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Zhang YS, Tu B, Song K, Lin LC, Liu ZY, Lu D, Chen Q, Tao H. Epigenetic hallmarks in pulmonary fibrosis: New advances and perspectives. Cell Signal 2023; 110:110842. [PMID: 37544633 DOI: 10.1016/j.cellsig.2023.110842] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2023] [Revised: 07/25/2023] [Accepted: 08/03/2023] [Indexed: 08/08/2023]
Abstract
Epigenetics indicates that certain phenotypes of an organism can undergo heritable changes in the absence of changes in the genetic DNA sequence. Many studies have shown that epigenetic patterns play an important role in the lung and lung diseases. Pulmonary fibrosis (PF) is also a type of lung disease. PF is an end-stage change of a large group of lung diseases, characterized by fibroblast proliferation and massive accumulation of extracellular matrix, accompanied by inflammatory injury and histological destruction, that is, structural abnormalities caused by abnormal repair of normal alveolar tissue. It causes loss of lung function in patients with multiple complex diseases, leading to respiratory failure and subsequent death. However, current treatment options for IPF are very limited and no drugs have been shown to significantly prolong the survival of patients. Therefore, based on a systematic understanding of the disease mechanisms of PF, this review integrates the role of epigenetics in the development and course of PF, describes preventive and potential therapeutic targets for PF, and provides a theoretical basis for further exploration of the mechanisms of PF.
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Affiliation(s)
- Yun-Sen Zhang
- Department of Anesthesiology and Perioperative Medicine, The Second Affiliated Hospital of Anhui Medical University, Hefei 230601, PR China
| | - Bin Tu
- Department of Cardiothoracic Surgery, The Second Affiliated Hospital of Anhui Medical University, Hefei 230601, PR China
| | - Kai Song
- Department of Cardiothoracic Surgery, The Second Affiliated Hospital of Anhui Medical University, Hefei 230601, PR China
| | - Li-Chan Lin
- Department of Anesthesiology and Perioperative Medicine, The Second Affiliated Hospital of Anhui Medical University, Hefei 230601, PR China
| | - Zhi-Yan Liu
- Department of Anesthesiology and Perioperative Medicine, The Second Affiliated Hospital of Anhui Medical University, Hefei 230601, PR China
| | - Dong Lu
- Department of Interventional Radiology, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, PR China.
| | - Qi Chen
- Department of Anesthesiology and Perioperative Medicine, The Second Affiliated Hospital of Anhui Medical University, Hefei 230601, PR China.
| | - Hui Tao
- Department of Anesthesiology and Perioperative Medicine, The Second Affiliated Hospital of Anhui Medical University, Hefei 230601, PR China; Department of Cardiothoracic Surgery, The Second Affiliated Hospital of Anhui Medical University, Hefei 230601, PR China.
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Du S, Qu H, Zhang Y, Zhu S, Wang Y, Zhang S, Wang Z, Yang Q, Fu S, Dong K. MiR-375 promotes cisplatin sensitivity of lung adenocarcinoma. Pathol Res Pract 2023; 249:154765. [PMID: 37625279 DOI: 10.1016/j.prp.2023.154765] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/23/2023] [Revised: 07/30/2023] [Accepted: 08/12/2023] [Indexed: 08/27/2023]
Abstract
BACKGROUND Cisplatin-based chemotherapy has been widely used in the treatment of lung adenocarcinoma (LUAD). However, the development of cisplatin resistance becomes a major obstacle impeding the curative effect. It remains necessary to uncover the molecular mechanism of cisplatin resistance. METHODS Based on the CCLE database, lung cancer cell lines were divided into cisplatin-resistant and cisplatin-sensitive groups. The differentially expressed miRNAs were filtered and further identified by survival prognosis analysis. After transfection with miR-375 inhibitor or mimic, cell cytotoxicity assay, flow cytometry and western blot were conducted to validate the role of miR-375. The transcription factor (TF)-miRNA network was constructed based on TransmiR. The target genes of miR-375 were predicted by Starbase and further verified by RT-qPCR and immunohistochemistry results in the Human Protein Atlas. Functional enrichment analysis was performed with GO terms and KEGG. RESULTS In this study, miR-375 showed the ability to promote cisplatin sensitivity and apoptosis of LUAD. Genes correlated with miR-375 in LUAD were analyzed and ABCC8 showed the strongest positive correlation. Moreover, transcription factors that regulate miR-375 expression were predicted. MBNL1, PTPN3, PRKD1 and RPN1 were identified as the target genes of miR-375. Enrichment analysis demonstrated that miR-375-related genes associated with promoting cell proliferation and anti-apoptosis were involved in the MAPK signaling pathway. CONCLUSION Overall, this study provides new insights into the role of miR-375 in the cisplatin sensitivity of LUAD. Our present findings may serve as a theoretical basis for new therapeutic strategies and predictive models of cisplatin resistance in LUAD.
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Affiliation(s)
- Shuomeng Du
- Key Laboratory of Preservation of Human Genetic Resources and Disease Control in China (Harbin Medical University), Ministry of Education, Harbin 150081, China; Laboratory of Medical Genetics, Harbin Medical University, Harbin 150081, China
| | - Han Qu
- Key Laboratory of Preservation of Human Genetic Resources and Disease Control in China (Harbin Medical University), Ministry of Education, Harbin 150081, China; Laboratory of Medical Genetics, Harbin Medical University, Harbin 150081, China
| | - Ying Zhang
- Key Laboratory of Preservation of Human Genetic Resources and Disease Control in China (Harbin Medical University), Ministry of Education, Harbin 150081, China; Laboratory of Medical Genetics, Harbin Medical University, Harbin 150081, China
| | - Shihao Zhu
- Key Laboratory of Preservation of Human Genetic Resources and Disease Control in China (Harbin Medical University), Ministry of Education, Harbin 150081, China; Laboratory of Medical Genetics, Harbin Medical University, Harbin 150081, China
| | - Yang Wang
- Key Laboratory of Preservation of Human Genetic Resources and Disease Control in China (Harbin Medical University), Ministry of Education, Harbin 150081, China; Laboratory of Medical Genetics, Harbin Medical University, Harbin 150081, China
| | - Shuopeng Zhang
- Key Laboratory of Preservation of Human Genetic Resources and Disease Control in China (Harbin Medical University), Ministry of Education, Harbin 150081, China; Laboratory of Medical Genetics, Harbin Medical University, Harbin 150081, China
| | - Zhao Wang
- Department of Gynecological Radiotherapy, Harbin Medical University Cancer Hospital, Harbin 150081, China
| | - Qian Yang
- Key Laboratory of Preservation of Human Genetic Resources and Disease Control in China (Harbin Medical University), Ministry of Education, Harbin 150081, China; Laboratory of Medical Genetics, Harbin Medical University, Harbin 150081, China
| | - Songbin Fu
- Key Laboratory of Preservation of Human Genetic Resources and Disease Control in China (Harbin Medical University), Ministry of Education, Harbin 150081, China; Laboratory of Medical Genetics, Harbin Medical University, Harbin 150081, China
| | - Kexian Dong
- Key Laboratory of Preservation of Human Genetic Resources and Disease Control in China (Harbin Medical University), Ministry of Education, Harbin 150081, China; Laboratory of Medical Genetics, Harbin Medical University, Harbin 150081, China.
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Delivery of anti-microRNA-21 by lung-targeted liposomes for pulmonary fibrosis treatment. MOLECULAR THERAPY. NUCLEIC ACIDS 2023; 32:36-47. [PMID: 36919116 PMCID: PMC9972768 DOI: 10.1016/j.omtn.2023.02.031] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/08/2022] [Accepted: 02/24/2023] [Indexed: 03/06/2023]
Abstract
Idiopathic pulmonary fibrosis (IPF) is a chronic lung disorder with a low survival rate. Pulmonary fibrosis is one of the complications of COVID-19 and has a high prevalence in COVID-19 patients. Currently, no effective therapies other than lung transplantation are available to cure IPF and post-COVID-19 pulmonary fibrosis. MicroRNAs are small non-coding RNAs that mediate the development and progression of pulmonary fibrosis, thus making them potent drug candidates for this serious disease. MicroRNA-21 (miR-21) promotes not only the differentiation of fibroblasts to myofibroblasts but also epithelial-mesenchymal transition, both of which have been proposed as fundamental processes in pulmonary fibrosis development. Delivery of anti-miR-21 to block the miR-21-associated fibrogenic pathways represents a promising therapy for pulmonary fibrosis. However, microRNA treatment is challenged by quick degradation of RNA in blood, poor cellular uptake, and off-target effects. To overcome these challenges, we developed a lung-targeted, cationic liposome formulation to encapsulate anti-miR-21, enhance its delivery efficiency, and improve the therapeutic efficacy. We optimized the liposome formulation and demonstrated the anti-fibrotic effects using both in vitro and in vivo lung fibrosis models. Our results showed that anti-miR-21 delivered by cationic liposomes suppressed myofibroblast differentiation, reduced the synthesis of extracellular matrix, and inhibited fibrosis progression.
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SIRT3 improves alveolar epithelial cell damage caused by bronchopulmonary dysplasia through deacetylation of FOXO1. Allergol Immunopathol (Madr) 2023; 51:191-204. [PMID: 36916106 DOI: 10.15586/aei.v51i2.710] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Accepted: 12/15/2022] [Indexed: 03/08/2023]
Abstract
BACKGROUND Bronchopulmonary dysplasia (BPD) is a serious and long-term lung condition commonly observed in premature babies. Sirtuin 3 (SIRT3) has been reported to reduce pulmonary injury and pulmonary fibrosis. OBJECTIVE The present study investigated the specific role of SIRT3 in BPD by establishing hyperoxia-induced BPD rat and cell models. Hematoxylin and eosin staining was used to observe pathological changes in lung tissues. MATERIALS AND METHODS The expression levels of SIRT3 and forkhead box protein O1 (FOXO1), as well as its acetylation levels, were detected in hyperoxia-induced lung tissues and cells by Western blot analysis and reverse transcription-quantitative polymerase chain reaction (RT-qPCR). Levels of reactive oxygen species, superoxide dismutase, and malondialdehyde were assessed by using biochemical kits. Following SIRT3 overexpression, the levels of inflammatory cytokines were assessed by RT-qPCR. Apoptosis was determined by terminal deoxynucleotidyl transferase dUTP nickend labeling (TUNEL) and Western blot analysis. Upon FOXO1 knockout, cell inflammation, oxidative stress and apoptosis were evaluated again. RESULTS Compared to the control group, the SIRT3 and FOXO1 expression levels were decreased and the FOXO1 acetylation levels were increased in hyperoxia-induced lung tissues and cells. In addition, SIRT3 reduced hyperoxia-induced inflammation, oxidative stress, and apoptosis in A549 cells, and inhibited FOXO1 acetylation to activate FOXO1. However, FOXO1 knockdown reversed the effects of SIRT3 overexpression in hyperoxia-induced A549 cells. CONCLUSION SIRT3 relieved alveolar epithelial cell damage caused by BPD via deacetylation of FOXO1, suggesting that SIRT3 could be a therapeutic target in BPD.
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Bao T, Zhu H, Zheng Y, Hu J, Wang H, Cheng H, Zhang Y, Tian Z. Expression of long noncoding RNA uc.375 in bronchopulmonary dysplasia and its function in the proliferation and apoptosis of mouse alveolar epithelial cell line MLE 12. Front Physiol 2022; 13:971732. [PMID: 36111163 PMCID: PMC9468891 DOI: 10.3389/fphys.2022.971732] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2022] [Accepted: 07/21/2022] [Indexed: 11/13/2022] Open
Abstract
Background: According to our previous gene ChIP results, long noncoding RNA uc.375 was down-regulated in lung tissue of bronchopulmonary dysplasia (BPD) mice induced by hyperoxia. FoxA1 gene showed higher levels in lung tissue of BPD mice and is reported to promote the apoptosis of alveolar epithelial cells. We aimed to clarify the expression pattern of uc.375 in BPD and explore the interaction between uc.375 and FoxA1.Methods: Newborn mice were placed in a 95% high-oxygen environment for 7 days. Lung tissue samples from mice were used for lncRNA microarray to screen BPD related lncRNAs. Mouse alveolar epithelial cell line MLE 12 was stably transfected with uc.375 and FoxA1 silencing or overexpression lentiviral vectors. The proliferation activity of MLE 12 cells was detected by a cell counting kit 8 (CCK-8) assay. MLE 12 cell apoptosis was determined by Hoechst/PI staining and flow cytometry analysis. The protein levels of Cleaved Caspase-3, FoxA1, SP-C and UCP2 were investigated by western blot. The relative mRNA expression levels were detected by quantitative real-time PCR.Results: uc.375 is mainly distributed in the nucleus of alveolar epithelial cells, as revealed by In Situ Hybridization assay results. uc.375 was lowly expressed in the lung tissues of BPD mice. According to the results of CCK-8 assay, analysis of Hoechst/PI staining and western blotting, uc.375 silencing inhibited cell proliferation, facilitated apoptosis of MLE 12 cells, promoted caspase 3 and FoxA1 expression, and inhibited the expression of SP-C and UCP2. On the contrary, after overexpressing uc.375, the opposite results were obtained. Silencing FoxA1 inhibited MLE 12 apoptosis, promoted proliferation, inhibited apoptosis-related factor caspase 3, and promoted the expression of SP-C and UCP2. FoxA1 silencing also reversed the effect induced by uc.375 knockdown on the proliferation and apoptosis of MLE 12 cells.Conclusion: Based on the biomedical images-derived analysis results, uc.375 negatively regulates FoxA1 expression, affects alveolar development, and plays an important role in the initiation and progression of BPD, providing a new molecular target for the prevention and treatment of BPD.
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Hawkins S, Namboori SC, Tariq A, Blaker C, Flaxman C, Dey NS, Henley P, Randall A, Rosa A, Stanton LW, Bhinge A. Upregulation of β-catenin due to loss of miR-139 contributes to motor neuron death in amyotrophic lateral sclerosis. Stem Cell Reports 2022; 17:1650-1665. [PMID: 35750046 PMCID: PMC9287677 DOI: 10.1016/j.stemcr.2022.05.019] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2021] [Revised: 05/25/2022] [Accepted: 05/26/2022] [Indexed: 01/12/2023] Open
Abstract
Amyotrophic lateral sclerosis (ALS) is a fatal neurodegenerative disease characterized by the loss of motor neurons (MNs). There are no effective treatments and patients usually die within 2-5 years of diagnosis. Emerging commonalities between familial and sporadic cases of this complex multifactorial disorder include disruption to RNA processing and cytoplasmic inclusion bodies containing TDP-43 and/or FUS protein aggregates. Both TDP-43 and FUS have been implicated in RNA processing functions, including microRNA biogenesis, transcription, and splicing. In this study, we explore the misexpression of microRNAs in an iPSC-based disease model of FUS ALS. We identify the downregulation of miR-139, an MN-enriched microRNA, in FUS and sporadic ALS MN. We discover that miR-139 downregulation leads to the activation of canonical WNT signaling and demonstrate that the WNT transcriptional mediator β-catenin is a major driver of MN degeneration in ALS. Our results highlight the importance of homeostatic RNA networks in ALS.
