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Yousefi B, Sadoughi F, Asemi Z, Mansournia MA, Hallajzadeh J. Novel Perspectives for the Diagnosis and Treatment of Gynecological Cancers using Dysregulation of PIWI Protein and PiRNAs as Biomarkers. Curr Med Chem 2024; 31:453-463. [PMID: 36786140 DOI: 10.2174/0929867330666230214101837] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2022] [Revised: 11/23/2022] [Accepted: 12/23/2022] [Indexed: 02/15/2023]
Abstract
The term "gynecological cancer" is used for a group of cancers occurring in the female reproductive system. Some of these cancers are ranked as the leading causes of death in developed and developing countries. The lack of proper diagnostic strategies is one of the most important reasons that make them lethal. PIWI-interacting RNAs or piRNAs are a class of small non-coding RNAs, which contain 24-32 nucleotides. These RNAs take part in some cellular mechanisms, and their role in diverse kinds of cancer is confirmed by accumulative evidence. In this review, we gather some information on the roles of these RNAs and members of the PIWI protein family to provide new insight into accurate diagnostic biomarkers and more effective anti-cancer drugs with fewer side effects.
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Affiliation(s)
- Bahman Yousefi
- Molecular Medicine Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
- Department of Biochemistry, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Fatemeh Sadoughi
- Research Center for Biochemistry and Nutrition in Metabolic Diseases, Institute for Basic Sciences, Kashan University of Medical Sciences, Kashan, I.R. Iran
| | - Zatollah Asemi
- Research Center for Biochemistry and Nutrition in Metabolic Diseases, Institute for Basic Sciences, Kashan University of Medical Sciences, Kashan, I.R. Iran
| | - Mohammad Ali Mansournia
- Department of Epidemiology and Biostatistics, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran
| | - Jamal Hallajzadeh
- Department of Biochemistry and Nutrition, Research Center for Evidence-Based Health Management, Maragheh University of Medical Sciences, Maragheh, Iran
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2
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Hashemi M, Hasani S, Hajimazdarany S, Mirmazloomi SR, Makvandy S, Zabihi A, Goldoost Y, Gholinia N, Kakavand A, Tavakolpournegari A, Salimimoghadam S, Nabavi N, Zarrabi A, Taheriazam A, Entezari M, Hushmandi K. Non-coding RNAs targeting notch signaling pathway in cancer: From proliferation to cancer therapy resistance. Int J Biol Macromol 2022; 222:1151-1167. [DOI: 10.1016/j.ijbiomac.2022.09.203] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2022] [Accepted: 09/22/2022] [Indexed: 11/26/2022]
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3
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Bao HJ, Chen X, Liu X, Wu W, Li QH, Xian JY, Zhao Y, Chen S. Box C/D snoRNA SNORD89 influences the occurrence and development of endometrial cancer through 2'-O-methylation modification of Bim. Cell Death Dis 2022; 8:309. [PMID: 35790714 PMCID: PMC9256700 DOI: 10.1038/s41420-022-01102-5] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2022] [Accepted: 06/24/2022] [Indexed: 11/23/2022]
Abstract
The small nucleolar RNA (snoRNA) is a type of small non-coding RNA widely distributed in the nucleoli of eukaryotic cells, promoting cancer development. The aim of this study was to assess box C/D snoRNA 89 (SNORD89) dysregulations in endometrial cancer. According to the TCGA database as well as the International Federation of Gynecology and Obstetrics (FIGO), higher SNORD89 expression is found in endometrial cancer tissues. In addition, the SNORD89 expression level was higher in endometrial carcinoma with lymph node metastasis than in endometrial carcinoma without lymph node metastasis. By interacting with the conservative chaperone protein methylase fibrillarin (Fbl), SNORD89 inhibits the translation process of the Bim gene, leading to a decrease in Bim protein. Cancer-promoting effect of SNORD89 can be reversed by Fbl knockdown or Bim overexpressing. What’s more, ASO-mediated silencing of SNORD89 could inhibit endometrial cancer cell proliferation and migration ability. Taken together, SNORD89 can modify Bim through 2′-O-methylation and affect downstream signaling pathways to promote endometrial cancer occurrence and development. The role of methylation modification in the prevention and treatment of endometrial cancer provides a new understanding and SNORD89 may be a new diagnostic and therapeutic target for endometrial cancer. Mechanism of action of SNORD89 ![]()
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Affiliation(s)
- Hai-Juan Bao
- Department of Obstetrics and Gynecology, Department of Gynecologic Oncology Research Office, Guangdong Provincial Key Laboratory of Major Obstetric Diseases, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510150, China
| | - Xi Chen
- Department of Obstetrics and Gynecology, Department of Gynecologic Oncology Research Office, Guangdong Provincial Key Laboratory of Major Obstetric Diseases, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510150, China
| | - Xin Liu
- Department of Obstetrics and Gynecology, Department of Gynecologic Oncology Research Office, Guangdong Provincial Key Laboratory of Major Obstetric Diseases, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510150, China
| | - Wu Wu
- Department of Obstetrics and Gynecology, Department of Gynecologic Oncology Research Office, Guangdong Provincial Key Laboratory of Major Obstetric Diseases, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510150, China
| | - Qian-Hui Li
- Department of Obstetrics and Gynecology, Department of Gynecologic Oncology Research Office, Guangdong Provincial Key Laboratory of Major Obstetric Diseases, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510150, China
| | - Jing-Yuan Xian
- Department of Obstetrics and Gynecology, Department of Gynecologic Oncology Research Office, Guangdong Provincial Key Laboratory of Major Obstetric Diseases, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510150, China
| | - Yang Zhao
- Department of Obstetrics and Gynecology, Department of Gynecologic Oncology Research Office, Guangdong Provincial Key Laboratory of Major Obstetric Diseases, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510150, China
| | - Shuo Chen
- Department of Obstetrics and Gynecology, Department of Gynecologic Oncology Research Office, Guangdong Provincial Key Laboratory of Major Obstetric Diseases, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510150, China.
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Karimpour M, Ravanbakhsh R, Maydanchi M, Rajabi A, Azizi F, Saber A. Cancer driver gene and non-coding RNA alterations as biomarkers of brain metastasis in lung cancer: A review of the literature. Biomed Pharmacother 2021; 143:112190. [PMID: 34560543 DOI: 10.1016/j.biopha.2021.112190] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2021] [Revised: 09/08/2021] [Accepted: 09/10/2021] [Indexed: 02/07/2023] Open
Abstract
Brain metastasis (BM) is the most common event in patients with lung cancer. Despite multimodal treatments and advances in systemic therapies, development of BM remains one of the main factors associated with poor prognosis and mortality in patients with lung cancer. Therefore, better understanding of mechanisms involved in lung cancer brain metastasis (LCBM) is of great importance to suppress cancer cells and to improve the overall survival of patients. Several cancer-related genes such as EGFR and KRAS have been proposed as potential predictors of LCBM. In addition, there is ample evidence supporting crucial roles of non-coding RNAs (ncRNAs) in mediating LCBM. In this review, we provide comprehensive information on risk assessment, predictive, and prognostic panels for early detection of BM in patients with lung cancer. Moreover, we present an overview of LCBM molecular mechanisms, cancer driver genes, and ncRNAs which may predict the risk of BM in lung cancer patients. Recent clinical studies have focused on determining mechanisms involved in LCBM and their association with diagnosis, prognosis, and treatment outcomes. These studies have shown that alterations in EGFR, KRAS, BRAF, and ALK, as the most frequent coding gene alterations, and dysregulation of ncRNAs such as miR-423, miR-330-3p, miR-145, piR-651, and MALAT1 can be considered as potential biomarkers of LCBM.
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Affiliation(s)
- Mina Karimpour
- Department of Genetics, Faculty of Biological Sciences, Tarbiat Modares University, Tehran, Iran
| | - Reyhaneh Ravanbakhsh
- Department of Aquatic Biotechnology, Artemia and Aquaculture Research Institute, Urmia University, Urmia, Iran
| | - Melika Maydanchi
- Zimagene Medical Genetics Laboratory, Avicenna St., Hamedan, Iran
| | - Ali Rajabi
- Department of Animal Biology, Faculty of Natural Sciences, University of Tabriz, Tabriz, Iran
| | - Faezeh Azizi
- Genetics Office, Non-Communicable Disease Control Department, Public Health Department, Ministry of Health and Medical Education, Tehran, Iran
| | - Ali Saber
- Zimagene Medical Genetics Laboratory, Avicenna St., Hamedan, Iran.
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Knockdown of PAK1 Inhibits the Proliferation and Invasion of Non-Small Cell Lung Cancer Cells Through the ERK Pathway. Appl Immunohistochem Mol Morphol 2021; 28:602-610. [PMID: 31394555 DOI: 10.1097/pai.0000000000000803] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
The p21-activated kinase (PAK) family of serine/threonine kinases plays a pivotal role in various human tumors, as supported by our previous report on the overexpressed PAK isoforms in non-small cell lung cancer (NSCLC). To better understand the role of PAKs in tumorigenesis, the authors examined PAK1 expression patterns and its significance in NSCLC. It was demonstrated by immunohistochemical staining that PAK1 was increased and localized in the cytoplasm in 151 of 207 cases. High levels of PAK1 expression correlated with a histologic type of tumor (squamous cell carcinoma), tumor node metastasis stage, and lymph nodal status. We also examined the biological role of PAK1 in lung cancer cell lines transfected with PAK1-small interfering RNA. Decreased expression of PAK1 inhibited lung cancer cell proliferation and invasion, which is the major cause of lung cancer malignancy. Downregulated expression of PAK1 hampered rapidly accelerated fibrosarcoma/mitogen-activated extracellular signal-regulated kinase/extracellular signal-regulated kinase pathway activity but did not affect Wnt/β-catenin signaling. Our findings suggest that PAK1 is an important oncogene in NSCLC, as decreased expression of PAK1 inhibited the proliferation and invasion of NSCLC cells by blocking the ERK pathway. These results provide evidence for using PAK1 inhibition as potential anticancer therapy.
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Yuan C, Qin H, Ponnusamy M, Chen Y, Lin Z. PIWI‑interacting RNA in cancer: Molecular mechanisms and possible clinical implications (Review). Oncol Rep 2021; 46:209. [PMID: 34328192 DOI: 10.3892/or.2021.8160] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2021] [Accepted: 07/05/2021] [Indexed: 11/06/2022] Open
Abstract
PIWI‑interacting RNA is a class of non‑coding small RNA that is ~30 nt long and is primarily found in mammalian germ cells from mice and humans. In cooperation with the members of PIWI protein family, this macromolecule participates in germ cell development, inhibits DNA self‑-replication and maintains genomic stability. Increasing evidence has demonstrated that PIWI‑interacting RNA (piRNAs) are abnormally expressed in various human cancers, such as liver cancer, stomach cancer, colorectal cancer, osteosarcoma, breast cancer, lung cancer, prostate cancer, etc. piRNAs abnormal expression is also associated with the occurrence and development of human cancers, such as liver cancer, stomach cancer, colorectal cancer, etc. Despite their unclear molecular mechanisms, piRNAs may act as oncogenes or tumor suppressors by interacting with multiple cancer‑related signal pathways including STAT3/Bcl‑xl or coding genes, such as heat shock transcription factor‑1. Hence, piRNAs may be potential markers and targets and provide new opportunities for cancer diagnosis, treatment or prognosis monitoring. The current review mainly aims to highlight the latest research progress made in the biological functions and regulation of piRNAs in mammals, their involvement in various cancer forms and their potential clinical applications.
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Affiliation(s)
- Chao Yuan
- Department of Basic Medicine, Key Lab for Immunology in Universities of Shandong Province, Immunology Lab, Weifang Medical University, Weifang, Shandong 261053, P.R. China
| | - Hao Qin
- Department of Public Health, Weifang Medical University, Weifang, Shandong 261053, P.R. China
| | - Murugavel Ponnusamy
- Department of Basic Medicine, Institute for Translational Medicine, Qingdao University, Qingdao, Shandong 266021, P.R. China
| | - Yong Chen
- Department of Basic Medicine, Key Lab for Immunology in Universities of Shandong Province, Immunology Lab, Weifang Medical University, Weifang, Shandong 261053, P.R. China
| | - Zhijuan Lin
- Department of Basic Medicine, Key Lab for Immunology in Universities of Shandong Province, Immunology Lab, Weifang Medical University, Weifang, Shandong 261053, P.R. China
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Klicka K, Grzywa TM, Klinke A, Mielniczuk A, Włodarski PK. The Role of miRNAs in the Regulation of Endometrial Cancer Invasiveness and Metastasis-A Systematic Review. Cancers (Basel) 2021; 13:3393. [PMID: 34298609 PMCID: PMC8304659 DOI: 10.3390/cancers13143393] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2021] [Revised: 06/18/2021] [Accepted: 07/02/2021] [Indexed: 12/17/2022] Open
Abstract
Endometrial cancer (EC) is the most common genital cancer in women with increasing death rates. MiRNAs are short non-coding RNAs that regulate gene expression on the post-transcriptional levels. Multiple studies demonstrated a fundamental role of miRNAs in the regulation of carcinogenesis. This systematic review is a comprehensive overview of the role of miRNAs in the regulation of cancer cell invasiveness and metastasis in EC. The literature was searched for studies investigating the role of miRNAs in the regulation of invasiveness and metastasis in EC. We explored PubMed, Embase, and Scopus using the following keywords: miRNA, metastasis, invasiveness, endometrial cancer. Data were collected from 163 articles that described the expression and role of 106 miRNAs in the regulation of EC invasiveness and metastasis out of which 63 were tumor suppressor miRNAs, and 38 were oncomiRNAs. Five miRNAs had a discordant role in different studies. Moreover, we identified 66 miRNAs whose expression in tumor tissue or concentration in serum correlated with at least one clinical parameter. These findings suggest a crucial role of miRNAs in the regulation of EC invasiveness and metastasis and present them as potential prognostic factors for patients with EC.
