1
|
Del Val C, Díaz de la Guardia-Bolívar E, Zwir I, Mishra PP, Mesa A, Salas R, Poblete GF, de Erausquin G, Raitoharju E, Kähönen M, Raitakari O, Keltikangas-Järvinen L, Lehtimäki T, Cloninger CR. Gene expression networks regulated by human personality. Mol Psychiatry 2024; 29:2241-2260. [PMID: 38433276 PMCID: PMC11408262 DOI: 10.1038/s41380-024-02484-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/02/2023] [Revised: 02/03/2024] [Accepted: 02/08/2024] [Indexed: 03/05/2024]
Abstract
Genome-wide association studies of human personality have been carried out, but transcription of the whole genome has not been studied in relation to personality in humans. We collected genome-wide expression profiles of adults to characterize the regulation of expression and function in genes related to human personality. We devised an innovative multi-omic approach to network analysis to identify the key control elements and interactions in multi-modular networks. We identified sets of transcribed genes that were co-expressed in specific brain regions with genes known to be associated with personality. Then we identified the minimum networks for the co-localized genes using bioinformatic resources. Subjects were 459 adults from the Young Finns Study who completed the Temperament and Character Inventory and provided peripheral blood for genomic and transcriptomic analysis. We identified an extrinsic network of 45 regulatory genes from seed genes in brain regions involved in self-regulation of emotional reactivity to extracellular stimuli (e.g., self-regulation of anxiety) and an intrinsic network of 43 regulatory genes from seed genes in brain regions involved in self-regulation of interpretations of meaning (e.g., production of concepts and language). We discovered that interactions between the two networks were coordinated by a control hub of 3 miRNAs and 3 protein-coding genes shared by both. Interactions of the control hub with proteins and ncRNAs identified more than 100 genes that overlap directly with known personality-related genes and more than another 4000 genes that interact indirectly. We conclude that the six-gene hub is the crux of an integrative network that orchestrates information-transfer throughout a multi-modular system of over 4000 genes enriched in liquid-liquid-phase-separation (LLPS)-related RNAs, diverse transcription factors, and hominid-specific miRNAs and lncRNAs. Gene expression networks associated with human personality regulate neuronal plasticity, epigenesis, and adaptive functioning by the interactions of salience and meaning in self-awareness.
Collapse
Affiliation(s)
- Coral Del Val
- University of Granada, Department of Computer Science and Artificial Intelligence, Andalusian Research Institute in Data Science and Computational Intelligence, Granada, Spain
- Instituto de Investigación Biosanitaria de Granada (ibs. GRANADA), Granada, Spain
| | - Elisa Díaz de la Guardia-Bolívar
- University of Granada, Department of Computer Science and Artificial Intelligence, Andalusian Research Institute in Data Science and Computational Intelligence, Granada, Spain
| | - Igor Zwir
- University of Granada, Department of Computer Science and Artificial Intelligence, Andalusian Research Institute in Data Science and Computational Intelligence, Granada, Spain
- Washington University School of Medicine, Department of Psychiatry, St. Louis, MO, USA
| | - Pashupati P Mishra
- Tampere University, Department of Clinical Chemistry, Fimlab Laboratories, and Finnish Cardiovascular Research Center - Tampere, Faculty of Medicine and Health Technology, Tampere, Finland
| | - Alberto Mesa
- University of Granada, Department of Computer Science and Artificial Intelligence, Andalusian Research Institute in Data Science and Computational Intelligence, Granada, Spain
| | - Ramiro Salas
- The Menninger Clinic, Baylor College of Medicine, and DeBakey VA Medical Center, Houston, TX, USA
| | | | - Gabriel de Erausquin
- University of Texas Health San Antonio, Long School of Medicine, Department of Neurology, Biggs Institute of Alzheimer's & Neurodegenerative Disorders, San Antonio, TX, USA
| | - Emma Raitoharju
- Tampere University, Department of Clinical Chemistry, Fimlab Laboratories, and Finnish Cardiovascular Research Center - Tampere, Faculty of Medicine and Health Technology, Tampere, Finland
| | - Mika Kähönen
- Department of Clinical Physiology, Tampere University Hospital, and Finnish Cardiovascular Research Center - Tampere, Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
| | - Olli Raitakari
- University of Turku and Turku University Hospital, Center for Population Health Research; University of Turku, Research Center of Applied and Preventive Cardiovascular Medicine; Turku University Hospital, Department of Clinical Physiology and Nuclear Medicine, Turku, Finland
| | | | - Terho Lehtimäki
- Tampere University, Department of Clinical Chemistry, Fimlab Laboratories, and Finnish Cardiovascular Research Center - Tampere, Faculty of Medicine and Health Technology, Tampere, Finland
| | | |
Collapse
|
2
|
Shibamoto A, Kitsu Y, Shibata K, Kaneko Y, Moriizumi H, Takahashi T. microRNA-guided immunity against respiratory virus infection in human and mouse lung cells. Biol Open 2024; 13:bio060172. [PMID: 38875000 PMCID: PMC11212637 DOI: 10.1242/bio.060172] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2023] [Accepted: 05/16/2024] [Indexed: 06/15/2024] Open
Abstract
Viral infectivity depends on multiple factors. Recent studies showed that the interaction between viral RNAs and endogenous microRNAs (miRNAs) regulates viral infectivity; viral RNAs function as a sponge of endogenous miRNAs and result in upregulation of its original target genes, while endogenous miRNAs target viral RNAs directly and result in repression of viral gene expression. In this study, we analyzed the possible interaction between parainfluenza virus RNA and endogenous miRNAs in human and mouse lungs. We showed that the parainfluenza virus can form base pairs with human miRNAs abundantly than mouse miRNAs. Furthermore, we analyzed that the sponge effect of endogenous miRNAs on viral RNAs may induce the upregulation of transcription regulatory factors. Then, we performed RNA-sequence analysis and observed the upregulation of transcription regulatory factors in the early stages of parainfluenza virus infection. Our studies showed how the differential expression of endogenous miRNAs in lungs could contribute to respiratory virus infection and species- or tissue-specific mechanisms and common mechanisms could be conserved in humans and mice and regulated by miRNAs during viral infection.
Collapse
Affiliation(s)
- Ayaka Shibamoto
- Department of Biochemistry and Molecular Biology, Faculty of Science, Saitama University, Saitama 338-8570, Japan
| | - Yoshiaki Kitsu
- Department of Biochemistry and Molecular Biology, Faculty of Science, Saitama University, Saitama 338-8570, Japan
| | - Keiko Shibata
- Department of Biochemistry and Molecular Biology, Graduate School of Science and Engineering, Saitama University, Saitama 338-8570, Japan
| | - Yuka Kaneko
- Department of Biochemistry and Molecular Biology, Graduate School of Science and Engineering, Saitama University, Saitama 338-8570, Japan
| | - Harune Moriizumi
- Department of Biochemistry and Molecular Biology, Graduate School of Science and Engineering, Saitama University, Saitama 338-8570, Japan
| | - Tomoko Takahashi
- Department of Biochemistry and Molecular Biology, Faculty of Science, Saitama University, Saitama 338-8570, Japan
- Department of Biochemistry and Molecular Biology, Graduate School of Science and Engineering, Saitama University, Saitama 338-8570, Japan
| |
Collapse
|
3
|
Srivastava S, Garg I, Ghosh N, Varshney R. Therapeutic implication of MicroRNA-320a antagonist in attenuating blood clots formed during venous thrombosis. J Thromb Thrombolysis 2024; 57:699-709. [PMID: 38393674 DOI: 10.1007/s11239-024-02947-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 12/31/2023] [Indexed: 02/25/2024]
Abstract
Venous thrombosis (VT) is a complex multi-factorial disease and a major health concern worldwide. Its clinical implications include deep vein thrombosis (DVT) and pulmonary embolism (PE). VT pathogenesis involves intricate interplay of various coagulants and anti-coagulants. Growing evidences from epidemiological studies have shown that many non-coding microRNAs play significant regulatory role in VT pathogenesis by modulating expressions of large number of gene involved in blood coagulation. Present study aimed to investigate the effect of human micro RNA (hsa-miR)-320a antagonist on thrombus formation in VT. Surgery was performed on Sprague-Dawley (SD) rats, wherein the inferior vena cava (IVC) was ligated to introduce DVT. Animals were divided into four groups (n = 5 in each group); Sham controls (Sham), IVC ligated-DVT (DVT), IVC ligated-DVT + transfection reagent (DVT-NC) and IVC ligated-DVT + miR320a antagonist (DVT-miR-320a antagonist). IVC was dissected after 6 h and 24 h of surgery to estimate thrombus weight and coagulatory parameters such as levels of D-dimer, clotting time and bleeding time. Also, ELISA based biochemical assays were formed to assess toxicity of miRNA antagonist in animals. Our experimental analysis demonstrated that there was a marked reduction in size of thrombus in hsa-miR-320a antagonist treated animals, both at 6 h and 24 h. There was a marked reduction in D-dimer levels in hsa-miR-320a antagonist treated animals. Also, blood clotting time was delayed and bleeding time was increased significantly in hsa-miR-320a antagonist treated rats compared to the non-treated and Sham rats. There was no sign of toxicity in treated group compared to control animals. Hsa-miR-320a antagonist could be promising therapeutic target for management of VT.
