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Parvizi M, Vaezi M, Jeddi F, Bakhshandeh M, Eghdam-Zamiri R, Mobaraki-Asl N, Esmati E, Karimi A. The role and diagnostic value of deregulated miRNAs in cervical cancer. Discov Oncol 2025; 16:922. [PMID: 40413660 DOI: 10.1007/s12672-025-02744-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/10/2025] [Accepted: 05/17/2025] [Indexed: 05/27/2025] Open
Abstract
Cervical cancer (CC) remains a significant global health concern, particularly affecting women in low-income countries. Despite advancements in screening programs, CC continues to pose a substantial mortality risk, highlighting the need to explore diagnostic and treatment modalities. This review focuses on the role of deregulated microRNAs (miRNAs) in CC development, emphasizing their potential as biomarkers for early detection and prognosis in body fluids. miRNAs have emerged as critical regulators of key cellular processes, including proliferation, migration, invasion, and apoptosis, and their dysregulation is closely linked to CC progression. Upregulated miRNAs such as miR-146b-3p, miR-1908, and miR-21 promote CC progression by targeting tumor suppressor genes, while downregulated miRNAs like miR-23-3p and miR-4262 are associated with reduced tumor aggressiveness. miRNAs also hold significant promise as non-invasive prognostic biomarkers. Their expression levels correlate with clinical outcomes, including tumor stage, metastasis, and overall survival, making them valuable tools for risk stratification and personalized treatment strategies. Liquid biopsies, which detect circulating miRNAs in bodily fluids, offer a minimally invasive approach to monitor tumor dynamics and predict patient outcomes. Furthermore, exosomal miRNAs are emerging as promising diagnostic and prognostic tools for CC. Advanced diagnostic technologies and bioinformatics tools are anticipated to enhance the identification of evident miRNA biomarkers in the clinical settings. Standardized protocols for sample collection and analysis will improve the reproducibility of miRNA studies, while a deeper understanding of miRNA biology may unlock their potential as therapeutic targets. In conclusion, this review consolidates current research on deregulated miRNAs in CC, highlighting their diagnostic and prognostic significance. The findings underscore the potential of miRNAs to revolutionize CC management through innovative diagnostic and therapeutic strategies.
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Affiliation(s)
- Masoumeh Parvizi
- Department of Molecular Medicine, Faculty of Advanced Medical Sciences, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Maryam Vaezi
- Obstetric and Oncology Department, School of Medicine, Women's Reproductive Health Research Center, Clinical Research Institute, Alzahra Hospital, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Farhad Jeddi
- Department of Genetics and Pathology, School of Medicine, Ardabil University of Medical Sciences, Ardabil, Iran
| | - Masoumeh Bakhshandeh
- Obstetric and Oncology Department, School of Medicine, Women's Reproductive Health Research Center, Clinical Research Institute, Alzahra Hospital, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Reza Eghdam-Zamiri
- Department of Radiation Oncology, School of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Noushin Mobaraki-Asl
- Department of Obstetrics and Gynecology, School of Medicine, Alavi Hospital, Ardabil University of Medical Sciences, Ardabil, Iran
| | - Ebrahim Esmati
- Department of Radiation Oncology, Cancer Institute, IKHC, Tehran University of Medical Sciences, Tehran, Iran
| | - Abbas Karimi
- Department of Molecular Medicine, Faculty of Advanced Medical Sciences, Tabriz University of Medical Sciences, Tabriz, Iran.
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Ahi EP. Fish Evo-Devo: Moving Toward Species-Specific and Knowledge-Based Interactome. JOURNAL OF EXPERIMENTAL ZOOLOGY. PART B, MOLECULAR AND DEVELOPMENTAL EVOLUTION 2025; 344:158-168. [PMID: 40170296 DOI: 10.1002/jez.b.23287] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/14/2024] [Revised: 12/13/2024] [Accepted: 01/12/2025] [Indexed: 04/03/2025]
Abstract
A knowledge-based interactome maps interactions among proteins and molecules within a cell using experimental data, computational predictions, and literature mining. These interactomes are vital for understanding cellular functions, pathways, and the evolutionary conservation of protein interactions. They reveal how interactions regulate growth, differentiation, and development. Transitioning to functionally validated interactomes is crucial in evolutionary developmental biology (Evo-Devo), especially for non-model species, to uncover unique regulatory networks, evolutionary novelties, and reliable gene interaction models. This enhances our understanding of complex trait evolution across species. The European Evo-Devo 2024 conference in Helsinki hosted the first fish-specific Evo-Devo symposium, highlighting the growing interest in fish models. Advances in genome annotation, genome editing, imaging, and molecular screening are expanding fish Evo-Devo research. High-throughput molecular data have enabled the deduction of gene regulatory networks. The next steps involve creating species-specific interactomes, validating them functionally, and integrating additional molecular data to deepen the understanding of complex regulatory interactions in fish Evo-Devo. This short review aims to address the logical steps for this transition, as well as the necessities and limitations of this journey.
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Affiliation(s)
- Ehsan Pashay Ahi
- Organismal and Evolutionary Biology Research Programme, University of Helsinki, Helsinki, Finland
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3
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Kim H, Lee YY, Kim VN. The biogenesis and regulation of animal microRNAs. Nat Rev Mol Cell Biol 2025; 26:276-296. [PMID: 39702526 DOI: 10.1038/s41580-024-00805-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/28/2024] [Indexed: 12/21/2024]
Abstract
MicroRNAs (miRNAs) are small, yet profoundly influential, non-coding RNAs that base-pair with mRNAs to induce RNA silencing. Although the basic principles of miRNA biogenesis and function have been established, recent breakthroughs have yielded important new insights into the molecular mechanisms of miRNA biogenesis. In this Review, we discuss the metazoan miRNA biogenesis pathway step-by-step, focusing on the key biogenesis machinery, including the Drosha-DGCR8 complex (Microprocessor), exportin-5, Dicer and Argonaute. We also highlight newly identified cis-acting elements and their impact on miRNA maturation, informed by advanced high-throughput and structural studies, and discuss recently discovered mechanisms of clustered miRNA processing, target recognition and target-directed miRNA decay (TDMD). Lastly, we explore multiple regulatory layers of miRNA biogenesis, mediated by RNA-protein interactions, miRNA tailing (uridylation or adenylation) and RNA modifications.
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Affiliation(s)
- Haedong Kim
- Center for RNA Research, Institute for Basic Science, Seoul, Republic of Korea
- School of Biological Sciences, Seoul National University, Seoul, Republic of Korea
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - Young-Yoon Lee
- Center for RNA Research, Institute for Basic Science, Seoul, Republic of Korea
- School of Biological Sciences, Seoul National University, Seoul, Republic of Korea
| | - V Narry Kim
- Center for RNA Research, Institute for Basic Science, Seoul, Republic of Korea.
- School of Biological Sciences, Seoul National University, Seoul, Republic of Korea.
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4
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Ghani MU, Zhao G, Pei D, Ma T, Zhao Y, Qu X, Cui H. Inter-species dynamics of non-coding RNAs: Impact on host immunomodulation and pathogen survival. DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY 2025; 164:105318. [PMID: 39809336 DOI: 10.1016/j.dci.2025.105318] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/19/2024] [Revised: 01/09/2025] [Accepted: 01/11/2025] [Indexed: 01/16/2025]
Abstract
Non-coding RNAs (ncRNAs) are composed of nucleotides that do not encode proteins but instead serve as guides. It interacts with amino acids at precise genomic sites, influencing chromatin structure and gene expression. These ncRNAs contribute to numerous inter-species dynamics, including those within the vector-host-pathogen triad. Vector-associated ncRNAs are released into hosts to combat the host immune system and sustain arthropod viability. Conversely, hosts may utilize specific ncRNAs as part of their defences to counteract pathogen-carrying vectors. Moreover, pathogens transmitted through vectors' saliva into hosts carry ncRNAs that enhances their virulence. While recent investigations have primarily focused on vector-associated ncRNAs in animal hosts, only a few have explored the functions of pathogen-associated ncRNAs and their role in initiating infections. Our review delves into the historical prospects of ncRNAs, mechanisms by which pathogen-derived ncRNAs influence host-pathogen interactions, regulate gene expression, and evade host defences. Ultimately, it underscores the importance ncRNAs mediated regulatory network in vector-host-pathogen dynamics, offering new strategies to combat vector-borne diseases and enhance public health outcomes.
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Affiliation(s)
- Muhammad Usman Ghani
- State Key Laboratory of Resource Insects, Southwest University, Chongqing, 400715, China; Medical Research Institute, Southwest University, Chongqing, 400715, China
| | - Gaichao Zhao
- State Key Laboratory of Resource Insects, Southwest University, Chongqing, 400715, China; Medical Research Institute, Southwest University, Chongqing, 400715, China
| | - Dakun Pei
- State Key Laboratory of Resource Insects, Southwest University, Chongqing, 400715, China; Jinfeng Laboratory, Chongqing, 401329, China
| | - Tao Ma
- State Key Laboratory of Resource Insects, Southwest University, Chongqing, 400715, China; Medical Research Institute, Southwest University, Chongqing, 400715, China
| | - Yuhan Zhao
- Medical Research Institute, Southwest University, Chongqing, 400715, China
| | - Xiaoxuan Qu
- Medical Research Institute, Southwest University, Chongqing, 400715, China
| | - Hongjuan Cui
- State Key Laboratory of Resource Insects, Southwest University, Chongqing, 400715, China; Medical Research Institute, Southwest University, Chongqing, 400715, China; Jinfeng Laboratory, Chongqing, 401329, China.
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5
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Sriharikrishnaa S, Jishnu PV, Varghese VK, Shukla V, Mallya S, Chakrabarty S, Sharan K, Pandey D, Kabekkodu SP. Identification of differentially expressed MiRNA clusters in cervical cancer. Discov Oncol 2025; 16:172. [PMID: 39946028 PMCID: PMC11825440 DOI: 10.1007/s12672-025-01946-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/31/2024] [Accepted: 02/06/2025] [Indexed: 02/16/2025] Open
Abstract
BACKGROUND Aberrant miRNA expression has been associated with cervical cancer (CC) progression. The present study aimed to identify the miRNA clusters (MCs) altered in CC, identify their clinical utility, and understand their biological functions via computational analysis. METHODS We used small RNA sequencing and qRT‒PCR to identify and validate abnormally expressed MCs in cervical squamous cell carcinoma (CSCC) samples. We compared our data with publicly available CC datasets to identify the differentially expressed MCs in CC. The potential targets, pathways, biological functions, and clinical utility of abnormally expressed MCs were predicted via several computational tools. RESULTS Small RNA sequencing revealed that 229 miRNAs belonging to 48 MCs were significantly differentially expressed in CSCC (p-value ≤ 0.05). Validation by qRT‒PCR confirmed the downregulation of members of the miR-379/656, namely, hsa-miR-376c-3p (2.8-fold; p-value 0.03), hsa-miR-494-3p (3.4-fold; p-value 0.02), hsa-miR-495-3p (eightfold; p-value 0.01), and hsa-miR-409-3p (fivefold; p-value 0.03), in CSCC samples compared with normal samples. The prognostic model generated via miRNA expression and random forest analysis showed robust sensitivity and specificity (0.88 to 0.92) in predicting overall survival. In addition, we report 22 prognostically important miRNAs in CC. Pathway analysis revealed the enrichment of several cancer-related pathways, notably p53, the cell cycle, viral infection and MAPK signalling. CDC25A, CCNE1, E2F1, CCNE2, RBL1, E2F3, CDK2, RBL2, E2F2 and CCND2 were identified as the top ten gene targets of MC. Drug‒gene interaction analysis revealed enrichment of 548 approved drugs and 62 unique genes. CONCLUSION Our study identified MCs, their target genes, their prognostic utility, and their potential functions in CC and recommended their usefulness in CC management.
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Affiliation(s)
- S Sriharikrishnaa
- Department of Cell and Molecular Biology, Manipal School of Life Sciences, Manipal Academy of Higher Education, Manipal, Karnataka, 576104, India
| | - Padacherri Vethil Jishnu
- Department of Cell and Molecular Biology, Manipal School of Life Sciences, Manipal Academy of Higher Education, Manipal, Karnataka, 576104, India
| | - Vinay Koshy Varghese
- Department of Cell and Molecular Biology, Manipal School of Life Sciences, Manipal Academy of Higher Education, Manipal, Karnataka, 576104, India
| | - Vaibhav Shukla
- Department of Cell and Molecular Biology, Manipal School of Life Sciences, Manipal Academy of Higher Education, Manipal, Karnataka, 576104, India
| | - Sandeep Mallya
- Department of Bioinformatics, Manipal School of Life Sciences, Manipal Academy of Higher Education, Manipal, Karnataka, India
| | - Sanjiban Chakrabarty
- Department of Cell and Molecular Biology, Manipal School of Life Sciences, Manipal Academy of Higher Education, Manipal, Karnataka, 576104, India
- Center for DNA Repair and Genome Stability (CDRGS), Manipal Academy of Higher Education, Manipal, Karnataka, India
| | - Krishna Sharan
- Department of Radiotherapy Oncology, Kasturba Medical College, Manipal, Karnataka, India
| | - Deeksha Pandey
- Department of Obstetrics and Gynecology, Kasturba Medical College, Manipal, Karnataka, India
| | - Shama Prasada Kabekkodu
- Department of Cell and Molecular Biology, Manipal School of Life Sciences, Manipal Academy of Higher Education, Manipal, Karnataka, 576104, India.
- Center for DNA Repair and Genome Stability (CDRGS), Manipal Academy of Higher Education, Manipal, Karnataka, India.
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Gheitasi I, Akbari G, Savari F. Physiological and cellular mechanisms of ischemic preconditioning microRNAs-mediated in underlying of ischemia/reperfusion injury in different organs. Mol Cell Biochem 2025; 480:855-868. [PMID: 39001984 DOI: 10.1007/s11010-024-05052-7] [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: 03/28/2024] [Accepted: 06/10/2024] [Indexed: 07/15/2024]
Abstract
Ischemia-reperfusion (I/R) injury, as a pathological phenomenon, takes place when blood supply to an organ is disrupted and then aggravated during restoration of blood flow. Ischemic preconditioning (IPC) is a potent method for attenuating subsequent events of IR damage in numerous organs. IPC protocol is determined by a brief and sequential time periods of I/R before the main ischemia. MicroRNAs are endogenous non-coding RNAs that regulate post-transcriptionally target mRNA translation via degrading it and/or suppressing protein synthesis. This review introduces the physiological and cellular mechanisms of ischemic preconditioning microRNAs-mediated after I/R insult in different organs such as the liver, kidney, heart, brain, and intestine. Data of this review have been collected from the scientific articles published in databases such as Science Direct, Scopus, PubMed, Web of Science, and Scientific Information Database from 2000 to 2023. Based on these literature studies, IPC/IR intervention can affect cellular mechanisms including oxidative stress, apoptosis, angiogenesis, and inflammation through up-regulation or down-regulation of multiple microRNAs and their target genes.
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Affiliation(s)
- Izadpanah Gheitasi
- Department of Physiology, Faculty of Medicine, Yasuj University of Medical Sciences, Yasuj, Iran
| | - Ghaidafeh Akbari
- Department of Physiology, Faculty of Medicine, Yasuj University of Medical Sciences, Yasuj, Iran.
| | - Feryal Savari
- Department of Medical Basic Sciences, Shoushtar Faculty of Medical Sciences, Shoushtar, Iran.
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7
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Yari AH, Aghbash PS, Bayat M, Lahouti S, Jalilzadeh N, Zadeh LN, Yari AM, Tabrizi-Nezhadi P, Nahand JS, MotieGhader H, Baghi HB. Novel bioinformatic approaches show the role of driver genes in the progression of cervical cancer: An in-silico study. Heliyon 2024; 10:e40179. [PMID: 39634417 PMCID: PMC11616557 DOI: 10.1016/j.heliyon.2024.e40179] [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: 02/12/2024] [Revised: 10/31/2024] [Accepted: 11/05/2024] [Indexed: 12/07/2024] Open
Abstract
Background The goal of this bioinformatics research is to get a comprehensive understanding of the driver genes and their function in the development, progression, and treatment of cervical cancer. This study constitutes a pioneering attempt, adding to our knowledge of genetic diversity and its ramifications. Material and methods In this project, we use bioinformatics and systems biology methods to identify candidate transcription factors and the genes they regulate in order to identify microRNAs and LncRNAs that regulate these transcription factors and lead to the discovery of new medicines for the treatment of cervical cancer. From the differentially expressed genes available via GEO's GSE63514 accession, we use driver genes to choose these candidates. We then used the WGCNA tool in R to rebuild the co-expression network and its modules. The hub genes of each module were determined using CytoHubba, a Cystoscope plugin. The biomarker potential of hub genes was analyzed using the UCSC Xena browser and the GraphPad prism program. The TRRUST database is used to locate the TFs that regulate the expression of these genes. In order to learn how drugs, MicroRNAs, and LncRNAs interact with transcription factors, we consulted the Drug Target Information Database (DGIDB), the miRWalk database, and the LncHub database. Finally, the online database Enrichr is utilized to analyze the enrichment of Gene Ontology and KEGG pathways. Results By combining the mRNA expression levels of 2041 driver genes from 14 early-stage Cervical cancer and 24 control samples, a co-expression network was built. The cluster analysis shows that the collection of shared genes may be broken down into seven distinct groups, or "modules." According to the average linkage hierarchical clustering and Summary smaller than 2, we found five modules (represented by the colors blue, brown, red, green, and grey) in our research. Then, we identify 5 high-degree genes from these modules that may serve as diagnostic biomarkers (ZBBX, PLCH1, TTC7B, DNAH7, and ZMYND10). In addition, we identify four transcription factors (SRF, RELA, NFKB1, and SP1) that regulate the expression of genes in the co-expression module. Drugs, microRNAs, and long noncoding RNAs are then shown to cooperate with transcription factors. At last, the KEGG database's pathways were mined for information on how the co-expression module fits within them. More clinical trials are required for more trustworthy outcomes, and we collected this data using bioinformatics methods. Conclusion The major goal of this research was to identify diagnostic and therapeutic targets for cervical cancer by learning more about the involvement of driver genes in cancer's earliest stages.