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Affiliation(s)
- Sophie Hawkins
- College of Medicine and Health, University of Exeter, Exeter EX1 2LU, UK; Living Systems Institute, University of Exeter, Exeter EX4 4QD, UK
| | - Seema C Namboori
- College of Medicine and Health, University of Exeter, Exeter EX1 2LU, UK; Living Systems Institute, University of Exeter, Exeter EX4 4QD, UK
| | - Ammarah Tariq
- Living Systems Institute, University of Exeter, Exeter EX4 4QD, UK; Biosciences, University of Exeter, Exeter EX4 4QD, UK
| | - Catherine Blaker
- College of Medicine and Health, University of Exeter, Exeter EX1 2LU, UK
| | - Christine Flaxman
- College of Medicine and Health, University of Exeter, Exeter EX1 2LU, UK
| | - Nidhi S Dey
- York Biomedical Research Institute, Hull York Medical School, University of York, York YO10 5DD, UK
| | - Peter Henley
- College of Medicine and Health, University of Exeter, Exeter EX1 2LU, UK
| | - Andrew Randall
- College of Medicine and Health, University of Exeter, Exeter EX1 2LU, UK
| | - Alessandro Rosa
- Department of Biology and Biotechnologies Charles Darwin, Sapienza University of Rome, P.le A. Moro 5, 00185 Rome, Italy; Center for Life Nano- & Neuro-Science, Fondazione Istituto Italiano di Tecnologia (IIT), 00161 Rome, Italy
| | - Lawrence W Stanton
- Qatar Biomedical Research Institute, Hamad Bin Khalifa University, Doha, Qatar
| | - Akshay Bhinge
- College of Medicine and Health, University of Exeter, Exeter EX1 2LU, UK; Living Systems Institute, University of Exeter, Exeter EX4 4QD, UK.
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Zhu D, Krause M, Yawno T, Kusuma GD, Schwab R, Barabadi M, Maleken AS, Chan ST, Hunt R, Greening D, Wallace EM, Lim R. Assessing the impact of gestational age of donors on the efficacy of amniotic epithelial cell-derived extracellular vesicles in experimental bronchopulmonary dysplasia. Stem Cell Res Ther 2022; 13:196. [PMID: 35550006 PMCID: PMC9102678 DOI: 10.1186/s13287-022-02874-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2022] [Accepted: 04/27/2022] [Indexed: 11/20/2022] Open
Abstract
Background and rationale Extracellular vesicles (EVs) are a potential cell-free regenerative medicine. Human amniotic epithelial cells (hAECs) are a viable source of cell therapy for diseases like bronchopulmonary dysplasia (BPD). However, little is known about the impact of gestational age of the donor on the quality of hAEC-derived EVs.
Aims To determine the impact of gestational age on hAEC-derived EVs in experimental BPD.
Results Term hAEC-derived EVs displayed a significantly higher density of surface epitopes (CD142 and CD133) and induced greater macrophage phagocytosis compared to preterm hAEC-EVs. However, T cell proliferation was more significantly suppressed by preterm hAEC-EVs. Using a model of experimental BPD, we observed that term but not preterm hAEC-EVs improved tissue-to-airspace ratio and septal crest density. While both term and preterm hAEC-EVs reduced the levels of inflammatory cytokines on postnatal day 7, the improvement in lung injury was associated with increased type II alveolar cells which was only observed in term hAEC-EV treatment group. Furthermore, only neonatal term hAEC-EVs reduced airway hyper-responsiveness, mitigated pulmonary hypertension and protected against right ventricular hypertrophy at 6 weeks of age. Conclusion Term hAEC-EVs, but not preterm hAEC-EVs, have therapeutic efficacy in a mouse model of BPD-like lung injury. Therefore, the impact of donor criteria should be considered when applying perinatal cells-derived EV therapy for clinical use.
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Affiliation(s)
- Dandan Zhu
- The Ritchie Centre, Hudson Institute of Medical Research, Clayton, VIC, 3168, Australia.,Department of Obstetrics and Gynaecology, Monash University, Clayton, VIC, 3168, Australia
| | - Mirja Krause
- The Ritchie Centre, Hudson Institute of Medical Research, Clayton, VIC, 3168, Australia.,Department of Obstetrics and Gynaecology, Monash University, Clayton, VIC, 3168, Australia
| | - Tamara Yawno
- The Ritchie Centre, Hudson Institute of Medical Research, Clayton, VIC, 3168, Australia. .,Department of Obstetrics and Gynaecology, Monash University, Clayton, VIC, 3168, Australia. .,Department of Paediatrics, Monash University, Clayton, VIC, 3168, Australia.
| | - Gina D Kusuma
- The Ritchie Centre, Hudson Institute of Medical Research, Clayton, VIC, 3168, Australia.,Department of Obstetrics and Gynaecology, Monash University, Clayton, VIC, 3168, Australia
| | - Renate Schwab
- The Ritchie Centre, Hudson Institute of Medical Research, Clayton, VIC, 3168, Australia.,Department of Obstetrics and Gynaecology, Monash University, Clayton, VIC, 3168, Australia
| | - Mehri Barabadi
- The Ritchie Centre, Hudson Institute of Medical Research, Clayton, VIC, 3168, Australia
| | - Amina S Maleken
- The Ritchie Centre, Hudson Institute of Medical Research, Clayton, VIC, 3168, Australia.,Department of Obstetrics and Gynaecology, Monash University, Clayton, VIC, 3168, Australia
| | - Siow T Chan
- The Ritchie Centre, Hudson Institute of Medical Research, Clayton, VIC, 3168, Australia.,Department of Obstetrics and Gynaecology, Monash University, Clayton, VIC, 3168, Australia
| | - Rod Hunt
- Department of Paediatrics, Monash University, Clayton, VIC, 3168, Australia
| | - David Greening
- Baker Heart and Diabetes Institute, Melbourne, VIC, Australia.,Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Bundoora, VIC, Australia.,Central Clinical School, Monash University, Clayton, VIC, Australia.,Baker Department of Cardiometabolic Health, University of Melbourne, Parkville, VIC, Australia
| | - Euan M Wallace
- The Ritchie Centre, Hudson Institute of Medical Research, Clayton, VIC, 3168, Australia.,Department of Obstetrics and Gynaecology, Monash University, Clayton, VIC, 3168, Australia
| | - Rebecca Lim
- The Ritchie Centre, Hudson Institute of Medical Research, Clayton, VIC, 3168, Australia.,Department of Obstetrics and Gynaecology, Monash University, Clayton, VIC, 3168, Australia
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Fülöp Á, Torma G, Moldován N, Szenthe K, Bánáti F, Almsarrhad IAA, Csabai Z, Tombácz D, Minárovits J, Boldogkői Z. Integrative profiling of Epstein-Barr virus transcriptome using a multiplatform approach. Virol J 2022; 19:7. [PMID: 34991630 PMCID: PMC8740505 DOI: 10.1186/s12985-021-01734-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2021] [Accepted: 12/20/2021] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Epstein-Barr virus (EBV) is an important human pathogenic gammaherpesvirus with carcinogenic potential. The EBV transcriptome has previously been analyzed using both Illumina-based short read-sequencing and Pacific Biosciences RS II-based long-read sequencing technologies. Since the various sequencing methods have distinct strengths and limitations, the use of multiplatform approaches have proven to be valuable. The aim of this study is to provide a more complete picture on the transcriptomic architecture of EBV. METHODS In this work, we apply the Oxford Nanopore Technologies MinION (long-read sequencing) platform for the generation of novel transcriptomic data, and integrate these with other's data generated by another LRS approach, Pacific BioSciences RSII sequencing and Illumina CAGE-Seq and Poly(A)-Seq approaches. Both amplified and non-amplified cDNA sequencings were applied for the generation of sequencing reads, including both oligo-d(T) and random oligonucleotide-primed reverse transcription. EBV transcripts are identified and annotated using the LoRTIA software suite developed in our laboratory. RESULTS This study detected novel genes embedded into longer host genes containing 5'-truncated in-frame open reading frames, which potentially encode N-terminally truncated proteins. We also detected a number of novel non-coding RNAs and transcript length isoforms encoded by the same genes but differing in their start and/or end sites. This study also reports the discovery of novel splice isoforms, many of which may represent altered coding potential, and of novel replication-origin-associated transcripts. Additionally, novel mono- and multigenic transcripts were identified. An intricate meshwork of transcriptional overlaps was revealed. CONCLUSIONS An integrative approach applying multi-technique sequencing technologies is suitable for reliable identification of complex transcriptomes because each techniques has different advantages and limitations, and the they can be used for the validation of the results obtained by a particular approach.
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Affiliation(s)
- Ádám Fülöp
- Department of Medical Biology, Albert Szent-Györgyi Medical School, University of Szeged, Somogyi B. u. 4., Szeged, 6720 Hungary
| | - Gábor Torma
- Department of Medical Biology, Albert Szent-Györgyi Medical School, University of Szeged, Somogyi B. u. 4., Szeged, 6720 Hungary
| | - Norbert Moldován
- Department of Medical Biology, Albert Szent-Györgyi Medical School, University of Szeged, Somogyi B. u. 4., Szeged, 6720 Hungary
| | - Kálmán Szenthe
- Carlsbad Research Organization Ltd., Szabadság u. 2., Újrónafő, 9244 Hungary
| | - Ferenc Bánáti
- RT-Europe Research Center, Vár tér 2., Mosonmagyaróvár, 9200 Hungary
| | - Islam A. A. Almsarrhad
- Department of Medical Biology, Albert Szent-Györgyi Medical School, University of Szeged, Somogyi B. u. 4., Szeged, 6720 Hungary
| | - Zsolt Csabai
- Department of Medical Biology, Albert Szent-Györgyi Medical School, University of Szeged, Somogyi B. u. 4., Szeged, 6720 Hungary
| | - Dóra Tombácz
- Department of Medical Biology, Albert Szent-Györgyi Medical School, University of Szeged, Somogyi B. u. 4., Szeged, 6720 Hungary
| | - János Minárovits
- Department of Oral Biology and Experimental Dental Research, University of Szeged, Tisza Lajos krt. 64, Szeged, 6720 Hungary
| | - Zsolt Boldogkői
- Department of Medical Biology, Albert Szent-Györgyi Medical School, University of Szeged, Somogyi B. u. 4., Szeged, 6720 Hungary
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Dai Y, Jian C, Wang X, Dai X. Comprehensive expression profiles of mRNAs, lncRNAs and miRNAs in Kashin-Beck disease identified by RNA-sequencing. Mol Omics 2021; 18:154-166. [PMID: 34913457 DOI: 10.1039/d1mo00370d] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Kashin-Beck disease (KBD) is a chronic, endemic and deforming osteochondropathy, whose basic pathological alterations include apoptosis and necrosis of chondrocytes in articular cartilage and growth plates and imbalanced extracellular matrix metabolism. Numerous studies have reported that long noncoding RNAs (lncRNAs) and microRNA (miRNAs) are aberrantly expressed in KBD. Our study was comprised of 5 KBD patients and 5 healthy individuals and we compared the expression profiles of mRNAs, lncRNAs and miRNAs through RNA-sequencing (RNA-seq). Bioinformatic analysis of GO and KEGG was employed to conduct functional annotation and pathway enriched analysis. In total, 3194 mRNAs, 4103 lncRNAs and 1550 miRNAs were detected to be differentially expressed by RNA-seq (P < 0.05; |log2FC| ≥1). The lysosome pathway, Wnt signaling pathway, TNF signaling pathway, endocytosis and mTOR signaling pathway were identified to be involved in the KBD development according to the result of the KEGG analysis. In addition, a ceRNA network based on lncRNA-miRNA-mRNA was constructed to probe the intricate regulatory mechanism and interaction between transcripts, which was visualized using the Cytoscape software. The ce-lncRNAs of four aberrantly expressed genes, FOSB, EGR3, BCAM and SOX6, were determined through the network. Among the identified DElncRNAs, we selected 8 differentially expressed lncRNAs to confirm the reliability of RNA-seq data by qRT-PCR in 11 KBD patients and 11 healthy individuals. We aimed to provide a comprehensive understanding ofmRNA, lncRNA and miRNA alterations between KBD patients and healthy individuals, and meanwhile reveal several potential causative molecular and signaling pathways involved in KBD.
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Affiliation(s)
- Yu Dai
- School of Public Health, Xi'an Jiaotong University Health Science Center, No. 76 Yanta West Road, Xi'an, Shaanxi 710061, China
| | - Can Jian
- School of Public Health, Xi'an Jiaotong University Health Science Center, No. 76 Yanta West Road, Xi'an, Shaanxi 710061, China
| | - Xiaofeng Wang
- School of Public Health, Xi'an Jiaotong University Health Science Center, No. 76 Yanta West Road, Xi'an, Shaanxi 710061, China
| | - Xiaoxia Dai
- School of Public Health, Xi'an Jiaotong University Health Science Center, No. 76 Yanta West Road, Xi'an, Shaanxi 710061, China.,Key Laboratory of Trace Elements and Endemic Diseases, National Health Commission of the People's Republic of China, No. 76 Yanta West Road, Xi'an, Shaanxi 710061, China.
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10
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Ji Z, Tang T, Chen M, Dong B, Sun W, Wu N, Chen H, Feng Q, Yang X, Jin R, Jiang L. C-Myc-activated long non-coding RNA LINC01050 promotes gastric cancer growth and metastasis by sponging miR-7161-3p to regulate SPZ1 expression. J Exp Clin Cancer Res 2021; 40:351. [PMID: 34749766 PMCID: PMC8573944 DOI: 10.1186/s13046-021-02155-7] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2021] [Accepted: 10/25/2021] [Indexed: 12/24/2022] Open
Abstract
BACKGROUND Growing evidence shows that long non-coding RNAs (lncRNAs) play significant roles in cancer development. However, the functions of most lncRNAs in human gastric cancer are still not fully understood. Here, we explored the role of a novel c-Myc-activated lncRNA, LINC01050, in gastric cancer progression. METHODS The expression of LINC01050 in the context of gastric cancer was assessed using The Cancer Genome Atlas datasets. Its functions in gastric cancer were investigated through gain- and loss-of-function experiments combined with the Cell Counting Kit-8 assays, colony-forming assays, Transwell assays, flow cytometry, Western blot analyses, and xenograft tumor and mouse metastasis models. Potential LINC01050 transcription activators were screened via bioinformatics and validated by chromatin immunoprecipitation and luciferase assays. The interaction between LINC01050 and miR-7161-3p and the targets of miR-7161-3p were predicted by bioinformatics analysis and confirmed by a luciferase assay, RNA immunoprecipitation, RNA pull-down, and rescue experiments. RESULTS LINC01050 was significantly up-regulated in gastric cancer, and its high expression was positively correlated with a poor prognosis. The transcription factor c-Myc was found to directly bind to the LINC01050 promoter region and activate its transcription. Furthermore, overexpression of LINC01050 was confirmed to promote gastric cancer cell proliferation, migration, invasion, and epithelial-mesenchymal transition in vitro and tumor growth in vivo. At the same time, its knockdown inhibited gastric cancer cell proliferation, migration, invasion, and epithelial-mesenchymal transition in vitro along with tumor growth and metastasis in vivo. Moreover, mechanistic investigations revealed that LINC01050 functions as a molecular sponge to absorb cytosolic miR-7161-3p, which reduces the miR-7161-3p-mediated translational repression of SPZ1, thus contributing to gastric cancer progression. CONCLUSIONS Taken together, our results identified a novel gastric cancer-associated lncRNA, LINC01050, which is activated by c-Myc. LINC01050 may be considered a potential therapeutic target for gastric cancer.
