1
|
Zhao L, Wu Q, Long Y, Qu Q, Qi F, Liu L, Zhang L, Ai K. microRNAs: critical targets for treating rheumatoid arthritis angiogenesis. J Drug Target 2024; 32:1-20. [PMID: 37982157 DOI: 10.1080/1061186x.2023.2284097] [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: 08/07/2023] [Accepted: 11/09/2023] [Indexed: 11/21/2023]
Abstract
Vascular neogenesis, an early event in the development of rheumatoid arthritis (RA) inflammation, is critical for the formation of synovial vascular networks and plays a key role in the progression and persistence of chronic RA inflammation. microRNAs (miRNAs), a class of single-stranded, non-coding RNAs with approximately 21-23 nucleotides in length, regulate gene expression by binding to the 3' untranslated region (3'-UTR) of specific mRNAs. Increasing evidence suggests that miRNAs are differently expressed in diseases associated with vascular neogenesis and play a crucial role in disease-related vascular neogenesis. However, current studies are not sufficient and further experimental studies are needed to validate and establish the relationship between miRNAs and diseases associated with vascular neogenesis, and to determine the specific role of miRNAs in vascular development pathways. To better treat vascular neogenesis in diseases such as RA, we need additional studies on the role of miRNAs and their target genes in vascular development, and to provide more strategic references. In addition, future studies can use modern biotechnological methods such as proteomics and transcriptomics to investigate the expression and regulatory mechanisms of miRNAs, providing a more comprehensive and in-depth research basis for the treatment of related diseases such as RA.
Collapse
Affiliation(s)
- Lingyun Zhao
- College of Acupuncture, Tuina and Rehabilitation, Hunan University of Chinese Medicine, Changsha, China
| | - Qingze Wu
- College of Acupuncture, Tuina and Rehabilitation, Hunan University of Chinese Medicine, Changsha, China
| | - Yiying Long
- Hunan Traditional Chinese Medical College, Zhuzhou, China
| | - Qirui Qu
- College of Acupuncture, Tuina and Rehabilitation, Hunan University of Chinese Medicine, Changsha, China
| | - Fang Qi
- College of Acupuncture, Tuina and Rehabilitation, Hunan University of Chinese Medicine, Changsha, China
| | - Li Liu
- The First Affiliated Hospital of Hunan University of Chinese Medicine, Changsha, China
| | - Liang Zhang
- College of Acupuncture, Tuina and Rehabilitation, Hunan University of Chinese Medicine, Changsha, China
| | - Kun Ai
- College of Acupuncture, Tuina and Rehabilitation, Hunan University of Chinese Medicine, Changsha, China
| |
Collapse
|
2
|
Sumaira S, Vijayarathna S, Hemagirri M, Adnan M, Hassan MI, Patel M, Gupta R, Shanmugapriya, Chen Y, Gopinath SC, Kanwar JR, Sasidharan S. Plant bioactive compounds driven microRNAs (miRNAs): A potential source and novel strategy targeting gene and cancer therapeutics. Noncoding RNA Res 2024; 9:1140-1158. [PMID: 39022680 PMCID: PMC11250886 DOI: 10.1016/j.ncrna.2024.06.003] [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: 04/10/2023] [Revised: 05/21/2024] [Accepted: 06/03/2024] [Indexed: 07/20/2024] Open
Abstract
Irrespective of medical technology improvements, cancer ranks among the leading causes of mortality worldwide. Although numerous cures and treatments exist, creating alternative cancer therapies with fewer adverse side effects is vital. Since ancient times, plant bioactive compounds have already been used as a remedy to heal cancer. These plant bioactive compounds and their anticancer activity can also deregulate the microRNAs (miRNAs) in the cancerous cells. Therefore, the deregulation of miRNAs in cancer cells by plant bioactive compounds and the usage of the related miRNA could be a promising approach for cancer cure, mainly to prevent cancer and overcome chemotherapeutic side effect problems. Hence, this review highlights the function of plant bioactive compounds as an anticancer agent through the underlying mechanism that alters the miRNA expression in cancer cells, ultimately leading to apoptosis. Moreover, this review provides insight into using plant bioactive compounds -driven miRNAs as an anticancer agent to develop miRNA-based cancer gene therapy. They can be the potential resource for gene therapy and novel strategies targeting cancer therapeutics.
Collapse
Affiliation(s)
- Sahreen Sumaira
- Institute for Research in Molecular Medicine (INFORMM), Universiti Sains Malaysia, USM, 11800, Pulau Pinang, Malaysia
| | - Soundararajan Vijayarathna
- Institute for Research in Molecular Medicine (INFORMM), Universiti Sains Malaysia, USM, 11800, Pulau Pinang, Malaysia
| | - Manisekaran Hemagirri
- Institute for Research in Molecular Medicine (INFORMM), Universiti Sains Malaysia, USM, 11800, Pulau Pinang, Malaysia
| | - Mohd Adnan
- Department of Biology, College of Science, University of Hail, Hail, P.O. Box 2440, Saudi Arabia
| | - Md Imtaiyaz Hassan
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, Jamia Nagar, New Delhi, 110025, India
| | - Mitesh Patel
- Research and Development Cell and Department of Biotechnology, Parul Institute of Applied Sciences, Parul University, Vadodara, 391760, Gujarat, India
| | - Reena Gupta
- Institute of Pharmaceutical Research, Department. Pharmaceutical Research, GLA University, Mathura, India
| | - Shanmugapriya
- Institute for Research in Molecular Medicine (INFORMM), Universiti Sains Malaysia, USM, 11800, Pulau Pinang, Malaysia
| | - Yeng Chen
- Department of Oral & Craniofacial Sciences, Faculty of Dentistry, University of Malaya, 50603, Kuala Lumpur, Malaysia
| | - Subash C.B. Gopinath
- Faculty of Chemical Engineering Technology, Universiti Malaysia Perlis, Perlis, Malaysia
| | - Jagat R. Kanwar
- Department of Biochemistry, All India Institute of Medical Sciences (AIIMS), 174001, Bilaspur, Himachal Pradesh, India
| | - Sreenivasan Sasidharan
- Institute for Research in Molecular Medicine (INFORMM), Universiti Sains Malaysia, USM, 11800, Pulau Pinang, Malaysia
| |
Collapse
|
3
|
Garg A, Shang R, Cvetanovic T, Lai EC, Joshua-Tor L. The structural landscape of Microprocessor-mediated processing of pri-let-7 miRNAs. Mol Cell 2024:S1097-2765(24)00741-X. [PMID: 39368465 DOI: 10.1016/j.molcel.2024.09.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2024] [Revised: 07/25/2024] [Accepted: 09/06/2024] [Indexed: 10/07/2024]
Abstract
MicroRNA (miRNA) biogenesis is initiated upon cleavage of a primary miRNA (pri-miRNA) hairpin by the Microprocessor (MP), composed of the Drosha RNase III enzyme and its partner DGCR8. Multiple pri-miRNA sequence motifs affect MP recognition, fidelity, and efficiency. Here, we performed cryoelectron microscopy (cryo-EM) and biochemical studies of several let-7 family pri-miRNAs in complex with human MP. We show that MP has the structural plasticity to accommodate a range of pri-miRNAs. These structures revealed key features of the 5' UG sequence motif, more comprehensively represented as the "flipped U with paired N" (fUN) motif. Our analysis explains how cleavage of class-II pri-let-7 members harboring a bulged nucleotide generates a non-canonical precursor with a 1-nt 3' overhang. Finally, the MP-SRSF3-pri-let-7f1 structure reveals how SRSF3 contributes to MP fidelity by interacting with the CNNC motif and Drosha's Piwi/Argonaute/Zwille (PAZ)-like domain. Overall, this study sheds light on the mechanisms for flexible recognition, accurate cleavage, and regulated processing of different pri-miRNAs by MP.
Collapse
Affiliation(s)
- Ankur Garg
- W. M. Keck Structural Biology Laboratory, Cold Spring Harbor Laboratory, One Bungtown Road, Cold Spring Harbor, NY 11724, USA; Howard Hughes Medical Institute, Cold Spring Harbor Laboratory, One Bungtown Road, Cold Spring Harbor, NY 11724, USA
| | - Renfu Shang
- Developmental Biology Program, Sloan Kettering Institute, 430 East 67th St, ROC-10, New York, NY 10065, USA
| | - Todor Cvetanovic
- W. M. Keck Structural Biology Laboratory, Cold Spring Harbor Laboratory, One Bungtown Road, Cold Spring Harbor, NY 11724, USA
| | - Eric C Lai
- Developmental Biology Program, Sloan Kettering Institute, 430 East 67th St, ROC-10, New York, NY 10065, USA
| | - Leemor Joshua-Tor
- W. M. Keck Structural Biology Laboratory, Cold Spring Harbor Laboratory, One Bungtown Road, Cold Spring Harbor, NY 11724, USA; Howard Hughes Medical Institute, Cold Spring Harbor Laboratory, One Bungtown Road, Cold Spring Harbor, NY 11724, USA.
| |
Collapse
|
4
|
Li JN, Wang MY, Ruan JW, Lyu YJ, Weng YH, Brindangnanam P, Coumar MS, Chen PS. A transcription-independent role for HIF-1α in modulating microprocessor assembly. Nucleic Acids Res 2024:gkae792. [PMID: 39319577 DOI: 10.1093/nar/gkae792] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2024] [Revised: 08/22/2024] [Accepted: 08/31/2024] [Indexed: 09/26/2024] Open
Abstract
Microprocessor is an essential nuclear complex responsible for the initial RNase-mediated cleavage of primary miRNA, which is a tightly controlled maturation process that requires the proper assembly of Drosha and DGCR8. Unlike previously identified mechanisms directly targeting the enzymatic subunit Drosha, current knowledge about the biological ways of controlling miRNA nuclear maturation through DGCR8 is less addressed. In this study, we unveiled that the microprocessor assembly is governed by a master gene regulator HIF-1α irrespective of its canonical transcriptional activity. First, a widespread protein binding of HIF-1α with DGCR8 instead of Drosha was observed in response to biological stimulations. Similar protein interactions between their corresponding orthologues in model organisms were also observed. After dissecting the essential protein domains, we noticed that HIF-1α suppresses microprocessor assembly via binding to DGCR8. Furthermore, our results showed that HIF-1α hijacks monomeric DGCR8 thus reducing its dimer formation prior to microprocessor assembly, and consequently, the suppressed microprocessor formation and nuclear processing of primary miRNA were demonstrated. In conclusion, here we unveiled the mechanism of how microprocessor assembly is regulated by HIF-1α, which not only demonstrates a non-transcriptional function of nuclear HIF-1α but also provides new molecular insights into the regulation of microprocessor assembly through DGCR8.
Collapse
Affiliation(s)
- Jie-Ning Li
- Institute of Basic Medical Sciences, College of Medicine, National Cheng Kung University, Tainan, Taiwan
- Department of Medical Laboratory Science and Biotechnology, College of Medicine, National Cheng Kung University, Tainan, Taiwan
- Breast Medical Center, National Cheng Kung University Hospital, Tainan, Taiwan
- Research Center for Medical Laboratory Biotechnology, National Cheng Kung University, Tainan, Taiwan
| | - Ming-Yang Wang
- Department of Surgery, National Taiwan University Hospital, Taipei, Taiwan
- Department of Surgical Oncology, National Taiwan University Cancer Center, Taipei, Taiwan
| | - Jhen-Wei Ruan
- Institute of Basic Medical Sciences, College of Medicine, National Cheng Kung University, Tainan, Taiwan
- Department of Medical Laboratory Science and Biotechnology, College of Medicine, National Cheng Kung University, Tainan, Taiwan
- Research Center for Medical Laboratory Biotechnology, National Cheng Kung University, Tainan, Taiwan
| | - Yu-Jhen Lyu
- Department of Medical Laboratory Science and Biotechnology, College of Medicine, National Cheng Kung University, Tainan, Taiwan
- Department of Surgery, National Taiwan University Hospital, Taipei, Taiwan
| | - Yi-Hsiu Weng
- Institute of Basic Medical Sciences, College of Medicine, National Cheng Kung University, Tainan, Taiwan
- Department of Medical Laboratory Science and Biotechnology, College of Medicine, National Cheng Kung University, Tainan, Taiwan
- Research Center for Medical Laboratory Biotechnology, National Cheng Kung University, Tainan, Taiwan
| | - Pownraj Brindangnanam
- Department of Bioinformatics, School of Life Sciences, Pondicherry University, Kalapet, Pondicherry 605014, India
| | - Mohane Selvaraj Coumar
- Department of Bioinformatics, School of Life Sciences, Pondicherry University, Kalapet, Pondicherry 605014, India
| | - Pai-Sheng Chen
- Institute of Basic Medical Sciences, College of Medicine, National Cheng Kung University, Tainan, Taiwan
- Department of Medical Laboratory Science and Biotechnology, College of Medicine, National Cheng Kung University, Tainan, Taiwan
- Breast Medical Center, National Cheng Kung University Hospital, Tainan, Taiwan
- Research Center for Medical Laboratory Biotechnology, National Cheng Kung University, Tainan, Taiwan
| |
Collapse
|
5
|
Fujiwara Y, Takahashi RU, Saito M, Umakoshi M, Shimada Y, Koyama K, Yatabe Y, Watanabe SI, Koyota S, Minamiya Y, Tahara H, Kono K, Shiraishi K, Kohno T, Goto A, Tsuchiya N. Oncofetal IGF2BP3-mediated control of microRNA structural diversity in the malignancy of early-stage lung adenocarcinoma. Proc Natl Acad Sci U S A 2024; 121:e2407016121. [PMID: 39196622 PMCID: PMC11388381 DOI: 10.1073/pnas.2407016121] [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: 04/08/2024] [Accepted: 08/02/2024] [Indexed: 08/29/2024] Open
Abstract
The nature of microRNA (miRNA) dysfunction in carcinogenesis remains controversial because of the complex connection between miRNA structural diversity and biological processes. Here, we found that oncofetal IGF2BP3 regulates the selective production of a subset of 3'-isoforms (3'-isomiRs), including miR-21-5p and Let-7 family, which induces significant changes in their cellular seed occupancy and structural components, establishing a cancer-specific gene expression profile. The D-score, reflecting dominant production of a representative miR-21-5p+C (a 3'-isomiR), discriminated between clinical early-stage lung adenocarcinoma (LUAD) cases with low and high recurrence risks, and was associated with molecular features of cell cycle progression, epithelial-mesenchymal transition pressure, and immune evasion. We found that IGF2BP3 controls the production of miR-21-5p+C by directing the nuclear Drosha complex to select the cleavage site. IGF2BP3 was also involved in the production of 3'-isomiRs of miR-425-5p and miR-454-3p. IGF2BP3-regulated these three miRNAs are suggested to be associated with the regulation of p53, TGF-β, and TNF pathways in LUAD. Knockdown of IGF2BP3 also induced a selective upregulation of Let-7 3'-isomiRs, leading to increased cellular Let-7 seed occupancy and broad repression of its target genes encoding cell cycle regulators. The D-score is an index that reflects this cellular situation. Our results suggest that the aberrant regulation of miRNA structural diversity is a critical component for controlling cellular networks, thus supporting the establishment of a malignant gene expression profile in early stage LUAD.
Collapse
Affiliation(s)
- Yuko Fujiwara
- Laboratory of Molecular Carcinogenesis, National Cancer Center Research Institute, Tokyo 104-0045, Japan
| | - Ryou-U Takahashi
- Department of Cellular and Molecular Biology, Graduate School of Biomedical and Health Sciences, Hiroshima University, Hiroshima 734-8553, Japan
| | - Motonobu Saito
- Department of Gastrointestinal Tract Surgery, Fukushima Medical University School of Medicine, Fukushima 960-1295, Japan
| | - Michinobu Umakoshi
- Department of Cellular and Organ Pathology, Graduate School of Medicine, Akita University, Akita 010-8543, Japan
| | - Yoko Shimada
- Division of Genome Biology, National Cancer Center Research Institute, Tokyo 104-0045, Japan
| | - Kei Koyama
- Department of Cellular and Organ Pathology, Graduate School of Medicine, Akita University, Akita 010-8543, Japan
| | - Yasushi Yatabe
- Department of Diagnostic Pathology, National Cancer Center Hospital, Tokyo 104-0045, Japan
| | - Shun-Ichi Watanabe
- Department of Thoracic Surgery, National Cancer Center Hospital, Tokyo 104-0045, Japan
| | - Souichi Koyota
- Molecular Medicine Laboratory, Bioscience Education and Research Support Center, Akita University, Akita 010-8543, Japan
| | - Yoshihiro Minamiya
- Department of Thoracic Surgery, Akita University Hospital, Akita 010-8543, Japan
| | - Hidetoshi Tahara
- Department of Cellular and Molecular Biology, Graduate School of Biomedical and Health Sciences, Hiroshima University, Hiroshima 734-8553, Japan
| | - Koji Kono
- Department of Gastrointestinal Tract Surgery, Fukushima Medical University School of Medicine, Fukushima 960-1295, Japan
| | - Kouya Shiraishi
- Division of Genome Biology, National Cancer Center Research Institute, Tokyo 104-0045, Japan
- Department of Clinical Genomics, National Cancer Center Research Institute, Tokyo 104-0045, Japan
| | - Takashi Kohno
- Division of Genome Biology, National Cancer Center Research Institute, Tokyo 104-0045, Japan
| | - Akiteru Goto
- Department of Cellular and Organ Pathology, Graduate School of Medicine, Akita University, Akita 010-8543, Japan
| | - Naoto Tsuchiya
- Laboratory of Molecular Carcinogenesis, National Cancer Center Research Institute, Tokyo 104-0045, Japan
| |
Collapse
|
6
|
Owens DDG, Maitland MER, Khalili Yazdi A, Song X, Reber V, Schwalm MP, Machado RAC, Bauer N, Wang X, Szewczyk MM, Dong C, Dong A, Loppnau P, Calabrese MF, Dowling MS, Lee J, Montgomery JI, O'Connell TN, Subramanyam C, Wang F, Adamson EC, Schapira M, Gstaiger M, Knapp S, Vedadi M, Min J, Lajoie GA, Barsyte-Lovejoy D, Owen DR, Schild-Poulter C, Arrowsmith CH. A chemical probe to modulate human GID4 Pro/N-degron interactions. Nat Chem Biol 2024; 20:1164-1175. [PMID: 38773330 DOI: 10.1038/s41589-024-01618-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2023] [Accepted: 04/12/2024] [Indexed: 05/23/2024]
Abstract
The C-terminal to LisH (CTLH) complex is a ubiquitin ligase complex that recognizes substrates with Pro/N-degrons via its substrate receptor Glucose-Induced Degradation 4 (GID4), but its function and substrates in humans remain unclear. Here, we report PFI-7, a potent, selective and cell-active chemical probe that antagonizes Pro/N-degron binding to human GID4. Use of PFI-7 in proximity-dependent biotinylation and quantitative proteomics enabled the identification of GID4 interactors and GID4-regulated proteins. GID4 interactors are enriched for nucleolar proteins, including the Pro/N-degron-containing RNA helicases DDX21 and DDX50. We also identified a distinct subset of proteins whose cellular levels are regulated by GID4 including HMGCS1, a Pro/N-degron-containing metabolic enzyme. These data reveal human GID4 Pro/N-degron targets regulated through a combination of degradative and nondegradative functions. Going forward, PFI-7 will be a valuable research tool for investigating CTLH complex biology and facilitating development of targeted protein degradation strategies that highjack CTLH E3 ligase activity.
