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Kumar R, Kamboj H, Dhanda S, Verma A, Chander Y, Nehra K, Bhati A, Dedar RK, Sharma DK, Barua S, Tripathi BN, Sharma S, Kumar N. Identification of miR-29a as a novel biomarker for lumpy skin disease virus exposure in cattle. Virulence 2024; 15:2324711. [PMID: 38527940 PMCID: PMC10965105 DOI: 10.1080/21505594.2024.2324711] [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: 10/11/2023] [Accepted: 02/04/2024] [Indexed: 03/27/2024] Open
Abstract
Micro RNAs (miRNAs) have been implicated in the regulation of maturation, proliferation, differentiation, and activation of immune cells. In this study, we demonstrated that miR-29a antagonizes IFN-γ production at early times post-LSDV infection in cattle. miR-29a was predicted to target upstream IFN-γ regulators, and its inhibition resulted in enhanced IFN-γ production in sensitized peripheral blood mononuclear cells (PBMCs). Further, stimulation of PBMCs with LSDV antigen exhibited lower levels of miR-29a, concomitant with a potent cell-mediated immune response (CMI), characterized by an increase in LSDV-specific CD8+ T cell counts and enhanced levels of IFN-γ, which eventually facilitated virus clearance. In addition, a few immunocompromised cattle (developed secondary LSDV infection at ~ 6 months) that failed to mount a potent cell-mediated immune response, were shown to maintain higher miR-29a levels. Furthermore, as compared to the sensitized crossbred cattle, PBMCs from sensitized Rathi (a native Indian breed) animals exhibited lower levels of miR-29a along with an increase in CD8+ T cell counts and enhanced levels of IFN-γ. Finally, we analysed that a ≥ 60% decrease in miR-29a expression levels in the PBMCs of sensitized cattle correlated with a potent CMI response. In conclusion, miR-29a expression is involved in antagonizing the IFN-γ response in LSDV-infected cattle and may serve as a novel biomarker for the acute phase of LSDV infection, as well as predicting the functionality of T cells in sensitized cattle. In addition, Rathi cattle mount a more potent CMI response against LSDV than crossbred cattle.
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Affiliation(s)
- Ram Kumar
- National Centre for Veterinary Type Cultures, ICAR-National Research Centre on Equines, Hisar, India
| | - Himanshu Kamboj
- National Centre for Veterinary Type Cultures, ICAR-National Research Centre on Equines, Hisar, India
| | - Shweta Dhanda
- National Centre for Veterinary Type Cultures, ICAR-National Research Centre on Equines, Hisar, India
| | - Assim Verma
- National Centre for Veterinary Type Cultures, ICAR-National Research Centre on Equines, Hisar, India
| | - Yogesh Chander
- National Centre for Veterinary Type Cultures, ICAR-National Research Centre on Equines, Hisar, India
| | - Kuldeep Nehra
- Livestock Research Station, Rajasthan University of Veterinary and Animal Sciences, Nohar, Rajasthan, India
| | | | - Ramesh Kumar Dedar
- National Centre for Veterinary Type Cultures, ICAR-National Research Centre on Equines, Hisar, India
| | - Deepak Kumar Sharma
- Department of Veterinary Microbiology, Rajasthan University of Veterinary and Animal Sciences, Udaipur, India
| | - Sanjay Barua
- National Centre for Veterinary Type Cultures, ICAR-National Research Centre on Equines, Hisar, India
| | - Bhupendra N. Tripathi
- National Centre for Veterinary Type Cultures, ICAR-National Research Centre on Equines, Hisar, India
| | - Shalini Sharma
- National Centre for Veterinary Type Cultures, ICAR-National Research Centre on Equines, Hisar, India
| | - Naveen Kumar
- National Centre for Veterinary Type Cultures, ICAR-National Research Centre on Equines, Hisar, India
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Sprang M, Möllmann J, Andrade-Navarro MA, Fontaine JF. Overlooked poor-quality patient samples in sequencing data impair reproducibility of published clinically relevant datasets. Genome Biol 2024; 25:222. [PMID: 39152483 PMCID: PMC11328481 DOI: 10.1186/s13059-024-03331-6] [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: 06/13/2023] [Accepted: 07/08/2024] [Indexed: 08/19/2024] Open
Abstract
BACKGROUND Reproducibility is a major concern in biomedical studies, and existing publication guidelines do not solve the problem. Batch effects and quality imbalances between groups of biological samples are major factors hampering reproducibility. Yet, the latter is rarely considered in the scientific literature. RESULTS Our analysis uses 40 clinically relevant RNA-seq datasets to quantify the impact of quality imbalance between groups of samples on the reproducibility of gene expression studies. High-quality imbalance is frequent (14 datasets; 35%), and hundreds of quality markers are present in more than 50% of the datasets. Enrichment analysis suggests common stress-driven effects among the low-quality samples and highlights a complementary role of transcription factors and miRNAs to regulate stress response. Preliminary ChIP-seq results show similar trends. Quality imbalance has an impact on the number of differential genes derived by comparing control to disease samples (the higher the imbalance, the higher the number of genes), on the proportion of quality markers in top differential genes (the higher the imbalance, the higher the proportion; up to 22%) and on the proportion of known disease genes in top differential genes (the higher the imbalance, the lower the proportion). We show that removing outliers based on their quality score improves the resulting downstream analysis. CONCLUSIONS Thanks to a stringent selection of well-designed datasets, we demonstrate that quality imbalance between groups of samples can significantly reduce the relevance of differential genes, consequently reducing reproducibility between studies. Appropriate experimental design and analysis methods can substantially reduce the problem.
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Affiliation(s)
- Maximilian Sprang
- Faculty of Biology, Johannes Gutenberg-Universität Mainz, Biozentrum I, Hans-Dieter-Hüsch-Weg 15, Mainz, 55128, Germany
| | - Jannik Möllmann
- Faculty of Biology, Johannes Gutenberg-Universität Mainz, Biozentrum I, Hans-Dieter-Hüsch-Weg 15, Mainz, 55128, Germany
| | - Miguel A Andrade-Navarro
- Faculty of Biology, Johannes Gutenberg-Universität Mainz, Biozentrum I, Hans-Dieter-Hüsch-Weg 15, Mainz, 55128, Germany.
| | - Jean-Fred Fontaine
- Faculty of Biology, Johannes Gutenberg-Universität Mainz, Biozentrum I, Hans-Dieter-Hüsch-Weg 15, Mainz, 55128, Germany
- Central Institute for Decision Support Systems in Crop Protection (ZEPP), Rüdesheimer Str. 60-68, Bad Kreuznach, 55545, Germany
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3
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Pandita S, Verma A, Kamboj H, Kumar R, Chander Y, Barua S, Tripathi BN, Kumar N. miRNA profiling of primary lamb testicle cells infected with lumpy skin disease virus. Arch Virol 2023; 168:290. [PMID: 37955695 DOI: 10.1007/s00705-023-05917-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2023] [Accepted: 09/27/2023] [Indexed: 11/14/2023]
Abstract
In this study, miRNA profiling of cells infected with lumpy skin disease virus (LSDV) was conducted for the first time. When compared to mock-infected cells, LSDV-infected primary lamb testicle (LT) cells showed dysregulation of 64, 85, and 85 miRNAs at 12 hours postinfection (hpi), 48 hpi, and 72 hpi, respectively. While some of these miRNAs were found to be dysregulated at a particular time point following LSDV infection, others were dysregulated at all three time points. Analysis of the differentially expressed miRNA-mRNA interaction networks, Gene Ontology analysis of the predicted targets, and KEGG analysis of highly enriched pathways revealed several cellular factors/pathways involved in protein/ion/enzyme binding, cell differentiation, movement of subcellular components, calcium reabsorption, aldosterone synthesis and secretion, and melanogenesis. Some selected upregulated (oar-mir-379-5p, oar-let-7d, Chr10-18769, Chr2_5162 and oar-miR-493-5p) and downregulated (ChrX-33741, Chr3_8257 and Chr26_32680) miRNAs were further confirmed by quantitative real-time PCR. These findings contribute to our understanding of virus replication, virus-host interactions, and disease pathogenesis, and the differentially expressed miRNAs and their cellular targets may serve as biomarkers as well as novel targets for therapeutic intervention against LSDV.
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Affiliation(s)
- Sakshi Pandita
- National Centre for Veterinary Type Cultures, ICAR-National Research Centre on Equines, Hisar, Haryana, 125001, India
- Lala Lajpat Rai University of Veterinary and Animal Sciences, Hisar, Haryana, 125004, India
| | - Assim Verma
- National Centre for Veterinary Type Cultures, ICAR-National Research Centre on Equines, Hisar, Haryana, 125001, India
| | - Himanshu Kamboj
- National Centre for Veterinary Type Cultures, ICAR-National Research Centre on Equines, Hisar, Haryana, 125001, India
| | - Ram Kumar
- National Centre for Veterinary Type Cultures, ICAR-National Research Centre on Equines, Hisar, Haryana, 125001, India
| | - Yogesh Chander
- National Centre for Veterinary Type Cultures, ICAR-National Research Centre on Equines, Hisar, Haryana, 125001, India
| | - Sanjay Barua
- National Centre for Veterinary Type Cultures, ICAR-National Research Centre on Equines, Hisar, Haryana, 125001, India
| | - Bhupendra Nath Tripathi
- National Centre for Veterinary Type Cultures, ICAR-National Research Centre on Equines, Hisar, Haryana, 125001, India
| | - Naveen Kumar
- National Centre for Veterinary Type Cultures, ICAR-National Research Centre on Equines, Hisar, Haryana, 125001, India.
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Holzhausen EA, Kupsco A, Chalifour BN, Patterson WB, Schmidt KA, Mokhtari P, Lurmann F, Baccarelli AA, Goran MI, Alderete TL. Human milk EV-miRNAs: a novel biomarker for air pollution exposure during pregnancy. ENVIRONMENTAL RESEARCH, HEALTH : ERH 2023; 1:035002. [PMID: 37692372 PMCID: PMC10486183 DOI: 10.1088/2752-5309/ace075] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/13/2023] [Revised: 05/23/2023] [Accepted: 06/21/2023] [Indexed: 09/12/2023]
Abstract
Exposure to ambient and near-roadway air pollution during pregnancy has been linked with several adverse health outcomes for pregnant women and their babies. Emerging research indicates that microRNA (miRNA) expression can be altered by exposure to air pollutants in a variety of tissues. Additionally, miRNAs from breast tissue and circulating miRNAs have previously been proposed as a biomarker for breast cancer diagnosis and prognosis. Therefore, this study sought to evaluate the associations between pregnancy exposures to ambient (PM10, PM2.5, NO2, O3) and near-roadway air pollution (total NOx, freeway NOx, non-freeway NOx) with breast milk extracellular vesicle miRNA (EV-miRNA), measured at 1-month postpartum, in a cohort of 108 Latina women living in Southern California. We found that PM10 exposure during pregnancy was positively associated with hsa-miR-200c-3p, hsa-miR-200b-3p, and hsa-let-7c-5p, and was negatively associated with hsa-miR-378d. We also found that pregnancy PM2.5 exposure was positively associated with hsa-miR-200c-3p and hsa-miR-200b-3p. First and second trimester exposure to PM10 and PM2.5 was associated with several EV-miRNAs with putative messenger RNA targets related to cancer. This study provides preliminary evidence that air pollution exposure during pregnancy is associated with human milk EV-miRNA expression.
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Affiliation(s)
- Elizabeth A Holzhausen
- Department of Integrative Physiology, University of Colorado Boulder, Boulder, CO,
United States of America
| | - Allison Kupsco
- Department of Environmental Health Sciences, Columbia University Mailman School of Public
Health, New York, NY, United States of America
| | - Bridget N Chalifour
- Department of Integrative Physiology, University of Colorado Boulder, Boulder, CO,
United States of America
| | - William B Patterson
- Department of Integrative Physiology, University of Colorado Boulder, Boulder, CO,
United States of America
| | - Kelsey A Schmidt
- Department of Pediatrics, Children’s Hospital Los Angeles, Los Angeles, CA, United
States of America
| | - Pari Mokhtari
- Department of Pediatrics, Children’s Hospital Los Angeles, Los Angeles, CA, United
States of America
| | | | - Andrea A Baccarelli
- Department of Environmental Health Sciences, Columbia University Mailman School of Public
Health, New York, NY, United States of America
| | - Michael I Goran
- Department of Pediatrics, Children’s Hospital Los Angeles, Los Angeles, CA, United
States of America
| | - Tanya L Alderete
- Department of Integrative Physiology, University of Colorado Boulder, Boulder, CO,
United States of America
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5
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Mikhailov VF, Shulenina LV. Regulation of Gene Activity Is One of the Mechanisms for Changing Radiosensitivity. BIOL BULL+ 2022. [DOI: 10.1134/s1062359022110140] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/15/2023]
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6
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Ravegnini G, De Iaco P, Gorini F, Dondi G, Klooster I, De Crescenzo E, Bovicelli A, Hrelia P, Perrone AM, Angelini S. Role of Circulating miRNAs in Therapeutic Response in Epithelial Ovarian Cancer: A Systematic Revision. Biomedicines 2021; 9:biomedicines9101316. [PMID: 34680433 PMCID: PMC8533254 DOI: 10.3390/biomedicines9101316] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2021] [Revised: 09/17/2021] [Accepted: 09/20/2021] [Indexed: 12/11/2022] Open
Abstract
Epithelial ovarian cancer (EOC) is one of the most lethal cancers worldwide, mostly due to nonspecific symptoms and a lack of screening tests, which, taken together, contribute to delayed diagnosis and treatment. The current clinical biomarker is serum CA-125, which allows the identification of most advanced primary and relapsed disease and correlates with disease burden; however, as well highlighted in the literature, CA-125 often lacks sensitivity and specificity, and is not helpful in monitoring chemotherapeutic response or in predicting the risk of relapse. Given that, the identification of novel biomarkers able to foster more precise medical approaches and the personalization of patient management represents an unmet clinical requirement. In this context, circulating miRNAs may represent an interesting opportunity as they can be easily detected in all biological fluids. This is particularly relevant when looking for non-invasive approaches that can be repeated over time, with no pain and stress for the oncological patient. Given that, the present review aims to describe the circulating miRNAs currently identified as associated with therapeutic treatments in OC and presents a complete overview of the available evidence.