Collapse
Affiliation(s)
- Swati Srivastava
- Pathophysiology and Disruptive Technology Division (PDT), Defence Research and Development Organization (DRDO), Defence Institute of Physiology and Allied Sciences (DIPAS), Lucknow Road, Timarpur, Delhi, 110054, India.
| | - Iti Garg
- Pathophysiology and Disruptive Technology Division (PDT), Defence Research and Development Organization (DRDO), Defence Institute of Physiology and Allied Sciences (DIPAS), Lucknow Road, Timarpur, Delhi, 110054, India
| | - Nilanjana Ghosh
- Pathophysiology and Disruptive Technology Division (PDT), Defence Research and Development Organization (DRDO), Defence Institute of Physiology and Allied Sciences (DIPAS), Lucknow Road, Timarpur, Delhi, 110054, India
| | - Rajeev Varshney
- Pathophysiology and Disruptive Technology Division (PDT), Defence Research and Development Organization (DRDO), Defence Institute of Physiology and Allied Sciences (DIPAS), Lucknow Road, Timarpur, Delhi, 110054, India
| |
Collapse
|
4
|
Zhang J, Yu X, Guo Y, Wang D. HPV16 E6 promoting cervical cancer progression through down-regulation of miR-320a to increase TOP2A expression. Cancer Med 2024; 13:e6875. [PMID: 38205938 PMCID: PMC10905336 DOI: 10.1002/cam4.6875] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2023] [Revised: 12/10/2023] [Accepted: 12/13/2023] [Indexed: 01/12/2024] Open
Abstract
BACKGROUND Cervical cancer (CC) has become the fourth most common cancer worldwide and it is mainly caused by the infection of human papillomavirus (HPV), especially high-risk HPV16. Aberrant miRNA expression in CC is closely related to HPV16 infection, and the regulation of HPV16 E6 expression can affect a variety of miRNA expression. This study aims to exploring the miRNAs involved in E6 regulation in CC. METHODS Our study screened differentially expressed miRNAs in cervical cells of HPV16 infected and uninfected cervical cancer patients by analyzing the GSE81137 dataset of the gene expression omnibus database (GEO), and identified miR-320a that plays an anti-tumor role and is associated with good prognosis of cervical cancer. Explore the effect of HPV16 E6 on the expression of miR-320a in cervical cancer, and verify whether HPV16 E6 regulates the downstream target gene TOP2A expression through miR-320a, thereby affecting cervical cancer cell proliferation, apoptosis, migration, invasion, and EMT in vitro and in vivo. RESULTS The bioinformatic methods selected the miR-320a, which was differentially expressed in cervical cells from HPV16-infected patients compared to uninfected patients. We further demonstrated that miR-320a level was regulated by HPV16 E6, which promoted the CC cell proliferation, migration, invasion, and inhibited apoptosis. In addition, we predicted the downstream target genes of miR-320a and confirmed that TOP2A was one of its targeting proteins. Moreover, HPV16 E6 promoted the TOP2A expression in CC cells through down-regulating miR-320a, leading to promoting CC development. CONCLUSIONS We confirmed that HPV16 E6 promoted the TOP2A expression through down-regulation of miR-320a, thus promoting CC development, and the HPV16 E6/miR-320a/TOP2A axis may perform as a potential target for CC treatment.
Collapse
Affiliation(s)
- Jianing Zhang
- Department of Gynecology, Dalian Women and Children's Medical Group, Dalian, Liaoning, China
| | - Xiaohui Yu
- Department of Gynecology, Dalian Women and Children's Medical Group, Dalian, Liaoning, China
| | - Yi Guo
- Department of Gynecology, The First Hospital of China Medical University, Shenyang, Liaoning, China
| | - Daqing Wang
- Department of Gynecology, Dalian Women and Children's Medical Group, Dalian, Liaoning, China
| |
Collapse
|
5
|
Gillis RF, Palmour RM. miRNA Expression Analysis of the Hippocampus in a Vervet Monkey Model of Fetal Alcohol Spectrum Disorder Reveals a Potential Role in Global mRNA Downregulation. Brain Sci 2023; 13:934. [PMID: 37371413 DOI: 10.3390/brainsci13060934] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2023] [Revised: 06/03/2023] [Accepted: 06/06/2023] [Indexed: 06/29/2023] Open
Abstract
MicroRNAs (miRNAs) are short-length non-protein-coding RNA sequences that post-transcriptionally regulate gene expression in a broad range of cellular processes including neuro- development and have previously been implicated in fetal alcohol spectrum disorders (FASD). In this study, we use our vervet monkey model of FASD to follow up on a prior multivariate (developmental age × ethanol exposure) mRNA analysis (GSE173516) to explore the possibility that the global mRNA downregulation we observed in that study could be related to miRNA expression and function. We report here a predominance of upregulated and differentially expressed miRNAs. Further, the 24 most upregulated miRNAs were significantly correlated with their predicted targets (Target Scan 7.2). We then explored the relationship between these 24 miRNAs and the fold changes observed in their paired mRNA targets using two prediction platforms (Target Scan 7.2 and miRwalk 3.0). Compared to a list of non-differentially expressed miRNAs from our dataset, the 24 upregulated and differentially expressed miRNAs had a greater impact on the fold changes of their corresponding mRNA targets across both platforms. Taken together, this evidence raises the possibility that ethanol-induced upregulation of specific miRNAs might contribute functionally to the general downregulation of mRNAs observed by multiple investigators in response to prenatal alcohol exposure.
Collapse
Affiliation(s)
- Rob F Gillis
- Department of Human Genetics, Faculty of Medicine and Health Sciences, McGill University, Montreal, QC H3A 0C7, Canada
| | - Roberta M Palmour
- Department of Human Genetics, Faculty of Medicine and Health Sciences, McGill University, Montreal, QC H3A 0C7, Canada
- Department of Psychiatry, Faculty of Medicine and Health Sciences, McGill University, Montreal, QC H3A 0G4, Canada
- Behavioural Science Foundation, Mansion KN 0101, Saint Kitts and Nevis
| |
Collapse
|
6
|
Novak TE, Bailey NP, Stevison LS. Genetic characterization of Macaca arctoides: A highlight of key genes and pathways. Primates 2023:10.1007/s10329-023-01064-x. [PMID: 37142891 DOI: 10.1007/s10329-023-01064-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2022] [Accepted: 03/15/2023] [Indexed: 05/06/2023]
Abstract
When compared to the approximately 22 other macaque species, Macaca arctoides has many unique phenotypes. These traits fall into various phenotypic categories, including genitalia, coloration, mating, and olfactory traits. Here we used a previously identified whole genome set of 690 outlier genes to look for possible genetic explanations of these unique traits. Of these, 279 genes were annotated miRNAs, which are non-coding. Patterns within the remaining outliers in coding genes were investigated using GO (n = 370) and String (n = 383) analysis, which showed many interconnected immune-related genes. Further, we compared the outliers to candidate pathways associated with M. arcotides' unique phenotypes, revealing 10/690 outlier genes that overlapped these four pathways: hedgehog signaling, WNT signaling, olfactory, and melanogenesis. Of these, genes in all pathways except olfactory had higher FST values than the rest of the genes in the genome based on permutation tests. Overall, our results point to many genes each having a small impact on phenotype, working in tandem to cause large systemic changes. Additionally, these results may indicate pleiotropy. This seems to be especially true with the development and coloration of M. arctoides. Our results highlight that development, melanogenesis, immune function, and miRNAs may be heavily involved in M. arctoides' evolutionary history.
Collapse
Affiliation(s)
- Taylor E Novak
- Department of Biological Sciences, Auburn University, Auburn, AL, USA.
| | - Nick P Bailey
- Department of Biological Sciences, Auburn University, Auburn, AL, USA
| | - Laurie S Stevison
- Department of Biological Sciences, Auburn University, Auburn, AL, USA.
| |
Collapse
|
7
|
Vand-Rajabpour F, Savage M, Belote RL, Judson-Torres RL. Critical Considerations for Investigating MicroRNAs during Tumorigenesis: A Case Study in Conceptual and Contextual Nuances of miR-211-5p in Melanoma. EPIGENOMES 2023; 7:9. [PMID: 37218870 PMCID: PMC10204420 DOI: 10.3390/epigenomes7020009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2023] [Revised: 04/11/2023] [Accepted: 04/13/2023] [Indexed: 05/24/2023] Open
Abstract
MicroRNAs are non-coding RNAs fundamental to metazoan development and disease. Although the aberrant regulation of microRNAs during mammalian tumorigenesis is well established, investigations into the contributions of individual microRNAs are wrought with conflicting observations. The underlying cause of these inconsistencies is often attributed to context-specific functions of microRNAs. We propose that consideration of both context-specific factors, as well as underappreciated fundamental concepts of microRNA biology, will permit a more harmonious interpretation of ostensibly diverging data. We discuss the theory that the biological function of microRNAs is to confer robustness to specific cell states. Through this lens, we then consider the role of miR-211-5p in melanoma progression. Using literature review and meta-analyses, we demonstrate how a deep understating of domain-specific contexts is critical for moving toward a concordant understanding of miR-211-5p and other microRNAs in cancer biology.
Collapse
Affiliation(s)
- Fatemeh Vand-Rajabpour
- Department of Medical Genetics, School of Medicine, Tehran University of Medical Sciences, P.O. Box 14155-6447, Tehran 14176-13151, Iran
| | - Meghan Savage
- Department of Oncological Sciences, University of Utah, Salt Lake City, UT 84112, USA
| | - Rachel L. Belote
- Huntsman Cancer Institute, University of Utah, Salt Lake City, UT 84112, USA
| | - Robert L. Judson-Torres
- Department of Oncological Sciences, University of Utah, Salt Lake City, UT 84112, USA
- Huntsman Cancer Institute, University of Utah, Salt Lake City, UT 84112, USA
- Department of Dermatology, University of Utah, Salt Lake City, UT 84112, USA
| |
Collapse
|
8
|
Bovari-Biri J, Garai K, Banfai K, Csongei V, Pongracz JE. miRNAs as Predictors of Barrier Integrity. BIOSENSORS 2023; 13:bios13040422. [PMID: 37185497 PMCID: PMC10136429 DOI: 10.3390/bios13040422] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/24/2023] [Revised: 03/16/2023] [Accepted: 03/21/2023] [Indexed: 05/17/2023]
Abstract
The human body has several barriers that protect its integrity and shield it from mechanical, chemical, and microbial harm. The various barriers include the skin, intestinal and respiratory epithelia, blood-brain barrier (BBB), and immune system. In the present review, the focus is on the physical barriers that are formed by cell layers. The barrier function is influenced by the molecular microenvironment of the cells forming the barriers. The integrity of the barrier cell layers is maintained by the intricate balance of protein expression that is partly regulated by microRNAs (miRNAs) both in the intracellular space and the extracellular microenvironment. The detection of changes in miRNA patterns has become a major focus of diagnostic, prognostic, and disease progression, as well as therapy-response, markers using a great variety of detection systems in recent years. In the present review, we highlight the importance of liquid biopsies in assessing barrier integrity and challenges in differential miRNA detection.
