1
|
Li Y, Mondaza-Hernandez JL, Moura DS, Revenko AS, Tolentino A, Nguyen JT, Tran N, Meyer CA, Merino-Garcia J, Ramos R, Di Lernia D, Martin-Broto J, Hayenga HN, Bleris L. STAT6-targeting antisense oligonucleotides against solitary fibrous tumor. Mol Ther Nucleic Acids 2024; 35:102154. [PMID: 38511173 PMCID: PMC10950871 DOI: 10.1016/j.omtn.2024.102154] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/30/2023] [Accepted: 02/13/2024] [Indexed: 03/22/2024]
Abstract
Solitary fibrous tumor (SFT) is a rare, non-hereditary soft tissue sarcoma thought to originate from fibroblastic mesenchymal stem cells. The etiology of SFT is thought to be due to an environmental intrachromosomal gene fusion between NGFI-A-binding protein 2 (NAB2) and signal transducer and activator protein 6 (STAT6) genes on chromosome 12, wherein the activation domain of STAT6 is fused with the DNA-binding domain of NAB2 resulting in the oncogenesis of SFT. All NAB2-STAT6 fusion variations discovered in SFTs contain the C-terminal of STAT6 transcript, and thus can serve as target site for antisense oligonucleotides (ASOs)-based therapies. Indeed, our in vitro studies show the STAT6 3' untranslated region (UTR)-targeting ASO (ASO 993523) was able to reduce expression of NAB2-STAT6 fusion transcripts in multiple SFT cell models with high efficiency (half-maximal inhibitory concentration: 116-300 nM). Encouragingly, in vivo treatment of SFT patient-derived xenograft mouse models with ASO 993523 resulted in acceptable tolerability profiles, reduced expression of NAB2-STAT6 fusion transcripts in xenograft tissues (21.9%), and, importantly, reduced tumor growth (32.4% decrease in tumor volume compared with the untreated control). Taken together, our study established ASO 993523 as a potential agent for the treatment of SFTs.
Collapse
Affiliation(s)
- Yi Li
- Department of Bioengineering, University of Texas at Dallas, Richardson, TX 75080, USA
- Center for Systems Biology, University of Texas at Dallas, Richardson, TX 75080, USA
| | - Jose L. Mondaza-Hernandez
- Health Research Institute Fundacion Jimenez Diaz, Universidad Autonoma de Madrid (IIS/FJD-UAM), 28049 Madrid, Spain
- University Hospital General de Villalba, 28400 Madrid, Spain
| | - David S. Moura
- Health Research Institute Fundacion Jimenez Diaz, Universidad Autonoma de Madrid (IIS/FJD-UAM), 28049 Madrid, Spain
| | - Alexey S. Revenko
- Department of Antisense Drug Discovery, Ionis Pharmaceuticals, Inc, Carlsbad, CA 92010, USA
| | - Angelica Tolentino
- Department of Antisense Drug Discovery, Ionis Pharmaceuticals, Inc, Carlsbad, CA 92010, USA
| | - John T. Nguyen
- Department of Bioengineering, University of Texas at Dallas, Richardson, TX 75080, USA
- Center for Systems Biology, University of Texas at Dallas, Richardson, TX 75080, USA
| | - Nam Tran
- Neurosurgical Oncology, Department of Neuro-Oncology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL 33612, USA
| | - Clark A. Meyer
- Department of Bioengineering, University of Texas at Dallas, Richardson, TX 75080, USA
| | - Jose Merino-Garcia
- Pathology Department, University Hospital Fundacion Jimenez Diaz, Universidad Autonoma, Av. Reyes Catolicos 2, 28040 Madrid, Spain
| | - Rafael Ramos
- Pathology Department, University Hospital Son Espases, 07120 Palma de Mallorca, Spain
| | - Davide Di Lernia
- Health Research Institute Fundacion Jimenez Diaz, Universidad Autonoma de Madrid (IIS/FJD-UAM), 28049 Madrid, Spain
| | - Javier Martin-Broto
- Health Research Institute Fundacion Jimenez Diaz, Universidad Autonoma de Madrid (IIS/FJD-UAM), 28049 Madrid, Spain
- University Hospital General de Villalba, 28400 Madrid, Spain
- Medical Oncology Department, University Hospital Fundacion Jimenez Diaz, 28040 Madrid, Spain
| | - Heather N. Hayenga
- Department of Bioengineering, University of Texas at Dallas, Richardson, TX 75080, USA
| | - Leonidas Bleris
- Department of Bioengineering, University of Texas at Dallas, Richardson, TX 75080, USA
- Center for Systems Biology, University of Texas at Dallas, Richardson, TX 75080, USA
- Department of Biological Sciences, University of Texas at Dallas, Richardson, TX 75080, USA
| |
Collapse
|
2
|
Gubu A, Ma Y, Yu S, Zhang H, Chen Z, Ni S, Abdullah R, Xiao H, Zhang Y, Dai H, Luo H, Yu Y, Wang L, Jiang H, Zhang N, Tian Y, Li H, Lu A, Zhang B, Zhang G. Unique quinoline orientations shape the modified aptamer to sclerostin for enhanced binding affinity and bone anabolic potential. Mol Ther Nucleic Acids 2024; 35:102146. [PMID: 38444701 PMCID: PMC10914587 DOI: 10.1016/j.omtn.2024.102146] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/06/2023] [Accepted: 02/09/2024] [Indexed: 03/07/2024]
Abstract
Osteogenesis imperfecta (OI) is a rare genetic disease characterized by bone fragility and bone formation. Sclerostin could negatively regulate bone formation by antagonizing the Wnt signal pathway, whereas it imposes severe cardiac ischemic events in clinic. Our team has screened an aptamer that could promote bone anabolic potential without cardiovascular risk. However, the affinity of the aptamer is lower and needs to be improved. In the study, hydrophobic quinoline molecule with unique orientations (seven subtypes) were incorporated into key sites of a bone anabolic aptamer against sclerostin to form a modified aptamer library. Among all the quinoline modifications, 5-quinoline modification could shape the molecular recognition of modified aptamers to sclerostin to facilitate enhancing its binding to sclerostin toward the highest affinity by interacting with newly participated binding sites in sclerostin. Further, 5-quinoline modification could facilitate the modified aptamer attenuating the suppressed effect of the transfected sclerostin on both Wnt signaling and bone formation marker expression levels in vitro, promoting bone anabolism in OI mice (Col1a2+/G610C). The proposed quinoline-oriented modification strategy could shape the molecular recognition of modified aptamers to proteins to facilitate enhancing its binding affinity and therapeutic potency.
Collapse
Affiliation(s)
- Amu Gubu
- Guangdong-Hong Kong-Macao Greater Bay Area International Research Platform for Aptamer-based Translational Medicine and Drug Discovery, Hong Kong SAR 999077, China
- Law Sau Fai Institute for Advancing Translational Medicine in Bone & Joint Diseases, School of Chinese Medicine, Hong Kong Baptist University, Hong Kong SAR 999077, China
| | - Yuan Ma
- Guangdong-Hong Kong-Macao Greater Bay Area International Research Platform for Aptamer-based Translational Medicine and Drug Discovery, Hong Kong SAR 999077, China
- Law Sau Fai Institute for Advancing Translational Medicine in Bone & Joint Diseases, School of Chinese Medicine, Hong Kong Baptist University, Hong Kong SAR 999077, China
- Increasepharm & Hong Kong Baptist University Joint Centre for Nucleic Acid Drug Discovery, Hong Kong Science Park, New Territories, Hong Kong, China
| | - Sifan Yu
- Guangdong-Hong Kong-Macao Greater Bay Area International Research Platform for Aptamer-based Translational Medicine and Drug Discovery, Hong Kong SAR 999077, China
- School of Chinese Medicine, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong SAR 999077, China
- Shenzhen Research Institute, The Chinese University of Hong Kong, School of Chinese Medicine, The Chinese University of Hong Kong, Shen Zhen 518063, China
| | - Huarui Zhang
- Guangdong-Hong Kong-Macao Greater Bay Area International Research Platform for Aptamer-based Translational Medicine and Drug Discovery, Hong Kong SAR 999077, China
- School of Chinese Medicine, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong SAR 999077, China
| | - Zefeng Chen
- Guangdong-Hong Kong-Macao Greater Bay Area International Research Platform for Aptamer-based Translational Medicine and Drug Discovery, Hong Kong SAR 999077, China
- Law Sau Fai Institute for Advancing Translational Medicine in Bone & Joint Diseases, School of Chinese Medicine, Hong Kong Baptist University, Hong Kong SAR 999077, China
- Increasepharm & Hong Kong Baptist University Joint Centre for Nucleic Acid Drug Discovery, Hong Kong Science Park, New Territories, Hong Kong, China
| | - Shuaijian Ni
- Guangdong-Hong Kong-Macao Greater Bay Area International Research Platform for Aptamer-based Translational Medicine and Drug Discovery, Hong Kong SAR 999077, China
| | - Razack Abdullah
- Guangdong-Hong Kong-Macao Greater Bay Area International Research Platform for Aptamer-based Translational Medicine and Drug Discovery, Hong Kong SAR 999077, China
- Law Sau Fai Institute for Advancing Translational Medicine in Bone & Joint Diseases, School of Chinese Medicine, Hong Kong Baptist University, Hong Kong SAR 999077, China
- Institute of Integrated Bioinfomedicine and Translational Science, School of Chinese Medicine, Hong Kong Baptist University, Kowloon Tsai, Hong Kong 999077, China
| | - Huan Xiao
- Guangdong-Hong Kong-Macao Greater Bay Area International Research Platform for Aptamer-based Translational Medicine and Drug Discovery, Hong Kong SAR 999077, China
- School of Chinese Medicine, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong SAR 999077, China
| | - Yihao Zhang
- Guangdong-Hong Kong-Macao Greater Bay Area International Research Platform for Aptamer-based Translational Medicine and Drug Discovery, Hong Kong SAR 999077, China
- School of Chinese Medicine, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong SAR 999077, China
| | - Hong Dai
- Guangdong-Hong Kong-Macao Greater Bay Area International Research Platform for Aptamer-based Translational Medicine and Drug Discovery, Hong Kong SAR 999077, China
| | - Hang Luo
- Guangdong-Hong Kong-Macao Greater Bay Area International Research Platform for Aptamer-based Translational Medicine and Drug Discovery, Hong Kong SAR 999077, China
- School of Chinese Medicine, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong SAR 999077, China
| | - Yuanyuan Yu
- Guangdong-Hong Kong-Macao Greater Bay Area International Research Platform for Aptamer-based Translational Medicine and Drug Discovery, Hong Kong SAR 999077, China
- Law Sau Fai Institute for Advancing Translational Medicine in Bone & Joint Diseases, School of Chinese Medicine, Hong Kong Baptist University, Hong Kong SAR 999077, China
| | - Luyao Wang
- Guangdong-Hong Kong-Macao Greater Bay Area International Research Platform for Aptamer-based Translational Medicine and Drug Discovery, Hong Kong SAR 999077, China
- Law Sau Fai Institute for Advancing Translational Medicine in Bone & Joint Diseases, School of Chinese Medicine, Hong Kong Baptist University, Hong Kong SAR 999077, China
| | - Hewen Jiang
- Guangdong-Hong Kong-Macao Greater Bay Area International Research Platform for Aptamer-based Translational Medicine and Drug Discovery, Hong Kong SAR 999077, China
- School of Chinese Medicine, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong SAR 999077, China
| | - Ning Zhang
- Guangdong-Hong Kong-Macao Greater Bay Area International Research Platform for Aptamer-based Translational Medicine and Drug Discovery, Hong Kong SAR 999077, China
- School of Chinese Medicine, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong SAR 999077, China
| | - Yuan Tian
- Law Sau Fai Institute for Advancing Translational Medicine in Bone & Joint Diseases, School of Chinese Medicine, Hong Kong Baptist University, Hong Kong SAR 999077, China
- Institute of Integrated Bioinfomedicine and Translational Science, School of Chinese Medicine, Hong Kong Baptist University, Kowloon Tsai, Hong Kong 999077, China
| | - Haitian Li
- Law Sau Fai Institute for Advancing Translational Medicine in Bone & Joint Diseases, School of Chinese Medicine, Hong Kong Baptist University, Hong Kong SAR 999077, China
- Institute of Integrated Bioinfomedicine and Translational Science, School of Chinese Medicine, Hong Kong Baptist University, Kowloon Tsai, Hong Kong 999077, China
| | - Aiping Lu
- Guangdong-Hong Kong-Macao Greater Bay Area International Research Platform for Aptamer-based Translational Medicine and Drug Discovery, Hong Kong SAR 999077, China
| | - Baoting Zhang
- School of Chinese Medicine, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong SAR 999077, China
| | - Ge Zhang
- Guangdong-Hong Kong-Macao Greater Bay Area International Research Platform for Aptamer-based Translational Medicine and Drug Discovery, Hong Kong SAR 999077, China
- Law Sau Fai Institute for Advancing Translational Medicine in Bone & Joint Diseases, School of Chinese Medicine, Hong Kong Baptist University, Hong Kong SAR 999077, China
| |
Collapse
|
3
|
Spangsberg Petersen US, Dembic M, Martínez-Pizarro A, Richard E, Holm LL, Havelund JF, Doktor TK, Larsen MR, Færgeman NJ, Desviat LR, Andresen BS. Regulating PCCA gene expression by modulation of pseudoexon splicing patterns to rescue enzyme activity in propionic acidemia. Mol Ther Nucleic Acids 2024; 35:102101. [PMID: 38204914 PMCID: PMC10776996 DOI: 10.1016/j.omtn.2023.102101] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/10/2023] [Accepted: 12/08/2023] [Indexed: 01/12/2024]
Abstract
Pseudoexons are nonfunctional intronic sequences that can be activated by deep-intronic sequence variation. Activation increases pseudoexon inclusion in mRNA and interferes with normal gene expression. The PCCA c.1285-1416A>G variation activates a pseudoexon and causes the severe metabolic disorder propionic acidemia by deficiency of the propionyl-CoA carboxylase enzyme encoded by PCCA and PCCB. We characterized this pathogenic pseudoexon activation event in detail and identified hnRNP A1 to be important for normal repression. The PCCA c.1285-1416A>G variation disrupts an hnRNP A1-binding splicing silencer and simultaneously creates a splicing enhancer. We demonstrate that blocking this region of regulation with splice-switching antisense oligonucleotides restores normal splicing and rescues enzyme activity in patient fibroblasts and in a cellular model created by CRISPR gene editing. Interestingly, the PCCA pseudoexon offers an unexploited potential to upregulate gene expression because healthy tissues show relatively high inclusion levels. By blocking inclusion of the nonactivated wild-type pseudoexon, we can increase both PCCA and PCCB protein levels, which increases the activity of the heterododecameric enzyme. Surprisingly, we can increase enzyme activity from residual levels in not only patient fibroblasts harboring PCCA missense variants but also those harboring PCCB missense variants. This is a potential treatment strategy for propionic acidemia.
Collapse
Affiliation(s)
- Ulrika Simone Spangsberg Petersen
- Department of Biochemistry and Molecular Biology and the Villum Center for Bioanalytical Sciences, University of Southern Denmark, 5230 Odense M, Denmark
| | - Maja Dembic
- Department of Biochemistry and Molecular Biology and the Villum Center for Bioanalytical Sciences, University of Southern Denmark, 5230 Odense M, Denmark
- Department of Clinical Genetics, Odense University Hospital, 5000 Odense C, Denmark
- Department of Mathematics and Computer Science, University of Southern Denmark, 5230 Odense M, Denmark
| | - Ainhoa Martínez-Pizarro
- Centro de Biología Molecular Severo Ochoa, UAM-CSIC, CEDEM, CIBERER, IdiPaz, Universidad Autónoma de Madrid, 28049 Madrid, Spain
| | - Eva Richard
- Centro de Biología Molecular Severo Ochoa, UAM-CSIC, CEDEM, CIBERER, IdiPaz, Universidad Autónoma de Madrid, 28049 Madrid, Spain
| | - Lise Lolle Holm
- Department of Biochemistry and Molecular Biology and the Villum Center for Bioanalytical Sciences, University of Southern Denmark, 5230 Odense M, Denmark
| | - Jesper Foged Havelund
- Department of Biochemistry and Molecular Biology and the Villum Center for Bioanalytical Sciences, University of Southern Denmark, 5230 Odense M, Denmark
| | - Thomas Koed Doktor
- Department of Biochemistry and Molecular Biology and the Villum Center for Bioanalytical Sciences, University of Southern Denmark, 5230 Odense M, Denmark
| | - Martin Røssel Larsen
- Department of Biochemistry and Molecular Biology and the Villum Center for Bioanalytical Sciences, University of Southern Denmark, 5230 Odense M, Denmark
| | - Nils J. Færgeman
- Department of Biochemistry and Molecular Biology and the Villum Center for Bioanalytical Sciences, University of Southern Denmark, 5230 Odense M, Denmark
| | - Lourdes Ruiz Desviat
- Centro de Biología Molecular Severo Ochoa, UAM-CSIC, CEDEM, CIBERER, IdiPaz, Universidad Autónoma de Madrid, 28049 Madrid, Spain
| | - Brage Storstein Andresen
- Department of Biochemistry and Molecular Biology and the Villum Center for Bioanalytical Sciences, University of Southern Denmark, 5230 Odense M, Denmark
| |
Collapse
|
4
|
Duan C, Kang M, Pan X, Gan Z, Huang V, Li G, Place RF, Li LC. Intrathecal administration of a novel siRNA modality extends survival and improves motor function in the SOD1 G93A ALS mouse model. Mol Ther Nucleic Acids 2024; 35:102147. [PMID: 38435120 PMCID: PMC10907209 DOI: 10.1016/j.omtn.2024.102147] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Accepted: 02/12/2024] [Indexed: 03/05/2024]
Abstract
Antisense oligonucleotides (ASOs) were the first modality to pioneer targeted gene knockdown in the treatment of amyotrophic lateral sclerosis (ALS) caused by mutant superoxide dismutase 1 (SOD1). RNA interference (RNAi) is another mechanism of gene silencing in which short interfering RNAs (siRNAs) effectively degrade complementary transcripts. However, delivery to extrahepatic tissues like the CNS has been a bottleneck in the clinical development of RNAi. Herein, we identify potent siRNA duplexes for the knockdown of human SOD1 in which medicinal chemistry and conjugation to an accessory oligonucleotide (ACO) enable activity in CNS tissues. Local delivery via intracerebroventricular or intrathecal injection into SOD1G93A mice delayed disease progression and extended animal survival with superior efficacy compared with an ASO resembling tofersen in sequence and chemistry. Treatment also prevented disease-related declines in motor function, including improvements in animal mobility, muscle strength, and coordination. The ACO itself does not target any specific complementary nucleic acid sequence; rather, it imparts benefits conducive to bioavailability and delivery through its chemistry. The complete conjugate (i.e., siRNA-ACO) represents a novel modality for delivery of duplex RNA (e.g., siRNA) to the CNS that is currently being tested in the clinic for treatment of ALS.
Collapse
Affiliation(s)
- Chunling Duan
- Ractigen Therapeutics, Nantong, Jiangsu Province, China
| | - Moorim Kang
- Ractigen Therapeutics, Nantong, Jiangsu Province, China
| | - Xiaojie Pan
- Ractigen Therapeutics, Nantong, Jiangsu Province, China
| | - Zubao Gan
- Ractigen Therapeutics, Nantong, Jiangsu Province, China
| | - Vera Huang
- Ractigen Therapeutics, Nantong, Jiangsu Province, China
| | - Guanlin Li
- Ractigen Therapeutics, Nantong, Jiangsu Province, China
| | | | - Long-Cheng Li
- Ractigen Therapeutics, Nantong, Jiangsu Province, China
- Institute of Reproductive Medicine, Nantong University School of Medicine, Nantong, Jiangsu, China
| |
Collapse
|
5
|
Wang W, Chen X, Chen J, Xu M, Liu Y, Yang S, Zhao W, Tan S. Engineering lentivirus envelope VSV-G for liver targeted delivery of IDOL-shRNA to ameliorate hypercholesterolemia and atherosclerosis. Mol Ther Nucleic Acids 2024; 35:102115. [PMID: 38314097 PMCID: PMC10835450 DOI: 10.1016/j.omtn.2024.102115] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/12/2023] [Accepted: 01/05/2024] [Indexed: 02/06/2024]
Abstract
Lentiviral vectors (LVs) have been widely used as a tool for gene therapies. However, tissue-selective transduction after systemic delivery remains a challenge. Inducible degrader of low-density lipoprotein receptor is an attractive target for treating hypercholesterolemia. Here, a liver-targeted LV, CS8-LV-shIDOL, is developed by incorporating a hepatocyte-targeted peptide derived from circumsporozoite protein (CSP) into the lentivirus envelope for liver-targeted delivery of IDOL-shRNA (short hairpin RNA) to alleviate hypercholesterolemia. Tail-vein injection of CS8-LV-shIDOL results in extremely high accumulation in liver and nearly undetectable levels in other organs in mice. In addition, it shows superior therapeutic efficacy in lowering serum low-density lipoprotein cholesterol (LDL-C) and reducing atherosclerotic lesions over unmodified LV-shIDOL in hyperlipidemic mice. Mechanically, the envelope-engineered CS8-LV-shIDOL can enter liver cells via low-density lipoprotein receptor-related protein (LRP). Thus, this study provides a novel approach for liver-targeted delivery of IDOL-shRNA to treat hypercholesterolemia by using an envelope-engineered LV, and this delivery system has great potential for liver-targeted transgene therapy.
