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Toden S, Zumwalt TJ, Goel A. Non-coding RNAs and potential therapeutic targeting in cancer. Biochim Biophys Acta Rev Cancer 2021; 1875:188491. [PMID: 33316377 PMCID: PMC7856203 DOI: 10.1016/j.bbcan.2020.188491] [Citation(s) in RCA: 185] [Impact Index Per Article: 46.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2020] [Revised: 12/02/2020] [Accepted: 12/02/2020] [Indexed: 12/11/2022]
Abstract
Recent advances have begun to clarify the physiological and pathological roles of non-coding RNAs (ncRNAs) in various diseases, including cancer. Among these, microRNAs (miRNAs) have been the most studied and have emerged as key players that are involved in the regulation of important growth regulatory pathways in cancer pathogenesis. The ability of a single ncRNA to modulate the expression of multiple downstream gene targets and associated pathways, have provided a rationale to pursue them for therapeutic drug development in cancer. In this context, early data from pre-clinical studies have demonstrated that synthetic miRNA-based therapeutic molecules, along with various protective coating approaches, has allowed for their efficient delivery and anti-tumor activity. In fact, some of the miRNA-based cancer therapeutic strategies have shown promising results even in early-phase human clinical trials. While the enthusiasm for ncRNA-based cancer therapeutics continue to evolve, the field is still in the midst of unraveling a more precise understanding of the molecular mechanisms and specific downstream therapeutic targets of other lesser studied ncRNAs such as the long-non-coding RNAs, transfer RNAs, circular RNAs, small nucleolar RNAs, and piwi-interacting RNAs. This review article provides the current state of knowledge and the evolving principles for ncRNA-based therapeutic approaches in cancer, and specifically highlights the importance of data to date and the approaches that are being developed to overcome the challenges associated with their delivery and mitigating the off-target effects in human cancers.
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Affiliation(s)
- Shusuke Toden
- Center for Gastrointestinal Research; Center for Translational Genomics and Oncology, Baylor Scott & White Research Institute and Charles A. Sammons Cancer Center, Baylor Research Institute and Sammons Cancer Center, Baylor University Medical Center, Dallas, Texas, USA
| | - Timothy J Zumwalt
- Center for Gastrointestinal Research; Center for Translational Genomics and Oncology, Baylor Scott & White Research Institute and Charles A. Sammons Cancer Center, Baylor Research Institute and Sammons Cancer Center, Baylor University Medical Center, Dallas, Texas, USA
| | - Ajay Goel
- Center for Gastrointestinal Research; Center for Translational Genomics and Oncology, Baylor Scott & White Research Institute and Charles A. Sammons Cancer Center, Baylor Research Institute and Sammons Cancer Center, Baylor University Medical Center, Dallas, Texas, USA; Department of Molecular Diagnostics and Experimental Therapeutics, Beckman Research Institute of City of Hope Comprehensive Cancer Center, Duarte, CA, USA.
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Ding L, Jiang M, Wang R, Shen D, Wang H, Lu Z, Zheng Q, Wang L, Xia L, Li G. The emerging role of small non-coding RNA in renal cell carcinoma. Transl Oncol 2020; 14:100974. [PMID: 33395751 PMCID: PMC7719974 DOI: 10.1016/j.tranon.2020.100974] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2020] [Revised: 10/14/2020] [Accepted: 11/24/2020] [Indexed: 12/12/2022] Open
Abstract
SncRNAs contribute to the progress of renal cell carcinoma. SncRNAs are promising biomarkers for diagnosis and prognosis of renal cell carcinoma. Despite the potential of sncRNA-based cancer therapy, some obstacles remain, including several severe adverse effect.
Noncoding RNAs are transcribed in the most regions of the human genome, divided into small noncoding RNAs (less than 200 nt) and long noncoding RNAs (more than 200 nt) according to their size. Compelling evidences suggest that small noncoding RNAs play critical roles in tumorigenesis and tumor progression, especially in renal cell carcinoma. MiRNA, the most famous small noncoding RNA, has been comprehensively explored for its fundamental role in cancer. And several miRNA-based therapeutic strategies have been applied to several ongoing clinical trials. However, piRNAs and tsRNAs, have not received as much research attention, because of several technological limitations. Nevertheless, some studies have revealed the presence of aberration of piRNAs and tsRNAs in renal cell carcinoma, highlighting a potentially novel mechanism for tumor onset and progression. In this review, we provide an overview of three classes of small noncoding RNA: miRNAs, piRNAs and tsRNAs, that have been reported dysregulation in renal cell carcinoma and have the potential for advancing diagnosis, prognosis and therapeutic applications of this disease.
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Affiliation(s)
- Lifeng Ding
- Department of Urology, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou 310016, China
| | - Minxiao Jiang
- Department of Urology, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou 310016, China
| | - Ruyue Wang
- Department of Urology, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou 310016, China
| | - Danyang Shen
- Department of Urology, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou 310016, China
| | - Huan Wang
- Department of Urology, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou 310016, China
| | - Zeyi Lu
- Department of Urology, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou 310016, China
| | - Qiming Zheng
- Department of Urology, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou 310016, China
| | - Liya Wang
- Department of Urology, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou 310016, China
| | - Liqun Xia
- Department of Urology, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou 310016, China
| | - Gonghui Li
- Department of Urology, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou 310016, China.
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Ahmadi A, De Toma I, Vilor-Tejedor N, Eftekhariyan Ghamsari MR, Sadeghi I. Transposable elements in brain health and disease. Ageing Res Rev 2020; 64:101153. [PMID: 32977057 DOI: 10.1016/j.arr.2020.101153] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2019] [Revised: 07/22/2020] [Accepted: 08/19/2020] [Indexed: 12/17/2022]
Abstract
Transposable elements (TEs) occupy a large fraction of the human genome but only a small proportion of these elements are still active today. Recent works have suggested that TEs are expressed and active in the brain, challenging the dogma that neuronal genomes are static and revealing that they are susceptible to somatic genomic alterations. These new findings have major implications for understanding the neuroplasticity of the brain, which could hypothetically have a role in behavior and cognition, and contribute to vulnerability to disease. As active TEs could induce genetic diversity and mutagenesis, their influences on human brain development and diseases are of great interest. In this review, we will focus on the active TEs in the human genome and discuss in detail their impacts on human brain development. Furthermore, the association between TEs and brain-related diseases is discussed.
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Vinasco-Sandoval T, Moreira FC, F. Vidal A, Pinto P, Ribeiro-dos-Santos AM, Cruz RLS, Fonseca Cabral G, Anaissi AKM, Lopes KDP, Ribeiro-dos-Santos A, Demachki S, de Assumpção PP, Ribeiro-dos-Santos Â, Santos S. Global Analyses of Expressed Piwi-Interacting RNAs in Gastric Cancer. Int J Mol Sci 2020; 21:E7656. [PMID: 33081152 PMCID: PMC7593925 DOI: 10.3390/ijms21207656] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2020] [Revised: 08/07/2020] [Accepted: 08/18/2020] [Indexed: 12/15/2022] Open
Abstract
Gastric cancer (GC) represents a notable amount of morbidity and mortality worldwide. Understanding the molecular basis of CG will offer insight into its pathogenesis in an attempt to identify new molecular biomarkers to early diagnose this disease. Therefore, studies involving small non-coding RNAs have been widely explored. Among these, PIWI-interacting RNAs (piRNAs) are an emergent class that can play important roles in carcinogenesis. In this study, small-RNA sequencing was used to identify the global piRNAs expression profile (piRNome) of gastric cancer patients. We found 698 piRNAs in gastric tissues, 14 of which were differentially expressed (DE) between gastric cancer (GC), adjacent to gastric cancer (ADJ), and non-cancer tissues (NC). Moreover, three of these DE piRNAs (piR-48966*, piR-49145, piR-31335*) were differently expressed in both GC and ADJ samples in comparison to NC samples, indicating that the tumor-adjacent tissue was molecularly altered and should not be considered as a normal control. These three piRNAs are potential risk biomarkers for GC, especially piR-48966* and piR-31335*. Furthermore, an in-silico search for mRNAs targeted by the differentially expressed piRNAs revealed that these piRNAs may regulate genes that participate in cancer-related pathways, suggesting that these small non-coding RNAs may be directly and indirectly involved in gastric carcinogenesis.
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Affiliation(s)
- Tatiana Vinasco-Sandoval
- Graduate Program in Genetics and Molecular Biology, Laboratory of Human and Medical Genetics, Federal University of Pará, Belém, Pará 66075-110, Brazil; (T.V.-S.); (F.C.M.); (A.F.V.); (P.P.); (A.M.R.-d.-S.); (R.L.S.C.); (G.F.C.); (K.d.P.L.); (A.R.-d.-S.); (Â.R.-d.-S.)
| | - Fabiano Cordeiro Moreira
- Graduate Program in Genetics and Molecular Biology, Laboratory of Human and Medical Genetics, Federal University of Pará, Belém, Pará 66075-110, Brazil; (T.V.-S.); (F.C.M.); (A.F.V.); (P.P.); (A.M.R.-d.-S.); (R.L.S.C.); (G.F.C.); (K.d.P.L.); (A.R.-d.-S.); (Â.R.-d.-S.)
- Graduate Program in Oncology and Medical Sciences, Center of Oncology Research, Federal University of Pará, Belém, Pará 66063-023, Brazil; (A.K.M.A.); (S.D.); (P.P.d.A.)
| | - Amanda F. Vidal
- Graduate Program in Genetics and Molecular Biology, Laboratory of Human and Medical Genetics, Federal University of Pará, Belém, Pará 66075-110, Brazil; (T.V.-S.); (F.C.M.); (A.F.V.); (P.P.); (A.M.R.-d.-S.); (R.L.S.C.); (G.F.C.); (K.d.P.L.); (A.R.-d.-S.); (Â.R.-d.-S.)
| | - Pablo Pinto
- Graduate Program in Genetics and Molecular Biology, Laboratory of Human and Medical Genetics, Federal University of Pará, Belém, Pará 66075-110, Brazil; (T.V.-S.); (F.C.M.); (A.F.V.); (P.P.); (A.M.R.-d.-S.); (R.L.S.C.); (G.F.C.); (K.d.P.L.); (A.R.-d.-S.); (Â.R.-d.-S.)
- Graduate Program in Oncology and Medical Sciences, Center of Oncology Research, Federal University of Pará, Belém, Pará 66063-023, Brazil; (A.K.M.A.); (S.D.); (P.P.d.A.)
| | - André M. Ribeiro-dos-Santos
- Graduate Program in Genetics and Molecular Biology, Laboratory of Human and Medical Genetics, Federal University of Pará, Belém, Pará 66075-110, Brazil; (T.V.-S.); (F.C.M.); (A.F.V.); (P.P.); (A.M.R.-d.-S.); (R.L.S.C.); (G.F.C.); (K.d.P.L.); (A.R.-d.-S.); (Â.R.-d.-S.)
| | - Rebecca L. S. Cruz
- Graduate Program in Genetics and Molecular Biology, Laboratory of Human and Medical Genetics, Federal University of Pará, Belém, Pará 66075-110, Brazil; (T.V.-S.); (F.C.M.); (A.F.V.); (P.P.); (A.M.R.-d.-S.); (R.L.S.C.); (G.F.C.); (K.d.P.L.); (A.R.-d.-S.); (Â.R.-d.-S.)
| | - Gleyce Fonseca Cabral
- Graduate Program in Genetics and Molecular Biology, Laboratory of Human and Medical Genetics, Federal University of Pará, Belém, Pará 66075-110, Brazil; (T.V.-S.); (F.C.M.); (A.F.V.); (P.P.); (A.M.R.-d.-S.); (R.L.S.C.); (G.F.C.); (K.d.P.L.); (A.R.-d.-S.); (Â.R.-d.-S.)
| | - Ana K. M. Anaissi
- Graduate Program in Oncology and Medical Sciences, Center of Oncology Research, Federal University of Pará, Belém, Pará 66063-023, Brazil; (A.K.M.A.); (S.D.); (P.P.d.A.)
| | - Katia de Paiva Lopes
- Graduate Program in Genetics and Molecular Biology, Laboratory of Human and Medical Genetics, Federal University of Pará, Belém, Pará 66075-110, Brazil; (T.V.-S.); (F.C.M.); (A.F.V.); (P.P.); (A.M.R.-d.-S.); (R.L.S.C.); (G.F.C.); (K.d.P.L.); (A.R.-d.-S.); (Â.R.-d.-S.)
| | - Arthur Ribeiro-dos-Santos
- Graduate Program in Genetics and Molecular Biology, Laboratory of Human and Medical Genetics, Federal University of Pará, Belém, Pará 66075-110, Brazil; (T.V.-S.); (F.C.M.); (A.F.V.); (P.P.); (A.M.R.-d.-S.); (R.L.S.C.); (G.F.C.); (K.d.P.L.); (A.R.-d.-S.); (Â.R.-d.-S.)
| | - Samia Demachki
- Graduate Program in Oncology and Medical Sciences, Center of Oncology Research, Federal University of Pará, Belém, Pará 66063-023, Brazil; (A.K.M.A.); (S.D.); (P.P.d.A.)
| | - Paulo Pimentel de Assumpção
- Graduate Program in Oncology and Medical Sciences, Center of Oncology Research, Federal University of Pará, Belém, Pará 66063-023, Brazil; (A.K.M.A.); (S.D.); (P.P.d.A.)
| | - Ândrea Ribeiro-dos-Santos
- Graduate Program in Genetics and Molecular Biology, Laboratory of Human and Medical Genetics, Federal University of Pará, Belém, Pará 66075-110, Brazil; (T.V.-S.); (F.C.M.); (A.F.V.); (P.P.); (A.M.R.-d.-S.); (R.L.S.C.); (G.F.C.); (K.d.P.L.); (A.R.-d.-S.); (Â.R.-d.-S.)
- Graduate Program in Oncology and Medical Sciences, Center of Oncology Research, Federal University of Pará, Belém, Pará 66063-023, Brazil; (A.K.M.A.); (S.D.); (P.P.d.A.)
| | - Sidney Santos
- Graduate Program in Genetics and Molecular Biology, Laboratory of Human and Medical Genetics, Federal University of Pará, Belém, Pará 66075-110, Brazil; (T.V.-S.); (F.C.M.); (A.F.V.); (P.P.); (A.M.R.-d.-S.); (R.L.S.C.); (G.F.C.); (K.d.P.L.); (A.R.-d.-S.); (Â.R.-d.-S.)
- Graduate Program in Oncology and Medical Sciences, Center of Oncology Research, Federal University of Pará, Belém, Pará 66063-023, Brazil; (A.K.M.A.); (S.D.); (P.P.d.A.)
