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Gravina T, Favero F, Rosano S, Parab S, Diaz Alcalde A, Bussolino F, Doronzo G, Corà D. Integrative Bioinformatics Analysis Reveals a Transcription Factor EB-Driven MicroRNA Regulatory Network in Endothelial Cells. Int J Mol Sci 2024; 25:7123. [PMID: 39000232 PMCID: PMC11241138 DOI: 10.3390/ijms25137123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2024] [Revised: 06/19/2024] [Accepted: 06/21/2024] [Indexed: 07/16/2024] Open
Abstract
Various human diseases are triggered by molecular alterations influencing the fine-tuned expression and activity of transcription factors, usually due to imbalances in targets including protein-coding genes and non-coding RNAs, such as microRNAs (miRNAs). The transcription factor EB (TFEB) modulates human cellular networks, overseeing lysosomal biogenesis and function, plasma-membrane trafficking, autophagic flux, and cell cycle progression. In endothelial cells (ECs), TFEB is essential for the maintenance of endothelial integrity and function, ensuring vascular health. However, the comprehensive regulatory network orchestrated by TFEB remains poorly understood. Here, we provide novel mechanistic insights into how TFEB regulates the transcriptional landscape in primary human umbilical vein ECs (HUVECs), using an integrated approach combining high-throughput experimental data with dedicated bioinformatics analysis. By analyzing HUVECs ectopically expressing TFEB using ChIP-seq and examining both polyadenylated mRNA and small RNA sequencing data from TFEB-silenced HUVECs, we have developed a bioinformatics pipeline mapping the different gene regulatory interactions driven by TFEB. We show that TFEB directly regulates multiple miRNAs, which in turn post-transcriptionally modulate a broad network of target genes, significantly expanding the repertoire of gene programs influenced by this transcription factor. These insights may have significant implications for vascular biology and the development of novel therapeutics for vascular disease.
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Affiliation(s)
- Teresa Gravina
- Department of Translational Medicine, University of Piemonte Orientale, 28100 Novara, Italy
- Center for Translational Research on Allergic and Autoimmune Diseases (CAAD), University of Piemonte Orientale, 28100 Novara, Italy
| | - Francesco Favero
- Department of Translational Medicine, University of Piemonte Orientale, 28100 Novara, Italy
- Center for Translational Research on Allergic and Autoimmune Diseases (CAAD), University of Piemonte Orientale, 28100 Novara, Italy
| | - Stefania Rosano
- Department of Oncology, University of Torino, 10124 Orbassano, Italy
- Candiolo Cancer Institute, IRCCS-FPO, 10060 Candiolo, Italy
| | - Sushant Parab
- Department of Oncology, University of Torino, 10124 Orbassano, Italy
- Candiolo Cancer Institute, IRCCS-FPO, 10060 Candiolo, Italy
| | - Alejandra Diaz Alcalde
- Department of Oncology, University of Torino, 10124 Orbassano, Italy
- Candiolo Cancer Institute, IRCCS-FPO, 10060 Candiolo, Italy
| | - Federico Bussolino
- Department of Oncology, University of Torino, 10124 Orbassano, Italy
- Candiolo Cancer Institute, IRCCS-FPO, 10060 Candiolo, Italy
| | - Gabriella Doronzo
- Department of Oncology, University of Torino, 10124 Orbassano, Italy
- Candiolo Cancer Institute, IRCCS-FPO, 10060 Candiolo, Italy
| | - Davide Corà
- Department of Translational Medicine, University of Piemonte Orientale, 28100 Novara, Italy
- Center for Translational Research on Allergic and Autoimmune Diseases (CAAD), University of Piemonte Orientale, 28100 Novara, Italy
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2
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Ayed A. The role of natural products versus miRNA in renal cell carcinoma: implications for disease mechanisms and diagnostic markers. NAUNYN-SCHMIEDEBERG'S ARCHIVES OF PHARMACOLOGY 2024:10.1007/s00210-024-03121-8. [PMID: 38691151 DOI: 10.1007/s00210-024-03121-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/18/2024] [Accepted: 04/24/2024] [Indexed: 05/03/2024]
Abstract
Natural products are chemical compounds produced by living organisms. They are isolated and purified to determine their function and can potentially be used as therapeutic agents. The ability of some bioactive natural products to modify the course of cancer is fascinating and promising. In the past 50 years, there have been advancements in cancer therapy that have increased survival rates for localized tumors. However, there has been little progress in treating advanced renal cell carcinoma (RCC), which is resistant to radiation and chemotherapy. Oncogenes and tumor suppressors are two roles played by microRNAs (miRNAs). They are involved in important pathogenetic mechanisms like hypoxia and epithelial-mesenchymal transition (EMT); they control apoptosis, cell growth, migration, invasion, angiogenesis, and proliferation through target proteins involved in various signaling pathways. Depending on their expression pattern, miRNAs may identify certain subtypes of RCC or distinguish tumor tissue from healthy renal tissue. As diagnostic biomarkers of RCC, circulating miRNAs show promise. There is a correlation between the expression patterns of several miRNAs and the prognosis and diagnosis of patients with RCC. Potentially high-risk primary tumors may be identified by comparing original tumor tissue with metastases. Variations in miRNA expression between treatment-sensitive and therapy-resistant patients' tissues and serum allow for the estimation of responsiveness to target therapy. Our knowledge of miRNAs' function in RCC etiology has a tremendous uptick. Finding and validating their gene targets could have an immediate effect on creating anticancer treatments based on miRNAs. Several miRNAs have the potential to be used as biomarkers for diagnosis and prognosis. This review provides an in-depth analysis of the current knowledge regarding natural compounds and their modes of action in combating cancer. Also, this study aims to give information about the diagnostic and prognostic value of miRNAs as cancer biomarkers and their involvement in the pathogenesis of RCC.
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Affiliation(s)
- Abdullah Ayed
- Department of Surgery, College of Medicine, University of Bisha, P.O Box 551, 61922, Bisha, Saudi Arabia.
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3
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Dominguez LJ, Veronese N, Barbagallo M. Magnesium and the Hallmarks of Aging. Nutrients 2024; 16:496. [PMID: 38398820 PMCID: PMC10892939 DOI: 10.3390/nu16040496] [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: 12/31/2023] [Revised: 02/01/2024] [Accepted: 02/05/2024] [Indexed: 02/25/2024] Open
Abstract
Magnesium is an essential ion in the human body that regulates numerous physiological and pathological processes. Magnesium deficiency is very common in old age. Age-related chronic diseases and the aging process itself are frequently associated with low-grade chronic inflammation, called 'inflammaging'. Because chronic magnesium insufficiency has been linked to excessive generation of inflammatory markers and free radicals, inducing a chronic inflammatory state, we formerly hypothesized that magnesium inadequacy may be considered among the intermediaries helping us explain the link between inflammaging and aging-associated diseases. We show in this review evidence of the relationship of magnesium with all the hallmarks of aging (genomic instability, telomere attrition, epigenetic alterations, loss of proteostasis, deregulated nutrient sensing, mitochondrial dysfunction, cellular senescence, stem cell exhaustion, altered intercellular communication, disabled autophagy, dysbiosis, and chronic inflammation), which may positively affect the human healthspan. It is feasible to hypothesize that maintaining an optimal balance of magnesium during one's life course may turn out to be a safe and economical strategy contributing to the promotion of healthy aging. Future well-designed studies are necessary to further explore this hypothesis.
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Affiliation(s)
- Ligia J. Dominguez
- School of Medicine, “Kore” University of Enna, 94100 Enna, Italy;
- Geriatric Unit, Department of Medicine, University of Palermo, 90127 Palermo, Italy;
| | - Nicola Veronese
- Geriatric Unit, Department of Medicine, University of Palermo, 90127 Palermo, Italy;
| | - Mario Barbagallo
- Geriatric Unit, Department of Medicine, University of Palermo, 90127 Palermo, Italy;
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4
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Shi M, Lu Q, Zhao Y, Ding Z, Yu S, Li J, Ji M, Fan H, Hou S. miR-223: a key regulator of pulmonary inflammation. Front Med (Lausanne) 2023; 10:1187557. [PMID: 37465640 PMCID: PMC10350674 DOI: 10.3389/fmed.2023.1187557] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2023] [Accepted: 06/14/2023] [Indexed: 07/20/2023] Open
Abstract
Small noncoding RNAs, known as microRNAs (miRNAs), are vital for the regulation of diverse biological processes. miR-223, an evolutionarily conserved anti-inflammatory miRNA expressed in cells of the myeloid lineage, has been implicated in the regulation of monocyte-macrophage differentiation, proinflammatory responses, and the recruitment of neutrophils. The biological functions of this gene are regulated by its expression levels in cells or tissues. In this review, we first outline the regulatory role of miR-223 in granulocytes, macrophages, endothelial cells, epithelial cells and dendritic cells (DCs). Then, we summarize the possible role of miR-223 in chronic obstructive pulmonary disease (COPD), acute lung injury (ALI), coronavirus disease 2019 (COVID-19) and other pulmonary inflammatory diseases to better understand the molecular regulatory networks in pulmonary inflammatory diseases.
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Affiliation(s)
- Mingyu Shi
- Institute of Disaster and Emergency Medicine, Tianjin University, Tianjin, China
| | - Qianying Lu
- Institute of Disaster and Emergency Medicine, Tianjin University, Tianjin, China
| | - Yanmei Zhao
- Institute of Disaster and Emergency Medicine, Tianjin University, Tianjin, China
| | - Ziling Ding
- Institute of Disaster and Emergency Medicine, Tianjin University, Tianjin, China
| | - Sifan Yu
- Institute of Disaster and Emergency Medicine, Tianjin University, Tianjin, China
| | - Junfeng Li
- Institute of Disaster and Emergency Medicine, Tianjin University, Tianjin, China
| | - Mengjun Ji
- Institute of Disaster and Emergency Medicine, Tianjin University, Tianjin, China
| | - Haojun Fan
- Institute of Disaster and Emergency Medicine, Tianjin University, Tianjin, China
- Wenzhou Safety (Emergency) Institute of Tianjin University, Wenzhou, China
| | - Shike Hou
- Institute of Disaster and Emergency Medicine, Tianjin University, Tianjin, China
- Wenzhou Safety (Emergency) Institute of Tianjin University, Wenzhou, China
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5
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Mazloom AR, Xu H, Reig-Palou J, Vasileva A, Román AC, Mulero-Navarro S, Lemischka IR, Sevilla A. Esrrb Regulates Specific Feed-Forward Loops to Transit From Pluripotency Into Early Stages of Differentiation. Front Cell Dev Biol 2022; 10:820255. [PMID: 35652095 PMCID: PMC9149258 DOI: 10.3389/fcell.2022.820255] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2021] [Accepted: 03/24/2022] [Indexed: 01/15/2023] Open
Abstract
Characterization of pluripotent states, in which cells can both self-renew or differentiate, with the irreversible loss of pluripotency, are important research areas in developmental biology. Although microRNAs (miRNAs) have been shown to play a relevant role in cellular differentiation, the role of miRNAs integrated into gene regulatory networks and its dynamic changes during these early stages of embryonic stem cell (ESC) differentiation remain elusive. Here we describe the dynamic transcriptional regulatory circuitry of stem cells that incorporate protein-coding and miRNA genes based on miRNA array expression and quantitative sequencing of short transcripts upon the downregulation of the Estrogen Related Receptor Beta (Esrrb). The data reveals how Esrrb, a key stem cell transcription factor, regulates a specific stem cell miRNA expression program and integrates dynamic changes of feed-forward loops contributing to the early stages of cell differentiation upon its downregulation. Together these findings provide new insights on the architecture of the combined transcriptional post-transcriptional regulatory network in embryonic stem cells.
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Affiliation(s)
- Amin R. Mazloom
- Department of Pharmacology and Systems Therapeutics, Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | - Huilei Xu
- Department of Pharmacology and Systems Therapeutics, Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | - Jaume Reig-Palou
- Department of Cell Biology, Physiology and Immunology, Faculty of Biology, University of Barcelona, Barcelona, Spain
| | - Ana Vasileva
- Center for Radiological Research, Columbia University, New York, NY, United States
| | - Angel-Carlos Román
- Department of Biochemistry, Molecular Biology and Genetics, University of Extremadura, Badajoz, Spain
| | - Sonia Mulero-Navarro
- Department of Biochemistry, Molecular Biology and Genetics, University of Extremadura, Badajoz, Spain
| | - Ihor R. Lemischka
- Department of Developmental and Regenerative Biology, Icahn School of Medicine at Mount Sinai, New York, NY, United States
- Black Family Stem Cell Institute, Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | - Ana Sevilla
- Department of Cell Biology, Physiology and Immunology, Faculty of Biology, University of Barcelona, Barcelona, Spain
- Department of Developmental and Regenerative Biology, Icahn School of Medicine at Mount Sinai, New York, NY, United States
- Black Family Stem Cell Institute, Icahn School of Medicine at Mount Sinai, New York, NY, United States
- Institute of Biomedicine of the University of Barcelona (IBUB), Barcelona, Spain
- *Correspondence: Ana Sevilla,
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6
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Liu HN, Dong WH, Lin Y, Zhang ZH, Wang TY. The Effect of microRNA on the Production of Recombinant Protein in CHO Cells and its Mechanism. Front Bioeng Biotechnol 2022; 10:832065. [PMID: 35387297 PMCID: PMC8977551 DOI: 10.3389/fbioe.2022.832065] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2021] [Accepted: 02/25/2022] [Indexed: 11/13/2022] Open
Abstract
Recombinant protein production by mammalian cells is the initial step in the manufacture of many therapeutic proteins. Chinese hamster ovary (CHO) cells are the most common host system to produce recombinant therapeutic proteins (RTPs). However, it is still challenging to maintain high productivity ensuring the good quality of RTPs produced by CHO cells. MicroRNAs(miRNAs) are short regulatory non-coding RNAs that can regulate cellular behavior and complex phenotypes. It has been found that miRNAs can enhance the expression level of recombinant proteins in CHO cells by promoting proliferation, resisting apoptosis, and regulating metabolism. miRNAs also can affect the quality of RTPs. In this review, we will discuss the effect and mechanism of miRNA on the expression level and quality of recombinant proteins in CHO cells.
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Affiliation(s)
- Hui-Ning Liu
- The First Affiliated Hospital of Xinxiang Medical University, Xinxiang, China.,International Joint Research Laboratory for Recombinant Pharmaceutical Protein Expression System of Henan, Xinxiang, China
| | - Wei-Hua Dong
- International Joint Research Laboratory for Recombinant Pharmaceutical Protein Expression System of Henan, Xinxiang, China.,Department of Biochemistry and Molecular Biology, Basic Medical School, Xinxiang Medical University, Xinxiang, China
| | - Yan Lin
- International Joint Research Laboratory for Recombinant Pharmaceutical Protein Expression System of Henan, Xinxiang, China
| | - Zhao-Hui Zhang
- The First Affiliated Hospital of Xinxiang Medical University, Xinxiang, China
| | - Tian-Yun Wang
- International Joint Research Laboratory for Recombinant Pharmaceutical Protein Expression System of Henan, Xinxiang, China.,Department of Biochemistry and Molecular Biology, Basic Medical School, Xinxiang Medical University, Xinxiang, China
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7
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Effect and Role of miR-196b in Ectopic Pregnancy. JOURNAL OF HEALTHCARE ENGINEERING 2022; 2022:7797484. [PMID: 35265305 PMCID: PMC8901340 DOI: 10.1155/2022/7797484] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/12/2022] [Revised: 01/25/2022] [Accepted: 02/02/2022] [Indexed: 11/30/2022]
Abstract
Ectopic pregnancy (EP) is associated with significant morbidity and mortality, but the molecular mechanism of this condition is still unclear. miR-196b, a hot research direction for the past few years, participates in the occurrence of various diseases but whether it plays a regulatory role in EP is still unclear. This research was set to investigate the expression and potential value of miR-196b in EP. qRT-PCR was utilized to determine the relative expression of miR-196b in peripheral blood of EP patients and to observe the expression changes of miR-196b before and after treatment. Correlation analysis of miR-196b with HCG and progesterone was performed. Logistic regression analysis was applied to independent risk factors affecting EP patients. TargetScan was utilized to predict the downstream target genes of miR-196b, and GO and KEGG analysis was carried out using the R language pack. qRT-PCR showed that miR-196b expression in peripheral blood of EP patients was lower than that of normal people. miR-196b expression in patients after treatment was notably higher than that before treatment. In addition, correlation analysis showed that miR-196b was positively correlated with the expression of HCG, progesterone, and estradiol. Risk factor analysis revealed that abortion history, pelvic inflammatory disease history, lower abdominal surgery history, and miR-196b were independent risk factors for EP, and the AUC of the combined ROC curve was 0.899. GO function enrichment and KEGG signal pathway enrichment found 10 potential functions and 2 potential signal pathways of miR-196b. miR-196b is expressed in EP patients, is differentially expressed according to the change in EP condition, and is expected to become a promising index for clinical diagnosis of EP.
