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Shavali M, Moradi A, Tahmaseb M, Mohammadian K, Ganji SM. Circulating-tumour DNA methylation of HAND1 gene: a promising biomarker in early detection of colorectal cancer. BMC Med Genomics 2024; 17:117. [PMID: 38689296 PMCID: PMC11061902 DOI: 10.1186/s12920-024-01893-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2024] [Accepted: 04/25/2024] [Indexed: 05/02/2024] Open
Abstract
BACKGROUND Colorectal cancer (CRC) is one of the significant global health concerns with an increase in cases. Regular screening tests are crucial for early detection as it is often asymptomatic in the initial stages. Liquid biopsies, a non-invasive approach that examines biomarkers in biofluids, offer a promising future in diagnosing and screening cancer. Circulating-tumour DNA (ctDNA) is the genetic material in biofluids released into the circulatory system by cells. ctDNA is a promising marker for monitoring patients since cancer cells display distinct DNA methylation patterns compared to normal cells. The potential of our research to contribute to early detection and improved patient outcomes is significant. AIMS The primary objective of this research project was to explore the HAND1 methylation levels in plasma ctDNA as a potential biomarker for diagnosing CRC and evaluate the methylation level of the well-established gene SPET9 to compare it with the methylation level of HAND1. MATERIALS AND METHODS Plasma samples were collected from 30 CRC patients and 15 healthy individuals, with CRC samples obtained pre-treatment. ctDNA was extracted and treated with bisulfite for methylation status assessment. Quantitative methylation-specific PCR (qMS-PCR) was performed for HAND1 and SEPT9, using β-actin (ACTB gene) as a reference. The study aims to evaluate the potential of these genes as diagnostic biomarkers for CRC, contributing to early detection and improved patient outcomes. RESULTS Our study yielded significant results: 90% of CRC patients (27 out of 30) had hypermethylation in the SEPT9 gene, and 83% (25 out of 30) exhibited hypermethylation in the HAND1 gene. The methylation levels of both genes were significantly higher in CRC patients than in healthy donors. These findings underscore the potential of SEPT9 and HAND1 methylation as promising biomarkers for diagnosing CRC, potentially leading to early detection and improved patient outcomes. CONCLUSION These findings highlight the potential of SEPT9 and HAND1 methylation as promising biomarkers for diagnosing CRC. However, further research and validation studies are needed to confirm these findings and to explore their clinical utility in CRC diagnosis and management.
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Affiliation(s)
- Mehrdad Shavali
- Department of Cell and Molecular Biology, Faculty of Biological Science, Kharazmi University, Tehran, Iran
| | - Arash Moradi
- Department of Medical Biotechnology, National Institute of Genetic Engineering and Biotechnology, Shahrak-e Pajoohesh, km 15, P.O. Box 14965/161, Tehran, Tehran - Karaj Highway, Iran
| | - Mohammad Tahmaseb
- Department of Cell and Molecular Biology, Faculty of Biological Science, Kharazmi University, Tehran, Iran
| | - Kamal Mohammadian
- Department of Radiation Oncology, Hamadan University of Medical Sciences, Hamadan, Iran
- Cancer Research Center, Hamadan University of Medical Sciences, Hamadan, Iran
| | - Shahla Mohammad Ganji
- Department of Medical Biotechnology, National Institute of Genetic Engineering and Biotechnology, Shahrak-e Pajoohesh, km 15, P.O. Box 14965/161, Tehran, Tehran - Karaj Highway, Iran.
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2
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Kuang Y, He Z, Li L, Wang C, Cheng X, Shi Q, Fu G, Ying J, Tao Q, Hu X. The developmental regulator HAND1 inhibits gastric carcinogenesis through enhancing ER stress apoptosis via targeting CHOP and BAK which is augmented by cisplatin. Int J Biol Sci 2023; 19:120-136. [PMID: 36594085 PMCID: PMC9760445 DOI: 10.7150/ijbs.76345] [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: 06/20/2022] [Accepted: 10/02/2022] [Indexed: 11/24/2022] Open
Abstract
Epigenetic disruption of tumor suppressor genes, particularly aberrant CpG methylation, plays a crucial role in gastric cancer (GC) pathogenesis. Through CpG methylome and expression profiling, a developmental transcription factor - Hand-And-Neural-crest-Derivative-expressed 1 (HAND1), was identified methylated and downregulated in GC. However, its role and underlying mechanisms in GC progression are poorly understood. Here, we show that HAND1 was frequently downregulated in GC by promoter methylation, and significantly correlated with tumor progression and poor prognosis of GC patients. High expression of HAND1 in GC patients was associated with significantly higher 5-year overall survival rates. Ectopic expression of HAND1 inhibited GC cell growth and migration in vitro and in vivo. HAND1 expression increased ROS levels and cytosolic Ca2+ concentration, enhanced cisplatin-induced apoptosis through endoplasmic reticulum (ER) stress/mitochondria-mediated apoptosis. Knockdown of CHOP and BAK attenuated HAND1-induced cell apoptosis. Overexpression of CHOP increased BAK expression. HAND1 interacts with CHOP, also directly binds to CHOP and BAK promoters and positively regulates BAK transcription. Thus, the present study demonstrates that HAND1 is a tumor suppressor gene methylated in GC, induces ER stress and apoptosis via CHOP and BAK, which is augmented by cisplatin. Low HAND1 expression is an independent poor prognostic factor for GC. The tumor-specific methylation of HAND1 promoter could be a candidate biomarker for GC.
