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Taheri Z, Zaki-Dizaji M. Epigenetically Regulating Non-coding RNAs in Colorectal Cancer: Promises and Potentials. Middle East J Dig Dis 2025; 17:40-53. [PMID: 40322568 PMCID: PMC12048831 DOI: 10.34172/mejdd.2025.404] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/27/2024] [Accepted: 12/09/2024] [Indexed: 05/08/2025] Open
Abstract
Colorectal cancer (CRC) is a common malignancy with high mortality. Despite advancements in understanding its molecular causes and improved drug therapies, patient survival rates remain low. The main reasons for the high mortality rate are cancer metastasis and the emergence of drug-resistant cancer cell populations. While genetic changes are recognized as the main driver of CRC occurrence and progression, recent studies suggest that epigenetic regulation is a crucial marker in cancer, influencing the interplay between genetics and the environment. Research has shown the significant regulatory roles of non-coding RNAs (ncRNAs) in CRC development. This review explores epigenetically regulated ncRNAs and their functions, aiming to understand key regulatory mechanisms that impact CRC development. Additionally, it discusses the potential use of these ncRNAs in CRC diagnosis, prognosis, and targeted treatments.
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Affiliation(s)
- Zahra Taheri
- Department of Biology, Science and Research Branch, Islamic Azad University, Tehran, Iran
| | - Majid Zaki-Dizaji
- Human Genetics Research Center, Baqiyatallah University of Medical Sciences, Tehran, Iran
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Ponomaryova AA, Rykova EY, Solovyova AI, Tarasova AS, Kostromitsky DN, Dobrodeev AY, Afanasiev SA, Cherdyntseva NV. Dynamic Changes in Circulating Methylated Markers in Response to Antitumor Therapy of Rectal Cancer. J Gastrointest Cancer 2024; 55:1190-1198. [PMID: 38829580 DOI: 10.1007/s12029-024-01066-y] [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] [Accepted: 05/05/2024] [Indexed: 06/05/2024]
Abstract
BACKGROUND Rectal cancer (RC) occupies a leading position in the structure of oncological morbidity and mortality. Aberrant methylation of tumor-suppressor genes and hypomethylation of retrotransposons were shown to be detectable in cell-free DNA, circulating in the blood (cfDNA) of cancer patients, indicating the possibility to use them as diagnostic and prognosis markers. PURPOSE Evaluation of the changes in the methylation level of LINE-1 elements and SEPTIN9 and IKZF1 genes in the cell-surface-bound cfDNA (csb-cfDNA) from the blood of RC patients after antitumor therapy at a long-term follow-up. METHODS Blood samples were obtained from RC patients (n = 25) before treatment, after preoperative chemotherapy (3 courses according to the XELOX scheme), 10-15 days after surgery, and every 3 months during 12 months of dynamic observation. The methylation level of LINE-1, SEPTIN9, and IKZF1 in the csb-cfDNA was evaluated by quantitative methyl-specific PCR. RESULTS The LINE-1 methylation level in the csb-cfDNA increased 1.6 times in RC patients after chemotherapy and 3 times after tumor resection versus methylation level before therapy. The SEPTIN9 gene methylation level in the csb-cfDNA decreased by 1.7 times in RC patients after chemotherapy and by 2.3 times after tumor resection compared with the values before the treatment. The IKZF1 gene methylation level decreased by 2 times in RC patients after combined therapy. Notably, all patients with relapses (n = 5) showed an increase in methylation level for the SEPTIN9 and IKZF1 genes and a decrease of methylation level for the LINE-1 elements by 2 times or more in comparison with the level 10-15 days after surgery. There were no changes in the circulating SEPTIN9, IKZF1, and LINE-1 methylation levels during the 12-month follow-up period after the combined therapy of RC patients (n = 20) without relapses. CONCLUSION The results indicate that SEPTIN9, IKZF1, and LINE-1 methylation levels in the csb-cfDNA are potential markers of the effectiveness of antitumor therapy and early detection of relapse in RC patients.
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Affiliation(s)
- Anastasia A Ponomaryova
- Cancer Research Institute, Tomsk National Research Medical Center of the Russian Academy of Sciences, 634009, Tomsk, Russia.
| | - Elena Yu Rykova
- Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences, 630090, Novosibirsk, Russia
- Department of Engineering Problems of Ecology, Novosibirsk State Technical University, 630087, Novosibirsk, Russia
| | - Anastasia I Solovyova
- Department of Biochemistry, Medico-Biological Faculty, Siberian State Medical University, 634050, Tomsk, Russia
| | - Anna S Tarasova
- Cancer Research Institute, Tomsk National Research Medical Center of the Russian Academy of Sciences, 634009, Tomsk, Russia
| | - Dmitry N Kostromitsky
- Cancer Research Institute, Tomsk National Research Medical Center of the Russian Academy of Sciences, 634009, Tomsk, Russia
| | - Alexey Yu Dobrodeev
- Cancer Research Institute, Tomsk National Research Medical Center of the Russian Academy of Sciences, 634009, Tomsk, Russia
| | - Sergey A Afanasiev
- Cancer Research Institute, Tomsk National Research Medical Center of the Russian Academy of Sciences, 634009, Tomsk, Russia
| | - Nadezhda V Cherdyntseva
- Cancer Research Institute, Tomsk National Research Medical Center of the Russian Academy of Sciences, 634009, Tomsk, Russia
- Faculty of Chemistry, National Research Tomsk State University, 634050, Tomsk, Russia
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Khabbazpour M, Tat M, Karbasi A, Abyazi MA, Khodadoustan G, Heidary Z, Zaki-Dizaji M. Advances in blood DNA methylation-based assay for colorectal cancer early detection: a systematic updated review. GASTROENTEROLOGY AND HEPATOLOGY FROM BED TO BENCH 2024; 17:225-240. [PMID: 39308542 PMCID: PMC11413380 DOI: 10.22037/ghfbb.v17i3.2978] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/02/2024] [Accepted: 07/04/2024] [Indexed: 09/25/2024]
Abstract
Aim A systematic review was conducted to summarize the methylated circulating tumor DNA (ctDNA) markers reported over the last decade for early detection of colorectal cancer (CRC) and to identify the main technical challenges that are impeding their clinical implementation. Background CRC is a major cause of cancer deaths worldwide, but early detection is key for successful treatment. Non-invasive methods such as methylated ctDNA testing show promise for improving detection and monitoring of CRC. Methods A comprehensive search was performed using Web of Science, PubMed, and Scopus up to December 30, 2023, limited to articles published in the last 10 years (after 2012), while including advanced adenoma/stage 0 or stage I/II samples in biomarker validation. Results After identifying 694 articles, removing duplicates and screening titles, abstracts, and full texts, a total of 62 articles were found to meet the inclusion criteria. Among the single biomarkers, MYO1-G, SEPT9, SDC2, and JAM3 revealed the highest sensitivity for polyps and stage I/II CRC. For multi-biomarkers with suitable sensitivity, combinations of SFRP1, SFRP2, SDC2, PRIMA1, or ALX4, BMP3, NPTX2, RARB, SDC2, SEPT9, VIM or ZFHX4, ZNF334, ELOVL2, UNC5C, LOC146880, SFMBT2, GFRA1 were identified for polyps and stage I/II CRC. Conclusion Enhancing sensitivity and specificity of molecular screening methods is crucial for improving CRC detection. Identifying a select few valuable biomarkers is key to reducing costs, despite challenges posed by low ctDNA levels in plasma, particularly in early-stage cancers.
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Affiliation(s)
- Milad Khabbazpour
- Human Genetics Research Center, Baqiyatallah University of Medical Sciences, Tehran, Iran
| | - Masoud Tat
- Human Genetics Research Center, Baqiyatallah University of Medical Sciences, Tehran, Iran
| | - Ashraf Karbasi
- Baqiyatallah Research Center for Gastroenterology and Liver Diseases (BRCGL), Clinical Sciences Institute, Baqiyatallah University of Medical Sciences, Tehran, Iran
| | - Mohammad Ali Abyazi
- Baqiyatallah Research Center for Gastroenterology and Liver Diseases (BRCGL), Clinical Sciences Institute, Baqiyatallah University of Medical Sciences, Tehran, Iran
| | - Ghazal Khodadoustan
- Department of Cell and Molecular Biology and Microbiology, Faculty of biological science and technology, University of Isfahan, Isfahan, Iran
| | - Zohreh Heidary
- Vali-e-Asr Reproductive Health Research Center, Family Health Research Institute, Tehran University of Medical Sciences, Tehran, Iran
| | - Majid Zaki-Dizaji
- Human Genetics Research Center, Baqiyatallah University of Medical Sciences, Tehran, Iran
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Danos P, Giannoni‐Luza S, Murillo Carrasco AG, Acosta O, Guevara‐Fujita ML, Cotrina Concha JM, Guerra Miller H, Pinto Oblitas J, Aguilar Cartagena A, Araujo JM, Fujita R, Buleje Sono JL. Promoter hypermethylation of RARB and GSTP1 genes in plasma cell-free DNA as breast cancer biomarkers in Peruvian women. Mol Genet Genomic Med 2023; 11:e2260. [PMID: 37548362 PMCID: PMC10724513 DOI: 10.1002/mgg3.2260] [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: 04/07/2022] [Revised: 04/30/2023] [Accepted: 07/19/2023] [Indexed: 08/08/2023] Open
Abstract
BACKGROUND Promoter hypermethylation is one of the enabling mechanisms of hallmarks of cancer. Tumor suppressor genes like RARB and GSTP1 have been reported as hypermethylated in breast cancer tumors compared with normal tissues in several populations. This case-control study aimed to determine the association between the promoter methylation ratio (PMR) of RARB and GSTP1 genes (separately and as a group) with breast cancer and its clinical-pathological variables in Peruvian patients, using a liquid biopsy approach. METHODS A total of 58 breast cancer patients and 58 healthy controls, matched by age, participated in the study. We exacted cell-free DNA (cfDNA) from blood plasma and converted it by bisulfite salts. Methylight PCR was performed to obtain the PMR value of the studied genes. We determined the association between PMR and breast cancer, in addition to other clinicopathological variables. The sensitivity and specificity of the PMR of these genes were obtained. RESULTS A significant association was not found between breast cancer and the RARB PMR (OR = 1.90; 95% CI [0.62-6.18]; p = 0.210) or the GSTP1 PMR (OR = 6.57; 95% CI [0.75-307.66]; p = 0.114). The combination of the RARB + GSTP1 PMR was associated with breast cancer (OR = 2.81; 95% CI [1.02-8.22]; p = 0.026), controls under 50 years old (p = 0.048), patients older than 50 (p = 0.007), and postmenopausal (p = 0.034). The PMR of both genes showed a specificity of 86.21% and a sensitivity of 31.03%. CONCLUSION Promoter hypermethylation of RARB + GSTP1 genes is associated with breast cancer, older age, and postmenopausal Peruvian patients. The methylated promoter of the RARB + GSTP1 genes needs further validation to be used as a biomarker for liquid biopsy and as a recommendation criterion for additional tests in asymptomatic women younger than 50 years.
