51
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Berulava T, Buchholz E, Elerdashvili V, Pena T, Islam MR, Lbik D, Mohamed BA, Renner A, von Lewinski D, Sacherer M, Bohnsack KE, Bohnsack MT, Jain G, Capece V, Cleve N, Burkhardt S, Hasenfuss G, Fischer A, Toischer K. Changes in m6A RNA methylation contribute to heart failure progression by modulating translation. Eur J Heart Fail 2019; 22:54-66. [PMID: 31849158 DOI: 10.1002/ejhf.1672] [Citation(s) in RCA: 179] [Impact Index Per Article: 35.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/28/2019] [Revised: 09/15/2019] [Accepted: 10/15/2019] [Indexed: 12/27/2022] Open
Abstract
AIMS Deregulation of epigenetic processes and aberrant gene expression are important mechanisms in heart failure. Here we studied the potential relevance of m6A RNA methylation in heart failure development. METHODS AND RESULTS We analysed m6A RNA methylation via next-generation sequencing. We found that approximately one quarter of the transcripts in the healthy mouse and human heart exhibit m6A RNA methylation. During progression to heart failure we observed that changes in m6A RNA methylation exceed changes in gene expression both in mouse and human. RNAs with altered m6A RNA methylation were mainly linked to metabolic and regulatory pathways, while changes in RNA expression level mainly represented changes in structural plasticity. Mechanistically, we could link m6A RNA methylation to altered RNA translation and protein production. Interestingly, differentially methylated but not differentially expressed RNAs showed differential polysomal occupancy, indicating transcription-independent modulation of translation. Furthermore, mice with a cardiomyocyte restricted knockout of the RNA demethylase Fto exhibited an impaired cardiac function compared to control mice. CONCLUSIONS We could show that m6A landscape is altered in heart hypertrophy and heart failure. m6A RNA methylation changes lead to changes in protein abundance, unconnected to mRNA levels. This uncovers a new transcription-independent mechanisms of translation regulation. Therefore, our data suggest that modulation of epitranscriptomic processes such as m6A methylation might be an interesting target for therapeutic interventions.
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Affiliation(s)
- Tea Berulava
- Department for Epigenetics and Systems Medicine in Neurodegenerative Diseases, German Center for Neurodegenerative Diseases (DZNE), Göttingen, Germany
| | - Eric Buchholz
- Clinic for Cardiology and Pneumology, University Medical Center, Göttingen, Germany.,German Centre for Cardiovascular Research (DZHK), partner site Göttingen, Göttingen, Germany
| | - Vakhtang Elerdashvili
- Department for Epigenetics and Systems Medicine in Neurodegenerative Diseases, German Center for Neurodegenerative Diseases (DZNE), Göttingen, Germany.,Bioinformatics Unit, German Center for Neurodegenerative Diseases (DZNE), Göttingen, Germany
| | - Tonatiuh Pena
- Department for Epigenetics and Systems Medicine in Neurodegenerative Diseases, German Center for Neurodegenerative Diseases (DZNE), Göttingen, Germany.,Bioinformatics Unit, German Center for Neurodegenerative Diseases (DZNE), Göttingen, Germany
| | - Md Rezaul Islam
- Department for Epigenetics and Systems Medicine in Neurodegenerative Diseases, German Center for Neurodegenerative Diseases (DZNE), Göttingen, Germany
| | - Dawid Lbik
- Clinic for Cardiology and Pneumology, University Medical Center, Göttingen, Germany.,German Centre for Cardiovascular Research (DZHK), partner site Göttingen, Göttingen, Germany
| | - Belal A Mohamed
- Clinic for Cardiology and Pneumology, University Medical Center, Göttingen, Germany.,German Centre for Cardiovascular Research (DZHK), partner site Göttingen, Göttingen, Germany
| | - Andre Renner
- Clinic for Thoracic and Cardiovascular Surgery, Heart and Diabetes Centre NRW, Ruhr-University Bochum, Bochum, Germany
| | | | - Michael Sacherer
- Department of Cardiology, Medical University Graz, Graz, Austria
| | | | - Markus T Bohnsack
- Department of Molecular Biology, University Medical Center, Göttingen, Germany
| | - Gaurav Jain
- Department for Epigenetics and Systems Medicine in Neurodegenerative Diseases, German Center for Neurodegenerative Diseases (DZNE), Göttingen, Germany.,Bioinformatics Unit, German Center for Neurodegenerative Diseases (DZNE), Göttingen, Germany
| | - Vincenzo Capece
- Department for Epigenetics and Systems Medicine in Neurodegenerative Diseases, German Center for Neurodegenerative Diseases (DZNE), Göttingen, Germany
| | - Nicole Cleve
- Department for Epigenetics and Systems Medicine in Neurodegenerative Diseases, German Center for Neurodegenerative Diseases (DZNE), Göttingen, Germany
| | - Susanne Burkhardt
- Department for Epigenetics and Systems Medicine in Neurodegenerative Diseases, German Center for Neurodegenerative Diseases (DZNE), Göttingen, Germany
| | - Gerd Hasenfuss
- Clinic for Cardiology and Pneumology, University Medical Center, Göttingen, Germany.,German Centre for Cardiovascular Research (DZHK), partner site Göttingen, Göttingen, Germany
| | - Andre Fischer
- Department for Epigenetics and Systems Medicine in Neurodegenerative Diseases, German Center for Neurodegenerative Diseases (DZNE), Göttingen, Germany.,Department of Psychiatry and Psychotherapy, University Medical Center, Göttingen, Germany.,Cluster of Excellence "Multiscale Bioimaging: from Molecular Machines to Networks of Excitable Cells" (MBExC), University of Göttingen, Germany
| | - Karl Toischer
- Clinic for Cardiology and Pneumology, University Medical Center, Göttingen, Germany.,German Centre for Cardiovascular Research (DZHK), partner site Göttingen, Göttingen, Germany
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52
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Bartoszewski R, Sikorski AF. Editorial focus: understanding off-target effects as the key to successful RNAi therapy. Cell Mol Biol Lett 2019; 24:69. [PMID: 31867046 PMCID: PMC6902517 DOI: 10.1186/s11658-019-0196-3] [Citation(s) in RCA: 79] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2019] [Accepted: 12/03/2019] [Indexed: 12/21/2022] Open
Abstract
With the first RNA interference (RNAi) drug (ONPATTRO (patisiran)) on the market, we witness the RNAi therapy field reaching a critical turning point, when further improvements in drug candidate design and delivery pipelines should enable fast delivery of novel life changing treatments to patients. Nevertheless, ignoring parallel development of RNAi dedicated in vitro pharmacological profiling aiming to identify undesirable off-target activity may slow down or halt progress in the RNAi field. Since academic research is currently fueling the RNAi development pipeline with new therapeutic options, the objective of this article is to briefly summarize the basics of RNAi therapy, as well as to discuss how to translate basic research into better understanding of related drug candidate safety profiles early in the process.
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Affiliation(s)
- Rafal Bartoszewski
- Department of Biology and Pharmaceutical Botany, Medical University of Gdansk, Gdansk, Poland
| | - Aleksander F. Sikorski
- Department of Cytobiochemistry, Faculty of Biotechnology, University of Wroclaw, Wroclaw, Poland
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53
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Zheng Y, Tai W. Insight into the siRNA transmembrane delivery—From cholesterol conjugating to tagging. WILEY INTERDISCIPLINARY REVIEWS-NANOMEDICINE AND NANOBIOTECHNOLOGY 2019; 12:e1606. [DOI: 10.1002/wnan.1606] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/31/2019] [Revised: 11/05/2019] [Accepted: 11/06/2019] [Indexed: 01/25/2023]
Affiliation(s)
- Yan Zheng
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery Ministry of Education, School of Pharmaceutical Sciences, Wuhan University Wuhan China
| | - Wanyi Tai
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery Ministry of Education, School of Pharmaceutical Sciences, Wuhan University Wuhan China
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54
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Abstract
The RNA interference (RNAi) pathway regulates mRNA stability and translation in nearly all human cells. Small double-stranded RNA molecules can efficiently trigger RNAi silencing of specific genes, but their therapeutic use has faced numerous challenges involving safety and potency. However, August 2018 marked a new era for the field, with the US Food and Drug Administration approving patisiran, the first RNAi-based drug. In this Review, we discuss key advances in the design and development of RNAi drugs leading up to this landmark achievement, the state of the current clinical pipeline and prospects for future advances, including novel RNAi pathway agents utilizing mechanisms beyond post-translational RNAi silencing.