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Affiliation(s)
- Klaudia Klicka
- Department of Methodology, Medical University of Warsaw, 02-091 Warsaw, Poland; (K.K.); (T.M.G.); (A.K.); (A.M.)
- Doctoral School, Medical University of Warsaw, 02-091 Warsaw, Poland
| | - Tomasz M. Grzywa
- Department of Methodology, Medical University of Warsaw, 02-091 Warsaw, Poland; (K.K.); (T.M.G.); (A.K.); (A.M.)
- Doctoral School, Medical University of Warsaw, 02-091 Warsaw, Poland
- Department of Immunology, Medical University of Warsaw, 02-097 Warsaw, Poland
| | - Alicja Klinke
- Department of Methodology, Medical University of Warsaw, 02-091 Warsaw, Poland; (K.K.); (T.M.G.); (A.K.); (A.M.)
| | - Aleksandra Mielniczuk
- Department of Methodology, Medical University of Warsaw, 02-091 Warsaw, Poland; (K.K.); (T.M.G.); (A.K.); (A.M.)
| | - Paweł K. Włodarski
- Department of Methodology, Medical University of Warsaw, 02-091 Warsaw, Poland; (K.K.); (T.M.G.); (A.K.); (A.M.)
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8
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Zivarpour P, Asemi Z, Jamilian H, Hallajzadeh J. PiRNAs and PIWI proteins as new biomarkers for diagnosis and treatment of liver cancer. GENE REPORTS 2021. [DOI: 10.1016/j.genrep.2021.101103] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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9
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Seddon AR, Liau Y, Pace PE, Miller AL, Das AB, Kennedy MA, Hampton MB, Stevens AJ. Genome-wide impact of hydrogen peroxide on maintenance DNA methylation in replicating cells. Epigenetics Chromatin 2021; 14:17. [PMID: 33761969 PMCID: PMC7992848 DOI: 10.1186/s13072-021-00388-6] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2020] [Accepted: 03/01/2021] [Indexed: 12/22/2022] Open
Abstract
Background Environmental factors, such as oxidative stress, have the potential to modify the epigenetic landscape of cells. We have previously shown that DNA methyltransferase (DNMT) activity can be inhibited by sublethal doses of hydrogen peroxide (H2O2). However, site-specific changes in DNA methylation and the reversibility of any changes have not been explored. Using bead chip array technology, differential methylation was assessed in Jurkat T-lymphoma cells following exposure to H2O2. Results Sublethal H2O2 exposure was associated with an initial genome-wide decrease in DNA methylation in replicating cells, which was largely corrected 72 h later. However, some alterations were conserved through subsequent cycles of cell division. Significant changes to the variability of DNA methylation were also observed both globally and at the site-specific level. Conclusions This research indicates that increased exposure to H2O2 can result in long-term alterations to DNA methylation patterns, providing a mechanism for environmental factors to have prolonged impact on gene expression. Supplementary Information The online version contains supplementary material available at 10.1186/s13072-021-00388-6.
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Affiliation(s)
- Annika R Seddon
- Department of Pathology and Biomedical Science, University of Otago, PO Box 4345, Christchurch, 8140, New Zealand.
| | - Yusmiati Liau
- Department of Pathology and Biomedical Science, University of Otago, PO Box 4345, Christchurch, 8140, New Zealand
| | - Paul E Pace
- Department of Pathology and Biomedical Science, University of Otago, PO Box 4345, Christchurch, 8140, New Zealand
| | - Allison L Miller
- Department of Pathology and Biomedical Science, University of Otago, PO Box 4345, Christchurch, 8140, New Zealand
| | - Andrew B Das
- Department of Pathology and Biomedical Science, University of Otago, PO Box 4345, Christchurch, 8140, New Zealand
| | - Martin A Kennedy
- Department of Pathology and Biomedical Science, University of Otago, PO Box 4345, Christchurch, 8140, New Zealand
| | - Mark B Hampton
- Department of Pathology and Biomedical Science, University of Otago, PO Box 4345, Christchurch, 8140, New Zealand
| | - Aaron J Stevens
- Department of Pathology and Biomedical Science, University of Otago, PO Box 4345, Christchurch, 8140, New Zealand.
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10
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Dwivedi SKD, Rao G, Dey A, Mukherjee P, Wren JD, Bhattacharya R. Small Non-Coding-RNA in Gynecological Malignancies. Cancers (Basel) 2021; 13:1085. [PMID: 33802524 PMCID: PMC7961667 DOI: 10.3390/cancers13051085] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2021] [Revised: 02/18/2021] [Accepted: 02/25/2021] [Indexed: 12/12/2022] Open
Abstract
Gynecologic malignancies, which include cancers of the cervix, ovary, uterus, vulva, vagina, and fallopian tube, are among the leading causes of female mortality worldwide, with the most prevalent being endometrial, ovarian, and cervical cancer. Gynecologic malignancies are complex, heterogeneous diseases, and despite extensive research efforts, the molecular mechanisms underlying their development and pathology remain largely unclear. Currently, mechanistic and therapeutic research in cancer is largely focused on protein targets that are encoded by about 1% of the human genome. Our current understanding of 99% of the genome, which includes noncoding RNA, is limited. The discovery of tens of thousands of noncoding RNAs (ncRNAs), possessing either structural or regulatory functions, has fundamentally altered our understanding of genetics, physiology, pathophysiology, and disease treatment as they relate to gynecologic malignancies. In recent years, it has become clear that ncRNAs are relatively stable, and can serve as biomarkers for cancer diagnosis and prognosis, as well as guide therapy choices. Here we discuss the role of small non-coding RNAs, i.e., microRNAs (miRs), P-Element induced wimpy testis interacting (PIWI) RNAs (piRNAs), and tRNA-derived small RNAs in gynecological malignancies, specifically focusing on ovarian, endometrial, and cervical cancer.
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Affiliation(s)
- Shailendra Kumar Dhar Dwivedi
- Department of Obstetrics and Gynecology, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104, USA; (S.K.D.D.); (A.D.)
| | - Geeta Rao
- Department of Pathology, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104, USA; (G.R.); (P.M.)
| | - Anindya Dey
- Department of Obstetrics and Gynecology, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104, USA; (S.K.D.D.); (A.D.)
| | - Priyabrata Mukherjee
- Department of Pathology, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104, USA; (G.R.); (P.M.)
- Peggy and Charles Stephenson Cancer Center, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104, USA
| | - Jonathan D. Wren
- Biochemistry and Molecular Biology Department, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104, USA;
- Oklahoma Center for Neuroscience, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104, USA
- Genes & Human Disease Research Program, Oklahoma Medical Research Foundation, Oklahoma City, OK 73104, USA
| | - Resham Bhattacharya
- Department of Obstetrics and Gynecology, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104, USA; (S.K.D.D.); (A.D.)
- Peggy and Charles Stephenson Cancer Center, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104, USA
- Department of Cell Biology, University of Oklahoma Health Science Center, Oklahoma City, OK 73104, USA
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11
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Salimimoghadam S, Taefehshokr S, Loveless R, Teng Y, Bertoli G, Taefehshokr N, Musaviaroo F, Hajiasgharzadeh K, Baradaran B. The role of tumor suppressor short non-coding RNAs on breast cancer. Crit Rev Oncol Hematol 2020; 158:103210. [PMID: 33385514 DOI: 10.1016/j.critrevonc.2020.103210] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2020] [Revised: 12/15/2020] [Accepted: 12/20/2020] [Indexed: 12/11/2022] Open
Abstract
Characterized by remarkable levels of aggression and malignancy, BC remains one of the leading causes of death in females world wide. Accordingly, significant efforts have been made to develop early diagnostic tools, increase treatment efficacy, and improve patient prognosis. Hopefully, many of the molecular mechanisms underlying BC have been detected and show promising targeting potential. In particular, short and long non-coding RNAs (ncRNAs) are a class of endogenous BC controllers and include a number of different species including microRNAs, Piwi-interacting RNAs, small nucleolar RNA, short interfering RNAs, and tRNA-derivatives. In this review, we discuss the tumor suppressing roles of ncRNAs in the context of BC, and the mechanisms by which ncRNAs target tumor hallmarks, including apoptosis, proliferation, invasion, metastasis, epithelial-mesenchymal transition, angiogenesis, and cell cycle progression, in addition to their diagnostic and prognostic significance in cancer treatment.
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Affiliation(s)
| | - Sina Taefehshokr
- Immunology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran.
| | - Reid Loveless
- Department of Oral Biology and Diagnostic Sciences, Augusta University, Augusta, GA, USA; Georgia Cancer Center, Augusta University, Augusta, GA, USA.
| | - Yong Teng
- Department of Oral Biology and Diagnostic Sciences, Augusta University, Augusta, GA, USA; Georgia Cancer Center, Augusta University, Augusta, GA, USA.
| | - Gloria Bertoli
- Institute of Molecular Bioimaging and Physiology, National Research Council (IBFM-CNR), Segrate, Milan, Italy.
| | - Nima Taefehshokr
- Department of Microbiology and Immunology, Center for Human Immunology, The University of Western Ontario, London, Ontario, Canada.
| | | | | | - Behzad Baradaran
- Immunology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran.
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12
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Razavi ZS, Tajiknia V, Majidi S, Ghandali M, Mirzaei HR, Rahimian N, Hamblin MR, Mirzaei H. Gynecologic cancers and non-coding RNAs: Epigenetic regulators with emerging roles. Crit Rev Oncol Hematol 2020; 157:103192. [PMID: 33290823 DOI: 10.1016/j.critrevonc.2020.103192] [Citation(s) in RCA: 81] [Impact Index Per Article: 20.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2020] [Revised: 11/30/2020] [Accepted: 12/01/2020] [Indexed: 12/24/2022] Open
Abstract
Gynecologic cancers involve the female genital organs, such as the vulva, vagina, cervix, endometrium, ovaries, and fallopian tubes. The occurrence and frequency of gynecologic cancer depends on personal lifestyle, history of exposure to viruses or carcinogens, genetics, body shape, and geographical habitat. For a long time, research into the molecular biology of cancer was broadly restricted to protein-coding genes. Recently it has been realized that non-coding RNAs (ncRNA), including long noncoding RNAs (LncRNAs), microRNAs, circular RNAs and piRNAs (PIWI-interacting RNAs), can all play a role in the regulation of cellular function within gynecological cancer. It is now known that ncRNAs are able to play dual roles, i.e. can exert both oncogenic or tumor suppressive functions in gynecological cancer. Moreover, several clinical trials are underway looking at the biomarker and therapeutic roles of ncRNAs. These efforts may provide a new horizon for the diagnosis and treatment of gynecological cancer. Herein, we summarize some of the ncRNAs that have been shown to be important in gynecological cancers.
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Affiliation(s)
| | - Vida Tajiknia
- Department of Surgery, School of Medicine, Iran University of Medical Sciences, Tehran, Iran
| | - Shahab Majidi
- Student Research Committee, Fasa University of Medical Sciences, Fasa, Iran
| | - Maryam Ghandali
- School of Medicine, Iran University of Medical Sciences, Tehran, Iran
| | - Hamid Reza Mirzaei
- Department of Medical Immunology, School of Medicine, Tehran University of Medical Sciences, Tehran, Iran
| | - Neda Rahimian
- Endocrine Research Center, Institute of Endocrinology and Metabolism, Iran University of Medical Sciences (IUMS), Tehran, Iran.
| | - Michael R Hamblin
- Wellman Center for Photomedicine, Massachusetts General Hospital, Boston, MA, 02114, USA; Department of Dermatology, Harvard Medical School, Boston, MA, 02115, USA; Laser Research Centre, Faculty of Health Science, University of Johannesburg, Doornfontein, 2028, South Africa.
| | - Hamed Mirzaei
- Research Center for Biochemistry and Nutrition in Metabolic Diseases, Institute for Basic Sciences, Kashan University of Medical Sciences, Kashan, Iran.