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Affiliation(s)
- Pierina Danos
- Centro de Genética y Biología MolecularUniversidad de San Martín de PorresLimaPeru
| | | | | | - Oscar Acosta
- Facultad de Medicina HumanaUniversidad de San Martín de PorresChiclayoPeru
- Facultad de Farmacia y BioquímicaUniversidad Nacional Mayor de San MarcosLimaPeru
| | | | | | | | | | | | | | - Ricardo Fujita
- Centro de Genética y Biología MolecularUniversidad de San Martín de PorresLimaPeru
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Ma Y, Sun Y, Zhao X, Li J, Fu X, Gong T, Zhang X. Identification of m 5C-related lncRNAs signature to predict prognosis and therapeutic responses in esophageal squamous cell carcinoma patients. Sci Rep 2023; 13:14499. [PMID: 37666951 PMCID: PMC10477299 DOI: 10.1038/s41598-023-41495-6] [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: 09/28/2022] [Accepted: 08/28/2023] [Indexed: 09/06/2023] Open
Abstract
Esophageal squamous cell carcinoma (ESCC) has a dismal prognosis because of atypical early symptoms and heterogeneous therapeutic responses. 5-methylcytosine (m5C) modification plays an important role in the onset and development of many tumors and is widespread in long non-coding RNA (lncRNA) transcripts. However, the functions of m5C and lncRNAs in ESCC have not been completely elucidated. Herein, this study aimed to explore the role of m5C-related lncRNAs in ESCC. The RNA-seq transcriptome profiles and clinical information were downloaded from the TCGA-ESCC database. Pearson analysis was used to identify m5C-related lncRNAs. Then we established the m5C-related lncRNAs prognostic signature (m5C-LPS) using univariate Cox and least absolute shrinkage and selection operator (LASSO) regression analysis. Then, the prognostic value of m5C-LPS was evaluated internally and externally using the TCGA-ESCC and GSE53622 databases through multiple methods. We also detected the expression of these lncRNAs in ESCC cell lines and patient tissues. Fluorescence in situ hybridization (FISH) was used to detect the prognostic value of specific lncRNA. In addition, clinical parameters, immune status, genomic variants, oncogenic pathways, enrichment pathways, and therapeutic response features associated with m5C-LPS were explored using bioinformatics methods. We constructed and validated a prognostic signature based on 9 m5C-related lncRNAs (AC002091.2, AC009275.1, CAHM, LINC02057.1, AC0006329.1, AC037459.3, AC064807.1, ATP2B1-AS1, and UBAC2-AS1). The quantitative real-time polymerase chain reaction (qRT-PCR) revealed that most lncRNAs were upregulated in ESCC cell lines and patient tissues. And AC002091.2 was validated to have significant prognostic value in ESCC patients. A composite nomogram was generated to facilitate clinical practice by integrating this signature with the N stage. Besides, patients in the low-risk group were characterized by good clinical outcomes, favorable immune status, and low oncogenic alteration. Function enrichment analysis indicated that the risk score was associated with mRNA splicing, ncRNA processing, and DNA damage repair response. At the same time, we found significant differences in the responses to chemoradiotherapy between the two groups, proving the value of m5C-LPS in treatment decision-making in ESCC. This study established a novel prognostic signature based on 9 m5C-related lncRNAs, which is a promising biomarker for predicting clinical outcomes and therapeutic response in ESCC.
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Affiliation(s)
- Yuan Ma
- Department of Radiation Oncology, The First Affiliated Hospital of Xi'an Jiaotong University, Yanta West Road 277, Xi'an, 710061, Shaanxi, China
| | - Yuchen Sun
- Department of Radiation Oncology, The First Affiliated Hospital of Xi'an Jiaotong University, Yanta West Road 277, Xi'an, 710061, Shaanxi, China
| | - Xu Zhao
- Department of Radiation Oncology, The First Affiliated Hospital of Xi'an Jiaotong University, Yanta West Road 277, Xi'an, 710061, Shaanxi, China
| | - Jing Li
- Department of Radiation Oncology, The First Affiliated Hospital of Xi'an Jiaotong University, Yanta West Road 277, Xi'an, 710061, Shaanxi, China
| | - Xing Fu
- Department of Radiation Oncology, The First Affiliated Hospital of Xi'an Jiaotong University, Yanta West Road 277, Xi'an, 710061, Shaanxi, China
| | - Tuotuo Gong
- Department of Radiation Oncology, The First Affiliated Hospital of Xi'an Jiaotong University, Yanta West Road 277, Xi'an, 710061, Shaanxi, China.
| | - Xiaozhi Zhang
- Department of Radiation Oncology, The First Affiliated Hospital of Xi'an Jiaotong University, Yanta West Road 277, Xi'an, 710061, Shaanxi, China.
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Ponomaryova AA, Rykova EY, Solovyova AI, Tarasova AS, Kostromitsky DN, Dobrodeev AY, Afanasiev SA, Cherdyntseva NV. Genomic and Transcriptomic Research in the Discovery and Application of Colorectal Cancer Circulating Markers. Int J Mol Sci 2023; 24:12407. [PMID: 37569782 PMCID: PMC10419249 DOI: 10.3390/ijms241512407] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2023] [Revised: 07/24/2023] [Accepted: 08/02/2023] [Indexed: 08/13/2023] Open
Abstract
Colorectal cancer (CRC) is the most frequently occurring malignancy in the world. However, the mortality from CRC can be reduced through early diagnostics, selection of the most effective treatment, observation of the therapy success, and the earliest possible diagnosis of recurrences. A comprehensive analysis of genetic and epigenetic factors contributing to the CRC development is needed to refine diagnostic, therapeutic, and preventive strategies and to ensure appropriate decision making in managing specific CRC cases. The liquid biopsy approach utilizing circulating markers has demonstrated its good performance as a tool to detect the changes in the molecular pathways associated with various cancers. In this review, we attempted to brief the main tendencies in the development of circulating DNA and RNA-based markers in CRC such as cancer-associated DNA mutations, DNA methylation changes, and non-coding RNA expression shifts. Attention is devoted to the existing circulating nucleic acid-based CRC markers, the possibility of their application in clinical practice today, and their future improvement. Approaches to the discovery and verification of new markers are described, and the existing problems and potential solutions for them are highlighted.
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Affiliation(s)
- Anastasia A. Ponomaryova
- Cancer Research Institute, Tomsk National Research Medical Center of the Russian Academy of Sciences, 634009 Tomsk, Russia
| | - Elena Yu. Rykova
- Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences, 630090 Novosibirsk, Russia
- Department of Engineering Problems of Ecology, Novosibirsk State Technical University, 630087 Novosibirsk, Russia
| | - Anastasia I. Solovyova
- Department of Biochemistry, Medico-Biological Faculty, Siberian State Medical University, 634050 Tomsk, Russia
| | - Anna S. Tarasova
- Cancer Research Institute, Tomsk National Research Medical Center of the Russian Academy of Sciences, 634009 Tomsk, Russia
| | - Dmitry N. Kostromitsky
- Cancer Research Institute, Tomsk National Research Medical Center of the Russian Academy of Sciences, 634009 Tomsk, Russia
| | - Alexey Yu. Dobrodeev
- Cancer Research Institute, Tomsk National Research Medical Center of the Russian Academy of Sciences, 634009 Tomsk, Russia
| | - Sergey A. Afanasiev
- Cancer Research Institute, Tomsk National Research Medical Center of the Russian Academy of Sciences, 634009 Tomsk, Russia
| | - Nadezhda V. Cherdyntseva
- Cancer Research Institute, Tomsk National Research Medical Center of the Russian Academy of Sciences, 634009 Tomsk, Russia
- Faculty of Chemistry, National Research Tomsk State University, 634050 Tomsk, Russia
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Yin Q, Huang X, Yang Q, Lin S, Song Q, Fan W, Li W, Li Z, Gao L. LncRNA model predicts liver cancer drug resistance and validate in vitro experiments. Front Cell Dev Biol 2023; 11:1174183. [PMID: 37077416 PMCID: PMC10106610 DOI: 10.3389/fcell.2023.1174183] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2023] [Accepted: 03/17/2023] [Indexed: 04/05/2023] Open
Abstract
Introduction: Hepatocellular carcinoma (HCC) patients may benefit from chemotherapy, but drug resistance is an important obstacle to favorable prognoses. Overcoming drug resistance is an urgent problem to be solved.Methods: Differential expression analysis was used to identify long non-coding RNAs (LncRNAs) that differed in chemotherapy-sensitive and chemotherapy-resistant patients. Machine learning algorithms including random forest (RF), lasso regression (LR), and support vector machines (SVMs) were used to identify important chemotherapy-related LncRNAs. A back propagation (BP) network was then used to validate the predictive capacity of important LncRNAs. The molecular functions of hub LncRNAs were investigated via qRT-PCR and cell proliferation assay. Molecular-docking technique was used to explore candidate drug of targets of hub LncRNA in the model.Results: A total of 125 differentially expressed LncRNAs between sensitive and resistant patients. Seventeen important LncRNAs were identified via RF, and seven factors were identified via LR. With respect to SVM, the top 15 LncRNAs of AvgRank were selected. Five merge chemotherapy-related LncRNAs were used to predict chemotherapy resistance with high accuracy. CAHM was a hub LncRNA of model and expression high in sorafenib resistance cell lines. In addition, the results of CCK8 showed that the sensitivity of HepG2-sorafenib cells to sorafenib was significantly lower than that of HepG2; and the sensitivity of HepG2-sorafenib cells transfected with sh-CAHM was significantly higher than that of Sorafenib. In the non-transfection group, the results of clone formation experiments showed that the number of clones formed by HepG2-sorafenib cells treated with sorafenib was significantly more than that of HepG2; after HepG2-sorafenib cells were transfected with sh-CAHM, the number of clones formed by Sorafenib treatment was significantly higher than that of HepG2 cells. The number was significantly less than that of HepG2-s + sh-NC group. Molecular Docking results indicate that Moschus was candidate drug for target protein of CAHM.Conclusion: Five chemotherapy-related LncRNAs could predict drug resistance in HCC with high accuracy, and the hub LncRNA CAHM has potential as a new biomarker for HCC chemotherapy resistance.
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Affiliation(s)
- Qiushi Yin
- Department of Hepatobiliary Surgery, The First Affiliated Hospital of Hainan Medical University, Haikou, Hainan Province, China
| | - Xiaolong Huang
- Department of Hepatobiliary Surgery, The First Affiliated Hospital of Hainan Medical University, Haikou, Hainan Province, China
| | - Qiuxi Yang
- Department of Hepatobiliary Surgery, The First Affiliated Hospital of Hainan Medical University, Haikou, Hainan Province, China
| | - Shibu Lin
- Department of Hepatobiliary Surgery, The First Affiliated Hospital of Hainan Medical University, Haikou, Hainan Province, China
| | - Qifeng Song
- Department of Hepatobiliary Surgery, The First Affiliated Hospital of Hainan Medical University, Haikou, Hainan Province, China
| | - Weiqiang Fan
- Department of Hepatobiliary Surgery, The First Affiliated Hospital of Hainan Medical University, Haikou, Hainan Province, China
| | - Wang Li
- Department of Hepatobiliary Surgery, The First Affiliated Hospital of Hainan Medical University, Haikou, Hainan Province, China
| | - Zhongyi Li
- Department of General, Visceral, and Transplant Surgery, Ludwig-Maximilians-University Munich, Munich, Germany
| | - Lianghui Gao
- Department of Hepatobiliary Surgery, The First Affiliated Hospital of Hainan Medical University, Haikou, Hainan Province, China
- *Correspondence: Lianghui Gao,
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Li W, Xu Y, Chen W. Bone mesenchymal stem cells deliver exogenous lncRNA CAHM via exosomes to regulate macrophage polarization and ameliorate intervertebral disc degeneration. Exp Cell Res 2022; 421:113408. [PMID: 36334792 DOI: 10.1016/j.yexcr.2022.113408] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2022] [Revised: 10/18/2022] [Accepted: 10/29/2022] [Indexed: 11/06/2022]
Abstract
Exosomes derived from bone marrow mesenchymal stem cells (BMSC-Exos) were reported to have therapeutic potential in degenerative diseases. This study aimed to explore the effects of BMSC-Exos on inhibiting M1 macrophage polarization, reducing excessive nucleus pulposus cells (NPCs) apoptosis, and inhibiting ECM degradation during intervertebral disc degeneration (IDD). Rat IDD models were established by acupuncture. For the co-culture experiment, we used BMSC-Exo or human monocyte leukemia (THP-1) medium to incubate THP-1 or NPCs, respectively. BMSC-Exo was isolated from the BMSC medium, identified by TEM and NTA, and injected into the intervertebral discs of IDD rats. The macrophage infiltration in intervertebral disc tissue was evaluated by immunohistochemistry and immunofluorescence. ELISA was used to measure the levels of TNF-α, IL-6 and IL-10. The ECM degradation was analyzed by Western blot. The cell proportion and apoptosis were measured by flow cytometry. The morphological change of the intervertebral disc was analyzed by HE and safranin O fixation staining. In intervertebral disc tissues of IDD rats, we found the increased infiltration of M1 macrophages, with upregulated iNOS, TNF-α and IL-6 levels. Compared with BMSCs, the expression of CAHM in BMSC-Exo was significantly higher. Using co-cultured experiments, we proved that BMSC-Exo reduced apoptosis and ECM degradation of NPCs by inhibiting M1-type macrophage polarization by delivering CAHM. In addition, BMSC-Exo could improve IDD in vivo, including increased proteoglycan content, reduced macrophage infiltration and ECM degradation, and decrease expression of inflammatory factors by delivering CAHM. In conclusion, BMSC-Exo delivered exogenous CAHM via exosomes to regulate macrophage polarization and ameliorate IDD.