Collapse
Affiliation(s)
- Judit Bovari-Biri
- Department of Pharmaceutical Biotechnology, Faculty of Pharmacy, University of Pecs, 2 Rokus Str, H-7624 Pecs, Hungary
- Szentagothai Research Centre, University of Pecs, 20 Ifjusag Str, H-7624 Pecs, Hungary
| | - Kitti Garai
- Department of Pharmaceutical Biotechnology, Faculty of Pharmacy, University of Pecs, 2 Rokus Str, H-7624 Pecs, Hungary
- Szentagothai Research Centre, University of Pecs, 20 Ifjusag Str, H-7624 Pecs, Hungary
| | - Krisztina Banfai
- Department of Pharmaceutical Biotechnology, Faculty of Pharmacy, University of Pecs, 2 Rokus Str, H-7624 Pecs, Hungary
- Szentagothai Research Centre, University of Pecs, 20 Ifjusag Str, H-7624 Pecs, Hungary
| | - Veronika Csongei
- Department of Pharmaceutical Biotechnology, Faculty of Pharmacy, University of Pecs, 2 Rokus Str, H-7624 Pecs, Hungary
- Szentagothai Research Centre, University of Pecs, 20 Ifjusag Str, H-7624 Pecs, Hungary
| | - Judit E Pongracz
- Department of Pharmaceutical Biotechnology, Faculty of Pharmacy, University of Pecs, 2 Rokus Str, H-7624 Pecs, Hungary
- Szentagothai Research Centre, University of Pecs, 20 Ifjusag Str, H-7624 Pecs, Hungary
| |
Collapse
|
9
|
Akaba Y, Takahashi S, Suzuki K, Kosaki K, Tsujimura K. miR-514a promotes neuronal development in human iPSC-derived neurons. Front Cell Dev Biol 2023; 11:1096463. [PMID: 36824367 PMCID: PMC9941156 DOI: 10.3389/fcell.2023.1096463] [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: 11/12/2022] [Accepted: 01/26/2023] [Indexed: 02/10/2023] Open
Abstract
Proper development and function of the central nervous system require precise regulation of gene expression. MicroRNAs (miRNAs), a group of small non-coding RNAs that can negatively regulate gene expression at the post-transcriptional level, are critical regulators of neuronal development, and dysregulation of microRNAs has been implicated in various neurological disorders. Changes in microRNA expression and repertoire are related to the emergence of social and behavioral variations in closely related primates, including humans, during evolution. MicroRNA-514a (miR-514a) is an X-linked miRNA that is conserved in species with higher social and cognitive functions, and frequent tandem duplications of miR-514a have been found in primate genomes. Here, we demonstrate that miR-514a plays a crucial role in neuronal development in neurons derived from human induced pluripotent stem cells (iPSCs). Overexpression of miR-514a increased dendritic length, soma size, and activity levels of mammalian target of rapamycin (mTOR) signaling in induced pluripotent stem cell-derived neurons, whereas blocking of endogenous miR-514a inhibited neuronal development. Furthermore, we performed a functional analysis of the miR-514a variation found during primate evolution, to investigate the impact of miR-514a sequence variation and associated changes in expression on brain development during evolution. We found that mutation in miR-514a significantly reduced the expression of the mature form and abolished the effects observed when native miR-514a was expressed. Our findings provide new insights into the functional role of miR-514a in the regulation of neuronal development and evolution of primate brain development.
Collapse
Affiliation(s)
- Yuichi Akaba
- Group of Brain Function and Development, Neuroscience Institute of the Graduate School of Science, Nagoya University, Nagoya, Aichi, Japan,Research Unit for Developmental Disorders, Institute for Advanced Research, Nagoya University, Nagoya, Aichi, Japan,Department of Pediatrics, Asahikawa Medical University, Asahikawa, Hokkaido, Japan
| | - Satoru Takahashi
- Department of Pediatrics, Asahikawa Medical University, Asahikawa, Hokkaido, Japan
| | - Keiichiro Suzuki
- Institute for Advanced Co-Creation Studies, Osaka University, Osaka, Japan,Graduate School of Engineering Science, Osaka University, Osaka, Japan,Graduate School of Frontier Bioscience, Osaka University, Osaka, Japan
| | - Kenjiro Kosaki
- Center for Medical Genetics, Keio University School of Medicine, Tokyo, Japan
| | - Keita Tsujimura
- Group of Brain Function and Development, Neuroscience Institute of the Graduate School of Science, Nagoya University, Nagoya, Aichi, Japan,Research Unit for Developmental Disorders, Institute for Advanced Research, Nagoya University, Nagoya, Aichi, Japan,*Correspondence: Keita Tsujimura,
| |
Collapse
|
10
|
Aggio-Bruce R, Schumann U, Cioanca AV, Chen FK, McLenachan S, Heath Jeffery RC, Das S, Natoli R. Serum miRNA modulations indicate changes in retinal morphology. Front Mol Neurosci 2023; 16:1130249. [PMID: 36937046 PMCID: PMC10020626 DOI: 10.3389/fnmol.2023.1130249] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2022] [Accepted: 02/13/2023] [Indexed: 03/06/2023] Open
Abstract
Background Age-related macular degeneration (AMD) is the leading cause of vision loss in the developed world and the detection of its onset and progression are based on retinal morphological assessments. MicroRNA (miRNA) have been explored extensively as biomarkers for a range of neurological diseases including AMD, however differences in experimental design and the complexity of human biology have resulted in little overlap between studies. Using preclinical animal models and clinical samples, this study employs a novel approach to determine a serum signature of AMD progression. Methods Serum miRNAs were extracted from mice exposed to photo-oxidative damage (PD; 0, 1, 3 and 5 days), and clinical samples from patients diagnosed with reticular pseudodrusen or atrophic AMD. The expression of ~800 miRNAs was measured using OpenArray™, and differential abundance from controls was determined using the HTqPCR R package followed by pathway analysis with DAVID. MiRNA expression changes were compared against quantifiable retinal histological indicators. Finally, the overlap of miRNA changes observed in the mouse model and human patient samples was investigated. Results Differential miRNA abundance was identified at all PD time-points and in clinical samples. Importantly, these were associated with inflammatory pathways and histological changes in the retina. Further, we were able to align findings in the mouse serum to those of clinical patients. Conclusion In conclusion, serum miRNAs are a valid tool as diagnostics for the early detection of retinal degeneration, as they reflect key changes in retinal health. The combination of pre-clinical animal models and human patient samples led to the identification of a preliminary serum miRNA signature for AMD. This study is an important platform for the future development of a diagnostic serum miRNA panel for the early detection of retinal degeneration.
Collapse
Affiliation(s)
- Riemke Aggio-Bruce
- The John Curtin School of Medical Research, The Australian National University, Acton, ACT, Australia
- The School of Medicine and Psychology, Acton, ACT, Australia
| | - Ulrike Schumann
- The John Curtin School of Medical Research, The Australian National University, Acton, ACT, Australia
- The Save Sight Institute, Faculty of Medicine and Health, The University of Sydney, Sydney, NSW, Australia
| | - Adrian V. Cioanca
- The John Curtin School of Medical Research, The Australian National University, Acton, ACT, Australia
| | - Fred K. Chen
- Centre of Ophthalmology and Visual Science, The University of Western Australia, Perth, WA, Australia
- Lions Eye Institute, Perth, WA, Australia
- Ophthalmology, Department of Surgery, University of Melbourne, East Melbourne, VIC, Australia
- Centre for Eye Research Australia, Royal Victorian Eye and Ear Hospital, East Melbourne, VIC, Australia
| | - Samuel McLenachan
- Centre of Ophthalmology and Visual Science, The University of Western Australia, Perth, WA, Australia
- Lions Eye Institute, Perth, WA, Australia
| | - Rachael C. Heath Jeffery
- Centre of Ophthalmology and Visual Science, The University of Western Australia, Perth, WA, Australia
- Lions Eye Institute, Perth, WA, Australia
- Centre for Eye Research Australia, Royal Victorian Eye and Ear Hospital, East Melbourne, VIC, Australia
| | - Shannon Das
- The John Curtin School of Medical Research, The Australian National University, Acton, ACT, Australia
| | - Riccardo Natoli
- The John Curtin School of Medical Research, The Australian National University, Acton, ACT, Australia
- The School of Medicine and Psychology, Acton, ACT, Australia
- *Correspondence: Riccardo Natoli,
| |
Collapse
|
11
|
The Role of miRNAs in the Prognosis of Triple-Negative Breast Cancer: A Systematic Review and Meta-Analysis. Diagnostics (Basel) 2022; 13:diagnostics13010127. [PMID: 36611419 PMCID: PMC9818368 DOI: 10.3390/diagnostics13010127] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2022] [Revised: 07/15/2022] [Accepted: 07/18/2022] [Indexed: 01/03/2023] Open
Abstract
Breast cancer is one of the most common malignancies among women around the world. The basal or triple-negative subtype (TNBC) is a heterogeneous group of tumors, characterized by its aggressive and metastatic nature, with low survival and worse prognosis. Research on genetic biomarkers, such as microRNAs (miRs) in TNBC, demonstrate their relevance in the prognosis of the disease. Therefore, the objective of this research was to verify the role of miRs in the prognosis of TNBC. A search was carried out in the PubMed (MEDLINE), Web of Science, and Scopus databases, with articles in the English language from 2010 to 2022. Only articles that analyzed the role of miRNAs in the prognosis of TNBC and that met the criteria of the MOOSE method were included. For the preparation and planning of this systematic review, a PRISMA checklist and the MOOSE method were used. The Newcastle-Ottawa Scale was used to analyze the quality of the included studies. The excluded criteria considered were: (1) studies that presented duplication in the databases; (2) reviews of the literature, clinical case reports, meta-analyses, conference abstracts, letters to the editor, theses, dissertations, and book chapters; (3) studies that stratified only women diagnosed with other subtypes of breast cancer subtypes; (4) experiments without a control or comparison group. After the bibliographic survey of the 2.274 articles found, 43 articles met the inclusion criteria, totaling 5421 patients with TNBC analyzed for this review. Six miRs (miR-155, miR-21, miR-27a/b/, miR-374a/b, miR-30a/c/e, and miR-301a) were included in the meta-analysis. A low expression of miR-155 was associated with reduced overall survival (OS) (HR: 0.68, 95% CI: 0.58-0.81). A high expression of miR-21 was a predictor of OS reduction (HR: 2.56; 95% CI: 1.49-4.40). In addition, high levels of miR-27a/b and miR-301a/b were associated with lower OS, while the decreased expression levels of miR-30 and miR-374a/b were associated with worse relapse-free survival (RFS) and shorter disease-free survival (DFS), respectively. The present study revealed that miRs play essential roles in the development of metastases, in addition to acting as suppressors of the disease, thus improving the prognosis of TNBC. However, the clinical application of these findings has not yet been investigated.