Collapse
Affiliation(s)
- Dominic D G Owens
- Structural Genomics Consortium, University of Toronto, Toronto, Ontario, Canada
| | - Matthew E R Maitland
- Structural Genomics Consortium, University of Toronto, Toronto, Ontario, Canada
- Robarts Research Institute, Schulich School of Medicine and Dentistry, University of Western Ontario, London, Ontario, Canada
- Department of Biochemistry, Schulich School of Medicine and Dentistry, University of Western Ontario, London, Ontario, Canada
- Don Rix Protein Identification Facility, Schulich School of Medicine and Dentistry, University of Western Ontario, London, Ontario, Canada
| | | | - Xiaosheng Song
- Structural Genomics Consortium, University of Toronto, Toronto, Ontario, Canada
| | - Viviane Reber
- Institute of Molecular Systems Biology at ETH Zurich, Zurich, Switzerland
| | - Martin P Schwalm
- Institut für Pharmazeutische Chemie, Goethe-University Frankfurt, Biozentrum, Frankfurt am Main, Germany
- Structural Genomics Consortium, Goethe-University Frankfurt, Buchmann Institute for Life Sciences, Frankfurt am Main, Germany
| | - Raquel A C Machado
- Structural Genomics Consortium, University of Toronto, Toronto, Ontario, Canada
| | - Nicolas Bauer
- Institut für Pharmazeutische Chemie, Goethe-University Frankfurt, Biozentrum, Frankfurt am Main, Germany
- Structural Genomics Consortium, Goethe-University Frankfurt, Buchmann Institute for Life Sciences, Frankfurt am Main, Germany
| | - Xu Wang
- Robarts Research Institute, Schulich School of Medicine and Dentistry, University of Western Ontario, London, Ontario, Canada
| | | | - Cheng Dong
- Structural Genomics Consortium, University of Toronto, Toronto, Ontario, Canada
| | - Aiping Dong
- Structural Genomics Consortium, University of Toronto, Toronto, Ontario, Canada
| | - Peter Loppnau
- Structural Genomics Consortium, University of Toronto, Toronto, Ontario, Canada
| | | | | | - Jisun Lee
- Development and Medical, Pfizer Worldwide Research, Groton, CT, USA
| | | | | | | | - Feng Wang
- Development and Medical, Pfizer Worldwide Research, Groton, CT, USA
| | - Ella C Adamson
- Structural Genomics Consortium, University of Toronto, Toronto, Ontario, Canada
| | - Matthieu Schapira
- Structural Genomics Consortium, University of Toronto, Toronto, Ontario, Canada
- Department of Pharmacology and Toxicology, University of Toronto, Toronto, Ontario, Canada
| | - Matthias Gstaiger
- Institute of Molecular Systems Biology at ETH Zurich, Zurich, Switzerland
| | - Stefan Knapp
- Institut für Pharmazeutische Chemie, Goethe-University Frankfurt, Biozentrum, Frankfurt am Main, Germany
- Structural Genomics Consortium, Goethe-University Frankfurt, Buchmann Institute for Life Sciences, Frankfurt am Main, Germany
| | - Masoud Vedadi
- Structural Genomics Consortium, University of Toronto, Toronto, Ontario, Canada
- Department of Pharmacology and Toxicology, University of Toronto, Toronto, Ontario, Canada
| | - Jinrong Min
- Structural Genomics Consortium, University of Toronto, Toronto, Ontario, Canada
- Department of Physiology, University of Toronto, Toronto, Ontario, Canada
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences, Central China Normal University, Wuhan, China
| | - Gilles A Lajoie
- Department of Biochemistry, Schulich School of Medicine and Dentistry, University of Western Ontario, London, Ontario, Canada
- Don Rix Protein Identification Facility, Schulich School of Medicine and Dentistry, University of Western Ontario, London, Ontario, Canada
| | - Dalia Barsyte-Lovejoy
- Structural Genomics Consortium, University of Toronto, Toronto, Ontario, Canada
- Department of Pharmacology and Toxicology, University of Toronto, Toronto, Ontario, Canada
| | - Dafydd R Owen
- Development and Medical, Pfizer Worldwide Research, Groton, CT, USA
| | - Caroline Schild-Poulter
- Robarts Research Institute, Schulich School of Medicine and Dentistry, University of Western Ontario, London, Ontario, Canada
- Department of Biochemistry, Schulich School of Medicine and Dentistry, University of Western Ontario, London, Ontario, Canada
| | - Cheryl H Arrowsmith
- Structural Genomics Consortium, University of Toronto, Toronto, Ontario, Canada.
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada.
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada.
| |
Collapse
|
7
|
Zhu L, Song L, Zheng C, Wang N, Xue C, Shen Z, Huang X. Intracellular nonenzymatic in situ growth of layered nanosheet DNA architectures based on palindrome-chained dumbbell probes for miRNA imaging. Talanta 2024; 277:126333. [PMID: 38850801 DOI: 10.1016/j.talanta.2024.126333] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2023] [Revised: 05/07/2024] [Accepted: 05/28/2024] [Indexed: 06/10/2024]
Abstract
MicroRNA (miRNA) represents a class of important potential biomarkers, and their intracellular imaging is extremely useful for fundamental research and early diagnosis of human cancers. Hybridization chain reaction (HCR) has been shown to be effective in detecting miRNA in living cells. However, its practical applications are still hampered by inefficient reaction kinetics and poor biological stability under complex intracellular conditions. To address these issues, we report a palindrome-mediated multiple hybridization chain reaction (P-HCR) system to better visualize intracellular miRNAs. In the presence of the target miRNA, a layered nanosheet DNA architecture (LSDA) can be assembled in situ via the palindrome-mediated multiple HCR process. We demonstrate that the biological stability of this reaction system could be significantly improved by designing the probes to dumbbell-shaped structures and the distance of hairpins was effectively decreased due to palindrome-chained effect. Consequently, miRNA can be quantitatively identified even at extremely low concentrations of 4.7 pM. The P-HCR system can effectively differentiate the expression levels of miRNA in different tumor cells and normal cells, as demonstrated in live cell tests and the results were in agreement with the PCR, which is considered the gold standard. The new (P-HCR) system has the potential to revolutionize miRNA imaging in living cells.
Collapse
Affiliation(s)
- Lingye Zhu
- Pulmonary Division, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou Key Laboratory of Interdiscipline and Translational Medicine, Wenzhou Key Laboratory of Heart and Lung, Wenzhou, Zhejiang, 325035, China; Emergency and Critical Care Center, Intensive Care Unit, Zhejiang Provincial People's Hospital (Affiliated People's Hospital), Hangzhou Medical College, Hangzhou, Zhejiang, China
| | - Lanlan Song
- Pulmonary Division, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou Key Laboratory of Interdiscipline and Translational Medicine, Wenzhou Key Laboratory of Heart and Lung, Wenzhou, Zhejiang, 325035, China
| | - Cheng Zheng
- Pulmonary Division, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou Key Laboratory of Interdiscipline and Translational Medicine, Wenzhou Key Laboratory of Heart and Lung, Wenzhou, Zhejiang, 325035, China
| | - Ning Wang
- Pulmonary Division, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou Key Laboratory of Interdiscipline and Translational Medicine, Wenzhou Key Laboratory of Heart and Lung, Wenzhou, Zhejiang, 325035, China
| | - Chang Xue
- Key Laboratory of Laboratory Medicine, Ministry of Education of China, and Zhejiang Provincial Key Laboratory of Medical Genetics, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, Zhejiang, 325035, China.
| | - Zhifa Shen
- Key Laboratory of Laboratory Medicine, Ministry of Education of China, and Zhejiang Provincial Key Laboratory of Medical Genetics, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, Zhejiang, 325035, China.
| | - Xiaoying Huang
- Pulmonary Division, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou Key Laboratory of Interdiscipline and Translational Medicine, Wenzhou Key Laboratory of Heart and Lung, Wenzhou, Zhejiang, 325035, China.
| |
Collapse
|
8
|
Bahojb Mahdavi SZ, Jebelli A, Aghbash PS, Baradaran B, Amini M, Oroojalian F, Pouladi N, Baghi HB, de la Guardia M, Mokhtarzadeh AA. A comprehensive overview on the crosstalk between microRNAs and viral pathogenesis and infection. Med Res Rev 2024. [PMID: 39185567 DOI: 10.1002/med.22073] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2021] [Revised: 04/11/2023] [Accepted: 08/04/2024] [Indexed: 08/27/2024]
Abstract
Infections caused by viruses as the smallest infectious agents, pose a major threat to global public health. Viral infections utilize different host mechanisms to facilitate their own propagation and pathogenesis. MicroRNAs (miRNAs), as small noncoding RNA molecules, play important regulatory roles in different diseases, including viral infections. They can promote or inhibit viral infection and have a pro-viral or antiviral role. Also, viral infections can modulate the expression of host miRNAs. Furthermore, viruses from different families evade the host immune response by producing their own miRNAs called viral miRNAs (v-miRNAs). Understanding the replication cycle of viruses and their relation with host miRNAs and v-miRNAs can help to find new treatments against viral infections. In this review, we aim to outline the structure, genome, and replication cycle of various viruses including hepatitis B, hepatitis C, influenza A virus, coronavirus, human immunodeficiency virus, human papillomavirus, herpes simplex virus, Epstein-Barr virus, Dengue virus, Zika virus, and Ebola virus. We also discuss the role of different host miRNAs and v-miRNAs and their role in the pathogenesis of these viral infections.
Collapse
Affiliation(s)
- Seyedeh Zahra Bahojb Mahdavi
- Department of Biology, Faculty of Basic Sciences, Azarbaijan Shahid Madani University, Tabriz, Iran
- Immunology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Asiyeh Jebelli
- Department of Biological Science, Faculty of Basic Science, Higher Education Institute of Rab-Rashid, Tabriz, Iran
- Tuberculosis and Lung Diseases Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | | | - Behzad Baradaran
- Immunology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Mohammad Amini
- Immunology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Fatemeh Oroojalian
- Department of Advanced Sciences and Technologies in Medicine, School of Medicine, North Khorasan University of Medical Sciences, Bojnurd, Iran
| | - Nasser Pouladi
- Department of Biology, Faculty of Basic Sciences, Azarbaijan Shahid Madani University, Tabriz, Iran
| | - Hossein Bannazadeh Baghi
- Department of Virology, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Miguel de la Guardia
- Department of Analytical Chemistry, University of Valencia, Burjassot, Valencia, Spain
| | | |
Collapse
|
9
|
Garg A, Shang R, Cvetanovic T, Lai EC, Joshua-Tor L. The structural landscape of Microprocessor mediated pri- let-7 miRNA processing. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.09.593372. [PMID: 38766155 PMCID: PMC11100773 DOI: 10.1101/2024.05.09.593372] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2024]
Abstract
miRNA biogenesis is initiated upon cleavage of a primary miRNA (pri-miRNA) hairpin by the Microprocessor (MP), composed of the Drosha RNase III enzyme and its partner DGCR8. Multiple pri-miRNA sequence motifs affect MP recognition, fidelity, and efficiency. Here, we performed cryo-EM and biochemical studies of several let-7 family pri-miRNAs in complex with human MP. We show that MP has the structural plasticity to accommodate a range of pri-miRNAs. These structures revealed key features of the 5' UG sequence motif, more comprehensively represented as the "fUN" motif. Our analysis explains how cleavage of class-II pri-let-7 members harboring a bulged nucleotide generates a noncanonical precursor with a 1-nt 3' overhang. Finally, the MP-SRSF3-pri-let-7f1 structure reveals how SRSF3 contributes to MP fidelity by interacting with the CNNC-motif and Drosha's PAZ-like domain. Overall, this study sheds light on the mechanisms for flexible recognition, accurate cleavage, and regulated processing of different pri-miRNAs by MP.
Collapse
Affiliation(s)
- Ankur Garg
- W. M. Keck Structural Biology Laboratory, Cold Spring Harbor Laboratory, One Bungtown Road, Cold Spring Harbor, New York, 11724 USA
- Howard Hughes Medical Institute, Cold Spring Harbor laboratory, One Bungtown Road, Cold Spring Harbor, New York, 11724 USA
| | - Renfu Shang
- Developmental Biology Program, Sloan Kettering Institute, 430 East 67th St, ROC-10, New York, NY 10065, USA
| | - Todor Cvetanovic
- W. M. Keck Structural Biology Laboratory, Cold Spring Harbor Laboratory, One Bungtown Road, Cold Spring Harbor, New York, 11724 USA
| | - Eric C Lai
- Developmental Biology Program, Sloan Kettering Institute, 430 East 67th St, ROC-10, New York, NY 10065, USA
| | - Leemor Joshua-Tor
- W. M. Keck Structural Biology Laboratory, Cold Spring Harbor Laboratory, One Bungtown Road, Cold Spring Harbor, New York, 11724 USA
- Howard Hughes Medical Institute, Cold Spring Harbor laboratory, One Bungtown Road, Cold Spring Harbor, New York, 11724 USA
- Lead Contact
| |
Collapse
|
10
|
Phan P, Fogarty CE, Eamens AL, Duke MG, McManus DP, Wang T, Cummins SF. ARGONAUTE2 Localizes to Sites of Sporocysts in the Schistosome-Infected Snail, Biomphalaria glabrata. Genes (Basel) 2024; 15:1023. [PMID: 39202383 PMCID: PMC11353429 DOI: 10.3390/genes15081023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2024] [Revised: 07/30/2024] [Accepted: 08/01/2024] [Indexed: 09/03/2024] Open
Abstract
MicroRNAs (miRNAs) are a class of small regulatory RNA that are generated via core protein machinery. The miRNAs direct gene-silencing mechanisms to mediate an essential role in gene expression regulation. In mollusks, miRNAs have been demonstrated to be required to regulate gene expression in various biological processes, including normal development, immune responses, reproduction, and stress adaptation. In this study, we aimed to establishment the requirement of the miRNA pathway as part of the molecular response of exposure of Biomphalaria glabrata (snail host) to Schistosoma mansoni (trematode parasite). Initially, the core pieces of miRNA pathway protein machinery, i.e., Drosha, DGCR8, Exportin-5, Ran, and Dicer, together with the central RNA-induced silencing complex (RISC) effector protein Argonaute2 (Ago2) were elucidated from the B. glabrata genome. Following exposure of B. glabrata to S. mansoni miracidia, we identified significant expression up-regulation of all identified pieces of miRNA pathway protein machinery, except for Exportin-5, at 16 h post exposure. For Ago2, we went on to show that the Bgl-Ago2 protein was localized to regions surrounding the sporocysts in the digestive gland of infected snails 20 days post parasite exposure. In addition to documenting elevated miRNA pathway protein machinery expression at the early post-exposure time point, a total of 13 known B. glabrata miRNAs were significantly differentially expressed. Of these thirteen B. glabrata miRNAs responsive to S. mansoni miracidia exposure, five were significantly reduced in their abundance, and correspondingly, these five miRNAs were determined to putatively target six genes with significantly elevated expression and that have been previously associated with immune responses in other animal species, including humans. In conclusion, this study demonstrates the central importance of a functional miRNA pathway in snails, which potentially forms a critical component of the immune response of snails to parasite exposure. Further, the data reported in this study provide additional evidence of the complexity of the molecular response of B. glabrata to S. mansoni infection: a molecular response that could be targeted in the future to overcome parasite infection and, in turn, human schistosomiasis.
Collapse
Affiliation(s)
- Phong Phan
- Centre for Bioinnovation, University of the Sunshine Coast, Maroochydore, QLD 4558, Australia; (P.P.); (C.E.F.); (T.W.)
- School of Science, Technology and Engineering, University of the Sunshine Coast, Maroochydore, QLD 4558, Australia
| | - Conor E. Fogarty
- Centre for Bioinnovation, University of the Sunshine Coast, Maroochydore, QLD 4558, Australia; (P.P.); (C.E.F.); (T.W.)
- School of Science, Technology and Engineering, University of the Sunshine Coast, Maroochydore, QLD 4558, Australia
| | - Andrew L. Eamens
- School of Health, University of the Sunshine Coast, Maroochydore, QLD 4558, Australia;
| | - Mary G. Duke
- Molecular Parasitology Laboratory, QIMR Berghofer Medical Research Institute, Brisbane, QLD 4006, Australia;
| | - Donald P. McManus
- Molecular Parasitology Laboratory, QIMR Berghofer Medical Research Institute, Brisbane, QLD 4006, Australia;
| | - Tianfang Wang
- Centre for Bioinnovation, University of the Sunshine Coast, Maroochydore, QLD 4558, Australia; (P.P.); (C.E.F.); (T.W.)
- School of Science, Technology and Engineering, University of the Sunshine Coast, Maroochydore, QLD 4558, Australia
| | - Scott F. Cummins
- Centre for Bioinnovation, University of the Sunshine Coast, Maroochydore, QLD 4558, Australia; (P.P.); (C.E.F.); (T.W.)