Collapse
Affiliation(s)
- Wei Wang
- Department of Cell and Molecular Biology, School of Life Science and Technology, State Key Laboratory of Natural Medicines, Jiangsu Key Laboratory of Druggability of Biopharmaceuticals, China Pharmaceutical University, Nanjing 210009, China
| | - Xuemei Chen
- Department of Cell and Molecular Biology, School of Life Science and Technology, State Key Laboratory of Natural Medicines, Jiangsu Key Laboratory of Druggability of Biopharmaceuticals, China Pharmaceutical University, Nanjing 210009, China
| | - Jiali Chen
- Department of Cell and Molecular Biology, School of Life Science and Technology, State Key Laboratory of Natural Medicines, Jiangsu Key Laboratory of Druggability of Biopharmaceuticals, China Pharmaceutical University, Nanjing 210009, China
| | - Menglong Xu
- Department of Cell and Molecular Biology, School of Life Science and Technology, State Key Laboratory of Natural Medicines, Jiangsu Key Laboratory of Druggability of Biopharmaceuticals, China Pharmaceutical University, Nanjing 210009, China
| | - Ying Liu
- Department of Cell and Molecular Biology, School of Life Science and Technology, State Key Laboratory of Natural Medicines, Jiangsu Key Laboratory of Druggability of Biopharmaceuticals, China Pharmaceutical University, Nanjing 210009, China
| | - Shijie Yang
- Department of Cell and Molecular Biology, School of Life Science and Technology, State Key Laboratory of Natural Medicines, Jiangsu Key Laboratory of Druggability of Biopharmaceuticals, China Pharmaceutical University, Nanjing 210009, China
| | - Wenfeng Zhao
- Department of Cell and Molecular Biology, School of Life Science and Technology, State Key Laboratory of Natural Medicines, Jiangsu Key Laboratory of Druggability of Biopharmaceuticals, China Pharmaceutical University, Nanjing 210009, China
| | - Shuhua Tan
- Department of Cell and Molecular Biology, School of Life Science and Technology, State Key Laboratory of Natural Medicines, Jiangsu Key Laboratory of Druggability of Biopharmaceuticals, China Pharmaceutical University, Nanjing 210009, China
| |
Collapse
|
6
|
Cheng SY, Caiazzi J, Biscans A, Alterman JF, Echeverria D, McHugh N, Hassler M, Jolly S, Giguere D, Cipi J, Khvorova A, Punzo C. Single intravitreal administration of a tetravalent siRNA exhibits robust and efficient gene silencing in mouse and pig photoreceptors. Mol Ther Nucleic Acids 2024; 35:102088. [PMID: 38192611 PMCID: PMC10772295 DOI: 10.1016/j.omtn.2023.102088] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/28/2023] [Accepted: 11/30/2023] [Indexed: 01/10/2024]
Abstract
Inherited retinal dystrophies caused by dominant mutations in photoreceptor (PR) cell expressed genes are a major cause of irreversible vision loss. Oligonucleotide therapy has been of interest in diseases that conventional medicine cannot target. In the early days, small interfering RNAs (siRNAs) were explored in clinical trials for retinal disorders with limited success due to a lack of stability and efficient cellular delivery. Thus, an unmet need exists to identify siRNA chemistry that targets PR cell expressed genes. Here, we evaluated 12 different fully chemically modified siRNA configurations, where the valency and conjugate structure were systematically altered. The impact on retinal distribution following intravitreal delivery was examined. We found that the increase in valency (tetravalent siRNA) supports the best PR accumulation. A single intravitreal administration induces multimonths efficacy in rodent and porcine retinas while demonstrating a good safety profile. The data suggest that this configuration can treat retinal diseases caused by PR cell expressed genes with 1-2 intravitreal injections per year.
Collapse
Affiliation(s)
- Shun-Yun Cheng
- Department of Ophthalmology and Visual Sciences, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA
- Horae Gene Therapy Center, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA
- Department of Neurobiology, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA
| | - Jillian Caiazzi
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA
| | - Annabelle Biscans
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA
| | - Julia F. Alterman
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA
| | - Dimas Echeverria
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA
| | - Nicholas McHugh
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA
| | - Matthew Hassler
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA
| | - Samson Jolly
- Department of Ophthalmology and Visual Sciences, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA
| | - Delaney Giguere
- Department of Ophthalmology and Visual Sciences, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA
| | - Joris Cipi
- Department of Ophthalmology and Visual Sciences, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA
| | - Anastasia Khvorova
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA
| | - Claudio Punzo
- Department of Ophthalmology and Visual Sciences, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA
- Horae Gene Therapy Center, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA
- Department of Neurobiology, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA
| |
Collapse
|
7
|
Moreira L, Guimarães NM, Santos RS, Loureiro JA, Pereira MC, Azevedo NF. Promising strategies employing nucleic acids as antimicrobial drugs. Mol Ther Nucleic Acids 2024; 35:102122. [PMID: 38333674 PMCID: PMC10850860 DOI: 10.1016/j.omtn.2024.102122] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/10/2024]
Abstract
Antimicrobial resistance (AMR) is a growing concern because it causes microorganisms to develop resistance to drugs commonly used to treat infections. This results in increased difficulty in treating infections, leading to higher mortality rates and significant economic effects. Investing in new antimicrobial agents is, therefore, necessary to prevent and control AMR. Antimicrobial nucleic acids have arisen as potential key players in novel therapies for AMR infections. They have been designed to serve as antimicrobials and to act as adjuvants to conventional antibiotics or to inhibit virulent mechanisms. This new category of antimicrobial drugs consists of antisense oligonucleotides and oligomers, DNAzymes, and transcription factor decoys, differing in terms of structure, target molecules, and mechanisms of action. They are synthesized using nucleic acid analogs to enhance their resistance to nucleases. Because bacterial envelopes are generally impermeable to oligonucleotides, delivery into the cytoplasm typically requires the assistance of nanocarriers, which can affect their therapeutic potency. Given that numerous factors contribute to the success of these antimicrobial drugs, this review aims to provide a summary of the key advancements in the use of oligonucleotides for treating bacterial infections. Their mechanisms of action and the impact of factors such as nucleic acid design, target sequence, and nanocarriers on the antimicrobial potency are discussed.
Collapse
Affiliation(s)
- Luís Moreira
- LEPABE–Laboratory for Process Engineering, Environment, Biotechnology, and Energy, Faculty of Engineering, University of Porto, Rua Dr. Roberto Frias, 4200-465 Porto, Portugal
- ALiCE–Associate Laboratory in Chemical Engineering, Faculty of Engineering, University of Porto, Rua Dr. Roberto Frias, 4200-465 Porto, Portugal
| | - Nuno M. Guimarães
- LEPABE–Laboratory for Process Engineering, Environment, Biotechnology, and Energy, Faculty of Engineering, University of Porto, Rua Dr. Roberto Frias, 4200-465 Porto, Portugal
- ALiCE–Associate Laboratory in Chemical Engineering, Faculty of Engineering, University of Porto, Rua Dr. Roberto Frias, 4200-465 Porto, Portugal
| | - Rita S. Santos
- LEPABE–Laboratory for Process Engineering, Environment, Biotechnology, and Energy, Faculty of Engineering, University of Porto, Rua Dr. Roberto Frias, 4200-465 Porto, Portugal
- ALiCE–Associate Laboratory in Chemical Engineering, Faculty of Engineering, University of Porto, Rua Dr. Roberto Frias, 4200-465 Porto, Portugal
| | - Joana A. Loureiro
- LEPABE–Laboratory for Process Engineering, Environment, Biotechnology, and Energy, Faculty of Engineering, University of Porto, Rua Dr. Roberto Frias, 4200-465 Porto, Portugal
- ALiCE–Associate Laboratory in Chemical Engineering, Faculty of Engineering, University of Porto, Rua Dr. Roberto Frias, 4200-465 Porto, Portugal
| | - Maria C. Pereira
- LEPABE–Laboratory for Process Engineering, Environment, Biotechnology, and Energy, Faculty of Engineering, University of Porto, Rua Dr. Roberto Frias, 4200-465 Porto, Portugal
- ALiCE–Associate Laboratory in Chemical Engineering, Faculty of Engineering, University of Porto, Rua Dr. Roberto Frias, 4200-465 Porto, Portugal
| | - Nuno F. Azevedo
- LEPABE–Laboratory for Process Engineering, Environment, Biotechnology, and Energy, Faculty of Engineering, University of Porto, Rua Dr. Roberto Frias, 4200-465 Porto, Portugal
- ALiCE–Associate Laboratory in Chemical Engineering, Faculty of Engineering, University of Porto, Rua Dr. Roberto Frias, 4200-465 Porto, Portugal
| |
Collapse
|
8
|
Hall J, Zhang Z, Bhattacharya S, Wang D, Alcantara M, Liang Y, Swiderski P, Forman S, Kwak L, Vaidehi N, Kortylewski M. Oligo-PROTAC strategy for cell-selective and targeted degradation of activated STAT3. Mol Ther Nucleic Acids 2024; 35:102137. [PMID: 38384444 PMCID: PMC10879796 DOI: 10.1016/j.omtn.2024.102137] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/03/2023] [Accepted: 01/31/2024] [Indexed: 02/23/2024]
Abstract
Decoy oligodeoxynucleotides (ODNs) allow targeting undruggable transcription factors, such as STAT3, but their limited potency and lack of delivery methods hampered translation. To overcome these challenges, we conjugated a STAT3-specific decoy to thalidomide, a ligand to cereblon in E3 ubiquitin ligase complex, to generate a proteolysis-targeting chimera (STAT3DPROTAC). STAT3DPROTAC downregulated STAT3 in target cells, but not STAT1 or STAT5. Computational modeling of the STAT3DPROTAC ternary complex predicted two surface lysines, K601 and K626, in STAT3 as potential ubiquitination sites. Accordingly, K601/K626 point mutations in STAT3, as well as proteasome inhibition or cereblon deletion, alleviated STAT3DPROTAC effect. Next, we conjugated STAT3DPROTAC to a CpG oligonucleotide targeting Toll-like receptor 9 (TLR9) to generate myeloid/B cell-selective C-STAT3DPROTAC. Naked C-STAT3DPROTAC was spontaneously internalized by TLR9+ myeloid cells, B cells, and human and mouse lymphoma cells but not by T cells. C-STAT3DPROTAC effectively decreased STAT3 protein levels and also STAT3-regulated target genes critical for lymphoma cell proliferation and/or survival (BCL2L1, CCND2, and MYC). Finally, local C-STAT3DPROTAC administration to human Ly3 lymphoma-bearing mice triggered tumor regression, while control C-STAT3D and C-SCR treatments had limited effects. Our results underscore the feasibility of using a PROTAC strategy for cell-selective, decoy oligonucleotide-based STAT3 targeting of and potentially other tumorigenic transcription factors for cancer therapy.
Collapse
Affiliation(s)
- Jeremy Hall
- Department of Immuno-Oncology, Beckman Research Institute, City of Hope, Duarte, CA 91010, USA
| | - Zhuoran Zhang
- Department of Immuno-Oncology, Beckman Research Institute, City of Hope, Duarte, CA 91010, USA
| | - Supriyo Bhattacharya
- Department of Computational and Quantitative Medicine, Beckman Research Institute, City of Hope, Duarte, CA 91010, USA
| | - Dongfang Wang
- Department of Immuno-Oncology, Beckman Research Institute, City of Hope, Duarte, CA 91010, USA
| | - Marice Alcantara
- Department of Immuno-Oncology, Beckman Research Institute, City of Hope, Duarte, CA 91010, USA
| | - Yong Liang
- DNA/RNA Synthesis Core Facility, Beckman Research Institute, City of Hope, Duarte, CA 91010, USA
| | - Piotr Swiderski
- DNA/RNA Synthesis Core Facility, Beckman Research Institute, City of Hope, Duarte, CA 91010, USA
| | - Stephen Forman
- Department of Hematology & Hematopoietic Cell Transplantation, Beckman Research Institute, City of Hope, Duarte, CA 91010, USA
| | - Larry Kwak
- Department of Hematology & Hematopoietic Cell Transplantation, Beckman Research Institute, City of Hope, Duarte, CA 91010, USA
| | - Nagarajan Vaidehi
- Department of Computational and Quantitative Medicine, Beckman Research Institute, City of Hope, Duarte, CA 91010, USA
| | - Marcin Kortylewski
- Department of Immuno-Oncology, Beckman Research Institute, City of Hope, Duarte, CA 91010, USA
| |
Collapse
|
9
|
Autiero I, Vitagliano L. Enhanced molecular dynamic simulation studies unravel long-range effects caused by sequence variations and partner binding in RNA aptamers. Mol Ther Nucleic Acids 2023; 34:102039. [PMID: 37869259 PMCID: PMC10585333 DOI: 10.1016/j.omtn.2023.102039] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/25/2022] [Accepted: 09/23/2023] [Indexed: 10/24/2023]
Abstract
Intrinsic flexibility and structural modularity are two common features of RNA molecules. Although functionally crucial, RNA plasticity often represents a major complication in high-resolution structural studies. To overcome this problem, RNAs may be rigidified through the complexation with high-affinity partners such as Fab molecules. This approach has been previously used to characterize the DIR2-aptamer. However, possible perturbations induced by the insertion of the Fab binding site on the DIR2-aptamer conformational properties were not investigated. Here, using enhanced molecular dynamics simulations, we compared the dynamics of the DIR2 aptamer holding the Fab binding site with that of the parental sequence. Our results suggest that the L2-loop modification for the Fab recognition leads to a significant increase in local flexibility that also affects the mobility of distant regions. The trajectories provide clear indications of the groups and the interactions mediating the dynamics transfer in DIR2. The effectiveness of our approach in addressing RNA flexibility was further corroborated by showing its ability to reproduce the most important events affecting the NF-κB RNA aptamer upon dissociation from the partner. Therefore, REMD analyses, a rarely adopted technique to unravel the structural/dynamical properties of aptamers, could efficiently complement experimental data guiding the rational design of nucleic acid therapeutics.
Collapse
Affiliation(s)
- Ida Autiero
- Institute of Biostructures and Bioimaging, Via Pietro Castellino 111, 80131 Naples, Italy
| | - Luigi Vitagliano
- Institute of Biostructures and Bioimaging, Via Pietro Castellino 111, 80131 Naples, Italy
| |
Collapse
|
10
|
Watanabe N, Tone Y, Nagata T, Masuda S, Saito T, Motohashi N, Takagaki K, Aoki Y, Takeda S. Exon 44 skipping in Duchenne muscular dystrophy: NS-089/NCNP-02, a dual-targeting antisense oligonucleotide. Mol Ther Nucleic Acids 2023; 34:102034. [PMID: 37854955 PMCID: PMC10579524 DOI: 10.1016/j.omtn.2023.102034] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/10/2022] [Accepted: 09/15/2023] [Indexed: 10/20/2023]
Abstract
Exon-skipping therapy mediated by antisense oligonucleotides is expected to provide a therapeutic option for Duchenne muscular dystrophy. Antisense oligonucleotides for exon skipping reported so far target a single continuous sequence in or around the target exon. In the present study, we investigated antisense oligonucleotides for exon 44 skipping (applicable to approximately 6% of all Duchenne muscular dystrophy patients) to improve activity by using a novel antisense oligonucleotide design incorporating two connected sequences. Phosphorodiamidate morpholino oligomers targeting two separate sequences in exon 44 were created to target two splicing regulators in exon 44 simultaneously, and their exon 44 skipping was measured. NS-089/NCNP-02 showed the highest skipping activity among the oligomers. NS-089/NCNP-02 also induced exon 44 skipping and dystrophin protein expression in cells from a Duchenne muscular dystrophy patient to whom exon 44 skipping is applicable. We also assessed the in vivo activity of NS-089/NCNP-02 by intravenous administration to cynomolgus monkeys. NS-089/NCNP-02 induced exon 44 skipping in skeletal and cardiac muscle of cynomolgus monkeys. In conclusion, NS-089/NCNP-02, an antisense oligonucleotide with a novel connected-sequence design, showed highly efficient exon skipping both in vitro and in vivo.
Collapse
Affiliation(s)
- Naoki Watanabe
- Discovery Research Laboratories in Tsukuba, Nippon Shinyaku Co., Ltd, Tsukuba, Ibaraki, Japan
| | - Yuichiro Tone
- Discovery Research Laboratories in Tsukuba, Nippon Shinyaku Co., Ltd, Tsukuba, Ibaraki, Japan
| | - Tetsuya Nagata
- Department of Molecular Therapy, National Institute of Neuroscience, National Center of Neurology and Psychiatry (NCNP), Kodaira, Tokyo, Japan
- Department of Neurology and Neurological Science, Graduate School of Medicine, Tokyo Medical and Dental University, Tokyo, Japan
| | - Satoru Masuda
- Department of Molecular Therapy, National Institute of Neuroscience, National Center of Neurology and Psychiatry (NCNP), Kodaira, Tokyo, Japan
| | - Takashi Saito
- Department of Molecular Therapy, National Institute of Neuroscience, National Center of Neurology and Psychiatry (NCNP), Kodaira, Tokyo, Japan
| | - Norio Motohashi
- Department of Molecular Therapy, National Institute of Neuroscience, National Center of Neurology and Psychiatry (NCNP), Kodaira, Tokyo, Japan
| | - Kazuchika Takagaki
- Discovery Research Laboratories in Tsukuba, Nippon Shinyaku Co., Ltd, Tsukuba, Ibaraki, Japan
| | - Yoshitsugu Aoki
- Department of Molecular Therapy, National Institute of Neuroscience, National Center of Neurology and Psychiatry (NCNP), Kodaira, Tokyo, Japan
| | - Shin’ichi Takeda
- Department of Molecular Therapy, National Institute of Neuroscience, National Center of Neurology and Psychiatry (NCNP), Kodaira, Tokyo, Japan
| |
Collapse
|
11
|
Gwon MG, Leem J, An HJ, Gu H, Bae S, Kim JH, Park KK. The decoy oligodeoxynucleotide against HIF-1α and STAT5 ameliorates atopic dermatitis-like mouse model. Mol Ther Nucleic Acids 2023; 34:102036. [PMID: 37799329 PMCID: PMC10550406 DOI: 10.1016/j.omtn.2023.102036] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/02/2023] [Accepted: 09/15/2023] [Indexed: 10/07/2023]
Abstract
Atopic dermatitis (AD) is a common inflammatory skin disease caused by an immune disorder. Mast cells are known to be activated and granulated to maintain an allergic reaction, including rhinitis, asthma, and AD. Although hypoxia-inducible factor-1 alpha (HIF-1α) and signal transducer and activator of transcription 5 (STAT5) play crucial roles in mast cell survival and granulation, their effects need to be clarified in allergic disorders. Thus, we designed decoy oligodeoxynucleotide (ODN) synthetic DNA, without open ends, containing complementary sequences for HIF-1α and STAT5 to suppress the transcriptional activities of HIF-1α and STAT5. In this study, we demonstrated the effects of HIF-1α/STAT5 ODN using AD-like in vivo and in vitro models. The HIF-1α/STAT5 decoy ODN significantly alleviated cutaneous symptoms similar to AD, including morphology changes, immune cell infiltration, skin barrier dysfunction, and inflammatory response. In the AD model, it also inhibited mast cell infiltration and degranulation in skin tissue. These results suggest that the HIF-1α/STAT5 decoy ODN ameliorates the AD-like disorder and immunoglobulin E (IgE)-induced mast cell activation by disrupting HIF-1α/STAT5 signaling pathways. Taken together, these findings suggest the possibility of HIF-1α/STAT5 as therapeutic targets and their decoy ODN as a potential therapeutic tool for AD.
Collapse
Affiliation(s)
- Mi-Gyeong Gwon
- Department of Pathology, School of Medicine, Daegu Catholic University, Daegu 42472, Republic of Korea
| | - Jaechan Leem
- Department of Immunology, School of Medicine, Daegu Catholic University, Daegu 42472, Republic of Korea
| | - Hyun-Jin An
- Department of Pathology, School of Medicine, Daegu Catholic University, Daegu 42472, Republic of Korea
| | - Hyemin Gu
- Department of Pathology, School of Medicine, Daegu Catholic University, Daegu 42472, Republic of Korea
| | - Seongjae Bae
- Department of Pathology, School of Medicine, Daegu Catholic University, Daegu 42472, Republic of Korea
| | - Jong Hyun Kim
- Department of Biochemistry, School of Medicine, Daegu Catholic University, Daegu 42472, Republic of Korea
| | - Kwan-Kyu Park
- Department of Pathology, School of Medicine, Daegu Catholic University, Daegu 42472, Republic of Korea
| |
Collapse
|
12
|
Chu Z, Zhang B, Zhou X, Yuan H, Gao C, Liu L, Xiao Y, Zhang J, Hong J, Liang J, Chen D, Yao N. A DNA/RNA heteroduplex oligonucleotide coupling asparagine depletion restricts FGFR2 fusion-driven intrahepatic cholangiocarcinoma. Mol Ther Nucleic Acids 2023; 34:102047. [PMID: 37869260 PMCID: PMC10589379 DOI: 10.1016/j.omtn.2023.102047] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/25/2023] [Accepted: 09/29/2023] [Indexed: 10/24/2023]
Abstract
Pemigatinib, a pan-FGFR inhibitor, is approved to treat intrahepatic cholangiocarcinoma (ICC) harboring FGFR2 fusion mutations. Improving its targeting of FGFR2 fusions remains an unmet clinical need due to its pan selectivity and resistance. Here, we report a cholesterol-conjugated DNA/RNA heteroduplex oligonucleotide targeting the chimeric site in FGFR2-AHCYL1 (F-A Cho-HDO) that accumulates in ICC through endocytosis of low-density lipoprotein receptor (LDLR), which is highly expressed in both human and murine ICC. F-A Cho-HDO was determined to be a highly specific, sustainable, and well-tolerated agent for inhibiting ICC progression through posttranscriptional suppression of F-A in ICC patient-derived xenograft mouse models. Moreover, we identified an EGFR-orchestrated bypass signaling axis that partially offset the efficacy of F-A Cho-HDO. Mechanistically, EGFR-induced STAT1 upregulation promoted asparagine (Asn) synthesis through direct transcriptional upregulation of asparagine synthetase (ASNS) and dictated cell survival by preventing p53-dependent cell cycle arrest. Asn restriction with ASNase or ASNS inhibitors reduced the intracellular Asn, thereby reactivating p53 and sensitizing ICC to F-A Cho-HDO. Our findings highlight the application of genetic engineering therapies in ICC harboring FGFR2 fusions and reveal an axis of adaptation to FGFR2 inhibition that presents a rationale for the clinical evaluation of a strategy combining FGFR2 inhibitors with Asn depletion.