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55
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Zhao L, Wang L, Zhang C, Liu Z, Piao Y, Yan J, Xiang R, Yao Y, Shi Y. E6-induced selective translation of WNT4 and JIP2 promotes the progression of cervical cancer via a noncanonical WNT signaling pathway. Signal Transduct Target Ther 2019; 4:32. [PMID: 31637011 PMCID: PMC6799841 DOI: 10.1038/s41392-019-0060-y] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2019] [Revised: 05/16/2019] [Accepted: 05/17/2019] [Indexed: 12/24/2022] Open
Abstract
mRNA translation reprogramming occurs frequently in many pathologies, including cancer and viral infection. It remains largely unknown whether viral-induced alterations in mRNA translation contribute to carcinogenesis. Most cervical cancer is caused by high-risk human papillomavirus infection, resulting in the malignant transformation of normal epithelial cells mainly via viral E6 and E7 oncoproteins. Here, we utilized polysome profiling and deep RNA sequencing to systematically evaluate E6-regulated mRNA translation in HPV18-infected cervical cancer cells. We found that silencing E6 can cause over a two-fold change in the translation efficiency of ~653 mRNAs, most likely in an eIF4E- and eIF2α-independent manner. In addition, we identified that E6 can selectively upregulate the translation of WNT4, JIP1, and JIP2, resulting in the activation of the noncanonical WNT/PCP/JNK pathway to promote cell proliferation in vitro and tumor growth in vivo. Ectopic expression of WNT4/JIP2 can effectively rescue the decreased cell proliferation caused by E6 silencing, strongly suggesting that the WNT4/JIP2 pathway mediates the role of E6 in promoting cell proliferation. Thus, our results revealed a novel oncogenic mechanism of E6 via regulating the translation of mRNAs.
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Affiliation(s)
- Lin Zhao
- School of Medicine, Nankai University, 94 Weijin Road, 300071 Tianjin, China
- Department of Obstetrics and Gynecology, Chinese PLA General Hospital, 28 Fuxing Road, 100853 Beijing, China
| | - Longlong Wang
- School of Medicine, Nankai University, 94 Weijin Road, 300071 Tianjin, China
| | - Chenglan Zhang
- School of Medicine, Nankai University, 94 Weijin Road, 300071 Tianjin, China
| | - Ze Liu
- School of Medicine, Nankai University, 94 Weijin Road, 300071 Tianjin, China
| | - Yongjun Piao
- School of Medicine, Nankai University, 94 Weijin Road, 300071 Tianjin, China
| | - Jie Yan
- School of Medicine, Nankai University, 94 Weijin Road, 300071 Tianjin, China
| | - Rong Xiang
- School of Medicine, Nankai University, 94 Weijin Road, 300071 Tianjin, China
| | - Yuanqing Yao
- School of Medicine, Nankai University, 94 Weijin Road, 300071 Tianjin, China
- Department of Obstetrics and Gynecology, Chinese PLA General Hospital, 28 Fuxing Road, 100853 Beijing, China
| | - Yi Shi
- School of Medicine, Nankai University, 94 Weijin Road, 300071 Tianjin, China
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56
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Gong C, Tian J, Wang Z, Gao Y, Wu X, Ding X, Qiang L, Li G, Han Z, Yuan Y, Gao S. Functional exosome-mediated co-delivery of doxorubicin and hydrophobically modified microRNA 159 for triple-negative breast cancer therapy. J Nanobiotechnology 2019; 17:93. [PMID: 31481080 PMCID: PMC6721253 DOI: 10.1186/s12951-019-0526-7] [Citation(s) in RCA: 184] [Impact Index Per Article: 36.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2019] [Accepted: 08/22/2019] [Indexed: 02/08/2023] Open
Abstract
Exosomes (Exo) hold great promise as endogenous nanocarriers that can deliver biological information between cells. However, Exo are limited in terms of their abilities to target specific recipient cell types. We developed a strategy to isolate Exo exhibiting increased binding to integrin αvβ3. Binding occurred through a modified version of a disintegrin and metalloproteinase 15 (A15) expressed on exosomal membranes (A15-Exo), which facilitated co-delivery of therapeutic quantities of doxorubicin (Dox) and cholesterol-modified miRNA 159 (Cho-miR159) to triple-negative breast cancer (TNBC) cells, both in vitro and in vivo. The targeted A15-Exo were derived from continuous protein kinase C activation in monocyte-derived macrophages. These cell-derived Exo displayed targeting properties and had a 2.97-fold higher production yield. In vitro, A15-Exo co-loaded with Dox and Cho-miR159 induced synergistic therapeutic effects in MDA-MB-231 cells. In vivo, miR159 and Dox delivery in a vesicular system effectively silenced the TCF-7 gene and exhibited improved anticancer effects, without adverse effects. Therefore, our data demonstrate the synergistic efficacy of co-delivering miR159 and Dox by targeted Exo for TNBC therapy.
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Affiliation(s)
- Chunai Gong
- Department of Pharmaceutics, Changhai Hospital, Second Military Medical University, Shanghai, 200433, People's Republic of China.,Department of Pharmacy, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200011, People's Republic of China
| | - Jing Tian
- Department of Pharmaceutics, Changhai Hospital, Second Military Medical University, Shanghai, 200433, People's Republic of China
| | - Zhuo Wang
- Department of Pharmaceutics, Changhai Hospital, Second Military Medical University, Shanghai, 200433, People's Republic of China
| | - Yuan Gao
- Department of Clinical Pharmacy and Pharmaceutical Management, School of Pharmacy, Fudan University, Shanghai, 201203, People's Republic of China
| | - Xin Wu
- Department of Pharmaceutics, Changhai Hospital, Second Military Medical University, Shanghai, 200433, People's Republic of China
| | - Xueying Ding
- Department of Clinical Pharmacy, Shanghai General Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200080, People's Republic of China
| | - Lei Qiang
- Department of Pharmaceutics, Changhai Hospital, Second Military Medical University, Shanghai, 200433, People's Republic of China
| | - Guorui Li
- Department of Pharmaceutics, Changhai Hospital, Second Military Medical University, Shanghai, 200433, People's Republic of China
| | - Zhimin Han
- Department of Pharmaceutics, Changhai Hospital, Second Military Medical University, Shanghai, 200433, People's Republic of China
| | - Yongfang Yuan
- Department of Pharmacy, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200011, People's Republic of China.
| | - Shen Gao
- Department of Pharmaceutics, Changhai Hospital, Second Military Medical University, Shanghai, 200433, People's Republic of China.
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57
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Abstract
The PDCD1 gene encodes PD-1, an important immune checkpoint protein and key immunotherapy target to treat cancer. PDCD1 is alternatively spliced to generate an exon 3-skipped isoform PD-1Δ3 that has been suggested to play an antagonistic role to PD-1, but the mechanism underlying alternative splicing of PDCD1 has never been explored. Here using a minigene system, we analysed the splicing pattern of PDCD1 in multiple cell lines and confirmed exon 3 skipping as the main alternative splicing event. Using deletion analysis of exon 3, we mapped two splicing enhancers in the exon: ESE3a and ESE3b. Using mutagenesis, RNA-affinity chromatography, mass spectrometry as well as depletion and overexpression of MATR3, we defined MATR3 as a splicing activator during PDCD1 exon 3 splicing that operates through binding to ESE3b. MATR3's splicing-stimulatory activity is counteracted by an RNA secondary structure around ESE3b and an RNA helicase DDX5. Furthermore, we identified ASOs that efficiently promotes PDCD1 exon 3 skipping in both minigene and endogenous-gene contexts. Our data support further study of the ASOs as potential drug candidates to treat cancer.
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Affiliation(s)
- Junjie Sun
- Institute of Neuroscience, Soochow University, Suzhou, Jiangsu, China
| | - Jialin Bai
- Institute of Neuroscience, Soochow University, Suzhou, Jiangsu, China
| | - Tao Jiang
- Institute of Neuroscience, Soochow University, Suzhou, Jiangsu, China
| | - Yuan Gao
- Institute of Neuroscience, Soochow University, Suzhou, Jiangsu, China
| | - Yimin Hua
- Institute of Neuroscience, Soochow University, Suzhou, Jiangsu, China.,Jiangsu Key Laboratory for Molecular and Medical Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing, China
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58
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A divalent siRNA chemical scaffold for potent and sustained modulation of gene expression throughout the central nervous system. Nat Biotechnol 2019; 37:884-894. [PMID: 31375812 PMCID: PMC6879195 DOI: 10.1038/s41587-019-0205-0] [Citation(s) in RCA: 128] [Impact Index Per Article: 25.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2018] [Accepted: 06/27/2019] [Indexed: 12/20/2022]
Abstract
Sustained silencing of gene expression in deep regions of the brain using small interfering RNAs (siRNAs) has not been achieved. Here we describe an siRNA architecture, divalent-siRNA (Di-siRNA), that supports potent, sustained gene silencing in the central nervous system (CNS) of mice and non-human primates following a single injection into cerebrospinal fluid. Di-siRNAs are composed of two fully chemically modified, phosphorothioate-containing siRNAs connected by a linker. In mice, Di-siRNAs induced potent silencing of huntingtin, the causative gene in Huntington’s disease, reducing mRNA and protein throughout the brain. Silencing persisted for at least six months, with the degree of gene silencing correlating to guide strand tissue accumulation levels. In Cynomolgus macaques, a bolus injection of Di-siRNA showed substantial distribution and robust silencing throughout the brain and spinal cord without detectable toxicity and with minimal off-target effects. This siRNA design may enable RNAi-based gene silencing in the CNS for the treatment of neurological disorders.