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The piRNA CHAPIR regulates cardiac hypertrophy by controlling METTL3-dependent N 6-methyladenosine methylation of Parp10 mRNA. Nat Cell Biol 2020; 22:1319-1331. [PMID: 33020597 DOI: 10.1038/s41556-020-0576-y] [Citation(s) in RCA: 128] [Impact Index Per Article: 25.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2019] [Accepted: 08/11/2020] [Indexed: 12/21/2022]
Abstract
PIWI-interacting RNAs (piRNAs) are abundantly expressed during cardiac hypertrophy. However, their functions and molecular mechanisms remain unknown. Here, we identified a cardiac-hypertrophy-associated piRNA (CHAPIR) that promotes pathological hypertrophy and cardiac remodelling by targeting METTL3-mediated N6-methyladenosine (m6A) methylation of Parp10 mRNA transcripts. CHAPIR deletion markedly attenuates cardiac hypertrophy and restores heart function, while administration of a CHAPIR mimic enhances the pathological hypertrophic response in pressure-overloaded mice. Mechanistically, CHAPIR-PIWIL4 complexes directly interact with METTL3 and block the m6A methylation of Parp10 mRNA transcripts, which upregulates PARP10 expression. The CHAPIR-dependent increase in PARP10 promotes the mono-ADP-ribosylation of GSK3β and inhibits its kinase activity, which results in the accumulation of nuclear NFATC4 and the progression of pathological hypertrophy. Hence, our findings reveal that a piRNA-mediated RNA epigenetic mechanism is involved in the regulation of cardiac hypertrophy and that the CHAPIR-METTL3-PARP10-NFATC4 signalling axis could be therapeutically targeted for treating pathological hypertrophy and maladaptive cardiac remodelling.
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The critical impacts of small RNA biogenesis proteins on aging, longevity and age-related diseases. Ageing Res Rev 2020; 62:101087. [PMID: 32497728 DOI: 10.1016/j.arr.2020.101087] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2019] [Revised: 04/01/2020] [Accepted: 05/11/2020] [Indexed: 12/13/2022]
Abstract
Small RNAs and enzymes that provide their biogenesis and functioning are involved in the organism development and coordination of biological processes, including metabolism, maintaining genome integrity, immune and stress responses. In this review, we focused on the role of small RNA biogenesis proteins in determining the aging and longevity of animals and human. A number of studies have revealed that changes in expression profiles of key enzymes, in particular proteins of the Drosha, Dicer and Argonaute families, are associated with the aging process, as well as with some age-related diseases and progeroid syndromes. Down-regulation of small RNA biogenesis proteins leads to global alterations in the expression of regulatory RNAs, disruption of key molecular, cellular and systemic processes, which leads to a lifespan shortening. In contrast, overexpression of Dicer prolongs lifespan and improves cellular defense. Additionally, the role of small RNA biogenesis proteins in the pathogenesis of age-related diseases, including cancer, inflammaging, neurodegeneration, cardiovascular, metabolic and immune disorders, has been conclusively evidenced. Recent advances in biomedicine allow using these proteins as diagnostic and prognostic biomarkers and therapeutic targets.
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Lin Y, Zheng J, Lin D. PIWI-interacting RNAs in human cancer. Semin Cancer Biol 2020; 75:15-28. [PMID: 32877760 DOI: 10.1016/j.semcancer.2020.08.012] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2020] [Revised: 08/16/2020] [Accepted: 08/23/2020] [Indexed: 12/11/2022]
Abstract
P-element-induced wimpy testis (PIWI) interacting RNAs (piRNAs) are a class of small regulatory RNAs mechanistically similar to but much less studied than microRNAs and small interfering RNAs. Today the best understood function of piRNAs is transposon control in animal germ cells, which has earned them the name 'guardians of the germline'. Several molecular/cellular characteristics of piRNAs, including high sequence diversity, lack of secondary structures, and target-oriented generation seem to serve this purpose. Recently, aberrant expressions of piRNAs and PIWI proteins have been implicated in a variety of malignant tumors and associated with cancer hallmarks such as cell proliferation, inhibited apoptosis, invasion, metastasis and increased stemness. Researchers have also demonstrated multiple mechanisms of piRNA-mediated target deregulation associated with cancer initiation, progression or dissemination. We review current research findings on the biogenesis, normal functions and cancer associations of piRNAs, highlighting their potentials as cancer diagnostic/prognostic biomarkers and therapeutic tools. Whenever applicable, we draw connections with other research fields to encourage intercommunity conversations. We also offer recommendations and cautions regarding the general process of cancer-related piRNA studies and the methods/tools used at each step. Finally, we call attention to some issues that, if left unsolved, might impede the future development of this field.
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Affiliation(s)
- Yuan Lin
- Beijing Advanced Innovation Center for Genomics (ICG), Biomedical Pioneering Innovation Center (BIOPIC), Peking University, Beijing, 100871, China.
| | - Jian Zheng
- Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China and Collaborative Innovation Center for Cancer Medicine, Guangzhou, 510060, China
| | - Dongxin Lin
- Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China and Collaborative Innovation Center for Cancer Medicine, Guangzhou, 510060, China; Department of Etiology and Carcinogenesis, National Cancer Center/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China
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58
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Abstract
Targeted cancer therapy aims to achieve specific elimination of cancerous but not normal cells. Recently, PIWI proteins, a subfamily of the PAZ-PIWI domain (PPD) protein family, have emerged as promising candidates for targeted cancer therapy. PPD proteins are essential for small noncoding RNA pathways. The Argonaute subfamily partners with microRNA and small interfering RNA, whereas the PIWI subfamily partners with PIWI-interacting RNA (piRNA). Both PIWI proteins and piRNA are mostly expressed in the germline and best known for their function in transposon silencing, with no detectable function in mammalian somatic tissues. However, PIWI proteins become aberrantly expressed in multiple types of somatic cancers, thus gaining interest in targeted therapy. Despite this, little is known about the regulatory mechanism of PIWI proteins in cancer. Here we report that one of the four PIWI proteins in humans, PIWIL1, is highly expressed in gastric cancer tissues and cell lines. Knocking out the PIWIL1 gene (PIWIL1-KO) drastically reduces gastric cancer cell proliferation, migration, metastasis, and tumorigenesis. RNA deep sequencing of gastric cancer cell line SNU-1 reveals that KO significantly changes the transcriptome, causing the up-regulation of most of its associated transcripts. Surprisingly, few bona fide piRNAs exist in gastric cancer cells. Furthermore, abolishing the piRNA-binding activity of PIWIL1 does not affect its oncogenic function. Thus, PIWIL1 function in gastric cancer cells is independent of piRNA. This piRNA-independent regulation involves interaction with the UPF1-mediated nonsense-mediated mRNA decay (NMD) mechanism. Altogether, our findings reveal a piRNA-independent function of PIWIL1 in promoting gastric cancer.
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Zeng C, Weng C, Wang X, Yan YH, Li WJ, Xu D, Hong M, Liao S, Dong MQ, Feng X, Xu C, Guang S. Functional Proteomics Identifies a PICS Complex Required for piRNA Maturation and Chromosome Segregation. Cell Rep 2020; 27:3561-3572.e3. [PMID: 31216475 DOI: 10.1016/j.celrep.2019.05.076] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2018] [Revised: 04/08/2019] [Accepted: 05/20/2019] [Indexed: 01/19/2023] Open
Abstract
piRNAs play significant roles in suppressing transposons and nonself nucleic acids, maintaining genome integrity, and defending against viral infections. In C. elegans, piRNA precursors are transcribed in the nucleus and are subjected to a number of processing and maturation steps. The biogenesis of piRNAs is not fully understood. We use functional proteomics in C. elegans and identify a piRNA biogenesis and chromosome segregation (PICS) complex. The PICS complex contains TOFU-6, PID-1, PICS-1, TOST-1, and ERH-2, which exhibit dynamic localization among different subcellular compartments. In the germlines, the PICS complex contains TOFU-6/PICS-1/ERH-2/PID-1, is largely concentrated at the perinuclear granule zone, and engages in piRNA processing. During embryogenesis, the TOFU-6/PICS-1/ERH-2/TOST-1 complex accumulates in the nucleus and plays essential roles in chromosome segregation. The functions of these factors in mediating chromosome segregation are independent of piRNA production. We speculate that differential compositions of PICS factors may help cells coordinate distinct cellular processes.
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Affiliation(s)
- Chenming Zeng
- Hefei National Laboratory for Physical Sciences at the Microscale, School of Life Sciences, University of Science and Technology of China, Hefei, Anhui 230027, P.R. China
| | - Chenchun Weng
- Hefei National Laboratory for Physical Sciences at the Microscale, School of Life Sciences, University of Science and Technology of China, Hefei, Anhui 230027, P.R. China
| | - Xiaoyang Wang
- Hefei National Laboratory for Physical Sciences at the Microscale, School of Life Sciences, University of Science and Technology of China, Hefei, Anhui 230027, P.R. China
| | - Yong-Hong Yan
- National Institute of Biological Sciences, Beijing 102206, China
| | - Wen-Jun Li
- National Institute of Biological Sciences, Beijing 102206, China
| | - Demin Xu
- Hefei National Laboratory for Physical Sciences at the Microscale, School of Life Sciences, University of Science and Technology of China, Hefei, Anhui 230027, P.R. China
| | - Minjie Hong
- Hefei National Laboratory for Physical Sciences at the Microscale, School of Life Sciences, University of Science and Technology of China, Hefei, Anhui 230027, P.R. China
| | - Shanhui Liao
- Hefei National Laboratory for Physical Sciences at the Microscale, School of Life Sciences, University of Science and Technology of China, Hefei, Anhui 230027, P.R. China
| | - Meng-Qiu Dong
- National Institute of Biological Sciences, Beijing 102206, China
| | - Xuezhu Feng
- Hefei National Laboratory for Physical Sciences at the Microscale, School of Life Sciences, University of Science and Technology of China, Hefei, Anhui 230027, P.R. China.
| | - Chao Xu
- Hefei National Laboratory for Physical Sciences at the Microscale, School of Life Sciences, University of Science and Technology of China, Hefei, Anhui 230027, P.R. China.
| | - Shouhong Guang
- Hefei National Laboratory for Physical Sciences at the Microscale, School of Life Sciences, University of Science and Technology of China, Hefei, Anhui 230027, P.R. China; CAS Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Hefei, Anhui 230027, P.R. China.
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60
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Pinto P, da Silva MB, Moreira FC, Bouth RC, Gobbo AR, Sandoval TV, Ribeiro-Dos-Santos AM, Vidal AF, Barreto JG, Santos S, Spencer JS, Salgado CG, Ribeiro-Dos-Santos Â. Leprosy piRnome: exploring new possibilities for an old disease. Sci Rep 2020; 10:12648. [PMID: 32724108 PMCID: PMC7387468 DOI: 10.1038/s41598-020-69355-7] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2020] [Accepted: 07/03/2020] [Indexed: 12/19/2022] Open
Abstract
Leprosy, which is caused by the human pathogen Mycobacterium leprae, causes nerve damage, deformity and disability in over 200,000 people every year. Because of the long doubling time of M. leprae (13 days) and the delayed onset of detectable symptoms, which is estimated to be approximately 3-7 years after infection, there is always a large percentage of subclinically infected individuals in the population who will eventually develop the disease, mainly in endemic countries. piRNAs comprise the largest group of small noncoding RNAs found in humans, and they are distinct from microRNAs (miRNAs) and small interfering RNAs (siRNAs). piRNAs function in transposon silencing, epigenetic regulation, and germline development. The functional role of piRNAs and their associated PIWI proteins have started to emerge in the development of human cancers and viral infections, but their relevance to bacterial diseases has not been investigated. The present study reports the piRNome of human skin, revealing that all but one of the piRNAs examined are downregulated in leprosy skin lesions. Considering that one of the best characterized functions of piRNAs in humans is posttranscriptional mRNA silencing, their functions are similar to what we have described for miRNAs, including acting on apoptosis, M. leprae recognition and engulfment, Schwann cell (SC) demyelination, epithelial-mesenchymal transition (EMT), loss of sensation and neuropathic pain. In addition to new findings on leprosy physiopathology, the discovery of relevant piRNAs involved in disease processes in human skin may provide new clues for therapeutic targets, specifically to control nerve damage, a prominent feature of leprosy that has no currently available pharmaceutical treatment.
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Affiliation(s)
- Pablo Pinto
- Human and Medical Genetics Laboratory, Institute of Biological Sciences (ICB), UFPA, Belém, 66075110, Brazil
- Oncology Research Center (NPO), UFPA, Belém, 66075110, Brazil
| | - Moisés Batista da Silva
- Dermato-Immunology Laboratory, Institute of Biological Sciences (ICB), UFPA, Marituba, 67200000, Brazil
| | | | - Raquel Carvalho Bouth
- Dermato-Immunology Laboratory, Institute of Biological Sciences (ICB), UFPA, Marituba, 67200000, Brazil
| | - Angélica Rita Gobbo
- Dermato-Immunology Laboratory, Institute of Biological Sciences (ICB), UFPA, Marituba, 67200000, Brazil
| | - Tatiana Vinasco Sandoval
- Human and Medical Genetics Laboratory, Institute of Biological Sciences (ICB), UFPA, Belém, 66075110, Brazil
| | | | - Amanda Ferreira Vidal
- Human and Medical Genetics Laboratory, Institute of Biological Sciences (ICB), UFPA, Belém, 66075110, Brazil
| | | | - Sidney Santos
- Human and Medical Genetics Laboratory, Institute of Biological Sciences (ICB), UFPA, Belém, 66075110, Brazil
- Oncology Research Center (NPO), UFPA, Belém, 66075110, Brazil
| | - John Stewart Spencer
- Mycobacteria Research Laboratories, Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, 80523-1601, USA
| | - Claudio Guedes Salgado
- Dermato-Immunology Laboratory, Institute of Biological Sciences (ICB), UFPA, Marituba, 67200000, Brazil.
| | - Ândrea Ribeiro-Dos-Santos
- Human and Medical Genetics Laboratory, Institute of Biological Sciences (ICB), UFPA, Belém, 66075110, Brazil.
- Oncology Research Center (NPO), UFPA, Belém, 66075110, Brazil.
