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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: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [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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102
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Liu Z, Chen Q, Hann SS. The functions and oncogenic roles of CCAT1 in human cancer. Biomed Pharmacother 2019; 115:108943. [PMID: 31078038 DOI: 10.1016/j.biopha.2019.108943] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2019] [Revised: 04/24/2019] [Accepted: 04/29/2019] [Indexed: 02/07/2023] Open
Abstract
In various human cancers, long non-coding RNAs (lncRNAs), a novel class of RNAs longer than 200 nucleotides without protein-coding potential, are implicated in a variety of biological processes, such as cell proliferation, invasion, metastasis, and apoptosis through regulation of gene expression at various levels including chromatin, splicing, transcriptional and post-transcriptional levels. However, the mechanisms underlying these are still elusive. Colon cancer-associated transcript 1(CCAT1) has received increased attention among those lncRNAs. Studies have shown high expression pattern and oncogenic role of CCAT1 in different types of cancer, and aberrant expression of CCAT1 has been involved in tumor-genesis, progression, metastasis, and patient survival via regulating different target genes and signaling pathways. In this review, we first introduce the concept, identification, and biological function of CCAT1; we then describe the mechanisms by which CCAT1 regulate the cancer proliferation and progression. In the last, we discuss emerging insights into the role of CCAT1 as potential biomarker and therapeutic target for novel treatment paradigms in cancer.
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Affiliation(s)
- Zheng Liu
- Laboratory of Tumor Biology, The Second Clinical Collage of Guangzhou University of Chinese Medicine, Guangzhou, Guangdong Province, 510120, China
| | - QianJun Chen
- Department of Mammary Diseases, The Second Clinical Collage of Guangzhou University of Chinese Medicine, Guangzhou, Guangdong Province, 510120, China.
| | - Swei Sunny Hann
- Laboratory of Tumor Biology, The Second Clinical Collage of Guangzhou University of Chinese Medicine, Guangzhou, Guangdong Province, 510120, China; Guangdong Provincial Key Laboratory of Clinical Research on Traditional Chinese Medicine Syndrome, The Second Clinical Collage of Guangzhou University of Chinese Medicine, Guangzhou, Guangdong Province, 510120, China.
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103
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Hashoul D, Shapira R, Falchenko M, Tepper O, Paviov V, Nissan A, Yavin E. Red-emitting FIT-PNAs: "On site" detection of RNA biomarkers in fresh human cancer tissues. Biosens Bioelectron 2019; 137:271-278. [PMID: 31121464 DOI: 10.1016/j.bios.2019.04.056] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2019] [Revised: 04/15/2019] [Accepted: 04/29/2019] [Indexed: 01/17/2023]
Abstract
To date, there are limited approaches for the direct and rapid visualization (on site) of tumor tissues for pathological assessment and for aiding cytoreductive surgery. Herein, we have designed FIT-PNAs (forced-intercalation-peptide nucleic acids) to detect two RNA cancer biomarkers. Firstly, a lncRNA (long noncoding RNA) termed CCAT1, has been shown as an oncogenic lncRNA over-expressed in a variety of cancers. The latter, an mRNA termed KRT20, has been shown to be over-expressed in metastases originating from colorectal cancer (CRC). To these FIT-PNAs, we have introduced the bis-quinoline (BisQ) cyanine dye that emits light in the red region (605-610 nm) of the visible spectrum. Most strikingly, spraying fresh human tissue taken from patients during cytoreductive surgery for peritoneal metastasis of colon cancer with an aqueous solution of CCAT1 FIT-PNA results in bright fluorescence in a matter of minutes. In fresh healthy tissue (from bariatric surgeries), no appreciable fluorescence is detected. In addition, a non-targeted FIT-PNA shows no fluorescent signal after spraying this FIT-PNA on fresh tumor tissue emphasizing the specificity of these molecular sensors. This study is the first to show on-site direct and immediate visualization of an RNA cancer biomarker on fresh human cancer tissues by topical application (spraying) of a molecular sensor.
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Affiliation(s)
- Dina Hashoul
- School of Pharmacy, Faculty of Medicine, The Hebrew University of Jerusalem, Hadassah Ein-Kerem, Jerusalem, 91120, Israel
| | - Rachel Shapira
- Department of General and Oncological Surgery, The Chaim Sheba Medical Center, Tel Hashomer, Israel
| | - Maria Falchenko
- School of Pharmacy, Faculty of Medicine, The Hebrew University of Jerusalem, Hadassah Ein-Kerem, Jerusalem, 91120, Israel
| | - Odelia Tepper
- School of Pharmacy, Faculty of Medicine, The Hebrew University of Jerusalem, Hadassah Ein-Kerem, Jerusalem, 91120, Israel
| | - Vera Paviov
- Department of General and Oncological Surgery, The Chaim Sheba Medical Center, Tel Hashomer, Israel
| | - Aviram Nissan
- Department of General and Oncological Surgery, The Chaim Sheba Medical Center, Tel Hashomer, Israel.
| | - Eylon Yavin
- School of Pharmacy, Faculty of Medicine, The Hebrew University of Jerusalem, Hadassah Ein-Kerem, Jerusalem, 91120, Israel.
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104
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Yang C, Pan Y, Deng SP. Downregulation of lncRNA CCAT1 enhances 5-fluorouracil sensitivity in human colon cancer cells. BMC Mol Cell Biol 2019; 20:9. [PMID: 31039730 PMCID: PMC6480879 DOI: 10.1186/s12860-019-0188-1] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2018] [Accepted: 03/19/2019] [Indexed: 01/22/2023] Open
Abstract
BACKGROUND The purpose of this study was to determine the aberrant expression of the long noncoding RNA (lncRNA) colon cancer-associated transcript 1 (CCAT1) in 5-fluorouracil-resistant colonic neoplasm cells and to elucidate its effects on the 5-fluorouracil sensitivity of human colonic neoplasm cells. The aberrant expression of lncRNAs in normal tissues and colonic neoplasm tissues was detected by microarray assay. qRT-PCR analysis was performed to assess CCAT1 expression levels in colonic neoplasm cell lines and corresponding normal tissues. After constructing the 5-FU-resistant cell lines and validating the resistance by measuring the IC50 value, the CCAT1 expression levels in parental and artificially resistant cell lines were determined by qRT-PCR. Transfection was used to modulate the expression of CCAT1. Cell proliferation and apoptosis were then detected by CCK-8 and flow cytometry, respectively. RESULTS CCAT1 in colon cancer tissues was higher than that in noncancer tissues, and the levels of CCAT1 in HCT 116, SW1417, HT-29, and KM12 cell lines were higher than those in the human normal colon epithelial NCM460 cell line. Moreover, the expression levels of CCAT1 were high in HCT 116/5-FU and HT-29/5-FU cell lines, whose apoptosis rates induced by 5-FU were lower than those in corresponding parental cells. The results of qRT-PCR and CCK-8 assay showed that enhancement of lncRNA CCAT1 expression levels in HCT 116 and HT-29 cell lines increased their IC50 of 5-FU and decreased their apoptosis rates. Meanwhile, siRNA-CCAT1 effectively inhibited the expression of CCAT1 and enhanced the 5-FU-sensitivity of HCT 116/5-FU and HT-29/5-FU, in which apoptosis rates were increased at the same time. CONCLUSIONS Downregulation of CCAT1 effectively reversed the resistance of HCT 116/5-FU and HT-29/5-FU cells to 5-FU chemotherapeutic, opening a new avenue in colon cancer therapy.
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Affiliation(s)
- Chun Yang
- Department of Gastrointestinal Surgery, Sichuan Academy of Medical Sciences & Sichuan Provincial People's Hospital, School of Medicine, University of Electronic Science and Technology, No.32 Western Section 2 Yihuan Road, Chengdu, 610072, Sichuan, China
| | - Yong Pan
- Department of Gastrointestinal Surgery, Sichuan Academy of Medical Sciences & Sichuan Provincial People's Hospital, School of Medicine, University of Electronic Science and Technology, No.32 Western Section 2 Yihuan Road, Chengdu, 610072, Sichuan, China.
| | - Shao Ping Deng
- Department of Gastrointestinal Surgery, Sichuan Academy of Medical Sciences & Sichuan Provincial People's Hospital, School of Medicine, University of Electronic Science and Technology, No.32 Western Section 2 Yihuan Road, Chengdu, 610072, Sichuan, China.
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105
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Ma D, Cao Y, Wang Z, He J, Chen H, Xiong H, Ren L, Shen C, Zhang X, Yan Y, Yan T, Guo F, Xuan B, Cui Z, Ye G, Fang JY, Chen H, Hong J. CCAT1 lncRNA Promotes Inflammatory Bowel Disease Malignancy by Destroying Intestinal Barrier via Downregulating miR-185-3p. Inflamm Bowel Dis 2019; 25:862-874. [PMID: 30615124 DOI: 10.1093/ibd/izy381] [Citation(s) in RCA: 45] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/24/2018] [Indexed: 01/17/2023]
Abstract
BACKGROUND The long noncoding RNA (lncRNA) colon cancer-associated transcript-1 (CCAT1) has been reported to play a vital role in the development of cancer. Although the link between inflammation and cancer initiation is well established, whether CCAT1 is involved in inflammation and promotes inflammatory bowel disease (IBD) malignancy remains undetermined. We aimed to investigate the expression of CCAT1 in IBD and the effect of CCAT1 overexpression on intestinal epithelial barrier function. METHODS The relationship between CCAT1 and the inflammation-related pathway was analyzed in both colorectal cancer (CRC) and IBD patients. Gene expression was detected by real-time polymerase chain reaction and Western blot. Transepithelial electrical resistance (TEER) and FD-4 flux measurement were used to test the effect of CCAT1 and miR-185-3p on intestinal epithelial barrier function. Luciferase assay was performed to validate the target site of miR-185-3p on 3'-UTR of MLCK mRNA. RESULTS Gene set enrichment analysis revealed that several inflammation-related genes were enriched in the CCAT1 high-expressed group of CRC patients. The relationship between CCAT1 and inflammation activation in IBD patients was further confirmed. CCAT1 expression positively correlated with MLCK, which acts as a protein kinase to phosphorylate myosin light chain and induces tight junction protein distribution, whereas it was negatively correlated with miR-185-3p in IBD tissues. We also determined that CCAT1 overexpression increased Caco-2 monolayer permeability and upregulated MLCK. Furthermore, CCAT1-induced MLCK overexpression and IBD disease progression were significantly attenuated by miR-185-3p. CONCLUSIONS The CCAT1/miR-185-3p/MLCK signaling pathway is strongly activated to destroy barrier function and promotes the pathogenesis of IBD.
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Affiliation(s)
- Dan Ma
- State Key Laboratory for Oncogenes and Related Genes, Key Laboratory of Gastroenterology & Hepatology, Ministry of Health, Division of Gastroenterology and Hepatology, Shanghai Cancer Institute, Shanghai Institute of Digestive Disease, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Yingying Cao
- State Key Laboratory for Oncogenes and Related Genes, Key Laboratory of Gastroenterology & Hepatology, Ministry of Health, Division of Gastroenterology and Hepatology, Shanghai Cancer Institute, Shanghai Institute of Digestive Disease, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Zhenhua Wang
- State Key Laboratory for Oncogenes and Related Genes, Key Laboratory of Gastroenterology & Hepatology, Ministry of Health, Division of Gastroenterology and Hepatology, Shanghai Cancer Institute, Shanghai Institute of Digestive Disease, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Jie He
- Department of Gastroenterology and Guangzhou Key Laboratory of Digestive Disease, Guangzhou Digestive Disease Center, Guangzhou First People's Hospital, School of Medicine, South China University of Technology, Guangdong, China
| | - Huimin Chen
- State Key Laboratory for Oncogenes and Related Genes, Key Laboratory of Gastroenterology & Hepatology, Ministry of Health, Division of Gastroenterology and Hepatology, Shanghai Cancer Institute, Shanghai Institute of Digestive Disease, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Hua Xiong
- State Key Laboratory for Oncogenes and Related Genes, Key Laboratory of Gastroenterology & Hepatology, Ministry of Health, Division of Gastroenterology and Hepatology, Shanghai Cancer Institute, Shanghai Institute of Digestive Disease, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Linlin Ren
- Department of Gastroenterology, the Affiliated Hospital of Qingdao University, Qingdao, China
| | - Chaoqin Shen
- State Key Laboratory for Oncogenes and Related Genes, Key Laboratory of Gastroenterology & Hepatology, Ministry of Health, Division of Gastroenterology and Hepatology, Shanghai Cancer Institute, Shanghai Institute of Digestive Disease, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Xinyu Zhang
- State Key Laboratory for Oncogenes and Related Genes, Key Laboratory of Gastroenterology & Hepatology, Ministry of Health, Division of Gastroenterology and Hepatology, Shanghai Cancer Institute, Shanghai Institute of Digestive Disease, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Yuqing Yan
- State Key Laboratory for Oncogenes and Related Genes, Key Laboratory of Gastroenterology & Hepatology, Ministry of Health, Division of Gastroenterology and Hepatology, Shanghai Cancer Institute, Shanghai Institute of Digestive Disease, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Tingting Yan
- State Key Laboratory for Oncogenes and Related Genes, Key Laboratory of Gastroenterology & Hepatology, Ministry of Health, Division of Gastroenterology and Hepatology, Shanghai Cancer Institute, Shanghai Institute of Digestive Disease, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Fangfang Guo
- State Key Laboratory for Oncogenes and Related Genes, Key Laboratory of Gastroenterology & Hepatology, Ministry of Health, Division of Gastroenterology and Hepatology, Shanghai Cancer Institute, Shanghai Institute of Digestive Disease, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Baoqin Xuan
- State Key Laboratory for Oncogenes and Related Genes, Key Laboratory of Gastroenterology & Hepatology, Ministry of Health, Division of Gastroenterology and Hepatology, Shanghai Cancer Institute, Shanghai Institute of Digestive Disease, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Zhe Cui
- Department of Gastrointestinal Surgery, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Guangyao Ye
- Department of Gastrointestinal Surgery, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Jing-Yuan Fang
- State Key Laboratory for Oncogenes and Related Genes, Key Laboratory of Gastroenterology & Hepatology, Ministry of Health, Division of Gastroenterology and Hepatology, Shanghai Cancer Institute, Shanghai Institute of Digestive Disease, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Haoyan Chen
- State Key Laboratory for Oncogenes and Related Genes, Key Laboratory of Gastroenterology & Hepatology, Ministry of Health, Division of Gastroenterology and Hepatology, Shanghai Cancer Institute, Shanghai Institute of Digestive Disease, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Jie Hong
- State Key Laboratory for Oncogenes and Related Genes, Key Laboratory of Gastroenterology & Hepatology, Ministry of Health, Division of Gastroenterology and Hepatology, Shanghai Cancer Institute, Shanghai Institute of Digestive Disease, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
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106
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Tang X, Qiao X, Chen C, Liu Y, Zhu J, Liu J. Regulation Mechanism of Long Noncoding RNAs in Colon Cancer Development and Progression. Yonsei Med J 2019; 60:319-325. [PMID: 30900417 PMCID: PMC6433576 DOI: 10.3349/ymj.2019.60.4.319] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/19/2018] [Revised: 01/23/2019] [Accepted: 01/24/2019] [Indexed: 12/24/2022] Open
Abstract
Colorectal cancer (CRC) is the second most common cause of cancer-related death worldwide, and its high rates of relapse and metastasis are associated with a poor prognosis. Despite extensive research, the underlying regulatory mechanisms of CRC remain unclear. Long noncoding RNAs (lncRNAs) are a major type of noncoding RNAs that have received increasing attention in the past few years, and studies have shown that they play a role in many biological processes in CRC. Here, we summarize recent studies on lncRNAs associated with CRC and the signaling pathways and mechanisms underlying this association. We show that dysregulated lncRNAs may be new prognostic and diagnostic biomarkers or therapeutic targets for clinical application. This review contributes not only to our understanding of CRC, but also suggests novel signaling pathways associated with lncRNAs that can be targeted to block or eradicate CRC.