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59
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Chemical modulation of siRNA lipophilicity for efficient delivery. J Control Release 2019; 307:98-107. [DOI: 10.1016/j.jconrel.2019.06.022] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2019] [Revised: 06/17/2019] [Accepted: 06/19/2019] [Indexed: 11/19/2022]
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60
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Shen X, Corey DR. Chemistry, mechanism and clinical status of antisense oligonucleotides and duplex RNAs. Nucleic Acids Res 2019; 46:1584-1600. [PMID: 29240946 PMCID: PMC5829639 DOI: 10.1093/nar/gkx1239] [Citation(s) in RCA: 439] [Impact Index Per Article: 87.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2017] [Accepted: 11/29/2017] [Indexed: 12/12/2022] Open
Abstract
RNA plays a central role in the expression of all genes. Because any sequence within RNA can be recognized by complementary base pairing, synthetic oligonucleotides and oligonucleotide mimics offer a general strategy for controlling processes that affect disease. The two primary antisense approaches for regulating expression through recognition of cellular RNAs are single-stranded antisense oligonucleotides and duplex RNAs. This review will discuss the chemical modifications and molecular mechanisms that make synthetic nucleic acid drugs possible. Lessons learned from recent clinical trials will be summarized. Ongoing clinical trials are likely to decisively test the adequacy of our current generation of antisense nucleic acid technologies and highlight areas where more basic research is needed.
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Affiliation(s)
- Xiulong Shen
- Departments of Pharmacology & Biochemistry, University of Texas Southwestern Medical Center, 6001 Forest Park Road, Dallas, TX 75390-9041, USA
| | - David R Corey
- Departments of Pharmacology & Biochemistry, University of Texas Southwestern Medical Center, 6001 Forest Park Road, Dallas, TX 75390-9041, USA
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61
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Shmushkovich T, Monopoli KR, Homsy D, Leyfer D, Betancur-Boissel M, Khvorova A, Wolfson AD. Functional features defining the efficacy of cholesterol-conjugated, self-deliverable, chemically modified siRNAs. Nucleic Acids Res 2019; 46:10905-10916. [PMID: 30169779 PMCID: PMC6237813 DOI: 10.1093/nar/gky745] [Citation(s) in RCA: 49] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2018] [Accepted: 08/24/2018] [Indexed: 12/14/2022] Open
Abstract
Progress in oligonucleotide chemistry has produced a shift in the nature of siRNA used, from formulated, minimally modified siRNAs, to unformulated, heavily modified siRNA conjugates. The introduction of extensive chemical modifications is essential for conjugate-mediated delivery. Modifications have a significant impact on siRNA efficacy through interference with recognition and processing by RNAi enzymatic machinery, severely restricting the sequence space available for siRNA design. Many algorithms available publicly can successfully predict the activity of non-modified siRNAs, but the efficiency of the algorithms for designing heavily modified siRNAs has never been systematically evaluated experimentally. Here we screened 356 cholesterol-conjugated siRNAs with extensive modifications and developed a linear regression-based algorithm that effectively predicts siRNA activity using two independent datasets. We further demonstrate that predictive determinants for modified and non-modified siRNAs differ substantially. The algorithm developed from the non-modified siRNAs dataset has no predictive power for modified siRNAs and vice versa. In the context of heavily modified siRNAs, the introduction of chemical asymmetry fully eliminates the requirement for thermodynamic bias, the major determinant for non-modified siRNA efficacy. Finally, we demonstrate that in addition to the sequence of the target site, the accessibility of the neighboring 3′ region significantly contributes to siRNA efficacy.
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Affiliation(s)
| | | | - Diana Homsy
- Advirna, 60 Prescott Street, Worcester, MA 01605, USA
| | - Dmitriy Leyfer
- Advirna, 60 Prescott Street, Worcester, MA 01605, USA.,Boston University, 44 Cummington Mall, Boston, MA 02215, USA
| | | | - Anastasia Khvorova
- University of Massachusetts Medical School, 368 Plantation Street. Worcester, MA 01655, USA
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62
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Current Aspects of siRNA Bioconjugate for In Vitro and In Vivo Delivery. Molecules 2019; 24:molecules24122211. [PMID: 31200490 PMCID: PMC6631009 DOI: 10.3390/molecules24122211] [Citation(s) in RCA: 53] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2019] [Revised: 06/03/2019] [Accepted: 06/08/2019] [Indexed: 02/07/2023] Open
Abstract
Studies on siRNA delivery have seen intense growth in the past decades since siRNA has emerged as a new class of gene therapeutics for the treatment of various diseases. siRNA bioconjugate, as one of the major delivery strategies, offers the potential to enhance and broaden pharmacological properties of siRNA, while minimizing the heterogeneity and stability-correlated toxicology. This review summarizes the recent developments of siRNA bioconjugate, including the conjugation with antibody, peptide, aptamer, small chemical, lipidoid, cell-penetrating peptide polymer, and nanoparticle. These siRNA bioconjugate, either administrated alone or formulated with other agents, could significantly improve pharmacokinetic behavior, enhance the biological half-life, and increase the targetability while maintaining sufficient gene silencing activity, with a concomitant improvement of the therapeutic outcomes and diminishment of adverse effects. This review emphasizes the delivery application of these siRNA bioconjugates, especially the conjugation strategy that control the integrity, stability and release of siRNA bioconjugates. The limitations conferred by these conjugation strategies have also been covered.
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63
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Biscans A, Coles A, Echeverria D, Khvorova A. The valency of fatty acid conjugates impacts siRNA pharmacokinetics, distribution, and efficacy in vivo. J Control Release 2019; 302:116-125. [PMID: 30940496 PMCID: PMC6546539 DOI: 10.1016/j.jconrel.2019.03.028] [Citation(s) in RCA: 46] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2018] [Revised: 03/02/2019] [Accepted: 03/29/2019] [Indexed: 12/17/2022]
Abstract
Lipid-conjugated small-interfering RNAs (siRNAs) exhibit accumulation and gene silencing in extrahepatic tissues, providing an opportunity to expand therapeutic siRNA utility beyond the liver. Chemically engineering lipids may further improve siRNA delivery and efficacy, but the relationship between lipid structure/configuration and siRNA pharmacodynamics is unclear. Here, we synthesized a panel of mono-, di-, and tri-meric fatty acid-conjugated siRNAs to systematically evaluate the impact of fatty acid structure and valency on siRNA clearance, distribution, and efficacy. Fatty acid valency significantly altered the physicochemical properties of conjugated siRNAs, including hydrophobicity and micelle formation, which affected distribution. Trivalent lipid-conjugated siRNAs were predominantly retained at the site of injection with minimal systemic exposure, whereas monovalent lipid-conjugated siRNAs were quickly released into the circulation and accumulated primarily in kidney. Divalent lipid-conjugated siRNAs showed intermediate behavior, and preferentially accumulated in liver with functional distribution to lung, heart, and fat. The chemical structure of the conjugate, rather than overall physicochemical properties (i.e. hydrophobicity), predicted the degree of extrahepatic tissue accumulation necessary for productive gene silencing. Our findings will inform chemical engineering strategies for enhancing the extrahepatic delivery of lipophilic siRNAs.
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Affiliation(s)
- Annabelle Biscans
- RNA Therapeutics Institute, University of Massachusetts Medical School, Worcester, MA 01604, USA; Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA 01604, USA
| | - Andrew Coles
- RNA Therapeutics Institute, University of Massachusetts Medical School, Worcester, MA 01604, USA; Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA 01604, USA
| | - Dimas Echeverria
- RNA Therapeutics Institute, University of Massachusetts Medical School, Worcester, MA 01604, USA; Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA 01604, USA
| | - Anastasia Khvorova
- RNA Therapeutics Institute, University of Massachusetts Medical School, Worcester, MA 01604, USA; Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA 01604, USA.