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8
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microRNA-Mediated Encoding and Decoding of Time-Dependent Signals in Tumorigenesis. Biomolecules 2022; 12:biom12020213. [PMID: 35204714 PMCID: PMC8961662 DOI: 10.3390/biom12020213] [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: 11/22/2021] [Revised: 01/13/2022] [Accepted: 01/21/2022] [Indexed: 02/01/2023] Open
Abstract
microRNAs, pivotal post-transcriptional regulators of gene expression, in the past decades have caught the attention of researchers for their involvement in different biological processes, ranging from cell development to cancer. Although lots of effort has been devoted to elucidate the topological features and the equilibrium properties of microRNA-mediated motifs, little is known about how the information encoded in frequency, amplitude, duration, and other features of their regulatory signals can affect the resulting gene expression patterns. Here, we review the current knowledge about microRNA-mediated gene regulatory networks characterized by time-dependent input signals, such as pulses, transient inputs, and oscillations. First, we identify the general characteristic of the main motifs underlying temporal patterns. Then, we analyze their impact on two commonly studied oncogenic networks, showing how their dysfunction can lead to tumorigenesis.
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9
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Yuan S, Wu Q, Wang Z, Che Y, Zheng S, Chen Y, Zhong X, Shi F. miR-223: An Immune Regulator in Infectious Disorders. Front Immunol 2021; 12:781815. [PMID: 34956210 PMCID: PMC8702553 DOI: 10.3389/fimmu.2021.781815] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2021] [Accepted: 11/24/2021] [Indexed: 12/12/2022] Open
Abstract
MicroRNAs (miRNAs) are diminutive noncoding RNAs that can influence disease development and progression by post-transcriptionally regulating gene expression. The anti-inflammatory miRNA, miR-223, was first identified as a regulator of myelopoietic differentiation in 2003. This miR-223 exhibits multiple regulatory functions in the immune response, and abnormal expression of miR-223 is shown to be associated with multiple infectious diseases, including viral hepatitis, human immunodeficiency virus type 1 (HIV-1), and tuberculosis (TB) by influencing neutrophil infiltration, macrophage function, dendritic cell (DC) maturation and inflammasome activation. This review summarizes the current understanding of miR-223 physiopathology and highlights the molecular mechanism by which miR-223 regulates immune responses to infectious diseases and how it may be targeted for diagnosis and treatment.
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Affiliation(s)
- Shun Yuan
- Department of Cardiovascular Surgery, Renmin Hospital of Wuhan University, Wuhan, China
| | - Qi Wu
- Department of Cardiovascular Surgery, Renmin Hospital of Wuhan University, Wuhan, China
| | - Zhiwei Wang
- Department of Cardiovascular Surgery, Renmin Hospital of Wuhan University, Wuhan, China
| | - Yanjia Che
- Department of Cardiovascular Surgery, Renmin Hospital of Wuhan University, Wuhan, China
| | - Sihao Zheng
- Department of Cardiovascular Surgery, Renmin Hospital of Wuhan University, Wuhan, China
| | - Yuanyang Chen
- Department of Cardiovascular Surgery, Renmin Hospital of Wuhan University, Wuhan, China
| | - Xiaohan Zhong
- Department of Cardiovascular Surgery, Renmin Hospital of Wuhan University, Wuhan, China
| | - Feng Shi
- Department of Cardiovascular Surgery, Renmin Hospital of Wuhan University, Wuhan, China
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10
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Corrêa S, Lopes FP, Panis C, Basili T, Binato R, Abdelhay E. miRNome Profiling Reveals Shared Features in Breast Cancer Subtypes and Highlights miRNAs That Potentially Regulate MYB and EZH2 Expression. Front Oncol 2021; 11:710919. [PMID: 34646766 PMCID: PMC8502886 DOI: 10.3389/fonc.2021.710919] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2021] [Accepted: 08/30/2021] [Indexed: 01/03/2023] Open
Abstract
Breast cancer (BC) has been extensively studied, as it is one of the more commonly diagnosed cancer types worldwide. The study of miRNAs has increased what is known about the complexity of pathways and signaling and has identified potential biomarkers and therapeutic targets. Thus, miRNome profiling could provide important information regarding the molecular mechanisms involved in BC. On average, more than 430 miRNAs were identified as differentially expressed between BC cell lines and normal breast HMEC cells. From these, 110 miRNAs were common to BC subtypes. The miRNome enrichment analysis and interaction maps highlighted epigenetic-related pathways shared by all BC cell lines and revealed potential miRNA targets. Quantitative evaluation of BC patient samples and GETx/TCGA-BRCA datasets confirmed MYB and EZH2 as potential targets from BC miRNome. Moreover, overall survival was impacted by EZH2 expression. The expression of 15 miRNAs, selected according to aggressiveness of BC subtypes, was confirmed in TCGA-BRCA dataset. Of these miRNAs, miRNA-mRNA interaction prediction revealed 7 novel or underexplored miRNAs in BC: miR-1271-5p, miR-130a-5p, and miR-134 as MYB regulators and miR-138-5p, miR-455-3p, miR-487a, and miR-487b as EZH2 regulators. Herein, we report a novel molecular miRNA signature for BC and identify potential miRNA/mRNAs involved in disease subtypes.
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Affiliation(s)
- Stephany Corrêa
- Centro de Transplante de Medula Óssea (CEMO), Instituto Nacional de Câncer (INCA), Rio de Janeiro, Brazil
| | - Francisco P Lopes
- Grupo de Biologia do Desenvolvimento e Sistemas Dinâmicos, Universidade Federal do Rio de Janeiro (UFRJ), Duque de Caxias, Brazil
| | - Carolina Panis
- Laboratório de Biologia de Tumores, Universidade Estadual do Oeste do Paraná (UNIOESTE), Francisco Beltrão, Brazil
| | - Thais Basili
- Centro de Transplante de Medula Óssea (CEMO), Instituto Nacional de Câncer (INCA), Rio de Janeiro, Brazil.,Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, United States
| | - Renata Binato
- Centro de Transplante de Medula Óssea (CEMO), Instituto Nacional de Câncer (INCA), Rio de Janeiro, Brazil
| | - Eliana Abdelhay
- Centro de Transplante de Medula Óssea (CEMO), Instituto Nacional de Câncer (INCA), Rio de Janeiro, Brazil
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11
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Shannon OM, Ashor AW, Scialo F, Saretzki G, Martin-Ruiz C, Lara J, Matu J, Griffiths A, Robinson N, Lillà L, Stevenson E, Stephan BCM, Minihane AM, Siervo M, Mathers JC. Mediterranean diet and the hallmarks of ageing. Eur J Clin Nutr 2021; 75:1176-1192. [PMID: 33514872 DOI: 10.1038/s41430-020-00841-x] [Citation(s) in RCA: 66] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2020] [Revised: 11/09/2020] [Accepted: 12/07/2020] [Indexed: 12/21/2022]
Abstract
Ageing is a multifactorial process associated with reduced function and increased risk of morbidity and mortality. Recently, nine cellular and molecular hallmarks of ageing have been identified, which characterise the ageing process, and collectively, may be key determinants of the ageing trajectory. These include genomic instability, telomere attrition, epigenetic alterations, loss of proteostasis, deregulated nutrient sensing, mitochondrial dysfunction, cellular senescence, stem cell exhaustion and altered intercellular communication. Healthier dietary patterns reduce the risk of age-related diseases and increase longevity and may influence positively one or more of these hallmarks. The Mediterranean dietary pattern (MedDiet) is a plant-based eating pattern that was typical of countries such as Greece, Spain, and Italy pre-globalisation of the food system and which is associated with better health during ageing. Here we review the potential effects of a MedDiet on each of the nine hallmarks of ageing, and provide evidence that the MedDiet as a whole, or individual elements of this dietary pattern, may influence each hallmark positively-effects which may contribute to the beneficial effects of this dietary pattern on age-related disease risk and longevity. We also highlight potential avenues for future research.
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Affiliation(s)
- Oliver M Shannon
- Human Nutrition Research Centre, Population Health Sciences Institute, Newcastle University, Newcastle upon Tyne,, NE2 4HH, UK
| | - Ammar W Ashor
- Department of Pharmacology, College of Medicine, Al-Mustansiriyah University, Baghdad, Iraq
| | - Filippo Scialo
- Biosciences Institute, Campus for Ageing and Vitality, Newcastle University, Newcastle upon Tyne,, NE4 5PL, UK
- Dipartimento di Scienze Mediche Traslazionali, University of Campania "L. Vanvitelli", Naples, Italy
| | - Gabriele Saretzki
- Biosciences Institute, Campus for Ageing and Vitality, Newcastle University, Newcastle upon Tyne,, NE4 5PL, UK
| | - Carmen Martin-Ruiz
- Bioscience Institute, Bioscreening Core Facility, Campus for Ageing and Vitality, Newcastle University, Newcastle upon Tyne,, NE4 5PL, UK
| | - Jose Lara
- Department of Applied Sciences, Faculty of Health and Life Sciences, Northumbria University, Newcastle upon Tyne,, NE1 8ST, UK
| | - Jamie Matu
- School of Clinical Applied Sciences, Leeds Beckett University, Leeds,, LS1 3HE, UK
| | - Alex Griffiths
- Institute for Sport, Physical Activity & Leisure, Leeds Beckett University, Leeds,, LS163QS, UK
| | - Natassia Robinson
- Biosciences Institute, Campus for Ageing and Vitality, Newcastle University, Newcastle upon Tyne,, NE4 5PL, UK
| | - Lionetti Lillà
- Department of Chemistry and Biology, University of Salerno, via Giovanni Paolo II, 132, 84084, Fisciano, SA, Italy
| | - Emma Stevenson
- Human Nutrition Research Centre, Population Health Sciences Institute, Newcastle University, Newcastle upon Tyne,, NE2 4HH, UK
| | - Blossom C M Stephan
- Institute of Mental Health, The University of Nottingham Medical School, Nottingham, UK
| | - Anne Marie Minihane
- Department of Nutrition and Preventive Medicine, Norwich Medical School, University of East Anglia (UEA), Norwich, UK
| | - Mario Siervo
- School of Life Sciences, The University of Nottingham Medical School, Queen's Medical Centre, Nottingham,, NG7 2UH, UK.
| | - John C Mathers
- Human Nutrition Research Centre, Population Health Sciences Institute, Newcastle University, Newcastle upon Tyne,, NE2 4HH, UK
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12
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Corà D, Bussolino F, Doronzo G. TFEB Signalling-Related MicroRNAs and Autophagy. Biomolecules 2021; 11:985. [PMID: 34356609 PMCID: PMC8301958 DOI: 10.3390/biom11070985] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2021] [Revised: 06/28/2021] [Accepted: 06/30/2021] [Indexed: 12/26/2022] Open
Abstract
The oncogenic Transcription Factor EB (TFEB), a member of MITF-TFE family, is known to be the most important regulator of the transcription of genes responsible for the control of lysosomal biogenesis and functions, autophagy, and vesicles flux. TFEB activation occurs in response to stress factors such as nutrient and growth factor deficiency, hypoxia, lysosomal stress, and mitochondrial damage. To reach the final functional status, TFEB is regulated in multimodal ways, including transcriptional rate, post-transcriptional regulation, and post-translational modifications. Post-transcriptional regulation is in part mediated by miRNAs. miRNAs have been linked to many cellular processes involved both in physiology and pathology, such as cell migration, proliferation, differentiation, and apoptosis. miRNAs also play a significant role in autophagy, which exerts a crucial role in cell behaviour during stress or survival responses. In particular, several miRNAs directly recognise TFEB transcript or indirectly regulate its function by targeting accessory molecules or enzymes involved in its post-translational modifications. Moreover, the transcriptional programs triggered by TFEB may be influenced by the miRNA-mediated regulation of TFEB targets. Finally, recent important studies indicate that the transcription of many miRNAs is regulated by TFEB itself. In this review, we describe the interplay between miRNAs with TFEB and focus on how these types of crosstalk affect TFEB activation and cellular functions.
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Affiliation(s)
- Davide Corà
- Department of Translational Medicine, Piemonte Orientale University, 28100 Novara, Italy;
- Center for Translational Research on Autoimmune and Allergic Diseases—CAAD, 28100 Novara, Italy
| | - Federico Bussolino
- Department of Oncology, University of Torino, 10060 Candiolo, Italy
- Candiolo Cancer Institute-IRCCS-FPO, Laboratory of Vascular Oncology, 10060 Candiolo, Italy
| | - Gabriella Doronzo
- Department of Oncology, University of Torino, 10060 Candiolo, Italy
- Candiolo Cancer Institute-IRCCS-FPO, Laboratory of Vascular Oncology, 10060 Candiolo, Italy
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13
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MicroRNA Sequences Modulated by Beta Cell Lipid Metabolism: Implications for Type 2 Diabetes Mellitus. BIOLOGY 2021; 10:biology10060534. [PMID: 34203703 PMCID: PMC8232095 DOI: 10.3390/biology10060534] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/15/2021] [Revised: 06/08/2021] [Accepted: 06/09/2021] [Indexed: 12/23/2022]
Abstract
Alterations in lipid metabolism within beta cells and islets contributes to dysfunction and apoptosis of beta cells, leading to loss of insulin secretion and the onset of type 2 diabetes. Over the last decade, there has been an explosion of interest in understanding the landscape of gene expression which influences beta cell function, including the importance of small non-coding microRNA sequences in this context. This review sought to identify the microRNA sequences regulated by metabolic challenges in beta cells and islets, their targets, highlight their function and assess their possible relevance as biomarkers of disease progression in diabetic individuals. Predictive analysis was used to explore networks of genes targeted by these microRNA sequences, which may offer new therapeutic strategies to protect beta cell function and delay the onset of type 2 diabetes.