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Affiliation(s)
- Yeye Kuang
- Biomedical Research Center, Sir Run Shaw Hospital, Zhejiang University, Hangzhou, China.,Department of Pathology, Sir Run Shaw Hospital, Zhejiang University, Hangzhou, China.,Key Laboratory of Cancer Prevention and Intervention, Ministry of Education, Hangzhou 310016, Zhejiang, China
| | - Zhanglian He
- Biomedical Research Center, Sir Run Shaw Hospital, Zhejiang University, Hangzhou, China.,Key Laboratory of Cancer Prevention and Intervention, Ministry of Education, Hangzhou 310016, Zhejiang, China
| | - Lili Li
- Cancer Epigenetics Laboratory, Department of Clinical Oncology, State Key Laboratory of Translational Oncology, Sir YK Pao Center for Cancer and Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Hong Kong
| | - Chan Wang
- Biomedical Research Center, Sir Run Shaw Hospital, Zhejiang University, Hangzhou, China.,Department of Pathology, Sir Run Shaw Hospital, Zhejiang University, Hangzhou, China.,Key Laboratory of Cancer Prevention and Intervention, Ministry of Education, Hangzhou 310016, Zhejiang, China
| | - Xiaoqing Cheng
- Department of Pathology, Sir Run Shaw Hospital, Zhejiang University, Hangzhou, China
| | - Qinglan Shi
- Biomedical Research Center, Sir Run Shaw Hospital, Zhejiang University, Hangzhou, China.,Key Laboratory of Cancer Prevention and Intervention, Ministry of Education, Hangzhou 310016, Zhejiang, China
| | - Guoxiang Fu
- Department of Pathology, Sir Run Shaw Hospital, Zhejiang University, Hangzhou, China
| | - Jianming Ying
- Cancer Epigenetics Laboratory, Department of Clinical Oncology, State Key Laboratory of Translational Oncology, Sir YK Pao Center for Cancer and Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Hong Kong
| | - Qian Tao
- Cancer Epigenetics Laboratory, Department of Clinical Oncology, State Key Laboratory of Translational Oncology, Sir YK Pao Center for Cancer and Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Hong Kong.,✉ Corresponding authors: X Hu () or Q Tao ()
| | - Xiaotong Hu
- Biomedical Research Center, Sir Run Shaw Hospital, Zhejiang University, Hangzhou, China.,Department of Pathology, Sir Run Shaw Hospital, Zhejiang University, Hangzhou, China.,Key Laboratory of Cancer Prevention and Intervention, Ministry of Education, Hangzhou 310016, Zhejiang, China.,✉ Corresponding authors: X Hu () or Q Tao ()
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3
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Game-theoretic link relevance indexing on genome-wide expression dataset identifies putative salient genes with potential etiological and diapeutics role in colorectal cancer. Sci Rep 2022; 12:13409. [PMID: 35927308 PMCID: PMC9352798 DOI: 10.1038/s41598-022-17266-0] [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: 10/01/2021] [Accepted: 07/22/2022] [Indexed: 11/08/2022] Open
Abstract
Diapeutics gene markers in colorectal cancer (CRC) can help manage mortality caused by the disease. We applied a game-theoretic link relevance Index (LRI) scoring on the high-throughput whole-genome transcriptome dataset to identify salient genes in CRC and obtained 126 salient genes with LRI score greater than zero. The biomarkers database lacks preliminary information on the salient genes as biomarkers for all the available cancer cell types. The salient genes revealed eleven, one and six overrepresentations for major Biological Processes, Molecular Function, and Cellular components. However, no enrichment with respect to chromosome location was found for the salient genes. Significantly high enrichments were observed for several KEGG, Reactome and PPI terms. The survival analysis of top protein-coding salient genes exhibited superior prognostic characteristics for CRC. MIR143HG, AMOTL1, ACTG2 and other salient genes lack sufficient information regarding their etiological role in CRC. Further investigation in LRI methodology and salient genes to augment the existing knowledge base may create new milestones in CRC diapeutics.