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Affiliation(s)
- Xiaohuan Tang
- Department of Gastrointestinal Nutrition and Hernia Surgery, The Second Hospital of Jilin University, Changchun, China
| | - Xiaofang Qiao
- Department of Gastrointestinal Nutrition and Hernia Surgery, The Second Hospital of Jilin University, Changchun, China
| | - Chao Chen
- Department of Gastrointestinal Nutrition and Hernia Surgery, The Second Hospital of Jilin University, Changchun, China
| | - Yuanda Liu
- Department of Gastrointestinal Nutrition and Hernia Surgery, The Second Hospital of Jilin University, Changchun, China
| | - Jiaming Zhu
- Department of Gastrointestinal Nutrition and Hernia Surgery, The Second Hospital of Jilin University, Changchun, China.
| | - Jingjing Liu
- Department of Gastrointestinal Nutrition and Hernia Surgery, The Second Hospital of Jilin University, Changchun, China.
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107
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Sarfi M, Abbastabar M, Khalili E. Long noncoding RNAs biomarker-based cancer assessment. J Cell Physiol 2019; 234:16971-16986. [PMID: 30835829 DOI: 10.1002/jcp.28417] [Citation(s) in RCA: 62] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2018] [Revised: 02/04/2019] [Accepted: 02/14/2019] [Indexed: 12/18/2022]
Abstract
Cancer diagnosis have mainly relied on the incorporation of molecular biomarkers as part of routine diagnostic tool. The molecular alteration ranges from those involving DNA, RNA, noncoding RNAs (microRNAs and long noncoding RNAs [lncRNAs]) and proteins. lncRNAs are recently discovered noncoding endogenous RNAs that critically regulates the development, invasion, and metastasis of cancer cells. They are dysregulated in different types of malignancies and have the potential to serve as diagnostic markers for cancer. The expression of noncoding RNAs is altered following many diseases, and besides, some of them can be secreted from the cells into the circulation following the apoptotic and necrotic cell death. These secreted noncoding RNAs are known as cell free RNA. These RNAs can be secreted from the cell through the apoptotic body, extracellular vesicles including microvesicle and exosome, and bind to proteins. Since, lncRNAs display high organ and cell specificity, can be found in the blood, urine, tumor tissue, or other tissues or bodily fluids of some patients with cancer, this review summarizes the most significant and up-to-date findings of research on lncRNAs involvement in different cancers, focusing on the potential of cancer-related lncRNAs as biomarkers for diagnosis, prognosis, and therapy.
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Affiliation(s)
- Mohammad Sarfi
- Department of Clinical Biochemistry, School of Medicine, Tehran University of Medical Sciences, Tehran, Iran.,Students Scientific Research Center, Tehran University of Medical Sciences, Tehran, Iran
| | - Maryam Abbastabar
- Department of Clinical Biochemistry, School of Medicine, Tehran University of Medical Sciences, Tehran, Iran.,Students Scientific Research Center, Tehran University of Medical Sciences, Tehran, Iran
| | - Ehsan Khalili
- Department of Clinical Biochemistry, School of Medicine, Tehran University of Medical Sciences, Tehran, Iran
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108
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Farooqi AA, Fuentes-Mattei E, Fayyaz S, Raj P, Goblirsch M, Poltronieri P, Calin GA. Interplay between epigenetic abnormalities and deregulated expression of microRNAs in cancer. Semin Cancer Biol 2019; 58:47-55. [PMID: 30742906 DOI: 10.1016/j.semcancer.2019.02.003] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2018] [Revised: 01/23/2019] [Accepted: 02/07/2019] [Indexed: 02/07/2023]
Abstract
Epigenetic abnormalities and aberrant expression of non-coding RNAs are two emerging features of cancer cells, both of which are responsible for deregulated gene expression. In this review, we describe the interplay between the two. Specific themes include epigenetic silencing of tumor suppressor miRNAs, epigenetic activation of oncogenic miRNAs, epigenetic aberrations caused by miRNAs, and naturally occurring compounds which modulate miRNA expression through epigenetic mechanisms.
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Affiliation(s)
| | - Enrique Fuentes-Mattei
- Department of Experimental Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | | | - Priyank Raj
- Department of Experimental Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Matthew Goblirsch
- College of Science, Department of Chemistry & Biochemistry, University of Notre Dame, Notre Dame, IN 46556, USA
| | - Palmiro Poltronieri
- National Research Council Italy Institute of Sciences of Food Productions (CNR-ISPA), Via Lecce-Monteroni km 7, 73100 Lecce, Italy
| | - George A Calin
- Department of Experimental Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, TX, USA; Center for RNA Interference and Non-Coding RNAs, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.
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109
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Identification of marker genes and pathways specific to precancerous duodenal adenomas and early stage adenocarcinomas. J Gastroenterol 2019; 54:131-140. [PMID: 29951927 DOI: 10.1007/s00535-018-1489-4] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/07/2017] [Accepted: 06/22/2018] [Indexed: 02/04/2023]
Abstract
BACKGROUND The mechanism behind the pathogenesis and carcinogenesis of these neoplasms is not fully understood. The objective of this study was to identify genetic markers and pathways specific to precancerous duodenal adenomas and early stage adenocarcinomas through gene expression analysis. METHODS Gene expression profiling was performed in 4 pairs of duodenal adenoma/adenocarcinomas and corresponding matched normal tissue. Genes with consistent expression differences were identified and confirmed in 7 independent pairs. Gene set enrichment analysis (GSEA) was performed to characterize gene expression profiles of duodenal adenoma/adenocarcinomas, together with immunohistochemical staining of candidate oncogenic genes. RESULTS 626 probes consistently demonstrated over a twofold expression difference between tumor-normal pairs. Reverse transcriptase polymerase chain reaction of genes with the most prominent difference in expression between tumors and normal mucosa (KLK7, KLK6, CEMIP, MMP7, KRT17, LGR5, G6PC, S100G, APOA1) validated the results of gene expression analysis. GSEA demonstrated a strong association between duodenal adenoma/adenocarcinomas with colorectal adenomas (p < 10-5) and gene expression patterns seen after APC gene knockout (p < 10-5), suggesting that the Wnt/β-catenin pathway plays a crucial role in the carcinogenesis of these neoplasms. Immunohistochemical staining of an independent group of duodenal adenomas confirmed over-accumulation of β-catenin in 80.0% (16/20). CONCLUSIONS Precancerous duodenal adenomas and early stage adenocarcinomas demonstrate gene expression characteristics with a strong resemblance to colorectal adenomas. The results of this study strongly suggest that upregulation of the Wnt/β-catenin pathway is the major factor involved in the initial stages of the carcinogenesis of duodenal adenocarcinomas.
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110
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Carlevaro-Fita J, Polidori T, Das M, Navarro C, Zoller TI, Johnson R. Ancient exapted transposable elements promote nuclear enrichment of human long noncoding RNAs. Genome Res 2019. [PMID: 30587508 DOI: 10.1101/gr.229922.117.freely] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/24/2023]
Abstract
The sequence domains underlying long noncoding RNA (lncRNA) activities, including their characteristic nuclear enrichment, remain largely unknown. It has been proposed that these domains can originate from neofunctionalized fragments of transposable elements (TEs), otherwise known as RIDLs (repeat insertion domains of lncRNA), although just a handful have been identified. It is challenging to distinguish functional RIDL instances against a numerous genomic background of neutrally evolving TEs. We here show evidence that a subset of TE types experience evolutionary selection in the context of lncRNA exons. Together these comprise an enrichment group of 5374 TE fragments in 3566 loci. Their host lncRNAs tend to be functionally validated and associated with disease. This RIDL group was used to explore the relationship between TEs and lncRNA subcellular localization. By using global localization data from 10 human cell lines, we uncover a dose-dependent relationship between nuclear/cytoplasmic distribution and evolutionarily conserved L2b, MIRb, and MIRc elements. This is observed in multiple cell types and is unaffected by confounders of transcript length or expression. Experimental validation with engineered transgenes shows that these TEs drive nuclear enrichment in a natural sequence context. Together these data reveal a role for TEs in regulating the subcellular localization of lncRNAs.
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Affiliation(s)
- Joana Carlevaro-Fita
- Department for BioMedical Research (DBMR), University of Bern, 3008 Bern, Switzerland
- Department of Medical Oncology, Inselspital, University Hospital and University of Bern, 3010 Bern, Switzerland
- Graduate School of Cellular and Biomedical Sciences, University of Bern, 3012 Bern, Switzerland
| | - Taisia Polidori
- Department for BioMedical Research (DBMR), University of Bern, 3008 Bern, Switzerland
- Department of Medical Oncology, Inselspital, University Hospital and University of Bern, 3010 Bern, Switzerland
- Graduate School of Cellular and Biomedical Sciences, University of Bern, 3012 Bern, Switzerland
| | - Monalisa Das
- Department for BioMedical Research (DBMR), University of Bern, 3008 Bern, Switzerland
- Department of Medical Oncology, Inselspital, University Hospital and University of Bern, 3010 Bern, Switzerland
| | - Carmen Navarro
- Department of Computer Science and Artificial Intelligence, University of Granada, 18071 Granada, Spain
| | - Tatjana I Zoller
- Department for BioMedical Research (DBMR), University of Bern, 3008 Bern, Switzerland
- Department of Medical Oncology, Inselspital, University Hospital and University of Bern, 3010 Bern, Switzerland
| | - Rory Johnson
- Department for BioMedical Research (DBMR), University of Bern, 3008 Bern, Switzerland
- Department of Medical Oncology, Inselspital, University Hospital and University of Bern, 3010 Bern, Switzerland
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111
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Laneve P, Rea J, Caffarelli E. Long Noncoding RNAs: Emerging Players in Medulloblastoma. Front Pediatr 2019; 7:67. [PMID: 30923703 PMCID: PMC6426782 DOI: 10.3389/fped.2019.00067] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/08/2018] [Accepted: 02/18/2019] [Indexed: 01/02/2023] Open
Abstract
Central Nervous System tumors are the leading cause of cancer-related death in children, and medulloblastoma has the highest incidence rate. The current therapies achieve a 5-year survival rate of 50-80%, but often inflict severe secondary effects demanding the urgent development of novel, effective, and less toxic therapeutic strategies. Historically identified on a histopathological basis, medulloblastoma was later classified into four major subgroups-namely WNT, SHH, Group 3, and Group 4-each characterized by distinct transcriptional profiles, copy-number aberrations, somatic mutations, and clinical outcomes. Additional complexity was recently provided by integrating gene- and non-gene-based data, which indicates that each subclass can be further subdivided into specific subtypes. These deeper classifications, while getting over the typical tumor heterogeneity, indicate that different forms of medulloblastoma hold different molecular drivers that can be successfully exploited for a greater diagnostic accuracy and for the development of novel, targeted treatments. Long noncoding RNAs are transcripts that lack coding potential and play relevant roles as regulators of gene expression in mammalian differentiation and developmental processes. Their cell type- and tissue-specificity, higher than mRNAs, make them more informative about cell- type identity than protein-coding genes. Remarkably, about 40% of long noncoding RNAs are expressed in the brain and their aberrant expression has been linked to neuro-oncological disorders. However, while their involvement in gliomas and neuroblastomas has been extensively studied, their role in medulloblastoma is still poorly explored. Here, we present an overview of current knowledge regarding the function played by long noncoding RNAs in medulloblastoma biology.
