1
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Wang Z, Che S, Yu Z. PROTAC: Novel degradable approach for different targets to treat breast cancer. Eur J Pharm Sci 2024; 198:106793. [PMID: 38740076 DOI: 10.1016/j.ejps.2024.106793] [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: 03/21/2024] [Revised: 04/22/2024] [Accepted: 05/05/2024] [Indexed: 05/16/2024]
Abstract
The revolutionary Proteolysis Targeting Chimera (PROTACs) have the exciting potential to reshape the pharmaceutical industry landscape by leveraging the ubiquitin-proteasome system for targeted protein degradation. Breast cancer, the most prevalent cancer in women, could be treated using PROTAC therapy. Although substantial work has been conducted, there is not yet a comprehensive overview or progress update on PROTAC therapy for breast cancer. Hence, in this article, we've compiled recent research progress focusing on different breast cancer target proteins, such as estrogen receptor (ER), BET, CDK, HER2, PARP, EZH2, etc. This resource aims to serve as a guide for future PROTAC-based breast cancer treatment design.
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Affiliation(s)
- Zhenjie Wang
- Guangdong Provincial Key Laboratory of New Drug Screening, School of Pharmaceutical Sciences, Southern Medical University, Guangzhou 510515, PR China; Office of Drug Clinical Trials, The People's Hospital of Gaozhou, Maoming, 525200, PR China
| | - Siyao Che
- Hepatological Surgery Department, The People's Hospital of Gaozhou, Maoming, 525200, PR China.
| | - Zhiqiang Yu
- Department of Laboratory Medicine, Dongguan Institute of Clinical Cancer Research, The Tenth Affiliated Hospital of Southern Medical University (Dongguan People's Hospital), Dongguan 523018, PR China.
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2
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Yuan W, Shi X, Lee LTO. RNA therapeutics in targeting G protein-coupled receptors: Recent advances and challenges. MOLECULAR THERAPY. NUCLEIC ACIDS 2024; 35:102195. [PMID: 38741614 PMCID: PMC11089380 DOI: 10.1016/j.omtn.2024.102195] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 05/16/2024]
Abstract
G protein-coupled receptors (GPCRs) are the major targets of existing drugs for a plethora of human diseases and dominate the pharmaceutical market. However, over 50% of the GPCRs remain undruggable. To pursue a breakthrough and overcome this situation, there is significant clinical research for developing RNA-based drugs specifically targeting GPCRs, but none has been approved so far. RNA therapeutics represent a unique and promising approach to selectively targeting previously undruggable targets, including undruggable GPCRs. However, the development of RNA therapeutics faces significant challenges in areas of RNA stability and efficient in vivo delivery. This review presents an overview of the advances in RNA therapeutics and the diverse types of nanoparticle RNA delivery systems. It also describes the potential applications of GPCR-targeted RNA drugs for various human diseases.
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Affiliation(s)
- Wanjun Yuan
- Cancer Centre, Faculty of Health Sciences, University of Macau, Taipa 999078, Macau, China
| | - Xiangyang Shi
- State Key Laboratory for Modification of Chemical Fibers and Polymer Materials, Shanghai Engineering Research Center of Nano-Biomaterials and Regenerative Medicine, College of Biological Science and Medical Engineering, Donghua University, Shanghai 201620, People’s Republic of China
| | - Leo Tsz On Lee
- Cancer Centre, Faculty of Health Sciences, University of Macau, Taipa 999078, Macau, China
- Ministry of Education Frontiers Science Center for Precision Oncology, University of Macau, Taipa 999078, Macau, China
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3
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Bosio S, Bernetti M, Rocchia W, Masetti M. Similarities and Differences in Ligand Binding to Protein and RNA Targets: The Case of Riboflavin. J Chem Inf Model 2024; 64:4570-4586. [PMID: 38800845 DOI: 10.1021/acs.jcim.4c00420] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/29/2024]
Abstract
It is nowadays clear that RNA molecules can play active roles in several biological processes. As a result, an increasing number of RNAs are gradually being identified as potentially druggable targets. In particular, noncoding RNAs can adopt highly organized conformations that are suitable for drug binding. However, RNAs are still considered challenging targets due to their complex structural dynamics and high charge density. Thus, elucidating relevant features of drug-RNA binding is fundamental for advancing drug discovery. Here, by using Molecular Dynamics simulations, we compare key features of ligand binding to proteins with those observed in RNA. Specifically, we explore similarities and differences in terms of (i) conformational flexibility of the target, (ii) electrostatic contribution to binding free energy, and (iii) water and ligand dynamics. As a test case, we examine binding of the same ligand, namely riboflavin, to protein and RNA targets, specifically the riboflavin (RF) kinase and flavin mononucleotide (FMN) riboswitch. The FMN riboswitch exhibited enhanced fluctuations and explored a wider conformational space, compared to the protein target, underscoring the importance of RNA flexibility in ligand binding. Conversely, a similar electrostatic contribution to the binding free energy of riboflavin was found. Finally, greater stability of water molecules was observed in the FMN riboswitch compared to the RF kinase, possibly due to the different shape and polarity of the pockets.
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Affiliation(s)
- Stefano Bosio
- Department of Pharmacy and Biotechnology, Alma Mater Studiorum - University of Bologna, Via Belmeloro 6, 40126 Bologna, Italy
- Computational and Chemical Biology, Fondazione Istituto Italiano di Tecnologia, Via Morego 30, I-16163 Genova, Italy
| | - Mattia Bernetti
- Department of Pharmacy and Biotechnology, Alma Mater Studiorum - University of Bologna, Via Belmeloro 6, 40126 Bologna, Italy
- Computational and Chemical Biology, Fondazione Istituto Italiano di Tecnologia, Via Morego 30, I-16163 Genova, Italy
| | - Walter Rocchia
- Computational mOdelling of NanosCalE and bioPhysical sysTems (CONCEPT) Lab, Istituto Italiano di Tecnologia, Via Melen - 83, B Block, 16152 Genova, Italy
| | - Matteo Masetti
- Department of Pharmacy and Biotechnology, Alma Mater Studiorum - University of Bologna, Via Belmeloro 6, 40126 Bologna, Italy
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4
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Song Y, Cui J, Zhu J, Kim B, Kuo ML, Potts PR. RNATACs: Multispecific small molecules targeting RNA by induced proximity. Cell Chem Biol 2024:S2451-9456(24)00207-1. [PMID: 38876100 DOI: 10.1016/j.chembiol.2024.05.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2024] [Revised: 05/09/2024] [Accepted: 05/22/2024] [Indexed: 06/16/2024]
Abstract
RNA-targeting small molecules (rSMs) have become an attractive modality to tackle traditionally undruggable proteins and expand the druggable space. Among many innovative concepts, RNA-targeting chimeras (RNATACs) represent a new class of multispecific, induced proximity small molecules that act by chemically bringing RNA targets into proximity with an endogenous RNA effector, such as a ribonuclease (RNase). Depending on the RNA effector, RNATACs can alter the stability, localization, translation, or splicing of the target RNA. Although still in its infancy, this new modality has the potential for broad applications in the future to treat diseases with high unmet need. In this review, we discuss potential advantages of RNATACs, recent progress in the field, and challenges to this cutting-edge technology.
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Affiliation(s)
- Yan Song
- Induced Proximity Platform, Amgen Research, Thousand Oaks, CA 91320, USA.
| | - Jia Cui
- Induced Proximity Platform, Amgen Research, Thousand Oaks, CA 91320, USA
| | - Jiaqiang Zhu
- Induced Proximity Platform, Amgen Research, Thousand Oaks, CA 91320, USA
| | - Boseon Kim
- Induced Proximity Platform, Amgen Research, Thousand Oaks, CA 91320, USA
| | - Mei-Ling Kuo
- Induced Proximity Platform, Amgen Research, Thousand Oaks, CA 91320, USA
| | - Patrick Ryan Potts
- Induced Proximity Platform, Amgen Research, Thousand Oaks, CA 91320, USA.
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5
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Yasir Khan H, Fawad Ansari M, Tabassum S, Arjmand F. A review on the recent advances of interaction studies of anticancer metal-based drugs with therapeutic targets, DNA and RNAs. Drug Discov Today 2024:104055. [PMID: 38852835 DOI: 10.1016/j.drudis.2024.104055] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2023] [Revised: 05/18/2024] [Accepted: 05/30/2024] [Indexed: 06/11/2024]
Abstract
Metal-based drugs hold promise as potent anticancer agents owing to their unique interactions with cellular targets. This review discusses recent advances in our understanding of the intricate molecular interactions of metal-based anticancer compounds with specific therapeutic targets in cancer cells. Advanced computational and experimental methodologies delineate the binding mechanisms, structural dynamics and functional outcomes of these interactions. In addition, the review sheds light on the precise modes of action of these drugs, their efficacy and the potential avenues for further optimization in cancer-treatment strategies and the development of targeted and effective metal-based therapies for combating various forms of cancer.
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Affiliation(s)
- Huzaifa Yasir Khan
- Department of Chemistry, Aligarh Muslim University, Aligarh-202002, UP, India
| | | | - Sartaj Tabassum
- Department of Chemistry, Aligarh Muslim University, Aligarh-202002, UP, India
| | - Farukh Arjmand
- Department of Chemistry, Aligarh Muslim University, Aligarh-202002, UP, India.
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6
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Cappello M, Barbara G, Bellini M, Consalvo D, Di Sabatino A, Marasco G, Principi M, Savarino EV, Tortora A, Obici L. Identification and management of gastrointestinal manifestations of hereditary transthyretin amyloidosis: Recommendations from an Italian group of experts. Dig Liver Dis 2024; 56:1014-1020. [PMID: 38105149 DOI: 10.1016/j.dld.2023.11.025] [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: 10/26/2023] [Accepted: 11/23/2023] [Indexed: 12/19/2023]
Abstract
Gastrointestinal manifestations are common across all hereditary transthyretin amyloidosis (ATTRv) genotypes. However, they are poorly specific, and their recognition as part of ATTRv is difficult, resulting in misdiagnosis with more common conditions. Moreover, delays in diagnosis occur because of fragmented knowledge, a shortage of centers of excellence and specialists dedicated to ATTRv management, and the scarce involvement of gastroenterologists in multidisciplinary teams. A group of Italian gastroenterologists with experience in the management of ATTRv took part in a project aimed at assessing the awareness of ATTRv among the community of Italian gastroenterologists through an online survey and providing education about practical aspects of ATTRv management. Survey results reported low participation, and very few patients with ATTRv were cared for by gastroenterologists. This highlights the need for greater attention to rare diseases in gastroenterology and emphasizes increasing awareness of ATTRv and diagnostic suspicion. Based on the experts' recommendations, a diagnosis of ATTRv should be suspected when at least one of the 'red flags' is detected. Subsequently, it is suggested to promptly ask for genetic testing and exclude a serum and urinary monoclonal protein, even before the detection of amyloid in biopsy samples, particularly in non-endemic areas.
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Affiliation(s)
- Maria Cappello
- Gastroenterology and Hepatology Section, ProMiSe Department, University of Palermo, Piazza delle Cliniche 2, 90127, Palermo, Italy.
| | - Giovanni Barbara
- Department of Medical and Surgical Sciences, University of Bologna, via Massarenti 9, 40138, Bologna, Italy; IRCCS Azienda Ospedaliero-Universitaria di Bologna, Via Albertoni 15, 40138, Bologna, Italy
| | - Massimo Bellini
- Gastroenterology Unit, Department of Translational Research and New Technologies in Medicine and Surgery, University of Pisa, Via Savi 10, 56126, Pisa, Italy
| | - Danilo Consalvo
- Department of Gastroenterology and Digestive Endoscopy, AORN ``Antonio Cardarelli'', Via Antonio Cardarelli 9, 80131, Napoli, Italy
| | - Antonio Di Sabatino
- Department of Internal Medicine and Therapeutics, University of Pavia, Piazzale Golgi 19, 27100 Pavia, Italy; First Department of Internal Medicine, IRCCS San Matteo Hospital Foundation, Piazzale Golgi 19, 27100 Pavia, Italy
| | - Giovanni Marasco
- Department of Medical and Surgical Sciences, University of Bologna, via Massarenti 9, 40138, Bologna, Italy; IRCCS Azienda Ospedaliero-Universitaria di Bologna, Via Albertoni 15, 40138, Bologna, Italy
| | - Mariabeatrice Principi
- Department of Precision and Regenerative Medicine and Ionian Area (DiMePRe-J), University of Bari, Piazza Umberto I, 70121, Bari, Italy
| | - Edoardo Vincenzo Savarino
- Gastroenterology Unit, Azienda Ospedale Università di Padova, via Nicolò Giustiniani 2, 35100, Padova, Italy; Department of Surgery, Oncology and Gastroenterology, University of Padua, via Nicolò Giustiniani 2, 35100, Italy
| | - Annalisa Tortora
- UOC Gastroenterologia, Azienda Ospedaliera Universitaria Integrata di Verona, Piazzale L.A. Scuro, 10, 37134 Verona VR, Italy
| | - Laura Obici
- Rare Diseases Unit and Amyloidosis Research and Treatment Centre, IRCCS San Matteo Hospital Foundation, viale Camillo Golgi 19, 27100, Pavia, Italy
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Zhou Y, Chen SJ. Advances in machine-learning approaches to RNA-targeted drug design. ARTIFICIAL INTELLIGENCE CHEMISTRY 2024; 2:100053. [PMID: 38434217 PMCID: PMC10904028 DOI: 10.1016/j.aichem.2024.100053] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/05/2024]
Abstract
RNA molecules play multifaceted functional and regulatory roles within cells and have garnered significant attention in recent years as promising therapeutic targets. With remarkable successes achieved by artificial intelligence (AI) in different fields such as computer vision and natural language processing, there is a growing imperative to harness AI's potential in computer-aided drug design (CADD) to discover novel drug compounds that target RNA. Although machine-learning (ML) approaches have been widely adopted in the discovery of small molecules targeting proteins, the application of ML approaches to model interactions between RNA and small molecule is still in its infancy. Compared to protein-targeted drug discovery, the major challenges in ML-based RNA-targeted drug discovery stem from the scarcity of available data resources. With the growing interest and the development of curated databases focusing on interactions between RNA and small molecule, the field anticipates a rapid growth and the opening of a new avenue for disease treatment. In this review, we aim to provide an overview of recent advancements in computationally modeling RNA-small molecule interactions within the context of RNA-targeted drug discovery, with a particular emphasis on methodologies employing ML techniques.