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Affiliation(s)
- Amir Hossein Yari
- Department of Biology, Tabriz Branch, Islamic Azad University, Tabriz, Iran
- Immunology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Parisa Shiri Aghbash
- Immunology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
- Department of Virology, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Mobina Bayat
- Department of Virology, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran
- Infectious and Tropical Diseases Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Shiva Lahouti
- Immunology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Nazila Jalilzadeh
- Immunology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Leila Nariman Zadeh
- Immunology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Amir Mohammad Yari
- Department of Biology, Tabriz Branch, Islamic Azad University, Tabriz, Iran
| | | | - Javid Sadri Nahand
- Infectious and Tropical Diseases Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Habib MotieGhader
- Department of Biology, Tabriz Branch, Islamic Azad University, Tabriz, Iran
- Department of Software Engineering, Engineering Faculty, Istanbul Topkapi University, Istanbul, Turkey
| | - Hossein Bannazadeh Baghi
- Immunology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
- Department of Virology, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran
- Infectious and Tropical Diseases Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
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8
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Tao J, Shen X, Qian H, Ding Q, Wang L. TIM proteins and microRNAs: distinct impact and promising interactions on transplantation immunity. Front Immunol 2024; 15:1500228. [PMID: 39650660 PMCID: PMC11621082 DOI: 10.3389/fimmu.2024.1500228] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2024] [Accepted: 11/06/2024] [Indexed: 12/11/2024] Open
Abstract
Achieving sustained activity and tolerance in of allogeneic grafts after post-transplantation remains a substantial challenge. The response of the immune system to "non-self" MHC-antigenic peptides initiates a crucial phase, wherein blocking positive co-stimulatory signals becomes imperative to ensure graft survival and tolerance. MicroRNAs (miRNAs) inhibit mRNA translation or promote mRNA degradation by complementary binding of mRNA seed sequences, which ultimately affects protein synthesis. These miRNAs exhibit substantial promise as diagnostic, prognostic, and therapeutic candidates for within the realm of solid organ transplantations. Current research has highlighted three members of the T cell immunoglobulin and mucin domain (TIM) family as a novel therapeutic avenue in transplantation medicine and alloimmunization. The interplay between miRNAs and TIM proteins has been extensively explored in viral infections, inflammatory responses, and post-transplantation ischemia-reperfusion injuries. This review aims to elucidate the distinct roles of miRNAs and TIM in transplantation immunity and delineate their interdependent relationships in terms of targeted regulation. Specifically, this investigation sought seeks to uncover the potential of miRNA interaction with TIM, aiming to induce immune tolerance and bolster allograft survival after transplantation. This innovative strategy holds substantial promise in for the future of transplantation science and practice.
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Affiliation(s)
- Jialing Tao
- Translational Medical Innovation Center, Zhangjiagang TCM Hospital Affiliated to Nanjing University of Chinese Medicine, Zhangjiagang, Jiangsu, China
| | - Xiaoxuan Shen
- Department of Endocrinology, Zhangjiagang TCM Hospital Affiliated to Nanjing University of Chinese Medicine, Zhangjiagang, Jiangsu, China
| | - Haiqing Qian
- Department of Reproduction, Zhangjiagang TCM Hospital Affiliated to Nanjing University of Chinese Medicine, Jiangsu, Zhangjiagang, China
| | - Qing Ding
- Department of Surgery, Thomas E. Starzl Transplantation Institute, University of Pittsburgh School of Medicine, Pittsburgh, PA, United States
| | - Lihong Wang
- Department of Reproduction, Zhangjiagang TCM Hospital Affiliated to Nanjing University of Chinese Medicine, Jiangsu, Zhangjiagang, China
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Li Q, Li Y, Zhu J, Liu Z, Sun Y, Lv Y, Li J, Luo L, Zhang C, Zhang W. Cadmium Exposure in Male Rats Results in Ovarian Granulosa Cell Apoptosis in Female Offspring and Paternal Genetic Effects. ENVIRONMENTAL TOXICOLOGY 2024; 39:5187-5198. [PMID: 39119833 DOI: 10.1002/tox.24375] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/02/2023] [Revised: 02/01/2024] [Accepted: 06/01/2024] [Indexed: 08/10/2024]
Abstract
The aim of this study was to investigate whether the damage to male offspring induced by cadmium (Cd) exposure during embryonic period leads to the apoptosis of ovarian granulosa cells (OGCs) in the next generation of female offspring, and whether this apoptosis in the offspring was due to paternal genetic effects. Pregnant Sprague-Dawley (SD) rats were exposed to CdCl2 (0, 0.5, 2.0, or 8.0 mg/kg) by gavage daily for 20 days to produce the filial 1 (F1) generation. F1 males were mated with newly purchased females to produce the F2 generation, and the F3 generation was generated in the same way. No apoptotic bodies were observed in the OGCs of either the F2 or F3 generation as shown by electron microscopy, and a reduced OGC apoptosis rate (detected by flow cytometry) was observed in F2 OGCs from the Cd-exposed group. Moreover, the mRNA (qRT-PCR) levels of Bax and Bcl-2 and the protein (western blotting) level of pro-caspase-8 increased in the F2 generation (p < 0.05). The expression of apoptosis-related miRNAs (qRT-PCR) and methylation of apoptosis-related genes (determined via bisulfite-sequencing PCR) in OGCs were further determined. Compared with those of the controls, the expression patterns of microRNAs (miRNAs) in the F2 offspring were different in the Cd-exposed group. The miR-92a-2-5p expression levels were decreased in both the F2 and F3 generations (p < 0.05), while the average methylation level of apoptosis-related genes did not change significantly (except for individual loci). In summary, this study showed that the paternal genetic intergenerational effect of male Cd exposure during embryonic period induced apoptosis of OGCs in the offspring was weakened, and the transgenerational effect disappeared; nevertheless, intergenerational and transgenerational changes in apoptosis-related genes, epigenetic modifications, DNA methylation, and miRNAs were observed, and may be important for understanding the homeostatic mechanisms of the body to alleviate the intergenerational transmission of Cd-induced damage.
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Affiliation(s)
- Qingyu Li
- Department of Preventive Medicine, Fujian Provincial Key Laboratory of Environment Factors and Cancer, Key Laboratory of Environment and Health, School of Public Health, Fujian Medical University, Fuzhou, Fujian, China
| | - Yuchen Li
- Department of Preventive Medicine, Fujian Provincial Key Laboratory of Environment Factors and Cancer, Key Laboratory of Environment and Health, School of Public Health, Fujian Medical University, Fuzhou, Fujian, China
| | - Jianlin Zhu
- Department of Preventive Medicine, Fujian Provincial Key Laboratory of Environment Factors and Cancer, Key Laboratory of Environment and Health, School of Public Health, Fujian Medical University, Fuzhou, Fujian, China
| | - Zhangpin Liu
- Department of Preventive Medicine, Fujian Provincial Key Laboratory of Environment Factors and Cancer, Key Laboratory of Environment and Health, School of Public Health, Fujian Medical University, Fuzhou, Fujian, China
| | - Yi Sun
- Department of Preventive Medicine, Fujian Provincial Key Laboratory of Environment Factors and Cancer, Key Laboratory of Environment and Health, School of Public Health, Fujian Medical University, Fuzhou, Fujian, China
| | - Yake Lv
- Department of Preventive Medicine, Fujian Provincial Key Laboratory of Environment Factors and Cancer, Key Laboratory of Environment and Health, School of Public Health, Fujian Medical University, Fuzhou, Fujian, China
| | - Jingwen Li
- Department of Preventive Medicine, Fujian Provincial Key Laboratory of Environment Factors and Cancer, Key Laboratory of Environment and Health, School of Public Health, Fujian Medical University, Fuzhou, Fujian, China
| | - Lingfeng Luo
- Department of Preventive Medicine, Fujian Provincial Key Laboratory of Environment Factors and Cancer, Key Laboratory of Environment and Health, School of Public Health, Fujian Medical University, Fuzhou, Fujian, China
| | - Chenyun Zhang
- Department of Health Law and Policy, School of Public Health, Fujian Medical University, Fuzhou, Fujian, China
| | - Wenchang Zhang
- Department of Preventive Medicine, Fujian Provincial Key Laboratory of Environment Factors and Cancer, Key Laboratory of Environment and Health, School of Public Health, Fujian Medical University, Fuzhou, Fujian, China
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10
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Zhang X, Zhu X, Chen L, Fan H, Liu X, Yang N, Wang Y, Duan Y. Functional Identification of miR2119 Targeting ADHs in Modulating Soybean Resistance to Heterodera glycines. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2024; 72:21461-21474. [PMID: 39311099 PMCID: PMC11450968 DOI: 10.1021/acs.jafc.4c05000] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/08/2024] [Revised: 09/07/2024] [Accepted: 09/17/2024] [Indexed: 10/03/2024]
Abstract
Soybean cyst nematode (SCN, Heterodera glycines) is a sedentary endoparasite nematode that results in severe economic losses in soybean crops. miRNAs play crucial roles in plant responses to nematode. However, the role of miR2119 responding to SCN stress in soybean. Here, we demonstrated that the transcript levels of polycistronic precursors containing miR2119 and miR398a were significantly reduced in soybean upon nematode infection. Promoter of the miR2119-398a precursor analysis was conducted containing a GUS reporter gene. GUS activity assays demonstrated a decrease in miR2119-398a promoter during SCN infection. Overexpression of polycistronic precursor miR2119-398a (OE-premiR2119-398a) and miR2119 precursor (OE-premiR2119) rendered soybean more susceptible to SCN. Conversely, silencing miR2119 (STTM2119) increased soybean resistance against SCN. Furthermore, RNA-seq analysis revealed that miR2119 is involved in many defense signaling pathways. GUS reporter gene assays demonstrated that miR2119 targets GmADH1.1a and GmADH1.1b. Functional analysis indicated that ADHs act as a major role in responding to H. glycines by modulating reactive oxygen species (ROS) levels. Together, the findings reveal a novel mechanism by which the polycistronic precursor miR2119-398a coordinately regulates in response to H. glycines. Additionally, miR2119 becomes an essential element contributing to H. glycines by modulating ADH activity and ROS homeostasis in soybean.
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Affiliation(s)
- Xiaoyu Zhang
- Nematology
Institute of Northern China, Shenyang Agricultural
University, Shenyang 110866, China
- College
of Plant Protection, Shenyang Agricultural
University, Shenyang 110866, China
| | - Xiaofeng Zhu
- Nematology
Institute of Northern China, Shenyang Agricultural
University, Shenyang 110866, China
- College
of Plant Protection, Shenyang Agricultural
University, Shenyang 110866, China
| | - Lijie Chen
- Nematology
Institute of Northern China, Shenyang Agricultural
University, Shenyang 110866, China
- College
of Plant Protection, Shenyang Agricultural
University, Shenyang 110866, China
| | - Haiyan Fan
- Nematology
Institute of Northern China, Shenyang Agricultural
University, Shenyang 110866, China
- College
of Plant Protection, Shenyang Agricultural
University, Shenyang 110866, China
| | - Xiaoyu Liu
- Nematology
Institute of Northern China, Shenyang Agricultural
University, Shenyang 110866, China
- College
of Sciences, Shenyang Agricultural University, Shenyang 110866, China
| | - Ning Yang
- Nematology
Institute of Northern China, Shenyang Agricultural
University, Shenyang 110866, China
- College
of Plant Protection, Shenyang Agricultural
University, Shenyang 110866, China
| | - Yuanyuan Wang
- Nematology
Institute of Northern China, Shenyang Agricultural
University, Shenyang 110866, China
- College
of Biological Science and Technology, Shenyang
Agricultural University, Shenyang 110866, China
| | - Yuxi Duan
- Nematology
Institute of Northern China, Shenyang Agricultural
University, Shenyang 110866, China
- College
of Plant Protection, Shenyang Agricultural
University, Shenyang 110866, China
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11
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Sebutsoe XM, Tsotetsi NJN, Jantjies ZE, Raphela-Choma PP, Choene MS, Motadi LR. Therapeutic Strategies in Advanced Cervical Cancer Detection, Prevention and Treatment. Onco Targets Ther 2024; 17:785-801. [PMID: 39345275 PMCID: PMC11439348 DOI: 10.2147/ott.s475132] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2024] [Accepted: 08/08/2024] [Indexed: 10/01/2024] Open
Abstract
Cervical cancer is ranked the fourth most common cause of cancer related deaths amongst women. The situation is particularly dire in low to lower middle-income countries. It continues to affect these countries due to poor vaccine coverage and screening. Cervical cancer is mostly detected in the advanced stages leading to poor outcomes. This review focuses on the progress made to date to improve early detection and targeted therapy using both circulating RNA. Vaccine has played a major role in cervical cancer control in vaccinated young woman in mainly developed countries yet in low-income countries with challenges of 3 dose vaccination affordability, cervical cancer continues to be the second most deadly amongst women. In this review, we show the progress made in reducing cervical cancer using vaccination that in combination with other treatments that might improve survival in cervical cancer. We further show with both miRNA and siRNA that targeted therapy and specific markers might be ideal for early detection of cervical cancer in low-income countries. These markers are either upregulated or down regulated in cancer providing clue to the stage of the cancer.
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Affiliation(s)
- Xolisiwe M Sebutsoe
- Department of Biochemistry C2 Lab, University of Johannesburg, Auckland Park Kingsway Campus, Johannesburg, South Africa
| | | | - Zodwa Edith Jantjies
- Department of Biochemistry C2 Lab, University of Johannesburg, Auckland Park Kingsway Campus, Johannesburg, South Africa
| | - Portia Pheladi Raphela-Choma
- Department of Biochemistry C2 Lab, University of Johannesburg, Auckland Park Kingsway Campus, Johannesburg, South Africa
| | - Mpho S Choene
- Department of Biochemistry C2 Lab, University of Johannesburg, Auckland Park Kingsway Campus, Johannesburg, South Africa
| | - Lesetja R Motadi
- Department of Biochemistry C2 Lab, University of Johannesburg, Auckland Park Kingsway Campus, Johannesburg, South Africa
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12
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Ware AP, Satyamoorthy K, Paul B. CmirC update 2024: a multi-omics database for clustered miRNAs. Funct Integr Genomics 2024; 24:133. [PMID: 39085735 PMCID: PMC11291601 DOI: 10.1007/s10142-024-01410-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2024] [Revised: 07/18/2024] [Accepted: 07/19/2024] [Indexed: 08/02/2024]
Abstract
Clustered miRNAs consist of two or more miRNAs transcribed together and may coordinately regulate gene expression. Differential expression of clustered miRNAs is found to be controlled by crosstalk of genetic or epigenetic mechanisms. It has been demonstrated that clustered miRNA expression patterns greatly impact cancer cell progression. With the CmirC initiative, we initially developed a comprehensive database to identify copy number variation (CNV) driven clustered miRNAs in cancer. Now, we extended the analysis and identified three miRNAs, mir-96, mir-183, and mir-21, were found to be significantly upregulated in 17 cancer types. Further, CmirC is now upgraded to determine the impact of changes in the DNA methylation status at clustered miRNAs by utilizing The Cancer Genomic Atlas (TCGA) cancer datasets. We examined specific methylation datasets from 9,639 samples, pinpointing 215,435 methylation sites and 27,949 CpG islands with miRNA cluster information. The integrated analysis identified 34 clusters exhibiting differentially methylated CpG sites across 14 cancer types. Furthermore, we determined that CpG islands in the promoter region of 20 miRNA clusters could play a regulatory role. Along with ensuring a straightforward and convenient user experience, CmirC has been updated with improved data browsing and analysis functionalities, as well as enabled hyperlinks to literature and miR-cancer databases. The enhanced version of CmirC is anticipated to play an important role in providing information on the regulation of clustered miRNA expression, and their targeted oncogenes and tumor suppressors. The newly updated version of CmirC is available at https://slsdb.manipal.edu/cmirclust/ .
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Affiliation(s)
- Akshay Pramod Ware
- Department of Bioinformatics, Manipal School of Life Sciences, Manipal Academy of Higher Education, Manipal, Karnataka, 576104, India
- Institute of Cardiovascular Regeneration, Johann Wolfgang Goethe University, Theodor-Stern-Kai 7, Frankfurt Am Main, 60590, Germany
| | - Kapaettu Satyamoorthy
- SDM College of Medical Sciences and Hospital, Shri Dharmasthala Manjunatheshwara (SDM) University, Manjushree Nagar, Sattur, Dharwad, Karnataka, 580009, India
| | - Bobby Paul
- Department of Bioinformatics, Manipal School of Life Sciences, Manipal Academy of Higher Education, Manipal, Karnataka, 576104, India.
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13
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Rossi M, Breman E. Engineering strategies to safely drive CAR T-cells into the future. Front Immunol 2024; 15:1411393. [PMID: 38962002 PMCID: PMC11219585 DOI: 10.3389/fimmu.2024.1411393] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2024] [Accepted: 05/27/2024] [Indexed: 07/05/2024] Open
Abstract
Chimeric antigen receptor (CAR) T-cell therapy has proven a breakthrough in cancer treatment in the last decade, giving unprecedented results against hematological malignancies. All approved CAR T-cell products, as well as many being assessed in clinical trials, are generated using viral vectors to deploy the exogenous genetic material into T-cells. Viral vectors have a long-standing clinical history in gene delivery, and thus underwent iterations of optimization to improve their efficiency and safety. Nonetheless, their capacity to integrate semi-randomly into the host genome makes them potentially oncogenic via insertional mutagenesis and dysregulation of key cellular genes. Secondary cancers following CAR T-cell administration appear to be a rare adverse event. However several cases documented in the last few years put the spotlight on this issue, which might have been underestimated so far, given the relatively recent deployment of CAR T-cell therapies. Furthermore, the initial successes obtained in hematological malignancies have not yet been replicated in solid tumors. It is now clear that further enhancements are needed to allow CAR T-cells to increase long-term persistence, overcome exhaustion and cope with the immunosuppressive tumor microenvironment. To this aim, a variety of genomic engineering strategies are under evaluation, most relying on CRISPR/Cas9 or other gene editing technologies. These approaches are liable to introduce unintended, irreversible genomic alterations in the product cells. In the first part of this review, we will discuss the viral and non-viral approaches used for the generation of CAR T-cells, whereas in the second part we will focus on gene editing and non-gene editing T-cell engineering, with particular regard to advantages, limitations, and safety. Finally, we will critically analyze the different gene deployment and genomic engineering combinations, delineating strategies with a superior safety profile for the production of next-generation CAR T-cell.
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14
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Lasser S, Ozbay Kurt FG, Fritz L, Gutzeit N, De La Torre C, Altevogt P, Utikal J, Umansky V. Generation of Myeloid-Derived Suppressor Cells Mediated by MicroRNA-125a-5p in Melanoma. Int J Mol Sci 2024; 25:6693. [PMID: 38928399 PMCID: PMC11203613 DOI: 10.3390/ijms25126693] [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: 03/28/2024] [Revised: 06/13/2024] [Accepted: 06/13/2024] [Indexed: 06/28/2024] Open
Abstract
The ability of tumor-derived extracellular vesicles (EVs) to modulate the function of myeloid cells is widely recognized. Hence, a comprehensive understanding of the distinct components associated with EVs and the signals that they deliver to myeloid cells could provide potential approaches to impede the immunosuppression by myeloid-derived suppressor cells (MDSCs). We investigated melanoma EV-associated microRNAs (miRs) using the RET transgenic melanoma mouse model and simulated their transfer to normal myeloid cells by transfecting immature mouse myeloid cells and human monocytes. We observed elevated levels of miR-125a-5p, -125b-5p, and let-7e-5p in mouse melanoma-infiltrating MDSCs. In addition, miR-125a-5p levels in the tumor microenvironment correlated with mouse melanoma progression. The delivery of miR-125a-5p, alone or in combination with let-7e-5p and miR-99b-5p from the same genomic cluster, to normal myeloid cells resulted in their conversion to MDSC-like cells. Our findings indicate that miR-125a-5p could modulate myeloid cell activation in the melanoma microenvironment via a NF-κB-dependent mechanism.