- School of Science, Technology and Engineering, University of the Sunshine Coast, Maroochydore, QLD 4558, Australia
| |
Collapse
|
11
|
Alkhazaali-Ali Z, Sahab-Negah S, Boroumand AR, Tavakol-Afshari J. MicroRNA (miRNA) as a biomarker for diagnosis, prognosis, and therapeutics molecules in neurodegenerative disease. Biomed Pharmacother 2024; 177:116899. [PMID: 38889636 DOI: 10.1016/j.biopha.2024.116899] [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: 04/11/2024] [Revised: 05/29/2024] [Accepted: 06/06/2024] [Indexed: 06/20/2024] Open
Abstract
Neurodegenerative diseases that include Alzheimer's disease (AD), amyotrophic lateral sclerosis (ALS), Parkinson's disease (PD), Huntington's disease (HD), and multiple sclerosis (MS) that arise due to numerous causes like protein accumulation and autoimmunity characterized by neurologic depletion which lead to incapacity in normal physiological function such as thinking and movement in these patients. Glial cells perform an important role in protective neuronal function; in the case of neuroinflammation, glial cell dysfunction can promote the development of neurodegenerative diseases. miRNA that participates in gene regulation and plays a vital role in many biological processes in the body; in the central nervous system (CNS), it can play an essential part in neural maturation and differentiation. In neurodegenerative diseases, miRNA dysregulation occurs, enhancing the development of these diseases. In this review, we discuss neurodegenerative disease (Alzheimer's disease (AD), Parkinson's disease (PD), amyotrophic lateral sclerosis (ALS), and multiple sclerosis (MS)) and how miRNA is preserved as a diagnostic biomarker or therapeutic agent in these disorders. Finally, we highlight miRNA as therapy.
Collapse
Affiliation(s)
- Zahraa Alkhazaali-Ali
- Department of Immunology, Immunology Research Center, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran; Student Research Committee, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Sajad Sahab-Negah
- Neuroscience Research Center, Mashhad University of Medical Sciences, Mashhad, Iran; Shefa Neuroscience Research Center, Khatam Alanbia Hospital, Tehran, Iran
| | - Amir Reza Boroumand
- Neuroscience Research Center, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Jalil Tavakol-Afshari
- Department of Immunology, Immunology Research Center, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran.
| |
Collapse
|
12
|
Huang Y, Guan Y, Zhang X. METTL3-Mediated Maturation of miR-99a-5p Promotes Cell Migration and Invasion in Oral Squamous Cell Carcinoma by Targeting ZBTB7A. Mol Biotechnol 2024; 66:1942-1953. [PMID: 37498409 DOI: 10.1007/s12033-023-00815-x] [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: 01/06/2023] [Accepted: 06/29/2023] [Indexed: 07/28/2023]
Abstract
METTL3 is an important methyltransferase in N(6)-methyladenosine (m6A) modification. Recently, METTL3 mediates methylation of pri-microRNA (miRNA) to accelerate miRNA maturation, regulating tumor development. This study explored whether METTL3 mediated miR-99a-5p to influence oral squamous cell carcinoma (OSCC) cell metastasis. MiR-99a-5p, ZBTB7A, and MATTL3 expression was measured using quantitative real-time PCR. Biological behaviors were assessed using cell counting kit-8, flow cytometry, Transwell assay, as well as western blot. Luciferase reporter assay evaluated the interaction between miR-99a-5p and ZBTB7A. METTL3-regulated pri-miR-99a-5p processing was determined by RNA binding protein immunoprecipitation (RIP) and methylated RNA immunoprecipitation (MeRIP) assays. The consequences clarified that miR-99a-5p was upregulated in OSCC cells. Downregulation of miR-99a-5p suppressed cellular viability, migration, invasion, and epithelial-mesenchymal transition (EMT), and induced apoptosis. ZBTB7A acted as a miR-99a-5p target and reversed the effects on cellular behaviors induced by miR-99a-5p inhibitor. m6A content and METTL3 expression were increased in OSCC cells. METTL3 promoted the m6A modification of pri-miR-99a-5p and thereby facilitated miR-99a-5p processing. Moreover, knockdown of METTL3 inhibited OSCC metastasis by downregulating miR-99a-5p. Taken together, METTL3 promoted miR-99a-5p maturation in an m6A-dependent manner, which further targets ZBTB7A to accelerate the progression of OSCC. These findings suggest potential targets for OSCC therapy.
Collapse
Affiliation(s)
- Yuhua Huang
- Department of stomatology, The Second Affiliated Hospital of Guangzhou, University of Chinese Medicine, 6/F, East Zone, No. 111, Dade Road, Yuexiu District, Guangzhou, 510000, Guangdong, China
| | - Yun Guan
- Department of stomatology, The Second Affiliated Hospital of Guangzhou, University of Chinese Medicine, 6/F, East Zone, No. 111, Dade Road, Yuexiu District, Guangzhou, 510000, Guangdong, China
| | - Xing Zhang
- Department of stomatology, The Second Affiliated Hospital of Guangzhou, University of Chinese Medicine, 6/F, East Zone, No. 111, Dade Road, Yuexiu District, Guangzhou, 510000, Guangdong, China.
| |
Collapse
|
13
|
Wang Y, Tu MJ, Yu AM. Efflux ABC transporters in drug disposition and their posttranscriptional gene regulation by microRNAs. Front Pharmacol 2024; 15:1423416. [PMID: 39114355 PMCID: PMC11303158 DOI: 10.3389/fphar.2024.1423416] [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: 04/25/2024] [Accepted: 07/11/2024] [Indexed: 08/10/2024] Open
Abstract
ATP-binding cassette (ABC) transporters are transmembrane proteins expressed commonly in metabolic and excretory organs to control xenobiotic or endobiotic disposition and maintain their homeostasis. Changes in ABC transporter expression may directly affect the pharmacokinetics of relevant drugs involving absorption, distribution, metabolism, and excretion (ADME) processes. Indeed, overexpression of efflux ABC transporters in cancer cells or bacteria limits drug exposure and causes therapeutic failure that is known as multidrug resistance (MDR). With the discovery of functional noncoding microRNAs (miRNAs) produced from the genome, many miRNAs have been revealed to govern posttranscriptional gene regulation of ABC transporters, which shall improve our understanding of complex mechanism behind the overexpression of ABC transporters linked to MDR. In this article, we first overview the expression and localization of important ABC transporters in human tissues and their clinical importance regarding ADME as well as MDR. Further, we summarize miRNA-controlled posttranscriptional gene regulation of ABC transporters and effects on ADME and MDR. Additionally, we discuss the development and utilization of novel bioengineered miRNA agents to modulate ABC transporter gene expression and subsequent influence on cellular drug accumulation and chemosensitivity. Findings on posttranscriptional gene regulation of ABC transporters shall not only improve our understanding of mechanisms behind variable ADME but also provide insight into developing new means towards rational and more effective pharmacotherapies.
Collapse
Affiliation(s)
| | | | - Ai-Ming Yu
- Department of Biochemistry and Molecular Medicine, School of Medicine, University of California at Davis, Sacramento, CA, United States
| |
Collapse
|
14
|
da Silva Feltran G, Augusto da Silva R, da Costa Fernandes CJ, Ferreira MR, Dos Santos SAA, Justulin Junior LA, Del Valle Sosa L, Zambuzzi WF. Vascular smooth muscle cells exhibit elevated hypoxia-inducible Factor-1α expression in human blood vessel organoids, influencing osteogenic performance. Exp Cell Res 2024; 440:114136. [PMID: 38909881 DOI: 10.1016/j.yexcr.2024.114136] [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: 11/09/2023] [Revised: 03/14/2024] [Accepted: 06/15/2024] [Indexed: 06/25/2024]
Abstract
Considering the importance of alternative methodologies to animal experimentation, we propose an organoid-based biological model for in vitro blood vessel generation, achieved through co-culturing endothelial and vascular smooth muscle cells (VSMCs). Initially, the organoids underwent comprehensive characterization, revealing VSMCs (α-SMA + cells) at the periphery and endothelial cells (CD31+ cells) at the core. Additionally, ephrin B2 and ephrin B4, genes implicated in arterial and venous formation respectively, were used to validate the obtained organoid. Moreover, the data indicates exclusive HIF-1α expression in VSMCs, identified through various methodologies. Subsequently, we tested the hypothesis that the generated blood vessels have the capacity to modulate the osteogenic phenotype, demonstrating the ability of HIF-1α to promote osteogenic signals, primarily by influencing Runx2 expression. Overall, this study underscores that the methodology employed to create blood vessel organoids establishes an experimental framework capable of producing a 3D culture model of both venous and arterial endothelial tissues. This model effectively guides morphogenesis from mesenchymal stem cells through paracrine signaling, ultimately leading to an osteogenic acquisition phenotype, with the dynamic involvement of HIF-1α.
Collapse
Affiliation(s)
- Geórgia da Silva Feltran
- Department of Chemical and Biological Sciences, Institute of Biosciences, Universidade Estadual Paulista - UNESP, Campus Botucatu, Botucatu, São Paulo, 18618-970, Brazil
| | - Rodrigo Augusto da Silva
- CEEpiRG, Program in Environmental and Experimental Pathology, Paulista University - UNIP, São Paulo, São Paulo, Brazil
| | - Célio Junior da Costa Fernandes
- Department of Chemical and Biological Sciences, Institute of Biosciences, Universidade Estadual Paulista - UNESP, Campus Botucatu, Botucatu, São Paulo, 18618-970, Brazil
| | - Marcel Rodrigues Ferreira
- Department of Chemical and Biological Sciences, Institute of Biosciences, Universidade Estadual Paulista - UNESP, Campus Botucatu, Botucatu, São Paulo, 18618-970, Brazil
| | | | - Luis Antônio Justulin Junior
- Department of Structural and Functional Biology, Institute of Biosciences, São Paulo State University - UNESP, Botucatu, São Paulo, Brazil
| | - Liliana Del Valle Sosa
- Electron Microscopy Center, Faculty of Medical Sciences, National University of Cordoba, Córdoba, Argentina
| | - Willian Fernando Zambuzzi
- Department of Chemical and Biological Sciences, Institute of Biosciences, Universidade Estadual Paulista - UNESP, Campus Botucatu, Botucatu, São Paulo, 18618-970, Brazil.
| |
Collapse
|
15
|
Pathak AS, Stouffer GA. Differential responses to thrombospondin-1 and PDGF-BB in smooth muscle cells from atherosclerotic coronary arteries and internal thoracic arteries. Sci Rep 2024; 14:15847. [PMID: 38982274 PMCID: PMC11233497 DOI: 10.1038/s41598-024-66860-x] [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: 07/18/2023] [Accepted: 07/04/2024] [Indexed: 07/11/2024] Open
Abstract
Atherosclerosis is rare in internal thoracic arteries (ITA) even in patients with severe atherosclerotic coronary artery (ACA) disease. To explore cellular differences, ITA SMC from 3 distinct donors and ACA SMC from 3 distinct donors were grown to sub-confluence and growth arrested for 48 h. Proliferation and thrombospondin-1 (TSP1) production were determined using standard techniques. ITA SMC were larger, grew more slowly and survived more passages than ACA SMC. ACA SMC had a more pronounced proliferative response to 10% serum than ITA SMC. Both ACA SMC and ITA SMC proliferated in response to exogenous TSP1 (12.5 µg/ml and 25 µg/ml) and platelet derived growth factor-BB (PDGF-BB; 20 ng/ml) but TSP1- and PDGF-BB-induced proliferation were partially inhibited by anti-TSP1 antibody A4.1, microRNA-21(miR-21)-3p inhibitors and miR-21-5p inhibitors in each of the 3 ACA SMC lines, but not in any of the ITA SMC lines. PDGF-BB stimulated TSP1 production in ACA SMC but not in ITA SMC but there was no increase in TSP1 levels in conditioned media in either SMC type. In summary, there are significant differences in morphology, proliferative capacity and in responses to TSP1 and PDGF-BB in SMC derived from ITA compared to SMC derived from ACA.
Collapse
Affiliation(s)
- Alokkumar S Pathak
- Division of Cardiology and McAllister Heart Institute, University of North Carolina, Chapel Hill, NC, 27599-7075, USA
| | - George A Stouffer
- Division of Cardiology and McAllister Heart Institute, University of North Carolina, Chapel Hill, NC, 27599-7075, USA.
| |
Collapse
|
16
|
Chang JJS, Lin T, Jhang XY, Chan SP. hnRNP Q/SYNCRIP interacts with LIN28B and modulates the LIN28B/let-7 axis in human hepatoma cells. PLoS One 2024; 19:e0304947. [PMID: 38976670 PMCID: PMC11230530 DOI: 10.1371/journal.pone.0304947] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2023] [Accepted: 05/21/2024] [Indexed: 07/10/2024] Open
Abstract
The RNA-binding protein LIN28B represses the biogenesis of the tumor suppressor let-7. The LIN28B/let-7 axis regulates cell differentiation and is associated with various cancers. The RNA-binding protein Q (hnRNP Q) or SYNCRIP (Synaptotagmin Binding Cytoplasmic RNA Interacting Protein) has been implicated in mRNA splicing, mRNA transport, translation, and miRNAs biogenesis as well as metabolism in cancer. To determine whether hnRNP Q plays a role in the LIN28B/let-7 axis, we tested for interactions between hnRNP Q and LIN28B. We demonstrated that hnRNP Q interacts with LIN28B in an RNA-dependent manner. Knockdown of hnRNP Q caused reduced expression of a well-known let-7 target TRIM71, an E3 ubiquitin ligase that belongs to the RBCC/TRIM family, and also LIN28B, whose mRNA itself is down-regulated by let-7. In addition, hnRNP Q knockdown increased let-7 family miRNA levels and reduced the activity of luciferase reporters fused with the TRIM71 3'UTR or a synthetic 3'UTR carrying 8X let-7 complementary sites. Finally, depletion of hnRNP Q inhibited the proliferation of a hepatocellular carcinoma cell line, Huh7. This observation is consistent with the survival curve for liver cancer patients from the TCGA database, which indicates that high expression of hnRNP Q is a prognostic marker for a poor outcome in individuals afflicted with hepatocellular carcinoma. Together, our findings suggest that hnRNP Q interacts with LIN28B and modulates the LIN28B/let-7 axis in hepatocellular carcinoma.
Collapse
Affiliation(s)
- Jason Jei-Sheng Chang
- Graduate Institute of Microbiology, College of Medicine, National Taiwan University, Taipei, Taiwan
- Institute of Biomedical Sciences, Academia Sinica, Taipei, Taiwan
| | - Ti Lin
- Graduate Institute of Microbiology, College of Medicine, National Taiwan University, Taipei, Taiwan
| | - Xin-Yue Jhang
- Graduate Institute of Microbiology, College of Medicine, National Taiwan University, Taipei, Taiwan
| | - Shih-Peng Chan
- Graduate Institute of Microbiology, College of Medicine, National Taiwan University, Taipei, Taiwan
- Genome and Systems Biology Degree Program, College of Life Science, National Taiwan University, Taipei, Taiwan
| |
Collapse
|
17
|
Valizadeh M, Derafsh E, Abdi Abyaneh F, Parsamatin SK, Noshabad FZR, Alinaghipour A, Yaghoobi Z, Taheri AT, Dadgostar E, Aschner M, Mirzaei H, Tamtaji OR, Nabavizadeh F. Non-Coding RNAs and Neurodegenerative Diseases: Information of their Roles in Apoptosis. Mol Neurobiol 2024; 61:4508-4537. [PMID: 38102518 DOI: 10.1007/s12035-023-03849-z] [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: 03/22/2023] [Accepted: 11/16/2023] [Indexed: 12/17/2023]
Abstract
Apoptosis can be known as a key factor in the pathogenesis of neurodegenerative disorders. In disease conditions, the rate of apoptosis expands and tissue damage may become apparent. Recently, the scientific studies of the non-coding RNAs (ncRNAs) has provided new information of the molecular mechanisms that contribute to neurodegenerative disorders. Numerous reports have documented that ncRNAs have important contributions to several biological processes associated with the increase of neurodegenerative disorders. In addition, microRNAs (miRNAs), circular RNAs (circRNAs), as well as, long ncRNAs (lncRNAs) represent ncRNAs subtypes with the usual dysregulation in neurodegenerative disorders. Dysregulating ncRNAs has been associated with inhibiting or stimulating apoptosis in neurodegenerative disorders. Therefore, this review highlighted several ncRNAs linked to apoptosis in neurodegenerative disorders. CircRNAs, lncRNAs, and miRNAs were also illustrated completely regarding the respective signaling pathways of apoptosis.
Collapse
Affiliation(s)
| | - Ehsan Derafsh
- Windsor University School of Medicine, Cayon, Canada
| | | | - Sayedeh Kiana Parsamatin
- Department of Neurology, School of Medicine, Isfahan University of Medical Sciences, Isfahan, Iran
| | | | - Azam Alinaghipour
- School of Medical Sciences, Yazd Branch, Islamic Azad University, Yazd, Iran
| | - Zahra Yaghoobi
- Electrophysiology Research Center, Neuroscience Institute, Tehran University of Medical Sciences, Tehran, IR, Iran
- Department of Physiology, School of Medicine, Tehran University of Medical Sciences, Tehran, IR, Iran
| | - Abdolkarim Talebi Taheri
- Student Research Committee, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Ehsan Dadgostar
- Behavioral Sciences Research Center, Isfahan University of Medical Sciences, Isfahan, IR, Iran
- Student Research Committee, Isfahan University of Medical Sciences, Isfahan, IR, Iran
| | - Michael Aschner
- Department of Molecular Pharmacology, Albert Einstein College of Medicine, Bronx, NY, 10461, USA
| | - Hamed Mirzaei
- Research Center for Biochemistry and Nutrition in Metabolic Diseases, Kashan University of Medical Sciences, Kashan, IR, Iran.
| | - Omid Reza Tamtaji
- Electrophysiology Research Center, Neuroscience Institute, Tehran University of Medical Sciences, Tehran, IR, Iran.
- Department of Physiology, School of Medicine, Tehran University of Medical Sciences, Tehran, IR, Iran.
| | - Fatemeh Nabavizadeh
- Electrophysiology Research Center, Neuroscience Institute, Tehran University of Medical Sciences, Tehran, IR, Iran
- Department of Physiology, School of Medicine, Tehran University of Medical Sciences, Tehran, IR, Iran
| |
Collapse
|
18
|
Jang D, Kim CJ, Shin BH, Lim DH. The Biological Roles of microRNAs in Drosophila Development. INSECTS 2024; 15:491. [PMID: 39057224 PMCID: PMC11277110 DOI: 10.3390/insects15070491] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/23/2024] [Revised: 06/24/2024] [Accepted: 06/27/2024] [Indexed: 07/28/2024]
Abstract
Drosophila is a well-established insect model system for studying various physiological phenomena and developmental processes, with a focus on gene regulation. Drosophila development is controlled by programmed regulatory mechanisms specific to individual tissues. When key developmental processes are shared among various insects, the associated regulatory networks are believed to be conserved across insects. Thus, studies of developmental regulation in Drosophila have substantially contributed to our understanding of insect development. Over the past two decades, studies on microRNAs (miRNAs) in Drosophila have revealed their crucial regulatory roles in various developmental processes. This review focuses on the biological roles of miRNAs in specific tissues and processes associated with Drosophila development. Additionally, as a future direction, we discuss sequencing technologies that can analyze the interactions between miRNAs and their target genes, with the aim of enhancing miRNA studies in Drosophila development.
