1
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Zhang J, Yang L, Sun Y, Zhang L, Wang Y, Liu M, Li X, Liang Y, Zhao H, Liu Z, Qiu Z, Zhang T, Xie J. Up-regulation of miR-10a-5p expression inhibits the proliferation and differentiation of neural stem cells by targeting Chl1. Acta Biochim Biophys Sin (Shanghai) 2024. [PMID: 38841745 DOI: 10.3724/abbs.2024078] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/07/2024] Open
Abstract
Neural tube defects (NTDs) are characterized by the failure of neural tube closure during embryogenesis and are considered the most common and severe central nervous system anomalies during early development. Recent microRNA (miRNA) expression profiling studies have revealed that the dysregulation of several miRNAs plays an important role in retinoic acid (RA)-induced NTDs. However, the molecular functions of these miRNAs in NTDs remain largely unidentified. Here, we show that miR-10a-5p is significantly upregulated in RA-induced NTDs and results in reduced cell growth due to cell cycle arrest and dysregulation of cell differentiation. Moreover, the cell adhesion molecule L1-like ( Chl1) is identified as a direct target of miR-10a-5p in neural stem cells (NSCs) in vitro, and its expression is reduced in RA-induced NTDs. siRNA-mediated knockdown of intracellular Chl1 affects cell proliferation and differentiation similar to those of miR-10a-5p overexpression, which further leads to the inhibition of the expressions of downstream ERK1/2 MAPK signaling pathway proteins. These cellular responses are abrogated by either increased expression of the direct target of miR-10a-5p ( Chl1) or an ERK agonist such as honokiol. Overall, our study demonstrates that miR-10a-5p plays a major role in the process of NSC growth and differentiation by directly targeting Chl1, which in turn induces the downregulation of the ERK1/2 cascade, suggesting that miR-10a-5p and Chl1 are critical for NTD formation in the development of embryos.
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Affiliation(s)
- Juan Zhang
- Department of Biochemistry and Molecular Biology, School of Basic Medical Science, Shanxi Key Laboratory of Birth Defect and Cell Regeneration, MOE Key Laboratory of Coal Environmental Pathogenicity and Prevention, Shanxi Medical University, Taiyuan 030001, China
- Department of Cell Biology and Genetics, School of Basic Medical Science, Shanxi Medical University, Taiyuan 030001, China
| | - Lihong Yang
- Department of Biochemistry and Molecular Biology, School of Basic Medical Science, Shanxi Key Laboratory of Birth Defect and Cell Regeneration, MOE Key Laboratory of Coal Environmental Pathogenicity and Prevention, Shanxi Medical University, Taiyuan 030001, China
| | - Yuqing Sun
- Department of Biochemistry and Molecular Biology, School of Basic Medical Science, Shanxi Key Laboratory of Birth Defect and Cell Regeneration, MOE Key Laboratory of Coal Environmental Pathogenicity and Prevention, Shanxi Medical University, Taiyuan 030001, China
| | - Li Zhang
- Department of Biochemistry and Molecular Biology, School of Basic Medical Science, Shanxi Key Laboratory of Birth Defect and Cell Regeneration, MOE Key Laboratory of Coal Environmental Pathogenicity and Prevention, Shanxi Medical University, Taiyuan 030001, China
| | - Yufei Wang
- Department of Biochemistry and Molecular Biology, School of Basic Medical Science, Shanxi Key Laboratory of Birth Defect and Cell Regeneration, MOE Key Laboratory of Coal Environmental Pathogenicity and Prevention, Shanxi Medical University, Taiyuan 030001, China
| | - Ming Liu
- Department of Cell Biology and Genetics, School of Basic Medical Science, Shanxi Medical University, Taiyuan 030001, China
| | - Xiujuan Li
- Department of Biochemistry and Molecular Biology, School of Basic Medical Science, Shanxi Key Laboratory of Birth Defect and Cell Regeneration, MOE Key Laboratory of Coal Environmental Pathogenicity and Prevention, Shanxi Medical University, Taiyuan 030001, China
| | - Yuxiang Liang
- Department of Biochemistry and Molecular Biology, School of Basic Medical Science, Shanxi Key Laboratory of Birth Defect and Cell Regeneration, MOE Key Laboratory of Coal Environmental Pathogenicity and Prevention, Shanxi Medical University, Taiyuan 030001, China
| | - Hong Zhao
- Department of Biochemistry and Molecular Biology, School of Basic Medical Science, Shanxi Key Laboratory of Birth Defect and Cell Regeneration, MOE Key Laboratory of Coal Environmental Pathogenicity and Prevention, Shanxi Medical University, Taiyuan 030001, China
| | - Zhizhen Liu
- Department of Biochemistry and Molecular Biology, School of Basic Medical Science, Shanxi Key Laboratory of Birth Defect and Cell Regeneration, MOE Key Laboratory of Coal Environmental Pathogenicity and Prevention, Shanxi Medical University, Taiyuan 030001, China
| | - Zhiyong Qiu
- Beijing Municipal Key Laboratory of Child Development and Nutriomics, Capital Institute of Pediatrics, Beijing 100020, China
| | - Ting Zhang
- Beijing Municipal Key Laboratory of Child Development and Nutriomics, Capital Institute of Pediatrics, Beijing 100020, China
| | - Jun Xie
- Department of Biochemistry and Molecular Biology, School of Basic Medical Science, Shanxi Key Laboratory of Birth Defect and Cell Regeneration, MOE Key Laboratory of Coal Environmental Pathogenicity and Prevention, Shanxi Medical University, Taiyuan 030001, China
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2
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Shuai Y, Xu N, Zhao C, Yang F, Ning Z, Li G. MicroRNA-10 Family Promotes Renal Fibrosis through the VASH-1/Smad3 Pathway. Int J Mol Sci 2024; 25:5232. [PMID: 38791272 PMCID: PMC11120755 DOI: 10.3390/ijms25105232] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2024] [Revised: 05/06/2024] [Accepted: 05/09/2024] [Indexed: 05/26/2024] Open
Abstract
Renal fibrosis (RF) stands as a pivotal pathological process in the advanced stages of chronic kidney disease (CKD), and impeding its progression is paramount for delaying the advancement of CKD. The miR-10 family, inclusive of miR-10a and miR-10b, has been implicated in the development of various fibrotic diseases. Nevertheless, the precise role of miR-10 in the development of RF remains enigmatic. In this study, we utilized both an in vivo model involving unilateral ureteral obstruction (UUO) in mice and an in vitro model employing TGF-β1 stimulation in HK-2 cells to unravel the mechanism underlying the involvement of miR-10a/b in RF. The findings revealed heightened expression of miR-10a and miR-10b in the kidneys of UUO mice, accompanied by a substantial increase in p-Smad3 and renal fibrosis-related proteins. Conversely, the deletion of these two genes led to a notable reduction in p-Smad3 levels and the alleviation of RF in mouse kidneys. In the in vitro model of TGF-β1-stimulated HK-2 cells, the co-overexpression of miR-10a and miR-10b fostered the phosphorylation of Smad3 and RF, while the inhibition of miR-10a and miR-10b resulted in a decrease in p-Smad3 levels and RF. Further research revealed that miR-10a and miR-10b, through binding to the 3'UTR region of Vasohibin-1 (VASH-1), suppressed the expression of VASH-1, thereby promoting the elevation of p-Smad3 and exacerbating the progression of RF. The miR-10 family may play a pivotal role in RF.
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Affiliation(s)
| | | | | | | | | | - Guoxia Li
- Department of Pharmacology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin 300070, China
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3
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Seo Y, Rhim J, Kim JH. RNA-binding proteins and exoribonucleases modulating miRNA in cancer: the enemy within. Exp Mol Med 2024; 56:1080-1106. [PMID: 38689093 PMCID: PMC11148060 DOI: 10.1038/s12276-024-01224-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2023] [Revised: 02/20/2024] [Accepted: 02/25/2024] [Indexed: 05/02/2024] Open
Abstract
Recent progress in the investigation of microRNA (miRNA) biogenesis and the miRNA processing machinery has revealed previously unknown roles of posttranscriptional regulation in gene expression. The molecular mechanistic interplay between miRNAs and their regulatory factors, RNA-binding proteins (RBPs) and exoribonucleases, has been revealed to play a critical role in tumorigenesis. Moreover, recent studies have shown that the proliferation of hepatocellular carcinoma (HCC)-causing hepatitis C virus (HCV) is also characterized by close crosstalk of a multitude of host RBPs and exoribonucleases with miR-122 and its RNA genome, suggesting the importance of the mechanistic interplay among these factors during the proliferation of HCV. This review primarily aims to comprehensively describe the well-established roles and discuss the recently discovered understanding of miRNA regulators, RBPs and exoribonucleases, in relation to various cancers and the proliferation of a representative cancer-causing RNA virus, HCV. These have also opened the door to the emerging potential for treating cancers as well as HCV infection by targeting miRNAs or their respective cellular modulators.
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Affiliation(s)
- Yoona Seo
- Cancer Molecular Biology Branch, Research Institute, National Cancer Center, Goyang, 10408, Korea
- Department of Cancer Biomedical Science, Graduate School of Cancer Science and Policy, National Cancer Center, Goyang, 10408, Korea
| | - Jiho Rhim
- Cancer Molecular Biology Branch, Research Institute, National Cancer Center, Goyang, 10408, Korea
- Department of Cancer Biomedical Science, Graduate School of Cancer Science and Policy, National Cancer Center, Goyang, 10408, Korea
| | - Jong Heon Kim
- Cancer Molecular Biology Branch, Research Institute, National Cancer Center, Goyang, 10408, Korea.
- Department of Cancer Biomedical Science, Graduate School of Cancer Science and Policy, National Cancer Center, Goyang, 10408, Korea.
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4
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Singh R, Ha SE, Park HS, Debnath S, Cho H, Baek G, Yu TY, Ro S. Sustained Effectiveness and Safety of Therapeutic miR-10a/b in Alleviating Diabetes and Gastrointestinal Dysmotility without Inducing Cancer or Inflammation in Murine Liver and Colon. Int J Mol Sci 2024; 25:2266. [PMID: 38396943 PMCID: PMC10888952 DOI: 10.3390/ijms25042266] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2024] [Revised: 02/10/2024] [Accepted: 02/11/2024] [Indexed: 02/25/2024] Open
Abstract
microRNAs (miRNAs) are key regulators of both physiological and pathophysiological mechanisms in diabetes and gastrointestinal (GI) dysmotility. Our previous studies have demonstrated the therapeutic potential of miR-10a-5p mimic and miR-10b-5p mimic (miR-10a/b mimics) in rescuing diabetes and GI dysmotility in murine models of diabetes. In this study, we elucidated the safety profile of a long-term treatment with miR-10a/b mimics in diabetic mice. Male C57BL/6 mice were fed a high-fat, high-sucrose diet (HFHSD) to induce diabetes and treated by five subcutaneous injections of miR-10a/b mimics for a 5 month period. We examined the long-term effects of the miRNA mimics on diabetes and GI dysmotility, including an assessment of potential risks for cancer and inflammation in the liver and colon using biomarkers. HFHSD-induced diabetic mice subcutaneously injected with miR-10a/b mimics on a monthly basis for 5 consecutive months exhibited a marked reduction in fasting blood glucose levels with restoration of insulin and significant weight loss, improved glucose and insulin intolerance, and restored GI transit time. In addition, the miR-10a/b mimic-treated diabetic mice showed no indication of risk for cancer development or inflammation induction in the liver, colon, and blood for 5 months post-injections. This longitudinal study demonstrates that miR-10a/b mimics, when subcutaneously administered in diabetic mice, effectively alleviate diabetes and GI dysmotility for 5 months with no discernible risk for cancer or inflammation in the liver and colon. The sustained efficacy and favorable safety profiles position miR-10a/b mimics as promising candidates in miRNA-based therapeutics for diabetes and GI dysmotility.
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Affiliation(s)
- Rajan Singh
- Department of Physiology and Cell Biology, School of Medicine, University of Nevada, Reno, NV 89557, USA; (R.S.); (S.E.H.); (H.S.P.); (S.D.); (H.C.); (G.B.); (T.Y.Y.)
| | - Se Eun Ha
- Department of Physiology and Cell Biology, School of Medicine, University of Nevada, Reno, NV 89557, USA; (R.S.); (S.E.H.); (H.S.P.); (S.D.); (H.C.); (G.B.); (T.Y.Y.)
| | - Han Sung Park
- Department of Physiology and Cell Biology, School of Medicine, University of Nevada, Reno, NV 89557, USA; (R.S.); (S.E.H.); (H.S.P.); (S.D.); (H.C.); (G.B.); (T.Y.Y.)
| | - Sushmita Debnath
- Department of Physiology and Cell Biology, School of Medicine, University of Nevada, Reno, NV 89557, USA; (R.S.); (S.E.H.); (H.S.P.); (S.D.); (H.C.); (G.B.); (T.Y.Y.)
| | - Hayeong Cho
- Department of Physiology and Cell Biology, School of Medicine, University of Nevada, Reno, NV 89557, USA; (R.S.); (S.E.H.); (H.S.P.); (S.D.); (H.C.); (G.B.); (T.Y.Y.)
| | - Gain Baek
- Department of Physiology and Cell Biology, School of Medicine, University of Nevada, Reno, NV 89557, USA; (R.S.); (S.E.H.); (H.S.P.); (S.D.); (H.C.); (G.B.); (T.Y.Y.)
| | - Tae Yang Yu
- Department of Physiology and Cell Biology, School of Medicine, University of Nevada, Reno, NV 89557, USA; (R.S.); (S.E.H.); (H.S.P.); (S.D.); (H.C.); (G.B.); (T.Y.Y.)
| | - Seungil Ro
- Department of Physiology and Cell Biology, School of Medicine, University of Nevada, Reno, NV 89557, USA; (R.S.); (S.E.H.); (H.S.P.); (S.D.); (H.C.); (G.B.); (T.Y.Y.)
- RosVivo Therapeutics, Applied Research Facility, 1664 N. Virginia St., Reno, NV 89557, USA
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5
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Chakraborty S, Banerjee S. Understanding crosstalk of organ tropism, tumor microenvironment and noncoding RNAs in breast cancer metastasis. Mol Biol Rep 2023; 50:9601-9623. [PMID: 37792172 DOI: 10.1007/s11033-023-08852-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2023] [Accepted: 09/26/2023] [Indexed: 10/05/2023]
Abstract
Cancer metastasis is one of the major clinical challenges worldwide due to limited existing effective treatments. Metastasis roots from the host organ of origin and gradually migrates to different regional and distant organs. In different breast cancer subtypes, different organs like bones, liver, lungs and brain are targeted by the metastatic tumor cells. Cancer renders mortality to their respective metastasizing sites like bones, brain, liver, and lungs. Metastatic breast cancers are best treated and managed if detected at an early stage. Metastasis is regulated by various molecular activators and suppressors. The conventional theory of 'seed and soil' states that metastatic tumor cells move to tumor microenvironment that has favorable conditions like blood flow for them to grow just like seeds grows when planted in fertile land. Additionally, different coding as well as non-coding RNAs play a very significant role in the process of metastasis by modulating their expression levels leading to a crosstalk of various tumorigenic cascades. Treatments for metastasis is also very critical in controlling this lethal process. Detecting breast cancer metastasis at an early stage is crucial for managing and predicting metastatic progression. In this review, we have compiled several factors that can be targeted to manage the onset and gradual stages of breast cancer metastasis.
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Affiliation(s)
- Sohini Chakraborty
- Department of Biotechnology, School of Biosciences and Technology, Vellore Institute of Technology, Vellore, 632014, Tamil Nadu, India
| | - Satarupa Banerjee
- Department of Biotechnology, School of Biosciences and Technology, Vellore Institute of Technology, Vellore, 632014, Tamil Nadu, India.
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6
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Mierzejewski B, Grabowska I, Michalska Z, Zdunczyk K, Zareba F, Irhashava A, Chrzaszcz M, Patrycy M, Streminska W, Janczyk-Ilach K, Koblowska M, Iwanicka-Nowicka R, Gromadka A, Kowalski K, Ciemerych MA, Brzoska E. SDF-1 and NOTCH signaling in myogenic cell differentiation: the role of miRNA10a, 425, and 5100. Stem Cell Res Ther 2023; 14:204. [PMID: 37582765 PMCID: PMC10426160 DOI: 10.1186/s13287-023-03429-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2022] [Accepted: 07/25/2023] [Indexed: 08/17/2023] Open
Abstract
BACKGROUND Skeletal muscle regeneration is a complex process regulated by many cytokines and growth factors. Among the important signaling pathways regulating the myogenic cell identity are these involving SDF-1 and NOTCH. SDF-1 participates in cell mobilization and acts as an important chemoattractant. NOTCH, on the other hand, controls cell activation and myogenic determination of satellite cells. Knowledge about the interaction between SDF-1 and NOTCH signaling is limited. METHODS We analyzed two populations of myogenic cells isolated from mouse skeletal muscle, that is, myoblasts derived from satellite cells (SCs) and muscle interstitial progenitor cells (MIPCs). First, microRNA level changes in response to SDF-1 treatment were analyzed with next-generation sequencing (NGS). Second, myogenic cells, i.e., SC-derived myoblasts and MIPCs were transfected with miRNA mimics, selected on the basis of NGS results, or their inhibitors. Transcriptional changes, as well as proliferation, migration, and differentiation abilities of SC-derived myoblasts and MIPCs, were analyzed in vitro. Naive myogenic potential was assessed in vivo, using subcutaneous engrafts and analysis of cell contribution to regeneration of the skeletal muscles. RESULTS SDF-1 treatment led to down-regulation of miR10a, miR151, miR425, and miR5100 in myoblasts. Interestingly, miR10a, miR425, and miR5100 regulated the expression of factors involved in the NOTCH signaling pathway, including Dll1, Jag2, and NICD. Furthermore, miR10a, miR425, and miR5100 down-regulated the expression of factors involved in cell migration: Acta1, MMP12, and FAK, myogenic differentiation: Pax7, Myf5, Myod, Mef2c, Myog, Musk, and Myh3. However, these changes did not significantly affect myogenic cell migration or fusion either in vitro or in vivo, except when miR425 was overexpressed, or miR5100 inhibitor was used. These two molecules increased the fusion of MIPCs and myoblasts, respectively. Furthermore, miR425-transfected MIPC transplantation into injured skeletal muscle resulted in more efficient regeneration, compared to control cell transplantation. However, skeletal muscles that were injected with miR10a transfected myoblasts regenerated less efficiently. CONCLUSIONS SDF-1 down-regulates miR10a, miR425, and miR5100, what could affect NOTCH signaling, differentiation of myogenic cells, and their participation in skeletal muscle regeneration.