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Affiliation(s)
- Pietro Laneve
- Institute of Molecular Biology and Pathology, National Research Council, Rome, Italy
| | - Jessica Rea
- Department of Biology and Biotechnology, Sapienza University of Rome, Rome, Italy
| | - Elisa Caffarelli
- Institute of Molecular Biology and Pathology, National Research Council, Rome, Italy
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112
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Carlevaro-Fita J, Polidori T, Das M, Navarro C, Zoller TI, Johnson R. Ancient exapted transposable elements promote nuclear enrichment of human long noncoding RNAs. Genome Res 2018; 29:208-222. [PMID: 30587508 PMCID: PMC6360812 DOI: 10.1101/gr.229922.117] [Citation(s) in RCA: 50] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2018] [Accepted: 12/18/2018] [Indexed: 01/02/2023]
Abstract
The sequence domains underlying long noncoding RNA (lncRNA) activities, including their characteristic nuclear enrichment, remain largely unknown. It has been proposed that these domains can originate from neofunctionalized fragments of transposable elements (TEs), otherwise known as RIDLs (repeat insertion domains of lncRNA), although just a handful have been identified. It is challenging to distinguish functional RIDL instances against a numerous genomic background of neutrally evolving TEs. We here show evidence that a subset of TE types experience evolutionary selection in the context of lncRNA exons. Together these comprise an enrichment group of 5374 TE fragments in 3566 loci. Their host lncRNAs tend to be functionally validated and associated with disease. This RIDL group was used to explore the relationship between TEs and lncRNA subcellular localization. By using global localization data from 10 human cell lines, we uncover a dose-dependent relationship between nuclear/cytoplasmic distribution and evolutionarily conserved L2b, MIRb, and MIRc elements. This is observed in multiple cell types and is unaffected by confounders of transcript length or expression. Experimental validation with engineered transgenes shows that these TEs drive nuclear enrichment in a natural sequence context. Together these data reveal a role for TEs in regulating the subcellular localization of lncRNAs.
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Affiliation(s)
- Joana Carlevaro-Fita
- Department for BioMedical Research (DBMR), University of Bern, 3008 Bern, Switzerland.,Department of Medical Oncology, Inselspital, University Hospital and University of Bern, 3010 Bern, Switzerland.,Graduate School of Cellular and Biomedical Sciences, University of Bern, 3012 Bern, Switzerland
| | - Taisia Polidori
- Department for BioMedical Research (DBMR), University of Bern, 3008 Bern, Switzerland.,Department of Medical Oncology, Inselspital, University Hospital and University of Bern, 3010 Bern, Switzerland.,Graduate School of Cellular and Biomedical Sciences, University of Bern, 3012 Bern, Switzerland
| | - Monalisa Das
- Department for BioMedical Research (DBMR), University of Bern, 3008 Bern, Switzerland.,Department of Medical Oncology, Inselspital, University Hospital and University of Bern, 3010 Bern, Switzerland
| | - Carmen Navarro
- Department of Computer Science and Artificial Intelligence, University of Granada, 18071 Granada, Spain
| | - Tatjana I Zoller
- Department for BioMedical Research (DBMR), University of Bern, 3008 Bern, Switzerland.,Department of Medical Oncology, Inselspital, University Hospital and University of Bern, 3010 Bern, Switzerland
| | - Rory Johnson
- Department for BioMedical Research (DBMR), University of Bern, 3008 Bern, Switzerland.,Department of Medical Oncology, Inselspital, University Hospital and University of Bern, 3010 Bern, Switzerland
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113
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Wang N, Yu Y, Xu B, Zhang M, Li Q, Miao L. Pivotal prognostic and diagnostic role of the long non‑coding RNA colon cancer‑associated transcript 1 expression in human cancer (Review). Mol Med Rep 2018; 19:771-782. [PMID: 30535444 PMCID: PMC6323215 DOI: 10.3892/mmr.2018.9721] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2018] [Accepted: 10/30/2018] [Indexed: 01/17/2023] Open
Abstract
Long non‑coding RNAs (lncRNAs) have been classically defined as regulatory RNA members >200 nucleotides in length, without detectable open‑reading frames to encode proteins. Previous studies have demonstrated that lncRNAs serve critical roles in multiple cancer types. Colon cancer‑associated transcript 1 (CCAT1), a novel cancer‑associated lncRNA, is significantly overexpressed in a number of malignancies. Functionally, as an oncogenic lncRNA, CCAT1 is involved in proliferation, migration, cell cycle progression, apoptosis, chemoresistance and other biological processes of cancer cells through complex regulation mechanisms in the cytoplasm or nucleus. In clinical applications, CCAT1 is additionally positively associated with histological differentiation, tumour node metastasis stage, vascular invasion, overall survival and recurrence‑free survival, which demonstrates its important role as a diagnostic and prognostic marker in cancer. The present review summarises the current research progress of the oncogenic potential and clinical uses of CCAT1 in various human cancer types.
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Affiliation(s)
- Ni Wang
- Medical Center for Digestive Diseases, Second Affiliated Hospital, Nanjing Medical University, Nanjing, Jiangsu 21001, P.R. China
| | - Yang Yu
- Medical Center for Digestive Diseases, Second Affiliated Hospital, Nanjing Medical University, Nanjing, Jiangsu 21001, P.R. China
| | - Boming Xu
- Department of Gastroenterology, The Quanzhou First Hospital Affiliated to Fujian Medical University, Quanzhou, Fujian 362000, P.R. China
| | - Mingjiong Zhang
- Medical Center for Digestive Diseases, Second Affiliated Hospital, Nanjing Medical University, Nanjing, Jiangsu 21001, P.R. China
| | - Quanpeng Li
- Medical Center for Digestive Diseases, Second Affiliated Hospital, Nanjing Medical University, Nanjing, Jiangsu 21001, P.R. China
| | - Lin Miao
- Medical Center for Digestive Diseases, Second Affiliated Hospital, Nanjing Medical University, Nanjing, Jiangsu 21001, P.R. China
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Fanelli GN, Gasparini P, Coati I, Cui R, Pakula H, Chowdhury B, Valeri N, Loupakis F, Kupcinskas J, Cappellesso R, Fassan M. LONG-NONCODING RNAs in gastroesophageal cancers. Noncoding RNA Res 2018; 3:195-212. [PMID: 30533569 PMCID: PMC6257886 DOI: 10.1016/j.ncrna.2018.10.001] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2018] [Revised: 10/26/2018] [Accepted: 10/26/2018] [Indexed: 02/07/2023] Open
Abstract
Despite continuing improvements in multimodal therapies, gastro-esophageal malignances remain widely prevalent in the population and is characterized by poor overall and disease-free survival rates. Due to the lack of understanding about the pathogenesis and absence of reliable markers, gastro-esophageal cancers are associated with delayed diagnosis. The increasing understanding about cancer's molecular landscape in the recent years, offers the possibility of identifying 'targetable' molecular events and in particular facilitates novel treatment strategies and development of biomarkers for early stage diagnosis. At least 98% of our genome is actively transcribed into non-coding RNAs encompassing long non-coding RNAs (lncRNAs) constituted of transcripts longer than 200 nucleotides with no protein-coding capacity. Many studies have demonstrated that lncRNAs are functional genomic elements playing pivotal roles in main oncogenic processes. LncRNA can act at multiple levels developing a complex molecular network that can modulate directly or indirectly the expression of genes involved in tumorigenesis. In this review, we focus on lncRNAs as emerging players in gastro-esophageal carcinogenesis and critically assess their potential as reliable noninvasive biomarkers and in next generation targeted therapies.
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Affiliation(s)
- Giuseppe Nicolò Fanelli
- Department of Medicine (DIMED), Surgical Pathology & Cytopathology Unit, University of Padua, Padua, PD, Italy
- Department of Oncologic Pathology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Pierluigi Gasparini
- Department of Cancer Biology and Genetics, College of Medicine, The Ohio State University Comprehensive Cancer Center, Columbus, OH, USA
| | - Irene Coati
- Department of Medicine (DIMED), Surgical Pathology & Cytopathology Unit, University of Padua, Padua, PD, Italy
| | - Ri Cui
- Department of Cancer Biology and Genetics, College of Medicine, The Ohio State University Comprehensive Cancer Center, Columbus, OH, USA
- School of Pharmaceutical Sciences, Wenzhou Medical University, Wenzhou, Zhejiang, China
| | - Hubert Pakula
- Department of Oncologic Pathology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Basudev Chowdhury
- Department of Oncologic Pathology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Nicola Valeri
- Division of Molecular Pathology, The Institute of Cancer Research, London, UK
- Department of Medicine, The Royal Marsden NHS Trust, London, UK
| | - Fotios Loupakis
- Oncology Unit, Istituto Oncologico Veneto, IOV-IRCCS, Padua, PD, Italy
| | - Juozas Kupcinskas
- Department of Gastroenterology and Institute for Digestive Research, Lithuanian University of Health Sciences, Kaunas, Lithuania
| | - Rocco Cappellesso
- Department of Medicine (DIMED), Surgical Pathology & Cytopathology Unit, University of Padua, Padua, PD, Italy
| | - Matteo Fassan
- Department of Medicine (DIMED), Surgical Pathology & Cytopathology Unit, University of Padua, Padua, PD, Italy
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CX-3543 Promotes Cell Apoptosis through Downregulation of CCAT1 in Colon Cancer Cells. BIOMED RESEARCH INTERNATIONAL 2018; 2018:9701957. [PMID: 30519593 PMCID: PMC6241339 DOI: 10.1155/2018/9701957] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/26/2018] [Revised: 09/04/2018] [Accepted: 10/08/2018] [Indexed: 01/17/2023]
Abstract
Aim Colon cancer-associated transcript-1 (CCAT1), located in the vicinity of transcription factor c-Myc, was first identified in colon cancer. A small-molecule compound CX3543 (Quarfloxin) selectively targeting Myc G-quadruplexes has entered phase II clinical trials for neuroendocrine carcinomas. The aim of the study was to explore the relationship between CX3543, CCAT1, and cell apoptosis in colon cancer cells. Methods Semiquantitative PCR was used to detect the relative expression of CCAT1 in colon cancer (CC) tissues and HT29 cell lines. Real-time PCR (RT-PCR) was also used to investigate the expression of CCAT1 and c-Myc after HT29 cells being treated by CX3543 for 24 h. Cell apoptosis assay and cell proliferation assay were conducted in HT29 cells after being treated by CX3543. Results The results showed that the expression of CCAT1 was remarkably increased in CC tissues and HT29 cells compared to controls. CX3543 treatment reduced the expression of c-Myc and CCAT1 and promoted cell apoptosis and inhibited cell proliferation. After the expression of CCAT1 was inhibited by sh-CCAT1 transfection, the cell apoptosis rate was higher than that of control group. After the cells were treated by CCAT1 overexpression plasmid transfection and CX3543, the cell apoptosis rate was lower than that of control group. In vivo results showed that CX3543 inhibited the xenograft tumor growth of rats through downregulation of CCAT1. Conclusion Our study demonstrated that CX3543 could inhibit the progression of colon cancer by downregulating CCAT1 expression and might be a potential drug for the treatment of colon cancer.
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Zare K, Shademan M, Ghahramani Seno MM, Dehghani H. CRISPR/Cas9 Knockout Strategies to Ablate CCAT1 lncRNA Gene in Cancer Cells. Biol Proced Online 2018; 20:21. [PMID: 30410426 PMCID: PMC6211572 DOI: 10.1186/s12575-018-0086-5] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2018] [Accepted: 10/11/2018] [Indexed: 02/01/2023] Open
Abstract
Background With the increasing discovery of long noncoding RNAs (lncRNAs), the application of functional techniques that could have very specific, efficient, and robust effects and readouts is necessary. Here, we have applied and analyzed three gene knockout (KO) strategies to ablate the CCAT1 gene in different colorectal adenocarcinoma cell lines. We refer to these strategies as “CRISPR excision”, “CRISPR HDR”, and “CRISPR du-HITI”. Results In order to obstruct the transcription of lncRNA or to alter its structure, in these strategies either a significant segment of the gene is removed, or a transcription termination signal is inserted in the target gene. We use RT-qPCR, RNA-seq, MTT, and colony formation assay to confirm the functional effects of CCAT1 gene ablation in knockout colorectal adenocarcinoma cell lines. We applied three different CRISPR/Cas9 mediated knockout strategies to abolish the transcription of CCAT1 lncRNA. CCAT1 knockout cells displayed dysregulation of genes involved in several biological processes, and a significant reduction for anchorage-independent growth. The du-HITI strategy introduced in this study removes a gene segment and inserts a reporter and a transcription termination signal in each of the two target alleles. The preparation of donor vector for this strategy is much easier than that in “CRISPR HDR”, and the selection of cells in this strategy is also much more practical than that in “CRISPR excision”. In addition, use of this technique in the first attempt of transfection, generates single cell knockouts for both alleles. Conclusions The strategies applied and introduced in this study can be used for the generation of CCAT1 knockout cell lines and in principle can be applied to the deletion of other lncRNAs for the study of their function. Electronic supplementary material The online version of this article (10.1186/s12575-018-0086-5) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Khadijeh Zare
- 1Department of Basic Sciences, Faculty of Veterinary Medicine, Ferdowsi University of Mashhad, Azadi Square, Mashhad, Iran
| | - Milad Shademan
- 1Department of Basic Sciences, Faculty of Veterinary Medicine, Ferdowsi University of Mashhad, Azadi Square, Mashhad, Iran
| | - Mohammad M Ghahramani Seno
- 1Department of Basic Sciences, Faculty of Veterinary Medicine, Ferdowsi University of Mashhad, Azadi Square, Mashhad, Iran.,2Division of Biotechnology, Faculty of Veterinary Medicine, Ferdowsi University of Mashhad, Azadi Square, Mashhad, Iran
| | - Hesam Dehghani
- 1Department of Basic Sciences, Faculty of Veterinary Medicine, Ferdowsi University of Mashhad, Azadi Square, Mashhad, Iran.,2Division of Biotechnology, Faculty of Veterinary Medicine, Ferdowsi University of Mashhad, Azadi Square, Mashhad, Iran.,3Stem Cell Biology and Regenerative Medicine Research Group, Research Institute of Biotechnology, Ferdowsi University of Mashhad, Azadi Square, Mashhad, Iran
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Identification of abnormally expressed lncRNAs induced by PM2.5 in human bronchial epithelial cells. Biosci Rep 2018; 38:BSR20171577. [PMID: 29899163 PMCID: PMC6131355 DOI: 10.1042/bsr20171577] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2017] [Revised: 05/21/2018] [Accepted: 06/11/2018] [Indexed: 01/17/2023] Open
Abstract
To investigate the effect of stimulation of human bronchial epithelial cells (HBECs) by arterial traffic ambient PM2.5 (TAPM2.5) and wood smoke PM2.5 (WSPM2.5) on the expression of long non-coding RNAs (lncRNAs) in order to find new therapeutic targets for treatment of chronic obstructive pulmonary disease (COPD). HBECs were exposed to TAPM2.5 and WSPM2.5 at a series of concentrations. The microarray analysis was used to detect the lncRNA and mRNA expression profiles. Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis and gene ontology (GO) enrichment were conducted to analyze the differentially expressed lncRNAs and mRNAs. Quantitative real-time PCR (qRT-PCR) was performed to confirm the differential expression of lncRNAs. Western blot was performed to study the expression of autophagy and apoptosis-associated proteins. Flow cytometry was used to detect the apoptotic cells. The results indicated that fine particulate matter (PM2.5)-induced cell damage of HBECs occurred in a dose-dependent manner. The microarray analysis indicated that treatment with TAPM2.5 and WSPM2.5 led to the alteration of lncRNA and mRNA expression profiles. LncRNA maternally expressed gene 3 (MEG3) was significantly up-regulated in HBECs after PM2.5 treatment. The results of Western blot showed that PM2.5 induced cell apoptosis and autophagy by up-regulating apoptosis-associated gene, caspase-3, and down-regulating autophagy-associated markers, Bcl-2 and LC3 expression. In addition, we demonstrated that TAPM2.5 and WSPM2.5 accelerated apoptosis of human bronchial (HBE) cells, silencing of MEG3 suppressed apoptosis and autophagy of HBE cells. These findings suggested that the lncRNA MEG3 mediates PM2.5-induced cell apoptosis and autophagy, and probably through regulating the expression of p53.