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61
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Hsieh CL, Xia J, Lin H. MIWI prevents aneuploidy during meiosis by cleaving excess satellite RNA. EMBO J 2020; 39:e103614. [PMID: 32677148 DOI: 10.15252/embj.2019103614] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2019] [Revised: 06/10/2020] [Accepted: 06/16/2020] [Indexed: 01/01/2023] Open
Abstract
MIWI, a murine member of PIWI proteins mostly expressed during male meiosis, is crucial for piRNA biogenesis, post-transcriptional regulation, and spermiogenesis. However, its meiotic function remains unknown. Here, we report that MIWI deficiency alters meiotic kinetochore assembly, significantly increases chromosome misalignment at the meiosis metaphase I plate, and causes chromosome mis-segregation. Consequently, Miwi-deficient mice show elevated aneuploidy in metaphase II and spermatid death. Furthermore, in Miwi-null and Miwi slicer-deficient mutants, major and minor satellite RNAs from centromeric and pericentromeric satellite repeats accumulate in excess. Over-expression of satellite repeats in wild-type spermatocytes also causes elevated chromosome misalignment, whereas reduction of both strands of major or minor satellite RNAs results in lower frequencies of chromosome misalignment. We show that MIWI, guided by piRNA, cleaves major satellite RNAs, generating RNA fragments that may form substrates for subsequent Dicer cleavage. Furthermore, Dicer cleaves all satellite RNAs in conjunction with MIWI. These findings reveal a novel mechanism in which MIWI- and Dicer-mediated cleavage of the satellite RNAs prevents the over-expression of satellite RNAs, thus ensuring proper kinetochore assembly and faithful chromosome segregation during meiosis.
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Affiliation(s)
- Chia-Ling Hsieh
- Yale Stem Cell Center and Department of Cell Biology, Yale University School of Medicine, New Haven, CT, USA
| | - Jing Xia
- Yale Stem Cell Center and Department of Cell Biology, Yale University School of Medicine, New Haven, CT, USA
| | - Haifan Lin
- Yale Stem Cell Center and Department of Cell Biology, Yale University School of Medicine, New Haven, CT, USA
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62
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Chang Z, Ji G, Huang R, Chen H, Gao Y, Wang W, Sun X, Zhang J, Zheng J, Wei Q. PIWI-interacting RNAs piR-13643 and piR-21238 are promising diagnostic biomarkers of papillary thyroid carcinoma. Aging (Albany NY) 2020; 12:9292-9310. [PMID: 32428871 PMCID: PMC7288952 DOI: 10.18632/aging.103206] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2019] [Accepted: 04/17/2020] [Indexed: 04/11/2023]
Abstract
Emerging studies demonstrate that PIWI-interacting RNAs (piRNAs) participate in the development of cancers. 75 pairs of papillary thyroid carcinoma (PTC) samples and 31 benign thyroid nodule samples were included in this three-phase biomarker identifying study. First, piRNA expression profiles of five pairs of PTC samples were acquired piRNA sequencing. The expression of all upregulated piRNAs were further validated by RT-qPCR. Paired t and nonparametric test were used to evaluate the association between all upregulated piRNAs and clinic stage. The expression levels of key piRNAs were corrected by demographic data to construct a multivariate model to distinguish malignant nodules from benign. Additionally, the intersection between target genes of key piRNAs and differentially expressed genes in The Cancer Genome Atlas (TCGA) PTC samples were used to perform enrichment analysis. Only piR-13643 and piR-21238 were significantly upregulated in PTC and associated with clinic stage. Moreover, both piR-13643 (Area Under Curve (AUC): 0.821) and piR-21238 (AUC: 0.823) showed better performance in distinguishing malignant nodules from benign than currently used biomarkers HBME1 (AUC: 0.590). Based on our findings, piR-13643 and piR-21238 were observed to be significantly upregulated in human PTC. PIWI-interacting RNAs could serve as promising novel biomarkers for accurate detection of PTC.
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Affiliation(s)
- Zhengyan Chang
- Department of Pathology, Shanghai Tenth People’s Hospital, Tongji University School of Medicine, Shanghai
| | - Guo Ji
- Department of Pathology, Shanghai Tenth People’s Hospital, Tongji University School of Medicine, Shanghai
| | - Runzhi Huang
- Division of Spine, Department of Orthopedics, Tongji Hospital Affiliated to Tongji University School of Medicine, Shanghai, China
- Key Laboratory of Spine and Spinal Cord Injury Repair and Regeneration (Tongji University), Ministry of Education, Shanghai, China
| | - Hong Chen
- Center for Difficult and Complicated Abdominal Surgery, Shanghai Tenth People’s Hospital, Tongji University School of Medicine, Shanghai, China
| | - Yaohui Gao
- Department of Pathology, Shanghai Tenth People’s Hospital, Tongji University School of Medicine, Shanghai
| | - Weifeng Wang
- Central Laboratory, Shanghai Tenth People's Hospital, Shanghai, China
| | - Xuechen Sun
- Department of Pathology, Shanghai Tenth People’s Hospital, Tongji University School of Medicine, Shanghai
| | - Jie Zhang
- Key Laboratory of Spine and Spinal Cord Injury Repair and Regeneration (Tongji University), Ministry of Education, Shanghai, China
- Department of Prevention, Tongji University School of Medicine, Tongji University, Shanghai, China
| | - Jiayi Zheng
- Department of Pathology, Shanghai Tenth People’s Hospital, Tongji University School of Medicine, Shanghai
- Human Province Key Laboratory of Tumor Cellular and Molecular Pathology, Cancer Research Institute, University of South China, Hengyang, China
| | - Qing Wei
- Department of Pathology, Shanghai Tenth People’s Hospital, Tongji University School of Medicine, Shanghai
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63
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Li F, Yuan P, Rao M, Jin CH, Tang W, Rong YF, Hu YP, Zhang F, Wei T, Yin Q, Liang T, Wu L, Li J, Li D, Liu Y, Lou W, Zhao S, Liu MF. piRNA-independent function of PIWIL1 as a co-activator for anaphase promoting complex/cyclosome to drive pancreatic cancer metastasis. Nat Cell Biol 2020; 22:425-438. [PMID: 32203416 DOI: 10.1038/s41556-020-0486-z] [Citation(s) in RCA: 43] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2019] [Accepted: 02/17/2020] [Indexed: 12/19/2022]
Abstract
Piwi proteins are normally restricted in germ cells to suppress transposons through associations with Piwi-interacting RNAs (piRNAs), but they are also frequently activated in many types of human cancers. A great puzzle is the lack of significant induction of corresponding piRNAs in cancer cells, as we document here in human pancreatic ductal adenocarcinomas (PDACs), which implies that such germline-specific proteins are somehow hijacked to promote tumorigenesis through a different mode of action. Here, we show that in the absence of piRNAs, human PIWIL1 in PDAC functions as an oncoprotein by activating the anaphase promoting complex/cyclosome (APC/C) E3 complex, which then targets a critical cell adhesion-related protein, Pinin, to enhance PDAC metastasis. This is in contrast to piRNA-dependent PIWIL1 ubiquitination and removal by APC/C during late spermiogenesis. These findings unveil a piRNA-dependent mechanism to switch PIWIL1 from a substrate in spermatids to a co-activator of APC/C in human cancer cells.
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Affiliation(s)
- Feng Li
- State Key Laboratory of Molecular Biology, Shanghai Key Laboratory of Molecular Andrology, Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences-University of Chinese Academy of Sciences, Shanghai, China
| | - Peng Yuan
- State Key Laboratory of Molecular Biology, Shanghai Key Laboratory of Molecular Andrology, Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences-University of Chinese Academy of Sciences, Shanghai, China
| | - Ming Rao
- State Key Laboratory of Molecular Biology, Shanghai Key Laboratory of Molecular Andrology, Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences-University of Chinese Academy of Sciences, Shanghai, China
| | - Chun-Hui Jin
- School of Life Science and Technology, Shanghai Tech University, Shanghai, China
| | - Wei Tang
- The Animal Core Facility, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, Shanghai, China
| | - Ye-Fei Rong
- Department of Pancreatic Surgery, Zhong Shan Hospital, Shanghai, China
| | - Yun-Ping Hu
- Department of General Surgery, Xinhua Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Fengjuan Zhang
- State Key Laboratory of Molecular Biology, Shanghai Key Laboratory of Molecular Andrology, Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences-University of Chinese Academy of Sciences, Shanghai, China
| | - Tao Wei
- Department of Hepatobiliary and Pancreatic Surgery, The First Affiliated Hospital of Zhejiang University, School of Medicine, Hangzhou, China
| | - Qi Yin
- State Key Laboratory of Cell Biology, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences-University of Chinese Academy of Sciences, Shanghai, China
| | - Tingbo Liang
- Department of Hepatobiliary and Pancreatic Surgery, The First Affiliated Hospital of Zhejiang University, School of Medicine, Hangzhou, China
| | - Ligang Wu
- State Key Laboratory of Molecular Biology, Shanghai Key Laboratory of Molecular Andrology, Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences-University of Chinese Academy of Sciences, Shanghai, China
| | - Jinsong Li
- School of Life Science and Technology, Shanghai Tech University, Shanghai, China
- State Key Laboratory of Cell Biology, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences-University of Chinese Academy of Sciences, Shanghai, China
| | - Dangsheng Li
- State Key Laboratory of Molecular Biology, Shanghai Key Laboratory of Molecular Andrology, Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences-University of Chinese Academy of Sciences, Shanghai, China
| | - Yingbin Liu
- Department of General Surgery, Xinhua Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Wenhui Lou
- Department of Pancreatic Surgery, Zhong Shan Hospital, Shanghai, China
| | - Shuang Zhao
- State Key Laboratory of Molecular Biology, Shanghai Key Laboratory of Molecular Andrology, Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences-University of Chinese Academy of Sciences, Shanghai, China.
| | - Mo-Fang Liu
- State Key Laboratory of Molecular Biology, Shanghai Key Laboratory of Molecular Andrology, Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences-University of Chinese Academy of Sciences, Shanghai, China.
- School of Life Science and Technology, Shanghai Tech University, Shanghai, China.
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64
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Fonseca Cabral G, Azevedo dos Santos Pinheiro J, Vidal AF, Santos S, Ribeiro-dos-Santos Â. piRNAs in Gastric Cancer: A New Approach Towards Translational Research. Int J Mol Sci 2020; 21:ijms21062126. [PMID: 32204558 PMCID: PMC7139476 DOI: 10.3390/ijms21062126] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2020] [Revised: 02/11/2020] [Accepted: 02/18/2020] [Indexed: 12/12/2022] Open
Abstract
Background: Gastric cancer is currently the third leading cause of cancer-related deaths worldwide, usually diagnosed at late stages. The development of new biomarkers to improve its prevention and patient management is critical for disease control. piRNAs are small regulatory RNAs important for gene silencing mechanisms, mainly associated with the silencing of transposable elements. piRNA pathways may also be involved in gene regulation and the deregulation of piRNAs may be an important factor in carcinogenic processes. Thus, several studies suggest piRNAs as potential cancer biomarkers. Translational studies suggest that piRNAs may regulate key genes and pathways associated with gastric cancer progression, though there is no functional annotation in piRNA databases. The impacts of genetic variants in piRNA genes and their influence in gastric cancer development remains elusive, highlighting the gap in piRNA regulatory mechanisms knowledge. Here, we discuss the current state of understanding of piRNA-mediated regulation and piRNA functions and suggest that genetic alterations in piRNA genes may affect their functionality, thus, it may be associated with gastric carcinogenesis. Conclusions: In the era of precision medicine, investigations about genetic and epigenetic mechanisms are essential to further comprehend gastric carcinogenesis and the role of piRNAs as potential biomarkers for translational research.
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Affiliation(s)
- Gleyce Fonseca Cabral
- Laboratório de Genética Humana e Médica, Programa de Pós-Graduação em Genética e Biologia Molecular, Universidade Federal do Pará, Belém 66.075-110, PA, Brazil; (G.F.C.); (J.A.d.S.P.); (A.F.V.); (S.S.)
| | - Jhully Azevedo dos Santos Pinheiro
- Laboratório de Genética Humana e Médica, Programa de Pós-Graduação em Genética e Biologia Molecular, Universidade Federal do Pará, Belém 66.075-110, PA, Brazil; (G.F.C.); (J.A.d.S.P.); (A.F.V.); (S.S.)
| | - Amanda Ferreira Vidal
- Laboratório de Genética Humana e Médica, Programa de Pós-Graduação em Genética e Biologia Molecular, Universidade Federal do Pará, Belém 66.075-110, PA, Brazil; (G.F.C.); (J.A.d.S.P.); (A.F.V.); (S.S.)
| | - Sidney Santos
- Laboratório de Genética Humana e Médica, Programa de Pós-Graduação em Genética e Biologia Molecular, Universidade Federal do Pará, Belém 66.075-110, PA, Brazil; (G.F.C.); (J.A.d.S.P.); (A.F.V.); (S.S.)
- Programa de Pós-Graduacão em Oncologia e Ciências Médicas, Núcleo de Pesquisas em Oncologia, Universidade Federal do Pará, Belém 66.073-000, PA, Brazil
| | - Ândrea Ribeiro-dos-Santos
- Laboratório de Genética Humana e Médica, Programa de Pós-Graduação em Genética e Biologia Molecular, Universidade Federal do Pará, Belém 66.075-110, PA, Brazil; (G.F.C.); (J.A.d.S.P.); (A.F.V.); (S.S.)
- Programa de Pós-Graduacão em Oncologia e Ciências Médicas, Núcleo de Pesquisas em Oncologia, Universidade Federal do Pará, Belém 66.073-000, PA, Brazil
- Correspondence: ; Tel.: +55-091-3201-7843
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Das B, Jain N, Mallick B. piR‐39980 promotes cell proliferation, migration and invasion, and inhibits apoptosis via repression of SERPINB1 in human osteosarcoma. Biol Cell 2020; 112:73-91. [DOI: 10.1111/boc.201900063] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2019] [Revised: 12/14/2019] [Accepted: 12/16/2019] [Indexed: 12/12/2022]
Affiliation(s)
- Basudeb Das
- RNAi and Functional Genomics LaboratoryDepartment of Life ScienceNational Institute of Technology Rourkela 769008 Odisha India
| | - Neha Jain
- RNAi and Functional Genomics LaboratoryDepartment of Life ScienceNational Institute of Technology Rourkela 769008 Odisha India
| | - Bibekanand Mallick
- RNAi and Functional Genomics LaboratoryDepartment of Life ScienceNational Institute of Technology Rourkela 769008 Odisha India
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66
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Xue Z, Yang B, Xu Q, Zhu X, Qin G. Long non-coding RNA SSTR5-AS1 facilitates gemcitabine resistance via stabilizing NONO in gallbladder carcinoma. Biochem Biophys Res Commun 2019; 522:952-959. [PMID: 31810606 DOI: 10.1016/j.bbrc.2019.10.104] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2019] [Accepted: 10/12/2019] [Indexed: 01/13/2023]
Abstract
Gallbladder carcinoma (GBC) is the most aggressive carcinoma of the biliary tract, effective chemotherapy was critical for the patients with unresectable GBC. However, chemotherapy resistance is still problematic for clinicians. Here, we identified a specific long non-coding RNA, SSTR5-AS1, in GBC patient that facilitates gemcitabine resistance. SSTR5-AS1 is significantly increased in GBC samples and cell lines, especially in gemcitabine-resistant cell lines, and higher SSTR5-AS1 expression was correlated with poorer overall survival rate in GBC patients. Our data revealed that upregulated SSTR5-AS1 facilitates gemcitabine resistance via inhibiting apoptosis. Knockdown of SSTR5-AS1 sensitized drug resistant GBC cells to gemcitabine in vitro and strongly inhibited xenografts formed by drug resistant GBC cells in vivo. Moreover, we found via streptavidin pull down assay that NONO specifically binds to sense sequence of SSTR5-AS1 and prevented proteasome mediated NONO degradation, which resulted in increased NONO protein level without affecting the transcription of NONO. NONO functions as the downstream effector of SSTR5-AS1 and is required for SSTR5-AS1 mediated gemcitabine resistance. Collectively, our data provided novel insights into lncRNA-mediated chemotherapy resistance and suggested a novel therapeutic target to improve chemotherapy strategies for unresectable GBC patients.