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Affiliation(s)
- Ziwei Ji
- Department of Gastroenterology, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, 325000, China
| | - Tianbin Tang
- Central Laboratory, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, 325000, China
| | - Mengxia Chen
- Department of Gastroenterology, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, 325000, China
| | - Buyuan Dong
- Department of Gastroenterology, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, 325000, China
| | - Wenjing Sun
- Central Laboratory, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, 325000, China
| | - Nan Wu
- Department of Gastroenterology, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, 325000, China
| | - Hao Chen
- Department of Gastroenterology, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, 325000, China
| | - Qian Feng
- Department of Gastroenterology, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, 325000, China
| | - Xingyi Yang
- Department of Gastroenterology, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, 325000, China
| | - Rong Jin
- Department of Gastroenterology, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, 325000, China.
| | - Lei Jiang
- Central Laboratory, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, 325000, China.
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11
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Long Noncoding RNA FENDRR Inhibits Lung Fibroblast Proliferation via a Reduction of β-Catenin. Int J Mol Sci 2021; 22:ijms22168536. [PMID: 34445242 PMCID: PMC8395204 DOI: 10.3390/ijms22168536] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2021] [Revised: 07/30/2021] [Accepted: 08/01/2021] [Indexed: 02/06/2023] Open
Abstract
Idiopathic Pulmonary Fibrosis (IPF) is a chronic, progressive, and usually lethal lung disease and it has been widely accepted that fibroblast proliferation is one of the key characteristics of IPF. Long noncoding RNAs (lncRNAs) play vital roles in the pathogenesis of many diseases. In this study, we investigated the role of lncRNA FENDRR on fibroblast proliferation. Human lung fibroblasts stably overexpressing FENDRR showed a reduced cell proliferation compared to those expressing the control vector. On the other hand, FENDRR silencing increased fibroblast proliferation. FENDRR bound serine-arginine rich splicing factor 9 (SRSF9) and inhibited the phosphorylation of p70 ribosomal S6 kinase 1 (PS6K), a downstream protein of the mammalian target of rapamycin (mTOR) signaling. Silencing SRSF9 reduced fibroblast proliferation. FENDRR reduced β-catenin protein, but not mRNA levels. The reduction of β-catenin protein levels in lung fibroblasts by gene silencing or chemical inhibitor decreased fibroblast proliferation. Adenovirus-mediated FENDRR transfer to the lungs of mice reduced asbestos-induced fibrotic lesions and collagen deposition. RNA sequencing of lung tissues identified 7 cell proliferation-related genes that were up-regulated by asbestos but reversed by FENDRR. In conclusion, FENDRR inhibits fibroblast proliferation and functions as an anti-fibrotic lncRNA.
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12
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Li J, Li H, Ye X, Zhang L, Xu Q, Ping Y, Jing X, Jiang W, Liao Q, Liu B, Wang Y. IIMLP: integrated information-entropy-based method for LncRNA prediction. BMC Bioinformatics 2021; 22:243. [PMID: 33980144 PMCID: PMC8117603 DOI: 10.1186/s12859-020-03884-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2020] [Accepted: 11/17/2020] [Indexed: 11/26/2022] Open
Abstract
BACKGROUND The prediction of long non-coding RNA (lncRNA) has attracted great attention from researchers, as more and more evidence indicate that various complex human diseases are closely related to lncRNAs. In the era of bio-med big data, in addition to the prediction of lncRNAs by biological experimental methods, many computational methods based on machine learning have been proposed to make better use of the sequence resources of lncRNAs. RESULTS We developed the lncRNA prediction method by integrating information-entropy-based features and machine learning algorithms. We calculate generalized topological entropy and generate 6 novel features for lncRNA sequences. By employing these 6 features and other features such as open reading frame, we apply supporting vector machine, XGBoost and random forest algorithms to distinguish human lncRNAs. We compare our method with the one which has more K-mer features and results show that our method has higher area under the curve up to 99.7905%. CONCLUSIONS We develop an accurate and efficient method which has novel information entropy features to analyze and classify lncRNAs. Our method is also extendable for research on the other functional elements in DNA sequences.
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Affiliation(s)
- Junyi Li
- School of Computer Science and Technology, Harbin Institute of Technology (Shenzhen), Shenzhen, 518055, Guangdong, China.
| | - Huinian Li
- School of Computer Science and Technology, Harbin Institute of Technology (Shenzhen), Shenzhen, 518055, Guangdong, China
| | - Xiao Ye
- School of Computer Science and Technology, Harbin Institute of Technology (Shenzhen), Shenzhen, 518055, Guangdong, China
| | - Li Zhang
- School of Computer Science and Technology, Harbin Institute of Technology (Shenzhen), Shenzhen, 518055, Guangdong, China
| | - Qingzhe Xu
- School of Computer Science and Technology, Harbin Institute of Technology (Shenzhen), Shenzhen, 518055, Guangdong, China
| | - Yuan Ping
- School of Computer Science and Technology, Harbin Institute of Technology (Shenzhen), Shenzhen, 518055, Guangdong, China
| | - Xiaozhu Jing
- School of Computer Science and Technology, Harbin Institute of Technology (Shenzhen), Shenzhen, 518055, Guangdong, China
| | - Wei Jiang
- School of Computer Science and Technology, Harbin Institute of Technology (Shenzhen), Shenzhen, 518055, Guangdong, China
| | - Qing Liao
- School of Computer Science and Technology, Harbin Institute of Technology (Shenzhen), Shenzhen, 518055, Guangdong, China
| | - Bo Liu
- Center for Bioinformatics, School of Computer Science and Technology, Harbin Institute of Technology, Harbin, 150001, Heilongjiang, China
| | - Yadong Wang
- School of Computer Science and Technology, Harbin Institute of Technology (Shenzhen), Shenzhen, 518055, Guangdong, China.
- Center for Bioinformatics, School of Computer Science and Technology, Harbin Institute of Technology, Harbin, 150001, Heilongjiang, China.
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Role of various imbalances centered on alveolar epithelial cell/fibroblast apoptosis imbalance in the pathogenesis of idiopathic pulmonary fibrosis. Chin Med J (Engl) 2021; 134:261-274. [PMID: 33522725 PMCID: PMC7846426 DOI: 10.1097/cm9.0000000000001288] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
There have been recent extensive studies and rapid advancement on the pathogenesis underlying idiopathic pulmonary fibrosis (IPF), and intricate pathogenesis of IPF has been suggested. The purpose of this study was to clarify the logical relationship between these mechanisms. An extensive search was undertaken of the PubMed using the following keywords: “etiology,” “pathogenesis,” “alveolar epithelial cell (AEC),” “fibroblast,” “lymphocyte,” “macrophage,” “epigenomics,” “histone,” acetylation,” “methylation,” “endoplasmic reticulum stress,” “mitochondrial dysfunction,” “telomerase,” “proteases,” “plasminogen,” “epithelial-mesenchymal transition,” “oxidative stress,” “inflammation,” “apoptosis,” and “idiopathic pulmonary fibrosis.” This search covered relevant research articles published up to April 30, 2020. Original articles, reviews, and other articles were searched and reviewed for content; 240 highly relevant studies were obtained after screening. IPF is likely the result of complex interactions between environmental, genetic, and epigenetic factors: environmental exposures affect epigenetic marks; epigenetic processes translate environmental exposures into the regulation of chromatin; epigenetic processes shape gene expression profiles; in turn, an individual's genetic background determines epigenetic marks; finally, these genetic and epigenetic factors act in concert to dysregulate gene expression in IPF lung tissue. The pathogenesis of IPF involves various imbalances including endoplasmic reticulum, telomere length homeostasis, mitochondrial dysfunction, oxidant/antioxidant imbalance, Th1/Th2 imbalance, M1–M2 polarization of macrophages, protease/antiprotease imbalance, and plasminogen activation/inhibition imbalance. These affect each other, promote each other, and ultimately promote AEC/fibroblast apoptosis imbalance directly or indirectly. Excessive AEC apoptosis and impaired apoptosis of fibroblasts contribute to fibrosis. IPF is likely the result of complex interactions between environmental, genetic, and epigenetic factors. The pathogenesis of IPF involves various imbalances centered on AEC/fibroblast apoptosis imbalance.
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Bartczak K, Białas AJ, Kotecki MJ, Górski P, Piotrowski WJ. More than a Genetic Code: Epigenetics of Lung Fibrosis. Mol Diagn Ther 2020; 24:665-681. [PMID: 32926347 PMCID: PMC7677145 DOI: 10.1007/s40291-020-00490-7] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
At the end of the last century, genetic studies reported that genetic information is not transmitted solely by DNA, but is also transmitted by other mechanisms, named as epigenetics. The well-described epigenetic mechanisms include DNA methylation, biochemical modifications of histones, and microRNAs. The role of altered epigenetics in the biology of various fibrotic diseases is well-established, and recent advances demonstrate its importance in the pathogenesis of pulmonary fibrosis-predominantly referring to idiopathic pulmonary fibrosis, the most lethal of the interstitial lung diseases. The deficiency in effective medications suggests an urgent need to better understand the underlying pathobiology. This review summarizes the current knowledge concerning epigenetic changes in pulmonary fibrosis and associations of these changes with several cellular pathways of known significance in its pathogenesis. It also designates the most promising substances for further research that may bring us closer to new therapeutic options.
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Affiliation(s)
- Krystian Bartczak
- Department of Pneumology and Allergology, The Medical University of Lodz, Kopcińskiego 22, 90-153, Lodz, Poland.
| | - Adam J Białas
- Department of Pathobiology of Respiratory Diseases, The Medical University of Lodz, Lodz, Poland
| | - Mateusz J Kotecki
- Department of Pneumology and Allergology, The Medical University of Lodz, Kopcińskiego 22, 90-153, Lodz, Poland
| | - Paweł Górski
- Department of Pneumology and Allergology, The Medical University of Lodz, Kopcińskiego 22, 90-153, Lodz, Poland
| | - Wojciech J Piotrowski
- Department of Pneumology and Allergology, The Medical University of Lodz, Kopcińskiego 22, 90-153, Lodz, Poland
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15
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Chen Y, Liu W, Ma J, Wang Y, Huang H. Comprehensive physiological and transcriptomic analysis revealing the responses of hybrid grouper (Epinephelus fuscoguttatus♀ × E. lanceolatus♂) to the replacement of fish meal with soy protein concentrate. FISH PHYSIOLOGY AND BIOCHEMISTRY 2020; 46:2037-2053. [PMID: 32767005 DOI: 10.1007/s10695-020-00851-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/21/2019] [Accepted: 07/28/2020] [Indexed: 06/11/2023]
Abstract
Plant proteins are suitable and alternative to fish meals (FMs), with less cost compared with that of all other types of fish feeds. In recent years, soy protein concentrate (SPC) has emerged as a cost-effective alternative to FM; however, little is known regarding the effects of dietary SPC on general fish physiology and well-being. This study aimed to perform comprehensive physiological and transcriptomic analysis for testing the applicability of SPC as fish feeds in hybrid grouper (Epinephelus fuscoguttatus♀ × E. lanceolatus♂) [SPC replaced 0% (CK), 30% (SPC30), and 75% (SPC75) of FM protein]. Generally, SPC30 promoted fish survival and had less effects on the phenotype, while SPC75 reduced fish survival, promoted inflammation, and regulated multiple physiological responses. Thousands of differentially expressed genes (DEGs) by SPC were identified in the intestine, liver, and muscle, which were enriched in biological regulation, cellular process, metabolic process, single-organism process, cell, cell part, membrane, binding, and catalytic activity based on RNA-seq. Notably, some DEGs involved in amino acid and lipid metabolism in the digestive system highlighted the modulatory effect of SPC on these metabolic processes, consistent with the physiological responses including enzyme activities. The enriched aspects of these predominant DEGs might be directly related to the different effects of SPC30 and SPC75 on fish growth, digestibility, and underlying enzyme activities and histology. In conclusion, the comprehensive physiological and transcriptomic comparative analysis of CK, SPC30, and SPC75 was also effective in testing the applicability of SPC as fish feeds and in designing a proper diet with the best impact on the growth performance and health of fish in hybrid grouper.
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Affiliation(s)
- Yan Chen
- Hainan Key Laboratory for Conservation and Utilization of Tropical Marine Fishery Resources, Sanya, 572022, Hainan province, People's Republic of China
- College of Fisheries and Life Science, Hainan Tropical Ocean University, Sanya, 572022, Hainan Province, People's Republic of China
| | - Wenkan Liu
- Hainan Key Laboratory for Conservation and Utilization of Tropical Marine Fishery Resources, Sanya, 572022, Hainan province, People's Republic of China
- College of Fisheries and Life Science, Hainan Tropical Ocean University, Sanya, 572022, Hainan Province, People's Republic of China
| | - Jun Ma
- Hainan Key Laboratory for Conservation and Utilization of Tropical Marine Fishery Resources, Sanya, 572022, Hainan province, People's Republic of China.
- College of Fisheries and Life Science, Hainan Tropical Ocean University, Sanya, 572022, Hainan Province, People's Republic of China.
| | - Yaorong Wang
- Fisheries College, Guangdong Ocean University, Zhanjiang, 524088, Guangdong Province, People's Republic of China
| | - Hai Huang
- Hainan Key Laboratory for Conservation and Utilization of Tropical Marine Fishery Resources, Sanya, 572022, Hainan province, People's Republic of China
- College of Fisheries and Life Science, Hainan Tropical Ocean University, Sanya, 572022, Hainan Province, People's Republic of China
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16
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Yin X, Yi K, Zhao Y, Hu Y, Li X, He T, Liu J, Cui G. Revealing the full-length transcriptome of caucasian clover rhizome development. BMC PLANT BIOLOGY 2020; 20:429. [PMID: 32938399 PMCID: PMC7493993 DOI: 10.1186/s12870-020-02637-4] [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: 03/11/2020] [Accepted: 09/03/2020] [Indexed: 06/02/2023]
Abstract
BACKGROUND Caucasian clover (Trifolium ambiguum M. Bieb.) is a strongly rhizomatous, low-crowned perennial leguminous and ground-covering grass. The species may be used as an ornamental plant and is resistant to cold, arid temperatures and grazing due to a well-developed underground rhizome system and a strong clonal reproduction capacity. However, the posttranscriptional mechanism of the development of the rhizome system in caucasian clover has not been comprehensively studied. Additionally, a reference genome for this species has not yet been published, which limits further exploration of many important biological processes in this plant. RESULT We adopted PacBio sequencing and Illumina sequencing to identify differentially expressed genes (DEGs) in five tissues, including taproot (T1), horizontal rhizome (T2), swelling of taproot (T3), rhizome bud (T4) and rhizome bud tip (T5) tissues, in the caucasian clover rhizome. In total, we obtained 19.82 GB clean data and 80,654 nonredundant transcripts were analysed. Additionally, we identified 78,209 open reading frames (ORFs), 65,227 coding sequences (CDSs), 58,276 simple sequence repeats (SSRs), 6821 alternative splicing (AS) events, 2429 long noncoding RNAs (lncRNAs) and 4501 putative transcription factors (TFs) from 64 different families. Compared with other tissues, T5 exhibited more DEGs, and co-upregulated genes in T5 are mainly annotated as involved in phenylpropanoid biosynthesis. We also identified betaine aldehyde dehydrogenase (BADH) as a highly expressed gene-specific to T5. A weighted gene co-expression network analysis (WGCNA) of transcription factors and physiological indicators were combined to reveal 11 hub genes (MEgreen-GA3), three of which belong to the HB-KNOX family, that are up-regulated in T3. We analysed 276 DEGs involved in hormone signalling and transduction, and the largest number of genes are associated with the auxin (IAA) signalling pathway, with significant up-regulation in T2 and T5. CONCLUSIONS This study contributes to our understanding of gene expression across five different tissues and provides preliminary insight into rhizome growth and development in caucasian clover.