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Affiliation(s)
- Gloria Ravegnini
- Department of Pharmacy and Biotechnology, University of Bologna, 40126 Bologna, Italy; (F.G.); (P.H.); (S.A.)
- Correspondence:
| | - Pierandrea De Iaco
- Division of Oncologic Gynecology, IRCCS Azienda Ospedaliero-Universitaria di Bologna, 40138 Bologna, Italy; (P.D.I.); (G.D.); (E.D.C.); (A.B.); (A.M.P.)
- Department of Medical and Surgical Sciences, DIMEC, University of Bologna, 40138 Bologna, Italy
- Centro di Studio e Ricerca delle Neoplasie Ginecologiche, University of Bologna, 40138 Bologna, Italy
| | - Francesca Gorini
- Department of Pharmacy and Biotechnology, University of Bologna, 40126 Bologna, Italy; (F.G.); (P.H.); (S.A.)
| | - Giulia Dondi
- Division of Oncologic Gynecology, IRCCS Azienda Ospedaliero-Universitaria di Bologna, 40138 Bologna, Italy; (P.D.I.); (G.D.); (E.D.C.); (A.B.); (A.M.P.)
| | - Isabella Klooster
- Department of Pathology, Brigham and Women’s Hospital, 75 Francis Street, Boston, MA 02115, USA;
| | - Eugenia De Crescenzo
- Division of Oncologic Gynecology, IRCCS Azienda Ospedaliero-Universitaria di Bologna, 40138 Bologna, Italy; (P.D.I.); (G.D.); (E.D.C.); (A.B.); (A.M.P.)
| | - Alessandro Bovicelli
- Division of Oncologic Gynecology, IRCCS Azienda Ospedaliero-Universitaria di Bologna, 40138 Bologna, Italy; (P.D.I.); (G.D.); (E.D.C.); (A.B.); (A.M.P.)
| | - Patrizia Hrelia
- Department of Pharmacy and Biotechnology, University of Bologna, 40126 Bologna, Italy; (F.G.); (P.H.); (S.A.)
| | - Anna Myriam Perrone
- Division of Oncologic Gynecology, IRCCS Azienda Ospedaliero-Universitaria di Bologna, 40138 Bologna, Italy; (P.D.I.); (G.D.); (E.D.C.); (A.B.); (A.M.P.)
- Department of Medical and Surgical Sciences, DIMEC, University of Bologna, 40138 Bologna, Italy
- Centro di Studio e Ricerca delle Neoplasie Ginecologiche, University of Bologna, 40138 Bologna, Italy
| | - Sabrina Angelini
- Department of Pharmacy and Biotechnology, University of Bologna, 40126 Bologna, Italy; (F.G.); (P.H.); (S.A.)
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7
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Li D, Ge Y, Zhao Z, Zhu R, Wang X, Bi X. Distinct and Coordinated Regulation of Small Non-coding RNAs by E2f1 and p53 During Drosophila Development and in Response to DNA Damage. Front Cell Dev Biol 2021; 9:695311. [PMID: 34368144 PMCID: PMC8339594 DOI: 10.3389/fcell.2021.695311] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2021] [Accepted: 06/18/2021] [Indexed: 01/22/2023] Open
Abstract
Small non-coding RNAs (ncRNAs), including microRNAs (miRNAs) and PIWI-interacting RNAs (piRNAs), play a pivotal role in biological processes. A comprehensive quantitative reference of small ncRNAs expression during development and in DNA damage response (DDR) would significantly advance our understanding of their roles. In this study, we systemically analyzed the expression profile of miRNAs and piRNAs in wild-type flies, e2f1 mutant, p53 mutant and e2f1 p53 double mutant during development and after X-ray irradiation. By using small RNA sequencing and bioinformatic analysis, we found that both miRNAs and piRNAs were expressed in a dynamic mode and formed 4 distinct clusters during development. Notably, the expression pattern of miRNAs and piRNAs was changed in e2f1 mutant at multiple developmental stages, while retained in p53 mutant, indicating a critical role of E2f1 played in mediating small ncRNAs expression. Moreover, we identified differentially expressed (DE) small ncRNAs in e2f1 mutant and p53 mutant after X-ray irradiation. Furthermore, we mapped the binding motif of E2f1 and p53 around the small ncRNAs. Our data suggested that E2f1 and p53 work differently yet coordinately to regulate small ncRNAs expression, and E2f1 may play a major role to regulate miRNAs during development and after X-ray irradiation. Collectively, our results provide comprehensive characterization of small ncRNAs, as well as the regulatory roles of E2f1 and p53 in small ncRNAs expression, during development and in DNA damage response, which reveal new insights into the small ncRNAs biology.
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Affiliation(s)
- Dong Li
- School of Medicine, Nantong University, Nantong, China
| | - Ying Ge
- Institute of Cancer Stem Cell, Dalian Medical University, Dalian, China
| | - Ze Zhao
- Institute of Cancer Stem Cell, Dalian Medical University, Dalian, China
| | - Rui Zhu
- Institute of Cancer Stem Cell, Dalian Medical University, Dalian, China
| | - Xiang Wang
- Institute of Cancer Stem Cell, Dalian Medical University, Dalian, China
| | - Xiaolin Bi
- School of Medicine, Nantong University, Nantong, China.,College of Basic Medical Sciences, Dalian Medical University, Dalian, China
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8
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Zhan J, Diao Y, Yin G, Sajjad M, Wei X, Lu Z, Wang Y. Integration of mRNA and miRNA Analysis Reveals the Molecular Mechanism of Cotton Response to Salt Stress. FRONTIERS IN PLANT SCIENCE 2021; 12:767984. [PMID: 34956267 PMCID: PMC8695560 DOI: 10.3389/fpls.2021.767984] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Accepted: 11/09/2021] [Indexed: 05/13/2023]
Abstract
To identify the regulatory network of known and novel microRNAs (miRNAs) and their targets responding to salt stress, a combined analysis of mRNA libraries, small RNA libraries, and degradome libraries were performed. In this study, we used unique molecular identifiers (UMIs), which are more sensitive, accurate, and reproducible than traditional methods of sequencing, to quantify the number of molecules and correct for amplification bias. We identified a total of 312 cotton miRNAs using seedlings at 0, 1, 3, and 6 h after NaCl treatment, including 80 known ghr-miRNAs and 232 novel miRNAs and found 155 miRNAs that displayed significant differential expression under salt stress. Among them, fifty-nine differentially expressed miRNAs were simultaneously induced in two or three tissues, while 66, 11, and 19 were specifically expressed in the roots, leaves, and stems, respectively. It is indicated there were different populations of miRNAs against salt stress in roots, leaves and stems. 399 candidate targets of salt-induced miRNAs showed significant differential expression before and after salt treatment, and 72 targets of 25 miRNAs were verified by degradome sequencing data. Furthermore, the regulatory relationship of miRNA-target gene was validated experimentally via 5'RLM-RACE, proving our data reliability. Gene ontology and KEGG pathway analysis found that salt-responsive miRNA targets among the differentially expressed genes were significantly enriched, and mainly involved in response to the stimulus process and the plant hormone signal transduction pathway. Furthermore, the expression levels of newly identified miRNA mir1 and known miRNAs miR390 and miR393 gradually decreased when subjected to continuous salt stress, while overexpression of these miRNAs both increased sensitivity to salt stress. Those newly identified miRNAs and mRNA pairs were conducive to genetic engineering and better understanding the mechanisms responding to salt stress in cotton.
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Affiliation(s)
- Jingjing Zhan
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Anyang, China
| | - Yangyang Diao
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Anyang, China
| | - Guo Yin
- Handan Academy of Agricultural Sciences, Handan, China
| | - Muhammad Sajjad
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Anyang, China
| | - Xi Wei
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Anyang, China
| | - Zhengying Lu
- Handan Academy of Agricultural Sciences, Handan, China
- *Correspondence: Zhengying Lu,
| | - Ye Wang
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Anyang, China
- Ye Wang,
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9
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Sun JL, Zhao LL, He K, Liu Q, Luo J, Zhang DM, Liang J, Liao L, Ma JD, Yang S. MicroRNA regulation in hypoxic environments: differential expression of microRNAs in the liver of largemouth bass (Micropterus salmoides). FISH PHYSIOLOGY AND BIOCHEMISTRY 2020; 46:2227-2242. [PMID: 32948974 DOI: 10.1007/s10695-020-00877-7] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/09/2020] [Accepted: 09/08/2020] [Indexed: 06/11/2023]
Abstract
Environmental changes in intensive aquaculture commonly lead to hypoxic stress for cultured largemouth bass (Micropterus salmoides). To better to understand the hypoxic stress response mechanisms, the miRNA expression profiles of the livers of largemouth bass exposed for 24 h to three different dissolved oxygen levels (7.0 ± 0.2 mg/L as control, 3.0 ± 0.2 mg/L and 1.2 ± 0.2 mg/L) were compared. In this study, a total of 266 known miRNAs were identified, 84 of which were differentially expressed compared with the control group. Thirteen of the differentially expressed miRNAs (miR-15b-5p, miR-30a-3p, miR-133a-3p, miR-19d-5p, miR-1288-3p, miR456, miR-96-5p, miR-23a-3p, miR-23b-5p, miR-214, miR-24, miR-20a-3p, and miR-2188-5p) were significantly enriched in VEGF signaling pathway, MAPK signaling pathway, and phosphatidylinositol signaling system. These miRNAs were significantly downregulated during stress, especially after a 4-h exposure to hypoxia. In contrast, their target genes (vegfa, pla2g4a, raf1a, pik3c2a, clam2a, inpp1, pi4k2b, mtmr14, ip6k, itpkca, map3k7, and Jun) were significant upregulated after 4 h of hypoxic stress. Moreover, two potential hypoxia-tolerance signal transduction pathways (MAPK signaling pathway and phosphatidylinositol signaling system) were revealed, both of which may play important roles in responding to acute hypoxic stress. We see that miRNAs played an important role in regulating gene expression related to physiological responses to hypoxia. Potential functional network regulated by miRNAs under hypoixic stress in the liver of largemouth bass (Micropterus salmoides). Blue boxes indicated that the expression of miRNA or target genes were down-regulated. Red boxes indicated that the expression of miRNA or target genes wasere up-regulated.
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Affiliation(s)
- Jun Long Sun
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
- State Key Laboratory of Marine Resource Utilization in South China Sea, Hainan Aquaculture Breeding Engineering Research Center, Hainan University, Haikou, 570228, Hainan, China
| | - Liu Lan Zhao
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
| | - Kuo He
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
| | - Qiao Liu
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
| | - Jie Luo
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
| | - Dong Mei Zhang
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
| | - Ji Liang
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
| | - Lei Liao
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
| | - Ji Deng Ma
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
| | - Song Yang
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China.
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Lopez-Rincon A, Mendoza-Maldonado L, Martinez-Archundia M, Schönhuth A, Kraneveld AD, Garssen J, Tonda A. Machine Learning-Based Ensemble Recursive Feature Selection of Circulating miRNAs for Cancer Tumor Classification. Cancers (Basel) 2020; 12:cancers12071785. [PMID: 32635415 PMCID: PMC7407482 DOI: 10.3390/cancers12071785] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2020] [Revised: 06/25/2020] [Accepted: 06/29/2020] [Indexed: 02/07/2023] Open
Abstract
Circulating microRNAs (miRNA) are small noncoding RNA molecules that can be detected in bodily fluids without the need for major invasive procedures on patients. miRNAs have shown great promise as biomarkers for tumors to both assess their presence and to predict their type and subtype. Recently, thanks to the availability of miRNAs datasets, machine learning techniques have been successfully applied to tumor classification. The results, however, are difficult to assess and interpret by medical experts because the algorithms exploit information from thousands of miRNAs. In this work, we propose a novel technique that aims at reducing the necessary information to the smallest possible set of circulating miRNAs. The dimensionality reduction achieved reflects a very important first step in a potential, clinically actionable, circulating miRNA-based precision medicine pipeline. While it is currently under discussion whether this first step can be taken, we demonstrate here that it is possible to perform classification tasks by exploiting a recursive feature elimination procedure that integrates a heterogeneous ensemble of high-quality, state-of-the-art classifiers on circulating miRNAs. Heterogeneous ensembles can compensate inherent biases of classifiers by using different classification algorithms. Selecting features then further eliminates biases emerging from using data from different studies or batches, yielding more robust and reliable outcomes. The proposed approach is first tested on a tumor classification problem in order to separate 10 different types of cancer, with samples collected over 10 different clinical trials, and later is assessed on a cancer subtype classification task, with the aim to distinguish triple negative breast cancer from other subtypes of breast cancer. Overall, the presented methodology proves to be effective and compares favorably to other state-of-the-art feature selection methods.
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Affiliation(s)
- Alejandro Lopez-Rincon
- Division of Pharmacology, Utrecht Institute for Pharmaceutical Sciences, Faculty of Science, Utrecht University, Universiteitsweg 99, 3584 CG Utrecht, The Netherlands; (A.D.K.); (J.G.)