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Affiliation(s)
- Wan Li
- Department of Ophthalmology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, 1277 Jiefang Avenue, Wuhan, Hubei, 430022, China
| | - Yong Xu
- Department of Orthopedic, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, 1095 Jiefang Avenue, Wuhan, Hubei, 430030, China
| | - Wenjian Chen
- Department of Orthopedic, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, 1095 Jiefang Avenue, Wuhan, Hubei, 430030, China.
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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] [MESH Headings] [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 the third most common cancer with the second most frequent 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 mRNAs, 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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10
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Xu Y, Li Z, Huai T, Huo X, Wang H, Bian E, Zhao B. DNMT1 Mediated CAHM Repression Promotes Glioma Invasion via SPAK/JNK Pathway. Cell Mol Neurobiol 2022; 42:2643-2653. [PMID: 34227028 PMCID: PMC11421610 DOI: 10.1007/s10571-021-01125-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2021] [Accepted: 07/02/2021] [Indexed: 10/20/2022]
Abstract
Gliomas are the most common and fatal brain tumors worldwide. Abnormal DNA promoter methylation is an important mechanism for gene loss of tumor suppressors. A long non-coding RNA colorectal adenocarcinoma hypermethylated (CAHM) has been reported to be nearly deleted in glioblastomas (GBMs). Nevertheless, the roles of CAHM in gliomas remain unknown up to now. In the present study, 969 glioma samples downloaded from the CGGA and Gravendeel databases were included. We found that CAHM expression was correlated with glioma grades, molecular subtype, IDH mutation status, and 1q/19p codel status. In glioma cells, CAHM is hypermethylated by DNA methyltransferase1 (DNMT1) and the loss of CAHM expression could be reversed by 5-Aza-2'-deoxycytidine (5-Aza), a specific inhibitor of DNA methyltransferases. Besides, the expression of CAHM was negatively associated with overall survival in both primary and recurrent gliomas. Moreover, the result of Gene Ontology (GO) analysis suggested that CAHM participated in negatively regulating cell development, nervous system development, neurogenesis, and integrin-mediated signaling pathway. Overexpression of CAHM inhibited glioma cell proliferation, clone formation, and invasion. Further exploring results showed that CAHM overexpression suppressed glioma migration and invasion through SPAK/MAPK pathway. Collectively, this study disclosed that CAHM might be a suppressor in gliomas.
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Affiliation(s)
- Yadi Xu
- Ultrasonography Department, Hubei Hospital of Traditional Chinese Medicine, Wuhan, China
| | - Zelin Li
- Department of Neurosurgery, The Second Affiliated Hospital of Anhui Medical University, Anhui Medical University, 678 Fu Rong Road, Hefei, 230601, Anhui, China
- Cerebral Vascular Disease Research Center, Anhui Medical University, Hefei, 230601, China
| | - Tian Huai
- Department of Neurosurgery, The Second Affiliated Hospital of Anhui Medical University, Anhui Medical University, 678 Fu Rong Road, Hefei, 230601, Anhui, China
- Cerebral Vascular Disease Research Center, Anhui Medical University, Hefei, 230601, China
| | - Xiuhao Huo
- Department of Neurosurgery, The Second Affiliated Hospital of Anhui Medical University, Anhui Medical University, 678 Fu Rong Road, Hefei, 230601, Anhui, China
- Cerebral Vascular Disease Research Center, Anhui Medical University, Hefei, 230601, China
| | - Hongliang Wang
- Department of Neurosurgery, The Second Affiliated Hospital of Anhui Medical University, Anhui Medical University, 678 Fu Rong Road, Hefei, 230601, Anhui, China
- Cerebral Vascular Disease Research Center, Anhui Medical University, Hefei, 230601, China
| | - Erbao Bian
- Department of Neurosurgery, The Second Affiliated Hospital of Anhui Medical University, Anhui Medical University, 678 Fu Rong Road, Hefei, 230601, Anhui, China
- Cerebral Vascular Disease Research Center, Anhui Medical University, Hefei, 230601, China
| | - Bing Zhao
- Department of Neurosurgery, The Second Affiliated Hospital of Anhui Medical University, Anhui Medical University, 678 Fu Rong Road, Hefei, 230601, Anhui, China.
- Cerebral Vascular Disease Research Center, Anhui Medical University, Hefei, 230601, China.
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11
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Zhang L, Li D, Gao L, Fu J, Sun S, Huang H, Zhang D, Jia C, Zheng T, Cui B, Liu Y, Zhao Y. Promoter Methylation of QKI as a Potential Specific Biomarker for Early Detection of Colorectal Cancer. Front Genet 2022; 13:928150. [PMID: 36017498 PMCID: PMC9395658 DOI: 10.3389/fgene.2022.928150] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2022] [Accepted: 06/24/2022] [Indexed: 11/16/2022] Open
Abstract
Early and specific detection of cancer provides an opportunity for appropriate treatment. Although studies have suggested that QKI is a tumor suppressor gene, no studies have evaluated the diagnostic utility of QKI methylation in colorectal cancer (CRC). Here, we evaluated the methylation status of QKI by integrating the methylation data of tissues and cell lines of multiple cancer types. The diagnostic performance of QKI was analyzed in the discovery dataset from the TCGA CRC 450K array (n = 440) and tested in the test sets (n = 845) from the GEO. The methylation level of QKI was further validated in our independent dataset (n = 388) using targeted bisulfite sequencing. All detected CpG sites in the QKI promoter showed CRC-specific hypermethylation in 31 types of tumor tissues. In the discovery dataset, six consecutive CpG sites achieved high diagnostic performances, with AUCs ranging from 0.821 to 0.930. In the test set, a region (chr6: 163,834,452–163,834,924) including four consecutive CpG sites had robust diagnostic ability in distinguishing CRC and adenoma from normal samples. In the validation dataset, similar robust results were observed in both early- and advanced-stage CRC patients. In addition, QKI exhibited hypermethylation in the cfDNA of patients with CRC (n = 14). Collectively, the QKI promoter is a CRC-specific methylation biomarker and holds great promise for improving the diagnosis using minimally invasive biopsy.
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Affiliation(s)
- Lei Zhang
- Department of Epidemiology, College of Public Health, Harbin Medical University, Harbin, China
| | - Dapeng Li
- Department of Epidemiology, College of Public Health, Harbin Medical University, Harbin, China
| | - Lijing Gao
- Department of Epidemiology, College of Public Health, Harbin Medical University, Harbin, China
| | - Jinming Fu
- Department of Epidemiology, College of Public Health, Harbin Medical University, Harbin, China
| | - Simin Sun
- Department of Epidemiology, College of Public Health, Harbin Medical University, Harbin, China
| | - Hao Huang
- Department of Epidemiology, College of Public Health, Harbin Medical University, Harbin, China
| | - Ding Zhang
- Department of Epidemiology, College of Public Health, Harbin Medical University, Harbin, China
| | - Chenyang Jia
- Department of Epidemiology, College of Public Health, Harbin Medical University, Harbin, China
| | - Ting Zheng
- Department of Epidemiology, College of Public Health, Harbin Medical University, Harbin, China
| | - Binbin Cui
- Department of Colorectal Surgery, Harbin Medical University Cancer Hospital, Harbin Medical University, Harbin, China
- *Correspondence: Yashuang Zhao, ; Yanlong Liu, ; Binbin Cui,
| | - Yanlong Liu
- Department of Colorectal Surgery, Harbin Medical University Cancer Hospital, Harbin Medical University, Harbin, China
- *Correspondence: Yashuang Zhao, ; Yanlong Liu, ; Binbin Cui,
| | - Yashuang Zhao
- Department of Epidemiology, College of Public Health, Harbin Medical University, Harbin, China
- *Correspondence: Yashuang Zhao, ; Yanlong Liu, ; Binbin Cui,
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12
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Lin S, Gu S, Qian S, Liu Y, Sheng J, Li Q, Yang J, Ying X, Li Z, Tang M, Wang J, Chen K, Jin M. Genome-Wide Methylation Profiling of lncRNAs Reveals a Novel Progression-Related and Prognostic Marker for Colorectal Cancer. Front Oncol 2022; 11:782077. [PMID: 35127488 PMCID: PMC8811200 DOI: 10.3389/fonc.2021.782077] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2021] [Accepted: 12/29/2021] [Indexed: 01/05/2023] Open
Abstract
Sporadic colorectal cancer (CRC) develops principally through the adenoma-carcinoma sequence. Previous studies revealed that DNA methylation alterations play a significant role in colorectal neoplastic transformation. On the other hand, long noncoding RNAs (lncRNAs) have been identified to be associated with some critical tumorigenic processes of CRC. Accumulating evidence indicates more intricate regulatory relationships between DNA methylation and lncRNAs in CRC. Nevertheless, the methylation alterations of lncRNAs at different stages of colorectal carcinogenesis based on a genome-wide scale remain elusive. Therefore, in this study, we first used an Illumina MethylationEPIC BeadChip (850K array) to identify the methylation status of lncRNAs in 12 pairs of colorectal cancerous and adjacent normal tissues from cohort I, followed by cross-validation with The Cancer Genome Atlas (TCGA) database and the Gene Expression Omnibus (GEO) database. Then, the abnormal hypermethylation of candidate genes in colorectal lesions was successfully confirmed by MassARRAY EpiTYPER in cohort II including 48 CRC patients, and cohort III including 286 CRC patients, 81 advanced adenoma (AA) patients and 81 nonadvanced adenoma (NAA) patients. DLX6-AS1 hypermethylation was detected at all stages of colorectal neoplasms and occurred as early as the NAA stage during colorectal neoplastic progression. The methylation levels were significantly higher in the comparisons of CRC vs. NAA (P < 0.001) and AA vs. NAA (P = 0.004). Moreover, the hypermethylation of DLX6-AS1 promoter was also found in cell-free DNA samples collected from CRC patients as compared to healthy controls (P adj = 0.003). Multivariate Cox proportional hazards regression analysis revealed DLX6-AS1 promoter hypermethylation was independently associated with poorer disease-specific survival (HR = 2.52, 95% CI: 1.35-4.69, P = 0.004) and overall survival (HR = 1.64, 95% CI: 1.02-2.64, P = 0.042) in CRC patients. Finally, a nomogram was constructed and verified by a calibration curve to predict the survival probability of individual CRC patients (C-index: 0.789). Our findings indicate DLX6-AS1 hypermethylation might be an early event during colorectal carcinogenesis and has the potential to be a novel biomarker for CRC progression and prognosis.