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Affiliation(s)
- Xiujie Yin
- College of Animal Science and Technology, Northeast Agricultural University, No.600 Changjiang Street, Xiangfang District, Harbin, 150030, Heilongjiang, China
| | - Kun Yi
- College of Animal Science and Technology, Northeast Agricultural University, No.600 Changjiang Street, Xiangfang District, Harbin, 150030, Heilongjiang, China
| | - Yihang Zhao
- College of Animal Science and Technology, Northeast Agricultural University, No.600 Changjiang Street, Xiangfang District, Harbin, 150030, Heilongjiang, China
| | - Yao Hu
- College of Animal Science and Technology, Northeast Agricultural University, No.600 Changjiang Street, Xiangfang District, Harbin, 150030, Heilongjiang, China
| | - Xu Li
- College of Animal Science and Technology, Northeast Agricultural University, No.600 Changjiang Street, Xiangfang District, Harbin, 150030, Heilongjiang, China
| | - Taotao He
- College of Animal Science and Technology, Northeast Agricultural University, No.600 Changjiang Street, Xiangfang District, Harbin, 150030, Heilongjiang, China
| | - Jiaxue Liu
- College of Animal Science and Technology, Northeast Agricultural University, No.600 Changjiang Street, Xiangfang District, Harbin, 150030, Heilongjiang, China
| | - Guowen Cui
- College of Animal Science and Technology, Northeast Agricultural University, No.600 Changjiang Street, Xiangfang District, Harbin, 150030, Heilongjiang, China.
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Rezaei S, Mahjoubin-Tehran M, Aghaee-Bakhtiari SH, Jalili A, Movahedpour A, Khan H, Moghoofei M, Shojaei Z, R Hamblin M, Mirzaei H. Autophagy-related MicroRNAs in chronic lung diseases and lung cancer. Crit Rev Oncol Hematol 2020; 153:103063. [DOI: 10.1016/j.critrevonc.2020.103063] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2019] [Revised: 06/11/2020] [Accepted: 07/12/2020] [Indexed: 12/24/2022] Open
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18
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Kong C, Yao YX, Bing ZT, Guo BH, Huang L, Huang ZG, Lai YC. Dynamical network analysis reveals key microRNAs in progressive stages of lung cancer. PLoS Comput Biol 2020; 16:e1007793. [PMID: 32428028 PMCID: PMC7295246 DOI: 10.1371/journal.pcbi.1007793] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2019] [Revised: 06/15/2020] [Accepted: 03/17/2020] [Indexed: 11/19/2022] Open
Abstract
Non-coding RNAs are fundamental to the competing endogenous RNA (CeRNA) hypothesis in oncology. Previous work focused on static CeRNA networks. We construct and analyze CeRNA networks for four sequential stages of lung adenocarcinoma (LUAD) based on multi-omics data of long non-coding RNAs (lncRNAs), microRNAs and mRNAs. We find that the networks possess a two-level bipartite structure: common competing endogenous network (CCEN) composed of an invariant set of microRNAs over all the stages and stage-dependent, unique competing endogenous networks (UCENs). A systematic enrichment analysis of the pathways of the mRNAs in CCEN reveals that they are strongly associated with cancer development. We also find that the microRNA-linked mRNAs from UCENs have a higher enrichment efficiency. A key finding is six microRNAs from CCEN that impact patient survival at all stages, and four microRNAs that affect the survival from a specific stage. The ten microRNAs can then serve as potential biomarkers and prognostic tools for LUAD.
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Affiliation(s)
- Chao Kong
- The Key Laboratory of Biomedical Information Engineering of Ministry of Education, Institute of Health and Rehabilitation Science, School of Life Science and Technology, Xi’an Jiaotong University, The Key Laboratory of Neuro-informatics & Rehabilitation Engineering of Ministry of Civil Affairs, Xi’an, Shaanxi, P. R. China
- National Engineering Research Center for Healthcare Devices. Guangzhou, Guangdong, P.R. China
- Institute of Computational Physics and Complex Systems, School of Physical Science and Technology, Lanzhou University, Lanzhou, China
| | - Yu-Xiang Yao
- Institute of Computational Physics and Complex Systems, School of Physical Science and Technology, Lanzhou University, Lanzhou, China
| | - Zhi-Tong Bing
- Evidence Based Medicine Center, School of Basic Medical Science of Lanzhou University, Lanzhou, China
- Key Laboratory of Evidence Based Medicine and Knowledge Translation of Gansu Province, Lanzhou, China
- Department of Computational Physics, Institute of Modern Physics, Chinese Academy of Sciences, Lanzhou, China
| | - Bing-Hui Guo
- Beijing Advanced Innovation Center for Big Data and Brain Computing, LMIB and School of Mathematics and System Sciences, Beihang University, Beijing, China
| | - Liang Huang
- Institute of Computational Physics and Complex Systems, School of Physical Science and Technology, Lanzhou University, Lanzhou, China
| | - Zi-Gang Huang
- The Key Laboratory of Biomedical Information Engineering of Ministry of Education, Institute of Health and Rehabilitation Science, School of Life Science and Technology, Xi’an Jiaotong University, The Key Laboratory of Neuro-informatics & Rehabilitation Engineering of Ministry of Civil Affairs, Xi’an, Shaanxi, P. R. China
- * E-mail:
| | - Ying-Cheng Lai
- School of Electrical, Computer and Energy Engineering, Arizona State University, Tempe, Arizona, United States of America
- Department of Physics, Arizona State University, Tempe, Arizona, United States of America
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19
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Castaldi A, Horie M, Rieger ME, Dubourd M, Sunohara M, Pandit K, Zhou B, Offringa IA, Marconett CN, Borok Z. Genome-wide integration of microRNA and transcriptomic profiles of differentiating human alveolar epithelial cells. Am J Physiol Lung Cell Mol Physiol 2020; 319:L173-L184. [PMID: 32432919 DOI: 10.1152/ajplung.00519.2019] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
The alveolar epithelium is comprised of two cell types, alveolar epithelial type 1 (AT1) and type 2 (AT2) cells, the latter being capable of self-renewal and transdifferentiation into AT1 cells for normal maintenance and restoration of epithelial integrity following injury. MicroRNAs (miRNAs) are critical regulators of several biological processes, including cell differentiation; however, their role in establishment/maintenance of cellular identity in adult alveolar epithelium is not well understood. To investigate this question, we performed genome-wide analysis of sequential changes in miRNA and gene expression profiles using a well-established model in which human AT2 (hAT2) cells transdifferentiate into AT1-like cells over time in culture that recapitulates many aspects of transdifferentiation in vivo. We defined three phases of miRNA expression during the transdifferentiation process as "early," "late," and "consistently" changed, which were further subclassified as up- or downregulated. miRNAs with altered expression at all time points during transdifferentiation were the largest subgroup, suggesting the need for consistent regulation of signaling pathways to mediate this process. Target prediction analysis and integration with previously published gene expression data identified glucocorticoid signaling as the top pathway regulated by miRNAs. Serum/glucocorticoid-regulated kinase 1 (SGK1) emerged as a central regulatory factor, whose downregulation correlated temporally with gain of hsa-miR-424 and hsa-miR-503 expression. Functional validation demonstrated specific targeting of these miRNAs to the 3'-untranslated region of SGK1. These data demonstrate the time-related contribution of miRNAs to the alveolar transdifferentiation process and suggest that inhibition of glucocorticoid signaling is necessary to achieve the AT1-like cell phenotype.
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Affiliation(s)
- Alessandra Castaldi
- Hastings Center for Pulmonary Research and Division of Pulmonary, Critical Care and Sleep Medicine, Department of Medicine, Keck School of Medicine, University of Southern California, Los Angeles, California
| | - Masafumi Horie
- Hastings Center for Pulmonary Research and Division of Pulmonary, Critical Care and Sleep Medicine, Department of Medicine, Keck School of Medicine, University of Southern California, Los Angeles, California
| | - Megan E Rieger
- Hastings Center for Pulmonary Research and Division of Pulmonary, Critical Care and Sleep Medicine, Department of Medicine, Keck School of Medicine, University of Southern California, Los Angeles, California
| | - Mickael Dubourd
- Hastings Center for Pulmonary Research and Division of Pulmonary, Critical Care and Sleep Medicine, Department of Medicine, Keck School of Medicine, University of Southern California, Los Angeles, California
| | - Mitsuhiro Sunohara
- Hastings Center for Pulmonary Research and Division of Pulmonary, Critical Care and Sleep Medicine, Department of Medicine, Keck School of Medicine, University of Southern California, Los Angeles, California
| | - Kusum Pandit
- Department of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania
| | - Beiyun Zhou
- Hastings Center for Pulmonary Research and Division of Pulmonary, Critical Care and Sleep Medicine, Department of Medicine, Keck School of Medicine, University of Southern California, Los Angeles, California
| | - Ite A Offringa
- Department of Surgery, Keck School of Medicine, University of Southern California, Los Angeles, California.,USC Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, California.,Department of Biochemistry and Molecular Medicine, Keck School of Medicine, University of Southern California, Los Angeles, California
| | - Crystal N Marconett
- Department of Surgery, Keck School of Medicine, University of Southern California, Los Angeles, California.,USC Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, California.,Department of Biochemistry and Molecular Medicine, Keck School of Medicine, University of Southern California, Los Angeles, California
| | - Zea Borok
- Hastings Center for Pulmonary Research and Division of Pulmonary, Critical Care and Sleep Medicine, Department of Medicine, Keck School of Medicine, University of Southern California, Los Angeles, California.,USC Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, California.,Department of Biochemistry and Molecular Medicine, Keck School of Medicine, University of Southern California, Los Angeles, California
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Therapeutic Strategies for Corneal Wound Angiogenesis. CURRENT PATHOBIOLOGY REPORTS 2020. [DOI: 10.1007/s40139-020-00206-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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21
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Malmuthuge N, Liang G, Guan LL. Regulation of rumen development in neonatal ruminants through microbial metagenomes and host transcriptomes. Genome Biol 2019; 20:172. [PMID: 31443695 PMCID: PMC6708143 DOI: 10.1186/s13059-019-1786-0] [Citation(s) in RCA: 95] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2019] [Accepted: 08/07/2019] [Indexed: 01/05/2023] Open
Abstract
BACKGROUND In ruminants, early rumen development is vital for efficient fermentation that converts plant materials to human edible food such as milk and meat. Here, we investigate the extent and functional basis of host-microbial interactions regulating rumen development during the first 6 weeks of life. RESULTS The use of microbial metagenomics, together with quantification of volatile fatty acids (VFAs) and qPCR, reveals the colonization of an active bacterial community in the rumen at birth. Colonization of active complex carbohydrate fermenters and archaea with methyl-coenzyme M reductase activity was also observed from the first week of life in the absence of a solid diet. Integrating microbial metagenomics and host transcriptomics reveals only 26.3% of mRNA transcripts, and 46.4% of miRNAs were responsive to VFAs, while others were ontogenic. Among these, one host gene module was positively associated with VFAs, while two other host gene modules and one miRNA module were negatively associated with VFAs. Eight host genes and five miRNAs involved in zinc ion binding-related transcriptional regulation were associated with a rumen bacterial cluster consisting of Prevotella, Bacteroides, and Ruminococcus. CONCLUSION This three-way interaction suggests a potential role of bacteria-driven transcriptional regulation in early rumen development via miRNAs. Our results reveal a highly active early microbiome that regulates rumen development of neonatal calves at the cellular level, and miRNAs may coordinate these host-microbial interactions.
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Affiliation(s)
- Nilusha Malmuthuge
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, Alberta, T6G 2P5, Canada
| | - Guanxiang Liang
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, Alberta, T6G 2P5, Canada
| | - Le Luo Guan
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, Alberta, T6G 2P5, Canada.
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22
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Zheng J, He Q, Tang H, Xia H. miR-455-5p Overexpression Reduces Rat Lung Alveolar Type II Cell Proliferation by Downregulating STRA6. Anat Rec (Hoboken) 2019; 302:2062-2069. [PMID: 31087788 PMCID: PMC6851624 DOI: 10.1002/ar.24145] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2018] [Revised: 11/26/2018] [Accepted: 12/26/2018] [Indexed: 11/12/2022]
Abstract
miR‐455‐5p and retinoid signaling pathway and its membrane receptor, STRA6, are associated with lung development. Software copredictions indicate that the miRNA upstream of the STRA6 gene is miR‐455‐5p. We hypothesized that miR‐455‐5p participates in rat lung alveolar Type II cell proliferation by targeting STRA6 and designed this study to investigate the effects of miR‐455‐5p overexpression on rat lung alveolar Type II cells. Dual luciferase reporter gene assay was utilized to confirm the relationship between miR‐455‐5p and STRA6. An miR‐455‐5p‐expressing adenoviral vector was constructed and transfected into rat lung alveolar Type II cells. STRA6 protein expression was detected in rat lung alveolar Type II cells by Western blotting at 72 hr posttransfection. Retinol concentration was detected by ELISA at 72 hr posttransfection. The cell proliferation was detected by CCK8 assay at 24, 48, and 72 hr posttransfection. Our results showed that STRA6 is a target gene of miR‐455‐5p. STRA6 protein expression was significantly lower in the miR‐455‐5p‐overexpression group than in the NC group (0.615 ± 0.131 vs. 0.958 ± 0.246, P = 0.029). Similar results were observed for retinol concentration (2.985 ± 0.061 vs. 3.949 ± 0.118, P = 0.000). Rat lung alveolar Type II cell proliferation was lower in the miR‐455‐5p‐overexpression group than in the NC group at 24, 48, and 72 hr posttransfection (24 hr: 0.280 ± 0.184 vs. 1.354 ± 0.169 P = 0.026; 48 hr: 0.881 ± 0.016 vs. 1.992 ± 0.050 P = 0.001; 72 hr: 2.105 ± 0.148 vs. 2.937 ± 0.079 P = 0.016). In summary, miR‐455‐5p is associated with lung development. miR‐455‐5p overexpression downregulates STRA6, leading to reduced retinol concentration and rat lung alveolar Type II cell proliferation. Anat Rec, 302:2062–2069, 2019. © 2019 The Authors. The Anatomical Record published by Wiley Periodicals, Inc. on behalf of American Association of Anatomists.