- Correspondence:
| | - Lucero Mendoza-Maldonado
- Nuevo Hospital Civil de Guadalajara “Dr. Juan I. Menchaca”, Salvador Quevedo y Zubieta 750, Independencia Oriente, Guadalajara C.P. 44340, Jalisco, Mexico;
| | - Marlet Martinez-Archundia
- Laboratorio de Modelado Molecular, Bioinformática y Diseno de farmacos, Seccion de Estudios de Posgrado e Investigación, Escuela Superior de Medicina, Instituto Politécnico Nacional, Mexico City 11340, Mexico;
| | - Alexander Schönhuth
- Life Sciences and Health, Centrum Wiskunde & Informatica, Science Park 123, 1098 XG Amsterdam, The Netherlands;
- Genome Data Science, Faculty of Technology, Bielefeld University, Universitätsstraße 25, 33615 Bielefeld, Germany
| | - Aletta D. Kraneveld
- Division of Pharmacology, Utrecht Institute for Pharmaceutical Sciences, Faculty of Science, Utrecht University, Universiteitsweg 99, 3584 CG Utrecht, The Netherlands; (A.D.K.); (J.G.)
| | - Johan Garssen
- Division of Pharmacology, Utrecht Institute for Pharmaceutical Sciences, Faculty of Science, Utrecht University, Universiteitsweg 99, 3584 CG Utrecht, The Netherlands; (A.D.K.); (J.G.)
- Global Centre of Excellence Immunology Danone Nutricia Research, Uppsalaan 12, 3584 CT Utrecht, The Netherlands
| | - Alberto Tonda
- UMR 518 MIA-Paris, INRAE, Université Paris-Saclay, 75013 Paris, France;
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11
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Ma L, Yu H, Wang X, Li D, Zhang Y, Pei X, Duan Z, Ma M. The effects of maternal exposure to BPA during pregnancy on the male reproductive system and the testicular microRNA expression profile. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2020; 27:17290-17302. [PMID: 32157532 DOI: 10.1007/s11356-020-08156-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/14/2019] [Accepted: 02/19/2020] [Indexed: 06/10/2023]
Abstract
The effect of prenatal bisphenol A (BPA) exposure is increasingly concerned. We investigated the effect of maternal BPA exposure during pregnancy on male offspring and its potential mechanism. Thirty pregnant Sprague Dawley (SD) rats were randomly divided into exposed and control groups. At PND56, the number of sperm, luteinizing hormone, and testosterone in the BPA-exposed group decreased, and testicular tissue structure was damaged in offsprings. At GD20, the miRNA profile in the testis of male offspring was examined and the expression levels of 28 deregulated miRNAs were validated by qRT-PCR. We found that miR-361-5p, miR-203a-3p, and miR-19b-2-5p had significantly different expression levels in the testis. These results suggest that maternal exposure to BPA can lead to differential changes in progeny miRNAs, which will provide direction for future in-depth mechanisms of reproductive injury.
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Affiliation(s)
- Lin Ma
- Department of Toxicology, School of Public Heath, Shenyang Medical College, Shenyang, 110034, Liaoning Province, People's Republic of China
| | - Haiyang Yu
- Department of Toxicology, School of Public Heath, Shenyang Medical College, Shenyang, 110034, Liaoning Province, People's Republic of China
| | - Xu Wang
- Department of Environmental Engineering and Bioengineering, Shenyang Institute of Science and Technology, Shenyang, 110167, Liaoning Province, People's Republic of China
| | - Dan Li
- Department of Toxicology, School of Public Heath, Shenyang Medical College, Shenyang, 110034, Liaoning Province, People's Republic of China
| | - Yumin Zhang
- Department of Toxicology, School of Public Heath, Shenyang Medical College, Shenyang, 110034, Liaoning Province, People's Republic of China
| | - Xiucong Pei
- Department of Toxicology, School of Public Heath, Shenyang Medical College, Shenyang, 110034, Liaoning Province, People's Republic of China
| | - Zhiwen Duan
- Department of Toxicology, School of Public Heath, Shenyang Medical College, Shenyang, 110034, Liaoning Province, People's Republic of China
| | - Mingyue Ma
- Department of Toxicology, School of Public Heath, Shenyang Medical College, Shenyang, 110034, Liaoning Province, People's Republic of China.
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12
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Gusev EY, Zotova NV. Cellular Stress and General Pathological Processes. Curr Pharm Des 2020; 25:251-297. [PMID: 31198111 DOI: 10.2174/1381612825666190319114641] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2019] [Accepted: 03/13/2019] [Indexed: 02/06/2023]
Abstract
From the viewpoint of the general pathology, most of the human diseases are associated with a limited number of pathogenic processes such as inflammation, tumor growth, thrombosis, necrosis, fibrosis, atrophy, pathological hypertrophy, dysplasia and metaplasia. The phenomenon of chronic low-grade inflammation could be attributed to non-classical forms of inflammation, which include many neurodegenerative processes, pathological variants of insulin resistance, atherosclerosis, and other manifestations of the endothelial dysfunction. Individual and universal manifestations of cellular stress could be considered as a basic element of all these pathologies, which has both physiological and pathophysiological significance. The review examines the causes, main phenomena, developmental directions and outcomes of cellular stress using a phylogenetically conservative set of genes and their activation pathways, as well as tissue stress and its role in inflammatory and para-inflammatory processes. The main ways towards the realization of cellular stress and its functional blocks were outlined. The main stages of tissue stress and the classification of its typical manifestations, as well as its participation in the development of the classical and non-classical variants of the inflammatory process, were also described. The mechanisms of cellular and tissue stress are structured into the complex systems, which include networks that enable the exchange of information with multidirectional signaling pathways which together make these systems internally contradictory, and the result of their effects is often unpredictable. However, the possible solutions require new theoretical and methodological approaches, one of which includes the transition to integral criteria, which plausibly reflect the holistic image of these processes.
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Affiliation(s)
- Eugeny Yu Gusev
- Laboratory of the Immunology of Inflammation, Institute of Immunology and Physiology, Yekaterinburg, Russian Federation
| | - Natalia V Zotova
- Laboratory of the Immunology of Inflammation, Institute of Immunology and Physiology, Yekaterinburg, Russian Federation.,Department of Medical Biochemistry and Biophysics, Ural Federal University named after B.N.Yeltsin, Yekaterinburg, Russian Federation
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13
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Jackson L, Qifti A, Pearce KM, Scarlata S. Regulation of bifunctional proteins in cells: Lessons from the phospholipase Cβ/G protein pathway. Protein Sci 2019; 29:1258-1268. [PMID: 31867822 DOI: 10.1002/pro.3809] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2019] [Revised: 12/17/2019] [Accepted: 12/18/2019] [Indexed: 12/14/2022]
Abstract
Some proteins can serve multiple functions depending on different cellular conditions. An example of a bifunctional protein is inositide-specific mammalian phospholipase Cβ (PLCβ). PLCβ is activated by G proteins in response to hormones and neurotransmitters to increase intracellular calcium. Recently, alternate cellular function(s) of PLCβ have become uncovered. However, the conditions that allow these different functions to be operative are unclear. Like many mammalian proteins, PLCβ has a conserved catalytic core along with several regulatory domains. These domains modulate the intensity and duration of calcium signals in response to external sensory information, and allow this enzyme to inhibit protein translation in a noncatalytic manner. In this review, we first describe PLCβ's cellular functions and regulation of the switching between these functions, and then discuss the thermodynamic considerations that offer insight into how cells manage multiple and competitive associations allowing them to rapidly shift between functional states.
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Affiliation(s)
- Lela Jackson
- Department of Chemistry and Biochemistry, Worcester Polytechnic Institute, Worcester, Massachusetts
| | - Androniqi Qifti
- Department of Chemistry and Biochemistry, Worcester Polytechnic Institute, Worcester, Massachusetts
| | - Katherine M Pearce
- Department of Chemistry and Biochemistry, Worcester Polytechnic Institute, Worcester, Massachusetts
| | - Suzanne Scarlata
- Department of Chemistry and Biochemistry, Worcester Polytechnic Institute, Worcester, Massachusetts
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14
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Sun J, Liu Q, Zhao L, Cui C, Wu H, Liao L, Tang G, Yang S, Yang S. Potential regulation by miRNAs on glucose metabolism in liver of common carp (Cyprinus carpio) at different temperatures. COMPARATIVE BIOCHEMISTRY AND PHYSIOLOGY D-GENOMICS & PROTEOMICS 2019; 32:100628. [PMID: 31677400 DOI: 10.1016/j.cbd.2019.100628] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/20/2019] [Revised: 09/13/2019] [Accepted: 09/13/2019] [Indexed: 12/12/2022]
Abstract
Water temperature can affect the metabolism of fish. Common carp (Cyprinus carpio) is a representative eurythermic fish that can survive at a wide range of ambient temperatures, allowing it to live in an extensive geographical range. The goal of this work was to study the glucose metabolism of common carp at different temperatures and determine the miRNAs involved in the regulation of glucose metabolism. We determined the indicators related to glucose metabolism after long-term temperature stress and constructed nine small RNA libraries of livers under different temperature stress (5 °C, 17 °C, and 30 °C, with three biological replicates for each temperature), and subjected these samples to high-throughput sequencing. A positive relationship was observed between weight gain rate (WGR) and temperature increase after 18 days of temperature stress. However, the glucose level in the plasma maintained a gentle decrease. Unexpectedly, liver lactic acid levels were elevated in HTG (high temperature group) and LTG (low temperature group). Six down-regulated miRNAs (miR-122, miR-30b, miR-15b-5p, miR-20a-5p, miR-1, and miR-7b) were identified as involved in the regulation of glycolysis. Twelve genes were predicted as targets of these miRNAs, and these genes are in pathways related to pyruvate metabolism, glycolysis/gluconeogenesis, and the citrate cycle (TCA cycle). The results allowed prediction of a potential regulatory network of miRNAs involved in the regulation of glycolysis. The target genes of six down-regulated miRNAs were up-regulated under temperature stress, including Aldolase C, fructose-bisphosphate, b (ALDOCB), multiple inositol-polyphosphate phosphatase 1 (MINPP1), phosphoenolpyruvate carboxykinase 1 (PCK1), pyruvate dehydrogenase E1 alpha 1 (PDHA1), aldehyde dehydrogenase 9 family member A1a (ALDH9A1A), Acetyl-coenzyme A synthetase (ACSS), lactate dehydrogenase b (LDH-b), and glyoxylate reductase/hydroxypyruvate reductase (GRHPR). Other key genes of glycolysis, glucose transporter 1 (GLUT-1), pyruvate kinase PKM (PKM), and mitochondrial pyruvate carrier (MPC) were significantly up-regulated in LTG and HTG. Overall, the results suggest that miRNAs maintain their energy requirements by regulating glycolysis and play an important role in the molecular response to cold and heat stress of common carp. These data provide the foundation for further studies of the role of miRNAs in environmental adaptation in fish.
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Affiliation(s)
- JunLong Sun
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, Sichuan 611130, China
| | - Qiao Liu
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, Sichuan 611130, China
| | - LiuLan Zhao
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, Sichuan 611130, China
| | - Can Cui
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, Sichuan 611130, China
| | - Hao Wu
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, Sichuan 611130, China
| | - Lei Liao
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, Sichuan 611130, China
| | - Gang Tang
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, Sichuan 611130, China
| | - ShiYong Yang
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, Sichuan 611130, China
| | - Song Yang
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, Sichuan 611130, China.
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15
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Wang P, Yang Y, Shi H, Wang Y, Ren F. Small RNA and degradome deep sequencing reveal respective roles of cold-related microRNAs across Chinese wild grapevine and cultivated grapevine. BMC Genomics 2019; 20:740. [PMID: 31615400 PMCID: PMC6794902 DOI: 10.1186/s12864-019-6111-5] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2019] [Accepted: 09/20/2019] [Indexed: 12/28/2022] Open
Abstract
Background Chinese wild grapevine (Vitis amurensis) has remarkable cold stress tolerance, exceeding that of the common cultivated grapevine (Vitis vinifera L.). Result Here, we surveyed the expression dynamics of microRNAs (miRNAs) across Chinese wild grapevine (cv. Beibinghong) and cultivated grapevine (cv. Cabernet Sauvignon) under cold stress using high-throughput sequencing. We identified 186 known miRNAs in cultivated grape and 427 known miRNAs in Beibinghong. Of the identified miRNAs, 59 are conserved miRNAs orthologous in Cabernet Sauvignon and Beibinghong. In addition, 105 and 129 novel miRNAs were identified in Cabernet Sauvignon and Beibinghong, respectively. The expression of some miRNAs was related to cold stress both in Cabernet Sauvignon and Beibinghong. Many cold-related miRNAs in Cabernet Sauvignon and Beibinghong were predicted to target stress response-related genes such as MYB, WRKY, bHLH transcription factor genes, and heat shock protein genes. However, the expression tendency under cold treatment of many of these miRNAs was different between Cabernet Sauvignon and Beibinghong. Different modes of expression of cultivated and Chinese wild grape miRNAs were indicated in key pathways under cold stress by degradome, target prediction, GO, and KEGG analyses. Conclusion Our study indicated three likely reasons that led to the different cold stress tolerance levels of Cabernet Sauvignon and Beibinghong. Specifically, there may be (1) differential expression of orthologous miRNAs between cultivated grapevine and Chinese wild grape; (2) species-specific miRNAs or target genes; or (3) different regulatory models of miRNAs in cultivated and Chinese wild grape in some key pathways.