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Affiliation(s)
- Yuanzhe Zhou
- Department of Physics and Astronomy, University of Missouri, Columbia, MO 65211-7010, USA
| | - Shi-Jie Chen
- Department of Physics and Astronomy, Department of Biochemistry, Institute of Data Sciences and Informatics, University of Missouri, Columbia, MO 65211-7010, USA
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8
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Tolbatov I, Umari P, Marrone A. The binding of diruthenium (II,III) and dirhodium (II,II) paddlewheel complexes at DNA/RNA nucleobases: Computational evidences of an appreciable selectivity toward the AU base pairs. J Mol Graph Model 2024; 131:108806. [PMID: 38824876 DOI: 10.1016/j.jmgm.2024.108806] [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: 02/20/2024] [Revised: 05/21/2024] [Accepted: 05/28/2024] [Indexed: 06/04/2024]
Abstract
Multiple medicinal strategies involve modifications of the structure of DNA or RNA, which disrupt their correct functioning. Metal complexes with medicinal effects, also known as metallodrugs, are among the agents intended specifically for the attack onto nucleosides. The diruthenium (II,III) and dirhodium (II,II) paddlewheel complexes constitute promising dual acting drugs due to their ability to release the therapeutically active bridging ligands upon their substitution by endogenous ligands. In this paper, we study the structure and the stability of the complexes formed by the diruthenium (II,III) and dirhodium (II,II) paddlewheel complexes coordinated in axial positions with the DNA/RNA nucleobases or base pairs, assuming the attainable metalation at all the accessible pyridyl nitrogens. Dirhodium complexes coordinate at the pyridyl nitrogens more strongly than the diruthenium complexes. On the other hand, we found that the diruthenium scaffold binds more selectively to nucleobase targets. Furthermore, we reveal a tighter coordination of diruthenium complex at the adenine-uracil base pair, compared to adenine-thymine, hence constituting a scarce instance of RNA-selectivity. We envision that the here reported computational outcomes may pace future experiments addressing the binding of diruthenium and dirhodium paddlewheel complexes at either single nucleobases or DNA/RNA fragments.
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Affiliation(s)
- Iogann Tolbatov
- Department of Physics and Astronomy, University of Padova, via F. Marzolo 8, 35131, Padova, Italy.
| | - Paolo Umari
- Department of Physics and Astronomy, University of Padova, via F. Marzolo 8, 35131, Padova, Italy
| | - Alessandro Marrone
- Dipartimento di Farmacia, Università degli Studi "G. D'Annunzio" Chieti-Pescara, Via dei Vestini, 66100, Chieti, Italy
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9
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Heel SV, Breuker K. Investigating the Intramolecular Competition of Different RNA Binding Motifs for Neomycin B by Native Top-Down Mass Spectrometry. Chempluschem 2024:e202400178. [PMID: 38758051 DOI: 10.1002/cplu.202400178] [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: 04/13/2024] [Indexed: 05/18/2024]
Abstract
The ongoing search for small molecule drugs that target ribonucleic acids (RNA) is complicated by a limited understanding of the principles that govern RNA-small molecule interactions. Here we have used stoichiometry-resolved native top-down mass spectrometry (MS) to study the binding of neomycin B to small model hairpin RNAs, an unstructured RNA, and a viral RNA construct. For 15-22 nt model RNAs with hairpin structure, we found that neomycin B binding to hairpin loops relies on interactions with both the nucleobases and the 2'-OH groups, and that a simple 5' or 3' overhang can introduce an additional binding motif. For a 47 nt RNA construct derived from stem IA of the human immunodeficiency virus 1 (HIV-1) rev response element (RRE) RNA, native top-down MS identified four different binding motifs, of which the purine-rich internal loop showed the highest affinity for neomycin B. Stoichiometry-resolved binding site mapping by native top-down MS allows for a new perspective on binding specificity, and has the potential to reveal unexpected principles of small molecule binding to RNA.
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Affiliation(s)
- Sarah Viola Heel
- Institute of Organic Chemistry and Center for Molecular Biosciences Innsbruck (CMBI), University of Innsbruck, Innrain 80/82, 6020, Innsbruck, Austria
| | - Kathrin Breuker
- Institute of Organic Chemistry and Center for Molecular Biosciences Innsbruck (CMBI), University of Innsbruck, Innrain 80/82, 6020, Innsbruck, Austria
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10
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Traber GM, Yi C, Batra N, Tu MJ, Yu AM. Novel RNA molecular bioengineering technology efficiently produces functional miRNA agents. RNA (NEW YORK, N.Y.) 2024; 30:680-694. [PMID: 38429100 PMCID: PMC11098458 DOI: 10.1261/rna.079904.123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/28/2023] [Accepted: 02/19/2024] [Indexed: 03/03/2024]
Abstract
Genome-derived microRNAs (miRNAs or miRs) govern posttranscriptional gene regulation and play important roles in various cellular processes and disease progression. While chemo-engineered miRNA mimics or biosimilars made in vitro are widely available and used, miRNA agents produced in vivo are emerging to closely recapitulate natural miRNA species for research. Our recent work has demonstrated the success of high-yield, in vivo production of recombinant miRNAs by using human tRNA (htRNA) fused precursor miRNA (pre-miR) carriers. In this study, we aim to compare the production of bioengineered RNA (BioRNA) molecules with glycyl versus leucyl htRNA fused hsa-pre-miR-34a carriers, namely, BioRNAGly and BioRNALeu, respectively, and perform the initial functional assessment. We designed, cloned, overexpressed, and purified a total of 48 new BioRNA/miRNAs, and overall expression levels, final yields, and purities were revealed to be comparable between BioRNAGly and BioRNALeu molecules. Meanwhile, the two versions of BioRNA/miRNAs showed similar activities to inhibit non-small cell lung cancer cell viability. Interestingly, functional analyses using model BioRNA/miR-7-5p demonstrated that BioRNAGly/miR-7-5p exhibited greater efficiency to regulate a known target gene expression (EGFR) than BioRNALeu/miR-7-5p, consistent with miR-7-5p levels released in cells. Moreover, BioRNAGly/miR-7-5p showed comparable or slightly greater activities to modulate MRP1 and VDAC1 expression, compared with miRCURY LNA miR-7-5p mimic. Computational modeling illustrated overall comparable 3D structures for exemplary BioRNA/miRNAs with noticeable differences in htRNA species and payload miRNAs. These findings support the utility of hybrid htRNA/hsa-pre-miR-34a as reliable carriers for RNA molecular bioengineering, and the resultant BioRNAs serve as functional biologic RNAs for research and development.
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Affiliation(s)
- Gavin M Traber
- Department of Biochemistry and Molecular Medicine, University of California-Davis, School of Medicine, Sacramento, California 95817, USA
| | - Colleen Yi
- Department of Biochemistry and Molecular Medicine, University of California-Davis, School of Medicine, Sacramento, California 95817, USA
| | - Neelu Batra
- Department of Biochemistry and Molecular Medicine, University of California-Davis, School of Medicine, Sacramento, California 95817, USA
| | - Mei-Juan Tu
- Department of Biochemistry and Molecular Medicine, University of California-Davis, School of Medicine, Sacramento, California 95817, USA
| | - Ai-Ming Yu
- Department of Biochemistry and Molecular Medicine, University of California-Davis, School of Medicine, Sacramento, California 95817, USA
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11
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Batra N, Tu MJ, Yu AM. Molecular Engineering of Functional SiRNA Agents. ACS Synth Biol 2024. [PMID: 38733599 DOI: 10.1021/acssynbio.4c00181] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/13/2024]
Abstract
Synthetic biology constitutes a scientific domain focused on intentional redesign of organisms to confer novel functionalities or create new products through strategic engineering of their genetic makeup. Leveraging the inherent capabilities of nature, one may address challenges across diverse sectors including medicine. Inspired by this concept, we have developed an innovative bioengineering platform, enabling high-yield and large-scale production of biological small interfering RNA (BioRNA/siRNA) agents via bacterial fermentation. Herein, we show that with the use of a new tRNA fused pre-miRNA carrier, we can produce various forms of BioRNA/siRNA agents within living host cells. We report a high-level overexpression of nine target BioRNA/siRNA molecules at 100% success rate, yielding 3-10 mg of BioRNA/siRNA per 0.25 L of bacterial culture with high purity (>98%) and low endotoxin (<5 EU/μg RNA). Furthermore, we demonstrate that three representative BioRNA/siRNAs against GFP, BCL2, and PD-L1 are biologically active and can specifically and efficiently silence their respective targets with the potential to effectively produce downstream antiproliferation effects by PD-L1-siRNA. With these promising results, we aim to advance the field of synthetic biology by offering a novel platform to bioengineer functional siRNA agents for research and drug development.
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Affiliation(s)
- Neelu Batra
- Department of Biochemistry and Molecular Medicine, UC Davis School of Medicine, Sacramento, California 95817, United States
| | - Mei-Juan Tu
- Department of Biochemistry and Molecular Medicine, UC Davis School of Medicine, Sacramento, California 95817, United States
| | - Ai-Ming Yu
- Department of Biochemistry and Molecular Medicine, UC Davis School of Medicine, Sacramento, California 95817, United States
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12
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Heel SV, Juen F, Bartosik K, Micura R, Kreutz C, Breuker K. Resolving the intricate binding of neomycin B to multiple binding motifs of a neomycin-sensing riboswitch aptamer by native top-down mass spectrometry and NMR spectroscopy. Nucleic Acids Res 2024; 52:4691-4701. [PMID: 38567725 PMCID: PMC11077050 DOI: 10.1093/nar/gkae224] [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: 08/07/2023] [Revised: 03/05/2024] [Accepted: 03/25/2024] [Indexed: 05/09/2024] Open
Abstract
Understanding small molecule binding to RNA can be complicated by an intricate interplay between binding stoichiometry, multiple binding motifs, different occupancies of different binding motifs, and changes in the structure of the RNA under study. Here, we use native top-down mass spectrometry (MS) and nuclear magnetic resonance (NMR) spectroscopy to experimentally resolve these factors and gain a better understanding of the interactions between neomycin B and the 40 nt aptamer domain of a neomycin-sensing riboswitch engineered in yeast. Data from collisionally activated dissociation of the 1:1, 1:2 and 1:3 RNA-neomycin B complexes identified a third binding motif C of the riboswitch in addition to the two motifs A and B found in our previous study, and provided occupancies of the different binding motifs for each complex stoichiometry. Binding of a fourth neomycin B molecule was unspecific according to both MS and NMR data. Intriguingly, all major changes in the aptamer structure can be induced by the binding of the first neomycin B molecule regardless of whether it binds to motif A or B as evidenced by stoichiometry-resolved MS data together with titration data from 1H NMR spectroscopy in the imino proton region. Specific binding of the second and third neomycin B molecules further stabilizes the riboswitch aptamer, thereby allowing for a gradual response to increasing concentrations of neomycin B, which likely leads to a fine-tuning of the cellular regulatory mechanism.
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Affiliation(s)
- Sarah Viola Heel
- Institute of Organic Chemistry and Center for Molecular Biosciences Innsbruck (CMBI), University of Innsbruck, Innrain 80/82, 6020 Innsbruck, Austria
| | - Fabian Juen
- Institute of Organic Chemistry and Center for Molecular Biosciences Innsbruck (CMBI), University of Innsbruck, Innrain 80/82, 6020 Innsbruck, Austria
| | - Karolina Bartosik
- Institute of Organic Chemistry and Center for Molecular Biosciences Innsbruck (CMBI), University of Innsbruck, Innrain 80/82, 6020 Innsbruck, Austria
| | - Ronald Micura
- Institute of Organic Chemistry and Center for Molecular Biosciences Innsbruck (CMBI), University of Innsbruck, Innrain 80/82, 6020 Innsbruck, Austria
| | - Christoph Kreutz
- Institute of Organic Chemistry and Center for Molecular Biosciences Innsbruck (CMBI), University of Innsbruck, Innrain 80/82, 6020 Innsbruck, Austria
| | - Kathrin Breuker
- Institute of Organic Chemistry and Center for Molecular Biosciences Innsbruck (CMBI), University of Innsbruck, Innrain 80/82, 6020 Innsbruck, Austria
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13
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Wang Z, Zhou P, Li Y, Zhang D, Chu F, Yuan F, Pan B, Gao F. A Bimetallic Polymerization Network for Effective Increase in Labile Iron Pool and Robust Activation of cGAS/STING Induces Ferroptosis-Based Tumor Immunotherapy. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2024; 20:e2308397. [PMID: 38072786 DOI: 10.1002/smll.202308397] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/21/2023] [Revised: 11/13/2023] [Indexed: 12/20/2023]
Abstract
Due to the inherent low immunogenicity and immunosuppressive tumor microenvironment (TME) of malignant cancers, the clinical efficacy and application of tumor immunotherapy have been limited. Herein, a bimetallic drug-gene co-loading network (Cu/ZIF-8@U-104@siNFS1-HA) is developed that increased the intracellular labile iron pool (LIP) and enhanced the weakly acidic TME by co-suppressing the dual enzymatic activities of carbonic anhydrase IX (CA IX) and cysteine desulfurylase (NFS1), inducing a safe and efficient initial tumor immunogenic ferroptosis. During this process, Cu2+ is responsively released to deplete glutathione (GSH) and reduce the enzyme activity of glutathione peroxidase 4 (GPX4), achieving the co-inhibition of the three enzymes and further inducing lipid peroxidation (LPO). Additionally, the reactive oxygen species (ROS) storm in target cells promoted the generation of large numbers of double-stranded DNA breaks. The presence of Zn2+ substantially increased the expression of cGAS/STING, which cooperated with ferroptosis to strengthen the immunogenic cell death (ICD) response and remodel the immunosuppressive TME. In brief, Cu/ZIF-8@U-104@siNFS1-HA linked ferroptosis with immunotherapy through multiple pathways, including the increase in LIP, regulation of pH, depletion of GSH/GPX4, and activation of STING, effectively inhibiting cancer growth and metastasis.
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Affiliation(s)
- Zhenxin Wang
- Department of Orthopedics, The Affiliated Hospital of Xuzhou Medical University, Jiangsu, 221002, P. R. China
- Jiangsu Key Laboratory of New Drug Research and Clinical Pharmacy, Xuzhou Medical University, Jiangsu, 221002, P. R. China
| | - Peng Zhou
- Department of Orthopedics, The Affiliated Huai'an Hospital of Xuzhou Medical University, The Second People's Hospital of Huai'an, Jiangsu, 223002, P. R. China
| | - Yuting Li
- Jiangsu Key Laboratory of New Drug Research and Clinical Pharmacy, Xuzhou Medical University, Jiangsu, 221002, P. R. China
| | - Dazhen Zhang
- Department of Orthopedics, The Affiliated Hospital of Xuzhou Medical University, Jiangsu, 221002, P. R. China
| | - Fuchao Chu
- Department of Orthopedics, The Affiliated Hospital of Xuzhou Medical University, Jiangsu, 221002, P. R. China
| | - Feng Yuan
- Department of Orthopedics, The Affiliated Hospital of Xuzhou Medical University, Jiangsu, 221002, P. R. China
- Jiangsu Key Laboratory of New Drug Research and Clinical Pharmacy, Xuzhou Medical University, Jiangsu, 221002, P. R. China
| | - Bin Pan
- Department of Orthopedics, The Affiliated Hospital of Xuzhou Medical University, Jiangsu, 221002, P. R. China
- Jiangsu Key Laboratory of New Drug Research and Clinical Pharmacy, Xuzhou Medical University, Jiangsu, 221002, P. R. China
| | - Fenglei Gao
- Department of Orthopedics, The Affiliated Hospital of Xuzhou Medical University, Jiangsu, 221002, P. R. China
- Jiangsu Key Laboratory of New Drug Research and Clinical Pharmacy, Xuzhou Medical University, Jiangsu, 221002, P. R. China
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14
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Yamaguchi S, Miyamoto K, Jones XM, Ciullo A, Morris A, Tsi K, Marbán E, Ibrahim AG. Oral bioavailability of a noncoding RNA drug, TY1, that acts on macrophages. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.27.591474. [PMID: 38746093 PMCID: PMC11092517 DOI: 10.1101/2024.04.27.591474] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2024]
Abstract
All approved RNA therapeutics require parenteral delivery. Here we demonstrate an orally bioavailable formulation wherein synthetic noncoding (nc) RNA, packaged into lipid nanoparticles, is loaded into casein-chitosan (C2) micelles. We used the C2 formulation to deliver TY1, a 24-nucleotide synthetic ncRNA which targets the DNA damage response pathway in macrophages. C2-formulated TY1 (TY1C2) efficiently packages and protects TY1 against degradative enzymes. In healthy mice, oral TY1C2 was well-tolerated and nontoxic. Oral TY1C2 exhibited disease-modifying bioactivity in 2 models of tissue injury: 1) rat myocardial infarction, where a single oral dose of TY1C2 was cardioprotective, on par with intravenously-delivered TY1; and 2) mouse acute lung injury, where a single dose of TY1C2 attenuated pulmonary inflammation. Mechanistic dissection revealed that TY1C2 is not absorbed into the systemic circulation but is, instead, taken up by intestinal macrophages, namely those of the lamina propria and Peyer's patches. This route of absorption may rationalize why an antisense oligonucleotide against Factor VII, which acts on hepatocytes, is not effective when administered in the C2 formulation. Thus, some (but not all) ncRNA drugs are bioavailable when delivered by mouth. Oral RNA delivery and uptake, relying on uptake via the gastrointestinal immune system, has broad-ranging therapeutic implications.