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4
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Gu L, Jiang C, Xu C, Liu Y, Zhou H. Based on Molecular Subtypes, Immune Characteristics and Genomic Variation to Constructing and Verifying Multi-Gene Prognostic Characteristics of Colorectal Cancer. Front Cell Dev Biol 2022; 10:828415. [PMID: 35281077 PMCID: PMC8905350 DOI: 10.3389/fcell.2022.828415] [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: 12/03/2021] [Accepted: 01/31/2022] [Indexed: 11/25/2022] Open
Abstract
Background: Colon cancer (COAD) has been identified as being among the most prevalent tumors globally and ranked the third major contributor to cancer-related mortality. COAD is a molecularly heterogeneous disease. There are great differences in clinical manifestations and prognosis among different molecular subtypes. Methods:379 TCGA-COAD samples were divided into four subtypes: primary proliferative, with collective, crypt-like, and EMT invasion. The differences among the four subtypes were analyzed from the multidimensional perspectives of immunity, genomic variation, and prognosis. The limma package was utilized to identify differentially expressed genes (DEGs) amongst different molecular subtypes. Phenotype-related coexpressed gene modules were identified using WGCNA. The polygenic prognosis model was created utilizing the lasso Cox analysis and verified by time-dependent subject operating characteristics (ROC). Results: There are some differences in prognosis, TMB and common gene variation, immune score, and immunotherapy/chemotherapy between proliferative and three invasive molecular subtypes. 846 differential genes (DEGs) were obtained by limma packet analysis. Differential gene analysis was utilized to screen the DEGs among distinct subtypes, which were significantly enriched in the pathways related to tumorigenesis and development. Co-expression network analysis found 46 co-expressed genes correlated with proliferative and three invasive phenotypes. Based on differentially co-expressed genes, we developed a prognostic risk model of 8-genes signature, which exhibited strong stability regardless of external and internal validation. RT-PCR experiments proved the expression of eight genes in tumor and normal samples. Conclusion: We have developed an eight-gene signature prognostic stratification system. Furthermore, we proposed that this classifier can serve as a molecular diagnostic tool to assess the prognosis of colon cancer patients.
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Affiliation(s)
- Lei Gu
- Department of Gastrointestinal Surgery, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Chunhui Jiang
- Department of Gastrointestinal Surgery, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Chunjie Xu
- Department of Gastrointestinal Surgery, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Ye Liu
- Department of Gastrointestinal Surgery, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Hong Zhou
- Department of Gastrointestinal Surgery, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
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5
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Chen X, Wu H, Feng J, Li Y, Lv J, Shi W, Fan W, Xiao L, Sun D, Jiang M, Shi M. Transcriptome profiling unveils GAP43 regulates ABC transporters and EIF2 signaling in colorectal cancer cells. BMC Cancer 2021; 21:24. [PMID: 33402155 PMCID: PMC7786480 DOI: 10.1186/s12885-020-07728-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2020] [Accepted: 12/11/2020] [Indexed: 02/08/2023] Open
Abstract
Background The growth- and plasticity-associated protein-43 (GAP43) is biasedly expressed in indigestive system and nervous system. Recent study has shown that GAP43 is responsible for the development of neuronal growth and axonal regeneration in normal nervous tissue, while serves as a specific biomarker of relapsed or refractory neuroblastoma. However, its expression pattern and function in digestive system cancer remains to be clarified. Methods In this study, we examined the GAP43 status with qRT-PCR and bisulfite genomic sequencing in colorectal cancer (CRC). We investigated the effect of overexpressed GAP43 in CRC cells with RNA-seq. The RNA-seq data was analyzed with DAVID and IPA. Results GAP43 was downregulated in CRC compared to the adjacent tissues. DNA methylase inhibitor 5-Aza-CdR treatment could significantly induce GAP43, indicated that the silencing of GAP43 gene in CRC is closely related to DNA methylation. Bisulfite genomic sequencing confirmed the promoter methylation of GAP43 in CRC. To explore the transcriptional alterations by overexpressed GAP43 in CRC, we performed RNA-seq and found that upregulated genes were significantly enriched in the signaling pathways of ABC transporters and ECM-receptor interaction, while downregulated genes were significantly enriched in Ribosome signaling pathway. Further Ingenuity Pathway Analysis (IPA) showed that EIF2 signaling pathway was significantly repressed by overexpression of GAP43. Conclusion Our findings provide a novel mechanistic insight of GAP43 in CRC. Transcriptome profiling of overexpressed GAP43 in CRC uncovered the functional roles of GAP43 in the development of human CRC. Supplementary Information The online version contains supplementary material available at 10.1186/s12885-020-07728-x.
