgery, Anhui Provincial Hospital, Cheeloo College of Medicine, Shandong University, No. 27, Shanda South Road, Jinan, 250012, Shandong, People's Republic of China.
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Zinc finger protein 280C contributes to colorectal tumorigenesis by maintaining epigenetic repression at H3K27me3-marked loci. Proc Natl Acad Sci U S A 2022; 119:e2120633119. [PMID: 35605119 PMCID: PMC9295756 DOI: 10.1073/pnas.2120633119] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
This study uncovered the role of ZNF280C, a known DNA damage response protein, as a tumorigenic transcription regulator that contributes to colorectal tumorigenesis and metastasis through maintaining an epigenetic repression program at key cancer gene loci. These findings identified a contributor with potential prognostic value to colorectal pathogenesis and provide mechanistic insight to the essential function of transcription factor in fine-tuning the activity of chromatin regulators for proper transcription control. Dysregulated epigenetic and transcriptional programming due to abnormalities of transcription factors (TFs) contributes to and sustains the oncogenicity of cancer cells. Here, we unveiled the role of zinc finger protein 280C (ZNF280C), a known DNA damage response protein, as a tumorigenic TF in colorectal cancer (CRC), required for colitis-associated carcinogenesis and Apc deficiency–driven intestinal tumorigenesis in mice. Consistently, ZNF280C silencing in human CRC cells inhibited proliferation, clonogenicity, migration, xenograft growth, and liver metastasis. As a C2H2 (Cys2-His2) zinc finger-containing TF, ZNF280C occupied genomic intervals with both transcriptionally active and repressive states and coincided with CCCTC-binding factor (CTCF) and cohesin binding. Notably, ZNF280C was crucial for the repression program of trimethylation of histone H3 at lysine 27 (H3K27me3)-marked genes and the maintenance of both focal and broad H3K27me3 levels. Mechanistically, ZNF280C counteracted CTCF/cohesin activities and condensed the chromatin environment at the cis elements of certain tumor suppressor genes marked by H3K27me3, at least partially through recruiting the epigenetic repressor structural maintenance of chromosomes flexible hinge domain-containing 1 (SMCHD1). In clinical relevance, ZNF280C was highly expressed in primary CRCs and distant metastases, and a higher ZNF280C level independently predicted worse prognosis of CRC patients. Thus, our study uncovered a contributor with good prognostic value to CRC pathogenesis and also elucidated the essence of DNA-binding TFs in orchestrating the epigenetic programming of gene regulation.
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Liu Y, Xu L, Hao C, Wu J, Jia X, Ding X, Lin C, Zhu H, Zhang Y. Identification and Validation of Novel Immune-Related Alternative Splicing Signatures as a Prognostic Model for Colon Cancer. Front Oncol 2022; 12:866289. [PMID: 35692800 PMCID: PMC9178000 DOI: 10.3389/fonc.2022.866289] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Accepted: 04/25/2022] [Indexed: 12/24/2022] Open
Abstract
BackgroundIndividual immune-related alternative splicing (AS) events have been found to be significant in immune regulation and cancer prognosis. However, a comprehensive analysis of AS events in cancer cells based on immune-related genes (IRGs) has not been performed, and its clinical value is unknown.MethodsColon cancer cases with AS data were obtained from TCGA, and then, we identified overall survival-related AS events (OS-ASEs) based on IRGs by univariate analyses. Using Lasso regression, multivariate Cox regression, Kaplan–Meier analysis and nomograms, we constructed an AS risk model based on the calculated risk score. Furthermore, associations of the risk score with clinical and immune features were confirmed through the Wilcoxon rank sum test, association analysis, etc. Finally, by qRT–PCR, cell coculture and CCK-8 analyses, we validated the significance of OS-ASEs in colon cancer cell lines and clinical samples.ResultsA total of 3,119 immune-related AS events and 183 OS-ASEs were identified, and 9 OS-ASEs were ultimately used to construct a comprehensive risk model for colon cancer patients. Low-risk patients had better OS and DFS rates than high risk patients. Furthermore, a high risk score corresponded to high numbers of multiple tumour-infiltrating immune cells and high expression of HLA-D region genes and immune checkpoint genes. Notably, we identified for the first time that anti-PD-L1 or anti-CTLA-4 antibodies may decrease the OS of specific colon cancer patients in the low-risk group. Additionally, the in vitro experiment validated that CD46-9652-ES and PSMC5-43011-ES are positively correlated with the infiltration of immune cells and promote the growth of colon cancer cells. CD46-9652-ES can contribute to T cell-mediated tumour cell killing. PSMC5-43011-ES was observed to induce M2 polarization of macrophages.ConclusionsThis study identified and validated immune-related prognostic AS signatures that can be used as a novel AS prognostic model and provide a novel understanding of the relationship between the immune microenvironment and clinical outcomes.