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64
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Malik N, Yan H, Moshkovich N, Palangat M, Yang H, Sanchez V, Cai Z, Peat TJ, Jiang S, Liu C, Lee M, Mock BA, Yuspa SH, Larson D, Wakefield LM, Huang J. The transcription factor CBFB suppresses breast cancer through orchestrating translation and transcription. Nat Commun 2019; 10:2071. [PMID: 31061501 PMCID: PMC6502810 DOI: 10.1038/s41467-019-10102-6] [Citation(s) in RCA: 50] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2018] [Accepted: 04/18/2019] [Indexed: 02/06/2023] Open
Abstract
Translation and transcription are frequently dysregulated in cancer. These two processes are generally regulated by distinct sets of factors. The CBFB gene, which encodes a transcription factor, has recently emerged as a highly mutated driver in a variety of human cancers including breast cancer. Here we report a noncanonical role of CBFB in translation regulation. RNA immunoprecipitation followed by deep sequencing (RIP-seq) reveals that cytoplasmic CBFB binds to hundreds of transcripts and regulates their translation. CBFB binds to mRNAs via hnRNPK and enhances translation through eIF4B, a general translation initiation factor. Interestingly, the RUNX1 mRNA, which encodes the transcriptional partner of CBFB, is bound and translationally regulated by CBFB. Furthermore, nuclear CBFB/RUNX1 complex transcriptionally represses the oncogenic NOTCH signaling pathway in breast cancer. Thus, our data reveal an unexpected function of CBFB in translation regulation and propose that breast cancer cells evade translation and transcription surveillance simultaneously through downregulating CBFB. CBFB is highly mutated in breast cancers and is known to interact with RUNX proteins to regulate transcription. Here, the authors describe a non-canonical role of CBFB in translation regulation in which it binds to mRNAs through hnRNPK, facilitating translation by eIF4B.
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Affiliation(s)
- Navdeep Malik
- Cancer and Stem Cell Epigenetics Section, Laboratory of Cancer Biology and Genetics, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Hualong Yan
- Cancer and Stem Cell Epigenetics Section, Laboratory of Cancer Biology and Genetics, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Nellie Moshkovich
- Cancer Biology of TGF-beta Section, Laboratory of Cancer Biology and Genetics, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Murali Palangat
- Laboratory of Receptor Biology & Gene Expression, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Howard Yang
- High-Dimension Data Analysis Group, Laboratory of Cancer Biology and Genetics, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Vanesa Sanchez
- In Vitro Pathogenesis Section, Laboratory of Cancer Biology and Genetics, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Zhuo Cai
- Cancer and Stem Cell Epigenetics Section, Laboratory of Cancer Biology and Genetics, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Tyler J Peat
- Cancer Genetics Section, Laboratory of Cancer Biology and Genetics, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Shunlin Jiang
- Cancer and Stem Cell Epigenetics Section, Laboratory of Cancer Biology and Genetics, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Chengyu Liu
- Transgenic Core, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Maxwell Lee
- High-Dimension Data Analysis Group, Laboratory of Cancer Biology and Genetics, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Beverly A Mock
- Cancer Genetics Section, Laboratory of Cancer Biology and Genetics, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Stuart H Yuspa
- In Vitro Pathogenesis Section, Laboratory of Cancer Biology and Genetics, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Daniel Larson
- Laboratory of Receptor Biology & Gene Expression, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Lalage M Wakefield
- Cancer Biology of TGF-beta Section, Laboratory of Cancer Biology and Genetics, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Jing Huang
- Cancer and Stem Cell Epigenetics Section, Laboratory of Cancer Biology and Genetics, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20892, USA.
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65
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Chernikov IV, Vlassov VV, Chernolovskaya EL. Current Development of siRNA Bioconjugates: From Research to the Clinic. Front Pharmacol 2019; 10:444. [PMID: 31105570 PMCID: PMC6498891 DOI: 10.3389/fphar.2019.00444] [Citation(s) in RCA: 135] [Impact Index Per Article: 27.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2019] [Accepted: 04/08/2019] [Indexed: 12/12/2022] Open
Abstract
Small interfering RNAs (siRNAs) acting via RNA interference mechanisms are able to recognize a homologous mRNA sequence in the cell and induce its degradation. The main problems in the development of siRNA-based drugs for therapeutic use are the low efficiency of siRNA delivery to target cells and the degradation of siRNAs by nucleases in biological fluids. Various approaches have been proposed to solve the problem of siRNA delivery in vivo (e.g., viruses, cationic lipids, polymers, nanoparticles), but all have limitations for therapeutic use. One of the most promising approaches to solve the problem of siRNA delivery to target cells is bioconjugation; i.e., the covalent connection of siRNAs with biogenic molecules (lipophilic molecules, antibodies, aptamers, ligands, peptides, or polymers). Bioconjugates are "ideal nanoparticles" since they do not need a positive charge to form complexes, are less toxic, and are less effectively recognized by components of the immune system because of their small size. This review is focused on strategies and principles for constructing siRNA bioconjugates for in vivo use.
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Affiliation(s)
- Ivan V Chernikov
- Laboratory of Nucleic Acids Biochemistry, Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - Valentin V Vlassov
- Laboratory of Nucleic Acids Biochemistry, Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - Elena L Chernolovskaya
- Laboratory of Nucleic Acids Biochemistry, Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
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66
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Manganese-induced cellular disturbance in the baker's yeast, Saccharomyces cerevisiae with putative implications in neuronal dysfunction. Sci Rep 2019; 9:6563. [PMID: 31024033 PMCID: PMC6484083 DOI: 10.1038/s41598-019-42907-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2018] [Accepted: 04/09/2019] [Indexed: 12/24/2022] Open
Abstract
Manganese (Mn) is an essential element, but in humans, chronic and/or acute exposure to this metal can lead to neurotoxicity and neurodegenerative disorders including Parkinsonism and Parkinson’s Disease by unclear mechanisms. To better understand the effects that exposure to Mn2+ exert on eukaryotic cell biology, we exposed a non-essential deletion library of the yeast Saccharomyces cerevisiae to a sub-inhibitory concentration of Mn2+ followed by targeted functional analyses of the positive hits. This screen produced a set of 43 sensitive deletion mutants that were enriched for genes associated with protein biosynthesis. Our follow-up investigations demonstrated that Mn reduced total rRNA levels in a dose-dependent manner and decreased expression of a β-galactosidase reporter gene. This was subsequently supported by analysis of ribosome profiles that suggested Mn-induced toxicity was associated with a reduction in formation of active ribosomes on the mRNAs. Altogether, these findings contribute to the current understanding of the mechanism of Mn-triggered cytotoxicity. Lastly, using the Comparative Toxicogenomic Database, we revealed that Mn shared certain similarities in toxicological mechanisms with neurodegenerative disorders including amyotrophic lateral sclerosis, Alzheimer’s, Parkinson’s and Huntington’s diseases.
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67
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Qu X, Hu Y, Wang H, Song H, Young M, Xu F, Liu Y, Cheng G. Biomimetic Dextran–Peptide Vectors for Efficient and Safe siRNA Delivery. ACS APPLIED BIO MATERIALS 2019; 2:1456-1463. [DOI: 10.1021/acsabm.8b00714] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
- Xinjian Qu
- School of Life Science and Medicine, Dalian University of Technology, Panjin 124221, China
- Department of Chemical Engineering, University of Illinois at Chicago, Chicago, Illinois 60607, United States
| | - Yang Hu
- Department of Chemical Engineering, University of Illinois at Chicago, Chicago, Illinois 60607, United States
- State Key Laboratory of Chemical Resource Engineering, Beijing Laboratory of Biomedical Materials, Beijing University of Chemical Technology, Beijing 100029, China
| | - Huifeng Wang
- Department of Chemical Engineering, University of Illinois at Chicago, Chicago, Illinois 60607, United States
| | - Haiqing Song
- Department of Chemical Engineering, University of Illinois at Chicago, Chicago, Illinois 60607, United States
| | - Megan Young
- Department of Chemical Engineering, University of Illinois at Chicago, Chicago, Illinois 60607, United States
| | - Fujian Xu
- State Key Laboratory of Chemical Resource Engineering, Beijing Laboratory of Biomedical Materials, Beijing University of Chemical Technology, Beijing 100029, China
| | - Ying Liu
- Department of Chemical Engineering, University of Illinois at Chicago, Chicago, Illinois 60607, United States
| | - Gang Cheng
- Department of Chemical Engineering, University of Illinois at Chicago, Chicago, Illinois 60607, United States
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68
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Park Y, Koga Y, Su C, Waterbury AL, Johnny CL, Liau BB. Versatile Synthetic Route to Cycloheximide and Analogues That Potently Inhibit Translation Elongation. Angew Chem Int Ed Engl 2019; 58:5387-5391. [PMID: 30802354 DOI: 10.1002/anie.201901386] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2019] [Indexed: 02/05/2023]
Abstract
Cycloheximide (CHX) is an inhibitor of eukaryotic translation elongation that has played an essential role in the study of protein synthesis. Despite its ubiquity, few studies have been directed towards accessing synthetic CHX derivatives, even though such efforts may lead to protein synthesis inhibitors with improved or alternate properties. Described here is the total synthesis of CHX and analogues, and the establishment of structure-activity relationships (SAR) responsible for translation inhibition. The SAR studies aided the design of more potent compounds, one of which irreversibly blocks ribosomal elongation, preserves polysome profiles, and may be a broadly useful tool for investigating protein synthesis.