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Zhou Z, Zheng X, Mei X, Li W, Qi S, Deng Y, Lei B. Hsa_circ_0080229 upregulates the expression of murine double minute-2 (MDM2) and promotes glioma tumorigenesis and invasion via the miR-1827 sponging mechanism. ANNALS OF TRANSLATIONAL MEDICINE 2021; 9:762. [PMID: 34268375 PMCID: PMC8246201 DOI: 10.21037/atm-20-7123] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/26/2020] [Accepted: 02/21/2021] [Indexed: 12/17/2022]
Abstract
Background Glioma is the most common and fatal primary cranial tumor. The epidermal growth factor receptor (EGFR) plays an important role in the occurrence and treatment of glioma, which might function through a circular ribonucleic acid (circRNA)-related mechanism. Hsa_circ_0080229 (circ_0080229) has been identified as a circRNA arising from an EGFR gene in gliomas; however, little is known about its molecular mechanism to date. Methods To address this question, a series of experiments were conducted to confirm the effect of circ_0080229 in gliomas and identify the downstream mechanism. A quantitative real-time polymerase chain reaction (qRT-PCR) analysis and in-situ hybridization/fluorescence in-situ hybridization (ISH/FISH) testing were performed to identify the expression of circ_0080229 in patient samples. Bioinformatic analysis was carried out to explore the possible mechanism. Next, a series of in-vitro functional assays and in-vivo assays with a xenograft subcutaneous glioma model was carried out to confirm the effect of circ_0080229. Finally, qRT-PCR analysis and a Western Blot analysis were performed to verify the related mechanism. Results The expression of circ_0080229 was upregulated in both glioma tissues and cell lines related to unfavorable clinicopathologic characteristics. The expression of circ_0080229 was found to be inversely correlated with miR-1827, a micro-ribonucleic acid (miRNA) targeting murine double minute-2 (MDM2). The downregulation of circ_0080229 inhibited gliomas in vivo and suppressed U87 and U251 cell lines in vitro, which the transfection of the miR-1827 inhibitor could reverse. Concerning the mechanism, a block of circ_0080229 decreased MDM2 expression, while the inhibition of miR-1827 reversed this effect. Thus, circ_0080229 appears to target the downstream miR-1827/MDM2 signaling pathway. Conclusions Our results showed that the silencing of circ_0080229 upregulates the expression of miR-1827, which in turn resulted in the suppression of MDM2, and the mediation of the downstream P53 signaling pathway. Circ_0080229 exerted an effect in mediating tumor progression through the MDM2 signaling pathway by sponging miR-1827. Its importance as a potential prognostic biomarker in gliomas has thus been established.
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Affiliation(s)
- Zhiwei Zhou
- Department of Neurosurgery, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, China.,Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, China.,Faculty of Health Sciences, University of Macau, Taipa, Macau, China
| | - Xiuyuan Zheng
- Department of Rehabilitation Medicine, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, China
| | - Xin Mei
- Department of Neurosurgery, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, China.,Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, China
| | - Wengpeng Li
- Department of Neurosurgery, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, China
| | - Songtao Qi
- Department of Neurosurgery, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Yuefei Deng
- Department of Neurosurgery, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, China
| | - Bingxi Lei
- Department of Neurosurgery, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, China.,Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, China.,Department of Neurosurgery, Nanfang Hospital, Southern Medical University, Guangzhou, China
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15
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Tej S, Mukherji S. Small RNA-driven feed-forward loop: fine-tuning of protein synthesis through sRNA-mediated crosstalk. THE EUROPEAN PHYSICAL JOURNAL. E, SOFT MATTER 2021; 44:55. [PMID: 33871749 DOI: 10.1140/epje/s10189-021-00013-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/11/2020] [Accepted: 01/05/2021] [Indexed: 06/12/2023]
Abstract
Often in bacterial regulatory networks, small non-coding RNAs (sRNA) interact with several mRNA species. The competition among mRNAs for binding to the common pool of sRNA might lead to crosstalk between the mRNAs. This is similar to the competing endogenous RNA effect that leads to complex gene regulation with stabilized gene expression in Eukaryotes. Here, we study an sRNA-driven feed-forward loop (sFFL) where the top-tier regulator, an sRNA, translationally activates the target protein (TP) as well as a transcriptional activator of the TP through binding to the respective mRNAs. We show that the sRNA-mediated crosstalk between the two mRNA species enables the sFFL to function in three different regimes depending on the synthesis rate of the transcriptional activator mRNA. Of these three regimes, there exists a sensitive regime where the TP level shows interesting features depending on the precise mechanism of target translation. In the case of translation entirely from sRNA-mRNA bound complexes, the TP level becomes maximum around the sensitive regime. Through stochastic analysis and simulations, we show that relative fluctuations in the TP level is minimized here. For translation both from mRNA and sRNA-mRNA bound complexes, the target expression shows a threshold response across the sensitive regime.
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Affiliation(s)
- Swathi Tej
- Protein Chemistry and Technology, Central Food Technological Research Institute, Mysore, Karnataka, 570 020, India
| | - Sutapa Mukherji
- Protein Chemistry and Technology, Central Food Technological Research Institute, Mysore, Karnataka, 570 020, India.
- Mathematical and Physical Sciences Division, School of Arts and Sciences, Ahmedabad University, Navrangpura, Ahmedabad, 380009, India.
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16
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Differential Response of Grapevine to Infection with ' Candidatus Phytoplasma solani' in Early and Late Growing Season through Complex Regulation of mRNA and Small RNA Transcriptomes. Int J Mol Sci 2021; 22:ijms22073531. [PMID: 33805429 PMCID: PMC8037961 DOI: 10.3390/ijms22073531] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2021] [Revised: 03/24/2021] [Accepted: 03/25/2021] [Indexed: 02/08/2023] Open
Abstract
Bois noir is the most widespread phytoplasma grapevine disease in Europe. It is associated with ‘Candidatus Phytoplasma solani’, but molecular interactions between the causal pathogen and its host plant are not well understood. In this work, we combined the analysis of high-throughput RNA-Seq and sRNA-Seq data with interaction network analysis for finding new cross-talks among pathways involved in infection of grapevine cv. Zweigelt with ‘Ca. P. solani’ in early and late growing seasons. While the early growing season was very dynamic at the transcriptional level in asymptomatic grapevines, the regulation at the level of small RNAs was more pronounced later in the season when symptoms developed in infected grapevines. Most differentially expressed small RNAs were associated with biotic stress. Our study also exposes the less-studied role of hormones in disease development and shows that hormonal balance was already perturbed before symptoms development in infected grapevines. Analysis at the level of communities of genes and mRNA-microRNA interaction networks revealed several new genes (e.g., expansins and cryptdin) that have not been associated with phytoplasma pathogenicity previously. These novel actors may present a new reference framework for research and diagnostics of phytoplasma diseases of grapevine.
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17
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Protection against Glucolipotoxicity by High Density Lipoprotein in Human PANC-1 Hybrid 1.1B4 Pancreatic Beta Cells: The Role of microRNA. BIOLOGY 2021; 10:biology10030218. [PMID: 33805674 PMCID: PMC8000094 DOI: 10.3390/biology10030218] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/26/2021] [Accepted: 03/11/2021] [Indexed: 02/06/2023]
Abstract
High-density lipoproteins provide protection against the damaging effects of glucolipotoxicity in beta cells, a factor which sustains insulin secretion and staves off onset of type 2 diabetes mellitus. This study examines epigenetic changes in small non-coding microRNA sequences induced by high density lipoproteins in a human hybrid beta cell model, and tests the impact of delivery of a single sequence in protecting against glucolipotoxicity. Human PANC-1.1B4 cells were used to establish Bmax and Kd for [3H]cholesterol efflux to high density lipoprotein, and minimum concentrations required to protect cell viability and reduce apoptosis to 30mM glucose and 0.25 mM palmitic acid. Microchip array identified the microRNA signature associated with high density lipoprotein treatment, and one sequence, hsa-miR-21-5p, modulated via delivery of a mimic and inhibitor. The results confirm that low concentrations of high-density lipoprotein can protect against glucolipotoxicity, and report the global microRNA profile associated with this lipoprotein; delivery of miR-21-5p mimic altered gene targets, similar to high density lipoprotein, but could not provide sufficient protection against glucolipotoxicity. We conclude that the complex profile of microRNA changes due to HDL treatment may be difficult to replicate using a single microRNA, findings which may inform current drug strategies focused on this approach.
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18
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A critical approach for successful use of circulating microRNAs as biomarkers in cardiovascular diseases: the case of hypertrophic cardiomyopathy. Heart Fail Rev 2021; 27:281-294. [PMID: 33656618 DOI: 10.1007/s10741-021-10084-y] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 02/10/2021] [Indexed: 10/22/2022]
Abstract
MicroRNAs (miRNAs) are small noncoding RNA molecules that act as major regulators of gene expression at the post-transcriptional level. As the potential applications of miRNAs in the diagnosis and treatment of human diseases have become more evident, many studies of hypertrophic cardiomyopathy (HCM) have focused on the systemic identification and quantification of miRNAs in biofluids and myocardial tissues. HCM is a hereditary cardiomyopathy caused by mutations in genes encoding proteins of the sarcomere. Despite overall improvements in survival, progression to heart failure, stroke, and sudden cardiac death remain prominent features of living with HCM. Several miRNAs have been shown to be promising biomarkers of HCM; however, there are many challenges to ensuring the validity, consistency, and reproducibility of these biomarkers for clinical use. In particular, miRNA testing may be limited by pre-analytical and analytical caveats, making our interpretation of results challenging. Such factors that may affect miRNA testing include sample type selection, hemolysis, platelet activation, and renal dysfunction. Therefore, researchers should be careful when developing appropriate standards for the design of miRNA profiling studies in order to ensure that all results provided are both accurate and reliable. In this review, we discuss the application of miRNAs as biomarkers for HCM.
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19
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Inhibition of lncRNA-NEAT1 sensitizes 5-Fu resistant cervical cancer cells through de-repressing the microRNA-34a/LDHA axis. Biosci Rep 2021; 41:227998. [PMID: 33645623 PMCID: PMC8298262 DOI: 10.1042/bsr20200533] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2020] [Revised: 01/03/2021] [Accepted: 01/04/2021] [Indexed: 12/25/2022] Open
Abstract
Cervical cancer is one of the most diagnosed malignancies among females. The 5-fluorouracil (5-Fu) is a widely used chemotherapeutic agent against diverse cancers. Despite the initially encouraging progresses, a fraction of cervical cancer patients developed 5-Fu resistance. We detected that nuclear-rich transcripts 1 (NEAT1) was significantly up-regulated in cervical cancer tissues and cell lines. Moreover, NEAT1 was positively associated with 5-Fu resistance. Furthermore, expression of NEAT1 was significantly up-regulated in 5-Fu resistant CaSki cervical cancer cells. Knocking down NEAT1 by shRNA dramatically promoted the sensitivity of 5-Fu resistant CaSki cells. We observed a negative correlation between long noncoding RNA (lncRNA)-NEAT1 and miR-34a in cervical cancer patient tissues. Overexpression of miR-34a significantly sensitized 5-Fu resistant cells. Bioinformatics analysis uncovered that NEAT1 functions as a competitive endogenous RNA (ceRNA) of miR-34a in cervical cancer cells via sponging it at multiple sites to suppress expression of miR-34a. This negative association between NEAT1 and miR-34a was further verified in cervical cancer tissues. We found the 5-Fu resistant cells displayed significantly increased glycolysis rate. Overexpression of miR-34a suppressed cellular glycolysis rate and sensitized 5-Fu resistant cells through direct targeting the 3′-untranslated region (UTR) of LDHA, a glycolysis key enzyme. Importantly, knocking down NEAT1 successfully down-regulated LDHA expressions and glycolysis rate of cervical cancer cells by up-regulating miR-34a, a process could be further rescued by miR-34a inhibition. Finally, we demonstrated inhibition of NEAT1 significantly sensitized cervical cancer cells to 5-Fu through the miR-34a/LDHA pathway. In summary, the present study suggests a new molecular mechanism for the NEAT1-mediated 5-Fu resistance via the miR-34a/LDHA-glycolysis axis.
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20
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Pirim D. Integrative analyses of molecular pathways and key candidate biomarkers associated with colorectal cancer. Cancer Biomark 2020; 27:555-568. [PMID: 32176635 DOI: 10.3233/cbm-191263] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
BACKGROUND Colorectal cancer (CRC) is one of the leading causes of cancer-related deaths and mining the molecular factors underlying CRC pathogenesis is imperative for alleviating the disease burden. OBJECTIVE To highlight key molecular pathways, prioritize hub genes and their regulators related to CRC. METHODS Data sets of TCGA-COAD and GTEx were used to identify differentially expressed genes (DEGs) and their functional enrichments in pathways and biological processes were analyzed using bioinformatics tools. Protein-protein interaction network was constructed and hub genes were identified using Cytoscape. Ingenuity Pathway Analysis was used to analyze the relations of the hub genes with diseases and canonical pathways. Key regulators targeting the hub genes such as TFs, miRNAs and their interactions were identified using in silico tools. RESULTS AURKA, CDK1, MYC, CDH1, CCNB1, CDC20, UBE2C, PLK1, KIF11, and CCNA2 were prioritized as hub genes based on their topological properties. Enrichment analyses emphasized the roles of DEGs and hub genes in the cell cycle process. Interactions of the hub genes with TFs and miRNAs suggested TP53, EZH2 and KLF4 as being promising candidate biomarkers for CRC. CONCLUSIONS Our results provide in silico evidence for candidate biomolecules that may have strong biomarker potential for CRC-related translational strategies.
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21
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Gilyazova IR, Beeraka NM, Klimentova EA, Bulygin KV, Nikolenko VN, Izmailov AA, Gilyazova GR, Pavlov VN, Khusnutdinova EK, Somasundaram SG, Kirkland CE, Aliev G. Novel MicroRNA Binding Site SNPs and the Risk of Clear Cell Renal Cell Carcinoma (ccRCC): A Case-Control Study. Curr Cancer Drug Targets 2020; 21:CCDT-EPUB-111697. [PMID: 33222672 DOI: 10.2174/1568009620666201120151226] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2020] [Revised: 10/14/2020] [Accepted: 10/14/2020] [Indexed: 12/14/2022]
Abstract
BACKGROUND Renal cell carcinoma represents 3% of all adult malignancies. MicroRNAs exhibit specific functions in various biological processes through their interaction with cellular mRNA involved in apoptosis and cell cycle control. Recent studies have reported the potential association of single-nucleotide polymorphisms (SNPs) in miRNA-binding sites of VHL-HIF1α pathway genes with renal cancer development and progression. OBJECTIVE The objective of this study is to investigate SNPs invoking an alteration in the nature of interaction with miRNA binding sites of VHL-HIF1α pathway genes. PATIENTS & METHODS Total 450 cases of histologically and clinically verified ccRCC and 490 controls were included in our study. Genotyping was performed using a TaqMan PCR allelic discrimination method. Kaplan-Meier method of statistical analysis was implemented to analyze the overall patient survival rate. RESULTS Polymorphism rs10491534 in TSC1 gene was significantly associated with risk of developing advanced ccRCC. Allele G of rs1642742 in VHL gene was significantly prevalent in ccRCC compared with control group aged 55 and older (OR = 1.5566; CI [1.1532-2.1019]). Results from the dominant model combining individuals with AG or AA genotype showed that the A allele bearers of CDCP1 rs6773576 exhibited higher risk of death compared to GG carriers (HR 3.93, 95% CI 1.76-17.21, log-rank P = 0.0033). CONCLUSION The present study delineated the association of miRNA binding site variants in VHL-HIF1α pathway genes with the ccRCC risk, which may affect clinical outcome.