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13
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Hallal S, Ebrahim Khani S, Wei H, Lee MYT, Sim HW, Sy J, Shivalingam B, Buckland ME, Alexander-Kaufman KL. Deep Sequencing of Small RNAs from Neurosurgical Extracellular Vesicles Substantiates miR-486-3p as a Circulating Biomarker that Distinguishes Glioblastoma from Lower-Grade Astrocytoma Patients. Int J Mol Sci 2020; 21:ijms21144954. [PMID: 32668808 PMCID: PMC7404297 DOI: 10.3390/ijms21144954] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2020] [Revised: 07/01/2020] [Accepted: 07/07/2020] [Indexed: 02/07/2023] Open
Abstract
Extracellular vesicles (EVs) play key roles in glioblastoma (GBM; astrocytoma grade IV) biology and are novel sources of biomarkers. EVs released from GBM tumors can cross the blood-brain-barrier into the periphery carrying GBM molecules, including small non-coding RNA (sncRNA). Biomarkers cargoed in circulating EVs have shown great promise for assessing the molecular state of brain tumors in situ. Neurosurgical aspirate fluids captured during tumor resections are a rich source of GBM-EVs isolated directly from tumor microenvironments. Using density gradient ultracentrifugation, EVs were purified from cavitron ultrasonic surgical aspirate (CUSA) washings from GBM (n = 12) and astrocytoma II-III (GII-III, n = 5) surgeries. The sncRNA contents of surgically captured EVs were profiled using the Illumina® NextSeqTM 500 NGS System. Differential expression analysis identified 27 miRNA and 10 piRNA species in GBM relative to GII-III CUSA-EVs. Resolved CUSA-EV sncRNAs could discriminate serum-EV sncRNA profiles from GBM and GII-III patients and healthy controls and 14 miRNAs (including miR-486-3p and miR-106b-3p) and cancer-associated piRNAs (piR_016658, _016659, _020829 and _204090) were also significantly expressed in serum-EVs. Circulating EV markers that correlate with histological, neuroradiographic and clinical parameters will provide objective measures of tumor activity and improve the accuracy of GBM tumor surveillance.
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Affiliation(s)
- Susannah Hallal
- Department of Neurosurgical Services, Chris O’Brien Lifehouse, Camperdown 2050, Australia; (S.H.); (B.S.)
- Discipline of Pathology, School of Medical Sciences, The University of Sydney, Camperdown 2006, Australia; (S.E.K.); (M.E.B.)
- Brainstorm Brain Cancer Research, Brain and Mind Centre, The University of Sydney, Camperdown 2050, Australia; (H.W.); (M.Y.T.L.)
- Neuropathology Department, Royal Prince Alfred Hospital, Camperdown 2050, Australia;
| | - Saeideh Ebrahim Khani
- Discipline of Pathology, School of Medical Sciences, The University of Sydney, Camperdown 2006, Australia; (S.E.K.); (M.E.B.)
| | - Heng Wei
- Brainstorm Brain Cancer Research, Brain and Mind Centre, The University of Sydney, Camperdown 2050, Australia; (H.W.); (M.Y.T.L.)
- Neuropathology Department, Royal Prince Alfred Hospital, Camperdown 2050, Australia;
| | - Maggie Yuk Ting Lee
- Brainstorm Brain Cancer Research, Brain and Mind Centre, The University of Sydney, Camperdown 2050, Australia; (H.W.); (M.Y.T.L.)
- Neuropathology Department, Royal Prince Alfred Hospital, Camperdown 2050, Australia;
| | - Hao-Wen Sim
- Department of Medical Oncology and NHMRC Clinical Trials Centre, Chris O’Brien Lifehouse, Camperdown 2050, Australia;
- Central Clinical School, The University of Sydney, Camperdown 2006, Australia
- The Kinghorn Cancer Centre, St Vincent’s Hospital, Darlinghurst 2010, Australia
| | - Joanne Sy
- Neuropathology Department, Royal Prince Alfred Hospital, Camperdown 2050, Australia;
| | - Brindha Shivalingam
- Department of Neurosurgical Services, Chris O’Brien Lifehouse, Camperdown 2050, Australia; (S.H.); (B.S.)
- Brainstorm Brain Cancer Research, Brain and Mind Centre, The University of Sydney, Camperdown 2050, Australia; (H.W.); (M.Y.T.L.)
| | - Michael E. Buckland
- Discipline of Pathology, School of Medical Sciences, The University of Sydney, Camperdown 2006, Australia; (S.E.K.); (M.E.B.)
- Brainstorm Brain Cancer Research, Brain and Mind Centre, The University of Sydney, Camperdown 2050, Australia; (H.W.); (M.Y.T.L.)
- Neuropathology Department, Royal Prince Alfred Hospital, Camperdown 2050, Australia;
| | - Kimberley L. Alexander-Kaufman
- Department of Neurosurgical Services, Chris O’Brien Lifehouse, Camperdown 2050, Australia; (S.H.); (B.S.)
- Discipline of Pathology, School of Medical Sciences, The University of Sydney, Camperdown 2006, Australia; (S.E.K.); (M.E.B.)
- Brainstorm Brain Cancer Research, Brain and Mind Centre, The University of Sydney, Camperdown 2050, Australia; (H.W.); (M.Y.T.L.)
- Neuropathology Department, Royal Prince Alfred Hospital, Camperdown 2050, Australia;
- Correspondence: ; Tel.: +61-2-8514-0675
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14
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Feng J, Yang M, Wei Q, Song F, Zhang Y, Wang X, Liu B, Li J. Novel evidence for oncogenic piRNA-823 as a promising prognostic biomarker and a potential therapeutic target in colorectal cancer. J Cell Mol Med 2020; 24:9028-9040. [PMID: 32596991 PMCID: PMC7417729 DOI: 10.1111/jcmm.15537] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2019] [Revised: 05/29/2020] [Accepted: 06/02/2020] [Indexed: 12/16/2022] Open
Abstract
piRNA‐823 as a member of the piRNA family is reported to promote tumour cell proliferation in multiple myeloma and hepatocellular cancer. However, few studies on the function of piRNA‐823 in colorectal cancer (CRC). Our present study data showed that piRNA‐823 plays an oncogene role in CRC cells. Inhibition of piRNA‐823 can significantly inhibit the proliferation, invasion and apoptosis resistance of CRC cells. Mechanism studies have shown that piRNA‐823 inhibits the ubiquitination of hypoxia‐inducible factor‐1 alpha (HIF‐1α) by up‐regulating the expression of Glucose‐6‐phosphate dehydrogenase (G6PD) and ultimately up‐regulates the glucose consumption of carcinoma cells and inhibits the content of intracellular reactive oxygen species (ROS). Therefore, we speculate piRNA‐823 promotes the proliferation, invasion and apoptosis resistance of CRC cells by regulating G6PD/HIF‐1α pathway. In this study, we set up the cancer‐promoting function recovery experiment of piRNA‐823 by silencing G6PD gene to confirm the dominance of the above‐mentioned pathways. Using clinical samples, we found that overexpression of piRNA‐823 correlated with poor overall survival and predicted a poor response to adjuvant chemotherapy of patients with CRC. In a word, our research has further enriched the theory of piRNA‐823 promoting the progression of CRC, and laid a solid foundation for the development of piRNA‐823‐based gene therapy for CRC and its use as a promising prognostic biomarker in CRC patients.
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Affiliation(s)
- Junlan Feng
- Department of General Surgery, School of Medicine, Shanghai Tenth People's Hospital, Tongji University, Shanghai, China
| | - Muqing Yang
- Department of General Surgery, School of Medicine, Shanghai Tenth People's Hospital, Tongji University, Shanghai, China
| | - Qing Wei
- Department of Pathology, School of Medicine, Shanghai Tenth People's Hospital, Tongji University, Shanghai, China
| | - Feifei Song
- Department of Pathology, School of Medicine, Shanghai Tenth People's Hospital, Tongji University, Shanghai, China
| | - Youhua Zhang
- Department of Pathology, School of Medicine, Shanghai Tenth People's Hospital, Tongji University, Shanghai, China
| | - Xiaodong Wang
- Department of General Surgery, School of Medicine, Shanghai Tenth People's Hospital, Tongji University, Shanghai, China
| | - Bin Liu
- Department of General Surgery, School of Medicine, Shanghai Tenth People's Hospital, Tongji University, Shanghai, China
| | - Jiyu Li
- Department of General Surgery, School of Medicine, Shanghai Tenth People's Hospital, Tongji University, Shanghai, China
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15
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Bauersachs S, Mermillod P, Almiñana C. The Oviductal Extracellular Vesicles' RNA Cargo Regulates the Bovine Embryonic Transcriptome. Int J Mol Sci 2020; 21:ijms21041303. [PMID: 32075098 PMCID: PMC7072903 DOI: 10.3390/ijms21041303] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2020] [Revised: 02/11/2020] [Accepted: 02/12/2020] [Indexed: 12/11/2022] Open
Abstract
Oviductal extracellular vesicles (oEVs) are emerging as key players in the gamete/embryo–oviduct interactions that contribute to successful pregnancy. Various positive effects of oEVs on gametes and early embryos have been found in vitro. To determine whether these effects are associated with changes of embryonic gene expression, the transcriptomes of embryos supplemented with bovine fresh (FeEVs) or frozen (FoEVs) oEVs during in vitro culture compared to controls without oEVs were analyzed by low-input RNA sequencing. Analysis of RNA-seq data revealed 221 differentially expressed genes (DEGs) between FoEV treatment and control, 67 DEGs for FeEV and FoEV treatments, and minor differences between FeEV treatment and control (28 DEGs). An integrative analysis of mRNAs and miRNAs contained in oEVs obtained in a previous study with embryonic mRNA alterations pointed to direct effects of oEV cargo on embryos (1) by increasing the concentration of delivered transcripts; (2) by translating delivered mRNAs to proteins that regulate embryonic gene expression; and (3) by oEV-derived miRNAs which downregulate embryonic mRNAs or modify gene expression in other ways. Our study provided the first high-throughput analysis of the embryonic transcriptome regulated by oEVs, increasing our knowledge on the impact of oEVs on the embryo and revealing the oEV RNA components that potentially regulate embryonic development.
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Affiliation(s)
- Stefan Bauersachs
- Genetics and Functional Genomics, VetSuisse Faculty Zurich, University of Zurich, 8315 Lindau (ZH), Switzerland;
| | - Pascal Mermillod
- UMR85 PRC, INRA, CNRS 7247, Université de Tours, IFCE, 37380 Nouzilly, France;
| | - Carmen Almiñana
- Genetics and Functional Genomics, VetSuisse Faculty Zurich, University of Zurich, 8315 Lindau (ZH), Switzerland;
- UMR85 PRC, INRA, CNRS 7247, Université de Tours, IFCE, 37380 Nouzilly, France;
- Correspondence:
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16
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Sundar IK, Li D, Rahman I. Small RNA-sequence analysis of plasma-derived extracellular vesicle miRNAs in smokers and patients with chronic obstructive pulmonary disease as circulating biomarkers. J Extracell Vesicles 2019; 8:1684816. [PMID: 31762962 PMCID: PMC6848892 DOI: 10.1080/20013078.2019.1684816] [Citation(s) in RCA: 92] [Impact Index Per Article: 18.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2019] [Revised: 09/24/2019] [Accepted: 10/20/2019] [Indexed: 12/12/2022] Open
Abstract
Extracellular vesicles (EVs) play a vital role in normal lung physiology to maintain homeostasis in the airways via intercellular communication. EVs include exosomes and microvesicles, and are characterized by their phospholipid bilayers. EVs have been recognized as novel circulating biomarkers of disease, which are released by different cell types. In this study, we used different EV isolation and purification methods to characterize the plasma-derived EV miRNAs from non-smokers, smokers and patients with COPD. A small RNA sequencing (RNA-seq) approach was adapted to identify novel circulating EV miRNAs. We found that plasma-derived EVs from non-smokers, smokers and patients with COPD vary in their size, concentration, distribution and phenotypic characteristics as confirmed by nanoparticle tracking analysis, transmission electron microscopy, and immunoblot analysis of EV surface markers. RNA-seq analysis confirmed the most abundant types of small RNAs, such as miRNAs, tRNAs, piRNAs snRNAs, snoRNAs and other biotypes in plasma-derived EVs. We mainly focused on miRNAs as novel biomarkers in smokers and patients with COPD for further analysis. Differential expression by DESeq2 identified distinct miRNA profiles (up-regulated: miR-22-3p, miR-99a-5p, miR-151a-5p, miR-320b, miR-320d; and down-regulated: miR-335-5p, miR-628-3p, miR-887-5p and miR-937-3p) in COPD versus smokers or non-smokers in a pairwise comparison. Gene set enrichment analysis (GSEA) of differentially expressed miRNAs revealed the top pathways, gene ontology and diseases associated with smokers and patients with COPD. We selectively validated miRNAs in EVs isolated from BEAS-2B cells treated with cigarette smoke extract by quantitative PCR analysis. For the first time, we report that plasma-derived EV miRNAs are novel circulating pulmonary disease biomarkers. Thus, molecular profiling of EV miRNAs has great translational potential for the development of biomarkers that may be used in the diagnosis, prognosis, and therapeutics of COPD.