Collapse
Affiliation(s)
- Zhenzhen Chu
- Department of Pathophysiology, School of Medicine, Jinan University, Guangzhou, Guangdong 510632, China
| | - Baohuan Zhang
- Morphology Experimental Teaching Center, School of Medicine, Jinan University, Guangzhou, Guangdong 510632, China
| | - Xuxuan Zhou
- Department of Pathophysiology, School of Medicine, Jinan University, Guangzhou, Guangdong 510632, China
| | - Hui Yuan
- Department of Gastroenterology, Huizhou Municipal Central Hospital, Huizhou, Guangdong 516001, China
| | - Chongqing Gao
- Department of Pathophysiology, School of Medicine, Jinan University, Guangzhou, Guangdong 510632, China
| | - Lihao Liu
- School of Medicine, Jinan University, Guangzhou, Guangdong 510632, China
| | - Yang Xiao
- Department of Hepatobiliary Surgery, the First Affiliated Hospital, Jinan University, Guangzhou, Guangdong 510632, China
| | - Jichun Zhang
- Department of Physiology, School of Medicine, Jinan University, Guangzhou, Guangdong 510632, China
| | - Jian Hong
- Department of Pathophysiology, School of Medicine, Jinan University, Guangzhou, Guangdong 510632, China
- Department of Hepatobiliary Surgery, the First Affiliated Hospital, Jinan University, Guangzhou, Guangdong 510632, China
| | - Junjie Liang
- Department of Hepatobiliary Surgery, the First Affiliated Hospital, Jinan University, Guangzhou, Guangdong 510632, China
| | - Dong Chen
- Department of Pancreato-Biliary Surgery, the First Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong 510080, China
| | - Nan Yao
- Department of Pathophysiology, School of Medicine, Jinan University, Guangzhou, Guangdong 510632, China
| |
Collapse
|
13
|
Obata T, Tsutsumi K, Ueta E, Oda T, Kikuchi T, Ako S, Fujii Y, Yamazaki T, Uchida D, Matsumoto K, Horiguchi S, Kato H, Okada H, Otsuka M. MicroRNA-451a inhibits gemcitabine-refractory biliary tract cancer progression by suppressing the MIF-mediated PI3K/AKT pathway. Mol Ther Nucleic Acids 2023; 34:102054. [PMID: 38111913 PMCID: PMC10726424 DOI: 10.1016/j.omtn.2023.102054] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/01/2023] [Accepted: 10/11/2023] [Indexed: 12/20/2023]
Abstract
Gemcitabine is an effective chemotherapeutic agent for biliary tract cancers (BTCs), including gallbladder cancer (GBC) and cholangiocarcinoma (CCA). However, few other effective agents are currently available, particularly for GEM-refractory BTCs. We previously identified microRNA-451a (miR-451a) as a potential therapeutic target in GBC. To elucidate the antineoplastic effects of miR-451a and its underlying mechanisms, we transfected miR-451a into GBC, gemcitabine-resistant GBC (GR-GBC), and gemcitabine-resistant CCA (GR-CCA) cell lines. Furthermore, mimicking in vivo conditions, tumorigenic GBC organoids and three-dimensional (3D) cell culture systems were employed to investigate the anti-proliferative effects of miR-451a on BTCs, and its effect on stem cell properties. We found that miR-451a significantly inhibited cell proliferation, induced apoptosis, and reduced chemoresistant phenotypes, such as epithelial-mesenchymal transition, in both GBC and GR-GBC. The principal mechanism is probably the negative regulation of the phosphatidylinositol 3-kinase/AKT pathway, partially accomplished by directly downregulating macrophage migration inhibitory factor. The Gene Expression Omnibus database revealed that miR-451a was the most significantly downregulated microRNA in CCA tissues. The introduction of miR-451a resulted in similar antineoplastic effects in GR-CCA. Furthermore, miR-451a reduced cell viability in 3D spheroid models and tumorigenic GBC organoids. These findings suggest that the supplementation of miR-451a is a potential treatment strategy for GEM-refractory BTCs.
Collapse
Affiliation(s)
- Taisuke Obata
- Department of Gastroenterology and Hepatology, Okayama University Graduate School of Medicine, Dentistry, and Pharmaceutical Science, Okayama 700-8558, Japan
| | - Koichiro Tsutsumi
- Department of Gastroenterology and Hepatology, Okayama University Hospital, Okayama 700-8558, Japan
| | - Eijiro Ueta
- Department of Gastroenterology and Hepatology, Okayama University Hospital, Okayama 700-8558, Japan
| | - Takashi Oda
- Department of Gastroenterology and Hepatology, Okayama University Graduate School of Medicine, Dentistry, and Pharmaceutical Science, Okayama 700-8558, Japan
| | - Tatsuya Kikuchi
- Department of Gastroenterology and Hepatology, Okayama University Graduate School of Medicine, Dentistry, and Pharmaceutical Science, Okayama 700-8558, Japan
| | - Soichiro Ako
- Department of Gastroenterology and Hepatology, Okayama University Hospital, Okayama 700-8558, Japan
| | - Yuki Fujii
- Department of Gastroenterology and Hepatology, Okayama University Hospital, Okayama 700-8558, Japan
| | - Tatsuhiro Yamazaki
- Department of Gastroenterology and Hepatology, Okayama University Hospital, Okayama 700-8558, Japan
| | - Daisuke Uchida
- Department of Gastroenterology and Hepatology, Okayama University Hospital, Okayama 700-8558, Japan
| | - Kazuyuki Matsumoto
- Department of Gastroenterology and Hepatology, Okayama University Hospital, Okayama 700-8558, Japan
| | - Shigeru Horiguchi
- Department of Gastroenterology and Hepatology, Okayama University Hospital, Okayama 700-8558, Japan
| | - Hironari Kato
- Department of Gastroenterology and Hepatology, Okayama University Hospital, Okayama 700-8558, Japan
| | - Hiroyuki Okada
- Department of Gastroenterology and Hepatology, Okayama University Graduate School of Medicine, Dentistry, and Pharmaceutical Science, Okayama 700-8558, Japan
- Department of Gastroenterology and Hepatology, Okayama University Hospital, Okayama 700-8558, Japan
| | - Motoyuki Otsuka
- Department of Gastroenterology and Hepatology, Okayama University Graduate School of Medicine, Dentistry, and Pharmaceutical Science, Okayama 700-8558, Japan
- Department of Gastroenterology and Hepatology, Okayama University Hospital, Okayama 700-8558, Japan
| |
Collapse
|
14
|
Radloff K, Gutbier B, Dunne CM, Moradian H, Schwestka M, Gossen M, Ahrens K, Kneller L, Wang Y, Moga A, Gkionis L, Keil O, Fehring V, Tondera D, Giese K, Santel A, Kaufmann J, Witzenrath M. Cationic LNP-formulated mRNA expressing Tie2-agonist in the lung endothelium prevents pulmonary vascular leakage. Mol Ther Nucleic Acids 2023; 34:102068. [PMID: 38034031 PMCID: PMC10682670 DOI: 10.1016/j.omtn.2023.102068] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/26/2023] [Accepted: 10/25/2023] [Indexed: 12/02/2023]
Abstract
Dysfunction of endothelial cells (ECs) lining the inner surface of blood vessels are causative for a number of diseases. Hence, the ability to therapeutically modulate gene expression within ECs is of high therapeutic value in treating diseases such as those associated with lung edema. mRNAs formulated with lipid nanoparticles (LNPs) have emerged as a new drug modality to induce transient protein expression for modulating disease-relevant signal transduction pathways. In the study presented here, we tested the effect of a novel synthetic, nucleoside-modified mRNA encoding COMP-Ang1 (mRNA-76) formulated into a cationic LNP on attenuating inflammation-induced vascular leakage. After intravenous injection, the respective mRNA was found to be delivered almost exclusively to the ECs of the lung, while sparing other vascular beds and bypassing the liver. The mode of action of mRNA-76, such as its activation of the Tie2 signal transduction pathway, was tested by pharmacological studies in vitro and in vivo in respective mouse models. mRNA-76 was found to prevent lung vascular leakage/lung edema as well as neutrophil infiltration in a lipopolysaccharide-challenging model.
Collapse
Affiliation(s)
| | - Birgitt Gutbier
- Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Department of Infectious Diseases, Respiratory Medicine, and Critical Care, 10117 Berlin, Germany
| | | | - Hanieh Moradian
- Institute of Active Polymers, Helmholtz-Zentrum Hereon, 14513 Teltow, Germany
- Berlin-Brandenburg Center for Regenerative Therapies (BCRT) Charité Campus Virchow Klinikum, 13353 Berlin, Germany
| | - Marko Schwestka
- Institute of Active Polymers, Helmholtz-Zentrum Hereon, 14513 Teltow, Germany
- Berlin-Brandenburg Center for Regenerative Therapies (BCRT) Charité Campus Virchow Klinikum, 13353 Berlin, Germany
| | - Manfred Gossen
- Institute of Active Polymers, Helmholtz-Zentrum Hereon, 14513 Teltow, Germany
- Berlin-Brandenburg Center for Regenerative Therapies (BCRT) Charité Campus Virchow Klinikum, 13353 Berlin, Germany
| | - Katharina Ahrens
- Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Department of Infectious Diseases, Respiratory Medicine, and Critical Care, 10117 Berlin, Germany
| | - Laura Kneller
- Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Department of Infectious Diseases, Respiratory Medicine, and Critical Care, 10117 Berlin, Germany
| | - Yadong Wang
- Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Department of Infectious Diseases, Respiratory Medicine, and Critical Care, 10117 Berlin, Germany
| | - Akanksha Moga
- Pantherna Therapeutics GmbH, 16761 Hennigsdorf, Germany
| | | | - Oliver Keil
- Pantherna Therapeutics GmbH, 16761 Hennigsdorf, Germany
| | | | | | - Klaus Giese
- Pantherna Therapeutics GmbH, 16761 Hennigsdorf, Germany
| | - Ansgar Santel
- Pantherna Therapeutics GmbH, 16761 Hennigsdorf, Germany
| | - Jörg Kaufmann
- Pantherna Therapeutics GmbH, 16761 Hennigsdorf, Germany
| | - Martin Witzenrath
- Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Department of Infectious Diseases, Respiratory Medicine, and Critical Care, 10117 Berlin, Germany
| |
Collapse
|
15
|
Rossi M, Steklov M, Huberty F, Nguyen T, Marijsse J, Jacques-Hespel C, Najm P, Lonez C, Breman E. Efficient shRNA-based knockdown of multiple target genes for cell therapy using a chimeric miRNA cluster platform. Mol Ther Nucleic Acids 2023; 34:102038. [PMID: 37799328 PMCID: PMC10548280 DOI: 10.1016/j.omtn.2023.102038] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/20/2023] [Accepted: 09/15/2023] [Indexed: 10/07/2023]
Abstract
Genome engineering technologies are powerful tools in cell-based immunotherapy to optimize or fine-tune cell functionalities. However, their use for multiple gene edits poses relevant biological and technical challenges. Short hairpin RNA (shRNA)-based cell engineering bypasses these criticalities and represents a valid alternative to CRISPR-based gene editing. Here, we describe a microRNA (miRNA)-based multiplex shRNA platform obtained by combining highly efficient miRNA scaffolds into a chimeric cluster, to deliver up to four shRNA-like sequences. Thanks to its limited size, our cassette could be deployed in a one-step process along with all the CAR components, streamlining the generation of engineered CAR T cells. The plug-and-play design of the shRNA platform allowed us to swap each shRNA-derived guide sequence without affecting the system performance. Appropriately choosing the target sequences, we were able to either achieve a functional KO, or fine-tune the expression levels of the target genes, all without the need for gene editing. Through our strategy we achieved easy, safe, efficient, and tunable modulation of multiple target genes simultaneously. This approach allows for the effective introduction of multiple functionally relevant tweaks in the transcriptome of the engineered cells, which may lead to increased performance in challenging environments, e.g., solid tumors.
Collapse
Affiliation(s)
- Matteo Rossi
- Celyad Oncology, 1435 Mont-Saint-Guibert, Belgium
| | | | | | - Thuy Nguyen
- Celyad Oncology, 1435 Mont-Saint-Guibert, Belgium
| | | | | | - Paul Najm
- Celyad Oncology, 1435 Mont-Saint-Guibert, Belgium
| | | | - Eytan Breman
- Celyad Oncology, 1435 Mont-Saint-Guibert, Belgium
| |
Collapse
|
16
|
Wallings RL, Mark JR, Staley HA, Gillett DA, Neighbarger N, Kordasiewicz H, Hirst WD, Tansey MG. ASO-mediated knockdown or kinase inhibition of G2019S-Lrrk2 modulates lysosomal tubule-associated antigen presentation in macrophages. Mol Ther Nucleic Acids 2023; 34:102064. [PMID: 38028198 PMCID: PMC10661462 DOI: 10.1016/j.omtn.2023.102064] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/14/2023] [Accepted: 10/18/2023] [Indexed: 12/01/2023]
Abstract
Genetic variation around the LRRK2 gene affects risk for both familial and sporadic Parkinson's disease (PD). LRRK2 levels have become an appealing target for potential PD therapeutics with LRRK2 antisense oligonucleotides (ASOs) now moving toward clinical trials. However, LRRK2 has been suggested to play a fundamental role in peripheral immunity, and it is currently unknown if targeting increased LRRK2 levels in peripheral immune cells will be beneficial or deleterious. Here it was observed that G2019S macrophages exhibited increased stimulation-dependent lysosomal tubule formation (LTF) and MHC-II trafficking from the perinuclear lysosome to the plasma membrane in an mTOR-dependent manner with concomitant increases in pro-inflammatory cytokine release. Both ASO-mediated knockdown of mutant Lrrk2 and LRRK2 kinase inhibition ameliorated this phenotype and decreased these immune responses in control cells. Given the critical role of antigen presentation, lysosomal function, and cytokine release in macrophages, it is likely LRRK2-targeting therapies with systemic activity may have therapeutic value with regard to mutant LRRK2, but deleterious effects on the peripheral immune system, such as altered pathogen control in these cells, should be considered when reducing levels of non-mutant LRRK2.
Collapse
Affiliation(s)
- Rebecca L. Wallings
- Department of Neuroscience, University of Florida, College of Medicine, McKnight Brain Institute, Gainesville, FL 32610, USA
- Center for Translational Research in Neurodegenerative Disease, University of Florida, College of Medicine, McKnight Brain Institute, Gainesville, FL 32610, USA
| | - Julian R. Mark
- Department of Neuroscience, University of Florida, College of Medicine, McKnight Brain Institute, Gainesville, FL 32610, USA
- Center for Translational Research in Neurodegenerative Disease, University of Florida, College of Medicine, McKnight Brain Institute, Gainesville, FL 32610, USA
| | - Hannah A. Staley
- Department of Neuroscience, University of Florida, College of Medicine, McKnight Brain Institute, Gainesville, FL 32610, USA
- Center for Translational Research in Neurodegenerative Disease, University of Florida, College of Medicine, McKnight Brain Institute, Gainesville, FL 32610, USA
| | - Drew A. Gillett
- Department of Neuroscience, University of Florida, College of Medicine, McKnight Brain Institute, Gainesville, FL 32610, USA
- Center for Translational Research in Neurodegenerative Disease, University of Florida, College of Medicine, McKnight Brain Institute, Gainesville, FL 32610, USA
| | - Noelle Neighbarger
- Department of Neuroscience, University of Florida, College of Medicine, McKnight Brain Institute, Gainesville, FL 32610, USA
- Center for Translational Research in Neurodegenerative Disease, University of Florida, College of Medicine, McKnight Brain Institute, Gainesville, FL 32610, USA
| | - Holly Kordasiewicz
- Neurology, Ionis Pharmaceuticals, 2855 Gazelle Court, Carlsbad, CA 92010, USA
| | - Warren D. Hirst
- Neurodegenerative Diseases Research Unit, Biogen, 115 Broadway, Cambridge, MA 02142, USA
| | - Malú Gámez Tansey
- Department of Neuroscience, University of Florida, College of Medicine, McKnight Brain Institute, Gainesville, FL 32610, USA
- Center for Translational Research in Neurodegenerative Disease, University of Florida, College of Medicine, McKnight Brain Institute, Gainesville, FL 32610, USA
- Department of Neurology and Fixel Institute for Neurological Diseases, University of Florida Health, Gainesville, FL 32608, USA
| |
Collapse
|
17
|
González-Martínez I, Cerro-Herreros E, Moreno N, García-Rey A, Espinosa-Espinosa J, Carrascosa-Sàez M, Piqueras-Losilla D, Arzumanov A, Seoane-Miraz D, Jad Y, Raz R, Wood MJ, Varela MA, Llamusí B, Artero R. Peptide-conjugated antimiRs improve myotonic dystrophy type 1 phenotypes by promoting endogenous MBNL1 expression. Mol Ther Nucleic Acids 2023; 34:102024. [PMID: 37744174 PMCID: PMC10514136 DOI: 10.1016/j.omtn.2023.09.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/12/2022] [Accepted: 09/01/2023] [Indexed: 09/26/2023]
Abstract
Myotonic dystrophy type 1 (DM1) is a rare neuromuscular disease caused by a CTG repeat expansion in the DMPK gene that generates toxic RNA with a myriad of downstream alterations in RNA metabolism. A key consequence is the sequestration of alternative splicing regulatory proteins MBNL1/2 by expanded transcripts in the affected tissues. MBNL1/2 depletion interferes with a developmental alternative splicing switch that causes the expression of fetal isoforms in adults. Boosting the endogenous expression of MBNL proteins by inhibiting the natural translational repressors miR-23b and miR-218 has previously been shown to be a promising therapeutic approach. We designed antimiRs against both miRNAs with a phosphorodiamidate morpholino oligonucleotide (PMO) chemistry conjugated to cell-penetrating peptides (CPPs) to improve delivery to affected tissues. In DM1 cells, CPP-PMOs significantly increased MBNL1 levels. In some candidates, this was achieved using concentrations less than two orders of magnitude below the median toxic concentration, with up to 5.38-fold better therapeutic window than previous antagomiRs. In HSALR mice, intravenous injections of CPP-PMOs improve molecular, histopathological, and functional phenotypes, without signs of toxicity. Our findings place CPP-PMOs as promising antimiR candidates to overcome the treatment delivery challenge in DM1 therapy.