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Affiliation(s)
- Samantha Lasser
- Department of Dermatology, Venereology and Allergology, University Medical Center Mannheim, Heidelberg University, 68167 Mannheim, Germany; (S.L.); (F.G.O.K.); (L.F.); (N.G.); (P.A.); (J.U.)
- Skin Cancer Unit, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
- DFKZ-Hector Cancer Institute, University Medical Center Mannheim, 68167 Mannheim, Germany
- Mannheim Institute for Innate Immunoscience (MI3), Medical Faculty Mannheim, Heidelberg University, 68167 Mannheim, Germany
| | - Feyza Gul Ozbay Kurt
- Department of Dermatology, Venereology and Allergology, University Medical Center Mannheim, Heidelberg University, 68167 Mannheim, Germany; (S.L.); (F.G.O.K.); (L.F.); (N.G.); (P.A.); (J.U.)
- Skin Cancer Unit, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
- DFKZ-Hector Cancer Institute, University Medical Center Mannheim, 68167 Mannheim, Germany
- Mannheim Institute for Innate Immunoscience (MI3), Medical Faculty Mannheim, Heidelberg University, 68167 Mannheim, Germany
| | - Lennart Fritz
- Department of Dermatology, Venereology and Allergology, University Medical Center Mannheim, Heidelberg University, 68167 Mannheim, Germany; (S.L.); (F.G.O.K.); (L.F.); (N.G.); (P.A.); (J.U.)
- Skin Cancer Unit, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
- DFKZ-Hector Cancer Institute, University Medical Center Mannheim, 68167 Mannheim, Germany
- Mannheim Institute for Innate Immunoscience (MI3), Medical Faculty Mannheim, Heidelberg University, 68167 Mannheim, Germany
| | - Nina Gutzeit
- Department of Dermatology, Venereology and Allergology, University Medical Center Mannheim, Heidelberg University, 68167 Mannheim, Germany; (S.L.); (F.G.O.K.); (L.F.); (N.G.); (P.A.); (J.U.)
- Skin Cancer Unit, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
- DFKZ-Hector Cancer Institute, University Medical Center Mannheim, 68167 Mannheim, Germany
- Mannheim Institute for Innate Immunoscience (MI3), Medical Faculty Mannheim, Heidelberg University, 68167 Mannheim, Germany
| | - Carolina De La Torre
- NGS Core Facility, Medical Faculty Mannheim, Heidelberg University, 68167 Mannheim, Germany;
| | - Peter Altevogt
- Department of Dermatology, Venereology and Allergology, University Medical Center Mannheim, Heidelberg University, 68167 Mannheim, Germany; (S.L.); (F.G.O.K.); (L.F.); (N.G.); (P.A.); (J.U.)
- Skin Cancer Unit, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
- DFKZ-Hector Cancer Institute, University Medical Center Mannheim, 68167 Mannheim, Germany
- Mannheim Institute for Innate Immunoscience (MI3), Medical Faculty Mannheim, Heidelberg University, 68167 Mannheim, Germany
| | - Jochen Utikal
- Department of Dermatology, Venereology and Allergology, University Medical Center Mannheim, Heidelberg University, 68167 Mannheim, Germany; (S.L.); (F.G.O.K.); (L.F.); (N.G.); (P.A.); (J.U.)
- Skin Cancer Unit, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
- DFKZ-Hector Cancer Institute, University Medical Center Mannheim, 68167 Mannheim, Germany
| | - Viktor Umansky
- Department of Dermatology, Venereology and Allergology, University Medical Center Mannheim, Heidelberg University, 68167 Mannheim, Germany; (S.L.); (F.G.O.K.); (L.F.); (N.G.); (P.A.); (J.U.)
- Skin Cancer Unit, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
- DFKZ-Hector Cancer Institute, University Medical Center Mannheim, 68167 Mannheim, Germany
- Mannheim Institute for Innate Immunoscience (MI3), Medical Faculty Mannheim, Heidelberg University, 68167 Mannheim, Germany
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15
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Schlossbauer P, Naumann L, Klingler F, Burkhart M, Handrick R, Korff K, Neusüß C, Otte K, Hesse F. Stable overexpression of native and artificial miRNAs for the production of differentially fucosylated antibodies in CHO cells. Eng Life Sci 2024; 24:2300234. [PMID: 38845814 PMCID: PMC11151017 DOI: 10.1002/elsc.202300234] [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: 08/08/2023] [Revised: 03/04/2024] [Accepted: 03/17/2024] [Indexed: 06/09/2024] Open
Abstract
Cell engineering strategies typically rely on energy-consuming overexpression of genes or radical gene-knock out. Both strategies are not particularly convenient for the generation of slightly modulated phenotypes, as needed in biosimilar development of for example differentially fucosylated monoclonal antibodies (mAbs). Recently, transiently transfected small noncoding microRNAs (miRNAs), known to be regulators of entire gene networks, have emerged as potent fucosylation modulators in Chinese hamster ovary (CHO) production cells. Here, we demonstrate the applicability of stable miRNA overexpression in CHO production cells to adjust the fucosylation pattern of mAbs as a model phenotype. For this purpose, we applied a miRNA chaining strategy to achieve adjustability of fucosylation in stable cell pools. In addition, we were able to implement recently developed artificial miRNAs (amiRNAs) based on native miRNA sequences into a stable CHO expression system to even further fine-tune fucosylation regulation. Our results demonstrate the potential of miRNAs as a versatile tool to control mAb fucosylation in CHO production cells without adverse side effects on important process parameters.
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Affiliation(s)
- Patrick Schlossbauer
- Institute for Applied BiotechnologyUniversity of Applied Sciences BiberachBiberachGermany
| | | | - Florian Klingler
- Institute for Applied BiotechnologyUniversity of Applied Sciences BiberachBiberachGermany
| | - Madina Burkhart
- Institute for Applied BiotechnologyUniversity of Applied Sciences BiberachBiberachGermany
| | - René Handrick
- Institute for Applied BiotechnologyUniversity of Applied Sciences BiberachBiberachGermany
| | | | | | - Kerstin Otte
- Institute for Applied BiotechnologyUniversity of Applied Sciences BiberachBiberachGermany
| | - Friedemann Hesse
- Institute for Applied BiotechnologyUniversity of Applied Sciences BiberachBiberachGermany
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16
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Kappari L, Dasireddy JR, Applegate TJ, Selvaraj RK, Shanmugasundaram R. MicroRNAs: exploring their role in farm animal disease and mycotoxin challenges. Front Vet Sci 2024; 11:1372961. [PMID: 38803799 PMCID: PMC11129562 DOI: 10.3389/fvets.2024.1372961] [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: 01/21/2024] [Accepted: 04/04/2024] [Indexed: 05/29/2024] Open
Abstract
MicroRNAs (miRNAs) serve as key regulators in gene expression and play a crucial role in immune responses, holding a significant promise for diagnosing and managing diseases in farm animals. This review article summarizes current research on the role of miRNAs in various farm animal diseases and mycotoxicosis, highlighting their potential as biomarkers and using them for mitigation strategies. Through an extensive literature review, we focused on the impact of miRNAs in the pathogenesis of several farm animal diseases, including viral and bacterial infections and mycotoxicosis. They regulate gene expression by inducing mRNA deadenylation, decay, or translational inhibition, significantly impacting cellular processes and protein synthesis. The research revealed specific miRNAs associated with the diseases; for instance, gga-miR-M4 is crucial in Marek's disease, and gga-miR-375 tumor-suppressing function in Avian Leukosis. In swine disease such as Porcine Respiratory and Reproductive Syndrome (PRRS) and swine influenza, miRNAs like miR-155 and miR-21-3p emerged as key regulatory factors. Additionally, our review highlighted the interaction between miRNAs and mycotoxins, suggesting miRNAs can be used as a biomarker for mycotoxin exposure. For example, alterations in miRNA expression, such as the dysregulation observed in response to Aflatoxin B1 (AFB1) in chickens, may indicate potential mechanisms for toxin-induced changes in lipid metabolism leading to liver damage. Our findings highlight miRNAs potential for early disease detection and intervention in farm animal disease management, potentially reducing significant economic losses in agriculture. With only a fraction of miRNAs functionally characterized in farm animals, this review underlines more focused research on specific miRNAs altered in distinct diseases, using advanced technologies like CRISPR-Cas9 screening, single-cell sequencing, and integrated multi-omics approaches. Identifying specific miRNA targets offers a novel pathway for early disease detection and the development of mitigation strategies against mycotoxin exposure in farm animals.
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Affiliation(s)
- Laharika Kappari
- Department of Poultry Science, The University of Georgia, Athens, GA, United States
| | | | - Todd J. Applegate
- Department of Poultry Science, The University of Georgia, Athens, GA, United States
| | - Ramesh K. Selvaraj
- Department of Poultry Science, The University of Georgia, Athens, GA, United States
| | - Revathi Shanmugasundaram
- Toxicology and Mycotoxin Research Unit, U.S. National Poultry Research Center, Agricultural Research Service, U.S. Department of Agriculture, Athens, GA, United States
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17
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Sriharikrishnaa S, John FE, Bairy M, Shetty S, Suresh PS, Kabekkodu SP. A comprehensive review on the functional role of miRNA clusters in cervical cancer. Epigenomics 2024; 16:493-511. [PMID: 38511231 DOI: 10.2217/epi-2023-0244] [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: 07/08/2023] [Accepted: 03/04/2024] [Indexed: 03/22/2024] Open
Abstract
Cervical cancer (CC) poses a significant health threat in women globally. MicroRNA clusters (MCs), comprising multiple miRNA-encoding genes, are pivotal in gene regulation. Various factors, including circular RNA and DNA methylation, govern MC expression. Dysregulated MC expression correlates strongly with CC development via promoting the acquisition of cancer hallmarks. Certain MCs show promise for diagnosis, prognosis and therapy selection due to their distinct expression patterns in normal, premalignant and tumor tissues. This review explains the regulation and biological functions of MCs and highlights the clinical relevance of abnormal MC expression in CC.
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Affiliation(s)
- Srinath Sriharikrishnaa
- Department of Cell & Molecular Biology, Manipal School of Life Sciences, Manipal Academy of Higher Education, Manipal, Karnataka, 576104, India
| | - Femi E John
- Department of Cell & Molecular Biology, Manipal School of Life Sciences, Manipal Academy of Higher Education, Manipal, Karnataka, 576104, India
| | - Medha Bairy
- Department of Cell & Molecular Biology, Manipal School of Life Sciences, Manipal Academy of Higher Education, Manipal, Karnataka, 576104, India
| | - Sachin Shetty
- Department of Cell & Molecular Biology, Manipal School of Life Sciences, Manipal Academy of Higher Education, Manipal, Karnataka, 576104, India
| | - Padmanaban S Suresh
- Department of Bioscience and Engineering, National Institute of Technology Calicut, Kerala, India
| | - Shama P Kabekkodu
- Department of Cell & Molecular Biology, Manipal School of Life Sciences, Manipal Academy of Higher Education, Manipal, Karnataka, 576104, India
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18
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Wang Y, Tang X, Lu J. Convergent and divergent evolution of microRNA-mediated regulation in metazoans. Biol Rev Camb Philos Soc 2024; 99:525-545. [PMID: 37987240 DOI: 10.1111/brv.13033] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2023] [Revised: 11/12/2023] [Accepted: 11/14/2023] [Indexed: 11/22/2023]
Abstract
The evolution of microRNAs (miRNAs) has been studied extensively to understand their roles in gene regulation and evolutionary processes. This review focuses on how miRNA-mediated regulation has evolved in bilaterian animals, highlighting both convergent and divergent evolution. Since animals and plants display significant differences in miRNA biogenesis and target recognition, the 'independent origin' hypothesis proposes that miRNA pathways in these groups independently evolved from the RNA interference (RNAi) pathway, leading to modern miRNA repertoires through convergent evolution. However, recent evidence raises the alternative possibility that the miRNA pathway might have already existed in the last common ancestor of eukaryotes, and that the differences in miRNA pathway and miRNA repertoires among animal and plant lineages arise from lineage-specific innovations and losses of miRNA pathways, miRNA acquisition, and loss of miRNAs after eukaryotic divergence. The repertoire of miRNAs has considerably expanded during bilaterian evolution, primarily through de novo creation and duplication processes, generating new miRNAs. Although ancient functionally established miRNAs are rarely lost, many newly emerged miRNAs are transient and lineage specific, following a birth-death evolutionary pattern aligning with the 'out-of-the-testis' and 'transcriptional control' hypotheses. Our focus then shifts to the convergent molecular evolution of miRNAs. We summarize how miRNA clustering and seed mimicry contribute to this phenomenon, and we review how miRNAs from different sources converge to degrade maternal messenger RNAs (mRNAs) during animal development. Additionally, we describe how miRNAs evolve across species due to changes in sequence, seed shifting, arm switching, and spatiotemporal expression patterns, which can result in variations in target sites among orthologous miRNAs across distant strains or species. We also provide a summary of the current understanding regarding how the target sites of orthologous miRNAs can vary across strains or distantly related species. Although many paralogous miRNAs retain their seed or mature sequences after duplication, alterations can occur in the seed or mature sequences or expression patterns of paralogous miRNAs, leading to functional diversification. We discuss our current understanding of the functional divergence between duplicated miRNAs, and illustrate how the functional diversification of duplicated miRNAs impacts target site evolution. By investigating these topics, we aim to enhance our current understanding of the functions and evolutionary dynamics of miRNAs. Additionally, we shed light on the existing challenges in miRNA evolutionary studies, particularly the complexity of deciphering the role of miRNA-mediated regulatory network evolution in shaping gene expression divergence and phenotypic differences among species.
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Affiliation(s)
- Yirong Wang
- Bioinformatics Center, College of Biology, Hunan University, Changsha, 410082, China
| | - Xiaolu Tang
- State Key Laboratory of Protein and Plant Gene Research, Center for Bioinformatics, School of Life Sciences, Peking University, Beijing, 100871, China
| | - Jian Lu
- State Key Laboratory of Protein and Plant Gene Research, Center for Bioinformatics, School of Life Sciences, Peking University, Beijing, 100871, China
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19
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Ishibashi S, Kamei N, Tsuchikawa Y, Nakamae T, Akimoto T, Miyaki S, Adachi N. Myelin-Specific microRNA-23a/b Cluster Deletion Inhibits Myelination in the Central Nervous System during Postnatal Growth and Aging. Genes (Basel) 2024; 15:402. [PMID: 38674338 PMCID: PMC11049049 DOI: 10.3390/genes15040402] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2024] [Revised: 03/21/2024] [Accepted: 03/23/2024] [Indexed: 04/28/2024] Open
Abstract
Microribonucleic acids (miRNAs) comprising miR-23a/b clusters, specifically miR-23a and miR-27a, are recognized for their divergent roles in myelination within the central nervous system. However, cluster-specific miRNA functions remain controversial as miRNAs within the same cluster have been suggested to function complementarily. This study aims to clarify the role of miR-23a/b clusters in myelination using mice with a miR-23a/b cluster deletion (KO mice), specifically in myelin expressing proteolipid protein (PLP). Inducible conditional KO mice were generated by crossing miR-23a/b clusterflox/flox mice with PlpCre-ERT2 mice; the offspring were injected with tamoxifen at 10 days or 10 weeks of age to induce a myelin-specific miR-23a/b cluster deletion. Evaluation was performed at 10 weeks or 12 months of age and compared with control mice that were not treated with tamoxifen. KO mice exhibit impaired motor function and hypoplastic myelin sheaths in the brain and spinal cord at 10 weeks and 12 months of age. Simultaneously, significant decreases in myelin basic protein (MBP) and PLP expression occur in KO mice. The percentages of oligodendrocyte precursors and mature oligodendrocytes are consistent between the KO and control mice. However, the proportion of oligodendrocytes expressing MBP is significantly lower in KO mice. Moreover, changes in protein expression occur in KO mice, with increased leucine zipper-like transcriptional regulator 1 expression, decreased R-RAS expression, and decreased phosphorylation of extracellular signal-regulated kinases. These findings highlight the significant influence of miR-23a/b clusters on myelination during postnatal growth and aging.
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Affiliation(s)
- Shigeki Ishibashi
- Department of Orthopaedic Surgery, Graduate School of Biomedical and Health Sciences, Hiroshima University, Hiroshima 734-8551, Japan; (S.I.); (T.N.); (S.M.); (N.A.)
| | - Naosuke Kamei
- Department of Orthopaedic Surgery, Graduate School of Biomedical and Health Sciences, Hiroshima University, Hiroshima 734-8551, Japan; (S.I.); (T.N.); (S.M.); (N.A.)
| | - Yuji Tsuchikawa
- Orthopedics and Micro-Surgical Spine Center, Hiroshima City North Medical Center Asa Citizens Hospital, Hiroshima 731-0293, Japan;
| | - Toshio Nakamae
- Department of Orthopaedic Surgery, Graduate School of Biomedical and Health Sciences, Hiroshima University, Hiroshima 734-8551, Japan; (S.I.); (T.N.); (S.M.); (N.A.)
| | - Takayuki Akimoto
- Faculty of Sport Sciences, Waseda University, Tokorozawa 359-1192, Japan;
| | - Shigeru Miyaki
- Department of Orthopaedic Surgery, Graduate School of Biomedical and Health Sciences, Hiroshima University, Hiroshima 734-8551, Japan; (S.I.); (T.N.); (S.M.); (N.A.)
- Medical Center for Translational and Clinical Research, Hiroshima University Hospital, Hiroshima 734-8551, Japan
| | - Nobuo Adachi
- Department of Orthopaedic Surgery, Graduate School of Biomedical and Health Sciences, Hiroshima University, Hiroshima 734-8551, Japan; (S.I.); (T.N.); (S.M.); (N.A.)