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Fang H, Liu HM, Wu WH, Liu H, Pan Y, Li WJ. Upregulation of long noncoding RNA CCAT1-L promotes epithelial-mesenchymal transition in gastric adenocarcinoma. Onco Targets Ther 2018; 11:5647-5655. [PMID: 30254457 PMCID: PMC6141104 DOI: 10.2147/ott.s170553] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
Objective In this study, we aimed to investigate the role of a long-chain noncoding RNA, colorectal cancer-associated transcript 1-long (CCAT1-L) in gastric adenocarcinoma. Patients and methods Expressions of CCAT1-L and c-MYC mRNA and MYC protein in gastric adenocarcinoma tissue and adjacent normal tissues of 60 patients were analyzed using quantitative real-time polymerase chain reaction and Western blot, respectively. The CCAT1-L levels in the normal gastric epithelial cell line, GES1, and human gastric adenocarcinoma cell lines, MGC803, MKN-28, SGC7901, and BGC823 were analyzed by quantitative real-time polymerase chain reaction. CCAT1-L knockdown in MGC803 and MKN28 cells was performed using RNA interference, followed by evaluating cell proliferation, invasion, and migration with soft agar colony formation assay, scratch wound assay, and transwell assay. Twenty BALB/C-nu-nu nude mice were inoculated with gastric tumor xenografts and treated with CCAT1-L small-interfering RNA (siRNA), followed by monitoring survival and tumor growth. Western blot was also used to analyze the expression of epithelial–mesenchymal transition-related proteins, including MYC, RAS, T-ERK, P-ERK, E-cadherin, and vimentin, in gastric adenocarcinoma MKN-28 cells. Results The expression of CCAT1-L and MYC in tumor tissue was significantly higher than that in adjacent normal tissues (P<0.001). There was a positive correlation between the expression level of CCAT1-L mRNA and c-MYC mRNA (r=0.863, P<0.001). CCAT1-L expression was also significantly higher in gastric adenocarcinoma cell lines than that in normal cell lines (P<0.01). Knockdown of CCAT1-L in MGC803 and MKN-28 cells markedly reduced the cell proliferation, migration, and invasion (P<0.001). CCAT1-L knockdown also evidently inhibited tumor growth and improved survival in nude mice (P<0.001). Expressions of MYC, RAS, and vimentin, and the phosphorylation of ERK protein were dramatically decreased, while the expression of E-cadherin protein was increased by CCAT1-L knockdown in MKN-28 cell. Conclusion CCAT1-L is a pro-oncogenic marker in gastric adenocarcinoma. CCAT1-L knockdown inhibits epithelial–mesenchymal transition of gastric adenocarcinoma cells and thus suppresses the gastric adenocarcinoma metastasis.
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Affiliation(s)
- Hua Fang
- Department of Oncology, Fuxing Hospital, Capital Medical University, Beijing 100038, China
| | - Hui-Min Liu
- Department of Gastroenterology, The Affiliated Yantai Yuhuangding Hospital of Qingdao University, Yantai 264000, China
| | - Wei-Hua Wu
- Department of Oncology, Beijing Chest Hospital, Capital Medical University, Beijing 100038, China
| | - Han Liu
- Department of Oncology, Fuxing Hospital, Capital Medical University, Beijing 100038, China
| | - Yong Pan
- Department of Oncology, Fuxing Hospital, Capital Medical University, Beijing 100038, China
| | - Wen-Jun Li
- Department of Thoracic Surgery, The Affiliated Yantai Yuhuangding Hospital of Qingdao University, Yantai 264000, China,
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Co-activation of super-enhancer-driven CCAT1 by TP63 and SOX2 promotes squamous cancer progression. Nat Commun 2018; 9:3619. [PMID: 30190462 PMCID: PMC6127298 DOI: 10.1038/s41467-018-06081-9] [Citation(s) in RCA: 153] [Impact Index Per Article: 25.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2018] [Accepted: 08/13/2018] [Indexed: 01/17/2023] Open
Abstract
Squamous cell carcinomas (SCCs) are aggressive malignancies. Previous report demonstrated that master transcription factors (TFs) TP63 and SOX2 exhibited overlapping genomic occupancy in SCCs. However, functional consequence of their frequent co-localization at super-enhancers remains incompletely understood. Here, epigenomic profilings of different types of SCCs reveal that TP63 and SOX2 cooperatively and lineage-specifically regulate long non-coding RNA (lncRNA) CCAT1 expression, through activation of its super-enhancers and promoter. Silencing of CCAT1 substantially reduces cellular growth both in vitro and in vivo, phenotyping the effect of inhibiting either TP63 or SOX2. ChIRP analysis shows that CCAT1 forms a complex with TP63 and SOX2, which regulates EGFR expression by binding to the super-enhancers of EGFR, thereby activating both MEK/ERK1/2 and PI3K/AKT signaling pathways. These results together identify a SCC-specific DNA/RNA/protein complex which activates TP63/SOX2-CCAT1-EGFR cascade and promotes SCC tumorigenesis, advancing our understanding of transcription dysregulation in cancer biology mediated by master TFs and super-enhancers. Master regulator transcription factors TP63 and SOX2 have been reported to overlap in genomic occupancy in squamous cell carcinomas (SCCs). Here, the authors demonstrate that TP63 and SOX2 promote co-operatively long non-coding RNA CCAT1 expression through activating its super-enhancer, and CCAT1 forms a complex with TP63 and SOX2, which regulates EGFR super-enhancers and enhances both the MEK/ERK1/2 and PI3K/AKT signaling pathways in SCC.
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Barbagallo C, Brex D, Caponnetto A, Cirnigliaro M, Scalia M, Magnano A, Caltabiano R, Barbagallo D, Biondi A, Cappellani A, Basile F, Di Pietro C, Purrello M, Ragusa M. LncRNA UCA1, Upregulated in CRC Biopsies and Downregulated in Serum Exosomes, Controls mRNA Expression by RNA-RNA Interactions. MOLECULAR THERAPY-NUCLEIC ACIDS 2018; 12:229-241. [PMID: 30195762 PMCID: PMC6023947 DOI: 10.1016/j.omtn.2018.05.009] [Citation(s) in RCA: 149] [Impact Index Per Article: 24.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/26/2018] [Revised: 05/10/2018] [Accepted: 05/11/2018] [Indexed: 02/07/2023]
Abstract
Long non-coding RNAs (lncRNAs) and circular RNAs (circRNAs) contribute to the onset of many neoplasias through RNA-RNA competitive interactions; in addition, they could be secreted by cancer cells into biological fluids, suggesting their potential diagnostic application. By analyzing the expression of 17 lncRNAs and 31 circRNAs in biopsies and serum exosomes from colorectal cancer (CRC) patients through qRT-PCR, we detected CCAT1, CCAT2, HOTAIR, and UCA1 upregulation and CDR1AS, MALAT1, and TUG1 downregulation in biopsies. In serum exosomes, UCA1 was downregulated, while circHIPK3 and TUG1 were upregulated. Combined receiver operating characteristic (ROC) curves of TUG1:UCA1 and circHIPK3:UCA1 showed high values of sensitivity and specificity. Through in vitro (i.e., RNA silencing and mitogen-activated protein kinase [MAPK] inhibition) and in silico analyses (i.e., expression correlation and RNA-RNA-binding prediction), we found that UCA1 could (1) be controlled by MAPKs through CEBPB; (2) sequester miR-135a, miR-143, miR-214, and miR-1271, protecting ANLN, BIRC5, IPO7, KIF2A, and KIF23 from microRNA (miRNA)-induced degradation; and (3) interact with mRNA 3'-UTRs, preventing miRNA binding. UCA1 and its co-regulated antisense LINC01764 could interact and reciprocally mask their own miRNA-binding sites. Functional enrichment analysis of the RNA-RNA network controlled by UCA1 suggested its potential involvement in cellular migration. The UCA1 regulatory axis would represent a promising target to develop innovative RNA-based therapeutics against CRC.
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Affiliation(s)
- Cristina Barbagallo
- Department of Biomedical and Biotechnological Sciences, Section of Biology and Genetics G. Sichel, University of Catania, Catania 95123, Italy
| | - Duilia Brex
- Department of Biomedical and Biotechnological Sciences, Section of Biology and Genetics G. Sichel, University of Catania, Catania 95123, Italy
| | - Angela Caponnetto
- Department of Biomedical and Biotechnological Sciences, Section of Biology and Genetics G. Sichel, University of Catania, Catania 95123, Italy
| | - Matilde Cirnigliaro
- Department of Biomedical and Biotechnological Sciences, Section of Biology and Genetics G. Sichel, University of Catania, Catania 95123, Italy
| | - Marina Scalia
- Department of Biomedical and Biotechnological Sciences, Section of Biology and Genetics G. Sichel, University of Catania, Catania 95123, Italy
| | - Antonio Magnano
- Digestive Endoscopy Service, Vittorio Emanuele Hospital, Catania 95124, Italy
| | - Rosario Caltabiano
- Department of Medical and Surgical Sciences and Advanced Technologies G.F. Ingrassia, University of Catania, Catania 95123, Italy
| | - Davide Barbagallo
- Department of Biomedical and Biotechnological Sciences, Section of Biology and Genetics G. Sichel, University of Catania, Catania 95123, Italy
| | - Antonio Biondi
- Department of Surgery, Vittorio Emanuele Hospital, University of Catania, Catania 95124, Italy
| | - Alessandro Cappellani
- Department of Surgery, Vittorio Emanuele Hospital, University of Catania, Catania 95124, Italy
| | - Francesco Basile
- Department of Surgery, Vittorio Emanuele Hospital, University of Catania, Catania 95124, Italy
| | - Cinzia Di Pietro
- Department of Biomedical and Biotechnological Sciences, Section of Biology and Genetics G. Sichel, University of Catania, Catania 95123, Italy
| | - Michele Purrello
- Department of Biomedical and Biotechnological Sciences, Section of Biology and Genetics G. Sichel, University of Catania, Catania 95123, Italy
| | - Marco Ragusa
- Department of Biomedical and Biotechnological Sciences, Section of Biology and Genetics G. Sichel, University of Catania, Catania 95123, Italy; IRCCS Associazione Oasi Maria S.S., Institute for Research on Mental Retardation and Brain Aging, Troina (EN) 94018, Italy.
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Yang T, Zhai H, Yan R, Zhou Z, Gao L, Wang L. lncRNA CCAT1 promotes cell proliferation, migration, and invasion by down-regulation of miR-143 in FTC-133 thyroid carcinoma cell line. ACTA ACUST UNITED AC 2018; 51:e7046. [PMID: 29791590 PMCID: PMC6002139 DOI: 10.1590/1414-431x20187046] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2017] [Accepted: 02/16/2018] [Indexed: 01/17/2023]
Abstract
Thyroid cancer is a common malignant tumor. Long non-coding RNA colon
cancer-associated transcript 1 (lncRNA CCAT1) is highly expressed in many
cancers; however, the molecular mechanism of CCAT1 in thyroid cancer remains
unclear. Hence, this study aimed to investigate the effect of CCAT1 on human
thyroid cancer cell line FTC-133. FTC-133 cells were transfected with CCAT1
expressing vector, CCAT1 shRNA, miR-143 mimic, and miR-143 inhibitor,
respectively. After different treatments, cell viability, proliferation,
migration, invasion, and apoptosis were measured. Moreover, the regulatory
relationship of CCAT1 and miR-143, as well as miR-143 and VEGF were tested using
dual-luciferase reporter assay. The relative expressions of CCAT1, miR-143, and
VEGF were tested by qRT-PCR. The expressions of apoptosis-related factors and
corresponding proteins in PI3K/AKT and MAPK pathways were analyzed using western
blot analysis. The results suggested that CCAT1 was up-regulated in the FTC-133
cells. CCAT1 suppression decreased FTC-133 cell viability, proliferation,
migration, invasion, and miR-143 expression, while it increased apoptosis and
VEGF expression. CCAT1 might act as a competing endogenous RNA (ceRNA) for
miR-143. Moreover, CCAT1 activated PI3K/AKT and MAPK signaling pathways through
inhibition of miR-143. This study demonstrated that CCAT1 exhibited
pro-proliferative and pro-metastasis functions on FTC-133 cells and activated
PI3K/AKT and MAPK signaling pathways via down-regulation of miR-143. These
findings will provide a possible target for clinical treatment of thyroid
cancer.