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Affiliation(s)
- Shujuan Lin
- Department of Epidemiology and Biostatistics at School of Public Health and the Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Simeng Gu
- Department of Epidemiology and Biostatistics at School of Public Health and the Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
- Department of Environmental Health, Institute of Endemic Diseases, Zhejiang Provincial Center for Disease Control and Prevention, Hangzhou, China
| | - Sangni Qian
- Department of Epidemiology and Biostatistics at School of Public Health and the Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Yaxin Liu
- Institute of Environmental Medicine, and Cancer Center of the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Jinghao Sheng
- Institute of Environmental Medicine, and Cancer Center of the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Qilong Li
- Department of Screening, Jiashan Institute of Cancer Prevention and Treatment, Jiashan, China
| | - Jinhua Yang
- Department of Screening, Jiashan Institute of Cancer Prevention and Treatment, Jiashan, China
| | - Xiaojiang Ying
- Department of Anorectal Surgery, Shaoxing People’s Hospital, Shaoxing, China
| | - Zhenjun Li
- Department of Anorectal Surgery, Shaoxing People’s Hospital, Shaoxing, China
| | - Mengling Tang
- Department of Epidemiology and Biostatistics at School Public Health and the Fourth Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Jianbing Wang
- Department of Epidemiology and Biostatistics at School of Public Health and National Clinical Research Center for Child Health of the Children’s Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Kun Chen
- Department of Epidemiology and Biostatistics at School of Public Health and the Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Mingjuan Jin
- Department of Epidemiology and Biostatistics at School of Public Health and the Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
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13
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Neumann DP, Goodall GJ, Gregory PA. The Quaking RNA-binding proteins as regulators of cell differentiation. WILEY INTERDISCIPLINARY REVIEWS. RNA 2022; 13:e1724. [PMID: 35298877 PMCID: PMC9786888 DOI: 10.1002/wrna.1724] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/12/2022] [Revised: 02/18/2022] [Accepted: 02/21/2022] [Indexed: 12/30/2022]
Abstract
The RNA-binding protein Quaking (QKI) has emerged as a potent regulator of cellular differentiation in developmental and pathological processes. The QKI gene is itself alternatively spliced to produce three major isoforms, QKI-5, QKI-6, and QKI-7, that possess very distinct functions. Here, we highlight roles of the different QKI isoforms in neuronal, vascular, muscle, and monocyte cell differentiation, and during epithelial-mesenchymal transition in cancer progression. QKI isoforms control cell differentiation through regulating alternative splicing, mRNA stability and translation, with activities in gene transcription now also becoming evident. These diverse functions of the QKI isoforms contribute to their broad influences on RNA metabolism and cellular differentiation. This article is categorized under: RNA Interactions with Proteins and Other Molecules > Protein-RNA Interactions: Functional Implications RNA Processing > Splicing Regulation/Alternative Splicing RNA in Disease and Development > RNA in Development.
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Affiliation(s)
- Daniel P. Neumann
- Centre for Cancer BiologyUniversity of South Australia and SA PathologyAdelaideSouth Australia
| | - Gregory J. Goodall
- Centre for Cancer BiologyUniversity of South Australia and SA PathologyAdelaideSouth Australia,Faculty of Health and Medical SciencesThe University of AdelaideAdelaideSouth Australia
| | - Philip A. Gregory
- Centre for Cancer BiologyUniversity of South Australia and SA PathologyAdelaideSouth Australia,Faculty of Health and Medical SciencesThe University of AdelaideAdelaideSouth Australia
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14
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Expression level of long non-coding RNA colon adenocarcinoma hypermethylated serves as a novel prognostic biomarker in patients with thyroid carcinoma. Biosci Rep 2021; 41:228191. [PMID: 33792624 PMCID: PMC8056003 DOI: 10.1042/bsr20210284] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2021] [Revised: 03/09/2021] [Accepted: 03/24/2021] [Indexed: 12/13/2022] Open
Abstract
The present study attempts to identify the prognostic value and potential mechanism of action of colorectal adenocarcinoma hypermethylated (CAHM) in thyroid carcinoma (THCA) by using the RNA sequencing (RNA-seq) dataset from The Cancer Genome Atlas (TCGA). The functional mechanism of CAHM was explored by using RNA-seq dataset and multiple functional enrichment analysis approaches. Connectivity map (CMap) online analysis tool was also used to predict CAHM targeted drugs. Survival analysis suggests that THCA patients with high CAHM expression have lower risk of death than the low CAHM expression (log-rank P=0.022, adjusted P=0.011, HR = 0.187, 95% confidence interval (CI) = 0.051–0.685). Functional enrichment of CAHM co-expression genes suggests that CAHM may play a role in the following biological processes: DNA repair, cell adhesion, DNA replication, vascular endothelial growth factor receptor, Erb-B2 receptor tyrosine kinase 2, ErbB and thyroid hormone signaling pathways. Functional enrichment of differentially expressed genes (DEGs) between low- and high-CAHM phenotype suggests that different CAHM expression levels may have the following differences in biological processes in THCA: cell adhesion, cell proliferation, extracellular signal-regulated kinase (ERK) 1 (ERK1) and ERK2 cascade, G-protein coupled receptor, chemokine and phosphatidylinositol-3-kinase-Akt signaling pathways. Connectivity map have identified five drugs (levobunolol, NU-1025, quipazine, anisomycin and sulfathiazole) for CAHM targeted therapy in THCA. Gene set enrichment analysis (GSEA) suggest that low CAHM phenotype were notably enriched in p53, nuclear factor κB, Janus kinase-signal transducer and activators of transcription, tumor necrosis factor, epidermal growth factor receptor and other signaling pathways. In the present study, we have identified that CAHM may serve as novel prognostic biomarkers for predicting overall survival (OS) in patients with THCA.
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15
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Poursheikhani A, Abbaszadegan MR, Kerachian MA. Mechanisms of long non-coding RNA function in colorectal cancer tumorigenesis. Asia Pac J Clin Oncol 2020; 17:7-23. [PMID: 32970938 DOI: 10.1111/ajco.13452] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2020] [Accepted: 08/03/2020] [Indexed: 12/14/2022]
Abstract
Colorectal cancer (CRC) is one of the most common cancers globally. Although a variety of CRC screening methods have been developed, many patients are diagnosed at advanced stages of CRC with tumor invasion and distance metastasis. Several studies have suggested the long noncoding RNAs (lncRNAs) as one of the main contributors in CRC tumorigenesis, although the exact underlying mechanism of lncRNAs in CRC is still unknown. Numerous studies have indicated aberrant expression of lncRNAs in CRC through different modes of action such as cell proliferation, apoptosis, cell cycle, DNA repair response, drug-resistance, migration, and metastasis. Furthermore, lncRNA polymorphisms can influence the risk of CRC development. Accordingly, lncRNAs can be served as promising diagnostic or prognostic biomarkers and also desired therapeutic targets affecting the outcome of patients with CRC. In this review, we summarized the updated and novel evidence that identifies different roles of lncRNAs in the tumorigenesis of CRC.
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Affiliation(s)
- Arash Poursheikhani
- 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
| | - Mohammad Reza Abbaszadegan
- 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.,Immunology Research Center, Mashhad University of Medical Sciences, Mashhad, Iran
| | - 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.,Cancer Genetics Research Unit, Reza Radiotherapy, and Oncology Center, Mashhad, Iran
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16
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Constâncio V, Nunes SP, Henrique R, Jerónimo C. DNA Methylation-Based Testing in Liquid Biopsies as Detection and Prognostic Biomarkers for the Four Major Cancer Types. Cells 2020; 9:E624. [PMID: 32150897 PMCID: PMC7140532 DOI: 10.3390/cells9030624] [Citation(s) in RCA: 132] [Impact Index Per Article: 26.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2020] [Revised: 03/01/2020] [Accepted: 03/02/2020] [Indexed: 12/11/2022] Open
Abstract
Lung, breast, colorectal, and prostate cancers are the most incident worldwide. Optimal population-based cancer screening methods remain an unmet need, since cancer detection at early stages increases the prospects of successful and curative treatment, leading to a lower incidence of recurrences. Moreover, the current parameters for cancer patients' stratification have been associated with divergent outcomes. Therefore, new biomarkers that could aid in cancer detection and prognosis, preferably detected by minimally invasive methods are of major importance. Aberrant DNA methylation is an early event in cancer development and may be detected in circulating cell-free DNA (ccfDNA), constituting a valuable cancer biomarker. Furthermore, DNA methylation is a stable alteration that can be easily and rapidly quantified by methylation-specific PCR methods. Thus, the main goal of this review is to provide an overview of the most important studies that report methylation biomarkers for the detection and prognosis of the four major cancers after a critical analysis of the available literature. DNA methylation-based biomarkers show promise for cancer detection and management, with some studies describing a "PanCancer" detection approach for the simultaneous detection of several cancer types. Nonetheless, DNA methylation biomarkers still lack large-scale validation, precluding implementation in clinical practice.
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Affiliation(s)
- Vera Constâncio
- Cancer Biology & Epigenetics Group—Research Center, Portuguese Oncology Institute of Porto (CI-IPOP), 4200-072 Porto, Portugal; (V.C.); (S.P.N.); (R.H.)
- Master in Oncology, Institute of Biomedical Sciences Abel Salazar, University of Porto (ICBAS-UP), 4050-313 Porto, Portugal
| | - Sandra P. Nunes
- Cancer Biology & Epigenetics Group—Research Center, Portuguese Oncology Institute of Porto (CI-IPOP), 4200-072 Porto, Portugal; (V.C.); (S.P.N.); (R.H.)
| | - Rui Henrique
- Cancer Biology & Epigenetics Group—Research Center, Portuguese Oncology Institute of Porto (CI-IPOP), 4200-072 Porto, Portugal; (V.C.); (S.P.N.); (R.H.)
- Department of Pathology, Portuguese Oncology Institute of Porto, 4200-072 Porto, Portugal
- Department of Pathology and Molecular Immunology, Institute of Biomedical Sciences Abel Salazar–University of Porto (ICBAS-UP), 4050-313 Porto, Portugal
| | - Carmen Jerónimo
- Cancer Biology & Epigenetics Group—Research Center, Portuguese Oncology Institute of Porto (CI-IPOP), 4200-072 Porto, Portugal; (V.C.); (S.P.N.); (R.H.)
- Department of Pathology and Molecular Immunology, Institute of Biomedical Sciences Abel Salazar–University of Porto (ICBAS-UP), 4050-313 Porto, Portugal
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17
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Wang S, Wu D, Xu Y, Cao Y, Wang J, Zhang Y, Yang N, Sun L. Downregulated placental expression of linc00468 contributes to trophoblast dysfunction by inducing epithelial-mesenchymal transition. ANNALS OF TRANSLATIONAL MEDICINE 2020; 8:333. [PMID: 32355777 PMCID: PMC7186696 DOI: 10.21037/atm.2020.02.166] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Background Preeclampsia (PE) is a widespread progressive condition that can occur pregnancy and is related to high maternal morbidity and fetal mortality in the perinatal period. However, the exact mechanism responsible has not been specific. Accumulating evidence has highlighted the prominent role of the epithelial‐mesenchymal transition (EMT) in the biological behaviors of PE. Methods We explored the role of a lincRNA in extravillous trophoblast (EVTs) cell viability, migration, invasion and apoptosis in vitro, along with the use of linc00468 knockdown or overexpression. Clinically, we discovered that the expression of linc00468 was frequently correlated with adverse clinical features and poor prognosis of PE patients. Results We uncovered that linc00468 was downregulated in PE samples compared to in healthy tissues and in trophoblast cells. Functionally, gain and loss-of-function experiments demonstrated that linc00468 inhibited cell proliferation, migration, invasion and linc00468 accelerated apoptosis of the trophoblast phenotype in cell lines. Moreover, we demonstrated that downregulation of linc00468 promoted the expression of E-cadherin and β-catenin but reduced the expression of N-cadherin, Vimentin and Snail, resulting in progression of EMT. Conclusions In conclusion, linc00468 promoted EMT and a consequent increase in invasiveness in HTR-8/Svneo and JAR EVT cell lines. Our study provides the first evidence that linc00468 has a pivotal role in cell invasion and promotes intrinsic and extrinsic EMT ability of PE.