Collapse
|
12
|
Tielke A, Martins H, Pelzl MA, Maaser-Hecker A, David FS, Reinbold CS, Streit F, Sirignano L, Schwarz M, Vedder H, Kammerer-Ciernioch J, Albus M, Borrmann-Hassenbach M, Hautzinger M, Hünten K, Degenhardt F, Fischer SB, Beins EC, Herms S, Hoffmann P, Schulze TG, Witt SH, Rietschel M, Cichon S, Nöthen MM, Schratt G, Forstner AJ. Genetic and functional analyses implicate microRNA 499A in bipolar disorder development. Transl Psychiatry 2022; 12:437. [PMID: 36207305 PMCID: PMC9547016 DOI: 10.1038/s41398-022-02176-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/17/2021] [Revised: 08/10/2022] [Accepted: 09/12/2022] [Indexed: 11/09/2022] Open
Abstract
Bipolar disorder (BD) is a complex mood disorder with a strong genetic component. Recent studies suggest that microRNAs contribute to psychiatric disorder development. In BD, specific candidate microRNAs have been implicated, in particular miR-137, miR-499a, miR-708, miR-1908 and miR-2113. The aim of the present study was to determine the contribution of these five microRNAs to BD development. For this purpose, we performed: (i) gene-based tests of the five microRNA coding genes, using data from a large genome-wide association study of BD; (ii) gene-set analyses of predicted, brain-expressed target genes of the five microRNAs; (iii) resequencing of the five microRNA coding genes in 960 BD patients and 960 controls and (iv) in silico and functional studies for selected variants. Gene-based tests revealed a significant association with BD for MIR499A, MIR708, MIR1908 and MIR2113. Gene-set analyses revealed a significant enrichment of BD associations in the brain-expressed target genes of miR-137 and miR-499a-5p. Resequencing identified 32 distinct rare variants (minor allele frequency < 1%), all of which showed a non-significant numerical overrepresentation in BD patients compared to controls (p = 0.214). Seven rare variants were identified in the predicted stem-loop sequences of MIR499A and MIR2113. These included rs142927919 in MIR2113 (pnom = 0.331) and rs140486571 in MIR499A (pnom = 0.297). In silico analyses predicted that rs140486571 might alter the miR-499a secondary structure. Functional analyses showed that rs140486571 significantly affects miR-499a processing and expression. Our results suggest that MIR499A dysregulation might contribute to BD development. Further research is warranted to elucidate the contribution of the MIR499A regulated network to BD susceptibility.
Collapse
Affiliation(s)
- Aileen Tielke
- grid.10388.320000 0001 2240 3300Institute of Human Genetics, University of Bonn, School of Medicine & University Hospital Bonn, Bonn, Germany ,Salus Clinic Hürth, Hürth, Germany
| | - Helena Martins
- grid.5801.c0000 0001 2156 2780Lab of Systems Neuroscience, Department of Health Science and Technology, Institute for Neuroscience, Swiss Federal Institute of Technology ETH & Neuroscience Center Zurich (ZNZ), Zurich, Switzerland
| | - Michael A. Pelzl
- grid.10253.350000 0004 1936 9756Institute for Physiological Chemistry, Philipps-University Marburg, Marburg, Germany ,grid.10392.390000 0001 2190 1447Present Address: Clinic for Psychiatry and Psychotherapy, Eberhard Karls University Tübingen, Tübingen, Germany
| | - Anna Maaser-Hecker
- grid.10388.320000 0001 2240 3300Institute of Human Genetics, University of Bonn, School of Medicine & University Hospital Bonn, Bonn, Germany
| | - Friederike S. David
- grid.10388.320000 0001 2240 3300Institute of Human Genetics, University of Bonn, School of Medicine & University Hospital Bonn, Bonn, Germany
| | - Céline S. Reinbold
- grid.5510.10000 0004 1936 8921Center for Lifespan Changes in Brain and Cognition (LCBC), Department of Psychology, University of Oslo, Oslo, Norway ,grid.6612.30000 0004 1937 0642Department of Biomedicine, University of Basel, Basel, Switzerland ,grid.410567.1Institute of Medical Genetics and Pathology, University Hospital Basel, Basel, Switzerland
| | - Fabian Streit
- grid.7700.00000 0001 2190 4373Department of Genetic Epidemiology in Psychiatry, Central Institute of Mental Health, Medical Faculty Mannheim, University of Heidelberg, Mannheim, Germany
| | - Lea Sirignano
- grid.7700.00000 0001 2190 4373Department of Genetic Epidemiology in Psychiatry, Central Institute of Mental Health, Medical Faculty Mannheim, University of Heidelberg, Mannheim, Germany
| | | | | | | | - Margot Albus
- grid.419834.30000 0001 0690 3065Isar Amper Klinikum München Ost, kbo, Haar, Germany
| | | | - Martin Hautzinger
- grid.10392.390000 0001 2190 1447Department of Psychology, Clinical Psychology and Psychotherapy, Eberhard Karls University Tübingen, Tübingen, Germany
| | - Karola Hünten
- grid.10388.320000 0001 2240 3300Institute of Human Genetics, University of Bonn, School of Medicine & University Hospital Bonn, Bonn, Germany
| | - Franziska Degenhardt
- grid.10388.320000 0001 2240 3300Institute of Human Genetics, University of Bonn, School of Medicine & University Hospital Bonn, Bonn, Germany ,grid.410718.b0000 0001 0262 7331Department of Child and Adolescent Psychiatry, Psychosomatics and Psychotherapy, University Hospital Essen, University of Duisburg-Essen, Duisburg, Germany
| | - Sascha B. Fischer
- grid.6612.30000 0004 1937 0642Department of Biomedicine, University of Basel, Basel, Switzerland ,grid.410567.1Institute of Medical Genetics and Pathology, University Hospital Basel, Basel, Switzerland
| | - Eva C. Beins
- grid.10388.320000 0001 2240 3300Institute of Human Genetics, University of Bonn, School of Medicine & University Hospital Bonn, Bonn, Germany
| | - Stefan Herms
- grid.10388.320000 0001 2240 3300Institute of Human Genetics, University of Bonn, School of Medicine & University Hospital Bonn, Bonn, Germany ,grid.6612.30000 0004 1937 0642Department of Biomedicine, University of Basel, Basel, Switzerland ,grid.410567.1Institute of Medical Genetics and Pathology, University Hospital Basel, Basel, Switzerland
| | - Per Hoffmann
- grid.10388.320000 0001 2240 3300Institute of Human Genetics, University of Bonn, School of Medicine & University Hospital Bonn, Bonn, Germany ,grid.6612.30000 0004 1937 0642Department of Biomedicine, University of Basel, Basel, Switzerland ,grid.410567.1Institute of Medical Genetics and Pathology, University Hospital Basel, Basel, Switzerland
| | - Thomas G. Schulze
- grid.7700.00000 0001 2190 4373Department of Genetic Epidemiology in Psychiatry, Central Institute of Mental Health, Medical Faculty Mannheim, University of Heidelberg, Mannheim, Germany ,grid.5252.00000 0004 1936 973XInstitute of Psychiatric Phenomics and Genomics (IPPG), University Hospital, LMU Munich, Munich, Germany ,grid.411984.10000 0001 0482 5331Department of Psychiatry and Psychotherapy, University Medical Center Göttingen, Göttingen, Germany
| | - Stephanie H. Witt
- grid.7700.00000 0001 2190 4373Department of Genetic Epidemiology in Psychiatry, Central Institute of Mental Health, Medical Faculty Mannheim, University of Heidelberg, Mannheim, Germany ,grid.7700.00000 0001 2190 4373Center for Innovative Psychiatry and Psychotherapy Research, Central Institute of Mental Health, Medical Faculty Mannheim, University of Heidelberg, Mannheim, Germany
| | - Marcella Rietschel
- grid.7700.00000 0001 2190 4373Department of Genetic Epidemiology in Psychiatry, Central Institute of Mental Health, Medical Faculty Mannheim, University of Heidelberg, Mannheim, Germany
| | - Sven Cichon
- grid.10388.320000 0001 2240 3300Institute of Human Genetics, University of Bonn, School of Medicine & University Hospital Bonn, Bonn, Germany ,grid.6612.30000 0004 1937 0642Department of Biomedicine, University of Basel, Basel, Switzerland ,grid.410567.1Institute of Medical Genetics and Pathology, University Hospital Basel, Basel, Switzerland ,grid.8385.60000 0001 2297 375XInstitute of Neuroscience and Medicine (INM-1), Research Center Jülich, Jülich, Germany
| | - Markus M. Nöthen
- grid.10388.320000 0001 2240 3300Institute of Human Genetics, University of Bonn, School of Medicine & University Hospital Bonn, Bonn, Germany
| | - Gerhard Schratt
- grid.5801.c0000 0001 2156 2780Lab of Systems Neuroscience, Department of Health Science and Technology, Institute for Neuroscience, Swiss Federal Institute of Technology ETH & Neuroscience Center Zurich (ZNZ), Zurich, Switzerland
| | - Andreas J. Forstner
- grid.10388.320000 0001 2240 3300Institute of Human Genetics, University of Bonn, School of Medicine & University Hospital Bonn, Bonn, Germany ,grid.8385.60000 0001 2297 375XInstitute of Neuroscience and Medicine (INM-1), Research Center Jülich, Jülich, Germany ,grid.10253.350000 0004 1936 9756Centre for Human Genetics, University of Marburg, Marburg, Germany
| |
Collapse
|
13
|
Rojas-Pirela M, Andrade-Alviárez D, Medina L, Castillo C, Liempi A, Guerrero-Muñoz J, Ortega Y, Maya JD, Rojas V, Quiñones W, Michels PA, Kemmerling U. MicroRNAs: master regulators in host-parasitic protist interactions. Open Biol 2022; 12:210395. [PMID: 35702995 PMCID: PMC9198802 DOI: 10.1098/rsob.210395] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
MicroRNAs (miRNAs) are a group of small non-coding RNAs present in a wide diversity of organisms. MiRNAs regulate gene expression at a post-transcriptional level through their interaction with the 3' untranslated regions of target mRNAs, inducing translational inhibition or mRNA destabilization and degradation. Thus, miRNAs regulate key biological processes, such as cell death, signal transduction, development, cellular proliferation and differentiation. The dysregulation of miRNAs biogenesis and function is related to the pathogenesis of diseases, including parasite infection. Moreover, during host-parasite interactions, parasites and host miRNAs determine the probability of infection and progression of the disease. The present review is focused on the possible role of miRNAs in the pathogenesis of diseases of clinical interest caused by parasitic protists. In addition, the potential role of miRNAs as targets for the design of drugs and diagnostic and prognostic markers of parasitic diseases is also discussed.