Collapse
Affiliation(s)
- Irene González-Martínez
- University Research Institute for Biotechnology and Biomedicine (BIOTECMED), Universidad de Valencia, Valencia, Spain
- Translational Genomics Group, INCLIVA Biomedical Research Institute, Avenue Menéndez Pelayo 4 acc, 46010 Valencia, Spain
| | - Estefanía Cerro-Herreros
- University Research Institute for Biotechnology and Biomedicine (BIOTECMED), Universidad de Valencia, Valencia, Spain
- Translational Genomics Group, INCLIVA Biomedical Research Institute, Avenue Menéndez Pelayo 4 acc, 46010 Valencia, Spain
| | - Nerea Moreno
- University Research Institute for Biotechnology and Biomedicine (BIOTECMED), Universidad de Valencia, Valencia, Spain
- Translational Genomics Group, INCLIVA Biomedical Research Institute, Avenue Menéndez Pelayo 4 acc, 46010 Valencia, Spain
| | - Andrea García-Rey
- University Research Institute for Biotechnology and Biomedicine (BIOTECMED), Universidad de Valencia, Valencia, Spain
- Translational Genomics Group, INCLIVA Biomedical Research Institute, Avenue Menéndez Pelayo 4 acc, 46010 Valencia, Spain
| | - Jorge Espinosa-Espinosa
- University Research Institute for Biotechnology and Biomedicine (BIOTECMED), Universidad de Valencia, Valencia, Spain
- Translational Genomics Group, INCLIVA Biomedical Research Institute, Avenue Menéndez Pelayo 4 acc, 46010 Valencia, Spain
- Group of Emerging and Neglected Diseases, Ecoepidemiology and Biodiversity, Health Sciences Faculty, Universidad Internacional SEK, Quito 170521, Ecuador
| | - Marc Carrascosa-Sàez
- University Research Institute for Biotechnology and Biomedicine (BIOTECMED), Universidad de Valencia, Valencia, Spain
| | - Diego Piqueras-Losilla
- University Research Institute for Biotechnology and Biomedicine (BIOTECMED), Universidad de Valencia, Valencia, Spain
| | - Andrey Arzumanov
- Department of Paediatrics, Institute of Developmental and Regenerative Medicine (IDRM), University of Oxford, Roosevelt Dr, Oxford OX3 7TY, UK
- MDUK Oxford Neuromuscular Centre, University of Oxford, Oxford, UK
| | - David Seoane-Miraz
- Department of Paediatrics, Institute of Developmental and Regenerative Medicine (IDRM), University of Oxford, Roosevelt Dr, Oxford OX3 7TY, UK
- MDUK Oxford Neuromuscular Centre, University of Oxford, Oxford, UK
| | - Yahya Jad
- Department of Paediatrics, Institute of Developmental and Regenerative Medicine (IDRM), University of Oxford, Roosevelt Dr, Oxford OX3 7TY, UK
- MDUK Oxford Neuromuscular Centre, University of Oxford, Oxford, UK
| | - Richard Raz
- Department of Paediatrics, Institute of Developmental and Regenerative Medicine (IDRM), University of Oxford, Roosevelt Dr, Oxford OX3 7TY, UK
- MDUK Oxford Neuromuscular Centre, University of Oxford, Oxford, UK
| | - Matthew J. Wood
- Department of Paediatrics, Institute of Developmental and Regenerative Medicine (IDRM), University of Oxford, Roosevelt Dr, Oxford OX3 7TY, UK
- MDUK Oxford Neuromuscular Centre, University of Oxford, Oxford, UK
| | - Miguel A. Varela
- Department of Paediatrics, Institute of Developmental and Regenerative Medicine (IDRM), University of Oxford, Roosevelt Dr, Oxford OX3 7TY, UK
- MDUK Oxford Neuromuscular Centre, University of Oxford, Oxford, UK
| | - Beatriz Llamusí
- University Research Institute for Biotechnology and Biomedicine (BIOTECMED), Universidad de Valencia, Valencia, Spain
- Translational Genomics Group, INCLIVA Biomedical Research Institute, Avenue Menéndez Pelayo 4 acc, 46010 Valencia, Spain
| | - Rubén Artero
- University Research Institute for Biotechnology and Biomedicine (BIOTECMED), Universidad de Valencia, Valencia, Spain
- Translational Genomics Group, INCLIVA Biomedical Research Institute, Avenue Menéndez Pelayo 4 acc, 46010 Valencia, Spain
| |
Collapse
|
18
|
Zhang X, McLendon JM, Peck BD, Chen B, Song LS, Boudreau RL. Modulation of miR-29 influences myocardial compliance likely through coordinated regulation of calcium handling and extracellular matrix. Mol Ther Nucleic Acids 2023; 34:102081. [PMID: 38111915 PMCID: PMC10726423 DOI: 10.1016/j.omtn.2023.102081] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/20/2023] [Accepted: 11/14/2023] [Indexed: 12/20/2023]
Abstract
MicroRNAs (miRNAs) control the expression of diverse subsets of target mRNAs, and studies have found miRNA dysregulation in failing hearts. Expression of miR-29 is abundant in heart, increases with aging, and is altered in cardiomyopathies. Prior studies demonstrate that miR-29 reduction via genetic knockout or pharmacologic blockade can blunt cardiac hypertrophy and fibrosis in mice. Surprisingly, this depended on specifically blunting miR-29 actions in cardiomyocytes versus fibroblasts. To begin developing more translationally relevant vectors, we generated a novel transgene-encoded miR-29 inhibitor (TuD-29) that can be incorporated into a viral-mediated gene therapy for cardioprotection. Here, we corroborate that miR-29 expression and activity is higher in cardiomyocytes versus fibroblasts and demonstrate that TuD-29 effectively blunts hypertrophic responses in cultured cardiomyocytes and mouse hearts. Furthermore, we found that adeno-associated virus (AAV)-mediated miR-29 overexpression in mouse hearts induces early diastolic dysfunction, whereas AAV:TuD-29 treatment improves cardiac output by increasing end-diastolic and stroke volumes. The integration of RNA sequencing and miRNA-target interactomes reveals that miR-29 regulates genes involved in calcium handling, cell stress and hypertrophy, metabolism, ion transport, and extracellular matrix remodeling. These investigations support a likely versatile role for miR-29 in influencing myocardial compliance and relaxation, potentially providing a unique therapeutic avenue to improve diastolic function in heart failure patients.
Collapse
Affiliation(s)
- Xiaoming Zhang
- Department of Internal Medicine, Fraternal Order of Eagles Diabetes Research Center, Abboud Cardiovascular Research Center, Carver College of Medicine, University of Iowa, Iowa City, IA, USA
| | - Jared M. McLendon
- Department of Internal Medicine, Fraternal Order of Eagles Diabetes Research Center, Abboud Cardiovascular Research Center, Carver College of Medicine, University of Iowa, Iowa City, IA, USA
| | - Bailey D. Peck
- Department of Internal Medicine, Fraternal Order of Eagles Diabetes Research Center, Abboud Cardiovascular Research Center, Carver College of Medicine, University of Iowa, Iowa City, IA, USA
| | - Biyi Chen
- Department of Internal Medicine, Fraternal Order of Eagles Diabetes Research Center, Abboud Cardiovascular Research Center, Carver College of Medicine, University of Iowa, Iowa City, IA, USA
| | - Long-Sheng Song
- Department of Internal Medicine, Fraternal Order of Eagles Diabetes Research Center, Abboud Cardiovascular Research Center, Carver College of Medicine, University of Iowa, Iowa City, IA, USA
| | - Ryan L. Boudreau
- Department of Internal Medicine, Fraternal Order of Eagles Diabetes Research Center, Abboud Cardiovascular Research Center, Carver College of Medicine, University of Iowa, Iowa City, IA, USA
| |
Collapse
|
19
|
Wang Z, Fan X, Mu G, Zhao X, Wang Q, Wang J, Tang X. Cathepsin B-activatable cyclic antisense oligonucleotides for cell-specific target gene knockdown in vitro and in vivo. Mol Ther Nucleic Acids 2023; 33:548-558. [PMID: 37588686 PMCID: PMC10425675 DOI: 10.1016/j.omtn.2023.07.022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/19/2022] [Accepted: 07/20/2023] [Indexed: 08/18/2023]
Abstract
Trigger-activatable antisense oligonucleotides have been widely applied to regulate gene function. Among them, caged cyclic antisense oligonucleotides (cASOs) maintain a specific topology that temporarily inhibits their interaction with target genes. By inserting linkers that respond to cell-specific endogenous stimuli, they can be powerful tools and potential therapeutic agents for specific types of cancer cells with low off-target effects on normal cells. Here, we developed enzyme-activatable cASOs by tethering two terminals of linear antisense oligonucleotides through a cathepsin B (CB) substrate peptide (Gly-Phe-Leu-Gly [GFLG]), which could be efficiently uncaged by CB. CB-activatable cASOs were used to successfully knock down two disease-related endogenous genes in CB-abundant PC-3 tumor cells at the mRNA and protein levels but had much less effect on gene knockdown in CB-deficient human umbilical vein endothelial cell (HUVECs). In addition, reduced nonspecific immunostimulation was found using cASOs compared with their linear counterparts. Further in vivo studies indicated that CB-activatable cASOs showed effective tumor inhibition in PC-3 tumor model mice through downregulation of translationally controlled tumor protein (TCTP) protein in tumors. This study applies endogenous enzyme-activatable cASOs for antitumor therapy in tumor model mice, which demonstrates a promising stimulus-responsive cASO strategy for cell-specific gene knockdown upon endogenous activation and ASO prodrug development.
Collapse
Affiliation(s)
- Zhongyu Wang
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences and Chemical Biology Center, Peking University, No. 38, Xueyuan Road, Beijing 100191, People’s Republic of China
| | - Xinli Fan
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences and Chemical Biology Center, Peking University, No. 38, Xueyuan Road, Beijing 100191, People’s Republic of China
| | - Guanqun Mu
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences and Chemical Biology Center, Peking University, No. 38, Xueyuan Road, Beijing 100191, People’s Republic of China
| | - Xiaoran Zhao
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences and Chemical Biology Center, Peking University, No. 38, Xueyuan Road, Beijing 100191, People’s Republic of China
| | - Qian Wang
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences and Chemical Biology Center, Peking University, No. 38, Xueyuan Road, Beijing 100191, People’s Republic of China
| | - Jing Wang
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences and Chemical Biology Center, Peking University, No. 38, Xueyuan Road, Beijing 100191, People’s Republic of China
| | - Xinjing Tang
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences and Chemical Biology Center, Peking University, No. 38, Xueyuan Road, Beijing 100191, People’s Republic of China
- State Key Laboratory of Pharmaceutical Biotechnology, Nanjing University, Nanjing, Jiangsu 210023, People’s Republic of China
| |
Collapse
|
20
|
Zhou S, Chen M, Yuan Y, Xu Y, Pu Q, Ai X, Liu S, Du F, Huang X, Dong J, Cui X, Tang Z. Trans-acting aptazyme for conditional gene knockdown in eukaryotic cells. Mol Ther Nucleic Acids 2023; 33:367-375. [PMID: 37547296 PMCID: PMC10400872 DOI: 10.1016/j.omtn.2023.07.014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/13/2023] [Accepted: 07/11/2023] [Indexed: 08/08/2023]
Abstract
Trans-acting hammerhead ribozyme inherits the advantages of being the smallest and best-characterized RNA-cleaving ribozyme, offering high modularity and the ability to cleave any desired sequence without the aid of any protein, as long as the target sequence contains a cleavage site. However, achieving precise control over the trans-acting hammerhead ribozyme would enable safer and more accurate regulation of gene expression. Herein, we described an intracellular selection of hammerhead aptazyme that contains a theophylline aptamer on stem II based on toxin protein IbsC. Based on the intracellular selection, we obtained three new cis-acting hammerhead aptazymes. Moreover, the corresponding trans-acting aptazymes could be efficiently induced by theophylline to knock down different targeted genes in eukaryotic cells. Notably, the best one, T195, exhibited a ligand-dependent and dose-dependent response to theophylline, and the cleavage efficiency could be enhanced by incorporating multiplex aptazymes.
Collapse
Affiliation(s)
- Shan Zhou
- Natural Products Research Center, Chengdu Institution of Biology, Chinese Academy of Sciences, Chengdu 610041, P.R. China
- University of Chinese Academy of Sciences, Beijing 100049, P.R. China
| | - Meiyi Chen
- Natural Products Research Center, Chengdu Institution of Biology, Chinese Academy of Sciences, Chengdu 610041, P.R. China
| | - Yi Yuan
- Natural Products Research Center, Chengdu Institution of Biology, Chinese Academy of Sciences, Chengdu 610041, P.R. China
| | - Yan Xu
- Natural Products Research Center, Chengdu Institution of Biology, Chinese Academy of Sciences, Chengdu 610041, P.R. China
| | - Qinlin Pu
- Natural Products Research Center, Chengdu Institution of Biology, Chinese Academy of Sciences, Chengdu 610041, P.R. China
| | - Xilei Ai
- Natural Products Research Center, Chengdu Institution of Biology, Chinese Academy of Sciences, Chengdu 610041, P.R. China
| | - Shuai Liu
- Natural Products Research Center, Chengdu Institution of Biology, Chinese Academy of Sciences, Chengdu 610041, P.R. China
| | - Feng Du
- Natural Products Research Center, Chengdu Institution of Biology, Chinese Academy of Sciences, Chengdu 610041, P.R. China
| | - Xin Huang
- Natural Products Research Center, Chengdu Institution of Biology, Chinese Academy of Sciences, Chengdu 610041, P.R. China
| | - Juan Dong
- Natural Products Research Center, Chengdu Institution of Biology, Chinese Academy of Sciences, Chengdu 610041, P.R. China
| | - Xin Cui
- Natural Products Research Center, Chengdu Institution of Biology, Chinese Academy of Sciences, Chengdu 610041, P.R. China
| | - Zhuo Tang
- Natural Products Research Center, Chengdu Institution of Biology, Chinese Academy of Sciences, Chengdu 610041, P.R. China
| |
Collapse
|
21
|
Corydon IJ, Fabian-Jessing BK, Jakobsen TS, Jørgensen AC, Jensen EG, Askou AL, Aagaard L, Corydon TJ. 25 years of maturation: A systematic review of RNAi in the clinic. Mol Ther Nucleic Acids 2023; 33:469-482. [PMID: 37583575 PMCID: PMC10424002 DOI: 10.1016/j.omtn.2023.07.018] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 08/17/2023]
Abstract
The year 2023 marks the 25th anniversary of the discovery of RNAi. RNAi-based therapeutics enable sequence-specific gene knockdown by eliminating target RNA molecules through complementary base-pairing. A systematic review of published and ongoing clinical trials was performed. Web of Science, PubMed, and Embase were searched from January 1, 1998, to December 30, 2022 for clinical trials using RNAi. Following inclusion, data from the articles were extracted according to a predefined protocol. A total of 90 trials published in 81 articles were included. In addition, ongoing clinical trials were retrieved from ClinicalTrials.gov, resulting in the inclusion of 48 trials. We investigated how maturation of RNAi-based therapeutics and developments in delivery platforms, administration routes, and potential targets shape the current landscape of clinically applied RNAi. Notably, most contemporary clinical trials used either N-acetylgalactosamine delivery and subcutaneous administration or lipid nanoparticle delivery and intravenous administration. In conclusion, RNAi therapeutics have gained great momentum during the past decade, resulting in five approved therapeutics targeting the liver for treatment of severe diseases, and the trajectory depicted by the ongoing trials emphasizes that even more RNAi-based medicines also targeting extra-hepatic tissues are likely to be available in the years to come.
Collapse
Affiliation(s)
- Ida Juhl Corydon
- Department of Biomedicine, Aarhus University, Høegh-Guldbergs Gade 10, 8000 Aarhus C, Denmark
| | - Bjørn Kristensen Fabian-Jessing
- Department of Biomedicine, Aarhus University, Høegh-Guldbergs Gade 10, 8000 Aarhus C, Denmark
- Department of Ophthalmology, Aarhus University Hospital, Palle Juul-Jensens Boulevard 167, Aarhus N, Denmark
| | - Thomas Stax Jakobsen
- Department of Biomedicine, Aarhus University, Høegh-Guldbergs Gade 10, 8000 Aarhus C, Denmark
- Department of Ophthalmology, Aarhus University Hospital, Palle Juul-Jensens Boulevard 167, Aarhus N, Denmark
| | | | - Emilie Grarup Jensen
- Department of Biomedicine, Aarhus University, Høegh-Guldbergs Gade 10, 8000 Aarhus C, Denmark
| | - Anne Louise Askou
- Department of Biomedicine, Aarhus University, Høegh-Guldbergs Gade 10, 8000 Aarhus C, Denmark
- Department of Ophthalmology, Aarhus University Hospital, Palle Juul-Jensens Boulevard 167, Aarhus N, Denmark
| | - Lars Aagaard
- Department of Biomedicine, Aarhus University, Høegh-Guldbergs Gade 10, 8000 Aarhus C, Denmark
| | - Thomas Juhl Corydon
- Department of Biomedicine, Aarhus University, Høegh-Guldbergs Gade 10, 8000 Aarhus C, Denmark
- Department of Ophthalmology, Aarhus University Hospital, Palle Juul-Jensens Boulevard 167, Aarhus N, Denmark
| |
Collapse
|
22
|
Liao YC, Cheng TC, Tu SH, Chang J, Guo P, Chen LC, Ho YS. Tumor targeting and therapeutic assessments of RNA nanoparticles carrying α9-nAChR aptamer and anti-miR-21 in triple-negative breast cancers. Mol Ther Nucleic Acids 2023; 33:351-366. [PMID: 37547295 PMCID: PMC10400867 DOI: 10.1016/j.omtn.2023.07.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/15/2023] [Accepted: 07/11/2023] [Indexed: 08/08/2023]
Abstract
Triple-negative breast cancer (TNBC) is highly aggressive with a poor prognosis because of a lack of cell markers as drug targets. α9-Nicotinic acetylcholine receptor (nAChR) is expressed abundantly in TNBC; thus, it is a valuable biomarker for TNBC detection and treatment. In this study, we utilized thermodynamically stable three-way junction (3WJ) packaging RNA (pRNA) as the core to construct RNA nanoparticles with an α9-nAChR RNA aptamer as a targeting ligand and an anti-microRNA-21 (miR-21) as a therapeutic module. We compared the configuration of the two RNA nanoparticles and found that 3WJ-B-α9-nAChR-aptamer fluorescent RNA nanoparticles (3WJ-B-α9-apt-Alexa) exhibited better specificity for α9-nAChR in TNBC cells compared with 3WJ-C-α9-nAChR. Furthermore, 3WJ-B-α9-apt-Alexa bound more efficiently to TNBC patient-derived xenograft (PDX) tumors than 3WJ fluorescent RNA nanoparticles (3WJ-Alexa) with little or no accumulation in healthy organs after systemic injection in mice. Moreover, 3WJ-B-α9-nAChR-aptamer RNA nanoparticles carrying anti-miR-21 (3WJ-B-α9-apt-anti-miR-21) significantly suppressed TNBC-PDX tumor growth and induced cell apoptosis because of reduced miR-21 gene expression and upregulated the phosphatase and tensin homolog (PTEN) and programmed cell death 4 (PDCD4) proteins. In addition, no pathological changes were detected upon toxicity examination of treated mice. In conclusion, the 3WJ-B-α9-nAChR-aptamer RNA nanoparticles established in this study efficiently deliver therapeutic anti-miR-21, indicating their potential as a novel TNBC therapy.
Collapse
Affiliation(s)
- You-Cheng Liao
- Graduate Institute of Medical Sciences, College of Medicine, Taipei Medical University, Taipei 110031, Taiwan
| | - Tzu-Chun Cheng
- Institute of Biochemistry and Molecular Biology, College of Life Sciences, China Medical University, Taichung 406040, Taiwan
| | - Shih-Hsin Tu
- Department of Surgery, Taipei Medical University Hospital, Department of Surgery, School of Medicine, College of Medicine, Taipei Medical University, Taipei 110, Taiwan
| | - Jungshan Chang
- Graduate Institute of Medical Sciences, College of Medicine, Taipei Medical University, Taipei 110031, Taiwan
- International Master/PhD Program in Medicine, College of Medicine, Taipei Medical University, Taipei 110031, Taiwan
| | - Peixuan Guo
- Center for RNA Nanobiotechnology and Nanomedicine, The Ohio State University, Columbus, OH, USA
- Division of Pharmaceutics and Pharmacology, College of Pharmacy, The Ohio State University, Columbus, OH, USA
- James Comprehensive Cancer Center, The Ohio State University, Columbus, OH, USA
- College of Medicine, The Ohio State University, Columbus, OH, USA
- Dorothy M. Davis Heart and Lung Research Institute, The Ohio State University, Columbus, OH, USA
| | - Li-Ching Chen
- Department of Biological Science & Technology, College of Life Sciences, China Medical University, Taichung 406040, Taiwan
| | - Yuan-Soon Ho
- Institute of Biochemistry and Molecular Biology, College of Life Sciences, China Medical University, Taichung 406040, Taiwan
| |
Collapse
|
23
|
Fitzsimons S, Muñoz-San Martín M, Nally F, Dillon E, Fashina IA, Strowitzki MJ, Ramió-Torrentà L, Dowling JK, De Santi C, McCoy CE. Inhibition of pro-inflammatory signaling in human primary macrophages by enhancing arginase-2 via target site blockers. Mol Ther Nucleic Acids 2023; 33:941-959. [PMID: 37701067 PMCID: PMC10494319 DOI: 10.1016/j.omtn.2023.08.023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/27/2022] [Accepted: 08/17/2023] [Indexed: 09/14/2023]
Abstract
The modulation of macrophage phenotype from a pro-inflammatory to an anti-inflammatory state holds therapeutic potential in the treatment of inflammatory disease. We have previously shown that arginase-2 (Arg2), a mitochondrial enzyme, is a key regulator of the macrophage anti-inflammatory response. Here, we investigate the therapeutic potential of Arg2 enhancement via target site blockers (TSBs) in human macrophages. TSBs are locked nucleic acid antisense oligonucleotides that were specifically designed to protect specific microRNA recognition elements (MREs) in human ARG2 3' UTR mRNA. TSBs targeting miR-155 (TSB-155) and miR-3202 (TSB-3202) MREs increased ARG2 expression in human monocyte-derived macrophages. This resulted in decreased gene expression and cytokine production of TNF-α and CCL2 and, for TSB-3202, in an increase in the anti-inflammatory macrophage marker, CD206. Proteomic analysis demonstrated that a network of pro-inflammatory responsive proteins was modulated by TSBs. In silico bioinformatic analysis predicted that TSB-3202 suppressed upstream pro-inflammatory regulators including STAT-1 while enhancing anti-inflammatory associated proteins. Proteomic data were validated by confirming increased levels of sequestosome-1 and decreased levels of phosphorylated STAT-1 and STAT-1 upon TSB treatment. In conclusion, upregulation of Arg2 by TSBs inhibits pro-inflammatory signaling and is a promising novel therapeutic strategy to modulate inflammatory signaling in human macrophages.