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20
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Rossi M, Steklov M, Huberty F, Nguyen T, Marijsse J, Jacques-Hespel C, Najm P, Lonez C, Breman E. Efficient shRNA-based knockdown of multiple target genes for cell therapy using a chimeric miRNA cluster platform. MOLECULAR THERAPY. NUCLEIC ACIDS 2023; 34:102038. [PMID: 37799328 PMCID: PMC10548280 DOI: 10.1016/j.omtn.2023.102038] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/20/2023] [Accepted: 09/15/2023] [Indexed: 10/07/2023]
Abstract
Genome engineering technologies are powerful tools in cell-based immunotherapy to optimize or fine-tune cell functionalities. However, their use for multiple gene edits poses relevant biological and technical challenges. Short hairpin RNA (shRNA)-based cell engineering bypasses these criticalities and represents a valid alternative to CRISPR-based gene editing. Here, we describe a microRNA (miRNA)-based multiplex shRNA platform obtained by combining highly efficient miRNA scaffolds into a chimeric cluster, to deliver up to four shRNA-like sequences. Thanks to its limited size, our cassette could be deployed in a one-step process along with all the CAR components, streamlining the generation of engineered CAR T cells. The plug-and-play design of the shRNA platform allowed us to swap each shRNA-derived guide sequence without affecting the system performance. Appropriately choosing the target sequences, we were able to either achieve a functional KO, or fine-tune the expression levels of the target genes, all without the need for gene editing. Through our strategy we achieved easy, safe, efficient, and tunable modulation of multiple target genes simultaneously. This approach allows for the effective introduction of multiple functionally relevant tweaks in the transcriptome of the engineered cells, which may lead to increased performance in challenging environments, e.g., solid tumors.
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Affiliation(s)
- Matteo Rossi
- Celyad Oncology, 1435 Mont-Saint-Guibert, Belgium
| | | | | | - Thuy Nguyen
- Celyad Oncology, 1435 Mont-Saint-Guibert, Belgium
| | | | | | - Paul Najm
- Celyad Oncology, 1435 Mont-Saint-Guibert, Belgium
| | | | - Eytan Breman
- Celyad Oncology, 1435 Mont-Saint-Guibert, Belgium
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21
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Vaswani CM, Varkouhi AK, Gupta S, Ektesabi AM, Tsoporis JN, Yousef S, Plant PJ, da Silva AL, Cen Y, Tseng YC, Batah SS, Fabro AT, Advani SL, Advani A, Leong-Poi H, Marshall JC, Garcia CC, Rocco PRM, Albaiceta GM, Sebastian-Bolz S, Watts TH, Moraes TJ, Capelozzi VL, Dos Santos CC. Preventing occludin tight-junction disruption via inhibition of microRNA-193b-5p attenuates viral load and influenza-induced lung injury. Mol Ther 2023; 31:2681-2701. [PMID: 37340634 PMCID: PMC10491994 DOI: 10.1016/j.ymthe.2023.06.011] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2023] [Revised: 05/02/2023] [Accepted: 06/14/2023] [Indexed: 06/22/2023] Open
Abstract
Virus-induced lung injury is associated with loss of pulmonary epithelial-endothelial tight junction integrity. While the alveolar-capillary membrane may be an indirect target of injury, viruses may interact directly and/or indirectly with miRs to augment their replication potential and evade the host antiviral defense system. Here, we expose how the influenza virus (H1N1) capitalizes on host-derived interferon-induced, microRNA (miR)-193b-5p to target occludin and compromise antiviral defenses. Lung biopsies from patients infected with H1N1 revealed increased miR-193b-5p levels, marked reduction in occludin protein, and disruption of the alveolar-capillary barrier. In C57BL/6 mice, the expression of miR-193b-5p increased, and occludin decreased, 5-6 days post-infection with influenza (PR8). Inhibition of miR-193b-5p in primary human bronchial, pulmonary microvascular, and nasal epithelial cells enhanced antiviral responses. miR-193b-deficient mice were resistant to PR8. Knockdown of occludin, both in vitro and in vivo, and overexpression of miR-193b-5p reconstituted susceptibility to viral infection. miR-193b-5p inhibitor mitigated loss of occludin, improved viral clearance, reduced lung edema, and augmented survival in infected mice. Our results elucidate how the innate immune system may be exploited by the influenza virus and how strategies that prevent loss of occludin and preserve tight junction function may limit susceptibility to virus-induced lung injury.
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Affiliation(s)
- Chirag M Vaswani
- Department of Physiology, Temerty Faculty of Medicine, University of Toronto, Toronto, ON, Canada; Keenan Research Centre for Biomedical Science, St. Michael's Hospital, Toronto, ON, Canada
| | - Amir K Varkouhi
- Department of Chemistry and Environmental Science, New Jersey Institute of Technology, Newark, NJ, USA
| | - Sahil Gupta
- Keenan Research Centre for Biomedical Science, St. Michael's Hospital, Toronto, ON, Canada; Institute of Medical Sciences, Faculty of Medicine, University of Toronto, Toronto, ON, Canada; Faculty of Medicine, School of Medicine, The University of Queensland, Herston, QLD 4006, Australia
| | - Amin M Ektesabi
- Keenan Research Centre for Biomedical Science, St. Michael's Hospital, Toronto, ON, Canada; Institute of Medical Sciences, Faculty of Medicine, University of Toronto, Toronto, ON, Canada
| | - James N Tsoporis
- Keenan Research Centre for Biomedical Science, St. Michael's Hospital, Toronto, ON, Canada
| | - Sadiya Yousef
- Keenan Research Centre for Biomedical Science, St. Michael's Hospital, Toronto, ON, Canada
| | - Pamela J Plant
- Keenan Research Centre for Biomedical Science, St. Michael's Hospital, Toronto, ON, Canada
| | - Adriana L da Silva
- Laboratory of Pulmonary Investigation, Carlos Chagas Filho Institute of Biophysics, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil; COVID-19 Virus Network from Ministry of Science, Technology, and Innovation, Brazilian Council for Scientific and Technological Development, and Foundation Carlos Chagas Filho Research Support of the State of Rio de Janeiro, Brazil
| | - Yuchen Cen
- Program in Translational Medicine, SickKids Research Institute, Toronto, ON, Canada
| | - Yi-Chieh Tseng
- Program in Translational Medicine, SickKids Research Institute, Toronto, ON, Canada
| | - Sabrina S Batah
- Department of Pathology and Legal Medicine, Ribeirão Preto Medical School, University of São Paulo, São Paulo, Brazil
| | - Alexandre T Fabro
- Department of Pathology and Legal Medicine, Ribeirão Preto Medical School, University of São Paulo, São Paulo, Brazil
| | - Suzanne L Advani
- Keenan Research Centre for Biomedical Science, St. Michael's Hospital, Toronto, ON, Canada
| | - Andrew Advani
- Keenan Research Centre for Biomedical Science, St. Michael's Hospital, Toronto, ON, Canada
| | - Howard Leong-Poi
- Keenan Research Centre for Biomedical Science, St. Michael's Hospital, Toronto, ON, Canada; Institute of Medical Sciences, Faculty of Medicine, University of Toronto, Toronto, ON, Canada
| | - John C Marshall
- Keenan Research Centre for Biomedical Science, St. Michael's Hospital, Toronto, ON, Canada; Institute of Medical Sciences, Faculty of Medicine, University of Toronto, Toronto, ON, Canada
| | - Cristiana C Garcia
- Laboratory of Respiratory, Exanthematic Viruses, Enterovirus and Viral Emergencies, Oswaldo Cruz Institute, FIOCRUZ, Rio de Janeiro, Brazil; Integrated Research Group on Biomarkers. René Rachou Institute, FIOCRUZ Minas, Belo Horizonte, Brazil
| | - Patricia R M Rocco
- Laboratory of Pulmonary Investigation, Carlos Chagas Filho Institute of Biophysics, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil; COVID-19 Virus Network from Ministry of Science, Technology, and Innovation, Brazilian Council for Scientific and Technological Development, and Foundation Carlos Chagas Filho Research Support of the State of Rio de Janeiro, Brazil
| | - Guillermo M Albaiceta
- Departamento de Biología Funcional, Instituto Universitario de Oncología del Principado de Asturias, Universidad de Oviedo, Oviedo, Spain; Unidad de Cuidados Intensivos Cardiológicos, Hospital Universitario Central de Asturias, Oviedo, Spain; CIBER-Enfermedades Respiratorias, Instituto de Salud Carlos III, Madrid, Spain
| | - Steffen Sebastian-Bolz
- Department of Physiology, Temerty Faculty of Medicine, University of Toronto, Toronto, ON, Canada
| | - Tania H Watts
- Department of Immunology, Temerty Faculty of Medicine, University of Toronto, Toronto, ON, Canada
| | - Theo J Moraes
- Program in Translational Medicine, SickKids Research Institute, Toronto, ON, Canada; Department of Pediatrics University of Toronto and Respirology, Hospital for Sick Children, Toronto, ON, Canada
| | - Vera L Capelozzi
- Department of Pathology, University of São Paulo, São Paulo, Brazil
| | - Claudia C Dos Santos
- Department of Physiology, Temerty Faculty of Medicine, University of Toronto, Toronto, ON, Canada; Keenan Research Centre for Biomedical Science, St. Michael's Hospital, Toronto, ON, Canada; Institute of Medical Sciences, Faculty of Medicine, University of Toronto, Toronto, ON, Canada; Laboratory Medicine and Pathobiology, Faculty of Medicine, University of Toronto, Toronto, ON, Canada; Interdepartmental Division of Critical Care, St Michael's Hospital, University of Toronto, Toronto, ON, Canada.
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22
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Shafique R, Mahjabeen I, Bibi K, Kalsoom F, Rizwan M, Ashraf NS, Mehmood A, Ul Haq MF, Abbasi SF, Saeed N, Kayani MA. miRNA-767 and its binding site polymorphism in the mTOR gene act as potential biomarkers for female reproductive cancers. Future Oncol 2023; 19:1929-1943. [PMID: 37781867 DOI: 10.2217/fon-2022-1055] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/03/2023] Open
Abstract
Aims: The present study aimed to understand the relationship between the mTOR gene SNP (rs2536) and reproductive cancer risk. The expression level of miRNA-767 was also assessed. Methods: 700 tumor samples (300 breast, 200 ovarian and 200 cervical cancers), along with adjacent uninvolved control tissue, were used. rs2536 was screened using Tetra-ARMS PCR and expression level of miRNA-767 was assessed using quantitative PCR. Results: The frequency of the homozygous mutant genotype of rs2536 was observed significantly higher in breast (p < 0.04), ovarian (p < 0.005) and cervical (p < 0.003) cancers. Significant downregulation of miRNA-767 was observed in tumors compared with controls. Conclusion: The present study demonstrates that increased mutant frequency of rs2536 and deregulation of miRNA-767 are associated with increased reproductive cancer risk.
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Affiliation(s)
- Rabia Shafique
- Cancer Genetics & Epigenetics Research Group, Department of Biosciences, COMSATS University, Park Road Islamabad, Pakistan
| | - Ishrat Mahjabeen
- Cancer Genetics & Epigenetics Research Group, Department of Biosciences, COMSATS University, Park Road Islamabad, Pakistan
| | - Kashaf Bibi
- Cancer Genetics & Epigenetics Research Group, Department of Biosciences, COMSATS University, Park Road Islamabad, Pakistan
| | - Farah Kalsoom
- Department of Pathology, Sir Ganga Ram Hospital, Lahore, Pakistan
| | - Muhammad Rizwan
- Cancer Genetics & Epigenetics Research Group, Department of Biosciences, COMSATS University, Park Road Islamabad, Pakistan
| | - Nida Sarosh Ashraf
- Cancer Genetics & Epigenetics Research Group, Department of Biosciences, COMSATS University, Park Road Islamabad, Pakistan
| | - Azhar Mehmood
- Cancer Genetics & Epigenetics Research Group, Department of Biosciences, COMSATS University, Park Road Islamabad, Pakistan
| | - Maria Fazal Ul Haq
- Cancer Genetics & Epigenetics Research Group, Department of Biosciences, COMSATS University, Park Road Islamabad, Pakistan
| | - Sumaira Fida Abbasi
- Cancer Genetics & Epigenetics Research Group, Department of Biosciences, COMSATS University, Park Road Islamabad, Pakistan
| | - Nadia Saeed
- Cancer Genetics & Epigenetics Research Group, Department of Biosciences, COMSATS University, Park Road Islamabad, Pakistan
| | - Mahmood Akhtar Kayani
- Cancer Genetics & Epigenetics Research Group, Department of Biosciences, COMSATS University, Park Road Islamabad, Pakistan
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23
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Sprenkle NT, Winn NC, Bunn KE, Zhao Y, Park DJ, Giese BG, Karijolich JJ, Ansel KM, Serezani CH, Hasty AH, Pua HH. The miR-23-27-24 clusters drive lipid-associated macrophage proliferation in obese adipose tissue. Cell Rep 2023; 42:112928. [PMID: 37542720 PMCID: PMC10712211 DOI: 10.1016/j.celrep.2023.112928] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2023] [Revised: 06/19/2023] [Accepted: 07/17/2023] [Indexed: 08/07/2023] Open
Abstract
Identifying molecular circuits that control adipose tissue macrophage (ATM) function is necessary to understand how ATMs contribute to tissue homeostasis and obesity-induced insulin resistance. In this study, we find that mice with a myeloid-specific knockout of the miR-23-27-24 clusters of microRNAs (miRNAs) gain less weight on a high-fat diet but exhibit worsened glucose and insulin tolerance. Analysis of ATMs from these mice shows selectively reduced numbers and proliferation of a recently reported subset of lipid-associated CD9+Trem2+ ATMs (lipid-associated macrophages [LAMs]). Leveraging the role of miRNAs to control networks of genes, we use RNA sequencing (RNA-seq), functional screens, and biochemical assays to identify candidate target transcripts that regulate proliferation-associated signaling. We determine that miR-23 directly targets the mRNA of Eif4ebp2, a gene that restricts protein synthesis and proliferation in macrophages. Altogether, our study demonstrates that control of proliferation of a protective subset of LAMs by noncoding RNAs contributes to protection against diet-induced obesity metabolic dysfunction.
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Affiliation(s)
- Neil T Sprenkle
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Nathan C Winn
- Department of Molecular Physiology and Biophysics, Vanderbilt University, Nashville, TN, USA
| | - Kaitlyn E Bunn
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Yang Zhao
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Deborah J Park
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Brenna G Giese
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, TN, USA
| | - John J Karijolich
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, TN, USA; Vanderbilt Center for Immunobiology and Vanderbilt Institute for Infection, Immunology, and Inflammation, Vanderbilt University Medical Center, Nashville, TN, USA; Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN, USA; Vanerbilt-Ingram Cancer Center, Nashville, TN, USA
| | - K Mark Ansel
- Department of Microbiology and Immunology and Sandler Asthma Basic Research Center, University of California, San Francisco, San Francisco, CA, USA
| | - C Henrique Serezani
- Vanderbilt Center for Immunobiology and Vanderbilt Institute for Infection, Immunology, and Inflammation, Vanderbilt University Medical Center, Nashville, TN, USA; Division of Infectious Diseases, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Alyssa H Hasty
- Department of Molecular Physiology and Biophysics, Vanderbilt University, Nashville, TN, USA; Vanderbilt Center for Immunobiology and Vanderbilt Institute for Infection, Immunology, and Inflammation, Vanderbilt University Medical Center, Nashville, TN, USA; Veterans Affairs, Tennessee Valley Healthcare System, Nashville, TN, USA
| | - Heather H Pua
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, TN, USA; Vanderbilt Center for Immunobiology and Vanderbilt Institute for Infection, Immunology, and Inflammation, Vanderbilt University Medical Center, Nashville, TN, USA.
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24
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Jiménez-Ruiz CA, de la Herrán R, Robles F, Navajas-Pérez R, Cross I, Rebordinos L, Ruiz-Rejón C. miR-430 microRNA Family in Fishes: Molecular Characterization and Evolution. Animals (Basel) 2023; 13:2399. [PMID: 37570208 PMCID: PMC10417697 DOI: 10.3390/ani13152399] [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: 04/12/2023] [Revised: 07/21/2023] [Accepted: 07/22/2023] [Indexed: 08/13/2023] Open
Abstract
The miR-430 microRNA family has been described in multiple fish species as one of the first microRNAs expressed by the zygote. It has been suggested that this family is implicated in maternal mRNA elimination, but may also play a role in steroidogenesis, sexual differentiation, and flatfish metamorphosis. The miR-430 sequences have been found in multiple-copy tandem clusters but evidence of their conservation outside of teleost fishes is scarce. In the present study, we have characterized the tandem repeats organization of these microRNAs in different fish species, both model and of interest in aquaculture. A phylogenetic analysis of this family has allowed us to identify that the miR-430 duplication, which took place before the Chondrostei and Neopterygii groups' divergence, has resulted in three variants ("a", "b", and "c"). According to our data, variant "b" is the most closely related to the ancestral sequence. Furthermore, we have detected isolated instances of the miR-430 repeat subunit in some species, which suggests that this microRNA family may be affected by DNA rearrangements. This study provides new data about the abundance, variability, and organization of the miR-430 family in fishes.
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Affiliation(s)
- Claudio A. Jiménez-Ruiz
- Departamento de Genética, Facultad de Ciencias, Universidad de Granada, Avda. Fuentenueva s/n, 18071 Granada, Spain
| | - Roberto de la Herrán
- Departamento de Genética, Facultad de Ciencias, Universidad de Granada, Avda. Fuentenueva s/n, 18071 Granada, Spain
| | - Francisca Robles
- Departamento de Genética, Facultad de Ciencias, Universidad de Granada, Avda. Fuentenueva s/n, 18071 Granada, Spain
| | - Rafael Navajas-Pérez
- Departamento de Genética, Facultad de Ciencias, Universidad de Granada, Avda. Fuentenueva s/n, 18071 Granada, Spain
| | - Ismael Cross
- Área de Genética, Facultad de Ciencias del Mar y Ambientales, Instituto Universitario de Investigación Marina (INMAR), Universidad de Cádiz, 11510 Cádiz, Spain
| | - Laureana Rebordinos
- Área de Genética, Facultad de Ciencias del Mar y Ambientales, Instituto Universitario de Investigación Marina (INMAR), Universidad de Cádiz, 11510 Cádiz, Spain
| | - Carmelo Ruiz-Rejón
- Departamento de Genética, Facultad de Ciencias, Universidad de Granada, Avda. Fuentenueva s/n, 18071 Granada, Spain
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25
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Munkhzul C, Lee JM, Kim B, Nguyen TTM, Ginting RP, Jeong D, Kim YK, Lee MW, Lee M. H19X-encoded microRNAs induced by IL-4 in adipocyte precursors regulate proliferation to facilitate differentiation. Biol Direct 2023; 18:32. [PMID: 37322541 PMCID: PMC10273709 DOI: 10.1186/s13062-023-00388-4] [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: 12/29/2022] [Accepted: 06/06/2023] [Indexed: 06/17/2023] Open
Abstract
Adipose tissue, an organ critical for systemic energy homeostasis, is influenced by type 2 immunity in its development and function. The type 2 cytokine interleukin (IL)-4 induces the proliferation of bipotential adipocyte precursors (APs) in white fat tissue and primes these cells for differentiation into beige adipocytes, which are specialized for thermogenesis. However, the underlying mechanisms have not yet been comprehensively examined. Here, we identified six microRNA (miRNA) genes upregulated upon IL-4 stimulation in APs, miR-322, miR-503, miR-351, miR-542, miR-450a, and miR-450b; these are encoded in the H19X locus of the genome. Their expression is positively regulated by the transcription factor Klf4, whose expression also increases upon IL-4 stimulation. These miRNAs shared a large set of target genes, of which 381 genes were downregulated in mRNA expression upon IL-4 stimulation and enriched in Wnt signaling pathways. Two genes with downregulated expression, Ccnd1 and Fzd6, were repressed by H19X-encoded miRNAs. Additionally, the Wnt signaling activator LiCl downregulated the expression of this group of miRNAs in APs, indicating that Wnt signaling-related genes and these miRNAs form a double-negative feedback regulatory loop. This miRNA/Wnt feedback regulation modulated the elevated proliferation of APs induced by IL-4 stimulation and contributed to priming them for beige adipocyte differentiation. Moreover, the aberrant expression of these miRNAs attenuates the differentiation of APs into beige adipocytes. Collectively, our results suggest that H19X-encoded miRNAs facilitate the transition of APs from proliferation to differentiation in the IL-4-mediated regulation.