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Affiliation(s)
- Shukuro Yamaguchi
- Smidt Heart Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Kazutaka Miyamoto
- Smidt Heart Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Xaviar M. Jones
- Smidt Heart Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Alessandra Ciullo
- Smidt Heart Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Ashley Morris
- Smidt Heart Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Kara Tsi
- Smidt Heart Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Eduardo Marbán
- Smidt Heart Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Ahmed G.E. Ibrahim
- Smidt Heart Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA
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15
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Bouton L, Ecoutin A, Malard F, Campagne S. Small molecules modulating RNA splicing: a review of targets and future perspectives. RSC Med Chem 2024; 15:1109-1126. [PMID: 38665842 PMCID: PMC11042171 DOI: 10.1039/d3md00685a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2023] [Accepted: 01/03/2024] [Indexed: 04/28/2024] Open
Abstract
In eukaryotic cells, RNA splicing is crucial for gene expression. Dysregulation of this process can result in incorrect mRNA processing, leading to aberrant gene expression patterns. Such abnormalities are implicated in many inherited diseases and cancers. Historically, antisense oligonucleotides, which bind to specific RNA targets, have been used to correct these splicing abnormalities. Despite their high specificity of action, these oligonucleotides have drawbacks, such as lack of oral bioavailability and the need for chemical modifications to enhance cellular uptake and stability. As a result, recent efforts focused on the development of small organic molecules that can correct abnormal RNA splicing event under disease conditions. This review discusses known and potential targets of these molecules, including RNA structures, trans-acting splicing factors, and the spliceosome - the macromolecular complex responsible for RNA splicing. We also rely on recent advances to discuss therapeutic applications of RNA-targeting small molecules in splicing correction. Overall, this review presents an update on strategies for RNA splicing modulation, emphasizing the therapeutic promise of small molecules.
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Affiliation(s)
- Léa Bouton
- Inserm U1212, CNRS UMR5320, ARNA Laboratory, University of Bordeaux 146 rue Léo Saignat 33076 Bordeaux Cedex France
- Institut Européen de Chimie et de Biologie F-33600 Pessac France
| | - Agathe Ecoutin
- Inserm U1212, CNRS UMR5320, ARNA Laboratory, University of Bordeaux 146 rue Léo Saignat 33076 Bordeaux Cedex France
- Institut Européen de Chimie et de Biologie F-33600 Pessac France
| | - Florian Malard
- Inserm U1212, CNRS UMR5320, ARNA Laboratory, University of Bordeaux 146 rue Léo Saignat 33076 Bordeaux Cedex France
- Institut Européen de Chimie et de Biologie F-33600 Pessac France
| | - Sébastien Campagne
- Inserm U1212, CNRS UMR5320, ARNA Laboratory, University of Bordeaux 146 rue Léo Saignat 33076 Bordeaux Cedex France
- Institut Européen de Chimie et de Biologie F-33600 Pessac France
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16
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Min Y, Xiong W, Shen W, Liu X, Qi Q, Zhang Y, Fan R, Fu F, Xue H, Yang H, Sun X, Ning Y, Tian T, Zhou X. Developing nucleoside tailoring strategies against SARS-CoV-2 via ribonuclease targeting chimera. SCIENCE ADVANCES 2024; 10:eadl4393. [PMID: 38598625 PMCID: PMC11006213 DOI: 10.1126/sciadv.adl4393] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/18/2023] [Accepted: 03/06/2024] [Indexed: 04/12/2024]
Abstract
In response to the urgent need for potent severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) therapeutics, this study introduces an innovative nucleoside tailoring strategy leveraging ribonuclease targeting chimeras. By seamlessly integrating ribonuclease L recruiters into nucleosides, we address RNA recognition challenges and effectively inhibit severe acute respiratory syndrome coronavirus 2 replication in human cells. Notably, nucleosides tailored at the ribose 2'-position outperform those modified at the nucleobase. Our in vivo validation using hamster models further bolsters the promise of this nucleoside tailoring approach, positioning it as a valuable asset in the development of innovative antiviral drugs.
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Affiliation(s)
- Yuanqin Min
- Wuhan Institute of Virology; Hubei Jiangxia Laboratory; Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan 430200, Hubei, China
| | - Wei Xiong
- Key Laboratory of Biomedical Polymers of Ministry of Education, College of Chemistry and Molecular Sciences, Hubei Province Key Laboratory of Allergy and Immunology, Wuhan University, Wuhan 430072, Hubei, China
| | - Wei Shen
- Key Laboratory of Biomedical Polymers of Ministry of Education, College of Chemistry and Molecular Sciences, Hubei Province Key Laboratory of Allergy and Immunology, Wuhan University, Wuhan 430072, Hubei, China
| | - Xingyu Liu
- Key Laboratory of Biomedical Polymers of Ministry of Education, College of Chemistry and Molecular Sciences, Hubei Province Key Laboratory of Allergy and Immunology, Wuhan University, Wuhan 430072, Hubei, China
| | - Qianqian Qi
- Key Laboratory of Biomedical Polymers of Ministry of Education, College of Chemistry and Molecular Sciences, Hubei Province Key Laboratory of Allergy and Immunology, Wuhan University, Wuhan 430072, Hubei, China
| | - Yuanyuan Zhang
- Key Laboratory of Biomedical Polymers of Ministry of Education, College of Chemistry and Molecular Sciences, Hubei Province Key Laboratory of Allergy and Immunology, Wuhan University, Wuhan 430072, Hubei, China
| | - Ruochen Fan
- Key Laboratory of Biomedical Polymers of Ministry of Education, College of Chemistry and Molecular Sciences, Hubei Province Key Laboratory of Allergy and Immunology, Wuhan University, Wuhan 430072, Hubei, China
| | - Fang Fu
- Key Laboratory of Biomedical Polymers of Ministry of Education, College of Chemistry and Molecular Sciences, Hubei Province Key Laboratory of Allergy and Immunology, Wuhan University, Wuhan 430072, Hubei, China
| | - Heng Xue
- Wuhan Institute of Virology; Hubei Jiangxia Laboratory; Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan 430200, Hubei, China
| | - Hang Yang
- Wuhan Institute of Virology; Hubei Jiangxia Laboratory; Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan 430200, Hubei, China
| | - Xiulian Sun
- Wuhan Institute of Virology; Hubei Jiangxia Laboratory; Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan 430200, Hubei, China
| | - Yunjia Ning
- Wuhan Institute of Virology; Hubei Jiangxia Laboratory; Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan 430200, Hubei, China
| | - Tian Tian
- Key Laboratory of Biomedical Polymers of Ministry of Education, College of Chemistry and Molecular Sciences, Hubei Province Key Laboratory of Allergy and Immunology, Wuhan University, Wuhan 430072, Hubei, China
| | - Xiang Zhou
- Key Laboratory of Biomedical Polymers of Ministry of Education, College of Chemistry and Molecular Sciences, Hubei Province Key Laboratory of Allergy and Immunology, Wuhan University, Wuhan 430072, Hubei, China
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17
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Li Y, Xu Z, Li Y, Jiang T, Meng F, Fu J, Huang L, Wang F, Wang X, Wang F. Preclinical and phase I studies of an antisense oligonucleotide drug targeting IGF-1R in liver cancer. Future Oncol 2024:1-14. [PMID: 38573183 DOI: 10.2217/fon-2023-0872] [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: 10/12/2023] [Accepted: 02/14/2024] [Indexed: 04/05/2024] Open
Abstract
Aim: To evaluate a novel antisense oligonucleotide drug targeting human IGF-1R in preclinical and phase I studies of liver cancer. Materials & methods: The tolerability and safety of an investigational new drug were evaluated in a dose-escalation trial involving 17 patients with advanced liver cancer after preclinical assessment of pharmacokinetics and pharmacodynamics. Results: The drug exposure levels in the phase I trial were determined by the in vivo efficacy with pharmacokinetics evaluation in rats and rhesus monkeys. This clinical study showed that the maximum tolerated dose was 3.96 mg/kg, and the dose-limiting toxicity dose was 4.4 mg/kg. Conclusion: The drug was safe and tolerable in patients with advanced liver cancer.Clinical Trial Registration: ChiCTR2100044235 (www.chictr.org.cn).
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Affiliation(s)
- Yonggang Li
- Senior Department of Infectious Diseases, The Fifth Medical Center of Chinese PLA General Hospital, Beijing, 100039, China
| | - Zhe Xu
- Senior Department of Infectious Diseases, The Fifth Medical Center of Chinese PLA General Hospital, Beijing, 100039, China
| | - Yuanyuan Li
- Senior Department of Infectious Diseases, The Fifth Medical Center of Chinese PLA General Hospital, Beijing, 100039, China
| | - Tianjun Jiang
- Senior Department of Infectious Diseases, The Fifth Medical Center of Chinese PLA General Hospital, Beijing, 100039, China
| | - Fanping Meng
- Senior Department of Infectious Diseases, The Fifth Medical Center of Chinese PLA General Hospital, Beijing, 100039, China
| | - Junliang Fu
- Senior Department of Infectious Diseases, The Fifth Medical Center of Chinese PLA General Hospital, Beijing, 100039, China
| | - Lei Huang
- Senior Department of Infectious Diseases, The Fifth Medical Center of Chinese PLA General Hospital, Beijing, 100039, China
| | - Fengchao Wang
- Youcare Pharmaceutical Group Co Ltd, Beijing, 100176, China
| | - Xia Wang
- Youcare Pharmaceutical Group Co Ltd, Beijing, 100176, China
| | - Fusheng Wang
- Senior Department of Infectious Diseases, The Fifth Medical Center of Chinese PLA General Hospital, Beijing, 100039, China
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18
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Chen S, Navickas A, Goodarzi H. Translational adaptation in breast cancer metastasis and emerging therapeutic opportunities. Trends Pharmacol Sci 2024; 45:304-318. [PMID: 38453522 DOI: 10.1016/j.tips.2024.02.002] [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: 01/11/2024] [Revised: 02/07/2024] [Accepted: 02/13/2024] [Indexed: 03/09/2024]
Abstract
Breast cancer's tendency to metastasize poses a critical barrier to effective treatment, making it a leading cause of mortality among women worldwide. A growing body of evidence is showing that translational adaptation is emerging as a key mechanism enabling cancer cells to thrive in the dynamic tumor microenvironment (TME). Here, we systematically summarize how breast cancer cells utilize translational adaptation to drive metastasis, highlighting the intricate regulation by specific translation machinery and mRNA attributes such as sequences and structures, along with the involvement of tRNAs and other trans-acting RNAs. We provide an overview of the latest findings and emerging concepts in this area, discussing their potential implications for therapeutic strategies in breast cancer.
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Affiliation(s)
- Siyu Chen
- Department of Biochemistry and Biophysics, University of California, San Francisco, CA, USA; Department of Urology, University of California, San Francisco, CA, USA; Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, CA, USA; Bakar Computational Health Sciences Institute, University of California, San Francisco, CA, USA
| | - Albertas Navickas
- Institut Curie, PSL Research University, CNRS UMR3348, INSERM U1278, Orsay, France; Université Paris-Saclay, CNRS UMR3348, INSERM U1278, Orsay, France.
| | - Hani Goodarzi
- Department of Biochemistry and Biophysics, University of California, San Francisco, CA, USA; Department of Urology, University of California, San Francisco, CA, USA; Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, CA, USA; Bakar Computational Health Sciences Institute, University of California, San Francisco, CA, USA.
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19
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Zhang K, Shi Y, Jin Z, He J. Advances in tumor vascular growth inhibition. Clin Transl Oncol 2024:10.1007/s12094-024-03432-5. [PMID: 38504070 DOI: 10.1007/s12094-024-03432-5] [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: 01/04/2024] [Accepted: 03/01/2024] [Indexed: 03/21/2024]
Abstract
Tumor growth and metastasis require neovascularization, which is dependent on a complex array of factors, such as the production of various pro-angiogenic factors by tumor cells, intercellular signaling, and stromal remodeling. The hypoxic, acidic tumor microenvironment is not only conducive to tumor cell proliferation, but also disrupts the equilibrium of angiogenic factors, leading to vascular heterogeneity, which further promotes tumor development and metastasis. Anti-angiogenic strategies to inhibit tumor angiogenesis has, therefore, become an important focus for anti-tumor therapy. The traditional approach involves the use of anti-angiogenic drugs to inhibit tumor neovascularization by targeting upstream and downstream angiogenesis-related pathways or pro-angiogenic factors, thereby inhibiting tumor growth and metastasis. This review explores the mechanisms involved in tumor angiogenesis and summarizes currently used anti-angiogenic drugs, including monoclonal antibody, and small-molecule inhibitors, as well as the progress and challenges associated with their use in anti-tumor therapy. It also outlines the opportunities and challenges of treating tumors using more advanced anti-angiogenic strategies, such as immunotherapy and nanomaterials.
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Affiliation(s)
- Keyong Zhang
- State Key Laboratory of Targeting Oncology, National Center for International Research of Bio-Targeting Theranostics, Guangxi Key Laboratory of Bio-Targeting Theranostics, Collaborative Innovation Center for Targeting Tumor Diagnosis and Therapy, Guangxi Medical University, Nanning, 530021, Guangxi, China
| | - Yuanyuan Shi
- State Key Laboratory of Targeting Oncology, National Center for International Research of Bio-Targeting Theranostics, Guangxi Key Laboratory of Bio-Targeting Theranostics, Collaborative Innovation Center for Targeting Tumor Diagnosis and Therapy, Guangxi Medical University, Nanning, 530021, Guangxi, China
| | - Ze Jin
- State Key Laboratory of Targeting Oncology, National Center for International Research of Bio-Targeting Theranostics, Guangxi Key Laboratory of Bio-Targeting Theranostics, Collaborative Innovation Center for Targeting Tumor Diagnosis and Therapy, Guangxi Medical University, Nanning, 530021, Guangxi, China
| | - Jian He
- State Key Laboratory of Targeting Oncology, National Center for International Research of Bio-Targeting Theranostics, Guangxi Key Laboratory of Bio-Targeting Theranostics, Collaborative Innovation Center for Targeting Tumor Diagnosis and Therapy, Guangxi Medical University, Nanning, 530021, Guangxi, China.