Collapse
Affiliation(s)
- Stephen Fitzsimons
- School of Pharmacy and Biomolecular Science, Royal College of Surgeons in Ireland, 123 St Stephen’s Green, Dublin 2, Ireland
- FutureNeuro, SFI Research Centre for Chronic and Rare Neurological Diseases, Royal College of Surgeons in Ireland, 123 St. Stephen’s Green, Dublin 2, Ireland
| | - María Muñoz-San Martín
- School of Pharmacy and Biomolecular Science, Royal College of Surgeons in Ireland, 123 St Stephen’s Green, Dublin 2, Ireland
| | - Frances Nally
- School of Pharmacy and Biomolecular Science, Royal College of Surgeons in Ireland, 123 St Stephen’s Green, Dublin 2, Ireland
| | - Eugene Dillon
- School of Biomolecular and Biomedical Science, Conway Institute, University College Dublin, Belfield, Dublin 4, Ireland
| | - Ifeolutembi A. Fashina
- School of Pharmacy and Biomolecular Science, Royal College of Surgeons in Ireland, 123 St Stephen’s Green, Dublin 2, Ireland
| | - Moritz J. Strowitzki
- Department of General, Visceral & Transplantation Surgery, University Hospital Heidelberg, Heidelberg, Germany
| | - Lluís Ramió-Torrentà
- Neuroinflammation and Neurodegeneration Group, Girona Biomedical Research Institute (IDIBGI), CERCA Programme/Generalitat de Catalunya, Salt, Girona, Spain
| | - Jennifer K. Dowling
- School of Pharmacy and Biomolecular Science, Royal College of Surgeons in Ireland, 123 St Stephen’s Green, Dublin 2, Ireland
- FutureNeuro, SFI Research Centre for Chronic and Rare Neurological Diseases, Royal College of Surgeons in Ireland, 123 St. Stephen’s Green, Dublin 2, Ireland
| | - Chiara De Santi
- School of Pharmacy and Biomolecular Science, Royal College of Surgeons in Ireland, 123 St Stephen’s Green, Dublin 2, Ireland
| | - Claire E. McCoy
- School of Pharmacy and Biomolecular Science, Royal College of Surgeons in Ireland, 123 St Stephen’s Green, Dublin 2, Ireland
- FutureNeuro, SFI Research Centre for Chronic and Rare Neurological Diseases, Royal College of Surgeons in Ireland, 123 St. Stephen’s Green, Dublin 2, Ireland
| |
Collapse
|
24
|
Li X, Kheirabadi M, Dougherty PG, Kamer KJ, Shen X, Estrella NL, Peddigari S, Pathak A, Blake SL, Sizensky E, Genio CD, Gaur AB, Dhanabal M, Girgenrath M, Sethuraman N, Qian Z. The endosomal escape vehicle platform enhances delivery of oligonucleotides in preclinical models of neuromuscular disorders. Mol Ther Nucleic Acids 2023; 33:273-285. [PMID: 37538053 PMCID: PMC10393622 DOI: 10.1016/j.omtn.2023.06.022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/20/2023] [Accepted: 06/26/2023] [Indexed: 08/05/2023]
Abstract
Biological therapeutic agents are highly targeted and potent but limited in their ability to reach intracellular targets. These limitations often necessitate high therapeutic doses and can be associated with less-than-optimal therapeutic activity. One promising solution for therapeutic agent delivery is use of cell-penetrating peptides. Canonical cell-penetrating peptides, however, are limited by low efficiencies of cellular uptake and endosomal escape, minimal proteolytic stability, and toxicity. To overcome these limitations, we designed a family of proprietary cyclic cell-penetrating peptides that form the core of our endosomal escape vehicle technology capable of delivering therapeutic agent-conjugated cargo intracellularly. We demonstrated the therapeutic potential of this endosomal escape vehicle platform in preclinical models of muscular dystrophy with distinct disease etiology. An endosomal escape vehicle-conjugated, splice-modulating oligonucleotide restored dystrophin protein expression in striated muscles in the mdx mouse, a model for Duchenne muscular dystrophy. Furthermore, another endosomal escape vehicle-conjugated, sterically blocking oligonucleotide led to knockdown of aberrant transcript expression levels in facioscapulohumeral muscular dystrophy patient-derived skeletal muscle cells. These findings suggest a significant therapeutic potential of our endosomal escape vehicle conjugated oligonucleotides for targeted upregulation and downregulation of gene expression in neuromuscular diseases, with possible broader application of this platform for delivery of intracellular biological agents.
Collapse
Affiliation(s)
- Xiang Li
- Entrada Therapeutics, One Design Center Place, Suite 17-500, Boston, MA 02210, USA
| | - Mahboubeh Kheirabadi
- Entrada Therapeutics, One Design Center Place, Suite 17-500, Boston, MA 02210, USA
| | - Patrick G. Dougherty
- Entrada Therapeutics, One Design Center Place, Suite 17-500, Boston, MA 02210, USA
| | - Kimberli J. Kamer
- Entrada Therapeutics, One Design Center Place, Suite 17-500, Boston, MA 02210, USA
| | - Xiulong Shen
- Entrada Therapeutics, One Design Center Place, Suite 17-500, Boston, MA 02210, USA
| | - Nelsa L. Estrella
- Entrada Therapeutics, One Design Center Place, Suite 17-500, Boston, MA 02210, USA
| | - Suresh Peddigari
- Entrada Therapeutics, One Design Center Place, Suite 17-500, Boston, MA 02210, USA
| | - Anushree Pathak
- Entrada Therapeutics, One Design Center Place, Suite 17-500, Boston, MA 02210, USA
| | - Sara L. Blake
- Entrada Therapeutics, One Design Center Place, Suite 17-500, Boston, MA 02210, USA
| | - Emmanuelle Sizensky
- Entrada Therapeutics, One Design Center Place, Suite 17-500, Boston, MA 02210, USA
| | - Carmen del Genio
- Dartmouth Hitchcock Medical Center, 1 Medical Center Drive, Lebanon, NH 03756, USA
| | - Arti B. Gaur
- Dartmouth Hitchcock Medical Center, 1 Medical Center Drive, Lebanon, NH 03756, USA
| | - Mohanraj Dhanabal
- Entrada Therapeutics, One Design Center Place, Suite 17-500, Boston, MA 02210, USA
| | - Mahasweta Girgenrath
- Entrada Therapeutics, One Design Center Place, Suite 17-500, Boston, MA 02210, USA
| | - Natarajan Sethuraman
- Entrada Therapeutics, One Design Center Place, Suite 17-500, Boston, MA 02210, USA
| | - Ziqing Qian
- Entrada Therapeutics, One Design Center Place, Suite 17-500, Boston, MA 02210, USA
| |
Collapse
|
25
|
Pollak AJ, Zhao L, Crooke ST. Characterization of cooperative PS-oligo activation of human TLR9. Mol Ther Nucleic Acids 2023; 33:832-844. [PMID: 37675184 PMCID: PMC10477407 DOI: 10.1016/j.omtn.2023.08.011] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/23/2023] [Accepted: 08/11/2023] [Indexed: 09/08/2023]
Abstract
Single-stranded phosphorothioate oligonucleotides (PS-oligos) can activate TLR9, leading to an innate immune response. This can occur with PS-oligos containing unmethylated CpG sites, the canonical motif, or PS-oligos that do not contain those motifs (non-CpG). Structural evidence shows that TLR9 contains two PS-oligo binding sites, and recent data suggest that synergistic cooperative activation of TLR9 can be achieved by adding two separate PS-oligos to cells, each engaging with a separate site on TLR9 to enhance TLR9 activation as a pair. Here, we demonstrate and characterize this cooperativity phenomenon using PS-oligos in human cell lines, and we introduce several novel PS-oligo pairs (CpG and non-CpG pairs) that show cooperative activation. Indeed, we find that cooperative PS-oligos likely bind at different sites on TLR9. Interestingly, we find that PS-oligos that generate little TLR9 activation on their own can prime TLR9 to be activated by other PS-oligos. Finally, we determine that previous models of TLR9 activation cannot be used to fully explain data from systems using human TLR9 and PS-oligos. Overall, we reveal new details of TLR9 activation, but we also find that more work needs to be done to determine where certain PS-oligos are binding to TLR9.
Collapse
Affiliation(s)
| | - Luyi Zhao
- Ionis Pharmaceuticals, Inc., Carlsbad, CA 92010, USA
| | | |
Collapse
|
26
|
Ohara H, Hosokawa M, Awaya T, Hagiwara A, Kurosawa R, Sako Y, Ogawa M, Ogasawara M, Noguchi S, Goto Y, Takahashi R, Nishino I, Hagiwara M. Branchpoints as potential targets of exon-skipping therapies for genetic disorders. Mol Ther Nucleic Acids 2023; 33:404-412. [PMID: 37547287 PMCID: PMC10403725 DOI: 10.1016/j.omtn.2023.07.011] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/03/2023] [Accepted: 07/11/2023] [Indexed: 08/08/2023]
Abstract
Fukutin (FKTN) c.647+2084G>T creates a pseudo-exon with a premature stop codon, which causes Fukuyama congenital muscular dystrophy (FCMD). We aimed to ameliorate aberrant splicing of FKTN caused by this variant. We screened compounds focusing on splicing regulation using the c.647+2084G>T splicing reporter and discovered that the branchpoint, which is essential for splicing reactions, could be a potential therapeutic target. To confirm the effectiveness of branchpoints as targets for exon skipping, we designed branchpoint-targeted antisense oligonucleotides (BP-AONs). This restored normal FKTN mRNA and protein production in FCMD patient myotubes. We identified a functional BP by detecting splicing intermediates and creating BP mutations in the FKTN reporter gene; this BP was non-redundant and sufficiently blocked by BP-AONs. Next, a BP-AON was designed for a different FCMD-causing variant, which induces pathogenic exon trapping by a common SINE-VNTR-Alu-type retrotransposon. Notably, this BP-AON also restored normal FKTN mRNA and protein production in FCMD patient myotubes. Our findings suggest that BPs could be potential targets in exon-skipping therapeutic strategies for genetic disorders.
Collapse
Affiliation(s)
- Hiroaki Ohara
- Department of Anatomy and Developmental Biology, Graduate School of Medicine, Kyoto University, Kyoto 606-8501, Japan
- Department of Neurology, Graduate School of Medicine, Kyoto University, Kyoto 606-8507, Japan
- Department of Neuromuscular Research, National Institute of Neuroscience, National Center of Neurology and Psychiatry, Tokyo 187-8502, Japan
- Department of Drug Discovery for Intractable Diseases, Graduate School of Medicine, Kyoto University, Kyoto 606-8501, Japan
| | - Motoyasu Hosokawa
- Department of Anatomy and Developmental Biology, Graduate School of Medicine, Kyoto University, Kyoto 606-8501, Japan
| | - Tomonari Awaya
- Department of Anatomy and Developmental Biology, Graduate School of Medicine, Kyoto University, Kyoto 606-8501, Japan
- Laboratory of Tumor Microenvironment and Immunity, Graduate School of Medicine, Kyoto University, Kyoto 606-8501, Japan
| | - Atsuko Hagiwara
- Department of Anatomy and Developmental Biology, Graduate School of Medicine, Kyoto University, Kyoto 606-8501, Japan
| | - Ryo Kurosawa
- Department of Anatomy and Developmental Biology, Graduate School of Medicine, Kyoto University, Kyoto 606-8501, Japan
| | - Yukiya Sako
- Department of Anatomy and Developmental Biology, Graduate School of Medicine, Kyoto University, Kyoto 606-8501, Japan
| | - Megumu Ogawa
- Department of Neuromuscular Research, National Institute of Neuroscience, National Center of Neurology and Psychiatry, Tokyo 187-8502, Japan
| | - Masashi Ogasawara
- Department of Neuromuscular Research, National Institute of Neuroscience, National Center of Neurology and Psychiatry, Tokyo 187-8502, Japan
| | - Satoru Noguchi
- Department of Neuromuscular Research, National Institute of Neuroscience, National Center of Neurology and Psychiatry, Tokyo 187-8502, Japan
| | - Yuichi Goto
- Department of Mental Retardation and Birth Defect Research, National Institute of Neurology, National Center of Neurology and Psychiatry, Tokyo 187-8502, Japan
| | - Ryosuke Takahashi
- Department of Neurology, Graduate School of Medicine, Kyoto University, Kyoto 606-8507, Japan
| | - Ichizo Nishino
- Department of Neuromuscular Research, National Institute of Neuroscience, National Center of Neurology and Psychiatry, Tokyo 187-8502, Japan
| | - Masatoshi Hagiwara
- Department of Anatomy and Developmental Biology, Graduate School of Medicine, Kyoto University, Kyoto 606-8501, Japan
| |
Collapse
|
27
|
Abstract
Nucleic acid amphiphiles, referring to nucleic acids modified with large hydrophobic groups, have been widely used in programmable bioengineering. Since nucleic acids are intrinsically hydrophilic, the hydrophobic groups endow nucleic acid amphiphiles with unique properties, such as self-assembling, interactions with artificial or biological membranes, and transmembrane transport. Importantly, the hybridization or target binding capability of oligonucleotide itself supplies nucleic acid amphiphiles with excellent programmability. As a result, this type of molecule has attracted considerable attention in academic studies and has enormous potential for further applications. For a comprehensive understanding of nucleic acid amphiphiles, we review the reported research on nucleic acid amphiphiles from their molecular design to final applications, in which we summarize the synthetic strategies for nucleic acid amphiphiles and draw much attention to their unique properties in different contexts. Finally, a summary of the applications of nucleic acid amphiphiles in drug development, bioengineering, and bioanalysis are critically discussed.
Collapse
Affiliation(s)
- Amu Gubu
- Law Sau Fai Institute for Advancing Translational Medicine in Bone & Joint Diseases, School of Chinese Medicine, Hong Kong Baptist University, Hong Kong SAR, China
- Aptacure Therapeutics Limited, Kowloon, Hong Kong SAR, China
| | - Xueli Zhang
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences and Chemical Biology Center, Peking University, No. 38 Xueyuan Road, Beijing, China
| | - Aiping Lu
- Law Sau Fai Institute for Advancing Translational Medicine in Bone & Joint Diseases, School of Chinese Medicine, Hong Kong Baptist University, Hong Kong SAR, China
- Institute of Integrated Bioinfomedicine and Translational Science, School of Chinese Medicine, Hong Kong Baptist University, Kowloon Tsai, Hong Kong 999077, China
- Institute of Precision Medicine and Innovative Drug Discovery, HKBU Institute for Research and Continuing Education, Shenzhen 518000, China
| | - Baoting Zhang
- School of Chinese Medicine, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Yuan Ma
- Law Sau Fai Institute for Advancing Translational Medicine in Bone & Joint Diseases, School of Chinese Medicine, Hong Kong Baptist University, Hong Kong SAR, China
- Institute of Integrated Bioinfomedicine and Translational Science, School of Chinese Medicine, Hong Kong Baptist University, Kowloon Tsai, Hong Kong 999077, China
- Institute of Precision Medicine and Innovative Drug Discovery, HKBU Institute for Research and Continuing Education, Shenzhen 518000, China
| | - Ge Zhang
- Law Sau Fai Institute for Advancing Translational Medicine in Bone & Joint Diseases, School of Chinese Medicine, Hong Kong Baptist University, Hong Kong SAR, China
- Institute of Integrated Bioinfomedicine and Translational Science, School of Chinese Medicine, Hong Kong Baptist University, Kowloon Tsai, Hong Kong 999077, China
- Institute of Precision Medicine and Innovative Drug Discovery, HKBU Institute for Research and Continuing Education, Shenzhen 518000, China
| |
Collapse
|
28
|
Pleiko K, Haugas M, Parfejevs V, Pantelejevs T, Parisini E, Teesalu T, Riekstina U. Targeting triple-negative breast cancer cells with a β1-integrin binding aptamer. Mol Ther Nucleic Acids 2023; 33:871-884. [PMID: 37680989 PMCID: PMC10481362 DOI: 10.1016/j.omtn.2023.08.015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Accepted: 08/14/2023] [Indexed: 09/09/2023]
Abstract
Targeted therapies have increased the treatment options for triple-negative breast cancer patients. However, the paucity of targetable biomarkers and tumor heterogeneity have limited the ability of precision-guided interventions to live up to their full potential. As affinity-targeting ligands, aptamers show high selectivity toward target molecules. Compared with antibodies, aptamers have lower molecular weight, increased stability during transportation, reduced immunogenicity, and increased tissue uptake. Recently, we reported discovery of the GreenB1 aptamer, which is internalized in cultured triple-negative MDA-MB-231 human breast cancer cells. We show that the GreenB1 aptamer specifically targets β1-integrin, a protein linked previously to breast cancer cell invasiveness and migration. Aptamer binds to β1-integrin with low nanomolar affinity. Our findings suggest potential applications for GreenB1-guided precision agents for diagnosis and therapy of cancers overexpressing β1-integrin.
Collapse
Affiliation(s)
- Karlis Pleiko
- Faculty of Medicine, University of Latvia, House of Science, Jelgavas Str. 3, 1004 Riga, Latvia
- Laboratory of Precision- and Nanomedicine, Institute of Biomedicine and Translational Medicine, University of Tartu, 50411 Tartu, Estonia
| | - Maarja Haugas
- Laboratory of Precision- and Nanomedicine, Institute of Biomedicine and Translational Medicine, University of Tartu, 50411 Tartu, Estonia
| | - Vadims Parfejevs
- Faculty of Medicine, University of Latvia, House of Science, Jelgavas Str. 3, 1004 Riga, Latvia
| | | | - Emilio Parisini
- Latvian Institute of Organic Synthesis, Aizkraukles 21, 1006 Riga, Latvia
- Department of Chemistry “G. Ciamician”, University of Bologna, Via Selmi 2, 40126 Bologna, Italy
| | - Tambet Teesalu
- Laboratory of Precision- and Nanomedicine, Institute of Biomedicine and Translational Medicine, University of Tartu, 50411 Tartu, Estonia
- Materials Research Laboratory, University of California, Santa Barbara, Santa Barbara, CA 93106, USA
| | - Una Riekstina
- Faculty of Medicine, University of Latvia, House of Science, Jelgavas Str. 3, 1004 Riga, Latvia
| |
Collapse
|
29
|
Corbin JM, Georgescu C, Wang L, Wren JD, Bieniasz M, Xu C, Asch AS, Ruiz Echevarría MJ. An unbiased seed-based RNAi selection screen identifies small RNAs that inhibit androgen signaling and prostate cancer cell growth. Mol Ther Nucleic Acids 2023; 33:257-272. [PMID: 37554515 PMCID: PMC10404560 DOI: 10.1016/j.omtn.2023.06.021] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/04/2022] [Accepted: 06/26/2023] [Indexed: 08/10/2023]
Abstract
Blocking androgen receptor signaling is the mainstay of therapy for advanced prostate cancer (PCa). However, acquired resistance to single agents targeting this pathway results in the development of lethal castration-resistant PCa. Combination therapy approaches represent a promising strategy for the treatment of advanced disease. Here, we explore a therapeutic strategy for PCa based on the ability of shRNAs/siRNAs to function essentially as miRNAs and, via seed sequence complementarity, induce RNA interference of numerous targets simultaneously. We developed a library that contained shRNAs with all possible seed sequence combinations to identify those ones that most potently reduce cell growth and viability when expressed in PCa cells. Validation of some of these RNAi sequences indicated that the toxic effect is associated with seed sequence complementarity to the 3' UTR of AR coregulatory and essential genes. In fact, expression of siRNAs containing the identified toxic seed sequences led to global inhibition of AR-mediated gene expression and reduced expression of cell-cycle genes. When tested in mice, the toxic shRNAs also inhibited castration-resistant PCa and exhibited therapeutic efficacy in pre-established tumors. Our findings highlight RNAi of androgen signaling networks as a promising therapeutic strategy for PCa.