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Affiliation(s)
- Pengfei Wang
- Shandong Academy of Grape; Shandong engineering research center for Grape cultivation and deep-processing, Jinan, People's Republic of China.
| | - Yang Yang
- Shandong Academy of Grape; Shandong engineering research center for Grape cultivation and deep-processing, Jinan, People's Republic of China
| | - Hongmei Shi
- Shandong Academy of Grape; Shandong engineering research center for Grape cultivation and deep-processing, Jinan, People's Republic of China.
| | - Yongmei Wang
- Shandong Academy of Grape; Shandong engineering research center for Grape cultivation and deep-processing, Jinan, People's Republic of China.,Shandong engineering research center for cultivation and deep-processing of grape, Jinan, People's Republic of China.,Key Laboratory of Urban Agriculture (East China), Ministry of Agriculture, Jinan, People's Republic of China
| | - Fengshan Ren
- Shandong Academy of Grape; Shandong engineering research center for Grape cultivation and deep-processing, Jinan, People's Republic of China. .,Shandong engineering research center for cultivation and deep-processing of grape, Jinan, People's Republic of China. .,Key Laboratory of Urban Agriculture (East China), Ministry of Agriculture, Jinan, People's Republic of China.
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16
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Yang S, Luo J, Long Y, Du J, Xu G, Zhao L, Du Z, Luo W, Wang Y, He Z. Mixed Diets Reduce the Oxidative Stress of Common Carp ( Cyprinus carpio): Based on MicroRNA Sequencing. Front Physiol 2019; 10:631. [PMID: 31191340 PMCID: PMC6549001 DOI: 10.3389/fphys.2019.00631] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2018] [Accepted: 05/06/2019] [Indexed: 12/17/2022] Open
Abstract
The rice-fish mode, a mode of ecological aquaculture, has become a popular research topic in recent years. The antioxidant capacity of fish can be affected by the type of diet. Three groups of adult common carp (initial weight 517.8 ± 50 g) were fed earthworm (group A), earthworm + duckweed (group M), and duckweed (group P). The antioxidant capacity of common carp (Cyprinus carpio) was evaluated by histopathological sectioning, antioxidant enzyme activity, and the miRNA transcriptome profile. The pathological changes in group M were lighter than those in groups C and A. The activities of superoxide dismutase (SOD) and glutathione peroxidase (GSH-PX) significantly increased in group M, and the malondialdehyde content (MDA) significantly decreased (p < 0.05). Additionally, nine differentially expressed miRNAs (DEMs) were found between groups A and M, and eight DEMs found between groups P and M were identified in the liver of common carp. Five miRNAs were reported to be related to oxidative stress, including miR-137-3p, miR-143-3p, miR-146a-5p, miR-21-5p, and miR-125b-5p. Compared with group M, all five detected miRNAs were upregulated in group A, and four of the detected miRNAs were upregulated in group P. The targets of the five miRNAs were further predicted via functional analysis. Our study confirmed that omnivorous common carp exhibits stronger antioxidant capacity when feeding on both an animal diet and a plant diet.
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Affiliation(s)
- Song Yang
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, China
| | - Jie Luo
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, China
| | - Yalan Long
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, China
| | - Jie Du
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, China
| | - GangChun Xu
- Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Ministry of Agriculture, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi, China
| | - Liulan Zhao
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, China
| | - Zongjun Du
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, China
| | - Wei Luo
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, China
| | - Yan Wang
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, China
| | - Zhi He
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, China
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17
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Identification and functional prediction of cold-related long non-coding RNA (lncRNA) in grapevine. Sci Rep 2019; 9:6638. [PMID: 31036931 PMCID: PMC6488645 DOI: 10.1038/s41598-019-43269-5] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2018] [Accepted: 04/18/2019] [Indexed: 11/09/2022] Open
Abstract
Plant long non-coding RNA (lncRNA) undergoes dynamic regulation and acts in developmental and stress regulation. In this study, we surveyed the expression dynamics of lncRNAs in grapevine (Vitis vinifera L.) under cold stress using high-throughput sequencing. Two-hundred and three known lncRNAs were significantly up-regulated and 144 known lncRNAs were significantly down-regulated in cold-treated grapevine. In addition, 2 088 novel lncRNA transcripts were identified in this study, with 284 novel lncRNAs significantly up-regulated and 182 novel lncRNAs significantly down-regulated in cold-treated grapevine. Two-hundred and forty-two differentially expressed grapevine lncRNAs were predicted to target 326 protein-coding genes in a cis-regulatory relationship. Many differentially expressed grapevine lncRNAs targeted stress response-related genes, such as CBF4 transcription factor genes, late embryogenesis abundant protein genes, peroxisome biogenesis protein genes, and WRKY transcription factor genes. Sixty-two differentially expressed grapevine lncRNAs were predicted to target 100 protein-coding genes in a trans-regulatory relationship. The expression of overall target genes in both cis and trans-regulatory relationships were positively related to the expression of lncRNAs in grapevines under cold stress. We identified 31 known lncRNAs as 34 grapevine micro RNA (miRNA) precursors and some miRNAs may be derived from multiple lncRNAs. We found 212 lncRNAs acting as targets of miRNAs in grapevines, involving 150 miRNAs; additionally, 120 grapevine genes were predicted as targets of grapevine miRNAs and lncRNAs. We found one gene cluster that was up-regulated and showed the same expression trend. In this cluster, many genes may be involved in abiotic stress response such as WRKY, Hsf, and NAC transcription factor genes.
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18
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Analysis of miRNA-seq in the liver of common carp (Cyprinus carpio L.) in response to different environmental temperatures. Funct Integr Genomics 2018; 19:265-280. [DOI: 10.1007/s10142-018-0643-7] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2018] [Revised: 09/11/2018] [Accepted: 10/25/2018] [Indexed: 02/07/2023]
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19
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miR-34a Regulates Multidrug Resistance via Positively Modulating OAZ2 Signaling in Colon Cancer Cells. J Immunol Res 2018; 2018:7498514. [PMID: 30175154 PMCID: PMC6098920 DOI: 10.1155/2018/7498514] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2018] [Revised: 06/06/2018] [Accepted: 06/12/2018] [Indexed: 02/06/2023] Open
Abstract
Although aberrant expression of miR-34a, an essential tumor suppressor miRNA, has been frequently observed in colon cancer (CCa), whether miR-34a can regulate CCa progression by modulating other facets of this malignancy (such as multidrug resistance, MDR) remains unknown. Here, we report for the first time that miR-34a expression was significantly downregulated in clinical CCa samples from oxaliplatin-resistant patients and in experimentally established multidrug-resistant CCa cells. By using histoculture drug response assay, we further confirmed that clinical CCa samples with lower miR-34a expression appeared to be more resistant to chemotherapy. Functionally, ectopic expression of exogenous miR-34a resensitized multidrug-resistant HCT-8/OR cells to oxaliplatin treatment, whereas miR-34a inhibition augmented the oxaliplatin resistance in chemosensitive HCT-8 cells. Mechanistically, miR-34a positively regulated the mRNA stability of the ornithine decarboxylase antizyme 2 (OAZ2) by directly targeting its three prime untranslated region (3′UTR). Consequently, suppression of the expression of miR-34a/OAZ2 signaling by chemotherapeutic agents significantly enhanced the activation of MDR-associated ATP-binding cassette (ABC) transporters and antiapoptosis pathways, thus leading to MDR development in CCa cells. Collectively, our combined analysis reveals a critical role of miR-34a/OAZ2 cascade in conferring a proper cellular response to CCa chemotherapy.
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20
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Li X, Lv Y, Hao J, Sun H, Gao N, Zhang C, Lu R, Wang S, Yin L, Pu Y, Chen R. Role of microRNA-4516 involved autophagy associated with exposure to fine particulate matter. Oncotarget 2018; 7:45385-45397. [PMID: 27329587 PMCID: PMC5216729 DOI: 10.18632/oncotarget.9978] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2016] [Accepted: 05/23/2016] [Indexed: 12/22/2022] Open
Abstract
Metals are vital toxic components of fine particulate matter (PM2.5). Cellular responses to exposure to PM2.5 or PM metal components remain unknown. Post-transcriptional profiling and subsequent cell- and individual-based assays implied that the metal ion-binding miR-4516/RPL37/autophagy pathway could play a critical role in cellular responses to PM2.5 and PM metal stresses. miR-4516 was up-regulated in A549 cells exposed to PM2.5 and in the serum of individuals living in a city with moderate air pollution. The expression levels of the miR-4516 target genes, namely, RPL37 and UBA52, were involved in ribosome function and inhibited by exposure to PM2.5 and PM metal components. Autophagy in A549 cells was induced by PM2.5 exposure as a response to decreased RPL37 expression. Moreover, enhanced miR-4516 expression was positively correlated with the augmentation of the internal burden of aluminum and lead in individuals living in a city with moderate air pollution. Hereby, the miR-4516/RPL37/autophagy pathway may represent a novel mechanism that mediates responses to PM metal components.
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Affiliation(s)
- Xiaobo Li
- Key Laboratory of Environmental Medicine Engineering, Ministry of Education, School of Public Health, Southeast University, Nanjing 210009, China
| | - Yang Lv
- Department of Histology and Embryology, Hebei North University, Zhangjiakou 075000, China
| | - Jihong Hao
- Clinical Laboratory of The Second Hospital, Hebei Medical University, Shijiazhuang 050000, China
| | - Hao Sun
- Key Laboratory of Environmental Medicine Engineering, Ministry of Education, School of Public Health, Southeast University, Nanjing 210009, China
| | - Na Gao
- Key Laboratory of Environmental Medicine Engineering, Ministry of Education, School of Public Health, Southeast University, Nanjing 210009, China
| | - Chengcheng Zhang
- Key Laboratory of Environmental Medicine Engineering, Ministry of Education, School of Public Health, Southeast University, Nanjing 210009, China
| | - Runze Lu
- Key Laboratory of Environmental Medicine Engineering, Ministry of Education, School of Public Health, Southeast University, Nanjing 210009, China
| | - Shizhi Wang
- Key Laboratory of Environmental Medicine Engineering, Ministry of Education, School of Public Health, Southeast University, Nanjing 210009, China
| | - Lihong Yin
- Key Laboratory of Environmental Medicine Engineering, Ministry of Education, School of Public Health, Southeast University, Nanjing 210009, China
| | - Yuepu Pu
- Key Laboratory of Environmental Medicine Engineering, Ministry of Education, School of Public Health, Southeast University, Nanjing 210009, China
| | - Rui Chen
- Key Laboratory of Environmental Medicine Engineering, Ministry of Education, School of Public Health, Southeast University, Nanjing 210009, China.,State Key Laboratory of Bioelectronics, Southeast University, Nanjing 210096, China
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21
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Cavalleri T, Angelici L, Favero C, Dioni L, Mensi C, Bareggi C, Palleschi A, Rimessi A, Consonni D, Bordini L, Todaro A, Bollati V, Pesatori AC. Plasmatic extracellular vesicle microRNAs in malignant pleural mesothelioma and asbestos-exposed subjects suggest a 2-miRNA signature as potential biomarker of disease. PLoS One 2017; 12:e0176680. [PMID: 28472171 PMCID: PMC5417506 DOI: 10.1371/journal.pone.0176680] [Citation(s) in RCA: 54] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2016] [Accepted: 04/14/2017] [Indexed: 01/29/2023] Open
Abstract
Background Malignant Pleural Mesothelioma (MPM) is an aggressive cancer mainly caused by asbestos exposure and refractory to current therapies. Specific diagnostic markers for early MPM diagnosis are needed. Changes in miRNA expression have been implicated in several diseases and cancers, including MPM. We examined if a specific miRNA signature in plasmatic extracellular vesicles (EV) may help to discriminate between malignant pleural mesothelioma patients (MPM) and subjects with Past Asbestos Exposure (PAE). Methodology/Principal findings We investigated 23 MPM patients and 19 cancer-free subjects with past asbestos exposure (PAE). We screened 754 miRNAs in plasmatic EVs by OpenArray and found 55 differential miRNAs using logistic regression models adjusted for age, sex, BMI, and smoking. Among the top-20 differential miRNAs chosen for validation by Real time PCR, 16 were confirmed. Using receiver operating characteristic (ROC) curve analysis, the most discriminating miRNA combination was given by miR-103a-3p + miR-30e-3p, which generated an AUC of 0.942 (95% CI 0.87–1.00), with a sensitivity of 95.5% and a specificity of 80.0%. Using multivariate Cox regression analysis including gender, age, BMI and smoking we found a Hazard Ratio for miR-103a-3p above the median of 0.37 (95%CI 0.13–1.13) and of 0.51 (95%CI 0.17–1.52) for miR-30e-3p. Conclusions This study suggests EV-associated miR-103a-3p and miR-30e-3p are able to discriminate MPM from PAE subjects. Larger and prospective studies are needed to confirm these two-miRNA signature alone or in combination with other biomarkers as diagnostic tools for MPM.