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Affiliation(s)
- Yunze Liu
- Department of Traditional Chinese Medicine, Affiliated Hospital of Xuzhou Medical University, Xuzhou, China
- Dongzhimen Hospital, Beijing University of Chinese Medicine, Beijing, China
| | - Lei Xu
- Department of General Surgery, Affiliated Hospital of Xuzhou Medical University, Xuzhou, China
- Institute of Digestive Diseases, Xuzhou Medical University, Xuzhou, China
| | - Chuanchuan Hao
- Department of Traditional Chinese Medicine, Affiliated Hospital of Xuzhou Medical University, Xuzhou, China
| | - Jin Wu
- Department of General Surgery, Affiliated Hospital of Xuzhou Medical University, Xuzhou, China
| | - Xianhong Jia
- Department of Traditional Chinese Medicine, Affiliated Hospital of Xuzhou Medical University, Xuzhou, China
| | - Xia Ding
- Dongzhimen Hospital, Beijing University of Chinese Medicine, Beijing, China
| | - Changwei Lin
- Department of Gastrointestinal Surgery, The Third Xiang Ya Hospital of Central South University, Changsha, China
| | - Hongmei Zhu
- Department of Traditional Chinese Medicine, Affiliated Hospital of Xuzhou Medical University, Xuzhou, China
- *Correspondence: Yi Zhang, ; Hongmei Zhu,
| | - Yi Zhang
- Department of General Surgery, Affiliated Hospital of Xuzhou Medical University, Xuzhou, China
- Institute of Digestive Diseases, Xuzhou Medical University, Xuzhou, China
- *Correspondence: Yi Zhang, ; Hongmei Zhu,
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Sukocheva OA, Liu J, Neganova ME, Beeraka NM, Aleksandrova YR, Manogaran P, Grigorevskikh EM, Chubarev VN, Fan R. Perspectives of using microRNA-loaded nanocarriers for epigenetic reprogramming of drug resistant colorectal cancers. Semin Cancer Biol 2022; 86:358-375. [PMID: 35623562 DOI: 10.1016/j.semcancer.2022.05.012] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2022] [Revised: 05/19/2022] [Accepted: 05/20/2022] [Indexed: 02/07/2023]
Abstract
Epigenetic regulation by microRNAs (miRs) demonstrated a promising therapeutic potential of these molecules to regulate genetic activity in different cancers, including colorectal cancers (CRCs). The RNA-based therapy does not change genetic codes in tumor cells but can silence oncogenes and/or reactivate inhibited tumor suppressor genes. In many cancers, specific miRs were shown to promote or stop tumor progression. Among confirmed and powerful epigenetic regulators of colon carcinogenesis and development of resistance are onco-miRs, which include let-7, miR-21, miR-22, miR-23a, miR-27a, miR-34, miR-92, miR-96, miR-125b, miR-135b, miR-182, miR-200c, miR-203, miR-221, miR-421, miR-451, and others. Moreover, various tumor-suppressor miRs (miR-15b-5b, miR-18a, miR-20b, miR-22, miR-96, miR-139-5p, miR-145, miR-149, miR-197, miR-199b, miR-203, miR-214, miR-218, miR-320, miR-375-3p, miR-409-3p, miR-450b-5p, miR-494, miR-577, miR-874, and others) were found silenced in drug-resistant CRCs. Re-expression of tumor suppressor miR is complicated by the chemical nature of miRs that are not long-lasting compounds and require protection from the enzymatic degradation. Several recent studies explored application of miRs using nanocarrier complexes. This study critically describes the most successfully tested nanoparticle complexes used for intracellular delivery of nuclear acids and miRs, including micelles, liposomes, inorganic and polymeric NPs, dendrimers, and aptamers. Nanocarriers shield incorporated miRs and improve the agent stability in circulation. Attachment of antibodies and/or specific peptide or ligands facilitates cell-targeted miR delivery. Addressing in vivo challenges, a broad spectrum of non-toxic materials has been tested and indicated reliable advantages of lipid-based (lipoplexes) and polymer-based liposomes. Recent cutting-edge developments indicated that lipid-based complexes with multiple cargo, including several miRs, are the most effective approach to eradicate drug-resistant tumors. Focusing on CRC-specific miRs, this review provides a guidance and insights towards the most promising direction to achieve dramatic reduction in tumor growth and metastasis using miR-nanocarrier complexes.