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Affiliation(s)
- Zhuowei Xue
- Department of Obstetrics and Gynecology, Shanghai Jiao Tong University Affiliated Sixth People's Hospital, 600 Yishan Road, Shanghai, 200233, China
| | - Bikang Yang
- Department of Obstetrics and Gynecology, Shanghai Jiao Tong University Affiliated Sixth People's Hospital, 600 Yishan Road, Shanghai, 200233, China
| | - Qinyang Xu
- Department of Obstetrics and Gynecology, Shanghai Jiao Tong University Affiliated Sixth People's Hospital, 600 Yishan Road, Shanghai, 200233, China
| | - Xiaolu Zhu
- Department of Obstetrics and Gynecology, Shanghai Jiao Tong University Affiliated Sixth People's Hospital, 600 Yishan Road, Shanghai, 200233, China.
| | - Guangyi Qin
- Department of Obstetrics and Gynecology, Shanghai Jiao Tong University Affiliated Sixth People's Hospital, 600 Yishan Road, Shanghai, 200233, China.
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67
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Zhang X, Liang Z, Zhang Y, Zhu M, Zhu Y, Li S, Zhao W, Hu X, Wang J. Specific PIWI-interacting small noncoding RNA expression patterns in pulmonary tuberculosis patients. Epigenomics 2019; 11:1779-1794. [PMID: 31755303 DOI: 10.2217/epi-2018-0142] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2018] [Accepted: 10/25/2019] [Indexed: 12/17/2022] Open
Abstract
Aim: PIWI-interacting RNAs (piRNAs) play crucial roles in germline development and carcinogenesis. The expression patterns of piRNAs in pulmonary tuberculosis (PTB) are still unclear. Materials & methods: Small RNA sequencing was applied to investigate peripheral blood piRNA expression patterns in PTB patients and healthy individuals. Results: A total of 428 upregulated and 349 downregulated piRNAs were identified from PTB patients. Target genes of dysregulated piRNAs were mainly involved in transcription and protein binding. Dysregulated piRNAs were enriched in many pathways related with immunity. Many target genes were regulated by the same piRNAs. Nucleotide bias of these piRNAs showed that piRNAs in peripheral blood may be formed from the primary biogenesis pathway. Conclusion: Findings demonstrated that the PIWI-piRNA pathway is active in human peripheral blood, where it may represent a new player in the PTB pathogenesis.
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Affiliation(s)
- Xing Zhang
- School of Biology & Basic Medical Science, Soochow University, Suzhou 215123, PR China
| | - Zi Liang
- School of Biology & Basic Medical Science, Soochow University, Suzhou 215123, PR China
| | - Yunshan Zhang
- School of Biology & Basic Medical Science, Soochow University, Suzhou 215123, PR China
| | - Min Zhu
- School of Biology & Basic Medical Science, Soochow University, Suzhou 215123, PR China
| | - Yueping Zhu
- Department of Infectious Disease, First Affiliated Hospital of Soochow University, Suzhou 215006, PR China
| | - Sumei Li
- Department of Oncology, The Second Affiliated Hospital of Soochow University, Suzhou 215004, PR China
| | - Weifeng Zhao
- Department of Tuberculosis, The Fifth People's Hospital of Suzhou, Suzhou 215000, PR China
| | - Xiaolong Hu
- School of Biology & Basic Medical Science, Soochow University, Suzhou 215123, PR China
| | - Ji Wang
- Department of Infectious Disease, The Fifth People's Hospital of Suzhou, Suzhou 215000, PR China
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68
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Yao H, Wang X, Song J, Wang Y, Song Q, Han J. Coxsackievirus B3 infection induces changes in the expression of numerous piRNAs. Arch Virol 2019; 165:105-114. [PMID: 31741095 DOI: 10.1007/s00705-019-04451-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2019] [Accepted: 09/26/2019] [Indexed: 01/02/2023]
Abstract
Piwi-interacting RNAs (piRNAs) play pivotal roles in spermatogenesis and are widely distributed among somatic tissues. However, little is known about piRNAs in HeLa cells infected with coxsackievirus B3 (CVB3). In this study, we systematically investigated changes in piRNA expression in HeLa cells infected with CVB3 using high-throughput sequencing technology. piRNA expression profiles in CVB3-infected HeLa cells were examined at 3, 6 and 9 h postinfection (pi). Of the 32,826 piRNAs that were annotated in the NCBI database, 151,571, 89,698 and 76,626 piRNAs were detected in CVB3-infected HeLa cells at 3, 6 and 9 h pi, respectively. Compared with normal cells, 211, 72 and 94 piRNAs were differentially expressed in CVB3-infected HeLa cells at 3, 6 and 9 h pi, respectively. Thirteen piRNAs, including four novel piRNAs, exhibited concurrent changes in CVB3-infected HeLa cells. The changes in the expression of these 13 piRNAs was confirmed in CVB3-infected HeLa cells and 293T cells by stem-loop RT-qPCR at 3, 6 and 9 h pi. The target genes of 13 piRNAs were predicted. The four novel piRNAs were associated with LTR/ERV, LINE/L1 and LTR/ERVK repetitive elements located on different chromosomes. These findings may promote a better understanding of the regulatory mechanism of pathophysiological changes induced by CVB3 infection.
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Affiliation(s)
- Hailan Yao
- Molecular Immunology Laboratory, Capital Institute of Pediatrics, 2 YaBao Rd, Beijing, 100020, China
| | - Xinling Wang
- State Key Laboratory of Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, 155 Changbai Rd, Beijing, 102206, China
| | - Juan Song
- State Key Laboratory of Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, 155 Changbai Rd, Beijing, 102206, China
| | - Yanhai Wang
- State Key Laboratory of Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, 155 Changbai Rd, Beijing, 102206, China
| | - Qinqin Song
- State Key Laboratory of Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, 155 Changbai Rd, Beijing, 102206, China
| | - Jun Han
- State Key Laboratory of Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, 155 Changbai Rd, Beijing, 102206, China.
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Yusof AM, Jamal R, Saidin S, Muhammad R, Suhaimi SNA, Rose IM, Nazarie WFW, Fu FTY, Mutalib NSA. Deep Small RNA Sequencing of BRAF V600E Mutated Papillary Thyroid Carcinoma With Lymph Node Metastasis. Front Genet 2019; 10:941. [PMID: 31649724 PMCID: PMC6791926 DOI: 10.3389/fgene.2019.00941] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2019] [Accepted: 09/05/2019] [Indexed: 01/08/2023] Open
Affiliation(s)
- Azliana Mohamad Yusof
- Cytogenetics and Molecular Diagnostics Laboratory, Pantai Premier Pathology Sdn Bhd, Kuala Lumpur, Malaysia
| | - Rahman Jamal
- UKM Medical Molecular Biology Institute (UMBI), Universiti Kebangsaan Malaysia, Kuala Lumpur, Malaysia
| | - Sazuita Saidin
- UKM Medical Molecular Biology Institute (UMBI), Universiti Kebangsaan Malaysia, Kuala Lumpur, Malaysia
| | - Rohaizak Muhammad
- Department of Surgery, Faculty of Medicine, Universiti Kebangsaan Malaysia, Kuala Lumpur, Malaysia
| | | | - Isa Mohamed Rose
- Department of Pathology, Faculty of Medicine, Universiti Kebangsaan Malaysia, Kuala Lumpur, Malaysia
| | - Wan Fahmi Wan Nazarie
- UKM Medical Molecular Biology Institute (UMBI), Universiti Kebangsaan Malaysia, Kuala Lumpur, Malaysia
| | - Francis Tieng Yew Fu
- Institute of Bioscience (IBS), Universiti Putra Malaysia, UPM Serdang, Selangor, Malaysia
| | - Nurul-Syakima Ab Mutalib
- UKM Medical Molecular Biology Institute (UMBI), Universiti Kebangsaan Malaysia, Kuala Lumpur, Malaysia
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Rigoutsos I, Londin E, Kirino Y. Short RNA regulators: the past, the present, the future, and implications for precision medicine and health disparities. Curr Opin Biotechnol 2019; 58:202-210. [PMID: 31323485 DOI: 10.1016/j.copbio.2019.05.014] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2019] [Revised: 05/09/2019] [Accepted: 05/27/2019] [Indexed: 01/03/2023]
Abstract
We herein provide a brief review of the trajectory that the field of short RNA research followed in the last 25 years. We place emphasis on the unexpected discoveries and the ramifications of these discoveries for the field, as well as offer some thoughts about what the next 25 years may bring. Arguably, the uncovered dependence of different types of short RNAs on individual attributes such as a person's sex, population origin, race, and on tissue type, tissue state, and disease was most unexpected. This dependence has important ramifications in that it will provide a boost to our understanding of the molecular mechanisms of health disparities as well as pave the way for novel approaches to designing improved and personalized diagnostics and therapeutics.
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Affiliation(s)
- Isidore Rigoutsos
- Computational Medicine Center, Sidney Kimmel Medical College, Thomas Jefferson University, 1020 Locust Street, Philadelphia, PA 19107, United States.
| | - Eric Londin
- Computational Medicine Center, Sidney Kimmel Medical College, Thomas Jefferson University, 1020 Locust Street, Philadelphia, PA 19107, United States.
| | - Yohei Kirino
- Computational Medicine Center, Sidney Kimmel Medical College, Thomas Jefferson University, 1020 Locust Street, Philadelphia, PA 19107, United States.
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Yu Y, Xiao J, Hann SS. The emerging roles of PIWI-interacting RNA in human cancers. Cancer Manag Res 2019; 11:5895-5909. [PMID: 31303794 PMCID: PMC6612017 DOI: 10.2147/cmar.s209300] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2019] [Accepted: 05/14/2019] [Indexed: 12/17/2022] Open
Abstract
PIWI-interacting RNAs (piRNAs) are a type of non-coding RNAs that interact with PIWI proteins, which are members of the argonaute family. Originally described in the germline, piRNAs are also expressed in human somatic cells in a tissue-specific manner. piRNAs are involved in spermatogenesis, germ stem-cell maintenance, silencing of transposon, epigenetic and genomic regulation and rearrangement. A large number of studies have demonstrated that expression of piRNAs is involved in many kinds of disease, including cancer. Abnormal expression of piRNAs is emerging as a critical player in cancer cell proliferation, apoptosis, invasion, and migration in vitro and in vivo. Functionally, piRNAs maintain genomic integrity by repressing the mobilization of transposable elements, and regulate the expression of downstream target genes via transcriptional or post-transcriptional mechanisms. Furthermore, altered expression of piRNAs in cancer is linked to clinical outcome, highlighting the important role that they may play as novel diagnostic and prognostic biomarkers, and as therapeutic targets for cancer therapy. In this review, we focus on the biogenesis and the functional roles of piRNAs in cancers, discuss emerging insights into the roles of piRNAs in the occurrence, progression, and treatment of cancers, reveal various mechanisms underlying piRNAs-mediated gene regulation, and highlight their potential clinical utilities as biomarkers as well as potential targets for cancer treatment.
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Affiliation(s)
- Yaya Yu
- Laboratory of Tumor Biology, The Second Clinical College of Guangzhou University of Chinese Medicine , Guangzhou, Guangdong Province, 510120, People's Republic of China
| | - Jing Xiao
- Department of Gynecology, The Second Clinical College of Guangzhou University of Chinese Medicine, Guangzhou, Guangdong Province, 510120, People's Republic of China
| | - Swei Sunny Hann
- Laboratory of Tumor Biology, The Second Clinical College of Guangzhou University of Chinese Medicine , Guangzhou, Guangdong Province, 510120, People's Republic of China.,Guangdong Provincial Key Laboratory of Clinical Research on Traditional Chinese Medicine Syndrome, The Second Clinical College of Guangzhou University of Chinese Medicine, Guangzhou, Guangdong Province, 510120, People's Republic of China
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Baumann B, Lugli G, Gao S, Zenner M, Nonn L. High levels of PIWI-interacting RNAs are present in the small RNA landscape of prostate epithelium from vitamin D clinical trial specimens. Prostate 2019; 79:840-855. [PMID: 30905091 PMCID: PMC6593815 DOI: 10.1002/pros.23789] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/31/2019] [Revised: 01/31/2019] [Accepted: 02/19/2019] [Indexed: 02/02/2023]
Abstract
BACKGROUND Vitamin D, a hormone that acts through the nuclear vitamin D receptor (VDR), upregulates antitumorigenic microRNA in prostate epithelium. This may contribute to the lower levels of aggressive prostate cancer (PCa) observed in patients with high serum vitamin D. The small noncoding RNA (ncRNA) landscape includes many other RNA species that remain uncharacterized in prostate epithelium and their potential regulation by vitamin D is unknown. METHODS Laser capture microdissection (LCM) followed by small-RNA sequencing was used to identify ncRNAs in the prostate epithelium of tissues from a vitamin D-supplementation trial. VDR chromatin immunoprecipitation-sequencing was performed to identify vitamin D genomic targets in primary prostate epithelial cells. RESULTS Isolation of epithelium by LCM increased sample homogeneity and captured more diversity in ncRNA species compared with publicly available small-RNA sequencing data from benign whole prostate. An abundance of PIWI-interacting RNAs (piRNAs) was detected in normal prostate epithelium. The obligate binding partners of piRNAs, PIWI-like (PIWIL) proteins, were also detected in prostate epithelium. High prostatic vitamin D levels were associated with increased expression of piRNAs. VDR binding sites were located near several ncRNA biogenesis genes and genes regulating translation and differentiation. CONCLUSIONS Benign prostate epithelium expresses both piRNA and PIWIL proteins, suggesting that these small ncRNA may serve an unknown function in the prostate. Vitamin D may increase the expression of prostatic piRNAs. VDR binding sites in primary prostate epithelial cells are consistent with its reported antitumorigenic functions and a role in ncRNA biogenesis.