Collapse
Affiliation(s)
- Joshua M. Corbin
- Stephenson Cancer Center, 800 NE 10th Street, Oklahoma City, OK 73104, USA
- Department of Pathology, Biomedical Sciences Building, University of Oklahoma Health Sciences Center, 940 Stanton L. Young Boulevard, Oklahoma City, OK 73104, USA
| | - Constantin Georgescu
- Genes and Human Disease Research Program, Division of Genomics and Data Sciences, Oklahoma Medical Research Foundation, 825 NE 13th Street, Oklahoma City, OK 73104, USA
| | - Lin Wang
- Aging and Metabolism Program, Oklahoma Medical Research Foundation, 825 NE 13th Street, Oklahoma City, OK 73104, USA
| | - Jonathan D. Wren
- Genes and Human Disease Research Program, Division of Genomics and Data Sciences, Oklahoma Medical Research Foundation, 825 NE 13th Street, Oklahoma City, OK 73104, USA
| | - Magdalena Bieniasz
- Aging and Metabolism Program, Oklahoma Medical Research Foundation, 825 NE 13th Street, Oklahoma City, OK 73104, USA
| | - Chao Xu
- Stephenson Cancer Center, 800 NE 10th Street, Oklahoma City, OK 73104, USA
- Department of Biostatistics and Epidemiology, Hudson College of Public Health, University of Oklahoma Health Sciences Center, 801 N.E. 13 Street, Oklahoma City, OK 73104, USA
| | - Adam S. Asch
- Stephenson Cancer Center, 800 NE 10th Street, Oklahoma City, OK 73104, USA
- Department of Medicine, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104, USA
| | - Maria J. Ruiz Echevarría
- Stephenson Cancer Center, 800 NE 10th Street, Oklahoma City, OK 73104, USA
- Department of Pathology, Biomedical Sciences Building, University of Oklahoma Health Sciences Center, 940 Stanton L. Young Boulevard, Oklahoma City, OK 73104, USA
- Department of Medicine, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104, USA
| |
Collapse
|
30
|
de Carvalho Neves J, Moschovaki-Filippidou F, Böhm J, Laporte J. DNM2 levels normalization improves muscle phenotypes of a novel mouse model for moderate centronuclear myopathy. Mol Ther Nucleic Acids 2023; 33:321-334. [PMID: 37547294 PMCID: PMC10400865 DOI: 10.1016/j.omtn.2023.07.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/06/2022] [Accepted: 07/11/2023] [Indexed: 08/08/2023]
Abstract
Dynamin 2 (DNM2) is a ubiquitously expressed GTPase regulating membrane trafficking and cytoskeleton dynamics. Heterozygous dominant mutations in DNM2 cause centronuclear myopathy (CNM), associated with muscle weakness and atrophy and histopathological hallmarks as fiber hypotrophy and organelles mis-position. Different severities range from the severe neonatal onset form to the moderate form with childhood onset and to the mild adult onset form. No therapy is approved for CNM. Here we aimed to validate and rescue a mouse model for the moderate form of DNM2-CNM harboring the common DNM2 R369W missense mutation. Dnm2R369W/+ mice presented with increased DNM2 protein level in muscle and moderate CNM-like phenotypes with force deficit, muscle and fiber hypotrophy, impaired mTOR signaling, and progressive mitochondria and nuclei mis-position with age. Molecular analyses revealed a fiber type switch toward oxidative metabolism correlating with decreased force and alteration of mitophagy markers paralleling mitochondria structural defects. Normalization of DNM2 levels through intramuscular injection of AAV-shDnm2 targeting Dnm2 mRNA significantly improved histopathology and muscle and myofiber hypotrophy. These results showed that the Dnm2R369W/+ mouse is a faithful model for the moderate form of DNM2-CNM and revealed that DNM2 normalization after a short 4-week treatment is sufficient to improve the CNM phenotypes.
Collapse
Affiliation(s)
- Juliana de Carvalho Neves
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), CNRS UMR7104, INSERM U1258, 1 rue Laurent Fries, 67404 Illkirch Cedex, France
| | - Foteini Moschovaki-Filippidou
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), CNRS UMR7104, INSERM U1258, 1 rue Laurent Fries, 67404 Illkirch Cedex, France
| | - Johann Böhm
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), CNRS UMR7104, INSERM U1258, 1 rue Laurent Fries, 67404 Illkirch Cedex, France
| | - Jocelyn Laporte
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), CNRS UMR7104, INSERM U1258, 1 rue Laurent Fries, 67404 Illkirch Cedex, France
| |
Collapse
|
31
|
Monopoli KR, Korkin D, Khvorova A. Asymmetric trichotomous partitioning overcomes dataset limitations in building machine learning models for predicting siRNA efficacy. Mol Ther Nucleic Acids 2023; 33:93-109. [PMID: 37456778 PMCID: PMC10338369 DOI: 10.1016/j.omtn.2023.06.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/03/2022] [Accepted: 06/09/2023] [Indexed: 07/18/2023]
Abstract
Chemically modified small interfering RNAs (siRNAs) are promising therapeutics guiding sequence-specific silencing of disease genes. Identifying chemically modified siRNA sequences that effectively silence target genes remains challenging. Such determinations necessitate computational algorithms. Machine learning is a powerful predictive approach for tackling biological problems but typically requires datasets significantly larger than most available siRNA datasets. Here, we describe a framework applying machine learning to a small dataset (356 modified sequences) for siRNA efficacy prediction. To overcome noise and biological limitations in siRNA datasets, we apply a trichotomous, two-threshold, partitioning approach, producing several combinations of classification threshold pairs. We then test the effects of different thresholds on random forest machine learning model performance using a novel evaluation metric accounting for class imbalances. We identify thresholds yielding a model with high predictive power, outperforming a linear model generated from the same data, that was predictive upon experimental evaluation. Using a novel model feature extraction method, we observe target site base importances and base preferences consistent with our current understanding of the siRNA-mediated silencing mechanism, with the random forest providing higher resolution than the linear model. This framework applies to any classification challenge involving small biological datasets, providing an opportunity to develop high-performing design algorithms for oligonucleotide therapies.
Collapse
Affiliation(s)
- Kathryn R. Monopoli
- Department of Bioinformatics & Computational Biology, Worcester Polytechnic Institute, Worcester, MA 01609, USA
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, MA 01655, USA
| | - Dmitry Korkin
- Department of Bioinformatics & Computational Biology, Worcester Polytechnic Institute, Worcester, MA 01609, USA
| | - Anastasia Khvorova
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, MA 01655, USA
| |
Collapse
|
32
|
Baral B, Panigrahi B, Kar A, Tulsiyan KD, Suryakant U, Mandal D, Subudhi U. Peptide nanostructures-based delivery of DNA nanomaterial therapeutics for regulating gene expression. Mol Ther Nucleic Acids 2023; 33:493-510. [PMID: 37583574 PMCID: PMC10424151 DOI: 10.1016/j.omtn.2023.07.017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/13/2023] [Accepted: 07/14/2023] [Indexed: 08/17/2023]
Abstract
Self-assembled branched DNA (bDNA) nanomaterials have exhibited their functionality in various biomedical and diagnostic applications. However, the anionic cellular membrane has restricted the movement of bDNA nanostructures. Recently, amphiphilic peptides have been investigated as cationic delivery agents for nucleic acids. Herein, we demonstrate a strategy for delivering functional bDNA nanomaterials into mammalian cells using self-assembled linear peptides. In this study, antisense oligonucleotides of vascular endothelial growth factor (VEGF) were inserted in the overhangs of bDNAs. Novel linear peptides have been synthesized and the peptide-bound bDNA complex formation was examined using various biophysical experiments. Interestingly, the W4R4-bound bDNAs were found to be exceptionally stable against DNase I compared to other complexes. The delivery of fluorescent-labeled bDNAs into the mammalian cells confirmed the potential of peptide transporters. Furthermore, the functional efficacy of the peptide-bound bDNAs has been examined through RT-PCR and western blot analysis. The observed results revealed that W4R4 peptides exhibited excellent internalization of antisense bDNAs and significantly suppressed (3- to 4-fold) the transcripts and translated product of VEGF compared to the control. In summary, the results highlight the potential use of peptide-based nanocarrier for delivering bDNA nanostructures to regulate the gene expression in cell lines.
Collapse
Affiliation(s)
- Bineeth Baral
- DNA Nanotechnology & Application Laboratory, Environment & Sustainability Department, CSIR-Institute of Minerals & Materials Technology, Bhubaneswar 751013, Odisha, India
- Academy of Scientific & Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Bijayananda Panigrahi
- School of Biotechnology, Kalinga Institute of Industrial Technology Deemed to be University, Bhubaneswar 751024, Odisha, India
- Biopioneer Private Limited, Bhubaneswar 751024, Odisha, India
| | - Avishek Kar
- DNA Nanotechnology & Application Laboratory, Environment & Sustainability Department, CSIR-Institute of Minerals & Materials Technology, Bhubaneswar 751013, Odisha, India
- Academy of Scientific & Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Kiran D. Tulsiyan
- School of Chemical Sciences, National Institute of Science Education & Research, Bhubaneswar 752050, India
- Homi Bhaba National Institute, Mumbai 400094, India
| | - Uday Suryakant
- School of Biotechnology, Kalinga Institute of Industrial Technology Deemed to be University, Bhubaneswar 751024, Odisha, India
| | - Dindyal Mandal
- School of Biotechnology, Kalinga Institute of Industrial Technology Deemed to be University, Bhubaneswar 751024, Odisha, India
| | - Umakanta Subudhi
- DNA Nanotechnology & Application Laboratory, Environment & Sustainability Department, CSIR-Institute of Minerals & Materials Technology, Bhubaneswar 751013, Odisha, India
- Academy of Scientific & Innovative Research (AcSIR), Ghaziabad 201002, India
| |
Collapse
|
33
|
Golombek S, Hoffmann T, Hann L, Mandler M, Schmidhuber S, Weber J, Chang YT, Mehling R, Ladinig A, Knecht C, Leyens J, Schlensak C, Wendel HP, Schneeberger A, Avci-Adali M. Improved tropoelastin synthesis in the skin by codon optimization and nucleotide modification of tropoelastin-encoding synthetic mRNA. Mol Ther Nucleic Acids 2023; 33:642-654. [PMID: 37650117 PMCID: PMC10462787 DOI: 10.1016/j.omtn.2023.07.035] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/14/2022] [Accepted: 07/31/2023] [Indexed: 09/01/2023]
Abstract
Loss of elastin due to aging, disease, or injury can lead to impaired tissue function. In this study, de novo tropoelastin (TE) synthesis is investigated in vitro and in vivo using different TE-encoding synthetic mRNA variants after codon optimization and nucleotide modification. Codon optimization shows a strong effect on protein synthesis without affecting cell viability in vitro, whereas nucleotide modifications strongly modulate translation and reduce cell toxicity. Selected TE mRNA variants (3, 10, and 30 μg) are then analyzed in vivo in porcine skin after intradermal application. Administration of 30 μg of native TE mRNA with a me1 Ψ modification or 10 and 30 μg of unmodified codon-optimized TE mRNA is required to increase TE protein expression in vivo. In contrast, just 3 μg of a codon-optimized TE mRNA variant with the me1 Ψ modification is able to increase protein expression. Furthermore, skin toxicity is investigated in vitro by injecting 30 μg of mRNA of selected TE mRNA variants into a human full-thickness skin model, and no toxic effects are observed. Thereby, for the first time, an increased dermal TE synthesis by exogenous administration of synthetic mRNA is demonstrated in vivo. Codon optimization of a synthetic mRNA can significantly increase protein expression and therapeutic outcome.
Collapse
Affiliation(s)
- Sonia Golombek
- Department of Thoracic and Cardiovascular Surgery, University Hospital Tübingen, Calwerstraße 7/1, 72076 Tübingen, Germany
| | | | - Ludmilla Hann
- Department of Thoracic and Cardiovascular Surgery, University Hospital Tübingen, Calwerstraße 7/1, 72076 Tübingen, Germany
| | - Markus Mandler
- Accanis Biotech, Karl-Farkas-Gasse 22, Vienna 1030, Austria
| | | | - Josefin Weber
- Department of Thoracic and Cardiovascular Surgery, University Hospital Tübingen, Calwerstraße 7/1, 72076 Tübingen, Germany
| | - Young-Tae Chang
- Department of Chemistry, Pohang University of Science and Technology (POSTECH), Pohang 37673, Republic of Korea
| | - Roman Mehling
- Werner Siemens Imaging Center, Department of Preclinical Imaging and Radiopharmacy, Eberhard Karls University, Röntgenweg 13, 72076 Tübingen, Germany
| | - Andrea Ladinig
- University Clinic for Swine, Department of Farm Animals and Veterinary Public Health, University of Veterinary Medicine, Veterinärplatz 1, Vienna 1210, Austria
| | - Christian Knecht
- University Clinic for Swine, Department of Farm Animals and Veterinary Public Health, University of Veterinary Medicine, Veterinärplatz 1, Vienna 1210, Austria
| | - Johanna Leyens
- Department of Thoracic and Cardiovascular Surgery, University Hospital Tübingen, Calwerstraße 7/1, 72076 Tübingen, Germany
| | - Christian Schlensak
- Department of Thoracic and Cardiovascular Surgery, University Hospital Tübingen, Calwerstraße 7/1, 72076 Tübingen, Germany
| | - Hans Peter Wendel
- Department of Thoracic and Cardiovascular Surgery, University Hospital Tübingen, Calwerstraße 7/1, 72076 Tübingen, Germany
| | | | - Meltem Avci-Adali
- Department of Thoracic and Cardiovascular Surgery, University Hospital Tübingen, Calwerstraße 7/1, 72076 Tübingen, Germany
| |
Collapse
|
34
|
Nagano M, Kubota K, Sakata A, Nakamura R, Yoshitomi T, Wakui K, Yoshimoto K. A neutralizable dimeric anti-thrombin aptamer with potent anticoagulant activity in mice. Mol Ther Nucleic Acids 2023; 33:762-772. [PMID: 37621412 PMCID: PMC10445101 DOI: 10.1016/j.omtn.2023.07.038] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/08/2023] [Accepted: 07/31/2023] [Indexed: 08/26/2023]
Abstract
Heparin-induced thrombocytopenia (HIT) is a complication caused by administration of the anticoagulant heparin. Although the number of patients with HIT has drastically increased because of coronavirus disease 2019 (COVID-19), the currently used thrombin inhibitors for HIT therapy do not have antidotes to arrest the severe bleeding that occurs as a side effect; therefore, establishment of safer treatments for HIT patients is imperative. Here, we devised a potent thrombin inhibitor based on bivalent aptamers with a higher safety profile via combination with the antidote. Using an anti-thrombin DNA aptamer M08s-1 as a promising anticoagulant, its homodimer and heterodimer with TBA29 linked by a conformationally flexible linker or a rigid duplex linker were designed. The dimerized M08s-1-based aptamers had about 100-fold increased binding affinity to human and mouse thrombin compared with the monomer counterparts. Administration of these bivalent aptamers into mice revealed that the anticoagulant activity of the dimers significantly surpassed that of an approved drug for HIT treatment, argatroban. Moreover, adding protamine sulfate as an antidote against the most potent bivalent aptamer completely suppressed the anticoagulant activity of the dimer. Emerging potent and neutralizable anticoagulant aptamers will be promising candidates for HIT treatment with a higher safety profile.
Collapse
Affiliation(s)
- Masanobu Nagano
- Department of Life Sciences, Graduate School of Arts and Sciences, The University of Tokyo, 3-8-1 Komaba, Meguro, Tokyo 153-8902, Japan
| | - Kazuki Kubota
- Department of Life Sciences, Graduate School of Arts and Sciences, The University of Tokyo, 3-8-1 Komaba, Meguro, Tokyo 153-8902, Japan
| | - Asuka Sakata
- Medicinal Biology of Thrombosis and Hemostasis, Nara Medical University, 840 Shijo-cho, Kashihara, Nara 634-8521, Japan
| | - Rei Nakamura
- Department of Life Sciences, Graduate School of Arts and Sciences, The University of Tokyo, 3-8-1 Komaba, Meguro, Tokyo 153-8902, Japan
| | - Toru Yoshitomi
- Department of Life Sciences, Graduate School of Arts and Sciences, The University of Tokyo, 3-8-1 Komaba, Meguro, Tokyo 153-8902, Japan
| | - Koji Wakui
- Department of Life Sciences, Graduate School of Arts and Sciences, The University of Tokyo, 3-8-1 Komaba, Meguro, Tokyo 153-8902, Japan
| | - Keitaro Yoshimoto
- Department of Life Sciences, Graduate School of Arts and Sciences, The University of Tokyo, 3-8-1 Komaba, Meguro, Tokyo 153-8902, Japan
| |
Collapse
|
35
|
Weidner J, Kolosionek E, Holmila R, Ax E, Garreau M, Gnerlich F, Olsson H, Czechtizky W, Vollmer S, Rydzik AM. Gymnotic uptake of AntimiRs alter microRNA-34a levels in 2D and 3D epithelial cell culture. Mol Ther Nucleic Acids 2023; 33:898-907. [PMID: 37680982 PMCID: PMC10480572 DOI: 10.1016/j.omtn.2023.08.014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/24/2023] [Accepted: 08/14/2023] [Indexed: 09/09/2023]
Abstract
MicroRNAs are attractive therapeutic targets in many diseases, including chronic obstructive pulmonary disease and idiopathic pulmonary fibrosis. Among microRNA inhibitors antimiRs have been proven successful in lowering aberrant microRNA levels in the clinic. We present a set of antimiRs targeting miR-34a, which has been shown to be dysregulated in chronic lung diseases. The tool compounds were taken up by a bronchial epithelial cell line and primary human bronchial epithelial cells, followed by efficient knockdown of miR-34a. Similar results were observed in 3D differentiated primary human bronchial epithelial cells cultured at the air-liquid interface. Varying chemical properties of antimiRs had significant impact on cellular uptake and potency, resulting in effective tool compounds for use in lung-relevant cellular systems. This report demonstrates gymnotic antimiR uptake and activity in 3D epithelial cell culture after apical administration, mimicking inhalation conditions.
Collapse
Affiliation(s)
- Julie Weidner
- Translational Science Experimental Medicine, Research & Early Development, Respiratory & Immunology, BioPharmaceutical R&D, AstraZeneca, 431 83 Mölndal, Sweden
| | - Ewa Kolosionek
- Bioscience COPD/IPF, Research & Early Development, Respiratory & Immunology, BioPharmaceutical R&D, AstraZeneca, 431 83 Mölndal, Sweden
| | - Reetta Holmila
- Bioscience COPD/IPF, Research & Early Development, Respiratory & Immunology, BioPharmaceutical R&D, AstraZeneca, 431 83 Mölndal, Sweden
| | - Elisabeth Ax
- Translational Science Experimental Medicine, Research & Early Development, Respiratory & Immunology, BioPharmaceutical R&D, AstraZeneca, 431 83 Mölndal, Sweden
| | - Marion Garreau
- Medicinal Chemistry, Research & Early Development, Respiratory & Immunology, BioPharmaceutical R&D, AstraZeneca, 431 83 Mölndal, Sweden
| | - Felix Gnerlich
- Medicinal Chemistry, Research & Early Development, Respiratory & Immunology, BioPharmaceutical R&D, AstraZeneca, 431 83 Mölndal, Sweden
| | - Henric Olsson
- Translational Science Experimental Medicine, Research & Early Development, Respiratory & Immunology, BioPharmaceutical R&D, AstraZeneca, 431 83 Mölndal, Sweden
| | - Werngard Czechtizky
- Medicinal Chemistry, Research & Early Development, Respiratory & Immunology, BioPharmaceutical R&D, AstraZeneca, 431 83 Mölndal, Sweden
| | - Stefan Vollmer
- Bioscience COPD/IPF, Research & Early Development, Respiratory & Immunology, BioPharmaceutical R&D, AstraZeneca, 431 83 Mölndal, Sweden
| | - Anna M. Rydzik
- Medicinal Chemistry, Research & Early Development, Respiratory & Immunology, BioPharmaceutical R&D, AstraZeneca, 431 83 Mölndal, Sweden
| |
Collapse
|
36
|
Centa JL, Stratton MP, Pratt MA, Osterlund Oltmanns JR, Wallace DG, Miller SA, Weimer JM, Hastings ML. Protracted CLN3 Batten disease in mice that genetically model an exon-skipping therapeutic approach. Mol Ther Nucleic Acids 2023; 33:15-27. [PMID: 37359347 PMCID: PMC10285469 DOI: 10.1016/j.omtn.2023.05.025] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/17/2023] [Accepted: 05/31/2023] [Indexed: 06/28/2023]
Abstract
Genetic mutations that disrupt open reading frames and cause translation termination are frequent causes of human disease and are difficult to treat due to protein truncation and mRNA degradation by nonsense-mediated decay, leaving few options for traditional drug targeting. Splice-switching antisense oligonucleotides offer a potential therapeutic solution for diseases caused by disrupted open reading frames by inducing exon skipping to correct the open reading frame. We have recently reported on an exon-skipping antisense oligonucleotide that has a therapeutic effect in a mouse model of CLN3 Batten disease, a fatal pediatric lysosomal storage disease. To validate this therapeutic approach, we generated a mouse model that constitutively expresses the Cln3 spliced isoform induced by the antisense molecule. Behavioral and pathological analyses of these mice demonstrate a less severe phenotype compared with the CLN3 disease mouse model, providing evidence that antisense oligonucleotide-induced exon skipping can have therapeutic efficacy in treating CLN3 Batten disease. This model highlights how protein engineering through RNA splicing modulation can be an effective therapeutic approach.