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Affiliation(s)
- Jintao Zheng
- Department of Pediatric Surgery, Foshan Maternity and Children's Healthcare Hospital Affiliated to Southern Medical University, Guangzhou, Guangdong, China.,Department of Pediatric Surgery, Guangzhou Institute of Pediatrics, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, Guangdong, China
| | - Qiuming He
- Department of Pediatric Surgery, Guangzhou Institute of Pediatrics, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, Guangdong, China
| | - Huajian Tang
- Department of Pediatric Surgery, Foshan Maternity and Children's Healthcare Hospital Affiliated to Southern Medical University, Guangzhou, Guangdong, China
| | - Huimin Xia
- Department of Pediatric Surgery, Foshan Maternity and Children's Healthcare Hospital Affiliated to Southern Medical University, Guangzhou, Guangdong, China.,Department of Pediatric Surgery, Guangzhou Institute of Pediatrics, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, Guangdong, China
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The effects of tracheal occlusion on Wnt signaling in a rabbit model of congenital diaphragmatic hernia. J Pediatr Surg 2019; 54:937-944. [PMID: 30792093 DOI: 10.1016/j.jpedsurg.2019.01.024] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/23/2019] [Accepted: 01/27/2019] [Indexed: 12/22/2022]
Abstract
PURPOSE Tracheal occlusion (TO) reverses pulmonary hypoplasia (PH) in congenital diaphragmatic hernia (CDH), but its mechanism of action remains poorly understood. Wnt signaling plays a critical role in lung development, but few studies exist. The purpose of our study was to a) confirm that our CDH rabbit model produced PH which was reversed by TO and b) determine the effects of CDH +/- TO on Wnt signaling. METHODS CDH was created in fetal rabbits at 23 days, TO at 28 days, and lung collection at 31 days. Lung body weight ratio (LBWR) and mean terminal bronchiole density (MTBD) were determined. mRNA and miRNA expression was determined in the left lower lobe using RT-qPCR. RESULTS Fifteen CDH, 15 CDH + TO, 6 sham CDH, and 15 controls survived and were included in the study. LBWR was low in CDH, while CDH + TO was similar to controls (p = 0.003). MTBD was higher in CDH fetuses and restored to control levels in CDH + TO (p < 0.001). Reference genes TOP1, SDHA, and ACTB were consistently expressed within and between treatment groups. miR-33 and MKI67 were increased, and Lgl1 was decreased in CDH + TO. CONCLUSION TO reversed pulmonary hypoplasia and stimulated early Wnt signaling in CDH fetal rabbits. TYPE OF STUDY Basic science, prospective. LEVEL OF EVIDENCE II.
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24
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Overexpression of miR-27b-3p Targeting Wnt3a Regulates the Signaling Pathway of Wnt/ β-Catenin and Attenuates Atrial Fibrosis in Rats with Atrial Fibrillation. OXIDATIVE MEDICINE AND CELLULAR LONGEVITY 2019; 2019:5703764. [PMID: 31178968 PMCID: PMC6501122 DOI: 10.1155/2019/5703764] [Citation(s) in RCA: 55] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/16/2018] [Revised: 01/06/2019] [Accepted: 01/15/2019] [Indexed: 12/31/2022]
Abstract
MicroRNAs (miRNAs) are regarded as a potential method for the treatment of atrial fibrillation (AF) although its molecular mechanism remains unknown. We found in our previous study that the level of peripheral blood miR-27b-3p and the expression of atrial tissue CX43 were both significantly downregulated in AF patients. In the present study, we propose and test this hypothesis that overexpression of miR-27b-3p attenuates atrial fibrosis, increases CX43 expression, and regulates the signaling pathway of Wnt/β-Catenin by targeting Wnt3a. miR-27b-3p overexpression was induced by rat tail vein injection of adeno-associated virus. Two weeks after transfection of adeno-associated virus, the rat AF model was established by tail vein injection of acetylcholine- (ACh-) CaCl2 for 7 days, and 1 ml/kg was injected daily. The incidence and duration of AF were recorded with an electrocardiogram. Cardiac function was monitored by cardiac ultrasound. Serum cardiac enzyme was detected by ELISA. The expression of atrial miR-27b-3 and Wnt3a was assayed by quantitative RT-PCR. Atrial fibrosis was determined by Masson's trichrome staining. Expression of atrial Collagen-I and Collagen-III was tested by the immunohistochemical method. Expression of CX43 was measured by immunofluorescence. The expression of Collagen-I, a-SMA, Collagen-III, TGF-β1, CX43, Wnt3a, β-Catenin, and p-β-Catenin was assayed by western blot. Our results showed that miR-27b-3p overexpression could reduce the incidence and duration of AF, alleviate atrial fibrosis, increase atrial CX43 expression, and decrease the expression of Collagen-I, a-SMA, Collagen-III, TGF-β1, Wnt3a, and p-β-Catenin. In addition, the results of luciferase activity assay showed that Wnt3a is a validated miR-27b-3p target in HEK 293T cells. Our results provide a new evidence that miR-27b-3p regulates the signaling pathway of Wnt/β-Catenin by targeting Wnt3a, which may play an important role in the development of atrial fibrosis and AF.
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25
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Mukwaya A, Jensen L, Peebo B, Lagali N. MicroRNAs in the cornea: Role and implications for treatment of corneal neovascularization. Ocul Surf 2019; 17:400-411. [PMID: 30959113 DOI: 10.1016/j.jtos.2019.04.002] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2019] [Revised: 03/25/2019] [Accepted: 04/01/2019] [Indexed: 12/18/2022]
Abstract
With no safe and efficient approved therapy available for treating corneal neovascularization, the search for alternative and effective treatments is of great importance. Since the discovery of miRNAs as key regulators of gene expression, knowledge of their function in the eye has expanded continuously, facilitated by high throughput genomic tools such as microarrays and RNA sequencing. Recently, reports have emerged implicating miRNAs in pathological and developmental angiogenesis. This has led to the idea of targeting these regulatory molecules as a therapeutic approach for treating corneal neovascularization. With the growing volume of data generated from high throughput tools applied to study corneal neovascularization, we provide here a focused review of the known miRNAs related to corneal neovascularization, while presenting new experimental data and insights for future research and therapy development.
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Affiliation(s)
- Anthony Mukwaya
- Department of Ophthalmology, Institute for Clinical and Experimental Medicine, Faculty of Health Sciences, Linkoping University, Linköping, Sweden
| | - Lasse Jensen
- Department of Medical and Health Sciences, Division of Cardiovascular Medicine, Linköping University, Linköping, Sweden
| | - Beatrice Peebo
- Department of Ophthalmology, Institute for Clinical and Experimental Medicine, Faculty of Health Sciences, Linkoping University, Linköping, Sweden
| | - Neil Lagali
- Department of Ophthalmology, Institute for Clinical and Experimental Medicine, Faculty of Health Sciences, Linkoping University, Linköping, Sweden; Department of Ophthalmology, Sørlandet Hospital Arendal, Arendal, Norway.
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26
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Sedgeman LR, Beysen C, Ramirez Solano MA, Michell DL, Sheng Q, Zhao S, Turner S, Linton MF, Vickers KC. Beta cell secretion of miR-375 to HDL is inversely associated with insulin secretion. Sci Rep 2019; 9:3803. [PMID: 30846744 PMCID: PMC6405899 DOI: 10.1038/s41598-019-40338-7] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2018] [Accepted: 02/08/2019] [Indexed: 12/15/2022] Open
Abstract
Extracellular microRNAs (miRNAs) are a new class of biomarkers for cellular phenotypes and disease, and are bioactive signals within intercellular communication networks. Previously, we reported that miRNAs are secreted from macrophage to high-density lipoproteins (HDL) and delivered to recipient cells to regulate gene expression. Despite the potential importance of HDL-miRNAs, regulation of HDL-miRNA export from cells has not been fully studied. Here, we report that pancreatic islets and beta cells abundantly export miR-375-3p to HDL and this process is inhibited by cellular mechanisms that promote insulin secretion. Small RNA sequencing and PCR approaches were used to quantify beta cell miRNA export to HDL. Strikingly, high glucose conditions were found to inhibit HDL-miR-375-3p export, which was dependent on extracellular calcium. Likewise, stimulation of cAMP was found to repress HDL-miR-375-3p export. Furthermore, we found that beta cell ATP-sensitive potassium channel (KATP) channels are required for HDL-miRNA export as chemical inhibition (tolbutamide) and global genetic knockout (Abcc8−/−) approaches inhibited HDL-miR-375-3p export. This process is not likely associated with cholesterol flux, as gain-of-function and loss-of-function studies for cholesterol transporters failed to alter HDL-miR-375-3p export. In conclusion, results support that pancreatic beta cells export miR-375-3p to HDL and this process is inversely regulated to insulin secretion.
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Affiliation(s)
- Leslie R Sedgeman
- Department of Molecular Physiology and Biophysics, Vanderbilt University, Nashville, TN, USA
| | | | | | - Danielle L Michell
- Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Quanhu Sheng
- Department of Biostatistics, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Shilin Zhao
- Department of Biostatistics, Vanderbilt University Medical Center, Nashville, TN, USA
| | | | - MacRae F Linton
- Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Kasey C Vickers
- Department of Molecular Physiology and Biophysics, Vanderbilt University, Nashville, TN, USA. .,Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA.
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27
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Alveolar type 2 progenitor cells for lung injury repair. Cell Death Discov 2019; 5:63. [PMID: 30774991 PMCID: PMC6368612 DOI: 10.1038/s41420-019-0147-9] [Citation(s) in RCA: 102] [Impact Index Per Article: 20.4] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2018] [Revised: 12/24/2018] [Accepted: 01/02/2019] [Indexed: 12/19/2022] Open
Abstract
Alveolar type 2 progenitor cells (AT2) seem closest to clinical translation, specifying the evidence that AT2 may satisfactorily control the immune response to decrease lung injury by stabilizing host immune-competence and a classic and crucial resource for lung regeneration and repair. AT2 establish potential in benefiting injured lungs. However, significant discrepancies linger in our understanding vis-à-vis the mechanisms for AT2 as a regime for stem cell therapy as well as essential guiding information for clinical trials, including effectiveness in appropriate pre-clinical models, safety, mostly specifications for divergent lung injury patients. These important gaps shall be systematically investigated prior to the vast therapeutic perspective of AT2 cells for pulmonary diseases can be considered. This review focused on AT2 cells homeostasis, pathophysiological changes in the pathogenesis of lung injury, physiological function of AT2 cells, apoptosis of AT2 cells in lung diseases, the role of AT2 cells in repairing processes after lung injury, mechanism of AT2 cells activation promote repairing processes after lung injury, and potential therapy of lung disease by utilizing the AT2 progenitor cells. The advancement remains to causally connect the molecular and cellular alteration of AT2 cells to lung injury and repair. Conclusively, it is identified that AT2 cells can convert into AT1 cells; but, the comprehensive cellular mechanisms involved in this transition are unrevealed. Further investigation is mandatory to determine new strategies to prevent lung injury.
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28
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Shifts in ovine cardiopulmonary microRNA expression in late gestation and the perinatal period. PLoS One 2018; 13:e0204038. [PMID: 30231073 PMCID: PMC6145571 DOI: 10.1371/journal.pone.0204038] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2018] [Accepted: 09/01/2018] [Indexed: 12/23/2022] Open
Abstract
Background MicroRNAs (miRNAs) have been identified as important contributors to the regulation of early fetal cardiopulmonary development. However, miRNA expression profiles during late gestation and the early neonatal period are not fully elaborated in large mammals such as sheep (ovis aries). The aim of this study was to sequence miRNA from cardiopulmonary tissues in late gestation and neonate sheep to identify changes in miRNA expression. Methods Illumina HiSeq next-generation deep sequencing (NGS) was performed on ovine tissues from the left (LV) and right ventricles (RV), lungs and pulmonary artery (PA) of preterm fetuses (128 days), near-term fetuses (140 days) (term = 148 days) and neonatal lambs (5 days). NGS reads were mapped to the sheep genome (OviAri) and published miRNA sequences. Results Of 1345 cardiopulmonary miRNAs that were sequenced, relatively few major shifts in miRNA expression were detected with increased age from near term to neonates, and were confirmed by quantitative real-time PCR: bta-miR-146a (lung), bta-miR-22-3p (lung, LV), hsa-miR-335* (lung, PA), and miR-210 (lung, PA, LV). Conclusions Sequencing of miRNA led to identification of four predominant miRNA in ovine cardiopulmonary tissues which alter expression during late gestation and the early neonatal period, concurrent with important functional changes in heart and lungs.
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29
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Wang L, Huang W, Zhang L, Chen Q, Zhao H. Molecular pathogenesis involved in human idiopathic pulmonary fibrosis based on an integrated microRNA‑mRNA interaction network. Mol Med Rep 2018; 18:4365-4373. [PMID: 30221703 PMCID: PMC6172385 DOI: 10.3892/mmr.2018.9456] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2018] [Accepted: 07/06/2018] [Indexed: 01/27/2023] Open
Abstract
Idiopathic pulmonary fibrosis (IPF) is considered to be an ailment of the lungs that cannot be cured, wherein the lung tissues are characterized by increased thickness and stiffness, and/or scars. Despite the fact that extensive success has been achieved regarding the molecular diagnostics and pathobiology, the basic pathogenesis associated with IPF has not yet been fully elucidated and requires further clarification. In the current research, the changes in microRNA (miRNA) and mRNA expression in IPF were investigated through an integrative network technique. The authentic miRNA and mRNA expression profiling datasets were downloaded from Gene Expression Omnibus, followed by identification of differentially expressed miRNAs and mRNAs with use of the Significance Analysis of Microarrays algorithm. Expansion of the molecular targets associated with miRNAs was performed with the use of CyTargetLinker in Cytoscape, which was succeeded by validation with the use of mRNA array expression profiling. The incorporated miRNA‑mRNA network covered 27 genes, in addition to 22 miRNAs that were associated with IPF development. As revealed by the functional enrichment analysis, the cytokine‑cytokine receptor interaction and glycine, serine and threonine metabolism signalling pathways were extensively associated with IPF development. Overall, the present incorporated network illustrated the key link between miRNA and genes in IPF; in particular, it was elucidated that miR‑409‑5p and has‑miR‑376c, together with their target genes (C‑C motif chemokine ligand 20 and oncostatin M), are likely candidates involved in the promotion of IPF initiation and progression.
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Affiliation(s)
- Lijing Wang
- Department of Gerontology, Xiangya Hospital, Central South University, Changsha, Hunan 410008, P.R. China
| | - Wei Huang
- Division of Cellular Therapy, Duke University, Durham, NC 27710, USA
| | - Lemeng Zhang
- Department of Thoracic Oncology, Hunan Cancer Hospital, Changsha, Hunan 410008, P.R. China
| | - Qiong Chen
- Department of Gerontology, Xiangya Hospital, Central South University, Changsha, Hunan 410008, P.R. China
| | - Hongjun Zhao
- Department of Rheumatology and Immunology, Xiangya Hospital, Central South University, Changsha, Hunan 410008, P.R. China
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30
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Kim HR, Shin DY, Chung KH. A review of current studies on cellular and molecular mechanisms underlying pulmonary fibrosis induced by chemicals. ENVIRONMENTAL HEALTH AND TOXICOLOGY 2018; 33:e2018014-0. [PMID: 30286590 PMCID: PMC6182244 DOI: 10.5620/eht.e2018014] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/22/2018] [Accepted: 09/19/2018] [Indexed: 05/04/2023]
Abstract
Several studies showed that the inflammatory and fibrotic responses induced by polyhexamethylene guanidine phosphate (PHMG-p) were similar to those observed for idiopathic pulmonary fibrosis in South Korea in 2011. "Omic" technologies can be used to understand the mechanisms underlying chemical-induced diseases. Studies to determine the toxicity of chemicals may facilitate understanding of the mechanisms underlying the development of pulmonary fibrosis at a molecular level; thus, such studies may provide information about the toxic characteristics of various substances. In this review, we have outlined the cellular and molecular mechanisms underlying idiopathic pulmonary fibrosis and described pulmonary fibrosis induced by various chemicals, including bleomycin, paraquat, and PHMG-p, based on the results of studies performed to date.