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Affiliation(s)
- Bartosz Mierzejewski
- Department of Cytology, Faculty of Biology, University of Warsaw, Miecznikowa 1 St, 02-096, Warsaw, Poland
| | - Iwona Grabowska
- Department of Cytology, Faculty of Biology, University of Warsaw, Miecznikowa 1 St, 02-096, Warsaw, Poland
| | - Zuzanna Michalska
- Department of Cytology, Faculty of Biology, University of Warsaw, Miecznikowa 1 St, 02-096, Warsaw, Poland
| | - Kamila Zdunczyk
- Department of Cytology, Faculty of Biology, University of Warsaw, Miecznikowa 1 St, 02-096, Warsaw, Poland
| | - Franciszek Zareba
- Department of Cytology, Faculty of Biology, University of Warsaw, Miecznikowa 1 St, 02-096, Warsaw, Poland
| | - Aliksandra Irhashava
- Department of Cytology, Faculty of Biology, University of Warsaw, Miecznikowa 1 St, 02-096, Warsaw, Poland
| | - Marta Chrzaszcz
- Department of Cytology, Faculty of Biology, University of Warsaw, Miecznikowa 1 St, 02-096, Warsaw, Poland
| | - Magdalena Patrycy
- Department of Cytology, Faculty of Biology, University of Warsaw, Miecznikowa 1 St, 02-096, Warsaw, Poland
| | - Wladyslawa Streminska
- Department of Cytology, Faculty of Biology, University of Warsaw, Miecznikowa 1 St, 02-096, Warsaw, Poland
| | - Katarzyna Janczyk-Ilach
- Department of Cytology, Faculty of Biology, University of Warsaw, Miecznikowa 1 St, 02-096, Warsaw, Poland
| | - Marta Koblowska
- Laboratory of Systems Biology, Faculty of Biology, University of Warsaw, 02-096, Warsaw, Poland
- Laboratory of Microarray Analysis, Institute of Biochemistry and Biophysics, Polish Academy of Sciences, 02-106, Warsaw, Poland
| | - Roksana Iwanicka-Nowicka
- Laboratory of Systems Biology, Faculty of Biology, University of Warsaw, 02-096, Warsaw, Poland
- Laboratory of Microarray Analysis, Institute of Biochemistry and Biophysics, Polish Academy of Sciences, 02-106, Warsaw, Poland
| | - Agnieszka Gromadka
- Department of Bioinformatics, Institute of Biochemistry and Biophysics, Polish Academy of Sciences, 02-106, Warsaw, Poland
| | - Kamil Kowalski
- Department of Cytology, Faculty of Biology, University of Warsaw, Miecznikowa 1 St, 02-096, Warsaw, Poland
| | - Maria Anna Ciemerych
- Department of Cytology, Faculty of Biology, University of Warsaw, Miecznikowa 1 St, 02-096, Warsaw, Poland
| | - Edyta Brzoska
- Department of Cytology, Faculty of Biology, University of Warsaw, Miecznikowa 1 St, 02-096, Warsaw, Poland.
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7
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Murashov AK, Pak ES, Mar J, O’Brien K, Fisher-Wellman K, Bhat KM. Paternal Western diet causes transgenerational increase in food consumption in Drosophila with parallel alterations in the offspring brain proteome and microRNAs. FASEB J 2023; 37:e22966. [PMID: 37227156 PMCID: PMC10234493 DOI: 10.1096/fj.202300239rr] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2023] [Revised: 04/20/2023] [Accepted: 04/26/2023] [Indexed: 05/26/2023]
Abstract
Several lines of evidence indicate that ancestral diet might play an important role in determining offspring's metabolic traits. However, it is not yet clear whether ancestral diet can affect offspring's food choices and feeding behavior. In the current study, taking advantage of Drosophila model system, we demonstrate that paternal Western diet (WD) increases offspring food consumption up to the fourth generation. Paternal WD also induced alterations in F1 offspring brain proteome. Using enrichment analyses of pathways for upregulated and downregulated proteins, we found that upregulated proteins had significant enrichments in terms related to translation and translation factors, whereas downregulated proteins displayed enrichments in small molecule metabolic processes, TCA cycles, and electron transport chain (ETC). Using MIENTURNET miRNA prediction tool, dme-miR-10-3p was identified as the top conserved miRNA predicted to target proteins regulated by ancestral diet. RNAi-based knockdown of miR-10 in the brain significantly increased food consumption, implicating miR-10 as a potential factor in programming feeding behavior. Together, these findings suggest that ancestral nutrition may influence offspring feeding behavior through alterations in miRNAs.
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Affiliation(s)
- Alexander K. Murashov
- Department of Physiology & East Carolina Diabetes and Obesity Institute, East Carolina University, Greenville, NC
| | - Elena S. Pak
- Department of Physiology & East Carolina Diabetes and Obesity Institute, East Carolina University, Greenville, NC
| | - Jordan Mar
- Department of Molecular Medicine, University of South Florida, Tampa, FL
| | - Kevin O’Brien
- Department of Biostatistics, College of Allied Health Sciences, East Carolina University, Greenville, NC
| | - Kelsey Fisher-Wellman
- Department of Physiology & East Carolina Diabetes and Obesity Institute, East Carolina University, Greenville, NC
| | - Krishna M. Bhat
- Department of Molecular Medicine, University of South Florida, Tampa, FL
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8
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Yang M, Li XL, Zhang YT, Deng YW, Jiao Y. miR-10a-3p Participates in Nacre Formation in the Pearl Oyster Pinctada fucata martensii by Targeting NPY. MARINE BIOTECHNOLOGY (NEW YORK, N.Y.) 2023:10.1007/s10126-023-10216-5. [PMID: 37246207 DOI: 10.1007/s10126-023-10216-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/06/2022] [Accepted: 05/12/2023] [Indexed: 05/30/2023]
Abstract
MicroRNAs (miRNAs) are small noncoding RNAs that regulate gene expression via the recognition of their target messenger RNAs. MiR-10a-3p plays an important role in the process of ossification. In this study, we obtained the precursor sequence of miR-10a-3p in the pearl oyster Pinctada fucata martensii (Pm-miR-10a-3p) and verified its sequence by miR-RACE technology, and detected its expression level in the mantle tissues of the pearl oyster P. f. martensii. Pm-nAChRsα and Pm-NPY were identified as the potential target genes of Pm-miR-10a-3p. After the over-expression of Pm-miR-10a-3p, the target genes Pm-nAChRsα and Pm-NPY were downregulated, and the nacre microstructure became disordered. The Pm-miR-10a-3p mimic obviously inhibited the luciferase activity of the 3' untranslated region of the Pm-NPY gene. When the interaction site was mutated, the inhibitory effect disappeared. Our results suggested that Pm-miR-10a-3p participates in nacre formation in P. f. martensii by targeting Pm-NPY. This study can expand our understanding of the mechanism of biomineralization in pearl oysters.
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Affiliation(s)
- Min Yang
- Fishery College, Guangdong Ocean University, Zhanjiang, 524025, China
| | - Xin Lei Li
- Fishery College, Guangdong Ocean University, Zhanjiang, 524025, China
| | - Yu Ting Zhang
- Fishery College, Guangdong Ocean University, Zhanjiang, 524025, China
| | - Yue Wen Deng
- Fishery College, Guangdong Ocean University, Zhanjiang, 524025, China
- Pearl Breeding and Processing Engineering Technology Research Centre of Guangdong Province, Zhanjiang, 524088, China
- Guangdong Science and Innovation Center for Pearl Culture, Zhanjiang, 524088, China
- Guangdong Provincial Key Laboratory of Aquatic Animal Disease Control and Healthy culture, Zhanjiang, 524088, China
| | - Yu Jiao
- Fishery College, Guangdong Ocean University, Zhanjiang, 524025, China.
- Pearl Breeding and Processing Engineering Technology Research Centre of Guangdong Province, Zhanjiang, 524088, China.
- Guangdong Science and Innovation Center for Pearl Culture, Zhanjiang, 524088, China.
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9
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Brazane M, Dimitrova DG, Pigeon J, Paolantoni C, Ye T, Marchand V, Da Silva B, Schaefer E, Angelova MT, Stark Z, Delatycki M, Dudding-Byth T, Gecz J, Plaçais PY, Teysset L, Préat T, Piton A, Hassan BA, Roignant JY, Motorin Y, Carré C. The ribose methylation enzyme FTSJ1 has a conserved role in neuron morphology and learning performance. Life Sci Alliance 2023; 6:e202201877. [PMID: 36720500 PMCID: PMC9889914 DOI: 10.26508/lsa.202201877] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2022] [Revised: 01/08/2023] [Accepted: 01/10/2023] [Indexed: 02/02/2023] Open
Abstract
FTSJ1 is a conserved human 2'-O-methyltransferase (Nm-MTase) that modifies several tRNAs at position 32 and the wobble position 34 in the anticodon loop. Its loss of function has been linked to X-linked intellectual disability (XLID), and more recently to cancers. However, the molecular mechanisms underlying these pathologies are currently unclear. Here, we report a novel FTSJ1 pathogenic variant from an X-linked intellectual disability patient. Using blood cells derived from this patient and other affected individuals carrying FTSJ1 mutations, we performed an unbiased and comprehensive RiboMethSeq analysis to map the ribose methylation on all human tRNAs and identify novel targets. In addition, we performed a transcriptome analysis in these cells and found that several genes previously associated with intellectual disability and cancers were deregulated. We also found changes in the miRNA population that suggest potential cross-regulation of some miRNAs with these key mRNA targets. Finally, we show that differentiation of FTSJ1-depleted human neural progenitor cells into neurons displays long and thin spine neurites compared with control cells. These defects are also observed in Drosophila and are associated with long-term memory deficits. Altogether, our study adds insight into FTSJ1 pathologies in humans and flies by the identification of novel FTSJ1 targets and the defect in neuron morphology.
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Affiliation(s)
- Mira Brazane
- Transgenerational Epigenetics & Small RNA Biology, Sorbonne Université, Centre National de la Recherche Scientifique, Laboratoire de Biologie du Développement - Institut de Biologie Paris Seine, Paris, France
| | - Dilyana G Dimitrova
- Transgenerational Epigenetics & Small RNA Biology, Sorbonne Université, Centre National de la Recherche Scientifique, Laboratoire de Biologie du Développement - Institut de Biologie Paris Seine, Paris, France
| | - Julien Pigeon
- Paris Brain Institute-Institut du Cerveau (ICM), Sorbonne Université, Inserm, CNRS, Hôpital Pitié-Salpêtrière, Paris, France
| | - Chiara Paolantoni
- Center for Integrative Genomics, Génopode Building, Faculty of Biology and Medicine, University of Lausanne, Lausanne, Switzerland
| | - Tao Ye
- Institute of Genetics and Molecular and Cellular Biology, Strasbourg University, CNRS UMR7104, INSERM U1258, Illkirch, France
| | - Virginie Marchand
- Université de Lorraine, CNRS, INSERM, EpiRNASeq Core Facility, UMS2008/US40 IBSLor,Nancy, France
| | - Bruno Da Silva
- Transgenerational Epigenetics & Small RNA Biology, Sorbonne Université, Centre National de la Recherche Scientifique, Laboratoire de Biologie du Développement - Institut de Biologie Paris Seine, Paris, France
| | - Elise Schaefer
- Service de Génétique Médicale, Hôpitaux Universitaires de Strasbourg, Institut de Génétique Médicale d'Alsace, Strasbourg, France
| | - Margarita T Angelova
- Transgenerational Epigenetics & Small RNA Biology, Sorbonne Université, Centre National de la Recherche Scientifique, Laboratoire de Biologie du Développement - Institut de Biologie Paris Seine, Paris, France
| | - Zornitza Stark
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Melbourne, Australia; Department of Paediatrics, The University of Melbourne, Melbourne, Australia
| | - Martin Delatycki
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Melbourne, Australia; Department of Paediatrics, The University of Melbourne, Melbourne, Australia
| | | | - Jozef Gecz
- Adelaide Medical School and Robinson Research Institute, The University of Adelaide; South Australian Health and Medical Research Institute, Adelaide, Australia
| | - Pierre-Yves Plaçais
- Energy & Memory, Brain Plasticity Unit, CNRS, ESPCI Paris, PSL Research University, Paris, France
| | - Laure Teysset
- Transgenerational Epigenetics & Small RNA Biology, Sorbonne Université, Centre National de la Recherche Scientifique, Laboratoire de Biologie du Développement - Institut de Biologie Paris Seine, Paris, France
| | - Thomas Préat
- Energy & Memory, Brain Plasticity Unit, CNRS, ESPCI Paris, PSL Research University, Paris, France
| | - Amélie Piton
- Institute of Genetics and Molecular and Cellular Biology, Strasbourg University, CNRS UMR7104, INSERM U1258, Illkirch, France
| | - Bassem A Hassan
- Paris Brain Institute-Institut du Cerveau (ICM), Sorbonne Université, Inserm, CNRS, Hôpital Pitié-Salpêtrière, Paris, France
| | - Jean-Yves Roignant
- Center for Integrative Genomics, Génopode Building, Faculty of Biology and Medicine, University of Lausanne, Lausanne, Switzerland
- Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg-University Mainz, Mainz, Germany
| | - Yuri Motorin
- Université de Lorraine, CNRS, UMR7365 IMoPA, Nancy, France
| | - Clément Carré
- Transgenerational Epigenetics & Small RNA Biology, Sorbonne Université, Centre National de la Recherche Scientifique, Laboratoire de Biologie du Développement - Institut de Biologie Paris Seine, Paris, France
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10
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Zhang Y, Rabinovsky R, Wei Z, El Fatimy R, Deforzh E, Luan B, Peshkin L, Uhlmann EJ, Krichevsky AM. Secreted PGK1 and IGFBP2 contribute to the bystander effect of miR-10b gene editing in glioma. MOLECULAR THERAPY. NUCLEIC ACIDS 2023; 31:265-275. [PMID: 36700043 PMCID: PMC9852814 DOI: 10.1016/j.omtn.2022.12.018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/08/2022] [Accepted: 12/31/2022] [Indexed: 01/03/2023]
Abstract
MicroRNA-10b (miR-10b) is an essential glioma driver and one of the top candidates for targeted therapies for glioblastoma and other cancers. This unique miRNA controls glioma cell cycle and viability via an array of established conventional and unconventional mechanisms. Previously reported CRISPR-Cas9-mediated miR-10b gene editing of glioma cells in vitro and established orthotopic glioblastoma in mouse models demonstrated the efficacy of this approach and its promise for therapy development. However, therapeutic gene editing in patients' brain tumors may be hampered, among other factors, by the imperfect delivery and distribution of targeting vectors. Here, we demonstrate that miR-10b gene editing in glioma cells triggers a potent bystander effect that leads to the selective cell death of the unedited glioma cells without affecting the normal neuroglial cells. The effect is mediated by the secreted miR-10b targets phosphoglycerate kinase 1 (PGK1) and insulin-like growth factor binding protein 2 (IGFBP2) that block cell-cycle progression and induce glioma cell death. These findings further support the feasibility of therapeutic miR-10b editing without the need to target every cell of the tumor.
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Affiliation(s)
- Yanhong Zhang
- Department of Neurology, Brigham and Women’s Hospital and Harvard Medical School, Harvard Initiative for RNA Medicine, Boston, MA 02115, USA
| | - Rosalia Rabinovsky
- Department of Neurology, Brigham and Women’s Hospital and Harvard Medical School, Harvard Initiative for RNA Medicine, Boston, MA 02115, USA
| | - Zhiyun Wei
- Department of Neurology, Brigham and Women’s Hospital and Harvard Medical School, Harvard Initiative for RNA Medicine, Boston, MA 02115, USA
| | - Rachid El Fatimy
- Department of Neurology, Brigham and Women’s Hospital and Harvard Medical School, Harvard Initiative for RNA Medicine, Boston, MA 02115, USA
| | - Evgeny Deforzh
- Department of Neurology, Brigham and Women’s Hospital and Harvard Medical School, Harvard Initiative for RNA Medicine, Boston, MA 02115, USA
| | - Bai Luan
- Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Leonid Peshkin
- Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Erik J. Uhlmann
- Department of Neurology, Brigham and Women’s Hospital and Harvard Medical School, Harvard Initiative for RNA Medicine, Boston, MA 02115, USA
| | - Anna M. Krichevsky
- Department of Neurology, Brigham and Women’s Hospital and Harvard Medical School, Harvard Initiative for RNA Medicine, Boston, MA 02115, USA
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11
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Arshinchi Bonab R, Asfa S, Kontou P, Karakülah G, Pavlopoulou A. Identification of neoplasm-specific signatures of miRNA interactions by employing a systems biology approach. PeerJ 2022; 10:e14149. [PMID: 36213495 PMCID: PMC9536303 DOI: 10.7717/peerj.14149] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2022] [Accepted: 09/07/2022] [Indexed: 01/21/2023] Open
Abstract
MicroRNAs represent major regulatory components of the disease epigenome and they constitute powerful biomarkers for the accurate diagnosis and prognosis of various diseases, including cancers. The advent of high-throughput technologies facilitated the generation of a vast amount of miRNA-cancer association data. Computational approaches have been utilized widely to effectively analyze and interpret these data towards the identification of miRNA signatures for diverse types of cancers. Herein, a novel computational workflow was applied to discover core sets of miRNA interactions for the major groups of neoplastic diseases by employing network-based methods. To this end, miRNA-cancer association data from four comprehensive publicly available resources were utilized for constructing miRNA-centered networks for each major group of neoplasms. The corresponding miRNA-miRNA interactions were inferred based on shared functionally related target genes. The topological attributes of the generated networks were investigated in order to detect clusters of highly interconnected miRNAs that form core modules in each network. Those modules that exhibited the highest degree of mutual exclusivity were selected from each graph. In this way, neoplasm-specific miRNA modules were identified that could represent potential signatures for the corresponding diseases.