Collapse
Affiliation(s)
| | | | | | - Do-Hwan Lim
- School of Systems Biomedical Science, Soongsil University, Seoul 06978, Republic of Korea; (D.J.); (C.J.K.); (B.H.S.)
| |
Collapse
|
19
|
Wang F, Zhou C, Zhu Y, Keshavarzi M. The microRNA Let-7 and its exosomal form: Epigenetic regulators of gynecological cancers. Cell Biol Toxicol 2024; 40:42. [PMID: 38836981 PMCID: PMC11153289 DOI: 10.1007/s10565-024-09884-3] [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: 01/31/2024] [Accepted: 05/15/2024] [Indexed: 06/06/2024]
Abstract
Many types of gynecological cancer (GC) are often silent until they reach an advanced stage, and are therefore often diagnosed too late for effective treatment. Hence, there is a real need for more efficient diagnosis and treatment for patients with GC. During recent years, researchers have increasingly studied the impact of microRNAs cancer development, leading to a number of applications in detection and treatment. MicroRNAs are a particular group of tiny RNA molecules that regulate regular gene expression by affecting the translation process. The downregulation of numerous miRNAs has been observed in human malignancies. Let-7 is an example of a miRNA that controls cellular processes as well as signaling cascades to affect post-transcriptional gene expression. Recent research supports the hypothesis that enhancing let-7 expression in those cancers where it is downregulated may be a potential treatment option. Exosomes are tiny vesicles that move through body fluids and can include components like miRNAs (including let-7) that are important for communication between cells. Studies proved that exosomes are able to enhance tumor growth, angiogenesis, chemoresistance, metastasis, and immune evasion, thus suggesting their importance in GC management.
Collapse
Affiliation(s)
- Fei Wang
- Haiyan People's Hospital, Zhejiang Province, Jiaxing, 314300, Zhejiang, China
| | - Chundi Zhou
- Haiyan People's Hospital, Zhejiang Province, Jiaxing, 314300, Zhejiang, China
| | - Yanping Zhu
- Haiyan People's Hospital, Zhejiang Province, Jiaxing, 314300, Zhejiang, China.
| | - Maryam Keshavarzi
- School of Medicine, Tehran University of Medical Sciences, Tehran, Tehran, Iran.
| |
Collapse
|
20
|
Yu S, Li Y, Lu X, Han Z, Li C, Yuan X, Guo D. The regulatory role of miRNA and lncRNA on autophagy in diabetic nephropathy. Cell Signal 2024; 118:111144. [PMID: 38493883 DOI: 10.1016/j.cellsig.2024.111144] [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: 01/14/2024] [Revised: 03/09/2024] [Accepted: 03/14/2024] [Indexed: 03/19/2024]
Abstract
Diabetic nephropathy (DN) is a serious complication of diabetes that causes glomerular sclerosis and end-stage renal disease, leading to ascending morbidity and mortality in diabetic patients. Excessive accumulation of aberrantly modified proteins or damaged organelles, such as advanced glycation end-products, dysfunctional mitochondria, and inflammasomes is associated with the pathogenesis of DN. As one of the main degradation pathways, autophagy recycles toxic substances to maintain cellular homeostasis and autophagy dysregulation plays a crucial role in DN progression. MicroRNA (miRNA) and long non-coding RNA (lncRNA) are non-coding RNA (ncRNA) molecules that regulate gene expression and have been implicated in both physiological and pathological conditions. Recent studies have revealed that autophagy-regulating miRNA and lncRNA have been involved in pathological processes of DN, including renal cell injury, mitochondrial dysfunction, inflammation, and renal fibrosis. This review summarizes the role of autophagy in DN and emphasizes the modulation of miRNA and lncRNA on autophagy during disease progression, for the development of promising interventions by targeting these ncRNAs in this disease.
Collapse
Affiliation(s)
- Siming Yu
- Department of Nephrology II, First Affiliated Hospital of Heilongjiang University of Chinese Medicine, Harbin 150036, China
| | - Yue Li
- Heilongjiang University of Chinese Medicine, Harbin 150040, China
| | - Xinxin Lu
- Heilongjiang University of Chinese Medicine, Harbin 150040, China
| | - Zehui Han
- Heilongjiang University of Chinese Medicine, Harbin 150040, China
| | - Chunsheng Li
- Heilongjiang University of Chinese Medicine, Harbin 150040, China
| | - Xingxing Yuan
- Heilongjiang University of Chinese Medicine, Harbin 150040, China; Department of Gastroenterology, Heilongjiang Academy of Traditional Chinese Medicine, Harbin 150006, China
| | - Dandan Guo
- Department of Cardiology, Second Affiliated Hospital of Heilongjiang University of Chinese Medicine, Harbin 150001, China.
| |
Collapse
|
21
|
Azam HMH, Rößling RI, Geithe C, Khan MM, Dinter F, Hanack K, Prüß H, Husse B, Roggenbuck D, Schierack P, Rödiger S. MicroRNA biomarkers as next-generation diagnostic tools for neurodegenerative diseases: a comprehensive review. Front Mol Neurosci 2024; 17:1386735. [PMID: 38883980 PMCID: PMC11177777 DOI: 10.3389/fnmol.2024.1386735] [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: 02/15/2024] [Accepted: 04/12/2024] [Indexed: 06/18/2024] Open
Abstract
Neurodegenerative diseases (NDs) are characterized by abnormalities within neurons of the brain or spinal cord that gradually lose function, eventually leading to cell death. Upon examination of affected tissue, pathological changes reveal a loss of synapses, misfolded proteins, and activation of immune cells-all indicative of disease progression-before severe clinical symptoms become apparent. Early detection of NDs is crucial for potentially administering targeted medications that may delay disease advancement. Given their complex pathophysiological features and diverse clinical symptoms, there is a pressing need for sensitive and effective diagnostic methods for NDs. Biomarkers such as microRNAs (miRNAs) have been identified as potential tools for detecting these diseases. We explore the pivotal role of miRNAs in the context of NDs, focusing on Alzheimer's disease, Parkinson's disease, Multiple sclerosis, Huntington's disease, and Amyotrophic Lateral Sclerosis. The review delves into the intricate relationship between aging and NDs, highlighting structural and functional alterations in the aging brain and their implications for disease development. It elucidates how miRNAs and RNA-binding proteins are implicated in the pathogenesis of NDs and underscores the importance of investigating their expression and function in aging. Significantly, miRNAs exert substantial influence on post-translational modifications (PTMs), impacting not just the nervous system but a wide array of tissues and cell types as well. Specific miRNAs have been found to target proteins involved in ubiquitination or de-ubiquitination processes, which play a significant role in regulating protein function and stability. We discuss the link between miRNA, PTM, and NDs. Additionally, the review discusses the significance of miRNAs as biomarkers for early disease detection, offering insights into diagnostic strategies.
Collapse
Affiliation(s)
- Hafiz Muhammad Husnain Azam
- Institute of Biotechnology, Faculty of Environment and Natural Sciences, Brandenburg University of Technology Cottbus-Senftenberg, Senftenberg, Germany
| | - Rosa Ilse Rößling
- German Center for Neurodegenerative Diseases (DZNE), Berlin, Germany
- Department of Neurology, Charité - Universitätsmedizin Berlin, Berlin, Germany
| | - Christiane Geithe
- Institute of Biotechnology, Faculty of Environment and Natural Sciences, Brandenburg University of Technology Cottbus-Senftenberg, Senftenberg, Germany
- Faculty of Health Sciences, Joint Faculty of the Brandenburg University of Technology Cottbus - Senftenberg, The Brandenburg Medical School Theodor Fontane and the University of Potsdam, Berlin, Germany
| | - Muhammad Moman Khan
- Institute of Biotechnology, Faculty of Environment and Natural Sciences, Brandenburg University of Technology Cottbus-Senftenberg, Senftenberg, Germany
| | - Franziska Dinter
- Institute of Biotechnology, Faculty of Environment and Natural Sciences, Brandenburg University of Technology Cottbus-Senftenberg, Senftenberg, Germany
- PolyAn GmbH, Berlin, Germany
| | - Katja Hanack
- Institute of Biochemistry and Biology, University of Potsdam, Potsdam, Germany
| | - Harald Prüß
- German Center for Neurodegenerative Diseases (DZNE), Berlin, Germany
- Department of Neurology, Charité - Universitätsmedizin Berlin, Berlin, Germany
| | - Britta Husse
- Institute of Biotechnology, Faculty of Environment and Natural Sciences, Brandenburg University of Technology Cottbus-Senftenberg, Senftenberg, Germany
| | - Dirk Roggenbuck
- Institute of Biotechnology, Faculty of Environment and Natural Sciences, Brandenburg University of Technology Cottbus-Senftenberg, Senftenberg, Germany
| | - Peter Schierack
- Institute of Biotechnology, Faculty of Environment and Natural Sciences, Brandenburg University of Technology Cottbus-Senftenberg, Senftenberg, Germany
| | - Stefan Rödiger
- Institute of Biotechnology, Faculty of Environment and Natural Sciences, Brandenburg University of Technology Cottbus-Senftenberg, Senftenberg, Germany
- Faculty of Health Sciences, Joint Faculty of the Brandenburg University of Technology Cottbus - Senftenberg, The Brandenburg Medical School Theodor Fontane and the University of Potsdam, Berlin, Germany
| |
Collapse
|
22
|
Shibata K, Moriizumi H, Onomoto K, Kaneko Y, Miyakawa T, Zenno S, Tanokura M, Yoneyama M, Takahashi T, Ui-Tei K. Caspase-mediated processing of TRBP regulates apoptosis during viral infection. Nucleic Acids Res 2024; 52:5209-5225. [PMID: 38636948 PMCID: PMC11109963 DOI: 10.1093/nar/gkae246] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2023] [Revised: 03/14/2024] [Accepted: 03/26/2024] [Indexed: 04/20/2024] Open
Abstract
RNA silencing is a post-transcriptional gene-silencing mechanism mediated by microRNAs (miRNAs). However, the regulatory mechanism of RNA silencing during viral infection is unclear. TAR RNA-binding protein (TRBP) is an enhancer of RNA silencing that induces miRNA maturation by interacting with the ribonuclease Dicer. TRBP interacts with a virus sensor protein, laboratory of genetics and physiology 2 (LGP2), in the early stage of viral infection of human cells. Next, it induces apoptosis by inhibiting the maturation of miRNAs, thereby upregulating the expression of apoptosis regulatory genes. In this study, we show that TRBP undergoes a functional conversion in the late stage of viral infection. Viral infection resulted in the activation of caspases that proteolytically processed TRBP into two fragments. The N-terminal fragment did not interact with Dicer but interacted with type I interferon (IFN) signaling modulators, such as protein kinase R (PKR) and LGP2, and induced ER stress. The end results were irreversible apoptosis and suppression of IFN signaling. Our results demonstrate that the processing of TRBP enhances apoptosis, reducing IFN signaling during viral infection.
Collapse
Affiliation(s)
- Keiko Shibata
- Department of Biochemistry and Molecular Biology, Graduate School of Science and Engineering, Saitama University, Saitama 338-8570, Japan
| | - Harune Moriizumi
- Department of Biochemistry and Molecular Biology, Graduate School of Science and Engineering, Saitama University, Saitama 338-8570, Japan
| | - Koji Onomoto
- Division of Molecular Immunology, Medical Mycology Research Center, Chiba University, Chiba 260-8673, Japan
| | - Yuka Kaneko
- Department of Biochemistry and Molecular Biology, Graduate School of Science and Engineering, Saitama University, Saitama 338-8570, Japan
| | - Takuya Miyakawa
- Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo 113-8657, Japan
- Graduate School of Biostudies, Kyoto University, Kyoto 606-8502, Japan
| | - Shuhei Zenno
- Department of Biotechnology, Faculty of Engineering, Maebashi Institute of Technology, Gunma 371-0816, Japan
| | - Masaru Tanokura
- Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo 113-8657, Japan
| | - Mitsutoshi Yoneyama
- Division of Molecular Immunology, Medical Mycology Research Center, Chiba University, Chiba 260-8673, Japan
- Division of Pandemic and Post-disaster Infectious Diseases, Research Institute of Disaster Medicine, Chiba University, Chiba 260-8673, Japan
| | - Tomoko Takahashi
- Department of Biochemistry and Molecular Biology, Graduate School of Science and Engineering, Saitama University, Saitama 338-8570, Japan
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo 113-0033, Japan
| | - Kumiko Ui-Tei
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo 113-0033, Japan
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Chiba 277-8561, Japan
| |
Collapse
|
23
|
Lai C, Xu L, Dai S. The nuclear export protein exportin-1 in solid malignant tumours: From biology to clinical trials. Clin Transl Med 2024; 14:e1684. [PMID: 38783482 PMCID: PMC11116501 DOI: 10.1002/ctm2.1684] [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: 12/07/2023] [Revised: 04/15/2024] [Accepted: 04/19/2024] [Indexed: 05/25/2024] Open
Abstract
BACKGROUND Exportin-1 (XPO1), a crucial protein regulating nuclear-cytoplasmic transport, is frequently overexpressed in various cancers, driving tumor progression and drug resistance. This makes XPO1 an attractive therapeutic target. Over the past few decades, the number of available nuclear export-selective inhibitors has been increasing. Only KPT-330 (selinexor) has been successfully used for treating haematological malignancies, and KPT-8602 (eltanexor) has been used for treating haematologic tumours in clinical trials. However, the use of nuclear export-selective inhibitors for the inhibition of XPO1 expression has yet to be thoroughly investigated in clinical studies and therapeutic outcomes for solid tumours. METHODS We collected numerous literatures to explain the efficacy of XPO1 Inhibitors in preclinical and clinical studies of a wide range of solid tumours. RESULTS In this review, we focus on the nuclear export function of XPO1 and results from clinical trials of its inhibitors in solid malignant tumours. We summarized the mechanism of action and therapeutic potential of XPO1 inhibitors, as well as adverse effects and response biomarkers. CONCLUSION XPO1 inhibition has emerged as a promising therapeutic strategy in the fight against cancer, offering a novel approach to targeting tumorigenic processes and overcoming drug resistance. SINE compounds have demonstrated efficacy in a wide range of solid tumours, and ongoing research is focused on optimizing their use, identifying response biomarkers, and developing effective combination therapies. KEY POINTS Exportin-1 (XPO1) plays a critical role in mediating nucleocytoplasmic transport and cell cycle. XPO1 dysfunction promotes tumourigenesis and drug resistance within solid tumours. The therapeutic potential and ongoing researches on XPO1 inhibitors in the treatment of solid tumours. Additional researches are essential to address safety concerns and identify biomarkers for predicting patient response to XPO1 inhibitors.
Collapse
Affiliation(s)
- Chuanxi Lai
- Department of Colorectal SurgerySir Run Run Shaw HospitalSchool of MedicineZhejiang UniversityHangzhouChina
- Key Laboratory of Biotherapy of Zhejiang ProvinceHangzhouChina
| | - Lingna Xu
- Department of Colorectal SurgerySir Run Run Shaw HospitalSchool of MedicineZhejiang UniversityHangzhouChina
- Key Laboratory of Biotherapy of Zhejiang ProvinceHangzhouChina
| | - Sheng Dai
- Department of Colorectal SurgerySir Run Run Shaw HospitalSchool of MedicineZhejiang UniversityHangzhouChina
- Key Laboratory of Biotherapy of Zhejiang ProvinceHangzhouChina
| |
Collapse
|
24
|
Daniel Thomas S, Vijayakumar K, John L, Krishnan D, Rehman N, Revikumar A, Kandel Codi JA, Prasad TSK, S S V, Raju R. Machine Learning Strategies in MicroRNA Research: Bridging Genome to Phenome. OMICS : A JOURNAL OF INTEGRATIVE BIOLOGY 2024; 28:213-233. [PMID: 38752932 DOI: 10.1089/omi.2024.0047] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2024]
Abstract
MicroRNAs (miRNAs) have emerged as a prominent layer of regulation of gene expression. This article offers the salient and current aspects of machine learning (ML) tools and approaches from genome to phenome in miRNA research. First, we underline that the complexity in the analysis of miRNA function ranges from their modes of biogenesis to the target diversity in diverse biological conditions. Therefore, it is imperative to first ascertain the miRNA coding potential of genomes and understand the regulatory mechanisms of their expression. This knowledge enables the efficient classification of miRNA precursors and the identification of their mature forms and respective target genes. Second, and because one miRNA can target multiple mRNAs and vice versa, another challenge is the assessment of the miRNA-mRNA target interaction network. Furthermore, long-noncoding RNA (lncRNA)and circular RNAs (circRNAs) also contribute to this complexity. ML has been used to tackle these challenges at the high-dimensional data level. The present expert review covers more than 100 tools adopting various ML approaches pertaining to, for example, (1) miRNA promoter prediction, (2) precursor classification, (3) mature miRNA prediction, (4) miRNA target prediction, (5) miRNA- lncRNA and miRNA-circRNA interactions, (6) miRNA-mRNA expression profiling, (7) miRNA regulatory module detection, (8) miRNA-disease association, and (9) miRNA essentiality prediction. Taken together, we unpack, critically examine, and highlight the cutting-edge synergy of ML approaches and miRNA research so as to develop a dynamic and microlevel understanding of human health and diseases.