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Affiliation(s)
- Ha Ryong Kim
- College of Pharmacy, Daegu Catholic University, Gyeongsan, Gyeongsangbuk-do 38430, Republic of Korea
| | - Da Young Shin
- School of Pharmacy, Sungkyunkwan University, Suwon, Gyeonggi-do 16419, Republic of Korea
| | - Kyu Hyuck Chung
- School of Pharmacy, Sungkyunkwan University, Suwon, Gyeonggi-do 16419, Republic of Korea
- Corresponding author: Kyu Hyuck Chung School of Pharmacy, Sungkyunkwan University, 2066, Seobu-ro, Jangan-gu, Suwon, Gyeonggi 16419, Korea. E-mail:
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Miao C, Xiong Y, Zhang G, Chang J. MicroRNAs in idiopathic pulmonary fibrosis, new research progress and their pathophysiological implication. Exp Lung Res 2018; 44:178-190. [DOI: 10.1080/01902148.2018.1455927] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Affiliation(s)
- Chenggui Miao
- Department of Pharmacy, School of Life and Health Science, Anhui Science and Technology University, Fengyang, China
| | - Youyi Xiong
- Department of Pharmacy, School of Life and Health Science, Anhui Science and Technology University, Fengyang, China
| | - Guoxue Zhang
- School of Science and Technology of Tea and Food, Anhui Agricultural University, Hefei, China
| | - Jun Chang
- Fourth Affiliated Hospital, Anhui Medical University, Hefei, China
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32
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Zhang FY, Yang N, Rao YF, Du WH, Hao HS, Zhao XM, Zhu HB, Liu Y. Profiling of miRNAs in neonatal cloned bovines with collapsed lungs and respiratory distress. Reprod Domest Anim 2018; 53:550-555. [DOI: 10.1111/rda.13144] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2017] [Accepted: 12/28/2017] [Indexed: 01/05/2023]
Affiliation(s)
- FY Zhang
- Institute of Animal Sciences; Chinese Academy of Agricultural Sciences; Beijing China
- College of Biological Sciences; China Agricultural University; Beijing China
| | - N Yang
- Laboratory of Zoonosis of Liaoning Province; College of Animal Science & Veterinary Medicine; Shenyang Agricultural University; Shenyang Liaoning China
| | - YF Rao
- Institute of Animal Sciences; Chinese Academy of Agricultural Sciences; Beijing China
| | - WH Du
- Institute of Animal Sciences; Chinese Academy of Agricultural Sciences; Beijing China
| | - HS Hao
- Institute of Animal Sciences; Chinese Academy of Agricultural Sciences; Beijing China
| | - XM Zhao
- Institute of Animal Sciences; Chinese Academy of Agricultural Sciences; Beijing China
| | - HB Zhu
- Institute of Animal Sciences; Chinese Academy of Agricultural Sciences; Beijing China
| | - Y Liu
- Institute of Animal Sciences; Chinese Academy of Agricultural Sciences; Beijing China
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Deng F, Zhang X, Wang W, Yuan R, Shen F. Identification of Gossypium hirsutum long non-coding RNAs (lncRNAs) under salt stress. BMC PLANT BIOLOGY 2018; 18:23. [PMID: 29370759 PMCID: PMC5785843 DOI: 10.1186/s12870-018-1238-0] [Citation(s) in RCA: 82] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/23/2017] [Accepted: 01/17/2018] [Indexed: 05/22/2023]
Abstract
BACKGROUND Long non-coding RNAs (lncRNAs) represent a class of riboregulators that either directly act in long form or are processed into shorter microRNAs (miRNAs) and small interfering RNAs. Long noncoding RNAs (lncRNAs) are arbitrarily defined as RNA genes larger than 200 nt in length that have no apparent coding potential. lncRNAs have emerged as playing important roles in various biological regulatory processes and are expressed in a more tissue-specific manner than mRNA. Emerging evidence shows that lncRNAs participate in stress-responsive regulation. RESULTS In this study, in order to develop a comprehensive catalogue of lncRNAs in upland cotton under salt stress, we performed whole-transcriptome strand-specific RNA sequencing for three-leaf stage cotton seedlings treated with salt stress (S_NaCl) and controls (S_CK). In total we identified 1117 unique lncRNAs in this study and 44 differentially expressed RNAs were identified as potential non-coding RNAs. For the differentially expressed lncRNAs that were identified as intergenic lncRNAs (lincRNA), we analysed the gene ontology enrichment of cis targets and found that cis target protein-coding genes were mainly enriched in stress-related categories. Real-time quantitative PCR confirmed that all selected lincRNAs responsive to salt stress. We found lnc_388 was likely as regulator of Gh_A09G1182. And lnc_883 may participate in regulating tolerance to salt stress by modulating the expression of Gh_D03G0339 MS_channel. We then predicted the target mimics for miRNA in Gossypium. six miRNAs were identified, and the result of RT-qPCR with lncRNA and miRNA suggested that lnc_973 and lnc_253 may regulate the expression of ghr-miR399 and ghr-156e as a target mimic under salt stress. CONCLUSIONS We identified 44 lincRNAs that were differentially expressed under salt stress. These lincRNAs may target protein-coding genes via cis-acting regulation. We also discovered that specifically-expressed lincRNAs under salt stress may act as endogenous target mimics for conserved miRNAs. These findings extend the current view on lincRNAs as ubiquitous regulators under stress stress.
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Affiliation(s)
- Fenni Deng
- State Key Laboratory of Crop Biology, College of Agronomy, Shandong Agricultural University, Tai’an, 271018 Shandong People’s Republic of China
| | - Xiaopei Zhang
- State Key Laboratory of Crop Biology, College of Agronomy, Shandong Agricultural University, Tai’an, 271018 Shandong People’s Republic of China
| | - Wei Wang
- State Key Laboratory of Crop Biology, College of Agronomy, Shandong Agricultural University, Tai’an, 271018 Shandong People’s Republic of China
| | - Rui Yuan
- State Key Laboratory of Crop Biology, College of Agronomy, Shandong Agricultural University, Tai’an, 271018 Shandong People’s Republic of China
| | - Fafu Shen
- State Key Laboratory of Crop Biology, College of Agronomy, Shandong Agricultural University, Tai’an, 271018 Shandong People’s Republic of China
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Regulation of influenza virus replication by Wnt/β-catenin signaling. PLoS One 2018; 13:e0191010. [PMID: 29324866 PMCID: PMC5764324 DOI: 10.1371/journal.pone.0191010] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2017] [Accepted: 12/27/2017] [Indexed: 01/12/2023] Open
Abstract
Wnt/β-catenin signaling is an essential pathway in cell cycle control. Dysregulation of the Wnt/β-catenin signaling pathway during viral infection has been reported. In this study, we examined the effect of modulating Wnt/β-catenin signaling during influenza virus infection. The activation of the Wnt/β-catenin pathway by Wnt3a increased influenza virus mRNA and virus production in in vitro in mouse lung epithelial E10 cells and mRNA expresson of influenza virus genes in vivo in the lungs of mice infected with influenza virus A/Puerto Rico/8/34. However, the inhibition of Wnt/β-catenin signaling by iCRT14 reduced virus titer and viral gene expression in human lung epithelial A549 cells and viral replication in primary mouse alveolar epithelial cells infected with different influenza virus strains. Knockdown of β-catenin also reduced viral protein expression and virus production. iCRT14 acts at the early stage of virus replication. Treatment with iCRT14 inhibited the expression of the viral genes (vRNA, cRNA and mRNA) evaluated in this study. The intraperitoneal administration of iCRT14 reduced viral load, improved clinical signs, and partially protected mice from influenza virus infection.
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Genome-wide identification of miRNAs and lncRNAs in Cajanus cajan. BMC Genomics 2017; 18:878. [PMID: 29141604 PMCID: PMC5688659 DOI: 10.1186/s12864-017-4232-2] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2017] [Accepted: 10/23/2017] [Indexed: 01/24/2023] Open
Abstract
Background Non-coding RNAs (ncRNAs) are important players in the post transcriptional regulation of gene expression (PTGR). On one hand, microRNAs (miRNAs) are an abundant class of small ncRNAs (~22nt long) that negatively regulate gene expression at the levels of messenger RNAs stability and translation inhibition, on the other hand, long ncRNAs (lncRNAs) are a large and diverse class of transcribed non-protein coding RNA molecules (> 200nt) that play both up-regulatory as well as down-regulatory roles at the transcriptional level. Cajanus cajan, a leguminosae pulse crop grown in tropical and subtropical areas of the world, is a source of high value protein to vegetarians or very poor populations globally. Hence, genome-wide identification of miRNAs and lncRNAs in C. cajan is extremely important to understand their role in PTGR with a possible implication to generate improve variety of crops. Results We have identified 616 mature miRNAs in C. cajan belonging to 118 families, of which 578 are novel and not reported in MirBase21. A total of 1373 target sequences were identified for 180 miRNAs. Of these, 298 targets were characterized at the protein level. Besides, we have also predicted 3919 lncRNAs. Additionally, we have identified 87 of the predicted lncRNAs to be targeted by 66 miRNAs. Conclusions miRNA and lncRNAs in plants are known to control a variety of traits including yield, quality and stress tolerance. Owing to its agricultural importance and medicinal value, the identified miRNA, lncRNA and their targets in C. cajan may be useful for genome editing to improve better quality crop. A thorough understanding of ncRNA-based cellular regulatory networks will aid in the improvement of C. cajan agricultural traits. Electronic supplementary material The online version of this article (10.1186/s12864-017-4232-2) contains supplementary material, which is available to authorized users.
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Zhu D, Tan J, Maleken AS, Muljadi R, Chan ST, Lau SN, Elgass K, Leaw B, Mockler J, Chambers D, Leeman KT, Kim CF, Wallace EM, Lim R. Human amnion cells reverse acute and chronic pulmonary damage in experimental neonatal lung injury. Stem Cell Res Ther 2017; 8:257. [PMID: 29126435 PMCID: PMC5681809 DOI: 10.1186/s13287-017-0689-9] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2017] [Revised: 08/14/2017] [Accepted: 10/06/2017] [Indexed: 01/10/2023] Open
Abstract
Background Despite advances in neonatal care, bronchopulmonary dysplasia (BPD) remains a significant contributor to infant mortality and morbidity. While human amnion epithelial cells (hAECs) have shown promise in small and large animal models of BPD, there is scarce information on long-term benefit and clinically relevant questions surrounding administration strategy remain unanswered. In assessing the therapeutic potential of hAECs, we investigated the impact of cell dosage, administration routes and timing of treatment in a pre-clinical model of BPD. Methods Lipopolysaccharide was introduced intra-amniotically at day 16 of pregnancy prior to exposure to 65% oxygen (hyperoxia) at birth. hAECs were administered either 12 hours (early) or 4 days (late) after hyperoxia commenced. Collective lung tissues were subjected to histological analysis, multikine ELISA for inflammatory cytokines, FACS for immune cell populations and 3D lung stem cell culture at neonatal stage (postnatal day 7 and 14). Invasive lung function test and echocardiography were applied at 6 and 10 weeks of age. Results hAECs improved the tissue-to-airspace ratio and septal crest density in a dose-dependent manner, regardless of administration route. Early administration of hAECs, coinciding with the commencement of postnatal hyperoxia, was associated with reduced macrophages, dendritic cells and natural killer cells. This was not the case if hAECs were administered when lung injury was established. Fittingly, early hAEC treatment was more efficacious in reducing interleukin-1β, tumour necrosis factor alpha and monocyte chemoattractant protein-1 levels. Early hAEC treatment was also associated with reduced airway hyper-responsiveness and normalisation of pressure–volume loops. Pulmonary hypertension and right ventricle hypertrophy were also prevented in the early hAEC treatment group, and this persisted until 10 weeks of age. Conclusions Early hAEC treatment appears to be advantageous over late treatment. There was no difference in efficacy between intravenous and intratracheal administration. The benefits of hAEC administration resulted in long-term improvements in cardiorespiratory function. Electronic supplementary material The online version of this article (doi:10.1186/s13287-017-0689-9) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Dandan Zhu
- The Ritchie Centre, Hudson Institute of Medical Research, Clayton, VIC, Australia.,Department of Obstetrics and Gynaecology, Monash University, 27-31 Wright Street, Clayton, VIC, 3800, Australia
| | - Jean Tan
- The Ritchie Centre, Hudson Institute of Medical Research, Clayton, VIC, Australia.,Department of Obstetrics and Gynaecology, Monash University, 27-31 Wright Street, Clayton, VIC, 3800, Australia
| | - Amina S Maleken
- The Ritchie Centre, Hudson Institute of Medical Research, Clayton, VIC, Australia.,Department of Obstetrics and Gynaecology, Monash University, 27-31 Wright Street, Clayton, VIC, 3800, Australia
| | - Ruth Muljadi
- The Ritchie Centre, Hudson Institute of Medical Research, Clayton, VIC, Australia.,Department of Obstetrics and Gynaecology, Monash University, 27-31 Wright Street, Clayton, VIC, 3800, Australia
| | - Siow T Chan
- The Ritchie Centre, Hudson Institute of Medical Research, Clayton, VIC, Australia.,Department of Obstetrics and Gynaecology, Monash University, 27-31 Wright Street, Clayton, VIC, 3800, Australia
| | - Sin N Lau
- The Ritchie Centre, Hudson Institute of Medical Research, Clayton, VIC, Australia.,Department of Obstetrics and Gynaecology, Monash University, 27-31 Wright Street, Clayton, VIC, 3800, Australia
| | - Kirstin Elgass
- Monash Micro Imaging, Monash University, Clayton, Victoria, Australia
| | - Bryan Leaw
- The Ritchie Centre, Hudson Institute of Medical Research, Clayton, VIC, Australia.,Department of Obstetrics and Gynaecology, Monash University, 27-31 Wright Street, Clayton, VIC, 3800, Australia
| | - Joanne Mockler
- The Ritchie Centre, Hudson Institute of Medical Research, Clayton, VIC, Australia.,Department of Obstetrics and Gynaecology, Monash University, 27-31 Wright Street, Clayton, VIC, 3800, Australia
| | - Daniel Chambers
- Queensland Lung Transplant Service, The Prince Charles Hospital, Brisbane, QLD, Australia.,School of Medicine, The University of Queensland, Brisbane, QLD, Australia
| | - Kristen T Leeman
- Division of Newborn Medicine, Department of Paediatrics, Boston Children's Hospital Boston, Harvard Medical School, Clayton, Victoria, Australia.,Boston Children's Hospital Boston Stem Cell Program, Department of Genetics, Harvard Medical School and Harvard Stem Cell Institute, Clayton, Victoria, Australia
| | - Carla F Kim
- Boston Children's Hospital Boston Stem Cell Program, Department of Genetics, Harvard Medical School and Harvard Stem Cell Institute, Clayton, Victoria, Australia
| | - Euan M Wallace
- The Ritchie Centre, Hudson Institute of Medical Research, Clayton, VIC, Australia.,Department of Obstetrics and Gynaecology, Monash University, 27-31 Wright Street, Clayton, VIC, 3800, Australia
| | - Rebecca Lim
- The Ritchie Centre, Hudson Institute of Medical Research, Clayton, VIC, Australia. .,Department of Obstetrics and Gynaecology, Monash University, 27-31 Wright Street, Clayton, VIC, 3800, Australia.