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Affiliation(s)
- Isaac Kirubakaran Sundar
- Department of Environmental Medicine, University of Rochester Medical Center, Rochester, NY, USA
| | - Dongmei Li
- Department of Clinical & Translational Research, University of Rochester Medical Center, Rochester, NY, USA
| | - Irfan Rahman
- Department of Environmental Medicine, University of Rochester Medical Center, Rochester, NY, USA
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17
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Zeng JH, Lu W, Liang L, Chen G, Lan HH, Liang XY, Zhu X. Prognosis of clear cell renal cell carcinoma (ccRCC) based on a six-lncRNA-based risk score: an investigation based on RNA-sequencing data. J Transl Med 2019; 17:281. [PMID: 31443717 PMCID: PMC6708203 DOI: 10.1186/s12967-019-2032-y] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2019] [Accepted: 08/18/2019] [Indexed: 02/07/2023] Open
Abstract
Background The scientific understanding of long non-coding RNAs (lncRNAs) has improved in recent decades. Nevertheless, there has been little research into the role that lncRNAs play in clear cell renal cell carcinoma (ccRCC). More lncRNAs are assumed to influence the progression of ccRCC via their own molecular mechanisms. Methods This study investigated the prognostic significance of differentially expressed lncRNAs by mining high-throughput lncRNA-sequencing data from The Cancer Genome Atlas (TCGA) containing 13,198 lncRNAs from 539 patients. Differentially expressed lncRNAs were assessed using the R packages edgeR and DESeq. The prognostic significance of lncRNAs was measured using univariate Cox proportional hazards regression. ccRCC patients were then categorized into high- and low-score cohorts based on the cumulative distribution curve inflection point the of risk score, which was generated by the multivariate Cox regression model. Samples from the TCGA dataset were divided into training and validation subsets to verify the prognostic risk model. Bioinformatics methods, gene set enrichment analysis, and protein–protein interaction networks, Gene Ontology, and Kyoto Encyclopedia of Genes and Genomes analyses were subsequently used. Results It was found that the risk score based on 6 novel lncRNAs (CTA-384D8.35, CTD-2263F21.1, LINC01510, RP11-352G9.1, RP11-395B7.2, RP11-426C22.4) exhibited superior prognostic value for ccRCC. Moreover, we categorized the cases into two groups (high-risk and low-risk), and also examined related pathways and genetic differences between them. Kaplan–Meier curves indicated that the median survival time of patients in the high-risk group was 73.5 months, much shorter than that of the low-risk group (112.6 months; P < 0.05). Furthermore, the risk score predicted the 5-year survival of all 539 ccRCC patients (AUC at 5 years, 0.683; concordance index [C-index], 0.853; 95% CI 0.817–0.889). The training set and validation set also showed similar performance (AUC at 5 years, 0.649 and 0.681, respectively; C-index, 0.822 and 0.891; 95% CI 0.774–0.870 and 0.844–0.938). Conclusions The results of this study can be applied to analyzing various prognostic factors, leading to new possibilities for clinical diagnosis and prognosis of ccRCC.
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Affiliation(s)
- Jiang-Hui Zeng
- Department of Clinical Laboratory, The Third Affiliated Hospital of Guangxi Medical University/Nanning Second People's Hospital, 13 Dancun Road, Nanning, 530031, Guangxi Zhuang Autonomous Region, People's Republic of China
| | - Wei Lu
- Department of Pathology, The Third Affiliated Hospital of Guangxi Medical University/Nanning Second People's Hospital, 13 Dancun Road, Nanning, 530031, Guangxi Zhuang Autonomous Region, People's Republic of China
| | - Liang Liang
- Department of General Surgery, The Second Affiliated Hospital of Guangxi Medical University, 166 Daxuedong Road, Nanning, Guangxi Zhuang Autonomous Region, People's Republic of China
| | - Gang Chen
- Department of Pathology, First Affiliated Hospital of Guangxi Medical University, 6 Shuangyong Road, Nanning, 530021, Guangxi Zhuang Autonomous Region, People's Republic of China
| | - Hui-Hua Lan
- Department of Clinical Laboratory, The People's Hospital of Guangxi Zhuang Autonomous Region, 6 Taoyuan Road, Nanning, Guangxi Zhuang Autonomous Region, People's Republic of China
| | - Xiu-Yun Liang
- Department of Clinical Laboratory, The Third Affiliated Hospital of Guangxi Medical University/Nanning Second People's Hospital, 13 Dancun Road, Nanning, 530031, Guangxi Zhuang Autonomous Region, People's Republic of China
| | - Xu Zhu
- Department of Clinical Laboratory, The Third Affiliated Hospital of Guangxi Medical University/Nanning Second People's Hospital, 13 Dancun Road, Nanning, 530031, Guangxi Zhuang Autonomous Region, People's Republic of China.
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18
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Sun T, Han X. The disease-related biological functions of PIWI-interacting RNAs (piRNAs) and underlying molecular mechanisms. ACTA ACUST UNITED AC 2019. [DOI: 10.1186/s41544-019-0021-1] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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19
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Torella D, Iaconetti C, Tarallo R, Marino F, Giurato G, Veneziano C, Aquila I, Scalise M, Mancuso T, Cianflone E, Valeriano C, Marotta P, Tammè L, Vicinanza C, Sasso FC, Cozzolino D, Torella M, Weisz A, Indolfi C. miRNA Regulation of the Hyperproliferative Phenotype of Vascular Smooth Muscle Cells in Diabetes. Diabetes 2018; 67:2554-2568. [PMID: 30257973 DOI: 10.2337/db17-1434] [Citation(s) in RCA: 46] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/10/2017] [Accepted: 09/14/2018] [Indexed: 02/05/2023]
Abstract
Harnessing the mechanisms underlying the exacerbated vascular remodeling in diabetes mellitus (DM) is pivotal to prevent the high toll of vascular diseases in patients with DM. miRNA regulates vascular smooth muscle cell (VSMC) phenotypic switch. However, miRNA modulation of the detrimental diabetic VSMC phenotype is underexplored. Streptozotocin-induced type 1 DM (T1DM) Wistar rats and type 2 DM (T2DM) Zucker rats underwent right carotid artery experimental angioplasty, and global miRNA/mRNA expression profiling was obtained by RNA sequencing (RNA-Seq). Two days after injury, a set of six miRNAs were found to be uniquely downregulated or upregulated in VSMCs both in T1DM and T2DM. Among these miRNAs, miR-29c and miR-204 were the most significantly misregulated in atherosclerotic plaques from patients with DM. miR-29c overexpression and miR-204 inhibition per se attenuated VSMC phenotypic switch in DM. Concomitant miR-29c overexpression and miR-204 inhibition fostered an additive reduction in VSMC proliferation. Epithelial membrane protein 2 (Emp2) and Caveolin-1 (Cav1) mRNAs were identified as direct targets of miR-29c and miR-204, respectively. Importantly, contemporary miR-29c overexpression and miR-204 inhibition in the injured artery robustly reduced arterial stenosis in DM rats. Thus, contemporaneous miR-29c activation and miR-204 inhibition in DM arterial tissues is necessary and sufficient to prevent the exaggerated VSMC growth upon injury.
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MESH Headings
- Animals
- Cell Proliferation/physiology
- Diabetes Mellitus, Experimental/metabolism
- Diabetes Mellitus, Experimental/pathology
- Diabetes Mellitus, Type 1/metabolism
- Diabetes Mellitus, Type 1/pathology
- Diabetes Mellitus, Type 2/metabolism
- Diabetes Mellitus, Type 2/pathology
- Humans
- Male
- MicroRNAs/metabolism
- Muscle, Smooth, Vascular/metabolism
- Muscle, Smooth, Vascular/pathology
- Myocytes, Smooth Muscle/metabolism
- Myocytes, Smooth Muscle/pathology
- Plaque, Atherosclerotic/metabolism
- Plaque, Atherosclerotic/pathology
- Rats
- Rats, Wistar
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Affiliation(s)
- Daniele Torella
- Cardiovascular Institute, Department of Medical and Surgical Sciences, Magna Graecia University, Catanzaro, Italy
| | - Claudio Iaconetti
- Cardiovascular Institute, Department of Medical and Surgical Sciences, Magna Graecia University, Catanzaro, Italy
| | - Roberta Tarallo
- Laboratory of Molecular Medicine and Genomics, Department of Medicine, Surgery and Dentistry "Scuola Medica Salernitana," University of Salerno, Baronissi, Salerno, Italy
| | - Fabiola Marino
- Cardiovascular Institute, Department of Medical and Surgical Sciences, Magna Graecia University, Catanzaro, Italy
| | - Giorgio Giurato
- Laboratory of Molecular Medicine and Genomics, Department of Medicine, Surgery and Dentistry "Scuola Medica Salernitana," University of Salerno, Baronissi, Salerno, Italy
- Genomix4Life srl, Department of Medicine, Surgery and Dentistry "Scuola Medica Salernitana," University of Salerno, Baronissi, Salerno, Italy
| | - Claudia Veneziano
- Cardiovascular Institute, Department of Medical and Surgical Sciences, Magna Graecia University, Catanzaro, Italy
| | - Iolanda Aquila
- Cardiovascular Institute, Department of Medical and Surgical Sciences, Magna Graecia University, Catanzaro, Italy
| | - Mariangela Scalise
- Cardiovascular Institute, Department of Medical and Surgical Sciences, Magna Graecia University, Catanzaro, Italy
| | - Teresa Mancuso
- Cardiovascular Institute, Department of Medical and Surgical Sciences, Magna Graecia University, Catanzaro, Italy
| | - Eleonora Cianflone
- Cardiovascular Institute, Department of Medical and Surgical Sciences, Magna Graecia University, Catanzaro, Italy
| | - Chiara Valeriano
- Cardiovascular Institute, Department of Medical and Surgical Sciences, Magna Graecia University, Catanzaro, Italy
| | - Pina Marotta
- Cardiovascular Institute, Department of Medical and Surgical Sciences, Magna Graecia University, Catanzaro, Italy
| | - Laura Tammè
- Cardiovascular Institute, Department of Medical and Surgical Sciences, Magna Graecia University, Catanzaro, Italy
| | - Carla Vicinanza
- Cardiovascular Institute, Department of Medical and Surgical Sciences, Magna Graecia University, Catanzaro, Italy
| | - Ferdinando C Sasso
- Department of Internal and Experimental Medicine "Magrassi-Lanzara," University of Campania "L. Vanvitelli," Naples, Italy
| | - Domenico Cozzolino
- Department of Internal and Experimental Medicine "Magrassi-Lanzara," University of Campania "L. Vanvitelli," Naples, Italy
| | - Michele Torella
- Department of Cardiothoracic Sciences, University of Campania "L. Vanvitelli," Naples, Italy
| | - Alessandro Weisz
- Laboratory of Molecular Medicine and Genomics, Department of Medicine, Surgery and Dentistry "Scuola Medica Salernitana," University of Salerno, Baronissi, Salerno, Italy
| | - Ciro Indolfi
- Cardiovascular Institute, Department of Medical and Surgical Sciences, Magna Graecia University, Catanzaro, Italy
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20
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Lacunza E, Montanaro MA, Salvati A, Memoli D, Rizzo F, Henning MF, Quiroga IY, Guillou H, Abba MC, Gonzalez-Baro MDR, Weisz A, Pellon-Maison M. Small non-coding RNA landscape is modified by GPAT2 silencing in MDA-MB-231 cells. Oncotarget 2018; 9:28141-28154. [PMID: 29963267 PMCID: PMC6021339 DOI: 10.18632/oncotarget.25582] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2017] [Accepted: 04/28/2018] [Indexed: 01/13/2023] Open
Abstract
Glycerol-3-phosphate acyltransferase-2 is a member of "cancer-testis gene" family. Initially linked to lipid metabolism, this gene has been recently found involved also in PIWI-interacting RNAs biogenesis in germline stem cells. To investigate its role in piRNA metabolism in cancer, the gene was silenced in MDA-MB-231 breast cancer cells and small RNA sequencing was applied. PIWI-interacting RNAs and tRNA-derived fragments expression profiles showed changes following GPAT2 silencing. Interestingly, a marked shift in length distribution for both small RNAs was detected in GPAT2-silenced cells. Most downregulated PIWI-interacting RNAs are single copy in the genome, intragenic, hosted in snoRNAs and previously found to be upregulated in cancer cells. Putative targets of these PIWI-interacting RNAs are linked to lipid metabolism. Downregulated tRNA derived fragments derived from, so-called 'differentiation tRNAs', whereas upregulated ones derived from proliferation-linked tRNAs. miRNA amounts decrease after Glycerol-3-phosphate acyltransferase-2 silencing and functional enrichment analysis of deregulated miRNA putative targets point to mitochondrial biogenesis, IGF1R signaling and oxidative metabolism of lipids and lipoproteins. In addition, miRNAs known to be overexpressed in breast cancer tumors with poor prognosis where found downregulated in GPAT2-silenced cells. In conclusion, GPAT2 silencing quantitatively and qualitatively affects the population of PIWI-interacting RNAs, tRNA derived fragments and miRNAs which, in combination, result in a more differentiated cancer cell phenotype.