Collapse
Affiliation(s)
- Maura Rojas-Pirela
- Instituto de Ciencias Biomédicas, Facultad de Medicina, Universidad de Chile, Santiago de Chile 8380453, Chile,Instituto de Biología, Pontificia Universidad Católica de Valparaíso, Valparaíso 2373223, Chile,Facultad de Farmacia y Bioanálisis, Universidad de Los Andes, Mérida, Venezuela
| | - Diego Andrade-Alviárez
- Laboratorio de Enzimología de Parásitos, Facultad de Ciencias, Universidad de Los Andes, Mérida, Venezuela
| | - Lisvaneth Medina
- Instituto de Ciencias Biomédicas, Facultad de Medicina, Universidad de Chile, Santiago de Chile 8380453, Chile
| | - Christian Castillo
- Instituto de Ciencias Biomédicas, Facultad de Medicina, Universidad de Chile, Santiago de Chile 8380453, Chile,Núcleo de Investigación Aplicada en Ciencias Veterinarias y Agronómicas, Facultad de Medicina Veterinaria y Agronomía, Universidad de Las Américas, Chile
| | - Ana Liempi
- Instituto de Ciencias Biomédicas, Facultad de Medicina, Universidad de Chile, Santiago de Chile 8380453, Chile
| | - Jesús Guerrero-Muñoz
- Instituto de Ciencias Biomédicas, Facultad de Medicina, Universidad de Chile, Santiago de Chile 8380453, Chile
| | - Yessica Ortega
- Instituto de Ciencias Biomédicas, Facultad de Medicina, Universidad de Chile, Santiago de Chile 8380453, Chile,Facultad de Farmacia y Bioanálisis, Universidad de Los Andes, Mérida, Venezuela
| | - Juan Diego Maya
- Instituto de Ciencias Biomédicas, Facultad de Medicina, Universidad de Chile, Santiago de Chile 8380453, Chile
| | - Verónica Rojas
- Instituto de Biología, Pontificia Universidad Católica de Valparaíso, Valparaíso 2373223, Chile
| | - Wilfredo Quiñones
- Laboratorio de Enzimología de Parásitos, Facultad de Ciencias, Universidad de Los Andes, Mérida, Venezuela
| | - Paul A. Michels
- Centre for Immunity, Infection and Evolution and Centre for Translational and Chemical Biology, School of Biological Sciences, The University of Edinburgh, Edinburgh EH9 3FL, UK
| | - Ulrike Kemmerling
- Instituto de Ciencias Biomédicas, Facultad de Medicina, Universidad de Chile, Santiago de Chile 8380453, Chile
| |
Collapse
|
14
|
Ambrose JM, Anand DA, Kullappan M, Hussain S, James KM, Sreekandan RN, Suga SSD, Kamaraj D, Raghavan VPV, Mohan SK. A Computational approach to screen, predict and annotate human and chimpanzee PHEX intronic miRNAs, their gene targets, and regulatory interaction networks. Comput Biol Chem 2022; 98:107673. [DOI: 10.1016/j.compbiolchem.2022.107673] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2021] [Revised: 11/22/2021] [Accepted: 03/27/2022] [Indexed: 11/28/2022]
|
15
|
MiR-320-3p Regulates the Proliferation and Differentiation of Myogenic Progenitor Cells by Modulating Actin Remodeling. Int J Mol Sci 2022; 23:ijms23020801. [PMID: 35054986 PMCID: PMC8775871 DOI: 10.3390/ijms23020801] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2021] [Revised: 12/30/2021] [Accepted: 01/11/2022] [Indexed: 12/31/2022] Open
Abstract
Skeletal myogenesis is essential for the maintenance of muscle quality and quantity, and impaired myogenesis is intimately associated with muscle wasting diseases. Although microRNA (miRNA) plays a crucial role in myogenesis and relates to muscle wasting in obesity, the molecular targets and roles of miRNAs modulated by saturated fatty acids (SFA) are largely unknown. In the present study, we investigated the role of miR-320-3p on the differentiation of myogenic progenitor cells. Palmitic acid (PA), the most abundant dietary SFA, suppressed myogenic factors expression and impaired differentiation in C2C12 myoblasts, and these effects were accompanied by CFL2 downregulation and miR-320-3p upregulation. In particular, miR-320-3p appeared to target CFL2 mRNA directly and suppress the expression of CFL2, an essential factor for filamentous actin (F-actin) depolymerization. Transfection of myoblasts with miR-320-3p mimic increased F-actin formation and nuclear translocation of Yes-associated protein 1 (YAP1), a key component of mechanotransduction. Furthermore, miR-320-3p mimic increased myoblast proliferation and markedly impeded the expression of MyoD and MyoG, consequently inhibiting myoblast differentiation. In conclusion, our current study highlights the role of miR-320-3p on CFL2 expression, YAP1 activation, and myoblast differentiation and suggests that PA-inducible miR-320-3p is a significant mediator of muscle wasting in obesity.
Collapse
|
16
|
Naryzhnaya NV, Maslov LN, Derkachev IA, Ma H, Zhang Y, Prasad NR, Singh N, Fu F, Pei JM, Sarybaev A, Sydykov A. The effect of adaptation to hypoxia on cardiac tolerance to ischemia/reperfusion. J Biomed Res 2022:1-25. [PMID: 37183617 PMCID: PMC10387748 DOI: 10.7555/jbr.36.20220125] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022] Open
Abstract
The acute myocardial infarction (AMI) and sudden cardiac death (SCD), both associated with acute cardiac ischemia, are one of the leading causes of adult death in economically developed countries. The development of new approaches for the treatment and prevention of AMI and SCD remains the highest priority for medicine. A study on the cardiovascular effects of chronic hypoxia (CH) may contribute to the development of these methods. Chronic hypoxia exerts both positive and adverse effects. The positive effects are the infarct-reducing, vasoprotective, and antiarrhythmic effects, which can lead to the improvement of cardiac contractility in reperfusion. The adverse effects are pulmonary hypertension and right ventricular hypertrophy. This review presents a comprehensive overview of how CH enhances cardiac tolerance to ischemia/reperfusion. It is an in-depth analysis of the published data on the underlying mechanisms, which can lead to future development of the cardioprotective effect of CH. A better understanding of the CH-activated protective signaling pathways may contribute to new therapeutic approaches in an increase of cardiac tolerance to ischemia/reperfusion.
Collapse
|
17
|
Dattilo A, Ceccarini G, Scabia G, Magno S, Quintino L, Pelosini C, Salvetti G, Cusano R, Massidda M, Montanelli L, Gilio D, Gatti G, Giacomina A, Costa M, Santini F, Maffei M. Circulating Levels of MiRNAs From 320 Family in Subjects With Lipodystrophy: Disclosing Novel Signatures of the Disease. Front Endocrinol (Lausanne) 2022; 13:866679. [PMID: 35733784 PMCID: PMC9207177 DOI: 10.3389/fendo.2022.866679] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Accepted: 05/05/2022] [Indexed: 11/13/2022] Open
Abstract
Lipodystrophy (LD) indicates a group of rare disorders, with generalized or partial loss of white adipose tissue (WAT) often associated with metabolic derangements. Heterogeneity/wide spectrum of the disease and lack of biomarkers make diagnosis often difficult. MicroRNAs are important to maintain a correct WAT function and WAT is a source of circulating miRNAs (cmiRs). miRNAs from 320 family were previously detected in the WAT and variably associated to the metabolic syndrome. Our aim was then to investigate if LD can result in altered abundance of cmiRs-320. We collected samples from a cohort of LD subjects of various subtypes and from age matched controls. Use of quantitative PCR determined that cmiRs- 320a-3p, 320b, 320c, 320e are upregulated, while 320d is downregulated in LD. CmiRs-320 power as classifiers was more powerful in the most extreme and defined forms of LD, including the generalized and the Dunnigan subtypes. cmiR-320a-3p showed significant inverse relationships with plasma leptin (P < 0.0001), typically low in LD. The hepatic enzymes gamma-glutamyl transferase (GGT), aspartate aminotransferase (AST), alanine aminotransferase (ALT) and the marker of inflammation C-reactive protein (CRP) were inversely related to cmiR 320d (P < 0.05, for CRP and GGT; P < 0.01, for AST and ALT). Gene ontology analysis revealed cell-cell adhesion as a process regulated by 320 miRNAs targets, thus disclosing a novel route to investigate origin of WAT loss/dysfunction. In conclusion, cmiRs-320 constitute novel biomarkers of LD, abundance of miR320a-3p is inversely associated to indicators related to WAT function, while downregulation of cmiR-320d predicts an altered hepatic profile and higher inflammation.
Collapse
Affiliation(s)
- Alessia Dattilo
- Institute of Life Sciences, Scuola Superiore Sant’Anna, Pisa, Italy
- Obesity and Lipodystrophy Center, Endocrinology Unit, Pisa University Hospital, Pisa, Italy
| | - Giovanni Ceccarini
- Obesity and Lipodystrophy Center, Endocrinology Unit, Pisa University Hospital, Pisa, Italy
| | - Gaia Scabia
- Obesity and Lipodystrophy Center, Endocrinology Unit, Pisa University Hospital, Pisa, Italy
- National Research Council, Institute of Clinical Physiology, Pisa, Italy
| | - Silvia Magno
- Obesity and Lipodystrophy Center, Endocrinology Unit, Pisa University Hospital, Pisa, Italy
| | - Lara Quintino
- Obesity and Lipodystrophy Center, Endocrinology Unit, Pisa University Hospital, Pisa, Italy
| | - Caterina Pelosini
- Obesity and Lipodystrophy Center, Endocrinology Unit, Pisa University Hospital, Pisa, Italy
| | - Guido Salvetti
- Obesity and Lipodystrophy Center, Endocrinology Unit, Pisa University Hospital, Pisa, Italy
| | - Roberto Cusano
- Center for Advanced Studies, Research and Development in Sardinia, Pula (CA), Italy
| | - Matteo Massidda
- Center for Advanced Studies, Research and Development in Sardinia, Pula (CA), Italy
| | - Lucia Montanelli
- Department of Clinical and Experimental Medicine, Endocrinology Unit, Pisa University Hospital, Pisa, Italy
| | - Donatella Gilio
- Obesity and Lipodystrophy Center, Endocrinology Unit, Pisa University Hospital, Pisa, Italy
| | - Gianluca Gatti
- Plastic and Reconstructive Surgery Unit, Hospital of Pisa, Pisa, Italy
| | | | - Mario Costa
- National Research Council, Institute of Neuroscience, Pisa, Italy
- Centro Pisano Flash Radiotherapy, Center for Instrument Sharing of the University of Pisa (CPFR@CISUP), Pisa University Hospital, Pisa, Italy
| | - Ferruccio Santini
- Obesity and Lipodystrophy Center, Endocrinology Unit, Pisa University Hospital, Pisa, Italy
| | - Margherita Maffei
- Obesity and Lipodystrophy Center, Endocrinology Unit, Pisa University Hospital, Pisa, Italy
- National Research Council, Institute of Clinical Physiology, Pisa, Italy
- *Correspondence: Margherita Maffei,
| |
Collapse
|
18
|
Liu J, Mosti F, Silver DL. Human brain evolution: Emerging roles for regulatory DNA and RNA. Curr Opin Neurobiol 2021; 71:170-177. [PMID: 34861533 PMCID: PMC8756680 DOI: 10.1016/j.conb.2021.11.005] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2021] [Revised: 09/03/2021] [Accepted: 11/02/2021] [Indexed: 12/18/2022]
Abstract
Humans diverge from other primates in numerous ways, including their neuroanatomy and cognitive capacities. Human-specific features are particularly prominent in the cerebral cortex, which has undergone an expansion in size and acquired unique cellular composition and circuitry. Human-specific gene expression is postulated to explain neocortical anatomical differences across evolution. In particular, noncoding regulatory loci are strongly linked to human traits, including progenitor proliferation and cortical size. In this review, we highlight emerging noncoding elements implicated in human cortical evolution, including roles for regulatory DNA and RNA. Further, we discuss the association of human-specific genetic changes with neurodevelopmental diseases.