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Affiliation(s)
- Irina R Gilyazova
- Institute of Biochemistry and Genetics - Subdivision of the Ufa Federal Research Centre of the Russian Academy of Sciences, Ufa. Russian Federation
- Bashkir State Medical University, Ufa, Russian Federation
| | - Narasimha M Beeraka
- Center of Excellence in Regenerative Medicine and Molecular Biology (CEMR), Department of Biochemistry, JSS Academy of Higher Education and Research (JSS AHER), Mysuru, Karnataka. India
| | - Elizaveta A Klimentova
- Institute of Biochemistry and Genetics - Subdivision of the Ufa Federal Research Centre of the Russian Academy of Sciences, Ufa. Russian Federation
| | - Kirill V Bulygin
- I.M. Sechenov First Moscow State Medical University of the Ministry of Health of the Russian Federation (Sechenov University), 8/2 Trubetskaya Str., Moscow, 119991, Russia
- M.V. Lomonosov Moscow State University, Moscow, Russian Federation
| | - Vladimir N Nikolenko
- I.M. Sechenov First Moscow State Medical University of the Ministry of Health of the Russian Federation (Sechenov University), 8/2 Trubetskaya Str., Moscow, 119991, Russia
| | | | | | | | - Elsa K Khusnutdinova
- Institute of Biochemistry and Genetics - Subdivision of the Ufa Federal Research Centre of the Russian Academy of Sciences, Ufa. Russian Federation
- Bashkir State Medical University, Ufa, Russian Federation
| | | | - Cecil E Kirkland
- Department of Biological Sciences, Salem University, Salem, WV, 26426, USA
| | - Gjumrakch Aliev
- I.M. Sechenov First Moscow State Medical University of the Ministry of Health of the Russian Federation (Sechenov University), 8/2 Trubetskaya Str., Moscow, 119991, Russia
- GALLY International Research Institute, 7733 Louis Pasteur Drive, #330, San Antonio, TX, 78229, USA
- Research Institute of Human Morphology, 3 Tsyurupy Street, Moscow, 117418, Russian Federation
- Institute of Physiologically Active Compounds of Russian Academy of Sciences, Severny pr. 1, Chernogolovka, Moscow Region, 142432, Russia
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22
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Woods S, Charlton S, Cheung K, Hao Y, Soul J, Reynard LN, Crowe N, Swingler TE, Skelton AJ, Piróg KA, Miles CG, Tsompani D, Jackson RM, Dalmay T, Clark IM, Barter MJ, Young DA. microRNA-seq of cartilage reveals an overabundance of miR-140-3p which contains functional isomiRs. RNA (NEW YORK, N.Y.) 2020; 26:1575-1588. [PMID: 32660984 PMCID: PMC7566571 DOI: 10.1261/rna.075176.120] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/20/2020] [Accepted: 07/06/2020] [Indexed: 05/15/2023]
Abstract
miR-140 is selectively expressed in cartilage. Deletion of the entire Mir140 locus in mice results in growth retardation and early-onset osteoarthritis-like pathology; however, the relative contribution of miR-140-5p or miR-140-3p to the phenotype remains to be determined. An unbiased small RNA sequencing approach identified miR-140-3p as significantly more abundant (>10-fold) than miR-140-5p in human cartilage. Analysis of these data identified multiple miR-140-3p isomiRs differing from the miRBase annotation at both the 5' and 3' end, with >99% having one of two seed sequences (5' bases 2-8). Canonical (miR-140-3p.2) and shifted (miR-140-3p.1) seed isomiRs were overexpressed in chondrocytes and transcriptomics performed to identify targets. miR-140-3p.1 and miR-140-3p.2 significantly down-regulated 694 and 238 genes, respectively, of which only 162 genes were commonly down-regulated. IsomiR targets were validated using 3'UTR luciferase assays. miR-140-3p.1 targets were enriched within up-regulated genes in rib chondrocytes of Mir140-null mice and within down-regulated genes during human chondrogenesis. Finally, through imputing the expression of miR-140 from the expression of the host gene WWP2 in 124 previously published data sets, an inverse correlation with miR-140-3p.1 predicted targets was identified. Together these data suggest the novel seed containing isomiR miR-140-3p.1 is more functional than original consensus miR-140-3p seed containing isomiR.
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Affiliation(s)
- Steven Woods
- Division of Cell Matrix Biology and Regenerative Medicine, Faculty of Biology Medicine and Health, University of Manchester, Manchester M13 9PT, United Kingdom
| | - Sarah Charlton
- Skeletal Research Group, Biosciences Institute, Newcastle University, Newcastle upon Tyne NE1 3BZ, United Kingdom
| | - Kat Cheung
- Skeletal Research Group, Biosciences Institute, Newcastle University, Newcastle upon Tyne NE1 3BZ, United Kingdom
| | - Yao Hao
- Skeletal Research Group, Biosciences Institute, Newcastle University, Newcastle upon Tyne NE1 3BZ, United Kingdom
- Orthopedics Department, First Hospital of Shanxi Medical University, Yingze District, Taiyuan, 030000, China
| | - Jamie Soul
- Skeletal Research Group, Biosciences Institute, Newcastle University, Newcastle upon Tyne NE1 3BZ, United Kingdom
| | - Louise N Reynard
- Skeletal Research Group, Biosciences Institute, Newcastle University, Newcastle upon Tyne NE1 3BZ, United Kingdom
| | - Natalie Crowe
- School of Biological Sciences, University of East Anglia, Norwich NR4 7TJ, United Kingdom
| | - Tracey E Swingler
- School of Biological Sciences, University of East Anglia, Norwich NR4 7TJ, United Kingdom
| | - Andrew J Skelton
- Skeletal Research Group, Biosciences Institute, Newcastle University, Newcastle upon Tyne NE1 3BZ, United Kingdom
| | - Katarzyna A Piróg
- Skeletal Research Group, Biosciences Institute, Newcastle University, Newcastle upon Tyne NE1 3BZ, United Kingdom
| | - Colin G Miles
- Skeletal Research Group, Biosciences Institute, Newcastle University, Newcastle upon Tyne NE1 3BZ, United Kingdom
| | - Dimitra Tsompani
- Skeletal Research Group, Biosciences Institute, Newcastle University, Newcastle upon Tyne NE1 3BZ, United Kingdom
| | - Robert M Jackson
- Skeletal Research Group, Biosciences Institute, Newcastle University, Newcastle upon Tyne NE1 3BZ, United Kingdom
| | - Tamas Dalmay
- School of Biological Sciences, University of East Anglia, Norwich NR4 7TJ, United Kingdom
| | - Ian M Clark
- School of Biological Sciences, University of East Anglia, Norwich NR4 7TJ, United Kingdom
| | - Matt J Barter
- Skeletal Research Group, Biosciences Institute, Newcastle University, Newcastle upon Tyne NE1 3BZ, United Kingdom
| | - David A Young
- Skeletal Research Group, Biosciences Institute, Newcastle University, Newcastle upon Tyne NE1 3BZ, United Kingdom
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Regulatory Mechanisms of Epigenetic miRNA Relationships in Human Cancer and Potential as Therapeutic Targets. Cancers (Basel) 2020; 12:cancers12102922. [PMID: 33050637 PMCID: PMC7600069 DOI: 10.3390/cancers12102922] [Citation(s) in RCA: 72] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2020] [Revised: 10/03/2020] [Accepted: 10/07/2020] [Indexed: 12/15/2022] Open
Abstract
Simple Summary By the virtue of targeting multiple genes, a microRNA (miRNA) can infer variable consequences on tumorigenesis by appearing as both a tumour suppressor and oncogene. miRNAs can regulate gene expression by modulating genome-wide epigenetic status of genes that are involved in various cancers. These miRNAs perform direct inhibition of key mediators of the epigenetic machinery, such as DNA methyltransferases (DNMTs) and histone deacetylases (HDACs) genes. Along with miRNAs gene expression, similar to other protein-coding genes, miRNAs are also controlled by epigenetic mechanisms. Overall, this reciprocal interaction between the miRNAs and the epigenetic architecture is significantly implicated in the aberrant expression of miRNAs detected in various human cancers. Comprehensive knowledge of the miRNA-epigenetic dynamics in cancer is essential for the discovery of novel anticancer therapeutics. Abstract Initiation and progression of cancer are under both genetic and epigenetic regulation. Epigenetic modifications including alterations in DNA methylation, RNA and histone modifications can lead to microRNA (miRNA) gene dysregulation and malignant cellular transformation and are hereditary and reversible. miRNAs are small non-coding RNAs which regulate the expression of specific target genes through degradation or inhibition of translation of the target mRNA. miRNAs can target epigenetic modifier enzymes involved in epigenetic modulation, establishing a trilateral regulatory “epi–miR–epi” feedback circuit. The intricate association between miRNAs and the epigenetic architecture is an important feature through which to monitor gene expression profiles in cancer. This review summarises the involvement of epigenetically regulated miRNAs and miRNA-mediated epigenetic modulations in various cancers. In addition, the application of bioinformatics tools to study these networks and the use of therapeutic miRNAs for the treatment of cancer are also reviewed. A comprehensive interpretation of these mechanisms and the interwoven bond between miRNAs and epigenetics is crucial for understanding how the human epigenome is maintained, how aberrant miRNA expression can contribute to tumorigenesis and how knowledge of these factors can be translated into diagnostic and therapeutic tool development.
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Kinoshita C, Okamoto Y, Aoyama K, Nakaki T. MicroRNA: A Key Player for the Interplay of Circadian Rhythm Abnormalities, Sleep Disorders and Neurodegenerative Diseases. Clocks Sleep 2020; 2:282-307. [PMID: 33089205 PMCID: PMC7573810 DOI: 10.3390/clockssleep2030022] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Accepted: 07/21/2020] [Indexed: 02/06/2023] Open
Abstract
Circadian rhythms are endogenous 24-h oscillators that regulate the sleep/wake cycles and the timing of biological systems to optimize physiology and behavior for the environmental day/night cycles. The systems are basically generated by transcription-translation feedback loops combined with post-transcriptional and post-translational modification. Recently, evidence is emerging that additional non-coding RNA-based mechanisms are also required to maintain proper clock function. MicroRNA is an especially important factor that plays critical roles in regulating circadian rhythm as well as many other physiological functions. Circadian misalignment not only disturbs the sleep/wake cycle and rhythmic physiological activity but also contributes to the development of various diseases, such as sleep disorders and neurodegenerative diseases. The patient with neurodegenerative diseases often experiences profound disruptions in their circadian rhythms and/or sleep/wake cycles. In addition, a growing body of recent evidence implicates sleep disorders as an early symptom of neurodegenerative diseases, and also suggests that abnormalities in the circadian system lead to the onset and expression of neurodegenerative diseases. The genetic mutations which cause the pathogenesis of familial neurodegenerative diseases have been well studied; however, with the exception of Huntington's disease, the majority of neurodegenerative diseases are sporadic. Interestingly, the dysfunction of microRNA is increasingly recognized as a cause of sporadic neurodegenerative diseases through the deregulated genes related to the pathogenesis of neurodegenerative disease, some of which are the causative genes of familial neurodegenerative diseases. Here we review the interplay of circadian rhythm disruption, sleep disorders and neurodegenerative disease, and its relation to microRNA, a key regulator of cellular processes.
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Affiliation(s)
- Chisato Kinoshita
- Department of Pharmacology, Teikyo University School of Medicine, 2-11-1 Kaga, Itabashi, Tokyo 173-8605, Japan; (C.K.); (Y.O.); (K.A.)
| | - Yayoi Okamoto
- Department of Pharmacology, Teikyo University School of Medicine, 2-11-1 Kaga, Itabashi, Tokyo 173-8605, Japan; (C.K.); (Y.O.); (K.A.)
- Teikyo University Support Center for Women Physicians and Researchers, 2-11-1 Kaga, Itabashi, Tokyo 173-8605, Japan
| | - Koji Aoyama
- Department of Pharmacology, Teikyo University School of Medicine, 2-11-1 Kaga, Itabashi, Tokyo 173-8605, Japan; (C.K.); (Y.O.); (K.A.)
| | - Toshio Nakaki
- Department of Pharmacology, Teikyo University School of Medicine, 2-11-1 Kaga, Itabashi, Tokyo 173-8605, Japan; (C.K.); (Y.O.); (K.A.)
- Faculty of Pharma-Science, Teikyo University, 2-11-1 Kaga, Itabashi, Tokyo 173-8605, Japan
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25
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Lightbody RJ, Taylor JMW, Dempsie Y, Graham A. MicroRNA sequences modulating inflammation and lipid accumulation in macrophage “foam” cells: Implications for atherosclerosis. World J Cardiol 2020; 12:303-333. [PMID: 32843934 PMCID: PMC7415235 DOI: 10.4330/wjc.v12.i7.303] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/30/2020] [Revised: 06/03/2020] [Accepted: 06/10/2020] [Indexed: 02/06/2023] Open
Abstract
Accumulation of macrophage “foam” cells, laden with cholesterol and cholesteryl ester, within the intima of large arteries, is a hallmark of early “fatty streak” lesions which can progress to complex, multicellular atheromatous plaques, involving lipoproteins from the bloodstream and cells of the innate and adaptive immune response. Sterol accumulation triggers induction of genes encoding proteins mediating the atheroprotective cholesterol efflux pathway. Within the arterial intima, however, this mechanism is overwhelmed, leading to distinct changes in macrophage phenotype and inflammatory status. Over the last decade marked gains have been made in understanding of the epigenetic landscape which influence macrophage function, and in particular the importance of small non-coding micro-RNA (miRNA) sequences in this context. This review identifies some of the miRNA sequences which play a key role in regulating “foam” cell formation and atherogenesis, highlighting sequences involved in cholesterol accumulation, those influencing inflammation in sterol-loaded cells, and novel sequences and pathways which may offer new strategies to influence macrophage function within atherosclerotic lesions.
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Affiliation(s)
- Richard James Lightbody
- Department of Biological and Biomedical Sciences, School of Health and Life Sciences, Glasgow Caledonian University, Glasgow G4 0BA, United Kingdom
| | - Janice Marie Walsh Taylor
- Department of Biological and Biomedical Sciences, School of Health and Life Sciences, Glasgow Caledonian University, Glasgow G4 0BA, United Kingdom
| | - Yvonne Dempsie
- Department of Biological and Biomedical Sciences, School of Health and Life Sciences, Glasgow Caledonian University, Glasgow G4 0BA, United Kingdom
| | - Annette Graham
- Department of Biological and Biomedical Sciences, School of Health and Life Sciences, Glasgow Caledonian University, Glasgow G4 0BA, United Kingdom
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26
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Chetta M, Di Pietro L, Bukvic N, Lattanzi W. Rising Roles of Small Noncoding RNAs in Cotranscriptional Regulation: In Silico Study of miRNA and piRNA Regulatory Network in Humans. Genes (Basel) 2020; 11:genes11050482. [PMID: 32365489 PMCID: PMC7290514 DOI: 10.3390/genes11050482] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2020] [Revised: 04/09/2020] [Accepted: 04/27/2020] [Indexed: 01/10/2023] Open
Abstract
Gene expression regulation is achieved through an intricate network of molecular interactions, in which trans-acting transcription factors (TFs) and small noncoding RNAs (sncRNAs), including microRNAs (miRNAs) and PIWI-interacting RNAs (piRNAs), play a key role. Recent observations allowed postulating an interplay between TFs and sncRNAs, in that they may possibly share DNA-binding sites. The aim of this study was to analyze the complete subset of miRNA and piRNA sequences stored in the main databases in order to identify the occurrence of conserved motifs and subsequently predict a possible innovative interplay with TFs at a transcriptional level. To this aim, we adopted an original in silico workflow to search motifs and predict interactions within genome-scale regulatory networks. Our results allowed categorizing miRNA and piRNA motifs, with corresponding TFs sharing complementary DNA-binding motifs. The biological interpretation of the gene ontologies of the TFs permitted observing a selective enrichment in developmental pathways, allowing the distribution of miRNA motifs along a topological and chronological frame. In addition, piRNA motifs were categorized for the first time and revealed specific functional implications in somatic tissues. These data might pose experimental hypotheses to be tested in biological models, towards clarifying novel in gene regulatory routes.