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Affiliation(s)
- Reza Arshinchi Bonab
- Izmir International Biomedicine and Genome Institute, Dokuz Eylül University, Izmir, Turkey,Izmir Biomedicine and Genome Center, Izmir, Turkey
| | - Seyedehsadaf Asfa
- Izmir International Biomedicine and Genome Institute, Dokuz Eylül University, Izmir, Turkey,Izmir Biomedicine and Genome Center, Izmir, Turkey
| | - Panagiota Kontou
- Department of Mathematics, University of Thessaly, Lamia, Greece
| | - Gökhan Karakülah
- Izmir International Biomedicine and Genome Institute, Dokuz Eylül University, Izmir, Turkey,Izmir Biomedicine and Genome Center, Izmir, Turkey
| | - Athanasia Pavlopoulou
- Izmir International Biomedicine and Genome Institute, Dokuz Eylül University, Izmir, Turkey,Izmir Biomedicine and Genome Center, Izmir, Turkey
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12
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Elgeshy KM, Abdel Wahab AHA. The Role, Significance, and Association of MicroRNA-10a/b in Physiology of Cancer. Microrna 2022; 11:118-138. [PMID: 35616665 DOI: 10.2174/2211536611666220523104408] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2021] [Revised: 03/21/2022] [Accepted: 04/04/2022] [Indexed: 01/01/2023]
Abstract
MicroRNAs (miRNAs) are small non-coding RNAs that regulate the translation of mRNA and protein, mainly at the posttranscriptional level. Global expression profiling of miRNAs has demonstrated a broad spectrum of aberrations that correlated with several diseases, and miRNA- 10a and miRNA-10b were the first examined miRNAs to be involved in abnormal activities upon dysregulation, including many types of cancers and progressive diseases. It is expected that the same miRNAs behave inconsistently within different types of cancer. This review aims to provide a set of information about our updated understanding of miRNA-10a and miRNA-10b and their clinical significance, molecular targets, current research gaps, and possible future applications of such potent regulators.
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Affiliation(s)
- Khaled M Elgeshy
- Department of Botany and Microbiology, Faculty of Science, Cairo University, Cairo, Egypt
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13
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The Role of Extracellular Vesicles in Melanoma Progression. Cancers (Basel) 2022; 14:cancers14133086. [PMID: 35804857 PMCID: PMC9264817 DOI: 10.3390/cancers14133086] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2022] [Revised: 06/18/2022] [Accepted: 06/20/2022] [Indexed: 02/07/2023] Open
Abstract
Cutaneous melanoma arises from a malignant transformation of the melanocytes in the skin. It is the deadliest form of skin cancer owing to its potential to metastasize. While recent advances in immuno-oncology have been successful in melanoma treatment, not all the patients respond to the treatment equally, thus individual pre-screening and personalized combination therapies are essential to stratify and monitor patients. Extracellular vesicles (EVs) have emerged as promising biomarker candidates to tackle these challenges. EVs are ~50-1000-nm-sized, lipid bilayer-enclosed spheres, which are secreted by almost all cell types, including cancer cells. Their cargo, such as nucleic acids, proteins, lipids, amino acids, and metabolites, can be transferred to target cells. Thanks to these properties, EVs can both provide a multiplexed molecular fingerprint of the cell of origin and thus serve as potential biomarkers, or reveal pathways important for cancer progression that can be targeted pharmaceutically. In this review we give a general overview of EVs and focus on their impact on melanoma progression. In particular, we shed light on the role of EVs in shaping the tumor-stroma interactions that facilitate metastasis and summarize the latest findings on molecular profiling of EV-derived miRNAs and proteins that can serve as potential biomarkers for melanoma progression.
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14
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Methylation Status of Gene Bodies of Selected microRNA Genes Associated with Neoplastic Transformation in Equine Sarcoids. Cells 2022; 11:cells11121917. [PMID: 35741046 PMCID: PMC9221590 DOI: 10.3390/cells11121917] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2022] [Revised: 06/06/2022] [Accepted: 06/09/2022] [Indexed: 02/04/2023] Open
Abstract
Horses are of great importance in recreation, livestock production, as working animals in poorly developed countries, and for equine-assisted therapy. Equine sarcoids belong to the most commonly diagnosed tumors in this species. They may cause discomfort, pain, and can lead to the permanent impairment of motor function. The molecular bases of their formation are still under investigation. Our previous studies revealed altered microRNA (miRNA) expression and DNA methylation levels in sarcoid tumors. Abnormal patterns of methylation may be responsible for changes in gene expression levels, including microRNAs. Recently, the DNA methylation of gene bodies has also been shown to have an impact on gene expression. Thus, the aim of the study was to investigate the methylation pattern of gene bodies of chosen miRNAs identified in sarcoid tissue (miR-101, miR-10b, miR-200a, and miR-338-3p), which have also been established to play roles in neoplastic transformation. To this end, we applied qRT-PCR, Bisulfite Sequencing PCR (BSP), and Mquant methods. As a result, we identified the statistically significant downregulation of pri-mir-101-1, pri-mir-10b, and pri-mir-200a in the sarcoid samples in comparison to the control. The DNA methylation analysis revealed their hypermethylation. This suggests that DNA methylation may be one mechanism responsible for the downregulation of theses miRNAs. However, the identified differences in the methylation levels are not very high, which implies that other mechanisms may also underlie the downregulation of the expression of these miRNAs in equine sarcoids. For the first time, the results obtained shed light on microRNA expression regulation by gene body methylation in equine sarcoids and provide bases for further deeper studies on other mechanisms influencing the miRNA repertoire.
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15
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El Fatimy R, Zhang Y, Deforzh E, Ramadas M, Saravanan H, Wei Z, Rabinovsky R, Teplyuk NM, Uhlmann EJ, Krichevsky AM. A nuclear function for an oncogenic microRNA as a modulator of snRNA and splicing. Mol Cancer 2022; 21:17. [PMID: 35033060 PMCID: PMC8760648 DOI: 10.1186/s12943-022-01494-z] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2021] [Accepted: 12/23/2021] [Indexed: 01/09/2023] Open
Abstract
BACKGROUND miRNAs are regulatory transcripts established as repressors of mRNA stability and translation that have been functionally implicated in carcinogenesis. miR-10b is one of the key onco-miRs associated with multiple forms of cancer. Malignant gliomas exhibit particularly striking dependence on miR-10b. However, despite the therapeutic potential of miR-10b targeting, this miRNA's poorly investigated and largely unconventional properties hamper the clinical translation. METHODS We utilized Covalent Ligation of Endogenous Argonaute-bound RNAs and their high-throughput RNA sequencing to identify miR-10b interactome and a combination of biochemical and imaging approaches for target validation. They included Crosslinking and RNA immunoprecipitation with spliceosomal proteins, a combination of miRNA FISH with protein immunofluorescence in glioma cells and patient-derived tumors, native Northern blotting, and the transcriptome-wide analysis of alternative splicing. RESULTS We demonstrate that miR-10b binds to U6 snRNA, a core component of the spliceosomal machinery. We provide evidence of the direct binding between miR-10b and U6, in situ imaging of miR-10b and U6 co-localization in glioma cells and tumors, and biochemical co-isolation of miR-10b with the components of the spliceosome. We further demonstrate that miR-10b modulates U6 N-6-adenosine methylation and pseudouridylation, U6 binding to splicing factors SART3 and PRPF8, and regulates U6 stability, conformation, and levels. These effects on U6 result in global splicing alterations, exemplified by the altered ratio of the isoforms of a small GTPase CDC42, reduced overall CDC42 levels, and downstream CDC42 -mediated effects on cell viability. CONCLUSIONS We identified U6 snRNA, the key RNA component of the spliceosome, as the top miR-10b target in glioblastoma. We, therefore, present an unexpected intersection of the miRNA and splicing machineries and a new nuclear function for a major cancer-associated miRNA.
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Affiliation(s)
- Rachid El Fatimy
- Department of Neurology, Brigham and Women's Hospital and Harvard Medical School, 60 Fenwood Rd, Room 9002T, Boston, MA, 02115, USA
- Current Address: Institute of Biological Sciences (ISSB-P), Mohammed VI Polytechnic University (UM6P), 43150, Benguerir, Morocco
| | - Yanhong Zhang
- Department of Neurology, Brigham and Women's Hospital and Harvard Medical School, 60 Fenwood Rd, Room 9002T, Boston, MA, 02115, USA
| | - Evgeny Deforzh
- Department of Neurology, Brigham and Women's Hospital and Harvard Medical School, 60 Fenwood Rd, Room 9002T, Boston, MA, 02115, USA
| | - Mahalakshmi Ramadas
- Department of Neurology, Brigham and Women's Hospital and Harvard Medical School, 60 Fenwood Rd, Room 9002T, Boston, MA, 02115, USA
| | - Harini Saravanan
- Department of Neurology, Brigham and Women's Hospital and Harvard Medical School, 60 Fenwood Rd, Room 9002T, Boston, MA, 02115, USA
| | - Zhiyun Wei
- Department of Neurology, Brigham and Women's Hospital and Harvard Medical School, 60 Fenwood Rd, Room 9002T, Boston, MA, 02115, USA
- Current Address: Shanghai Key Laboratory of Maternal Fetal Medicine, Shanghai First Maternity and Infant Hospital, School of Medicine, Tongji University, Shanghai, 200092, China
| | - Rosalia Rabinovsky
- Department of Neurology, Brigham and Women's Hospital and Harvard Medical School, 60 Fenwood Rd, Room 9002T, Boston, MA, 02115, USA
| | - Nadiya M Teplyuk
- Department of Neurology, Brigham and Women's Hospital and Harvard Medical School, 60 Fenwood Rd, Room 9002T, Boston, MA, 02115, USA
| | - Erik J Uhlmann
- Department of Neurology, Brigham and Women's Hospital and Harvard Medical School, 60 Fenwood Rd, Room 9002T, Boston, MA, 02115, USA
| | - Anna M Krichevsky
- Department of Neurology, Brigham and Women's Hospital and Harvard Medical School, 60 Fenwood Rd, Room 9002T, Boston, MA, 02115, USA.
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16
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Liu W, Zhang F, Zheng Y, He S, Zhang T, Guo Q, Xu H, Chen H, Liu C, Yu S, Jiang K, Li H, Li G, Wang X, Liu X. The role of circulating blood microRNA-374 and microRNA-10 levels in the pathogenesis and therapeutic mechanisms of major depressive disorder. Neurosci Lett 2021; 763:136184. [PMID: 34418506 DOI: 10.1016/j.neulet.2021.136184] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2020] [Revised: 08/10/2021] [Accepted: 08/16/2021] [Indexed: 12/28/2022]
Abstract
Compelling recent evidence suggests that microRNAs (miRNAs) regulate specific mRNA transcripts at the transcriptomic level and coordinately influence complex regulatory networks, which may play a crucial role in the pathogenesis of major depressive disorder (MDD) and the treatment effects of antidepressants. To evaluate the possible involvement of miRNAs in the pathophysiology and therapeutic response of MDD, we conducted a miRNA expression array analysis of the peripheral blood mononuclear cells (PBMCs) of 5 depressed patients and 5 healthy controls (HCs). Subsequently, we chose 2 miRNAs for validation with real-time PCR (RT-PCR) analysis pre- and post-treatment in another group of 25 MDD patients and 25 HCs. In the array, 5 miRNAs were differentially expressed in medication-naïve MDD patients compared to HCs, of which 2 miRNAs were upregulated and 3 were downregulated. Furthermore, in comparison with HCs, MDD patients showed significantly lower expression levels of miR-374b and miR-10a before treatment. After 8 weeks of antidepressant treatment, both miR-374b and the miR-10a expression levels in MDD patients were significantly elevated only in responders. In conclusion, these results indicate the involvement of miR-374b and miR-10a in the biological mechanisms and therapeutic response of MDD, and provide new insights for exploring miRNAs as potential biomarkers for MDD.
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Affiliation(s)
- Wanying Liu
- Department of Psychiatry, Shanghai Mental Health Center, Shanghai Jiao Tong University School of Medicine, Shanghai, PR China
| | - Fuxu Zhang
- Department of Psychiatry, Shanghai Mental Health Center, Shanghai Jiao Tong University School of Medicine, Shanghai, PR China
| | - Yanqun Zheng
- Department of Psychiatry, Shanghai Mental Health Center, Shanghai Jiao Tong University School of Medicine, Shanghai, PR China
| | - Shen He
- Department of Psychiatry, Shanghai Mental Health Center, Shanghai Jiao Tong University School of Medicine, Shanghai, PR China
| | - Tianhong Zhang
- Department of Psychiatry, Shanghai Mental Health Center, Shanghai Jiao Tong University School of Medicine, Shanghai, PR China; Shanghai Key Laboratory of Psychotic Disorders, Shanghai Mental Health Center, Shanghai Jiao Tong University School of Medicine, Shanghai, PR China
| | - Qian Guo
- Department of Psychiatry, Shanghai Mental Health Center, Shanghai Jiao Tong University School of Medicine, Shanghai, PR China
| | - Hua Xu
- Department of Psychiatry, Shanghai Mental Health Center, Shanghai Jiao Tong University School of Medicine, Shanghai, PR China
| | - Haiying Chen
- Department of Psychiatry, Shanghai Mental Health Center, Shanghai Jiao Tong University School of Medicine, Shanghai, PR China
| | - Caiping Liu
- Department of Psychiatry, Shanghai Mental Health Center, Shanghai Jiao Tong University School of Medicine, Shanghai, PR China
| | - Shunying Yu
- Shanghai Key Laboratory of Psychotic Disorders, Shanghai Mental Health Center, Shanghai Jiao Tong University School of Medicine, Shanghai, PR China
| | - Kaida Jiang
- Department of Psychiatry, Shanghai Mental Health Center, Shanghai Jiao Tong University School of Medicine, Shanghai, PR China
| | - Huafang Li
- Department of Psychiatry, Shanghai Mental Health Center, Shanghai Jiao Tong University School of Medicine, Shanghai, PR China; Shanghai Key Laboratory of Psychotic Disorders, Shanghai Mental Health Center, Shanghai Jiao Tong University School of Medicine, Shanghai, PR China; Institution of Drug Clinical Trials, Shanghai Mental Health Center, Shanghai Jiao Tong University School of Medicine, Shanghai, PR China
| | - Guanjun Li
- Department of Psychiatry, Shanghai Mental Health Center, Shanghai Jiao Tong University School of Medicine, Shanghai, PR China
| | - Xiaoliang Wang
- Department of Psychiatry, Shanghai Mental Health Center, Shanghai Jiao Tong University School of Medicine, Shanghai, PR China
| | - Xiaohua Liu
- Department of Psychiatry, Shanghai Mental Health Center, Shanghai Jiao Tong University School of Medicine, Shanghai, PR China; Shanghai Key Laboratory of Psychotic Disorders, Shanghai Mental Health Center, Shanghai Jiao Tong University School of Medicine, Shanghai, PR China.
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17
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Abstract
Evidence has demonstrated that miRNAs play an irreplaceable role in tumorigenesis and progression of a broad range of cancers, including gastric cancer. Among these miRNAs, miR-10a and miR-10b have been identified to critically participate in gastric carcinogenesis and malignant progression. In this review, we briefly describe the role of miR-10a and miR-10b in gastric cancer, especially in the regulation of cell proliferation, apoptosis, cell cycle, migration, invasion and metastasis, drug resistance, and cancer stem cells. Furthermore, we highlight several compounds that target the miR-10 family and exhibit antitumor activity in cancer cells. Moreover, we conclude that targeting the miR-10 family might be a promising approach for the treatment of gastric cancer.
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Affiliation(s)
- Fang Liu
- Department of Emergency, The First Hospital of Jilin University, Changchun, Jilin, China
| | - Yanfen Shi
- Department of Pathology, China-Japan Friendship Hospital, Beijing, China
| | - Zuolong Liu
- Department of Emergency, The First Hospital of Jilin University, Changchun, Jilin, China
| | - Ziyi Li
- Key Laboratory of Organ Regeneration and Transplantation of Ministry of Education, The First Hospital of Jilin University, Changchun, Jilin, China
| | - Wei Xu
- Department of the Clinical Laboratory, The First Hospital of Jilin University, Changchun, Jilin, China
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18
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Lin CC, Liao WT, Yang TY, Lu HJ, Hsu SL, Wu CC. MicroRNA‑10b modulates cisplatin tolerance by targeting p53 directly in lung cancer cells. Oncol Rep 2021; 46:167. [PMID: 34165168 DOI: 10.3892/or.2021.8118] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2020] [Accepted: 03/04/2021] [Indexed: 12/24/2022] Open
Abstract
MicroRNA (miRNA or miR)‑10b is an oncogenic miRNA associated with metastasis that is present in various types of tumor, including lung cancer. However, whether miR‑10b is involved in different malignant characteristics, such as drug resistance or stemness, remains unclear. Therefore, the present study investigated whether miR‑10b is an upstream regulator of p53. Ectopic expression of miR‑10b‑agomir decreased the expression of p53 and its downstream effectors, such as Bax and p53 upregulated modulator of apoptosis. Two non‑canonical sites, including 1,580‑1,587 and 2,029‑2,035, located in p53 3'‑untranslated region (UTR) were affected by the presence of miR‑10b. In functional assays, upregulation of the p53 signaling pathway following cisplatin treatment was associated with decreased levels of miR‑10b and upregulation of the luciferase activity of wild‑type, but not 1,584, 2,032‑dual‑mutant, p53 3'‑UTR. The ectopic expression of miR‑10b‑agomir attenuated the stability of p53 3'‑UTR and the expression of p53 and its downstream effectors induced by cisplatin. By contrast, the knockdown of miR‑10b induced the stability of p53 3'‑UTR and increased levels of p53 and the sensitivity of A549 cells to cisplatin treatment. Similar results were also observed for Beas 2B cells. In the clinical investigation, p53 exhibited two distinct associations (cocurrent and countercurrent) with miR‑10b in patients with lung cancer. Patients with lung cancer with low p53 and high miR‑10b levels exhibited the poorest prognosis, while those with high p53 and low miR‑10b exhibited the most favorable prognosis. These findings indicate a novel pathway in which cisplatin induces the levels of p53 by increasing mRNA stability via miR‑10b, indicating a novel oncogenic role of miR‑10b in promoting the malignant characteristics of non‑small cell lung carcinoma.