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Affiliation(s)
- Ezequiel Lacunza
- Centro de Investigaciones Inmunológicas Básicas y Aplicadas, Facultad de Ciencias Médicas, Universidad Nacional de La Plata, La Plata, Argentina
| | - Mauro Aldo Montanaro
- Instituto de Investigaciones Bioquímicas de La Plata, Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Universidad Nacional de La Plata, La Plata, Argentina
| | - Annamaria Salvati
- Laboratory of Molecular Medicine and Genomics, Department of Medicine, Surgery and Dentistry "Scuola Medica Salernitana", University of Salerno, Baronissi, SA, Italy
| | - Domenico Memoli
- Laboratory of Molecular Medicine and Genomics, Department of Medicine, Surgery and Dentistry "Scuola Medica Salernitana", University of Salerno, Baronissi, SA, Italy
| | - Francesca Rizzo
- Laboratory of Molecular Medicine and Genomics, Department of Medicine, Surgery and Dentistry "Scuola Medica Salernitana", University of Salerno, Baronissi, SA, Italy.,Genomix4Life, Department of Medicine, Surgery and Dentistry "Schola Medica Salernitana", University of Salerno, Baronissi, SA, Italy
| | - Maria Florencia Henning
- Instituto de Investigaciones Bioquímicas de La Plata, Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Universidad Nacional de La Plata, La Plata, Argentina
| | - Ivana Yoseli Quiroga
- Instituto de Investigaciones Bioquímicas de La Plata, Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Universidad Nacional de La Plata, La Plata, Argentina
| | - Hervé Guillou
- Toxalim, Université de Toulouse, INRA, ENVT, INP-Purpan, UPS, Toulouse, France
| | - Martín Carlos Abba
- Centro de Investigaciones Inmunológicas Básicas y Aplicadas, Facultad de Ciencias Médicas, Universidad Nacional de La Plata, La Plata, Argentina
| | - María Del Rosario Gonzalez-Baro
- Instituto de Investigaciones Bioquímicas de La Plata, Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Universidad Nacional de La Plata, La Plata, Argentina
| | - Alessandro Weisz
- Laboratory of Molecular Medicine and Genomics, Department of Medicine, Surgery and Dentistry "Scuola Medica Salernitana", University of Salerno, Baronissi, SA, Italy.,Genomix4Life, Department of Medicine, Surgery and Dentistry "Schola Medica Salernitana", University of Salerno, Baronissi, SA, Italy
| | - Magalí Pellon-Maison
- Instituto de Investigaciones Bioquímicas de La Plata, Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Universidad Nacional de La Plata, La Plata, Argentina
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21
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Tusup M, Kundig T, Pascolo S. Epitranscriptomics of cancer. World J Clin Oncol 2018; 9:42-55. [PMID: 29900123 PMCID: PMC5997933 DOI: 10.5306/wjco.v9.i3.42] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/07/2018] [Revised: 04/18/2018] [Accepted: 05/23/2018] [Indexed: 02/06/2023] Open
Abstract
The functional impact of modifications of cellular RNAs, including mRNAs, miRNAs and lncRNAs, is a field of intense study. The role of such modifications in cancer has started to be elucidated. Diverse and sometimes opposite effects of RNA modifications have been reported. Some RNA modifications promote, while others decrease the growth and invasiveness of cancer. The present manuscript reviews the current knowledge on the potential impacts of N6-Methyladenosine, Pseudouridine, Inosine, 2’O-methylation or methylcytidine in cancer’s RNA. It also highlights the remaining questions and provides hints on research avenues and potential therapeutic applications, whereby modulating dynamic RNA modifications may be a new method to treat cancer.
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Affiliation(s)
- Marina Tusup
- Department of Dermatology, University Hospital of Zürich, Zurich 8091, Switzerland
- Faculty of Medicine, University of Zurich, Zurich 8091, Switzerland
| | - Thomas Kundig
- Department of Dermatology, University Hospital of Zürich, Zurich 8091, Switzerland
- Faculty of Medicine, University of Zurich, Zurich 8091, Switzerland
| | - Steve Pascolo
- Department of Dermatology, University Hospital of Zürich, Zurich 8091, Switzerland
- Faculty of Medicine, University of Zurich, Zurich 8091, Switzerland
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22
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Yang B, Xu B, Zhao H, Wang YB, Zhang J, Li CW, Wu Q, Cao YK, Li Y, Cao F. Dioscin protects against coronary heart disease by reducing oxidative stress and inflammation via Sirt1/Nrf2 and p38 MAPK pathways. Mol Med Rep 2018; 18:973-980. [PMID: 29845299 DOI: 10.3892/mmr.2018.9024] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2017] [Accepted: 01/11/2018] [Indexed: 11/06/2022] Open
Abstract
Cardiovascular diseases are common diseases in Sweden as in most countries. In 2016, 25,700 persons suffered from coronary heart disease (CHD) and 25% of these died within 28 days. The present study investigated whether dioscin may exert protective effects against CHD‑induced heart apoptosis, oxidative stress and inflammation in a pig model and the potential underlying mechanisms. Adult pigs were used to establish a CHD model group and 80 mg/kg dioscin was administered for 4 weeks. Histological analysis and measurement of serum levels of heart injury markers demonstrated that 80 mg/kg dioscin markedly alleviated CHD, while left ventricular ejection fraction and left ventricular systolic internal diameter measurements indicated that 80 mg/kg dioscin also increased heart function in the CHD pig model. Furthermore, western blotting demonstrated that 80 mg/kg dioscin significantly reduced protein levels of apoptosis markers in the heart of CHD model pigs, including Bcl‑2‑associated X and caspase‑3, potentially via the suppression of poly (ADP‑ribose) polymerase 1 (PARP)/p53 expression. Additionally, the results of ELISA and western blotting demonstrated that 80 mg/kg dioscin may reduce oxidative stress and inflammation in CHD model pigs through the promotion of sirtuin 1 (Sirt1)/nuclear factor erythroid 2‑related factor 2 (Nrf2) protein expression and the suppression of PARP/p53 and p38 mitogen‑activated protein kinase (MAPK) expression. The results of the current study indicate that dioscin may protect against CHD by regulating oxidative stress and inflammation via Sirt1/Nrf2 and p38 MAPK pathways.
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Affiliation(s)
- Bo Yang
- Department of Cardiology, Chinese PLA General Hospital, Beijing 100853, P.R. China
| | - Bin Xu
- Department of Cardiology, Chinese PLA General Hospital, Beijing 100853, P.R. China
| | - Hua Zhao
- Department of Cardiology, Chinese PLA General Hospital, Beijing 100853, P.R. China
| | - Ya-Bin Wang
- Department of Cardiology, Chinese PLA General Hospital, Beijing 100853, P.R. China
| | - Jian Zhang
- Department of Cardiology, Chinese PLA General Hospital, Beijing 100853, P.R. China
| | - Chuan-Wei Li
- Department of Cardiology, Chinese PLA General Hospital, Beijing 100853, P.R. China
| | - Qing Wu
- Department of Cardiology, Chinese PLA General Hospital, Beijing 100853, P.R. China
| | - Yu-Kang Cao
- Department of Cardiology, Chinese PLA General Hospital, Beijing 100853, P.R. China
| | - Yang Li
- Department of Cardiology, Chinese PLA General Hospital, Beijing 100853, P.R. China
| | - Feng Cao
- Department of Cardiology, Chinese PLA General Hospital, Beijing 100853, P.R. China
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23
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Chuang TD, Xie Y, Yan W, Khorram O. Next-generation sequencing reveals differentially expressed small noncoding RNAs in uterine leiomyoma. Fertil Steril 2018; 109:919-929. [PMID: 29778390 PMCID: PMC6445395 DOI: 10.1016/j.fertnstert.2018.01.034] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2017] [Revised: 01/20/2018] [Accepted: 01/24/2018] [Indexed: 12/12/2022]
Abstract
OBJECTIVE To determine the expression profile of small noncoding RNAs (sncRNAs) in leiomyoma, which has not been investigated to date. DESIGN Laboratory-based investigation. SETTING Academic center. PATIENT(S) Women undergoing hysterectomy for benign indications. INTERVENTION(S) Next-generation sequencing and screening of an sncRNA database with confirmatory analysis by quantitative reverse-transcription polymerase chain reaction (qRT-PCR). MAIN OUTCOME MEASURE(S) Expression profile of sncRNAs in leiomyoma and matched myometrium. RESULT(S) Screening our previously determined RNA sequencing data with the sncRNA database resulted in identification of 15 small nuclear (sn) RNAs, 284 small nucleolar (sno) RNAs, 98 Piwi-interacting (pi) RNAs, 152 transfer (t) RNAs, and 45 ribosomal (r) RNAs, of which 15 snoRNAs, 24 piRNAs, 7 tRNAs, and 6 rRNAs were differentially expressed at a 1.5-fold change cutoff in leiomyoma compared with myometrium. We selected 5 snoRNAs, 4 piRNAs, 1 tRNA, and 1 rRNA that were differentially expressed and confirmed their expression in paired tissues (n = 20) from both phases of the menstrual cycle with the use of qRT-PCR. The results indicated up-regulation of the snoRNAs (SNORD30, SNORD27, SNORA16A, SNORD46, and SNORD56) and down-regulation of the piRNAs (piR-1311, piR-16677, piR-20365, piR-4153), tRNA (TRG-GCC5-1), and rRNA (RNA5SP202) expression in leiomyoma compared with myometrium (P<.05). The pattern of expression of these sncRNAs was similar to RNA sequencing analysis, with no menstrual cycle-dependent differences detected except for SNORD30. Because Argonaute 2 (AGO2) is required for sncRNA-mediated gene silencing, we determined its expression and found greater abundance in leiomyoma. CONCLUSION(S) Our results provide the first evidence for the differential expression of additional classes of sncRNAs and AGO2 in leiomyoma, implicating their roles as a gene regulatory mechanism.
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Affiliation(s)
- Tsai-Der Chuang
- Department of Obstetrics and Gynecology, Harbor-UCLA Medical Center and LA-Biomed Research Institute, Torrance, California
| | - Yeming Xie
- Department of Physiology and Cell Biology, University of Nevada, Reno School of Medicine, Reno, Nevada
| | - Wei Yan
- Department of Physiology and Cell Biology, University of Nevada, Reno School of Medicine, Reno, Nevada
| | - Omid Khorram
- Department of Obstetrics and Gynecology, Harbor-UCLA Medical Center and LA-Biomed Research Institute, Torrance, California.
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24
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Non-Coding RNAs and Endometrial Cancer. Genes (Basel) 2018; 9:genes9040187. [PMID: 29596364 PMCID: PMC5924529 DOI: 10.3390/genes9040187] [Citation(s) in RCA: 42] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2018] [Revised: 03/13/2018] [Accepted: 03/27/2018] [Indexed: 01/03/2023] Open
Abstract
Non-coding RNAs (ncRNAs) are involved in the regulation of cell metabolism and neoplastic transformation. Recent studies have tried to clarify the significance of these information carriers in the genesis and progression of various cancers and their use as biomarkers for the disease; possible targets for the inhibition of growth and invasion by the neoplastic cells have been suggested. The significance of ncRNAs in lung cancer, bladder cancer, kidney cancer, and melanoma has been amply investigated with important results. Recently, the role of long non-coding RNAs (lncRNAs) has also been included in cancer studies. Studies on the relation between endometrial cancer (EC) and ncRNAs, such as small ncRNAs or micro RNAs (miRNAs), transfer RNAs (tRNAs), ribosomal RNAs (rRNAs), antisense RNAs (asRNAs), small nuclear RNAs (snRNAs), Piwi-interacting RNAs (piRNAs), small nucleolar RNAs (snoRNAs), competing endogenous RNAs (ceRNAs), lncRNAs, and long intergenic ncRNAs (lincRNAs) have been published. The recent literature produced in the last three years was extracted from PubMed by two independent readers, which was then selected for the possible relation between ncRNAs, oncogenesis in general, and EC in particular.
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25
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Rizzo F, Rinaldi A, Marchese G, Coviello E, Sellitto A, Cordella A, Giurato G, Nassa G, Ravo M, Tarallo R, Milanesi L, Destro A, Torzilli G, Roncalli M, Di Tommaso L, Weisz A. Specific patterns of PIWI-interacting small noncoding RNA expression in dysplastic liver nodules and hepatocellular carcinoma. Oncotarget 2018; 7:54650-54661. [PMID: 27429044 PMCID: PMC5342370 DOI: 10.18632/oncotarget.10567] [Citation(s) in RCA: 54] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2016] [Accepted: 06/06/2016] [Indexed: 11/25/2022] Open
Abstract
Hepatocellular carcinoma (HCC) is the result of a stepwise process, often beginning with development within a cirrhotic liver of premalignant lesions, morphologically characterized by low- (LGDN) and high-grade (HGDN) dysplastic nodules. PIWI-interacting RNAs (piRNAs) are small noncoding RNAs (sncRNAs), 23-35 nucleotide-long, exerting epigenetic and post-transcriptional regulation of gene expression. Recently the PIWI-piRNA pathway, best characterized in germline cells, has been identified also in somatic tissues, including stem and cancer cells, where it influences key cellular processes.Small RNA sequencing was applied to search for liver piRNAs and to profile their expression patterns in cirrhotic nodules (CNs), LGDN, HGDN, early HCC and progressed HCC (pHCC), analyzing 55 samples (14 CN, 9 LGDN, 6 HGDN, 6 eHCC and 20 pHCC) from 17 patients, aiming at identifying possible relationships between these sncRNAs and liver carcinogenesis. We identified a 125 piRNA expression signature that characterize HCC from matched CNs, correlating also to microvascular invasion in HCC. Functional analysis of the predicted RNA targets of deregulated piRNAs indicates that these can target key signaling pathways involved in hepatocarcinogenesis and HCC progression, thereby affecting their activity. Interestingly, 24 piRNAs showed specific expression patterns in dysplastic nodules, respect to cirrhotic liver and/or pHCC.The results demonstrate that the PIWI-piRNA pathway is active in human liver, where it represents a new player in the molecular events that characterize hepatocarcinogenesis, from early stages to pHCC. Furthermore, they suggest that piRNAs might be new disease biomarkers, useful for differential diagnosis of dysplastic and neoplastic liver lesions.