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Affiliation(s)
- Xi Chen
- School of Life Science and Technology, Harbin Institute of Technology, Harbin, 150001, China
| | - Hongjin Wu
- Department of Clinical Laboratory, Hangzhou Cancer Hospital, Hangzhou,, 320000, Zhejiang, China.,The NHC Key Laboratory of Drug Addition Medicine, The First Affiliated Hospital of Kunming Medical University, Kunming, 650000, China
| | - Jia Feng
- School of Life Science and Technology, Harbin Institute of Technology, Harbin, 150001, China
| | - Ying Li
- School of Life Science and Technology, Harbin Institute of Technology, Harbin, 150001, China
| | - Jiao Lv
- School of Life Science and Technology, Harbin Institute of Technology, Harbin, 150001, China
| | - Weikai Shi
- School of Life Science and Technology, Harbin Institute of Technology, Harbin, 150001, China
| | - Weiwei Fan
- Department of Infectious and Medicine, Heilongjiang Provincial Hospital, Harbin, 150036, China
| | - Li Xiao
- School of Life Science and Technology, Harbin Institute of Technology, Harbin, 150001, China
| | - Danmeng Sun
- Department of Pediatrics, Data People's hospital, Shenmu, 719301, China
| | - Mingfeng Jiang
- Department of Clinical Laboratory, Hangzhou Cancer Hospital, Hangzhou,, 320000, Zhejiang, China.
| | - Ming Shi
- School of Life Science and Technology, Harbin Institute of Technology, Harbin, 150001, China.
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Vincent A, Ouelkdite-Oumouchal A, Souidi M, Leclerc J, Neve B, Van Seuningen I. Colon cancer stemness as a reversible epigenetic state: Implications for anticancer therapies. World J Stem Cells 2019; 11:920-936. [PMID: 31768220 PMCID: PMC6851010 DOI: 10.4252/wjsc.v11.i11.920] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/25/2019] [Revised: 08/29/2019] [Accepted: 09/11/2019] [Indexed: 02/06/2023] Open
Abstract
The recent discovery of cancer cell plasticity, i.e. their ability to reprogram into cancer stem cells (CSCs) either naturally or under chemotherapy and/or radiotherapy, has changed, once again, the way we consider cancer treatment. If cancer stemness is a reversible epigenetic state rather than a genetic identity, opportunities will arise for therapeutic strategies that remodel epigenetic landscapes of CSCs. However, the systematic use of DNA methyltransferase and histone deacetylase inhibitors, alone or in combination, in advanced solid tumors including colorectal cancers, regardless of their molecular subtypes, does not seem to be the best strategy. In this review, we first summarize the knowledge researchers have gathered on the epigenetic signatures of CSCs with the difficulty of isolating rare populations of cells. We raise questions about the relevant use of currently available epigenetic inhibitors (epidrugs) while the expression of numerous cancer stem cell markers are often repressed by epigenetic mechanisms. These markers include the three cluster of differentiation CD133, CD44 and CD166 that have been extensively used for the isolation of colon CSCs.and . Finally, we describe current treatment strategies using epidrugs, and we hypothesize that, using correlation tools comparing associations of relevant CSC markers with chromatin modifier expression, we could identify better candidates for epienzyme targeting.
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Affiliation(s)
- Audrey Vincent
- Lille University, Institut National de la Santé et de la Recherche Médicale, CHU Lille, UMR-S 1172-Jean-Pierre Aubert Research Center, Lille F-59000, France
| | - Aïcha Ouelkdite-Oumouchal
- Lille University, Institut National de la Santé et de la Recherche Médicale, CHU Lille, UMR-S 1172-Jean-Pierre Aubert Research Center, Lille F-59000, France
| | - Mouloud Souidi
- Lille University, Institut National de la Santé et de la Recherche Médicale, CHU Lille, UMR-S 1172-Jean-Pierre Aubert Research Center, Lille F-59000, France
| | - Julie Leclerc
- Lille University, Institut National de la Santé et de la Recherche Médicale, CHU Lille, UMR-S 1172-Jean-Pierre Aubert Research Center, Lille F-59000, France
- Department of Biochemistry and Molecular Biology, Lille University Hospital, Lille F-59000, France
| | - Bernadette Neve
- Lille University, Institut National de la Santé et de la Recherche Médicale, CHU Lille, UMR-S 1172-Jean-Pierre Aubert Research Center, Lille F-59000, France
| | - Isabelle Van Seuningen
- Lille University, Institut National de la Santé et de la Recherche Médicale, CHU Lille, UMR-S 1172-Jean-Pierre Aubert Research Center, Lille F-59000, France
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7
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Lu M. An embedded method for gene identification problems involving unwanted data heterogeneity. Hum Genomics 2019; 13:45. [PMID: 31639059 PMCID: PMC6805328 DOI: 10.1186/s40246-019-0228-0] [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: 11/10/2022] Open
Abstract
BACKGROUND Modern applications such as bioinformatics collecting data in various ways can easily result in heterogeneous data. Traditional variable selection methods assume samples are independent and identically distributed, which however is not suitable for these applications. Some existing statistical models capable of taking care of unwanted variation were developed for gene identification involving heterogeneous data, but they lack model predictability and suffer from variable redundancy. RESULTS By accounting for the unwanted heterogeneity effectively, our method have shown its superiority over several state-of-the art methods, which is validated by the experimental results in both unsupervised and supervised gene identification problems. Moreover, we also applied our method to a pan-cancer study where our method can identify the most discriminative genes best distinguishing different cancer types. CONCLUSIONS This article provides an alternative gene identification method that can accounting for unwanted data heterogeneity. It is a promising method to provide new insights into the complex cancer biology and clues for understanding tumorigenesis and tumor progression.