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Affiliation(s)
- Chen-Chu Lin
- Institute of Medicine, Chung‑Shan Medical University, Taichung 402, Taiwan, R.O.C
| | - Wan-Ting Liao
- Institute of Medicine, Chung‑Shan Medical University, Taichung 402, Taiwan, R.O.C
| | - Tsung-Ying Yang
- Division of Chest Medicine, Department of Internal Medicine, Taichung Veterans General Hospital, Taichung 407, Taiwan, R.O.C
| | - Hsueh-Ju Lu
- Division of Medical Oncology, Department of Internal Medicine, Chung-Shan Medical University Hospital, Taichung 402, Taiwan, R.O.C
| | - Shih-Lan Hsu
- Department of Medical Research, Taichung Veterans General Hospital, Taichung 407, Taiwan, R.O.C
| | - Chun-Chi Wu
- Institute of Medicine, Chung‑Shan Medical University, Taichung 402, Taiwan, R.O.C
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19
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Dika E, Broseghini E, Porcellini E, Lambertini M, Riefolo M, Durante G, Loher P, Roncarati R, Bassi C, Misciali C, Negrini M, Rigoutsos I, Londin E, Patrizi A, Ferracin M. Unraveling the role of microRNA/isomiR network in multiple primary melanoma pathogenesis. Cell Death Dis 2021; 12:473. [PMID: 33980826 PMCID: PMC8115306 DOI: 10.1038/s41419-021-03764-y] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2020] [Revised: 04/19/2021] [Accepted: 04/19/2021] [Indexed: 12/16/2022]
Abstract
Malignant cutaneous melanoma (CM) is a potentially lethal form of skin cancer whose worldwide incidence has been constantly increasing over the past decades. During their lifetime, about 8% of CM patients will develop multiple primary melanomas (MPMs), usually at a young age and within 3 years from the first tumor/diagnosis. With the aim of improving our knowledge on MPM biology and pathogenesis, we explored the miRNome of 24 single and multiple primary melanomas, including multiple tumors from the same patient, using a small RNA-sequencing approach. From a supervised analysis, 22 miRNAs were differentially expressed in MPM compared to single CM, including key miRNAs involved in epithelial-mesenchymal transition. The first and second melanoma from the same patient presented a different miRNA profile. Ten miRNAs, including miR-25-3p, 149-5p, 92b-3p, 211-5p, 125a-5p, 125b-5p, 205-5p, 200b-3p, 21-5p, and 146a-5p, were further validated in 47 single and multiple melanoma samples. Pathway enrichment analysis of miRNA target genes revealed a more differentiated and less invasive status of MPMs compared to CMs. Bioinformatic analyses at the miRNA isoform (isomiR) level detected a panel of highly expressed isomiRs belonging to miRNA families implicated in human tumorigenesis, including miR-200, miR-30, and miR-10 family. Moreover, we identified hsa-miR-125a-5p|0|-2 isoform as tenfold over-represented in melanoma than the canonical form and differentially expressed in MPMs arising in the same patient. Target prediction analysis revealed that the miRNA shortening could change the pattern of target gene regulation, specifically in genes implicated in cell adhesion and neuronal differentiation. Overall, we provided a putative and comprehensive characterization of the miRNA/isomiR regulatory network of MPMs, highlighting mechanisms of tumor development and molecular features differentiating this subtype from single melanomas.
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Affiliation(s)
- Emi Dika
- Department of Experimental, Diagnostic and Specialty Medicine (DIMES), University of Bologna, Bologna, Italy
- Dermatology Unit, IRCCS Azienda Ospedaliero-Universitaria di Bologna, Bologna, Italy
| | - Elisabetta Broseghini
- Department of Experimental, Diagnostic and Specialty Medicine (DIMES), University of Bologna, Bologna, Italy
| | - Elisa Porcellini
- Department of Experimental, Diagnostic and Specialty Medicine (DIMES), University of Bologna, Bologna, Italy
| | - Martina Lambertini
- Department of Experimental, Diagnostic and Specialty Medicine (DIMES), University of Bologna, Bologna, Italy
- Dermatology Unit, IRCCS Azienda Ospedaliero-Universitaria di Bologna, Bologna, Italy
| | - Mattia Riefolo
- Department of Experimental, Diagnostic and Specialty Medicine (DIMES), University of Bologna, Bologna, Italy
| | - Giorgio Durante
- Department of Experimental, Diagnostic and Specialty Medicine (DIMES), University of Bologna, Bologna, Italy
| | - Phillipe Loher
- Computational Medicine Center, Sidney Kimmel Medical College, Thomas Jefferson University, Philadelphia, PA, 19107, USA
| | - Roberta Roncarati
- Department of Translational Medicine and for Romagna, and "Laboratorio per le Tecnologie delle Terapie Avanzate" (LTTA), University of Ferrara, Ferrara, Italy
- CNR, Institute of Genetics and Biomedical Research, National Research Council of Italy, Milan, Italy
| | - Cristian Bassi
- Department of Translational Medicine and for Romagna, and "Laboratorio per le Tecnologie delle Terapie Avanzate" (LTTA), University of Ferrara, Ferrara, Italy
| | - Cosimo Misciali
- Dermatology Unit, IRCCS Azienda Ospedaliero-Universitaria di Bologna, Bologna, Italy
| | - Massimo Negrini
- Department of Translational Medicine and for Romagna, and "Laboratorio per le Tecnologie delle Terapie Avanzate" (LTTA), University of Ferrara, Ferrara, Italy
| | - Isidore Rigoutsos
- Computational Medicine Center, Sidney Kimmel Medical College, Thomas Jefferson University, Philadelphia, PA, 19107, USA
| | - Eric Londin
- Computational Medicine Center, Sidney Kimmel Medical College, Thomas Jefferson University, Philadelphia, PA, 19107, USA
| | - Annalisa Patrizi
- Department of Experimental, Diagnostic and Specialty Medicine (DIMES), University of Bologna, Bologna, Italy
- Dermatology Unit, IRCCS Azienda Ospedaliero-Universitaria di Bologna, Bologna, Italy
| | - Manuela Ferracin
- Department of Experimental, Diagnostic and Specialty Medicine (DIMES), University of Bologna, Bologna, Italy.
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20
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Simultaneous learning of individual microRNA-gene interactions and regulatory comodules. BMC Bioinformatics 2021; 22:237. [PMID: 33971820 DOI: 10.1186/s12859-021-04151-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2020] [Accepted: 04/23/2021] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND MicroRNAs (miRNAs) function in post-transcriptional regulation of gene expression by binding to target messenger RNAs (mRNAs). Because of the key part that miRNAs play, understanding the correct regulatory role of miRNAs in diverse patho-physiological conditions is of great interest. Although it is known that miRNAs act combinatorially to regulate genes, precise identification of miRNA-gene interactions and their specific functional roles in regulatory comodules remains a challenge. We developed THEIA, an effective method for simultaneously predicting miRNA-gene interactions and regulatory comodules, which group functionally related miRNAs and genes via non-negative matrix factorization (NMF). RESULTS We apply THEIA to RNA sequencing data from breast invasive carcinoma samples and demonstrate its effectiveness in discovering biologically significant regulatory comodules that are significantly enriched in spatial miRNA clusters, biological pathways, and various cancers. CONCLUSIONS THEIA is a theoretically rigorous optimization algorithm that simultaneously predicts the strength and direction (i.e., up-regulation or down-regulation) of the effect of modules of miRNAs on a gene. We posit that if THEIA is capable of recovering known clusters of genes and miRNA, then the clusters found by our method not previously identified by literature are also likely to have biological significance. We believe that these novel regulatory comodules found by our method will be a springboard for further research into the specific functional roles of these new functional ensembles of miRNAs and genes,especially those related to diseases like breast cancer.
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21
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Expression profiling of Echinococcus multilocularis miRNAs throughout metacestode development in vitro. PLoS Negl Trop Dis 2021; 15:e0009297. [PMID: 33750964 PMCID: PMC8016320 DOI: 10.1371/journal.pntd.0009297] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2020] [Revised: 04/01/2021] [Accepted: 03/08/2021] [Indexed: 12/30/2022] Open
Abstract
The neglected zoonotic disease alveolar echinococcosis (AE) is caused by the metacestode stage of the tapeworm parasite Echinococcus multilocularis. MicroRNAs (miRNAs) are small non-coding RNAs with a major role in regulating gene expression in key biological processes. We analyzed the expression profile of E. multilocularis miRNAs throughout metacestode development in vitro, determined the spatial expression of miR-71 in metacestodes cultured in vitro and predicted miRNA targets. Small cDNA libraries from different samples of E. multilocularis were sequenced. We confirmed the expression of 37 miRNAs in E. multilocularis being some of them absent in the host, such as miR-71. We found a few miRNAs highly expressed in all life cycle stages and conditions analyzed, whereas most miRNAs showed very low expression. The most expressed miRNAs were miR-71, miR-9, let-7, miR-10, miR-4989 and miR-1. The high expression of these miRNAs was conserved in other tapeworms, suggesting essential roles in development, survival, or host-parasite interaction. We found highly regulated miRNAs during the different transitions or cultured conditions analyzed, which might suggest a role in the regulation of developmental timing, host-parasite interaction, and/or in maintaining the unique developmental features of each developmental stage or condition. We determined that miR-71 is expressed in germinative cells and in other cell types of the germinal layer in E. multilocularis metacestodes cultured in vitro. MiRNA target prediction of the most highly expressed miRNAs and in silico functional analysis suggested conserved and essential roles for these miRNAs in parasite biology. We found relevant targets potentially involved in development, cell growth and death, lifespan regulation, transcription, signal transduction and cell motility. The evolutionary conservation and expression analyses of E. multilocularis miRNAs throughout metacestode development along with the in silico functional analyses of their predicted targets might help to identify selective therapeutic targets for treatment and control of AE. Alveolar echinococcosis (AE) is a zoonotic disease caused by the metacestode stage of the helminth parasite Echinococcus multilocularis. Current treatment requires surgery and/or prolonged drug therapy. Thus, novel strategies for the treatment of AE are needed. MicroRNAs (miRNAs), a class of small ~22-nucleotide (nt) non-coding RNAs with a major role in regulating gene expression, have been suggested as potential therapeutic targets for treatment and control of helminth parasite infections. In this work, we analyzed the expression profile of E. multilocularis miRNAs throughout metacestode development in vitro. We predicted functional roles for highly expressed miRNAs and found that they could be involved in essential roles for survival and development in the host. We determined that E. multilocularis miR-71, a highly expressed miRNA that is absent in the human host, is expressed in germinative cells and in other cell types of the germinal layer in E. multilocularis metacestodes cultured in vitro. Germinative cells are a relevant cell type to target for anti-echinococcosis drug development. MiRNAs that are absent in the human host, involved in essential functions, highly expressed and/or expressed in germinative cells in E. multilocularis metacestodes may represent selective therapeutic targets for treatment and control of AE.
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22
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Wang J, Yin X, Zhang YQ, Ji X. Identification and Validation of a Novel Immune-Related Four-lncRNA Signature for Lung Adenocarcinoma. Front Genet 2021; 12:639254. [PMID: 33708243 PMCID: PMC7940686 DOI: 10.3389/fgene.2021.639254] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2020] [Accepted: 01/18/2021] [Indexed: 12/20/2022] Open
Abstract
Lung adenocarcinoma (LUAD) is a major subtype of lung cancer, the prognosis of patients with which is associated with both lncRNAs and cancer immunity. In this study, we collected gene expression data of 585 LUAD patients from The Cancer Genome Atlas (TCGA) database and 605 subjects from the Gene Expression Omnibus (GEO) database. LUAD patients were divided into high and low immune-cell-infiltrated groups according to the single sample gene set enrichment analysis (ssGSEA) algorithm to identify differentially expressed genes (DEGs). Based on the 49 immune-related DE lncRNAs, a four-lncRNA prognostic signature was constructed by applying least absolute shrinkage and selection operator (LASSO) regression, univariate Cox regression, and stepwise multivariate Cox regression in sequence. Kaplan–Meier curve, ROC analysis, and the testing GEO datasets verified the effectiveness of the signature in predicting overall survival (OS). Univariate Cox regression and multivariate Cox regression suggested that the signature was an independent prognostic factor. The correlation analysis revealed that the infiltration immune cell subtypes were related to these lncRNAs.
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Affiliation(s)
- Jixin Wang
- Zhejiang University-University of Edinburgh Institute, Zhejiang University, Zhejiang, China
| | - Xiangjun Yin
- School of Basic Medical Science, Zhejiang Chinese Medical University, Zhejiang, China
| | - Yin-Qiang Zhang
- Department of Hepatic Diseases, Xiyuan Hospital, China Academy of Chinese Medical Sciences, Beijing, China
| | - Xuming Ji
- School of Basic Medical Science, Zhejiang Chinese Medical University, Zhejiang, China
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23
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Mishra N, Raina K, Agarwal R. Deciphering the role of microRNAs in mustard gas-induced toxicity. Ann N Y Acad Sci 2020; 1491:25-41. [PMID: 33305460 DOI: 10.1111/nyas.14539] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2020] [Revised: 10/26/2020] [Accepted: 11/01/2020] [Indexed: 12/16/2022]
Abstract
Mustard gas (sulfur mustard, SM), a highly vesicating chemical warfare agent, was first deployed in warfare in 1917 and recently during the Iraq-Iran war (1980s) and Syrian conflicts (2000s); however, the threat of exposure from stockpiles and old artillery shells still looms large. Whereas research has been long ongoing on SM-induced toxicity, delineating the precise molecular pathways is still an ongoing area of investigation; thus, it is important to attempt novel approaches to decipher these mechanisms and develop a detailed network of pathways associated with SM-induced toxicity. One such avenue is exploring the role of microRNAs (miRNAs) in SM-induced toxicity. Recent research on the regulatory role of miRNAs provides important results to fill in the gaps in SM toxicity-associated mechanisms. In addition, differentially expressed miRNAs can also be used as diagnostic markers to determine the extent of toxicity in exposed individuals. Thus, in our review, we have summarized the studies conducted so far in cellular and animal models, including human subjects, on the expression profiles and roles of miRNAs in SM- and/or SM analog-induced toxicity. Further detailed research in this area will guide us in devising preventive strategies, diagnostic tools, and therapeutic interventions against SM-induced toxicity.
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Affiliation(s)
- Neha Mishra
- Department of Pharmaceutical Sciences, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of Colorado-Anschutz Medical Campus, Aurora, Colorado
| | - Komal Raina
- Department of Pharmaceutical Sciences, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of Colorado-Anschutz Medical Campus, Aurora, Colorado.,Department of Pharmaceutical Sciences, South Dakota State University, Brookings, South Dakota
| | - Rajesh Agarwal
- Department of Pharmaceutical Sciences, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of Colorado-Anschutz Medical Campus, Aurora, Colorado
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Imasato Y, Nakao R, Irie T, Kouguchi H, Yagi K, Nariaki N, Katakura K. Characterization of microRNAs expressed in the cystic legion of the liver of Mus musculus perorally infected with Echinococcus multilocularis Nemuro strain. Parasitol Int 2020; 81:102247. [PMID: 33238214 DOI: 10.1016/j.parint.2020.102247] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2020] [Revised: 10/02/2020] [Accepted: 11/15/2020] [Indexed: 11/18/2022]
Abstract
Alveolar echinococcosis (AE) is a zoonosis caused by the metacestode of Echinococcus multilocularis. The published genome of E. multilocularis showed that approximately 86% of its genome is non-coding. Micro RNAs (miRNAs) are small non-coding regulatory RNAs, and recent studies on parasitic helminths expect miRNAs as a promising target for drug development and diagnostic markers. Prior to this study, only a few studies reported the E. multilocularis miRNA profiles in the intermediate host. The primary objective of this study was to characterize miRNA profiles via small RNA-seq in E. multilocularis Nemuro strain, a laboratory strain of Asian genotype, using mice perorally infected with the parasite eggs. The data were then compared with two previously published small RNA-seq data. We identified 44 mature miRNAs as E. multilocularis origin out of the 68 mature miRNA sequences registered in the miRNA database miRbase. The highest quantities of miRNAs detected were miR-10-5p, followed by bantam-3p, let-7-5p, miR-61-3p, and miR-71-5p. The top two most abundant miRNAs (miR-10-5p and bantam-3p) accounted for approximately 80.9% of the total parasite miRNAs. The highly expressed miRNA repertoire is mostly comparable to that obtained from the previous experiment using secondary echinococcosis created by an intraperitoneal administration of metacestodes. A detailed characterization and functional annotations of these shared miRNAs will lead to a better understanding of parasitic dynamics, which could provide a basis for the development of novel diagnostic and treatment methods for AE.