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Affiliation(s)
- Choijamts Munkhzul
- Soonchunhyang Institute of Medi-bio Science, Soonchunhyang University, Cheonan, 31151, Korea
- Department of Integrated Biomedical Science, Soonchunhyang University, Cheonan, 31151, Korea
| | - Ji-Min Lee
- Soonchunhyang Institute of Medi-bio Science, Soonchunhyang University, Cheonan, 31151, Korea
| | - Boseon Kim
- Soonchunhyang Institute of Medi-bio Science, Soonchunhyang University, Cheonan, 31151, Korea
- Department of Integrated Biomedical Science, Soonchunhyang University, Cheonan, 31151, Korea
| | - Thi Thanh My Nguyen
- Soonchunhyang Institute of Medi-bio Science, Soonchunhyang University, Cheonan, 31151, Korea
| | - Rehna Paula Ginting
- Soonchunhyang Institute of Medi-bio Science, Soonchunhyang University, Cheonan, 31151, Korea
- Department of Integrated Biomedical Science, Soonchunhyang University, Cheonan, 31151, Korea
| | - Dahee Jeong
- Soonchunhyang Institute of Medi-bio Science, Soonchunhyang University, Cheonan, 31151, Korea
- Department of Integrated Biomedical Science, Soonchunhyang University, Cheonan, 31151, Korea
| | - Young-Kook Kim
- Department of Biochemistry, Chonnam National University Medical School, Hwasun, 58128, Korea
| | - Min-Woo Lee
- Soonchunhyang Institute of Medi-bio Science, Soonchunhyang University, Cheonan, 31151, Korea.
- Department of Integrated Biomedical Science, Soonchunhyang University, Cheonan, 31151, Korea.
| | - Mihye Lee
- Soonchunhyang Institute of Medi-bio Science, Soonchunhyang University, Cheonan, 31151, Korea.
- Department of Integrated Biomedical Science, Soonchunhyang University, Cheonan, 31151, Korea.
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26
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Zhang D, Lu W, Zhuo Z, Wang Y, Zhang W, Zhang M. Comprehensive analysis of a cuproptosis-related ceRNA network implicates a potential endocrine therapy resistance mechanism in ER-positive breast cancer. BMC Med Genomics 2023; 16:96. [PMID: 37143115 PMCID: PMC10161630 DOI: 10.1186/s12920-023-01511-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2022] [Accepted: 04/07/2023] [Indexed: 05/06/2023] Open
Abstract
BACKGROUND While adjuvant endocrine therapy (ET) may decrease the mortality rate of estrogen receptor-positive (ER+) breast cancer (BC), the likelihood of relapse and metastasis due to ET resistance remains high. Cuproptosis is a recently discovered regulated cell death (RCD), whose role in tumors has yet to be elucidated. Thus, there is a need to study its specific regulatory mechanism in resistance to ET in BC, to identify novel therapeutic targets. METHODS The prognostic cuproptosis-related genes (CRGs) in ER+ BC were filtered by undergoing Cox regression and least absolute shrinkage and selection operator (LASSO) regression analyses in TCGA-BRCA, and a CRGs risk signature was constructed using the correlation coefficient. Immune infiltration analysis, immune function analysis, tumor microenvironment (TME) analysis, immune checkpoint analysis, immunotherapy response analysis, drug sensitivity analysis, and pathway activation analysis were carried out among the high- and low-risk groups in turn. The central CRG of cuproptosis in ER+ BC resistance to ET was acquired through the intersection of protein interaction network (PPI) analysis, genes differentially expressed (DEGs) between human BC cells LCC9 and MCF-7 (GSE159968), and CRGs with prognostic significance in TCGA-BRCA ER+ BC. The miRNAs upstream of the core CRGs were predicted based on the intersection of 4 databases, miRDB, RNA22, miRWalk, and RNAlnter. Candidate miRNAs consisted of the intersection of predicted miRNAs and miRNAs differentially expressed in the LCC9 and MCF-7 cell lines (GSE159979). Candidate lncRNAs were the intersection of the differential lncRNAs from the LCC9 and MCF-7 cell lines and the survival-related lncRNAs obtained from a univariate Cox regression analysis. Pearson's correlation analysis was performed between mRNA-miRNA, miRNA-lncRNA, and mRNA-lncRNA expression separately. RESULTS We constructed A risk signature of 4-CRGs to predict the prognosis of ER+ BC in TCGA-BRCA, a risk score = DLD*0.378 + DBT*0.201 + DLAT*0.380 + ATP7A*0.447 was used as the definition of the formula. There were significant differences between the high- and low-risk groups based on the risk score of 4-CRGs in aspects of immune infiltration, immune function, expression levels of immune checkpoint genes, and signaling pathways. DLD was determined to be the central CRG of cuproptosis in ER+ BC resistance to ET through the intersection of the PPI network analysis, DEGs between LCC9 and MCF-7 and 4-CRGs. Two miRNAs hsa-miR-370-3p and hsa-miR-432-5p were found taking DLD mRNA as a target, and the lncRNA C6orf99 has been hypothesized to be a competitive endogenous RNA that regulates DLD mRNA expression by sponging off hsa-miR-370-3p and hsa-miR-432-5p. CONCLUSION This study built a prognostic model based on genes related to cuproptosis in ER+ BC. We considered DLD to be the core gene associated with resistance to ET in ER+ BC via copper metabolism. The search for promising therapeutic targets led to the establishment of a cuproptosis-related ceRNA network C6orf99/hsa-miR-370-3p and hsa-miR-432-5p/DLD.
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Affiliation(s)
- Dongni Zhang
- Oncology Department, China Academy of Chinese Medical Sciences Guang'anmen Hospital, Beijing, China
| | - Wenping Lu
- Oncology Department, China Academy of Chinese Medical Sciences Guang'anmen Hospital, Beijing, China.
| | - Zhili Zhuo
- Oncology Department, China Academy of Chinese Medical Sciences Guang'anmen Hospital, Beijing, China
| | - Yanan Wang
- Oncology Department, China Academy of Chinese Medical Sciences Guang'anmen Hospital, Beijing, China
| | - Weixuan Zhang
- Oncology Department, China Academy of Chinese Medical Sciences Guang'anmen Hospital, Beijing, China
| | - Mengfan Zhang
- Oncology Department, China Academy of Chinese Medical Sciences Guang'anmen Hospital, Beijing, China
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27
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Tsuchikawa Y, Kamei N, Sanada Y, Nakamae T, Harada T, Imaizumi K, Akimoto T, Miyaki S, Adachi N. Deficiency of MicroRNA-23-27-24 Clusters Exhibits the Impairment of Myelination in the Central Nervous System. Neural Plast 2023; 2023:8938674. [PMID: 37006814 PMCID: PMC10060068 DOI: 10.1155/2023/8938674] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2022] [Revised: 01/25/2023] [Accepted: 03/12/2023] [Indexed: 04/04/2023] Open
Abstract
Several microRNAs (miRNAs), including miR-23 and miR-27a have been reportedly involved in regulating myelination in the central nervous system. Although miR-23 and miR-27a form clusters in vivo and the clustered miRNAs are known to perform complementary functions, the role of these miRNA clusters in myelination has not been studied. To investigate the role of miR-23-27-24 clusters in myelination, we generated miR-23-27-24 cluster knockout mice and evaluated myelination in the brain and spinal cord. Our results showed that 10-week-old knockout mice had reduced motor function in the hanging wire test compared to the wild-type mice. At 4 weeks, 10 weeks, and 12 months of age, knockout mice showed reduced myelination compared to wild-type mice. The expression levels of myelin basic protein and myelin proteolipid protein were also significantly lower in the knockout mice compared to the wild-type mice. Although differentiation of oligodendrocyte progenitor cells to oligodendrocytes was not inhibited in the knockout mice, the percentage of oligodendrocytes expressing myelin basic protein was significantly lower in 4-week-old knockout mice than that in wild-type mice. Proteome analysis and western blotting showed increased expression of leucine-zipper-like transcription regulator 1 (LZTR1) and decreased expression of R-RAS and phosphorylated extracellular signal-regulated kinase 1/2 (pERK1/2) in the knockout mice. In summary, loss of miR-23-27-24 clusters reduces myelination and compromises motor functions in mice. Further, LZTR1, which regulates R-RAS upstream of the ERK1/2 pathway, a signal that promotes myelination, has been identified as a novel target of the miR-23-27-24 cluster in this study.
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Affiliation(s)
- Yuji Tsuchikawa
- Department of Orthopaedic Surgery, Graduate School of Biomedical and Health Sciences, Hiroshima University, Hiroshima 7348551, Japan
| | - Naosuke Kamei
- Department of Orthopaedic Surgery, Graduate School of Biomedical and Health Sciences, Hiroshima University, Hiroshima 7348551, Japan
| | - Yohei Sanada
- Department of Orthopaedic Surgery, Graduate School of Biomedical and Health Sciences, Hiroshima University, Hiroshima 7348551, Japan
- Medical Center for Translational and Clinical Research, Hiroshima University Hospital, Hiroshima 7348551, Japan
| | - Toshio Nakamae
- Department of Orthopaedic Surgery, Graduate School of Biomedical and Health Sciences, Hiroshima University, Hiroshima 7348551, Japan
| | - Takahiro Harada
- Department of Orthopaedic Surgery, Graduate School of Biomedical and Health Sciences, Hiroshima University, Hiroshima 7348551, Japan
| | - Kazunori Imaizumi
- Department of Biochemistry, Graduate School of Biomedical and Health Sciences, Hiroshima University, Hiroshima 7348551, Japan
| | - Takayuki Akimoto
- Faculty of Sport Sciences, Waseda University, Tokorozawa 3591192, Japan
| | - Shigeru Miyaki
- Department of Orthopaedic Surgery, Graduate School of Biomedical and Health Sciences, Hiroshima University, Hiroshima 7348551, Japan
- Medical Center for Translational and Clinical Research, Hiroshima University Hospital, Hiroshima 7348551, Japan
| | - Nobuo Adachi
- Department of Orthopaedic Surgery, Graduate School of Biomedical and Health Sciences, Hiroshima University, Hiroshima 7348551, Japan
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28
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Fedorova V, Amruz Cerna K, Oppelt J, Pospisilova V, Barta T, Mraz M, Bohaciakova D. MicroRNA Profiling of Self-Renewing Human Neural Stem Cells Reveals Novel Sets of Differentially Expressed microRNAs During Neural Differentiation In Vitro. Stem Cell Rev Rep 2023:10.1007/s12015-023-10524-2. [PMID: 36918496 PMCID: PMC10366325 DOI: 10.1007/s12015-023-10524-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/28/2023] [Indexed: 03/16/2023]
Abstract
The involvement of microRNAs (miRNAs) in orchestrating self-renewal and differentiation of stem cells has been revealed in a number of recent studies. And while in human pluripotent stem cells, miRNAs have been directly linked to the core pluripotency network, including the cell cycle regulation and the maintenance of the self-renewing capacity, their role in the onset of differentiation in other contexts, such as determination of neural cell fate, remains poorly described. To bridge this gap, we used three model cell types to study miRNA expression patterns: human embryonic stem cells (hESCs), hESCs-derived self-renewing neural stem cells (NSCs), and differentiating NSCs. The comprehensive miRNA profiling presented here reveals novel sets of miRNAs differentially expressed during human neural cell fate determination in vitro. Furthermore, we report a miRNA expression profile of self-renewing human NSCs, which has been lacking to this date. Our data also indicates that miRNA clusters enriched in NSCs share the target-determining seed sequence with cell cycle regulatory miRNAs expressed in pluripotent hESCs. Lastly, our mechanistic experiments confirmed that cluster miR-17-92, one of the NSCs-enriched clusters, is directly transcriptionally regulated by transcription factor c-MYC.
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Affiliation(s)
- Veronika Fedorova
- Department of Histology and Embryology, Faculty of Medicine, Masaryk University, Brno, Czech Republic
| | - Katerina Amruz Cerna
- Department of Histology and Embryology, Faculty of Medicine, Masaryk University, Brno, Czech Republic
| | - Jan Oppelt
- Department of Pathology and Laboratory Medicine, Division of Neuropathology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Veronika Pospisilova
- Department of Histology and Embryology, Faculty of Medicine, Masaryk University, Brno, Czech Republic
| | - Tomas Barta
- Department of Histology and Embryology, Faculty of Medicine, Masaryk University, Brno, Czech Republic
| | - Marek Mraz
- Central European Institute of Technology, Masaryk University, Brno, Czech Republic.,Department of Internal Medicine, Hematology and Oncology, University Hospital Brno and Faculty of Medicine, Masaryk University, Brno, Czech Republic
| | - Dasa Bohaciakova
- Department of Histology and Embryology, Faculty of Medicine, Masaryk University, Brno, Czech Republic. .,International Clinical Research Center (ICRC), St. Anne's University Hospital, Brno, Czech Republic.
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29
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Vilimova M, Pfeffer S. Post-transcriptional regulation of polycistronic microRNAs. WILEY INTERDISCIPLINARY REVIEWS. RNA 2023; 14:e1749. [PMID: 35702737 DOI: 10.1002/wrna.1749] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Revised: 05/20/2022] [Accepted: 05/24/2022] [Indexed: 02/02/2023]
Abstract
An important proportion of microRNA (miRNA) genes tend to lie close to each other within animal genomes. Such genomic organization is generally referred to as miRNA clusters. Even though many miRNA clusters have been greatly studied, most attention has been usually focused on functional impacts of clustered miRNA co-expression. However, there is also another compelling aspect about these miRNA clusters, their polycistronic nature. Being transcribed on a single RNA precursor, polycistronic miRNAs benefit from common transcriptional regulation allowing their coordinated expression. And yet, numerous reports have revealed striking discrepancies in the accumulation of mature miRNAs produced from the same cluster. Indeed, the larger polycistronic transcripts can act as platforms providing unforeseen post-transcriptional regulatory mechanisms controlling individual miRNA processing, thus leading to differential miRNA expression, and sometimes even challenging the general assumption that polycistronic miRNAs are co-expressed. In this review, we aim to address the current knowledge about how miRNA polycistrons are post-transcriptionally regulated. In particular, we will focus on the mechanisms occurring at the level of the primary transcript, which are highly relevant for individual miRNA processing and as such have a direct repercussion on miRNA function within the cell. This article is categorized under: RNA Processing > Processing of Small RNAs Regulatory RNAs/RNAi/Riboswitches > Biogenesis of Effector Small RNAs RNA Interactions with Proteins and Other Molecules > RNA-Protein Complexes.
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Affiliation(s)
- Monika Vilimova
- Architecture et Réactivité de l'ARN, Institut de Biologie Moléculaire et Cellulaire du CNRS, Université de Strasbourg, Strasbourg, France
| | - Sébastien Pfeffer
- Architecture et Réactivité de l'ARN, Institut de Biologie Moléculaire et Cellulaire du CNRS, Université de Strasbourg, Strasbourg, France
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30
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Niu H, Pang Y, Xie L, Yu Q, Shen Y, Li J, Xu X. Clustering pattern and evolution characteristic of microRNAs in grass carp (Ctenopharyngodon idella). BMC Genomics 2023; 24:73. [PMID: 36782132 PMCID: PMC9926789 DOI: 10.1186/s12864-023-09159-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2022] [Accepted: 01/31/2023] [Indexed: 02/15/2023] Open
Abstract
BACKGROUND A considerable fraction of microRNAs (miRNAs) are highly conserved, and certain miRNAs correspond to genomic clusters. The clustering of miRNAs can be advantageous, possibly by allowing coordinated expression. However, little is known about the evolutionary forces responsible for the loss and acquisition of miRNA and miRNA clusters. RESULTS The results demonstrated that several novel miRNAs arose throughout grass carp evolution. Duplication and de novo production were critical strategies for miRNA cluster formation. Duplicates accounted for a smaller fraction of the expansion in the grass carp miRNA than de novo creation. Clustered miRNAs are more conserved and change slower, whereas unique miRNAs usually have high evolution rates and low expression levels. The expression level of miRNA expression in clusters is strongly correlated. CONCLUSIONS This study examines the genomic distribution, evolutionary background, and expression regulation of grass carp miRNAs. Our findings provide novel insights into the genesis and development of miRNA clusters in teleost.
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Affiliation(s)
- Huiqin Niu
- grid.412514.70000 0000 9833 2433Key Laboratory of Freshwater Aquatic Genetic Resources Ministry of Agriculture and Rural Affairs, Shanghai Ocean University, Shanghai, China ,grid.412514.70000 0000 9833 2433National Demonstration Center for Experimental Fisheries Science Education, Shanghai Ocean University, Shanghai, China ,grid.412514.70000 0000 9833 2433Shanghai Engineering Research Center of Aquaculture, Shanghai Ocean University, Shanghai, China
| | - Yifan Pang
- grid.412514.70000 0000 9833 2433Key Laboratory of Freshwater Aquatic Genetic Resources Ministry of Agriculture and Rural Affairs, Shanghai Ocean University, Shanghai, China ,grid.412514.70000 0000 9833 2433National Demonstration Center for Experimental Fisheries Science Education, Shanghai Ocean University, Shanghai, China ,grid.412514.70000 0000 9833 2433Shanghai Engineering Research Center of Aquaculture, Shanghai Ocean University, Shanghai, China
| | - Lingli Xie
- grid.412514.70000 0000 9833 2433Key Laboratory of Freshwater Aquatic Genetic Resources Ministry of Agriculture and Rural Affairs, Shanghai Ocean University, Shanghai, China ,grid.412514.70000 0000 9833 2433National Demonstration Center for Experimental Fisheries Science Education, Shanghai Ocean University, Shanghai, China ,grid.412514.70000 0000 9833 2433Shanghai Engineering Research Center of Aquaculture, Shanghai Ocean University, Shanghai, China
| | - Qiaozhen Yu
- grid.412514.70000 0000 9833 2433Key Laboratory of Freshwater Aquatic Genetic Resources Ministry of Agriculture and Rural Affairs, Shanghai Ocean University, Shanghai, China ,grid.412514.70000 0000 9833 2433National Demonstration Center for Experimental Fisheries Science Education, Shanghai Ocean University, Shanghai, China ,grid.412514.70000 0000 9833 2433Shanghai Engineering Research Center of Aquaculture, Shanghai Ocean University, Shanghai, China
| | - Yubang Shen
- grid.412514.70000 0000 9833 2433Key Laboratory of Freshwater Aquatic Genetic Resources Ministry of Agriculture and Rural Affairs, Shanghai Ocean University, Shanghai, China ,grid.412514.70000 0000 9833 2433National Demonstration Center for Experimental Fisheries Science Education, Shanghai Ocean University, Shanghai, China ,grid.412514.70000 0000 9833 2433Shanghai Engineering Research Center of Aquaculture, Shanghai Ocean University, Shanghai, China
| | - Jiale Li
- Key Laboratory of Freshwater Aquatic Genetic Resources Ministry of Agriculture and Rural Affairs, Shanghai Ocean University, Shanghai, China. .,National Demonstration Center for Experimental Fisheries Science Education, Shanghai Ocean University, Shanghai, China. .,Shanghai Engineering Research Center of Aquaculture, Shanghai Ocean University, Shanghai, China.
| | - Xiaoyan Xu
- Key Laboratory of Freshwater Aquatic Genetic Resources Ministry of Agriculture and Rural Affairs, Shanghai Ocean University, Shanghai, China. .,National Demonstration Center for Experimental Fisheries Science Education, Shanghai Ocean University, Shanghai, China. .,Shanghai Engineering Research Center of Aquaculture, Shanghai Ocean University, Shanghai, China.