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Yang H, Fu J, Yao L, Hou A, Xue X. Runx3 is a key modulator during the epithelial-mesenchymal transition of alveolar type II cells in animal models of BPD. Int J Mol Med 2017; 40:1466-1476. [PMID: 28949375 PMCID: PMC5627869 DOI: 10.3892/ijmm.2017.3135] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2016] [Accepted: 08/31/2017] [Indexed: 01/01/2023] Open
Abstract
Bronchopulmonary dysplasia (BPD) is a major challenge for premature infants; however, the underlying mechanisms remain unclear. We previously reported that epithelial-mesenchymal transition (EMT) in alveolar type II (AT2) epithelial cells influences the normal alveolar development process. In this study, we wished to examine whether Runx3 is an important factor for BPD by regulating EMT in AT2 cells. In vivo, animal models of BPD were established by placing newborn rats in hyperoxia tanks. Lung tissue and isolated AT2 cells were collected on different days following exposure to oxygen. The pathological changes in lung tissue, alveolar development and Runx3 expression were then investigated. In vitro, RLE-6TN cells were divided into 5 groups as follows: the cont-rol, Runx3, siRunx3, transforming growth factor-β1 (TGF-β1) and Runx3 + TGF-β1 groups, and the biomarkers of EMT were investigated. In the newborn rat model of BPD, Runx3 protein and mRNA levels in both lung tissue and BPD-derived AT2 cells were significantly lower than those in the control group. The correlation between Runx3 protein expression and pulmonary development indicators was analyzed; Runx3 expression positively correlated with the radial alveolar count (RAC) and the percentage of smooth muscle actin-positive secondary septa, but negatively correlated with alveolar wall thickness. EMT was observed in the RLE-6TN cells in which the Runx3 gene was knocked down and follwoing TGF-β1‑induced EMT stimulation; however, TGF-β1 failed to induce EMT in the RLE-6TN cells overexpressing Runx3. On the whole, our data indicte that low Runx3 levels may promote EMT, while high Runx3 levels inhibit TGF-β1-induced EMT. Therefore, we predict that low levels of Runx3 in BPD lung tissue may promote EMT in AT2 cells, thus affecting alveolar development.
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Affiliation(s)
- Haiping Yang
- Department of Pediatrics, Cangzhou Central Hospital, Cangzhou, Hebei 061000, P.R. China
| | - Jianhua Fu
- Department of Pediatrics, Shengjing Hospital of China Medical University, Shenyang, Liaoning 110004, P.R. China
| | - Li Yao
- Department of Pediatrics, Shengjing Hospital of China Medical University, Shenyang, Liaoning 110004, P.R. China
| | - Ana Hou
- Department of Pediatrics, Shengjing Hospital of China Medical University, Shenyang, Liaoning 110004, P.R. China
| | - Xindong Xue
- Department of Pediatrics, Shengjing Hospital of China Medical University, Shenyang, Liaoning 110004, P.R. China
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Cheng Z, Dai LL, Wang X, Jia LQ, Jing XG, Li PF, Liu M, Wang H, An L. MicroRNA-145 down-regulates mucin 5AC to alleviate airway remodeling and targets EGFR to inhibit cytokine expression. Oncotarget 2017; 8:46312-46325. [PMID: 28564633 PMCID: PMC5542269 DOI: 10.18632/oncotarget.17933] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2016] [Accepted: 02/20/2017] [Indexed: 01/14/2023] Open
Abstract
This study aims to explore how microRNA-145 (miR-145) affects airway remodeling and cytokine expression by targeting epidermal growth factor receptor (EGFR) to regulate mucin 5AC (MUC5AC).Mice alveolar epithelial cells (AECs) were divided into a control, blank, miR-145 mimics, mimic control, miR-145 inhibitors, inhibitor control, si-EGFR and miR-145 inhibitors + si-EGFR group. Asthma mice models with airway remodeling were induced with an Ovalbumin (OVA) solution and randomly divided into a normal, asthma, asthma + miR-145 mimics, asthma + miR-145 mimic control, asthma + si-EGFR or asthma + si-EGFR NC group. Airway remodeling degree and histomorphology was measured using hematoxylin-eosin (HE), Masson and periodic acid-Schiff (PAS) staining. Flow cytometry was used to detect Th2 and Th17 cells in peripheral blood, ELISA was used to measure inflammatory factors. qRT-PCR and western blotting was adapted to detect the expressions of EGFR and the relevant cytokines that are regulated by miR-145.The control, miR-145 mimics and si-EGFR groups showed a higher expression of miR-145 and a lower expression of EGFR and cytokines than the blank, mimic control, inhibitor control and miR-145 inhibitor + si-EGFR groups. Mice in the asthma + miR-145 mimics and asthma + si-EGFR groups showed lower WAt/Pbm, WAi/Pbm and WAm/Pbm, less inflammatory cells, less airway modeling and alleviated goblet cell hyperplasia and mucus obstruction than the asthma group. Furthermore, the expressions of EGFR and cytokines of transfected cells and lung tissues were negatively related to those of miR-145. MiR-145 can down-regulate MUC5AC by negatively targeting EGFR and thereby relieving airway remodeling.
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Affiliation(s)
- Zhe Cheng
- Department of Respiratory and Critical Care Medicine, Institute of Clinical Medicine, The First Affiliated Hospital of Zhengzhou University, Zhengzhou 450052, P.R. China
| | - Ling-Ling Dai
- Department of Respiratory and Critical Care Medicine, Institute of Clinical Medicine, The First Affiliated Hospital of Zhengzhou University, Zhengzhou 450052, P.R. China
| | - Xi Wang
- Department of Respiratory and Critical Care Medicine, Institute of Clinical Medicine, The First Affiliated Hospital of Zhengzhou University, Zhengzhou 450052, P.R. China
| | - Liu-Qun Jia
- Department of Respiratory and Critical Care Medicine, Institute of Clinical Medicine, The First Affiliated Hospital of Zhengzhou University, Zhengzhou 450052, P.R. China
| | - Xiao-Gang Jing
- Department of Respiratory and Critical Care Medicine, Institute of Clinical Medicine, The First Affiliated Hospital of Zhengzhou University, Zhengzhou 450052, P.R. China
| | - Peng-Fei Li
- Department of Respiratory and Critical Care Medicine, Institute of Clinical Medicine, The First Affiliated Hospital of Zhengzhou University, Zhengzhou 450052, P.R. China
| | - Meng Liu
- Department of Respiratory and Critical Care Medicine, Institute of Clinical Medicine, The First Affiliated Hospital of Zhengzhou University, Zhengzhou 450052, P.R. China
| | - Huan Wang
- Department of Respiratory and Critical Care Medicine, Institute of Clinical Medicine, The First Affiliated Hospital of Zhengzhou University, Zhengzhou 450052, P.R. China
| | - Lin An
- Department of Respiratory and Critical Care Medicine, Institute of Clinical Medicine, The First Affiliated Hospital of Zhengzhou University, Zhengzhou 450052, P.R. China
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Zhang L, Zhao S, Yuan L, Wu H, Jiang H, Luo G. Hyperoxia-mediated LC3B activation contributes to the impaired transdifferentiation of type II alveolar epithelial cells (AECIIs) to type I cells (AECIs). Clin Exp Pharmacol Physiol 2017; 43:834-43. [PMID: 27187184 DOI: 10.1111/1440-1681.12592] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2016] [Revised: 05/05/2016] [Accepted: 05/12/2016] [Indexed: 12/14/2022]
Abstract
Life-saving mechanical ventilation can also cause lung injury through the overproduction of reactive oxygen species (ROS), leading to bronchopulmonary dysplasia (BPD)-like symptoms in preterm infants. It is reported that the autophagic protein microtubule-associated protein-1 light chain (LC)-3B can confer protection against hyperoxia-induced DNA damage in lung alveolar epithelium. However, its role in the transdifferentiation of type II alveolar epithelial cells (AECIIs) to type I cells (AECIs) is unclear and requires further investigation. In this study, newborn Sprague-Dawley rats were exposed to 90% oxygen for up to 14 days to mimic BPD in human infants, with neonatal pups exposed to room air (21% oxygen) as controls. Primary rat AECIIs were cultured under hyperoxic conditions for up to 24 hours to further investigate the underlying mechanisms. This study found that hyperoxia promoted a significant and time-dependent increase of AECII marker surfactant protein (SP)-C in the lung. The increase of AECI marker T1α was repressed by hyperoxia during lung development. These results indicated an impaired AECII transdifferentiation. Pulmonary ROS concentration and expression of autophagic protein LC-3B were increased gradually in response to hyperoxia exposure. Furthermore, AECIIs produced more ROS when cultured under hyperoxic conditions in vitro. Both the LC3B expression and the conversion from LC3BI to LC3BII were enhanced in hyperoxic AECs. Interestingly, inhibition of LC3B either by ROS inhibitor N-acetyl-l-cysteine (NAC) or adenovirus-mediated LC3B shRNA could partly restore AECII transdifferentiation under hyperoxia condition. In summary, the current study reveals a novel role of activated LC3B induced by hyperoxia in AECII transdifferentiation.
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Affiliation(s)
- Liang Zhang
- Department of Neonatology, The First Affiliated Hospital of China Medical University, Shenyang, China
| | - Shuang Zhao
- Department of Paediatrics, Shenyang Fourth People's Hospital, Shenyang, China
| | - Lijie Yuan
- Department of Biochemistry and Molecular Biology, Harbin Medical University (Daqing Campus), Daqing, China
| | - Hongmin Wu
- Department of Neonatology, The First Affiliated Hospital of China Medical University, Shenyang, China
| | - Hong Jiang
- Department of Paediatrics, The First Affiliated Hospital of China Medical University, Shenyang, China
| | - Gang Luo
- Department of Paediatrics, The First Affiliated Hospital of China Medical University, Shenyang, China
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Sun T, Li CT, Xiong L, Ning Z, Leung F, Peng S, Lu WW. miR-375-3p negatively regulates osteogenesis by targeting and decreasing the expression levels of LRP5 and β-catenin. PLoS One 2017; 12:e0171281. [PMID: 28158288 PMCID: PMC5291413 DOI: 10.1371/journal.pone.0171281] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2016] [Accepted: 01/18/2017] [Indexed: 12/18/2022] Open
Abstract
Wnt signaling pathways are essential for bone formation. Previous studies showed that Wnt signaling pathways were regulated by miR-375. Thus, we aim to explore whether miR-375 could affect osteogenesis. In the present study, we investigated the roles of miR-375 and its downstream targets. Firstly, we revealed that miR-375-3p negatively modulated osteogenesis by suppressing positive regulators of osteogenesis and promoting negative regulators of osteogenesis. In addition, the results of TUNEL cell apoptosis assay showed that miR-375-3p induced MC3T3-E1 cell apoptosis. Secondly, miR-375-3p targeted low-density lipoprotein receptor-related protein 5 (LRP5), a co-receptor of the Wnt signaling pathways, and β-catenin as determined by luciferase activity assay, and it decreased the expression levels of LRP5 and β-catenin. Thirdly, the decline of protein levels of β-catenin was determined by immunocytochemistry and immunofluorescence. Finally, silence of LRP5 in osteoblast precursor cells resulted in diminished cell viability and cell proliferation as detected by WST-1-based colorimetric assay. Additionally, all the parameters including the relative bone volume from μCT measurement suggested that LRP5 knockout in mice resulted in a looser and worse-connected trabeculae. The mRNA levels of important negative modulators relating to osteogenesis increased after the functions of LRP5 were blocked in mice. Last but not least, the expression levels of LRP5 increased during the osteogenesis of MC3T3-E1, while the levels of β-catenin decreased in bone tissues from osteoporotic patients with vertebral compression fractures. In conclusion, we revealed miR-375-3p negatively regulated osteogenesis by targeting LRP5 and β-catenin. In addition, loss of functions of LRP5 damaged bone formation in vivo. Clinically, miR-375-3p and its targets might be used as diagnostic biomarkers for osteoporosis and might be also as novel therapeutic agents in osteoporosis treatment. The relevant products of miR-375-3p might be developed into molecular drugs in the future. These molecules could be used in translational medicine.
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Affiliation(s)
- Tianhao Sun
- Department of Orthopaedics and Traumatology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
- Department of Spine Surgery, Shenzhen People's Hospital, Jinan University Second College of Medicine, Shenzhen, China
| | - Chen-Tian Li
- Department of Orthopaedics and Traumatology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
| | - Lifeng Xiong
- Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
| | - Ziyu Ning
- Department of Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
| | - Frankie Leung
- Department of Orthopaedics and Traumatology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
| | - Songlin Peng
- Department of Spine Surgery, Shenzhen People's Hospital, Jinan University Second College of Medicine, Shenzhen, China
| | - William W. Lu
- Department of Orthopaedics and Traumatology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
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Peck BCE, Mah AT, Pitman WA, Ding S, Lund PK, Sethupathy P. Functional Transcriptomics in Diverse Intestinal Epithelial Cell Types Reveals Robust MicroRNA Sensitivity in Intestinal Stem Cells to Microbial Status. J Biol Chem 2017; 292:2586-2600. [PMID: 28053090 DOI: 10.1074/jbc.m116.770099] [Citation(s) in RCA: 84] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2016] [Revised: 12/23/2016] [Indexed: 01/01/2023] Open
Abstract
Gut microbiota play an important role in regulating the development of the host immune system, metabolic rate, and at times, disease pathogenesis. The factors and mechanisms that mediate interactions between microbiota and the intestinal epithelium are not fully understood. We provide novel evidence that microbiota may control intestinal epithelial stem cell (IESC) proliferation in part through microRNAs (miRNAs). We demonstrate that miRNA profiles differ dramatically across functionally distinct cell types of the mouse jejunal intestinal epithelium and that miRNAs respond to microbiota in a highly cell type-specific manner. Importantly, we also show that miRNAs in IESCs are more prominently regulated by microbiota compared with miRNAs in any other intestinal epithelial cell subtype. We identify miR-375 as one miRNA that is significantly suppressed by the presence of microbiota in IESCs. Using a novel method to knockdown gene and miRNA expression ex vivo enteroids, we demonstrate that we can knock down gene expression in Lgr5+ IESCs. Furthermore, when we knock down miR-375 in IESCs, we observe significantly increased proliferative capacity. Understanding the mechanisms by which microbiota regulate miRNA expression in IESCs and other intestinal epithelial cell subtypes will elucidate a critical molecular network that controls intestinal homeostasis and, given the heightened interest in miRNA-based therapies, may offer novel therapeutic strategies in the treatment of gastrointestinal diseases associated with altered IESC function.