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Affiliation(s)
- Tianzheng Yang
- Department of Nuclear Medicine, Liaocheng People's Hospital, Liaocheng, Shandong, China
| | - Hongyan Zhai
- Department of Nuclear Medicine, Liaocheng People's Hospital, Liaocheng, Shandong, China
| | - Ruihong Yan
- Department of Nuclear Medicine, Liaocheng People's Hospital, Liaocheng, Shandong, China
| | - Zhenhu Zhou
- Department of Nuclear Medicine, Liaocheng People's Hospital, Liaocheng, Shandong, China
| | - Lei Gao
- Department of Nuclear Medicine, Liaocheng People's Hospital, Liaocheng, Shandong, China
| | - Luqing Wang
- Department of Radioimmunoassay, Liaocheng People's Hospital, Liaocheng, Shandong, China
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Long noncoding RNA CCAT1 promotes cell proliferation and metastasis in human medulloblastoma via MAPK pathway. TUMORI JOURNAL 2018; 104:43-50. [PMID: 28777430 DOI: 10.5301/tj.5000662] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
BACKGROUND Medulloblastoma is the most common posterior fossa tumor in children and one that easily metastasizes. The mechanisms of how the medulloblastoma develops and progresses remain to be elucidated. The present study aimed to assess the role of long noncoding colon cancer-associated transcript-1 (lncRNA CCAT1) in cell proliferation and metastasis in human medulloblastoma. METHODS Levels of CCAT1 were measured in samples and cell lines of medulloblastoma. Cell cycle progression, cell viability assay, colony formation assay, wound-healing and Transwell assays Corning, Cambridge, MA, USA were used to investigate the viability and motility of cells. Western blot assay was used to investigate the levels of CCAT1 and other proteins. RESULTS The initial findings indicated that CCAT1 was significantly up-regulated in clinical cancerous tissues and expressed differently in a series of medulloblastoma cell lines. CCAT1 knockdown significantly slowed cell proliferation rates and inhibited cell clonogenic potential in Daoy cells and D283 cells. Cell cycle progression was disrupted with cell proportions in the G0/G1 phase decreased and the proportion in the S phase and G2/M phases increased, in Daoy cells and D283 cells. Concordantly, medulloblastoma tumor cell growth rates were found to be impaired in xenotransplanted mice. After CCAT1 knockdown, cell wound recovery ability was significantly inhibited. Furthermore, the phosphorylated levels of MAPK, ERK and MEK, but not their total levels decreased after the down-regulation of CCAT1 in Daoy and D283 cells. CONCLUSIONS Our results suggested that the lncRNA CCAT1 promotes cell proliferation and metastasis in human medulloblastoma by possibly regulating the MAPK pathway.
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Luo Y, Ouyang J, Zhou D, Zhong S, Wen M, Ou W, Yu H, Jia L, Huang Y. Long Noncoding RNA GAPLINC Promotes Cells Migration and Invasion in Colorectal Cancer Cell by Regulating miR-34a/c-MET Signal Pathway. Dig Dis Sci 2018; 63:890-899. [PMID: 29427222 DOI: 10.1007/s10620-018-4915-9] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/21/2017] [Accepted: 01/03/2018] [Indexed: 01/17/2023]
Abstract
BACKGROUND Gastric adenocarcinoma predictive long intergenic noncoding RNA (GAPLINC) has been detected in colorectal cancer (CRC) cells and reportedly performs many functions related to tumor proliferation and metastasis. Aim The present study aimed to comprehensively explore the biological functions of GAPLINC and their underlying mechanism in CRC cell. METHODS The human cancer LncRNA PCR array was used to detect the differentially expressed long noncoding RNAs in human CRC samples. Real-time PCR, dual-luciferase assay, RNA pull-down assay, Transwell assay, and western blot analysis were performed to explore the molecular mechanism underlying GAPLINC functions related to migration and invasion of a human CRC cell line (HCT116). RESULTS Compared to the non-cancerous tissues, GAPLINC expression was obviously increased in CRC tissues. In HCT116, silencing of GAPLINC weakened cell migration and invasion, while overexpression of GAPLINC significantly promoted cell migration and invasion. Through dual-luciferase, RNA pull-down, and Transwell assays, we verified that miR-34a was the downstream molecule of GAPLINC and that miR-34a negatively regulated the migration and invasion of HCT116 cell. Furthermore, we found that GAPLINC positively regulated the miR-34a target gene c-MET in CRC tissues. CONCLUSIONS Our findings revealed that GAPLINC was up-regulated in CRC tissues and was involved in the migration and invasion of CRC cells by regulating miR-34a/c-MET signaling pathway.
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Affiliation(s)
- Yuqi Luo
- Department of Anatomy, School of Basic Medical Sciences, Southern Medical University, Guangzhou, 510515, China.,Department of General Surgery, Nansha Hospital of Guangzhou First People's Hospital, Guangzhou Medical University, Guangzhou, 511457, China
| | - Jun Ouyang
- Department of Anatomy, School of Basic Medical Sciences, Southern Medical University, Guangzhou, 510515, China.
| | - Donggen Zhou
- Ningbo international Travel Healthcare Center, Ningbo, 315000, China
| | - Shizhen Zhong
- Department of Anatomy, School of Basic Medical Sciences, Southern Medical University, Guangzhou, 510515, China
| | - Minjie Wen
- Department of General Surgery, Nansha Hospital of Guangzhou First People's Hospital, Guangzhou Medical University, Guangzhou, 511457, China
| | - Wentao Ou
- Department of General Surgery, Nansha Hospital of Guangzhou First People's Hospital, Guangzhou Medical University, Guangzhou, 511457, China
| | - Haitao Yu
- Department of General Surgery, Nansha Hospital of Guangzhou First People's Hospital, Guangzhou Medical University, Guangzhou, 511457, China
| | - Lin Jia
- Department of Gastroenterology, Nansha Hospital of Guangzhou First People's Hospital, Guangzhou Medical University, Guangzhou, 511457, China
| | - Yaoxin Huang
- Department of Gastroenterology, Nansha Hospital of Guangzhou First People's Hospital, Guangzhou Medical University, Guangzhou, 511457, China
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Kim T, Croce CM. Long noncoding RNAs: Undeciphered cellular codes encrypting keys of colorectal cancer pathogenesis. Cancer Lett 2018; 417:89-95. [PMID: 29306015 PMCID: PMC5825189 DOI: 10.1016/j.canlet.2017.12.033] [Citation(s) in RCA: 42] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2017] [Revised: 12/15/2017] [Accepted: 12/27/2017] [Indexed: 12/16/2022]
Abstract
Long noncoding RNAs are non-protein coding transcripts longer than 200 nucleotides in length. By the advance in genetic and bioinformatic technologies, the new genomic landscape including noncoding transcripts has been revealed. Despite their non-capacity to be translated into proteins, lncRNAs have a versatile functions through various mechanisms interacting with other cellular molecules including DNA, protein, and RNA. Recent research interest and endeavor have identified the functional role of lncRNAs in various diseases including cancer. Colorectal cancer (CRC) is not only one of the most frequent cancer but also one of the cancer types with remarkable achievements in lncRNA research. Of the numerous notable lncRNAs identified and characterized in CRC, we will focus on key lncRNAs with the high potential as CRC-specific biomarkers in this review.
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Affiliation(s)
- Taewan Kim
- The Ohio State University Comprehensive Cancer Center, Columbus, OH 43210, USA.
| | - Carlo M Croce
- Department of Cancer Biology and Genetics, College of Medicine, The Ohio State University, Columbus, OH 43210, USA.
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Chen J, Zhang K, Song H, Wang R, Chu X, Chen L. Long noncoding RNA CCAT1 acts as an oncogene and promotes chemoresistance in docetaxel-resistant lung adenocarcinoma cells. Oncotarget 2018; 7:62474-62489. [PMID: 27566568 PMCID: PMC5308740 DOI: 10.18632/oncotarget.11518] [Citation(s) in RCA: 67] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2016] [Accepted: 08/11/2016] [Indexed: 01/17/2023] Open
Abstract
Chemoresistance remains one of the major obstacles in clinical treatment of lung adenocarcinoma (LAD). Indeed, docetaxel-resistant LAD cells present chemoresistance and epithelial-to-mesenchymal transition phenotypes. Long non-coding RNAs (lncRNAs) are known to promote tumorigenesis in many cancer types. Here, we showed that the lncRNA colon cancer-associated transcript-1 (CCAT1) was upregulated in docetaxel-resistant LAD cells. Furthermore, downregulation of CCAT1 decreased chemoresistance, inhibited proliferation, enhanced apoptosis and reversed the epithelial-to-mesenchymal transition phenotype of docetaxel-resistant LAD cells. We also found that the oncogenic function of CCAT1 in docetaxel-resistant LAD cells depended on the sponging of let-7c. In turn, the sponging of let-7c by CCAT1 released Bcl-xl (a let-7c target), thereby promoting the acquisition of chemoresistance and epithelial-to-mesenchymal transition phenotypes in docetaxel-resistant LAD cells. Our data reveal a novel pathway underlying chemoresistance and the epithelial-to-mesenchymal transition in docetaxel-resistant LAD cells.
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Affiliation(s)
- Jing Chen
- Department of Medical Oncology, Jinling Hospital, School of Medicine, Nanjing University, Nanjing, Jiangsu, China
| | - Kai Zhang
- Department of Medical Oncology, Jinling Hospital, School of Medicine, Nanjing University, Nanjing, Jiangsu, China
| | - Haizhu Song
- Department of Medical Oncology, Jinling Hospital, School of Medicine, Nanjing University, Nanjing, Jiangsu, China
| | - Rui Wang
- Department of Medical Oncology, Jinling Hospital, School of Medicine, Nanjing University, Nanjing, Jiangsu, China
| | - Xiaoyuan Chu
- Department of Medical Oncology, Jinling Hospital, School of Medicine, Nanjing University, Nanjing, Jiangsu, China
| | - Longbang Chen
- Department of Medical Oncology, Jinling Hospital, School of Medicine, Nanjing University, Nanjing, Jiangsu, China
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Zhou W, Wang L, Miao Y, Xing R. Novel long noncoding RNA GACAT3 promotes colorectal cancer cell proliferation, invasion, and migration through miR-149. Onco Targets Ther 2018; 11:1543-1552. [PMID: 29593420 PMCID: PMC5865577 DOI: 10.2147/ott.s144103] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Aim To explore the expression and clinical significance of long noncoding RNA (lncRNA) gastric cancer-associated transcript 3 (GACAT3) in human colorectal cancer (CRC). Methods Expression of GACAT3 in CRC tissues and cell lines was measured using quantitative real-time PCR. CCK-8 and colony formation assays were used to assess the effect of GACAT3 on CRC cell line proliferation. Transwell invasion and migration assays were performed to detect the effect of GACAT3 on CRC cell line invasion and migration. Bioinformatics prediction, luciferase reporter assay, and pull-down assay were used to determine if miR-149 was a target of GACAT3. In addition, we also conducted colony formation assays and invasion assays to verify that GACAT3 promotes tumor progression through miR-149. Finally, in vivo tumorigenesis studies were used to demonstrate subcutaneous tumor growth. Results In the present study, we found that GACAT3 was highly expressed in CRC tissues and cell lines. Si-GACAT3 significantly decreased cell proliferation, motility, and invasiveness both in vitro and in vivo. We confirmed that downregulated GACAT3 significantly increased the expression of miR-149, and miR-149 binds to GACAT3 in a sequence-specific manner using luciferase reporter assays and pull-down assay. Further functional experiments indicated that GACAT3 could directly upregulate SP1 and STAT3 expressions by functioning as a competing endogenous RNA for miR-149, and consequentially, promoting CRC cell proliferation and invasion in vitro. Conclusion This study demonstrated that GACAT3 promotes tumor progression through competitive binding to miR-149 and suggests a promising new strategy for anti-CRC therapy.
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Affiliation(s)
- Weiwei Zhou
- Department of Pathology, Central Hospital of Cangzhou, Hebei
| | - Lei Wang
- Department of Pharmacy, Cangzhou Medical College, Hebei, China
| | - Yu Miao
- Department of Pathology, Central Hospital of Cangzhou, Hebei
| | - Rongge Xing
- Department of Pathology, Central Hospital of Cangzhou, Hebei
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128
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Arun G, Diermeier SD, Spector DL. Therapeutic Targeting of Long Non-Coding RNAs in Cancer. Trends Mol Med 2018; 24:257-277. [PMID: 29449148 PMCID: PMC5840027 DOI: 10.1016/j.molmed.2018.01.001] [Citation(s) in RCA: 419] [Impact Index Per Article: 69.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2017] [Revised: 01/09/2018] [Accepted: 01/14/2018] [Indexed: 02/07/2023]
Abstract
Long non-coding RNAs (lncRNAs) represent a significant population of the human transcriptome. Many lncRNAs exhibit cell- and/or tissue/tumor-specific expression, making them excellent candidates for therapeutic applications. In this review we discuss examples of lncRNAs that demonstrate the diversity of their function in various cancer types. We also discuss recent advances in nucleic acid drug development with a focus on oligonucleotide-based therapies as a novel approach to inhibit tumor progression. The increased success rates of nucleic acid therapeutics provide an outstanding opportunity to explore lncRNAs as viable therapeutic targets to combat various aspects of cancer progression.
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Affiliation(s)
- Gayatri Arun
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA; These authors contributed equally
| | - Sarah D Diermeier
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA; These authors contributed equally
| | - David L Spector
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA.