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Affiliation(s)
- Yongho Park
- Department of Chemistry and Chemical Biology, Harvard University, 12 Oxford Street, Cambridge, MA, 02138, USA
| | - Yumi Koga
- Department of Chemistry and Chemical Biology, Harvard University, 12 Oxford Street, Cambridge, MA, 02138, USA
| | - Cindy Su
- Department of Chemistry and Chemical Biology, Harvard University, 12 Oxford Street, Cambridge, MA, 02138, USA
| | - Amanda L Waterbury
- Department of Chemistry and Chemical Biology, Harvard University, 12 Oxford Street, Cambridge, MA, 02138, USA
| | - Christopher L Johnny
- Department of Chemistry and Chemical Biology, Harvard University, 12 Oxford Street, Cambridge, MA, 02138, USA
| | - Brian B Liau
- Department of Chemistry and Chemical Biology, Harvard University, 12 Oxford Street, Cambridge, MA, 02138, USA
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69
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Park Y, Koga Y, Su C, Waterbury AL, Johnny CL, Liau BB. Versatile Synthetic Route to Cycloheximide and Analogues That Potently Inhibit Translation Elongation. Angew Chem Int Ed Engl 2019. [DOI: 10.1002/ange.201901386] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Yongho Park
- Department of Chemistry and Chemical BiologyHarvard University 12 Oxford Street Cambridge MA 02138 USA
| | - Yumi Koga
- Department of Chemistry and Chemical BiologyHarvard University 12 Oxford Street Cambridge MA 02138 USA
| | - Cindy Su
- Department of Chemistry and Chemical BiologyHarvard University 12 Oxford Street Cambridge MA 02138 USA
| | - Amanda L. Waterbury
- Department of Chemistry and Chemical BiologyHarvard University 12 Oxford Street Cambridge MA 02138 USA
| | - Christopher L. Johnny
- Department of Chemistry and Chemical BiologyHarvard University 12 Oxford Street Cambridge MA 02138 USA
| | - Brian B. Liau
- Department of Chemistry and Chemical BiologyHarvard University 12 Oxford Street Cambridge MA 02138 USA
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70
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Ohmer M, Tzivelekidis T, Niedenführ N, Volceanov-Hahn L, Barth S, Vier J, Börries M, Busch H, Kook L, Biniossek ML, Schilling O, Kirschnek S, Häcker G. Infection of HeLa cells with Chlamydia trachomatis inhibits protein synthesis and causes multiple changes to host cell pathways. Cell Microbiol 2019; 21:e12993. [PMID: 30551267 DOI: 10.1111/cmi.12993] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2018] [Revised: 10/31/2018] [Accepted: 12/07/2018] [Indexed: 12/12/2022]
Abstract
The obligate intracellular bacterium Chlamydia trachomatis replicates in a cytosolic vacuole in human epithelial cells. Infection of human cells with C. trachomatis causes substantial changes to many host cell-signalling pathways, but the molecular basis of such influence is not well understood. Studies of gene transcription of the infected cell have shown altered transcription of many host cell genes, indicating a transcriptional response of the host cell to the infection. We here describe that infection of HeLa cells with C. trachomatis as well as infection of murine cells with Chlamydia muridarum substantially inhibits protein synthesis of the infected host cell. This inhibition was accompanied by changes to the ribosomal profile of the infected cell indicative of a block of translation initiation, most likely as part of a stress response. The Chlamydia protease-like activity factor (CPAF) also reduced protein synthesis in uninfected cells, although CPAF-deficient C. trachomatis showed no defect in this respect. Analysis of polysomal mRNA as a proxy of actively transcribed mRNA identified a number of biological processes differentially affected by chlamydial infection. Mapping of differentially regulated genes onto a protein interaction network identified nodes of up- and down-regulated networks during chlamydial infection. Proteomic analysis of protein synthesis further suggested translational regulation of host cell functions by chlamydial infection. These results demonstrate reprogramming of the host cell during chlamydial infection through the alteration of protein synthesis.
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Affiliation(s)
- Michaela Ohmer
- Institute for Microbiology and Hygiene, Medical Center, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Tina Tzivelekidis
- Institute for Microbiology and Hygiene, Medical Center, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Nora Niedenführ
- Institute for Microbiology and Hygiene, Medical Center, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Larisa Volceanov-Hahn
- Institute for Microbiology and Hygiene, Medical Center, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Svenja Barth
- Institute for Microbiology and Hygiene, Medical Center, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Juliane Vier
- Institute for Microbiology and Hygiene, Medical Center, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Melanie Börries
- Institute of Molecular Medicine and Cell Research, Faculty of Medicine, University of Freiburg, Freiburg, Germany.,German Cancer Consortium (DKTK), Freiburg, Germany.,German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Hauke Busch
- Institute of Molecular Medicine and Cell Research, Faculty of Medicine, University of Freiburg, Freiburg, Germany.,Luebeck Institute for Experimental Dermatology; Institute for Cardiogenetics, University of Lübeck, Lübeck, Germany
| | - Lucas Kook
- Institute of Molecular Medicine and Cell Research, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Martin L Biniossek
- Institute of Molecular Medicine and Cell Research, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Oliver Schilling
- Institute of Molecular Medicine and Cell Research, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Susanne Kirschnek
- Institute for Microbiology and Hygiene, Medical Center, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Georg Häcker
- Institute for Microbiology and Hygiene, Medical Center, Faculty of Medicine, University of Freiburg, Freiburg, Germany.,BIOSS Centre for Biological Signalling Studies, University of Freiburg, Freiburg, Germany
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71
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Chandela A, Ueno Y. Systemic Delivery of Small Interfering RNA Therapeutics: Obstacles and Advances. ACTA ACUST UNITED AC 2019. [DOI: 10.7831/ras.7.10] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Akash Chandela
- United Graduate School of Agricultural Science, Gifu University
| | - Yoshihito Ueno
- United Graduate School of Agricultural Science, Gifu University
- Course of Applied Life Science, Faculty of Applied Biological Sciences, Gifu University
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72
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Makwana K, Gosai N, Poe A, Kondratov RV. Calorie restriction reprograms diurnal rhythms in protein translation to regulate metabolism. FASEB J 2018; 33:4473-4489. [PMID: 30566374 DOI: 10.1096/fj.201802167r] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Calorie restriction (CR) delays aging and affects the circadian clocks by reprogramming circadian rhythms in gene expression. To expand on the circadian mechanisms in CR, we assayed rhythms in the protein translation by analyzing polysome-associated mRNAs in the liver of mice fed ad libitum (AL) and CR diets. Global comparison of the diets revealed that <1% of transcripts were differentially abundant in the polysomes. In contrast, the large differential, up to 10%, was detected when CR and AL diets were compared at individual times throughout the day. Most transcripts that were rhythmic under AL lost their rhythms, and many new transcripts gained rhythms under CR. Only a small fraction of transcripts, including the circadian clock genes, were rhythmic under both diets. Thus, CR strongly reprograms translation. CR affected translation of enzymes regulating long-chain acetyl-coenzyme A (Acyl-CoA) metabolism. The expression of the Acyl-CoA thioesterase (ACOT) family was induced upon CR, leading to the increased transcriptional activity of peroxisome proliferator-activated receptor α, the transcriptional factor regulated by the ACOT products. We propose that the differential translation induced by CR leads to a temporal partition and reprogramming of metabolic processes and provides a link between CR, lipid metabolism, and the circadian clock.-Makwana, K., Gosai, N., Poe, A., Kondratov, R. V. Calorie restriction reprograms diurnal rhythms in protein translation to regulate metabolism.