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Affiliation(s)
- Sailan Wang
- Department of Obstetrics and Gynecology, The First Affiliated Hospital of Nanjing Medical University, Nanjing 210029, China.,Department of Neurobiology, Care Science and Society, Karolinska Institutet, Solna, Sweden
| | - Dan Wu
- Department of Obstetrics and Gynecology, The First Affiliated Hospital of Nanjing Medical University, Nanjing 210029, China
| | - Yetao Xu
- Department of Obstetrics and Gynecology, The First Affiliated Hospital of Nanjing Medical University, Nanjing 210029, China
| | - Yueying Cao
- Department of Obstetrics and Gynecology, The First Affiliated Hospital of Nanjing Medical University, Nanjing 210029, China
| | - Jiawei Wang
- Department of Oncology, The First Affiliated Hospital of Nanjing Medical University, Nanjing 210029, China
| | - Yuanyuan Zhang
- Department of Obstetrics and Gynecology, The First Affiliated Hospital of Nanjing Medical University, Nanjing 210029, China
| | - Nana Yang
- Department of Obstetrics and Gynecology, The First Affiliated Hospital of Nanjing Medical University, Nanjing 210029, China
| | - Lizhou Sun
- Department of Obstetrics and Gynecology, The First Affiliated Hospital of Nanjing Medical University, Nanjing 210029, China
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18
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Tian S, Wang C, Zhang J, Yu D. The cox-filter method identifies respective subtype-specific lncRNA prognostic signatures for two human cancers. BMC Med Genomics 2020; 13:18. [PMID: 32024523 PMCID: PMC7003323 DOI: 10.1186/s12920-020-0691-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2019] [Accepted: 01/29/2020] [Indexed: 12/17/2022] Open
Abstract
BACKGROUND The most common histological subtypes of esophageal cancer are squamous cell carcinoma (ESCC) and adenocarcinoma (EAC). It has been demonstrated that non-marginal differences in gene expression and somatic alternation exist between these two subtypes; consequently, biomarkers that have prognostic values for them are expected to be distinct. In contrast, laryngeal squamous cell cancer (LSCC) has a better prognosis than hypopharyngeal squamous cell carcinoma (HSCC). Likewise, subtype-specific prognostic signatures may exist for LSCC and HSCC. Long non-coding RNAs (lncRNAs) hold promise for identifying prognostic signatures for a variety of cancers including esophageal cancer and head and neck squamous cell carcinoma (HNSCC). METHODS In this study, we applied a novel feature selection method capable of identifying specific prognostic signatures uniquely for each subtype - the Cox-filter method - to The Cancer Genome Atlas esophageal cancer and HSNCC RNA-Seq data, with the objectives of constructing subtype-specific prognostic lncRNA expression signatures for esophageal cancer and HNSCC. RESULTS By incorporating biological relevancy information, the lncRNA lists identified by the Cox-filter method were further refined. The resulting signatures include genes that are highly related to cancer, such as H19 and NEAT1, which possess perfect prognostic values for esophageal cancer and HNSCC, respectively. CONCLUSIONS The Cox-filter method is indeed a handy tool to identify subtype-specific prognostic lncRNA signatures. We anticipate the method will gain wider applications.
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Affiliation(s)
- Suyan Tian
- Division of Clinical Research, The First Hospital of Jilin University, 1Xinmin Street, Changchun, Jilin, 130021, People's Republic of China.
| | - Chi Wang
- Department of Biostatistics, College of Public Health, University of Kentucky, 800 Rose St, Lexington, KY, 40536, USA
- Markey Cancer Center, University of Kentucky, 800 Rose St, Lexington, KY, 40536, USA
| | - Jing Zhang
- School of Life Science, 2699 Qianjin Street, Changchun, Jilin, 130012, People's Republic of China
| | - Dan Yu
- Department of Otolaryngology Head and Neck Surgery, The Second Hospital of Jilin University, 218 Ziqiang Road, Changchun, Jilin, 130041, People's Republic of China.
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19
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Zheng S, Lin F, Zhang M, Fu J, Ge X, Mu N. AK001058 promotes the proliferation and migration of colorectal cancer cells by regulating methylation of ADAMTS12. Am J Transl Res 2019; 11:5869-5878. [PMID: 31632555 PMCID: PMC6789239] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2019] [Accepted: 07/27/2019] [Indexed: 06/10/2023]
Abstract
BACKGROUND Long noncoding RNA (LncRNA) functions as multiple mechanisms, including DNA methylation in colorectal cancer (CRC). ADAMTS12 was applied as biomarkers in CRC via abnormally DNA methylation. Lnc-AK001058 gene, which was reported dysregulated in CRC, is located adjacent to the gene ADAMTS12. However, little is known about the role of AK001058 during the proliferation and migration of CRC. MATERIAL AND METHODS In present study, quantitative RT-PCR were used to measure AK001058 and ADAMTS12 expression levels, and western blotting assays were performed to measure ADAMTS12 expression in CRC cells. Methylation-specific PCR (MSP) was applied to measure the methylation of the CpG islands of the ADAMTS12 promoter. Cell proliferation, migration, invasion and cycle assays ware utilized to analyze the role of AK001058 in CRC. RESULTS The results indicated that the expression of AK001058 was significantly increased in CRC. Overexpression of AK001058 could suppress the expression of ADAMTS12. AK001058 also significantly promoted cell proliferation, migration and invasion, and prolonged S stage of CRC, while silencing the expression of AK001058 showed contrary effects. Moreover, compared with negative control and AK001058-NC groups, overexpression of AK001058 could increase the DNA methylation level of ADAMTS12 gene promoter in CRC, while si-AK001058 could reverse this effect. CONCLUSION In conclusion, AK001058 promotes the proliferation, invasion, migration, and prolonged S stage of CRC by regulating methylation of ADAMTS12. Our research will provide new insights for the biomarker of colorectal cancer diagnose and new clues for clinical treatment.
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Affiliation(s)
- Shuang Zheng
- Department of General Surgery, Huangyan Hospital of Wenzhou Medical University, Taizhou First People's Hospital Taizhou 318020, Zhejiang Province, China
| | - Feng Lin
- Department of General Surgery, Huangyan Hospital of Wenzhou Medical University, Taizhou First People's Hospital Taizhou 318020, Zhejiang Province, China
| | - Meng Zhang
- Department of General Surgery, Huangyan Hospital of Wenzhou Medical University, Taizhou First People's Hospital Taizhou 318020, Zhejiang Province, China
| | - Junhui Fu
- Department of General Surgery, Huangyan Hospital of Wenzhou Medical University, Taizhou First People's Hospital Taizhou 318020, Zhejiang Province, China
| | - Xiaogang Ge
- Department of General Surgery, Huangyan Hospital of Wenzhou Medical University, Taizhou First People's Hospital Taizhou 318020, Zhejiang Province, China
| | - Ning Mu
- Department of General Surgery, Huangyan Hospital of Wenzhou Medical University, Taizhou First People's Hospital Taizhou 318020, Zhejiang Province, China
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Galamb O, Barták BK, Kalmár A, Nagy ZB, Szigeti KA, Tulassay Z, Igaz P, Molnár B. Diagnostic and prognostic potential of tissue and circulating long non-coding RNAs in colorectal tumors. World J Gastroenterol 2019; 25:5026-5048. [PMID: 31558855 PMCID: PMC6747286 DOI: 10.3748/wjg.v25.i34.5026] [Citation(s) in RCA: 83] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/25/2019] [Revised: 07/26/2019] [Accepted: 08/07/2019] [Indexed: 02/06/2023] Open
Abstract
Long non-coding RNAs (lncRNAs) are members of the non-protein coding RNA family longer than 200 nucleotides. They participate in the regulation of gene and protein expression influencing apoptosis, cell proliferation and immune responses, thereby playing a critical role in the development and progression of various cancers, including colorectal cancer (CRC). As CRC is one of the most frequently diagnosed malignancies worldwide with high mortality, its screening and early detection are crucial, so the identification of disease-specific biomarkers is necessary. LncRNAs are promising candidates as they are involved in carcinogenesis, and certain lncRNAs (e.g., CCAT1, CRNDE, CRCAL1-4) show altered expression in adenomas, making them potential early diagnostic markers. In addition to being useful as tissue-specific markers, analysis of circulating lncRNAs (e.g., CCAT1, CCAT2, BLACAT1, CRNDE, NEAT1, UCA1) in peripheral blood offers the possibility to establish minimally invasive, liquid biopsy-based diagnostic tests. This review article aims to describe the origin, structure, and functions of lncRNAs and to discuss their contribution to CRC development. Moreover, our purpose is to summarise lncRNAs showing altered expression levels during tumor formation in both colon tissue and plasma/serum samples and to demonstrate their clinical implications as diagnostic or prognostic biomarkers for CRC.
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Affiliation(s)
- Orsolya Galamb
- Molecular Medicine Research Group, Hungarian Academy of Sciences, Budapest H-1088, Hungary
| | - Barbara K Barták
- 2nd Department of Internal Medicine, Semmelweis University, Budapest H-1088, Hungary
| | - Alexandra Kalmár
- Molecular Medicine Research Group, Hungarian Academy of Sciences, Budapest H-1088, Hungary
| | - Zsófia B Nagy
- 2nd Department of Internal Medicine, Semmelweis University, Budapest H-1088, Hungary
| | - Krisztina A Szigeti
- 2nd Department of Internal Medicine, Semmelweis University, Budapest H-1088, Hungary
| | - Zsolt Tulassay
- Molecular Medicine Research Group, Hungarian Academy of Sciences, Budapest H-1088, Hungary
| | - Peter Igaz
- Molecular Medicine Research Group, Hungarian Academy of Sciences, Budapest H-1088, Hungary
- 2nd Department of Internal Medicine, Semmelweis University, Budapest H-1088, Hungary
| | - Béla Molnár
- Molecular Medicine Research Group, Hungarian Academy of Sciences, Budapest H-1088, Hungary
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Molnár B, Galamb O, Kalmár A, Barták BK, Nagy ZB, Tóth K, Tulassay Z, Igaz P, Dank M. Circulating cell-free nucleic acids as biomarkers in colorectal cancer screening and diagnosis - an update. Expert Rev Mol Diagn 2019; 19:477-498. [PMID: 31046485 DOI: 10.1080/14737159.2019.1613891] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2019] [Accepted: 04/29/2019] [Indexed: 12/15/2022]
Abstract
Introduction: Screening methods for one of the most frequently diagnosed malignancy, colorectal cancer (CRC), have limitations. Circulating cell-free nucleic acids (cfNA) hold clinical relevance as screening, prognostic and therapy monitoring markers. Area covered: In this review, we summarize potential CRC-specific cfNA biomarkers, the recently developed sample preparation techniques, their applications, and pitfalls. Expert opinion: Automated extraction of cfDNA is highly reproducible, however, cfDNA yield is less compared to manual isolation. Quantitative and highly sensitive detection techniques (e.g. digital PCR, NGS) can be applied to analyze genetic and epigenetic changes. Detection of DNA mutations or methylation in cfDNA and related altered levels of mRNA, miRNA, and lncRNA may improve early cancer recognition, based on specific, CRC-related patterns. Detection of cfDNA mutations (e.g. TP53, KRAS, APC) has limited diagnostic sensitivity (40-60%), however, methylated DNA including SEPT9, SFRP1, SDC2 can be applied with higher sensitivity (up to 90%) for CRC. Circulating miRNAs (e.g. miR-21, miR-92, miR-141) provide comparably high sensitivity for CRC as the circulating tumor cell mRNA markers (e.g. EGFR, CK19, CK20, CEA). Automation of cfNA isolation coupled with quantitative analysis of CRC-related, highly sensitive biomarkers may enhance CRC screening and early detection in the future.