Collapse
Affiliation(s)
- Jessica L. Centa
- Center for Genetic Diseases, Chicago Medical School, Rosalind Franklin University of Medicine and Science, North Chicago, IL 60064, USA
| | - Matthew P. Stratton
- Center for Genetic Diseases, Chicago Medical School, Rosalind Franklin University of Medicine and Science, North Chicago, IL 60064, USA
- School of Graduate and Postdoctoral Studies, Rosalind Franklin University of Medicine and Science, North Chicago, IL 60064, USA
| | - Melissa A. Pratt
- Pediatrics and Rare Diseases Group, Sanford Research, Sioux Falls, SD 57104, USA
| | | | - Douglas G. Wallace
- Department of Psychology, Northern Illinois University, DeKalb, IL 60115, USA
| | - Steven A. Miller
- Psychology Department, College of Health Professionals, Rosalind Franklin University of Medicine and Science, North Chicago, IL 60064, USA
| | - Jill M. Weimer
- Pediatrics and Rare Diseases Group, Sanford Research, Sioux Falls, SD 57104, USA
- Department of Pediatrics, Sanford School of Medicine, University of South Dakota, Sioux Falls, SD 57104, USA
| | - Michelle L. Hastings
- Center for Genetic Diseases, Chicago Medical School, Rosalind Franklin University of Medicine and Science, North Chicago, IL 60064, USA
- Department of Pharmacology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| |
Collapse
|
37
|
Yan L, Su Y, Hsia I, Xu Y, Vincent-Chong VK, Mojica W, Seshadri M, Zhao R, Wu Y. Delivery of anti-microRNA-21 by lung-targeted liposomes for pulmonary fibrosis treatment. Mol Ther Nucleic Acids 2023; 32:36-47. [PMID: 36919116 DOI: 10.1016/j.omtn.2023.02.031] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/08/2022] [Accepted: 02/24/2023] [Indexed: 03/06/2023]
Abstract
Idiopathic pulmonary fibrosis (IPF) is a chronic lung disorder with a low survival rate. Pulmonary fibrosis is one of the complications of COVID-19 and has a high prevalence in COVID-19 patients. Currently, no effective therapies other than lung transplantation are available to cure IPF and post-COVID-19 pulmonary fibrosis. MicroRNAs are small non-coding RNAs that mediate the development and progression of pulmonary fibrosis, thus making them potent drug candidates for this serious disease. MicroRNA-21 (miR-21) promotes not only the differentiation of fibroblasts to myofibroblasts but also epithelial-mesenchymal transition, both of which have been proposed as fundamental processes in pulmonary fibrosis development. Delivery of anti-miR-21 to block the miR-21-associated fibrogenic pathways represents a promising therapy for pulmonary fibrosis. However, microRNA treatment is challenged by quick degradation of RNA in blood, poor cellular uptake, and off-target effects. To overcome these challenges, we developed a lung-targeted, cationic liposome formulation to encapsulate anti-miR-21, enhance its delivery efficiency, and improve the therapeutic efficacy. We optimized the liposome formulation and demonstrated the anti-fibrotic effects using both in vitro and in vivo lung fibrosis models. Our results showed that anti-miR-21 delivered by cationic liposomes suppressed myofibroblast differentiation, reduced the synthesis of extracellular matrix, and inhibited fibrosis progression.
Collapse
|
38
|
Lin G, Yan H, Sun J, Zhao J, Zhang Y. Self-replicating RNA nanoparticle vaccine elicits protective immune responses against SARS-CoV-2. Mol Ther Nucleic Acids 2023; 32:650-666. [PMID: 37151990 PMCID: PMC10122567 DOI: 10.1016/j.omtn.2023.04.021] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/22/2022] [Accepted: 04/19/2023] [Indexed: 05/09/2023]
Abstract
The creation of safe and effective vaccines that induce potent cellular and humoral immune responses against SARS-CoV-2 is urgently needed to end the global COVID-19 epidemic. Here, we developed an alphavirus-derived self-replicating RNA (repRNA)-based vaccine platform encoding the receptor-binding domain (RBD) of SARS-CoV-2 spike glycoprotein. The repRNA triggers prolonged antigen expression compared with conventional mRNA due to the replication machinery of repRNA. To improve the delivery and vaccine efficacy of repRNA, we developed a self-assembling liposome-protamine-RNA (LPR) nanoparticle with highly efficient encapsulation and transfection of repRNA. LPR-repRNA vaccines substantially activated type I interferon response and innate immune signaling pathways. Subcutaneous immunization of LPR-repRNA-RBD led to prolonged antigen expression, stimulation of innate immune cells, and induction of germinal center response in draining lymph nodes. LPR-repRNA-RBD induced antigen-specific T cell responses and skewed cellular immunity toward an effector memory CD8+ T cell response. Immunizations with LPR-repRNA-RBD triggered the production of anti-RBD IgG antibodies and induced neutralizing antibody response against SARS-CoV-2 pseudovirus. LPR-repRNA-RBD vaccines reduced SARS-CoV-2 infection and lung inflammation in mice. Altogether, these data suggest that the LPR-repRNA platform can be a promising avenue for COVID-19 vaccine development.
Collapse
Affiliation(s)
- Guibin Lin
- The Second Affiliated Hospital, School of Biomedical Sciences and Engineering, South China University of Technology, Guangzhou, Guangdong 511442, China
- National Engineering Research Center for Tissue Restoration and Reconstruction, South China University of Technology, Guangzhou, Guangdong 510006, China
- Guangdong Provincial Key Laboratory of Biomedical Engineering, South China University of Technology, Guangzhou, Guangdong 510006, China
- Key Laboratory of Biomedical Materials and Engineering of the Ministry of Education, South China University of Technology, Guangzhou, Guangdong 510006, China
| | - Huan Yan
- The Second Affiliated Hospital, School of Biomedical Sciences and Engineering, South China University of Technology, Guangzhou, Guangdong 511442, China
- National Engineering Research Center for Tissue Restoration and Reconstruction, South China University of Technology, Guangzhou, Guangdong 510006, China
- Guangdong Provincial Key Laboratory of Biomedical Engineering, South China University of Technology, Guangzhou, Guangdong 510006, China
- Key Laboratory of Biomedical Materials and Engineering of the Ministry of Education, South China University of Technology, Guangzhou, Guangdong 510006, China
| | - Jing Sun
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, the First Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong 510182, China
| | - Jincun Zhao
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, the First Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong 510182, China
- Institute of Infectious Disease, Guangzhou Eighth People's Hospital of Guangzhou Medical University, Guangzhou, Guangdong 510060, China
| | - Yuan Zhang
- The Second Affiliated Hospital, School of Biomedical Sciences and Engineering, South China University of Technology, Guangzhou, Guangdong 511442, China
- National Engineering Research Center for Tissue Restoration and Reconstruction, South China University of Technology, Guangzhou, Guangdong 510006, China
- Guangdong Provincial Key Laboratory of Biomedical Engineering, South China University of Technology, Guangzhou, Guangdong 510006, China
- Key Laboratory of Biomedical Materials and Engineering of the Ministry of Education, South China University of Technology, Guangzhou, Guangdong 510006, China
| |
Collapse
|
39
|
McKenzie C, El-Kholy M, Parekh F, Robson M, Lamb K, Allen C, Sillibourne J, Cordoba S, Thomas S, Pule M. Novel Fas-TNFR chimeras that prevent Fas ligand-mediated kill and signal synergistically to enhance CAR T cell efficacy. Mol Ther Nucleic Acids 2023; 32:603-621. [PMID: 37200859 PMCID: PMC10185706 DOI: 10.1016/j.omtn.2023.04.017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/22/2023] [Accepted: 04/18/2023] [Indexed: 05/20/2023]
Abstract
The hostile tumor microenvironment limits the efficacy of adoptive cell therapies. Activation of the Fas death receptor initiates apoptosis and disrupting these receptors could be key to increasing CAR T cell efficacy. We screened a library of Fas-TNFR proteins identifying several novel chimeras that not only prevented Fas ligand-mediated kill, but also enhanced CAR T cell efficacy by signaling synergistically with the CAR. Upon binding Fas ligand, Fas-CD40 activated the NF-κB pathway, inducing greatest proliferation and IFN-γ release out of all Fas-TNFRs tested. Fas-CD40 induced profound transcriptional modifications, particularly genes relating to the cell cycle, metabolism, and chemokine signaling. Co-expression of Fas-CD40 with either 4-1BB- or CD28-containing CARs increased in vitro efficacy by augmenting CAR T cell proliferation and cancer target cytotoxicity, and enhanced tumor killing and overall mouse survival in vivo. Functional activity of the Fas-TNFRs were dependent on the co-stimulatory domain within the CAR, highlighting crosstalk between signaling pathways. Furthermore, we show that a major source for Fas-TNFR activation derives from CAR T cells themselves via activation-induced Fas ligand upregulation, highlighting a universal role of Fas-TNFRs in augmenting CAR T cell responses. We have identified Fas-CD40 as the optimal chimera for overcoming Fas ligand-mediated kill and enhancing CAR T cell efficacy.
Collapse
Affiliation(s)
| | | | | | | | | | | | | | | | | | - Martin Pule
- Autolus Therapeutics, London W12 7FP, UK
- Department of Haematology, UCL Cancer Institute, University College, 72 Huntley Street, London WC1E 6DD, UK
- Corresponding author Martin Pule, Autolus Therapeutics, London W12 7FP, UK.
| |
Collapse
|
40
|
Colombani T, Haudebourg T, Pitard B. 704/DNA vaccines leverage cytoplasmic DNA stimulation to promote anti-HIV neutralizing antibody production in mice and strong immune response against alpha-fetoprotein in non-human primates. Mol Ther Nucleic Acids 2023; 32:743-757. [PMID: 37251693 PMCID: PMC10213191 DOI: 10.1016/j.omtn.2023.04.029] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/13/2022] [Accepted: 04/28/2023] [Indexed: 05/31/2023]
Abstract
Genetic immunization is an attractive approach for prophylactic and therapeutic vaccination using synthetic vectors to deliver antigen-encoding nucleic acids. Recently, DNA delivered by a physical means or RNA by liposomes consisting of four different lipids demonstrated good protection in human phase III clinical trials and received Drugs Controller General of India and US FDA approval to protect against COVID-19, respectively. However, the development of a system allowing for efficient and simple delivery of nucleic acids while improving immune response priming has the potential to unleash the full therapeutic potential of genetic immunization. DNA-based gene therapies and vaccines have the potential for rapid development, as exemplified by the recent approval of Collategene, a gene therapy to treat human critical limb ischemia, and ZyCoV, a DNA vaccine delivered by spring-powered jet injector to protect against SARS-CoV2 infection. Recently, we reported amphiphilic block copolymer 704 as a promising synthetic vector for DNA vaccination in various models of human diseases. This vector allows dose sparing of antigen-encoding plasmid DNA. Here, we report the capacity of 704-mediated HIV and anti-hepatocellular carcinoma DNA vaccines to induce the production of specific antibodies against gp120 HIV envelope proteins in mice and against alpha-fetoprotein antigen in non-human primates, respectively. An investigation of the underlying mechanisms showed that 704-mediated vaccination did trigger a strong immune response by (1) allowing a direct DNA delivery into the cytosol, (2) promoting an intracytoplasmic DNA sensing leading to both interferon and NF-κB cascade stimulation, and (3) inducing antigen expression by muscle cells and presentation by antigen-presenting cells, leading to the induction of a robust adaptive response. Overall, our findings suggest that the 704-mediated DNA vaccination platform is an attractive method to develop both prophylactic and therapeutic vaccines.
Collapse
Affiliation(s)
- Thibault Colombani
- Nantes Université, University of Angers, INSERM, CNRS, Immunology and New Concepts in Immunotherapy, INSERM UMR1302, CNRS EMR6001, 44000 Nantes, France
| | - Thomas Haudebourg
- Nantes Université, University of Angers, INSERM, CNRS, Immunology and New Concepts in Immunotherapy, INSERM UMR1302, CNRS EMR6001, 44000 Nantes, France
| | - Bruno Pitard
- Nantes Université, University of Angers, INSERM, CNRS, Immunology and New Concepts in Immunotherapy, INSERM UMR1302, CNRS EMR6001, 44000 Nantes, France
| |
Collapse
|
41
|
Lax A, Soler F, Fernandez del Palacio MJ, Pascual-Oliver S, Ballester MR, Fuster JJ, Pascual-Figal D, Asensio-Lopez MDC. Silencing of microRNA-106b-5p prevents doxorubicin-mediated cardiotoxicity through modulation of the PR55α/YY1/sST2 signaling axis. Mol Ther Nucleic Acids 2023; 32:704-720. [PMID: 37234747 PMCID: PMC10208836 DOI: 10.1016/j.omtn.2023.04.031] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/15/2022] [Accepted: 04/28/2023] [Indexed: 05/28/2023]
Abstract
Clinical use of doxorubicin (Dox), an anthracycline with potent anti-tumor effects, is limited because of its highly chemotherapy-induced cardiotoxicity (CIC). After myocardial infarction (MI), we have recently identified Yin Yang-1 (YY1) and histone deacetylase 4 (HDAC4) as two factors involved in the overexpression of the isoform soluble suppression of tumorigenicity 2 (sST2) protein, which acts as a decoy receptor blocking the favorable effects of IL-33. Therefore, high levels of sST2 are associated with increased fibrosis, remodeling, and worse cardiovascular outcomes. No data exist on the role of the YY1/HDAC4/sST2 axis in CIC. This study aimed to evaluate the pathophysiological implication of the molecular YY1/HDAC4/sST2 axis in remodeling that is developed in patients treated with Dox as well as to suggest a novel molecular therapy to prevent anthracycline-induced cardiotoxicity. Here, we have characterized a novel nexus between miR106b-5p (miR-106b) levels and the YY1/HDAC4 axis in relation to the cardiac expression of sST2 using two experimental models with Dox-induced cardiotoxicity. The addition of Dox (5 μM) to human induced pluripotent stem cell-derived cardiomyocytes induced cellular apoptotic death via upregulation of miR-106b-5p (miR-106b), which was confirmed by specific mimic sequences. A functional blockage of miR-106b using the locked nucleic acid antagomir inhibited Dox-induced cardiotoxicity.
Collapse
Affiliation(s)
- Antonio Lax
- Biomedical Research Institute Virgen de la Arrixaca (IMIB-Arrixaca), University of Murcia, 30120 Murcia, Spain
| | - Fernando Soler
- Biomedical Research Institute Virgen de la Arrixaca (IMIB-Arrixaca), University of Murcia, 30120 Murcia, Spain
| | | | - Silvia Pascual-Oliver
- Biomedical Research Institute Virgen de la Arrixaca (IMIB-Arrixaca), University of Murcia, 30120 Murcia, Spain
| | - Miriam Ruiz Ballester
- Biomedical Research Institute Virgen de la Arrixaca (IMIB-Arrixaca), University of Murcia, 30120 Murcia, Spain
| | - Jose Javier Fuster
- Centro Nacional de Investigaciones Cardiovasculares (CNIC), 28029 Madrid, Spain
| | - Domingo Pascual-Figal
- Centro Nacional de Investigaciones Cardiovasculares (CNIC), 28029 Madrid, Spain
- Cardiology Department, Hospital Virgen de la Arrixaca, IMIB-Arrixaca and University of Murcia, 30120 Murcia, Spain
- Centro de Investigación Biomédica en Red Enfermedades Cardiovasculares (CIBERCV), 28029 Madrid, Spain
| | | |
Collapse
|
42
|
Schellens RT, Broekman S, Peters T, Graave P, Malinar L, Venselaar H, Kremer H, De Vrieze E, Van Wijk E. A protein domain-oriented approach to expand the opportunities of therapeutic exon skipping for USH2A-associated retinitis pigmentosa. Mol Ther Nucleic Acids 2023; 32:980-994. [PMID: 37313440 PMCID: PMC10258241 DOI: 10.1016/j.omtn.2023.05.020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/18/2022] [Accepted: 05/17/2023] [Indexed: 06/15/2023]
Abstract
Loss-of-function mutations in USH2A are among the most common causes of syndromic and non-syndromic retinitis pigmentosa (RP). We previously presented skipping of USH2A exon 13 as a promising treatment paradigm for USH2A-associated RP. However, RP-associated mutations are often private, and evenly distributed along the USH2A gene. In order to broaden the group of patients that could benefit from therapeutic exon skipping strategies, we expanded our approach to other USH2A exons in which unique loss-of-function mutations have been reported by implementing a protein domain-oriented dual exon skipping strategy. We first generated zebrafish mutants carrying a genomic deletion of the orthologous exons of the frequently mutated human USH2A exons 30-31 or 39-40 using CRISPR-Cas9. Excision of these in-frame combinations of exons restored usherin expression in the zebrafish retina and rescued the photopigment mislocalization typically observed in ush2a mutants. To translate these findings into a future treatment in humans, we employed in vitro assays to identify and validate antisense oligonucleotides (ASOs) with a high potency for sequence-specific dual exon skipping. Together, the in vitro and in vivo data demonstrate protein domain-oriented ASO-induced dual exon skipping to be a highly promising treatment option for RP caused by mutations in USH2A.
Collapse
Affiliation(s)
- Renske T.W. Schellens
- Department of Otorhinolaryngology, Hearing and Genes, Radboud University Medical Center, 6525GA Nijmegen, the Netherlands
- Donders Institute for Brain, Cognition and Behaviour, 6500 GL Nijmegen, the Netherlands
| | - Sanne Broekman
- Department of Otorhinolaryngology, Hearing and Genes, Radboud University Medical Center, 6525GA Nijmegen, the Netherlands
| | - Theo Peters
- Department of Otorhinolaryngology, Hearing and Genes, Radboud University Medical Center, 6525GA Nijmegen, the Netherlands
| | - Pam Graave
- Department of Human Genetics, Radboud University Medical Center, 6525 GA Nijmegen, the Netherlands
| | - Lucija Malinar
- Center for Molecular and Biomolecular Informatics, Radboud University Medical Center, 6525 GA Nijmegen, the Netherlands
| | - Hanka Venselaar
- Center for Molecular and Biomolecular Informatics, Radboud University Medical Center, 6525 GA Nijmegen, the Netherlands
| | - Hannie Kremer
- Department of Otorhinolaryngology, Hearing and Genes, Radboud University Medical Center, 6525GA Nijmegen, the Netherlands
- Donders Institute for Brain, Cognition and Behaviour, 6500 GL Nijmegen, the Netherlands
- Department of Human Genetics, Radboud University Medical Center, 6525 GA Nijmegen, the Netherlands
| | - Erik De Vrieze
- Department of Otorhinolaryngology, Hearing and Genes, Radboud University Medical Center, 6525GA Nijmegen, the Netherlands
- Donders Institute for Brain, Cognition and Behaviour, 6500 GL Nijmegen, the Netherlands
| | - Erwin Van Wijk
- Department of Otorhinolaryngology, Hearing and Genes, Radboud University Medical Center, 6525GA Nijmegen, the Netherlands
- Donders Institute for Brain, Cognition and Behaviour, 6500 GL Nijmegen, the Netherlands
| |
Collapse
|
43
|
Bayat H, Pourgholami MH, Rahmani S, Pournajaf S, Mowla SJ. Synthetic miR-21 decoy circularized by tRNA splicing mechanism inhibited tumorigenesis in glioblastoma in vitro and in vivo models. Mol Ther Nucleic Acids 2023; 32:432-444. [PMID: 37181451 PMCID: PMC10173299 DOI: 10.1016/j.omtn.2023.04.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/30/2022] [Accepted: 04/04/2023] [Indexed: 05/16/2023]
Abstract
Glioblastoma multiforme (GBM) is the deadliest primary central nervous system tumor. miRNAs (miRs), a class of non-coding RNAs, are considered pivotal post-transcriptional regulators of cell signaling pathways. miR-21 is a reliable oncogene that promotes tumorigenesis of cancer cells. We first performed an in silico analysis on 10 microarray datasets retrieved from TCGA and GEO databases to elucidate top differentially expressed miRs. Furthermore, we generated a circular miR-21 decoy, CM21D, using the tRNA-splicing mechanism in GBM cell models, U87 and C6. The inhibitory efficacy of CM21D with that of a linear form, LM21D, was compared under in vitro conditions and an intracranial C6 rat glioblastoma model. miR-21 significantly overexpressed in GBM samples and confirmed in GBM cell models using qRT-PCR. CM21D was more efficient than LM21D at inducing apoptosis, inhibiting cell proliferation and migration, and interrupting the cell cycle by restoring the expression of miR-21 target genes at RNA and protein levels. Moreover, CM21D suppressed tumor growth more effectively than LM21D in the C6-rat GBM model (p < 0.001). Our findings validate miR-21 as a promising therapeutic target for GBM. The introduced CM21D by sponging miR-21 reduced tumorigenesis of GBM and can be considered a potential RNA-base therapy to inhibit cancers.
Collapse
Affiliation(s)
- Hadi Bayat
- Department of Molecular Genetics, Faculty of Biological Sciences, Tarbiat Modares University, Tehran 14115-111, Iran
| | | | - Saeid Rahmani
- School of Computer Science, Institute for Research in Fundamental Sciences (IPM), Tehran 19538-33511, Iran
| | - Safura Pournajaf
- Department of Physiology, Faculty of Medical Sciences, Tarbiat Modares University, Tehran 14115-111, Iran
| | - Seyed Javad Mowla
- Department of Molecular Genetics, Faculty of Biological Sciences, Tarbiat Modares University, Tehran 14115-111, Iran
- Corresponding author: Seyed Javad Mowla, Department of Molecular Genetics, Faculty of Biological Sciences, Tarbiat Modares University, Tehran 14115-111, Iran.
| |
Collapse
|
44
|
Bernard MC, Bazin E, Petiot N, Lemdani K, Commandeur S, Verdelet C, Margot S, Perkov V, Ripoll M, Garinot M, Ruiz S, Boudet F, Rokbi B, Haensler J. The impact of nucleoside base modification in mRNA vaccine is influenced by the chemistry of its lipid nanoparticle delivery system. Mol Ther Nucleic Acids 2023; 32:794-806. [PMID: 37346973 PMCID: PMC10280092 DOI: 10.1016/j.omtn.2023.05.004] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/11/2022] [Accepted: 05/04/2023] [Indexed: 06/23/2023]
Abstract
The use of modified nucleosides is an important approach to mitigate the intrinsic immunostimulatory activity of exogenous mRNA and to increase its translation for mRNA therapeutic applications. However, for vaccine applications, the intrinsic immunostimulatory nature of unmodified mRNA could help induce productive immunity. Additionally, the ionizable lipid nanoparticles (LNPs) used to deliver mRNA vaccines can possess immunostimulatory properties that may influence the impact of nucleoside modification. Here we show that uridine replacement with N1-methylpseudouridine in an mRNA vaccine encoding influenza hemagglutinin had a significant impact on the induction of innate chemokines/cytokines and a positive impact on the induction of functional antibody titers in mice and macaques when MC3 or KC2 LNPs were used as delivery systems, while it impacted only minimally the titers obtained with L319 LNPs, indicating that the impact of nucleoside modification on mRNA vaccine efficacy varies with LNP composition. In line with previous observations, we noticed an inverse correlation between the induction of high innate IFN-α titers in the macaques and antigen-specific immune responses. Furthermore, and consistent with the species specificity of pathogen recognition receptors, we found that the effect of uridine replacement did not strictly translate from mice to non-human primates.