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Affiliation(s)
- Kuldeep Makwana
- Department of Biological, Geological, and Environmental Sciences, Center for Gene Regulation in Health and Diseases, Cleveland State University, Cleveland, Ohio, USA
| | - Neha Gosai
- Department of Biological, Geological, and Environmental Sciences, Center for Gene Regulation in Health and Diseases, Cleveland State University, Cleveland, Ohio, USA
| | - Allan Poe
- Department of Biological, Geological, and Environmental Sciences, Center for Gene Regulation in Health and Diseases, Cleveland State University, Cleveland, Ohio, USA
| | - Roman V Kondratov
- Department of Biological, Geological, and Environmental Sciences, Center for Gene Regulation in Health and Diseases, Cleveland State University, Cleveland, Ohio, USA
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73
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Chernikov IV, Gladkikh DV, Meschaninova MI, Karelina UA, Ven'yaminova AG, Zenkova MA, Vlassov VV, Chernolovskaya EL. Fluorophore Labeling Affects the Cellular Accumulation and Gene Silencing Activity of Cholesterol-Modified siRNAs In Vitro. Nucleic Acid Ther 2018; 29:33-43. [PMID: 30562146 DOI: 10.1089/nat.2018.0745] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
The objective of this study was to analyze the effects of fluorophores on the intracellular accumulation and biological activity of small interfering RNA (siRNA) and its cholesterol conjugates. In this study, we used stem-loop real-time PCR and calibration curves to quantitate cellular siRNA accumulation. Attachment of fluorophores significantly affected both the accumulation and biological activity of siRNA conjugates. The severity of this effect depended significantly on the structure of the conjugate; fluorophores (Cy5.5 or Alexa-488) attached to siRNA, facing the side of the duplex opposite to cholesterol, enhanced the unproductive intracellular accumulation of the conjugate when delivered in carrier-free mode. Enhanced cellular accumulation of siRNA conjugates did not result in enhanced biological activity of the conjugate. Moreover, the attachment of a hydrophobic fluorophore, such as Cy5.5, to conventional siRNA also enhanced its apparent intracellular accumulation, but not its biological activity. Thus, the use of fluorescent labels for the study of the intracellular accumulation of siRNA and its conjugates formed with different molecules is possible only for a limited range of structures, and requires verification using alternative methods.
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Affiliation(s)
- Ivan V Chernikov
- 1 Laboratory of Nucleic Acids Biochemistry, Institute of Chemical Biology and Fundamental Medicine SB RAS, Novosibirsk, Russia
| | - Daniil V Gladkikh
- 1 Laboratory of Nucleic Acids Biochemistry, Institute of Chemical Biology and Fundamental Medicine SB RAS, Novosibirsk, Russia
| | - Mariya I Meschaninova
- 2 Laboratory of RNA Chemistry, Institute of Chemical Biology and Fundamental Medicine SB RAS, Novosibirsk, Russia
| | - Ulyana A Karelina
- 1 Laboratory of Nucleic Acids Biochemistry, Institute of Chemical Biology and Fundamental Medicine SB RAS, Novosibirsk, Russia
| | - Alya G Ven'yaminova
- 2 Laboratory of RNA Chemistry, Institute of Chemical Biology and Fundamental Medicine SB RAS, Novosibirsk, Russia
| | - Marina A Zenkova
- 1 Laboratory of Nucleic Acids Biochemistry, Institute of Chemical Biology and Fundamental Medicine SB RAS, Novosibirsk, Russia
| | - Valentin V Vlassov
- 1 Laboratory of Nucleic Acids Biochemistry, Institute of Chemical Biology and Fundamental Medicine SB RAS, Novosibirsk, Russia
| | - Elena L Chernolovskaya
- 1 Laboratory of Nucleic Acids Biochemistry, Institute of Chemical Biology and Fundamental Medicine SB RAS, Novosibirsk, Russia
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74
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Turanov AA, Lo A, Hassler MR, Makris A, Ashar-Patel A, Alterman JF, Coles AH, Haraszti RA, Roux L, Godinho BMDC, Echeverria D, Pears S, Iliopoulos J, Shanmugalingam R, Ogle R, Zsengeller ZK, Hennessy A, Karumanchi SA, Moore MJ, Khvorova A. RNAi modulation of placental sFLT1 for the treatment of preeclampsia. Nat Biotechnol 2018; 36:nbt.4297. [PMID: 30451990 PMCID: PMC6526074 DOI: 10.1038/nbt.4297] [Citation(s) in RCA: 124] [Impact Index Per Article: 20.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2017] [Accepted: 10/05/2018] [Indexed: 12/14/2022]
Abstract
Preeclampsia is a placentally induced hypertensive disorder of pregnancy that is associated with substantial morbidity and mortality to mothers and fetuses. Clinical manifestations of preterm preeclampsia result from excess circulating soluble vascular endothelial growth factor receptor FLT1 (sFLT1 or sVEGFR1) of placental origin. Here we identify short interfering RNAs (siRNAs) that selectively silence the three sFLT1 mRNA isoforms primarily responsible for placental overexpression of sFLT1 without reducing levels of full-length FLT1 mRNA. Full chemical stabilization in the context of hydrophobic modifications enabled productive siRNA accumulation in the placenta (up to 7% of injected dose) and reduced circulating sFLT1 in pregnant mice (up to 50%). In a baboon preeclampsia model, a single dose of siRNAs suppressed sFLT1 overexpression and clinical signs of preeclampsia. Our results demonstrate RNAi-based extrahepatic modulation of gene expression with nonformulated siRNAs in nonhuman primates and establish a path toward a new treatment paradigm for patients with preterm preeclampsia.
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Affiliation(s)
- Anton A Turanov
- RNA Therapeutics Institute, University of Massachusetts Medical School, Worcester, Massachusetts, USA
| | - Agnes Lo
- Center for Vascular Biology Research, Beth Israel Deaconess Medical Center, Boston, Massachusetts, USA
- Harvard Medical School, Boston, Massachusetts, USA
| | - Matthew R Hassler
- RNA Therapeutics Institute, University of Massachusetts Medical School, Worcester, Massachusetts, USA
| | - Angela Makris
- Heart Research Institute, Sydney, New South Wales, Australia
- School of Medicine, Western Sydney University, Sydney, New South Wales, Australia
- Renal Department, Liverpool Hospital, Sydney, New South Wales, Australia
| | - Ami Ashar-Patel
- RNA Therapeutics Institute, University of Massachusetts Medical School, Worcester, Massachusetts, USA
| | - Julia F Alterman
- RNA Therapeutics Institute, University of Massachusetts Medical School, Worcester, Massachusetts, USA
| | - Andrew H Coles
- RNA Therapeutics Institute, University of Massachusetts Medical School, Worcester, Massachusetts, USA
| | - Reka A Haraszti
- RNA Therapeutics Institute, University of Massachusetts Medical School, Worcester, Massachusetts, USA
| | - Loic Roux
- RNA Therapeutics Institute, University of Massachusetts Medical School, Worcester, Massachusetts, USA
| | - Bruno M D C Godinho
- RNA Therapeutics Institute, University of Massachusetts Medical School, Worcester, Massachusetts, USA
| | - Dimas Echeverria
- RNA Therapeutics Institute, University of Massachusetts Medical School, Worcester, Massachusetts, USA
| | - Suzanne Pears
- Heart Research Institute, Sydney, New South Wales, Australia
| | - Jim Iliopoulos
- School of Medicine, Western Sydney University, Sydney, New South Wales, Australia
| | - Renuka Shanmugalingam
- Heart Research Institute, Sydney, New South Wales, Australia
- School of Medicine, Western Sydney University, Sydney, New South Wales, Australia
- Renal Department, Liverpool Hospital, Sydney, New South Wales, Australia
| | - Robert Ogle
- Women's and Babies, Royal Prince Alfred Hospital, Sydney, New South Wales, Australia
| | - Zsuzsanna K Zsengeller
- Center for Vascular Biology Research, Beth Israel Deaconess Medical Center, Boston, Massachusetts, USA
- Harvard Medical School, Boston, Massachusetts, USA
| | - Annemarie Hennessy
- Heart Research Institute, Sydney, New South Wales, Australia
- School of Medicine, Western Sydney University, Sydney, New South Wales, Australia
| | - S Ananth Karumanchi
- Center for Vascular Biology Research, Beth Israel Deaconess Medical Center, Boston, Massachusetts, USA
- Harvard Medical School, Boston, Massachusetts, USA
- Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, California, USA
| | - Melissa J Moore
- RNA Therapeutics Institute, University of Massachusetts Medical School, Worcester, Massachusetts, USA
- Moderna Therapeutics, Cambridge, Massachusetts, USA
| | - Anastasia Khvorova
- RNA Therapeutics Institute, University of Massachusetts Medical School, Worcester, Massachusetts, USA
- Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, Massachusetts
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75
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Shen P, Reineke LC, Knutsen E, Chen M, Pichler M, Ling H, Calin GA. Metformin blocks MYC protein synthesis in colorectal cancer via mTOR-4EBP-eIF4E and MNK1-eIF4G-eIF4E signaling. Mol Oncol 2018; 12:1856-1870. [PMID: 30221473 PMCID: PMC6210051 DOI: 10.1002/1878-0261.12384] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2018] [Revised: 08/04/2018] [Accepted: 08/14/2018] [Indexed: 12/26/2022] Open
Abstract
The antidiabetic drug metformin has been associated with reduced colorectal cancer (CRC) risk and improved prognosis of CRC patients. However, the detailed mechanisms underlying such beneficial effects remain unknown. In this study, we aimed to evaluate metformin activity in CRC models and unveil the underlying molecular mechanisms. We showed that metformin inhibits CRC cell proliferation by arresting cells in the G1 phase of the cell cycle and dramatically reduces colony formation of CRC cells. We discovered that metformin causes a robust reduction of MYC protein level. Through the use of luciferase assay and coincubation with either protein synthesis or proteasome inhibitors, we demonstrated that regulation of MYC by metformin is independent of the proteasome and 3' UTR-mediated regulation, but depends on protein synthesis. Data from polysome profiling and ribopuromycylation assays showed that metformin induced widespread inhibition of protein synthesis. Repression of protein synthesis by metformin preferentially affects cell cycle-associated proteins, by altering signaling through the mTOR-4EBP-eIF4E and MNK1-eIF4G-eIF4E axes. The inhibition of MYC protein synthesis may underlie metformin's beneficial effects on CRC risk and prognosis.