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Affiliation(s)
- Massimiliano Chetta
- U.O.C. Genetica Medica e di Laboratorio, Ospedale Antonio Cardarelli, 80131 Napoli, Italy
- Correspondence: (M.C.); (L.D.P.); Tel.: +39-333187551 (M.C.); +39-0630154464 (L.D.P.)
| | - Lorena Di Pietro
- Dipartimento Scienze della Vita e Sanità Pubblica, Sezione di Biologia Applicata, Università Cattolica del Sacro Cuore, 00168 Rome, Italy
- Correspondence: (M.C.); (L.D.P.); Tel.: +39-333187551 (M.C.); +39-0630154464 (L.D.P.)
| | - Nenad Bukvic
- UOC Lab. di Genetica Medica, Azienda Ospedaliero Universitaria Consorziale Policlinico di Bari, 70124 Bari, Italy
| | - Wanda Lattanzi
- Dipartimento Scienze della Vita e Sanità Pubblica, Sezione di Biologia Applicata, Università Cattolica del Sacro Cuore, 00168 Rome, Italy
- Fondazione Policlinico Universitario A. Gemelli IRCCS, 00168 Rome, Italy
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27
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Martyniuk CJ, Martínez R, Kostyniuk DJ, Mennigen JA, Zubcevic J. Genetic ablation of bone marrow beta-adrenergic receptors in mice modulates miRNA-transcriptome networks of neuroinflammation in the paraventricular nucleus. Physiol Genomics 2020; 52:169-177. [PMID: 32089076 PMCID: PMC7191424 DOI: 10.1152/physiolgenomics.00001.2020] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2020] [Revised: 02/07/2020] [Accepted: 02/16/2020] [Indexed: 12/21/2022] Open
Abstract
Elucidating molecular pathways regulating neuroimmune communication is critical for therapeutic interventions in conditions characterized by overactive immune responses and dysfunctional autonomic nervous system. We generated a bone marrow-specific adrenergic beta 1 and beta 2 knockout mouse chimera (AdrB1.B2 KO) to determine how sympathetic drive to the bone affects transcripts and miRNAs in the hypothalamic paraventricular nucleus (PVN). This model has previously exhibited a dampened systemic immune response and decreased blood pressure compared with control animals. Reduced sympathetic responsiveness of the bone marrow hematopoietic cells of AdrB1.B2 KO chimera led to suppression of transcriptional networks that included leukocyte cell adhesion and migration and T cell-activation and recruitment. Transcriptome responses related to IL-17a signaling and the renin-angiotensin system were also suppressed in the PVN. Based on the transcriptome response, we next computationally predicted miRNAs in the PVN that may underscore the reduced sympathetic responsiveness of the bone marrow cells. These included miR-27b-3p, miR-150, miR-223-3p, and miR-326. Using real-time PCR, we measured a downregulation in the expression of miR-150-5p, miR-205-5p, miR-223-3p, miR-375-5p, miR-499a-5p, miR-27b-3p, let-7a-5p, and miR-21a-5p in the PVN of AdrB1.B2 KO chimera, confirming computational predictions that these miRNAs are associated with reduced neuro-immune responses and the loss of sympathetic responsiveness in the bone marrow. Intriguingly, directional responses of the miRNA corresponded to mRNAs, suggesting complex temporal or circuit-dependent posttranscriptional control of gene expression in the PVN. This study identifies molecular pathways involved in neural-immune interactions that may act as targets of therapeutic intervention for a dysfunctional autonomic nervous system.
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Affiliation(s)
- Christopher J Martyniuk
- Department of Physiological Sciences, College of Veterinary Medicine, University of Florida, Gainesville, Florida
| | - Ruben Martínez
- Department of Environmental Chemistry, Institute of Environmental Assessment and Water Research, IDAEA-CSIC, Jordi Girona, Barcelona, Spain
- Department of Cellular Biology, Physiology and Immunology, Universidad de Barcelona (UB), Barcelona, Spain
| | | | - Jan A Mennigen
- Department of Biology, University of Ottawa, Ottawa, Ontario, Canada
| | - Jasenka Zubcevic
- Department of Physiological Sciences, College of Veterinary Medicine, University of Florida, Gainesville, Florida
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28
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Ferro E, Enrico Bena C, Grigolon S, Bosia C. microRNA-mediated noise processing in cells: A fight or a game? Comput Struct Biotechnol J 2020; 18:642-649. [PMID: 32257047 PMCID: PMC7103774 DOI: 10.1016/j.csbj.2020.02.020] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2019] [Revised: 02/27/2020] [Accepted: 02/27/2020] [Indexed: 12/17/2022] Open
Abstract
In the past decades, microRNAs (miRNA) have much attracted the attention of researchers at the interface between life and theoretical sciences for their involvement in post-transcriptional regulation and related diseases. Thanks to the always more sophisticated experimental techniques, the role of miRNAs as "noise processing units" has been further elucidated and two main ways of miRNA noise-control have emerged by combinations of theoretical and experimental studies. While on one side miRNAs were thought to buffer gene expression noise, it has recently been suggested that miRNAs could also increase the cell-to-cell variability of their targets. In this Mini Review, we focus on the role of miRNAs in molecular noise processing and on the advantages as well as current limitations of theoretical modelling.
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Affiliation(s)
- Elsi Ferro
- Italian Institute for Genomic Medicine, Italy
| | | | - Silvia Grigolon
- The Francis Crick Institute, 1, Midland Road, London NW1 1AT, UK
| | - Carla Bosia
- Italian Institute for Genomic Medicine, Italy
- Department of Applied Science and Technology, Politecnico di Torino, Italy
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29
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Rosano S, Corà D, Parab S, Zaffuto S, Isella C, Porporato R, Hoza RM, Calogero RA, Riganti C, Bussolino F, Noghero A. A regulatory microRNA network controls endothelial cell phenotypic switch during sprouting angiogenesis. eLife 2020; 9:48095. [PMID: 31976858 PMCID: PMC7299339 DOI: 10.7554/elife.48095] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2019] [Accepted: 01/07/2020] [Indexed: 12/11/2022] Open
Abstract
Angiogenesis requires the temporal coordination of the proliferation and the migration of endothelial cells. Here, we investigated the regulatory role of microRNAs (miRNAs) in harmonizing angiogenesis processes in a three-dimensional in vitro model. We described a microRNA network which contributes to the observed down- and upregulation of proliferative and migratory genes, respectively. Global analysis of miRNA-target gene interactions identified two sub-network modules, the first organized in upregulated miRNAs connected with downregulated target genes and the second with opposite features. miR-424-5p and miR-29a-3p were selected for the network validation. Gain- and loss-of-function approaches targeting these microRNAs impaired angiogenesis, suggesting that these modules are instrumental to the temporal coordination of endothelial migration and proliferation. Interestingly, miR-29a-3p and its targets belong to a selective biomarker that is able to identify colorectal cancer patients who are responding to anti-angiogenic treatments. Our results provide a view of higher-order interactions in angiogenesis that has potential to provide diagnostic and therapeutic insights.
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Affiliation(s)
- Stefania Rosano
- Department of Oncology, University of Turin, Candiolo, Italy.,Candiolo Cancer Institute FPO-IRCCS, Candiolo, Italy
| | - Davide Corà
- Department of Translational Medicine, Piemonte Orientale University, Novara, Italy.,Center for Translational Research on Autoimmune and Allergic Diseases - CAAD, Novara, Italy
| | - Sushant Parab
- Department of Oncology, University of Turin, Candiolo, Italy.,Candiolo Cancer Institute FPO-IRCCS, Candiolo, Italy
| | - Serena Zaffuto
- Department of Oncology, University of Turin, Candiolo, Italy.,Candiolo Cancer Institute FPO-IRCCS, Candiolo, Italy
| | - Claudio Isella
- Department of Oncology, University of Turin, Candiolo, Italy.,Candiolo Cancer Institute FPO-IRCCS, Candiolo, Italy
| | | | - Roxana Maria Hoza
- Department of Oncology, University of Turin, Candiolo, Italy.,Candiolo Cancer Institute FPO-IRCCS, Candiolo, Italy
| | - Raffaele A Calogero
- Molecular Biotechnology Center, Department of Biotechnology and Health Sciences, University of Turin, Turin, Italy
| | - Chiara Riganti
- Department of Oncology, University of Turin, Candiolo, Italy
| | - Federico Bussolino
- Department of Oncology, University of Turin, Candiolo, Italy.,Candiolo Cancer Institute FPO-IRCCS, Candiolo, Italy
| | - Alessio Noghero
- Department of Oncology, University of Turin, Candiolo, Italy.,Candiolo Cancer Institute FPO-IRCCS, Candiolo, Italy
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30
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Ferro E, Enrico Bena C, Grigolon S, Bosia C. From Endogenous to Synthetic microRNA-Mediated Regulatory Circuits: An Overview. Cells 2019; 8:E1540. [PMID: 31795372 PMCID: PMC6952906 DOI: 10.3390/cells8121540] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2019] [Revised: 11/22/2019] [Accepted: 11/25/2019] [Indexed: 12/13/2022] Open
Abstract
MicroRNAs are short non-coding RNAs that are evolutionarily conserved and are pivotal post-transcriptional mediators of gene regulation. Together with transcription factors and epigenetic regulators, they form a highly interconnected network whose building blocks can be classified depending on the number of molecular species involved and the type of interactions amongst them. Depending on their topology, these molecular circuits may carry out specific functions that years of studies have related to the processing of gene expression noise. In this review, we first present the different over-represented network motifs involving microRNAs and their specific role in implementing relevant biological functions, reviewing both theoretical and experimental studies. We then illustrate the recent advances in synthetic biology, such as the construction of artificially synthesised circuits, which provide a controlled tool to test experimentally the possible microRNA regulatory tasks and constitute a starting point for clinical applications.
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Affiliation(s)
- Elsi Ferro
- IIGM—Italian Institute for Genomic Medicine, c/o IRCCS, 10060 Candiolo (Torino), Italy
- Candiolo Cancer Institute, FPO-IRCCS, 10060 Candiolo (Torino), Italy
| | - Chiara Enrico Bena
- IIGM—Italian Institute for Genomic Medicine, c/o IRCCS, 10060 Candiolo (Torino), Italy
- Candiolo Cancer Institute, FPO-IRCCS, 10060 Candiolo (Torino), Italy
| | - Silvia Grigolon
- The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Carla Bosia
- IIGM—Italian Institute for Genomic Medicine, c/o IRCCS, 10060 Candiolo (Torino), Italy
- Department of Applied Science and Technology, Politecnico di Torino, Corso Duca degli Abruzzi 24, 10129 Torino, Italy
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31
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Miotto M, Marinari E, De Martino A. Competing endogenous RNA crosstalk at system level. PLoS Comput Biol 2019; 15:e1007474. [PMID: 31675359 PMCID: PMC6853376 DOI: 10.1371/journal.pcbi.1007474] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2019] [Revised: 11/13/2019] [Accepted: 10/10/2019] [Indexed: 12/14/2022] Open
Abstract
microRNAs (miRNAs) regulate gene expression at post-transcriptional level by repressing target RNA molecules. Competition to bind miRNAs tends in turn to correlate their targets, establishing effective RNA-RNA interactions that can influence expression levels, buffer fluctuations and promote signal propagation. Such a potential has been characterized mathematically for small motifs both at steady state and away from stationarity. Experimental evidence, on the other hand, suggests that competing endogenous RNA (ceRNA) crosstalk is rather weak. Extended miRNA-RNA networks could however favour the integration of many crosstalk interactions, leading to significant large-scale effects in spite of the weakness of individual links. To clarify the extent to which crosstalk is sustained by the miRNA interactome, we have studied its emergent systemic features in silico in large-scale miRNA-RNA network reconstructions. We show that, although generically weak, system-level crosstalk patterns (i) are enhanced by transcriptional heterogeneities, (ii) can achieve high-intensity even for RNAs that are not co-regulated, (iii) are robust to variability in transcription rates, and (iv) are significantly non-local, i.e. correlate weakly with miRNA-RNA interaction parameters. Furthermore, RNA levels are generically more stable when crosstalk is strongest. As some of these features appear to be encoded in the network's topology, crosstalk may functionally be favoured by natural selection. These results suggest that, besides their repressive role, miRNAs mediate a weak but resilient and context-independent network of cross-regulatory interactions that interconnect the transcriptome, stabilize expression levels and support system-level responses.
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Affiliation(s)
- Mattia Miotto
- Dipartimento di Fisica, Sapienza Università di Roma, Rome, Italy
| | - Enzo Marinari
- Dipartimento di Fisica, Sapienza Università di Roma, Rome, Italy
| | - Andrea De Martino
- Soft & Living Matter Lab, CNR NANOTEC, Rome, Italy
- Italian Institute for Genomic Medicine, Turin, Italy
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Song SK, Park MG, Park SK, Chung CW, Park Y. MicroRNAs associated with microvascular invasion in hepatocellular carcinoma and their prognostic impacts in patients undergoing hepatic resection. Oncol Lett 2019; 18:6293-6303. [PMID: 31788107 DOI: 10.3892/ol.2019.10987] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2019] [Accepted: 08/30/2019] [Indexed: 12/12/2022] Open
Abstract
Although microvascular invasion (McVI) has prognostic value for patients with hepatocellular carcinoma (HCC) who have undergone hepatic resection, few studies have investigated the relationship between McVI and the aberrant expression of microRNAs (miRNAs). The present study identified the miRNAs that were selectively expressed in HCC with McVI and investigated their prognostic value. Clinical data and the miRNA expression profiles of 372 patients with HCC were extracted from The Cancer Genome Atlas database. miRNAs that were differentially expressed between patients with McVI and those without vascular invasion (VI) were identified and investigated as potential prognostic factors for HCC. The results demonstrated that McVI was a significant predictor of shortened recurrence-free survival (RFS). The 3 year RFS rate in patients with HCC accompanied by McVI was 28.2 and 49.3% in HCC without VI (P<0.001). miRNA-141/-582/-9 were upregulated, while miRNA-675 was downregulated in patients with McVI when compared with HCC patients without VI. Log2 fold-changes of miRNA-141/-582/-675/-9 were 0.80 [false discovery rate (FDR), 0.005], 0.55 (FDR, 0.045), -0.99 (FDR, 0.005) and 1.22 (FDR, <0.001), respectively. Kaplan-Meier analysis indicated that the overexpression of miR-141/-582/-9 was significantly associated with poor RFS and a poor overall survival. A text mining analysis revealed that these miRNAs were significantly associated with multifaceted hallmarks of cancer, including 'invasion and metastasis'. In conclusion, the overexpression of miRNA-141/-582/-9 was associated with McVI and a poor survival in patients undergoing hepatic resection for HCC.
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Affiliation(s)
- Sung Kyu Song
- Department of Surgery, Catholic Kwandong University International St. Mary's Hospital, Catholic Kwandong University College of Medicine, Incheon 22711, Republic of Korea
| | - Min Geun Park
- Department of Surgery, Catholic Kwandong University International St. Mary's Hospital, Catholic Kwandong University College of Medicine, Incheon 22711, Republic of Korea
| | - Seung-Keun Park
- Department of Supercomputing M&S Technology Development, Korea Institute of Science and Technology Information, Daejeon 34141, Republic of Korea
| | - Chul-Woon Chung
- Department of Surgery, Catholic Kwandong University International St. Mary's Hospital, Catholic Kwandong University College of Medicine, Incheon 22711, Republic of Korea
| | - Yongkeun Park
- Department of Surgery, Catholic Kwandong University International St. Mary's Hospital, Catholic Kwandong University College of Medicine, Incheon 22711, Republic of Korea
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Cai J, Yu Y, Xu Y, Liu H, Shou J, You L, Jiang H, Han X, Xie B, Han W. Exploring the role of Mir204/211 in HNSCC by the combination of bioinformatic analysis of ceRNA and transcription factor regulation. Oral Oncol 2019; 96:153-160. [PMID: 31422208 DOI: 10.1016/j.oraloncology.2019.07.024] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2019] [Revised: 07/22/2019] [Accepted: 07/24/2019] [Indexed: 12/12/2022]
Abstract
OBJECTIVES This study aimed to reveal the regulatory roles of microRNAs in head and neck squamous cell carcinoma (HNSCC) through comprehensive ceRNA, miRNA-transcription factor (TF)-hub gene network and survival analysis. MATERIALS AND METHODS Expression analysis was performed using the 'edgeR' package based on The Cancer Genome Atlas database. The ceRNA network was screened by intersecting prediction results from miRcode, miRTarBase, miRDB and TargetScan. GSE30784, GSE59102 and GSE107591 from the Gene Expression Omnibus repository were chosen for cross-validation. Hub genes were identified using a protein-protein interaction network constructed by Search Tool for the Retrieval of Interacting Genes. The Transcriptional Regulatory Relationships Unraveled by Sentence-based Text mining (TTRUST) was utilized to map the miRNA-TF-Hub gene network. Patient overall survival was analyzed using the 'survival' package in R. Structural and functional analysis of miR-204/211 was based on miRbase and RNAstructure. RESULTS A ceRNA network of 178 lncRNAs, 19 miRNAs and 55 mRNAs was generated, and a TF regulatory network with 11 miRNAs, 11 TFs and 18 hub genes was constructed from the 52 hub genes identified through the protein-protein interaction (PPI) network. Survival analysis demonstrated that the dysregulated expression of 11 lncRNAs and 14 mRNAs was highly related to overall survival. Furthermore, miR-204 and miR-211 were significantly involved in the network with identical mature structures, indicating them as key miRNAs in HNSCC. CONCLUSION This study reveals the comprehensive molecular regulatory networks centralized by miRNAs in HNSCC and uncovers the crucial role of miR-204 and miR-211, which may become potential diagnostic and therapeutic targets.