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129
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Nasrollahzadeh-Khakiani M, Emadi-Baygi M, Schulz WA, Nikpour P. Long noncoding RNAs in gastric cancer carcinogenesis and metastasis. Brief Funct Genomics 2018; 16:129-145. [PMID: 27122631 DOI: 10.1093/bfgp/elw011] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
Abstract
Recent studies of the human transcriptome, most prominently by the ENCyclopedia Of DNA Elements project, have revealed an unexpected number of noncoding RNAs (ncRNAs). Long noncoding RNAs (lncRNAs) are typically referred to a heterogeneous group of polyadenylated long ncRNAs, with a length of > 200 nt. LncRNAs constitute an integral part of tumor biology, with many lncRNAs discovered to be aberrantly expressed in various cancer types. They are involved in many aspects of cancer pathogenesis from its initiation to progression, metastasis and treatment response. Gastric cancer (GC) is the third leading cause of cancer death worldwide. Despite the current improvements of life expectancy and survival rate, most of the patients are diagnosed when their cancer has been progressed to advanced stages. Therefore, unraveling the molecular mechanisms of GC to find early-stage biomarkers is urgent. As the list of lncRNAs with deregulated expression in GC is steadily expanding, these molecules offer a source for developing GC-specific biomarkers. In this review, we will present and discuss those lncRNAs whose expression has been shown to be deregulated in GC.
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130
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Li Y, Jing F, Ding Y, He Q, Zhong Y, Fan C. Long noncoding RNA CCAT1 polymorphisms are associated with the risk of colorectal cancer. Cancer Genet 2018; 222-223:13-19. [PMID: 29666003 DOI: 10.1016/j.cancergen.2018.02.003] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2017] [Revised: 01/18/2018] [Accepted: 02/13/2018] [Indexed: 12/27/2022]
Abstract
Colorectal cancer associated transcript 1 (CCAT1) is a novel long noncoding RNA, whose overexpression is evident in both early phase of tumorigenesis and later disease stages in colorectal cancer (CRC). No study has explored the relationship between CCAT1 polymorphisms and CRC risk. In the present study, a case-control study was conducted to investigate the association between CCAT1 polymorphisms and CRC risk in Chinese population. We identified that CCAT1 rs67085638 polymorphism was associated with an increased risk of CRC (OR = 1.72, 95%CI = 1.14-2.58, P = 0.009 in heterozygote codominant model; OR = 1.67, 95%CI = 1.13-2.47, P = 0.010 in dominant model). Moreover, CCAT1 rs7013433 polymorphism was associated with late clinical stage (OR = 1.82, 95%CI = 1.16-2.86, P = 0.009 in heterozygote codominant model; OR = 1.72, 95%CI = 1.13-2.63, P = 0.012 in dominant model). Our finding proposed a link between CCAT1 polymorphisms with CRC risk as well as different clinical stages.
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Affiliation(s)
- Yingjun Li
- Department of Public Health, Hangzhou Medical College, Hangzhou, Zhejiang, China
| | - Fangyuan Jing
- Department of Public Health, Hangzhou Medical College, Hangzhou, Zhejiang, China
| | - Ye Ding
- Department of Public Health, Hangzhou Medical College, Hangzhou, Zhejiang, China
| | - Qingfang He
- Department of Chronic Non-Communicable Diseases Control and Prevention, Zhejiang Provincial Center for Disease Control and Prevention, Hangzhou, Zhejiang, China
| | - Yaohong Zhong
- Department of Public Health, Hangzhou Medical College, Hangzhou, Zhejiang, China
| | - Chunhong Fan
- Department of Public Health, Hangzhou Medical College, Hangzhou, Zhejiang, China.
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131
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Liu T, Zhang X, Gao S, Jing F, Yang Y, Du L, Zheng G, Li P, Li C, Wang C. Exosomal long noncoding RNA CRNDE-h as a novel serum-based biomarker for diagnosis and prognosis of colorectal cancer. Oncotarget 2018; 7:85551-85563. [PMID: 27888803 PMCID: PMC5356757 DOI: 10.18632/oncotarget.13465] [Citation(s) in RCA: 242] [Impact Index Per Article: 40.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2016] [Accepted: 10/27/2016] [Indexed: 12/19/2022] Open
Abstract
Cancer-secreted long non-coding RNAs (lncRNAs) are emerging mediators of cancer-host cross talk. The aim of our study was to illustrate the clinical significance of the lncRNA CRNDE-h in exosomes purified from the serum of patients with colorectal cancer (CRC). The study was divided into four parts: (1) The exosome isolated methods and lncRNA detected methods which accurately and reproducibly measure CRC-related exosomal CRNDE-h in serum were optimized in preliminary pilot stage; (2) The stability of exosomal CRNDE-h was evaluated systematically; (3) The origin of exosomal CRNDE-h was explorated in vitro and in vivo; (4) The diagnostic and prognostic value of exosomal CRNDE-h for CRC were validated in 468 patients. In pilot study, our results indicated that exosomal CRNDE-h was detectable and stable in serum of CRC patients, and derived from tumor cells. Then, the increased expression of exosomal CRNDE-h was successfully validated in 148 CRC patients when compared with colorectal benign disease patients and healthy donors. Exosomal CRNDE-h level significantly correlated with CRC regional lymph node metastasis (P = 0.019) and distant metastasis (P = 0.003). Moreover, at the cut-off value of 0.020 exosomal CRNDE-h level of serum, the area under ROC curve distinguishing CRC from colorectal benign disease patients and healthy donors was 0.892, with 70.3% sensitivity and 94.4% specificity, which was superior to carcinoembryogenic antigen. In addition, high exosomal CRNDE-h level has a lower overall survival rates than that for low groups (34.6% vs. 68.2%, P < 0.001). In conclusion, detection of lncRNA CRNDE-h in exosome shed a light on utilizing exosomal CRNDE-h as a noninvasive serum-based tumor marker for diagnosis and prognosis of CRC.
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Affiliation(s)
- Tong Liu
- Department of Clinical Laboratory, Qilu Hospital, Shandong University, Jinan, People's Republic of China
| | - Xin Zhang
- Department of Clinical Laboratory, Qilu Hospital, Shandong University, Jinan, People's Republic of China
| | - Shanyu Gao
- Department of Anorectal Surgery, Shandong Provincial Traditional Chinese Medical Hospital, Jinan, People's Republic of China
| | - Fangmiao Jing
- Oncology Center, Qilu Hospital, Shandong University, Jinan, People's Republic of China
| | - Yongmei Yang
- Department of Clinical Laboratory, Qilu Hospital, Shandong University, Jinan, People's Republic of China
| | - Lutao Du
- Department of Clinical Laboratory, Qilu Hospital, Shandong University, Jinan, People's Republic of China
| | - Guixi Zheng
- Department of Clinical Laboratory, Qilu Hospital, Shandong University, Jinan, People's Republic of China
| | - Peilong Li
- Department of Clinical Laboratory, Qilu Hospital, Shandong University, Jinan, People's Republic of China
| | - Chen Li
- Department of Clinical Laboratory, Qilu Hospital, Shandong University, Jinan, People's Republic of China
| | - Chuanxin Wang
- Department of Clinical Laboratory, Qilu Hospital, Shandong University, Jinan, People's Republic of China
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Alteration of Epigenetic Regulation by Long Noncoding RNAs in Cancer. Int J Mol Sci 2018; 19:ijms19020570. [PMID: 29443889 PMCID: PMC5855792 DOI: 10.3390/ijms19020570] [Citation(s) in RCA: 112] [Impact Index Per Article: 18.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2017] [Revised: 02/13/2018] [Accepted: 02/13/2018] [Indexed: 02/06/2023] Open
Abstract
Long noncoding RNAs (lncRNAs) are important regulators of the epigenetic status of the human genome. Besides their participation to normal physiology, lncRNA expression and function have been already associated to many diseases, including cancer. By interacting with epigenetic regulators and by controlling chromatin topology, their misregulation may result in an aberrant regulation of gene expression that may contribute to tumorigenesis. Here, we review the functional role and mechanisms of action of lncRNAs implicated in the aberrant epigenetic regulation that has characterized cancer development and progression.
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133
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Chen L, Hu N, Wang C, Zhao H, Gu Y. Long non-coding RNA CCAT1 promotes multiple myeloma progression by acting as a molecular sponge of miR-181a-5p to modulate HOXA1 expression. Cell Cycle 2018; 17:319-329. [PMID: 29228867 DOI: 10.1080/15384101.2017.1407893] [Citation(s) in RCA: 70] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
Abstract
Multiple myeloma (MM) is the second most common hematological cancer all over the world. Long non-coding RNA (lncRNA) colon cancer associated transcript-1 (CCAT1) has been reported to play important roles in the development and progression of multiple human malignancies. However, little is known about its functional role and molecular mechanism in MM. The aim of this study was to investigate the clinical and biological significance of CCAT1 in MM. Our data showed that the relative expression levels of CCAT1 were significantly upregulated in MM tissues and cell lines compared with healthy donors and normal plasma cells (nPCs). High expression of CCAT1 was correlated shorter overall survival of MM patients. CCAT1 knockdown significantly inhibited cell proliferation, induced cell cycle arrest at G0/G1 phase and promoted cell apoptosis in vitro, and suppressed tumor growth in vivo. MiR-181a-5p was a direct target of CCAT1, and repression of miR-181a-5p could rescue the inhibition of CCAT1 knockdown on MM progression. In addition, CCAT1 positively regulated HOXA1 expression through sponging miR-181a-5p in MM cells.taken together, lncRNA CCAT1 exerted an oncogenic role in MM by acting as a ceRNA of miR-181a-5p. These results suggest that CCAT1 may serve as a novel diagnostic marker and therapeutic target for MM.
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Affiliation(s)
- Li Chen
- a Department of Hematology , Huaihe Hospital of Henan University , Kaifeng 475000 , Henan China
| | - Ning Hu
- a Department of Hematology , Huaihe Hospital of Henan University , Kaifeng 475000 , Henan China
| | - Chao Wang
- a Department of Hematology , Huaihe Hospital of Henan University , Kaifeng 475000 , Henan China
| | - Hongmian Zhao
- a Department of Hematology , Huaihe Hospital of Henan University , Kaifeng 475000 , Henan China
| | - Yueli Gu
- b Department of Hematology , The First People's Hospital of Shangqiu , Shangqiu 476100 , Henan China
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Gao T, Liu X, He B, Nie Z, Zhu C, Zhang P, Wang S. Exosomal lncRNA 91H is associated with poor development in colorectal cancer by modifying HNRNPK expression. Cancer Cell Int 2018; 18:11. [PMID: 29410604 PMCID: PMC5781274 DOI: 10.1186/s12935-018-0506-2] [Citation(s) in RCA: 80] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2017] [Accepted: 01/10/2018] [Indexed: 02/07/2023] Open
Abstract
Background Exosomes mediated transfer of lncRNA 91H may play a critical role in the development of CRC. However, few studies have proved the mechanism. So we performed this study to deeply explore the biological functions of exosomal 91H in the development and progression of CRC. Methods The association between lncRNA 91H and exosomes was detected in vitro and vivo. Then RNA pulldown and RIP were used to detect how lncRNA 91H affect CRC IGF2 express. At last, clinic pathological significance of exosomal 91H was evaluated by Cox proportional hazards model. Results We found that serum lncRNA 91H expression was closely related to cancer exosomes in vitro and vivo which may enhance tumor-cell migration and invasion in tumor development by modifying HNRNPK expression. Then the clinic pathological significance of exosomal 91H was evaluated which demonstrated that CRC patients with high lncRNA 91H expression usually showed a higher risk in tumor recurrence and metastasis than patients with low lncRNA 91H expression (P < 0.05). Conclusion All these data suggested that exosomal lncRNA 91H enhancing CRC metastasis by modifying HNRNPK expression might be an early plasma-based biomarker for CRC recurrence or metastasis. Further large-scale studies are needed to confirm our findings.
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Affiliation(s)
- Tianyi Gao
- 1Department of Clinical Laboratory, Nanjing First Hospital, Nanjing Medical University, 68 Changle Road, Nanjing, 210006 Jiangsu China
| | - Xiangxiang Liu
- 2Central Laboratory, Nanjing First Hospital, Nanjing Medical University, 68 Changle Road, Nanjing, 210006 Jiangsu China
| | - Bangshun He
- 2Central Laboratory, Nanjing First Hospital, Nanjing Medical University, 68 Changle Road, Nanjing, 210006 Jiangsu China
| | - Zhenlin Nie
- 1Department of Clinical Laboratory, Nanjing First Hospital, Nanjing Medical University, 68 Changle Road, Nanjing, 210006 Jiangsu China
| | - Chengbin Zhu
- 1Department of Clinical Laboratory, Nanjing First Hospital, Nanjing Medical University, 68 Changle Road, Nanjing, 210006 Jiangsu China
| | - Pei Zhang
- 1Department of Clinical Laboratory, Nanjing First Hospital, Nanjing Medical University, 68 Changle Road, Nanjing, 210006 Jiangsu China
| | - Shukui Wang
- 1Department of Clinical Laboratory, Nanjing First Hospital, Nanjing Medical University, 68 Changle Road, Nanjing, 210006 Jiangsu China.,2Central Laboratory, Nanjing First Hospital, Nanjing Medical University, 68 Changle Road, Nanjing, 210006 Jiangsu China
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135
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White NM, Maher CA. The potential use of lncRNAs found in the 8q24 region as biomarkers for colon cancer. Ann Oncol 2018; 28:1688-1689. [PMID: 28838213 DOI: 10.1093/annonc/mdx337] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Affiliation(s)
- N M White
- Division of Oncology, Department of Medicine, School of Medicine, Washington University, St. Louis, USA
| | - C A Maher
- Division of Oncology, Department of Medicine, School of Medicine, Washington University, St. Louis, USA
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136
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A RNA-Sequencing approach for the identification of novel long non-coding RNA biomarkers in colorectal cancer. Sci Rep 2018; 8:575. [PMID: 29330370 PMCID: PMC5766599 DOI: 10.1038/s41598-017-18407-6] [Citation(s) in RCA: 65] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2017] [Accepted: 12/05/2017] [Indexed: 12/18/2022] Open
Abstract
Long non-coding RNAs (lncRNAs) have been implicated in human pathology, however, their role in colorectal carcinogenesis have not been fully elucidated. In the current study, whole-transcriptome analysis was performed in 3 pairs of colorectal cancer (CRC) and matched normal mucosa (NM) by RNA sequencing (RNA-seq). Followed by confirmation using the Cancer Genome Atlas (TCGA) dataset, we identified 27 up-regulated and 22 down-regulated lncRNAs in CRC. Up-regulation of four lncRNAs, hereby named colorectal cancer associated lncRNA (CRCAL)-1 [AC021218.2], CRCAL-2 [LINC00858], CRCAL-3 [RP11-138J23.1] and CRCAL-4 [RP11-435O5.2], was further validated by real-time RT-PCR in 139 colorectal neoplasms and matched NM tissues. Knockdown of CRCAL-3 and CRCAL-4 in colon cancer cells reduced cell viability and colony formation ability, and induced cell cycle arrest. TCGA dataset supported the associations of CRCAL-3 and CRCAL-4 with cell cycle and revealed a co-expression network comprising dysregulated lncRNAs associated with protein-coding genes. In conclusion, RNA-seq identified numbers of novel lncRNAs dysregulated in CRC. In vitro experiments and GO term enrichment analysis indicated the functional relevance of CRCAL-3 and CRCAL-4 in association with cell cycle. Our data highlight the capability of RNA-seq to discover novel lncRNAs involved in human carcinogenesis, which may serve as alternative biomarkers and/or molecular treatment targets.