Collapse
Affiliation(s)
- Jing Liu
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, NC 27710, USA
| | - Federica Mosti
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, NC 27710, USA; Department of Neurobiology, Duke University Medical Center, Durham, NC 27710, USA
| | - Debra L Silver
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, NC 27710, USA; Department of Neurobiology, Duke University Medical Center, Durham, NC 27710, USA; Department of Cell Biology, Duke University Medical Center, Durham, NC 27710, USA; Duke Regeneration Center and Duke Institute for Brain Sciences, Duke University Medical Center, Durham, NC 277710, USA.
| |
Collapse
|
19
|
Caus M, Eritja À, Bozic M. Role of microRNAs in Obesity-Related Kidney Disease. Int J Mol Sci 2021; 22:ijms222111416. [PMID: 34768854 PMCID: PMC8583993 DOI: 10.3390/ijms222111416] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2021] [Revised: 10/19/2021] [Accepted: 10/20/2021] [Indexed: 12/14/2022] Open
Abstract
Obesity is a major global health problem and is associated with a significant risk of renal function decline. Obesity-related nephropathy, as one of the complications of obesity, is characterized by a structural and functional damage of the kidney and represents one of the important contributors to the morbidity and mortality worldwide. Despite increasing data linking hyperlipidemia and lipotoxicity to kidney injury, the apprehension of molecular mechanisms leading to a development of kidney damage is scarce. MicroRNAs (miRNAs) are endogenously produced small noncoding RNA molecules with an important function in post-transcriptional regulation of gene expression. miRNAs have been demonstrated to be important regulators of a vast array of physiological and pathological processes in many organs, kidney being one of them. In this review, we present an overview of miRNAs, focusing on their functional role in the pathogenesis of obesity-associated renal pathologies. We explain novel findings regarding miRNA-mediated signaling in obesity-related nephropathies and highlight advantages and future perspectives of the therapeutic application of miRNAs in renal diseases.
Collapse
|
20
|
Simultaneous Detection of Drug-Induced Liver Injury Protein and microRNA Biomarkers Using Dynamic Chemical Labelling on a Luminex MAGPIX System. ANALYTICA 2021. [DOI: 10.3390/analytica2040013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022] Open
Abstract
Drug-induced liver injury (DILI) is a potentially fatal adverse event and a leading cause for pre- and post-marketing drug withdrawal. Several multinational DILI initiatives have now recommended a panel of protein and microRNA (miRNA) biomarkers that can detect early liver injury and inform about mechanistic basis. This manuscript describes the development of seqCOMBO, a unique combo-multiplexed assay which combines the dynamic chemical labelling approach and an antibody-dependant method on the Luminex MAGPIX system. SeqCOMBO enables a versatile multiplexing platform to perform qualitative and quantitative analysis of proteins and miRNAs in patient serum samples simultaneously. To the best of our knowledge, this is the first method to profile protein and miRNA biomarkers to diagnose DILI in a single-step assay.
Collapse
|
21
|
Evolution and Phylogeny of MicroRNAs - Protocols, Pitfalls, and Problems. Methods Mol Biol 2021. [PMID: 34432281 DOI: 10.1007/978-1-0716-1170-8_11] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/17/2023]
Abstract
MicroRNAs are important regulators in many eukaryotic lineages. Typical miRNAs have a length of about 22nt and are processed from precursors that form a characteristic hairpin structure. Once they appear in a genome, miRNAs are among the best-conserved elements in both animal and plant genomes. Functionally, they play an important role in particular in development. In contrast to protein-coding genes, miRNAs frequently emerge de novo. The genomes of animals and plants harbor hundreds of mutually unrelated families of homologous miRNAs that tend to be persistent throughout evolution. The evolution of their genomic miRNA complement closely correlates with important morphological innovation. In addition, miRNAs have been used as valuable characters in phylogenetic studies. An accurate and comprehensive annotation of miRNAs is required as a basis to understand their impact on phenotypic evolution. Since experimental data on miRNA expression are limited to relatively few species and are subject to unavoidable ascertainment biases, it is inevitable to complement miRNA sequencing by homology based annotation methods. This chapter reviews the state of the art workflows for homology based miRNA annotation, with an emphasis on their limitations and open problems.
Collapse
|
22
|
Sharma RK, Calderon C, Vivas-Mejia PE. Targeting Non-coding RNA for Glioblastoma Therapy: The Challenge of Overcomes the Blood-Brain Barrier. FRONTIERS IN MEDICAL TECHNOLOGY 2021; 3:678593. [PMID: 35047931 PMCID: PMC8757885 DOI: 10.3389/fmedt.2021.678593] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2021] [Accepted: 07/16/2021] [Indexed: 12/12/2022] Open
Abstract
Glioblastoma (GBM) is the most malignant form of all primary brain tumors, and it is responsible for around 200,000 deaths each year worldwide. The standard therapy for GBM treatment includes surgical resection followed by temozolomide-based chemotherapy and/or radiotherapy. With this treatment, the median survival rate of GBM patients is only 15 months after its initial diagnosis. Therefore, novel and better treatment modalities for GBM treatment are urgently needed. Mounting evidence indicates that non-coding RNAs (ncRNAs) have critical roles as regulators of gene expression. Long non-coding RNAs (lncRNAs) and microRNAs (miRNAs) are among the most studied ncRNAs in health and disease. Dysregulation of ncRNAs is observed in virtually all tumor types, including GBMs. Several dysregulated miRNAs and lncRNAs have been identified in GBM cell lines and GBM tumor samples. Some of them have been proposed as diagnostic and prognostic markers, and as targets for GBM treatment. Most ncRNA-based therapies use oligonucleotide RNA molecules which are normally of short life in circulation. Nanoparticles (NPs) have been designed to increase the half-life of oligonucleotide RNAs. An additional challenge faced not only by RNA oligonucleotides but for therapies designed for brain-related conditions, is the presence of the blood-brain barrier (BBB). The BBB is the anatomical barrier that protects the brain from undesirable agents. Although some NPs have been derivatized at their surface to cross the BBB, optimal NPs to deliver oligonucleotide RNA into GBM cells in the brain are currently unavailable. In this review, we describe first the current treatments for GBM therapy. Next, we discuss the most relevant miRNAs and lncRNAs suggested as targets for GBM therapy. Then, we compare the current drug delivery systems (nanocarriers/NPs) for RNA oligonucleotide delivery, the challenges faced to send drugs through the BBB, and the strategies to overcome this barrier. Finally, we categorize the critical points where research should be the focus in order to design optimal NPs for drug delivery into the brain; and thus move the Oligonucleotide RNA-based therapies from the bench to the clinical setting.
Collapse
Affiliation(s)
- Rohit K. Sharma
- Comprehensive Cancer Center, University of Puerto Rico, San Juan, PR, United States
| | - Carlos Calderon
- Comprehensive Cancer Center, University of Puerto Rico, San Juan, PR, United States
| | - Pablo E. Vivas-Mejia
- Comprehensive Cancer Center, University of Puerto Rico, San Juan, PR, United States
- Department of Biochemistry, University of Puerto Rico, Medical Sciences Campus, San Juan, PR, United States
| |
Collapse
|
23
|
Liang Y, Li S, Tang L. MicroRNA 320, an Anti-Oncogene Target miRNA for Cancer Therapy. Biomedicines 2021; 9:biomedicines9060591. [PMID: 34071109 PMCID: PMC8224659 DOI: 10.3390/biomedicines9060591] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2021] [Revised: 05/18/2021] [Accepted: 05/20/2021] [Indexed: 12/11/2022] Open
Abstract
MicroRNAs are a set of highly conserved non-coding RNAs that control gene expression at the post-transcriptional/translational levels by binding to the 3′-UTR of diverse target genes. Increasing evidence indicates that miRNAs not only play a vital role in many biological processes, but they are also frequently deregulated in pathological conditions, including cancer. The miR-320 family is one of many tumor suppressor families and is composed of five members, which has been demonstrated to be related to the repression of epithelial-mesenchymal transition (EMT) inhibition, cell proliferation, and apoptosis. Moreover, this family has been shown to regulate drug resistance, and act as a potential biomarker for the diagnosis, prognosis, and prediction of cancer. In this review, we summarized recent research with reference to the tumor suppressor function of miR-320 and the regulation mechanisms of miR-320 expression. The collected evidence shown here supports that miR-320 may act as a novel biomarker for cancer prognosis and therapeutic response to cancer treatment.