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Affiliation(s)
- Jingyi Cai
- Department of Medical Oncology, Sir Run Run Shaw Hospital, College of Medicine, Zhejiang University, Hangzhou, Zhejiang, China; Department of Stomatology, Zhejiang University, School of Medicine, Yuhangtang Rd, No.866, Hangzhou 310058, Zhejiang Province, China
| | - Yeke Yu
- Department of Medical Oncology, Sir Run Run Shaw Hospital, College of Medicine, Zhejiang University, Hangzhou, Zhejiang, China; Department of Stomatology, Zhejiang University, School of Medicine, Yuhangtang Rd, No.866, Hangzhou 310058, Zhejiang Province, China
| | - Yuzi Xu
- Department of Medical Oncology, Sir Run Run Shaw Hospital, College of Medicine, Zhejiang University, Hangzhou, Zhejiang, China; Department of Stomatology, Zhejiang University, School of Medicine, Yuhangtang Rd, No.866, Hangzhou 310058, Zhejiang Province, China
| | - Hao Liu
- Department of Medical Oncology, Sir Run Run Shaw Hospital, College of Medicine, Zhejiang University, Hangzhou, Zhejiang, China
| | - Jiawei Shou
- Department of Medical Oncology, Sir Run Run Shaw Hospital, College of Medicine, Zhejiang University, Hangzhou, Zhejiang, China
| | - Liangkun You
- Department of Medical Oncology, Sir Run Run Shaw Hospital, College of Medicine, Zhejiang University, Hangzhou, Zhejiang, China
| | - Hanliang Jiang
- Department of Respiratory Medicine, Sir Run Run Shaw Hospital, College of Medicine, Zhejiang University, Hangzhou, Zhejiang, China
| | - XuFeng Han
- Department of Internal Medicine, Yuyao Traditional Chinese Medicine Hospital, Yuyao, Zhejiang, China
| | - Binbin Xie
- Department of Medical Oncology, Sir Run Run Shaw Hospital, College of Medicine, Zhejiang University, Hangzhou, Zhejiang, China.
| | - Weidong Han
- Department of Medical Oncology, Sir Run Run Shaw Hospital, College of Medicine, Zhejiang University, Hangzhou, Zhejiang, China.
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Kostyniuk DJ, Marandel L, Jubouri M, Dias K, de Souza RF, Zhang D, Martyniuk CJ, Panserat S, Mennigen JA. Profiling the rainbow trout hepatic miRNAome under diet-induced hyperglycemia. Physiol Genomics 2019; 51:411-431. [PMID: 31282806 DOI: 10.1152/physiolgenomics.00032.2019] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
Carnivorous rainbow trout exhibit prolonged postprandial hyperglycemia when fed a diet exceeding 20% carbohydrate content. This poor capacity to utilize carbohydrates has led to rainbow trout being classified as "glucose-intolerant" (GI). The metabolic phenotype has spurred research to identify the underlying cellular and molecular mechanisms of glucose intolerance, largely because carbohydrate-rich diets provide economic and ecological advantages over traditionally used fish meal, considered unsustainable for rainbow trout aquaculture operations. Evidence points to a contribution of hepatic intermediary carbohydrate and lipid metabolism, as well as upstream insulin signaling. Recently, microRNAs (miRNAs), small noncoding RNAs acting as negative posttranscriptional regulators affecting target mRNA stability and translation, have emerged as critical regulators of hepatic control of glucose-homeostasis in mammals, revealing that dysregulated hepatic miRNAs might play a role in organismal hyperglycemia in metabolic disease. To determine whether hepatic regulatory miRNA networks may contribute to GI in rainbow trout, we induced prolonged postprandial hyperglycemia in rainbow trout by using a carbohydrate-rich diet and profiled genome-wide hepatic miRNAs in hyperglycemic rainbow trout compared with fasted trout and trout fed a diet devoid of carbohydrates. Using small RNA next-generation sequencing and real-time RT-PCR validation, we identified differentially regulated hepatic miRNAs between these groups and used an in silico approach to predict bona fide mRNA targets and enriched pathways. Diet-induced hyperglycemia resulted in differential regulation of hepatic miRNAs compared with fasted fish. Some of the identified miRNAs, such as miRNA-27b-3p and miRNA-200a-3p, are known to be responsive to hyperglycemia in the liver of hyperglycemic glucose-tolerant fish and mammals, suggesting an evolutionary conserved regulation. Using Gene Ontology term-based enrichment analysis, we identify intermediate carbohydrate and lipid metabolism and insulin signaling as potential targets of posttranscriptional regulation by hyperglycemia-regulated miRNAs and provide correlative expression analysis of specific predicted miRNA-target pairs. This study identifies hepatic miRNAs in rainbow trout that exhibit differential postprandial expression in response to diets with different carbohydrate content and predicts posttranscriptionally regulated target mRNAs enriched for pathways involved in glucoregulation. Together, these results provide a framework for testable hypotheses of functional involvement of specific hepatic miRNAs in GI in rainbow trout.
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Affiliation(s)
| | - Lucie Marandel
- INRA, Université de Pau et Pays d'Adour, UMR 1419, Nutrition, Metabolism and Aquaculture, E2S UPPA, Saint Pée-sur-Nivelle, France
| | - Mais Jubouri
- Department of Biology, University of Ottawa, Ottawa, Ontario, Canada
| | - Karine Dias
- INRA, Université de Pau et Pays d'Adour, UMR 1419, Nutrition, Metabolism and Aquaculture, E2S UPPA, Saint Pée-sur-Nivelle, France
| | - Robson F de Souza
- Microbiology Department, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
| | - Dapeng Zhang
- Department of Biology, Saint Louis University, Saint Louis, Missouri
| | - Christopher J Martyniuk
- Department of Physiological Sciences and Center for Environmental and Human Toxicology, UF Genetics Institute, College of Veterinary Medicine, University of Florida, Gainesville, Florida
| | - Stéphane Panserat
- INRA, Université de Pau et Pays d'Adour, UMR 1419, Nutrition, Metabolism and Aquaculture, E2S UPPA, Saint Pée-sur-Nivelle, France
| | - Jan A Mennigen
- Department of Biology, University of Ottawa, Ottawa, Ontario, Canada
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35
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Social status regulates the hepatic miRNAome in rainbow trout: Implications for posttranscriptional regulation of metabolic pathways. PLoS One 2019; 14:e0217978. [PMID: 31194802 PMCID: PMC6563994 DOI: 10.1371/journal.pone.0217978] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2018] [Accepted: 05/21/2019] [Indexed: 11/19/2022] Open
Abstract
Juvenile rainbow trout develop social hierarchies when held in dyads, and the development of socially subordinate (SS) and social dominance (SD) phenotypes in this context has been linked to specific changes in the hepatic energy metabolism of all major macronutrients. Following our recently reported finding that transcript abundance of drosha, a key component of the microRNA (miRNA) biogenesis pathway, is increased in paired juvenile rainbow trout irrespective of social status compared to socially isolated (SI) controls, we here determined global changes of the hepatic miRNA pathway genes in detail at the transcript and protein level. Both SD and SS rainbow trout exhibited increased Ago2 protein abundance compared to SI rainbow trout, suggesting that hepatic miRNA function is increased in rainbow trout maintained in dyads. Given the well-described differences in hepatic intermediary metabolism between SD and SS rainbow trout, and the important role of miRNAs in the posttranscriptional regulation of metabolic pathways, we also identified changes in hepatic miRNA abundance between SS and SD rainbow trout using small RNA next generation sequencing. We identified a total of 24 differentially regulated miRNAs, with 15 miRNAs that exhibited increased expression, and 9 miRNAs that exhibited decreased expression in the liver of SS trout compared to SD trout. To identify potential miRNA-dependent posttranscriptional regulatory pathways important for social status-dependent regulation of hepatic metabolism in rainbow trout, we used an in silico miRNA target prediction and pathway enrichment approach. We identified enrichment for pathways related to metabolism of carbohydrates, lipids and proteins in addition to organelle-specific processes involved in energy metabolism, especially mitochondrial fusion and fission. Select predicted miRNA-mRNA target pairs within these categories were quantitatively analyzed by real-time RT-PCR to validate candidates for future studies that will probe the functional metabolic roles of specific hepatic miRNAs in the development of SD and SS metabolic phenotypes.
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Kittelmann S, McGregor AP. Modulation and Evolution of Animal Development through microRNA Regulation of Gene Expression. Genes (Basel) 2019; 10:genes10040321. [PMID: 31027314 PMCID: PMC6523689 DOI: 10.3390/genes10040321] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2019] [Revised: 04/20/2019] [Accepted: 04/23/2019] [Indexed: 12/20/2022] Open
Abstract
microRNAs regulate gene expression by blocking the translation of mRNAs and/or promoting their degradation. They, therefore, play important roles in gene regulatory networks (GRNs) by modulating the expression levels of specific genes and can tune GRN outputs more broadly as part of feedback loops. These roles for microRNAs provide developmental buffering on one hand but can facilitate evolution of development on the other. Here we review how microRNAs can modulate GRNs during animal development as part of feedback loops and through their individual or combinatorial targeting of multiple different genes in the same network. We then explore how changes in the expression of microRNAs and consequently targets can facilitate changes in GRNs that alter development and lead to phenotypic evolution. The reviewed studies exemplify the key roles played by microRNAs in the regulation and evolution of gene expression during developmental processes in animals.
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Affiliation(s)
- Sebastian Kittelmann
- Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford, OX1 3RE, UK.
| | - Alistair P McGregor
- Department of Biological and Medical Sciences, Oxford Brookes University, Gipsy Lane, Oxford, OX3 0BP, UK.
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Braga EA, Fridman MV, Loginov VI, Dmitriev AA, Morozov SG. Molecular Mechanisms in Clear Cell Renal Cell Carcinoma: Role of miRNAs and Hypermethylated miRNA Genes in Crucial Oncogenic Pathways and Processes. Front Genet 2019; 10:320. [PMID: 31110513 PMCID: PMC6499217 DOI: 10.3389/fgene.2019.00320] [Citation(s) in RCA: 57] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2018] [Accepted: 03/22/2019] [Indexed: 12/13/2022] Open
Abstract
Clear cell renal cell carcinoma (ccRCC) is the third most common urological cancer, and it has the highest mortality rate. The increasing drug resistance of metastatic ccRCC has resulted in the search for new biomarkers. Epigenetic regulatory mechanisms, such as genome-wide DNA methylation and inhibition of protein translation by interaction of microRNA (miRNA) with its target messenger RNA (mRNA), are deeply involved in the pathogenesis of human cancers, including ccRCC, and may be used in its diagnosis and prognosis. Here, we review oncogenic and oncosuppressive miRNAs, their putative target genes, and the crucial pathways they are involved in. The contradictory behavior of a number of miRNAs, such as suppressive and anti-metastatic miRNAs with oncogenic potential (for example, miR-99a, miR-106a, miR-125b, miR-144, miR-203, miR-378), is examined. miRNAs that contribute mostly to important pathways and processes in ccRCC, for instance, PI3K/AKT/mTOR, Wnt-β, histone modification, and chromatin remodeling, are discussed in detail. We also separately consider their participation in crucial oncogenic processes, such as hypoxia and angiogenesis, metastasis, and epithelial-mesenchymal transition (EMT). The review also considers the interactions of long non-coding RNAs (lncRNAs) and miRNAs of significance in ccRCC. Recent advances in the understanding of the role of hypermethylated miRNA genes in ccRCC and their usefulness as biomarkers are reviewed based on our own data and those available in the literature. Finally, new data and perspectives concerning the clinical applications of miRNAs in the diagnosis, prognosis, and treatment of ccRCC are discussed.
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Affiliation(s)
| | - Marina V. Fridman
- Vavilov Institute of General Genetics, Russian Academy of Sciences, Moscow, Russia
| | - Vitaly I. Loginov
- Institute of General Pathology and Pathophysiology, Moscow, Russia
- Research Center of Medical Genetics, Moscow, Russia
| | - Alexey A. Dmitriev
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
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Zhao C, Zhang Y, Popel AS. Mechanistic Computational Models of MicroRNA-Mediated Signaling Networks in Human Diseases. Int J Mol Sci 2019; 20:E421. [PMID: 30669429 PMCID: PMC6358731 DOI: 10.3390/ijms20020421] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2018] [Revised: 01/14/2019] [Accepted: 01/15/2019] [Indexed: 12/17/2022] Open
Abstract
MicroRNAs (miRs) are endogenous non-coding RNA molecules that play important roles in human health and disease by regulating gene expression and cellular processes. In recent years, with the increasing scientific knowledge and new discovery of miRs and their gene targets, as well as the plentiful experimental evidence that shows dysregulation of miRs in a wide variety of human diseases, the computational modeling approach has emerged as an effective tool to help researchers identify novel functional associations between differential miR expression and diseases, dissect the phenotypic expression patterns of miRs in gene regulatory networks, and elucidate the critical roles of miRs in the modulation of disease pathways from mechanistic and quantitative perspectives. Here we will review the recent systems biology studies that employed different kinetic modeling techniques to provide mechanistic insights relating to the regulatory function and therapeutic potential of miRs in human diseases. Some of the key computational aspects to be discussed in detail in this review include (i) models of miR-mediated network motifs in the regulation of gene expression, (ii) models of miR biogenesis and miR⁻target interactions, and (iii) the incorporation of such models into complex disease pathways in order to generate mechanistic, molecular- and systems-level understanding of pathophysiology. Other related bioinformatics tools such as computational platforms that predict miR-disease associations will also be discussed, and we will provide perspectives on the challenges and opportunities in the future development and translational application of data-driven systems biology models that involve miRs and their regulatory pathways in human diseases.
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Affiliation(s)
- Chen Zhao
- Department of Biomedical Engineering, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA.
| | - Yu Zhang
- Department of Biomedical Engineering, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA.
| | - Aleksander S Popel
- Department of Biomedical Engineering, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA.