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20
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Smith PR, Campbell ZT. RNA-binding proteins in pain. WILEY INTERDISCIPLINARY REVIEWS. RNA 2024; 15:e1843. [PMID: 38576117 PMCID: PMC11003723 DOI: 10.1002/wrna.1843] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/01/2024] [Revised: 03/13/2024] [Accepted: 03/14/2024] [Indexed: 04/06/2024]
Abstract
RNAs are meticulously controlled by proteins. Through direct and indirect associations, every facet in the brief life of an mRNA is subject to regulation. RNA-binding proteins (RBPs) permeate biology. Here, we focus on their roles in pain. Chronic pain is among the largest challenges facing medicine and requires new strategies. Mounting pharmacologic and genetic evidence obtained in pre-clinical models suggests fundamental roles for a broad array of RBPs. We describe their diverse roles that span RNA modification, splicing, stability, translation, and decay. Finally, we highlight opportunities to expand our understanding of regulatory interactions that contribute to pain signaling. This article is categorized under: RNA Interactions with Proteins and Other Molecules > Protein-RNA Interactions: Functional Implications Translation > Regulation RNA in Disease and Development > RNA in Disease.
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Affiliation(s)
- Patrick R. Smith
- Department of Anaesthesiology, University of Wisconsin-Madison, Madison, WI, USA 53792
| | - Zachary T. Campbell
- Department of Anaesthesiology, University of Wisconsin-Madison, Madison, WI, USA 53792
- Department of Biomolecular Chemistry, University of Wisconsin-Madison, Madison, WI, USA 53792
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21
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Zhang S, Liang Y, Ji P, Zheng R, Lu F, Hou G, Yang G, Yuan L. Truncated PD1 Engineered Gas-Producing Extracellular Vesicles for Ultrasound Imaging and Subsequent Degradation of PDL1 in Tumor Cells. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024; 11:e2305891. [PMID: 38263860 DOI: 10.1002/advs.202305891] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/21/2023] [Revised: 01/05/2024] [Indexed: 01/25/2024]
Abstract
PDL1 blockade therapy holds great promise in cancer immunotherapy. Ultrasound imaging of PDL1 expression in the tumor is of great importance in predicting the therapeutic efficacy. As a proof-of-concept study, a novel ultrasound contrast agent has been innovated here to image and block PDL1 in the tumor tissue. Briefly, extracellular vesicles (EVs) are engineered to display truncated PD1 (tPD1) on the surface to bind PDL1 with high affinity by fusion to EV-abundant transmembrane protein PTGFRN. The engineered EVs are then encapsulated with Ca(HCO3)2 via electroporation and designated as Gp-EVtPD1, which would recognize PDL1 highly expressed cells and produce gas in the endosomes and lysosomes. On the one hand, the echogenic signal intensity correlates well with the PDL1 expression and immune response inhibition in the tumor. On the other hand, during the trajectory of Gp-EVtPD1 in the recipient cells, tPD1 on the EV binds PDL1 and triggers the PDL1 endocytosis and degradation in endosomes/lysosomes in a sequential manner, and thus boosts the anti-tumor immunity of cytotoxic T cells. In summary, Gp-EVtPD1 serves as a novel ultrasound contrast agent and blocker of PDL1, which might be of great advantage in imaging PDL1 expression and conquering immune checkpoint blocker resistance.
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Affiliation(s)
- Siyan Zhang
- Department of Ultrasound Diagnostics, Tangdu Hospital, Fourth Military Medical University, Xinsi Road No. 569th, Xi'an, 710038, P. R. China
| | - Yuan Liang
- Department of Ultrasound Diagnostics, Tangdu Hospital, Fourth Military Medical University, Xinsi Road No. 569th, Xi'an, 710038, P. R. China
| | - Panpan Ji
- Department of Digestive Surgery, Xijing Hospital, Fourth Military Medical University, Shaanxi, 710032, P. R. China
| | - Rui Zheng
- State Key Laboratory of Holistic Integrative Management of Gastrointestinal Cancers and Department of Biochemistry and Molecular Biology, Fourth Military Medical University, Changlexi Road No. 169th, Xi'an, 710032, P. R. China
| | - Fan Lu
- State Key Laboratory of Holistic Integrative Management of Gastrointestinal Cancers and Department of Biochemistry and Molecular Biology, Fourth Military Medical University, Changlexi Road No. 169th, Xi'an, 710032, P. R. China
| | - Guangdong Hou
- Department of Urology, Xijing Hospital, Fourth Military Medical University, Xi'an, 710032, P. R. China
| | - Guodong Yang
- State Key Laboratory of Holistic Integrative Management of Gastrointestinal Cancers and Department of Biochemistry and Molecular Biology, Fourth Military Medical University, Changlexi Road No. 169th, Xi'an, 710032, P. R. China
| | - Lijun Yuan
- Department of Ultrasound Diagnostics, Tangdu Hospital, Fourth Military Medical University, Xinsi Road No. 569th, Xi'an, 710038, P. R. China
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22
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Wang M, Yan M, Tan L, Zhao X, Liu G, Zhang Z, Zhang J, Gao H, Qin W. Non-coding RNAs: targets for Chinese herbal medicine in treating myocardial fibrosis. Front Pharmacol 2024; 15:1337623. [PMID: 38476331 PMCID: PMC10928947 DOI: 10.3389/fphar.2024.1337623] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2023] [Accepted: 02/07/2024] [Indexed: 03/14/2024] Open
Abstract
Cardiovascular diseases have become the leading cause of death in urban and rural areas. Myocardial fibrosis is a common pathological manifestation at the adaptive and repair stage of cardiovascular diseases, easily predisposing to cardiac death. Non-coding RNAs (ncRNAs), RNA molecules with no coding potential, can regulate gene expression in the occurrence and development of myocardial fibrosis. Recent studies have suggested that Chinese herbal medicine can relieve myocardial fibrosis through targeting various ncRNAs, mainly including microRNAs (miRNAs), long non-coding RNAs (lncRNAs), and circular RNAs (circRNAs). Thus, ncRNAs are novel drug targets for Chinese herbal medicine. Herein, we summarized the current understanding of ncRNAs in the pathogenesis of myocardial fibrosis, and highlighted the contribution of ncRNAs to the therapeutic effect of Chinese herbal medicine on myocardial fibrosis. Further, we discussed the future directions regarding the potential applications of ncRNA-based drug screening platform to screen drugs for myocardial fibrosis.
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Affiliation(s)
- Minghui Wang
- School of Pharmacy, Shandong University of Traditional Chinese Medicine, Jinan, Shandong, China
- School of Pharmacy, Jining Medical University, Rizhao, Shandong, China
| | - Maocai Yan
- School of Pharmacy, Jining Medical University, Rizhao, Shandong, China
| | - Liqiang Tan
- Department of Nasopharyngeal Carcinoma, Sun Yat-Sen University Cancer Center, Guangzhou, Guangdong, China
| | - Xiaona Zhao
- School of Pharmacy, Jining Medical University, Rizhao, Shandong, China
- School of Pharmacy, Weifang Medical University, Weifang, Shandong, China
| | - Guoqing Liu
- School of Pharmacy, Shandong University of Traditional Chinese Medicine, Jinan, Shandong, China
- School of Pharmacy, Jining Medical University, Rizhao, Shandong, China
| | - Zejin Zhang
- School of Pharmacy, Jining Medical University, Rizhao, Shandong, China
- School of Pharmacy, Binzhou Medical University, Yantai, Shandong, China
| | - Jing Zhang
- School of Pharmacy, Jining Medical University, Rizhao, Shandong, China
| | - Honggang Gao
- School of Pharmacy, Jining Medical University, Rizhao, Shandong, China
| | - Wei Qin
- School of Pharmacy, Jining Medical University, Rizhao, Shandong, China
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23
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Dzau VJ, Hodgkinson CP. RNA Therapeutics for the Cardiovascular System. Circulation 2024; 149:707-716. [PMID: 38408142 DOI: 10.1161/circulationaha.123.067373] [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] [Indexed: 02/28/2024]
Abstract
RNA therapeutics hold significant promise in the treatment of cardiovascular diseases. RNAs are biologically diverse and functionally specific and can be used for gain- or loss-of-function purposes. The effectiveness of mRNA-based vaccines in the recent COVID-19 pandemic has undoubtedly proven the benefits of an RNA-based approach. RNA-based therapies are becoming more common as a treatment modality for cardiovascular disease. This is most evident in hypertension where several small interfering RNA-based drugs have proven to be effective in managing high blood pressure in several clinical trials. As befits a rapidly burgeoning field, there is significant interest in other classes of RNA. Revascularization of the infarcted heart through an mRNA drug is under clinical investigation. mRNA technology may provide the platform for the expression of paracrine factors for myocardial protection and regeneration. Emergent technologies on the basis of microRNAs and gene editing are tackling complex diseases in a novel fashion. RNA-based gene editing offers hope of permanent cures for monogenic cardiovascular diseases, and long-term control of complex diseases such as essential hypertension, as well. Likewise, microRNAs are proving effective in regenerating cardiac muscle. The aim of this review is to provide an overview of the current landscape of RNA-based therapies for the treatment of cardiovascular disease. The review describes the large number of RNA molecules that exist with a discussion of the clinical development of each RNA type. In addition, the review also presents a number of avenues for future development.
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Affiliation(s)
- Victor J Dzau
- Mandel Center for Hypertension and Atherosclerosis, and the Duke Cardiovascular Research Center, Duke University Medical Center, Durham, NC (V.J.D., C.P.H.)
- National Academy of Medicine, Washington, DC (V.J.D.)
| | - Conrad P Hodgkinson
- Mandel Center for Hypertension and Atherosclerosis, and the Duke Cardiovascular Research Center, Duke University Medical Center, Durham, NC (V.J.D., C.P.H.)
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24
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Kamath D, Iwakuma T, Bossmann SH. Therapeutic potential of combating cancer by restoring wild-type p53 through mRNA nanodelivery. NANOMEDICINE : NANOTECHNOLOGY, BIOLOGY, AND MEDICINE 2024; 56:102732. [PMID: 38199451 PMCID: PMC11108594 DOI: 10.1016/j.nano.2024.102732] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/28/2023] [Revised: 12/27/2023] [Accepted: 01/02/2024] [Indexed: 01/12/2024]
Abstract
Among the tumor suppressor genes, TP53 is the most frequently mutated in human cancers, and most mutations are missense mutations causing production of mutant p53 (mutp53) proteins. TP53 mutations not only results in loss of function (LOH) as a transcription factor and a tumor suppressor, but also gain wild-type p53 (WTp53)-independent oncogenic functions that enhance cancer metastasis and progression (Yamamoto and Iwakuma, 2018; Zhang et al., 2022). TP53 has extensively been studied as a therapeutic target as well as for drug development and therapies, however with limited success. Achieving targeted therapies for restoration of WTp53 function and depletion or repair of mutant p53 (mutp53) will have far reaching implication in cancer treatment and therapies. This review briefly discusses the role of p53 mutation in cancer and the therapeutic potential of restoring WTp53 through the advances in mRNA nanomedicine.
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Affiliation(s)
- Divya Kamath
- The University of Kansas Medical Center, Department of Cancer Biology, 3901 Rainbow Blvd, mailstop 1071, 66160 Kansas City, KS, USA.
| | - Tomoo Iwakuma
- Children's Mercy Hospital, Adele Hall Campus, 2401 Gillham Rd, Kansas City, MO 64108, USA.
| | - Stefan H Bossmann
- The University of Kansas Medical Center, Department of Cancer Biology, 3901 Rainbow Blvd, mailstop 1071, 66160 Kansas City, KS, USA.
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25
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Loyer G, Reinharz V. Concurrent prediction of RNA secondary structures with pseudoknots and local 3D motifs in an integer programming framework. Bioinformatics 2024; 40:btae022. [PMID: 38230755 PMCID: PMC10868335 DOI: 10.1093/bioinformatics/btae022] [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: 07/18/2023] [Revised: 11/30/2023] [Accepted: 01/12/2024] [Indexed: 01/18/2024] Open
Abstract
MOTIVATION The prediction of RNA structure canonical base pairs from a single sequence, especially pseudoknotted ones, remains challenging in a thermodynamic models that approximates the energy of the local 3D motifs joining canonical stems. It has become more and more apparent in recent years that the structural motifs in the loops, composed of noncanonical interactions, are essential for the final shape of the molecule enabling its multiple functions. Our capacity to predict accurate 3D structures is also limited when it comes to the organization of the large intricate network of interactions that form inside those loops. RESULTS We previously developed the integer programming framework RNA Motifs over Integer Programming (RNAMoIP) to reconcile RNA secondary structure and local 3D motif information available in databases. We further develop our model to now simultaneously predict the canonical base pairs (with pseudoknots) from base pair probability matrices with or without alignment. We benchmarked our new method over the all nonredundant RNAs below 150 nucleotides. We show that the joined prediction of canonical base pairs structure and local conserved motifs (i) improves the ratio of well-predicted interactions in the secondary structure, (ii) predicts well canonical and Wobble pairs at the location where motifs are inserted, (iii) is greatly improved with evolutionary information, and (iv) noncanonical motifs at kink-turn locations. AVAILABILITY AND IMPLEMENTATION The source code of the framework is available at https://gitlab.info.uqam.ca/cbe/RNAMoIP and an interactive web server at https://rnamoip.cbe.uqam.ca/.
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Affiliation(s)
- Gabriel Loyer
- Department of Computer Science, Université du Québec à Montréal, Montréal, QC H2X 3Y7, Canada
| | - Vladimir Reinharz
- Department of Computer Science, Université du Québec à Montréal, Montréal, QC H2X 3Y7, Canada
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Goleij P, Babamohamadi M, Rezaee A, Sanaye PM, Tabari MAK, Sadreddini S, Arefnezhad R, Motedayyen H. Types of RNA therapeutics. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2024; 203:41-63. [PMID: 38360005 DOI: 10.1016/bs.pmbts.2023.12.022] [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: 02/17/2024]
Abstract
RNA therapy is one of the new treatments using small RNA molecules to target and regulate gene expression. It involves the application of synthetic or modified RNA molecules to inhibit the expression of disease-causing genes specifically. In other words, it silences genes and suppresses the transcription process. The main theory behind RNA therapy is that RNA molecules can prevent the translation into proteins by binding to specific messenger RNA (mRNA) molecules. By targeting disease-related mRNA molecules, RNA therapy can effectively silence or reduce the development of harmful proteins. There are different types of RNA molecules used in therapy, including small interfering RNAs (siRNAs), microRNAs (miRNAs), aptamer, ribozyme, and antisense oligonucleotides (ASOs). These molecules are designed to complement specific mRNA sequences, allowing them to bind and degrade the targeted mRNA or prevent its translation into protein. Nanotechnology is also highlighted to increase the efficacy of RNA-based drugs. In this chapter, while examining various methods of RNA therapy, we discuss the advantages and challenges of each.