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Affiliation(s)
- Tommaso Cavalleri
- Department of Gastroenterology, Humanitas Clinical and Research Center, Via Manzoni 56, Rozzano (Milan), Italy
| | - Laura Angelici
- EPIGET—Epidemiology, Epigenetics and Toxicology Lab—Department of Clinical Sciences and Community Health, Università degli Studi di Milano, Via San Barnaba 8, Milan, Italy
| | - Chiara Favero
- EPIGET—Epidemiology, Epigenetics and Toxicology Lab—Department of Clinical Sciences and Community Health, Università degli Studi di Milano, Via San Barnaba 8, Milan, Italy
| | - Laura Dioni
- EPIGET—Epidemiology, Epigenetics and Toxicology Lab—Department of Clinical Sciences and Community Health, Università degli Studi di Milano, Via San Barnaba 8, Milan, Italy
| | - Carolina Mensi
- Fondazione IRCCS Ca’ Granda Ospedale Maggiore Policlinico, Department of Preventive Medicine, Epidemiology Unit, Via San Barnaba 8, Milan, Italy
| | - Claudia Bareggi
- Fondazione IRCCS Ca’ Granda Ospedale Maggiore Policlinico, Medical Oncology Unit, Via F.Sforza 28, Milan, Italy
| | - Alessandro Palleschi
- Fondazione IRCCS Ca’ Granda Ospedale Maggiore Policlinico, Thoracic Surgery and Lung Transplantation Unit, Via F. Sforza 28, Milan, Italy
| | - Arianna Rimessi
- Fondazione IRCCS Ca’ Granda Ospedale Maggiore Policlinico, Thoracic Surgery and Lung Transplantation Unit, Via F. Sforza 28, Milan, Italy
| | - Dario Consonni
- Fondazione IRCCS Ca’ Granda Ospedale Maggiore Policlinico, Department of Preventive Medicine, Epidemiology Unit, Via San Barnaba 8, Milan, Italy
| | - Lorenzo Bordini
- Fondazione IRCCS Ca’ Granda Ospedale Maggiore Policlinico, Department of Preventive Medicine, Occupational Health Unit, Via San Barnaba 8, Milan, Italy
| | - Aldo Todaro
- Fondazione IRCCS Ca’ Granda Ospedale Maggiore Policlinico, Department of Preventive Medicine, Occupational Health Unit, Via San Barnaba 8, Milan, Italy
| | - Valentina Bollati
- EPIGET—Epidemiology, Epigenetics and Toxicology Lab—Department of Clinical Sciences and Community Health, Università degli Studi di Milano, Via San Barnaba 8, Milan, Italy
- Fondazione IRCCS Ca’ Granda Ospedale Maggiore Policlinico, Department of Preventive Medicine, Epidemiology Unit, Via San Barnaba 8, Milan, Italy
| | - Angela Cecilia Pesatori
- EPIGET—Epidemiology, Epigenetics and Toxicology Lab—Department of Clinical Sciences and Community Health, Università degli Studi di Milano, Via San Barnaba 8, Milan, Italy
- Fondazione IRCCS Ca’ Granda Ospedale Maggiore Policlinico, Department of Preventive Medicine, Epidemiology Unit, Via San Barnaba 8, Milan, Italy
- * E-mail:
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Abstract
Kelch-like ECH-associated protein 1 (Keap1), nuclear factor erythroid 2-like factor 2-related factor 2 (Nrf2), and the antioxidant response element (ARE) are interacting components of a master regulatory signaling pathway that coordinates redox homeostasis, cytoprotective responses, and shifts in stem cell state. This study reexamined detailed dose–response (DR) data reported for in vitro Nrf2-ARE activation in human hepatoblastoma HepG2 cell lines containing either a ARE-bla or ARE-luc reporter at 12 different concentrations of each of 15 chemicals. The normalized study data were combined among chemicals exhibiting a positive response, yielding n = 531 (179) DR data for 9 (7) chemicals using the ARE-bla (ARE-luc) assay. Three-parameter linear/kth-power regression fits obtained to each combined set of ARE-bla- or ARE-luc-assay response data provided good fits (R2 = .99 or .91, respectively, Pfit > .99) that each incorporate a highly significant negative initial linear slope (P = 4 × 10−5 or .00025) and an overall J-shaped DR pattern. Results from this reanalysis of high-resolution ARE response data support the hypothesis that nonlinear ARE-mediated adaptive cellular responses to oxidative stress are governed by an ultrasensitive molecular switch.
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Differential processing of small RNAs during endoplasmic reticulum stress. Sci Rep 2017; 7:46080. [PMID: 28452371 PMCID: PMC5408347 DOI: 10.1038/srep46080] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2016] [Accepted: 03/10/2017] [Indexed: 12/30/2022] Open
Abstract
The accumulation of misfolded proteins in the endoplasmic reticulum (ER) lumen due to the disruption of the homeostatic system of the ER leads to the induction of the ER stress response. Cellular stress-induced pathways globally transform genes expression on both the transcriptional and post-transcriptional levels with small RNA involvement as regulators of the stress response. The modulation of small RNA processing might represent an additional layer of a complex stress response program. However, it is poorly understood. Here, we studied changes in expression and small RNAs processing upon ER stress in Jurkat T-cells. Induced by ER-stress, depletion of miRNAs among small RNA composition was accompanied by a global decrease of 3′ mono-adenylated, mono-cytodinylated and a global increase of 3′ mono-uridinylated miRNA isoforms. We observed the specific subset of differentially expressed microRNAs, and also the dramatic induction of 32-nt tRNA fragments precisely phased to 5′ and 3′ ends of tRNA from a subset of tRNA isotypes. The induction of these tRNA fragments was linked to Angiogenin RNase, which mediates translation inhibition. Overall, the global perturbations of the expression and processing of miRNAs and tiRNAs were the most prominent features of small RNA transcriptome changes upon ER stress.
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α-Syntrophin is involved in the survival signaling pathway in myoblasts under menadione-induced oxidative stress. Exp Cell Res 2016; 344:1-10. [DOI: 10.1016/j.yexcr.2016.04.001] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2015] [Revised: 03/31/2016] [Accepted: 04/02/2016] [Indexed: 01/24/2023]
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25
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Bian DL, Wang XM, Huang K, Zhai QX, Yu GB, Wu CH. Expression and regulatory effects of microRNA-182 in osteosarcoma cells: A pilot study. Oncol Lett 2016; 11:3040-3048. [PMID: 27123060 PMCID: PMC4840939 DOI: 10.3892/ol.2016.4375] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2015] [Accepted: 02/19/2016] [Indexed: 12/21/2022] Open
Abstract
The aim of the present study was to evaluate the expression level of microRNA-182 (miRNA-182) in human osteosarcoma (OS) MG-63 cells and OS tissues, and to elucidate the effect of miRNA-182 on the biological activity of tumors. In the present study, the expression of miRNA-182 in human OS MG-63 cells, OS tissues and normal osteoblast hFOB1.19 cells was determined using quantitative polymerase chain reaction. Subsequently, a miRNA-182 mimic and inhibitor were utilized to regulate the expression level of this miRNA in MG-63 cells. Cell viability and proliferation were examined using cell counting kit-8 assays, and cell apoptosis was detected by flow cytometry. Cell invasion and migration assays were performed using Transwell chambers to analyze the biological functions of miRNA-182 in vitro. The present study demonstrated that the expression level of miRNA-182 in MG-63 cells and OS tissues was significantly increased compared with the hFOB1.19 cell line (P<0.05). The present study successfully performed cell transfections of miRNA-182 inhibitor and miRNA-182 mimic into MG-63 cells and achieved the desired transfection efficiency. The present study confirmed that upregulation of miRNA-182 promotes cell apoptosis and inhibits cell viability, proliferation, invasion and migration. The present findings additionally demonstrated that miRNA-182 is a tumor suppressor gene in OS. Therefore, regulating the expression of miRNA-182 may affect the biological behavior of OS cells, which suggests a potential role for miRNA-182 in molecular therapy for malignant tumors.
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Affiliation(s)
- Dong-Lin Bian
- Department of Ultrasound, The First Affiliated Hospital of China Medical University, Shenyang, Liaoning 110001, P.R. China
| | - Xue-Mei Wang
- Department of Ultrasound, The First Affiliated Hospital of China Medical University, Shenyang, Liaoning 110001, P.R. China
| | - Kun Huang
- Department of Ultrasound, The First Affiliated Hospital of China Medical University, Shenyang, Liaoning 110001, P.R. China
| | - Qi-Xi Zhai
- Department of Ultrasound, The First Affiliated Hospital of China Medical University, Shenyang, Liaoning 110001, P.R. China
| | - Gui-Bo Yu
- Key Laboratory of Diagnosis and Interventional Therapy of Liaoning Province, The First Affiliated Hospital of China Medical University, Shenyang, Liaoning 110001, P.R. China
| | - Cheng-Hua Wu
- Department of Radiology, The First Affiliated Hospital of China Medical University, Shenyang, Liaoning 110001, P.R. China
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Gao M, Liu Y, Chen Y, Yin C, Chen JJ, Liu S. miR-214 protects erythroid cells against oxidative stress by targeting ATF4 and EZH2. Free Radic Biol Med 2016; 92:39-49. [PMID: 26791102 DOI: 10.1016/j.freeradbiomed.2016.01.005] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/22/2015] [Revised: 12/23/2015] [Accepted: 01/09/2016] [Indexed: 12/30/2022]
Abstract
Nuclear factor (erythroid-derived 2) like 2 (Nrf2) is a key regulator in protecting cells against stress by targeting many anti-stress response genes. Recent evidence also reveals that Nrf2 functions partially by targeting mircroRNAs (miRNAs). However, the understanding of Nrf2-mediated cytoprotection through miRNA-dependent mechanisms is largely unknown. In the current study, we identified a direct Nrf2 targeting miRNA, miR-214, and demonstrated a protective role of miR-214 in erythroid cells against oxidative stresses generated by radiation, excess iron and arsenic (As) exposure. miR-214 expression was transcriptionally repressed by Nrf2 through a canonical antioxidant response element (ARE) within its promoter region, and this repression is ROS-dependence. The suppression of miR-214 by Nrf2 could antagonize oxidative stress-induced cell death in erythroid cells by two ways. First, miR-214 directly targeted ATF4, a crucial transcriptional factor involved in anti-stress responses, down regulation of miR-214 releases the repression of ATF4 translation and leads to increased ATF4 protein content. Second, miR-214 was able to prevent cell death by targeting EZH2, the catalytic core component of PRC2 complex that is responsible for tri-methylation reaction at lysine 27 (K27) of histone 3 (H3) (H3K27me3), by which As-induced miR-214 reduction resulted in an increased global H3K27me3 level and a compromised overexpression of a pro-apoptotic gene Bim. These two pathways downstream of miR-214 synergistically cooperated to antagonize erythroid cell death upon oxidative stress. Our combined data revealed a protective role of miR-214 signaling in erythroid cells against oxidative stress, and also shed new light on Nrf2-mediated cytoprotective machinery.
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Affiliation(s)
- Ming Gao
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
| | - Yun Liu
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; Key Laboratory of Ion Beam Bioengineering, Hefei Institutes of Physical Science, Chinese Academy of Sciences and Anhui Province, Hefei, Anhui 230031, China
| | - Yue Chen
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; Department of Urology, The Second Hospital of Tianjin Medical University, Tianjin Institute of Urology, Tianjin 300211, China
| | - Chunyang Yin
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
| | - Jane-Jane Chen
- Institute for Medical Engineering and Science, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Sijin Liu
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China.
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Genome-Wide Investigation of MicroRNAs and Their Targets in Response to Freezing Stress in Medicago sativa L., Based on High-Throughput Sequencing. G3-GENES GENOMES GENETICS 2016; 6:755-65. [PMID: 26801649 PMCID: PMC4777136 DOI: 10.1534/g3.115.025981] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Winter damage, especially in northern climates, is a major limitation of the utilization of perennial forages such as alfalfa. Therefore, improving freezing tolerance is imperative in alfalfa genetic breeding. However, freezing tolerance is a complex trait that is determined by many genes. To understand the complex regulation mechanisms of freezing tolerance in alfalfa, we performed small RNA sequencing analysis under cold (4°) and freezing (-8°) stress. The sequencing results revealed that 173 known, and 24 novel miRNAs were expressed, and that the expression of 35 miRNAs was affected by cold and/or freezing stress. Meanwhile, 105 target genes cleaved by these miRNAs were characterized by degradome sequencing. These targets were associated with biological regulation, cellular processes, metabolic processes, and response to stress. Interestingly, most of them were characterized as transcription factors (TFs), including auxin response factors, SBP, NAC, AP2/ERF, and GRF, which play important roles in plant abiotic responses. In addition, important miRNAs and mRNAs involved in nodulation were also identified, for example, the relationship between miR169 and the TF CCAAT (also named as NF-YA/HAP2), which suggested that nodulation has an important function in freezing tolerance in alfalfa. Our results provide valuable information to help determine the molecular mechanisms of freezing tolerance in alfalfa, which will aid the application of these miRNAs and their targets in the improvement of freezing tolerance in alfalfa and related plants.
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Polycyclic Aromatic Hydrocarbons–Associated MicroRNAs and Heart Rate Variability in Coke Oven Workers. J Occup Environ Med 2016; 58:e24-31. [DOI: 10.1097/jom.0000000000000564] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
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29
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Gupta A, Hossain MM, Read DE, Hetz C, Samali A, Gupta S. PERK regulated miR-424(322)-503 cluster fine-tunes activation of IRE1 and ATF6 during Unfolded Protein Response. Sci Rep 2015; 5:18304. [PMID: 26674075 PMCID: PMC4682135 DOI: 10.1038/srep18304] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2015] [Accepted: 11/16/2015] [Indexed: 12/30/2022] Open
Abstract
The endoplasmic reticulum (ER) responds to changes in intracellular homeostasis through activation of the unfolded protein response (UPR). UPR can facilitate the restoration of cellular homeostasis, via the concerted activation of three ER stress sensors, namely IRE1, PERK and ATF6. Global approaches in several cellular contexts have revealed that UPR regulates the expression of many miRNAs that play an important role in the regulation of life and death decisions during UPR. Here we show that expression of miR-424(322)-503 cluster is downregulated during UPR. IRE1 inhibitor (4 μ8C) and deficiency of XBP1 had no effect on downregulation of miR-424(322)-503 during UPR. Treatment of cells with CCT030312, a selective activator of EIF2AK3/PERK signalling, leads to the downregulation of miR-424(322)-503 expression. The repression of miR-424(322)-503 cluster during conditions of ER stress is compromised in PERK-deficient MEFs. miR-424 regulates the expression of ATF6 via a miR-424 binding site in its 3′ UTR and attenuates the ATF6 transcriptional activity during UPR. Further miR-424 had no effect on IRE1-XBP1 axis but enhanced the regulated IRE1-dependent decay (RIDD). Our results suggest that miR-424 constitutes an obligatory fine-tuning mechanism where PERK-mediated downregulation of miR-424(322)-503 cluster regulates optimal activation of IRE1 and ATF6 during conditions of ER stress.