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Affiliation(s)
- Béla Molnár
- a 2nd Department of Internal Medicine , Semmelweis University , Budapest , Hungary
- b MTA-SE Molecular Medicine Research Unit , Hungarian Academy of Sciences and Semmelweis University , Budapest , Hungary
| | - Orsolya Galamb
- a 2nd Department of Internal Medicine , Semmelweis University , Budapest , Hungary
- b MTA-SE Molecular Medicine Research Unit , Hungarian Academy of Sciences and Semmelweis University , Budapest , Hungary
| | - Alexandra Kalmár
- a 2nd Department of Internal Medicine , Semmelweis University , Budapest , Hungary
- b MTA-SE Molecular Medicine Research Unit , Hungarian Academy of Sciences and Semmelweis University , Budapest , Hungary
| | - Barbara Kinga Barták
- a 2nd Department of Internal Medicine , Semmelweis University , Budapest , Hungary
| | - Zsófia Brigitta Nagy
- a 2nd Department of Internal Medicine , Semmelweis University , Budapest , Hungary
| | - Kinga Tóth
- a 2nd Department of Internal Medicine , Semmelweis University , Budapest , Hungary
| | - Zsolt Tulassay
- a 2nd Department of Internal Medicine , Semmelweis University , Budapest , Hungary
- b MTA-SE Molecular Medicine Research Unit , Hungarian Academy of Sciences and Semmelweis University , Budapest , Hungary
| | - Péter Igaz
- a 2nd Department of Internal Medicine , Semmelweis University , Budapest , Hungary
- b MTA-SE Molecular Medicine Research Unit , Hungarian Academy of Sciences and Semmelweis University , Budapest , Hungary
| | - Magdolna Dank
- c Department of Oncology , Semmelweis University , Budapest , Hungary
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LncRNAs with miRNAs in regulation of gastric, liver, and colorectal cancers: updates in recent years. Appl Microbiol Biotechnol 2019; 103:4649-4677. [PMID: 31062053 DOI: 10.1007/s00253-019-09837-5] [Citation(s) in RCA: 95] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2018] [Revised: 04/07/2019] [Accepted: 04/08/2019] [Indexed: 12/15/2022]
Abstract
Long noncoding RNA (lncRNA) is a kind of RNAi molecule composed of hundreds to thousands of nucleotides. There are several major types of functional lncRNAs which participate in some important cellular pathways. LncRNA-RNA interaction controls mRNA translation and degradation or serves as a microRNA (miRNA) sponge for silencing. LncRNA-protein interaction regulates protein activity in transcriptional activation and silencing. LncRNA guide, decoy, and scaffold regulate transcription regulators of enhancer or repressor region of the coding genes for alteration of expression. LncRNA plays a role in cellular responses including the following activities: regulation of chromatin structural modification and gene expression for epigenetic and cell function control, promotion of hematopoiesis and maturation of immunity, cell programming in stem cell and somatic cell development, modulation of pathogen infection, switching glycolysis and lipid metabolism, and initiation of autoimmune diseases. LncRNA, together with miRNA, are considered the critical elements in cancer development. It has been demonstrated that tumorigenesis could be driven by homeostatic imbalance of lncRNA/miRNA/cancer regulatory factors resulting in biochemical and physiological alterations inside the cells. Cancer-driven lncRNAs with other cellular RNAs, epigenetic modulators, or protein effectors may change gene expression level and affect the viability, immortality, and motility of the cells that facilitate cancer cell cycle rearrangement, angiogenesis, proliferation, and metastasis. Molecular medicine will be the future trend for development. LncRNA/miRNA could be one of the potential candidates in this category. Continuous studies in lncRNA functional discrepancy between cancer cells and normal cells and regional and rational genetic differences of lncRNA profiles are critical for clinical research which is beneficial for clinical practice.
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Yang Y, Junjie P, Sanjun C, Ma Y. Long non-coding RNAs in Colorectal Cancer: Progression and Future Directions. J Cancer 2017; 8:3212-3225. [PMID: 29158793 PMCID: PMC5665037 DOI: 10.7150/jca.19794] [Citation(s) in RCA: 53] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2017] [Accepted: 08/29/2017] [Indexed: 12/25/2022] Open
Abstract
Identification of the colorectal adenoma-carcinoma sequence with its corresponding genetic and epigenetic alterations has significantly increased our knowledge of the etiopathogenesis of colorectal cancer (CRC). However, the molecular mechanisms of colorectal carcinogenesis and metastasis haven't been clearly elucidated. Long non-coding ribonucleic acids (lncRNAs) are key participants of gene regulations rather than “noises”. Accumulative studies have implicated that the aberrant expressions of lncRNAs are tightly corelated to CRC screening, diagnosis, prognosis and therapeutic outcomes. Our review focuses on recent findings on the involvement of lncRNAs in CRC oncogenesis and the lncRNA-based clinical implications in patients with CRC.
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Affiliation(s)
- Yongzhi Yang
- Department of Colorectal Surgery, Fudan University Shanghai Cancer Center, Shanghai, 200032, China.,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, 200032, China
| | - Peng Junjie
- Department of Colorectal Surgery, Fudan University Shanghai Cancer Center, Shanghai, 200032, China.,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, 200032, China
| | - Cai Sanjun
- Department of Colorectal Surgery, Fudan University Shanghai Cancer Center, Shanghai, 200032, China.,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, 200032, China
| | - Yanlei Ma
- Department of Colorectal Surgery, Fudan University Shanghai Cancer Center, Shanghai, 200032, China.,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, 200032, China
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Yang Y, Du Y, Liu X, Cho WC. Involvement of Non-coding RNAs in the Signaling Pathways of Colorectal Cancer. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2017; 937:19-51. [PMID: 27573893 DOI: 10.1007/978-3-319-42059-2_2] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Colorectal cancer (CRC) is one of the most common diagnosed cancers worldwide. The metastasis and development of resistance to anti-cancer treatment are major challenges in the treatment of CRC. Understanding mechanisms underpinning the pathogenesis is therefore critical in developing novel agents for CRC treatments. A large number of evidence has demonstrated that non-coding RNAs (ncRNAs), including microRNAs (miRNAs), long non-coding RNAs (lncRNAs), and circular RNAs have functional roles in both the physiological and pathological processes by regulating the expression of their target genes. These molecules are engaged in the pathobiology of neoplastic diseases and are targets for the diagnosis, prognosis and therapy of a variety of cancers, including CRC. In this regard, ncRNAs have emerged as one of the hallmarks of CRC pathogenesis and they also play key roles in metastasis, drug resistance and the stemness of CRC stem cell by regulating various signaling networks. Therefore, a better understanding the ncRNAs involved in the signaling pathways of CRC may lead to the development of novel strategy for diagnosis, prognosis and treatment of CRC. In this chapter, we summarize the latest findings on ncRNAs, with a focus on miRNAs and lncRNAs involving in signaling networks and in the regulation of pathogenic signaling pathways in CRC.
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Affiliation(s)
- Yinxue Yang
- The General Hospital, Ningxia Medical University, Yinchuan, 750004, Ningxia, China
| | - Yong Du
- The General Hospital, Ningxia Medical University, Yinchuan, 750004, Ningxia, China
| | - Xiaoming Liu
- The General Hospital, Ningxia Medical University, Yinchuan, 750004, Ningxia, China
| | - William C Cho
- Department of Clinical Oncology, Queen Elizabeth Hospital, Hong Kong, China.
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Non-coding RNAs as Biomarkers for Colorectal Cancer Screening and Early Detection. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2017; 937:153-70. [PMID: 27573899 DOI: 10.1007/978-3-319-42059-2_8] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Early detection of colorectal cancer (CRC) is the key for prevention and the ability to impact long-term survival of CRC patients. Current CRC screening modalities are inadequate for global application because of low sensitivity and specificity in case of conventional stool-based screening tests, and high costs and a low participation compliance in colonoscopy. An accurate stool- or blood-based screening test with use of innovative biomarkers is an appealing alternative as it is non-invasive and poses minimal risk to patients. It is easy to perform, can be repeated at shorter intervals, and therefore would likely lead to a much higher compliance rates. Non-coding RNAs (ncRNAs) have recently gained attention because of their involvement in different biological processes, such as proliferation, differentiation, migration, angiogenesis and apoptosis. An increasing number of studies have demonstrated that mutations or abnormal expression of ncRNAs are closely associated with various cancers, including CRC. The discovery that ncRNAs (mainly microRNAs) are stable in stool and in blood plasma and serum presents the opportunity to develop novel strategies taking advantage of circulating ncRNAs as early diagnostic biomarkers of CRC. This chapter is a comprehensive examination of aberrant ncRNAs expression levels in tumor tissue, stool and blood of CRC patients and a summary of the current findings on ncRNAs, including microRNAs, small nucleolar RNAs, small nuclear RNAs, Piwi-interacting RNAs, circular RNAs and long ncRNAs in regards to their potential usage for screening or early detection of CRC.
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Fang C, Zan J, Yue B, Liu C, He C, Yan D. Long non-coding ribonucleic acid zinc finger antisense 1 promotes the progression of colonic cancer by modulating ZEB1 expression. J Gastroenterol Hepatol 2017; 32:1204-1211. [PMID: 27862275 DOI: 10.1111/jgh.13646] [Citation(s) in RCA: 51] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/24/2016] [Revised: 10/09/2016] [Accepted: 11/07/2016] [Indexed: 12/13/2022]
Abstract
BACKGROUND AND AIM Long non-coding RNA zinc finger antisense 1 (ZFAS1) is frequently amplified in hepatocellular carcinoma and promotes metastasis by increasing zinc finger E-box binding homeobox 1 (ZEB1), which can potentiate the progression of epithelial-to-mesenchymal transition (EMT). However, the expression pattern and role of ZFAS1 in colonic cancer remains unknown. The present study aimed to investigate the role of ZFAS1 and its clinical significance in colonic cancer. METHODS Paired clinical colonic cancer tissue samples and clinicopathologic characteristics of 73 patients were analyzed. Quantitative real-time polymerase chain reaction analysis was used to evaluate expression levels of ZFAS1 in colonic cancer tissues, cell lines, and plasma. ZEB1 and EMT-related markers expression levels also were explored. Cell biology assays were used to explore the biologic consequences of ZFAS1 in regulating cell proliferation and invasion, as well as the roles in regulating EMT. RESULTS Zinc finger antisense 1 was up-regulated in colonic cancer tissues compared with adjacent mucosa (P < 0.01), and its expression level was significantly correlated with TNM stage, vascular invasion, and lymph node metastasis (P < 0.05). ZFAS1 and ZEB1 were also increased in patients' plasma. Moreover, ZFAS1 promoted proliferation, invasion, and impeded apoptosis. Knockdown of ZFAS1 decreased expression of ZEB1 and increased the epithelial markers E-cadherin, ZO-1 while decreasing mesenchymal markers vimentin and N-cadherin. CONCLUSIONS Long non-coding RNA ZFAS1 may function as an oncogene by modulating ZEB1 to induce EMT. Manipulation of ZFAS1 level may be a novel approach to suppress colonic cancer progression. In addition, ZFAS1 in plasma has the potential to be a diagnostic biomarker of colonic cancer.