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Affiliation(s)
- Meng Lu
- Department of Information Management,Tianjin University, Tianjin, China.
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8
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Portrait of Tissue-Specific Coexpression Networks of Noncoding RNAs (miRNA and lncRNA) and mRNAs in Normal Tissues. COMPUTATIONAL AND MATHEMATICAL METHODS IN MEDICINE 2019; 2019:9029351. [PMID: 31565069 PMCID: PMC6745163 DOI: 10.1155/2019/9029351] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/10/2019] [Revised: 08/01/2019] [Accepted: 08/10/2019] [Indexed: 02/01/2023]
Abstract
Genes that encode proteins playing a role in more than one biological process are frequently dependent on their tissue context, and human diseases result from the altered interplay of tissue- and cell-specific processes. In this work, we performed a computational approach that identifies tissue-specific co-expression networks by integrating miRNAs, long-non-coding RNAs, and mRNAs in more than eight thousands of human samples from thirty normal tissue types. Our analysis (1) shows that long-non coding RNAs and miRNAs have a high specificity, (2) confirms several known tissue-specific RNAs, and (3) identifies new tissue-specific co-expressed RNAs that are currently still not described in the literature. Some of these RNAs interact with known tissue-specific RNAs or are crucial in key cancer functions, suggesting that they are implicated in tissue specification or cell differentiation.
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Shimomura H, Sasahira T, Nakashima C, Shimomura-Kurihara M, Kirita T. Downregulation of DHRS9 is associated with poor prognosis in oral squamous cell carcinoma. Pathology 2018; 50:642-647. [PMID: 30149992 DOI: 10.1016/j.pathol.2018.06.002] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2018] [Revised: 06/12/2018] [Accepted: 06/27/2018] [Indexed: 01/06/2023]
Abstract
Oral squamous cell carcinoma (OSCC) has a high potential for local invasion and nodal metastasis. Therefore, early detection and elucidation of the detailed molecular mechanisms underlying OSCC are essential. Dehydrogenase/reductase member 9 (DHRS9) is downregulated in recurrent OSCC. Although DHRS9 is reported to act as a tumour suppressor in several malignancies, its expression in OSCC cells is unknown. In this study, we examined DHRS9 expression immunohistochemically in specimens from a sample of 98 OSCC patients. Reduced DHRS9 expression was observed in 68 of 98 patients (69.4%) with OSCC. A significant association was found between low DHRS9 expression and local progression (T factor) (p = 0.0135). Furthermore, patients with low DHRS9 expression had a significantly poorer prognosis than those with high DHRS9 expression (p = 0.0443). In multivariate analysis using the Cox proportional hazards model, decreased DHRS9 expression strongly correlated with worse prognosis. The study findings suggest that DHRS9 might be a useful diagnostic and prognostic marker for OSCC.
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Affiliation(s)
- Hiroyuki Shimomura
- Department of Oral and Maxillofacial Surgery, Nara Medical University, Kashihara, Japan
| | - Tomonori Sasahira
- Department of Molecular Pathology, Nara Medical University, Kashihara, Japan.