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Affiliation(s)
- Ananya Gupta
- Discipline of Pathology, School of medicine, Clinical Science Institute, National University of Ireland Galway, Ireland.,Lambe Institute for Translational Research, National University of Ireland Galway, Ireland
| | - Muhammad Mosaraf Hossain
- Discipline of Pathology, School of medicine, Clinical Science Institute, National University of Ireland Galway, Ireland.,Lambe Institute for Translational Research, National University of Ireland Galway, Ireland
| | - Danielle E Read
- Discipline of Pathology, School of medicine, Clinical Science Institute, National University of Ireland Galway, Ireland.,Lambe Institute for Translational Research, National University of Ireland Galway, Ireland
| | - Claudio Hetz
- Biomedical Neuroscience Institute, Faculty of Medicine, University of Chile, Santiago, Chile.,Program of Cellular and Molecular Biology, Center for Molecular Studies of the Cell, Institute of Biomedical Sciences, University of Chile, Santiago, Chile.,FONDAP Center for Geroscience, Brain Health and Metabolism, Santiago, Chile
| | - Afshin Samali
- Apoptosis Research Centre, School of Natural Sciences, National University of Ireland Galway, Ireland
| | - Sanjeev Gupta
- Discipline of Pathology, School of medicine, Clinical Science Institute, National University of Ireland Galway, Ireland.,Lambe Institute for Translational Research, National University of Ireland Galway, Ireland
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30
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Bansal S, Luu BE, Storey KB. MicroRNA regulation in heart and skeletal muscle over the freeze–thaw cycle in the freeze tolerant wood frog. J Comp Physiol B 2015; 186:229-41. [DOI: 10.1007/s00360-015-0951-3] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2015] [Revised: 11/09/2015] [Accepted: 11/25/2015] [Indexed: 01/14/2023]
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31
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De Felice B, Manfellotto F, Palumbo A, Troisi J, Zullo F, Di Carlo C, Di Spiezio Sardo A, De Stefano N, Ferbo U, Guida M, Guida M. Genome-wide microRNA expression profiling in placentas from pregnant women exposed to BPA. BMC Med Genomics 2015; 8:56. [PMID: 26345457 PMCID: PMC4562201 DOI: 10.1186/s12920-015-0131-z] [Citation(s) in RCA: 59] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2015] [Accepted: 08/18/2015] [Indexed: 11/10/2022] Open
Abstract
Background Bisphenol A (BPA) is an environmental compounds is known to possess endocrine disruption potentials. Bisphenol A has epigenetic effects as deregulated expression of microRNAs; such epigenetic marks can induce up/down alterations in gene expression that may persist throughout a lifetime. Bisphenol A (BPA) exposure has been documented in pregnant women, but consequences for development of offspring after BPA exposure during pregnancy are not yet widely studied. Therefore, the aim of this study was to gain a comprehensive understanding of microRNAs changes in the placenta transcriptome from pregnant women subjected to therapeutic abortion for fetal malformation and correlate the impact of gestational exposure to BPA on these developmental changes. Methods We performed a comparative analysis of genome wide miRNA expression in placentas from pregnant women exposed to BPA using microarray technology to identify miRNAs which were aberrantly expressed in placentas from malformed fetuses. The expression changes of differential expressed miRNAs in the samples used for microarray were confirmed by qPCR . Beside, we applied various bioinformatics tools to predict the target genes of the identified miR-146a and explore their biological function and downstream pathways. Results We found that miR-146a was significant overexpressed and correlated significantly with BPA accumulation in the placenta from pregnant women living in a polluted area and undergoing therapeutic abortion due to fetal malformations. Beside, we applied various bioinformatics tools to predict the target genes of miR-146a and explore their biological function and downstream pathways. Conclusions For the first time, we found, in humans, that miR-146a was significant over-expressed and correlated significantly with BPA accumulation in the placenta. Our results lead to the suggestion that miRNAs could be potential biomarkers to clarify the mechanisms of environmental diseases.
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Affiliation(s)
- Bruna De Felice
- DISTABIF-Department of Environmental, Biological and Pharmaceutical Sciences and Technologies, University of Naples II, Via Vivaldi 43, 81100, Caserta, Italy.
| | - Francesco Manfellotto
- DISTABIF-Department of Environmental, Biological and Pharmaceutical Sciences and Technologies, University of Naples II, Via Vivaldi 43, 81100, Caserta, Italy.
| | - Annarita Palumbo
- Department of Gynecology and Obstetrics, University of Salerno, Salerno, Italy.
| | - Jacopo Troisi
- Department of Gynecology and Obstetrics, University of Salerno, Salerno, Italy.
| | - Fulvio Zullo
- Department of Gynecology and Obstetrics, University of Salerno, Salerno, Italy.
| | - Costantino Di Carlo
- Department of Gynecology and Obstetrics, University of Naples "Federico II", Naples, Italy.
| | | | - Noè De Stefano
- Department of Pathology, S.Giuseppe Moscati Hosptal, Avellino, Italy.
| | - Umberto Ferbo
- Department of Pathology, S.Giuseppe Moscati Hosptal, Avellino, Italy.
| | - Marco Guida
- Department of Biological Sciences, University of Naples, Naples, Italy.
| | - Maurizio Guida
- Department of Gynecology and Obstetrics, University of Salerno, Salerno, Italy.
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Lambrecht J, Mannaerts I, van Grunsven LA. The role of miRNAs in stress-responsive hepatic stellate cells during liver fibrosis. Front Physiol 2015; 6:209. [PMID: 26283969 PMCID: PMC4516870 DOI: 10.3389/fphys.2015.00209] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2015] [Accepted: 07/13/2015] [Indexed: 12/12/2022] Open
Abstract
The progression of liver fibrosis and cirrhosis is associated with the persistence of an injury causing agent, leading to changes in the extracellular environment and a disruption of the cellular homeostasis of liver resident cells. Recruitment of inflammatory cells, apoptosis of hepatocytes, and changes in liver microvasculature are some examples of changing cellular environment that lead to the induction of stress responses in nearby cells. During liver fibrosis, the major stresses include hypoxia, oxidative stress, and endoplasmic reticulum stress. When hepatic stellate cells (HSCs) are subjected to such stress, they modulate fibrosis progression by induction of their activation toward a myofibroblastic phenotype, or by undergoing apoptosis, and thus helping fibrosis resolution. It is widely accepted that microRNAs are import regulators of gene expression, both during normal cellular homeostasis, as well as in pathologic conditions. MicroRNAs are short RNA sequences that regulate the gene expression by mRNA destabilization and inhibition of mRNA translation. Specific microRNAs have been identified to play a role in the activation process of HSCs on the one hand and in stress-responsive pathways on the other hand in other cell types (Table 2). However, so far there are no reports for the involvement of miRNAs in the different stress responses linked to HSC activation. Here, we review briefly the major stress response pathways and propose several miRNAs to be regulated by these stress responsive pathways in activating HSCs, and discuss their potential specific pro-or anti-fibrotic characteristics.
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Affiliation(s)
- Joeri Lambrecht
- Liver Cell Biology Lab, Department of Biomedical Sciences, Vrije Universiteit Brussel Brussels, Belgium
| | - Inge Mannaerts
- Liver Cell Biology Lab, Department of Biomedical Sciences, Vrije Universiteit Brussel Brussels, Belgium
| | - Leo A van Grunsven
- Liver Cell Biology Lab, Department of Biomedical Sciences, Vrije Universiteit Brussel Brussels, Belgium
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Casati L, Sendra R, Sibilia V, Celotti F. Endocrine disrupters: the new players able to affect the epigenome. Front Cell Dev Biol 2015; 3:37. [PMID: 26151052 PMCID: PMC4471431 DOI: 10.3389/fcell.2015.00037] [Citation(s) in RCA: 59] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2015] [Accepted: 05/17/2015] [Indexed: 01/27/2023] Open
Abstract
Epigenetics represents the way by which the environment is able to program the genome; there are three main levels of epigenetic control on genome: DNA methylation, post-translational histone modification and microRNA expression. The term Epigenetics has been widened by NIH to include “both heritable changes in gene activity and expression but also stable, long-term alterations in the transcriptional potential of a cell that are not necessarily heritable.” These changes might be produced mostly by the early life environment and might affect health influencing the susceptibility to develop diseases, from cancer to mental disorder, during the entire life span. The most studied environmental influences acting on epigenome are diet, infections, wasting, child care, smoking and environmental pollutants, in particular endocrine disrupters (EDs). These are environmental xenobiotics able to interfere with the normal development of the male and female reproductive systems of wildlife, of experimental animals and possibly of humans, disrupting the normal reproductive functions. Data from literature indicate that EDs can act at different levels of epigenetic control, in some cases transgenerationally, in particular when the exposure to these compounds occurs during the prenatal and earliest period of life. Some of the best characterized EDs will be considered in this review. Among the EDs, vinclozolin (VZ), and methoxychlor (MXC) promote epigenetic transgenerational effects. Polychlorinated biphenils (PCBs), the most widespread environmental EDs, affect histone post-translational modifications in a dimorphic way, possibly as the result of an alteration of gene expression of the enzymes involved in histone modification, as the demethylase Jarid1b, an enzyme also involved in regulating the interaction of androgens with their receptor.
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Affiliation(s)
- Lavinia Casati
- Department of Medical Biotechnology and Translational Medicine, University of Milan Milan, Italy
| | - Ramon Sendra
- Departament de Bioquímica i Biologia Molecular, Universitat de València Valencia, Spain
| | - Valeria Sibilia
- Department of Medical Biotechnology and Translational Medicine, University of Milan Milan, Italy
| | - Fabio Celotti
- Department of Pharmacological and Biomolecular Sciences, University of Milan Milan, Italy
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Riccio A, Gogliettino M, Palmieri G, Balestrieri M, Facchiano A, Rossi M, Palumbo S, Monti G, Cocca E. A New APEH Cluster with Antioxidant Functions in the Antarctic Hemoglobinless Icefish Chionodraco hamatus. PLoS One 2015; 10:e0125594. [PMID: 25946123 PMCID: PMC4422685 DOI: 10.1371/journal.pone.0125594] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2014] [Accepted: 03/16/2015] [Indexed: 11/19/2022] Open
Abstract
Acylpeptide hydrolase (APEH) is a ubiquitous cytosolic protease that plays an important role in the detoxification of oxidised proteins. In this work, to further explore the physiological role of this enzyme, two apeh cDNAs were isolated from the Chionodraco hamatus icefish, which lives in the highly oxygenated Antarctic marine environment. The encoded proteins (APEH-1(Ch) and APEH-2(Ch)) were characterised in comparison with the uniquely expressed isoform from the temperate fish Dicentrarchus labrax (APEH-1Dl) and the two APEHs from the red-blooded Antarctic fish Trematomus bernacchii (APEH-1(Tb) and APEH-2(Tb)). Homology modelling and kinetic characterisation of the APEH isoforms provided new insights into their structure/function properties. APEH-2 isoforms were the only ones capable of hydrolysing oxidised proteins, with APEH-2(Ch) being more efficient than APEH-2(Tb) at this specific function. Therefore, this ability of APEH-2 isoforms is the result of an evolutionary adaptation due to the pressure of a richly oxygenated environment. The lack of expression of APEH-2 in the tissues of the temperate fish used as the controls further supported this hypothesis. In addition, analysis of gene expression showed a significant discrepancy between the levels of transcripts and those of proteins, especially for apeh-2 genes, which suggests the presence of post-transcriptional regulation mechanisms, triggered by cold-induced oxidative stress, that produce high basal levels of APEH-2 mRNA as a reserve that is ready to use in case of the accumulation of oxidised proteins.
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Affiliation(s)
- Alessia Riccio
- National Research Council, Institute of Biosciences and BioResources (CNR-IBBR), Napoli, Italy
| | - Marta Gogliettino
- National Research Council, Institute of Biosciences and BioResources (CNR-IBBR), Napoli, Italy
| | - Gianna Palmieri
- National Research Council, Institute of Biosciences and BioResources (CNR-IBBR), Napoli, Italy
- * E-mail:
| | - Marco Balestrieri
- National Research Council, Institute of Biosciences and BioResources (CNR-IBBR), Napoli, Italy
| | - Angelo Facchiano
- National Research Council, Institute of Food Sciences (CNR-ISA), Avellino, Italy
| | - Mosè Rossi
- National Research Council, Institute of Biosciences and BioResources (CNR-IBBR), Napoli, Italy
| | - Stefania Palumbo
- National Research Council, Institute of Biosciences and BioResources (CNR-IBBR), Napoli, Italy
| | | | - Ennio Cocca
- National Research Council, Institute of Biosciences and BioResources (CNR-IBBR), Napoli, Italy
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35
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Hou N, Han J, Li J, Liu Y, Qin Y, Ni L, Song T, Huang C. MicroRNA profiling in human colon cancer cells during 5-fluorouracil-induced autophagy. PLoS One 2014; 9:e114779. [PMID: 25526515 PMCID: PMC4272278 DOI: 10.1371/journal.pone.0114779] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2014] [Accepted: 11/13/2014] [Indexed: 11/18/2022] Open
Abstract
Autophagy modulation is now recognized as a potential therapeutic approach for cancer (including colorectal cancer), yet the molecular mechanisms regulating autophagy in response to cellular stress are still not well understood. MicroRNAs (miRNAs) have been found to play important roles in controlling many cellular functions, including growth, metabolism and stress response. The physiological importance of the miRNA-autophagy interconnection is only beginning to be elucidated. MiRNA microarray technology facilitates analysis of global miRNA expression in certain situations. In this study, we explored the expression profile of miRNAs during the response of human colon cancer cells (HT29s) to 5-FU treatment and nutrient starvation using miRNA microarray analysis. The alteration of miRNA expression showed the same pattern under both conditions was further testified by qRT-PCR in three human colon cancer cell lines. In addition, bioinformatic prediction of target genes, pathway analysis and gene network analysis were performed to better understand the roles of these miRNAs in the regulation of autophagy. We identified and selected four downregulated miRNAs including hsa-miR-302a-3p and 27 upregulated miRNAs under these two conditions as having the potential to target genes involved in the regulation of autophagy in human colon cancer cells. They have the potential to modulate autophagy in 5-FU-based chemotherapy in colorectal cancer.