Collapse
Affiliation(s)
- Sonet Daniel Thomas
- Centre for Integrative Omics Data Science (CIODS), Yenepoya (Deemed to Be University), Manglore, Karnataka, India
- Centre for Systems Biology and Molecular Medicine (CSBMM), Yenepoya (Deemed to Be University), Manglore, Karnataka, India
| | - Krithika Vijayakumar
- Centre for Integrative Omics Data Science (CIODS), Yenepoya (Deemed to Be University), Manglore, Karnataka, India
| | - Levin John
- Centre for Integrative Omics Data Science (CIODS), Yenepoya (Deemed to Be University), Manglore, Karnataka, India
| | - Deepak Krishnan
- Centre for Systems Biology and Molecular Medicine (CSBMM), Yenepoya (Deemed to Be University), Manglore, Karnataka, India
| | - Niyas Rehman
- Centre for Integrative Omics Data Science (CIODS), Yenepoya (Deemed to Be University), Manglore, Karnataka, India
| | - Amjesh Revikumar
- Centre for Integrative Omics Data Science (CIODS), Yenepoya (Deemed to Be University), Manglore, Karnataka, India
- Kerala Genome Data Centre, Kerala Development and Innovation Strategic Council, Thiruvananthapuram, Kerala, India
| | - Jalaluddin Akbar Kandel Codi
- Department of Surgical Oncology, Yenepoya Medical College, Yenepoya (Deemed to Be University), Manglore, Karnataka, India
| | | | - Vinodchandra S S
- Department of Computer Science, University of Kerala, Thiruvananthapuram, Kerala, India
| | - Rajesh Raju
- Centre for Integrative Omics Data Science (CIODS), Yenepoya (Deemed to Be University), Manglore, Karnataka, India
- Centre for Systems Biology and Molecular Medicine (CSBMM), Yenepoya (Deemed to Be University), Manglore, Karnataka, India
| |
Collapse
|
25
|
Montgomery BE, Knittel TL, Reed KJ, Chong MC, Isolehto IJ, Cafferty ER, Smith MJ, Sprister RA, Magelky CN, Scherman H, Ketting RF, Montgomery TA. Regulation of Microprocessor assembly and localization via Pasha's WW domain in C. elegans. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.23.590772. [PMID: 38712061 PMCID: PMC11071396 DOI: 10.1101/2024.04.23.590772] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2024]
Abstract
Primary microRNA (pri-miRNA) transcripts are processed by the Microprocessor, a protein complex that includes the ribonuclease Drosha and its RNA binding partner DGCR8/Pasha. We developed a live, whole animal, fluorescence-based sensor that reliably monitors pri-miRNA processing with high sensitivity in C. elegans. Through a forward genetic selection for alleles that desilence the sensor, we identified a mutation in the conserved G residue adjacent to the namesake W residue of Pasha's WW domain. Using genome editing we also mutated the W residue and reveal that both the G and W residue are required for dimerization of Pasha and proper assembly of the Microprocessor. Surprisingly, we find that the WW domain also facilitates nuclear localization of Pasha, which in turn promotes nuclear import or retention of Drosha. Furthermore, depletion of Pasha or Drosha causes both components of the Microprocessor to mislocalize to the cytoplasm. Thus, Pasha and Drosha mutually regulate each other's spatial expression in C. elegans.
Collapse
Affiliation(s)
| | - Thiago L. Knittel
- Department of Biology, Colorado State University, Fort Collins, CO 80523, USA
| | - Kailee J. Reed
- Department of Biology, Colorado State University, Fort Collins, CO 80523, USA
- Cell and Molecular Biology Program, Colorado State University, Fort Collins, CO 80523, USA
| | - Madeleine C. Chong
- Department of Biology, Colorado State University, Fort Collins, CO 80523, USA
| | - Ida J. Isolehto
- Biology of Non-coding RNA group, Institute of Molecular Biology, Mainz, Germany
- International PhD Program on Gene Regulation, Epigenetics and Genome Stability, Mainz, Germany
| | - Erin R. Cafferty
- Department of Biology, Colorado State University, Fort Collins, CO 80523, USA
| | - Margaret J. Smith
- Department of Biology, Colorado State University, Fort Collins, CO 80523, USA
| | - Reese A. Sprister
- Department of Biology, Colorado State University, Fort Collins, CO 80523, USA
| | - Colin N. Magelky
- Department of Biology, Colorado State University, Fort Collins, CO 80523, USA
| | - Hataichanok Scherman
- Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, CO 80523, USA
| | - Rene F. Ketting
- Biology of Non-coding RNA group, Institute of Molecular Biology, Mainz, Germany
- Institute of Developmental Biology and Neurobiology, Johannes Gutenberg University, Mainz, Germany
| | - Taiowa A. Montgomery
- Department of Biology, Colorado State University, Fort Collins, CO 80523, USA
- Cell and Molecular Biology Program, Colorado State University, Fort Collins, CO 80523, USA
| |
Collapse
|
26
|
Westemeier-Rice ES, Winters MT, Rawson TW, Martinez I. More than the SRY: The Non-Coding Landscape of the Y Chromosome and Its Importance in Human Disease. Noncoding RNA 2024; 10:21. [PMID: 38668379 PMCID: PMC11054740 DOI: 10.3390/ncrna10020021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2024] [Revised: 03/31/2024] [Accepted: 04/08/2024] [Indexed: 04/29/2024] Open
Abstract
Historically, the Y chromosome has presented challenges to classical methodology and philosophy of understanding the differences between males and females. A genetic unsolved puzzle, the Y chromosome was the last chromosome to be fully sequenced. With the advent of the Human Genome Project came a realization that the human genome is more than just genes encoding proteins, and an entire universe of RNA was discovered. This dark matter of biology and the black box surrounding the Y chromosome have collided over the last few years, as increasing numbers of non-coding RNAs have been identified across the length of the Y chromosome, many of which have played significant roles in disease. In this review, we will uncover what is known about the connections between the Y chromosome and the non-coding RNA universe that originates from it, particularly as it relates to long non-coding RNAs, microRNAs and circular RNAs.
Collapse
Affiliation(s)
- Emily S. Westemeier-Rice
- West Virginia University Cancer Institute, West Virginia University School of Medicine, Morgantown, WV 26506, USA;
| | - Michael T. Winters
- Department of Microbiology, Immunology and Cell Biology, West Virginia University School of Medicine, Morgantown, WV 26506, USA; (M.T.W.); (T.W.R.)
| | - Travis W. Rawson
- Department of Microbiology, Immunology and Cell Biology, West Virginia University School of Medicine, Morgantown, WV 26506, USA; (M.T.W.); (T.W.R.)
| | - Ivan Martinez
- West Virginia University Cancer Institute, West Virginia University School of Medicine, Morgantown, WV 26506, USA;
- Department of Microbiology, Immunology and Cell Biology, West Virginia University School of Medicine, Morgantown, WV 26506, USA; (M.T.W.); (T.W.R.)
| |
Collapse
|
27
|
Li J, Wang Z, Tan H, Tang M. ALKBH5-mediated m6A demethylation of pri-miR-199a-5p exacerbates myocardial ischemia/reperfusion injury by regulating TRAF3-mediated pyroptosis. J Biochem Mol Toxicol 2024; 38:e23710. [PMID: 38605440 DOI: 10.1002/jbt.23710] [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: 12/28/2023] [Revised: 02/22/2024] [Accepted: 03/29/2024] [Indexed: 04/13/2024]
Abstract
Myocardial ischemia‒reperfusion injury (MI/RI) is closely related to pyroptosis. alkB homolog 5 (ALKBH5) is abnormally expressed in the MI/RI models. However, the detailed molecular mechanism of ALKBH5 in MI/RI has not been elucidated. In this study, rats and H9C2 cells served as experimental subjects and received MI/R induction and H/R induction, respectively. The abundance of the targeted molecules was evaluated using RT-qPCR, Western blotting, immunohistochemistry, immunofluorescence, and enzyme-linked immunosorbent assay. The heart functions of the rats were evaluated using echocardiography, and heart injury was evaluated. Cell viability and pyroptosis were determined using cell counting Kit-8 and flow cytometry, respectively. Total m6A modification was measured using a commercial kit, and pri-miR-199a-5p m6A modification was detected by Me-RNA immunoprecipitation (RIP) assay. The interactions among the molecules were validated using RIP and luciferase experiments. ALKBH5 was abnormally highly expressed in H/R-induced H9C2 cells and MI/RI rats. ALKBH5 silencing improved injury and inhibited pyroptosis. ALKBH5 reduced pri-miR-199a-5p m6A methylation to block miR-199a-5p maturation and inhibit its expression. TNF receptor-associated Factor 3 (TRAF3) is a downstream gene of miR-199a-5p. Furthermore, in H/R-induced H9C2 cells, the miR-199a-5p inhibitor-mediated promotion of pyroptosis was reversed by ALKBH5 silencing, and the TRAF3 overexpression-mediated promotion of pyroptosis was offset by miR-199a-5p upregulation. ALKBH5 silencing inhibited pri-miR-199a-5p expression and enhanced pri-miR-199a-5p m6A modification to promote miR-199a-5p maturation and enhance its expression, thereby suppressing pyroptosis to alleviate MI/RI through decreasing TRAF3 expression.
Collapse
Affiliation(s)
- Jiarong Li
- Department of Cardiovascular Surgery, The Second Xiangya Hospital, Central South University, Changsha City, Hunan Province, P.R. China
| | - Zhirong Wang
- Department of Cardiovascular Surgery, The Second Xiangya Hospital, Central South University, Changsha City, Hunan Province, P.R. China
| | - Huayi Tan
- Department of Cardiovascular Surgery, The Second Xiangya Hospital, Central South University, Changsha City, Hunan Province, P.R. China
| | - Mi Tang
- Department of Cardiovascular Surgery, The Second Xiangya Hospital, Central South University, Changsha City, Hunan Province, P.R. China
| |
Collapse
|
28
|
Takeda K, Ohta S, Nagao M, Kobayashi E, Tago K, Funakoshi-Tago M. FL118 Is a Potent Therapeutic Agent against Chronic Myeloid Leukemia Resistant to BCR-ABL Inhibitors through Targeting RNA Helicase DDX5. Int J Mol Sci 2024; 25:3693. [PMID: 38612503 PMCID: PMC11011477 DOI: 10.3390/ijms25073693] [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: 02/09/2024] [Revised: 03/23/2024] [Accepted: 03/24/2024] [Indexed: 04/14/2024] Open
Abstract
Chronic myeloid leukemia (CML) is induced by the expression of the fused tyrosine kinase BCR-ABL, which is caused by a chromosomal translocation. BCR-ABL inhibitors have been used to treat CML; however, the acquisition of resistance by CML cells during treatment is a serious issue. We herein demonstrated that BCR-ABL induced the expression of the RNA helicase DDX5 in K562 cells derived from CML patients in a manner that was dependent on its kinase activity, which resulted in cell proliferation and survival. The knockout of DDX5 decreased the expression of BIRC5 (survivin) and activated caspase 3, leading to apoptosis in K562 cells. Similar results were obtained in cells treated with FL118, an inhibitor of DDX5 and a derivative compound of camptothecin (CPT). Furthermore, FL118 potently induced apoptosis not only in Ba/F3 cells expressing BCR-ABL, but also in those expressing the BCR-ABL T315I mutant, which is resistant to BCR-ABL inhibitors. Collectively, these results revealed that DDX5 is a critical therapeutic target in CML and that FL118 is an effective candidate compound for the treatment of BCR-ABL inhibitor-resistant CML.
Collapse
Affiliation(s)
- Kengo Takeda
- Division of Hygienic Chemistry, Faculty of Pharmacy, Keio University, 1-5-30 Shibakoen, Minato-ku, Tokyo 105-8512, Japan; (K.T.); (M.N.); (E.K.)
| | - Satoshi Ohta
- Division of Structural Biochemistry, Department of Biochemistry, School of Medicine, Jichi Medical University, 3311-1 Yakushiji, Shimotsuke-shi 329-0498, Tochigi, Japan;
| | - Miu Nagao
- Division of Hygienic Chemistry, Faculty of Pharmacy, Keio University, 1-5-30 Shibakoen, Minato-ku, Tokyo 105-8512, Japan; (K.T.); (M.N.); (E.K.)
| | - Erika Kobayashi
- Division of Hygienic Chemistry, Faculty of Pharmacy, Keio University, 1-5-30 Shibakoen, Minato-ku, Tokyo 105-8512, Japan; (K.T.); (M.N.); (E.K.)
| | - Kenji Tago
- Department of Laboratory Sciences, Gunma University Graduate School of Health Sciences, 3-39-22 Showa-Machi, Maebashi 371-8514, Gunma, Japan;
| | - Megumi Funakoshi-Tago
- Division of Hygienic Chemistry, Faculty of Pharmacy, Keio University, 1-5-30 Shibakoen, Minato-ku, Tokyo 105-8512, Japan; (K.T.); (M.N.); (E.K.)
| |
Collapse
|
29
|
Baek SC, Kim B, Jang H, Kim K, Park IS, Min DH, Kim VN. Structural atlas of human primary microRNAs generated by SHAPE-MaP. Mol Cell 2024; 84:1158-1172.e6. [PMID: 38447581 DOI: 10.1016/j.molcel.2024.02.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2023] [Revised: 12/01/2023] [Accepted: 02/06/2024] [Indexed: 03/08/2024]
Abstract
MicroRNA (miRNA) maturation is critically dependent on structural features of primary transcripts (pri-miRNAs). However, the scarcity of determined pri-miRNA structures has limited our understanding of miRNA maturation. Here, we employed selective 2'-hydroxyl acylation analyzed by primer extension and mutational profiling (SHAPE-MaP), a high-throughput RNA structure probing method, to unravel the secondary structures of 476 high-confidence human pri-miRNAs. Our SHAPE-based structures diverge substantially from those inferred solely from computation, particularly in the apical loop and basal segments, underlining the need for experimental data in RNA structure prediction. By comparing the structures with high-throughput processing data, we determined the optimal structural features of pri-miRNAs. The sequence determinants are influenced substantially by their structural contexts. Moreover, we identified an element termed the bulged GWG motif (bGWG) with a 3' bulge in the lower stem, which promotes processing. Our structure-function mapping better annotates the determinants of pri-miRNA processing and offers practical implications for designing small hairpin RNAs and predicting the impacts of miRNA mutations.
Collapse
Affiliation(s)
- S Chan Baek
- Center for RNA Research, Institute for Basic Science, Seoul 08826, South Korea; School of Biological Science, Seoul National University, Seoul 08826, South Korea
| | - Boseon Kim
- Center for RNA Research, Institute for Basic Science, Seoul 08826, South Korea; School of Biological Science, Seoul National University, Seoul 08826, South Korea
| | - Harim Jang
- Center for RNA Research, Institute for Basic Science, Seoul 08826, South Korea; School of Biological Science, Seoul National University, Seoul 08826, South Korea
| | - Kijun Kim
- Center for RNA Research, Institute for Basic Science, Seoul 08826, South Korea; School of Biological Science, Seoul National University, Seoul 08826, South Korea
| | - Il-Soo Park
- Center for RNA Research, Institute for Basic Science, Seoul 08826, South Korea; Department of Chemistry, Seoul National University, Seoul 08826, South Korea
| | - Dal-Hee Min
- Center for RNA Research, Institute for Basic Science, Seoul 08826, South Korea; Department of Chemistry, Seoul National University, Seoul 08826, South Korea
| | - V Narry Kim
- Center for RNA Research, Institute for Basic Science, Seoul 08826, South Korea; School of Biological Science, Seoul National University, Seoul 08826, South Korea.
| |
Collapse
|
30
|
Gu K, Mok L, Wakefield MJ, Chong MMW. Non-canonical RNA substrates of Drosha lack many of the conserved features found in primary microRNA stem-loops. Sci Rep 2024; 14:6713. [PMID: 38509178 PMCID: PMC10954719 DOI: 10.1038/s41598-024-57330-5] [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: 11/12/2023] [Accepted: 03/18/2024] [Indexed: 03/22/2024] Open
Abstract
The RNase III enzyme Drosha has a central role in microRNA (miRNA) biogenesis, where it is required to release the stem-loop intermediate from primary (pri)-miRNA transcripts. However, it can also cleave stem-loops embedded within messenger (m)RNAs. This destabilizes the mRNA causing target gene repression and appears to occur primarily in stem cells. While pri-miRNA stem-loops have been extensively studied, such non-canonical substrates of Drosha have yet to be characterized in detail. In this study, we employed high-throughput sequencing to capture all polyA-tailed RNAs that are cleaved by Drosha in mouse embryonic stem cells (ESCs) and compared the features of non-canonical versus miRNA stem-loop substrates. mRNA substrates are less efficiently processed than miRNA stem-loops. Sequence and structural analyses revealed that these mRNA substrates are also less stable and more likely to fold into alternative structures than miRNA stem-loops. Moreover, they lack the sequence and structural motifs found in miRNA stem-loops that are required for precise cleavage. Notably, we discovered a non-canonical Drosha substrate that is cleaved in an inverse manner, which is a process that is normally inhibited by features in miRNA stem-loops. Our study thus provides valuable insights into the recognition of non-canonical targets by Drosha.
Collapse
Affiliation(s)
- Karen Gu
- St Vincent's Institute of Medical Research, Fitzroy, VIC, 3065, Australia
- Department of Medicine (St Vincent's), University of Melbourne, Fitzroy, VIC, 3065, Australia
| | - Lawrence Mok
- St Vincent's Institute of Medical Research, Fitzroy, VIC, 3065, Australia
| | - Matthew J Wakefield
- Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, 3052, Australia
- Department of Obstetrics and Gynaecology, University of Melbourne, Parkville, VIC, 3010, Australia
| | - Mark M W Chong
- St Vincent's Institute of Medical Research, Fitzroy, VIC, 3065, Australia.
- Department of Medicine (St Vincent's), University of Melbourne, Fitzroy, VIC, 3065, Australia.
| |
Collapse
|
31
|
Hynes C, Kakumani PK. Regulatory role of RNA-binding proteins in microRNA biogenesis. Front Mol Biosci 2024; 11:1374843. [PMID: 38567098 PMCID: PMC10985210 DOI: 10.3389/fmolb.2024.1374843] [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: 01/22/2024] [Accepted: 03/06/2024] [Indexed: 04/04/2024] Open
Abstract
MicroRNAs (miRNAs) are small non-coding RNAs that silence gene expression through their interaction with complementary sequences in the 3' untranslated regions (UTR) of target mRNAs. miRNAs undergo a series of steps during their processing and maturation, which are tightly regulated to fine-tune their abundance and ability to function in post-transcriptional gene silencing. miRNA biogenesis typically involves core catalytic proteins, namely, Drosha and Dicer, and several other RNA-binding proteins (RBPs) that recognize and interact with miRNA precursors and/or their intermediates, and mature miRNAs along with their interacting proteins. The series of RNA-protein and protein-protein interactions are critical to maintaining miRNA expression levels and their function, underlying a variety of cellular processes. Throughout this article, we review RBPs that play a role in miRNA biogenesis and focus on their association with components of the miRNA pathway with functional consequences in the processing and generation of mature miRNAs.