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Affiliation(s)
- Bethany Baumann
- Department of Pathology, College of MedicineUniversity of Illinois at ChicagoChicagoIllinois
| | - Giovanni Lugli
- Department of Pathology, College of MedicineUniversity of Illinois at ChicagoChicagoIllinois
| | - Shang Gao
- Department of BioengineeringUniversity of Illinois at ChicagoChicagoIllinois
| | - Morgan Zenner
- Department of Pathology, College of MedicineUniversity of Illinois at ChicagoChicagoIllinois
| | - Larisa Nonn
- Department of Pathology, College of MedicineUniversity of Illinois at ChicagoChicagoIllinois
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73
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Tan L, Mai D, Zhang B, Jiang X, Zhang J, Bai R, Ye Y, Li M, Pan L, Su J, Zheng Y, Liu Z, Zuo Z, Zhao Q, Li X, Huang X, Yang J, Tan W, Zheng J, Lin D. PIWI-interacting RNA-36712 restrains breast cancer progression and chemoresistance by interaction with SEPW1 pseudogene SEPW1P RNA. Mol Cancer 2019; 18:9. [PMID: 30636640 PMCID: PMC6330501 DOI: 10.1186/s12943-019-0940-3] [Citation(s) in RCA: 150] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2018] [Accepted: 01/01/2019] [Indexed: 12/25/2022] Open
Abstract
Background Breast cancer is one of the most common malignancies and the major cause of cancer-related death in women. Although the importance of PIWI-interacting RNAs (piRNAs) in cancer has been increasingly recognized, few studies have been explored the functional mechanism of piRNAs in breast cancer development and progression. Methods We examined the top 20 highly expressed piRNAs based on the analysis of TCGA breast cancer data in two patient cohorts to test the roles of piRNAs in breast cancer. The effects of piRNA-36,712 on the malignant phenotypes and chemosensitivity of breast cancer cells were detected in vitro and in vivo. MS2-RIP and reporter gene assays were conducted to identify the interaction and regulation among piRNA-36,712, miRNAs and SEPW1P. Kaplan-Meier estimate with log-rank test was used to compare patient survival by different piRNA-36,712 expression levels. Results We found piRNA-36,712 level was significantly lower in breast cancer than in normal breast tissues and low level was correlated with poor clinical outcome in patients. Functional studies demonstrated that piRNA-36,712 interacts with RNAs produced by SEPW1P, a retroprocessed pseudogene of SEPW1, and subsequently inhibits SEPW1 expression through competition of SEPW1 mRNA with SEPW1P RNA for microRNA-7 and microRNA-324. We also found that higher SEPW1 expression due to downregulation of piRNA-36,712 in breast cancer may suppress P53, leading to the upregulated Slug but decreased P21 and E-cadherin levels, thus promoting cancer cell proliferation, invasion and migration. Furthermore, we found that piRNA-36,712 had synergistic anticancer effects with the paclitaxel and doxorubicin, two chemotherapeutic agents for breast cancer. Conclusions These findings suggest that piRNA-36,712 is a novel tumor suppressor and may serve as a potential predictor for the prognosis of breast cancer patients. Electronic supplementary material The online version of this article (10.1186/s12943-019-0940-3) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Liping Tan
- State Key Laboratory of Oncology in South China and Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Dongmei Mai
- State Key Laboratory of Oncology in South China and Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Bailin Zhang
- Department of Breast Surgery, National Cancer Center/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Xiaobing Jiang
- Department of Surgical Oncology, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Jialiang Zhang
- State Key Laboratory of Oncology in South China and Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Ruihong Bai
- State Key Laboratory of Oncology in South China and Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Ying Ye
- State Key Laboratory of Oncology in South China and Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Mei Li
- Department of Pathology, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Ling Pan
- State Key Laboratory of Oncology in South China and Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Jiachun Su
- State Key Laboratory of Oncology in South China and Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Yanfen Zheng
- State Key Laboratory of Oncology in South China and Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Zexian Liu
- State Key Laboratory of Oncology in South China and Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Zhixiang Zuo
- State Key Laboratory of Oncology in South China and Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Qi Zhao
- State Key Laboratory of Oncology in South China and Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Xiaoxing Li
- State Key Laboratory of Oncology in South China and Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Xudong Huang
- State Key Laboratory of Oncology in South China and Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Jie Yang
- Department of Etiology and Carcinogenesis, National Cancer Center/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Wen Tan
- Department of Etiology and Carcinogenesis, National Cancer Center/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Jian Zheng
- State Key Laboratory of Oncology in South China and Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, China.
| | - Dongxin Lin
- State Key Laboratory of Oncology in South China and Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, China.,Department of Etiology and Carcinogenesis, National Cancer Center/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
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74
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Liu X, Chen Q, Ding X, Zhao Y, Zhang K, Yu P, Cui F, Xue B. X-ray-induced reproductive dysfunction and differentially expressed piRNAs in male mice. Hum Exp Toxicol 2018; 38:533-546. [PMID: 30596273 DOI: 10.1177/0960327118812187] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
The effects of X-ray radiation on spermatogenesis, sperm motility, and PIWI-interacting RNAs (piRNAs) in mice were analyzed. Male C57BL/6 J mice were divided into control and two irradiation groups ( n = 9 mice/group). After irradiation of their reproductive regions, the mice were fed for 3 days (irradiation group 1) or 7 days (control and irradiation group 2). The sperm viability, motility, velocity, and motion curve were analyzed. After piRNA expression profiling, quantitative reverse-transcription polymerase chain reaction was conducted for validation. Ionizing radiation led to vessel dilation and congestion, fewer spermatogenic cells, and reduced sperm production compared to the control. At 3 and 7 days postirradiation, the sperm count (grade d) increased while sperm viability and sperm lateral head displacement decreased. At 7 days, the sperm abnormality rate was higher compared to the control. Many piRNAs were differentially expressed after irradiation, including decreased and increased expression of mmu_piR_009082 and mmu_piR_020217, respectively. Downregulated piRNAs were involved in Rap1 signaling, non-homologous end-joining, hedgehog signaling, oxytocin signaling, and cholinergic synapse. Upregulated piRNAs participated in pathways including proteoglycans in cancer, phosphatidylinositol signaling, cGMP-PKG signaling, and stem cell pluripotency regulation. X-ray irradiation inhibited spermatogenesis and increased abnormal sperm rate in mice. piRNA-related signaling pathways may be involved in this process.
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Affiliation(s)
- X Liu
- Department of Urology, the Second Affiliated Hospital of Suzhou University, Suzhou, China
- State Key Laboratory of Radiation Medicine and Protection, Soochow University, Suzhou, China
| | - Q Chen
- State Key Laboratory of Radiation Medicine and Protection, Soochow University, Suzhou, China
- Collaborative Innovation Center of Radiation Medicine of Jiangsu Higher Education Institutions, Suzhou, China
| | - X Ding
- Department of Urology, Suzhou University, Suzhou, China
| | - Y Zhao
- State Key Laboratory of Radiation Medicine and Protection, Soochow University, Suzhou, China
- Collaborative Innovation Center of Radiation Medicine of Jiangsu Higher Education Institutions, Suzhou, China
| | - K Zhang
- State Key Laboratory of Radiation Medicine and Protection, Soochow University, Suzhou, China
- Collaborative Innovation Center of Radiation Medicine of Jiangsu Higher Education Institutions, Suzhou, China
| | - P Yu
- Department of Urology, the Second Affiliated Hospital of Suzhou University, Suzhou, China
| | - F Cui
- State Key Laboratory of Radiation Medicine and Protection, Soochow University, Suzhou, China
- Collaborative Innovation Center of Radiation Medicine of Jiangsu Higher Education Institutions, Suzhou, China
| | - B Xue
- Department of Urology, the Second Affiliated Hospital of Suzhou University, Suzhou, China
- State Key Laboratory of Radiation Medicine and Protection, Soochow University, Suzhou, China
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75
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Weng W, Li H, Goel A. Piwi-interacting RNAs (piRNAs) and cancer: Emerging biological concepts and potential clinical implications. Biochim Biophys Acta Rev Cancer 2018; 1871:160-169. [PMID: 30599187 DOI: 10.1016/j.bbcan.2018.12.005] [Citation(s) in RCA: 86] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2018] [Revised: 11/09/2018] [Accepted: 12/24/2018] [Indexed: 12/12/2022]
Abstract
Piwi-interacting RNAs (piRNAs) are a very recently discovered class of small non-coding RNAs (ncRNAs), with approximately 20,000 piRNA genes already identified within the human genome. These short RNAs were originally described as key functional regulators for the germline maintenance and transposon silencing. However, due to our limited knowledge regarding their function, piRNAs were for a long time assumed to be the "dark matter" of ncRNAs in our genome. However, recent evidence has now changed our viewpoint of their biological and clinical significance in various diseases, as newly emerging data reveals that aberrant expression of piRNAs is a unique and distinct feature in many diseases, including multiple human cancers. Furthermore, their altered expression in cancer patients has been significantly associated with clinical outcomes, highlighting their important biological functional role in disease progression. Functionally, piRNAs maintain genomic integrity by silencing transposable elements, and are capable of regulating the expression of specific downstream target genes in a post-transcriptional manner. Moreover, accumulating evidences demonstrates that analogous to other small ncRNAs (e.g. miRNAs) piRNAs have both oncogenic and tumor suppressive roles in cancer development. In this article, we discuss emerging insights into roles of piRNAs in a variety of cancers, reveal new findings underpinning various mechanisms of piRNAs-mediated gene regulation, and highlight their potential clinical significance in the management of cancer patients.
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Affiliation(s)
- Wenhao Weng
- Department of Clinical Laboratory, Yangpu Hospital, Tongji University School of Medicine, Shanghai 200090, China; Center for Translational Medicine, Yangpu Hospital, Tongji University School of Medicine, Shanghai 200090, China
| | - Hanhua Li
- Department of Clinical Laboratory, Yangpu Hospital, Tongji University School of Medicine, Shanghai 200090, China
| | - Ajay Goel
- Center for Gastrointestinal Research, Center for Translational Genomics and Oncology, Baylor Scott & White Research Institute and Charles A Sammons Cancer Center, Baylor Research Institute and Sammons Cancer Center, Baylor University Medical Center, Dallas, TX 75246-2017, USA.
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76
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Jacobs DI, Qin Q, Fu A, Chen Z, Zhou J, Zhu Y. piRNA-8041 is downregulated in human glioblastoma and suppresses tumor growth in vitro and in vivo. Oncotarget 2018; 9:37616-37626. [PMID: 30701019 PMCID: PMC6340885 DOI: 10.18632/oncotarget.26331] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2016] [Accepted: 09/13/2017] [Indexed: 01/19/2023] Open
Abstract
PIWI-interacting RNAs (piRNAs) are small non-coding RNAs that partner with PIWI proteins to protect germline tissues from destabilizing transposon activity. While the aberrant expression of PIWI proteins has been linked with poor outcomes for many cancers, less is known about the expression or function of piRNAs in cancer. We performed array-based piRNA expression profiling in seven pairs of normal brain and glioblastoma multiforme (GBM) tissue specimens, and identified expression of ~350 piRNAs in both tissues and a subset with dysregulated expression in GBM. Over-expression of the most down-regulated piRNA in GBM tissue, piR-8041, was found to reduce glioma cell line proliferation, induce cell cycle arrest and apoptosis, and inhibit cell survival pathways. Furthermore, pre-treatment with piR-8041 significantly reduced the volume of intracranial mouse xenograft tumors. Taken together, our study reveals reduced expression in GBM of piR-8041 and other piRNAs with tumor suppressive properties, and suggests that restoration of such piRNAs may be a potential strategy for GBM therapy.
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Affiliation(s)
- Daniel I. Jacobs
- Department of Environmental Health Sciences, Yale School of Public Health, New Haven, CT, USA
| | - Qin Qin
- Department of Environmental Health Sciences, Yale School of Public Health, New Haven, CT, USA
- Current address: Division of Genetic and Molecular Toxicology, National Center for Toxicological Research, Food and Drug Administration, Jefferson, AR, USA
| | - Alan Fu
- Department of Environmental Health Sciences, Yale School of Public Health, New Haven, CT, USA
- Current Address: Department of Epidemiology, UCLA Fielding School of Public Health, Los Angeles, CA, USA
| | - Zeming Chen
- Department of Neurosurgery, Yale School of Medicine, New Haven, CT, USA
| | - Jiangbing Zhou
- Department of Neurosurgery, Yale School of Medicine, New Haven, CT, USA
- Department of Biomedical Engineering, Yale University, New Haven, CT, USA
| | - Yong Zhu
- Department of Environmental Health Sciences, Yale School of Public Health, New Haven, CT, USA
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77
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Klinge CM. Non-Coding RNAs in Breast Cancer: Intracellular and Intercellular Communication. Noncoding RNA 2018; 4:E40. [PMID: 30545127 PMCID: PMC6316884 DOI: 10.3390/ncrna4040040] [Citation(s) in RCA: 99] [Impact Index Per Article: 14.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2018] [Revised: 11/29/2018] [Accepted: 12/04/2018] [Indexed: 02/07/2023] Open
Abstract
Non-coding RNAs (ncRNAs) are regulators of intracellular and intercellular signaling in breast cancer. ncRNAs modulate intracellular signaling to control diverse cellular processes, including levels and activity of estrogen receptor α (ERα), proliferation, invasion, migration, apoptosis, and stemness. In addition, ncRNAs can be packaged into exosomes to provide intercellular communication by the transmission of microRNAs (miRNAs) and long non-coding RNAs (lncRNAs) to cells locally or systemically. This review provides an overview of the biogenesis and roles of ncRNAs: small nucleolar RNA (snRNA), circular RNAs (circRNAs), PIWI-interacting RNAs (piRNAs), miRNAs, and lncRNAs in breast cancer. Since more is known about the miRNAs and lncRNAs that are expressed in breast tumors, their established targets as oncogenic drivers and tumor suppressors will be reviewed. The focus is on miRNAs and lncRNAs identified in breast tumors, since a number of ncRNAs identified in breast cancer cells are not dysregulated in breast tumors. The identity and putative function of selected lncRNAs increased: nuclear paraspeckle assembly transcript 1 (NEAT1), metastasis-associated lung adenocarcinoma transcript 1 (MALAT1), steroid receptor RNA activator 1 (SRA1), colon cancer associated transcript 2 (CCAT2), colorectal neoplasia differentially expressed (CRNDE), myocardial infarction associated transcript (MIAT), and long intergenic non-protein coding RNA, Regulator of Reprogramming (LINC-ROR); and decreased levels of maternally-expressed 3 (MEG3) in breast tumors have been observed as well. miRNAs and lncRNAs are considered targets of therapeutic intervention in breast cancer, but further work is needed to bring the promise of regulating their activities to clinical use.
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Affiliation(s)
- Carolyn M Klinge
- Department of Biochemistry & Molecular Genetics, University of Louisville School of Medicine, Louisville, KY 40292, USA.