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Affiliation(s)
- Pouya Goleij
- Department of Genetics, Sana Institute of Higher Education, Sari, Iran; USERN Office, Kermanshah University of Medical Sciences, Kermanshah, Iran
| | - Mehregan Babamohamadi
- USERN Office, Kermanshah University of Medical Sciences, Kermanshah, Iran; Department of Biology, School of Natural Sciences, University of Tabriz, Tabriz, Iran; Stem Cell and Regenerative Medicine Innovation Center, Tehran University of Medical Sciences, Tehran, Iran
| | - Aryan Rezaee
- Student Research Committee, School of Medicine, Iran University of Medical Sciences, Tehran, Iran
| | | | - Mohammad Amin Khazeei Tabari
- Student Research Committee, Mazandaran University of Medical Sciences, Sari, Iran; USERN Office, Mazandaran University of Medical Sciences, Sari, Iran
| | - Sarvin Sadreddini
- Student Research Committee, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Reza Arefnezhad
- Coenzyme R Research Institute, Tehran, Iran; Student Research Committee, Shiraz University of Medical Sciences, Shiraz, Iran.
| | - Hossein Motedayyen
- Autoimmune Diseases Research Center, Kashan University of Medical Sciences, Kashan, Iran.
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27
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Thi HV, Thi LAN, Tang TL, Chu DT. Biosafety and regulatory issues of RNA therapeutics. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2024; 204:311-329. [PMID: 38458742 DOI: 10.1016/bs.pmbts.2023.12.008] [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: 03/10/2024]
Abstract
RNA therapy has recently emerged as a therapy targeting specific genes or proteins. With its outstanding advantages, this therapy has opened promising doors for treating and preventing diseases. The great application potential has driven the need for a comprehensive understanding of these therapies, particularly on biosafety and regulatory issues. This chapter began by discussing the risks to RNA therapy, such as off-target effects, immunogenicity and immune responses, and long-term effects. Since then, this therapy's intricate landscape of biosafety issues has been elucidated. Common biosecurity measures applied around the world have also been reviewed. In addition, this chapter emphasized the importance of regulations and laws in applying RNA therapy to prevent and treat human and animal diseases. At the same time, the current legal regulations in the world for RNA therapies have also been thoroughly discussed. To sum up, this chapter has provided a comprehensive perspective on biosafety and regulatory issues for developing RNA therapies. Understanding the biosafety and regulatory issues in RNA therapy can help researchers use this promising new technology safely and effectively in the future.
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Affiliation(s)
- Hue Vu Thi
- Center for Biomedicine and Community Health, International School, Vietnam National University, Hanoi, Vietnam; Faculty of Applied Sciences, International School, Vietnam National University, Hanoi, Vietnam
| | - Lan-Anh Nguyen Thi
- Center for Biomedicine and Community Health, International School, Vietnam National University, Hanoi, Vietnam
| | - Thuy Linh Tang
- Center for Biomedicine and Community Health, International School, Vietnam National University, Hanoi, Vietnam
| | - Dinh-Toi Chu
- Center for Biomedicine and Community Health, International School, Vietnam National University, Hanoi, Vietnam; Faculty of Applied Sciences, International School, Vietnam National University, Hanoi, Vietnam.
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28
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Bekker GJ, Fukunishi Y, Higo J, Kamiya N. Binding Mechanism of Riboswitch to Natural Ligand Elucidated by McMD-Based Dynamic Docking Simulations. ACS OMEGA 2024; 9:3412-3422. [PMID: 38284074 PMCID: PMC10809319 DOI: 10.1021/acsomega.3c06826] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/08/2023] [Revised: 12/16/2023] [Accepted: 12/28/2023] [Indexed: 01/30/2024]
Abstract
Flavin mononucleotide riboswitches are common among many pathogenic bacteria and are therefore considered to be an attractive target for antibiotics development. The riboswitch binds riboflavin (RBF, also known as vitamin B2), and although an experimental structure of their complex has been solved with the ligand bound deep inside the RNA molecule in a seemingly unreachable state, the binding mechanism between these molecules is not yet known. We have therefore used our Multicanonical Molecular Dynamics (McMD)-based dynamic docking protocol to analyze their binding mechanism by simulating the binding process between the riboswitch aptamer domain and the RBF, starting from the apo state of the riboswitch. Here, the refinement stage was crucial to identify the native binding configuration, as several other binding configurations were also found by McMD-based docking simulations. RBF initially binds the interface between P4 and P6 including U61 and G62, which forms a gateway where the ligand lingers until this gateway opens sufficiently to allow the ligand to pass through and slip into the hidden binding site including A48, A49, and A85.
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Affiliation(s)
- Gert-Jan Bekker
- Institute
for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Yoshifumi Fukunishi
- Cellular
and Molecular Biotechnology Research Institute, National Institute of Advanced Industrial Science and Technology
(AIST), 2-3-26, Aomi, Koto-ku, Tokyo 135-0064, Japan
| | - Junichi Higo
- Graduate
School of Information Science, University
of Hyogo, 7-1-28 minatojima
Minami-machi, Chuo-ku, Kobe, Hyogo 650-0047, Japan
| | - Narutoshi Kamiya
- Graduate
School of Information Science, University
of Hyogo, 7-1-28 minatojima
Minami-machi, Chuo-ku, Kobe, Hyogo 650-0047, Japan
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29
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Krishnan SR, Roy A, Gromiha MM. Reliable method for predicting the binding affinity of RNA-small molecule interactions using machine learning. Brief Bioinform 2024; 25:bbae002. [PMID: 38261341 PMCID: PMC10805179 DOI: 10.1093/bib/bbae002] [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: 05/24/2023] [Revised: 12/21/2023] [Accepted: 12/24/2023] [Indexed: 01/24/2024] Open
Abstract
Ribonucleic acids (RNAs) play important roles in cellular regulation. Consequently, dysregulation of both coding and non-coding RNAs has been implicated in several disease conditions in the human body. In this regard, a growing interest has been observed to probe into the potential of RNAs to act as drug targets in disease conditions. To accelerate this search for disease-associated novel RNA targets and their small molecular inhibitors, machine learning models for binding affinity prediction were developed specific to six RNA subtypes namely, aptamers, miRNAs, repeats, ribosomal RNAs, riboswitches and viral RNAs. We found that differences in RNA sequence composition, flexibility and polar nature of RNA-binding ligands are important for predicting the binding affinity. Our method showed an average Pearson correlation (r) of 0.83 and a mean absolute error of 0.66 upon evaluation using the jack-knife test, indicating their reliability despite the low amount of data available for several RNA subtypes. Further, the models were validated with external blind test datasets, which outperform other existing quantitative structure-activity relationship (QSAR) models. We have developed a web server to host the models, RNA-Small molecule binding Affinity Predictor, which is freely available at: https://web.iitm.ac.in/bioinfo2/RSAPred/.
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Affiliation(s)
- Sowmya R Krishnan
- Department of Biotechnology, Bhupat and Jyoti Mehta School of Biosciences, Indian Institute of Technology Madras, Chennai 600036, India
- TCS Research (Life Sciences division), Tata Consultancy Services, Hyderabad 500081, India
| | - Arijit Roy
- TCS Research (Life Sciences division), Tata Consultancy Services, Hyderabad 500081, India
| | - M Michael Gromiha
- Department of Biotechnology, Bhupat and Jyoti Mehta School of Biosciences, Indian Institute of Technology Madras, Chennai 600036, India
- International Research Frontiers Initiative, School of Computing, Tokyo Institute of Technology, Yokohama 226-8501, Japan
- Department of Computer Science, National University of Singapore, Singapore 117543
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30
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Chen Y, Wu M. Aitongping patch could alleviate cancer pain via suppressing microglia activation and modulating the miR-150-5p/CXCL12 signaling. Postgrad Med J 2024; 100:96-105. [PMID: 37978049 DOI: 10.1093/postmj/qgad102] [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: 08/07/2023] [Revised: 09/06/2023] [Accepted: 09/21/2023] [Indexed: 11/19/2023]
Abstract
PURPOSE We aimed to investigate the pharmacological effects and mechanisms of the Aitongping formula for treating cancer pain. METHODS We enrolled 60 cancer patients with Numeric Rating Scale above 4 and grouped them randomly as a Control group (N = 30) and a Patch group (N = 30). We also established bone cancer mice models via tumor implantation. And the animal groups were established as a Sham group, a tumor cell implantation (TCI) group, a TCI + Patch group, and a Patch group. RESULTS After the validation of successful tumor implantation, we identified candidate miRNAs and genes that were dysregulated in TCI mice and compared their expressions between different mice groups. We also observed the effect of Aitongping patch in vitro in mice primary microglia. The time to disease progression and cancer stability were prolonged by Aitongping patch in cancer patients. And the daily morphine dose was lower, and patients' quality of life was improved in the Patch group. Moreover, Aitongping patch alleviated cancer pain and inhibited microglia activation after the successful implantation of bone tumor in TCI mice. We also observed the dysregulation of miR-150-5p and chemokine CXC motif ligand 12 (CXCL12) mRNA in TCI mice. And CXCL12 was found to be targeted by miR-150-5p. Aitongping patch was found to upregulate miR-150-5p and downregulate CXCL12 in vivo and in vitro. CONCLUSION Aitongping patch could alleviate cancer pain via suppressing microglia activation, and the downregulation of miR-150-5p, as well as the upregulation of CXCL12 mRNA and protein, induced by tumor implantation or lipopolysaccharide stimulation, was restored by Aitongping treatment.
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Affiliation(s)
- Yunlong Chen
- Department of Oncology, Rudong County Hospital of Traditional Chinese Medicine, Rudong, Jiangsu 226400, China
| | - Mianhua Wu
- The First Clinical Medical College, Nanjing University of Chinese Medicine, Nanjing, Jiangsu 210046, China
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31
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Bravo-Vázquez LA, Paul S, Colín-Jurado MG, Márquez-Gallardo LD, Castañón-Cortés LG, Banerjee A, Pathak S, Duttaroy AK. Exploring the Therapeutic Significance of microRNAs and lncRNAs in Kidney Diseases. Genes (Basel) 2024; 15:123. [PMID: 38275604 PMCID: PMC10815231 DOI: 10.3390/genes15010123] [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: 12/26/2023] [Revised: 01/14/2024] [Accepted: 01/17/2024] [Indexed: 01/27/2024] Open
Abstract
MicroRNAs (miRNAs) and long non-coding RNAs (lncRNAs) are two crucial classes of transcripts that belong to the major group of non-coding RNAs (ncRNAs). These RNA molecules have significant influence over diverse molecular processes due to their crucial role as regulators of gene expression. However, the dysregulated expression of these ncRNAs constitutes a fundamental factor in the etiology and progression of a wide variety of multifaceted human diseases, including kidney diseases. In this context, over the past years, compelling evidence has shown that miRNAs and lncRNAs could be prospective targets for the development of next-generation drugs against kidney diseases as they participate in a number of disease-associated processes, such as podocyte and nephron death, renal fibrosis, inflammation, transition from acute kidney injury to chronic kidney disease, renal vascular changes, sepsis, pyroptosis, and apoptosis. Hence, in this current review, we critically analyze the recent findings concerning the therapeutic inferences of miRNAs and lncRNAs in the pathophysiological context of kidney diseases. Additionally, with the aim of driving advances in the formulation of ncRNA-based drugs tailored for the management of kidney diseases, we discuss some of the key challenges and future prospects that should be addressed in forthcoming investigations.
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Affiliation(s)
- Luis Alberto Bravo-Vázquez
- School of Engineering and Sciences, Tecnologico de Monterrey, Campus Queretaro, Av. Epigmenio Gonzalez, No. 500 Fracc. San Pablo, Queretaro 76130, Mexico (S.P.)
| | - Sujay Paul
- School of Engineering and Sciences, Tecnologico de Monterrey, Campus Queretaro, Av. Epigmenio Gonzalez, No. 500 Fracc. San Pablo, Queretaro 76130, Mexico (S.P.)
| | - Miriam Guadalupe Colín-Jurado
- School of Engineering and Sciences, Tecnologico de Monterrey, Campus Queretaro, Av. Epigmenio Gonzalez, No. 500 Fracc. San Pablo, Queretaro 76130, Mexico (S.P.)
| | - Luis David Márquez-Gallardo
- School of Engineering and Sciences, Tecnologico de Monterrey, Campus Queretaro, Av. Epigmenio Gonzalez, No. 500 Fracc. San Pablo, Queretaro 76130, Mexico (S.P.)
| | - Luis Germán Castañón-Cortés
- School of Engineering and Sciences, Tecnologico de Monterrey, Campus Queretaro, Av. Epigmenio Gonzalez, No. 500 Fracc. San Pablo, Queretaro 76130, Mexico (S.P.)
| | - Antara Banerjee
- Chettinad Academy of Research and Education (CARE), Chettinad Hospital and Research Institute (CHRI), Department of Medical Biotechnology, Faculty of Allied Health Sciences, Chennai 603103, India
| | - Surajit Pathak
- Chettinad Academy of Research and Education (CARE), Chettinad Hospital and Research Institute (CHRI), Department of Medical Biotechnology, Faculty of Allied Health Sciences, Chennai 603103, India
| | - Asim K. Duttaroy
- Department of Nutrition, Institute of Basic Medical Sciences, Faculty of Medicine, University of Oslo, N-0316 Oslo, Norway
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32
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Martinsen E, Jinnurine T, Subramani S, Rogne M. Advances in RNA therapeutics for modulation of 'undruggable' targets. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2024; 204:249-294. [PMID: 38458740 DOI: 10.1016/bs.pmbts.2023.12.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/10/2024]
Abstract
Over the past decades, drug discovery utilizing small pharmacological compounds, fragment-based therapeutics, and antibody therapy have significantly advanced treatment options for many human diseases. However, a major bottleneck has been that>70% of human proteins/genomic regions are 'undruggable' by the above-mentioned approaches. Many of these proteins constitute essential drug targets against complex multifactorial diseases like cancer, immunological disorders, and neurological diseases. Therefore, alternative approaches are required to target these proteins or genomic regions in human cells. RNA therapeutics is a promising approach for many of the traditionally 'undruggable' targets by utilizing methods such as antisense oligonucleotides, RNA interference, CRISPR/Cas-based genome editing, aptamers, and the development of mRNA therapeutics. In the following chapter, we will put emphasis on recent advancements utilizing these approaches against challenging drug targets, such as intranuclear proteins, intrinsically disordered proteins, untranslated genomic regions, and targets expressed in inaccessible tissues.
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Affiliation(s)
| | | | - Saranya Subramani
- Pioneer Research AS, Oslo Science Park, Oslo, Norway; Department of Pharmacy, Section for Pharmacology and Pharmaceutical Biosciences, University of Oslo, Oslo, Norway
| | - Marie Rogne
- Pioneer Research AS, Oslo Science Park, Oslo, Norway; Department of Molecular Medicine, Institute of Basic Medical Sciences, Faculty of Medicine, University of Oslo, Oslo, Norway.