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137
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Emerging role of non-coding RNA in oral cancer. Cell Signal 2018; 42:134-143. [DOI: 10.1016/j.cellsig.2017.10.009] [Citation(s) in RCA: 109] [Impact Index Per Article: 18.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2017] [Revised: 09/28/2017] [Accepted: 10/15/2017] [Indexed: 02/06/2023]
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138
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Advances in esophageal cancer: A new perspective on pathogenesis associated with long non-coding RNAs. Cancer Lett 2018; 413:94-101. [DOI: 10.1016/j.canlet.2017.10.046] [Citation(s) in RCA: 48] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2017] [Revised: 10/07/2017] [Accepted: 10/31/2017] [Indexed: 12/20/2022]
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139
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140
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Cao L, Zhang P, Li J, Wu M. LAST, a c-Myc-inducible long noncoding RNA, cooperates with CNBP to promote CCND1 mRNA stability in human cells. eLife 2017; 6:30433. [PMID: 29199958 PMCID: PMC5739540 DOI: 10.7554/elife.30433] [Citation(s) in RCA: 51] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2017] [Accepted: 12/02/2017] [Indexed: 12/13/2022] Open
Abstract
Cyclin D1 is a critical regulator of cell cycle progression and works at the G1 to S-phase transition. Here, we report the isolation and characterization of the novel c-Myc-regulated lncRNA LAST (LncRNA-Assisted Stabilization of Transcripts), which acts as a CCND1 mRNA stabilizer. Mechanistically, LAST was shown to cooperate with CNBP to bind to the 5′UTR of CCND1 mRNA to protect against possible nuclease targeting. In addition, data from CNBP RIP-seq and LAST RNA-seq showed that CCND1 mRNA might not be the only target of LAST and CNBP; three additional mRNAs were shown to be post-transcriptional targets of LAST and CNBP. In a xenograft model, depletion of LAST diminished and ectopic expression of LAST induced tumor formation, which are suggestive of its oncogenic function. We thus report a previously unknown lncRNA involved in the fine-tuned regulation of CCND1 mRNA stability, without which CCND1 exhibits, at most, partial expression. Cell division involves a series of steps in which the cell grows, duplicates its contents, and then divides into two. Together these steps are called the cell cycle, and the transition between each step must be controlled to make sure that events take place in the right order. Any loss of control can cause cells to divide in an unrestrained manner, which may lead to cancer. Proteins called cyclins control progression through the cell cycle. As such, these proteins need to be produced in the correct amounts and at the correct times. Transcription factors are proteins that switch genes on or off to help regulate how much protein is made from those genes. A transcription factor known as c-Myc regulates the expression of the genes that encode the cyclins. Among these genes, one called CCND1 is particularly important because it encodes a protein that controls a crucial transition in the cell cycle: it marks a ‘point of no return’, beyond which cells are committed to dividing. When a transcription factor switches on a gene, the gene gets copied into a molecule of messenger RNA, which is then translated into protein. But, cells also contain genes that do not code for proteins. Transcription factors can bind to such non-coding genes, leading to the production of so-called long non-coding RNAs (often abbreviated to lncRNAs). Many lncRNAs can affect the expression of other genes. Cao, Zhang et al. have now asked whether any lncRNAs regulate CCND1 in human cells. The analysis revealed that the transcription factor c-Myc promotes the expression of a previously unidentified lncRNA. Cao, Zhang et al. name this lncRNA LAST, which is officially short for LncRNA-assisted stabilization of transcripts, and show thatit makes the CCND1 messenger RNA more stable. In other words, it makes the messenger RNAs ‘last’ longer in the cell. This in turn, ensures that the cell cycle progresses in the correct manner, allowing cells to complete their division. In the absence of LAST, the CCND1 messenger RNA becomes unstable and as a result the cell cycle does not progress. Cao, Zhang et al. then explored the role of LAST in cancer cells. When human colon cancer cells that expressed LAST were implanted into mice, they formed tumors. Yet, reducing the expression of LAST in the colon cancer cells made the tumors grow slower. Future challenges will be to understand how LAST makes messenger RNAs stable and further explore its role in cancer. A better understanding of this molecule could reveal whether it can be used to help doctors diagnose or treat cancers.
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Affiliation(s)
- Limian Cao
- CAS Key Laboratory of Innate Immunity and Chronic Disease, CAS Center for Excellence in Molecular Cell Science, Innovation Center for Cell Signaling Network, School of Life Sciences, University of Science & Technology of China, Hefei, China
| | - Pengfei Zhang
- CAS Key Laboratory of Innate Immunity and Chronic Disease, CAS Center for Excellence in Molecular Cell Science, Innovation Center for Cell Signaling Network, School of Life Sciences, University of Science & Technology of China, Hefei, China
| | - Jinming Li
- Translational Research Institute, Henan Provincial People's Hospital, School of Medicine, Henan University, Zhengzhou, China
| | - Mian Wu
- CAS Key Laboratory of Innate Immunity and Chronic Disease, CAS Center for Excellence in Molecular Cell Science, Innovation Center for Cell Signaling Network, School of Life Sciences, University of Science & Technology of China, Hefei, China.,Translational Research Institute, Henan Provincial People's Hospital, School of Medicine, Henan University, Zhengzhou, China
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141
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Lagarde J, Uszczynska-Ratajczak B, Carbonell S, Pérez-Lluch S, Abad A, Davis C, Gingeras TR, Frankish A, Harrow J, Guigo R, Johnson R. High-throughput annotation of full-length long noncoding RNAs with capture long-read sequencing. Nat Genet 2017; 49:1731-1740. [PMID: 29106417 PMCID: PMC5709232 DOI: 10.1038/ng.3988] [Citation(s) in RCA: 166] [Impact Index Per Article: 23.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2017] [Accepted: 10/11/2017] [Indexed: 12/20/2022]
Abstract
Accurate annotation of genes and their transcripts is a foundation of genomics, but currently no annotation technique combines throughput and accuracy. As a result, reference gene collections remain incomplete-many gene models are fragmentary, and thousands more remain uncataloged, particularly for long noncoding RNAs (lncRNAs). To accelerate lncRNA annotation, the GENCODE consortium has developed RNA Capture Long Seq (CLS), which combines targeted RNA capture with third-generation long-read sequencing. Here we present an experimental reannotation of the GENCODE intergenic lncRNA populations in matched human and mouse tissues that resulted in novel transcript models for 3,574 and 561 gene loci, respectively. CLS approximately doubled the annotated complexity of targeted loci, outperforming existing short-read techniques. Full-length transcript models produced by CLS enabled us to definitively characterize the genomic features of lncRNAs, including promoter and gene structure, and protein-coding potential. Thus, CLS removes a long-standing bottleneck in transcriptome annotation and generates manual-quality full-length transcript models at high-throughput scales.
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Affiliation(s)
- Julien Lagarde
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, 08003 Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Barbara Uszczynska-Ratajczak
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, 08003 Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Silvia Carbonell
- R&D Department, Quantitative Genomic Medicine Laboratories (qGenomics), Barcelona, Spain
| | - Sílvia Pérez-Lluch
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, 08003 Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Amaya Abad
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, 08003 Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Carrie Davis
- Functional Genomics Group, Cold Spring Harbor Laboratory, 1 Bungtown Road, Cold Spring Harbor, New York 11724, USA
| | - Thomas R. Gingeras
- Functional Genomics Group, Cold Spring Harbor Laboratory, 1 Bungtown Road, Cold Spring Harbor, New York 11724, USA
| | - Adam Frankish
- Wellcome Trust Sanger Institute, Hinxton, Cambridgeshire, UK CB10 1HH
| | - Jennifer Harrow
- Wellcome Trust Sanger Institute, Hinxton, Cambridgeshire, UK CB10 1HH
| | - Roderic Guigo
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, 08003 Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Rory Johnson
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, 08003 Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
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142
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Liu W, Ma R, Yuan Y. Post-transcriptional Regulation of Genes Related to Biological Behaviors of Gastric Cancer by Long Noncoding RNAs and MicroRNAs. J Cancer 2017; 8:4141-4154. [PMID: 29187891 PMCID: PMC5706018 DOI: 10.7150/jca.22076] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2017] [Accepted: 10/10/2017] [Indexed: 12/18/2022] Open
Abstract
Noncoding RNAs play critical roles in regulating protein-coding genes and comprise two major classes: long noncoding RNAs (lncRNAs) and microRNAs (miRNAs). LncRNAs regulate gene expression at transcriptional, post-transcriptional, and epigenetic levels via multiple action modes. LncRNAs can also function as endogenous competitive RNAs for miRNAs and indirectly regulate gene expression post-transcriptionally. By binding to the 3'-untranslated regions (3'-UTR) of target genes, miRNAs post-transcriptionally regulate gene expression. Herein, we conducted a review of post-transcriptional regulation by lncRNAs and miRNAs of genes associated with biological behaviors of gastric cancer.
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Affiliation(s)
- Wenjing Liu
- Tumor Etiology and Screening Department of Cancer Institute and General Surgery, the First Hospital of China Medical University, and Key Laboratory of Cancer Etiology and Prevention (China Medical University), Liaoning Provincial Education Department, Shenyang, 110001, Liaoning Province, P R China.,Cancer Hospital of China Medical University, Liaoning Cancer Hospital & Institute, NO. 44 Xiaoheyan Road, Dadong District, Shenyang 110042, Liaoning Province, P R China
| | - Rui Ma
- Cancer Hospital of China Medical University, Liaoning Cancer Hospital & Institute, NO. 44 Xiaoheyan Road, Dadong District, Shenyang 110042, Liaoning Province, P R China
| | - Yuan Yuan
- Tumor Etiology and Screening Department of Cancer Institute and General Surgery, the First Hospital of China Medical University, and Key Laboratory of Cancer Etiology and Prevention (China Medical University), Liaoning Provincial Education Department, Shenyang, 110001, Liaoning Province, P R China.,National Clinical Research Center for Digestive Diseases, Xi'an, 110001 China
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143
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Mehra M, Chauhan R. Long Noncoding RNAs as a Key Player in Hepatocellular Carcinoma. BIOMARKERS IN CANCER 2017; 9:1179299X17737301. [PMID: 29147078 PMCID: PMC5673005 DOI: 10.1177/1179299x17737301] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/28/2017] [Indexed: 12/16/2022]
Abstract
Hepatocellular carcinoma (HCC) is a major malignancy in the liver and has emerged as one of the main cancers in the world with a high mortality rate. However, the molecular mechanisms of HCC are still poorly understood. Long noncoding RNAs (lncRNAs) have recently come to the forefront as functional non-protein-coding RNAs that are involved in a variety of cellular processes ranging from maintaining the structural integrity of chromosomes to gene expression regulation in a spatiotemporal manner. Many recent studies have reported the involvement of lncRNAs in HCC which has led to a better understanding of the underlying molecular mechanisms operating in HCC. Long noncoding RNAs have been shown to regulate development and progression of HCC, and thus, lncRNAs have both diagnostic and therapeutic potentials. In this review, we present an overview of the lncRNAs involved in different stages of HCC and their potential in clinical applications which have been studied so far.
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Affiliation(s)
- Mrigaya Mehra
- Studio of Computational Biology & Bioinformatics, Biotechnology Division, CSIR-Institute of Himalayan Bioresource Technology (CSIR-IHBT), Palampur, India
- Academy of Scientific & Innovative Research, Chennai, India
| | - Ranjit Chauhan
- Department of Hepatology, Loyola University Chicago, Chicago, IL, USA
- Molecular Virology and Hepatology Research Group, Division of BioMedical Sciences, Health Sciences Center, Memorial University, St John’s, Newfoundland and Labrador, Canada
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144
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Zhang S, Xiao J, Chai Y, Du YY, Liu Z, Huang K, Zhou X, Zhou W. LncRNA-CCAT1 Promotes Migration, Invasion, and EMT in Intrahepatic Cholangiocarcinoma Through Suppressing miR-152. Dig Dis Sci 2017; 62:3050-3058. [PMID: 28921383 DOI: 10.1007/s10620-017-4759-8] [Citation(s) in RCA: 54] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/27/2017] [Accepted: 09/08/2017] [Indexed: 01/17/2023]
Abstract
BACKGROUND Increasing evidence has suggested that lncRNA CCAT1 is upregulated and functions as a potential tumor promoter in many cancers. However, the potential biological roles and regulatory mechanisms of CCAT1 in intrahepatic cholangiocarcinoma (ICC) remain unclear. METHODS We used real-time PCR to measure CCAT1 expression in ICC tissues and the adjacent normal tissues. The statistical analyses were applied to evaluate the prognostic value and associations of CCAT1 expression with clinical parameters. The CCAT1 was silenced with siRNA in ICC cells. The migration and invasion of ICC cells were detected with Transwell assay. The expressions of epithelial-mesenchymal transition (EMT)-related proteins were evaluated to discover whether the process of EMT was involved. RESULTS We found that CCAT1 expression was elevated in ICC tissues compared to the adjacent normal tissues. We also found that high CCAT1 expression is closely correlated with tumor progression in ICC patients. Furthermore, our results show that knockdown of CCAT1 significantly suppressed the migration and invasion of ICC cells. Additionally, CCAT1 silencing remarkably reverses the EMT phenotype of ICC cells. Moreover, bioinformatics analysis and luciferase reporter assay revealed that CCAT1 directly bound to the miR-152, which has been reported to serve as a tumor suppressor in variety cancers. Further investigation demonstrated that CCAT1 led to the metastasis and EMT activation of ICC cells through inhibiting miR-152. CONCLUSIONS Our results suggested that CCAT1 functions as an oncogenic lncRNA in ICC, which could serve as a potential diagnostic and therapeutic target for ICC patients.