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78
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Kovalenko TF, Patrushev LI. Pseudogenes as Functionally Significant Elements of the Genome. BIOCHEMISTRY (MOSCOW) 2018; 83:1332-1349. [PMID: 30482145 DOI: 10.1134/s0006297918110044] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Pseudogene is a gene copy that has lost its original function. For a long time, pseudogenes have been considered as "junk DNA" that inevitably arises as a result of ongoing evolutionary process. However, experimental data obtained during recent years indicate this understanding of the nature of pseudogenes is not entirely correct, and many pseudogenes perform important genetic functions. In the review, we have addressed classification of pseudogenes, methods of their detection in the genome, and the problem of their evolutionary conservatism and prevalence among species belonging to different taxonomic groups in the light of modern data. The mechanisms of gene expression regulation by pseudogenes and the role of pseudogenes in pathogenesis of various human diseases are discussed.
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Affiliation(s)
- T F Kovalenko
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, 117997, Russia.
| | - L I Patrushev
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, 117997, Russia
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79
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Wang M, Jiang S, Wu W, Yu F, Chang W, Li P, Wang K. Non-coding RNAs Function as Immune Regulators in Teleost Fish. Front Immunol 2018; 9:2801. [PMID: 30546368 PMCID: PMC6279911 DOI: 10.3389/fimmu.2018.02801] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2018] [Accepted: 11/13/2018] [Indexed: 12/13/2022] Open
Abstract
Non-coding RNAs (ncRNAs) are functional RNA molecules that are transcribed from DNA but not translated into proteins. ncRNAs function as key regulators of gene expression and chromatin modification. Recently, the functional role of ncRNAs in teleost fish has been extensively studied. Teleost fish are a highly diverse group among the vertebrate lineage. Fish are also important in terms of aquatic ecosystem, food production and human life, being the source of animal proteins worldwide and models of biomedical research. However, teleost fish always suffer from the invasion of infectious pathogens including viruses and bacteria, which has resulted in a tremendous economic loss to the fishing industry worldwide. Emerging evidence suggests that ncRNAs, especially miRNAs and lncRNAs, may serve as important regulators in cytokine and chemokine signaling, antigen presentation, complement and coagulation cascades, and T cell response in teleost fish. In this review, we summarize current knowledge and understanding of the roles of both miRNAs and lncRNAs in immune regulation in teleost fish. Molecular mechanism insights into the function of ncRNAs in fish immune response may contribute to the development of potential biomarkers and therapeutic targets for the prevention and treatment of fish diseases.
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Affiliation(s)
- Man Wang
- Institute for Translational Medicine, Medical College of Qingdao University, Qingdao, China
| | - Shuai Jiang
- Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
| | - Wei Wu
- Institute for Translational Medicine, Medical College of Qingdao University, Qingdao, China
| | - Fei Yu
- Institute for Translational Medicine, Medical College of Qingdao University, Qingdao, China
| | - Wenguang Chang
- Institute for Translational Medicine, Medical College of Qingdao University, Qingdao, China
| | - Peifeng Li
- Institute for Translational Medicine, Medical College of Qingdao University, Qingdao, China
| | - Kun Wang
- Institute for Translational Medicine, Medical College of Qingdao University, Qingdao, China
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80
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Zhao C, Tolkach Y, Schmidt D, Toma M, Muders MH, Kristiansen G, Müller SC, Ellinger J. Mitochondrial PIWI-interacting RNAs are novel biomarkers for clear cell renal cell carcinoma. World J Urol 2018; 37:1639-1647. [DOI: 10.1007/s00345-018-2575-1] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2018] [Accepted: 11/22/2018] [Indexed: 12/20/2022] Open
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81
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Balaratnam S, West N, Basu S. A piRNA utilizes HILI and HIWI2 mediated pathway to down-regulate ferritin heavy chain 1 mRNA in human somatic cells. Nucleic Acids Res 2018; 46:10635-10648. [PMID: 30102404 PMCID: PMC6237762 DOI: 10.1093/nar/gky728] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2018] [Revised: 07/27/2018] [Accepted: 07/31/2018] [Indexed: 12/18/2022] Open
Abstract
The piwi interacting RNAs (piRNAs) are small non-coding RNAs that specifically bind to the PIWI proteins, a functional requirement. The piRNAs regulate germline development, transposons control, and gene expression. However, piRNA-mediated post-transcriptional gene regulation in human somatic cells is not well understood. We discovered a human piRNA (piR-FTH1) which has a complementary sequence in the ferritin heavy chain 1 (Fth1) mRNA. We demonstrated that expression of piR-FTH1 and Fth1 are inversely correlated in the tested tumor cell lines. We found that piR-FTH1 negatively regulates the Fth1 expression at post-transcriptional level in triple negative breast cancer (TNBC) cells. Additionally, we confirmed that transfected piR-FTH1 knocks down the Fth1 mRNA via the HIWI2 and HILI mediated mechanism. piR-FTH1 mediated Fth1 repression also increased doxorubicin sensitivity by a remarkable 20-fold in TNBC cells. Since the current piRNA-mediated knockdowns of target mRNA are mostly reported in germ line cells, piRNA-mediated post-transcriptional gene regulation in somatic cells is rather unique in its application and mechanistically uses an alternative pathway to siRNA and miRNA. This work begins to lay the groundwork with a broader impact on treatment of various diseases that are linked to elevated levels of specific mRNAs which have a piRNA target.
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Affiliation(s)
- Sumirtha Balaratnam
- Department of Chemistry and Biochemistry, Kent State University, Kent, OH 44242, USA
| | - Nicole West
- Department of Chemistry and Biochemistry, Kent State University, Kent, OH 44242, USA
| | - Soumitra Basu
- Department of Chemistry and Biochemistry, Kent State University, Kent, OH 44242, USA
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82
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A secondary structure within a human piRNA modulates its functionality. Biochimie 2018; 157:72-80. [PMID: 30414834 DOI: 10.1016/j.biochi.2018.11.002] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2018] [Accepted: 11/04/2018] [Indexed: 01/30/2023]
Abstract
The piwi-interacting RNAs (piRNAs) are small non-coding RNAs, mostly 24-32 nucleotides in length. The piRNAs are not known to have any conserved secondary structure or sequence motifs. Using bioinformatics analysis, we discovered the presence of putative G-quadruplex (GQ) forming sequences in human piRNAs. We studied human piR-48164/piR-GQ containing a potential GQ forming sequence and using biochemical and biophysical techniques confirmed its ability to form a GQ. Using EMSA, we discovered that the formation of GQ structure led to inhibition of the piRNA binding to the HIWI-PAZ domain as well as the complementary base pairing to a target RNA. The inability of the piR-GQ to interact with the PIWI protein might be detrimental to the function of the piRNA. To investigate if the formation of a GQ structure in piRNA prevents its target gene silencing in vivo, we used a reporter assay. The piR-GQ failed to inhibit the reporter gene expression while a mutated version that lacked the ability to form GQ inhibited reporter gene expression indicating that the presence of GQ in piRNA is detrimental to its function. These studies unraveled the dependence of a piRNA's functionality on an RNA secondary structure and added a new layer of regulation to their function.
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83
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Watanabe T, Cui X, Yuan Z, Qi H, Lin H. MIWI2 targets RNAs transcribed from piRNA-dependent regions to drive DNA methylation in mouse prospermatogonia. EMBO J 2018; 37:e95329. [PMID: 30108053 PMCID: PMC6138435 DOI: 10.15252/embj.201695329] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2016] [Revised: 07/06/2018] [Accepted: 07/09/2018] [Indexed: 12/24/2022] Open
Abstract
Argonaute/Piwi proteins can regulate gene expression via RNA degradation and translational regulation using small RNAs as guides. They also promote the establishment of suppressive epigenetic marks on repeat sequences in diverse organisms. In mice, the nuclear Piwi protein MIWI2 and Piwi-interacting RNAs (piRNAs) are required for DNA methylation of retrotransposon sequences and some other sequences. However, its underlying molecular mechanisms remain unclear. Here, we show that piRNA-dependent regions are transcribed at the stage when piRNA-mediated DNA methylation takes place. MIWI2 specifically interacts with RNAs from these regions. In addition, we generated mice with deletion of a retrotransposon sequence either in a representative piRNA-dependent region or in a piRNA cluster. Both deleted regions were required for the establishment of DNA methylation of the piRNA-dependent region, indicating that piRNAs determine the target specificity of MIWI2-mediated DNA methylation. Our results indicate that MIWI2 affects the chromatin state through base-pairing between piRNAs and nascent RNAs, as observed in other organisms possessing small RNA-mediated epigenetic regulation.
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Affiliation(s)
- Toshiaki Watanabe
- Yale Stem Cell Center and Department of Cell Biology, Yale University School of Medicine, New Haven, CT, USA
| | - Xiekui Cui
- Yale Stem Cell Center and Department of Cell Biology, Yale University School of Medicine, New Haven, CT, USA
| | - Zhongyu Yuan
- Zhiyuan College, Shanghai Jiaotong University, Shanghai, China
| | - Hongying Qi
- Yale Stem Cell Center and Department of Cell Biology, Yale University School of Medicine, New Haven, CT, USA
| | - Haifan Lin
- Yale Stem Cell Center and Department of Cell Biology, Yale University School of Medicine, New Haven, CT, USA
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Jehn J, Gebert D, Pipilescu F, Stern S, Kiefer JST, Hewel C, Rosenkranz D. PIWI genes and piRNAs are ubiquitously expressed in mollusks and show patterns of lineage-specific adaptation. Commun Biol 2018; 1:137. [PMID: 30272016 PMCID: PMC6128900 DOI: 10.1038/s42003-018-0141-4] [Citation(s) in RCA: 43] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2018] [Accepted: 08/17/2018] [Indexed: 12/14/2022] Open
Abstract
PIWI proteins and PIWI-interacting RNAs (piRNAs) suppress transposon activity in animals, thus protecting their genomes from detrimental insertion mutagenesis. Here, we reveal that PIWI genes and piRNAs are ubiquitously expressed in mollusks, similar to the situation in arthropods. We describe lineage-specific adaptations of transposon composition in piRNA clusters in the great pond snail and the pacific oyster, likely reflecting differential transposon activity in gastropods and bivalves. We further show that different piRNA clusters with unique transposon composition are dynamically expressed during oyster development. Finally, bioinformatics analyses suggest that different populations of piRNAs presumably bound to different PIWI paralogs participate in homotypic and heterotypic ping-pong amplification loops in a tissue- and sex-specific manner. Together with recent findings from other animal species, our results support the idea that somatic piRNA expression represents the ancestral state in metazoans.
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Affiliation(s)
- Julia Jehn
- Institute of Organismic and Molecular Evolution, Anthropology, Johannes Gutenberg University Mainz, Anselm-Franz-von-Bentzel-Weg 7, 55099, Mainz, Germany
| | - Daniel Gebert
- Institute of Organismic and Molecular Evolution, Anthropology, Johannes Gutenberg University Mainz, Anselm-Franz-von-Bentzel-Weg 7, 55099, Mainz, Germany
| | - Frank Pipilescu
- Institute of Organismic and Molecular Evolution, Anthropology, Johannes Gutenberg University Mainz, Anselm-Franz-von-Bentzel-Weg 7, 55099, Mainz, Germany
| | - Sarah Stern
- Institute of Organismic and Molecular Evolution, Anthropology, Johannes Gutenberg University Mainz, Anselm-Franz-von-Bentzel-Weg 7, 55099, Mainz, Germany
| | - Julian Simon Thilo Kiefer
- Institute of Organismic and Molecular Evolution, Anthropology, Johannes Gutenberg University Mainz, Anselm-Franz-von-Bentzel-Weg 7, 55099, Mainz, Germany
| | - Charlotte Hewel
- Institute of Organismic and Molecular Evolution, Anthropology, Johannes Gutenberg University Mainz, Anselm-Franz-von-Bentzel-Weg 7, 55099, Mainz, Germany
| | - David Rosenkranz
- Institute of Organismic and Molecular Evolution, Anthropology, Johannes Gutenberg University Mainz, Anselm-Franz-von-Bentzel-Weg 7, 55099, Mainz, Germany.
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85
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Lim MCJ, Baird AM, Aird J, Greene J, Kapoor D, Gray SG, McDermott R, Finn SP. RNAs as Candidate Diagnostic and Prognostic Markers of Prostate Cancer-From Cell Line Models to Liquid Biopsies. Diagnostics (Basel) 2018; 8:E60. [PMID: 30200254 PMCID: PMC6163368 DOI: 10.3390/diagnostics8030060] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2018] [Revised: 08/20/2018] [Accepted: 08/21/2018] [Indexed: 12/19/2022] Open
Abstract
The treatment landscape of prostate cancer has evolved rapidly over the past five years. The explosion in treatment advances has been witnessed in parallel with significant progress in the field of molecular biomarkers. The advent of next-generation sequencing has enabled the molecular profiling of the genomic and transcriptomic architecture of prostate and other cancers. Coupled with this, is a renewed interest in the role of non-coding RNA (ncRNA) in prostate cancer biology. ncRNA consists of several different classes including small non-coding RNA (sncRNA), long non-coding RNA (lncRNA), and circular RNA (circRNA). These families are under active investigation, given their essential roles in cancer initiation, development and progression. This review focuses on the evidence for the role of RNAs in prostate cancer, and their use as diagnostic and prognostic markers, and targets for treatment in this disease.
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Affiliation(s)
- Marvin C J Lim
- Department of Histopathology and Morbid Anatomy, Trinity Translational Medicine Institute, Trinity College Dublin, Dublin D08 W9RT, Ireland.
- Department of Medical Oncology, Tallaght University Hospital, Dublin D24 NR0A, Ireland.
| | - Anne-Marie Baird
- Cancer and Ageing Research Programme, Queensland University of Technology, Brisbane, QLD 4000, Australia.
- Department of Clinical Medicine, Trinity College Dublin, College Green, Dublin D02 PN40, Ireland.
- Thoracic Oncology Research Group, Labmed Directorate, St. James's Hospital, Dublin 08 W9RT, Ireland.
| | - John Aird
- Department of Histopathology and Morbid Anatomy, Trinity Translational Medicine Institute, Trinity College Dublin, Dublin D08 W9RT, Ireland.
| | - John Greene
- Department of Histopathology and Morbid Anatomy, Trinity Translational Medicine Institute, Trinity College Dublin, Dublin D08 W9RT, Ireland.
| | - Dhruv Kapoor
- Department of Histopathology and Morbid Anatomy, Trinity Translational Medicine Institute, Trinity College Dublin, Dublin D08 W9RT, Ireland.
| | - Steven G Gray
- Department of Clinical Medicine, Trinity College Dublin, College Green, Dublin D02 PN40, Ireland.
- Thoracic Oncology Research Group, Labmed Directorate, St. James's Hospital, Dublin 08 W9RT, Ireland.
- School of Biological Sciences, Dublin Institute of Technology, Dublin D08 NF82, Ireland.
| | - Ray McDermott
- Department of Medical Oncology, Tallaght University Hospital, Dublin D24 NR0A, Ireland.