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Affiliation(s)
- Olga A Sukocheva
- Cancer Center and Department of Radiation Oncology, The First Affiliated Hospital of Zhengzhou University, 1 Jianshedong Str., Zhengzhou, 450052, China; The National Centre for Neuroimmunology and Emerging Diseases, Menzies Health Institute, Griffith University, Queensland, Australia; Discipline of Health Sciences, College of Nursing and Health Sciences, Flinders University, Bedford Park, South Australia, 5042, Australia.
| | - Junqi Liu
- Cancer Center and Department of Radiation Oncology, The First Affiliated Hospital of Zhengzhou University, 1 Jianshedong Str., Zhengzhou, 450052, China
| | - Margarita E Neganova
- Institute of Physiologically Active Compounds of the Russian Academy of Sciences, 1, Severnii pr., Chernogolovka, 142432, Russia
| | - Narasimha M Beeraka
- Discipline of Health Sciences, College of Nursing and Health Sciences, Flinders University, Bedford Park, South Australia, 5042, Australia; Department of Human Anatomy, I.M. Sechenov First Moscow State Medical University (Sechenov University), 8/2 Trubetskaya Street, Moscow, 119991, Russia; Center of Excellence in Molecular Biology and Regenerative Medicine (CEMR), Department of Biochemistry, JSS Academy of Higher Education and Research (JSS AHER), JSS Medical College, Mysuru, Karnataka, India
| | - Yulia R Aleksandrova
- Institute of Physiologically Active Compounds of the Russian Academy of Sciences, 1, Severnii pr., Chernogolovka, 142432, Russia
| | - Prasath Manogaran
- Translational Research Laboratory, Department of Biotechnology, Bharathiar University, Coimbatore, Tamil Nadu 641046, India
| | - Ekaterina M Grigorevskikh
- Department of Human Anatomy, I.M. Sechenov First Moscow State Medical University (Sechenov University), 8/2 Trubetskaya Street, Moscow, 119991, Russia
| | - Vladimir N Chubarev
- Department of Human Anatomy, I.M. Sechenov First Moscow State Medical University (Sechenov University), 8/2 Trubetskaya Street, Moscow, 119991, Russia
| | - Ruitai Fan
- Cancer Center and Department of Radiation Oncology, The First Affiliated Hospital of Zhengzhou University, 1 Jianshedong Str., Zhengzhou, 450052, China.
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248
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Novel acetylation-related gene signatures for predicting the prognosis of patients with colorectal cancer. Hum Cell 2022; 35:1159-1173. [PMID: 35604486 DOI: 10.1007/s13577-022-00720-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2022] [Accepted: 05/07/2022] [Indexed: 11/04/2022]
Abstract
Histone acetylation may affect the tumorigenesis and prognosis of colorectal cancer (CRC). However, there is still a lack of studies exploring the effect of acetylation-related genes on the prognosis of CRC. To explore the role of acetylation-related genes in CRC prognosis using bioinformatics strategies, the expression data and survival information of CRC patients were collected from the Gene Expression Omnibus. The Molecular Signatures Database was used to select acetylation-related genes. Univariate and least absolute shrinkage and selection operator regression analyses were used to screen prognostic genes. Kaplan-Meier curves were plotted for survival analysis. Cibersort and pRRophetics were used to analyze immune infiltration and predict drug sensitivity, respectively. By implementing independent prognostic factors, a nomogram model was constructed. The result showed that a total of 48 prognostic genes which screened from the acetylation-related gene set were mainly enriched in ABC transporters and acetylation/deacetylation-related pathways. Three gene signatures (SDR16C5, MEAF6, and SOX4) were further defined, and a prognostic model was constructed that showed high sensitivity and specificity for predicting CRC prognosis in both training and validation cohorts. Patients with different prognostic risks also presented differential expression of gene signatures, infiltration of activated CD4 memory T cells, and drug sensitivity to bicalutamide, gefitinib, Lenalidomide, and imatinib. The nomogram suggested the potential of a risk score-based model in predicting 1- and 2-year survival in patients with CRC. In conclusion, we proposed three gene signatures from an acetylation-related gene set as potential targets for epigenetic therapy and constructed a prognostic model for CRC.