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Affiliation(s)
- Yuhei Imasato
- Laboratory of Parasitology, Division of Infectious Diseases, Graduate School of Infectious Diseases, Hokkaido University, Kita 18, Nishi 8, Sapporo, Hokkaido 060-0818, Japan.
| | - Ryo Nakao
- Laboratory of Parasitology, Division of Infectious Diseases, Graduate School of Infectious Diseases, Hokkaido University, Kita 18, Nishi 8, Sapporo, Hokkaido 060-0818, Japan; Laboratory of Parasitology, Faculty of Veterinary Medicine, Hokkaido University, Kita 18, Nishi 8, Sapporo, Hokkaido 060-0818, Japan.
| | - Takao Irie
- Department of Infectious Diseases, Hokkaido Institute of Public Health, Kita 19, Nishi 12, Sapporo, Hokkaido 060-0819, Japan.
| | - Hirokazu Kouguchi
- Department of Infectious Diseases, Hokkaido Institute of Public Health, Kita 19, Nishi 12, Sapporo, Hokkaido 060-0819, Japan.
| | - Kinpei Yagi
- Department of Infectious Diseases, Hokkaido Institute of Public Health, Kita 19, Nishi 12, Sapporo, Hokkaido 060-0819, Japan.
| | - Nonaka Nariaki
- Laboratory of Parasitology, Division of Infectious Diseases, Graduate School of Infectious Diseases, Hokkaido University, Kita 18, Nishi 8, Sapporo, Hokkaido 060-0818, Japan; Laboratory of Parasitology, Faculty of Veterinary Medicine, Hokkaido University, Kita 18, Nishi 8, Sapporo, Hokkaido 060-0818, Japan.
| | - Ken Katakura
- Laboratory of Parasitology, Division of Infectious Diseases, Graduate School of Infectious Diseases, Hokkaido University, Kita 18, Nishi 8, Sapporo, Hokkaido 060-0818, Japan; Laboratory of Parasitology, Faculty of Veterinary Medicine, Hokkaido University, Kita 18, Nishi 8, Sapporo, Hokkaido 060-0818, Japan.
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TWIST1-MicroRNA-10a-MAP3K7 Axis Ameliorates Synovitis of Osteoarthritis in Fibroblast-like Synoviocytes. MOLECULAR THERAPY-NUCLEIC ACIDS 2020; 22:1107-1120. [PMID: 33294296 PMCID: PMC7691159 DOI: 10.1016/j.omtn.2020.10.020] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/12/2020] [Accepted: 10/17/2020] [Indexed: 11/21/2022]
Abstract
Synovitis refers to the inflammation of the synovial membrane and is commonly detected in patients with osteoarthritis (OA). Recent reports have suggested that microRNAs (miRNAs) could be a promising target for diagnosis and prognosis in OA. This study examines the effect of microRNA-10a (miR-10a) in fibroblast-like synoviocyte (FLS)-mediated synovitis obtained from patients with OA. Expression of miR-10a is negatively associated with the severity of synovitis. miR-10a inhibited proliferation, migration, and secretion of pro-inflammatory cytokines of OA-FLS that were obtained from OA patients in vitro. By using a patient-derived xenograft (PDX) model, miR-10a repressed proliferation of OA-FLSs and production of OA synovium-derived pro-inflammatory cytokines in vivo. Twist Family BHLH Transcription Factor 1 (TWIST1) and mitogen-activated protein kinase kinase kinase 7 (MAP3K7) were identified as an upstream regulator and direct target of miR-10a in OA-FLSs, respectively. Nuclear factor κB (NF-κB) signaling pathway, a downstream pathway of MAP3K7, was also repressed by miR-10a in OA-FLSs. To summarize, the TWIST1-miR-10a-MAP3K7-NF-κB pathway mediates the development of synovitis in OA. miR-10a functions as an anti-inflammatory mediator in OA-FLS.
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Yi BS, Ma BQ, Li BZ, Tian F. MiR-10b induces cisplatin resistance in gastric cancer cells by inhibiting KLF4 expression. Shijie Huaren Xiaohua Zazhi 2020; 28:362-370. [DOI: 10.11569/wcjd.v28.i10.362] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND Gastric cancer (GC) chemotherapy is prone to acquired chemotherapy resistance. MiR-10b has been found to be involved in regulating cisplatin (DDP) resistance of esophageal and nasopharyngeal carcinoma cells, but its relationship with DDP chemotherapy sensitivity in GC is unclear.
AIM To investigate whether miR-10b is related to DDP chemoresistance in GC cells and the underlying molecular mechanism.
METHODS SGC-7901/DDP and MGC-803/DDP cell lines were established by repeated stimulation of SGC-7901 and MGC-803 cells with increasing concentrations of DDP. The expression levels of miR-10b and KLF4 in SGC-7901/DDP and MGC-803/DDP cells were detected. After SGC-7901 and MGC-803 cells were infected with a lentiviral vector overexpressing miR-10b, cell proliferation was detected by MTT assay, apoptosis was detected by Annexin V-FITC/PI staining, and KLF4 mRNA and protein expression was detected by RT- qPCR and Western blot, respectively. In addition, these cells were further used to construct a xenograft tumor model, and after DDP chemotherapy, tumor morphology was observed macroscopically and tumor weight was measured. After co-transfection of SGC-7901 and MGC-803 cells with miR-10b and KLF4, the sensitivity of cells to DDP was detected by MTT assay.
RESULTS Compared with SGC-7901 and MGC-803 cells, miR-10b expression levels in SGC-7901/DDP and MGC-803/DDP cells were significantly increased (P < 0.01), and KLF4 mRNA and protein levels were significantly decreased (P < 0.01). In vitro experiments showed that overexpression of miR-10b promoted DDP resistance in GC cells and inhibited KLF4 expression (P < 0.01). In vivo, after DDP treatment, tumor weight in the miR-10b group was significantly higher than that of the control group (P < 0.01). Overexpression of KLF4 could partially reverse DDP resistance of GC cells induced by overexpression of miR-10b.
CONCLUSION MiR-10b promotes DDP resistance in GC cells by inhibiting the expression of KLF4, however, the DDP resistance induced by miR-10b overexpression can be reversed by up-regulation of KLF4.
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Affiliation(s)
- Bi-Shun Yi
- Department of Trauma, Acute Abdomen and Hernia Surgery, Lishui City People's Hospital, Lishui 323000, Zhejiang Province, China
| | - Bai-Qiang Ma
- Department of Trauma, Acute Abdomen and Hernia Surgery, Lishui City People's Hospital, Lishui 323000, Zhejiang Province, China
| | - Bing-Zhen Li
- Department of Trauma, Acute Abdomen and Hernia Surgery, Lishui City People's Hospital, Lishui 323000, Zhejiang Province, China
| | - Feng Tian
- Department of Trauma, Acute Abdomen and Hernia Surgery, Lishui City People's Hospital, Lishui 323000, Zhejiang Province, China
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27
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Ochoa S, de Anda-Jáuregui G, Hernández-Lemus E. Multi-Omic Regulation of the PAM50 Gene Signature in Breast Cancer Molecular Subtypes. Front Oncol 2020; 10:845. [PMID: 32528899 PMCID: PMC7259379 DOI: 10.3389/fonc.2020.00845] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2019] [Accepted: 04/29/2020] [Indexed: 12/24/2022] Open
Abstract
Breast cancer is a disease that exhibits heterogeneity that goes from the genomic to the clinical levels. This heterogeneity is thought to be captured (at least partially) by the so-called breast cancer molecular subtypes. These molecular subtypes were initially defined based on the unsupervised clustering of gene expression and its correlate with histological, morphological, phenotypic and clinical features already known. Later, a 50-gene signature, PAM50, was defined in order to identify the biological subtype of a given sample within the clinical setting. The PAM50 signature was obtained by the use of unsupervised statistical methods, and therefore no limitation was set on the biological relevance (or lack of) of the selected genes beyond its predictive capacity. An open question that remains is what are the regulatory elements that drive the various expression behaviors of this set of genes in the different molecular subtypes. This question becomes more relevant as the measurement of more biological layers of regulation becomes accessible. In this work, we analyzed the gene expression regulation of the 50 genes in the PAM50 signature, in terms of (a) gene co-expression, (b) transcription factors, (c) micro-RNAs, and (d) methylation. Using data from the Cancer Genome Atlas (TCGA) for the Luminal A and B, Basal, and HER2-enriched molecular subtypes as well as normal tumor adjacent tissue, we identified predictors for gene expression through the use of an elastic net model. We compare and contrast the sets of identified regulators for the gene signature in each molecular subtype, and systematically compare them to current literature. We also identified a unique set of predictors for the expression of genes in the PAM50 signature associated with each of the molecular subtypes. Most selected predictors are exclusive for a PAM50 gene and predictors are not shared across subtypes. There are only 13 coding transcripts and 2 miRNAs selected for the four subtypes. MiR-21 and miR-10b connect almost all the PAM50 genes in all the subtypes and normal tissue, but do it in an exclusive manner, suggesting a cancer switch from miR-10b coordination in normal tissue to miR-21. The PAM50 gene sets of selected predictors that enrich for a function across subtypes, support that different regulatory molecular mechanisms are taking place. With this study we aim to a wider understanding of the regulatory mechanisms that differentiate the expression of the PAM50 signature, which in turn could perhaps help understand the molecular basis of the differences between the molecular subtypes.
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Affiliation(s)
- Soledad Ochoa
- Computational Genomics Division, National Institute of Genomic Medicine, Mexico City, Mexico.,Graduate Program in Biomedical Sciences, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Guillermo de Anda-Jáuregui
- Computational Genomics Division, National Institute of Genomic Medicine, Mexico City, Mexico.,Cátedras Conacyt para Jóvenes Investigadores', National Council on Science and Technology, Mexico City, Mexico
| | - Enrique Hernández-Lemus
- Computational Genomics Division, National Institute of Genomic Medicine, Mexico City, Mexico.,Center for Complexity Sciences, Universidad Nacional Autónoma de México, Mexico City, Mexico
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28
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Sharma J, Krupenko SA. Folate pathways mediating the effects of ethanol in tumorigenesis. Chem Biol Interact 2020; 324:109091. [PMID: 32283069 DOI: 10.1016/j.cbi.2020.109091] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2019] [Accepted: 04/02/2020] [Indexed: 02/08/2023]
Abstract
Folate and alcohol are dietary factors affecting the risk of cancer development in humans. The interaction between folate status and alcohol consumption in carcinogenesis involves multiple mechanisms. Alcoholism is typically associated with folate deficiency due to reduced dietary folate intake. Heavy alcohol consumption also decreases folate absorption, enhances urinary folate excretion and inhibits enzymes pivotal for one-carbon metabolism. While folate metabolism is involved in several key biochemical pathways, aberrant DNA methylation, due to the deficiency of methyl donors, is considered as a common downstream target of the folate-mediated effects of ethanol. The negative effects of low intakes of nutrients that provide dietary methyl groups, with high intakes of alcohol are additive in general. For example, low methionine, low-folate diets coupled with alcohol consumption could increase the risk for colorectal cancer in men. To counteract the negative effects of alcohol consumption, increased intake of nutrients, such as folate, providing dietary methyl groups is generally recommended. Here mechanisms involving dietary folate and folate metabolism in cancer disease, as well as links between these mechanisms and alcohol effects, are discussed. These mechanisms include direct effects on folate pathways and indirect mediation by oxidative stress, hypoxia, and microRNAs.
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Affiliation(s)
- Jaspreet Sharma
- Nutrition Research Institute and Department of Nutrition, University of North Carolina, Chapel Hill, USA
| | - Sergey A Krupenko
- Nutrition Research Institute and Department of Nutrition, University of North Carolina, Chapel Hill, USA; Department of Nutrition, University of North Carolina, Chapel Hill, USA.
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29
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Parrizas M, Mundet X, Castaño C, Canivell S, Cos X, Brugnara L, Giráldez-García C, Regidor E, Mata-Cases M, Franch-Nadal J, Novials A. miR-10b and miR-223-3p in serum microvesicles signal progression from prediabetes to type 2 diabetes. J Endocrinol Invest 2020; 43:451-459. [PMID: 31721085 DOI: 10.1007/s40618-019-01129-z] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/08/2019] [Accepted: 10/03/2019] [Indexed: 12/21/2022]
Abstract
PURPOSE Type 2 diabetes frequently remains undiagnosed for years, whereas early detection of affected individuals would facilitate the implementation of timely and cost-effective therapies, hence decreasing morbidity. With the intention of identifying novel diagnostic biomarkers, we characterized the miRNA profile of microvesicles isolated from retroactive serum samples of normoglycemic individuals and two groups of subjects with prediabetes that in the following 4 years either progressed to overt diabetes or remained stable. METHODS We profiled miRNAs in serum microvesicles of a selected group of control and prediabetic individuals participating in the PREDAPS cohort study. Half of the subjects with prediabetes were diagnosed with diabetes during the 4 years of follow-up, while the glycemic status of the other half remained unchanged. RESULTS We identified two miRNAs, miR-10b and miR-223-3p, which target components of the insulin signaling pathway and whose ratio discriminates between these two subgroups of prediabetic individuals at a stage at which other features, including glycemia, are less proficient at separating them. In global, the profile of miRNAs in microvesicles of prediabetic subjects primed to progress to overt diabetes was more similar to that of diabetic patients than the profile of prediabetic subjects who did not progress. CONCLUSION We have identified a miRNA signature in serum microvesicles that can be used as a new screening biomarker to identify subjects with prediabetes at high risk of developing diabetes, hence allowing the implementation of earlier, and probably more effective, therapeutic interventions.
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Affiliation(s)
- M Parrizas
- Spanish Biomedical Research Center in Diabetes and Associated Metabolic Disorders (CIBERDEM), Barcelona, Spain
- Pathogenesis and Prevention of Diabetes Laboratory, August Pi i Sunyer Biomedical Research Institute (IDIBAPS), Rosselló 149-153, 08036, Barcelona, Spain
| | - X Mundet
- redGDPS Foundation, Madrid, Spain
- DAP-Cat Group, Research Support Unit, University Institute for Research in Primary Care Jordi Gol (IDIAPJGol), Gran Via de les Corts Catalanes, 587, 08007, Barcelona, Spain
- Autonomous University of Barcelona, Barcelona, Spain
| | - C Castaño
- Spanish Biomedical Research Center in Diabetes and Associated Metabolic Disorders (CIBERDEM), Barcelona, Spain
- Pathogenesis and Prevention of Diabetes Laboratory, August Pi i Sunyer Biomedical Research Institute (IDIBAPS), Rosselló 149-153, 08036, Barcelona, Spain
| | - S Canivell
- DAP-Cat Group, Research Support Unit, University Institute for Research in Primary Care Jordi Gol (IDIAPJGol), Gran Via de les Corts Catalanes, 587, 08007, Barcelona, Spain
- Primary Health Care Center Sant Martí de Provençals, Catalan Health Institute, Barcelona, Spain
- Department of Internal Medicine, Health Sciences Research Institute and University Hospital Germans Trias i Pujol, Badalona, Barcelona, Spain
| | - X Cos
- DAP-Cat Group, Research Support Unit, University Institute for Research in Primary Care Jordi Gol (IDIAPJGol), Gran Via de les Corts Catalanes, 587, 08007, Barcelona, Spain
- Primary Health Care Center Sant Martí de Provençals, Catalan Health Institute, Barcelona, Spain
| | - L Brugnara
- Spanish Biomedical Research Center in Diabetes and Associated Metabolic Disorders (CIBERDEM), Barcelona, Spain
- Pathogenesis and Prevention of Diabetes Laboratory, August Pi i Sunyer Biomedical Research Institute (IDIBAPS), Rosselló 149-153, 08036, Barcelona, Spain
| | - C Giráldez-García
- redGDPS Foundation, Madrid, Spain
- Preventive Medicine Service, University Hospital Infanta Elena, Madrid, Spain
- Preventive Medicine, Public Health and History of Science Department, Complutense University of Madrid, Madrid, Spain
| | - E Regidor
- redGDPS Foundation, Madrid, Spain
- Preventive Medicine, Public Health and History of Science Department, Complutense University of Madrid, Madrid, Spain
- Epidemiology and Public Health Networking Biomedical Research Centre (CIBERESP), Madrid, Spain
- Health Research Institute, Hospital Clínico San Carlos (IdISSC), Madrid, Spain
| | - M Mata-Cases
- Spanish Biomedical Research Center in Diabetes and Associated Metabolic Disorders (CIBERDEM), Barcelona, Spain
- redGDPS Foundation, Madrid, Spain
- DAP-Cat Group, Research Support Unit, University Institute for Research in Primary Care Jordi Gol (IDIAPJGol), Gran Via de les Corts Catalanes, 587, 08007, Barcelona, Spain
- Primary Health Care Center La Mina, Catalan Health Institute, Sant Adrià De Besòs, Barcelona, Spain
| | - J Franch-Nadal
- Spanish Biomedical Research Center in Diabetes and Associated Metabolic Disorders (CIBERDEM), Barcelona, Spain.
- redGDPS Foundation, Madrid, Spain.
- DAP-Cat Group, Research Support Unit, University Institute for Research in Primary Care Jordi Gol (IDIAPJGol), Gran Via de les Corts Catalanes, 587, 08007, Barcelona, Spain.
- Department of Medicine, University of Barcelona, Barcelona, Spain.
| | - A Novials
- Spanish Biomedical Research Center in Diabetes and Associated Metabolic Disorders (CIBERDEM), Barcelona, Spain.
- Pathogenesis and Prevention of Diabetes Laboratory, August Pi i Sunyer Biomedical Research Institute (IDIBAPS), Rosselló 149-153, 08036, Barcelona, Spain.