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Affiliation(s)
- Bailey C E Peck
- From the Curriculum in Genetics and Molecular Biology, .,Department of Genetics
| | | | | | - Shengli Ding
- Department of Cell Biology and Physiology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599
| | - P Kay Lund
- From the Curriculum in Genetics and Molecular Biology.,Department of Nutrition, and.,Department of Cell Biology and Physiology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599
| | - Praveen Sethupathy
- From the Curriculum in Genetics and Molecular Biology, .,Department of Genetics
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MiR-218 Induces Neuronal Differentiation of ASCs in a Temporally Sequential Manner with Fibroblast Growth Factor by Regulation of the Wnt Signaling Pathway. Sci Rep 2017; 7:39427. [PMID: 28045049 PMCID: PMC5206743 DOI: 10.1038/srep39427] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2016] [Accepted: 11/22/2016] [Indexed: 12/22/2022] Open
Abstract
Differentiation of neural lineages from mesenchymal stem cells has raised the hope of generating functional cells as seed cells for nerve tissue engineering. As important gene regulators, microRNAs (miRNAs) have been speculated to play a vital role in accelerating stem cell differentiation and repairing neuron damage. However, miRNA roles in directing differentiation of stem cells in current protocols are underexplored and the mechanisms of miRNAs as regulators of neuronal differentiation remain ambiguous. In this study, we have determined that miR-218 serves as crucial constituent regulator in neuronal differentiation of adipose stem cells (ASCs) through Wnt signaling pathway based on comprehensive annotation of miRNA sequencing data. Moreover, we have also discovered that miR-218 and Fibroblast Growth Factor-2 (FGF2) modulate neuronal differentiation in a sequential manner. These findings provide additional understanding of the mechanisms regulating stem cell neuronal differentiation as well as a new method for neural lineage differentiation of ASCs.
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Li H, Zhao X, Shan H, Liang H. MicroRNAs in idiopathic pulmonary fibrosis: involvement in pathogenesis and potential use in diagnosis and therapeutics. Acta Pharm Sin B 2016; 6:531-539. [PMID: 27818919 PMCID: PMC5071633 DOI: 10.1016/j.apsb.2016.06.010] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2016] [Revised: 04/23/2016] [Accepted: 05/06/2016] [Indexed: 01/03/2023] Open
Abstract
MicroRNAs (miRNAs) are a class of phylogenetically conserved, non-coding short RNAs, 19-22 nt in length which suppress protein expression through base-pairing with the 3'-untranslated region of target mRNAs. miRNAs have been found to participate in cell proliferation, differentiation and apoptosis. Idiopathic pulmonary fibrosis (IPF) is a chronic, progressive, and high lethality fibrotic lung disease for which currently there is no effective treatment. Some miRNAs have been reported to be involved in the pathogenesis of pulmonary fibrosis. In this review, we discuss the role of miRNAs in the pathogenesis, diagnosis and treatment of IPF.
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MicroRNA-375 Functions as a Tumor-Suppressor Gene in Gastric Cancer by Targeting Recepteur d'Origine Nantais. Int J Mol Sci 2016; 17:ijms17101633. [PMID: 27689991 PMCID: PMC5085666 DOI: 10.3390/ijms17101633] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2016] [Revised: 09/01/2016] [Accepted: 09/12/2016] [Indexed: 12/13/2022] Open
Abstract
Emerging evidence supports a fundamental role for microRNAs (miRNA) in regulating cancer metastasis. Recently, microRNA-375 (miR-375) was reported to be downregulated in many types of cancers, including gastric cancer. Increase in the expression of Recepteur d'Origine Nantais (RON), a receptor tyrosine kinase, has been reported in tumors. However, the function of miR-375 and RON expression in gastric cancer metastasis has not been sufficiently studied. In silico analysis identified miR-375 binding sites in the 3'-untranslated regions (3'-UTR) of the RON-encoding gene. Expression of miR-375 resulted in reduced activity of a luciferase reporter containing the 3'-UTR fragments of RON-encoding mRNA, confirming that miR-375 directly targets the 3'-UTR of RON mRNA. Moreover, we found that overexpression of miR-375 inhibited mRNA and protein expression of RON, which was accompanied by the suppression of cell proliferation, migration, and invasion in gastric cancer AGS and MKN-28 cells. Ectopic miR-375 expression also induced G1 cell cycle arrest through a decrease in the expression of cyclin D1, cyclin D3, and in the phosphorylation of retinoblastoma (Rb). Knockdown of RON by RNAi, similar to miR-375 overexpression, suppressed tumorigenic properties and induced G1 arrest through a decrease in the expression of cyclin D1, cyclin D3, and in the phosphorylation of Rb. Thus, our study provides evidence that miR-375 acts as a suppressor of metastasis in gastric cancer by targeting RON, and might represent a new potential therapeutic target for gastric cancer.
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Zhu S, He Q, Zhang R, Wang Y, Zhong W, Xia H, Yu J. Decreased expression of miR-33 in fetal lungs of nitrofen-induced congenital diaphragmatic hernia rat model. J Pediatr Surg 2016; 51:1096-100. [PMID: 27041227 DOI: 10.1016/j.jpedsurg.2016.02.083] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/03/2015] [Revised: 02/11/2016] [Accepted: 02/22/2016] [Indexed: 02/06/2023]
Abstract
BACKGROUND The pathogenesis of congenital diaphragmatic hernia (CDH) and the causes of pulmonary hypoplasia and hypertension remain unclear. miRNAs have been identified to play important regulatory roles in pulmonary pathological processes and lung development. We carried out the study to investigate the hypothesis that specific miRNAs are expressed differently in the lungs of nitrofen-induced rats, and to explore the possible targeting genes and roles of miR-33 in the pathological process of CDH. METHODS Pregnant rats were divided into nitrofen and control group, and were exposed to nitrofen or vehicle respectively on D9. Fetuses were harvested on D21 and left lungs were dissected. 4 samples from each group underwent miRNAs microarray analysis using Agilent miRNA Array. Quantitative real-time polymerase chain reaction (qRT-PCR) was further performed to validate the miR-33 expression. RESULTS 11 miRNAs exhibited increased expression in nitrofen group compared with control (p<0.05): miR-3588, miR-382*, miR-363, miR-375, miR-487b, miR-483, miR-382, miR-495, miR-434, miR-181a, and miR-99a. 14 miRNAs showed decreased expression (p<0.05): miR-33, miR-193, miR-338, miR-30c-2*, miR-22, miR-18a, miR-532-5p, miR-28, miR-96, miR-551b, miR-141, miR-362*, miR-30a*, and miR-3559-5p. Among them, miR-33 expression was markedly decreased in CDH lungs compared to controls and the result was confirmed by qRT-PCR. CONCLUSION Decreased expression of miR-33 was found in the nitrofen-induced hypoplastic lung on D21. This finding suggests that pathogenesis of lung hypoplasia and CDH in the nitrofen model involve epigenetic layer of regulation.
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Affiliation(s)
- Shibo Zhu
- Surgical Department, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, China
| | - Qiuming He
- Surgical Department, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, China
| | - Ruizhong Zhang
- Surgical Department, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, China
| | - Yong Wang
- Surgical Department, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, China
| | - Wei Zhong
- Surgical Department, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, China
| | - Huimin Xia
- Surgical Department, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, China
| | - Jiakang Yu
- Surgical Department, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, China.
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48
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Xu L, Wen T, Liu Z, Xu F, Yang L, Liu J, Feng G, An G. MicroRNA-375 suppresses human colorectal cancer metastasis by targeting Frizzled 8. Oncotarget 2016; 7:40644-40656. [PMID: 27276676 PMCID: PMC5130033 DOI: 10.18632/oncotarget.9811] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2015] [Accepted: 05/17/2016] [Indexed: 01/01/2023] Open
Abstract
microRNAs are aberrantly expressed during the development and progression of a variety of human cancers, including colorectal cancer (CRC). Of these microRNAs, microRNA-375 (miR-375) was previously observed to be downregulated in human colorectal cancer(CRC) plasma and tissues, but its functions are largely unknown. Here, we investigated the impact of miR-375 on CRC metastasis. Specifically, miR-375 expression was significantly decreased in human CRC tissues compared with their matched noncancerous tissues (NCTs), and low levels of miR-375 predicted tumor metastatic potential. The up-regulation of miR-375 suppressed colorectal cancer cell migration and invasion in vitro and reduced tumor metastases in murine models established by both orthotopic implantation and spleen injection. Furthermore, we identified Frizzled 8 (FZD8) as a direct target of miR-375 in CRC, and miR-375 negatively regulated Wnt/β-catenin signaling by suppressing FZD8. More importantly, FZD8 expression inversely correlated with overall survival in human CRC patients and is a likely independent predictor of survival. Therefore, we concluded that miR-375 functions as a tumor-suppressive microRNA by directly acting upon FZD8, which may serve as a new therapeutic target to inhibit tumor metastasis in CRC.
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Affiliation(s)
- Lingling Xu
- Department of Oncology, Beijing Chao-Yang Hospital, Capital Medical University, Beijing 100020, China
| | - Tao Wen
- Medical Research Center, Beijing Chao-Yang Hospital, Capital Medical University, Beijing 100020, China
| | - Zhe Liu
- Department of Oncology, Beijing Chao-Yang Hospital, Capital Medical University, Beijing 100020, China
| | - Feng Xu
- Department of Oncology, Beijing Chao-Yang Hospital, Capital Medical University, Beijing 100020, China
| | - Lei Yang
- Medical Research Center, Beijing Chao-Yang Hospital, Capital Medical University, Beijing 100020, China
| | - Jian Liu
- Medical Research Center, Beijing Chao-Yang Hospital, Capital Medical University, Beijing 100020, China
| | - Guosheng Feng
- Department of Oncology, Beijing Chao-Yang Hospital, Capital Medical University, Beijing 100020, China
| | - Guangyu An
- Department of Oncology, Beijing Chao-Yang Hospital, Capital Medical University, Beijing 100020, China
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49
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Xu W, Zhao Y, Zhang B, Xu B, Yang Y, Wang Y, Liu C. Resveratrol attenuates hyperoxia-induced oxidative stress, inflammation and fibrosis and suppresses Wnt/β-catenin signalling in lungs of neonatal rats. Clin Exp Pharmacol Physiol 2016; 42:1075-83. [PMID: 26174235 DOI: 10.1111/1440-1681.12459] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2015] [Revised: 06/28/2015] [Accepted: 07/04/2015] [Indexed: 11/27/2022]
Abstract
Although survival rate of infants born prematurely has been raised by supplemental oxygen treatment, it is followed by high morbidity of hyperoxia-induced bronchopulmonary dysplasia. In this study, the effect of resveratrol on the lung injury was evaluated in hyperoxia-exposed rats of preterm birth. The results demonstrated that hyperoxia led to thickened alveolar wall, simplified alveolar architecture and fibrosis. In addition, elevated methane dicarboxylic aldehyde level, decreased glutathione level and superoxide dismutase activity were also found in hyperoxic lungs, as well as the increased tumor necrosis factor-α, interleukin-1β and interleukin-6 in the bronchoalveolar lavage fluid. Fibrotic-associated proteins transforming growth factor-β1, α-smooth muscle actin, collagen I and fibronectin deposition were also found in interstitial substance of lungs. Furthermore, Wnt/β-catenin signalling was found to be active in hyperoxia-induced lungs. In addition, expression of SP-C was increased and T1α was decreased in hyperoxia-exposed lungs. Resveratrol intraperitoneal administration alleviated hyperoxia-induced histological injury of lungs, regulated redox balance, decreased pro-inflammatory cytokine release, and down-regulated expression of fibrotic-associated proteins. Furthermore, Wnt/β-catenin signalling was also suppressed by resveratrol, as represented by diminished expression of lymphoid enhancer factor-1, Wnt induced signalling protein-1 and cyclin D1. In addition, the increase of SP-C and decrease of T1α expression was prevented as well. The present study showed that resveratrol could protect lungs from hyperoxia-induced injury through its antioxidant, anti-inflammatory and anti-fibrotic effects. The transdifferentiation of alveolar epithelial type II cells to alveolar epithelial type I cells promotion and Wnt/β-catenin signalling suppression are also involved in the protective effect.
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Affiliation(s)
- Wei Xu
- Department of Paediatrics, Shengjing Hospital of China Medical University, Shenyang, Liaoning, China
| | - Ying Zhao
- Department of Paediatrics, Shengjing Hospital of China Medical University, Shenyang, Liaoning, China
| | - Binglun Zhang
- Department of Paediatrics, Shengjing Hospital of China Medical University, Shenyang, Liaoning, China
| | - Bo Xu
- Department of Ophthalmology, The Affiliated People's Hospital of Jiangsu University, Zhenjiang, Jiangsu, China
| | - Yang Yang
- Department of Paediatrics, Shengjing Hospital of China Medical University, Shenyang, Liaoning, China
| | - Yujing Wang
- Department of Paediatrics, Shengjing Hospital of China Medical University, Shenyang, Liaoning, China
| | - Chunfeng Liu
- Department of Paediatrics, Shengjing Hospital of China Medical University, Shenyang, Liaoning, China
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50
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Guo Y, An R, Zhao R, Sun Y, Liu M, Tian L. miR-375 exhibits a more effective tumor-suppressor function in laryngeal squamous carcinoma cells by regulating KLF4 expression compared with simple co-transfection of miR-375 and miR-206. Oncol Rep 2016; 36:952-60. [PMID: 27279635 DOI: 10.3892/or.2016.4852] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2016] [Accepted: 02/26/2016] [Indexed: 11/06/2022] Open
Abstract
MicroRNAs (miRNAs) are reported to be important regulators of cancer-related processes, and function either as oncogenes or as tumor-suppressor genes. It was found that miR-375 was downregulated in samples of laryngeal squamous cell carcinomas (LSCCs) as compared to the level noted in adjacent non-tumor tissues, and it was inversely correlated with T grade, lymph node metastases and clinical tumor stage. Overexpression of miR-375 led to a decreased protein level of Krüppel-like factor 4 (KLF4) and marked suppression of the proliferation and invasion, and induced apoptosis of LSCC cell line Hep-2 using Cell Counting Kit-8, Transwell chamber and cell cycle assays. In addition, we examined the influence of the upregulation of miR-206 alone and upregulation of both miR-375 and miR-206 on the expression of KLF4 and Hep-2 cell behavior. The results showed that compared with the function of miR-375 in tumor suppression by regulating KLF4, co-transfection of miR-375 and miR-206 exhibited a less effective inhibitory effect not only on tumor cell proliferation and invasion, but also on tumor cell apoptosis. Taken together, miR-375 is possibly a tumor suppressor in LSCC by regulating KLF4. In addition, simple overexpression of several miRNAs did not entail higher efficacy than a single miRNA, similar to co-transfecions of miR-375 and miR-206.
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Affiliation(s)
- Yan Guo
- Service of Head and Neck Surgery, Department of Otolaryngology-Head and Neck Surgery, The Second Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang 150081, P.R. China
| | - Ran An
- Service of Head and Neck Surgery, Department of Otolaryngology-Head and Neck Surgery, The Second Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang 150081, P.R. China
| | - Rui Zhao
- Service of Laryngology, Department of Otolaryngology-Head and Neck Surgery, The Second Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang 150081, P.R. China
| | - Yanan Sun
- Service of Head and Neck Surgery, Department of Otolaryngology-Head and Neck Surgery, The Second Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang 150081, P.R. China
| | - Ming Liu
- Service of Head and Neck Surgery, Department of Otolaryngology-Head and Neck Surgery, The Second Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang 150081, P.R. China
| | - Linli Tian
- Service of Head and Neck Surgery, Department of Otolaryngology-Head and Neck Surgery, The Second Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang 150081, P.R. China
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