| | - Chie Nakashima
- Department of Oral and Maxillofacial Surgery, Nara Medical University, Kashihara, Japan
| | | | - Tadaaki Kirita
- Department of Oral and Maxillofacial Surgery, Nara Medical University, Kashihara, Japan
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Prognostic value of histone marks H3K27me3 and H3K9me3 and modifying enzymes EZH2, SETDB1 and LSD-1 in colorectal cancer. J Cancer Res Clin Oncol 2018; 144:2127-2137. [PMID: 30105513 DOI: 10.1007/s00432-018-2733-2] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2018] [Accepted: 08/04/2018] [Indexed: 12/27/2022]
Abstract
PURPOSE Studies on the performance of epigenetic-based biomarkers in colorectal cancer (CRC) are scarce and have shown contradictory results. Thus, we sought to examine the prognostic value of histone-modifying enzymes (EZH2, SETDB1 and LSD-1) and histone post-translational marks (H3K27me3 and H3K9me3) in CRC. METHODS A retrospective series of 207 CRC patients primarily submitted to surgery in a cancer center was included in this study. Clinicopathological data were retrieved. One representative paraffin block per case was selected for immunohistochemistry, including normal and CRC tissues whenever possible. The percentage of positive nuclear staining (digital image analysis) was used to classify patients into "low" and "high" expression groups for each biomarker. Correlations between immunoexpression levels, clinicopathological features and clinical outcomes [disease-specific (DSS) and disease-free (DFS) survival] were examined. Statistical significance was set at p < 0.05. RESULTS CRC tissues showed significantly lower expression of SETDB1 and higher expression of the remainder four biomarkers compared to normal mucosa. High EZH2 expression correlated with disease recurrence/progression, whereas low LSD1 expression and high H3K9me3 and H3K27me3 expression were associated with more advanced stage. In multivariable analysis, cases with high LSD1 expression displayed significantly better DSS and DFS (HR 0.477, 95% confidence interval: 0.247-0.923) adjusted for pathological TNM stage. CONCLUSION EZH2, SETDB1, LSD1, H3K9me3 and H3K27me3 expression are altered in CRC and may play a role in colorectal carcinogenesis. LSD1 immunoexpression levels independently predicted patient outcome in this cohort. Further investigations, using larger series, are warranted to confirm its potential clinical value and unravel underlying molecular mechanisms.
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Vilorio-Marqués L, Martín V, Diez-Tascón C, González-Sevilla MF, Fernández-Villa T, Honrado E, Davila-Batista V, Molina AJ. The role of EZH2 in overall survival of colorectal cancer: a meta-analysis. Sci Rep 2017; 7:13806. [PMID: 29061982 PMCID: PMC5653815 DOI: 10.1038/s41598-017-13670-z] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2017] [Accepted: 09/26/2017] [Indexed: 12/13/2022] Open
Abstract
Enhancer of zeste homolog 2 (EZH2) is the catalitic subunit of polycomb repressive complex 2 and mediates gene silencing. EZH2 is overexpressed in many cancers and correlates with poor prognosis. The role of the gene EZH2 in colorectal cancer survival is uncertainly, the aim of this study is clear this relationship. Relevant literaure was searched from electronic databases. A meta-analysis was performed with elegible studies which quantitatively evaluated the relationship between EZH2 overexpression and survival of patients with colorectal cancer. Survival data were aggregated and quantitatively analyzed. We performed a meta-analysis of 8 studies (n = 1059 patients) that evaluated the correlation between EZH2 overexpression and survival in patients with colorectal cancer. Combined hazard ratios suggested that EZH2 overexpression was associated with better prognosis of overall survival (OS) HR(hazard ratio) = 0.61 95% CI (0.38-0.84) We performed bias analysis according Egger and Begg,s test and we did not find publication bias. EZH2 overexpression indicates a better prognosis for colorectal cancer.
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Affiliation(s)
- Laura Vilorio-Marqués
- GIIGAS: Grupo de Investigación en Interacción Gen-Ambiente-Salud, Dpt of Biomedical Sciences, Area of Preventive Medicine and Public Health, Instituto de Biomedicina (IBIOMED), University of León, Leon, Spain
| | - Vicente Martín
- GIIGAS: Grupo de Investigación en Interacción Gen-Ambiente-Salud, Dpt of Biomedical Sciences, Area of Preventive Medicine and Public Health, Instituto de Biomedicina (IBIOMED), University of León, Leon, Spain
- CIBERESP, CIBER de Epidemiología y Salud Pública, Madrid, Spain
| | - Cristina Diez-Tascón
- Banco de Tumores, Servicio de Anatomía Patológica, Complejo Asistencial Universitario de León, Leon, Spain
| | - María Francisca González-Sevilla
- GIIGAS: Grupo en interacción Gen-Ambiente-Salud, Dpt of Biomedical Sciences, Area of Physiology, University of León, Leon, Spain
| | - Tania Fernández-Villa
- GIIGAS: Grupo de Investigación en Interacción Gen-Ambiente-Salud, Dpt of Biomedical Sciences, Area of Preventive Medicine and Public Health, Instituto de Biomedicina (IBIOMED), University of León, Leon, Spain
| | - Emiliano Honrado
- Servicio de Anatomía Patológica, Complejo Asistencial Universitario de León, Leon, Spain
| | - Veronica Davila-Batista
- GIIGAS: Grupo de Investigación en Interacción Gen-Ambiente-Salud, Dpt of Biomedical Sciences, Area of Preventive Medicine and Public Health, Instituto de Biomedicina (IBIOMED), University of León, Leon, Spain
| | - Antonio J Molina
- GIIGAS: Grupo de Investigación en Interacción Gen-Ambiente-Salud, Dpt of Biomedical Sciences, Area of Preventive Medicine and Public Health, Instituto de Biomedicina (IBIOMED), University of León, Leon, Spain.