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Affiliation(s)
- Ni Hou
- Department of Genetics and Molecular Biology, Xi'an Jiaotong University School of Medicine, Xi'an, China
| | - Jia Han
- Department of Genetics and Molecular Biology, Xi'an Jiaotong University School of Medicine, Xi'an, China
| | - Jie Li
- Department of General Surgery, the Second Affiliated Hospital, Xi'an Jiaotong University School of Medicine, Xi'an, China
| | - Yingxun Liu
- Department of Genetics and Molecular Biology, Xi'an Jiaotong University School of Medicine, Xi'an, China
| | - Yannan Qin
- Department of Genetics and Molecular Biology, Xi'an Jiaotong University School of Medicine, Xi'an, China
| | - Lei Ni
- Department of Genetics and Molecular Biology, Xi'an Jiaotong University School of Medicine, Xi'an, China
| | - Tusheng Song
- Department of Genetics and Molecular Biology, Xi'an Jiaotong University School of Medicine, Xi'an, China
| | - Chen Huang
- Department of Genetics and Molecular Biology, Xi'an Jiaotong University School of Medicine, Xi'an, China
- Key Laboratory of Environment and Genes Related to Diseases, Xi'an Jiaotong University School of Medicine, Xi'an, China
- Cardiovascular Research Center, Xi'an Jiaotong University School of Medicine, Xi'an, China
- * E-mail:
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36
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Read DE, Gupta A, Ladilov Y, Samali A, Gupta S. miRNA signature of unfolded protein response in H9c2 rat cardiomyoblasts. Cell Biosci 2014; 4:56. [PMID: 25302112 PMCID: PMC4190440 DOI: 10.1186/2045-3701-4-56] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2014] [Accepted: 09/11/2014] [Indexed: 11/28/2022] Open
Abstract
Background Glucose and oxygen deprivation during ischemia is known to affect the homeostasis of the endoplasmic reticulum (ER) in ways predicted to activate the unfolded protein response (UPR). Activation of UPR signalling due to ER stress is associated with the development of myocardial infarction (MI). MicroRNAs (miRNAs) are key regulators of cardiovascular development and deregulation of miRNA expression is involved in the onset of many cardiovascular diseases. However, little is known about the mechanisms regulating the miRNA expression in the cardiovascular system during disease development and progression. Here we performed genome-wide miRNA expression profiling in rat cardiomyoblasts to identify the miRNAs deregulated during UPR, a crucial component of ischemia. Results We found that expression of 86 microRNAs changed significantly during conditions of UPR in H9c2 cardiomyoblasts. We found that miRNAs with known function in cardiomyoblasts biology (miR-206, miR-24, miR-125b, miR-133b) were significantly deregulated during the conditions of UPR in H9c2 cells. The expression of miR-7a was upregulated by UPR and simulated in vitro ischemia in cardiomyoblasts. Further, ectopic expression of miR-7a provides resistance against UPR-mediated apoptosis in cardiomyoblasts. The ample overlap of miRNA expression signature between our analysis and different models of cardiac dysfunction further confirms the role of UPR in cardiovascular diseases. Conclusions This study demonstrates the role of UPR in deregulating the expression of miRNAs in MI. Our results provide novel insights about the molecular mechanisms of deregulated miRNA expression during the heart disease pathogenesis.
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Affiliation(s)
- Danielle E Read
- Discipline of Pathology, School of medicine, Clinical Science Institute, National University of Ireland Galway, Galway, Ireland
| | - Ananya Gupta
- Discipline of Pathology, School of medicine, Clinical Science Institute, National University of Ireland Galway, Galway, Ireland
| | - Yury Ladilov
- Center for Cardiovascular Research, Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Afshin Samali
- Apoptosis Research Centre, School of Natural Sciences, National University of Ireland Galway, Galway, Ireland
| | - Sanjeev Gupta
- Discipline of Pathology, School of medicine, Clinical Science Institute, National University of Ireland Galway, Galway, Ireland
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Kanherkar RR, Bhatia-Dey N, Csoka AB. Epigenetics across the human lifespan. Front Cell Dev Biol 2014; 2:49. [PMID: 25364756 PMCID: PMC4207041 DOI: 10.3389/fcell.2014.00049] [Citation(s) in RCA: 209] [Impact Index Per Article: 20.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2014] [Accepted: 08/22/2014] [Indexed: 12/17/2022] Open
Abstract
Epigenetics has the potential to explain various biological phenomena that have heretofore defied complete explication. This review describes the various types of endogenous human developmental milestones such as birth, puberty, and menopause, as well as the diverse exogenous environmental factors that influence human health, in a chronological epigenetic context. We describe the entire course of human life from periconception to death and chronologically note all of the potential internal timepoints and external factors that influence the human epigenome. Ultimately, the environment presents these various factors to the individual that influence the epigenome, and the unique epigenetic and genetic profile of each individual also modulates the specific response to these factors. During the course of human life, we are exposed to an environment that abounds with a potent and dynamic milieu capable of triggering chemical changes that activate or silence genes. There is constant interaction between the external and internal environments that is required for normal development and health maintenance as well as for influencing disease load and resistance. For example, exposure to pharmaceutical and toxic chemicals, diet, stress, exercise, and other environmental factors are capable of eliciting positive or negative epigenetic modifications with lasting effects on development, metabolism and health. These can impact the body so profoundly as to permanently alter the epigenetic profile of an individual. We also present a comprehensive new hypothesis of how these diverse environmental factors cause both direct and indirect epigenetic changes and how this knowledge can ultimately be used to improve personalized medicine.
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Affiliation(s)
- Riya R Kanherkar
- Epigenetics Laboratory, Department of Anatomy, Howard University Washington, DC, USA
| | - Naina Bhatia-Dey
- Epigenetics Laboratory, Department of Anatomy, Howard University Washington, DC, USA
| | - Antonei B Csoka
- Epigenetics Laboratory, Department of Anatomy, Howard University Washington, DC, USA
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38
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Identification and expression of microRNA in the brain of hibernating bats, Myotis lucifugus. Gene 2014; 544:67-74. [DOI: 10.1016/j.gene.2014.04.048] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2014] [Revised: 03/19/2014] [Accepted: 04/22/2014] [Indexed: 01/05/2023]
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Dorairaj JJ, Salzman DW, Wall D, Rounds T, Preskill C, Sullivan CAW, Lindner R, Curran C, Lezon-Geyda K, McVeigh T, Harris L, Newell J, Kerin MJ, Wood M, Miller N, Weidhaas JB. A germline mutation in the BRCA1 3'UTR predicts Stage IV breast cancer. BMC Cancer 2014; 14:421. [PMID: 24915755 PMCID: PMC4059881 DOI: 10.1186/1471-2407-14-421] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2013] [Accepted: 05/14/2014] [Indexed: 01/22/2023] Open
Abstract
Background A germline, variant in the BRCA1 3’UTR (rs8176318) was previously shown to predict breast and ovarian cancer risk in women from high-risk families, as well as increased risk of triple negative breast cancer. Here, we tested the hypothesis that this variant predicts tumor biology, like other 3’UTR mutations in cancer. Methods The impact of the BRCA1-3’UTR-variant on BRCA1 gene expression, and altered response to external stimuli was tested in vitro using a luciferase reporter assay. Gene expression was further tested in vivo by immunoflourescence staining on breast tumor tissue, comparing triple negative patient samples with the variant (TG or TT) or non-variant (GG) BRCA1 3’UTR. To determine the significance of the variant on clinically relevant endpoints, a comprehensive collection of West-Irish breast cancer patients were tested for the variant. Finally, an association of the variant with breast screening clinical phenotypes was evaluated using a cohort of women from the High Risk Breast Program at the University of Vermont. Results Luciferase reporters with the BRCA1-3’UTR-variant (T allele) displayed significantly lower gene expression, as well as altered response to external hormonal stimuli, compared to the non-variant 3’UTR (G allele) in breast cancer cell lines. This was confirmed clinically by the finding of reduced BRCA1 gene expression in triple negative samples from patients carrying the homozygous TT variant, compared to non-variant patients. The BRCA1-3’UTR-variant (TG or TT) also associated with a modest increased risk for developing breast cancer in the West-Irish cohort (OR = 1.4, 95% CI 1.1-1.8, p = 0.033). More importantly, patients with the BRCA1-3’UTR-variant had a 4-fold increased risk of presenting with Stage IV disease (p = 0.018, OR = 3.37, 95% CI 1.3-11.0). Supporting that this finding is due to tumor biology, and not difficulty screening, obese women with the BRCA1-3’UTR-variant had significantly less dense breasts (p = 0.0398) in the Vermont cohort. Conclusion A variant in the 3’UTR of BRCA1 is functional, leading to decreased BRCA1 expression, modest increased breast cancer risk, and most importantly, presentation with stage IV breast cancer, likely due to aggressive tumor biology.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | - Joanne B Weidhaas
- Department of Therapeutic Radiology, Yale School of Medicine, New Haven, CT 06510, USA.
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Bollati V, Angelici L, Rizzo G, Pergoli L, Rota F, Hoxha M, Nordio F, Bonzini M, Tarantini L, Cantone L, Pesatori AC, Apostoli P, Baccarelli AA, Bertazzi PA. Microvesicle-associated microRNA expression is altered upon particulate matter exposure in healthy workers and in A549 cells. J Appl Toxicol 2014; 35:59-67. [PMID: 24515752 PMCID: PMC4125569 DOI: 10.1002/jat.2987] [Citation(s) in RCA: 70] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2013] [Revised: 12/12/2013] [Accepted: 12/14/2013] [Indexed: 01/03/2023]
Abstract
Cardiovascular disease risk has been consistently linked with particulate matter (PM) exposure. Cell-derived microvesicles (MVs) are released into plasma and transfer microRNAs (miRNAs) between tissues. MVs can be produced by the respiratory system in response to proinflammatory triggers, enter the circulatory system and remotely modify gene expression in cardiovascular tissues. However, whether PM affects MV signaling has never been investigated. In this study, we evaluated expression of microRNAs contained within plasma MVs upon PM exposure both in vivo and in vitro. In the in vivo study, we isolated plasma MVs from healthy steel plant workers before and after workplace PM exposure. We measured the expression of 88 MV-associated miRNAs by real-time polymerase chain reaction. To assess a possible source of the MV miRNAs identified in vivo, we measured their miRNA expression in PM-treated A549 pulmonary cell lines in vitro. MiRNA profiling of plasma MVs showed 5.62- and 13.95-fold increased expression of miR-128 and miR-302c, respectively, after 3 days of workplace PM exposure (P < 0.001). According to Ingenuity Pathway Analysis, miR-128 is part of coronary artery disease pathways, and miR-302c is part of coronary artery disease, cardiac hypertrophy and heart failure pathways. In vitro experiments confirmed a dose-dependent expression of miR-128 in MVs released from A549 cells after 6 h of PM treatment (P = 0.030). MiR-302c was expressed neither from A549 cells nor in reference lung RNA. These results suggest novel PM-activated molecular mechanisms that may mediate the effects of air pollution and could lead to the identification of new diagnostic and therapeutic interventions.
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Affiliation(s)
- Valentina Bollati
- Center of Molecular and Genetic Epidemiology, Department of Clinical Sciences and Community Health, Università degli Studi di Milano, Milan, Italy; Epidemiology Unit, Fondazione Cà Granda IRCCS Ospedale Maggiore Policlinico, Milan, Italy
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Spatial and temporal expression levels of specific microRNAs in a spinal cord injury mouse model and their relationship to the duration of compression. Spine J 2014; 14:353-60. [PMID: 24269082 DOI: 10.1016/j.spinee.2013.08.015] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/16/2012] [Revised: 07/16/2013] [Accepted: 08/21/2013] [Indexed: 02/03/2023]
Abstract
BACKGROUND CONTEXT MicroRNAs, a class of small nonprotein-coding RNAs, are thought to control gene translation into proteins. The latter are the ultimate effectors of the biochemical cascade occurring in any physiological and pathological process. MicroRNAs have been shown to change their expression levels during injury of spinal cord in contusion rodent models. Compression is the most frequent mode of damage of neural elements in spinal cord injury. The cellular and molecular changes occurring in the spinal cord during prolonged compression are not very well elucidated. Understanding the underlying molecular events that occur during sustained compression is paramount in building new therapeutic strategies. PURPOSE The purpose of our study was to probe the relationship between the expression level changes of different miRNAs and the timing of spinal cord decompression in a mouse model. STUDY DESIGN A compression spinal cord injury mouse model was used for the study. METHODS A laminectomy was performed in the thoracic spine of C57BL/6 mice. Then, the thecal sac was compressed to create the injury. Decompression was performed early for one group and it was delayed in the second group. The spinal cord at the epicenter of the injury and one level rostral to it were removed at 3, 6, and 24 hours after trauma, and RNA was extracted. Expression levels of six different microRNAs and the relationship to the duration of compression were analyzed. This work was supported in part by the University Research Council Grants Program at the University of Texas Health Science Center San Antonio (Grant 130267). There are no specific conflicts of interest to be disclosed for this work. RESULTS Expression levels of microRNAs in the prolonged compression of spinal cord model were significantly different compared with the expression levels in the short duration of compression spinal cord injury model. Furthermore, microRNAs show a different expression pattern in different regions of the injured spinal cord. CONCLUSIONS Our findings demonstrate that spinal cord compression causes alterations in the expression of different miRNAs in the acute phase of injury. Their expression is related to the duration of the compression of the spinal cord. These findings suggest that early decompression of the spinal cord may have an important modulating effect on the molecular cascade triggered during secondary injury through the changes in expression levels of specific microRNAs.