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31
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Komatsu S, Kitai H, Suzuki HI. Network Regulation of microRNA Biogenesis and Target Interaction. Cells 2023; 12:306. [PMID: 36672241 PMCID: PMC9856966 DOI: 10.3390/cells12020306] [Citation(s) in RCA: 57] [Impact Index Per Article: 28.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2022] [Revised: 01/09/2023] [Accepted: 01/12/2023] [Indexed: 01/15/2023] Open
Abstract
MicroRNAs (miRNAs) are versatile, post-transcriptional regulators of gene expression. Canonical miRNAs are generated through the two-step DROSHA- and DICER-mediated processing of primary miRNA (pri-miRNA) transcripts with optimal or suboptimal features for DROSHA and DICER cleavage and loading into Argonaute (AGO) proteins, whereas multiple hairpin-structured RNAs are encoded in the genome and could be a source of non-canonical miRNAs. Recent advances in miRNA biogenesis research have revealed details of the structural basis of miRNA processing and cluster assistance mechanisms that facilitate the processing of suboptimal hairpins encoded together with optimal hairpins in polycistronic pri-miRNAs. In addition, a deeper investigation of miRNA-target interaction has provided insights into the complexity of target recognition with distinct outcomes, including target-mediated miRNA degradation (TDMD) and cooperation in target regulation by multiple miRNAs. Therefore, the coordinated or network regulation of both miRNA biogenesis and miRNA-target interaction is prevalent in miRNA biology. Alongside recent advances in the mechanistic investigation of miRNA functions, this review summarizes recent findings regarding the ordered regulation of miRNA biogenesis and miRNA-target interaction.
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Affiliation(s)
- Shintaro Komatsu
- Division of Molecular Oncology, Center for Neurological Diseases and Cancer, Nagoya University Graduate School of Medicine, Nagoya 466-8550, Japan
- Department of Nephrology, Nagoya University Graduate School of Medicine, Nagoya 466-8550, Japan
| | - Hiroki Kitai
- Department of Nephrology, Nagoya University Graduate School of Medicine, Nagoya 466-8550, Japan
- Division of Nephrology, Department of Medicine, Duke University School of Medicine, Durham, NC 27710, USA
| | - Hiroshi I. Suzuki
- Division of Molecular Oncology, Center for Neurological Diseases and Cancer, Nagoya University Graduate School of Medicine, Nagoya 466-8550, Japan
- Institute for Glyco-Core Research (iGCORE), Nagoya University, Nagoya 464-8601, Japan
- Center for One Medicine Innovative Translational Research, Gifu University Institute for Advanced Study, Gifu 501-1193, Japan
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32
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Lu B, Zhu Y, Wu J, Qiu H, Wang J, Ma Z, Jia K. LncRNA34977 promotes the proliferation, migration, and invasion and inhibits the apoptosis of canine mammary tumors by regulating the expression of miR-8881/ELAVL4. Funct Integr Genomics 2023; 23:31. [PMID: 36604379 PMCID: PMC9816241 DOI: 10.1007/s10142-022-00955-4] [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: 09/02/2022] [Revised: 12/27/2022] [Accepted: 12/28/2022] [Indexed: 01/07/2023]
Abstract
Long-stranded noncoding RNAs (lncRNAs) play different roles in various diseases. lncRNA34977 has been shown to play a relevant role the development of canine mammary tumors (CMTs). However, the mechanism of lncRNA34977 in canine mammary tumors has not been fully investigated. The aim of this study was to investigate the effects of lncRNA34977 on the proliferation, migration, invasion, and apoptosis of canine mammary tumor (CMT) cells through the regulation of miR-8881/ELAVL4 expression. The apoptosis was detected by an in situ fluorescence assay and flow cytometry. The expression levels were analyzed by RT-qPCR. CCK-8, colony formation, wound healing, and Transwell assays were used to assess the proliferation, migration, and invasion. The expression of protein was detected by western blot. The siRNA-induced silencing of lncRNA34977 promoted the apoptosis of CHMp cells, and in overexpression of lncRNA34977, the result is the opposite. LncRNA34977 has a direct targeting relationship with miR-8881 and that miR-8881 is correlated with ELAVL4. Transfection of miR-8881 mimics inhibited the proliferation, migration, invasion, and promoted the apoptosis of CHMp cells of CHMp cells. In the transfection with miR-8881 inhibitors, the result is the opposite. Co-transfected with lncRNA34977, miR-8881, or ELAVL4, we found that lncRNA34977 could regulate the expression of miR-8881 or ELAVL4. Our study shows that lncRNA34977 promotes the proliferation, migration, and invasion and suppresses the apoptosis of CMT cells by regulating the expression of miR-8881/ELAVL4.
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Affiliation(s)
- Baochun Lu
- College of Veterinary Medicine, South China Agricultural University, Guangzhou, 510642, China.,Guangdong Provincial Key Laboratory of Prevention and Control for Severe Clinical Animal Diseases, Guangzhou, 510642, China.,Guangdong Technological Engineering Research Center for Pet, Guangzhou, 510642, China
| | - Yufan Zhu
- College of Veterinary Medicine, South China Agricultural University, Guangzhou, 510642, China.,Guangdong Provincial Key Laboratory of Prevention and Control for Severe Clinical Animal Diseases, Guangzhou, 510642, China.,Guangdong Technological Engineering Research Center for Pet, Guangzhou, 510642, China
| | - Juye Wu
- College of Veterinary Medicine, South China Agricultural University, Guangzhou, 510642, China.,Guangdong Provincial Key Laboratory of Prevention and Control for Severe Clinical Animal Diseases, Guangzhou, 510642, China.,Guangdong Technological Engineering Research Center for Pet, Guangzhou, 510642, China
| | - Huidan Qiu
- College of Veterinary Medicine, South China Agricultural University, Guangzhou, 510642, China.,Guangdong Provincial Key Laboratory of Prevention and Control for Severe Clinical Animal Diseases, Guangzhou, 510642, China
| | - Jinyu Wang
- College of Veterinary Medicine, South China Agricultural University, Guangzhou, 510642, China.,Guangdong Provincial Key Laboratory of Prevention and Control for Severe Clinical Animal Diseases, Guangzhou, 510642, China.,Guangdong Technological Engineering Research Center for Pet, Guangzhou, 510642, China
| | - Zihang Ma
- College of Veterinary Medicine, South China Agricultural University, Guangzhou, 510642, China.,Guangdong Provincial Key Laboratory of Prevention and Control for Severe Clinical Animal Diseases, Guangzhou, 510642, China.,Guangdong Technological Engineering Research Center for Pet, Guangzhou, 510642, China
| | - Kun Jia
- College of Veterinary Medicine, South China Agricultural University, Guangzhou, 510642, China. .,Guangdong Provincial Key Laboratory of Prevention and Control for Severe Clinical Animal Diseases, Guangzhou, 510642, China. .,Guangdong Technological Engineering Research Center for Pet, Guangzhou, 510642, China.
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33
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Ste-Croix DT, Bélanger RR, Mimee B. Characterization of microRNAs in the cyst nematode Heterodera glycines identifies possible candidates involved in cross-kingdom interactions with its host Glycine max. RNA Biol 2023; 20:614-628. [PMID: 37599428 PMCID: PMC10443972 DOI: 10.1080/15476286.2023.2244790] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Revised: 07/21/2023] [Accepted: 07/31/2023] [Indexed: 08/22/2023] Open
Abstract
The soybean cyst nematode (SCN - Heterodera glycines) is one of the most damaging pests to the cultivated soybean worldwide. Using a wide array of stylet-secreted effector proteins, this nematode can restructure its host cells into a complex and highly active feeding structure called the syncytium. Tight regulation of these proteins is thought to be essential to the successful formation of this syncytium. To date, multiple mechanisms have been proposed to regulate the expression of these proteins including through post-transcriptional regulation. MicroRNAs (miRNAs) are a class of small, roughly 22-nucleotide-long, non-coding RNA shown to regulate gene expression through its interaction with the 3' untranslated region of genes. These same small RNAs have also been hypothesized to be able to cross over kingdom barriers and regulate genes in other species in a process called cross-kingdom interactions. In this study, we characterized the miRNome of the SCN via sequencing of small-RNAs isolated from whole nematodes and exosomes representing all developmental stages. We identified 121 miRNA loci encoding 96 distinct miRNA families including multiple lineage- and species-specific candidates. Using a combination of plant- and animal-specific miRNA target predictors, we generated a unique repertoire of miRNA:mRNA interacting partners in the nematode and its host plant leading to the identification of a set of nine probable cross-kingdom miRNA candidates.
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Affiliation(s)
- Dave T. Ste-Croix
- Saint-Jean-Sur-Richelieu Research and Development Centre, Agriculture and Agri-Food Canada, Saint-Jean-Sur-Richelieu, Canada
- Département de Phytologie, Université Laval, Québec, Canada
| | - Richard R. Bélanger
- Département de Phytologie, Université Laval, Québec, Canada
- Centre de Recherche et d’Innovation sur les Végétaux (CRIV), Université Laval, Québec, Canada
| | - Benjamin Mimee
- Saint-Jean-Sur-Richelieu Research and Development Centre, Agriculture and Agri-Food Canada, Saint-Jean-Sur-Richelieu, Canada
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34
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CmirC: an integrated database of clustered miRNAs co-localized with copy number variations in cancer. Funct Integr Genomics 2022; 22:1229-1241. [DOI: 10.1007/s10142-022-00909-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2022] [Revised: 10/08/2022] [Accepted: 10/14/2022] [Indexed: 11/25/2022]
Abstract
AbstractGenomic rearrangements and copy number variations (CNVs) are the major regulators of clustered microRNAs (miRNAs) expression. Several clustered miRNAs are harbored in and around chromosome fragile sites (CFSs) and cancer-associated genomic hotspots. Aberrant expression of such clusters can lead to oncogenic or tumor suppressor activities. Here, we developed CmirC (Clustered miRNAs co-localized with CNVs), a comprehensive database of clustered miRNAs co-localized with CNV regions. The database consists of 481 clustered miRNAs co-localized with CNVs and their expression patterns in 35 cancer types of the TCGA. The portal also provides information on CFSs, miRNA cluster candidates, genomic coordinates, target gene networks, and gene functionality. The web portal is integrated with advanced tools such as JBrowse, NCBI-BLAST, GeneSCF, visNetwork, and NetworkD3 to help the researchers in data analysis, visualization, and browsing. This portal provides a promising avenue for integrated data analytics and offers additional evidence for the complex regulation of clustered miRNAs in cancer. The web portal is freely accessible at http://slsdb.manipal.edu/cmirclust to explore clinically significant miRNAs.
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35
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Vu Hong A, Bourg N, Sanatine P, Poupiot J, Charton K, Gicquel E, Massourides E, Spinazzi M, Richard I, Israeli D. Dlk1-Dio3 cluster miRNAs regulate mitochondrial functions in the dystrophic muscle in Duchenne muscular dystrophy. Life Sci Alliance 2022; 6:6/1/e202201506. [PMID: 36265896 PMCID: PMC9585966 DOI: 10.26508/lsa.202201506] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2022] [Revised: 10/04/2022] [Accepted: 10/04/2022] [Indexed: 11/24/2022] Open
Abstract
Duchenne muscular dystrophy (DMD) is a severe muscle disease caused by impaired expression of dystrophin. Whereas mitochondrial dysfunction is thought to play an important role in DMD, the mechanism of this dysfunction remains to be clarified. Here we demonstrate that in DMD and other muscular dystrophies, a large number of Dlk1-Dio3 clustered miRNAs (DD-miRNAs) are coordinately up-regulated in regenerating myofibers and in the serum. To characterize the biological effect of this dysregulation, 14 DD-miRNAs were simultaneously overexpressed in vivo in mouse muscle. Transcriptomic analysis revealed highly similar changes between the muscle ectopically overexpressing 14 DD-miRNAs and the mdx diaphragm, with naturally up-regulated DD-miRNAs. Among the commonly dysregulated pathway we found repressed mitochondrial metabolism, and oxidative phosphorylation (OxPhos) in particular. Knocking down the DD-miRNAs in iPS-derived skeletal myotubes resulted in increased OxPhos activities. The data suggest that (1) DD-miRNAs are important mediators of dystrophic changes in DMD muscle, (2) mitochondrial metabolism and OxPhos in particular are targeted in DMD by coordinately up-regulated DD-miRNAs. These findings provide insight into the mechanism of mitochondrial dysfunction in muscular dystrophy.
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Affiliation(s)
- Ai Vu Hong
- Genethon, Evry, France,Université Paris-Saclay, Univ Evry, Inserm, Généthon, Integrare Research Unit UMR_S951, Evry, France
| | - Nathalie Bourg
- Genethon, Evry, France,Université Paris-Saclay, Univ Evry, Inserm, Généthon, Integrare Research Unit UMR_S951, Evry, France
| | - Peggy Sanatine
- Genethon, Evry, France,Université Paris-Saclay, Univ Evry, Inserm, Généthon, Integrare Research Unit UMR_S951, Evry, France
| | - Jerome Poupiot
- Genethon, Evry, France,Université Paris-Saclay, Univ Evry, Inserm, Généthon, Integrare Research Unit UMR_S951, Evry, France
| | - Karine Charton
- Genethon, Evry, France,Université Paris-Saclay, Univ Evry, Inserm, Généthon, Integrare Research Unit UMR_S951, Evry, France
| | - Evelyne Gicquel
- Genethon, Evry, France,Université Paris-Saclay, Univ Evry, Inserm, Généthon, Integrare Research Unit UMR_S951, Evry, France
| | | | - Marco Spinazzi
- Neuromuscular Reference Center, Department of Neurology, CHU d’Angers, Angers, France,Institute of Neurobiology and Neuropathology CHU d’Angers, Angers, France
| | - Isabelle Richard
- Genethon, Evry, France,Université Paris-Saclay, Univ Evry, Inserm, Généthon, Integrare Research Unit UMR_S951, Evry, France
| | - David Israeli
- Genethon, Evry, France .,Université Paris-Saclay, Univ Evry, Inserm, Généthon, Integrare Research Unit UMR_S951, Evry, France
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36
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Villegas-Mirón P, Gallego A, Bertranpetit J, Laayouni H, Espinosa-Parrilla Y. Signatures of genetic variation in human microRNAs point to processes of positive selection and population-specific disease risks. Hum Genet 2022; 141:1673-1693. [PMID: 35249174 PMCID: PMC9522702 DOI: 10.1007/s00439-021-02423-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2021] [Accepted: 12/19/2021] [Indexed: 12/11/2022]
Abstract
The occurrence of natural variation in human microRNAs has been the focus of numerous studies during the last 20 years. Most of them have been focused on the role of specific mutations in disease, while a minor proportion seek to analyse microRNA diversity in the genomes of human populations. We analyse the latest human microRNA annotations in the light of the most updated catalogue of genetic variation provided by the 1000 Genomes Project. By means of the in silico analysis of microRNA genetic variation we show that the level of evolutionary constraint of these sequences is governed by the interplay of different factors, like their evolutionary age or genomic location. The role of mutations in the shaping of microRNA-driven regulatory interactions is emphasized with the acknowledgement that, while the whole microRNA sequence is highly conserved, the seed region shows a pattern of higher genetic diversity that appears to be caused by the dramatic frequency shifts of a fraction of human microRNAs. We highlight the participation of these microRNAs in population-specific processes by identifying that not only the seed, but also the loop, are particularly differentiated regions among human populations. The quantitative computational comparison of signatures of population differentiation showed that candidate microRNAs with the largest differences are enriched in variants implicated in gene expression levels (eQTLs), selective sweeps and pathological processes. We explore the implication of these evolutionary-driven microRNAs and their SNPs in human diseases, such as different types of cancer, and discuss their role in population-specific disease risk.
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Affiliation(s)
- Pablo Villegas-Mirón
- Institut de Biologia Evolutiva (UPF-CSIC), Universitat Pompeu Fabra, Barcelona, Catalonia, Spain
| | - Alicia Gallego
- Centro de Biología Molecular Severo Ochoa, CSIC-UAM, Madrid, Spain
| | - Jaume Bertranpetit
- Institut de Biologia Evolutiva (UPF-CSIC), Universitat Pompeu Fabra, Barcelona, Catalonia, Spain
| | - Hafid Laayouni
- Institut de Biologia Evolutiva (UPF-CSIC), Universitat Pompeu Fabra, Barcelona, Catalonia, Spain.
- Bioinformatics Studies, ESCI-UPF, Pg. Pujades 1, 08003, Barcelona, Spain.
| | - Yolanda Espinosa-Parrilla
- Escuela de Medicina, Universidad de Magallanes, Punta Arenas, Chile.
- Laboratorio de Medicina Molecular-LMM, Centro Asistencial, Docente Y de Investigación-CADI, Universidad de Magallanes, Punta Arenas, Chile.
- Interuniversity Center on Healthy Aging, Punta Arenas, Chile.