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12
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Slattery ML, Pellatt AJ, Lee FY, Herrick JS, Samowitz WS, Stevens JR, Wolff RK, Mullany LE. Infrequently expressed miRNAs influence survival after diagnosis with colorectal cancer. Oncotarget 2017; 8:83845-83859. [PMID: 29137387 PMCID: PMC5663559 DOI: 10.18632/oncotarget.19863] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2017] [Accepted: 07/25/2017] [Indexed: 12/24/2022] Open
Abstract
Half of miRNAs expressed in colorectal tissue are expressed < 50% of the population. Many infrequently expressed miRNAs have low levels of expression. We hypothesize that less frequently expressed miRNAs, when expressed at higher levels, influence both disease stage and survival after diagnosis with colorectal cancer (CRC); low levels of expression may be background noise. We examine 304 infrequently expressed miRNAs in 1893 population-based cases of CRC with paired carcinoma and normal mucosa miRNA profiles. We evaluate miRNAs with disease stage and survival after adjusting for age, study center, sex, MSI status, and AJCC stage. These miRNAs were further evaluated with RNA-Seq data to identify miRNA::mRNA associations that may provide insight into the functionality of miRNAs. Eleven miRNAs were associated with advanced disease stage among colon cancer patients (Q value = 0.10). Eight infrequently expressed miRNAs influenced survival if highly expressed in overall CRC. Of these, five increased likelihood of dying if they were highly expressed, i.e. miR-124-3p, miR-143-5p, miR-145-3p, miR31-5p, and miR-99b-5p, while three were associated with better survival if highly expressed, i.e. miR-362-5p, miR-374a-5p, and miR-590-5p. Thirteen miRNAs infrequently expressed in colon-specific carcinoma tissue were associated with CRC survival if highly expressed. Evaluation of miRNAs::mRNA associations showed that mRNA expression influenced by infrequently expressed miRNA contributed to networks and pathways shown to influence disease progression and prognosis. Our large study enabled us to examine the implications of infrequently expressed miRNAs after removal of background noise. These results require replication in other studies. Confirmation of our findings in other studies could lead to important markers for prognosis.
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Affiliation(s)
- Martha L Slattery
- Department of Medicine, University of Utah, Salt Lake City, Utah, USA
| | | | | | | | - Wade S Samowitz
- Department of Pathology, University of Utah, Salt Lake City, Utah, USA
| | - John R Stevens
- Department of Mathematics and Statistics, Utah State University, Logan, Utah, USA
| | - Roger K Wolff
- Department of Medicine, University of Utah, Salt Lake City, Utah, USA
| | - Lila E Mullany
- Department of Medicine, University of Utah, Salt Lake City, Utah, USA
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Huang T, Lin C, Zhong LLD, Zhao L, Zhang G, Lu A, Wu J, Bian Z. Targeting histone methylation for colorectal cancer. Therap Adv Gastroenterol 2017; 10:114-131. [PMID: 28286564 PMCID: PMC5330608 DOI: 10.1177/1756283x16671287] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
As a leading cause of cancer deaths worldwide, colorectal cancer (CRC) results from accumulation of both genetic and epigenetic alterations. Disruption of epigenetic regulation in CRC, particularly aberrant histone methylation mediated by histone methyltransferases (HMTs) and demethylases (HDMs), have drawn increasing interest in recent years. In this paper, we aim to review the roles of histone methylation and associated enzymes in the pathogenesis of CRC, and the development of small-molecule modulators to regulate histone methylation for treating CRC. Multiple levels of evidence suggest that aberrant histone methylations play important roles in CRC. More than 20 histone-methylation enzymes are found to be clinically relevant to CRC, including 17 oncoproteins and 8 tumor suppressors. Inhibitors of EZH2 and DOT1L have demonstrated promising therapeutic effects in preclinical CRC treatment. Potent and selective chemical probes of histone-methylation enzymes are required for validation of their functional roles in carcinogenesis and clinical translations as CRC therapies. With EZH2 inhibitor EPZ-6438 entering into phase I/II trials for advanced solid tumors, histone methylation is emerging as a promising target for CRC.