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Suppression of miR-10a-5p in bone marrow mesenchymal stem cells enhances the therapeutic effect on spinal cord injury via BDNF. Neurosci Lett 2019; 714:134562. [PMID: 31626878 DOI: 10.1016/j.neulet.2019.134562] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2019] [Revised: 09/28/2019] [Accepted: 10/14/2019] [Indexed: 01/09/2023]
Abstract
BACKGROUNDS/AIMS Brain-derived neurotrophic factor (BDNF) plays a primary role in the maturation, proliferation, and differentiation of neuronal cells, can induce bone-marrow-derived mesenchymal stem cells (MSCs) to differentiate into nerve cells. This study aims to explore whether regulation of BDNF through microRNAs (miRNAs) in MSCs may further enhance the therapeutic effect on spinal cord injury (SCI). METHODS Bioinformatics analyses were done to predict miRNAs that target BDNF in MSCs. Dual-luciferase reporter gene assays were performed to verify the target relationship between microRNA and BDNF. We examined the mRNA and protein levels of BDNF in MSCs by RT-qPCR and Western blot, respectively. CCK 8 assay was chosen to assess cell viability. MSCs were transduced with miR-10a-5p-ASO, which were transplanted into rats that underwent SCI. The tissue integrity percentage, cavity volume, and Basso-Beattie-Bresnahan (BBB) scale were assessed. Neurofilament (NF) was detected using immunohistochemistry. Histological features of spinal cord tissues examined following HE staining. RESULTS MiR-10a-5p inhibited protein translation of BDNF, through binding to the 3'-UTR of the BDNF. MSCs transduced with MiR-10a-5p-ASO further increased the tissue integrity percentage, decreased cavity volume, and enhanced the recovery of BBB score in SCI model rats, compared to control MSCs. CONCLUSION Upregulation of BDNF by miR-10a-5p suppression in MSCs further improve the therapeutic potential of MSCs in treating SCI in rats.
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Diana A, Gaido G, Murtas D. MicroRNA Signature in Human Normal and Tumoral Neural Stem Cells. Int J Mol Sci 2019; 20:ijms20174123. [PMID: 31450858 PMCID: PMC6747235 DOI: 10.3390/ijms20174123] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2019] [Revised: 08/16/2019] [Accepted: 08/20/2019] [Indexed: 12/11/2022] Open
Abstract
MicroRNAs, also called miRNAs or simply miR-, represent a unique class of non-coding RNAs that have gained exponential interest during recent years because of their determinant involvement in regulating the expression of several genes. Despite the increasing number of mature miRNAs recognized in the human species, only a limited proportion is engaged in the ontogeny of the central nervous system (CNS). miRNAs also play a pivotal role during the transition of normal neural stem cells (NSCs) into tumor-forming NSCs. More specifically, extensive studies have identified some shared miRNAs between NSCs and neural cancer stem cells (CSCs), namely miR-7, -124, -125, -181 and miR-9, -10, -130. In the context of NSCs, miRNAs are intercalated from embryonic stages throughout the differentiation pathway in order to achieve mature neuronal lineages. Within CSCs, under a different cellular context, miRNAs perform tumor suppressive or oncogenic functions that govern the homeostasis of brain tumors. This review will draw attention to the most characterizing studies dealing with miRNAs engaged in neurogenesis and in the tumoral neural stem cell context, offering the reader insight into the power of next generation miRNA-targeted therapies against brain malignances.
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Affiliation(s)
- Andrea Diana
- Department of Biomedical Sciences, University of Cagliari, 09042 Monserrato (Cagliari), Italy.
| | - Giuseppe Gaido
- Department of Surgery, Cottolengo Mission Hospital Charia, 60200 Meru, Kenya
| | - Daniela Murtas
- Department of Biomedical Sciences, University of Cagliari, 09042 Monserrato (Cagliari), Italy.
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Datar I, Kalpana G, Choi J, Basuroy T, Trumbly R, Chaitanya Arudra SK, McPhee MD, de la Serna I, Yeung KC. Critical role of miR-10b in B-RafV600E dependent anchorage independent growth and invasion of melanoma cells. PLoS One 2019; 14:e0204387. [PMID: 30995246 PMCID: PMC6469749 DOI: 10.1371/journal.pone.0204387] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2018] [Accepted: 03/19/2019] [Indexed: 02/06/2023] Open
Abstract
Recent high-throughput-sequencing of cancer genomes has identified oncogenic mutations in the B-Raf genetic locus as one of the critical events in melanomagenesis. B-Raf encodes a serine/threonine kinase that regulates the MAPK/ERK kinase (MEK) and extracellular signal-regulated kinase (ERK) protein kinase cascade. In normal cells, the activity of B-Raf is tightly regulated and is required for cell growth and survival. B-Raf gain-of-function mutations in melanoma frequently lead to unrestrained growth, enhanced cell invasion and increased viability of cancer cells. Although it is clear that the invasive phenotypes of B-Raf mutated melanoma cells are stringently dependent on B-Raf-MEK-ERK activation, the downstream effector targets that are required for oncogenic B-Raf-mediated melanomagenesis are not well defined. miRNAs have regulatory functions towards the expression of genes that are important in carcinogenesis. We observed that miR-10b expression correlates with the presence of the oncogenic B-Raf (B-RafV600E) mutation in melanoma cells. While expression of miR-10b enhances anchorage-independent growth of B-Raf wild-type melanoma cells, miR-10b silencing decreases B-RafV600E cancer cell invasion in vitro. Importantly, the expression of miR-10b is required for B-RafV600E-mediated anchorage independent growth and invasion of melanoma cells in vitro. Taken together our results suggest that miR-10b is an important mediator of oncogenic B-RafV600E activity in melanoma.
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Affiliation(s)
- Ila Datar
- Case Comprehensive Cancer Center, Case Western Reserve University, Cleveland, OH, United States of America
| | - Gardiyawasam Kalpana
- Department of Cancer Biology, College of Medicine and Life Sciences, University of Toledo, Health Science Campus, Toledo, OH, United States of America
| | - Jungmin Choi
- Department of Genetics, Yale School of Medicine, New Haven, CT, United States of America
| | - Tupa Basuroy
- Department of Cancer Biology, College of Medicine and Life Sciences, University of Toledo, Health Science Campus, Toledo, OH, United States of America
| | - Robert Trumbly
- Department of Cancer Biology, College of Medicine and Life Sciences, University of Toledo, Health Science Campus, Toledo, OH, United States of America
| | | | | | - Ivana de la Serna
- Department of Cancer Biology, College of Medicine and Life Sciences, University of Toledo, Health Science Campus, Toledo, OH, United States of America
| | - Kam C. Yeung
- Department of Cancer Biology, College of Medicine and Life Sciences, University of Toledo, Health Science Campus, Toledo, OH, United States of America
- * E-mail:
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Macchiaroli N, Cucher M, Kamenetzky L, Yones C, Bugnon L, Berriman M, Olson PD, Rosenzvit MC. Identification and expression profiling of microRNAs in Hymenolepis. Int J Parasitol 2019; 49:211-223. [PMID: 30677390 DOI: 10.1016/j.ijpara.2018.07.005] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2018] [Revised: 07/20/2018] [Accepted: 07/23/2018] [Indexed: 02/08/2023]
Abstract
Tapeworms (cestodes) of the genus Hymenolepis are the causative agents of hymenolepiasis, a neglected zoonotic disease. Hymenolepis nana is the most prevalent human tapeworm, especially affecting children. The genomes of Hymenolepis microstoma and H. nana have been recently sequenced and assembled. MicroRNAs (miRNAs), a class of small non-coding RNAs, are principle regulators of gene expression at the post-transcriptional level and are involved in many different biological processes. In previous work, we experimentally identified miRNA genes in the cestodes Echinococcus, Taenia and Mesocestoides. However, current knowledge about miRNAs in Hymenolepis is limited. In this work we described for the first known time the expression profile of the miRNA complement in H. microstoma, and discovered miRNAs in H. nana. We found a reduced complement of 37 evolutionarily conserved miRNAs, putatively reflecting their low morphological complexity and parasitic lifestyle. We found high expression of a few miRNAs in the larval stage of H. microstoma that are conserved in other cestodes, suggesting that these miRNAs may have important roles in development, survival and for host-parasite interplay. We performed a comparative analysis of the identified miRNAs across the Cestoda and showed that most of the miRNAs in Hymenolepis are located in intergenic regions, implying that they are independently transcribed. We found a Hymenolepis-specific cluster composed of three members of the mir-36 family. Also, we found that one of the neighboring genes of mir-10 was a Hox gene as in most bilaterial species. This study provides a valuable resource for further experimental research in cestode biology that might lead to improved detection and control of these neglected parasites. The comprehensive identification and expression analysis of Hymenolepis miRNAs can help to identify novel biomarkers for diagnosis and/or novel therapeutic targets for the control of hymenolepiasis.
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Affiliation(s)
- Natalia Macchiaroli
- Instituto de Investigaciones en Microbiología y Parasitología Médicas (IMPaM), Facultad de Medicina, Universidad de Buenos Aires (UBA)-Consejo Nacional de Investigaciones Científicas y Tecnológicas (CONICET), Buenos Aires, Argentina
| | - Marcela Cucher
- Instituto de Investigaciones en Microbiología y Parasitología Médicas (IMPaM), Facultad de Medicina, Universidad de Buenos Aires (UBA)-Consejo Nacional de Investigaciones Científicas y Tecnológicas (CONICET), Buenos Aires, Argentina
| | - Laura Kamenetzky
- Instituto de Investigaciones en Microbiología y Parasitología Médicas (IMPaM), Facultad de Medicina, Universidad de Buenos Aires (UBA)-Consejo Nacional de Investigaciones Científicas y Tecnológicas (CONICET), Buenos Aires, Argentina
| | - Cristian Yones
- Research Institute for Signals, Systems and Computational Intelligence, (sinc(i)), FICH-UNL-Consejo Nacional de Investigaciones Científicas y Tecnológicas (CONICET), Santa Fe, Argentina
| | - Leandro Bugnon
- Research Institute for Signals, Systems and Computational Intelligence, (sinc(i)), FICH-UNL-Consejo Nacional de Investigaciones Científicas y Tecnológicas (CONICET), Santa Fe, Argentina
| | - Matt Berriman
- Parasite Genomics Group, Wellcome Trust Sanger Institute, Hinxton, UK
| | - Peter D Olson
- Department of Life Sciences, The Natural History Museum, London, UK
| | - Mara Cecilia Rosenzvit
- Instituto de Investigaciones en Microbiología y Parasitología Médicas (IMPaM), Facultad de Medicina, Universidad de Buenos Aires (UBA)-Consejo Nacional de Investigaciones Científicas y Tecnológicas (CONICET), Buenos Aires, Argentina.
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A new level of complexity in parasite-host interaction: The role of extracellular vesicles. ADVANCES IN PARASITOLOGY 2019; 104:39-112. [PMID: 31030771 DOI: 10.1016/bs.apar.2019.02.003] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Humans and animals have co-existed with parasites in a battle of constant adaptation to one another. It is becoming increasingly clear that extracellular vesicles (EVs) play important roles in this co-existence and pathology. This chapter reviews the current research on EVs released by protozoa, nematodes, trematodes, and cestodes with a special focus on EVs in parasite life cycles. The environmental changes experienced by the parasite during its life cycle is associated with distinct changes in EV release and content. The function of these EV seems to have a significant influence on parasite pathology and survival in the host by concomitantly modulating host immune responses and triggering parasite differentiation. The role of EVs in communication between the parasites and the host adds a new level of complexity in our understanding of parasite biology, which may be a key to further understand the complexity behind host-parasite interactions and communication. This increased understanding can, in turn, open up new avenues for vaccine, diagnostic, and therapeutic development for a wide variety of diseases such as parasite infection, cancers, and immunological disorders.
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Ma Y, Feng S, Wang X, Qazi IH, Long K, Luo Y, Li G, Ning C, Wang Y, Hu S, Xiao J, Li X, Lan D, Hu Y, Tang Q, Ma J, Jin L, Jiang A, Li M. Exploration of exosomal microRNA expression profiles in pigeon 'Milk' during the lactation period. BMC Genomics 2018; 19:828. [PMID: 30458711 PMCID: PMC6245878 DOI: 10.1186/s12864-018-5201-0] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2017] [Accepted: 10/25/2018] [Indexed: 11/10/2022] Open
Abstract
Background Pigeon crop has the unique ability to produce a nutrient rich substance termed pigeon ‘milk’ (PM), which has functional resemblance with the mammalian milk. Previous researches have demonstrated that a large number of exosomes and exosomal miRNAs exist in mammalian milk, and many of them are associated with immunity, growth and development. However, to date, little is known about the exosomes and exosomal miRNAs in PM. Results In this study, we isolated the exosomes from PM and used small RNA sequencing to investigate the distribution and expression profiles of exosomal miRNAs. A total of 301 mature miRNAs including 248 conserved and 53 novel miRNAs were identified in five lactation stages i.e. 1d, 5d, 10d, 15d, and 20d. From these, four top 10 conserved miRNAs (cli-miR-21-5p, cli-miR-148a-3p, cli-miR-10a-5p and cli-miR-26a-5p) were co-expressed in all five stages. We speculate that these miRNAs may have important role in the biosynthesis and metabolism of PM. Moreover, similar to the mammalian milk, a significant proportion of immune and growth-related miRNAs were also present and enriched in PM exosomes. Furthermore, we also identified 41 orthologous miRNAs group (giving rise to 81 mature miRNA) commonly shared with PM, human, bovine and porcine breast milk. Additionally, functional enrichment analysis revealed the role of exosomal miRNAs in organ development and in growth-related pathways including the MAPK, Wnt and insulin pathways. Conclusions To sum-up, this comprehensive analysis will contribute to a better understanding of the underlying functions and regulatory mechanisms of PM in squabs. Electronic supplementary material The online version of this article (10.1186/s12864-018-5201-0) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Yao Ma
- Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
| | - Siyuan Feng
- Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
| | - Xun Wang
- Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China.
| | - Izhar Hyder Qazi
- Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China.,Department of Veterinary Anatomy and Histology, Faculty of Bio-Sciences, Shaheed Benazir Bhutto University of Veterinary & Animal Sciences, Sakrand, Sindh, 67210, Pakistan
| | - Keren Long
- Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
| | - Yi Luo
- Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
| | - Guojun Li
- Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
| | - Chunyou Ning
- Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
| | - Yixin Wang
- Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
| | - Silu Hu
- Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
| | - Juan Xiao
- Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
| | - Xiaokai Li
- Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
| | - Dan Lan
- Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
| | - Yaodong Hu
- Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
| | - Qianzi Tang
- Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
| | - Jideng Ma
- Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
| | - Long Jin
- Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
| | - Anan Jiang
- Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
| | - Mingzhou Li
- Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China.
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Dumas PY, Mansier O, Prouzet-Mauleon V, Koya J, Villacreces A, Brunet de la Grange P, Luque Paz D, Bidet A, Pasquet JM, Praloran V, Salin F, Kurokawa M, Mahon FX, Cardinaud B, Lippert E. MiR-10a and HOXB4 are overexpressed in atypical myeloproliferative neoplasms. BMC Cancer 2018; 18:1098. [PMID: 30419846 PMCID: PMC6233495 DOI: 10.1186/s12885-018-4993-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2017] [Accepted: 10/24/2018] [Indexed: 11/19/2022] Open
Abstract
Background Atypical Myeloproliferative Neoplasms (aMPN) share characteristics of MPN and Myelodysplastic Syndromes. Although abnormalities in cytokine signaling are common in MPN, the pathophysiology of atypical MPN still remains elusive. Since deregulation of microRNAs is involved in the biology of various cancers, we studied the miRNome of aMPN patients. Methods MiRNome and mutations in epigenetic regulator genes ASXL1, TET2, DNMT3A, EZH2 and IDH1/2 were explored in aMPN patients. Epigenetic regulation of miR-10a and HOXB4 expression was investigated by treating hematopoietic cell lines with 5-aza-2’deoxycytidine, valproic acid and retinoic acid. Functional effects of miR-10a overexpression on cell proliferation, differentiation and self-renewal were studied by transducing CD34+ cells with lentiviral vectors encoding the pri-miR-10a precursor. Results MiR-10a was identified as the most significantly up-regulated microRNA in aMPN. MiR-10a expression correlated with that of HOXB4, sitting in the same genomic locus. The transcription of these two genes was increased by DNA demethylation and histone acetylation, both necessary for optimal expression induction by retinoic acid. Moreover, miR-10a and HOXB4 overexpression seemed associated with DNMT3A mutation in hematological malignancies. However, overexpression of miR-10a had no effect on proliferation, differentiation or self-renewal of normal hematopoietic progenitors. Conclusions MiR-10a and HOXB4 are overexpressed in aMPN. This overexpression seems to be the result of abnormalities in epigenetic regulation mechanisms. Our data suggest that miR-10a could represent a simple marker of transcription at this genomic locus including HOXB4, widely recognized as involved in stem cell expansion. Electronic supplementary material The online version of this article (10.1186/s12885-018-4993-2) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Pierre-Yves Dumas
- CHU de Bordeaux, Hématologie Clinique et Thérapie Cellulaire, F-33000, Bordeaux, France.,INSERM U1035, Université de Bordeaux, Bordeaux, France
| | - Olivier Mansier
- INSERM U1218, Université de Bordeaux, Bordeaux, France.,CHU de Bordeaux, Laboratoire d'Hématologie, F-33000, Bordeaux, France
| | | | - Junji Koya
- Department of Hematology and Oncology, Graduate School of Medicine, University of Tokyo, 7-3-1, Hongo, bunkyo-ku, Tokyo, 113-8655, Japan
| | | | - Philippe Brunet de la Grange
- Etablissement Français du Sang - Aquitaine Limousin, Laboratoire R&D d'Ingénierie Cellulaire, Université de Bordeaux, Bordeaux, France
| | | | - Audrey Bidet
- CHU de Bordeaux, Laboratoire d'Hématologie, F-33000, Bordeaux, France
| | | | - Vincent Praloran
- INSERM U1035, Université de Bordeaux, Bordeaux, France.,CHU de Bordeaux, Laboratoire d'Hématologie, F-33000, Bordeaux, France
| | - Franck Salin
- INRA, Plateforme Génome Transcriptome de Bordeaux, BIOGECO, UMR 1202, F-33610, Cestas, France
| | - Mineo Kurokawa
- Department of Hematology and Oncology, Graduate School of Medicine, University of Tokyo, 7-3-1, Hongo, bunkyo-ku, Tokyo, 113-8655, Japan
| | - François-Xavier Mahon
- INSERM U1218, Université de Bordeaux, Bordeaux, France.,Institut Bergonié, Bordeaux, France
| | - Bruno Cardinaud
- INSERM U1218, Université de Bordeaux, Bordeaux, France.,Bordeaux Institut National Polytechnique, F-33000, Bordeaux, France
| | - Eric Lippert
- INSERM U1035, Université de Bordeaux, Bordeaux, France. .,CHU de Bordeaux, Laboratoire d'Hématologie, F-33000, Bordeaux, France. .,CHRU de Brest, Service d'Hématologie Biologique et INSERM U1078, Université de Bretagne Occidentale, Brest, France.