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Affiliation(s)
- Shouhua Zhang
- Department of General Surgery, Jiangxi Children's Hospital, Nanchang, 330006, Jiangxi Province, China
| | - Juhua Xiao
- Department of Ultrasound, Jiangxi Provincial Maternal and Child Health Hospital, Nanchang, 330006, Jiangxi Province, China
| | - Yong Chai
- Department of General Surgery, Jiangxi Children's Hospital, Nanchang, 330006, Jiangxi Province, China
| | - Yun Yan Du
- Department of Otolaryngology, Jiangxi Provincial People's Hospital, Nanchang, 330006, Jiangxi Province, China
| | - Zhiqiang Liu
- Department of General Surgery, Jiangxi Children's Hospital, Nanchang, 330006, Jiangxi Province, China
| | - Kai Huang
- Department of Gastrointestinal Surgery, Jiangxi Provincial Cancer Hospital, No. 519, Beijing East Road, Nanchang, 330029, Jiangxi Province, China
| | - Xin Zhou
- Department of Ultrasound, Jiangxi Provincial Maternal and Child Health Hospital, Nanchang, 330006, Jiangxi Province, China
| | - Wei Zhou
- Department of Gastrointestinal Surgery, Jiangxi Provincial Cancer Hospital, No. 519, Beijing East Road, Nanchang, 330029, Jiangxi Province, China.
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145
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Luo J, Qu J, Wu DK, Lu ZL, Sun YS, Qu Q. Long non-coding RNAs: a rising biotarget in colorectal cancer. Oncotarget 2017; 8:22187-22202. [PMID: 28108736 PMCID: PMC5400657 DOI: 10.18632/oncotarget.14728] [Citation(s) in RCA: 66] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2016] [Accepted: 01/09/2017] [Indexed: 02/06/2023] Open
Abstract
Colorectal cancer (CRC) is a common gastrointestinal cancer, with a high incidence and high mortality. Long non-coding RNAs (lncRNAs) are involved in the development, invasion and metastasis, early diagnosis, prognosis, the chemoresistance and radioresistance of CRC through interference with mRNA activity, directly combining with proteins to regulate their activity or alter their localization, influencing downstream gene expression by inhibiting RNA polymerase and regulating gene expression as competing endogenous RNAs. Recent progress in next generation sequencing and transcriptome analysis has revealed that tissue and cancer-type specific lncRNAs could be useful prognostic markers. Here, the CRC-associated lncRNAs from recent studies until October 2016 are reviewed and multiple studies that have confirmed CRC-associated lncRNAs are summarized. This review may be helpful in understanding the overall relationships between the lncRNAs involved in CRC.
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Affiliation(s)
- Jian Luo
- Department of Pharmacy, Xiangya Hospital, Central South University, Changsha, P. R. China
| | - Jian Qu
- Department of Pharmacy, The Second Xiangya Hospital, Central South University, Institute of Clinical Pharmacy, Central South University, Changsha, P. R. China
| | - Dong-Kai Wu
- Department of Cardiothoracic Surgery, Xiangya Hospital, Central South University, Changsha, P. R. China
| | - Zhi-Li Lu
- Department of Pathology, The Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, P. R. China
| | - Yue-Sheng Sun
- Department of General Surgery, The Third Clinical College of Wenzhou Medical University, Wenzhou People's Hospital, Wenzhou, P. R. China
| | - Qiang Qu
- Department of Pharmacy, Xiangya Hospital, Central South University, Changsha, P. R. China
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146
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Long noncoding RNA CCAT1 functions as a ceRNA to antagonize the effect of miR-410 on the down-regulation of ITPKB in human HCT-116 and HCT-8 cells. Oncotarget 2017; 8:92855-92863. [PMID: 29190961 PMCID: PMC5696227 DOI: 10.18632/oncotarget.21612] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2017] [Accepted: 08/26/2017] [Indexed: 01/17/2023] Open
Abstract
Colorectal cancer is one of the most common malignancies, which has seriously affected people's health. Abnormal expression of long non-coding RNAs and microRNAs are closely related to the process of occurrence, development, invasion and metastasis of colorectal cancer. However, the effect of lnc CCAT1 on human HCT-116/HCT-8 cells and its potential mechanism were investigated. In present study, differential expression of CCAT1, miR-410 and ITPKB were detected in colon cancer tissues and adjacent parts. Then the prediction programs were applied to predict the target genes of miR-410. The complementary bindings of miR-410 with lnc CCAT1 and ITPKB were assessed by luciferase assays. The interaction between LncRNA CCAT1 and miR-410 was analyzed. In addition, the mRNA and protein of ITPKB and apoptosis factors were examined in cells after miR-410 overexpression or silencing. Meanwhile, MTT and flow cytometer were used to detect the cells proliferation and apoptosis level. Results showed that CCAT1 and miR-410 were up-regulated in colon cancer tissues, but ITPKB was down-regulated. Lnc CCAT1 and ITPKB were predicted to be the targets of miR-410 and the prediction were verified by luciferase assays. The expression of lnc CCAT1 and ITPKB were inhibited by miR-410 in human HCT-116/HCT-8 cells. Meanwhile, lnc CCAT1 could lead to a decrease of miR-410. Furthermore, miR-410 overexpression could promote cell proliferation and reduce apoptosis. In summary, these data demonstrated that miR-410 could promote cell proliferation and reduce apoptosis by inhibiting ITPKB expression and the expression of lnc CCAT1 antagonized the effect of miR-410.
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147
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Lu L, Qi H, Luo F, Xu H, Ling M, Qin Y, Yang P, Liu X, Yang Q, Xue J, Chen C, Lu J, Xiang Q, Liu Q, Bian Q. Feedback circuitry via let-7c between lncRNA CCAT1 and c-Myc is involved in cigarette smoke extract-induced malignant transformation of HBE cells. Oncotarget 2017; 8:19285-19297. [PMID: 28184029 PMCID: PMC5386684 DOI: 10.18632/oncotarget.15195] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2016] [Accepted: 01/09/2017] [Indexed: 01/17/2023] Open
Abstract
Cigarette smoking is a primary risk factor for the development of lung cancer, which is regarded as the leading cause of cancer-related deaths. The process of malignant transformation of cells, however, is complex and elusive. The present study investigated the roles of an lncRNA, CCAT1, and a transcriptional factor, c-Myc, in human bronchial epithelial (HBE) cell transformation induced by cigarette smoke extract. With acute and chronic treatment of HBE cells, cigarette smoke extract induced increases of CCAT1 and c-Myc levels and decreases of levels of let-7c, a microRNA. Down-regulation of c-Myc reduced the degree of malignancy and the invasion/migration capacity of HBE cells transformed by cigarette smoke extract. ChIP assays established that c-Myc, increased by cigarette smoke extract, binds to the promoter of CCAT1, activating its transcription. Further, let-7c suppressed the expression of c-Myc through binding to its 3'-UTR. In turn, CCAT1 promoted the accumulation of c-Myc through binding to let-7c and decreasing free let-7c, which influenced the neoplastic capacity of HBE cells transformed by cigarette smoke extract. These results indicate that a positive feedback loop ensures expression of cigarette smoke extract-induced CCAT1 and c-Myc via let-7c, which is involved in cigarette smoke extract-induced malignant transformation of HBE cells. Thus, the present research establishes a new mechanism for the reciprocal regulation between CCAT1 and c-Myc and provides an understanding of cigarette smoke extract-induced lung carcinogenesis.
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Affiliation(s)
- Lu Lu
- Institute of Toxicology, Ministry of Education, School of Public Health, Nanjing Medical University, Nanjing 211166, Jiangsu, People's Republic of China.,The Key Laboratory of Modern Toxicology, Ministry of Education, School of Public Health, Nanjing Medical University, Nanjing 211166, Jiangsu, People's Republic of China
| | - Hong Qi
- Institute of Toxicology, Ministry of Education, School of Public Health, Nanjing Medical University, Nanjing 211166, Jiangsu, People's Republic of China.,The Key Laboratory of Modern Toxicology, Ministry of Education, School of Public Health, Nanjing Medical University, Nanjing 211166, Jiangsu, People's Republic of China
| | - Fei Luo
- Institute of Toxicology, Ministry of Education, School of Public Health, Nanjing Medical University, Nanjing 211166, Jiangsu, People's Republic of China.,The Key Laboratory of Modern Toxicology, Ministry of Education, School of Public Health, Nanjing Medical University, Nanjing 211166, Jiangsu, People's Republic of China
| | - Hui Xu
- Institute of Toxicology, Ministry of Education, School of Public Health, Nanjing Medical University, Nanjing 211166, Jiangsu, People's Republic of China.,The Key Laboratory of Modern Toxicology, Ministry of Education, School of Public Health, Nanjing Medical University, Nanjing 211166, Jiangsu, People's Republic of China
| | - Min Ling
- Jiangsu Center for Disease Control and Prevention, Nanjing 210009, Jiangsu, People's Republic China
| | - Yu Qin
- Jiangsu Center for Disease Control and Prevention, Nanjing 210009, Jiangsu, People's Republic China
| | - Ping Yang
- The School of Public Health, Institute for Chemical Carcinogenesis, Guangzhou Medical University, Guangzhou 510182, Guangdong, People's Republic China
| | - Xinlu Liu
- Institute of Toxicology, Ministry of Education, School of Public Health, Nanjing Medical University, Nanjing 211166, Jiangsu, People's Republic of China.,The Key Laboratory of Modern Toxicology, Ministry of Education, School of Public Health, Nanjing Medical University, Nanjing 211166, Jiangsu, People's Republic of China
| | - Qianlei Yang
- Institute of Toxicology, Ministry of Education, School of Public Health, Nanjing Medical University, Nanjing 211166, Jiangsu, People's Republic of China.,The Key Laboratory of Modern Toxicology, Ministry of Education, School of Public Health, Nanjing Medical University, Nanjing 211166, Jiangsu, People's Republic of China
| | - Junchao Xue
- Institute of Toxicology, Ministry of Education, School of Public Health, Nanjing Medical University, Nanjing 211166, Jiangsu, People's Republic of China.,The Key Laboratory of Modern Toxicology, Ministry of Education, School of Public Health, Nanjing Medical University, Nanjing 211166, Jiangsu, People's Republic of China
| | - Chao Chen
- Institute of Toxicology, Ministry of Education, School of Public Health, Nanjing Medical University, Nanjing 211166, Jiangsu, People's Republic of China.,The Key Laboratory of Modern Toxicology, Ministry of Education, School of Public Health, Nanjing Medical University, Nanjing 211166, Jiangsu, People's Republic of China
| | - Jiachun Lu
- The School of Public Health, Institute for Chemical Carcinogenesis, Guangzhou Medical University, Guangzhou 510182, Guangdong, People's Republic China
| | - Quanyong Xiang
- Jiangsu Center for Disease Control and Prevention, Nanjing 210009, Jiangsu, People's Republic China
| | - Qizhan Liu
- Institute of Toxicology, Ministry of Education, School of Public Health, Nanjing Medical University, Nanjing 211166, Jiangsu, People's Republic of China.,The Key Laboratory of Modern Toxicology, Ministry of Education, School of Public Health, Nanjing Medical University, Nanjing 211166, Jiangsu, People's Republic of China
| | - Qian Bian
- Jiangsu Center for Disease Control and Prevention, Nanjing 210009, Jiangsu, People's Republic China
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148
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A novel SNP in promoter region of RP11-3N2.1 is associated with reduced risk of colorectal cancer. J Hum Genet 2017; 63:47-54. [PMID: 29167551 DOI: 10.1038/s10038-017-0361-3] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2017] [Revised: 08/07/2017] [Accepted: 08/23/2017] [Indexed: 12/12/2022]
Abstract
Single-nucleotide polymorphisms (SNPs) in the promoter region of long intergenic non-coding RNAs (lincRNAs) could play a regulatory role in its expression level and then get involved in colorectal cancer (CRC). Thus, we conducted a two-stage case-control study to investigate the associations of Tag SNPs within the promoter region of selected lincRNAs from microarray data with risk of CRC. A total of 320 cases and 319 controls were recruited in the test set to explore the associations between 16 SNPs with no deviations from Hardy-Weinberg equilibrium (HWE) and risk of CRC. Furthermore, 501 cases and 538 controls were included as the validation set to confirm the significant associations. RP11-3N2.1 rs13230517 polymorphism was found to be negatively associated with CRC in both test set (AA vs. GG, OR = 0.68, 95% CI = 0.48-0.96) and validation set (AA vs. GG, OR = 0.76, 95% CI = 0.59-0.98). Pooled analysis showed that individuals with GA/AA genotypes had a significantly decreased risk of CRC when compared with those carrying GG genotype (OR = 0.74, 95% CI = 0.60-0.90) in the combined set. The crossover analysis revealed that rs13230517 GA/AA carriers had a decreased risk of CRC than GG carriers among non-drinkers in both test and combined set. However, no gene-environment multiplicative interactions were found on risk of CRC. Our findings suggest that rs13230517 polymorphism might participate in the pathogenesis of CRC and have the potential to be a biomarker for predicting the risk of CRC.
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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: 7.6] [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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150
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Dandelion root extract suppressed gastric cancer cells proliferation and migration through targeting lncRNA-CCAT1. Biomed Pharmacother 2017; 93:1010-1017. [DOI: 10.1016/j.biopha.2017.07.007] [Citation(s) in RCA: 46] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2017] [Revised: 06/22/2017] [Accepted: 07/03/2017] [Indexed: 01/05/2023] Open
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