- Department of Medical Oncology, St. Vincent's University Hospital, Dublin D04 YN26, Ireland.
| | - Stephen P Finn
- Department of Histopathology and Morbid Anatomy, Trinity Translational Medicine Institute, Trinity College Dublin, Dublin D08 W9RT, Ireland.
- Department of Histopathology, St. James's Hospital, P.O. Box 580, James's Street, Dublin D08 X4RX, Ireland.
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86
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Kumar A, Srivastava P, Sirisena P, Dubey SK, Kumar R, Shrinet J, Sunil S. Mosquito Innate Immunity. INSECTS 2018; 9:insects9030095. [PMID: 30096752 PMCID: PMC6165528 DOI: 10.3390/insects9030095] [Citation(s) in RCA: 92] [Impact Index Per Article: 13.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/28/2018] [Revised: 06/17/2018] [Accepted: 06/18/2018] [Indexed: 12/19/2022]
Abstract
Mosquitoes live under the endless threat of infections from different kinds of pathogens such as bacteria, parasites, and viruses. The mosquito defends itself by employing both physical and physiological barriers that resist the entry of the pathogen and the subsequent establishment of the pathogen within the mosquito. However, if the pathogen does gain entry into the insect, the insect mounts a vigorous innate cellular and humoral immune response against the pathogen, thereby limiting the pathogen's propagation to nonpathogenic levels. This happens through three major mechanisms: phagocytosis, melanization, and lysis. During these processes, various signaling pathways that engage intense mosquito⁻pathogen interactions are activated. A critical overview of the mosquito immune system and latest information about the interaction between mosquitoes and pathogens are provided in this review. The conserved, innate immune pathways and specific anti-pathogenic strategies in mosquito midgut, hemolymph, salivary gland, and neural tissues for the control of pathogen propagation are discussed in detail.
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Affiliation(s)
- Ankit Kumar
- Vector Borne Diseases Group, International Centre for Genetic Engineering and Biotechnology (ICGEB), New Delhi-110067, India.
| | - Priyanshu Srivastava
- Vector Borne Diseases Group, International Centre for Genetic Engineering and Biotechnology (ICGEB), New Delhi-110067, India.
| | - Pdnn Sirisena
- Vector Borne Diseases Group, International Centre for Genetic Engineering and Biotechnology (ICGEB), New Delhi-110067, India.
| | - Sunil Kumar Dubey
- Vector Borne Diseases Group, International Centre for Genetic Engineering and Biotechnology (ICGEB), New Delhi-110067, India.
| | - Ramesh Kumar
- Vector Borne Diseases Group, International Centre for Genetic Engineering and Biotechnology (ICGEB), New Delhi-110067, India.
| | - Jatin Shrinet
- Vector Borne Diseases Group, International Centre for Genetic Engineering and Biotechnology (ICGEB), New Delhi-110067, India.
| | - Sujatha Sunil
- Vector Borne Diseases Group, International Centre for Genetic Engineering and Biotechnology (ICGEB), New Delhi-110067, India.
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87
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Diamantopoulos MA, Tsiakanikas P, Scorilas A. Non-coding RNAs: the riddle of the transcriptome and their perspectives in cancer. ANNALS OF TRANSLATIONAL MEDICINE 2018; 6:241. [PMID: 30069443 DOI: 10.21037/atm.2018.06.10] [Citation(s) in RCA: 78] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Non-coding RNAs (ncRNAs) constitute a heterogeneous group of RNA molecules in terms of biogenesis, biological function as well as length and structure. These biological molecules have gained attention recently as a potentially crucial layer of tumor cell progression or regulation. ncRNAs are expressed in a broad spectrum of tumors, and they play an important role not only in maintaining but also in promoting cancer development and progression. Recent discoveries have revealed that ncRNAs may act as key signal transduction mediators in tumor signaling pathways by interacting with RNA or proteins. These results reinforce the hypothesis, that ncRNAs constitute therapeutic targets, and point out their clinical potential as stratification markers. The major purpose of this review is to mention the emergence of the importance of ncRNAs, as molecules which are correlated with cancer, and to discuss their clinical implicit as prognostic diagnostic indicators, biomarkers, and therapeutic targets.
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Affiliation(s)
- Marios A Diamantopoulos
- Department of Biochemistry and Molecular Biology, National and Kapodistrian University of Athens, Athens, Greece
| | - Panagiotis Tsiakanikas
- Department of Biochemistry and Molecular Biology, National and Kapodistrian University of Athens, Athens, Greece
| | - Andreas Scorilas
- Department of Biochemistry and Molecular Biology, National and Kapodistrian University of Athens, Athens, Greece
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88
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The Challenges and Opportunities in the Clinical Application of Noncoding RNAs: The Road Map for miRNAs and piRNAs in Cancer Diagnostics and Prognostics. Int J Genomics 2018; 2018:5848046. [PMID: 29854719 PMCID: PMC5952559 DOI: 10.1155/2018/5848046] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2018] [Revised: 03/13/2018] [Accepted: 03/25/2018] [Indexed: 12/11/2022] Open
Abstract
Discoveries on nonprotein-coding RNAs have induced a paradigm shift in our overall understanding of gene expression and regulation. We now understand that coding and noncoding RNA machinery work in concert to maintain overall homeostasis. Based on their length, noncoding RNAs are broadly classified into two groups—long (>200 nt) and small noncoding RNAs (<200 nt). These RNAs perform diverse functions—gene regulation, splicing, translation, and posttranscriptional modifications. MicroRNAs (miRNAs) and PIWI-interacting RNAs (piRNAs) are two classes of small noncoding RNAs that are now classified as master regulators of gene expression. They have also demonstrated clinical significance as potential biomarkers and therapeutic targets for several diseases, including cancer. Despite these similarities, both these RNAs are generated through contrasting mechanisms, and one of the aims of this review is to cover the distance travelled since their discovery and compare and contrast the various facets of these RNAs. Although these RNAs show tremendous promise as biomarkers, translating the findings from bench to bedside is often met with roadblocks. The second aim of this review therefore is to highlight some of the challenges that hinder application of miRNA and piRNA as in guiding treatment decisions.
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89
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Wu Y, Xu K, Qi H. Domain-functional analyses of PIWIL1 and PABPC1 indicate their synergistic roles in protein translation via 3′-UTRs of meiotic mRNAs†. Biol Reprod 2018; 99:773-788. [DOI: 10.1093/biolre/ioy100] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2017] [Accepted: 04/24/2018] [Indexed: 12/12/2022] Open
Affiliation(s)
- Yaoyao Wu
- School of Life Science, University of Science and Technology of China, Hefei, China
- Key Laboratory of Regenerative Biology, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
| | - Kaibiao Xu
- Key Laboratory of Regenerative Biology, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
| | - Huayu Qi
- Key Laboratory of Regenerative Biology, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
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90
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Lieberman J. Tapping the RNA world for therapeutics. Nat Struct Mol Biol 2018; 25:357-364. [PMID: 29662218 DOI: 10.1038/s41594-018-0054-4] [Citation(s) in RCA: 140] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2018] [Accepted: 03/13/2018] [Indexed: 01/08/2023]
Abstract
A recent revolution in RNA biology has led to the identification of new RNA classes with unanticipated functions, new types of RNA modifications, an unexpected multiplicity of alternative transcripts and widespread transcription of extragenic regions. This development in basic RNA biology has spawned a corresponding revolution in RNA-based strategies to generate new types of therapeutics. Here, I review RNA-based drug design and discuss barriers to broader applications and possible ways to overcome them. Because they target nucleic acids rather than proteins, RNA-based drugs promise to greatly extend the domain of 'druggable' targets beyond what can be achieved with small molecules and biologics.
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Affiliation(s)
- Judy Lieberman
- Program in Cellular and Molecular Medicine, Boston Children's Hospital and Department of Pediatrics, Harvard Medical School, Boston, MA, USA.
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91
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Klinge CM. Non-coding RNAs: long non-coding RNAs and microRNAs in endocrine-related cancers. Endocr Relat Cancer 2018; 25:R259-R282. [PMID: 29440232 DOI: 10.1530/erc-17-0548] [Citation(s) in RCA: 87] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/18/2017] [Accepted: 02/12/2018] [Indexed: 12/11/2022]
Abstract
The human genome is 'pervasively transcribed' leading to a complex array of non-coding RNAs (ncRNAs) that far outnumber coding mRNAs. ncRNAs have regulatory roles in transcription and post-transcriptional processes as well numerous cellular functions that remain to be fully described. Best characterized of the 'expanding universe' of ncRNAs are the ~22 nucleotide microRNAs (miRNAs) that base-pair to target mRNA's 3' untranslated region within the RNA-induced silencing complex (RISC) and block translation and may stimulate mRNA transcript degradation. Long non-coding RNAs (lncRNAs) are classified as >200 nucleotides in length, but range up to several kb and are heterogeneous in genomic origin and function. lncRNAs fold into structures that interact with DNA, RNA and proteins to regulate chromatin dynamics, protein complex assembly, transcription, telomere biology and splicing. Some lncRNAs act as sponges for miRNAs and decoys for proteins. Nuclear-encoded lncRNAs can be taken up by mitochondria and lncRNAs are transcribed from mtDNA. Both miRNAs and lncRNAs are dysregulated in endocrine cancers. This review provides an overview on the current understanding of the regulation and function of selected lncRNAs and miRNAs, and their interaction, in endocrine-related cancers: breast, prostate, endometrial and thyroid.
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92
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Sage AP, Minatel BC, Ng KW, Stewart GL, Dummer TJB, Lam WL, Martinez VD. Oncogenomic disruptions in arsenic-induced carcinogenesis. Oncotarget 2018; 8:25736-25755. [PMID: 28179585 PMCID: PMC5421966 DOI: 10.18632/oncotarget.15106] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2016] [Accepted: 01/24/2017] [Indexed: 12/13/2022] Open
Abstract
Chronic exposure to arsenic affects more than 200 million people worldwide, and has been associated with many adverse health effects, including cancer in several organs. There is accumulating evidence that arsenic biotransformation, a step in the elimination of arsenic from the human body, can induce changes at a genetic and epigenetic level, leading to carcinogenesis. At the genetic level, arsenic interferes with key cellular processes such as DNA damage-repair and chromosomal structure, leading to genomic instability. At the epigenetic level, arsenic places a high demand on the cellular methyl pool, leading to global hypomethylation and hypermethylation of specific gene promoters. These arsenic-associated DNA alterations result in the deregulation of both oncogenic and tumour-suppressive genes. Furthermore, recent reports have implicated aberrant expression of non-coding RNAs and the consequential disruption of signaling pathways in the context of arsenic-induced carcinogenesis. This article provides an overview of the oncogenomic anomalies associated with arsenic exposure and conveys the importance of non-coding RNAs in the arsenic-induced carcinogenic process.
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Affiliation(s)
- Adam P Sage
- Department of Integrative Oncology, British Columbia Cancer Research Centre, Vancouver, British Columbia, Canada
| | - Brenda C Minatel
- Department of Integrative Oncology, British Columbia Cancer Research Centre, Vancouver, British Columbia, Canada
| | - Kevin W Ng
- Department of Integrative Oncology, British Columbia Cancer Research Centre, Vancouver, British Columbia, Canada
| | - Greg L Stewart
- Department of Integrative Oncology, British Columbia Cancer Research Centre, Vancouver, British Columbia, Canada
| | - Trevor J B Dummer
- Centre of Excellence in Cancer Prevention, School of Population and Public Health, University of British Columbia, Vancouver, British Columbia, Canada
| | - Wan L Lam
- Department of Integrative Oncology, British Columbia Cancer Research Centre, Vancouver, British Columbia, Canada
| | - Victor D Martinez
- Department of Integrative Oncology, British Columbia Cancer Research Centre, Vancouver, British Columbia, Canada
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93
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Piwi-interacting RNAs and PIWI genes as novel prognostic markers for breast cancer. Oncotarget 2018; 7:37944-37956. [PMID: 27177224 PMCID: PMC5122362 DOI: 10.18632/oncotarget.9272] [Citation(s) in RCA: 68] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2016] [Accepted: 04/28/2016] [Indexed: 02/07/2023] Open
Abstract
Piwi-interacting RNAs (piRNAs), whose role in germline maintenance has been established, are now also being classified as post-transcriptional regulators of gene expression in somatic cells. PIWI proteins, central to piRNA biogenesis, have been identified as genetic and epigenetic regulators of gene expression. piRNAs/PIWIs have emerged as potential biomarkers for cancer but their relevance to breast cancer has not been comprehensively studied. piRNAs and mRNAs were profiled from normal and breast tumor tissues using next generation sequencing and Agilent platforms, respectively. Gene targets for differentially expressed piRNAs were identified from mRNA expression dataset. piRNAs and PIWI genes were independently assessed for their prognostic significance (outcomes: Overall Survival, OS and Recurrence Free Survival, RFS). We discovered eight piRNAs as novel independent prognostic markers and their association with OS was confirmed in an external dataset (The Cancer Genome Atlas). Further, PIWIL3 and PIWIL4 genes showed prognostic relevance. 306 gene targets exhibited reciprocal relationship with piRNA expression. Cancer cell pathways such as apoptosis and cell signaling were the key Gene Ontology terms associated with the regulated gene targets. Overall, we have captured the entire cascade of events in a dysregulated piRNA pathway and have identified novel markers for breast cancer prognostication.
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94
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Cosacak MI, Yiğit H, Kizil C, Akgül B. Re-Arrangements in the Cytoplasmic Distribution of Small RNAs Following the Maternal-to-Zygotic Transition in Drosophila Embryos. Genes (Basel) 2018; 9:genes9020082. [PMID: 29439397 PMCID: PMC5852578 DOI: 10.3390/genes9020082] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2017] [Revised: 01/31/2018] [Accepted: 02/02/2018] [Indexed: 01/13/2023] Open
Abstract
Small ribonucleic acids (RNAs) are known to regulate gene expression during early development. However, the dynamics of interaction between small RNAs and polysomes during this process is largely unknown. To investigate this phenomenon, 0–1 h and 7–8 h Drosophila melanogaster embryos were fractionated on sucrose density gradients into four fractions based on A254 reading (1) translationally inactive messenger ribonucleoprotein (mRNP), (2) 60S, (3) monosome, and (4) polysome. Comparative analysis of deep-sequencing reads from fractionated and un-fractionated 0–1 h and 7–8 h embryos revealed development-specific co-sedimentation pattern of small RNAs with the cellular translation machinery. Although most micro RNAs (miRNAs) did not have a specific preference for any state of the translational machinery, we detected fraction-specific enrichment of a few miRNAs such as dme-miR-1-3p, -184-3p, 5-5p and 263-5p. More interestingly, we observed changes in the subcellular location of a subset of miRNAs in fractionated embryos despite no measurable difference in their amount in unfractionated embryos. Transposon-derived endo small interfering RNAs (siRNAs) were over-expressed in 7–8 h embryos and associated mainly with the mRNP fraction. In contrast, transposon-derived PIWI-interacting RNAs (piRNA), which were more abundant in 0–1 h embryos, co-sedimented primarily with the polysome fractions. These results suggest that there appears to be a complex interplay among the small RNAs with respect to their polysome-cosedimentation pattern during early development in Drosophila melanogaster.