Collapse
Affiliation(s)
| | - Pavan Kumar Kakumani
- Department of Biochemistry, Memorial University of Newfoundland, St. John’s, NL, Canada
| |
Collapse
|
32
|
Talebi Taheri A, Golshadi Z, Zare H, Alinaghipour A, Faghihi Z, Dadgostar E, Tamtaji Z, Aschner M, Mirzaei H, Tamtaji OR, Nabavizadeh F. The Potential of Targeting Autophagy-Related Non-coding RNAs in the Treatment of Alzheimer's and Parkinson's Diseases. Cell Mol Neurobiol 2024; 44:28. [PMID: 38461204 PMCID: PMC10924707 DOI: 10.1007/s10571-024-01461-w] [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: 05/30/2023] [Accepted: 01/29/2024] [Indexed: 03/11/2024]
Abstract
Clearance of accumulated protein aggregates is one of the functions of autophagy. Recently, a clearer understanding of non-coding RNAs (ncRNAs) functions documented that ncRNAs have important roles in several biological processes associated with the development and progression of neurodegenerative disorders. Subtypes of ncRNA, including microRNA (miRNA), long noncoding RNA (lncRNA), and circular RNA (circRNA), are commonly dysregulated in neurodegenerative disorders such as Alzheimer and Parkinson diseases. Dysregulation of these non-coding RNAs has been associated with inhibition or stimulation of autophagy. Decreased miR-124 led to decreased/increased autophagy in experimental model of Alzheimer and Parkinson diseases. Increased BACE1-AS showed enhanced autophagy in Alzheimer disease by targeting miR-214-3p, Beclin-1, LC3-I/LC3-II, p62, and ATG5. A significant increase in NEAT1led to stimulated autophagy in experimental model of PD by targeting PINK1, LC3-I, LC3-II, p62 and miR-374c-5p. In addition, increased BDNF-AS and SNHG1 decreased autophagy in MPTP-induced PD by targeting miR-125b-5p and miR-221/222, respectively. The upregulation of circNF1-419 and circSAMD4A resulted in an increased autophagy by regulating Dynamin-1 and miR-29c 3p, respectively. A detailed discussion of miRNAs, circRNAs, and lncRNAs in relation to their autophagy-related signaling pathways is presented in this study.
Collapse
Affiliation(s)
- Abdolkarim Talebi Taheri
- Students' Scientific Research Center, Tehran University of Medical Sciences, Tehran, Iran
- Department of Clinical Biochemistry, School of Medicine, Tehran University of Medical Sciences, Tehran, Iran
| | - Zakieh Golshadi
- Student Research Committee, Qazvin University of Medical Sciences, Qazvin, Iran
| | | | - Azam Alinaghipour
- School of Medical Sciences, Yazd Branch, Islamic Azad University, Yazd, Iran
| | - Zahra Faghihi
- Department of Physiology, School of Medicine, Tehran University of Medical Sciences, Tehran, I.R. of Iran
| | - Ehsan Dadgostar
- Behavioral Sciences Research Center, Isfahan University of Medical Sciences, Isfahan, I.R. of Iran
- Student Research Committee, Isfahan University of Medical Sciences, Isfahan, I.R. of Iran
| | - Zeinab Tamtaji
- Student Research Committee, Kashan University of Medical Sciences, Kashan, I.R. of Iran
| | - Michael Aschner
- Department of Molecular Pharmacology, Albert Einstein College of Medicine, Bronx, NY, 10461, USA
| | - Hamed Mirzaei
- Research Center for Biochemistry and Nutrition in Metabolic Diseases, Kashan University of Medical Sciences, Kashan, I.R. of Iran.
| | - Omid Reza Tamtaji
- Department of Physiology, School of Medicine, Tehran University of Medical Sciences, Tehran, I.R. of Iran.
- Electrophysiology Research Center, Neuroscience Institute, Tehran University of Medical Sciences, Tehran, I.R. of Iran.
| | - Fatemeh Nabavizadeh
- Department of Physiology, School of Medicine, Tehran University of Medical Sciences, Tehran, I.R. of Iran.
- Electrophysiology Research Center, Neuroscience Institute, Tehran University of Medical Sciences, Tehran, I.R. of Iran.
| |
Collapse
|
33
|
Zhang L, Li Y, Kuhn JH, Zhang K, Song Q, Liu F. Polyubiquitylated rice stripe virus NS3 translocates to the nucleus to promote cytosolic virus replication via miRNA-induced fibrillin 2 upregulation. PLoS Pathog 2024; 20:e1012112. [PMID: 38507423 PMCID: PMC10984529 DOI: 10.1371/journal.ppat.1012112] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2023] [Revised: 04/01/2024] [Accepted: 03/11/2024] [Indexed: 03/22/2024] Open
Abstract
Viruses are encapsidated mobile genetic elements that rely on host cells for replication. Several cytoplasmic RNA viruses synthesize proteins and/or RNAs that translocate to infected cell nuclei. However, the underlying mechanisms and role(s) of cytoplasmic-nuclear trafficking are unclear. We demonstrate that infection of small brown planthoppers with rice stripe virus (RSV), a negarnaviricot RNA virus, results in K63-linked polyubiquitylation of RSV's nonstructural protein 3 (NS3) at residue K127 by the RING ubiquitin ligase (E3) LsRING. In turn, ubiquitylation leads to NS3 trafficking from the cytoplasm to the nucleus, where NS3 regulates primary miRNA pri-miR-92 processing through manipulation of the microprocessor complex, resulting in accumulation of upregulated miRNA lst-miR-92. We show that lst-miR-92 regulates the expression of fibrillin 2, an extracellular matrix protein, thereby increasing RSV loads. Our results highlight the manipulation of intranuclear, cytoplasmic, and extracellular components by an RNA virus to promote its own replication in an insect vector.
Collapse
Affiliation(s)
- Lu Zhang
- College of Plant Protection; Yángzhōu University; Yángzhōu, Jiāngsū Province; China
| | - Yao Li
- College of Plant Protection; Yángzhōu University; Yángzhōu, Jiāngsū Province; China
| | - Jens H. Kuhn
- Integrated Research Facility at Fort Detrick; National Institute of Allergy and Infectious Diseases, National Institutes of Health, Fort Detrick; Frederick, Maryland; United States of America
| | - Kun Zhang
- College of Plant Protection; Yángzhōu University; Yángzhōu, Jiāngsū Province; China
| | - Qisheng Song
- Division of Plant Science and Technology; College of Agriculture; Food and Natural Resources; University of Missouri; Columbia, Missouri; United States of America
| | - Fang Liu
- College of Plant Protection; Yángzhōu University; Yángzhōu, Jiāngsū Province; China
| |
Collapse
|
34
|
La Sala L, Carlini V, Conte C, Macas-Granizo MB, Afzalpour E, Martin-Delgado J, D'Anzeo M, Pedretti RFE, Naselli A, Pontiroli AE, Cappato R. Metabolic disorders affecting the liver and heart: Therapeutic efficacy of miRNA-based therapies? Pharmacol Res 2024; 201:107083. [PMID: 38309383 DOI: 10.1016/j.phrs.2024.107083] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/14/2023] [Revised: 01/09/2024] [Accepted: 01/25/2024] [Indexed: 02/05/2024]
Abstract
Liver and heart disease are major causes of death worldwide. It is known that metabolic alteration causing type 2 diabetes (T2D) and Nonalcoholic fatty liver (NAFLD) coupled with a derangement in lipid homeostasis, may exacerbate hepatic and cardiovascular diseases. Some pharmacological treatments can mitigate organ dysfunctions but the important side effects limit their efficacy leading often to deterioration of the tissues. It needs to develop new personalized treatment approaches and recent progresses of engineered RNA molecules are becoming increasingly viable as alternative treatments. This review outlines the current use of antisense oligonucleotides (ASOs), RNA interference (RNAi) and RNA genome editing as treatment for rare metabolic disorders. However, the potential for small non-coding RNAs to serve as therapeutic agents for liver and heart diseases is yet to be fully explored. Although miRNAs are recognized as biomarkers for many diseases, they are also capable of serving as drugs for medical intervention; several clinical trials are testing miRNAs as therapeutics for type 2 diabetes, nonalcoholic fatty liver as well as cardiac diseases. Recent advances in RNA-based therapeutics may potentially facilitate a novel application of miRNAs as agents and as druggable targets. In this work, we sought to summarize the advancement and advantages of miRNA selective therapy when compared to conventional drugs. In particular, we sought to emphasise druggable miRNAs, over ASOs or other RNA therapeutics or conventional drugs. Finally, we sought to address research questions related to efficacy, side-effects, and range of use of RNA therapeutics. Additionally, we covered hurdles and examined recent advances in the use of miRNA-based RNA therapy in metabolic disorders such as diabetes, liver, and heart diseases.
Collapse
Affiliation(s)
- Lucia La Sala
- IRCCS MultiMedica, 20138 Milan, Italy; Dept. of Biomedical Sciences for Health, University of Milan, Milan, Italy.
| | | | - Caterina Conte
- IRCCS MultiMedica, 20138 Milan, Italy; Department of Human Sciences and Promotion of the Quality of Life, San Raffaele Roma Open University, Rome, Italy
| | | | - Elham Afzalpour
- Dept. of Biomedical Sciences and Clinic, University of Milan, Milan, Italy
| | - Jimmy Martin-Delgado
- Hospital Luis Vernaza, Junta de Beneficiencia de Guayaquil, 090603 Guayaquil, Ecuador; Instituto de Investigacion e Innovacion en Salud Integral, Universidad Catolica de Santiago de Guayaquil, Guayaquil 090603, Ecuador
| | - Marco D'Anzeo
- AUO delle Marche, SOD Medicina di Laboratorio, Ancona, Italy
| | | | | | | | | |
Collapse
|
35
|
Singh M, Krishnamoorthy VR, Kim S, Khurana S, LaPorte HM. Brain-derived neuerotrophic factor and related mechanisms that mediate and influence progesterone-induced neuroprotection. Front Endocrinol (Lausanne) 2024; 15:1286066. [PMID: 38469139 PMCID: PMC10925611 DOI: 10.3389/fendo.2024.1286066] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/30/2023] [Accepted: 01/15/2024] [Indexed: 03/13/2024] Open
Abstract
Historically, progesterone has been studied significantly within the context of reproductive biology. However, there is now an abundance of evidence for its role in regions of the central nervous system (CNS) associated with such non-reproductive functions that include cognition and affect. Here, we describe mechanisms of progesterone action that support its brain-protective effects, and focus particularly on the role of neurotrophins (such as brain-derived neurotrophic factor, BDNF), the receptors that are critical for their regulation, and the role of certain microRNA in influencing the brain-protective effects of progesterone. In addition, we describe evidence to support the particular importance of glia in mediating the neuroprotective effects of progesterone. Through this review of these mechanisms and our own prior published work, we offer insight into why the effects of a progestin on brain protection may be dependent on the type of progestin (e.g., progesterone versus the synthetic, medroxyprogesterone acetate) used, and age, and as such, we offer insight into the future clinical implication of progesterone treatment for such disorders that include Alzheimer's disease, stroke, and traumatic brain injury.
Collapse
Affiliation(s)
- Meharvan Singh
- Department of Cell and Molecular Physiology, Stritch School of Medicine, Loyola University Chicago, Maywood, IL, United States
| | | | | | | | | |
Collapse
|
36
|
Geleta U, Prajapati P, Bachstetter A, Nelson PT, Wang WX. Sex-Biased Expression and Response of microRNAs in Neurological Diseases and Neurotrauma. Int J Mol Sci 2024; 25:2648. [PMID: 38473893 PMCID: PMC10931569 DOI: 10.3390/ijms25052648] [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: 01/27/2024] [Revised: 02/16/2024] [Accepted: 02/21/2024] [Indexed: 03/14/2024] Open
Abstract
Neurological diseases and neurotrauma manifest significant sex differences in prevalence, progression, outcome, and therapeutic responses. Genetic predisposition, sex hormones, inflammation, and environmental exposures are among many physiological and pathological factors that impact the sex disparity in neurological diseases. MicroRNAs (miRNAs) are a powerful class of gene expression regulator that are extensively involved in mediating biological pathways. Emerging evidence demonstrates that miRNAs play a crucial role in the sex dimorphism observed in various human diseases, including neurological diseases. Understanding the sex differences in miRNA expression and response is believed to have important implications for assessing the risk of neurological disease, defining therapeutic intervention strategies, and advancing both basic research and clinical investigations. However, there is limited research exploring the extent to which miRNAs contribute to the sex disparities observed in various neurological diseases. Here, we review the current state of knowledge related to the sexual dimorphism in miRNAs in neurological diseases and neurotrauma research. We also discuss how sex chromosomes may contribute to the miRNA sexual dimorphism phenomenon. We attempt to emphasize the significance of sexual dimorphism in miRNA biology in human diseases and to advocate a gender/sex-balanced science.
Collapse
Affiliation(s)
- Urim Geleta
- Sanders-Brown Center on Aging, College of Medicine, University of Kentucky, Lexington, KY 40536, USA; (U.G.); (P.P.); (A.B.); (P.T.N.)
| | - Paresh Prajapati
- Sanders-Brown Center on Aging, College of Medicine, University of Kentucky, Lexington, KY 40536, USA; (U.G.); (P.P.); (A.B.); (P.T.N.)
| | - Adam Bachstetter
- Sanders-Brown Center on Aging, College of Medicine, University of Kentucky, Lexington, KY 40536, USA; (U.G.); (P.P.); (A.B.); (P.T.N.)
- Spinal Cord and Brain Injury Research Center, College of Medicine, University of Kentucky, Lexington, KY 40536, USA
- Neuroscience, College of Medicine, University of Kentucky, Lexington, KY 40536, USA
| | - Peter T. Nelson
- Sanders-Brown Center on Aging, College of Medicine, University of Kentucky, Lexington, KY 40536, USA; (U.G.); (P.P.); (A.B.); (P.T.N.)
- Spinal Cord and Brain Injury Research Center, College of Medicine, University of Kentucky, Lexington, KY 40536, USA
- Pathology and Laboratory Medicine, College of Medicine, University of Kentucky, Lexington, KY 40536, USA
| | - Wang-Xia Wang
- Sanders-Brown Center on Aging, College of Medicine, University of Kentucky, Lexington, KY 40536, USA; (U.G.); (P.P.); (A.B.); (P.T.N.)
- Spinal Cord and Brain Injury Research Center, College of Medicine, University of Kentucky, Lexington, KY 40536, USA
- Pathology and Laboratory Medicine, College of Medicine, University of Kentucky, Lexington, KY 40536, USA
| |
Collapse
|
37
|
Zhang H, Lu R, Huang J, Li L, Cao Y, Huang C, Chen R, Wang Y, Huang J, Zhao X, Yu J. N4-acetylcytidine modifies primary microRNAs for processing in cancer cells. Cell Mol Life Sci 2024; 81:73. [PMID: 38308713 PMCID: PMC10838262 DOI: 10.1007/s00018-023-05107-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2023] [Revised: 12/18/2023] [Accepted: 12/25/2023] [Indexed: 02/05/2024]
Abstract
N4 acetylcytidine (ac4C) modification mainly occurs on tRNA, rRNA, and mRNA, playing an important role in the expression of genetic information. However, it is still unclear whether microRNAs have undergone ac4C modification and their potential physiological and pathological functions. In this study, we identified that NAT10/THUMPD1 acetylates primary microRNAs (pri-miRNAs) with ac4C modification. Knockdown of NAT10 suppresses and augments the expression levels of mature miRNAs and pri-miRNAs, respectively. Molecular mechanism studies found that pri-miRNA ac4C promotes the processing of pri-miRNA into precursor miRNA (pre-miRNA) by enhancing the interaction of pri-miRNA and DGCR8, thereby increasing the biogenesis of mature miRNA. Knockdown of NAT10 attenuates the oncogenic characters of lung cancer cells by regulating miRNA production in cancers. Moreover, NAT10 is highly expressed in various clinical cancers and negatively correlated with poor prognosis. Thus, our results reveal that NAT10 plays a crucial role in cancer initiation and progression by modulating pri-miRNA ac4C to affect miRNA production, which would provide an attractive therapeutic strategy for cancers.