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Affiliation(s)
- Peng Shen
- Department of Oncology, Nanfang Hospital, Southern Medical University, Guangzhou, China.,The First School of Clinical Medicine, Southern Medical University, Guangzhou, China.,Department of Experimental Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Lucas C Reineke
- Department of Molecular Physiology and Biophysics, Baylor College of Medicine, Houston, TX, USA
| | - Erik Knutsen
- Department of Experimental Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.,Department of Medical Biology, Faculty of Health Sciences, UiT - The Arctic University of Norway, Tromsø, Norway
| | - Meng Chen
- Department of Experimental Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Martin Pichler
- Department of Experimental Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.,Division of Oncology, Research Unit of Non-Coding RNA and Genome Editing in Cancer, Medical University of Graz, Austria
| | - Hui Ling
- Department of Experimental Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - George A Calin
- Department of Experimental Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.,The Center for RNA Interference and Non-Coding RNAs, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
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76
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Panigrahi B, Singh RK, Mishra S, Mandal D. Cyclic peptide-based nanostructures as efficient siRNA carriers. ARTIFICIAL CELLS NANOMEDICINE AND BIOTECHNOLOGY 2018; 46:S763-S773. [DOI: 10.1080/21691401.2018.1511574] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Affiliation(s)
- Bijayananda Panigrahi
- School of Biotechnology, Kalinga Institute of Industrial Technology, Bhubaneswar, Odisha, India
| | - Rohit Kumar Singh
- School of Biotechnology, Kalinga Institute of Industrial Technology, Bhubaneswar, Odisha, India
| | - Sourav Mishra
- School of Biotechnology, Kalinga Institute of Industrial Technology, Bhubaneswar, Odisha, India
| | - Dindyal Mandal
- School of Biotechnology, Kalinga Institute of Industrial Technology, Bhubaneswar, Odisha, India
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77
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NLRP3 expression in mesencephalic neurons and characterization of a rare NLRP3 polymorphism associated with decreased risk of Parkinson's disease. NPJ PARKINSONS DISEASE 2018; 4:24. [PMID: 30131971 PMCID: PMC6093937 DOI: 10.1038/s41531-018-0061-5] [Citation(s) in RCA: 113] [Impact Index Per Article: 18.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/03/2017] [Revised: 06/26/2018] [Accepted: 06/29/2018] [Indexed: 12/22/2022]
Abstract
Neuroinflammation is a well-characterized pathophysiology occurring in association with the progression of Parkinson's disease. Characterizing the cellular and molecular basis of neuroinflammation is critical to understanding its impact on the incidence and progression of PD and other neurologic disorders. Inflammasomes are intracellular pro-inflammatory pattern-recognition receptors capable of initiating and propagating inflammation. These cellular complexes are well characterized in the innate immune system and activity of the NLRP3 inflammasome has been reported in microglia. NLRP3 inflammasome activity has been associated with Alzheimer's disease, and recent reports, from our laboratory and others, indicate that Nlrp3 is required for neuroinflammation and nigral cell loss in animal models of PD. NLRP3 has not yet been characterized in PD patients. Here we characterize NLRP3 in PD using immunohistologic and genetic approaches. Histologic studies revealed elevated NLRP3 expression in mesencephalic neurons of PD patients. Analysis of exome sequencing data for genetic variation of NLRP3 identified multiple single-nucleotide polymorphisms (SNPs) including rs7525979 that was associated with a significantly reduced risk of developing PD. Mechanistic studies conducted in HEK293 cells indicated that the synonymous SNP, NLRP3 rs7525979, alters the efficiency of NLRP3 translation impacting NLRP3 protein stability, ubiquitination state, and solubility. These data provide evidence that dopaminergic neurons are a cell-of-origin for inflammasome activity in PD and are consistent with recent animal studies, suggesting that inflammasome activity may impact the progression of PD.
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78
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Haraszti RA, Miller R, Didiot MC, Biscans A, Alterman JF, Hassler MR, Roux L, Echeverria D, Sapp E, DiFiglia M, Aronin N, Khvorova A. Optimized Cholesterol-siRNA Chemistry Improves Productive Loading onto Extracellular Vesicles. Mol Ther 2018; 26:1973-1982. [PMID: 29937418 DOI: 10.1016/j.ymthe.2018.05.024] [Citation(s) in RCA: 58] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2018] [Revised: 05/27/2018] [Accepted: 05/30/2018] [Indexed: 01/01/2023] Open
Abstract
Extracellular vesicles are promising delivery vesicles for therapeutic RNAs. Small interfering RNA (siRNA) conjugation to cholesterol enables efficient and reproducible loading of extracellular vesicles with the therapeutic cargo. siRNAs are typically chemically modified to fit an application. However, siRNA chemical modification pattern has not been specifically optimized for extracellular vesicle-mediated delivery. Here we used cholesterol-conjugated, hydrophobically modified asymmetric siRNAs (hsiRNAs) to evaluate the effect of backbone, 5'-phosphate, and linker chemical modifications on productive hsiRNA loading onto extracellular vesicles. hsiRNAs with a combination of 5'-(E)-vinylphosphonate and alternating 2'-fluoro and 2'-O-methyl backbone modifications outperformed previously used partially modified siRNAs in extracellular vesicle-mediated Huntingtin silencing in neurons. Between two commercially available linkers (triethyl glycol [TEG] and 2-aminobutyl-1-3-propanediol [C7]) widely used to attach cholesterol to siRNAs, TEG is preferred compared to C7 for productive exosomal loading. Destabilization of the linker completely abolished silencing activity of loaded extracellular vesicles. The loading of cholesterol-conjugated siRNAs was saturated at ∼3,000 siRNA copies per extracellular vesicle. Overloading impaired the silencing activity of extracellular vesicles. The data reported here provide an optimization scheme for the successful use of hydrophobic modification as a strategy for productive loading of RNA cargo onto extracellular vesicles.
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Affiliation(s)
- Reka Agnes Haraszti
- RNA Therapeutics Institute, University of Massachusetts Medical School, Worcester, MA, USA; Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA, USA
| | - Rachael Miller
- RNA Therapeutics Institute, University of Massachusetts Medical School, Worcester, MA, USA; Department of Medicine, University of Massachusetts Medical School, Worcester, MA, USA
| | - Marie-Cecile Didiot
- RNA Therapeutics Institute, University of Massachusetts Medical School, Worcester, MA, USA; Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA, USA
| | - Annabelle Biscans
- RNA Therapeutics Institute, University of Massachusetts Medical School, Worcester, MA, USA; Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA, USA
| | - Julia F Alterman
- RNA Therapeutics Institute, University of Massachusetts Medical School, Worcester, MA, USA; Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA, USA
| | - Matthew R Hassler
- RNA Therapeutics Institute, University of Massachusetts Medical School, Worcester, MA, USA; Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA, USA
| | - Loic Roux
- RNA Therapeutics Institute, University of Massachusetts Medical School, Worcester, MA, USA; Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA, USA
| | - Dimas Echeverria
- RNA Therapeutics Institute, University of Massachusetts Medical School, Worcester, MA, USA; Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA, USA
| | - Ellen Sapp
- Mass General Institute for Neurodegenerative Disease, Boston, MA, USA
| | - Marian DiFiglia
- Mass General Institute for Neurodegenerative Disease, Boston, MA, USA
| | - Neil Aronin
- RNA Therapeutics Institute, University of Massachusetts Medical School, Worcester, MA, USA; Department of Medicine, University of Massachusetts Medical School, Worcester, MA, USA.
| | - Anastasia Khvorova
- RNA Therapeutics Institute, University of Massachusetts Medical School, Worcester, MA, USA; Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA, USA.