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Affiliation(s)
- Mehmet Ilyas Cosacak
- Department of Molecular Biology and Genetics, İzmir Institute of Technology, Gülbahçeköyü, 35430 İzmir, Turkey.
- German Center for Neurodegenerative Diseases (DZNE) Dresden, Helmholtz Association, Arnoldstr. 18, 01307 Dresden, Germany.
- Center for Regenerative Therapies Dresden (CRTD), Technische Universität Dresden, Fetscherstr. 105, 01307 Dresden, Germany.
| | - Hatice Yiğit
- Department of Molecular Biology and Genetics, İzmir Institute of Technology, Gülbahçeköyü, 35430 İzmir, Turkey.
| | - Caghan Kizil
- German Center for Neurodegenerative Diseases (DZNE) Dresden, Helmholtz Association, Arnoldstr. 18, 01307 Dresden, Germany.
- Center for Regenerative Therapies Dresden (CRTD), Technische Universität Dresden, Fetscherstr. 105, 01307 Dresden, Germany.
| | - Bünyamin Akgül
- Department of Molecular Biology and Genetics, İzmir Institute of Technology, Gülbahçeköyü, 35430 İzmir, Turkey.
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95
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1700108J01Rik and 1700101O22Rik are mouse testis-specific long non-coding RNAs. Histochem Cell Biol 2018; 149:517-527. [PMID: 29411102 DOI: 10.1007/s00418-018-1642-4] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/24/2018] [Indexed: 01/29/2023]
Abstract
Long non-coding RNAs (lncRNAs; > 200 nucleotides in length) have attracted attention as fine-tuners of gene expression. However, little is known about the cell- and stage-specific expression pattern and function of lncRNAs in spermatogenesis. The purpose of this study was to identify mouse testis-associated lncRNAs using a combination of computational and experimental approaches. We first used the FANTOM5 database to survey lncRNA expression in the mouse testis and performed reverse transcription quantitative polymerase chain reaction (real-time PCR) and in situ hybridization (ISH) analyses. In silico analysis showed that most of the highly expressed lncRNAs in the adult mouse testis were testis-specific lncRNAs and were expressed at and following the initiation of spermatogenesis. We selected the antisense lncRNA 1700108J01Rik and long intergenic non-coding RNA 1700101O22Rik from the most highly expressed lncRNAs in the adult testis for further analysis. Real-time PCR analysis confirmed that 1700108J01Rik and 1700101O22Rik were specifically expressed in the testis. ISH analysis revealed that the two mouse-testis-specific lncRNAs were expressed exclusively in testicular germ cells in meiotic prophase and the round spermatid stage, which coincide with the period of transcriptional reactivation during spermatogenesis. The cytoplasmic distribution of these lncRNAs revealed by ISH suggests their involvement in post-transcriptional gene regulation rather than in epigenetic or transcriptional regulation. Our data provide new insight into testis-associated lncRNAs that will be useful in expression and functional studies of spermatogenesis.
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96
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Weng W, Liu N, Toiyama Y, Kusunoki M, Nagasaka T, Fujiwara T, Wei Q, Qin H, Lin H, Ma Y, Goel A. Novel evidence for a PIWI-interacting RNA (piRNA) as an oncogenic mediator of disease progression, and a potential prognostic biomarker in colorectal cancer. Mol Cancer 2018; 17:16. [PMID: 29382334 PMCID: PMC5791351 DOI: 10.1186/s12943-018-0767-3] [Citation(s) in RCA: 133] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2017] [Accepted: 01/15/2018] [Indexed: 02/06/2023] Open
Abstract
Background Emerging evidence suggests that PIWI-interacting RNAs (piRNAs) may be important epigenetic regulators of gene expression in human cancers; however, their functional and clinical significance in colorectal cancer (CRC) remains unknown. Methods We performed piRNA expression profiling in paired cancer and normal tissues through small RNA-sequencing. The clinical significance of candidate piRNAs was investigated, and independently validated in 771 CRC patients from three independent cohorts. The biological function of piRNAs was characterized in cell lines, followed by identification and validation of downstream target genes in CRC tissues. Results We identified piR-1245 as a novel and frequently overexpressed noncoding RNA in CRC, and its expression significantly correlated with advanced and metastatic disease. Patients with high piR-1245 expression experienced significantly shorter overall survival, and multivariate analysis identified its expression to serve as an independent prognostic biomarker in CRC. Functionally, piR-1245 acts as an oncogene and promotes tumor progression, and gene expression profiling results identified a panel of downstream target-genes involved in regulating cell survival pathway. Based upon piRNA:mRNA sequence complementarity, we identified a panel of tumor suppressor genes (ATF3, BTG1, DUSP1, FAS,NFKBIA, UPP1, SESN2, TP53INP1 and MDX1) as direct targets of piR-1245, and successfully validated an inverse correlation between their expression and piR-1245 in CRC. Conclusions We for the first time have identified the role for a PIWI-interacting noncoding RNA, piR-1245, as a novel oncogene and a potential prognostic biomarker in colorectal cancer. Electronic supplementary material The online version of this article (10.1186/s12943-018-0767-3) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Wenhao Weng
- Center for Gastrointestinal Research; Center for Translational Genomics and Oncology, Baylor Scott & White Research Institute and Charles A Sammons Cancer Center, Baylor University Medical Center, 3410 Worth Street, Suite 610, Dallas, TX, 75246, USA.,Department of Clinical Laboratory, Yangpu Hospital, Tongji University School of Medicine, Shanghai, China.,Center for Translational Medicine, Yangpu Hospital, Tongji University School of Medicine, Shanghai, China
| | - Na Liu
- Department of Cell Biology; Department of Genetics; Department of Obstetrics, Gynecology, and Reproductive Sciences; Yale Stem Cell Center, Yale University School of Medicine, New Haven, CT, USA
| | - Yuji Toiyama
- Department of Gastrointestinal and Pediatric Surgery, Division of Reparative Medicine, Institute of Life Sciences, Mie University Graduate School of Medicine, Mie, Japan
| | - Masato Kusunoki
- Department of Gastrointestinal and Pediatric Surgery, Division of Reparative Medicine, Institute of Life Sciences, Mie University Graduate School of Medicine, Mie, Japan
| | - Takeshi Nagasaka
- Department of Gastroenterological Surgery and Surgical Oncology, Okayama University Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama, Japan
| | - Toshiyoshi Fujiwara
- Department of Gastroenterological Surgery and Surgical Oncology, Okayama University Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama, Japan
| | - Qing Wei
- Department of Pathology, Shanghai Tenth People's Hospital, Tongji University, Shanghai, China
| | - Huanlong Qin
- Department of GI Surgery, Shanghai Tenth People's Hospital Affiliated to Tongji University, Shanghai, China
| | - Haifan Lin
- Department of Cell Biology; Department of Genetics; Department of Obstetrics, Gynecology, and Reproductive Sciences; Yale Stem Cell Center, Yale University School of Medicine, New Haven, CT, USA
| | - Yanlei Ma
- Department of Colorectal Surgery, Fudan University Shanghai Cancer Center, 270 Dong'an Road, Shanghai, 20032, China. .,Department of Oncology, Shanghai Medical College, Fudan University, 270 Dong'an Road, Shanghai, 20032, China.
| | - Ajay Goel
- Center for Gastrointestinal Research; Center for Translational Genomics and Oncology, Baylor Scott & White Research Institute and Charles A Sammons Cancer Center, Baylor University Medical Center, 3410 Worth Street, Suite 610, Dallas, TX, 75246, USA.
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97
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Afolabi LT, Saeed F, Hashim H, Petinrin OO. Ensemble learning method for the prediction of new bioactive molecules. PLoS One 2018; 13:e0189538. [PMID: 29329334 PMCID: PMC5766097 DOI: 10.1371/journal.pone.0189538] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2017] [Accepted: 11/27/2017] [Indexed: 12/31/2022] Open
Abstract
Pharmacologically active molecules can provide remedies for a range of different illnesses and infections. Therefore, the search for such bioactive molecules has been an enduring mission. As such, there is a need to employ a more suitable, reliable, and robust classification method for enhancing the prediction of the existence of new bioactive molecules. In this paper, we adopt a recently developed combination of different boosting methods (Adaboost) for the prediction of new bioactive molecules. We conducted the research experiments utilizing the widely used MDL Drug Data Report (MDDR) database. The proposed boosting method generated better results than other machine learning methods. This finding suggests that the method is suitable for inclusion among the in silico tools for use in cheminformatics, computational chemistry and molecular biology.
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Affiliation(s)
| | - Faisal Saeed
- College of Computer Science and Engineering, Taibah University, Medina, Saudi Arabia
- Information Systems Department, Faculty of Computing, Universiti Teknologi Malaysia, Skudai, Johor, Malaysia
| | - Haslinda Hashim
- Information Systems Department, Faculty of Computing, Universiti Teknologi Malaysia, Skudai, Johor, Malaysia
- Kolej Yayasan Pelajaran Johor, KM16, Jalan Kulai-Kota Tinggi, Kota Tinggi, Johor, Malaysia
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98
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Cordeiro A, Navarro A, Gaya A, Díaz-Beyá M, Gonzalez-Farré B, Castellano JJ, Fuster D, Martínez C, Martínez A, Monzó M. PiwiRNA-651 as marker of treatment response and survival in classical Hodgkin lymphoma. Oncotarget 2018; 7:46002-46013. [PMID: 27329591 PMCID: PMC5216777 DOI: 10.18632/oncotarget.10015] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2016] [Accepted: 05/26/2016] [Indexed: 01/31/2023] Open
Abstract
PiwiRNAs, small non-coding RNAs processed by Piwi proteins, are involved in maintaining genome stability in germline cells. Recently, piwiRNA expression has been identified in some tumors. We have examined the potential reactivation of the Piwi/piwiRNA pathway in classical Hodgkin lymphoma (cHL). We found that Piwi proteins and three selected piwiRNAs, including piR-651, were expressed in cHL patients and cell lines, indicating that the Piwi/piwiRNA pathway is active in cHL. Interestingly, low levels of piR-651 were associated with lack of complete response to first-line treatment, as well as shorter disease-free and overall survival in a cohort of 94 cHL patients. At diagnosis, piR-651 was underexpressed in cHL serum samples compared to healthy controls, while after complete remission, piR-651 levels increased to levels similar to healthy controls. This is the first evidence that piwiRNAs are active in tumor and serum samples and impact prognosis in cHL.
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Affiliation(s)
- Anna Cordeiro
- Molecular Oncology and Embryology Laboratory, Human Anatomy Unit, School of Medicine, University of Barcelona, IDIBAPS, Barcelona, Spain
| | - Alfons Navarro
- Molecular Oncology and Embryology Laboratory, Human Anatomy Unit, School of Medicine, University of Barcelona, IDIBAPS, Barcelona, Spain
| | - Anna Gaya
- Hematology Department, Hospital Clinic Barcelona, IDIBAPS, Barcelona, Spain
| | - Marina Díaz-Beyá
- Hematology Department, Hospital Clinic Barcelona, IDIBAPS, Barcelona, Spain
| | | | - Joan Josep Castellano
- Molecular Oncology and Embryology Laboratory, Human Anatomy Unit, School of Medicine, University of Barcelona, IDIBAPS, Barcelona, Spain
| | - Dolors Fuster
- Molecular Oncology and Embryology Laboratory, Human Anatomy Unit, School of Medicine, University of Barcelona, IDIBAPS, Barcelona, Spain
| | - Carmen Martínez
- Hematology Department, Hospital Clinic Barcelona, IDIBAPS, Barcelona, Spain
| | - Antonio Martínez
- Hematopathology Section, Hospital Clinic Barcelona, IDIBAPS, Barcelona, Spain
| | - Mariano Monzó
- Molecular Oncology and Embryology Laboratory, Human Anatomy Unit, School of Medicine, University of Barcelona, IDIBAPS, Barcelona, Spain
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99
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Fu Q, Liu CJ, Zhai ZS, Zhang X, Qin T, Zhang HW. Single-Cell Non-coding RNA in Embryonic Development. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2018; 1068:19-32. [DOI: 10.1007/978-981-13-0502-3_3] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
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100
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Zhu B, Pardeshi L, Chen Y, Ge W. Transcriptomic Analysis for Differentially Expressed Genes in Ovarian Follicle Activation in the Zebrafish. Front Endocrinol (Lausanne) 2018; 9:593. [PMID: 30364302 PMCID: PMC6193065 DOI: 10.3389/fendo.2018.00593] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/26/2018] [Accepted: 09/18/2018] [Indexed: 12/30/2022] Open
Abstract
In teleosts, the onset of puberty in females is marked by the appearance of the first wave of pre-vitellogenic (PV) follicles from the pool of primary growth (PG) follicles (follicle activation) in the ovary during sexual maturation. To understand the mechanisms underlying follicle activation and therefore puberty onset, we undertook this transcriptomic study to investigate gene expression profiles in the event. Our analysis revealed a total of 2,027 up-regulated and 859 down-regulated genes during the PG-PV transition. Gene Ontology (GO) analysis showed that in addition to basic cellular functions such as gene transcription, cell differentiation, and cell migration, other biological processes such as steroidogenesis, cell signaling and angiogenesis were also enriched in up-regulated genes; by comparison, some processes were down-regulated including piRNA metabolism, gene silencing and proteolysis. Further Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis identified a variety of signaling pathways that might play pivotal roles in PG-PV transition, including MAPK, TGF-β, Hedgehog, FoxO, VEGF, Jak-STAT, and phosphatidylinositol signaling pathways. Other pathways of particular interest included endocytosis and glycosaminoglycan biosynthesis. We also analyzed expression changes of genes expressed in different compartments viz. oocytes and follicle cells. Interestingly, most oocyte-specific genes remained unchanged in expression during follicle activation whereas a great number of genes specifically expressed in the follicle cells showed significant changes in expression. Overall, this study reported a comprehensive analysis for genes, biological processes and pathways involved in follicle activation, which also marks female puberty onset in the zebrafish when occurring for the first time in sexual maturation.
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Affiliation(s)
- Bo Zhu
- Centre of Reproduction, Development and Aging, Faculty of Health Sciences, University of Macau, Taipa, China
| | - Lakhansing Pardeshi
- Genomics and Bioinformatics Core, Faculty of Health Sciences, University of Macau, Taipa, China
| | - Yingying Chen
- Genomics and Bioinformatics Core, Faculty of Health Sciences, University of Macau, Taipa, China
| | - Wei Ge
- Centre of Reproduction, Development and Aging, Faculty of Health Sciences, University of Macau, Taipa, China
- *Correspondence: Wei Ge ;
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