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Affiliation(s)
- Francesca Rizzo
- Laboratory of Molecular Medicine and Genomics, Department of Medicine, Surgery and Dentistry 'Schola Medica Salernitana', University of Salerno, Baronissi (SA), Italy
| | - Antonio Rinaldi
- Laboratory of Molecular Medicine and Genomics, Department of Medicine, Surgery and Dentistry 'Schola Medica Salernitana', University of Salerno, Baronissi (SA), Italy
| | | | - Elena Coviello
- Laboratory of Molecular Medicine and Genomics, Department of Medicine, Surgery and Dentistry 'Schola Medica Salernitana', University of Salerno, Baronissi (SA), Italy
| | - Assunta Sellitto
- Laboratory of Molecular Medicine and Genomics, Department of Medicine, Surgery and Dentistry 'Schola Medica Salernitana', University of Salerno, Baronissi (SA), Italy
| | | | - Giorgio Giurato
- Laboratory of Molecular Medicine and Genomics, Department of Medicine, Surgery and Dentistry 'Schola Medica Salernitana', University of Salerno, Baronissi (SA), Italy.,Genomix4life, University of Salerno, Baronissi (SA), Italy
| | - Giovanni Nassa
- Laboratory of Molecular Medicine and Genomics, Department of Medicine, Surgery and Dentistry 'Schola Medica Salernitana', University of Salerno, Baronissi (SA), Italy.,Genomix4life, University of Salerno, Baronissi (SA), Italy
| | - Maria Ravo
- Laboratory of Molecular Medicine and Genomics, Department of Medicine, Surgery and Dentistry 'Schola Medica Salernitana', University of Salerno, Baronissi (SA), Italy
| | - Roberta Tarallo
- Laboratory of Molecular Medicine and Genomics, Department of Medicine, Surgery and Dentistry 'Schola Medica Salernitana', University of Salerno, Baronissi (SA), Italy
| | - Luciano Milanesi
- Institute for Biomedical Technologies, National Research Council, Milano, Italy
| | - Anna Destro
- Pathology Unit, Humanitas Clinical and Research Center, Rozzano-Milan, Italy
| | - Guido Torzilli
- Department of Biomedical Sciences, Humanitas University, Rozzano-Milan, Italy.,Hepatobiliary and General Surgery Division, Humanitas Clinical and Research Center, Rozzano-Milan, Italy
| | - Massimo Roncalli
- Pathology Unit, Humanitas Clinical and Research Center, Rozzano-Milan, Italy.,Department of Biomedical Sciences, Humanitas University, Rozzano-Milan, Italy
| | - Luca Di Tommaso
- Pathology Unit, Humanitas Clinical and Research Center, Rozzano-Milan, Italy.,Department of Biomedical Sciences, Humanitas University, Rozzano-Milan, Italy
| | - Alessandro Weisz
- Laboratory of Molecular Medicine and Genomics, Department of Medicine, Surgery and Dentistry 'Schola Medica Salernitana', University of Salerno, Baronissi (SA), Italy
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26
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Singh G, Roy J, Rout P, Mallick B. Genome-wide profiling of the PIWI-interacting RNA-mRNA regulatory networks in epithelial ovarian cancers. PLoS One 2018; 13:e0190485. [PMID: 29320577 PMCID: PMC5761873 DOI: 10.1371/journal.pone.0190485] [Citation(s) in RCA: 41] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2017] [Accepted: 12/17/2017] [Indexed: 12/27/2022] Open
Abstract
PIWI-interacting (piRNAs), ~23–36 nucleotide-long small non-coding RNAs (sncRNAs), earlier believed to be germline-specific, have now been identified in somatic cells, including cancer cells. These sncRNAs impact critical biological processes by fine-tuning gene expression at post-transcriptional and epigenetic levels. The expression of piRNAs in ovarian cancer, the most lethal gynecologic cancer is largely uncharted. In this study, we investigated the expression of PIWILs by qRT-PCR and western blotting and then identified piRNA transcriptomes in tissues of normal ovary and two most prevalent epithelial ovarian cancer subtypes, serous and endometrioid by small RNA sequencing. We detected 219, 256 and 234 piRNAs in normal ovary, endometrioid and serous ovarian cancer samples respectively. We observed piRNAs are encoded from various genomic regions, among which introns harbor the majority of them. Surprisingly, piRNAs originated from different genomic contexts showed the varied level of conservations across vertebrates. The functional analysis of predicted targets of differentially expressed piRNAs revealed these could modulate key processes and pathways involved in ovarian oncogenesis. Our study provides the first comprehensive piRNA landscape in these samples and a useful resource for further functional studies to decipher new mechanistic views of piRNA-mediated gene regulatory networks affecting ovarian oncogenesis. The RNA-seq data is submitted to GEO database (GSE83794).
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Affiliation(s)
- Garima Singh
- RNAi and Functional Genomics Laboratory, Department of Life Science, National Institute of Technology – Rourkela, Odisha, India
| | - Jyoti Roy
- RNAi and Functional Genomics Laboratory, Department of Life Science, National Institute of Technology – Rourkela, Odisha, India
| | - Pratiti Rout
- RNAi and Functional Genomics Laboratory, Department of Life Science, National Institute of Technology – Rourkela, Odisha, India
| | - Bibekanand Mallick
- RNAi and Functional Genomics Laboratory, Department of Life Science, National Institute of Technology – Rourkela, Odisha, India
- * E-mail: ,
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27
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Panero R, Rinaldi A, Memoli D, Nassa G, Ravo M, Rizzo F, Tarallo R, Milanesi L, Weisz A, Giurato G. iSmaRT: a toolkit for a comprehensive analysis of small RNA-Seq data. Bioinformatics 2017; 33:938-940. [PMID: 28057684 DOI: 10.1093/bioinformatics/btw734] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2016] [Accepted: 11/15/2016] [Indexed: 11/13/2022] Open
Abstract
Summary The interest in investigating the biological roles of small non-coding RNAs (sncRNAs) is increasing, due to the pleiotropic effects of these molecules exert in many biological contexts. While several methods and tools are available to study microRNAs (miRNAs), only few focus on novel classes of sncRNAs, in particular PIWI-interacting RNAs (piRNAs). To overcome these limitations, we implemented iSmaRT ( i ntegrative Sm all R NA T ool-kit), an automated pipeline to analyze smallRNA-Seq data. Availability and Implementation iSmaRT is a collection of bioinformatics tools and own algorithms, interconnected through a Graphical User Interface (GUI). In addition to performing comprehensive analyses on miRNAs, it implements specific computational modules to analyze piRNAs, predicting novel ones and identifying their RNA targets. A smallRNA-Seq dataset generated from brain samples of Huntington's Disease patients was used here to illustrate iSmaRT performances, demonstrating how the pipeline can provide, in a rapid and user friendly way, a comprehensive analysis of different classes of sncRNAs. iSmaRT is freely available on the web at ftp://labmedmolge-1.unisa.it (User: iSmart - Password: password). Contact aweisz@unisa.it or ggiurato@unisa.it. Supplementary information Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Riccardo Panero
- Laboratory of Molecular Medicine and Genomics, Department of Medicine, Surgery and Dentistry 'Scuola Medica Salernitana', University of Salerno, Baronissi, SA, Italy.,Department of Molecular Biotechnology and Health Sciences, University of Torino, via Nizza 52, Torino, Italy
| | - Antonio Rinaldi
- Laboratory of Molecular Medicine and Genomics, Department of Medicine, Surgery and Dentistry 'Scuola Medica Salernitana', University of Salerno, Baronissi, SA, Italy
| | - Domenico Memoli
- Laboratory of Molecular Medicine and Genomics, Department of Medicine, Surgery and Dentistry 'Scuola Medica Salernitana', University of Salerno, Baronissi, SA, Italy
| | - Giovanni Nassa
- Laboratory of Molecular Medicine and Genomics, Department of Medicine, Surgery and Dentistry 'Scuola Medica Salernitana', University of Salerno, Baronissi, SA, Italy.,Genomix4Life, University of Salerno, Baronissi, SA, Italy
| | - Maria Ravo
- Laboratory of Molecular Medicine and Genomics, Department of Medicine, Surgery and Dentistry 'Scuola Medica Salernitana', University of Salerno, Baronissi, SA, Italy
| | - Francesca Rizzo
- Laboratory of Molecular Medicine and Genomics, Department of Medicine, Surgery and Dentistry 'Scuola Medica Salernitana', University of Salerno, Baronissi, SA, Italy
| | - Roberta Tarallo
- Laboratory of Molecular Medicine and Genomics, Department of Medicine, Surgery and Dentistry 'Scuola Medica Salernitana', University of Salerno, Baronissi, SA, Italy
| | - Luciano Milanesi
- Institute for Biomedical Technologies, National Research Council, Segrate, MI, Italy
| | - Alessandro Weisz
- Laboratory of Molecular Medicine and Genomics, Department of Medicine, Surgery and Dentistry 'Scuola Medica Salernitana', University of Salerno, Baronissi, SA, Italy
| | - Giorgio Giurato
- Laboratory of Molecular Medicine and Genomics, Department of Medicine, Surgery and Dentistry 'Scuola Medica Salernitana', University of Salerno, Baronissi, SA, Italy.,Genomix4Life, University of Salerno, Baronissi, SA, Italy
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28
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Yoshida K, Toden S, Weng W, Shigeyasu K, Miyoshi J, Turner J, Nagasaka T, Ma Y, Takayama T, Fujiwara T, Goel A. SNORA21 - An Oncogenic Small Nucleolar RNA, with a Prognostic Biomarker Potential in Human Colorectal Cancer. EBioMedicine 2017; 22:68-77. [PMID: 28734806 PMCID: PMC5552212 DOI: 10.1016/j.ebiom.2017.07.009] [Citation(s) in RCA: 50] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2017] [Revised: 06/29/2017] [Accepted: 07/10/2017] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND Emerging evidence indicates that small nucleolar RNAs (snoRNAs) play a central role in oncogenesis. Herein, we systematically evaluated expression profiles of snoRNAs in colorectal cancer (CRC) and investigated their clinical and functional role in this malignancy. METHODS We compared expression levels of snoRNAs between cancer and normal tissues using publicly available datasets and identified the most differentially expressed and commonly upregulated snoRNAs in CRC. These results were examined in 489 colorectal tissues to assess their clinical significance, followed by a series of in vitro and in vivo experiments to evaluate the functional role of candidate snoRNAs. RESULTS Using multiple RNA profiling datasets, we identified consistent overexpression of SNORA21 in CRC. In the clinical validation cohorts, the expression level of SNORA21 was upregulated in colorectal adenomas and cancers. Furthermore, elevated SNORA21 emerged as an independent factor for predicting poor survival. Both in vitro and in vivo experiments revealed that CRISPR/Cas9-mediated inhibition of SNORA21 expression resulted in decreased cell proliferation and invasion through modulation of multiple cancer related pathways. CONCLUSIONS We systematically identified SNORA21 as a key oncogenic snoRNA in CRC, which plays an important role in cancer progression, and might serve as an important prognostic biomarker in CRC.
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Affiliation(s)
- Kazuhiro Yoshida
- Center for Gastrointestinal Research, Center for Translational Genomics and Oncology, Baylor Scott & White Research Institute, Charles A Sammons Cancer Center, Baylor University Medical Center, Dallas, TX, USA
| | - Shusuke Toden
- Center for Gastrointestinal Research, Center for Translational Genomics and Oncology, Baylor Scott & White Research Institute, Charles A Sammons Cancer Center, Baylor University Medical Center, Dallas, TX, USA
| | - Wenhao Weng
- Center for Gastrointestinal Research, Center for Translational Genomics and Oncology, Baylor Scott & White Research Institute, Charles A Sammons Cancer Center, Baylor University Medical Center, Dallas, TX, USA
| | - Kunitoshi Shigeyasu
- Center for Gastrointestinal Research, Center for Translational Genomics and Oncology, Baylor Scott & White Research Institute, Charles A Sammons Cancer Center, Baylor University Medical Center, Dallas, TX, USA; Department of Gastroenterological Surgery and Surgical Oncology, Okayama University Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama, Japan
| | - Jinsei Miyoshi
- Center for Gastrointestinal Research, Center for Translational Genomics and Oncology, Baylor Scott & White Research Institute, Charles A Sammons Cancer Center, Baylor University Medical Center, Dallas, TX, USA; Department of Gastroenterology and Oncology, Institute of Health Biosciences, University of Tokushima Graduate School, Tokushima, Japan
| | - Jacob Turner
- Center of Biostatistics, Baylor Research Institute, Baylor University Medical Center, Dallas, TX, USA
| | - Takeshi Nagasaka
- Department of Gastroenterological Surgery and Surgical Oncology, Okayama University Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama, Japan
| | - Yanlei Ma
- Department of Gastrointestinal Surgery, Shanghai Tenth People's Hospital, Shanghai, China
| | - Tetsuji Takayama
- Department of Gastroenterology and Oncology, Institute of Health Biosciences, University of Tokushima Graduate School, Tokushima, Japan
| | - Toshiyoshi Fujiwara
- Department of Gastroenterological Surgery and Surgical Oncology, Okayama University Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama, Japan
| | - Ajay Goel
- Center for Gastrointestinal Research, Center for Translational Genomics and Oncology, Baylor Scott & White Research Institute, Charles A Sammons Cancer Center, Baylor University Medical Center, Dallas, TX, USA.