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33
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Tidwell ED, Kilde IR, Leskaj S, Koutmos M. Fluorescent Ligand Equilibrium Displacement: A High-Throughput Method for Identification of FMN Riboswitch-Binding Small Molecules. Int J Mol Sci 2024; 25:735. [PMID: 38255809 PMCID: PMC11154562 DOI: 10.3390/ijms25020735] [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: 10/25/2023] [Revised: 12/27/2023] [Accepted: 12/28/2023] [Indexed: 01/24/2024] Open
Abstract
Antibiotic resistance remains a pressing global concern, with most antibiotics targeting the bacterial ribosome or a limited range of proteins. One class of underexplored antibiotic targets is bacterial riboswitches, structured RNA elements that regulate key biosynthetic pathways by binding a specific ligand. We developed a methodology termed Fluorescent Ligand Equilibrium Displacement (FLED) to rapidly discover small molecules that bind the flavin mononucleotide (FMN) riboswitch. FLED leverages intrinsically fluorescent FMN and the quenching effect on RNA binding to create a label-free, in vitro method to identify compounds that can bind the apo population of riboswitch in a system at equilibrium. The response difference between known riboswitch ligands and controls demonstrates the robustness of the method for high-throughput screening. An existing drug discovery library that was screened using FLED resulted in a final hit rate of 0.67%. The concentration response of each hit was determined and revealed a variety of approximate effective concentration values. Our preliminary screening data support the use of FLED to identify small molecules for medicinal chemistry development as FMN riboswitch-targeted antibiotic compounds. This robust, label-free, and cell-free method offers a strong alternative to other riboswitch screening methods and can be adapted to a variety of laboratory setups.
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Affiliation(s)
| | - Ingrid R. Kilde
- Program in Chemical Biology, University of Michigan, Ann Arbor, MI 48109, USA;
| | - Suada Leskaj
- Department of Chemistry, University of Michigan, Ann Arbor, MI 48109, USA;
| | - Markos Koutmos
- Program in Biophysics, University of Michigan, Ann Arbor, MI 48109, USA;
- Program in Chemical Biology, University of Michigan, Ann Arbor, MI 48109, USA;
- Department of Chemistry, University of Michigan, Ann Arbor, MI 48109, USA;
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34
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Vuong HL, Lan CT, Le HTT. The development and technologies of RNA therapeutics. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2024; 203:13-39. [PMID: 38359995 DOI: 10.1016/bs.pmbts.2023.12.017] [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: 02/17/2024]
Abstract
Since it was discovered for over 20 years ago, the potentiality of siRNAs in gene silencing in vitro and in vivo models has been recognized. Several studies in the new generation, molecular mechanisms, target attachment, and purification of RNA have supported the development of RNA therapeutics for a variety of applications. RNA therapeutics are growing rapidly with various platforms contributing to the standard of personalized medicine and rare disease treatment. Therefore, understanding the development and technologies of RNA therapeutics becomes a crucial point for new drug generation. Here, the primary purpose of this review is to provide a general view of six therapeutic categories that make up RNA-based therapeutic approaches, including RNA-target therapeutics, protein-targeted therapeutics, cellular reprogramming and tissues engineering, RNA-based protein replacement therapeutics, RNA-based genome editing, and RNA-based immunotherapies based on non-coding RNAs and coding RNA. Furthermore, we present an overview of the RNA strategies regarding viral approaches and nonviral approaches in designing a new generation of RNA technologies. The advantages and challenges of using RNA therapeutics are also discussed along with various approaches for RNA delivery. Therefore, this review is designed to provide updated reference evidence of RNA therapeutics in the battle against rare or difficult-to-treat diseases for researchers in this field.
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Affiliation(s)
- Huong Lan Vuong
- Pharmacy Department, National Hospital for Tropical Diseases, Hanoi, Vietnam
| | - Chu Thanh Lan
- Department of Regenerative Medicine, Institute of Tissue Regeneration, College of Medicine, Soonchunghyang University, South Korea
| | - Hien Thi Thu Le
- Intestinal Signaling and Epigenetics, Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland.
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35
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Zhang L, Xiao K, Kong L. A computational method for small molecule-RNA binding sites identification by utilizing position specificity and complex network information. Biosystems 2024; 235:105094. [PMID: 38056591 DOI: 10.1016/j.biosystems.2023.105094] [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: 09/03/2023] [Revised: 11/23/2023] [Accepted: 11/24/2023] [Indexed: 12/08/2023]
Abstract
Some computational methods have been given for small molecule-RNA binding site identification due to that it plays a significant role in revealing biology function researches. However, it is still challenging to design an accurate model, especially for MCC. We designed a feature extraction technology from two aspects (position specificity and complex network information). Specifically, complex network was employed to express the space topological structure and sequence position information for improving prediction effect. Then, the features fused position specificity and complex network information were input into random forest classifier for model construction. The AUC of 88.22%, 77.92% and 81.46% were obtained on three independent datasets (RB19, CS71, RB78). Compared with the existing method, the best MCC were obtained on three datasets, which were 8.19%, 0.59% and 4.35% higher than the state-of-the-art prediction methods, respectively. The outstanding performances show that our method is a powerful tool to identify RNA binding sites, helping to the design RNA-targeting small molecule drugs. The data and resource codes are available at https://github.com/Kangxiaoneuq/PCN_RNAsite.
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Affiliation(s)
- Lichao Zhang
- School of Mathematics and Statistics, Northeastern University at Qinhuangdao, Qinhuangdao, 066000, PR China; Hebei Innovation Center for Smart Perception and Applied Technology of Agricultural Data, Qinhuangdao, 066000, PR China.
| | - Kang Xiao
- School of Mathematics and Statistics, Northeastern University at Qinhuangdao, Qinhuangdao, 066000, PR China.
| | - Liang Kong
- Hebei Innovation Center for Smart Perception and Applied Technology of Agricultural Data, Qinhuangdao, 066000, PR China; School of Mathematics and Information Science & Technology, Hebei Normal University of Science & Technology, Qinhuangdao, 066000, PR China.
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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.
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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
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Harisa GI, Faris TM, Sherif AY, Alzhrani RF, Alanazi SA, Kohaf NA, Alanazi FK. Gene-editing technology, from macromolecule therapeutics to organ transplantation: Applications, limitations, and prospective uses. Int J Biol Macromol 2023; 253:127055. [PMID: 37758106 DOI: 10.1016/j.ijbiomac.2023.127055] [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: 04/04/2023] [Revised: 09/04/2023] [Accepted: 09/15/2023] [Indexed: 10/03/2023]
Abstract
Gene editing technologies (GETs) could induce gene knockdown or gene knockout for biomedical applications. The clinical success of gene silence by RNAi therapies pays attention to other GETs as therapeutic approaches. This review aims to highlight GETs, categories, mechanisms, challenges, current use, and prospective applications. The different academic search engines, electronic databases, and bibliographies of selected articles were used in the preparation of this review with a focus on the fundamental considerations. The present results revealed that, among GETs, CRISPR/Cas9 has higher editing efficiency and targeting specificity compared to other GETs to insert, delete, modify, or replace the gene at a specific location in the host genome. Therefore, CRISPR/Cas9 is talented in the production of molecular, tissue, cell, and organ therapies. Consequently, GETs could be used in the discovery of innovative therapeutics for genetic diseases, pandemics, cancer, hopeless diseases, and organ failure. Specifically, GETs have been used to produce gene-modified animals to spare human organ failure. Genetically modified pigs are used in clinical trials as a source of heart, liver, kidneys, and lungs for xenotransplantation (XT) in humans. Viral, non-viral, and hybrid vectors have been utilized for the delivery of GETs with some limitations. Therefore, extracellular vesicles (EVs) are proposed as intelligent and future cargoes for GETs delivery in clinical applications. This study concluded that GETs are promising for the production of molecular, cellular, and organ therapies. The use of GETs as XT is still in the early stage as well and they have ethical and biosafety issues.
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Affiliation(s)
- Gamaleldin I Harisa
- Kayyali Chair for Pharmaceutical Industry, College of Pharmacy, King Saud University, Riyadh, Saudi Arabia; Department of Pharmaceutics, College of Pharmacy, King Saud University, Riyadh, Saudi Arabia; Department of Biochemistry and Molecular Biology, College of Pharmacy, Al-Azhar University, Nasr City, Cairo, Egypt.
| | - Tarek M Faris
- Department of Pharmaceutical Sciences, College of Pharmacy, Princess Nourah bint Abdulrahman University, Saudi Arabia
| | - Abdelrahman Y Sherif
- Kayyali Chair for Pharmaceutical Industry, College of Pharmacy, King Saud University, Riyadh, Saudi Arabia; Department of Pharmaceutics, College of Pharmacy, King Saud University, Riyadh, Saudi Arabia
| | - Riyad F Alzhrani
- Department of Pharmaceutics, College of Pharmacy, King Saud University, Riyadh, Saudi Arabia; Nanobiotechnology Research Unit, College of Pharmacy, King Saud University, Riyadh, Saudi Arabia
| | - Saleh A Alanazi
- Pharmaceutical Care Services, King Abdulaziz Medical City, King Saud bin Abdulaziz University for Health Science Collage of Pharmacy, King Abdullah International Medical Research Center, Riyadh, Saudi Arabia
| | - Neveen A Kohaf
- Department of Clinical Pharmacy, Faculty of Pharmacy, Al-Azhar University, Cairo 11651, Egypt
| | - Fars K Alanazi
- Kayyali Chair for Pharmaceutical Industry, College of Pharmacy, King Saud University, Riyadh, Saudi Arabia; Department of Pharmaceutics, College of Pharmacy, King Saud University, Riyadh, Saudi Arabia
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38
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Gogate A, Belcourt J, Shah M, Wang AZ, Frankel A, Kolmel H, Chalon M, Stephen P, Kolli A, Tawfik SM, Jin J, Bahal R, Rasmussen TP, Manautou JE, Zhong XB. Targeting the Liver with Nucleic Acid Therapeutics for the Treatment of Systemic Diseases of Liver Origin. Pharmacol Rev 2023; 76:49-89. [PMID: 37696583 PMCID: PMC10753797 DOI: 10.1124/pharmrev.123.000815] [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: 01/03/2024] [Revised: 08/25/2023] [Accepted: 09/06/2023] [Indexed: 09/13/2023] Open
Abstract
Systemic diseases of liver origin (SDLO) are complex diseases in multiple organ systems, such as cardiovascular, musculoskeletal, endocrine, renal, respiratory, and sensory organ systems, caused by irregular liver metabolism and production of functional factors. Examples of such diseases discussed in this article include primary hyperoxaluria, familial hypercholesterolemia, acute hepatic porphyria, hereditary transthyretin amyloidosis, hemophilia, atherosclerotic cardiovascular diseases, α-1 antitrypsin deficiency-associated liver disease, and complement-mediated diseases. Nucleic acid therapeutics use nucleic acids and related compounds as therapeutic agents to alter gene expression for therapeutic purposes. The two most promising, fastest-growing classes of nucleic acid therapeutics are antisense oligonucleotides (ASOs) and small interfering RNAs (siRNAs). For each listed SDLO disease, this article discusses epidemiology, symptoms, genetic causes, current treatment options, and advantages and disadvantages of nucleic acid therapeutics by either ASO or siRNA drugs approved or under development. Furthermore, challenges and future perspectives on adverse drug reactions and toxicity of ASO and siRNA drugs for the treatment of SDLO diseases are also discussed. In summary, this review article will highlight the clinical advantages of nucleic acid therapeutics in targeting the liver for the treatment of SDLO diseases. SIGNIFICANCE STATEMENT: Systemic diseases of liver origin (SDLO) contain rare and common complex diseases caused by irregular functions of the liver. Nucleic acid therapeutics have shown promising clinical advantages to treat SDLO. This article aims to provide the most updated information on targeting the liver with antisense oligonucleotides and small interfering RNA drugs. The generated knowledge may stimulate further investigations in this growing field of new therapeutic entities for the treatment of SDLO, which currently have no or limited options for treatment.
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Affiliation(s)
- Anagha Gogate
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Connecticut, Storrs, Connecticut
| | - Jordyn Belcourt
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Connecticut, Storrs, Connecticut
| | - Milan Shah
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Connecticut, Storrs, Connecticut
| | - Alicia Zongxun Wang
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Connecticut, Storrs, Connecticut
| | - Alexis Frankel
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Connecticut, Storrs, Connecticut
| | - Holly Kolmel
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Connecticut, Storrs, Connecticut
| | - Matthew Chalon
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Connecticut, Storrs, Connecticut
| | - Prajith Stephen
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Connecticut, Storrs, Connecticut
| | - Aarush Kolli
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Connecticut, Storrs, Connecticut
| | - Sherouk M Tawfik
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Connecticut, Storrs, Connecticut
| | - Jing Jin
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Connecticut, Storrs, Connecticut
| | - Raman Bahal
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Connecticut, Storrs, Connecticut
| | - Theodore P Rasmussen
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Connecticut, Storrs, Connecticut
| | - José E Manautou
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Connecticut, Storrs, Connecticut
| | - Xiao-Bo Zhong
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Connecticut, Storrs, Connecticut
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Du J, Su Y, Gao J, Tai Y. The expression and function of long noncoding RNAs in hepatocellular carcinoma. CANCER INNOVATION 2023; 2:488-499. [PMID: 38125766 PMCID: PMC10730004 DOI: 10.1002/cai2.90] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/04/2023] [Revised: 06/23/2023] [Accepted: 07/07/2023] [Indexed: 12/23/2023]
Abstract
With the deepening of the genome project study, attention on noncoding RNAs is increasing. Long noncoding RNAs (lncRNAs) have become a new research hotspot. A growing number of studies have revealed that lncRNAs are involved in tumorigenesis and tumor suppressor pathways. Aberrant expressions of lncRNAs have been found in a variety of human tumors including hepatocellular carcinoma (HCC). In this review, we provide a brief introduction to lncRNA and highlight recent research on the functions and clinical significance of lncRNAs in HCC.