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Affiliation(s)
- Tao Huang
- Lab of Brain–Gut Research, School of Chinese Medicine, Hong Kong Baptist University, Hong Kong, PR China
| | - Chengyuan Lin
- Lab of Brain–Gut Research, School of Chinese Medicine, Hong Kong Baptist University, Hong Kong, PR China YMU-HKBU Joint Laboratory of Traditional Natural Medicine, Yunnan Minzu University, Kunming, PR China
| | - Linda L. D. Zhong
- Lab of Brain–Gut Research, School of Chinese Medicine, Hong Kong Baptist University, Hong Kong, PR China
| | - Ling Zhao
- Lab of Brain–Gut Research, School of Chinese Medicine, Hong Kong Baptist University, Hong Kong, PR China
| | - Ge Zhang
- Lab of Brain–Gut Research, School of Chinese Medicine, Hong Kong Baptist University, Hong Kong, PR China
| | - Aiping Lu
- Lab of Brain–Gut Research, School of Chinese Medicine, Hong Kong Baptist University, Hong Kong, PR China
| | - Jiang Wu
- State Key Laboratory of Applied Organic Chemistry, College of Chemistry and Chemical Engineering, Lanzhou University, Lanzhou, PR China
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14
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Packer JR, Maitland NJ. The molecular and cellular origin of human prostate cancer. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2016; 1863:1238-60. [DOI: 10.1016/j.bbamcr.2016.02.016] [Citation(s) in RCA: 57] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/04/2015] [Revised: 02/17/2016] [Accepted: 02/22/2016] [Indexed: 01/01/2023]
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15
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Identification of a DNA methylation signature to predict disease-free survival in locally advanced rectal cancer. Oncotarget 2015; 5:8123-35. [PMID: 25261372 PMCID: PMC4226671 DOI: 10.18632/oncotarget.2347] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
In locally advanced rectal cancer a preoperative predictive biomarker is necessary to adjust treatment specifically for those patients expected to suffer relapse. We applied whole genome methylation CpG island array analyses to an initial set of patients (n=11) to identify differentially methylated regions (DMRs) that separate a good from a bad prognosis group. Using a quantitative high-resolution approach, candidate DMRs were first validated in a set of 61 patients (test set) and then confirmed DMRs were further validated in additional independent patient cohorts (n=71, n=42). We identified twenty highly discriminative DMRs and validated them in the test set using the MassARRAY technique. Ten DMRs could be confirmed which allowed separation into prognosis groups (p=0.0207, HR=4.09). The classifier was validated in two additional cohorts (n=71, p=0.0345, HR=3.57 and n=42, p=0.0113, HR=3.78). Interestingly, six of the ten DMRs represented regions close to the transcriptional start sites of genes which are also marked by the Polycomb Repressor Complex component EZH2. In conclusion we present a classifier comprising 10 DMRs which predicts patient prognosis with a high degree of accuracy. These data may now help to discriminate between patients that may respond better to standard treatments from those that may require alternative modalities.
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Xin Z, Jiang S, Jiang P, Yan X, Fan C, Di S, Wu G, Yang Y, Reiter RJ, Ji G. Melatonin as a treatment for gastrointestinal cancer: a review. J Pineal Res 2015; 58:375-87. [PMID: 25752643 DOI: 10.1111/jpi.12227] [Citation(s) in RCA: 78] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/29/2015] [Accepted: 03/04/2015] [Indexed: 02/06/2023]
Abstract
Gastrointestinal cancer is a disease that affects the population worldwide with high morbidity and mortality. Melatonin, an endogenously produced molecule, may provide a defense against a variety of cancer types. In particular, the ability of melatonin to inhibit gastrointestinal cancer is substantial. In this review, we first clarify the relationship between the disruption of the melatonin rhythm and gastrointestinal cancer (based on epidemiologic surveys and animal and human studies) and summarize the preventive effect of melatonin on carcinogenesis. Thereafter, the mechanisms through which melatonin exerts its anti-gastrointestinal cancer actions are explained, including inhibition of proliferation, invasion, metastasis, and angiogenesis, and promotion of apoptosis and cancer immunity. Moreover, we discuss the drug synergy effects and the role of melatonin receptors involved in the growth-inhibitory effects on gastrointestinal cancer. Taken together, the information compiled here serves as a comprehensive reference for the anti-gastrointestinal cancer actions of melatonin that have been identified to date and will hopefully aid in the design of further experimental and clinical studies and increase the awareness of melatonin as a therapeutic agent in cancers of the gastrointestinal tract.
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Affiliation(s)
- Zhenlong Xin
- State Key Laboratory of Cancer Biology, Department of Gastroenterology, Xijing Hospital, The Fourth Military Medical University, Xi'an, China; Department of Biomedical Engineering, The Fourth Military Medical University, Xi'an, China
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