Collapse
Affiliation(s)
- Yuanyuan Liang
- Key Laboratory of Biorheological Science and Technology, Ministry of Education, College of Bioengineering, Chongqing University, Chongqing 400044, China;
| | - Shun Li
- Department of Immunology, School of Basic Medical Sciences, Chengdu Medical College, Chengdu 610500, China
- Non-Coding RNA and Drug Discovery Key Laboratory of Sichuan Province, Chengdu Medical College, Chengdu 610500, China
- Correspondence: (S.L.); (L.T.)
| | - Liling Tang
- Key Laboratory of Biorheological Science and Technology, Ministry of Education, College of Bioengineering, Chongqing University, Chongqing 400044, China;
- Correspondence: (S.L.); (L.T.)
| |
Collapse
|
24
|
Gowen AM, Odegaard KE, Hernandez J, Chand S, Koul S, Pendyala G, Yelamanchili SV. Role of microRNAs in the pathophysiology of addiction. WILEY INTERDISCIPLINARY REVIEWS. RNA 2021; 12:e1637. [PMID: 33336550 PMCID: PMC8026578 DOI: 10.1002/wrna.1637] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/18/2020] [Revised: 11/12/2020] [Accepted: 11/19/2020] [Indexed: 02/06/2023]
Abstract
Addiction is a chronic and relapsing brain disorder characterized by compulsive seeking despite adverse consequences. There are both heritable and epigenetic mechanisms underlying drug addiction. Emerging evidence suggests that non-coding RNAs (ncRNAs) such as microRNAs (miRNAs), long non-coding RNAs, and circular RNAs regulate synaptic plasticity and related behaviors caused by substances of abuse. These ncRNAs modify gene expression and may contribute to the behavioral phenotypes of addiction. Among the ncRNAs, the most widely researched and impactful are miRNAs. The goal in this systematic review is to provide a detailed account of recent research involving the role of miRNAs in addiction. This article is categorized under: RNA Interactions with Proteins and Other Molecules > Small Molecule-RNA Interactions RNA in Disease and Development > RNA in Disease.
Collapse
Affiliation(s)
- Austin M Gowen
- Department of Anesthesiology, University of Nebraska Medical Center, Omaha, Nebraska, USA
| | - Katherine E Odegaard
- Department of Anesthesiology, University of Nebraska Medical Center, Omaha, Nebraska, USA
| | - Jordan Hernandez
- Department of Anesthesiology, University of Nebraska Medical Center, Omaha, Nebraska, USA
| | - Subhash Chand
- Department of Anesthesiology, University of Nebraska Medical Center, Omaha, Nebraska, USA
| | - Sneh Koul
- Department of Anesthesiology, University of Nebraska Medical Center, Omaha, Nebraska, USA
| | - Gurudutt Pendyala
- Department of Anesthesiology, University of Nebraska Medical Center, Omaha, Nebraska, USA
| | - Sowmya V Yelamanchili
- Department of Anesthesiology, University of Nebraska Medical Center, Omaha, Nebraska, USA
| |
Collapse
|
25
|
Du H, Zhao Y, Yin Z, Wang DW, Chen C. The role of miR-320 in glucose and lipid metabolism disorder-associated diseases. Int J Biol Sci 2021; 17:402-416. [PMID: 33613101 PMCID: PMC7893589 DOI: 10.7150/ijbs.53419] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2020] [Accepted: 11/21/2020] [Indexed: 02/06/2023] Open
Abstract
Glucose and lipids are important nutrients that provide the majority of energy for each organ to maintain homeostasis of the body. With the continuous improvement in living standards, the incidence of metabolic disorder-associated diseases, such as diabetes, hyperlipidemia, and atherosclerosis, is increasing worldwide. Among them, diabetes, which could be induced by both glucose and lipid metabolic disorders, is one of the five diseases with the highest incidence and mortality worldwide. However, the detailed molecular mechanisms underlying glucose and lipid metabolism disorders and target-organ damage are still not fully defined. MicroRNAs (miRNAs) are small, non-coding, single-stranded RNAs, which usually affect their target mRNAs in the cytoplasm by post-transcriptional regulation. Previously, we have found that miR-320 contributed to glucose and lipid metabolism via different signaling pathways. Most importantly, we identified that nuclear miR-320 mediated diabetes-induced cardiac dysfunction by activating the transcription of fatty acid metabolic genes to cause lipotoxicity in the heart. Here, we reviewed the roles of miR-320 in glucose and lipid metabolism and target-organ damage.
Collapse
Affiliation(s)
| | | | | | | | - Chen Chen
- Division of Cardiology, Hubei Key Laboratory of Genetics and Molecular Mechanisms of Cardiological Disorders, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| |
Collapse
|
26
|
Ninsuwon J, Waiyamitra P, Roongsitthichai A, Surachetpong W. Expressions of miR-155 and miR-181 and predictions of their structures and targets in pigs ( Sus scrofa). Vet World 2020; 13:1667-1673. [PMID: 33061243 PMCID: PMC7522940 DOI: 10.14202/vetworld.2020.1667-1673] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2020] [Accepted: 06/30/2020] [Indexed: 12/17/2022] Open
Abstract
BACKGROUND AND AIM MicroRNAs (miRNAs) are responsible for gene expression control at the post-transcription level in many species. Several miRNAs are required in the regulation of immune responses, such as B-cell differentiation, T-cell receptor signaling pathway, CD4+ T cell selection, and so on. Studies on miRNAs have been extensively conducted in humans and mice; however, reports relevant to miRNAs, especially miR-155 and miR-181, in pigs are limited. Consequently, the present study aimed to investigate the structures, target genes, and expressions of miR-155 and miR-181 in various porcine cells and tissues. MATERIALS AND METHODS Five healthy male pigs from a porcine reproductive and respiratory syndrome virus-negative farm were studied. Before slaughter, blood samples were collected for peripheral blood mononuclear cell isolation. After slaughter, samples of spleen, lymph nodes, and forelimb muscles were collected. Both miR-155 and miR-181 were investigated for their structures with RNAfold web server, for their target genes from three online web servers, and for their expressions using polymerase chain reaction (PCR). RESULTS The structures of miR-155 and miR-181 contained hairpins with free energies of -35.27 and -35.29 kcal/mole, respectively. Target gene prediction revealed that miR-155 had perfect complementarity with Socs1 and Mapk3k14, while miR-181 had perfect complementarity with Ddx3x, Nfat5, Foxp1, and Mpp5. PCR showed that both miRNAs were detectable from all investigated cells and tissues. Moreover, the highest expression of both miRNAs was found from the lymph node of the pigs. CONCLUSION Both miR-155 and miR-181 might be involved with the regulation of porcine immune functions as both miRNAs were detected in several cells and tissues of the pigs. In addition, they had very high complementarities with the seed regions of several immune-related genes.
Collapse
Affiliation(s)
- Jirapat Ninsuwon
- Department of Veterinary Microbiology and Immunology, Faculty of Veterinary Medicine, Kasetsart University, Bangkok, Thailand
- Center for Advanced Studies for Agriculture and Food, Institute for Advanced Studies, Kasetsart University, Bangkok, Thailand
| | - Pitchaporn Waiyamitra
- Department of Veterinary Microbiology and Immunology, Faculty of Veterinary Medicine, Kasetsart University, Bangkok, Thailand
| | - Atthaporn Roongsitthichai
- Veterinary Clinic Research Unit, Faculty of Veterinary Sciences, Mahasarakham University, Maha Sarakham, Thailand
- Office of Academic Affairs, Faculty of Veterinary Sciences, Mahasarakham University, Maha Sarakham, Thailand
| | - Win Surachetpong
- Department of Veterinary Microbiology and Immunology, Faculty of Veterinary Medicine, Kasetsart University, Bangkok, Thailand
- Center for Advanced Studies for Agriculture and Food, Institute for Advanced Studies, Kasetsart University, Bangkok, Thailand
| |
Collapse
|
27
|
Huang X, Li S, Liu X, Huang S, Li S, Zhuo M. Analysis of conserved miRNAs in cynomolgus macaque genome using small RNA sequencing and homology searching. PeerJ 2020; 8:e9347. [PMID: 32728489 PMCID: PMC7357559 DOI: 10.7717/peerj.9347] [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: 06/03/2019] [Accepted: 05/21/2020] [Indexed: 11/23/2022] Open
Abstract
MicroRNAs (miRNAs) are important regulators that fine-tune diverse cellular activities. Cynomolgus macaques (Macaca fascicularis) are used extensively in biomedical and pharmaceutical research; however, substantially fewer miRNAs have been identified in this species than in humans. Consequently, we investigated conserved miRNA profiles in cynomolgus macaques by homology searching and small RNA sequencing. In total, 1,455 high-confidence miRNA gene loci were identified, 408 of which were also confirmed by RNA sequencing, including 73 new miRNA loci reported in cynomolgus macaques for the first time. Comparing miRNA expression with age, we found a positive correlation between sequence conservation and expression levels during miRNA evolution. Additionally, we found that the miRNA gene locations in cynomolgus macaque genome were very flexible. Most were embedded in intergenic spaces or introns and clustered together. Several miRNAs were found in certain gene locations, including 64 exon-resident miRNAs, six splice-site-overlapping miRNAs (SO-miRNAs), and two pairs of distinct mirror miRNAs. We also identified 78 miRNA clusters, 68 of which were conserved in the human genome, including 10 large miRNA clusters predicted to regulate diverse developmental and cellular processes in cynomolgus macaque. Thus, this study not only expands the number of identified miRNAs in cynomolgus macaques but also provides clues for future research on the differences in miRNA repertoire between macaques and humans.
Collapse
Affiliation(s)
- Xia Huang
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou, Guangdong, China
| | - Shijia Li
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou, Guangdong, China
| | - Xiaoming Liu
- Guangzhou Tulip Information Technologies Ltd., Guangzhou, Guangdong, China
| | - Shuting Huang
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou, Guangdong, China
| | - Shuang Li
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou, Guangdong, China
| | - Min Zhuo
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou, Guangdong, China
| |
Collapse
|
28
|
Lee HE, Huh JW, Kim HS. Bioinformatics Analysis of Evolution and Human Disease Related Transposable Element-Derived microRNAs. Life (Basel) 2020; 10:life10060095. [PMID: 32630504 PMCID: PMC7345915 DOI: 10.3390/life10060095] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2020] [Revised: 06/22/2020] [Accepted: 06/23/2020] [Indexed: 12/22/2022] Open
Abstract
Transposable element (TE) has the ability to insert into certain parts of the genome, and due to this event, it is possible for TEs to generate new factors and one of these factors are microRNAs (miRNA). miRNAs are non-coding RNAs made up of 19 to 24 nucleotides and numerous miRNAs are derived from TE. In this study, to support general knowledge on TE and miRNAs derived from TE, several bioinformatics tools and databases were used to analyze miRNAs derived from TE in two aspects: evolution and human disease. The distribution of TEs in diverse species presents that almost half of the genome is covered with TE in mammalians and less than a half in other vertebrates and invertebrates. Based on selected evolution-related miRNAs studies, a total of 51 miRNAs derived from TE were found and analyzed. For the human disease-related miRNAs, total of 34 miRNAs derived from TE were organized from the previous studies. In summary, abundant miRNAs derived from TE are found, however, the function of miRNAs derived from TE is not informed either. Therefore, this study provides theoretical understanding of miRNAs derived from TE by using various bioinformatics tools.