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37
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Tian FY, Kennedy EM, Hermetz K, Burt A, Everson TM, Punshon T, Jackson BP, Hao K, Chen J, Karagas MR, Koestler DC, Marsit C. Selenium-associated differentially expressed microRNAs and their targeted mRNAs across the placental genome in two U.S. birth cohorts. Epigenetics 2022; 17:1234-1245. [PMID: 34784848 PMCID: PMC9542509 DOI: 10.1080/15592294.2021.2003044] [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: 09/01/2021] [Revised: 10/21/2021] [Accepted: 11/02/2021] [Indexed: 10/19/2022] Open
Abstract
Selenium is an important micronutrient for foetal development. MicroRNAs play an important role in the function of the placenta, in communication between the placenta and maternal systems, and their expression can be altered through environmental and nutritional cues. To investigate the associations between placental selenium concentration and microRNA expression in the placenta, our observational study included 393 mother-child pairs from the New Hampshire Birth Cohort Study (NHBCS) and the Rhode Island Child Health Study (RICHS). Placental selenium concentrations were quantified using inductively coupled plasma mass spectrometry, and microRNA transcripts were measured using RNA-seq. We fit negative binomial additive models for assessing the association between selenium and microRNAs. We used the microRNA Data Integration Portal (mirDIP) to predict the target mRNAs of the differentially expressed microRNAs and verified the relationships between miRNA and mRNA targets in a subset of samples using existing whole transcriptome data (N = 199). We identified a non-monotonic association between selenium concentration and the expression of miR-216a-5p/miR-217-5p cluster (effective degrees of freedom, EDF = 2.44 and 2.08; FDR = 3.08 × 10-5) in placenta. Thirty putative target mRNAs of miR-216a-5p and/or miR-217-5p were identified computationally and empirically and were enriched in selenium metabolic pathways (driven by selenoprotein coding genes, TXNRD2 and SELENON). Our findings suggest that selenium influences placental microRNA expression. Further, miR-216a-5p and its putative target mRNAs could be the potential mechanistic targets of the health effect of selenium.
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Affiliation(s)
- Fu-Ying Tian
- Gangarosa Department of Environmental Health, Rollins School of Public Health, Emory University, Atlanta, Georgia, USA
| | - Elizabeth M. Kennedy
- Gangarosa Department of Environmental Health, Rollins School of Public Health, Emory University, Atlanta, Georgia, USA
| | - Karen Hermetz
- Gangarosa Department of Environmental Health, Rollins School of Public Health, Emory University, Atlanta, Georgia, USA
| | - Amber Burt
- Gangarosa Department of Environmental Health, Rollins School of Public Health, Emory University, Atlanta, Georgia, USA
| | - Todd M. Everson
- Gangarosa Department of Environmental Health, Rollins School of Public Health, Emory University, Atlanta, Georgia, USA
| | - Tracy Punshon
- Department of Biological Sciences, Dartmouth College, Hanover, New Hampshire, USA
| | - Brian P. Jackson
- Department of Earth Sciences, Dartmouth College, Hanover, New Hampshire, USA
| | - Ke Hao
- Department of Genetics and Genome Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Jia Chen
- Department of Environmental Medicine and Public Health, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Margaret R. Karagas
- Department of Epidemiology, Geisel School of Medicine, Dartmouth College, Hanover, New Hampshire, USA
- Children’s Environmental Health and Disease Prevention Research Center at Dartmouth, Dartmouth College, Hanover, New Hampshire, USA
| | - Devin C. Koestler
- The University Kansas Cancer Center, The University of Kansas Medical Center, Kansas City, Kansas, USA
- Department of Biostatistics & Data Science, The University of Kansas Medical Center, Kansas City, Kansas, USA
| | - Carmen Marsit
- Gangarosa Department of Environmental Health, Rollins School of Public Health, Emory University, Atlanta, Georgia, USA
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García-Andrade F, Vigueras-Villaseñor RM, Chávez-Saldaña MD, Rojas-Castañeda JC, Bahena-Ocampo IU, Aréchaga-Ocampo E, Díaz-Chávez J, Landero-Huerta DA. The Role of microRNAs in the Gonocyte Theory as Target of Malignancy: Looking for Potential Diagnostic Biomarkers. Int J Mol Sci 2022; 23:ijms231810526. [PMID: 36142439 PMCID: PMC9505168 DOI: 10.3390/ijms231810526] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Revised: 07/30/2022] [Accepted: 08/06/2022] [Indexed: 11/16/2022] Open
Abstract
Some pediatric patients with cryptorchidism preserve cells with gonocyte characteristics beyond their differentiation period, which could support the theory of the gonocyte as a target for malignancy in the development of testicular neoplasia. One of the key molecules in gonocyte malignancy is represented by microRNAs (miRNAs). The goal of this review is to give an overview of miRNAs, a class of small non-coding RNAs that participate in the regulation of gene expression. We also aim to review the crucial role of several miRNAs that have been further described in the regulation of gonocyte differentiation to spermatogonia, which, when transformed, could give rise to germ cell neoplasia in situ, a precursor lesion to testicular germ cell tumors. Finally, the potential use of miRNAs as diagnostic and prognostic biomarkers in testicular neoplasia is addressed, due to their specificity and sensitivity compared to conventional markers, as well as their applications in therapeutics.
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Affiliation(s)
- Fabiola García-Andrade
- Laboratorio de Biología de la Reproducción, Instituto Nacional de Pediatría, Ciudad de México 04530, Mexico
- Posgrado en Biología Experimental, Universidad Autónoma Metropolitana Unidad Iztapalapa, Ciudad de México 09310, Mexico
| | - Rosa María Vigueras-Villaseñor
- Laboratorio de Biología de la Reproducción, Instituto Nacional de Pediatría, Ciudad de México 04530, Mexico
- Correspondence: (R.M.V.-V.); (D.A.L.-H.); Tel.: +52-(55)-1084-0900 (ext. 1453) (R.M.V.-V. & D.A.L.-H.); Fax: +52-(55)-1084-5533 (R.M.V.-V. & D.A.L.-H.)
| | | | | | - Iván Uriel Bahena-Ocampo
- Departamento de Ciencias de la Salud, Universidad Autónoma Metropolitana Unidad Iztapalapa, Ciudad de México 09310, Mexico
| | - Elena Aréchaga-Ocampo
- Departamento de Ciencias Naturales, Universidad Autónoma Metropolitana Unidad Cuajimalpa, Ciudad de México 05348, Mexico
| | - José Díaz-Chávez
- Instituto Nacional de Cancerología, Ciudad de México 14080, Mexico
| | - Daniel Adrian Landero-Huerta
- Laboratorio de Biología de la Reproducción, Instituto Nacional de Pediatría, Ciudad de México 04530, Mexico
- Correspondence: (R.M.V.-V.); (D.A.L.-H.); Tel.: +52-(55)-1084-0900 (ext. 1453) (R.M.V.-V. & D.A.L.-H.); Fax: +52-(55)-1084-5533 (R.M.V.-V. & D.A.L.-H.)
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Rui T, Zhang X, Feng S, Huang H, Zhan S, Xie H, Zhou L, Zheng S, Ling Q. MiR-516a-3p is a Novel Mediator of Hepatocellular Carcinoma Oncogenic Activity and Cellular Metabolism. ENGINEERING 2022; 16:162-175. [DOI: 10.1016/j.eng.2021.07.020] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/19/2025]
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Singh J, Raina A, Sangwan N, Chauhan A, Avti PK. Structural, molecular hybridization and network based identification of miR-373-3p and miR-520e-3p as regulators of NR4A2 human gene involved in neurodegeneration. NUCLEOSIDES, NUCLEOTIDES & NUCLEIC ACIDS 2022; 41:419-443. [PMID: 35272569 DOI: 10.1080/15257770.2022.2048851] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
MicroRNAs (miRNAs) are short non-coding RNAs with a 22 nucleotide sequence length and docks to the 3'UTR/5'UTR of the gene to regulate their mRNA translation to play a vital role in neurodegenerative diseases. The Nuclear Receptor gene (NR4A2), a transcription factor, and a steroid-thyroid hormone retinoid receptor is involved in neural development, memory formation, dopaminergic neurotransmission, and cellular protection from inflammatory damage. Therefore, recognizing the miRNAs is essential to efficiently target the 3'UTR/5'UTR of the NR4A2 gene and regulate neurodegeneration. Highly stabilized top miRNA-mRNA hybridized structures, their homologs, and identification of the best structures based on their least free energy were evaluated using in silico techniques. The miR-gene, gene-gene network analysis, miR-disease association, and transcription factor binding sites were also investigated. Results suggest top 166 miRNAs targeting the NR4A2 mRNA, but with a total of 10 miRNAs bindings with 100% seed sequence identity (both at 3' and 5'UTR) at the same position on the NR4A2 mRNA region. The miR-373-3p and miR-520e-3p are considered the best candidate miRNAs hybridizing with high efficiency at both 3' and 5'UTR of NR4A2 mRNA. This could be due to the most significant seed sequence length complementary, supplementary pairing, and absence of non-canonical base pairs. Furthermore, the miR-gene network, target gene-gene interaction analysis, and miR-disease association provide an understanding of the molecular, cellular, and biological processes involved in various pathways regulated by four transcription factors (PPARG, ZNF740, NRF1, and RREB1). Therefore, miR-373-3p, 520e-3p, and four transcription factors can regulate the NR4A2 gene involved in the neurodegenerative process.
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Affiliation(s)
- Jitender Singh
- Department of Biophysics, Postgraduate Institute of Medical Education and Research (PGIMER), Chandigarh, India
| | - Ashvinder Raina
- Postgraduate Institute of Medical Education and Research (PGIMER), Chandigarh, India
| | - Namrata Sangwan
- Department of Biophysics, Postgraduate Institute of Medical Education and Research (PGIMER), Chandigarh, India
| | - Arushi Chauhan
- Department of Biophysics, Postgraduate Institute of Medical Education and Research (PGIMER), Chandigarh, India
| | - Pramod K Avti
- Department of Biophysics, Postgraduate Institute of Medical Education and Research (PGIMER), Chandigarh, India
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He Y, Liu Y, Yang Y, Liu Y, Jia X, Shen Y, Xu X, Li J. elk1/miR-462-731 Feedback Loop Regulates Macrophages Polarization and Phagocytosis in Grass Carp (Ctenopharyngodon idella). Front Immunol 2022; 13:946857. [PMID: 35911773 PMCID: PMC9330907 DOI: 10.3389/fimmu.2022.946857] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2022] [Accepted: 06/07/2022] [Indexed: 11/13/2022] Open
Abstract
MicroRNA clusters are microRNAs (miRNAs) that are distributed in close proximity on chromosomes. In this study, we report a miRNA cluster identified from grass carp (Ctenopharyngodon idella), miR-462-731, which plays a positive role in host antibacterial immunity. The expression of miR-462-731 was disrupted after infection by Aeromonas hydrophila. Transcription factor ETS transcription factor ELK1 was identified to bind to the promoter of the miR-462-731 cluster and suppress its expression. In addition, miR-731 negatively regulates the expression of elk1, forms an elk1/miR-462-731 double negative feedback loop. In addition, we found that miR-731 directly targets ezrin a (ezra), participates in inducing PI3K/AKT signaling in macrophage, to induce macrophage polarization to the M1 phenotype with stronger phagocytosis. Our results demonstrate a novel elk1/miR-462-731 feedback loop. The data deepen our understanding of the relationship between macrophage polarization and phagocytosis in teleost fish.
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Affiliation(s)
- Yan He
- Key Laboratory of Freshwater Aquatic Genetic Resources Ministry of Agriculture and Rural Affairs, Shanghai Ocean University, Shanghai, China
- National Demonstration Center for Experimental Fisheries Science Education, Shanghai Ocean University, Shanghai, China
- Shanghai Engineering Research Center of Aquaculture, Shanghai Ocean University, Shanghai, China
| | - Yuting Liu
- Key Laboratory of Freshwater Aquatic Genetic Resources Ministry of Agriculture and Rural Affairs, Shanghai Ocean University, Shanghai, China
- National Demonstration Center for Experimental Fisheries Science Education, Shanghai Ocean University, Shanghai, China
- Shanghai Engineering Research Center of Aquaculture, Shanghai Ocean University, Shanghai, China
| | - Yuyue Yang
- Key Laboratory of Freshwater Aquatic Genetic Resources Ministry of Agriculture and Rural Affairs, Shanghai Ocean University, Shanghai, China
| | - Yang Liu
- Key Laboratory of Freshwater Aquatic Genetic Resources Ministry of Agriculture and Rural Affairs, Shanghai Ocean University, Shanghai, China
- National Demonstration Center for Experimental Fisheries Science Education, Shanghai Ocean University, Shanghai, China
- Shanghai Engineering Research Center of Aquaculture, Shanghai Ocean University, Shanghai, China
| | - Xuewen Jia
- Key Laboratory of Freshwater Aquatic Genetic Resources Ministry of Agriculture and Rural Affairs, Shanghai Ocean University, Shanghai, China
- National Demonstration Center for Experimental Fisheries Science Education, Shanghai Ocean University, Shanghai, China
- Shanghai Engineering Research Center of Aquaculture, Shanghai Ocean University, Shanghai, China
| | - Yubang Shen
- Key Laboratory of Freshwater Aquatic Genetic Resources Ministry of Agriculture and Rural Affairs, Shanghai Ocean University, Shanghai, China
- National Demonstration Center for Experimental Fisheries Science Education, Shanghai Ocean University, Shanghai, China
- Shanghai Engineering Research Center of Aquaculture, Shanghai Ocean University, Shanghai, China
| | - Xiaoyan Xu
- Key Laboratory of Freshwater Aquatic Genetic Resources Ministry of Agriculture and Rural Affairs, Shanghai Ocean University, Shanghai, China
- National Demonstration Center for Experimental Fisheries Science Education, Shanghai Ocean University, Shanghai, China
- Shanghai Engineering Research Center of Aquaculture, Shanghai Ocean University, Shanghai, China
- *Correspondence: Xiaoyan Xu, ; Jiale Li,
| | - Jiale Li
- Key Laboratory of Freshwater Aquatic Genetic Resources Ministry of Agriculture and Rural Affairs, Shanghai Ocean University, Shanghai, China
- National Demonstration Center for Experimental Fisheries Science Education, Shanghai Ocean University, Shanghai, China
- Shanghai Engineering Research Center of Aquaculture, Shanghai Ocean University, Shanghai, China
- *Correspondence: Xiaoyan Xu, ; Jiale Li,
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Xu Z, Liu Q, Chen Y, He Y, Hu F. miR390 family of Cymbidium goeringii is involved in the development of reproductive organs in transgenic Arabidopsis. BMC PLANT BIOLOGY 2022; 22:149. [PMID: 35346036 PMCID: PMC8962573 DOI: 10.1186/s12870-022-03539-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/16/2021] [Accepted: 03/15/2022] [Indexed: 06/14/2023]
Abstract
BACKGROUND miR390s is an ancient family with a high level of conservation among plant miRNAs. Through the auxin signal transduction pathway, miR390 participates in diverse biological processes of plant growth and development. As an important Chinese traditional orchid, Cymbidium goeringii has unique flower shape and elegant fragrance. But its development has been greatly restricted because of the low flower bud differentiation and the difficult reproduction. This study aims to provide guidance for the role of cgo-miR390 in reproductive organ development to enhance the ornamental and economic value of Cymbidium. RESULTS MIR390a, MIR390b and MIR390c of C. goeringii were cloned, and their length ranged from 130 to 150 nt. Each precursor sequence of cgo-miR390 contains 2 to 3 mature miRNAs. Three kinds of cgo-miR390s displayed distinct temporal and spatial expression patterns during floral development in C. goeringii. The overexpression of MIR390s alters morphology and function of stamens and pistils in Arabidopsis, such as enlargement of anther aspect ratio and separation of stylar and stigmas, which affects the development of fruits and seeds. In particular, the pollen amount decreased and the seed abortion rate increased in cgo-MIR390c-overexpressed plants. CONCLUSIONS cgo-miR390 family affected the development of reproductive organs in transgenic Arabidopsis. The study provides references for the genetic improvement for orchid with potentially great economic benefit.
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Affiliation(s)
- Zihan Xu
- College of Landscape Architecture, Nanjing Forestry University, 210037, Nanjing, Jiangsu Province, China
| | - Qian Liu
- College of Landscape Architecture, Nanjing Forestry University, 210037, Nanjing, Jiangsu Province, China
| | - Yue Chen
- Institute of Horticulture, Zhejiang Academy of Agricultural Sciences, 310021, Hangzhou, Zhejiang Province, China
| | - Yuanhao He
- College of Landscape Architecture, Nanjing Forestry University, 210037, Nanjing, Jiangsu Province, China
| | - Fengrong Hu
- College of Landscape Architecture, Nanjing Forestry University, 210037, Nanjing, Jiangsu Province, China.
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Flowers E, Asam K, Allen IE, Kanaya AM, Aouizerat BE. Co‑expressed microRNAs, target genes and pathways related to metabolism, inflammation and endocrine function in individuals at risk for type 2 diabetes. Mol Med Rep 2022; 25:156. [PMID: 35244194 PMCID: PMC8941378 DOI: 10.3892/mmr.2022.12672] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2021] [Accepted: 02/03/2022] [Indexed: 11/25/2022] Open
Abstract
MicroRNAs (miRNAs) may be considered important regulators of risk for type 2 diabetes (T2D). The aim of the present study was to identify novel sets of miRNAs associated with T2D risk, as well as their gene and pathway targets. Circulating miRNAs (n=59) were measured in plasma from participants in a previously completed clinical trial (n=82). An agnostic statistical approach was applied to identify novel sets of miRNAs with optimal co-expression patterns. In silico analyses were used to identify the messenger RNA and biological pathway targets of the miRNAs within each factor. A total of three factors of miRNAs were identified, containing 18, seven and two miRNAs each. Eight biological pathways were revealed to contain genes targeted by the miRNAs in all three factors, 38 pathways contained genes targeted by the miRNAs in two factors, and 55, 18 and two pathways were targeted by the miRNAs in a single factor, respectively (all q<0.05). The pathways containing genes targeted by miRNAs in the largest factor shared a common theme of biological processes related to metabolism and inflammation. By contrast, the pathways containing genes targeted by miRNAs in the second largest factor were related to endocrine function and hormone activity. The present study focused on the pathways uniquely targeted by each factor of miRNAs in order to identify unique mechanisms that may be associated with a subset of individuals. Further exploration of the genes and pathways related to these biological themes may provide insights about the subtypes of T2D and lead to the identification of novel therapeutic targets.