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Affiliation(s)
- Jingli Du
- Senior Department of TuberculosisThe 8th Medical Center of PLA General HospitalBeijingChina
| | - Yue Su
- Senior Department of TuberculosisThe 8th Medical Center of PLA General HospitalBeijingChina
| | - Jianzhi Gao
- Department of OncologyZhuozhou Hospital, ZhuozhouHebeiChina
| | - Yanhong Tai
- Department of PathologyThe 5th Medical Center of PLA General HospitalBeijingChina
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Poller W, Sahoo S, Hajjar R, Landmesser U, Krichevsky AM. Exploration of the Noncoding Genome for Human-Specific Therapeutic Targets-Recent Insights at Molecular and Cellular Level. Cells 2023; 12:2660. [PMID: 37998395 PMCID: PMC10670380 DOI: 10.3390/cells12222660] [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: 10/06/2023] [Revised: 11/13/2023] [Accepted: 11/14/2023] [Indexed: 11/25/2023] Open
Abstract
While it is well known that 98-99% of the human genome does not encode proteins, but are nevertheless transcriptionally active and give rise to a broad spectrum of noncoding RNAs [ncRNAs] with complex regulatory and structural functions, specific functions have so far been assigned to only a tiny fraction of all known transcripts. On the other hand, the striking observation of an overwhelmingly growing fraction of ncRNAs, in contrast to an only modest increase in the number of protein-coding genes, during evolution from simple organisms to humans, strongly suggests critical but so far essentially unexplored roles of the noncoding genome for human health and disease pathogenesis. Research into the vast realm of the noncoding genome during the past decades thus lead to a profoundly enhanced appreciation of the multi-level complexity of the human genome. Here, we address a few of the many huge remaining knowledge gaps and consider some newly emerging questions and concepts of research. We attempt to provide an up-to-date assessment of recent insights obtained by molecular and cell biological methods, and by the application of systems biology approaches. Specifically, we discuss current data regarding two topics of high current interest: (1) By which mechanisms could evolutionary recent ncRNAs with critical regulatory functions in a broad spectrum of cell types (neural, immune, cardiovascular) constitute novel therapeutic targets in human diseases? (2) Since noncoding genome evolution is causally linked to brain evolution, and given the profound interactions between brain and immune system, could human-specific brain-expressed ncRNAs play a direct or indirect (immune-mediated) role in human diseases? Synergistic with remarkable recent progress regarding delivery, efficacy, and safety of nucleic acid-based therapies, the ongoing large-scale exploration of the noncoding genome for human-specific therapeutic targets is encouraging to proceed with the development and clinical evaluation of novel therapeutic pathways suggested by these research fields.
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Affiliation(s)
- Wolfgang Poller
- Department for Cardiology, Angiology and Intensive Care Medicine, Deutsches Herzzentrum Charité (DHZC), Charité-Universitätsmedizin Berlin, 12200 Berlin, Germany;
- Berlin-Brandenburg Center for Regenerative Therapies (BCRT), Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, 13353 Berlin, Germany
- German Center for Cardiovascular Research (DZHK), Site Berlin, 10785 Berlin, Germany
| | - Susmita Sahoo
- Cardiovascular Research Institute, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, Box 1030, New York, NY 10029, USA;
| | - Roger Hajjar
- Gene & Cell Therapy Institute, Mass General Brigham, 65 Landsdowne St, Suite 143, Cambridge, MA 02139, USA;
| | - Ulf Landmesser
- Department for Cardiology, Angiology and Intensive Care Medicine, Deutsches Herzzentrum Charité (DHZC), Charité-Universitätsmedizin Berlin, 12200 Berlin, Germany;
- German Center for Cardiovascular Research (DZHK), Site Berlin, 10785 Berlin, Germany
- Berlin Institute of Health, Charité-Universitätsmedizin Berlin, 10117 Berlin, Germany
| | - Anna M. Krichevsky
- Department of Neurology, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA 02115, USA;
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Wang L, Shui X, Diao Y, Chen D, Zhou Y, Lee TH. Potential Implications of miRNAs in the Pathogenesis, Diagnosis, and Therapeutics of Alzheimer's Disease. Int J Mol Sci 2023; 24:16259. [PMID: 38003448 PMCID: PMC10671222 DOI: 10.3390/ijms242216259] [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: 10/18/2023] [Revised: 11/10/2023] [Accepted: 11/12/2023] [Indexed: 11/26/2023] Open
Abstract
Alzheimer's disease (AD) is a complex multifactorial disorder that poses a substantial burden on patients, caregivers, and society. Considering the increased aging population and life expectancy, the incidence of AD will continue to rise in the following decades. However, the molecular pathogenesis of AD remains controversial, superior blood-based biomarker candidates for early diagnosis are still lacking, and effective therapeutics to halt or slow disease progression are urgently needed. As powerful genetic regulators, microRNAs (miRNAs) are receiving increasing attention due to their implications in the initiation, development, and theranostics of various diseases, including AD. In this review, we summarize miRNAs that directly target microtubule-associated protein tau (MAPT), amyloid precursor protein (APP), and β-site APP-cleaving enzyme 1 (BACE1) transcripts and regulate the alternative splicing of tau and APP. We also discuss related kinases, such as glycogen synthase kinase (GSK)-3β, cyclin-dependent kinase 5 (CDK5), and death-associated protein kinase 1 (DAPK1), as well as apolipoprotein E, that are directly targeted by miRNAs to control tau phosphorylation and amyloidogenic APP processing leading to Aβ pathologies. Moreover, there is evidence of miRNA-mediated modulation of inflammation. Furthermore, circulating miRNAs in the serum or plasma of AD patients as noninvasive biomarkers with diagnostic potential are reviewed. In addition, miRNA-based therapeutics optimized with nanocarriers or exosomes as potential options for AD treatment are discussed.
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Affiliation(s)
| | | | | | | | - Ying Zhou
- Fujian Key Laboratory of Translational Research in Cancer and Neurodegenerative Diseases, School of Basic Medical Sciences, Fujian Medical University, Fuzhou 350122, China; (L.W.)
| | - Tae Ho Lee
- Fujian Key Laboratory of Translational Research in Cancer and Neurodegenerative Diseases, School of Basic Medical Sciences, Fujian Medical University, Fuzhou 350122, China; (L.W.)
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Kaeffer B. Human Breast Milk miRNAs: Their Diversity and Potential for Preventive Strategies in Nutritional Therapy. Int J Mol Sci 2023; 24:16106. [PMID: 38003296 PMCID: PMC10671413 DOI: 10.3390/ijms242216106] [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: 10/02/2023] [Revised: 11/02/2023] [Accepted: 11/06/2023] [Indexed: 11/26/2023] Open
Abstract
The endogenous miRNAs of breast milk are the products of more than 1000 nonprotein-coding genes, giving rise to mature small regulatory molecules of 19-25 nucleotides. They are incorporated in macromolecular complexes, loaded on Argonaute proteins, sequestrated in exosomes and lipid complexes, or present in exfoliated cells of epithelial, endothelial, or immune origins. Their expression is dependent on the stage of lactation; however, their detection depends on progress in RNA sequencing and the reappraisal of the definition of small RNAs. Some miRNAs from plants are detected in breast milk, opening the possibility of the stimulation of immune cells from the allergy repertoire. Each miRNA harbors a seeding sequence, which targets mRNAs, gene promoters, or long noncoding RNAs. Their activities depend on their bioavailability. Efficient doses of miRNAs are estimated to be roughly 100 molecules in the cytoplasm of target cells from in vitro and in vivo experiments. Each miRNA is included in networks of stimulation/inhibition/sequestration, driving the expression of cellular phenotypes. Three types of stress applied during lactation to manipulate miRNA supply were explored using rodent offspring: a foster mother, a cafeteria diet, and early weaning. This review presents the main mature miRNAs described from current mothers' cohorts and their bioavailability in experimental models as well as studies assessing the potential of miR-26 or miR-320 miRNA families to alter offspring phenotypes.
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Affiliation(s)
- Bertrand Kaeffer
- Nantes Université, INRAE, UMR 1280, PhAN, F-44000 Nantes, France
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Huang X, Zhang Z, Wang Y, Xu M, Du X, Zhang Y. Circulating miRNAs drive personalized medicine based on subgroup classification in myasthenia gravis patients. Neurol Sci 2023; 44:3877-3884. [PMID: 37402938 DOI: 10.1007/s10072-023-06933-3] [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: 12/25/2022] [Accepted: 06/29/2023] [Indexed: 07/06/2023]
Abstract
Myasthenia gravis (MG) is a classic autoimmune neuromuscular disease with strong clinical heterogeneity. The concept of subgroup classification was proposed to guide the precise treatment of MG. Subgroups based on serum antibodies and clinical features include ocular MG, early-onset MG with AchR antibodies, late-onset MG with AchR antibodies, thymoma-associated MG, MuSK-associated MG, LRP4-associated MG, and seronegative MG. However, reliable objective biomarkers are still needed to reflect the individualized response to therapy. MicroRNAs (miRNAs) are small non-coding RNA molecules which can specifically bind to target genes and regulate gene expression at the post-transcriptional level, and then influence celluar biological processes. MiRNAs play an important role in the pathogenesis of autoimmune diseases, including MG. Several studies on circulating miRNAs in MG have been reported. However, there is rare systematic review to summarize the differences of these miRNAs in different subgroups of MG. Here, we summarize the potential role of circulating miRNAs in different subgroups of MG to promote personalized medicine.
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Affiliation(s)
- Xiaoyu Huang
- Department of Neurology, Affiliated Hospital of Xuzhou Medical University, No. 99 Huaihai West Road, Quanshan Distric, Xuzhou, Jiangsu, China
- Department of Neurology, Tianjin Neurological Institute, Tianjin Medical University General Hospital, Tianjin, China
| | - Zhouao Zhang
- Department of Neurology, Affiliated Hospital of Xuzhou Medical University, No. 99 Huaihai West Road, Quanshan Distric, Xuzhou, Jiangsu, China
| | - Yingying Wang
- Department of Neurology, Affiliated Hospital of Xuzhou Medical University, No. 99 Huaihai West Road, Quanshan Distric, Xuzhou, Jiangsu, China
| | - Mingming Xu
- Department of Neurology, Affiliated Hospital of Xuzhou Medical University, No. 99 Huaihai West Road, Quanshan Distric, Xuzhou, Jiangsu, China
| | - Xue Du
- Department of Neurology, Affiliated Hospital of Xuzhou Medical University, No. 99 Huaihai West Road, Quanshan Distric, Xuzhou, Jiangsu, China
| | - Yong Zhang
- Department of Neurology, Affiliated Hospital of Xuzhou Medical University, No. 99 Huaihai West Road, Quanshan Distric, Xuzhou, Jiangsu, China.
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Shankaranarayana AH, Meduri B, Pujar GV, Hariharapura RC, Sethu AK, Singh M, Bidye D. Restoration of p53 functions by suppression of mortalin-p53 sequestration: an emerging target in cancer therapy. Future Med Chem 2023; 15:2087-2112. [PMID: 37877348 DOI: 10.4155/fmc-2023-0061] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Accepted: 08/30/2023] [Indexed: 10/26/2023] Open
Abstract
Functional inactivation of wild-type p53 is a major trait of cancerous cells. In many cases, such inactivation occurs by either TP53 gene mutations or due to overexpression of p53 binding partners. This review focuses on an overexpressed p53 binding partner called mortalin, a mitochondrial heat shock protein that sequesters both wild-type and mutant p53 in malignant cells due to changes in subcellular localization. Clinical evidence suggests a drastic depletion of the overall survival time of cancer patients with high mortalin expression. Therefore, mortalin-p53 sequestration inhibitors could be game changers in improving overall survival rates. This review explores the consequences of mortalin overexpression and challenges, status and strategies for accelerating drug discovery to suppress mortalin-p53 sequestration.
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Affiliation(s)
- Akshatha Handattu Shankaranarayana
- Department of Pharmaceutical Chemistry, JSS College of Pharmacy, JSS Academy of Higher Education & Research, Sri Shivarathreeshwara Nagara, Mysuru, 570015, India
| | - Bhagyalalitha Meduri
- Department of Pharmaceutical Chemistry, JSS College of Pharmacy, JSS Academy of Higher Education & Research, Sri Shivarathreeshwara Nagara, Mysuru, 570015, India
| | - Gurubasavaraj Veeranna Pujar
- Department of Pharmaceutical Chemistry, JSS College of Pharmacy, JSS Academy of Higher Education & Research, Sri Shivarathreeshwara Nagara, Mysuru, 570015, India
| | - Raghu Chandrashekar Hariharapura
- Department of Pharmaceutical Biotechnology, Manipal College of Pharmaceutical Sciences, Manipal Academy of Higher Education, Manipal, 576104, India
| | - Arun Kumar Sethu
- Department of Pharmaceutical Chemistry, JSS College of Pharmacy, JSS Academy of Higher Education & Research, Sri Shivarathreeshwara Nagara, Mysuru, 570015, India
| | - Manisha Singh
- Department of Pharmaceutical Chemistry, JSS College of Pharmacy, JSS Academy of Higher Education & Research, Sri Shivarathreeshwara Nagara, Mysuru, 570015, India
| | - Durgesh Bidye
- Department of Pharmaceutical Chemistry, JSS College of Pharmacy, JSS Academy of Higher Education & Research, Sri Shivarathreeshwara Nagara, Mysuru, 570015, India
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Richard I. Basic notions about gene therapy from the nucleic acid perspective and applications in a pediatric disease: Duchenne muscular dystrophy. Arch Pediatr 2023; 30:8S2-8S11. [PMID: 38043979 DOI: 10.1016/s0929-693x(23)00221-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/05/2023]
Abstract
Gene therapy involves the introduction of genetic material into cells as a therapeutic molecule to cure a disease. Through the transfer of specific nucleic acid to the target tissue, gene expression can be downregulated, augmented, or corrected thanks to the nucleic acid sequence as a support of gene expression. This is achieved through molecular interactions according to the sequence arrangement or the secondary structure of the molecules or through their catalytic properties. Over the past two decades, the rapid advances of knowledge and technologies in gene therapy have led to the development of different strategies and to the extension of its use to numerous indications, including certain cancers. Major success has been achieved in clinical trials and the field of gene therapy is booming. Several gene therapy products are now on the market in Europe, the United States, and China. In this review, we cover the basic principles of gene therapy and the characteristics of the main vectors used to transfer genetic material into the cell. As an example of applications, we address the various strategies applied to a rare pediatric muscle disease: Duchenne muscular dystrophy. © 2023 Published by Elsevier Masson SAS on behalf of French Society of Pediatrics.
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Affiliation(s)
- Isabelle Richard
- Genethon, 91000, Evry, France; Université Paris-Saclay, Univ. Evry, Inserm, Integrare research unit UMR_S951, 91000, Evry-Courcouronnes, France; Atamyo Therapeutics, 1, bis rue de l'internationale, Evry, France.
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Li K, Guo J, Ming Y, Chen S, Zhang T, Ma H, Fu X, Wang J, Liu W, Peng Y. A circular RNA activated by TGFβ promotes tumor metastasis through enhancing IGF2BP3-mediated PDPN mRNA stability. Nat Commun 2023; 14:6876. [PMID: 37898647 PMCID: PMC10613289 DOI: 10.1038/s41467-023-42571-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2022] [Accepted: 10/16/2023] [Indexed: 10/30/2023] Open
Abstract
Metastasis is the leading cause of cancer-related death, where TGFβ-induced epithelial-mesenchymal transition (EMT) process confers on cancer cells increased metastatic potential. However, the involvement of circRNAs in this process is still obscure. Here, we identify a TGFβ-induced circRNA called circITGB6 as an indispensable factor during the TGFβ-mediated EMT process. circITGB6 is significantly upregulated in metastatic cancer samples and its higher abundance is closely correlated to worse prognosis of colorectal cancer (CRC) patients. Through gain- and loss-of-function assays, circITGB6 is found to potently promote EMT process and tumor metastasis in various models in vitro and in vivo. Mechanistically, circITGB6 enhances the mRNA stability of PDPN, an EMT-promoting gene, by directly interacting with IGF2BP3. Notably, interfering circITGB6 with PEI-coated specific siRNA effectively represses liver metastasis. Therefore, our study reveals the function of a TGFβ-regulated circRNA in tumor metastasis and suggests that targeting circITGB6 is a promising strategy for cancer therapy.