Collapse
Affiliation(s)
- Hailong Zhang
- Department of Biochemistry and Molecular Cell Biology, Shanghai Key Laboratory of Tumor Microenvironment and Inflammation, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
- Institute of Translational Medicine, National Center for Translational Medicine (Shanghai), Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Runhui Lu
- Department of Biochemistry and Molecular Cell Biology, Shanghai Key Laboratory of Tumor Microenvironment and Inflammation, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Jiayi Huang
- Department of Biochemistry and Molecular Cell Biology, Shanghai Key Laboratory of Tumor Microenvironment and Inflammation, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Lian Li
- Department of Biochemistry and Molecular Cell Biology, Shanghai Key Laboratory of Tumor Microenvironment and Inflammation, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Yingting Cao
- Department of Biochemistry and Molecular Cell Biology, Shanghai Key Laboratory of Tumor Microenvironment and Inflammation, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Caihu Huang
- Department of Biochemistry and Molecular Cell Biology, Shanghai Key Laboratory of Tumor Microenvironment and Inflammation, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Ran Chen
- Department of Biochemistry and Molecular Cell Biology, Shanghai Key Laboratory of Tumor Microenvironment and Inflammation, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Yanli Wang
- Department of Biochemistry and Molecular Cell Biology, Shanghai Key Laboratory of Tumor Microenvironment and Inflammation, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Jian Huang
- Department of Biochemistry and Molecular Cell Biology, Shanghai Key Laboratory of Tumor Microenvironment and Inflammation, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Xian Zhao
- Department of Biochemistry and Molecular Cell Biology, Shanghai Key Laboratory of Tumor Microenvironment and Inflammation, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China.
| | - Jianxiu Yu
- Department of Biochemistry and Molecular Cell Biology, Shanghai Key Laboratory of Tumor Microenvironment and Inflammation, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China.
| |
Collapse
|
38
|
Liu Z, Qiang Y, Shan S, Wang S, Liu Z, Yang Y, Huang Z, Song M, Zhao X, Song F. Aberrant mitochondrial aggregation of TDP-43 activated mitochondrial unfolded protein response and contributed to recovery of acetaminophen induced acute liver injury. Toxicol Res (Camb) 2024; 13:tfae008. [PMID: 38283824 PMCID: PMC10811519 DOI: 10.1093/toxres/tfae008] [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: 07/17/2023] [Revised: 11/02/2023] [Accepted: 12/14/2023] [Indexed: 01/30/2024] Open
Abstract
Mitochondrial dysfunction is a key pathological event in the acute liver injury following the overdose of acetaminophen (APAP). Calpain is the calcium-dependent protease, recent studies demonstrate that it is involved in the impairment of mitochondrial dynamics. The mitochondrial unfolded protein response (UPRmt) is commonly activated in the context of mitochondrial damage following pathological insults and contributes to the maintenance of the mitochondrial quality control through regulating a wide range of gene expression. More importantly, it is reported that abnormal aggregation of TDP-43 in mitochondria induced the activation of UPRmt. However, whether it is involved in APAP induced-hepatotoxicity remains unclear. In the present study, C57/BL6 mice were given 300 mg/kg APAP to establish a time-course model of acute liver injury. Furthermore, Calpeptin, the specific inhibiter of calpains, was used to conduct the intervention experiment. Our results showed, APAP exposure produced severe liver injury. Moreover, TDP-43 was obviously accumulated within mitochondria whereas mitochondrial protease LonP1 was significantly decreased. However, these changes exhibited significant recovery at 48 h. By contrast, the mitochondrial protease ClpP and chaperone mtHSP70 and HSP60 were consistently increased, which supported the UPRmt was activated to promote protein homeostasis. Further investigation revealed that calpain-mediated cleavage of TDP-43 could promote the accumulation of TDP-43 in mitochondria compartment, thereby facilitating the activation of UPRmt. Additionally, Calpeptin pretreatment not only protected against APAP-induced liver injury, but also suppressed the formation of TDP-43 aggregates and the activation of UPRmt. Taken together, our findings indicated that in APAP-induced acute liver injury, calpain-mediated cleavage of TDP43 caused its aberrant aggregation on the mitochondria. As a stress-protective response, the induction of UPRmt contributed to the recovery of mitochondrial function.
Collapse
Affiliation(s)
- Zhaoxiong Liu
- Department of Toxicology and Nutrition, School of Public Health, Cheeloo College of Medicine, Shandong University, 44 Wenhua Xi Road, Jinan, Shandong 250012, China
| | - Yalong Qiang
- Department of Toxicology and Nutrition, School of Public Health, Cheeloo College of Medicine, Shandong University, 44 Wenhua Xi Road, Jinan, Shandong 250012, China
| | - Shulin Shan
- Department of Toxicology and Nutrition, School of Public Health, Cheeloo College of Medicine, Shandong University, 44 Wenhua Xi Road, Jinan, Shandong 250012, China
| | - Shuai Wang
- Department of Toxicology and Nutrition, School of Public Health, Cheeloo College of Medicine, Shandong University, 44 Wenhua Xi Road, Jinan, Shandong 250012, China
| | - Zhidan Liu
- Department of Toxicology and Nutrition, School of Public Health, Cheeloo College of Medicine, Shandong University, 44 Wenhua Xi Road, Jinan, Shandong 250012, China
| | - Yiyu Yang
- Department of Toxicology and Nutrition, School of Public Health, Cheeloo College of Medicine, Shandong University, 44 Wenhua Xi Road, Jinan, Shandong 250012, China
| | - Zhengcheng Huang
- Department of Toxicology and Nutrition, School of Public Health, Cheeloo College of Medicine, Shandong University, 44 Wenhua Xi Road, Jinan, Shandong 250012, China
| | - Mingxue Song
- Department of Toxicology and Nutrition, School of Public Health, Cheeloo College of Medicine, Shandong University, 44 Wenhua Xi Road, Jinan, Shandong 250012, China
| | - Xiulan Zhao
- Department of Toxicology and Nutrition, School of Public Health, Cheeloo College of Medicine, Shandong University, 44 Wenhua Xi Road, Jinan, Shandong 250012, China
| | - Fuyong Song
- Department of Toxicology and Nutrition, School of Public Health, Cheeloo College of Medicine, Shandong University, 44 Wenhua Xi Road, Jinan, Shandong 250012, China
| |
Collapse
|
39
|
Fattahi M, Rahdan F, Shaterabadi D, Zamani Sani M, Alizadeh M, Khatami SH, Taheri-Anganeh M, Movahedpour A, Ghasemi H. MicroRNA biosensors for the detection of liver cancer. Clin Chim Acta 2024; 554:117796. [PMID: 38272250 DOI: 10.1016/j.cca.2024.117796] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2023] [Revised: 01/21/2024] [Accepted: 01/22/2024] [Indexed: 01/27/2024]
Abstract
Liver cancer is one of the deadliest types worldwide and early diagnosis is highly important for successful treatment. Therefore, it is necessary to develop rapid, sensitive, simple, and inexpensive analytical tools for its detection. MicroRNAs (miRNA) represent unique biomarkers whose expression in biofluids is strongly associated with cancer in general and miR-21, -31, -122, -145, -146a, -200c, -221, -222, and -223 in liver cancer, specifically. Various biosensors for miRNA detection have been developed. These include electrochemical biosensors based on amperometric, potentiometric, conductometric and impedimetric technology. Furthermore, the use of advanced nanomaterials with enhanced chemical stability, conductivity and electrocatalytic activity have greatly increased the sensitivity and specificity of these devices. The present review focuses on recent advances in electrochemical biosensors for miRNA detection in liver cancer.
Collapse
Affiliation(s)
- Mehdi Fattahi
- Institute of Research and Development, Duy Tan University, Da Nang, Vietnam; School of Engineering & Technology, Duy Tan University, Da Nang, Vietnam
| | - Fereshteh Rahdan
- Department of Medical Biotechnology, Faculty of Advanced Medical Sciences, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Donya Shaterabadi
- Department of Medical Nanotechnology, Faculty of Advanced Medical Sciences, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Maryam Zamani Sani
- Department of Biochemistry and Clinical Laboratories, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Mehdi Alizadeh
- Department of Clinical Biochemistry, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Seyyed Hossein Khatami
- Department of Clinical Biochemistry, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Mortaza Taheri-Anganeh
- Cellular and Molecular Research Center, Cellular and Molecular Medicine Research Institute, Urmia University of Medical Sciences, Urmia, Iran
| | | | | |
Collapse
|
40
|
Leopizzi M, Mundo L, Messina E, Campolo F, Lazzi S, Angeloni A, Marchese C, Leoncini L, Giordano C, Slack F, Trivedi P, Anastasiadou E. Epstein-Barr virus-encoded EBNA2 downregulates ICOSL by inducing miR-24 in B-cell lymphoma. Blood 2024; 143:429-443. [PMID: 37847858 PMCID: PMC10862363 DOI: 10.1182/blood.2023021346] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2023] [Revised: 09/12/2023] [Accepted: 09/27/2023] [Indexed: 10/19/2023] Open
Abstract
ABSTRACT Hematological malignancies such as Burkitt lymphoma (BL), Hodgkin lymphoma (HL), and diffuse large B-cell lymphoma (DLBCL) cause significant morbidity in humans. A substantial number of these lymphomas, particularly HL and DLBCLs have poorer prognosis because of their association with Epstein-Barr virus (EBV). Our earlier studies have shown that EBV-encoded nuclear antigen (EBNA2) upregulates programmed cell death ligand 1 in DLBCL and BLs by downregulating microRNA-34a. Here, we investigated whether EBNA2 affects the inducible costimulator (ICOS) ligand (ICOSL), a molecule required for efficient recognition of tumor cells by T cells through the engagement of ICOS on the latter. In virus-infected and EBNA2-transfected B-lymphoma cells, ICOSL expression was reduced. Our investigation of the molecular mechanisms revealed that this was due to an increase in microRNA-24 (miR-24) by EBNA2. By using ICOSL 3' untranslated region-luciferase reporter system, we validated that ICOSL is an authentic miR-24 target. Transfection of anti-miR-24 molecules in EBNA2-expressing lymphoma cells reconstituted ICOSL expression and increased tumor immunogenicity in mixed lymphocyte reactions. Because miR-24 is known to target c-MYC, an oncoprotein positively regulated by EBNA2, we analyzed its expression in anti-miR-24 transfected lymphoma cells. Indeed, the reduction of miR-24 in EBNA2-expressing DLBCL further elevated c-MYC and increased apoptosis. Consistent with the in vitro data, EBNA2-positive DLBCL biopsies expressed low ICOSL and high miR-24. We suggest that EBV evades host immune responses through EBNA2 by inducing miR-24 to reduce ICOSL expression, and for simultaneous rheostatic maintenance of proproliferative c-MYC levels. Overall, these data identify miR-24 as a potential therapeutically relevant target in EBV-associated lymphomas.
Collapse
Affiliation(s)
- Martina Leopizzi
- Department of Medico-surgical Sciences and Biotechnologies, Sapienza University, Latina, Italy
| | - Lucia Mundo
- Department of Medical Biotechnology, University of Siena, Siena, Italy
| | - Elena Messina
- Department of Experimental Medicine, Sapienza University, Rome, Italy
| | - Federica Campolo
- Department of Experimental Medicine, Sapienza University, Rome, Italy
| | - Stefano Lazzi
- Department of Medical Biotechnology, University of Siena, Siena, Italy
| | - Antonio Angeloni
- Department of Experimental Medicine, Sapienza University, Rome, Italy
| | - Cinzia Marchese
- Department of Experimental Medicine, Sapienza University, Rome, Italy
| | - Lorenzo Leoncini
- Department of Medical Biotechnology, University of Siena, Siena, Italy
| | - Carla Giordano
- Department of Radiology, Oncology and Pathology, Sapienza University, Rome, Italy
| | - Frank Slack
- Department of Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA
| | - Pankaj Trivedi
- Department of Experimental Medicine, Sapienza University, Rome, Italy
| | - Eleni Anastasiadou
- Department of Clinical and Molecular Medicine, Sapienza University, Rome, Italy
| |
Collapse
|
41
|
Zervou MI, Tarlatzis BC, Grimbizis GF, Spandidos DA, Niewold TB, Goulielmos GN. Association of endometriosis with Sjögren's syndrome: Genetic insights (Review). Int J Mol Med 2024; 53:20. [PMID: 38186322 PMCID: PMC10781419 DOI: 10.3892/ijmm.2024.5344] [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: 11/12/2023] [Accepted: 12/20/2023] [Indexed: 01/09/2024] Open
Abstract
Patients with a history of endometriosis have an increased risk of developing various autoimmune diseases such as rheumatoid arthritis, ankylosing spondylitis, systemic lupus erythematosus, multiple sclerosis and celiac disease. There is a potential association between endometriosis and an increased susceptibility for Sjögren's syndrome (SS). SS is a common chronic, inflammatory, systemic, autoimmune, multifactorial disease of complex pathology, with genetic, epigenetic and environmental factors contributing to the development of this condition. It occurs in 0.5‑1% of the population, is characterized by the presence of ocular dryness, lymphocytic infiltrations and contributes to neurological, gastrointestinal, vascular and dermatological manifestations. Endometriosis is an inflammatory, estrogen‑dependent, multifactorial, heterogeneous gynecological disease, affecting ≤10% of reproductive‑age women. It is characterized by the occurrence of endometrial tissue outside the uterine cavity, mainly in the pelvic cavity, and is associated with pelvic pain, dysmenorrhea, deep dyspareunia and either subfertility or infertility. It is still unclear whether SS appears as a secondary response to endometriosis, or it is developed due to any potential shared mechanisms of these conditions. The aim of the present review was to explore further the biological basis only of the co‑occurrence of these disorders but not their association at clinical basis, focusing on the analysis of the partially shared genetic background between endometriosis and SS, and the clarification of the possible similarities in the underlying pathogenetic mechanisms and the relevant molecular pathways.
Collapse
Affiliation(s)
- Maria I. Zervou
- Section of Molecular Pathology and Human Genetics, Department of Internal Medicine, School of Medicine, University of Crete, 71403 Heraklion, Greece
| | - Basil C. Tarlatzis
- First Department of Obstetrics and Gynecology, School of Medicine, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece
| | - Grigoris F. Grimbizis
- Unit for Human Reproduction, First Department of Obstetrics and Gynecology, 'Papageorgiou' General Hospital, Aristotle University Medical School, 56403 Thessaloniki, Greece
| | - Demetrios A. Spandidos
- Laboratory of Clinical Virology, School of Medicine, University of Crete, 71403 Heraklion, Greece
| | - Timothy B. Niewold
- Barbara Volcker Center for Women and Rheumatic Disease, New York, NY 10021, USA
- Hospital for Special Surgery, New York, NY 10021, USA
| | - George N. Goulielmos
- Section of Molecular Pathology and Human Genetics, Department of Internal Medicine, School of Medicine, University of Crete, 71403 Heraklion, Greece
- Department of Internal Medicine, University Hospital of Heraklion, 71500 Heraklion, Greece
| |
Collapse
|
42
|
Syed NH, Mussa A, Elmi AH, Jamal Al-Khreisat M, Ahmad Mohd Zain MR, Nurul AA. Role of MicroRNAs in Inflammatory Joint Diseases: A Review. Immunol Invest 2024; 53:185-209. [PMID: 38095847 DOI: 10.1080/08820139.2023.2293095] [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: 08/02/2023] [Accepted: 12/03/2023] [Indexed: 03/23/2024]
Abstract
Inflammatory arthritis commonly initiates in the soft tissues lining the joint. This lining swells, as do the cells in it and inside the joint fluid, producing chemicals that induce inflammation signs such as heat, redness, and swelling. MicroRNA (miRNA), a subset of non-coding small RNA molecules, post-transcriptionally controls gene expression by targeting their messenger RNA. MiRNAs modulate approximately 1/3 of the human genome with their multiple targets. Recently, they have been extensively studied as key modulators of the innate and adaptive immune systems in diseases such as allergic disorders, types of cancer, and cardiovascular diseases. However, research on the different inflammatory joint diseases, such as rheumatoid arthritis, gout, Lyme disease, ankylosing spondylitis, and psoriatic arthritis, remains in its infancy. This review presents a deeper understanding of miRNA biogenesis and the functions of miRNAs in modulating the immune and inflammatory responses in the above-mentioned inflammatory joint diseases. According to the literature, it has been demonstrated that the development of inflammatory joint disorders is closely related to different miRNAs and their specific regulatory mechanisms. Furthermore, they may present as possible prognostic and diagnostic biomarkers for all diseases and may help in developing a therapeutic response. However, further studies are needed to determine whether manipulating miRNAs can influence the development and progression of inflammatory joint disorders.
Collapse
Affiliation(s)
- Nazmul Huda Syed
- School of Health Sciences, Universiti Sains Malaysia, Kubang Kerian, Malaysia
- Center for Global Health Research, Saveetha Medical College and Hospitals, Saveetha Institute of Medical and Technical Sciences, Chennai, India
| | - Ali Mussa
- Center for Global Health Research, Saveetha Medical College and Hospitals, Saveetha Institute of Medical and Technical Sciences, Chennai, India
- Department of Haematology, School of Medical Sciences, Universiti Sains Malaysia, Kubang Kerian, Malaysia
- Department of Biology, Faculty of Education, Omdurman Islamic University, Omdurman, Sudan
| | - Abdirahman Hussein Elmi
- Department of Microbiology, School of Medical Sciences, Universiti Sains Malaysia, Kubang Kerian, Malaysia
| | - Mutaz Jamal Al-Khreisat
- Department of Haematology, School of Medical Sciences, Universiti Sains Malaysia, Kubang Kerian, Malaysia
| | | | - Asma Abdullah Nurul
- School of Health Sciences, Universiti Sains Malaysia, Kubang Kerian, Malaysia
| |
Collapse
|
43
|
Motta LF, Cerrudo CS, Belaich MN. A Comprehensive Study of MicroRNA in Baculoviruses. Int J Mol Sci 2024; 25:603. [PMID: 38203774 PMCID: PMC10778818 DOI: 10.3390/ijms25010603] [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: 11/27/2023] [Revised: 12/19/2023] [Accepted: 12/22/2023] [Indexed: 01/12/2024] Open
Abstract
Baculoviruses are viral pathogens that infect different species of Lepidoptera, Diptera, and Hymenoptera, with a global distribution. Due to their biological characteristics and the biotechnological applications derived from these entities, the Baculoviridae family is an important subject of study and manipulation in the natural sciences. With the advent of RNA interference mechanisms, the presence of baculoviral genes that do not code for proteins but instead generate transcripts similar to microRNAs (miRNAs) has been described. These miRNAs are functionally associated with the regulation of gene expression, both in viral and host sequences. This article provides a comprehensive review of miRNA biogenesis, function, and characterization in general, with a specific focus on those identified in baculoviruses. Furthermore, it delves into the specific roles of baculoviral miRNAs in regulating viral and host genes and presents structural and thermodynamic stability studies that are useful for detecting shared characteristics with predictive utility. This review aims to expand our understanding of the baculoviral miRNAome, contributing to improvements in the production of baculovirus-based biopesticides, management of resistance phenomena in pests, enhancement of recombinant protein production systems, and development of diverse and improved BacMam vectors to meet biomedical demands.