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Gao L, Yang X, Zhang H, Yu M, Long J, Yang T. Inhibition of miR-10a-5p suppresses cholangiocarcinoma cell growth through downregulation of Akt pathway. Onco Targets Ther 2018; 11:6981-6994. [PMID: 30410355 PMCID: PMC6199228 DOI: 10.2147/ott.s182225] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Backgrounds Cholangiocarcinoma (CCA) is epithelial cell malignancy with very poor prognosis. A lot of patients were diagnosed at advanced stage of CCA and no risk factors were identified. There are limited treatment options available for the management of CCA patients. It is urgent to develop effective targeted therapies for the treatment of CCA. miRNAs are small noncoding RNAs that negatively regulate the target genes. In this study, we investigated the role and mechanism of miR-10a-5p in CCA. Methods Human CCA cell lines (CCLP1 and SG-231) were transfected with miR-10a-5p mimic or miR-10a-5p inhibitor. qRT-PCR was performed to detect the miR-10a-5p level. Proliferation, colony formation, and apoptosis were analyzed. Luciferase reporter assay was used to explore the targeting of miR-10a-5p on PTEN. For in vivo tumorigenesis assay, CCLP1 cells with stable knockdown of miR-10a-5p or control CCLP1 cells were injected subcutaneously into the flank of the SCID mice and animals were monitored for tumor growth. Results miR-10a-5p expression was significantly upregulated in human CCA cell lines (CCLP1 and SG-231). Inhibition of miR-10a-5p significantly suppressed the proliferation and induced apoptosis in CCLP1 and SG-231. PTEN is a direct target of miR-10a-5p in CCA cells. Conclusion Inhibition of miR-10a-5p can decrease CCA cells growth by downregulation of Akt pathway. These results indicate that miR-10a-5p may serve as a potential target for the treatment of CCA and help to develop effective therapeutic strategies.
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Affiliation(s)
- Lili Gao
- Center for Medical Research and Innovation,
| | | | | | - Minghua Yu
- Department of Medical Oncology, Shanghai Pudong Hospital, Fudan University Pudong Medical Center, Shanghai 201399, People's Republic of China
| | - Jianting Long
- Department of Medical Oncology, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou 510080, Guangdong Province, People's Republic of China,
| | - Tao Yang
- Center for Medical Research and Innovation,
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Balatti V, Oghumu S, Bottoni A, Maharry K, Cascione L, Fadda P, Parwani A, Croce C, Iwenofu OH. MicroRNA Profiling of Salivary Duct Carcinoma Versus Her2/Neu Overexpressing Breast Carcinoma Identify miR-10a as a Putative Breast Related Oncogene. Head Neck Pathol 2018; 13:344-354. [PMID: 30259272 PMCID: PMC6684709 DOI: 10.1007/s12105-018-0971-x] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/26/2018] [Accepted: 09/20/2018] [Indexed: 12/19/2022]
Abstract
Salivary duct carcinomas (SDC) and Her2/Neu3-overexpressing invasive breast carcinomas (HNPIBC/IBC) are histologically indistinguishable. We investigated whether common histopathologic and immunophenotypic features of SDC and IBC are mirrored by a similar microRNA (miRNA) profile. MiRNA profiling of 5 SDCs, 6 IBCs Her2/Neu3+, and 5 high-grade ductal breast carcinoma in situ (DCIS) was performed by NanoString platform. Selected miRNAs and HOXA1 gene were validated by RT-PCR. We observed similar miRNA expression profiles between IBC and SDC with the exception of 2 miRNAs, miR-10a and miR-142-3p, which were higher in IBC tumors. DCIS tumors displayed increased expression of miR-10a, miR-99a, miR-331-3p and miR-335, and decreased expression of miR-15a, miR-16 and miR-19b compared to SDC. The normal salivary gland and breast tissues also showed similar expression profiles. Interestingly, miR-10a was selectively increased in both IBC and normal breast tissue compared to SDC and normal salivary gland tissue. Moreover, our NanoString and RT-PCR data confirmed that miR-10a was upregulated in IBC and DCIS compared to SDC. Finally, we show downregulation of HOXA1, a miR-10 target, in IBC tumors compared to normal breast tissue. Taken together, our data demonstrates that, based on miRNA profiling, SDC is closely related to HNPIBC. Our results also suggest that miR-10a is differentially expressed in IBC compared to SDC and may have potential utility as a diagnostic biomarker in synchronous or metachronous malignant epithelial malignancies involving both organs. In addition, miR-10a could be playing an important role as a mammary-specific oncogene, involved in breast cancer initiation (DCIS) and progression (IBC), through mechanisms that include modulation of HOXA1 gene expression.
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Affiliation(s)
- Veronica Balatti
- Department of Molecular Virology, Immunology and Medical Genetics, Comprehensive Cancer Center, The Ohio State University, Columbus, USA
| | - Steve Oghumu
- Department of Pathology and Laboratory Medicine, The Ohio State University, Columbus, USA
| | - Arianna Bottoni
- Department of Molecular Virology, Immunology and Medical Genetics, Comprehensive Cancer Center, The Ohio State University, Columbus, USA
| | - Kati Maharry
- Department of Epidemiology, College of Public Health, The Ohio State University, Columbus, USA
| | - Luciano Cascione
- Department of Molecular Virology, Immunology and Medical Genetics, Comprehensive Cancer Center, The Ohio State University, Columbus, USA ,Institute of Oncology Research, Bellinzona, Switzerland
| | - Paolo Fadda
- Department of Molecular Virology, Immunology and Medical Genetics, Comprehensive Cancer Center, The Ohio State University, Columbus, USA
| | - Anil Parwani
- Department of Pathology and Laboratory Medicine, The Ohio State University, Columbus, USA
| | - Carlo Croce
- Department of Molecular Virology, Immunology and Medical Genetics, Comprehensive Cancer Center, The Ohio State University, Columbus, USA
| | - O. Hans Iwenofu
- Department of Pathology and Laboratory Medicine, The Ohio State University, Columbus, USA
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Xu H, Li Y, Han B, Li Z, Wang B, Jiang P, Zhang J, Ma W, Zhou D, Li X, Ye X. Anti-breast-Cancer Activity Exerted by β-Sitosterol-d-glucoside from Sweet Potato via Upregulation of MicroRNA-10a and via the PI3K-Akt Signaling Pathway. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2018; 66:9704-9718. [PMID: 30160115 DOI: 10.1021/acs.jafc.8b03305] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Breast cancer (BC) is a prominent source of cancer mortality in women throughout the world. β-Sitosterol-d-glucoside (β-SDG), a newly isolated phytosterol from sweet potato, possibly displays potent anticancer activity. However, the probable anticancer mechanisms involved are still unclear. This study sought to study how β-SDG from sweet potato affects two BC cell lines (MCF7 and MDA-MB-231) and nude mice bearing MCF7-induced tumors. In addition, we assessed how β-SDG affects tumor suppressor miR-10a and PI3K-Akt signaling in BC cells. Cell viability and proliferation were determined via MTT and colony-formation assays, and apoptosis was quantified by Hoechst staining and flow cytometry. In addition, miR-10a expression and apoptosis-related protein levels were measured. Our study indicated that β-SDG exhibited cytotoxic activities on MCF7 and MDA-MB-231 cells via inducing apoptosis and activating caspase proteases in these cells. Furthermore, the experimental results in nude mice bearing MCF7-induced tumors demonstrated that oral β-SDG administration at medium (60 mg/kg) or high (120 mg/kg) doses was sufficient to substantially impair the growth of tumors and to decrease the levels of CEA, CA125, and CA153 by 64.71, 74.64, and 85.32%, respectively, relative to those of the controls ( P < 0.01). β-SDG was further found to regulate the expression of PI3K, p-Akt, Bcl-2-family members, and other factors involved in the PI3K-Akt-mediated mitochondrial signaling pathway via the tumor suppressor miR-10a. These findings indicated that β-SDG suppresses tumor growth by upregulating miR-10a expression and inactivating the PI3K-Akt signaling pathway. Furthermore, β-SDG could be developed as a potential therapeutic agent against MCF7-cell-related BC.
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Affiliation(s)
- Heshan Xu
- Chongqing Engineering Research Centre for Sweet Potato, School of Life Sciences , Southwest University , Chongqing 400715 , China
| | - Yuanfeng Li
- Chongqing Engineering Research Centre for Sweet Potato, School of Life Sciences , Southwest University , Chongqing 400715 , China
| | - Bing Han
- School of Pharmaceutical Sciences , Southwest University , Chongqing 400716 , China
| | - Zhaoxing Li
- School of Pharmaceutical Sciences , Southwest University , Chongqing 400716 , China
- McLean Hospital , Harvard Medical School , Belmont , Massachusetts 02478 , United States
| | - Bin Wang
- Chongqing Engineering Research Centre for Sweet Potato, School of Life Sciences , Southwest University , Chongqing 400715 , China
| | - Pu Jiang
- School of Pharmaceutical Sciences , Southwest University , Chongqing 400716 , China
| | - Jian Zhang
- Chongqing Engineering Research Centre for Sweet Potato, School of Life Sciences , Southwest University , Chongqing 400715 , China
| | - Wenyu Ma
- Chongqing Engineering Research Centre for Sweet Potato, School of Life Sciences , Southwest University , Chongqing 400715 , China
| | - Deqi Zhou
- Oncology Department , Chongqing Beibei District Hospital of Traditional Chinese Medicine , Chongqing 400700 , China
| | - Xuegang Li
- School of Pharmaceutical Sciences , Southwest University , Chongqing 400716 , China
| | - Xiaoli Ye
- Chongqing Engineering Research Centre for Sweet Potato, School of Life Sciences , Southwest University , Chongqing 400715 , China
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Romney ALT, Podrabsky JE. Small noncoding RNA profiles along alternative developmental trajectories in an annual killifish. Sci Rep 2018; 8:13364. [PMID: 30190591 PMCID: PMC6127099 DOI: 10.1038/s41598-018-31466-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2018] [Accepted: 08/13/2018] [Indexed: 11/24/2022] Open
Abstract
Embryonic development of Austrofundulus limnaeus can occur along two phenotypic trajectories that are physiologically and biochemically distinct. Phenotype appears to be influenced by maternal provisioning based on the observation that young females produce predominately non-diapausing embryos and older females produce mostly diapausing embryos. Embryonic incubation temperature can override this pattern and alter trajectory. We hypothesized that temperature-induced phenotypic plasticity may be regulated by post-transcriptional modification via noncoding RNAs. As a first step to exploring this possibility, RNA-seq was used to generate transcriptomic profiles of small noncoding RNAs in embryos developing along the two alternative trajectories. We find distinct profiles of mature sequences belonging to the miR-10 family expressed in increasing abundance during development and mature sequences of miR-430 that follow the opposite pattern. Furthermore, miR-430 sequences are enriched in escape trajectory embryos. MiR-430 family members are known to target maternally provisioned mRNAs in zebrafish and may operate similarly in A. limnaeus in the context of normal development, and also by targeting trajectory-specific mRNAs. This expression pattern and function for miR-430 presents a potentially novel model for maternal-embryonic conflict in gene regulation that provides the embryo the ability to override maternal programming in the face of altered environmental conditions.
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Affiliation(s)
- Amie L T Romney
- Department of Biology, Portland State University, P.O. Box 751, Portland, OR, 97207, USA.
- Department of Anatomy, Physiology & Cell Biology, University of California at Davis School of Veterinary Medicine, One Shields Ave, Davis, CA, 95616, USA.
| | - Jason E Podrabsky
- Department of Biology, Portland State University, P.O. Box 751, Portland, OR, 97207, USA.
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Hu J, Lin C, Liu M, Tong Q, Xu S, Wang D, Zhao Y. Analysis of the microRNA transcriptome of Daphnia pulex during aging. Gene 2018; 664:101-110. [PMID: 29684489 DOI: 10.1016/j.gene.2018.04.034] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2017] [Revised: 03/13/2018] [Accepted: 04/12/2018] [Indexed: 01/30/2023]
Abstract
Daphnia pulex is an important food organism that exhibits a particular mode of reproduction known as cyclical parthenogenesis (asexual) and sexual reproduction. Regulation of the aging process by microRNAs (miRNAs) is a research hotspot in miRNA studies. To investigate a possible role of miRNAs in regulating aging and senescence, we used Illumina HiSeq to sequence two miRNA libraries from 1-day-old (1d) and 25-day-old (25d) D. pulex specimens. In total, we obtained 11,218,097 clean reads and 28,569 unique miRNAs from 1d specimens and 11,819,106 clean reads and 44,709 unique miRNAs from 25d specimens. Bioinformatic analyses was used to identify 1335 differentially expressed miRNAs from known miRNAs, including 127 miRNAs that exhibited statistically significant differences (P < 0.01); 92 miRNAs were upregulated and 35 were downregulated. Quantitative real-time (qRT)-PCR experiments were performed for nine miRNAs from five samples (1d, 5d, 10d, 15d, 20d and 25d) during the aging process, and the sequencing and qRT-PCR data were found to be consistent. Ninety-four miRNAs were predicted to correspond to 2014 target genes in known miRNAs with 4032 target gene sites. Sixteen pathways changed significantly (P < 0.05) at different developmental stages, revealing many important principles of the miRNA regulatory aging network of D. pulex. Overall, the difference in miRNA expression profile during aging of D. pulex forms a basis for further studies aimed at understanding the role of miRNAs in regulating aging, reproductive transformation, senescence, and longevity.
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Affiliation(s)
- Jiabao Hu
- School of Marine Sciences, Ningbo University, Ningbo 315211, China
| | - Chongyuan Lin
- School of Marine Sciences, Ningbo University, Ningbo 315211, China
| | - Mengdi Liu
- School of Marine Sciences, Ningbo University, Ningbo 315211, China
| | - Qiaoqiong Tong
- School of Marine Sciences, Ningbo University, Ningbo 315211, China
| | - Shanliang Xu
- School of Marine Sciences, Ningbo University, Ningbo 315211, China
| | - Danli Wang
- School of Marine Sciences, Ningbo University, Ningbo 315211, China.
| | - Yunlong Zhao
- School of Life Science, East China Normal University, Shanghai 200062, China.
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Patel NA, Moss LD, Lee JY, Tajiri N, Acosta S, Hudson C, Parag S, Cooper DR, Borlongan CV, Bickford PC. Long noncoding RNA MALAT1 in exosomes drives regenerative function and modulates inflammation-linked networks following traumatic brain injury. J Neuroinflammation 2018; 15:204. [PMID: 30001722 PMCID: PMC6044101 DOI: 10.1186/s12974-018-1240-3] [Citation(s) in RCA: 133] [Impact Index Per Article: 22.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2018] [Accepted: 06/26/2018] [Indexed: 01/09/2023] Open
Abstract
BACKGROUND Neuroinflammation is a common therapeutic target for traumatic brain injury (TBI) due to its contribution to delayed secondary cell death and has the potential to occur for years after the initial insult. Exosomes from adipose-derived stem cells (hASCs) containing the long noncoding RNA MALAT1 are a novel, cell-free regenerative approach to long-term recovery after traumatic brain injury (TBI) that have the potential to modulate inflammation at the genomic level. The long noncoding RNA MALAT1 has been shown to be an important component of the secretome of hASCs. METHODS We isolated exosomes from hASC containing or depleted of MALAT1. The hASC-derived exosomes were then administered intravenously to rats following a mild controlled cortical impact (CCI). We followed the rats with behavior, in vivo imaging, histology, and RNA sequencing (RNA Seq). RESULTS Using in vivo imaging, we show that exosomes migrate into the spleen within 1 h following administration and enter the brain several hours later following TBI. Significant recovery of function on motor behavior as well as a reduction in cortical brain injury was observed after TBI in rats treated with exosomes. Treatment with either exosomes depleted of MALAT1 or conditioned media depleted of exosomes showed limited regenerative effects, demonstrating the importance of MALAT1 in exosome-mediated recovery. Analysis of the brain and spleen transcriptome using RNA Seq showed MALAT1-dependent modulation of inflammation-related pathways, cell cycle, cell death, and regenerative molecular pathways. Importantly, our data demonstrates that MALAT1 regulates expression of other noncoding RNAs including snoRNAs. CONCLUSION We demonstrate that MALAT1 in hASC-derived exosomes modulates multiple therapeutic targets, including inflammation, and has tremendous therapeutic potential for treatment of TBI.