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Vargas-Asencio JA, Perry KL. A Small RNA-Mediated Regulatory Network in Arabidopsis thaliana Demonstrates Connectivity Between phasiRNA Regulatory Modules and Extensive Co-Regulation of Transcription by miRNAs and phasiRNAs. FRONTIERS IN PLANT SCIENCE 2019; 10:1710. [PMID: 32082334 PMCID: PMC7001039 DOI: 10.3389/fpls.2019.01710] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/02/2019] [Accepted: 12/05/2019] [Indexed: 05/19/2023]
Abstract
Gene regulation involves the orchestrated action of multiple regulators to fine-tune the expression of genes. Hierarchical interactions and co-regulation among regulators are commonly observed in biological systems, leading to complex regulatory networks. Small RNA (sRNAs) have been shown to be important regulators of gene expression due to their involvement in multiple cellular processes. In plants, microRNA (miRNAs) and phased small interfering RNAs (phasiRNAs) correspond to two well-characterized types of sRNAs involved in the regulation of posttranscriptional gene expression, although information about their targets and interactions with other gene expression regulators is limited. We describe an extended sRNA-mediated regulatory network in Arabidopsis thaliana that provides a reference frame to understand sRNA biogenesis and activity at the genome-wide level. This regulatory network combines a comprehensive evaluation of phasiRNA production and sRNA targets supported by degradome data. The network includes ~17% of genes in the A. thaliana genome, representing ~50% annotated gene ontology (GO) functional categories. Approximately 14% of genes with GO annotations corresponding to regulation of gene expression were found to be under sRNA control. The unbiased bioinformatic approach used to produce the network was able to detect 107 PHAS loci (regions of phasiRNA production), 5,047 active phasiRNAs (~70% of which were non-canonical), and reconstruct 17 regulatory modules resulting from complex regulatory interactions between different sRNA-regulatory pathways. Known regulatory modules like miR173-TAS-PPR/TPR and miR390-TAS3-ARF/F-box were faithfully reconstructed and expanded, illustrating the accuracy and sensitivity of the methods and providing confidence for the validity of findings of previously unrecognized modules. The network presented here includes a 2X increase in the number of identified PHAS loci, a large complement (~70%) of non-canonical phasiRNAs, and the most comprehensive evaluation of sRNA cleavage activity in A. thaliana to date. Structural analysis showed similarities to networks of other biological systems and demonstrated connectivity between phasiRNA regulatory modules with extensive co-regulation of transcripts by miRNAs and phasiRNAs. The described regulatory network provides a reference that will facilitate global analyses of individual plant regulatory programs such as those that control homeostasis, development, and responses to biotic and abiotic environmental changes.
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Zhu Y, Xu J, Liang W, Li J, Feng L, Zheng P, Ji T, Bai S. miR-98-5p Alleviated Epithelial-to-Mesenchymal Transition and Renal Fibrosis via Targeting Hmga2 in Diabetic Nephropathy. Int J Endocrinol 2019; 2019:4946181. [PMID: 31885559 PMCID: PMC6925681 DOI: 10.1155/2019/4946181] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/26/2019] [Revised: 08/01/2019] [Accepted: 09/17/2019] [Indexed: 12/13/2022] Open
Abstract
Recently, microRNAs have been recognized as crucial regulators of diabetic nephropathy (DN) development. Epithelial-to-mesenchymal transition (EMT) can play a significant role in tubulointerstitial fibrosis, and it is a hallmark of diabetic nephropathy progression. Nevertheless, the function of miR-98-5p in the modulation of EMT and renal fibrosis during DN remains barely investigated. Hence, identifying the mechanisms of miR-98-5p in regulating EMT and fibrosis is of huge significance. In our present research, decreased miR-98-5p was demonstrated in db/db mice and mice mesangial cells treated with the high dose of glucose. Meanwhile, activated EMT and increased fibrosis was accompanied with the decrease of miR-98-5p in vitro and in vivo. Additionally, to further find out the roles of miR-98-5p in DN development, overexpression of miR-98-5p was applied. Firstly, in vivo investigation exhibited that elevation of miR-98-5p restrained proteinuria, serum creatinine, BUN, the EMT process, and fibrosis. Furthermore, high glucose was able to promote mice mesangial cell proliferation, EMT process, and induced renal fibrosis, which could be prevented by overexpression of miR-98-5p. Moreover, high mobility group A (HMGA2) can exhibit an important role in diverse biological processes. Here, HMGA2 was investigated as a target of miR-98-5p currently. Luciferase reporter assay was conducted and the correlation of miR-98-5p and HMGA2 was validated. Moreover, it was displayed that HMGA2 was remarkably elevated in db/db mice and mice mesangial cells. Furthermore, miR-98-5p strongly depressed HMGA2 protein and mRNA levels in mice mesangial cells. Overall, these revealed miR-98-5p could suppress the EMT process and renal fibrosis through targeting HMGA2 in DN.
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Affiliation(s)
- Yingchun Zhu
- Department of Nephrology, Qingpu Branch of Zhongshan Hospital Affiliated to Fudan University, 1158 Gongyuan East Road, Qingpu District, Shanghai 201700, China
| | - Jiang Xu
- Department of Rehabilitation, Huai'an Second People's Hospital, The Affiliated Hospital of Xuzhou Medical University, Huai'an, China
| | - Wenxing Liang
- Department of Nephrology, Qingpu Branch of Zhongshan Hospital Affiliated to Fudan University, 1158 Gongyuan East Road, Qingpu District, Shanghai 201700, China
| | - Ji Li
- Department of Nephrology, Qingpu Branch of Zhongshan Hospital Affiliated to Fudan University, 1158 Gongyuan East Road, Qingpu District, Shanghai 201700, China
| | - Linhong Feng
- Department of Nephrology, Qingpu Branch of Zhongshan Hospital Affiliated to Fudan University, 1158 Gongyuan East Road, Qingpu District, Shanghai 201700, China
| | - PengXi Zheng
- Department of Nephrology, Qingpu Branch of Zhongshan Hospital Affiliated to Fudan University, 1158 Gongyuan East Road, Qingpu District, Shanghai 201700, China
| | - Tingting Ji
- Department of Nephrology, Qingpu Branch of Zhongshan Hospital Affiliated to Fudan University, 1158 Gongyuan East Road, Qingpu District, Shanghai 201700, China
| | - Shoujun Bai
- Department of Nephrology, Qingpu Branch of Zhongshan Hospital Affiliated to Fudan University, 1158 Gongyuan East Road, Qingpu District, Shanghai 201700, China
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Doronzo G, Astanina E, Corà D, Chiabotto G, Comunanza V, Noghero A, Neri F, Puliafito A, Primo L, Spampanato C, Settembre C, Ballabio A, Camussi G, Oliviero S, Bussolino F. TFEB controls vascular development by regulating the proliferation of endothelial cells. EMBO J 2018; 38:embj.201798250. [PMID: 30591554 PMCID: PMC6356157 DOI: 10.15252/embj.201798250] [Citation(s) in RCA: 50] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2017] [Revised: 11/12/2018] [Accepted: 11/20/2018] [Indexed: 12/30/2022] Open
Abstract
Transcription factor TFEB is thought to control cellular functions—including in the vascular bed—primarily via regulation of lysosomal biogenesis and autophagic flux. Here, we report that TFEB also orchestrates a non‐canonical program that controls the cell cycle/VEGFR2 pathway in the developing vasculature. In endothelial cells, TFEB depletion halts proliferation at the G1‐S transition by inhibiting the CDK4/Rb pathway. TFEB‐deficient cells attempt to compensate for this limitation by increasing VEGFR2 levels at the plasma membrane via microRNA‐mediated mechanisms and controlled membrane trafficking. TFEB stimulates expression of the miR‐15a/16‐1 cluster, which limits VEGFR2 transcript stability and negatively modulates expression of MYO1C, a regulator of VEGFR2 trafficking to the cell surface. Altered levels of miR‐15a/16‐1 and MYO1C in TFEB‐depleted cells cause increased expression of plasma membrane VEGFR2, but in a manner associated with low signaling strength. An endothelium‐specific Tfeb‐knockout mouse model displays defects in fetal and newborn mouse vasculature caused by reduced endothelial proliferation and by anomalous function of the VEGFR2 pathway. These previously unrecognized functions of TFEB expand its role beyond regulation of the autophagic pathway in the vascular system.
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Affiliation(s)
- Gabriella Doronzo
- Department of Oncology, University of Turin, Candiolo, Italy .,Candiolo Cancer Institute-FPO-IRCCS, Candiolo, Italy
| | - Elena Astanina
- Department of Oncology, University of Turin, Candiolo, Italy.,Candiolo Cancer Institute-FPO-IRCCS, Candiolo, Italy
| | - Davide Corà
- Department of Translational Medicine, Piemonte Orientale University, Novara, Italy
| | - Giulia Chiabotto
- Department of Medical Sciences, University of Turin, Turin, Italy
| | - Valentina Comunanza
- Department of Oncology, University of Turin, Candiolo, Italy.,Candiolo Cancer Institute-FPO-IRCCS, Candiolo, Italy
| | - Alessio Noghero
- Department of Oncology, University of Turin, Candiolo, Italy.,Candiolo Cancer Institute-FPO-IRCCS, Candiolo, Italy
| | - Francesco Neri
- Leibniz Institute on Aging - Fritz Lipmann Institute, Jena, Germany
| | - Alberto Puliafito
- Department of Oncology, University of Turin, Candiolo, Italy.,Candiolo Cancer Institute-FPO-IRCCS, Candiolo, Italy
| | - Luca Primo
- Department of Oncology, University of Turin, Candiolo, Italy.,Candiolo Cancer Institute-FPO-IRCCS, Candiolo, Italy
| | - Carmine Spampanato
- Telethon Institute of Genetics and Medicine (TIGEM), Pozzuoli (Naples), Italy.,Department of Translational Medicine, Federico II University, Naples, Italy.,Department of Molecular and Human Genetics, Ian and Dan Duncan Neurological Research Institute, Baylor College of Medicine, Houston, TX, USA
| | - Carmine Settembre
- Telethon Institute of Genetics and Medicine (TIGEM), Pozzuoli (Naples), Italy.,Department of Translational Medicine, Federico II University, Naples, Italy.,Department of Molecular and Human Genetics, Ian and Dan Duncan Neurological Research Institute, Baylor College of Medicine, Houston, TX, USA
| | - Andrea Ballabio
- Telethon Institute of Genetics and Medicine (TIGEM), Pozzuoli (Naples), Italy.,Department of Translational Medicine, Federico II University, Naples, Italy.,Department of Molecular and Human Genetics, Ian and Dan Duncan Neurological Research Institute, Baylor College of Medicine, Houston, TX, USA
| | - Giovanni Camussi
- Department of Medical Sciences, University of Turin, Turin, Italy
| | - Salvatore Oliviero
- Department of Life Sciences and Systems Biology, University of Turin, Turin, Italy
| | - Federico Bussolino
- Department of Oncology, University of Turin, Candiolo, Italy .,Candiolo Cancer Institute-FPO-IRCCS, Candiolo, Italy
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42
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Characterization and expression profiling of microRNAs in response to plant feeding in two host-plant strains of the lepidopteran pest Spodoptera frugiperda. BMC Genomics 2018; 19:804. [PMID: 30400811 PMCID: PMC6219076 DOI: 10.1186/s12864-018-5119-6] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2018] [Accepted: 09/26/2018] [Indexed: 02/06/2023] Open
Abstract
Background A change in the environment may impair development or survival of living organisms leading them to adapt to the change. The resulting adaptation trait may reverse, or become fixed in the population leading to evolution of species. Deciphering the molecular basis of adaptive traits can thus give evolutionary clues. In phytophagous insects, a change in host-plant range can lead to emergence of new species. Among them, Spodoptera frugiperda is a major agricultural lepidopteran pest consisting of two host-plant strains having diverged 3 MA, based on mitochondrial markers. In this paper, we address the role of microRNAs, important gene expression regulators, in response to host-plant change and in adaptive evolution. Results Using small RNA sequencing, we characterized miRNA repertoires of the corn (C) and rice (R) strains of S. frugiperda, expressed during larval development on two different host-plants, corn and rice, in the frame of reciprocal transplant experiments. We provide evidence for 76 and 68 known miRNAs in C and R strains and 139 and 171 novel miRNAs. Based on read counts analysis, 34 of the microRNAs were differentially expressed in the C strain larvae fed on rice as compared to the C strain larvae fed on corn. Twenty one were differentially expressed on rice compared to corn in R strain. Nine were differentially expressed in the R strain compared to C strain when reared on corn. A similar ratio of microRNAs was differentially expressed between strains on rice. We could validate experimentally by QPCR, variation in expression of the most differentially expressed candidates. We used bioinformatics methods to determine the target mRNAs of known microRNAs. Comparison with the mRNA expression profile during similar reciprocal transplant experiment revealed potential mRNA targets of these host-plant regulated miRNAs. Conclusions In the current study, we performed the first systematic analysis of miRNAs in Lepidopteran pests feeding on host-plants. We identified a set of the differentially expressed miRNAs that respond to the plant diet, or differ constitutively between the two host plant strains. Among the latter, the ones that are also deregulated in response to host-plant are molecular candidates underlying a complex adaptive trait. Electronic supplementary material The online version of this article (10.1186/s12864-018-5119-6) contains supplementary material, which is available to authorized users.
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Migliore C, Morando E, Ghiso E, Anastasi S, Leoni VP, Apicella M, Cora' D, Sapino A, Pietrantonio F, De Braud F, Columbano A, Segatto O, Giordano S. miR-205 mediates adaptive resistance to MET inhibition via ERRFI1 targeting and raised EGFR signaling. EMBO Mol Med 2018; 10:e8746. [PMID: 30021798 PMCID: PMC6127885 DOI: 10.15252/emmm.201708746] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2017] [Revised: 06/25/2018] [Accepted: 06/27/2018] [Indexed: 12/24/2022] Open
Abstract
The onset of secondary resistance represents a major limitation to long-term efficacy of target therapies in cancer patients. Thus, the identification of mechanisms mediating secondary resistance is the key to the rational design of therapeutic strategies for resistant patients. MiRNA profiling combined with RNA-Seq in MET-addicted cancer cell lines led us to identify the miR-205/ERRFI1 (ERBB receptor feedback inhibitor-1) axis as a novel mediator of resistance to MET tyrosine kinase inhibitors (TKIs). In cells resistant to MET-TKIs, epigenetically induced miR-205 expression determined the downregulation of ERRFI1 which, in turn, caused EGFR activation, sustaining resistance to MET-TKIs. Anti-miR-205 transduction reverted crizotinib resistance in vivo, while miR-205 over-expression rendered wt cells refractory to TKI treatment. Importantly, in the absence of EGFR genetic alterations, miR-205/ERRFI1-driven EGFR activation rendered MET-TKI-resistant cells sensitive to combined MET/EGFR inhibition. As a proof of concept of the clinical relevance of this new mechanism of adaptive resistance, we report that a patient with a MET-amplified lung adenocarcinoma displayed deregulation of the miR-205/ERRFI1 axis in concomitance with onset of clinical resistance to anti-MET therapy.