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29
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Kurnit KC, Kim G, Fellman BM, Urbauer D, Mills GB, Zhang W, Broaddus RR. CTNNB1 (beta-catenin) mutation identifies low grade, early stage endometrial cancer patients at increased risk of recurrence. Mod Pathol 2017; 30:1032-1041. [PMID: 28281553 PMCID: PMC5493522 DOI: 10.1038/modpathol.2017.15] [Citation(s) in RCA: 197] [Impact Index Per Article: 28.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2016] [Revised: 01/27/2017] [Accepted: 01/27/2017] [Indexed: 12/12/2022]
Abstract
Although the majority of low grade, early stage endometrial cancer patients will have good survival outcomes with surgery alone, those patients who do recur tend to do poorly. Optimal identification of the subset of patients who are at high risk of recurrence and would benefit from adjuvant treatment has been difficult. The purpose of this study was to evaluate the impact of somatic tumor mutation on survival outcomes in this patient population. For this study, low grade was defined as endometrioid FIGO grades 1 or 2, while early stage was defined as endometrioid stages I or II (disease confined to the uterus). Next-generation sequencing was performed using panels comprised of 46-200 genes. Recurrence-free and overall survival was compared across gene mutational status in both univariate and multivariate analyses. In all, 342 patients were identified, 245 of which had endometrioid histology. For grades 1-2, stages I-II endometrioid endometrial cancer patients, age (HR 1.07, 95% CI 1.03-1.10), CTNNB1 mutation (HR 5.97, 95% CI 2.69-13.21), and TP53 mutation (HR 4.07, 95% CI 1.57-10.54) were associated with worse recurrence-free survival on multivariate analysis. When considering endometrioid tumors of all grades and stages, CTNNB1 mutant tumors were associated with significantly higher rates of grades 1-2 disease, lower rates of deep myometrial invasion, and lower rates of lymphatic/vascular space invasion. When both TP53 and CTNNB1 mutations were considered, presence of either TP53 mutation or CTNNB1 mutation remained a statistically significant predictor of recurrence-free survival on multivariate analysis and was associated with a more precise confidence interval (HR 4.69, 95% CI 2.38-9.24). Thus, mutational analysis of a 2 gene panel of CTNNB1 and TP53 can help to identify a subset of low grade, early stage endometrial cancer patients who are at high risk of recurrence.
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Affiliation(s)
- Katherine C. Kurnit
- The University of Texas MD Anderson Cancer Center, Houston, TX, Department of Gynecologic Oncology and Reproductive Medicine
| | - Grace Kim
- The University of California-Irvine School of Medicine, Irvine, California, Department of Pathology & Laboratory Medicine
| | - Bryan M. Fellman
- The University of Texas MD Anderson Cancer Center, Houston, TX, Department of Biostatistics
| | - Diana Urbauer
- The University of Texas MD Anderson Cancer Center, Houston, TX, Department of Biostatistics
| | - Gordon B. Mills
- The University of Texas MD Anderson Cancer Center, Houston, TX, Department of Systems Biology
| | - Wei Zhang
- Wake Forest University School of Medicine, Department of Cancer Biology, Winston-Salem, North Carolina
| | - Russell R. Broaddus
- The University of Texas MD Anderson Cancer Center, Houston, TX, Department of Pathology
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30
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Bartosch C, Lopes JM, Jerónimo C. Epigenetics in endometrial carcinogenesis - part 2: histone modifications, chromatin remodeling and noncoding RNAs. Epigenomics 2017; 9:873-892. [PMID: 28523964 DOI: 10.2217/epi-2016-0167] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Carcinogenesis is a multistep multifactorial process that involves the accumulation of genetic and epigenetic alterations. In the past two decades, there has been an exponential growth of knowledge establishing the importance of epigenetic changes in cancer. Our work focused on reviewing the main role of epigenetics in the pathogenesis of endometrial carcinoma, highlighting the reported results concerning each epigenetic mechanistic layer. In a previous review, we assessed DNA methylation alterations. The present review examines the contribution of histone modifications, chromatin remodeling and noncoding RNA alterations for endometrial carcinogenesis.
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Affiliation(s)
- Carla Bartosch
- Department of Pathology, Portuguese Oncology Institute of Porto (IPO-Porto), Porto, Portugal.,Cancer Biology & Epigenetics Group, Research Center (CI-IPOP), Portuguese Oncology Institute of Porto, Porto, Portugal.,Department of Pathology & Oncology, Medical Faculty, University of Porto, Porto, Portugal.,Porto Comprehensive Cancer Center (P.ccc), Porto, Portugal
| | - José Manuel Lopes
- Department of Pathology & Oncology, Medical Faculty, University of Porto, Porto, Portugal.,Department of Pathology, Centro Hospitalar São João (CHSJ), Porto, Portugal.,IPATIMUP (Institute of Molecular Pathology & Immunology, University of Porto); I3S-Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal
| | - Carmen Jerónimo
- Cancer Biology & Epigenetics Group, Research Center (CI-IPOP), Portuguese Oncology Institute of Porto, Porto, Portugal.,Porto Comprehensive Cancer Center (P.ccc), Porto, Portugal.,Department of Pathology & Molecular Immunology, Institute of Biomedical Sciences Abel Salazar (ICBAS), University of Porto, Porto, Portugal
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31
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Bam M, Yang X, Sen S, Zumbrun EE, Dennis L, Zhang J, Nagarkatti PS, Nagarkatti M. Characterization of Dysregulated miRNA in Peripheral Blood Mononuclear Cells from Ischemic Stroke Patients. Mol Neurobiol 2017; 55:1419-1429. [PMID: 28168424 DOI: 10.1007/s12035-016-0347-8] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2016] [Accepted: 12/07/2016] [Indexed: 12/31/2022]
Abstract
Epigenetic modification may play an important role in pathophysiology of ischemic stroke (IS) risk. MicroRNAs (miRNAs), which constitute one of the modes of epigenetic regulation, have been shown to be associated with a number of clinical disorders including IS. The purpose of this study was to investigate the miRNA profile in the peripheral blood mononuclear cells (PBMCs) of IS patients and compare it with stroke-free controls. Blood samples were obtained from 19 healthy age-gender-race matched individuals who served as controls to 20 IS patients. miRNA microarray analysis with RNA from PBMCs was performed and significantly dysregulated miRNAs common among IS patients were identified. We identified 117 miRNAs with linear fold values of at least ±1.5, of which, 29 were significantly altered (p value <0.05). Ingenuity Pathway Analysis (IPA) indicated a role for the dysregulated miRNAs in conditions relevant to IS (e.g., organismal injury and abnormalities, hematological disease and immunological disease). Pro-inflammatory genes like STAT3, interleukin (IL) 12A, and IL12B were some of the highly predicted targets for the dysregulated miRNAs. Notably, we further identified three common and significantly upregulated miRNAs (hsa-miR-4656, -432, -503) and one downregulated miRNA (hsa-miR-874) among all IS patients. Molecular interactive network analysis revealed that the commonly dysregulated miRNAs share several targets with roles relevant to IS. Altogether, we report dysregulation of miRNAs in IS PBMCs and provide evidence for their involvement in the immune system alteration during IS pathophysiology.
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Affiliation(s)
- Marpe Bam
- Department of Pathology, Microbiology and Immunology, University of South Carolina School of Medicine, Columbia, SC, 29209, USA
| | - Xiaoming Yang
- Department of Pathology, Microbiology and Immunology, University of South Carolina School of Medicine, Columbia, SC, 29209, USA
| | - Souvik Sen
- Department of Neurology, University of South Carolina School of Medicine, Columbia, SC, 29203, USA
| | - Elizabeth E Zumbrun
- Department of Pathology, Microbiology and Immunology, University of South Carolina School of Medicine, Columbia, SC, 29209, USA
| | - Lauren Dennis
- Department of Neurology, University of South Carolina School of Medicine, Columbia, SC, 29203, USA
| | - Jiajia Zhang
- Department of Epidemiology and Biostatistics, Arnold School of Public Health, University of South Carolina, Columbia, SC, 29206, USA
| | - Prakash S Nagarkatti
- Department of Pathology, Microbiology and Immunology, University of South Carolina School of Medicine, Columbia, SC, 29209, USA
| | - Mitzi Nagarkatti
- Department of Pathology, Microbiology and Immunology, University of South Carolina School of Medicine, Columbia, SC, 29209, USA. .,Department of Neurology, University of South Carolina School of Medicine, Columbia, SC, 29203, USA.
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32
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Su J, Liao J, Gao L, Shen J, Guarnera MA, Zhan M, Fang H, Stass SA, Jiang F. Analysis of small nucleolar RNAs in sputum for lung cancer diagnosis. Oncotarget 2017; 7:5131-42. [PMID: 26246471 PMCID: PMC4868676 DOI: 10.18632/oncotarget.4219] [Citation(s) in RCA: 46] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2014] [Accepted: 05/09/2015] [Indexed: 12/15/2022] Open
Abstract
Molecular analysis of sputum presents a noninvasive approach for diagnosis of lung cancer. We have shown that dysregulation of small nucleolar RNAs (snoRNAs) plays a vital role in lung tumorigenesis. We have also identified six snoRNAs whose changes are associated with lung cancer. Here we investigated if analysis of the snoRNAs in sputum could provide a potential tool for diagnosis of lung cancer. Using qRT-PCR, we determined expressions of the six snoRNAs in sputum of a training set of 59 lung cancer patients and 61 cancer-free smokers to develop a biomarker panel, which was validated in a testing set of 67 lung cancer patients and 69 cancer-free smokers for the diagnostic performance. The snoRNAs were robustly measurable in sputum. In the training set, a panel of two snoRNA biomarkers (snoRD66 and snoRD78) was developed, producing 74.58% sensitivity and 83.61% specificity for identifying lung cancer. The snoRNA biomarkers had a significantly higher sensitivity (74.58%) compared with sputum cytology (45.76%) (P < 0.05). The changes of the snoRNAs were not associated with stage and histology of lung cancer (All P >0.05). The performance of the biomarker panel was confirmed in the testing cohort. We report for the first time that sputum snoRNA biomarkers might be useful to improve diagnosis of lung cancer.
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Affiliation(s)
- Jian Su
- Department of Pathology, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Jeipi Liao
- Department of Pathology, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Lu Gao
- Department of Pathology, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Jun Shen
- Department of Pathology, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Maria A Guarnera
- Department of Pathology, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Min Zhan
- Department of Epidemiology and Public Health, University of Maryland School of Medicine, Baltimore, MD, USA
| | - HongBin Fang
- Department of Epidemiology and Public Health, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Sanford A Stass
- Department of Pathology, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Feng Jiang
- Department of Pathology, University of Maryland School of Medicine, Baltimore, MD, USA
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Suhaimi SS, Ab Mutalib NS, Jamal R. Understanding Molecular Landscape of Endometrial Cancer through Next Generation Sequencing: What We Have Learned so Far? Front Pharmacol 2016; 7:409. [PMID: 27847479 PMCID: PMC5088199 DOI: 10.3389/fphar.2016.00409] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2016] [Accepted: 10/14/2016] [Indexed: 01/06/2023] Open
Abstract
Endometrial cancer (EC) is among the most common gynecological cancers affecting women worldwide. Despite the early detection and rather high overall survival rate, around 20% of the cases recur with poor prognosis. The Next Generation Sequencing (NGS) technology, also known as massively parallel sequencing, symbolizes a high-throughput, fast, sensitive and accurate way to study the molecular landscape of a cancer and this has indeed revolutionized endometrial cancer research. Understanding the potential, advantages, and limitations of NGS will be crucial for the healthcare providers and scientists in providing the genome-driven care in this era of precision medicine and pharmacogenomics. This mini review aimed to compile and critically summarize the recent findings contributed by NGS technology pertaining to EC. Importantly, we also discussed the potential of this technology for fundamental discovery research, individualized therapy, screening of at-risk individual and early diagnosis.
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Affiliation(s)
- Siti-Syazani Suhaimi
- UKM Medical Molecular Biology Institute, Universiti Kebangsaan Malaysia Cheras, Malaysia
| | | | - Rahman Jamal
- UKM Medical Molecular Biology Institute, Universiti Kebangsaan Malaysia Cheras, Malaysia
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34
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Krishnan P, Ghosh S, Wang B, Heyns M, Graham K, Mackey JR, Kovalchuk O, Damaraju S. Profiling of Small Nucleolar RNAs by Next Generation Sequencing: Potential New Players for Breast Cancer Prognosis. PLoS One 2016; 11:e0162622. [PMID: 27631501 PMCID: PMC5025248 DOI: 10.1371/journal.pone.0162622] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2016] [Accepted: 08/25/2016] [Indexed: 01/09/2023] Open
Abstract
One of the most abundant, yet least explored, classes of RNA is the small nucleolar RNAs (snoRNAs), which are well known for their involvement in post-transcriptional modifications of other RNAs. Although snoRNAs were only considered to perform housekeeping functions for a long time, recent studies have highlighted their importance as regulators of gene expression and as diagnostic/prognostic markers. However, the prognostic potential of these RNAs has not been interrogated for breast cancer (BC). The objective of the current study was to identify snoRNAs as prognostic markers for BC. Small RNA sequencing (Illumina Genome Analyzer IIx) was performed for 104 BC cases and 11 normal breast tissues. Partek Genomics Suite was used for analyzing the sequencing files. Two independent and proven approaches were used to identify prognostic markers: case-control (CC) and case-only (CO). For both approaches, snoRNAs significant in the permutation test, following univariate Cox proportional hazards regression model were used for constructing risk scores. Risk scores were subsequently adjusted for potential confounders in a multivariate Cox model. For both approaches, thirteen snoRNAs were associated with overall survival and/or recurrence free survival. Patients belonging to the high-risk group were associated with poor outcomes, and the risk score was significant after adjusting for confounders. Validation of representative snoRNAs (SNORD46 and SNORD89) using qRT-PCR confirmed the observations from sequencing experiments. We also observed 64 snoRNAs harboring piwi-interacting RNAs and/or microRNAs that were predicted to target genes (mRNAs) involved in tumorigenesis. Our results demonstrate the potential of snoRNAs to serve (i) as novel prognostic markers for BC and (ii) as indirect regulators of gene expression.