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249
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Histone Modifications and Non-Coding RNAs: Mutual Epigenetic Regulation and Role in Pathogenesis. Int J Mol Sci 2022; 23:ijms23105801. [PMID: 35628612 PMCID: PMC9146199 DOI: 10.3390/ijms23105801] [Citation(s) in RCA: 33] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2022] [Revised: 05/12/2022] [Accepted: 05/18/2022] [Indexed: 12/07/2022] Open
Abstract
In the last few years, more and more scientists have suggested and confirmed that epigenetic regulators are tightly connected and form a comprehensive network of regulatory pathways and feedback loops. This is particularly interesting for a better understanding of processes that occur in the development and progression of various diseases. Appearing on the preclinical stages of diseases, epigenetic aberrations may be prominent biomarkers. Being dynamic and reversible, epigenetic modifications could become targets for a novel option for therapy. Therefore, in this review, we are focusing on histone modifications and ncRNAs, their mutual regulation, role in cellular processes and potential clinical application.
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250
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Chang L, Yang P, Zhang C, Zhu J, Zhang Y, Wang Y, Ding J, Wang K. Long intergenic non-protein-coding RNA 467 promotes tumor progression and angiogenesis via the microRNA-128-3p/vascular endothelial growth factor C axis in colorectal cancer. Bioengineered 2022; 13:12392-12408. [PMID: 35587748 PMCID: PMC9275949 DOI: 10.1080/21655979.2022.2074666] [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] [Indexed: 11/28/2022] Open
Abstract
Long non-coding RNAs (lncRNAs) are important regulators and biomarkers of tumorigenesis and tumor metastasis. Long intergenic non-protein-coding RNA 467 (LINC00467) is associated with various cancers. However, the role and mechanism of LINC00467 in colorectal cancer (CRC) promotion are poorly understood. This study aimed to present new details of LINC00467 in the progression of CRC. Reverse transcription–polymerase chain reaction demonstrated that the expression level of LINC00467 in CRC tissues and cell lines was significantly upregulated, which was closely related to the clinical features of CRC. Cell and animal studies showed that the downregulation of LINC00467 expression in CRC cells significantly inhibited cell proliferation, metastasis, and angiogenesis. Moreover, the overexpression of LINC00467 accelerated CRC promotion. Bioinformatics analysis and luciferase reporter assay confirmed that LINC00467 binds to miR-128-3p. Rescue experiments manifested that decreased miR-128-3p level reversed CRC cell inhibition by silencing LINC00467. Furthermore, vascular endothelial growth factor C (VEGFC) was identified as a target of miR-128-3p that could reverse the inhibition of cell growth that is mediated by miR-128-3p. Altogether, our results showed that LINC00467 contributes to CRC progression and angiogenesis via the miR-128-3p/VEGFC axis. Our findings expand the understanding of the mechanisms underlying CRC and suggest potential targets for clinical strategies against CRC.
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Affiliation(s)
- Lisha Chang
- Department of Oncology, Second Affiliated Hospital, Nanjing Medical University, Nanjing, Jiangsu, China
| | - Peipei Yang
- Department of Oncology, Second Affiliated Hospital, Nanjing Medical University, Nanjing, Jiangsu, China
| | - Chun Zhang
- Department of Oncology, Nanjing First Hospital, Nanjing Medical University, Nanjing, Jiangsu, China
| | - Jing Zhu
- Department of Oncology, Second Affiliated Hospital, Nanjing Medical University, Nanjing, Jiangsu, China
| | - Yirao Zhang
- Department of Oncology, Second Affiliated Hospital, Nanjing Medical University, Nanjing, Jiangsu, China
| | - Yang Wang
- Department of Oncology, Second Affiliated Hospital, Nanjing Medical University, Nanjing, Jiangsu, China
| | - Jie Ding
- Department of Oncology, Second Affiliated Hospital, Nanjing Medical University, Nanjing, Jiangsu, China
| | - Keming Wang
- Department of Oncology, Second Affiliated Hospital, Nanjing Medical University, Nanjing, Jiangsu, China
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