Collapse
Affiliation(s)
| | - Carolina Susana Cerrudo
- Laboratorio de Ingeniería Genética y Biología Celular y Molecular—Área Virosis de Insectos, Instituto de Microbiología Básica y Aplicada, Departamento de Ciencia y Tecnología, Universidad Nacional de Quilmes, Roque Sáenz Peña 352, Bernal B1876BXD, Buenos Aires, Argentina;
| | - Mariano Nicolás Belaich
- Laboratorio de Ingeniería Genética y Biología Celular y Molecular—Área Virosis de Insectos, Instituto de Microbiología Básica y Aplicada, Departamento de Ciencia y Tecnología, Universidad Nacional de Quilmes, Roque Sáenz Peña 352, Bernal B1876BXD, Buenos Aires, Argentina;
| |
Collapse
|
44
|
Ali M, Mishra D, Singh RP. Cancer Pathways Targeted by Berberine: Role of microRNAs. Curr Med Chem 2024; 31:5178-5198. [PMID: 38303534 DOI: 10.2174/0109298673275121231228124031] [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: 07/31/2023] [Revised: 11/26/2023] [Accepted: 12/06/2023] [Indexed: 02/03/2024]
Abstract
Cancer is a complex and heterogeneous malignant disease. Due to its multifactorial nature, including progressive changes in genetic, epigenetic, transcript, and protein levels, conventional therapeutics fail to save cancer patients. Evidence indicates that dysregulation of microRNA (miRNA) expression plays a crucial role in tumorigenesis, metastasis, cell proliferation, differentiation, metabolism, and signaling pathways. Moreover, miRNAs can be used as diagnostic and prognostic markers and therapeutic targets in cancer. Berberine, a naturally occurring plant alkaloid, has a wide spectrum of biological activities in different types of cancers. Inhibition of cell proliferation, metastasis, migration, invasion, and angiogenesis, as well as induction of cell cycle arrest and apoptosis in cancer cells, is reported by berberine. Recent studies suggested that berberine regulates many oncogenic and tumor suppressor miRNAs implicated in different phases of cancer. This review discussed how berberine inhibits cancer growth and propagation and regulates miRNAs in cancer cells. And how berberine-mediated miRNA regulation changes the landscape of transcripts and proteins that promote or suppress cancer progression. Overall, the underlying molecular pathways altered by berberine and miRNA influencing the tumor pathophysiology will enhance our understanding to combat the malignancy.
Collapse
Affiliation(s)
- Mansoor Ali
- Cancer Biology Laboratory, School of Life Sciences, Jawaharlal Nehru University, New Delhi, India
| | - Deepali Mishra
- Cancer Biology Laboratory, School of Life Sciences, Jawaharlal Nehru University, New Delhi, India
| | - Rana Pratap Singh
- Cancer Biology Laboratory, School of Life Sciences, Jawaharlal Nehru University, New Delhi, India
- Special Centre for Systems Medicine, Jawaharlal Nehru University, New Delhi, India
- Skaggs School of Pharmacy and Pharmaceutical Sciences, Department of Pharmaceutical Sciences, University of Colorado Denver, Aurora, CO, USA
| |
Collapse
|
45
|
Engin AB, Engin A. Next-Cell Hypothesis: Mechanism of Obesity-Associated Carcinogenesis. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2024; 1460:727-766. [PMID: 39287871 DOI: 10.1007/978-3-031-63657-8_25] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/19/2024]
Abstract
Higher body fat content is related to a higher risk of mortality, and obesity-related cancer represents approximately 40% of all cancer patients diagnosed each year. Furthermore, epigenetic mechanisms are involved in cellular metabolic memory and can determine one's predisposition to being overweight. Low-grade chronic inflammation, a well-established characteristic of obesity, is a central component of tumor development and progression. Cancer-associated adipocytes (CAA), which enhance inflammation- and metastasis-related gene sets within the cancer microenvironment, have pro-tumoral effects. Adipose tissue is a major source of the exosomal micro ribonucleic acids (miRNAs), which modulate pathways involved in the development of obesity and obesity-related comorbidities. Owing to their composition of cargo, exosomes can activate receptors at the target cell or transfer molecules to the target cells and thereby change the phenotype of these cells. Exosomes that are released into the extracellular environment are internalized with their cargo by neighboring cells. The tumor-secreted exosomes promote organ-specific metastasis of tumor cells that normally lack the capacity to metastasize to a specific organ. Therefore, the communication between neighboring cells via exosomes is defined as the "next-cell hypothesis." The reciprocal interaction between the adipocyte and tumor cell is realized through the adipocyte-derived exosomal miRNAs and tumor cell-derived oncogenic miRNAs. The cargo molecules of adipocyte-derived exosomes are important messengers for intercellular communication involved in metabolic responses and have very specific signatures that direct the metabolic activity of target cells. RNA-induced silencing regulates gene expression through various mechanisms. Destabilization of DICER enzyme, which catalyzes the conversion of primary miRNA (pri-miRNA) to precursor miRNA (pre-miRNA), is an important checkpoint in cancer development and progression. Interestingly, adipose tissue in obesity and tumors share similar pathogenic features, and the local hypoxia progress in both. While hypoxia in obesity leads to the adipocyte dysfunction and metabolic abnormalities, in obesity-related cancer cases, it is associated with worsened prognosis, increased metastatic potential, and resistance to chemotherapy. Notch-interleukin-1 (IL-1)-Leptin crosstalk outcome is referred to as "NILCO effect." In this chapter, obesity-related cancer development is discussed in the context of "next-cell hypothesis," miRNA biogenesis, and "NILCO effect."
Collapse
Affiliation(s)
- Ayse Basak Engin
- Faculty of Pharmacy, Department of Toxicology, Gazi University, Hipodrom, Ankara, Turkey.
| | - Atilla Engin
- Faculty of Medicine, Department of General Surgery, Gazi University, Besevler, Ankara, Turkey
- Mustafa Kemal Mah. 2137. Sok. 8/14, 06520, Cankaya, Ankara, Turkey
| |
Collapse
|
46
|
Bofill-De Ros X, Vang Ørom UA. Recent progress in miRNA biogenesis and decay. RNA Biol 2024; 21:1-8. [PMID: 38031325 PMCID: PMC10761092 DOI: 10.1080/15476286.2023.2288741] [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] [Accepted: 11/17/2023] [Indexed: 12/01/2023] Open
Abstract
MicroRNAs are a class of small regulatory RNAs that mediate regulation of protein synthesis by recognizing sequence elements in mRNAs. MicroRNAs are processed through a series of steps starting from transcription and primary processing in the nucleus to precursor processing and mature function in the cytoplasm. It is also in the cytoplasm where levels of mature microRNAs can be modulated through decay mechanisms. Here, we review the recent progress in the lifetime of a microRNA at all steps required for maintaining their homoeostasis. The increasing knowledge about microRNA regulation upholds great promise as therapeutic targets.
Collapse
Affiliation(s)
- Xavier Bofill-De Ros
- RNA Biology and Innovation, Institute of Molecular Biology and Genetics, Aarhus University, Aarhus, Denmark
- RNA Biology Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, Maryland, USA
| | - Ulf Andersson Vang Ørom
- RNA Biology and Innovation, Institute of Molecular Biology and Genetics, Aarhus University, Aarhus, Denmark
| |
Collapse
|
47
|
Min KW, Jo MH, Song M, Lee JW, Shim MJ, Kim K, Park HB, Ha S, Mun H, Polash A, Hafner M, Cho JH, Kim D, Jeong JH, Ko S, Hohng S, Kang SU, Yoon JH. Mature microRNA-binding protein QKI promotes microRNA-mediated gene silencing. RNA Biol 2024; 21:1-15. [PMID: 38372062 PMCID: PMC10878027 DOI: 10.1080/15476286.2024.2314846] [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] [Accepted: 01/29/2024] [Indexed: 02/20/2024] Open
Abstract
Although Argonaute (AGO) proteins have been the focus of microRNA (miRNA) studies, we observed AGO-free mature miRNAs directly interacting with RNA-binding proteins, implying the sophisticated nature of fine-tuning gene regulation by miRNAs. To investigate microRNA-binding proteins (miRBPs) globally, we analyzed PAR-CLIP data sets to identify RBP quaking (QKI) as a novel miRBP for let-7b. Potential existence of AGO-free miRNAs were further verified by measuring miRNA levels in genetically engineered AGO-depleted human and mouse cells. We have shown that QKI regulates miRNA-mediated gene silencing at multiple steps, and collectively serves as an auxiliary factor empowering AGO2/let-7b-mediated gene silencing. Depletion of QKI decreases interaction of AGO2 with let-7b and target mRNA, consequently controlling target mRNA decay. This finding indicates that QKI is a complementary factor in miRNA-mediated mRNA decay. QKI, however, also suppresses the dissociation of let-7b from AGO2, and slows the assembly of AGO2/miRNA/target mRNA complexes at the single-molecule level. We also revealed that QKI overexpression suppresses cMYC expression at post-transcriptional level, and decreases proliferation and migration of HeLa cells, demonstrating that QKI is a tumour suppressor gene by in part augmenting let-7b activity. Our data show that QKI is a new type of RBP implicated in the versatile regulation of miRNA-mediated gene silencing.
Collapse
Affiliation(s)
- Kyung-Won Min
- Department of Biochemistry and Molecular Biology, Medical University of South Carolina, Charleston, SC, USA
- Department of Biology, Gangneung-Wonju National University, Gangneung, Republic of Korea
| | - Myung Hyun Jo
- Department of Physics & Astronomy, Seoul National University, Seoul, Republic of Korea
| | - Minseok Song
- Department of Physics & Astronomy, Seoul National University, Seoul, Republic of Korea
| | - Ji Won Lee
- Department of Biology, Gangneung-Wonju National University, Gangneung, Republic of Korea
| | - Min Ji Shim
- Department of Biology, Gangneung-Wonju National University, Gangneung, Republic of Korea
| | - Kyungmin Kim
- Department of Biology, Gangneung-Wonju National University, Gangneung, Republic of Korea
| | - Hyun Bong Park
- Department of Biology, Gangneung-Wonju National University, Gangneung, Republic of Korea
| | - Shinwon Ha
- Neuroregeneration and Stem Cell Programs, Institute for Cell Engineering, Johns Hopkins University School of Medicine, Baltimore, USA
| | - Hyejin Mun
- Department of Biochemistry and Molecular Biology, Medical University of South Carolina, Charleston, SC, USA
- Department of Oncology Science, University of Oklahoma, Oklahoma City, USA
| | - Ahsan Polash
- Laboratory of Muscle Stem Cells and Gene Regulation, National Institute of Arthritis and Musculoskeletal and Skin Diseases, National Institutes of Health, Bethesda, USA
| | - Markus Hafner
- Laboratory of Muscle Stem Cells and Gene Regulation, National Institute of Arthritis and Musculoskeletal and Skin Diseases, National Institutes of Health, Bethesda, USA
| | - Jung-Hyun Cho
- Department of Biochemistry and Molecular Biology, Medical University of South Carolina, Charleston, SC, USA
| | - Dongsan Kim
- Neuroregeneration and Stem Cell Programs, Institute for Cell Engineering, Johns Hopkins University School of Medicine, Baltimore, USA
| | - Ji-Hoon Jeong
- Department of Oncology Science, University of Oklahoma, Oklahoma City, USA
- Department of Biochemistry and Molecular Biology, University of Ulsan College of Medicine, Seoul, Korea
| | - Seungbeom Ko
- Department of Biochemistry and Molecular Biology, Medical University of South Carolina, Charleston, SC, USA
| | - Sungchul Hohng
- Department of Physics & Astronomy, Seoul National University, Seoul, Republic of Korea
| | - Sung-Ung Kang
- Neuroregeneration and Stem Cell Programs, Institute for Cell Engineering, Johns Hopkins University School of Medicine, Baltimore, USA
| | - Je-Hyun Yoon
- Department of Biochemistry and Molecular Biology, Medical University of South Carolina, Charleston, SC, USA
- Department of Oncology Science, University of Oklahoma, Oklahoma City, USA
| |
Collapse
|
48
|
Sahu A, Verma R, Gupta U, Kashyap S, Sanyal I. An Overview of Targeted Genome Editing Strategies for Reducing the Biosynthesis of Phytic Acid: an Anti-nutrient in Crop Plants. Mol Biotechnol 2024; 66:11-25. [PMID: 37061991 DOI: 10.1007/s12033-023-00722-1] [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: 01/26/2023] [Accepted: 03/11/2023] [Indexed: 04/17/2023]
Abstract
Anti-nutrients are substances either found naturally or are of synthetic origin, which leads to the inactivation of nutrients and limits their utilization in metabolic processes. Phytic acid is classified as an anti-nutrient, as it has a strong binding affinity with most minerals like Fe, Zn, Mg, Ca, Mn, and Cd and impairs their proper metabolism. Removing anti-nutrients from cereal grains may enable the bioavailability of both macro- and micronutrients which is the desired goal of genetic engineering tools for the betterment of agronomic traits. Several strategies have been adopted to minimize phytic acid content in plants. Pursuing the molecular strategies, there are several studies, which result in the decrement of the total phytic acid content in grains of major as well as minor crops. Biosynthesis of phytic acid mainly takes place in the seed comprising lipid-dependent and lipid-independent pathways, involving various enzymes. Furthermore, some studies show that interruption of these enzymes may involve the pleiotropic effect. However, using modern biotechnological approaches, undesirable agronomic traits can be removed. This review presents an overview of different genes encoding the various enzymes involved in the biosynthetic pathway of phytic acid which is being targeted for its reduction. It also, highlights and enumerates the variety of potential applications of genome editing tools such as TALEN, ZFN, and CRISPR/Cas9 to knock out the desired genes, and RNAi for their silencing.
Collapse
Affiliation(s)
- Anshu Sahu
- Plant Transgenic Laboratory, Molecular Biology and Biotechnology Division, CSIR-National Botanical Research Institute, Rana Pratap Marg, Lucknow, U.P, 226001, India
| | - Rita Verma
- Plant Transgenic Laboratory, Molecular Biology and Biotechnology Division, CSIR-National Botanical Research Institute, Rana Pratap Marg, Lucknow, U.P, 226001, India
| | - Uma Gupta
- Plant Transgenic Laboratory, Molecular Biology and Biotechnology Division, CSIR-National Botanical Research Institute, Rana Pratap Marg, Lucknow, U.P, 226001, India
| | - Shashi Kashyap
- Plant Transgenic Laboratory, Molecular Biology and Biotechnology Division, CSIR-National Botanical Research Institute, Rana Pratap Marg, Lucknow, U.P, 226001, India
| | - Indraneel Sanyal
- Plant Transgenic Laboratory, Molecular Biology and Biotechnology Division, CSIR-National Botanical Research Institute, Rana Pratap Marg, Lucknow, U.P, 226001, India.
| |
Collapse
|
49
|
Yan B, Li Z, Su H, Xue H, Qiu D, Xu Z, Tan G. Regulatory mechanisms of autophagy-related ncRNAs in bone metabolic diseases. Front Pharmacol 2023; 14:1178310. [PMID: 38146458 PMCID: PMC10749346 DOI: 10.3389/fphar.2023.1178310] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2023] [Accepted: 11/27/2023] [Indexed: 12/27/2023] Open
Abstract
Bone metabolic diseases have been tormented and are plaguing people worldwide due to the lack of effective and thorough medical interventions and the poor understanding of their pathogenesis. Non-coding RNAs (ncRNAs) are heterogeneous transcripts that cannot encode the proteins but can affect the expressions of other genes. Autophagy is a fundamental mechanism for keeping cell viability, recycling cellular contents through the lysosomal pathway, and maintaining the homeostasis of the intracellular environment. There is growing evidence that ncRNAs, autophagy, and crosstalk between ncRNAs and autophagy play complex roles in progression of metabolic bone disease. This review investigated the complex mechanisms by which ncRNAs, mainly micro RNAs (miRNAs), long noncoding RNAs (lncRNAs), and circular RNAs (circRNAs), regulate autophagic pathway to assist in treating bone metabolism disorders. It aimed at identifying the autophagy role in bone metabolism disorders and understanding the role, potential, and challenges of crosstalk between ncRNAs and autophagy for bone metabolism disorders treatment.
Collapse
Affiliation(s)
- Binghan Yan
- College of First Clinical Medicine, Shandong University of Traditional Chinese Medicine, Jinan, China
| | - Zhichao Li
- College of First Clinical Medicine, Shandong University of Traditional Chinese Medicine, Jinan, China
| | - Hui Su
- College of First Clinical Medicine, Shandong University of Traditional Chinese Medicine, Jinan, China
| | - Haipeng Xue
- Affiliated Hospital of Shandong University of Traditional Chinese Medicine, Jinan, China
| | - Daodi Qiu
- Affiliated Hospital of Shandong University of Traditional Chinese Medicine, Jinan, China
| | - Zhanwang Xu
- Affiliated Hospital of Shandong University of Traditional Chinese Medicine, Jinan, China
| | - Guoqing Tan
- Affiliated Hospital of Shandong University of Traditional Chinese Medicine, Jinan, China
| |
Collapse
|
50
|
García Morato J, Gloeckner CJ, Kahle PJ. Proteomics elucidating physiological and pathological functions of TDP-43. Proteomics 2023; 23:e2200410. [PMID: 37671599 DOI: 10.1002/pmic.202200410] [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: 05/19/2023] [Revised: 08/02/2023] [Accepted: 08/10/2023] [Indexed: 09/07/2023]
Abstract
Trans-activation response DNA binding protein of 43 kDa (TDP-43) regulates a great variety of cellular processes in the nucleus and cytosol. In addition, a defined subset of neurodegenerative diseases is characterized by nuclear depletion of TDP-43 as well as cytosolic mislocalization and aggregation. To perform its diverse functions TDP-43 can associate with different ribonucleoprotein complexes. Combined with transcriptomics, MS interactome studies have unveiled associations between TDP-43 and the spliceosome machinery, polysomes and RNA granules. Moreover, the highly dynamic, low-valency interactions regulated by its low-complexity domain calls for innovative proximity labeling methodologies. In addition to protein partners, the analysis of post-translational modifications showed that they may play a role in the nucleocytoplasmic shuttling, RNA binding, liquid-liquid phase separation and protein aggregation of TDP-43. Here we review the various TDP-43 ribonucleoprotein complexes characterized so far, how they contribute to the diverse functions of TDP-43, and roles of post-translational modifications. Further understanding of the fluid dynamic properties of TDP-43 in ribonucleoprotein complexes, RNA granules, and self-assemblies will advance the understanding of RNA processing in cells and perhaps help to develop novel therapeutic approaches for TDPopathies.
Collapse
Affiliation(s)
- Jorge García Morato
- Laboratory of Functional Neurogenetics, Department of Neurodegeneration, German Center of Neurodegenerative Diseases and Hertie Institute for Clinical Brain Research, University of Tübingen, Tübingen, Germany
| | - Christian Johannes Gloeckner
- Research Group Functional Neuroproteomics, German Center of Neurodegenerative Diseases, Tübingen, Germany
- Core Facility for Medical Bioanalytics, Institute for Ophthalmic Research, Center for Ophthalmology, University of Tübingen, Tübingen, Germany
| | - Philipp J Kahle
- Laboratory of Functional Neurogenetics, Department of Neurodegeneration, German Center of Neurodegenerative Diseases and Hertie Institute for Clinical Brain Research, University of Tübingen, Tübingen, Germany
- Department of Biochemistry, University of Tübingen, Tübingen, Germany
| |
Collapse
|