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Savarimuthu Francis SM, Davidson MR, Tan ME, Wright CM, Clarke BE, Duhig EE, Bowman RV, Hayward NK, Fong KM, Yang IA. MicroRNA-34c is associated with emphysema severity and modulates SERPINE1 expression. BMC Genomics 2014; 15:88. [PMID: 24479666 PMCID: PMC3922660 DOI: 10.1186/1471-2164-15-88] [Citation(s) in RCA: 65] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2012] [Accepted: 01/23/2014] [Indexed: 12/11/2022] Open
Abstract
BACKGROUND MicroRNAs (MiRNA) are small non-coding RNAs that regulate gene expression. The aim of this study was to identify miRNAs differentially expressed between mild and moderately emphysematous lung, as well as their functional target mRNAs. Resected lung from patients with COPD undergoing lung cancer surgery was profiled using miRNA (Agilent Human miRNA profiler G4470 V1.01) and mRNA (OperonV2.0) microarrays. Cells of lung origin (BEAS-2B and HFL1) were profiled using mRNA microarrays (Illumina HumanHT-12 V3) after in vitro manipulation. RESULTS COPD patients had mean (SD) age 68 (6) years, FEV1 72 (17)% predicted and gas transfer (KCO) 70 (10)% predicted. Five miRNAs (miR-34c, miR-34b, miR-149, miR-133a and miR-133b) were significantly down-regulated in lung from patients with moderate compared to mild emphysema as defined by gas transfer (p < 0.01). In vitro upregulation of miR-34c in respiratory cells led to down-regulation of predicted target mRNAs, including SERPINE1, MAP4K4, ZNF3, ALDOA and HNF4A. The fold change in ex-vivo expression of all five predicted target genes inversely correlated with that of miR-34c in emphysematous lung, but this relationship was strongest for SERPINE1 (p = 0.05). CONCLUSION Differences in miRNA expression are associated with emphysema severity in COPD patients. MiR-34c modulates expression of its putative target gene, SERPINE1, in vitro in respiratory cell lines and ex vivo in emphysematous lung tissue.
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Izzotti A, Pulliero A. The effects of environmental chemical carcinogens on the microRNA machinery. Int J Hyg Environ Health 2014; 217:601-27. [PMID: 24560354 DOI: 10.1016/j.ijheh.2014.01.001] [Citation(s) in RCA: 86] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2013] [Revised: 01/03/2014] [Accepted: 01/06/2014] [Indexed: 12/29/2022]
Abstract
The first evidence that microRNA expression is early altered by exposure to environmental chemical carcinogens in still healthy organisms was obtained for cigarette smoke. To date, the cumulative experimental data indicate that similar effects are caused by a variety of environmental carcinogens, including polycyclic aromatic hydrocarbons, nitropyrenes, endocrine disruptors, airborne mixtures, carcinogens in food and water, and carcinogenic drugs. Accordingly, the alteration of miRNA expression is a general mechanism that plays an important pathogenic role in linking exposure to environmental toxic agents with their pathological consequences, mainly including cancer development. This review summarizes the existing experimental evidence concerning the effects of chemical carcinogens on the microRNA machinery. For each carcinogen, the specific microRNA alteration signature, as detected in experimental studies, is reported. These data are useful for applying microRNA alterations as early biomarkers of biological effects in healthy organisms exposed to environmental carcinogens. However, microRNA alteration results in carcinogenesis only if accompanied by other molecular damages. As an example, microRNAs altered by chemical carcinogens often inhibits the expression of mutated oncogenes. The long-term exposure to chemical carcinogens causes irreversible suppression of microRNA expression thus allowing the transduction into proteins of mutated oncogenes. This review also analyzes the existing knowledge regarding the mechanisms by which environmental carcinogens alter microRNA expression. The underlying molecular mechanism involves p53-microRNA interconnection, microRNA adduct formation, and alterations of Dicer function. On the whole, reported findings provide evidence that microRNA analysis is a molecular toxicology tool that can elucidate the pathogenic mechanisms activated by environmental carcinogens.
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Affiliation(s)
- A Izzotti
- Department of Health Sciences, University of Genoa, Italy; Mutagenesis Unit, IRCCS University Hospital San Martino - IST National Research Cancer Institute, Genoa, Italy.
| | - A Pulliero
- Department of Health Sciences, University of Genoa, Italy
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MiR-34a regulates apoptosis in liver cells by targeting the KLF4 gene. Cell Mol Biol Lett 2014; 19:52-64. [PMID: 24415058 PMCID: PMC6275989 DOI: 10.2478/s11658-013-0115-y] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2013] [Revised: 12/28/2013] [Indexed: 02/07/2023] Open
Abstract
MicroRNAs (miRNAs) regulate gene expression by inhibiting translation or targeting messenger RNA (mRNA) for degradation in a posttranscriptional fashion. In this study, we show that ectopic expression of miR-34a-5p reduces the mRNA and protein levels of Krüppel-like factor 4 (KLF4). We also demonstrate that miR-34a targets the 3′-untranslated mRNA region of KLF4 and show that overexpression of miR-34a induces a significant level of apoptosis in BNL CL.2 cells exposed to doxorubicin or 10 Gy X-ray. Our data suggest that the effects of miR-34a on apoptosis occur due to the downregulation of KLF4.
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Bao B, Azmi AS, Li Y, Ahmad A, Ali S, Banerjee S, Kong D, Sarkar FH. Targeting CSCs in tumor microenvironment: the potential role of ROS-associated miRNAs in tumor aggressiveness. Curr Stem Cell Res Ther 2014; 9:22-35. [PMID: 23957937 PMCID: PMC4493722 DOI: 10.2174/1574888x113089990053] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2013] [Revised: 08/01/2013] [Accepted: 08/06/2013] [Indexed: 02/07/2023]
Abstract
Reactive oxygen species (ROS) have been widely considered as critical cellular signaling molecules involving in various biological processes such as cell growth, differentiation, proliferation, apoptosis, and angiogenesis. The homeostasis of ROS is critical to maintain normal biological processes. Increased production of ROS, namely oxidative stress, due to either endogenous or exogenous sources causes irreversible damage of bio-molecules such as DNA, proteins, lipids, and sugars, leading to genomic instability, genetic mutation, and altered gene expression, eventually contributing to tumorigenesis. A great amount of experimental studies in vitro and in vivo have produced solid evidence supporting that oxidative stress is strongly associated with increased tumor cell growth, treatment resistance, and metastasis, and all of which contribute to tumor aggressiveness. More recently, the data have indicated that altered production of ROS is also associated with cancer stem cells (CSCs), epithelial-to-mesenchymal transition (EMT), and hypoxia, the most common features or phenomena in tumorigenesis and tumor progression. However, the exact mechanism by which ROS is involved in the regulation of CSC and EMT characteristics as well as hypoxia- and, especially, HIF-mediated pathways is not well known. Emerging evidence suggests the role of miRNAs in tumorigenesis and progression of human tumors. Recently, the data have indicated that altered productions of ROS are associated with deregulated expression of miRNAs, suggesting their potential roles in the regulation of ROS production. Therefore, targeting ROS mediated through the deregulation of miRNAs by novel approaches or by naturally occurring anti-oxidant agents such as genistein could provide a new therapeutic approach for the prevention and/or treatment of human malignancies. In this article, we will discuss the potential role of miRNAs in the regulation of ROS production during tumorigenesis. Finally, we will discuss the role of genistein, as a potent anti-tumor agent in the regulation of ROS production during tumorigenesis and tumor development.
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Affiliation(s)
| | | | | | | | | | | | | | - Fazlul H Sarkar
- Departments of Pathology and Oncology, Karmanos Cancer Institute, Wayne State University School of Medicine, 740 HWCRC, 4100 John R Street, Detroit, MI 48201, USA.
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DNA modifications in atherosclerosis: From the past to the future. Atherosclerosis 2013; 230:202-9. [DOI: 10.1016/j.atherosclerosis.2013.07.038] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/14/2013] [Revised: 07/08/2013] [Accepted: 07/15/2013] [Indexed: 11/19/2022]
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Abstract
Although severe stress can elicit toxicity, mild stress often elicits adaptations. Here we review the literature on stress-induced adaptations versus stress sensitization in models of neurodegenerative diseases. We also describe our recent findings that chronic proteotoxic stress can elicit adaptations if the dose is low but that high-dose proteotoxic stress sensitizes cells to subsequent challenges. In these experiments, long-term, low-dose proteasome inhibition elicited protection in a superoxide dismutase-dependent manner. In contrast, acute, high-dose proteotoxic stress sensitized cells to subsequent proteotoxic challenges by eliciting catastrophic loss of glutathione. However, even in the latter model of synergistic toxicity, several defensive proteins were upregulated by severe proteotoxicity. This led us to wonder whether high-dose proteotoxic stress can elicit protection against subsequent challenges in astrocytes, a cell type well known for their resilience. In support of this new hypothesis, we found that the astrocytes that survived severe proteotoxicity became harder to kill. The adaptive mechanism was glutathione dependent. If these findings can be generalized to the human brain, similar endogenous adaptations may help explain why neurodegenerative diseases are so delayed in appearance and so slow to progress. In contrast, sensitization to severe stress may explain why defenses eventually collapse in vulnerable neurons.
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Affiliation(s)
- Rehana K Leak
- Division of Pharmaceutical Sciences, Mylan School of Pharmacy, Duquesne University
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Abstract
MicroRNAs (miRNAs) are 18- to 22-nucleotide-long, single-stranded, noncoding RNAs that regulate important biological processes including differentiation, proliferation, and response to cellular stressors such as hypoxia, nutrient depletion, and traversion of the cell cycle by controlling protein expression within the cell. Many investigators have profiled cancer tissue and serum miRNAs to identify potential therapeutic targets, understand the pathways involved in tumorigenesis, and identify diagnostic tumor signatures. In the setting of pancreatic cancer, obtaining pancreatic tissue is invasive and impractical for early diagnosis. Several groups have profiled miRNAs that are present in the blood as a means to diagnose tumor progression and predict prognosis/survival or drug resistance. Several miRNA signatures found in pancreatic tissue and the peripheral blood, as well as the pathways that are associated with pancreatic cancer, are reviewed here in detail. Three miRNA biomarkers (miR-21, miR-155, and miR-200) have been repetitively identified in both pancreatic cancer tissue and patients' blood. Those miRNAs regulate and are regulated by the central genetic and epigenetic changes observed in pancreatic cancer including p53, transforming growth factor β, p16(INK4A), BRCA1/2, and Kras. These miRNAs are involved in DNA repair, cell cycle, and cell invasion and also play important roles in promoting metastases.
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Won KY, Kim YW, Kim HS, Lee SK, Jung WW, Park YK. MicroRNA-199b-5p is involved in the Notch signaling pathway in osteosarcoma. Hum Pathol 2013; 44:1648-55. [PMID: 23574781 DOI: 10.1016/j.humpath.2013.01.016] [Citation(s) in RCA: 60] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/26/2012] [Revised: 01/15/2013] [Accepted: 01/18/2013] [Indexed: 12/21/2022]
Abstract
MicroRNAs (miRNAs) play important roles in the development, differentiation, and function of different cell types and in the pathogenesis of various human diseases. miRNAs are differentially expressed in normal and cancer cells. The investigation of miRNA expression between healthy subjects and patients with osteosarcoma is crucial for future clinical trials. We performed miRNA microarray analysis on 8 formalin-fixed, paraffin-embedded osteosarcoma tissue samples. We confirmed the results of the microarray analysis using reverse transcription polymerase chain reaction. miRNA profiling of osteosarcoma tissue samples showed that expression of 10 miRNAs had increased 10-fold compared with normal controls. Among the 10 miRNAs, 3 miRNAs (miR-199b-5p, miR-338-3p, and miR-891a) were confirmed to have been up-regulated by reverse transcription polymerase chain reaction. After transfection of 4 osteosarcoma cell lines with miR-199b-5p inhibitor, the expression of Notch pathway components in the transfected cell lines was changed. These results revealed that miR-199b-5p plays a role in Notch signaling in osteosarcoma. Recently, the inhibition of Notch and HES1 signaling has been suggested as a potential therapeutic strategy to prevent metastasis in human osteosarcoma. Taken together with our results, we suggest that miR-199b-5p inhibitor may also be a therapeutic option for osteosarcoma.
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Affiliation(s)
- Kyu Yeoun Won
- Department of Pathology, Kyung Hee University Hospital at Gangdong, Kyung Hee University, Seoul 134-727, Korea
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Guida M, Marra M, Zullo F, Guida M, Trifuoggi M, Biffali E, Borra M, De Mieri G, D’Alessandro R, De Felice B. Association between exposure to dioxin-like polychlorinated biphenyls and miR-191 expression in human peripheral blood mononuclear cells. MUTATION RESEARCH-GENETIC TOXICOLOGY AND ENVIRONMENTAL MUTAGENESIS 2013; 753:36-41. [DOI: 10.1016/j.mrgentox.2012.12.018] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/14/2012] [Revised: 11/02/2012] [Accepted: 12/22/2012] [Indexed: 10/27/2022]
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