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Affiliation(s)
- Cristina Migliore
- Department of Oncology, University of Torino, Candiolo, Italy
- Candiolo Cancer Institute, FPO-IRCCS, Candiolo, Italy
| | - Elena Morando
- Candiolo Cancer Institute, FPO-IRCCS, Candiolo, Italy
| | - Elena Ghiso
- Candiolo Cancer Institute, FPO-IRCCS, Candiolo, Italy
| | - Sergio Anastasi
- Unit of Oncogenomics and Epigenetics, IRCCS Regina Elena National Cancer Institute, Rome, Italy
| | - Vera P Leoni
- Department of Biomedical Sciences, Unit of Oncology and Molecular Pathology, University of Cagliari, Cagliari, Italy
| | | | - Davide Cora'
- Department of Oncology, University of Torino, Candiolo, Italy
- Candiolo Cancer Institute, FPO-IRCCS, Candiolo, Italy
- Department of Translational Medicine, Piemonte Orientale University "Amedeo Avogadro", Novara, Italy
| | - Anna Sapino
- Candiolo Cancer Institute, FPO-IRCCS, Candiolo, Italy
- Department of Medical Science, University of Torino, Torino, Italy
| | - Filippo Pietrantonio
- Medical Oncology, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
- Department of Oncology and Hemato-oncology, University of Milano, Milan, Italy
| | - Filippo De Braud
- Medical Oncology, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
- Department of Oncology and Hemato-oncology, University of Milano, Milan, Italy
| | - Amedeo Columbano
- Department of Biomedical Sciences, Unit of Oncology and Molecular Pathology, University of Cagliari, Cagliari, Italy
| | - Oreste Segatto
- Unit of Oncogenomics and Epigenetics, IRCCS Regina Elena National Cancer Institute, Rome, Italy
| | - Silvia Giordano
- Department of Oncology, University of Torino, Candiolo, Italy
- Candiolo Cancer Institute, FPO-IRCCS, Candiolo, Italy
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Bros M, Youns M, Kollek V, Buchmüller D, Bollmann F, Seo EJ, Schupp J, Montermann E, Usanova S, Kleinert H, Efferth T, Reske-Kunz AB. Differentially Tolerized Mouse Antigen Presenting Cells Share a Common miRNA Signature Including Enhanced mmu-miR-223-3p Expression Which Is Sufficient to Imprint a Protolerogenic State. Front Pharmacol 2018; 9:915. [PMID: 30174602 PMCID: PMC6108336 DOI: 10.3389/fphar.2018.00915] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2018] [Accepted: 07/26/2018] [Indexed: 12/13/2022] Open
Abstract
Dendritic cells (DCs) are pivotal for the induction and maintenance of antigen-specific tolerance and immunity. miRNAs mediate post-transcriptional gene regulation and control in part the differentiation and stimulation-induced immunogenic function of DCs. However, the relevance of miRNAs for the induction and maintenance of a tolerogenic state of DCs has scarcely been highlighted yet. We differentiated mouse bone marrow cells to conventional/myeloid DCs or to tolerogenic antigen presenting cells (APCs) by using a glucocorticoid (dexamethasone) or interleukin-10, and assessed the miRNA expression patterns of unstimulated and LPS-stimulated cell populations by array analysis and QPCR. Differentially tolerized mouse APCs convergingly down-regulated a set of miRNA species at either state of activation as compared with the corresponding control DC population (mmu-miR-9-5p, mmu-miR-9-3p, mmu-miR-155-5p). These miRNAs were also upregulated in control DCs in response to stimulation. In contrast, miRNAs that were convergingly upregulated in both tolerized APC groups at stimulated state (mmu-miR-223-3p, mmu-miR-1224-5p) were downregulated in control DCs in response to stimulation. Overexpression of mmu-miR-223-3p in DCs was sufficient to prevent stimulation-associated acquisition of potent T cell stimulatory capacity. Overexpression of mmu-miR-223-3p in a DC line resulted in attenuated expression of known (Cflar, Rasa1, Ras) mRNA targets of this miRNA species shown to affect pathways that control DC activation. Taken together, we identified sets of miRNAs convergingly regulated in differentially tolerized APCs, which may contribute to imprint stimulation-resistant tolerogenic function as demonstrated for mmu-miR-223-3p. Knowledge of miRNAs with protolerogenic function enables immunotherapeutic approaches aimed to modulate immune responses by regulating miRNA expression.
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Affiliation(s)
- Matthias Bros
- Department of Dermatology, University Medical Center, Johannes Gutenberg University, Mainz, Germany
| | - Mahmoud Youns
- Department of Biochemistry and Molecular Biology, Faculty of Pharmacy, Helwan University, Cairo, Egypt
| | - Verena Kollek
- Department of Dermatology, University Medical Center, Johannes Gutenberg University, Mainz, Germany
| | - Diana Buchmüller
- Department of Dermatology, University Medical Center, Johannes Gutenberg University, Mainz, Germany
| | - Franziska Bollmann
- Department of Pharmacology, University Medical Center, Johannes Gutenberg University, Mainz, Germany
| | - Ean-Jeong Seo
- Department of Biochemistry and Molecular Biology, Faculty of Pharmacy, Helwan University, Cairo, Egypt
| | - Jonathan Schupp
- Department of Dermatology, University Medical Center, Johannes Gutenberg University, Mainz, Germany
| | - Evelyn Montermann
- Department of Dermatology, University Medical Center, Johannes Gutenberg University, Mainz, Germany
| | - Svetlana Usanova
- Department of Dermatology, University Medical Center, Johannes Gutenberg University, Mainz, Germany
| | - Hartmut Kleinert
- Department of Pharmacology, University Medical Center, Johannes Gutenberg University, Mainz, Germany
| | - Thomas Efferth
- Department of Biochemistry and Molecular Biology, Faculty of Pharmacy, Helwan University, Cairo, Egypt
| | - Angelika B Reske-Kunz
- Department of Dermatology, University Medical Center, Johannes Gutenberg University, Mainz, Germany
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Loginov VI, Filippova EA, Kurevlev SV, Fridman MV, Burdennyy AM, Braga EA. Suppressive and Hypermethylated MicroRNAs in the Pathogenesis of Breast Cancer. RUSS J GENET+ 2018. [DOI: 10.1134/s1022795418070086] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
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Zhao Y, Ma K, Yang S, Zhang X, Wang F, Zhang X, Liu H, Fan Q. MicroRNA-125a-5p enhances the sensitivity of esophageal squamous cell carcinoma cells to cisplatin by suppressing the activation of the STAT3 signaling pathway. Int J Oncol 2018; 53:644-658. [PMID: 29767234 PMCID: PMC6017156 DOI: 10.3892/ijo.2018.4409] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2018] [Accepted: 05/09/2018] [Indexed: 02/06/2023] Open
Abstract
Increasing evidence has demonstrated that microRNAs (miRNAs or miRs) play a variety of roles in tumor development, progression and chemosensitivity in a wide range of tumors. In this study, we found that miR-125a-5p exhibited a low expression in esophageal squamous cell carcinoma (ESCC) tissues and cells, and that its low expression was associated with higher tumor staging and shorter a survival time of patients with ESCC. Moreover, miR-125a-5p overexpression contributed to the suppression of cell proliferation, cell cycle arrest, cell apoptosis and a decrease in cell migratory and invasive abilities, whereas the downregulation of miR-125a-5p promoted cell proliferation, accelerated cell cycle progression, suppressed apoptosis and enhanced the migratory and invasive abilities of ESCC EC1 and TE1 cells, which may be tightly associated with the epithelial-mesenchymal transition (EMT) process in ESCC. Importantly, miR-125a-5p enhanced the cytotoxic effects of cisplatin on EC1 and TE1 cells, and co-treatment with miR-125a-5p and cisplatin significantly induced cell apoptosis and reduced the cell migratory and invasive abilities of EC1 and TE1 cells, coupled with an increase in the E-cadherin level and a decrease in the N-cadherin and Vimentin levels. Most notably, signal transducer and activator of transcription-3 (STAT3) was found to be a direct target of miR-125a-5p in ESCC cells, and miR-125a-5p overexpression significantly reduced the protein levels of t-STAT3, p-STAT3 and vascular endothelial growth factor (VEGF) in EC1 and TE1 cells. Furthermore, the combination of miR-125a-5p and cisplatin markedly inactivated the STAT3 signaling pathway; however, interleukin (IL)-6, a widely reported activator of the STAT3 signaling pathway, reversed the suppressive effects of miR-125a-5p/cisplatin in ESCC cells on the activation of the STAT3 signaling pathway. Of note, we found that IL-6 markedly reversed the altered cell phenotype mediated by the combination of miR-125a-5p and cisplatin in ESCC cells. These findings suggest that miR-125a-5p may play a pivotal role in the development and progression of ESCC, which may be achieved via the manipulation of the STAT3 signaling pathway.
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Affiliation(s)
- Yan Zhao
- Department of Oncology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan 450052, P.R. China
| | - Ke Ma
- College of Traditional Chinese Medicine, Shandong University of Traditional Chinese Medicine, Jinan, Shandong 250355, P.R. China
| | - Shujun Yang
- Department of Oncology, The Affiliated Cancer Hospital of Zhengzhou University, Zhengzhou, Henan 450003, P.R. China
| | - Xiaosan Zhang
- Department of Oncology, The Affiliated Cancer Hospital of Zhengzhou University, Zhengzhou, Henan 450003, P.R. China
| | - Feng Wang
- Department of Oncology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan 450052, P.R. China
| | - Xiaqing Zhang
- College of Life Sciences, Zhengzhou University, Zhengzhou, Henan 450001, P.R. China
| | - Hongtao Liu
- College of Life Sciences, Zhengzhou University, Zhengzhou, Henan 450001, P.R. China
| | - Qingxia Fan
- Department of Oncology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan 450052, P.R. China
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Cao Y, Shi X, Liu Y, Xu R, Ai Q. MicroRNA-338-3p Inhibits Proliferation and Promotes Apoptosis of Multiple Myeloma Cells Through Targeting Cyclin-Dependent Kinase 4. Oncol Res 2018; 27:117-124. [PMID: 29562955 PMCID: PMC7848273 DOI: 10.3727/096504018x15213031799835] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
MicroRNA-338-3p (miR-338-3p) has been reported to be a tumor suppressor in multiple cancer types. However, the biological role of miR-338-3p and its underlying mechanism in multiple myeloma (MM) remain unclear. In the present study, we investigated the biological role and potential of miR-338-3p in MM. We found that miR-338-3p was significantly decreased in newly diagnosed and relapsed MM tissues and cell lines. Overexpression of miR-338-3p in MM cells significantly inhibited proliferation and promoted apoptosis, caspase 3, and caspase 8 activity. Bioinformatics algorithm analysis predicted that cyclin-dependent kinase 4 (CDK4) was a direct target of miR-338-3p, and this was experimentally verified by a dual-luciferase reporter assay. Furthermore, overexpression of miR-338-3p inhibited CDK4 expression on mRNA and protein levels. Of note, the restoration of CDK4 expression markedly abolished the effect of miR-338-3p overexpression on cell proliferation, apoptosis, caspase 3, and caspase 8 activities in MM cells. Taken together, the present study is the first to demonstrate that miR-338-3p functions as a tumor suppressor in MM through inhibiting CDK4. This finding implies that miR-338-3p is a potential therapeutic target for the treatment of MM.
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Affiliation(s)
- Yang Cao
- Clinical Laboratory, the First Affiliated Hospital, Jilin University, Chaoyang District, Changchun, P.R. China
| | - Xu Shi
- Central Laboratory, the First Affiliated Hospital, Jilin University, Chaoyang District, Changchun, P.R. China
| | - Yingmin Liu
- Department of Hematology Cancer Center, the First Affiliated Hospital, Jilin University, Chaoyang District, Changchun, P.R. China
| | - Ren Xu
- Department of Respiratory, the First Affiliated Hospital, Jilin University, Chaoyang District, Changchun, P.R. China
| | - Qing Ai
- Clinical Laboratory, the First Affiliated Hospital, Jilin University, Chaoyang District, Changchun, P.R. China
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48
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Zhang H, Zhang L, Sun T. Cohesive Regulation of Neural Progenitor Development by microRNA miR-26, Its Host Gene Ctdsp and Target Gene Emx2 in the Mouse Embryonic Cerebral Cortex. Front Mol Neurosci 2018. [PMID: 29515367 PMCID: PMC5825903 DOI: 10.3389/fnmol.2018.00044] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Proper proliferation and differentiation of neural progenitors (NPs) in the developing cerebral cortex are critical for normal brain formation and function. Emerging evidence has shown the importance of microRNAs (miRNAs) in regulating cortical development and the etiology of neurological disorders. Here we show that miR-26 is co-expressed with its host gene Ctdsp in the mouse embryonic cortex. We demonstrate that similar to its host gene Ctdsp2, miR-26 positively regulates proliferation of NPs through controlling the cell-cycle progression, by using miR-26 overexpression and sponge approaches. On the contrary, miR-26 target gene Emx2 limits expansion of cortical NPs, and promotes transcription of miR-26 host gene Ctdsp. Our study suggests that miR-26, its target Emx2 and its host gene Ctdsp cohesively regulate proliferation of NPs during the mouse cortical development.
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Affiliation(s)
- Haijun Zhang
- Department of Cell and Developmental Biology, Weill Cornell Medical College, Cornell University, New York, NY, United States.,Department of Genetic Medicine, Weill Cornell Medical College, Cornell University, New York, NY, United States
| | - Longbin Zhang
- Center for Precision Medicine, School of Medicine and School of Biomedical Sciences, Huaqiao University, Xiamen, China
| | - Tao Sun
- Department of Cell and Developmental Biology, Weill Cornell Medical College, Cornell University, New York, NY, United States.,Center for Precision Medicine, School of Medicine and School of Biomedical Sciences, Huaqiao University, Xiamen, China
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Corella D, Coltell O, Macian F, Ordovás JM. Advances in Understanding the Molecular Basis of the Mediterranean Diet Effect. Annu Rev Food Sci Technol 2018; 9:227-249. [PMID: 29400994 DOI: 10.1146/annurev-food-032217-020802] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Increasingly, studies showing the protective effects of the Mediterranean diet (MedDiet) on different diseases (cardiovascular, diabetes, some cancers, and even total mortality and aging indicators) are being published. The scientific evidence level for each outcome is variable, and new studies are needed to better understand the molecular mechanisms whereby the MedDiet may exercise its effects. Here, we present recent advances in understanding the molecular basis of MedDiet effects, mainly focusing on cardiovascular diseases but also discussing other related diseases. There is heterogeneity in defining the MedDiet, and it can, owing to its complexity, be considered as an exposome with thousands of nutrients and phytochemicals. We review MedDiet composition and assessment as well as the latest advances in the genomic, epigenomic (DNA methylation, histone modifications, microRNAs, and other emerging regulators), transcriptomic (selected genes and whole transcriptome), and metabolomic and metagenomic aspects of the MedDiet effects (as a whole and for its most typical food components). We also present a critical review of the limitations of the studies undertaken and propose new analyses and greater bioinformatic integration to better understand the most important molecular mechanisms whereby the MedDiet as a whole, or its main food components, may exercise their protective effects.
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Affiliation(s)
- Dolores Corella
- Department of Preventive Medicine and Public Health, School of Medicine, University of Valencia, Valencia, 46010, Spain; .,CIBER Fisiopatología de la Obesidad y Nutrición, Instituto de Salud Carlos III, Madrid, 28029, Spain
| | - Oscar Coltell
- CIBER Fisiopatología de la Obesidad y Nutrición, Instituto de Salud Carlos III, Madrid, 28029, Spain.,Department of Computer Languages and Systems, School of Technology and Experimental Sciences, Universitat Jaume I, Castellón, 12071, Spain
| | - Fernando Macian
- Department of Pathology, Albert Einstein College of Medicine, New York, NY 10461, USA
| | - José M Ordovás
- Nutrition and Genomics Laboratory, JM-USDA Human Nutrition Research Center on Aging, Tufts University, Boston, Massachusetts 02111, USA.,Department of Cardiovascular Epidemiology and Population Genetics, Centro Nacional de Investigaciones Cardiovasculares (CNIC), Madrid, 28029, Spain.,IMDEA Alimentación, Madrid, 28049, Spain
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Methods for Using Small Non-Coding RNAs to Improve Recombinant Protein Expression in Mammalian Cells. Genes (Basel) 2018; 9:genes9010025. [PMID: 29315258 PMCID: PMC5793178 DOI: 10.3390/genes9010025] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2017] [Revised: 12/19/2017] [Accepted: 01/03/2018] [Indexed: 12/27/2022] Open
Abstract
The ability to produce recombinant proteins by utilizing different “cell factories” revolutionized the biotherapeutic and pharmaceutical industry. Chinese hamster ovary (CHO) cells are the dominant industrial producer, especially for antibodies. Human embryonic kidney cells (HEK), while not being as widely used as CHO cells, are used where CHO cells are unable to meet the needs for expression, such as growth factors. Therefore, improving recombinant protein expression from mammalian cells is a priority, and continuing effort is being devoted to this topic. Non-coding RNAs are RNA segments that are not translated into a protein and often have a regulatory role. Since their discovery, major progress has been made towards understanding their functions. Non-coding RNA has been investigated extensively in relation to disease, especially cancer, and recently they have also been used as a method for engineering cells to improve their protein expression capability. In this review, we provide information about methods used to identify non-coding RNAs with the potential of improving recombinant protein expression in mammalian cell lines.
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