Collapse
Affiliation(s)
- Hee-Eun Lee
- National Primate Research Center, Korea Research Institute of Bioscience and Biotechnology, Cheongju 28116, Korea; (H.-E.L.); (J.-W.H.)
| | - Jae-Won Huh
- National Primate Research Center, Korea Research Institute of Bioscience and Biotechnology, Cheongju 28116, Korea; (H.-E.L.); (J.-W.H.)
- Department of Functional Genomics, KRIBB School of Bioscience, Korea University of Science and Technology (UST), Daejeon 34113, Korea
| | - Heui-Soo Kim
- Department of Biological Sciences, College of Natural Sciences, Pusan National University, Busan 46241, Korea
- Institute of Systems Biology, Pusan National University, Busan 46241, Korea
- Correspondence: ; Tel.: +82-51-510-2259; Fax: +82-51-581-2962
| |
Collapse
|
29
|
Aryan L, Medzikovic L, Umar S, Eghbali M. Pregnancy-associated cardiac dysfunction and the regulatory role of microRNAs. Biol Sex Differ 2020; 11:14. [PMID: 32252821 PMCID: PMC7137306 DOI: 10.1186/s13293-020-00292-w] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/14/2020] [Accepted: 03/18/2020] [Indexed: 12/14/2022] Open
Abstract
Many crucial cardiovascular adaptations occur in the body during pregnancy to ensure successful gestation. Maladaptation of the cardiovascular system during pregnancy can lead to complications that promote cardiac dysfunction and may lead to heart failure (HF). About 12% of pregnancy-related deaths in the USA have been attributed to HF and the detrimental effects of cardiovascular complications on the heart can be long-lasting, pre-disposing the mother to HF later in life. Indeed, cardiovascular complications such as gestational diabetes mellitus, preeclampsia, gestational hypertension, and peripartum cardiomyopathy have been shown to induce cardiac metabolic dysfunction, oxidative stress, fibrosis, apoptosis, and diastolic and systolic dysfunction in the hearts of pregnant women, all of which are hallmarks of HF. The exact etiology and cardiac pathophysiology of pregnancy-related complications is not yet fully deciphered. Furthermore, diagnosis of cardiac dysfunction in pregnancy is often made only after clinical symptoms are already present, thus necessitating the need for novel diagnostic and prognostic biomarkers. Mounting data demonstrates an altered expression of maternal circulating miRNAs during pregnancy affected by cardiovascular complications. Throughout the past decade, miRNAs have become of growing interest as modulators and biomarkers of pathophysiology, diagnosis, and prognosis in cardiac dysfunction. While the association between pregnancy-related cardiovascular complications and cardiac dysfunction or HF is becoming increasingly evident, the roles of miRNA-mediated regulation herein remain poorly understood. Therefore, this review will summarize current reports on pregnancy-related cardiovascular complications that may lead to cardiac dysfunction and HF during and after pregnancy in previously healthy women, with a focus on the pathophysiological role of miRNAs.
Collapse
Affiliation(s)
- Laila Aryan
- Department of Anesthesiology, Division of Molecular Medicine, David Geffen School of Medicine at University of California, Los Angeles, BH-550 CHS, Los Angeles, CA, 90095-7115, USA
| | - Lejla Medzikovic
- Department of Anesthesiology, Division of Molecular Medicine, David Geffen School of Medicine at University of California, Los Angeles, BH-550 CHS, Los Angeles, CA, 90095-7115, USA
| | - Soban Umar
- Department of Anesthesiology, Division of Molecular Medicine, David Geffen School of Medicine at University of California, Los Angeles, BH-550 CHS, Los Angeles, CA, 90095-7115, USA
| | - Mansoureh Eghbali
- Department of Anesthesiology, Division of Molecular Medicine, David Geffen School of Medicine at University of California, Los Angeles, BH-550 CHS, Los Angeles, CA, 90095-7115, USA.
| |
Collapse
|
30
|
Chakraborty S, Islam MR, Ali MM, Nabi AHMN. Evolutionary Divergence of Brain-specific Precursor miRNAs Drives Efficient Processing and Production of Mature miRNAs in Human. Neuroscience 2018; 392:141-159. [PMID: 30273624 DOI: 10.1016/j.neuroscience.2018.09.010] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2018] [Revised: 08/09/2018] [Accepted: 09/07/2018] [Indexed: 12/18/2022]
Abstract
The hallmark of human evolution encompasses the dramatic increase in brain size and complexity. The intricate interplays of micro-RNAs (miRNAs) and their target genes are indispensable in brain development. Sequence divergence in distinct structural regions of Brain-specific precursor miRNAs (pre-miRNAs) and its consequence in the production of corresponding mature miRNAs in human are unknown. To address these questions, first we classified miRNAs into three categories based on tissue expression: Brain-specific (expressed exclusively in brain), Non-brain (expressed in Non-brain tissues) and Common (expressed in all tissues) and compared the sequence divergence of different structural regions (basal segment, lower and upper stem, internal and terminal loop) of categorized pre-miRNAs across human, non-human primates and rodents. Our analysis revealed that unpaired regions of Brain-specific pre-miRNAs in human bear traces of relatively high rate of evolutionary divergence compared to those in other species. Cross-tissue expression analysis unveiled the higher expression of the Brain-specific miRNAs in human compared to other species. Intriguingly, in human brain, expression levels of these miRNAs superseded the levels of the ubiquitously expressed "Common-miRNAs". Further analysis revealed that presence of certain motif and nucleotide preference in the Brain-specific pre-miRNAs may favor DROSHA and DICER to ameliorate miRNA processing. The higher processing efficiency of human Brain-specific miRNAs was reflected as an elevated production of corresponding mature miRNAs in the human brain. Finally, re-construction of gene-regulatory network uncovers different pathways driven by Brain-specific miRNAs that may contribute to the development of brain in human.
Collapse
Affiliation(s)
- Sajib Chakraborty
- Department of Biochemistry and Molecular Biology, University of Dhaka, Bangladesh.
| | - Md Rezaul Islam
- Department of Biochemistry and Molecular Biology, University of Dhaka, Bangladesh; Max Planck Research School for Neurosciences, Göttingen, Germany
| | - Md Muntasir Ali
- Department of Biochemistry and Molecular Biology, University of Dhaka, Bangladesh; Unit of Microbiology, Belgian Nuclear Research Centre (SCK•CEN), 2400 Mol, Belgium
| | - A H M Nurun Nabi
- Department of Biochemistry and Molecular Biology, University of Dhaka, Bangladesh.
| |
Collapse
|
31
|
Pradillo M, Santos JL. Genes involved in miRNA biogenesis affect meiosis and fertility. Chromosome Res 2018; 26:233-241. [PMID: 30343461 DOI: 10.1007/s10577-018-9588-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2018] [Revised: 10/03/2018] [Accepted: 10/07/2018] [Indexed: 01/01/2023]
Abstract
MicroRNAs (miRNAs) are a class of small (containing about 22 nucleotides) single-stranded non-coding RNAs that regulate gene expression at the post-transcriptional level in plants and animals, being absent from unicellular organisms. They act on diverse key physiological and cellular processes, such as development and tissue differentiation, cell identity, cell cycle progression, and programmed cell death. They are also likely to be involved in a broad spectrum of human diseases. Particularly, this review examines and summarizes work characterizing the function of miRNAs in gametogenesis and fertility. Although numerous studies have elucidated the involvement of reproductive-specific small interfering RNAs (siRNAs) in regulating germ cell development and meiosis, less is known about the role of miRNAs in these processes. We focus on the study of hypomorphic and null alleles of genes encoding components of miRNA biogenesis in both plants (Arabidopsis thaliana) and mammals (Mus musculus). We compare the consequences of the presence of these mutations on male meiosis in both species.
Collapse
Affiliation(s)
- Mónica Pradillo
- Department of Genetics, Physiology and Microbiology, Faculty of Biology, Complutense University, 28040, Madrid, Spain.
| | - Juan L Santos
- Department of Genetics, Physiology and Microbiology, Faculty of Biology, Complutense University, 28040, Madrid, Spain
| |
Collapse
|
32
|
Shah AA, Ahmad M, Ul-Haq T. Deciphering conserved identical sequences of mature miRNAs among six members of great apes. ZOOSYST EVOL 2018. [DOI: 10.3897/zse.94.28099] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
MicroRNAs (miRNAs) are a group of small RNA molecules which act as negative regulators of gene expression by controlling post-transcriptional regulation through binding to their corresponding mRNAs. Due to their small size, their nucleotide compositions are expected to be similar, but until now, the extent of similarity has not been reported in humans and their six phylogenetically closely related members of hominids. The present study allows direct comparison among six members of hominid species (Homosapiens, Gorillagorilla, Panpaniscus, Pongopygmaeus, Pantroglodytes and Symphalangussyndactylus) in terms of their miRNA repertoire, their evolutionary distance to human, as well as, the categorization of identical species-specific miRNAs. For this purpose, a total of 2694, 370, 157, 673, 590 and 10 mature miRNA sequences of Homosapiens, Gorillagorilla, Panpaniscus, Pongopygmaeus, Pantroglodytes and Symphalangussyndactylus respectively were retrieved from miRbase 22. A total of 12, 4, 4 and 3 conserved clusters with identical miRNA sequences that belong to the same gene families were found in Homosapiens, Gorillagorilla, Pongopygmaeus, Pantroglodytes respectively by neighbor-joining method using MEGA7 software. Interestingly, cross-species comparison has also shown a set of conserved identical miRNA sequences. Homologs of human mature miRNAs with 100% sequence identity are expected to have similar functions in the studied primates. Further in-vitro study is required to investigate common targets for identical miRNAs in the studied primates.
Collapse
|
33
|
Abstract
The noncoding portion of the genome, including microRNAs, has been fertile evolutionary soil for cortical development in primates. A major contribution to cortical expansion in primates is the generation of novel precursor cell populations. Because miRNA expression profiles track closely with cell identity, it is likely that numerous novel microRNAs have contributed to cellular diversity in the brain. The tools to determine the genomic context within which novel microRNAs emerge and how they become integrated into molecular circuitry are now in hand.
Collapse
Affiliation(s)
- Kenneth S Kosik
- Neuroscience Research Institute and Department of Molecular, Cellular, and Developmental Biology, University of California, Santa Barbara, California 93106, USA;
| | - Tomasz Nowakowski
- Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California, San Francisco, California 94143, USA.,Department of Anatomy, University of California, San Francisco, California 94158, USA
| |
Collapse
|