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Affiliation(s)
- Changyi Fang
- Department of General Surgery, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Jianbao Zan
- Department of General Surgery, Anqing Hospital Affiliated to Anhui Medical University, Anqing, China
| | - Ben Yue
- Department of General Surgery, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Chenchen Liu
- Department of General Surgery, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Chenglong He
- Department of General Surgery, Anqing Hospital Affiliated to Anhui Medical University, Anqing, China
| | - Dongwang Yan
- Department of General Surgery, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
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29
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Galanopoulos M, Tsoukalas N, Papanikolaou IS, Tolia M, Gazouli M, Mantzaris GJ. Abnormal DNA methylation as a cell-free circulating DNA biomarker for colorectal cancer detection: A review of literature. World J Gastrointest Oncol 2017; 9:142-152. [PMID: 28451061 PMCID: PMC5390299 DOI: 10.4251/wjgo.v9.i4.142] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/28/2016] [Revised: 12/28/2016] [Accepted: 03/12/2017] [Indexed: 02/05/2023] Open
Abstract
Colorectal cancer (CRC) is one of the most prevalent malignancies in the world. CRC-associated morbidity and mortality is continuously increasing, in part due to a lack of early detection. The existing screening tools such as colonoscopy, are invasive and yet high cost, affecting the willingness of patients to participate in screening programs. In recent years, evidence is accumulating that the interaction of aberrant genetic and epigenetic modifications is the cornerstone for the CRC development and progression by alternating the function of tumor suppressor genes, DNA repair genes and oncogenes of colonic cells. Apart from the understanding of the underlying mechanism(s) of carcinogenesis, the aforementioned interaction has also allowed identification of clinical biomarkers, especially epigenetic, for the early detection and prognosis of cancer patients. One of the ways to detect these epigenetic biomarkers is the cell-free circulating DNA (circDNA), a blood-based cancer diagnostic test, mainly focusing in the molecular alterations found in tumor cells, such as DNA mutations and DNA methylation. In this brief review, we epitomize the current knowledge on the research in circDNA biomarkers - mainly focusing on DNA methylation - as potential blood-based tests for early detection of colorectal cancer and the challenges for validation and globally implementation of this emergent technology.
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30
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Noncoding RNAs in the development, diagnosis, and prognosis of colorectal cancer. Transl Res 2017; 181:108-120. [PMID: 27810413 DOI: 10.1016/j.trsl.2016.10.001] [Citation(s) in RCA: 73] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/25/2016] [Revised: 09/29/2016] [Accepted: 10/06/2016] [Indexed: 12/17/2022]
Abstract
More than 90% of the human genome is actively transcribed, but less than 2% of the total genome encodes protein-coding RNA, and thus, noncoding RNA (ncRNA) is a major component of the human transcriptome. Recently, ncRNA was demonstrated to play important roles in multiple biological processes by directly or indirectly interfering with gene expression, and the dysregulation of ncRNA is associated with a variety of diseases, including cancer. In this review, we summarize the function and mechanism of miRNA, long intergenic ncRNA, and some other types of ncRNAs, such as small nucleolar RNA, circular ncRNA, pseudogene RNA, and even protein-coding mRNA, in the progression of colorectal cancer (CRC). We also presented their clinical application in the diagnosis and prognosis of CRC. The summary of the current state of ncRNA in CRC will contribute to our understanding of the complex processes of CRC initiation and development and will help in the discovery of novel biomarkers and therapeutic targets for CRC diagnosis and treatment.
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Wu W, Wagner EK, Hao Y, Rao X, Dai H, Han J, Chen J, Storniolo AMV, Liu Y, He C. Tissue-specific Co-expression of Long Non-coding and Coding RNAs Associated with Breast Cancer. Sci Rep 2016; 6:32731. [PMID: 27597120 PMCID: PMC5011741 DOI: 10.1038/srep32731] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2016] [Accepted: 08/12/2016] [Indexed: 02/01/2023] Open
Abstract
Inference of the biological roles of lncRNAs in breast cancer development remains a challenge. Here, we analyzed RNA-seq data in tumor and normal breast tissue samples from 18 breast cancer patients and 18 healthy controls and constructed a functional lncRNA-mRNA co-expression network. We revealed two distinctive co-expression patterns associated with breast cancer, reflecting different underlying regulatory mechanisms: (1) 516 pairs of lncRNA-mRNAs have differential co-expression pattern, in which the correlation between lncRNA and mRNA expression differs in tumor and normal breast tissue; (2) 291 pairs have dose-response co-expression pattern, in which the correlation is similar, but the expression level of lncRNA or mRNA differs in the two tissue types. We further validated our findings in TCGA dataset and annotated lncRNAs using TANRIC. One novel lncRNA, AC145110.1 on 8p12, was found differentially co-expressed with 127 mRNAs (including TOX4 and MAEL) in tumor and normal breast tissue and also highly correlated with breast cancer clinical outcomes. Functional enrichment and pathway analyses identified distinct biological functions for different patterns of co-expression regulations. Our data suggested that lncRNAs might be involved in breast tumorigenesis through the modulation of gene expression in multiple pathologic pathways.
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Affiliation(s)
- Wenting Wu
- Department of Epidemiology, Richard M. Fairbanks School of Public Health, Indiana University, Indianapolis, IN, USA
| | - Erin K. Wagner
- Department of Epidemiology, Richard M. Fairbanks School of Public Health, Indiana University, Indianapolis, IN, USA
| | - Yangyang Hao
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Xi Rao
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Hongji Dai
- Department of Epidemiology, Richard M. Fairbanks School of Public Health, Indiana University, Indianapolis, IN, USA
- Department of Epidemiology and Biostatistics, Tianjin Medical University Cancer Hospital and Institute, National Clinical Research Center for Cancer, Tianjin & Key Laboratory of Cancer Prevention and Therapy, Tianjin, China
| | - Jiali Han
- Department of Epidemiology, Richard M. Fairbanks School of Public Health, Indiana University, Indianapolis, IN, USA
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital, and Harvard Medical School, Boston, MA, USA
- Indiana University Melvin and Bren Simon Cancer Center, Indianapolis, IN, USA
| | - Jinhui Chen
- Spinal Cord and Brain Injury Research Group, Department of Neurosurgery, Stark Neuroscience Research Institute, Indiana University, Indianapolis, IN, USA
| | - Anna Maria V. Storniolo
- Susan G. Komen Tissue Bank at the Indiana University Melvin and Bren Simon Cancer Center, Indianapolis, IN, USA
| | - Yunlong Liu
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN, USA
- Center for Computational Biology and Bioinformatics, Indiana University, Indianapolis, IN 46202, USA
| | - Chunyan He
- Department of Epidemiology, Richard M. Fairbanks School of Public Health, Indiana University, Indianapolis, IN, USA
- Indiana University Melvin and Bren Simon Cancer Center, Indianapolis, IN, USA
- Center for Computational Biology and Bioinformatics, Indiana University, Indianapolis, IN 46202, USA
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Jiang X, Lei R, Ning Q. Circulating long noncoding RNAs as novel biomarkers of human diseases. Biomark Med 2016; 10:757-69. [PMID: 27347748 DOI: 10.2217/bmm-2016-0039] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Long noncoding RNAs (lncRNAs) are a kind of noncoding RNAs which are longer than ˜200 nucleotides, lacking of protein-encoding capacity and are implicated in the pathogenesis of various diseases. Recently, it was demonstrated that lncRNAs could be released into the circulation and be stable in blood. Circulating lncRNAs have been reported to have potential in distinguishing patients from healthy individuals. Therefore, the detection of circulating lncRNAs may be valuable for improving the diagnosis and prognosis of various diseases. This review summarized the current understanding of circulating lncRNAs as novel biomarkers of various human diseases, such as cancer, cardiovascular diseases, nervous system diseases and other diseases, which highlighted the significance of circulating lncRNAs as novel diagnostic and prognostic biomarkers of human diseases.
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Affiliation(s)
- Xiaoying Jiang
- Department of Biochemistry & Molecular Biology, School of Medicine, Xi'an Jiaotong University, Xi'an, 710061 Shaanxi, China
| | - Ronghui Lei
- Department of Biochemistry & Molecular Biology, School of Medicine, Xi'an Jiaotong University, Xi'an, 710061 Shaanxi, China
| | - Qilan Ning
- Department of Biochemistry & Molecular Biology, School of Medicine, Xi'an Jiaotong University, Xi'an, 710061 Shaanxi, China
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Guo W, Dong Z, Shi Y, Liu S, Liang J, Guo Y, Guo X, Shen S, Wang G. Methylation-mediated downregulation of long noncoding RNA LOC100130476 in gastric cardia adenocarcinoma. Clin Exp Metastasis 2016; 33:497-508. [PMID: 27189370 DOI: 10.1007/s10585-016-9794-x] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2015] [Accepted: 04/22/2016] [Indexed: 02/06/2023]
Abstract
Accumulating evidences indicate that long non-coding RNAs (lncRNAs) play important roles in several biological processes and dysregulated lncRNAs are involved in different kinds of cancer and are associated with carcinogenesis, metastasis, and prognosis of cancer. The role of a new lncRNA LOC100130476 in gastric cardia adenocarcinoma (GCA) has remained unknown. The present study investigated the role and methylation status of LOC100130476 in the pathogenesis of GCA, and further evaluated the potential prognostic role of LOC100130476 in GCA. Significant downregulation of LOC100130476 was detected in SGC-7901 and BGC-823 cell lines and primary GCA tissues. Methylation frequency of LOC100130476 was gradually increased from exon 1 to exon 2 both in tumor tissues and corresponding normal tissues; however, methylation status of region 1 closing to the transcription start site was more tumor-specific among the three regions examined. The findings of the association between LOC100130476 expression, methylation and TNM stage, pathological differentiation, and GCA patients' survival further identified the role of LOC100130476 as a tumor suppressor gene. Furthermore, the hypermethylation of LOC100130476 was also detected in peripheral white blood cells of GCA cases. Thus, LOC100130476 may be act as a tumor suppressor gene in GCA carcinogenesis and aberrant methylation at the CpG sites near the transcription start site within exon 1 may be critical for gene silencing. In addition, aberrant methylation of LOC100130476 in peripheral white blood cells and GCA tissues may be used as a potential valuable biomarker in GCA diagnosis and prognosis.
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Affiliation(s)
- Wei Guo
- Laboratory of Pathology, Hebei Cancer Institute, The Fourth Hospital of Hebei Medical University, Shijiazhuang, Hebei, China
| | - Zhiming Dong
- Laboratory of Pathology, Hebei Cancer Institute, The Fourth Hospital of Hebei Medical University, Shijiazhuang, Hebei, China
| | - Yabin Shi
- Laboratory of Pathology, Hebei Cancer Institute, The Fourth Hospital of Hebei Medical University, Shijiazhuang, Hebei, China
| | - Shengnan Liu
- Laboratory of Pathology, Hebei Cancer Institute, The Fourth Hospital of Hebei Medical University, Shijiazhuang, Hebei, China
| | - Jia Liang
- Laboratory of Pathology, Hebei Cancer Institute, The Fourth Hospital of Hebei Medical University, Shijiazhuang, Hebei, China
| | - Yanli Guo
- Laboratory of Pathology, Hebei Cancer Institute, The Fourth Hospital of Hebei Medical University, Shijiazhuang, Hebei, China
| | - Xin Guo
- Laboratory of Pathology, Hebei Cancer Institute, The Fourth Hospital of Hebei Medical University, Shijiazhuang, Hebei, China
| | - Supeng Shen
- Laboratory of Pathology, Hebei Cancer Institute, The Fourth Hospital of Hebei Medical University, Shijiazhuang, Hebei, China
| | - Guiying Wang
- Surgery Department, The Fourth Hospital of Hebei Medical University, Jiankang Road 12, Shijiazhuang, 050011, Hebei, China.