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Affiliation(s)
- Preethi Krishnan
- Department of Laboratory Medicine and Pathology, University of Alberta, Edmonton, Alberta, Canada
| | - Sunita Ghosh
- Department of Oncology, University of Alberta, Edmonton, Alberta, Canada.,Cross Cancer Institute, Alberta Health Services, Edmonton, Alberta, Canada
| | - Bo Wang
- Department of Biological Sciences, University of Lethbridge, Lethbridge, Alberta, Canada
| | - Mieke Heyns
- Department of Biological Sciences, University of Lethbridge, Lethbridge, Alberta, Canada
| | - Kathryn Graham
- Department of Oncology, University of Alberta, Edmonton, Alberta, Canada.,Cross Cancer Institute, Alberta Health Services, Edmonton, Alberta, Canada
| | - John R Mackey
- Department of Oncology, University of Alberta, Edmonton, Alberta, Canada.,Cross Cancer Institute, Alberta Health Services, Edmonton, Alberta, Canada
| | - Olga Kovalchuk
- Department of Biological Sciences, University of Lethbridge, Lethbridge, Alberta, Canada
| | - Sambasivarao Damaraju
- Department of Laboratory Medicine and Pathology, University of Alberta, Edmonton, Alberta, Canada.,Cross Cancer Institute, Alberta Health Services, Edmonton, Alberta, Canada
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35
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Liu Y. MicroRNAs and PIWI-interacting RNAs in oncology. Oncol Lett 2016; 12:2289-2292. [PMID: 27698791 PMCID: PMC5038388 DOI: 10.3892/ol.2016.4996] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2016] [Accepted: 07/28/2016] [Indexed: 12/19/2022] Open
Abstract
RNA molecules that are unable to translate into proteins are classified as non-coding RNA. Non-coding RNA (ncRNA) genes include highly abundant and functionally important RNAs such as transfer RNAs, microRNAs (miRNAs), siRNAs, snRNAs, exRNAs and piRNAs. The number of ncRNAs encoded within the human genome is unknown; however, recent transcriptomic and bioinformatic studies suggest the existence of thousands of ncRNAs. Furthermore, small ncRNAs, including miRNAs and PIWI-interacting RNAs (piRNAs), play an imperative role in the regulation of gene expression of numerous biological and pathological processes. Investigation into the expression and function of small RNA in cancer cells has contributed to gaining a greater understanding of the roles of small RNAs in carcinogenesis. The present review is aimed primarily to discuss the importance of the expression and functions of these small RNAs in carcinogenesis. These studies may provide useful information for future therapies in cancer.
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Affiliation(s)
- Yong Liu
- Department of Neurology, Xuzhou Central Hospital, The Affiliated Xuzhou Hospital of Medical College of Southeast University, Xuzhou, Jiangsu 221009, P.R. China
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36
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Esposito V, Baldi C, Zeppa P, Festa M, Guerriero L, d'Avenia M, Chetta M, Zullo F, De Laurenzi V, Turco MC, Rosati A, Guida M. BAG3 Protein Is Over-Expressed in Endometrioid Endometrial Adenocarcinomas. J Cell Physiol 2016; 232:309-311. [DOI: 10.1002/jcp.25489] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2016] [Accepted: 07/13/2016] [Indexed: 11/09/2022]
Affiliation(s)
- Veronica Esposito
- “SS. Giovanni di Dio e Ruggi d'Aragona-Schola Medica Salernitana”; University of Salerno Hospital; Salerno Italy
- Department of Medicine, Surgery and Dentistry “Scuola Medica Salernitana”; University of Salerno; Baronissi (SA) Italy
| | - Carlo Baldi
- “SS. Giovanni di Dio e Ruggi d'Aragona-Schola Medica Salernitana”; University of Salerno Hospital; Salerno Italy
| | - Pio Zeppa
- “SS. Giovanni di Dio e Ruggi d'Aragona-Schola Medica Salernitana”; University of Salerno Hospital; Salerno Italy
- Department of Medicine, Surgery and Dentistry “Scuola Medica Salernitana”; University of Salerno; Baronissi (SA) Italy
| | - Michelina Festa
- Department of Pharmacy; University of Salerno; Fisciano Italy
- BIOUNIVERSA s.r.l.; University of Salerno; Fisciano Italy
| | | | | | | | - Fulvio Zullo
- Department of Medicine, Surgery and Dentistry “Scuola Medica Salernitana”; University of Salerno; Baronissi (SA) Italy
| | - Vincenzo De Laurenzi
- BIOUNIVERSA s.r.l.; University of Salerno; Fisciano Italy
- Department of Experimental and Clinical Sciences; University G. D'Annunzio and Fondazione G. D'Annunzio, Ce.S.I.; Chieti Italy
| | - Maria Caterina Turco
- “SS. Giovanni di Dio e Ruggi d'Aragona-Schola Medica Salernitana”; University of Salerno Hospital; Salerno Italy
- Department of Medicine, Surgery and Dentistry “Scuola Medica Salernitana”; University of Salerno; Baronissi (SA) Italy
- BIOUNIVERSA s.r.l.; University of Salerno; Fisciano Italy
| | - Alessandra Rosati
- Department of Medicine, Surgery and Dentistry “Scuola Medica Salernitana”; University of Salerno; Baronissi (SA) Italy
- BIOUNIVERSA s.r.l.; University of Salerno; Fisciano Italy
| | - Maurizio Guida
- “SS. Giovanni di Dio e Ruggi d'Aragona-Schola Medica Salernitana”; University of Salerno Hospital; Salerno Italy
- Department of Medicine, Surgery and Dentistry “Scuola Medica Salernitana”; University of Salerno; Baronissi (SA) Italy
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Abstract
The past several years have seen dramatic leaps in our understanding of how gene expression is rewired at the translation level during tumorigenesis to support the transformed phenotype. This work has been driven by an explosion in technological advances and is revealing previously unimagined regulatory mechanisms that dictate functional expression of the cancer genome. In this Review we discuss emerging trends and exciting new discoveries that reveal how this translational circuitry contributes to specific aspects of tumorigenesis and cancer cell function, with a particular focus on recent insights into the role of translational control in the adaptive response to oncogenic stress conditions.
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Affiliation(s)
- Morgan L Truitt
- Department of Urology, University of California, San Francisco
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, California 94158, USA
| | - Davide Ruggero
- Department of Urology, University of California, San Francisco
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, California 94158, USA
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38
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Kuchta K, Muszewska A, Knizewski L, Steczkiewicz K, Wyrwicz LS, Pawlowski K, Rychlewski L, Ginalski K. FAM46 proteins are novel eukaryotic non-canonical poly(A) polymerases. Nucleic Acids Res 2016; 44:3534-48. [PMID: 27060136 PMCID: PMC4857005 DOI: 10.1093/nar/gkw222] [Citation(s) in RCA: 52] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2015] [Accepted: 03/22/2016] [Indexed: 12/22/2022] Open
Abstract
FAM46 proteins, encoded in all known animal genomes, belong to the nucleotidyltransferase (NTase) fold superfamily. All four human FAM46 paralogs (FAM46A, FAM46B, FAM46C, FAM46D) are thought to be involved in several diseases, with FAM46C reported as a causal driver of multiple myeloma; however, their exact functions remain unknown. By using a combination of various bioinformatics analyses (e.g. domain architecture, cellular localization) and exhaustive literature and database searches (e.g. expression profiles, protein interactors), we classified FAM46 proteins as active non-canonical poly(A) polymerases, which modify cytosolic and/or nuclear RNA 3′ ends. These proteins may thus regulate gene expression and probably play a critical role during cell differentiation. A detailed analysis of sequence and structure diversity of known NTases possessing PAP/OAS1 SBD domain, combined with state-of-the-art comparative modelling, allowed us to identify potential active site residues responsible for catalysis and substrate binding. We also explored the role of single point mutations found in human cancers and propose that FAM46 genes may be involved in the development of other major malignancies including lung, colorectal, hepatocellular, head and neck, urothelial, endometrial and renal papillary carcinomas and melanoma. Identification of these novel enzymes taking part in RNA metabolism in eukaryotes may guide their further functional studies.
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Affiliation(s)
- Krzysztof Kuchta
- Laboratory of Bioinformatics and Systems Biology, Centre of New Technologies, University of Warsaw, Zwirki i Wigury 93, 02-089 Warsaw, Poland College of Inter-Faculty Individual Studies in Mathematics and Natural Sciences, University of Warsaw, Banacha 2C, 02-097 Warsaw, Poland
| | - Anna Muszewska
- Laboratory of Bioinformatics and Systems Biology, Centre of New Technologies, University of Warsaw, Zwirki i Wigury 93, 02-089 Warsaw, Poland Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawinskiego 5a, 02-106 Warsaw, Poland
| | - Lukasz Knizewski
- Laboratory of Bioinformatics and Systems Biology, Centre of New Technologies, University of Warsaw, Zwirki i Wigury 93, 02-089 Warsaw, Poland
| | - Kamil Steczkiewicz
- Laboratory of Bioinformatics and Systems Biology, Centre of New Technologies, University of Warsaw, Zwirki i Wigury 93, 02-089 Warsaw, Poland
| | - Lucjan S Wyrwicz
- Laboratory of Bioinformatics and Biostatistics, M. Sklodowska-Curie Memorial Cancer Center and Institute of Oncology, WK Roentgena 5, 02-781 Warsaw, Poland
| | - Krzysztof Pawlowski
- Department of Experimental Design and Bioinformatics, Warsaw University of Life Sciences, Nowoursynowska 166, 02-787 Warsaw, Poland
| | | | - Krzysztof Ginalski
- Laboratory of Bioinformatics and Systems Biology, Centre of New Technologies, University of Warsaw, Zwirki i Wigury 93, 02-089 Warsaw, Poland
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Venkatesh T, Suresh PS, Tsutsumi R. Non-coding RNAs: Functions and applications in endocrine-related cancer. Mol Cell Endocrinol 2015; 416:88-96. [PMID: 26360585 DOI: 10.1016/j.mce.2015.08.026] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/26/2015] [Revised: 08/28/2015] [Accepted: 08/31/2015] [Indexed: 01/25/2023]
Abstract
A significant fraction of the human genome is transcribed as non-coding RNAs (ncRNAs). This non-coding transcriptome has challenged the notion of the central dogma and its involvement in transcriptional and post-transcriptional regulation of gene expression is well established. Interestingly, several ncRNAs are dysregulated in cancer and current non-coding transcriptome research aims to use our increasing knowledge of these ncRNAs for the development of cancer biomarkers and anti-cancer drugs. In endocrine-related cancers, for which survival rates can be relatively low, there is a need for such advancements. In this review, we aimed to summarize the roles and clinical implications of recently discovered ncRNAs, including long ncRNAs, PIWI-interacting RNAs, tRNA- and Y RNA-derived ncRNAs, and small nucleolar RNAs, in endocrine-related cancers affecting both sexes. We focus on recent studies highlighting discoveries in ncRNA biology and expression in cancer, and conclude with a discussion on the challenges and future directions, including clinical application. ncRNAs show great promise as diagnostic tools and therapeutic targets, but further work is necessary to realize the potential of these unconventional transcripts.
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MESH Headings
- Biomarkers, Tumor/classification
- Biomarkers, Tumor/genetics
- Biomarkers, Tumor/metabolism
- Endocrine Gland Neoplasms/genetics
- Endocrine Gland Neoplasms/metabolism
- Endocrine Gland Neoplasms/therapy
- Female
- Gene Expression Regulation
- Humans
- Male
- RNA, Long Noncoding/classification
- RNA, Long Noncoding/genetics
- RNA, Long Noncoding/metabolism
- RNA, Small Interfering/classification
- RNA, Small Interfering/genetics
- RNA, Small Interfering/metabolism
- RNA, Small Nucleolar/classification
- RNA, Small Nucleolar/genetics
- RNA, Small Nucleolar/metabolism
- Transcriptome
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Affiliation(s)
- Thejaswini Venkatesh
- Nitte University Centre for Science Education and Research (NUCSER), Nitte University, Deralakatte, Mangalore 575 018, Karnataka, India
| | - Padmanaban S Suresh
- Department of Biosciences, Mangalore University, Mangalagangothri, Mangalore 574 199, Karnataka, India.
| | - Rie Tsutsumi
- Division of Nutrition and Metabolism, Institute of Biomedical Science, Tokushima University, Tokushima, Japan
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