Collapse
Affiliation(s)
| | - Emilie Bazin
- Sanofi R&D, Campus Mérieux, 1541 Avenue Marcel Mérieux, 69280 Marcy l’Etoile, France
| | - Nadine Petiot
- Sanofi R&D, Campus Mérieux, 1541 Avenue Marcel Mérieux, 69280 Marcy l’Etoile, France
| | - Katia Lemdani
- Sanofi R&D, Campus Mérieux, 1541 Avenue Marcel Mérieux, 69280 Marcy l’Etoile, France
| | - Sylvie Commandeur
- Sanofi R&D, Campus Mérieux, 1541 Avenue Marcel Mérieux, 69280 Marcy l’Etoile, France
| | - Cécile Verdelet
- Sanofi R&D, Campus Mérieux, 1541 Avenue Marcel Mérieux, 69280 Marcy l’Etoile, France
| | - Sylvie Margot
- Sanofi R&D, Campus Mérieux, 1541 Avenue Marcel Mérieux, 69280 Marcy l’Etoile, France
| | - Vladimir Perkov
- Sanofi R&D, Campus Mérieux, 1541 Avenue Marcel Mérieux, 69280 Marcy l’Etoile, France
| | - Manon Ripoll
- Sanofi R&D, Campus Mérieux, 1541 Avenue Marcel Mérieux, 69280 Marcy l’Etoile, France
| | - Marie Garinot
- Sanofi R&D, Campus Mérieux, 1541 Avenue Marcel Mérieux, 69280 Marcy l’Etoile, France
| | - Sophie Ruiz
- Sanofi R&D, Campus Mérieux, 1541 Avenue Marcel Mérieux, 69280 Marcy l’Etoile, France
| | - Florence Boudet
- Sanofi R&D, Campus Mérieux, 1541 Avenue Marcel Mérieux, 69280 Marcy l’Etoile, France
| | - Bachra Rokbi
- Sanofi R&D, Campus Mérieux, 1541 Avenue Marcel Mérieux, 69280 Marcy l’Etoile, France
| | - Jean Haensler
- Sanofi R&D, Campus Mérieux, 1541 Avenue Marcel Mérieux, 69280 Marcy l’Etoile, France
| |
Collapse
|
45
|
El Boujnouni N, van der Bent ML, Willemse M, ’t Hoen PA, Brock R, Wansink DG. Block or degrade? Balancing on- and off-target effects of antisense strategies against transcripts with expanded triplet repeats in DM1. Mol Ther Nucleic Acids 2023; 32:622-636. [PMID: 37200862 PMCID: PMC10185704 DOI: 10.1016/j.omtn.2023.04.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/26/2022] [Accepted: 04/13/2023] [Indexed: 05/20/2023]
Abstract
Antisense oligonucleotide (ASO) therapies for myotonic dystrophy type 1 (DM1) are based on elimination of transcripts containing an expanded repeat or inhibition of sequestration of RNA-binding proteins. This activity is achievable by both degradation of expanded transcripts and steric hindrance, although it is unknown which approach is superior. We compared blocking ASOs with RNase H-recruiting gapmers of equivalent chemistries. Two DMPK target sequences were selected: the triplet repeat and a unique sequence upstream thereof. We assessed ASO effects on transcript levels, ribonucleoprotein foci and disease-associated missplicing, and performed RNA sequencing to investigate on- and off-target effects. Both gapmers and the repeat blocker led to significant DMPK knockdown and a reduction in (CUG)exp foci. However, the repeat blocker was more effective in MBNL1 protein displacement and had superior efficiency in splicing correction at the tested dose of 100 nM. By comparison, on a transcriptome level, the blocking ASO had the fewest off-target effects. In particular, the off-target profile of the repeat gapmer asks for cautious consideration in further therapeutic development. Altogether, our study demonstrates the importance of evaluating both on-target and downstream effects of ASOs in a DM1 context, and provides guiding principles for safe and effective targeting of toxic transcripts.
Collapse
Affiliation(s)
- Najoua El Boujnouni
- Department of Medical BioSciences, Research Institute for Medical Innovation, Radboud University Medical Center, 6525 GA Nijmegen, the Netherlands
| | - M. Leontien van der Bent
- Department of Medical BioSciences, Research Institute for Medical Innovation, Radboud University Medical Center, 6525 GA Nijmegen, the Netherlands
| | - Marieke Willemse
- Department of Medical BioSciences, Research Institute for Medical Innovation, Radboud University Medical Center, 6525 GA Nijmegen, the Netherlands
| | - Peter A.C. ’t Hoen
- Department of Medical BioSciences, Research Institute for Medical Innovation, Radboud University Medical Center, 6525 GA Nijmegen, the Netherlands
| | - Roland Brock
- Department of Medical BioSciences, Research Institute for Medical Innovation, Radboud University Medical Center, 6525 GA Nijmegen, the Netherlands
- Department of Medical Biochemistry, College of Medicine and Medical Sciences, Arabian Gulf University, Manama 293, Bahrain
- Corresponding author Roland Brock, Department of Medical BioSciences, Research Institute for Medical Innovation, Radboud University Medical Center, 6525 GA Nijmegen, the Netherlands.
| | - Derick G. Wansink
- Department of Medical BioSciences, Research Institute for Medical Innovation, Radboud University Medical Center, 6525 GA Nijmegen, the Netherlands
- Corresponding author Derick G. Wansink, Department of Medical BioSciences, Research Institute for Medical Innovation, Radboud University Medical Center, 6525 GA Nijmegen, the Netherlands.
| |
Collapse
|
46
|
Shibata A, Shirohzu H, Iwakami Y, Abe T, Emura C, Aoki E, Ohgi T. Terminal bridging of siRNA duplex at the ribose 2' position controls strand bias and target sequence preference. Mol Ther Nucleic Acids 2023; 32:468-477. [PMID: 37168798 PMCID: PMC10165404 DOI: 10.1016/j.omtn.2023.04.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/04/2022] [Accepted: 04/14/2023] [Indexed: 05/13/2023]
Abstract
Small interfering RNA (siRNA) and short hairpin RNA (shRNA) are widely used as RNA interference (RNAi) reagents. Recently, truncated shRNAs that trigger RNAi in a Dicer-independent manner have been developed. We generated a novel class of RNAi reagent, designated enforced strand bias (ESB) RNA, in which an siRNA duplex was chemically bridged between the 3' terminal overhang region of the guide strand and the 5' terminal nucleotide of the passenger strand. ESB RNA, which is chemically bridged at the 2' positions of ribose (2'-2' ESB RNA), functions in a Dicer-independent manner and was highly effective at triggering RNAi without the passenger strand-derived off-target effect. In addition, the 2'-2' ESB RNA exhibited a unique target sequence preference that differs from siRNA and silenced target sequences that could not be effectively suppressed by siRNA. Our results indicate that ESB RNA has the potential to be an effective RNAi reagent even when the target sequence is not suitable for siRNA.
Collapse
Affiliation(s)
- Atsushi Shibata
- Division of R&D, Bonac Corporation, 1488-4 Aikawa, Kurume, Fukuoka 839-0861, Japan
- Corresponding author Atsushi Shibata, Division of R&D, Bonac Corporation, 1488-4 Aikawa, Kurume, Fukuoka 839-0861, Japan.
| | - Hisao Shirohzu
- Division of R&D, Bonac Corporation, 1488-4 Aikawa, Kurume, Fukuoka 839-0861, Japan
- Fukuoka Center for Disease Control and Prevention, Kurume, Fukuoka, Japan
| | - Yusuke Iwakami
- Division of R&D, Bonac Corporation, 1488-4 Aikawa, Kurume, Fukuoka 839-0861, Japan
| | - Tomoaki Abe
- Division of R&D, Bonac Corporation, 1488-4 Aikawa, Kurume, Fukuoka 839-0861, Japan
| | - Chisato Emura
- Division of R&D, Bonac Corporation, 1488-4 Aikawa, Kurume, Fukuoka 839-0861, Japan
| | - Eriko Aoki
- Division of R&D, Bonac Corporation, 1488-4 Aikawa, Kurume, Fukuoka 839-0861, Japan
| | - Tadaaki Ohgi
- Division of R&D, Bonac Corporation, 1488-4 Aikawa, Kurume, Fukuoka 839-0861, Japan
| |
Collapse
|
47
|
Findlay AR, Paing MM, Daw JA, Haller M, Bengoechea R, Pittman SK, Li S, Wang F, Miller TM, True HL, Chou TF, Weihl CC. DNAJB6 isoform specific knockdown: Therapeutic potential for limb girdle muscular dystrophy D1. Mol Ther Nucleic Acids 2023; 32:937-948. [PMID: 37346979 PMCID: PMC10280091 DOI: 10.1016/j.omtn.2023.05.017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/17/2022] [Accepted: 05/10/2023] [Indexed: 06/23/2023]
Abstract
Dominant missense mutations in DNAJB6, a co-chaperone of HSP70, cause limb girdle muscular dystrophy (LGMD) D1. No treatments are currently available. Two isoforms exist, DNAJB6a and DNAJB6b, each with distinct localizations in muscle. Mutations reside in both isoforms, yet evidence suggests that DNAJB6b is primarily responsible for disease pathogenesis. Knockdown treatment strategies involving both isoforms carry risk, as DNAJB6 knockout is embryonic lethal. We therefore developed an isoform-specific knockdown approach using morpholinos. Selective reduction of each isoform was achieved in vitro in primary mouse myotubes and human LGMDD1 myoblasts, as well as in vivo in mouse skeletal muscle. To assess isoform specific knockdown in LGMDD1, we created primary myotube cultures from a knockin LGMDD1 mouse model. Using mass spectrometry, we identified an LGMDD1 protein signature related to protein homeostasis and myofibril structure. Selective reduction of DNAJB6b levels in LGMDD1 myotubes corrected much of the proteomic disease signature toward wild type levels. Additional in vivo functional data is required to determine if selective reduction of DNAJB6b is a viable therapeutic target for LGMDD1.
Collapse
Affiliation(s)
- Andrew R. Findlay
- Department of Neurology, Neuromuscular Division, Washington University School of Medicine, Saint Louis, MO 63110, USA
| | - May M. Paing
- Department of Neurology, Neuromuscular Division, Washington University School of Medicine, Saint Louis, MO 63110, USA
| | - Jil A. Daw
- Department of Neurology, Neuromuscular Division, Washington University School of Medicine, Saint Louis, MO 63110, USA
| | - Meade Haller
- Department of Neurology, Neuromuscular Division, Washington University School of Medicine, Saint Louis, MO 63110, USA
| | - Rocio Bengoechea
- Department of Neurology, Neuromuscular Division, Washington University School of Medicine, Saint Louis, MO 63110, USA
| | - Sara K. Pittman
- Department of Neurology, Neuromuscular Division, Washington University School of Medicine, Saint Louis, MO 63110, USA
| | - Shan Li
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Feng Wang
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Timothy M. Miller
- Department of Neurology, Neuromuscular Division, Washington University School of Medicine, Saint Louis, MO 63110, USA
| | - Heather L. True
- Department of Cell Biology and Physiology, Washington University School of Medicine, 660 South Euclid Avenue, Campus Box 8228, St. Louis, MO 63110, USA
| | - Tsui-Fen Chou
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Conrad C. Weihl
- Department of Neurology, Neuromuscular Division, Washington University School of Medicine, Saint Louis, MO 63110, USA
| |
Collapse
|
48
|
Yuan G, Yang ST, Yang S. Regulator of G protein signaling 12 drives inflammatory arthritis by activating synovial fibroblasts through MYCBP2/KIF2A signaling. Mol Ther Nucleic Acids 2023; 31:197-210. [PMID: 36700049 PMCID: PMC9843488 DOI: 10.1016/j.omtn.2022.12.017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/26/2022] [Accepted: 12/22/2022] [Indexed: 12/28/2022]
Abstract
Synovial fibroblasts are the active and aggressive drivers in the progression of arthritis, but the cellular and molecular mechanisms remain unknown. Here, our results showed that regulator of G protein signaling 12 (RGS12) maintained ciliogenesis in synovial fibroblasts, which is critical for the development of inflammatory arthritis. Deletion of RGS12 led to a significant decrease in ciliogenesis, adhesion, migration, and secretion of synovial fibroblasts. Mechanistically, RGS12 overexpression in synovial fibroblasts increased the length and number of cilia but decreased the protein level of kinesin family member 2A (KIF2A). The results of LC-MS analyses showed that RGS12 interacted with MYC binding protein 2 to enhance its ubiquitination activity, through which the KIF2A protein was degraded in synovial fibroblasts. Moreover, overexpression of KIF2A blocked the increases in cilia length and number. Mice with RGS12 deficiency or treatment of RGS12 shRNA nanoparticles significantly decreased the clinical score, paw swelling, synovitis, and cartilage destruction during inflammatory arthritis by inhibiting the activation of synovial fibroblasts. Therefore, this study provides evidence that RGS12 activates synovial fibroblasts' pathological function via promoting MCYBP2-mediated degradation of KIF2A and ciliogenesis. Our data suggest that RGS12 may be a potential drug target for the treatment of inflammatory arthritis.
Collapse
Affiliation(s)
- Gongsheng Yuan
- Department of Basic and Translational Sciences, School of Dental Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Shu-ting Yang
- Department of Basic and Translational Sciences, School of Dental Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Shuying Yang
- Department of Basic and Translational Sciences, School of Dental Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
- The Penn Center for Musculoskeletal Disorders, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
- Center for Innovation & Precision Dentistry, School of Engineering and Applied Sciences, University of Pennsylvania, Philadelphia, PA 19104, USA
| |
Collapse
|
49
|
Kaltak M, de Bruijn P, Piccolo D, Lee SE, Dulla K, Hoogenboezem T, Beumer W, Webster AR, Collin RW, Cheetham ME, Platenburg G, Swildens J. Antisense oligonucleotide therapy corrects splicing in the common Stargardt disease type 1-causing variant ABCA4 c.5461-10T>C. Mol Ther Nucleic Acids 2023; 31:674-688. [PMID: 36910710 PMCID: PMC9999166 DOI: 10.1016/j.omtn.2023.02.020] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/11/2022] [Accepted: 02/15/2023] [Indexed: 02/20/2023]
Abstract
Stargardt disease type 1 (STGD1) is the most common hereditary form of maculopathy and remains untreatable. STGD1 is caused by biallelic variants in the ABCA4 gene, which encodes the ATP-binding cassette (type 4) protein (ABCA4) that clears toxic byproducts of the visual cycle. The c.5461-10T>C p.[Thr1821Aspfs∗6,Thr1821Valfs∗13] variant is the most common severe disease-associated variant, and leads to exon skipping and out-of-frame ABCA4 transcripts that prevent translation of functional ABCA4 protein. Homozygous individuals typically display early onset STGD1 and are legally blind by early adulthood. Here, we applied antisense oligonucleotides (AONs) to promote exon inclusion and restore wild-type RNA splicing of ABCA4 c.5461-10T>C. The effect of AONs was first investigated in vitro using an ABCA4 midigene model. Subsequently, the best performing AONs were administered to homozygous c.5461-10T>C 3D human retinal organoids. Isoform-specific digital polymerase chain reaction revealed a significant increase in correctly spliced transcripts after treatment with the lead AON, QR-1011, up to 53% correct transcripts at a 3 μM dose. Furthermore, western blot and immunohistochemistry analyses identified restoration of ABCA4 protein after treatment. Collectively, we identified QR-1011 as a potent splice-correcting AON and a possible therapeutic intervention for patients harboring the severe ABCA4 c.5461-10T>C variant.
Collapse
Affiliation(s)
- Melita Kaltak
- ProQR Therapeutics, Zernikedreef 9, 2333 CK Leiden, the Netherlands
- Department of Human Genetics, Radboud University Medical Center, Geert Grooteplein-Zuid 10, 6525 GA Nijmegen, the Netherlands
- Academic Alliance Genetics, Radboud University Medical Center, Geert Grooteplein-Zuid 10, 6525 GA Nijmegen, and Maastricht University Medical Center+, P. Debyelaan 25, 6229 HX Maastricht, the Netherlands
| | - Petra de Bruijn
- ProQR Therapeutics, Zernikedreef 9, 2333 CK Leiden, the Netherlands
| | - Davide Piccolo
- UCL, Institute of Ophthalmology, 11-43 Bath Street, EC1V 9EL London, UK
| | - Sang-Eun Lee
- UCL, Institute of Ophthalmology, 11-43 Bath Street, EC1V 9EL London, UK
| | - Kalyan Dulla
- ProQR Therapeutics, Zernikedreef 9, 2333 CK Leiden, the Netherlands
| | | | - Wouter Beumer
- ProQR Therapeutics, Zernikedreef 9, 2333 CK Leiden, the Netherlands
| | - Andrew R. Webster
- UCL, Institute of Ophthalmology, 11-43 Bath Street, EC1V 9EL London, UK
- Moorfields Eye Hospital, 162 City Road, EC1V 2PD London, UK
| | - Rob W.J. Collin
- Department of Human Genetics, Radboud University Medical Center, Geert Grooteplein-Zuid 10, 6525 GA Nijmegen, the Netherlands
- Academic Alliance Genetics, Radboud University Medical Center, Geert Grooteplein-Zuid 10, 6525 GA Nijmegen, and Maastricht University Medical Center+, P. Debyelaan 25, 6229 HX Maastricht, the Netherlands
| | | | | | - Jim Swildens
- ProQR Therapeutics, Zernikedreef 9, 2333 CK Leiden, the Netherlands
| |
Collapse
|
50
|
Maksudov F, Kliuchnikov E, Pierson D, Ujwal M, Marx KA, Chanda A, Barsegov V. Therapeutic phosphorodiamidate morpholino oligonucleotides: Physical properties, solution structures, and folding thermodynamics. Mol Ther Nucleic Acids 2023; 31:631-647. [PMID: 36910708 PMCID: PMC9996446 DOI: 10.1016/j.omtn.2023.02.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/27/2022] [Accepted: 02/10/2023] [Indexed: 02/16/2023]
Abstract
Elucidating the structure-function relationships for therapeutic RNA mimicking phosphorodiamidate morpholino oligonucleotides (PMOs) is challenging due to the lack of information about their structures. While PMOs have been approved by the US Food and Drug Administration for treatment of Duchenne muscular dystrophy, no structural information on these unique, charge-neutral, and stable molecules is available. We performed circular dichroism and solution viscosity measurements combined with molecular dynamics simulations and machine learning to resolve solution structures of 22-mer, 25-mer, and 30-mer length PMOs. The PMO conformational dynamics are defined by the competition between non-polar nucleobases and uncharged phosphorodiamidate groups for shielding from solvent exposure. PMO molecules form non-canonical, partially helical, stable folded structures with a small 1.4- to 1.7-nm radius of gyration, low count of three to six base pairs and six to nine base stacks, characterized by -34 to -51 kcal/mol free energy, -57 to -103 kcal/mol enthalpy, and -23 to -53 kcal/mol entropy for folding. The 4.5- to 6.2-cm3/g intrinsic viscosity and Huggins constant of 4.5-9.9 are indicative of extended and aggregating systems. The results obtained highlight the importance of the conformational ensemble view of PMO solution structures, thermodynamic stability of their non-canonical structures, and concentration-dependent viscosity properties. These principles form a paradigm to understand the structure-properties-function relationship for therapeutic PMOs to advance the design of new RNA-mimic-based drugs.
Collapse
Affiliation(s)
- Farkhad Maksudov
- Department of Chemistry, University of Massachusetts, Lowell, MA 01854, USA
| | | | - Daniel Pierson
- Technical Operations, Sarepta Therapeutics, Cambridge, MA 02142, USA
| | | | - Kenneth A. Marx
- Department of Chemistry, University of Massachusetts, Lowell, MA 01854, USA
- Inciton, Inc., Andover, MA 01854, USA
| | - Arani Chanda
- Technical Operations, Sarepta Therapeutics, Cambridge, MA 02142, USA
- Corresponding author: Arani Chanda, Technical Operations, Sarepta Therapeutics, Cambridge, MA 02142, USA.
| | - Valeri Barsegov
- Department of Chemistry, University of Massachusetts, Lowell, MA 01854, USA
- Inciton, Inc., Andover, MA 01854, USA
- Corresponding author: Valeri Barsegov, Department of Chemistry, University of Massachusetts, Lowell, MA 01854, USA.
| |
Collapse
|