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Affiliation(s)
- Elena Flowers
- Department of Physiological Nursing, University of California San Francisco, San Francisco, CA 94143‑0610, USA
| | - Kesava Asam
- Bluestone Center for Clinical Research, New York University, New York, NY 10010, USA
| | - Isabel Elaine Allen
- Department of Epidemiology and Biostatistics, University of California San Francisco, San Francisco, CA 94143‑0610, USA
| | - Alka M Kanaya
- Department of Epidemiology and Biostatistics, University of California San Francisco, San Francisco, CA 94143‑0610, USA
| | - Bradley E Aouizerat
- Bluestone Center for Clinical Research, New York University, New York, NY 10010, USA
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Cheng J, Yang F, Liu S, Zhao H, Lu W, Zhang Q. Transcriptomic Analysis Reveals Functional Interaction of mRNA-lncRNA-miRNA in Steroidogenesis and Spermatogenesis of Gynogenetic Japanese Flounder ( Paralichthys olivaceus). BIOLOGY 2022; 11:biology11020213. [PMID: 35205081 PMCID: PMC8869744 DOI: 10.3390/biology11020213] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/30/2021] [Revised: 01/24/2022] [Accepted: 01/26/2022] [Indexed: 02/01/2023]
Abstract
Teleost fishes exhibit extraordinary diversity, plasticity and adaptability with their sex determination and sexual development, and there is growing evidence that non-coding RNAs (ncRNAs) are emerging as critical regulators of reproduction. Japanese flounder (Paralichthys olivaceus) is an important marine cultured fish that presents significant sexual dimorphism with bigger females, in which gynogenesis has been applied for aquaculture industry. In order to reveal the regulatory mechanisms of sexual development in gynogenetic female and sex-reversed neo-male P. olivaceus, the lncRNA-miRNA-mRNA interactions were investigated using high-throughput sequencing. A total of 6772 differentially expressed mRNAs (DEmRNAs), 2284 DElncRNAs, and 244 DEmiRNAs were obtained between gynogenetic female ovaries and sex-reversed neo-male testes. Genes in the steroid hormone biosynthesis and secretion pathway were enriched and mostly significantly upregulated in neo-male testes. Subsequently, network analysis uncovered high functional specificity for gynogenetic P. olivaceus sperm motility, as co-expressed DEmRNAs were significantly enriched in microtubule and cytoskeleton-related biological processes. Clustered miRNAs were characterized in the P. olivaceus genome with examples of the largest conserved let-7 clusters. The 20 let-7 members are distributed in 11 clusters and may not transcribe together with their neighboring miR-125b, with let-7 repressing cyp11a and miR-125b repressing esr2b, both as key steroidogenesis pathway genes. In summary, this study provides comprehensive insights into the mRNA-miRNA-lncRNA functional crosstalk in teleost sexual development and gametogenesis and will expand our understanding of ncRNA biology in teleost gynogenesis.
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Affiliation(s)
- Jie Cheng
- Key Laboratory of Marine Genetics and Breeding (Ocean University of China), Ministry of Education, 5 Yushan Road, Qingdao 266003, China; (F.Y.); (S.L.); (H.Z.); (W.L.)
- Laboratory for Marine Fisheries Science and Food Production Processes, Pilot National Laboratory for Marine Science and Technology (Qingdao), 1 Wenhai Road, Qingdao 266237, China
- Key Laboratory of Tropical Aquatic Germplasm of Hainan Province, Sanya Oceanographic Institution, Ocean University of China, Sanya 572024, China
- Correspondence: (J.C.); (Q.Z.); Tel.: +86-0532-82031986 (J.C.)
| | - Fan Yang
- Key Laboratory of Marine Genetics and Breeding (Ocean University of China), Ministry of Education, 5 Yushan Road, Qingdao 266003, China; (F.Y.); (S.L.); (H.Z.); (W.L.)
| | - Saisai Liu
- Key Laboratory of Marine Genetics and Breeding (Ocean University of China), Ministry of Education, 5 Yushan Road, Qingdao 266003, China; (F.Y.); (S.L.); (H.Z.); (W.L.)
| | - Haitao Zhao
- Key Laboratory of Marine Genetics and Breeding (Ocean University of China), Ministry of Education, 5 Yushan Road, Qingdao 266003, China; (F.Y.); (S.L.); (H.Z.); (W.L.)
| | - Wei Lu
- Key Laboratory of Marine Genetics and Breeding (Ocean University of China), Ministry of Education, 5 Yushan Road, Qingdao 266003, China; (F.Y.); (S.L.); (H.Z.); (W.L.)
| | - Quanqi Zhang
- Key Laboratory of Marine Genetics and Breeding (Ocean University of China), Ministry of Education, 5 Yushan Road, Qingdao 266003, China; (F.Y.); (S.L.); (H.Z.); (W.L.)
- Laboratory for Marine Fisheries Science and Food Production Processes, Pilot National Laboratory for Marine Science and Technology (Qingdao), 1 Wenhai Road, Qingdao 266237, China
- Key Laboratory of Tropical Aquatic Germplasm of Hainan Province, Sanya Oceanographic Institution, Ocean University of China, Sanya 572024, China
- Correspondence: (J.C.); (Q.Z.); Tel.: +86-0532-82031986 (J.C.)
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The miR-23b/27b/24-1 Cluster Inhibits Hepatic Fibrosis by Inactivating Hepatic Stellate Cells. Cell Mol Gastroenterol Hepatol 2022; 13:1393-1412. [PMID: 35093591 PMCID: PMC8938281 DOI: 10.1016/j.jcmgh.2022.01.016] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/04/2021] [Revised: 01/18/2022] [Accepted: 01/19/2022] [Indexed: 12/10/2022]
Abstract
BACKGROUND & AIMS Hepatic fibrosis is characterized by hepatic stellate cell (HSC) activation and transdifferentiation-mediated extracellular matrix (ECM) deposition, which both contribute to cirrhosis. However, no antifibrotic regimen is available in the clinic. microRNA-23b/27b/24-1 cluster inhibition of transforming growth factor-β (TGF-β) signaling during hepatic development prompted us to explore whether this cluster inhibits HSC activation and hepatic fibrosis. METHODS Experimental fibrosis was studied in carbon tetrachloride (CCl4)-treated C57BL/6 mice. After administration of miR-23b/27b/24-1 lentivirus or vehicle, animals were euthanized for liver histology. In primary rat HSC and HSC-T6, the anti-fibrotic effect of miR-23b/27b/24-1 cluster was furtherly investigated by RNA-sequencing, luciferase reporter assay, western blotting and bioinformatic means. RESULTS In this study, we showed that increasing the miR-23b/27b/24-1 level through intravenous delivery of miR-23b/27b/24-1 lentivirus ameliorated mouse hepatic fibrosis. Mechanistically, the miR-23b/27b/24-1 cluster directly targeted messenger RNAs, which reduced the protein expression of 5 secretory profibrotic genes (TGF-β2, Gremlin1, LOX, Itgα2, and Itgα5) in HSCs. Suppression of the TGF-β signaling pathway by down-regulation of TGF-β2, Itgα2, and Itgα5, and activation of the bone morphogenetic protein signaling pathway by inhibition of Gremlin1, decreased extracellular matrix secretion of HSCs. Furthermore, down-regulation of LOX expression softened the ECM. Moreover, a reduction in tissue inhibitors of metalloproteinase 1 expression owing to weakened TGF-β signaling increased ECM degradation. CONCLUSIONS Hepatic overexpression of the miR-23b/27b/24-1 cluster blocked hepatic fibrosis and may be a novel therapeutic regimen for patients with hepatic fibrosis.
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Geurts S, Mens MMJ, Bos MM, Ikram MA, Ghanbari M, Kavousi M. Circulatory MicroRNAs in Plasma and Atrial Fibrillation in the General Population: The Rotterdam Study. Genes (Basel) 2021; 13:genes13010011. [PMID: 35052352 PMCID: PMC8775308 DOI: 10.3390/genes13010011] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2021] [Revised: 12/14/2021] [Accepted: 12/16/2021] [Indexed: 01/07/2023] Open
Abstract
Background: MicroRNAs (miRNAs), small non-coding RNAs regulating gene expression, have been shown to play an important role in cardiovascular disease. However, limited population-based data regarding the relationship between circulatory miRNAs in plasma and atrial fibrillation (AF) exist. Moreover, it remains unclear if the relationship differs by sex. We therefore aimed to determine the (sex-specific) association between plasma circulatory miRNAs and AF at the population level. Methods: Plasma levels of miRNAs were measured using a targeted next-generation sequencing method in 1999 participants from the population-based Rotterdam Study. Logistic regression and Cox proportional hazards models were used to assess the associations of 591 well-expressed miRNAs with the prevalence and incidence of AF. Models were adjusted for cardiovascular risk factors. We further examined the link between predicted target genes of the identified miRNAs. Results: The mean age was 71.7 years (57.1% women), 98 participants (58 men and 40 women) had prevalent AF at baseline. Moreover, 196 participants (96 men and 100 women) developed AF during a median follow-up of 9.0 years. After adjusting for multiple testing, miR-4798-3p was significantly associated with the odds of prevalent AF among men (odds ratio, 95% confidence interval, 0.39, 0.24–0.66, p-value = 0.000248). No miRNAs were significantly associated with incident AF. MiR-4798-3p could potentially regulate the expression of a number of AF-related genes, including genes involved in calcium and potassium handling in myocytes, protection of cells against oxidative stress, and cardiac fibrosis. Conclusions: Plasma levels of miR-4798-3p were significantly associated with the odds of prevalent AF among men. Several target genes in relation to AF pathophysiology could potentially be regulated by miR-4798-3p that warrant further investigations in future experimental studies.
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Zhou H, Gao Y, Li X, Shang S, Wang P, Zhi H, Guo S, Sun D, Liu H, Li X, Zhang Y, Ning S. Identifying and characterizing lincRNA genomic clusters reveals its cooperative functions in human cancer. J Transl Med 2021; 19:509. [PMID: 34906173 PMCID: PMC8672572 DOI: 10.1186/s12967-021-03179-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2021] [Accepted: 12/03/2021] [Indexed: 02/01/2023] Open
Abstract
Background Emerging evidence has revealed that some long intergenic non-coding RNAs (lincRNAs) are likely to form clusters on the same chromosome, and lincRNA genomic clusters might play critical roles in the pathophysiological mechanism. However, the comprehensive investigation of lincRNA clustering is rarely studied, particularly the characterization of their functional significance across different cancer types. Methods In this study, we firstly constructed a computational method basing a sliding window approach for systematically identifying lincRNA genomic clusters. We then dissected these lincRNA genomic clusters to identify common characteristics in cooperative expression, conservation among divergent species, targeted miRNAs, and CNV frequency. Next, we performed comprehensive analyses in differentially-expressed patterns and overall survival outcomes for patients from The Cancer Genome Atlas (TCGA) and The Genotype-Tissue Expression (GTEx) across multiple cancer types. Finally, we explored the underlying mechanisms of lincRNA genomic clusters by functional enrichment analysis, pathway analysis, and drug-target interaction. Results We identified lincRNA genomic clusters according to the algorithm. Clustering lincRNAs tended to be co-expressed, highly conserved, targeted by more miRNAs, and with similar deletion and duplication frequency, suggesting that lincRNA genomic clusters may exert their effects by acting in combination. We further systematically explored conserved and cancer-specific lincRNA genomic clusters, indicating they were involved in some important mechanisms of disease occurrence through diverse approaches. Furthermore, lincRNA genomic clusters can serve as biomarkers with potential clinical significance and involve in specific pathological processes in the development of cancer. Moreover, a lincRNA genomic cluster named Cluster127 in DLK1-DIO3 imprinted locus was discovered, which contained MEG3, MEG8, MEG9, MIR381HG, LINC02285, AL132709.5, and AL132709.1. Further analysis indicated that Cluster127 may have the potential for predicting prognosis in cancer and could play their roles by participating in the regulation of PI3K-AKT signaling pathway. Conclusions Clarification of the lincRNA genomic clusters specific roles in human cancers could be beneficial for understanding the molecular pathogenesis of different cancer types. Supplementary Information The online version contains supplementary material available at 10.1186/s12967-021-03179-5.
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Affiliation(s)
- Hanxiao Zhou
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150081, Heilongjiang, China
| | - Yue Gao
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150081, Heilongjiang, China
| | - Xin Li
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150081, Heilongjiang, China
| | - Shipeng Shang
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150081, Heilongjiang, China
| | - Peng Wang
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150081, Heilongjiang, China
| | - Hui Zhi
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150081, Heilongjiang, China
| | - Shuang Guo
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150081, Heilongjiang, China
| | - Dailin Sun
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150081, Heilongjiang, China
| | - Hongjia Liu
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150081, Heilongjiang, China
| | - Xia Li
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150081, Heilongjiang, China.
| | - Yunpeng Zhang
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150081, Heilongjiang, China.
| | - Shangwei Ning
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150081, Heilongjiang, China.
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48
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Lyu Y, Liufu Z, Xiao J, Tang T. A Rapid Evolving microRNA Cluster Rewires Its Target Regulatory Networks in Drosophila. Front Genet 2021; 12:760530. [PMID: 34777478 PMCID: PMC8581666 DOI: 10.3389/fgene.2021.760530] [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: 08/18/2021] [Accepted: 10/11/2021] [Indexed: 11/13/2022] Open
Abstract
New miRNAs are evolutionarily important but their functional evolution remains unclear. Here we report that the evolution of a microRNA cluster, mir-972C rewires its downstream regulatory networks in Drosophila. Genomic analysis reveals that mir-972C originated in the common ancestor of Drosophila where it comprises six old miRNAs. It has subsequently recruited six new members in the melanogaster subgroup after evolving for at least 50 million years. Both the young and the old mir-972C members evolved rapidly in seed and non-seed regions. Combining target prediction and cell transfection experiments, we found that the seed and non-seed changes in individual mir-972C members cause extensive target divergence among D. melanogaster, D. simulans, and D. virilis, consistent with the functional evolution of mir-972C reported recently. Intriguingly, the target pool of the cluster as a whole remains relatively conserved. Our results suggest that clustering of young and old miRNAs broadens the target repertoires by acquiring new targets without losing many old ones. This may facilitate the establishment of new miRNAs in existing regulatory networks.
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Affiliation(s)
- Yang Lyu
- State Key Laboratory of Biocontrol and Guangdong Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Zhongqi Liufu
- State Key Laboratory of Biocontrol and Guangdong Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Juan Xiao
- State Key Laboratory of Biocontrol and Guangdong Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Tian Tang
- State Key Laboratory of Biocontrol and Guangdong Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
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49
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Vu Hong A, Sanson M, Richard I, Israeli D. A revised model for mitochondrial dysfunction in Duchenne muscular dystrophy. Eur J Transl Myol 2021; 31. [PMID: 34533019 PMCID: PMC8495359 DOI: 10.4081/ejtm.2021.10012] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2021] [Accepted: 09/12/2021] [Indexed: 12/27/2022] Open
Abstract
We recently identified a signaling pathway that links the upregulation of miR-379 with a mitochondrial response in dystrophic muscle. In the present commentary, we explain the significance that this pathway may have in mitochondrial dysfunction in Duchenne muscular dystrophy (DMD). We identified the upregulation of miR-379 in the serum and muscles of DMD animal models and patients. We found that miR-379 is one of very few miRNAs whose expression was normalized in DMD patients treated with glucocorticoid. We identified EIF4G2 as a miR-379 target, which may promote mitochondrial oxidative phosphorylation (OxPhos) in the skeletal muscle. We found enriched EIF4G2 expression in oxidative fibers, and identified the mitochondrial ATP synthase subunit DAPIT as a translational target of EIF4G2. The identified signaling cascade, which comprises miR-379, EIF4G2 and DAPIT, may link the glucocorticoid treatment in DMD to a recovered mitochondrial ATP synthesis rate. We propose an updated model of mitochondrial dysfunction in DMD.
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Affiliation(s)
- Ai Vu Hong
- Genethon, Evry, France; Université Paris-Saclay, Univ Evry, Inserm, Généthon, Integrare research unit UMR-S951, Evry.
| | - Mathilde Sanson
- Genethon, Evry, France; Université Paris-Saclay, Univ Evry, Inserm, Généthon, Integrare research unit UMR-S951, Evry.
| | - Isabelle Richard
- Genethon, Evry, France; Université Paris-Saclay, Univ Evry, Inserm, Généthon, Integrare research unit UMR-S951, Evry.
| | - David Israeli
- Genethon, Evry, France; Université Paris-Saclay, Univ Evry, Inserm, Généthon, Integrare research unit UMR-S951, Evry.
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50
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Kadkhoda S, Taslimi R, Noorbakhsh F, Darbeheshti F, Bazzaz JT, Ghafouri-Fard S, Shakoori A. Importance of Circ0009910 in colorectal cancer pathogenesis as a possible regulator of miR-145 and PEAK1. World J Surg Oncol 2021; 19:265. [PMID: 34479583 PMCID: PMC8417957 DOI: 10.1186/s12957-021-02378-0] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2021] [Accepted: 08/26/2021] [Indexed: 02/08/2023] Open
Abstract
Introduction Colorectal cancer (CRC) is one of the most frequent neoplasms in the world. Based on the emerging role of noncoding RNAs, particularly circular RNAs in pathogenesis of cancers, we designed this study to inspect the expression levels of a circ0009910-mediated regulatory pathway in colorectal cancer. Methods After bioinformatics analyses and construction of putative circ0009910/ miR-145-5p/PEAK1 pathway, the expression levels of these components were evaluated in 50 CRC tissues and adjacent specimens by quantitative real-time PCR. Moreover, we appraised the correlation coefficients between these transcripts and calculated the correlation between circ0009910 expression levels with clinicopathological features of patients. Results Circ0009910 and PEAK1 were significantly upregulated, while miR-145-5p was decreased in CRC samples compared with adjacent tissues (p < 0.05). Moreover, statistically significant correlations were observed between expression levels of circ0009910, miR-145-5p, and PEAK1. We also reported considerable correlations between circ0009910 expression and clinicopathological parameters including sex and perineural invasion. Finally, ROC curve analysis showed circ0009910 level as a discriminative biomarker for CRC. Conclusion For the first time, we could introduce circ0009910 as an important biomarker in CRC. Collectively, this investigation helped us to identify a newly diagnosed pathway in CRC that can be a potential axis for designing effective drugs for treatment of CRC patients. Supplementary Information The online version contains supplementary material available at 10.1186/s12957-021-02378-0.
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Affiliation(s)
- Sepideh Kadkhoda
- Department of Medical Genetics, School of Medicine, Tehran University of Medical Sciences, Tehran, Iran
| | - Reza Taslimi
- Department of Gastroenterology, Imam Khomeini Hospital, Tehran University of Medical Sciences, Tehran, Iran
| | - Farshid Noorbakhsh
- Department of Immunology, School of Medicine, Tehran University of Medical Sciences, Tehran, Iran
| | - Farzaneh Darbeheshti
- Department of Medical Genetics, School of Medicine, Tehran University of Medical Sciences, Tehran, Iran.,Medical Genetics Network (MeGeNe), Universal Scientific Education and Research Network (USERN), Tehran, Iran
| | - Javad Tavakkoly Bazzaz
- Department of Medical Genetics, School of Medicine, Tehran University of Medical Sciences, Tehran, Iran
| | - Soudeh Ghafouri-Fard
- Department of Medical Genetics, Shahid Beheshti University of Medical Sciences, Tehran, Iran.
| | - Abbas Shakoori
- Department of Medical Genetics, School of Medicine, Tehran University of Medical Sciences, Tehran, Iran. .,Department of Medical Genetics, Cancer Institute of Iran, Imam Khomeini Hospital Complex, Tehran University of Medical Sciences, Dr. Qarib St., Keshavarz Blvd, Tehran, Iran.
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