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A genomic screen for long noncoding RNA genes epigenetically silenced by aberrant DNA methylation in colorectal cancer. Sci Rep 2016; 6:26699. [PMID: 27215978 PMCID: PMC4877637 DOI: 10.1038/srep26699] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2015] [Accepted: 05/09/2016] [Indexed: 02/06/2023] Open
Abstract
Long noncoding RNAs (lncRNAs) have emerged as key components in multiple cellular processes, although their physiological and pathological functions are not fully understood. To identify cancer-related lncRNAs, we screened for those that are epigenetically silenced in colorectal cancer (CRC). Through a genome-wide analysis of histone modifications in CRC cells, we found that the transcription start sites (TSSs) of 1,027 lncRNA genes acquired trimethylation of histone H3 lysine 4 (H3K4me3) after DNA demethylation. Integrative analysis of chromatin signatures and the DNA methylome revealed that the promoter CpG islands (CGIs) of 66 lncRNA genes contained cancer-specific methylation. By validating the expression and methylation of lncRNA genes in CRC cells, we ultimately identified 20 lncRNAs, including ZNF582-AS1, as targets of epigenetic silencing in CRC. ZNF582-AS1 is frequently methylated in CRC cell lines (87.5%), primary CRCs (77.2%), colorectal adenomas (44.7%) and advanced adenomas (87.8%), suggesting that this methylation is an early event during colorectal tumorigenesis. Methylation of ZNF582-AS1 is associated with poor survival of CRC patients, and ectopic expression of ZNF582-AS1 suppressed colony formation by CRC cells. Our findings offer insight into the association between epigenetic alterations and lncRNA dysregulation in cancer and suggest that ZNF582-AS1 may be a novel tumor-suppressive lncRNA.
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Li B, Gan A, Chen X, Wang X, He W, Zhang X, Huang R, Zhou S, Song X, Xu A. Diagnostic Performance of DNA Hypermethylation Markers in Peripheral Blood for the Detection of Colorectal Cancer: A Meta-Analysis and Systematic Review. PLoS One 2016; 11:e0155095. [PMID: 27158984 PMCID: PMC4861294 DOI: 10.1371/journal.pone.0155095] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2016] [Accepted: 04/25/2016] [Indexed: 02/06/2023] Open
Abstract
DNA hypermethylation in blood is becoming an attractive candidate marker for colorectal cancer (CRC) detection. To assess the diagnostic accuracy of blood hypermethylation markers for CRC in different clinical settings, we conducted a meta-analysis of published reports. Of 485 publications obtained in the initial literature search, 39 studies were included in the meta-analysis. Hypermethylation markers in peripheral blood showed a high degree of accuracy for the detection of CRC. The summary sensitivity was 0.62 [95% confidence interval (CI), 0.56-0.67] and specificity was 0.91 (95% CI, 0.89-0.93). Subgroup analysis showed significantly greater sensitivity for the methylated Septin 9 gene (SEPT9) subgroup (0.75; 95% CI, 0.67-0.81) than for the non-methylated SEPT9 subgroup (0.58; 95% CI, 0.52-0.64). Sensitivity and specificity were not affected significantly by target gene number, CRC staging, study region, or methylation analysis method. These findings show that hypermethylation markers in blood are highly sensitive and specific for CRC detection, with methylated SEPT9 being particularly robust. The diagnostic performance of hypermethylation markers, which have varied across different studies, can be improved by marker optimization. Future research should examine variation in diagnostic accuracy according to non-neoplastic factors.
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Affiliation(s)
- Bingsheng Li
- Department of Gastroenterology, Huizhou First Hospital, Huizhou, 516003, China
| | - Aihua Gan
- Department of Gastroenterology, Huizhou First Hospital, Huizhou, 516003, China
| | - Xiaolong Chen
- Department of Gastroenterology, Hainan provincial people’s Hospital, Haikuo, 570100, China
| | - Xinying Wang
- Department of Gastroenterology, Nanfang Hospital, Southern Medical University, Guangzhou, 510515, China
| | - Weifeng He
- Department of Gastroenterology, Huizhou First Hospital, Huizhou, 516003, China
| | - Xiaohui Zhang
- Department of Gastroenterology, Huizhou First Hospital, Huizhou, 516003, China
| | - Renxiang Huang
- Huizhou Medicine Institute, Huizhou First Hospital, Huizhou, 516003, China
| | - Shuzhu Zhou
- Huizhou Medicine Institute, Huizhou First Hospital, Huizhou, 516003, China
| | - Xiaoxiao Song
- School of Public Health, Kunming Medical University, Kunming, 650500, China
| | - Angao Xu
- Huizhou Medicine Institute, Huizhou First Hospital, Huizhou, 516003, China
- * E-mail:
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Circulating Non-coding RNA as Biomarkers in Colorectal Cancer. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2016; 937:171-81. [DOI: 10.1007/978-3-319-42059-2_9] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
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Xue M, Lai SC, Xu ZP, Wang LJ. Noninvasive DNA methylation biomarkers in colorectal cancer: A systematic review. J Dig Dis 2015; 16:699-712. [PMID: 26565661 DOI: 10.1111/1751-2980.12299] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/23/2015] [Revised: 10/25/2015] [Accepted: 11/08/2015] [Indexed: 12/11/2022]
Abstract
OBJECTIVE To summarize the current evidence on the biomarkers associated with DNA methylation in the screening and diagnosis of colorectal cancer (CRC). METHODS A literature search was conducted on the databases of PubMed and Web of Science to identify articles published from 1 January 2000 to 6 June 2015 with language striction. Stuides focusing on the association between noninvasive biomarkers indicating DNA methylation and CRC were included. RESULTS Altogether 74 studies were finally included in the study. Varied genetic markers in the feces and blood samples were hypermethylated in patients with CRC than in the healthy controls. Some of them could even be detected at the early stage of the tumors. The sensitivity of the genetic markers was superior to that of fecal occult blood test and carcinoembryonic antigen. Multitarget DNA assays using a combination of different methylated genes could improve the diagnostic sensitivity. CONCLUSIONS Genetic markers might be minimally invasive, economical and accurate for the screening and surveillance of CRC. Large multicenter studies evaluating these biomarkers systematically and prospectively not only in CRC but also in other types of cancers are needed in the future.
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Affiliation(s)
- Meng Xue
- Department of Gastroenterology, The Second Affiliated Hospital, School of Medicine, Zhejiang University.,Institute of Gastroenterology, Zhejiang University
| | - San Chuan Lai
- Institute of Gastroenterology, Zhejiang University.,Department of Gastroenterology, Sir Run Run Shaw Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang Province, China
| | - Zhi Peng Xu
- Department of Gastroenterology, The Second Affiliated Hospital, School of Medicine, Zhejiang University
| | - Liang Jing Wang
- Department of Gastroenterology, The Second Affiliated Hospital, School of Medicine, Zhejiang University.,Institute of Gastroenterology, Zhejiang University
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Xue M, Wang LJ. Value of DNA methylation markers in colorectal cancer screening. Shijie Huaren Xiaohua Zazhi 2015; 23:4626-4635. [DOI: 10.11569/wcjd.v23.i29.4626] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Colorectal cancer (CRC) is one of the most common malignant tumors in the world. Recognizing CRC at an early stage by population-based screening is crucial in the prevention and treatment of CRC. Numerous candidate genes, which play important roles in the development and progression of CRC, have been found to be hyper-methylated in the promoter regions in recent studies. The promoter fragments of those hyper-methylated genes in tumor tissues have also been detected in the blood and fecal specimens, with higher sensitivity and specificity than traditional markers in the screening of CRC, including carcino-embryonic antigen (CEA) and fecal occult blood test. Here, we will discuss what we have already known about the DNA methylation markers for CRC screening and the potential research direction in the future.
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Fan H, Zhao H, Pang L, Liu L, Zhang G, Yu F, Liu T, Xu C, Xiao Y, Li X. Systematically Prioritizing Functional Differentially Methylated Regions (fDMRs) by Integrating Multi-omics Data in Colorectal Cancer. Sci Rep 2015; 5:12789. [PMID: 26239918 PMCID: PMC4523937 DOI: 10.1038/srep12789] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2015] [Accepted: 07/08/2015] [Indexed: 01/06/2023] Open
Abstract
While genome-wide differential DNA methylation regions (DMRs) have been extensively identified, the comprehensive prioritization of their functional importance is still poorly explored. Here, we aggregated multiple data resources rooted in the genome, epigenome and transcriptome to systematically prioritize functional DMRs (fDMRs) in colorectal cancer (CRC). As demonstrated, the top-ranked fDMRs from all of the data resources showed a strong enrichment for known methylated genes. Additionally, we analyzed those top 5% DMR-coupled coding genes using functional enrichment, which resulted in significant disease-related biological functions in contrast to the tail 5% genes. To further confirm the functional importance of the top-ranked fDMRs, we applied chromatin modification alterations of CRC cell lines to characterize their functional regulation. Specifically, we extended the utility of the top-ranked DMR-coupled genes to serve as classification and survival biomarkers, which showed a robust performance across diverse independent data sets. Collectively, our results established an integrative framework to prioritize fDMRs, which could help characterize aberrant DNA methylation-induced potential mechanisms underlying tumorigenesis and uncover epigenome-based biomarkers for clinical diagnosis and prognosis.
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Affiliation(s)
- Huihui Fan
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, Heilongjiang 150086, China
| | - Hongying Zhao
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, Heilongjiang 150086, China
| | - Lin Pang
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, Heilongjiang 150086, China
| | - Ling Liu
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, Heilongjiang 150086, China
| | - Guanxiong Zhang
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, Heilongjiang 150086, China
| | - Fulong Yu
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, Heilongjiang 150086, China
| | - Tingting Liu
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, Heilongjiang 150086, China
| | - Chaohan Xu
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, Heilongjiang 150086, China
| | - Yun Xiao
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, Heilongjiang 150086, China
| | - Xia Li
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, Heilongjiang 150086, China
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Warton K, Samimi G. Methylation of cell-free circulating DNA in the diagnosis of cancer. Front Mol Biosci 2015; 2:13. [PMID: 25988180 PMCID: PMC4428375 DOI: 10.3389/fmolb.2015.00013] [Citation(s) in RCA: 152] [Impact Index Per Article: 15.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2015] [Accepted: 04/07/2015] [Indexed: 01/04/2023] Open
Abstract
A range of molecular alterations found in tumor cells, such as DNA mutations and DNA methylation, is reflected in cell-free circulating DNA (circDNA) released from the tumor into the blood, thereby making circDNA an ideal candidate for the basis of a blood-based cancer diagnosis test. In many cancer types, mutations driving tumor development and progression are present in a wide range of oncogenes and tumor suppressor genes. However, even when a gene is consistently mutated in a particular cancer, the mutations can be spread over very large regions of its sequence, making evaluation difficult. This diversity of sequence changes in tumor DNA presents a challenge for the development of blood tests based on DNA mutations for cancer diagnosis. Unlike mutations, DNA methylation that can be consistently measured, as it tends to occur in specific regions of the DNA called CpG islands. Since DNA methylation is reflected within circDNA, detection of tumor-specific DNA methylation in patient plasma is a feasible approach for the development of a blood-based test. Aberrant circDNA methylation has been described in most cancer types and is actively being investigated for clinical applications. A commercial blood test for colorectal cancer based on the methylation of the SEPT9 promoter region in circDNA is under review for approval by the Federal Drug Administration (FDA) for clinical use. In this paper, we review the state of research in circDNA methylation as an application for blood-based diagnostic tests in colorectal, breast, lung, pancreatic and ovarian cancers, and we consider some of the future directions and challenges in this field. There are a number of potential circDNA biomarkers currently under investigation, and experience with SEPT9 shows that the time to clinical translation can be relatively rapid, supporting the promise of circDNA as a biomarker.
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Affiliation(s)
- Kristina Warton
- Garvan Institute of Medical Research, The Kinghorn Cancer Centre and St Vincent's Clinical School, University of New South Wales Sydney, NSW, Australia
| | - Goli Samimi
- Garvan Institute of Medical Research, The Kinghorn Cancer Centre and St Vincent's Clinical School, University of New South Wales Sydney, NSW, Australia
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