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Affiliation(s)
- Ke Li
- Laboratory of Molecular Oncology, Frontiers Science Center for Disease-related Molecular Network, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu, China
| | - Jiawei Guo
- Laboratory of Molecular Oncology, Frontiers Science Center for Disease-related Molecular Network, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu, China
| | - Yue Ming
- Laboratory of Molecular Oncology, Frontiers Science Center for Disease-related Molecular Network, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu, China
| | - Shuang Chen
- Laboratory of Molecular Oncology, Frontiers Science Center for Disease-related Molecular Network, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu, China
| | - Tingting Zhang
- Laboratory of Molecular Oncology, Frontiers Science Center for Disease-related Molecular Network, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu, China
| | - Hulin Ma
- Laboratory of Molecular Oncology, Frontiers Science Center for Disease-related Molecular Network, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu, China
| | - Xin Fu
- Laboratory of Molecular Oncology, Frontiers Science Center for Disease-related Molecular Network, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu, China
| | - Jin Wang
- Laboratory of Molecular Oncology, Frontiers Science Center for Disease-related Molecular Network, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu, China
| | - Wenrong Liu
- Laboratory of Molecular Oncology, Frontiers Science Center for Disease-related Molecular Network, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu, China
| | - Yong Peng
- Laboratory of Molecular Oncology, Frontiers Science Center for Disease-related Molecular Network, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu, China.
- Frontier Medical Center, Tianfu Jincheng Laboratory, 610212, Chengdu, China.
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Chan KH, Wang Y, Zheng BX, Long W, Feng X, Wong WL. RNA-Selective Small-Molecule Ligands: Recent Advances in Live-Cell Imaging and Drug Discovery. ChemMedChem 2023; 18:e202300271. [PMID: 37649155 DOI: 10.1002/cmdc.202300271] [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: 05/20/2023] [Revised: 08/13/2023] [Accepted: 08/24/2023] [Indexed: 09/01/2023]
Abstract
RNA structures, including those formed from coding and noncoding RNAs, alternative to protein-based drug targets, could be a promising target of small molecules for drug discovery against various human diseases, particularly in anticancer, antibacterial and antivirus development. The normal cellular activity of cells is critically dependent on the function of various RNA molecules generated from DNA transcription. Moreover, many studies support that mRNA-targeting small molecules may regulate the synthesis of disease-related proteins via the non-covalent mRNA-ligand interactions that do not involve gene modification. RNA-ligand interaction is thus an attractive approach to address the challenge of "undruggable" proteins in drug discovery because the intracellular activity of these proteins is hard to be suppressed with small molecule ligands. We selectively surveyed a specific area of RNA structure-selective small molecule ligands in fluorescence live cell imaging and drug discovery because the area was currently underexplored. This state-of-the-art review thus mainly focuses on the research published within the past three years and aims to provide the most recent information on this research area; hopefully, it could be complementary to the previously reported reviews and give new insights into the future development on RNA-specific small molecule ligands for live cell imaging and drug discovery.
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Affiliation(s)
- Ka Hin Chan
- State Key Laboratory of Chemical Biology and Drug Discovery, Department of Applied Biology and Chemical Technology, The Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong, SAR 999077, P. R. China
| | - Yakun Wang
- The Hong Kong Polytechnic University Shenzhen Research Institute, Shenzhen, 518057, P. R. China
| | - Bo-Xin Zheng
- State Key Laboratory of Chemical Biology and Drug Discovery, Department of Applied Biology and Chemical Technology, The Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong, SAR 999077, P. R. China
| | - Wei Long
- State Key Laboratory of Chemical Biology and Drug Discovery, Department of Applied Biology and Chemical Technology, The Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong, SAR 999077, P. R. China
| | - Xinxin Feng
- State Key Laboratory of Chem-/Bio-Sensing and Chemometrics, Hunan Provincial Key Laboratory of Biomacromolecular Chemical Biology and School of Chemistry and Chemical Engineering, Hunan University, Changsha, Hunan, 410082, P. R. China
| | - Wing-Leung Wong
- State Key Laboratory of Chemical Biology and Drug Discovery, Department of Applied Biology and Chemical Technology, The Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong, SAR 999077, P. R. China
- The Hong Kong Polytechnic University Shenzhen Research Institute, Shenzhen, 518057, P. R. China
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Safaei M, Khalighi F, Behabadi FA, Abpeikar Z, Goodarzi A, Kouhpayeh SA, Najafipour S, Ramezani V. Liposomal nanocarriers containing siRNA as small molecule-based drugs to overcome cancer drug resistance. Nanomedicine (Lond) 2023; 18:1745-1768. [PMID: 37965906 DOI: 10.2217/nnm-2023-0176] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2023] Open
Abstract
This review discusses the application of nanoliposomes containing siRNA/drug to overcome multidrug resistance for all types of cancer treatments. As drug resistance-associated factors are overexpressed in many cancer cell types, pumping chemotherapy drugs out of the cytoplasm leads to an inadequate therapeutic response. The siRNA/drug-loaded nanoliposomes are a promising approach to treating multidrug-resistant cancer, as they can effectively transmit a small-molecule drug into the target cytoplasm, ensuring that the drug binds efficiently. Moreover, nanoliposome-based therapeutics with advances in nanotechnology can effectively deliver siRNA to cancer cells. Overall, nanoliposomes have the potential to effectively deliver siRNA and small-molecule drugs in a targeted manner and are thus a promising tool for the treatment of cancer and other diseases.
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Affiliation(s)
- Mohsen Safaei
- Department of Tissue Engineering, School of Advanced Technologies in Medicine, Fasa University of Medical Sciences, Fasa, 7461686688, Iran
| | - Fatemeh Khalighi
- Department of Pharmaceutics, School of Pharmacy, Shahid Sadoughi University of Medical Sciences, Yazd, 9417694780, Iran
| | - Fatemeh Akhavan Behabadi
- Department of Pharmaceutics, School of Pharmacy, Shahid Sadoughi University of Medical Sciences, Yazd, 9417694780, Iran
| | - Zahra Abpeikar
- Department of Tissue Engineering, School of Advanced Technologies in Medicine, Fasa University of Medical Sciences, Fasa, 7461686688, Iran
| | - Arash Goodarzi
- Department of Tissue Engineering, School of Advanced Technologies in Medicine, Fasa University of Medical Sciences, Fasa, 7461686688, Iran
| | - Seyed Amin Kouhpayeh
- Department of Pharmacology, School of Medicine, Fasa University of Medical Sciences, Fasa, 7461686688, Iran
| | - Sohrab Najafipour
- Department of Microbiology, Faculty of Medicine, Fasa University of Medical Sciences, Fasa, 7461686688, Iran
| | - Vahid Ramezani
- Department of Pharmaceutics, School of Pharmacy, Shahid Sadoughi University of Medical Sciences, Yazd, 9417694780, Iran
- Pharmaceutical Sciences Research Center, School of Pharmacy, Shahid Sadoughi University of Medical Sciences, Yazd, 9417694780, Iran
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Chen Y, Tu MJ, Han F, Liu Z, Batra N, Lara PN, Chen HW, Bi H, Yu AM. Use of recombinant microRNAs as antimetabolites to inhibit human non-small cell lung cancer. Acta Pharm Sin B 2023; 13:4273-4290. [PMID: 37799388 PMCID: PMC10547963 DOI: 10.1016/j.apsb.2023.07.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2022] [Revised: 03/13/2023] [Accepted: 05/18/2023] [Indexed: 10/07/2023] Open
Abstract
During the development of therapeutic microRNAs (miRNAs or miRs), it is essential to define their pharmacological actions. Rather, miRNA research and therapy mainly use miRNA mimics synthesized in vitro. After experimental screening of unique recombinant miRNAs produced in vivo, three lead antiproliferative miRNAs against human NSCLC cells, miR-22-3p, miR-9-5p, and miR-218-5p, were revealed to target folate metabolism by bioinformatic analyses. Recombinant miR-22-3p, miR-9-5p, and miR-218-5p were shown to regulate key folate metabolic enzymes to inhibit folate metabolism and subsequently alter amino acid metabolome in NSCLC A549 and H1975 cells. Isotope tracing studies further confirmed the disruption of one-carbon transfer from serine to folate metabolites by all three miRNAs, inhibition of glucose uptake by miR-22-3p, and reduction of serine biosynthesis from glucose by miR-9-5p and -218-5p in NSCLC cells. With greater activities to interrupt NSCLC cell respiration, glycolysis, and colony formation than miR-9-5p and -218-5p, recombinant miR-22-3p was effective to reduce tumor growth in two NSCLC patient-derived xenograft mouse models without causing any toxicity. These results establish a common antifolate mechanism and differential actions on glucose uptake and metabolism for three lead anticancer miRNAs as well as antitumor efficacy for miR-22-3p nanomedicine, which shall provide insight into developing antimetabolite RNA therapies.
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Affiliation(s)
- Yixin Chen
- Department of Biochemistry and Molecular Medicine, School of Medicine, UC Davis, Sacramento, CA 95817, USA
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou 510006, China
| | - Mei-Juan Tu
- Department of Biochemistry and Molecular Medicine, School of Medicine, UC Davis, Sacramento, CA 95817, USA
| | - Fangwei Han
- School of Public Health, UNT Health Science Center, Fort Worth, TX 76107, USA
| | - Zhenzhen Liu
- Department of Biochemistry and Molecular Medicine, School of Medicine, UC Davis, Sacramento, CA 95817, USA
| | - Neelu Batra
- Department of Biochemistry and Molecular Medicine, School of Medicine, UC Davis, Sacramento, CA 95817, USA
| | - Primo N. Lara
- Department of Internal Medicine, School of Medicine, UC Davis, Sacramento, CA 95817, USA
| | - Hong-Wu Chen
- Department of Biochemistry and Molecular Medicine, School of Medicine, UC Davis, Sacramento, CA 95817, USA
| | - Huichang Bi
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou 510006, China
| | - Ai-Ming Yu
- Department of Biochemistry and Molecular Medicine, School of Medicine, UC Davis, Sacramento, CA 95817, USA
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Zogg H, Singh R, Ha SE, Wang Z, Jin B, Ha M, Dafinone M, Batalon T, Hoberg N, Poudrier S, Nguyen L, Yan W, Layden BT, Dugas LR, Sanders KM, Ro S. miR-10b-5p rescues leaky gut linked with gastrointestinal dysmotility and diabetes. United European Gastroenterol J 2023; 11:750-766. [PMID: 37723933 PMCID: PMC10576606 DOI: 10.1002/ueg2.12463] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/02/2023] [Accepted: 07/31/2023] [Indexed: 09/20/2023] Open
Abstract
BACKGROUND/AIM Diabetes has substantive co-occurrence with disorders of gut-brain interactions (DGBIs). The pathophysiological and molecular mechanisms linking diabetes and DGBIs are unclear. MicroRNAs (miRNAs) are key regulators of diabetes and gut dysmotility. We investigated whether impaired gut barrier function is regulated by a key miRNA, miR-10b-5p, linking diabetes and gut dysmotility. METHODS We created a new mouse line using the Mb3Cas12a/Mb3Cpf1 endonuclease to delete mir-10b globally. Loss of function studies in the mir-10b knockout (KO) mice were conducted to characterize diabetes, gut dysmotility, and gut barrier dysfunction phenotypes in these mice. Gain of function studies were conducted by injecting these mir-10b KO mice with a miR-10b-5p mimic. Further, we performed miRNA-sequencing analysis from colonic mucosa from mir-10b KO, wild type, and miR-10b-5p mimic injected mice to confirm (1) deficiency of miR-10b-5p in KO mice, and (2) restoration of miR-10b-5p after the mimic injection. RESULTS Congenital loss of mir-10b in mice led to the development of hyperglycemia, gut dysmotility, and gut barrier dysfunction. Gut permeability was increased, but expression of the tight junction protein Zonula occludens-1 was reduced in the colon of mir-10b KO mice. Patients with diabetes or constipation- predominant irritable bowel syndrome, a known DGBI that is linked to leaky gut, had significantly reduced miR-10b-5p expression. Injection of a miR-10b-5p mimic in mir-10b KO mice rescued these molecular alterations and phenotypes. CONCLUSIONS Our study uncovered a potential pathophysiologic mechanism of gut barrier dysfunction that links both the diabetes and gut dysmotility phenotypes in mice lacking miR-10b-5p. Treatment with a miR-10b-5p mimic reversed the leaky gut, diabetic, and gut dysmotility phenotypes, highlighting the translational potential of the miR-10b-5p mimic.
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Affiliation(s)
- Hannah Zogg
- Department of Physiology and Cell BiologySchool of MedicineUniversity of NevadaRenoNevadaUSA
| | - Rajan Singh
- Department of Physiology and Cell BiologySchool of MedicineUniversity of NevadaRenoNevadaUSA
| | - Se Eun Ha
- Department of Physiology and Cell BiologySchool of MedicineUniversity of NevadaRenoNevadaUSA
| | - Zhuqing Wang
- Department of Physiology and Cell BiologySchool of MedicineUniversity of NevadaRenoNevadaUSA
| | - Byungchang Jin
- Department of Physiology and Cell BiologySchool of MedicineUniversity of NevadaRenoNevadaUSA
| | - Mariah Ha
- Department of Physiology and Cell BiologySchool of MedicineUniversity of NevadaRenoNevadaUSA
| | - Mirabel Dafinone
- Department of Physiology and Cell BiologySchool of MedicineUniversity of NevadaRenoNevadaUSA
| | - Tylar Batalon
- Department of Physiology and Cell BiologySchool of MedicineUniversity of NevadaRenoNevadaUSA
| | - Nicholas Hoberg
- Department of Physiology and Cell BiologySchool of MedicineUniversity of NevadaRenoNevadaUSA
| | - Sandra Poudrier
- Department of Physiology and Cell BiologySchool of MedicineUniversity of NevadaRenoNevadaUSA
| | - Linda Nguyen
- Division of Gastroenterology & HepatologyStanford University School of MedicineStanfordCaliforniaUSA
| | - Wei Yan
- Department of Physiology and Cell BiologySchool of MedicineUniversity of NevadaRenoNevadaUSA
| | - Brian T. Layden
- Division of Endocrinology, Diabetes, and MetabolismDepartment of MedicineThe University of Illinois at ChicagoChicagoIllinoisUSA
- Jesse Brown Veterans Affairs Medical CenterChicagoIllinoisUSA
| | - Lara R. Dugas
- Loyola University ChicagoPublic Health SciencesMaywoodIllinoisUSA
- Division of Epidemiology & BiostatisticsSchool of Public HealthFaculty of Health SciencesUniversity of Cape TownCape TownSouth Africa
| | - Kenton M. Sanders
- Department of Physiology and Cell BiologySchool of MedicineUniversity of NevadaRenoNevadaUSA
| | - Seungil Ro
- Department of Physiology and Cell BiologySchool of MedicineUniversity of NevadaRenoNevadaUSA
- RosVivo TherapeuticsApplied Research FacilityRenoNevadaUSA
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