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Affiliation(s)
- Niketa A. Patel
- 0000 0001 0624 9286grid.281075.9James A Haley Veterans Hospital, Research Service, Tampa, FL USA ,0000 0001 2353 285Xgrid.170693.aDepartment of Molecular Medicine, University of South Florida Morsani College of Medicine, 12901 Bruce B Downs Blvd, Tampa, FL 33612 USA
| | - Lauren Daly Moss
- 0000 0001 2353 285Xgrid.170693.aDepartment of Neurosurgery and Brain Repair, University of South Florida Morsani College of Medicine, Tampa, FL USA
| | - Jea-Young Lee
- 0000 0001 2353 285Xgrid.170693.aDepartment of Neurosurgery and Brain Repair, University of South Florida Morsani College of Medicine, Tampa, FL USA
| | - Naoki Tajiri
- 0000 0001 2353 285Xgrid.170693.aDepartment of Neurosurgery and Brain Repair, University of South Florida Morsani College of Medicine, Tampa, FL USA ,0000 0001 0728 1069grid.260433.0Present address: Department of Neurophysiology & Brain Science, Graduate School of Medical Sciences & Medical School, Nagoya City University, 1 Kawasumi, Mizuho-cho, Mizuho-ku, Nagoya, Aichi 467-8601 Japan
| | - Sandra Acosta
- 0000 0001 2353 285Xgrid.170693.aDepartment of Neurosurgery and Brain Repair, University of South Florida Morsani College of Medicine, Tampa, FL USA
| | - Charles Hudson
- 0000 0001 0624 9286grid.281075.9James A Haley Veterans Hospital, Research Service, Tampa, FL USA
| | - Sajan Parag
- 0000 0001 2353 285Xgrid.170693.aDepartment of Molecular Medicine, University of South Florida Morsani College of Medicine, 12901 Bruce B Downs Blvd, Tampa, FL 33612 USA
| | - Denise R. Cooper
- 0000 0001 0624 9286grid.281075.9James A Haley Veterans Hospital, Research Service, Tampa, FL USA ,0000 0001 2353 285Xgrid.170693.aDepartment of Molecular Medicine, University of South Florida Morsani College of Medicine, 12901 Bruce B Downs Blvd, Tampa, FL 33612 USA
| | - Cesario V. Borlongan
- 0000 0001 2353 285Xgrid.170693.aDepartment of Neurosurgery and Brain Repair, University of South Florida Morsani College of Medicine, Tampa, FL USA ,0000 0001 2353 285Xgrid.170693.aUSF Health Center of Excellence for Aging and Brain Repair MDC-78, 12901 Bruce B Downs, Blvd, Tampa, FL 33612 USA
| | - Paula C. Bickford
- 0000 0001 0624 9286grid.281075.9James A Haley Veterans Hospital, Research Service, Tampa, FL USA ,0000 0001 2353 285Xgrid.170693.aDepartment of Neurosurgery and Brain Repair, University of South Florida Morsani College of Medicine, Tampa, FL USA ,0000 0001 2353 285Xgrid.170693.aUSF Health Center of Excellence for Aging and Brain Repair MDC-78, 12901 Bruce B Downs, Blvd, Tampa, FL 33612 USA
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Affiliation(s)
- Krung Phiwpan
- School of Allied Health Sciences, University of Phayao, Phayao province, Thailand
| | - Xuyu Zhou
- Institute of Microbiology, Chinese Academy of Sciences, Beijing, China; Savaid Medical School, University of Chinese Academy of Sciences, Beijing, 101408, China.
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Hou L, Ji Z, Wang G, Wang J, Chao T, Wang J. Identification and characterization of microRNAs in the intestinal tissues of sheep (Ovis aries). PLoS One 2018; 13:e0193371. [PMID: 29489866 PMCID: PMC5831392 DOI: 10.1371/journal.pone.0193371] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2017] [Accepted: 02/09/2018] [Indexed: 01/21/2023] Open
Abstract
Sheep are small ruminants, and their long intestines exhibit high digestive and absorptive capacity in many different rearing conditions; however, the genetic bases of this characteristic remains unclear. MicroRNAs (miRNAs) play a major role in maintaining both intestinal morphological structure as well as in regulating the physiological functions of this organ. However, no study has reported on the miRNA expression profile in the intestinal tissues of sheep. Here, we analyzed and identified the miRNA expression profile of three different intestinal tissues (i.e., duodenum, cecum, and colon) of sheep (Ovis aries) using high-throughput sequencing and bioinformatic methods. In total, 106 known miRNAs were identified, 458 conserved miRNAs were detected, 192 unannotated novel miRNAs were predicted, and 195 differentially expressed miRNAs were found between the different tissues. Additionally, 3,437 candidate target genes were predicted, and 17 non-redundant significantly enriched GO terms were identified using enrichment analysis. A total of 99 candidate target genes were found to significantly enriched in 4 KEGG biological pathways. A combined regulatory network was constructed based on 92 metabolism-related candidate target genes and 65 differentially expressed miRNAs, among which 7 miRNAs were identified as hub miRNAs. Via these mechanisms, miRNAs may play a role in maintaining intestinal homeostasis and metabolism. This study helps to further explain the mechanisms that underlie differences in tissue morphology and function in three intestinal segments of sheep.
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Affiliation(s)
- Lei Hou
- Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, Shandong Agricultural University, Taian City, Shandong Province, China
| | - Zhibin Ji
- Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, Shandong Agricultural University, Taian City, Shandong Province, China
| | - Guizhi Wang
- Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, Shandong Agricultural University, Taian City, Shandong Province, China
| | - Jin Wang
- Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, Shandong Agricultural University, Taian City, Shandong Province, China
| | - Tianle Chao
- Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, Shandong Agricultural University, Taian City, Shandong Province, China
| | - Jianmin Wang
- Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, Shandong Agricultural University, Taian City, Shandong Province, China
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Zhang H, Zhang L, Sun T. Cohesive Regulation of Neural Progenitor Development by microRNA miR-26, Its Host Gene Ctdsp and Target Gene Emx2 in the Mouse Embryonic Cerebral Cortex. Front Mol Neurosci 2018. [PMID: 29515367 PMCID: PMC5825903 DOI: 10.3389/fnmol.2018.00044] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Proper proliferation and differentiation of neural progenitors (NPs) in the developing cerebral cortex are critical for normal brain formation and function. Emerging evidence has shown the importance of microRNAs (miRNAs) in regulating cortical development and the etiology of neurological disorders. Here we show that miR-26 is co-expressed with its host gene Ctdsp in the mouse embryonic cortex. We demonstrate that similar to its host gene Ctdsp2, miR-26 positively regulates proliferation of NPs through controlling the cell-cycle progression, by using miR-26 overexpression and sponge approaches. On the contrary, miR-26 target gene Emx2 limits expansion of cortical NPs, and promotes transcription of miR-26 host gene Ctdsp. Our study suggests that miR-26, its target Emx2 and its host gene Ctdsp cohesively regulate proliferation of NPs during the mouse cortical development.
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Affiliation(s)
- Haijun Zhang
- Department of Cell and Developmental Biology, Weill Cornell Medical College, Cornell University, New York, NY, United States.,Department of Genetic Medicine, Weill Cornell Medical College, Cornell University, New York, NY, United States
| | - Longbin Zhang
- Center for Precision Medicine, School of Medicine and School of Biomedical Sciences, Huaqiao University, Xiamen, China
| | - Tao Sun
- Department of Cell and Developmental Biology, Weill Cornell Medical College, Cornell University, New York, NY, United States.,Center for Precision Medicine, School of Medicine and School of Biomedical Sciences, Huaqiao University, Xiamen, China
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46
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Zhang J, Yang J, Zhang X, Xu J, Sun Y, Zhang P. MicroRNA-10b expression in breast cancer and its clinical association. PLoS One 2018; 13:e0192509. [PMID: 29408861 PMCID: PMC5800653 DOI: 10.1371/journal.pone.0192509] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2017] [Accepted: 01/24/2018] [Indexed: 01/10/2023] Open
Abstract
MicroRNAs (miRNAs) are short non-coding RNA molecules that play a significant role in many types of cancers including breast cancer. In the current study, we evaluated the expression levels of microR-10b (miR-10b) in 115 breast cancer patients from Sichuan Cancer Center. Real time reverse transcription-PCR was used to assess miR-10b expression. Clinical data including disease stage, survival status, age, ER/PR/HER2 status, molecular subtypes, tumor size, lymph node status and Ki-67 expression levels were correlated with miR-10b expression levels. Our data showed that the miR-10b expression is correlated with disease stage, living status and tumor sizes. We also found that miR-10b expression levels are higher in the lymph node positive group and the Ki-67 higher scoring group (score > 20). No statistically significant differences were observed based on age or molecular sub-type grouping. In conclusion, miR-10b may be a biomarker for breast cancer and is a potential treatment target.
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Affiliation(s)
- Jianhui Zhang
- Sichuan Cancer Hospital & Institute, Sichuan Cancer Center, School of Medicine, University of Electronic Science and Technology of China, Chengdu, Sichuan, China
| | - Jing Yang
- Sichuan Cancer Hospital & Institute, Sichuan Cancer Center, School of Medicine, University of Electronic Science and Technology of China, Chengdu, Sichuan, China
| | - Xin Zhang
- Sichuan Cancer Hospital & Institute, Sichuan Cancer Center, School of Medicine, University of Electronic Science and Technology of China, Chengdu, Sichuan, China
| | - Jia Xu
- Sichuan Cancer Hospital & Institute, Sichuan Cancer Center, School of Medicine, University of Electronic Science and Technology of China, Chengdu, Sichuan, China
| | - Yiyi Sun
- Chengdu Medical College, Chengdu, Sichuan, China
| | - Purong Zhang
- Sichuan Cancer Hospital & Institute, Sichuan Cancer Center, School of Medicine, University of Electronic Science and Technology of China, Chengdu, Sichuan, China
- * E-mail:
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47
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Wang H, Liu L, Liu X, Zhang M, Li X. Correlation between miRNAs and target genes in response to Campylobacter jejuni inoculation in chicken. Poult Sci 2018; 97:485-493. [DOI: 10.3382/ps/pex343] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2017] [Accepted: 10/14/2017] [Indexed: 12/19/2022] Open
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Fu Y, Yang Y, Zhang H, Farley G, Wang J, Quarles KA, Weng Z, Zamore PD. The genome of the Hi5 germ cell line from Trichoplusia ni, an agricultural pest and novel model for small RNA biology. eLife 2018; 7:31628. [PMID: 29376823 PMCID: PMC5844692 DOI: 10.7554/elife.31628] [Citation(s) in RCA: 55] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2017] [Accepted: 01/26/2018] [Indexed: 12/30/2022] Open
Abstract
We report a draft assembly of the genome of Hi5 cells from the lepidopteran insect pest, Trichoplusia ni, assigning 90.6% of bases to one of 28 chromosomes and predicting 14,037 protein-coding genes. Chemoreception and detoxification gene families reveal T. ni-specific gene expansions that may explain its widespread distribution and rapid adaptation to insecticides. Transcriptome and small RNA data from thorax, ovary, testis, and the germline-derived Hi5 cell line show distinct expression profiles for 295 microRNA- and >393 piRNA-producing loci, as well as 39 genes encoding small RNA pathway proteins. Nearly all of the W chromosome is devoted to piRNA production, and T. ni siRNAs are not 2´-O-methylated. To enable use of Hi5 cells as a model system, we have established genome editing and single-cell cloning protocols. The T. ni genome provides insights into pest control and allows Hi5 cells to become a new tool for studying small RNAs ex vivo. A common moth called the cabbage looper is becoming increasingly relevant to the scientific community. Its caterpillars are a serious threat to cabbage, broccoli and cauliflower crops, and they have started to resist the pesticides normally used to control them. Moreover, the insect’s germline cells – the ones that will produce sperm and eggs – are used in laboratories as ‘factories’ to artificially produce proteins of interest. The germline cells also host a group of genetic mechanisms called RNA silencing. One of these processes is known as piRNA, and it protects the genome against ‘jumping genes’. These genetic elements can cause mutations by moving from place to place in the DNA: in germline cells, piRNA suppresses them before the genetic information is transmitted to the next generation. Not all germline cells grow equally well under experimental conditions, or are easy to use to examine piRNA mechanisms in a laboratory. The germline cells from the cabbage looper, on the other hand, have certain characteristics that would make them ideal to study piRNA in insects. However, the genome of the moth had not yet been fully resolved. This hinders research on new ways of controlling the pest, on how to use the germline cells to produce more useful proteins, or on piRNA. Decoding a genome requires several steps. First, the entire genetic information is broken in short sections that can then be deciphered. Next, these segments need to be ‘assembled’ – put together, and in the right order, to reconstitute the entire genome. Certain portions of the genome, which are formed of repeats of the same sections, can be difficult to assemble. Finally, the genome must be annotated: the different regions – such as the genes – need to be identified and labeled. Here, Fu et al. assembled and annotated the genome of the cabbage looper, and in the process developed strategies that could be used for other species with a lot of repeated sequences in their genomes. Having access to the looper’s full genetic information makes it possible to use their germline cells to produce new types of proteins, for example for pharmaceutical purposes. Fu et al. went on to make working with these cells even easier by refining protocols so that modern research techniques, such as the gene-editing technology CRISPR-Cas9, can be used on the looper germline cells. The mapping of the genome also revealed that the genes involved in removing toxins from the insects’ bodies are rapidly evolving, which may explain why the moths readily become resistant to insecticides. This knowledge could help finding new ways of controlling the pest. Finally, the genes involved in RNA silencing were labeled: results show that an entire chromosome is the source of piRNAs. Combined with the new protocols developed by Fu et al., this could make cabbage looper germline cells the default option for any research into the piRNA mechanism. How piRNA works in the moth could inform work on human piRNA, as these processes are highly similar across the animal kingdom.
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Affiliation(s)
- Yu Fu
- Bioinformatics Program, Boston University, Boston, United States.,Program in Bioinformatics and Integrative Biology, University of Massachusetts Medical School, Worcester, United States
| | - Yujing Yang
- RNA Therapeutics Institute and Howard Hughes Medical Institute, University of Massachusetts Medical School, Worcester, United States
| | - Han Zhang
- RNA Therapeutics Institute and Howard Hughes Medical Institute, University of Massachusetts Medical School, Worcester, United States
| | - Gwen Farley
- RNA Therapeutics Institute and Howard Hughes Medical Institute, University of Massachusetts Medical School, Worcester, United States
| | - Junling Wang
- RNA Therapeutics Institute and Howard Hughes Medical Institute, University of Massachusetts Medical School, Worcester, United States
| | - Kaycee A Quarles
- RNA Therapeutics Institute and Howard Hughes Medical Institute, University of Massachusetts Medical School, Worcester, United States
| | - Zhiping Weng
- Program in Bioinformatics and Integrative Biology, University of Massachusetts Medical School, Worcester, United States
| | - Phillip D Zamore
- RNA Therapeutics Institute and Howard Hughes Medical Institute, University of Massachusetts Medical School, Worcester, United States
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Differential microRNA expression in breast cancer with different onset age. PLoS One 2018; 13:e0191195. [PMID: 29324832 PMCID: PMC5764434 DOI: 10.1371/journal.pone.0191195] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2017] [Accepted: 12/29/2017] [Indexed: 11/28/2022] Open
Abstract
Purpose The lower breast cancer incidence in Asian populations compared with Western populations has been speculated to be caused by environmental and genetic variation. Early-onset breast cancer occupies a considerable proportion of breast cancers in Asian populations, but the reason for this is unclear. We aimed to examine miRNA expression profiles in different age-onset groups and pathological subtypes in Asian breast cancer. Methods At the first stage, 10 samples (tumor: n = 6, normal tissue: n = 4) were analyzed with an Agilent microRNA 470 probe microarray. Candidate miRNAs with expression levels that were significantly altered in breast cancer samples or selected from a literature review were further validated by quantitative real-time PCR (qPCR) of 145 breast cancer samples at the second stage of the process. Correlations between clinicopathological parameters of breast cancer patients from different age groups and candidate miRNA expression were elucidated. Results In the present study, the tumor subtypes were significantly different in each age group, and an onset age below 40 had poor disease-free and overall survival rates. For all breast cancer patients, miR-335 and miR-145 were down-regulated, and miR-21, miR-200a, miR-200c, and miR-141 were up-regulated. In very young patients (age < 35 y/o), the expression of 3 and 8 specific miRNAs were up- and down-regulated, respectively. In young patients (36–40 y/o), 3 and 3 specific miRNAs were up- and down-regulated, respectively. miR-532-5p was up-regulated in triple-negative breast cancer. Conclusions Differential miRNA expressions between normal and tumor tissues were observed in different age groups and tumor subtypes. Evolutionarily conserved miRNA clusters, which initiate malignancy transformation, were up-regulated in the breast cancers of very young patients. None of the significantly altered miRNAs were observed in postmenopausal patients.
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50
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Asiaf A, Ahmad ST, Arjumand W, Zargar MA. MicroRNAs in Breast Cancer: Diagnostic and Therapeutic Potential. Methods Mol Biol 2018; 1699:23-43. [PMID: 29086366 DOI: 10.1007/978-1-4939-7435-1_2] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
MicroRNAs (miRNAs) are a large family of small, approximately 20-22 nucleotide, noncoding RNAs that regulate the expression of target genes, at the post-transcriptional level. miRNAs are involved in virtually diverse biological processes and play crucial roles in cellular processes, such as cell differentiation, proliferation, and apoptosis. Accumulating lines of evidence have indicated that miRNAs play important roles in the maintenance of biological homeostasis and that aberrant expression levels of miRNAs are associated with the onset of many diseases, including cancer. It is possible that the diverse roles that miRNAs play, have potential to provide valuable information in a clinical setting, demonstrating the potential to act as both screening tools for the stratification of high-risk patients, while informing the treatment decision-making process. Increasing evidence suggests that some miRNAs may even provide assistance in the diagnosis of patients with breast cancer. In addition, miRNAs may themselves be considered therapeutic targets, with inhibition or reintroduction of a particular miRNA capable of inducing a response in-vivo. This chapter discusses the role of miRNAs as oncogenes and tumor suppressors in breast cancer development and metastasis . It focuses on miRNAs that have prognostic, diagnostic, or predictive potential in breast cancer as well as the possible challenges in the translation of such observations to the clinic.
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Affiliation(s)
- Asia Asiaf
- Department of Biochemistry, Faculty of Science, University of Kashmir, Hazratbal Srinagar, J&K, 190006, India
| | - Shiekh Tanveer Ahmad
- Clarke H. Smith Brain Tumour Centre, Arnie Charbonneau Cancer Institute, Cumming School of Medicine, 2A25 HRIC, University of Calgary, 3330 Hospital Drive NW, Calgary, AB, T2N 4N1, Canada
| | - Wani Arjumand
- Robson DNA Science Centre, Arnie Charbonneau Cancer Institute, Cumming School of Medicine, 2A32 HRIC, University of Calgary, 3330 Hospital Drive NW, Calgary, AB, T2N 4N1, Canada
| | - Mohammad Afzal Zargar
- Department of Biochemistry, Faculty of Science, University of Kashmir, Hazratbal Srinagar, J&K, 190006, India.
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