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79
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Optimized delivery of siRNA into 3D tumor spheroid cultures in situ. Sci Rep 2018; 8:7952. [PMID: 29785035 PMCID: PMC5962539 DOI: 10.1038/s41598-018-26253-3] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2016] [Accepted: 05/04/2018] [Indexed: 12/19/2022] Open
Abstract
3D tissue culture provides a physiologically relevant and genetically tractable system for studying normal and malignant human tissues. Despite this, gene-silencing studies using siRNA has proved difficult. In this study, we have identified a cause for why traditional siRNA transfection techniques are ineffective in eliciting gene silencing in situ within 3D cultures and proposed a simple method for significantly enhancing siRNA entry into spheroids/organoids. In 2D cell culture, the efficiency of gene silencing is significantly reduced when siRNA complexes are prepared in the presence of serum. Surprisingly, in both 3D tumour spheroids and primary murine organoids, the presence of serum during siRNA preparation rapidly promotes entry and internalization of Cy3-labelled siRNA in under 2 hours. Conversely, siRNA prepared in traditional low-serum transfection media fails to gain matrigel or spheroid/organoid entry. Direct measurement of CTNNB1 mRNA (encoding β-catenin) from transfected tumour spheroids confirmed a transient but significant knockdown of β-catenin when siRNA:liposome complexes were formed with serum, but not when prepared in the presence of reduced-serum media (Opti-MEM). Our studies suggest a simple modification to standard lipid-based transfection protocols facilitates rapid siRNA entry and transient gene repression, providing a platform for researchers to improve siRNA efficiency in established 3D cultures.
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80
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Osborn MF, Khvorova A. Improving siRNA Delivery In Vivo Through Lipid Conjugation. Nucleic Acid Ther 2018; 28:128-136. [PMID: 29746209 DOI: 10.1089/nat.2018.0725] [Citation(s) in RCA: 88] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
RNA interference (RNAi)-based therapeutics are approaching clinical approval for genetically defined diseases. Current clinical success is a result of significant innovations in the development of chemical architectures that support sustained, multi-month efficacy in vivo following a single administration. Conjugate-mediated delivery has established itself as the most promising platform for safe and targeted small interfering RNA (siRNA) delivery. Lipophilic conjugates represent a major class of modifications that improve siRNA pharmacokinetics and enable efficacy in a broad range of tissues. Here, we review current literature and define key features and limitations of this approach for in vivo modulation of gene expression.
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Affiliation(s)
- Maire F Osborn
- 1 RNA Therapeutics Institute, University of Massachusetts Medical School , Worcester, Massachusetts
| | - Anastasia Khvorova
- 1 RNA Therapeutics Institute, University of Massachusetts Medical School , Worcester, Massachusetts.,2 Department of Molecular Medicine, University of Massachusetts Medical School , Worcester, Massachusetts
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81
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Matsumura K, Taniguchi T, Reimer JD, Noguchi S, Fujita MJ, Sakai R. KB343, a Cyclic Tris-guanidine Alkaloid from Palauan Zoantharian Epizoanthus illoricatus. Org Lett 2018; 20:3039-3043. [DOI: 10.1021/acs.orglett.8b01069] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Ken Matsumura
- Faculty and Graduate School of Fisheries Sciences, Hokkaido University, 3-1-1 minato-cho, Hakodate, Hokkaido 041-8611, Japan
| | - Tohru Taniguchi
- Frontier Research Center for Advanced Material and Life Science, Faculty of Advanced Life Science, Hokkaido University, Kita 21 Nishi 11, Sapporo 001-0021, Japan
| | - James D. Reimer
- University of the Ryukyus Senbaru 1, Nishihara, Okinawa 903-0213, Japan
| | - Shuntaro Noguchi
- Faculty and Graduate School of Fisheries Sciences, Hokkaido University, 3-1-1 minato-cho, Hakodate, Hokkaido 041-8611, Japan
| | - Masaki J. Fujita
- Faculty and Graduate School of Fisheries Sciences, Hokkaido University, 3-1-1 minato-cho, Hakodate, Hokkaido 041-8611, Japan
| | - Ryuichi Sakai
- Faculty and Graduate School of Fisheries Sciences, Hokkaido University, 3-1-1 minato-cho, Hakodate, Hokkaido 041-8611, Japan
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82
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Juliano RL. Intracellular Trafficking and Endosomal Release of Oligonucleotides: What We Know and What We Don't. Nucleic Acid Ther 2018; 28:166-177. [PMID: 29708838 DOI: 10.1089/nat.2018.0727] [Citation(s) in RCA: 86] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Understanding the cellular uptake and intracellular trafficking of oligonucleotides provides an important basic underpinning for the developing field of oligonucleotide-based therapeutics. Whether delivered as "free" oligonucleotides, as ligand-oligonucleotide conjugates, or in association with various nanocarriers, all forms of oligonucleotide enter cells by endocytosis and are initially ensconced within membrane-limited vesicles. Accordingly, the locus and extent of release to the cytosol and nucleus are key determinants of the pharmacological actions of oligonucleotides. A number of recent studies have explored the intracellular trafficking of various forms of oligonucleotides and their release from endomembrane compartments. These studies reveal a surprising convergence on an early-intermediate compartment in the trafficking pathway as the key locus of release for oligonucleotides administered in "free" form as well as those delivered with lipid complexes. Thus, oligonucleotide release from multivesicular bodies or from late endosomes seems to be the crucial endogenous process for attaining pharmacological effects. This intrinsic process of oligonucleotide release may be amplified by delivery agents such as lipid complexes or small molecule enhancers.
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Affiliation(s)
- R L Juliano
- Initos Pharmaceuticals LLC, UNC Eshelman School of Pharmacy, University of North Carolina , Chapel Hill, North Carolina
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83
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Ligtenberg MA, Pico de Coaña Y, Shmushkovich T, Yoshimoto Y, Truxova I, Yang Y, Betancur-Boissel M, Eliseev AV, Wolfson AD, Kiessling R. Self-Delivering RNAi Targeting PD-1 Improves Tumor-Specific T Cell Functionality for Adoptive Cell Therapy of Malignant Melanoma. Mol Ther 2018; 26:1482-1493. [PMID: 29735366 PMCID: PMC5986970 DOI: 10.1016/j.ymthe.2018.04.015] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2017] [Revised: 04/05/2018] [Accepted: 04/10/2018] [Indexed: 12/12/2022] Open
Abstract
Adoptive cell therapy (ACT) is becoming a prominent alternative therapeutic treatment for cancer patients relapsing on traditional therapies. In parallel, antibodies targeting immune checkpoint molecules, such as cytotoxic-T-lymphocyte-associated antigen 4 (CTLA-4) and cell death protein 1 pathway (PD-1), are rapidly being approved for multiple cancer types, including as first line therapy for PD-L1-expressing non-small-cell lung cancer. The combination of ACT and checkpoint blockade could substantially boost the efficacy of ACT. In this study, we generated a novel self-delivering small interfering RNA (siRNA) (sdRNA) that knocked down PD-1 expression on healthy donor T cells as well as patient-derived tumor-infiltrating lymphocytes (TIL). We have developed an alternative chemical modification of RNA backbone for improved stability and increased efficacy. Our results show that T cells treated with sdRNA specific for PD-1 had increased interferon γ (IFN-γ) secreting capacity and that this modality of gene expression interference could be utilized in our rapid expansion protocol for production of TIL for therapy. TIL expanded in the presence of PD-1-specific sdRNA performed with increased functionality against autologous tumor as compared to control TIL. This method of introducing RNAi into T cells to modify the expression of proteins could easily be adopted into any ACT protocol and will lead to the exploration of new combination therapies.
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Affiliation(s)
- Maarten A Ligtenberg
- Department of Oncology and Pathology, Cancer Center Karolinska, Karolinska Institutet, Stockholm 17176, Sweden
| | - Yago Pico de Coaña
- Department of Oncology and Pathology, Cancer Center Karolinska, Karolinska Institutet, Stockholm 17176, Sweden.
| | | | - Yuya Yoshimoto
- Department of Oncology and Pathology, Cancer Center Karolinska, Karolinska Institutet, Stockholm 17176, Sweden; Department of Radiation Oncology, Gunma University Graduate School of Medicine, Maebashi 371-8510, Japan
| | - Iva Truxova
- Department of Oncology and Pathology, Cancer Center Karolinska, Karolinska Institutet, Stockholm 17176, Sweden; Charles University, 2(nd) Faculty of Medicine and University Hospital Motol, 150 06 Prague, Czech Republic; Sotio A.S., 170 00 Prague, Czech Republic
| | - Yuan Yang
- Department of Oncology and Pathology, Cancer Center Karolinska, Karolinska Institutet, Stockholm 17176, Sweden; Clinical Research Center, Guizhou Medical University Hospital, Guiyang 550025, People's Republic of China
| | | | | | | | - Rolf Kiessling
- Department of Oncology and Pathology, Cancer Center Karolinska, Karolinska Institutet, Stockholm 17176, Sweden
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84
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Biscans A, Haraszti RA, Echeverria D, Miller R, Didiot MC, Nikan M, Roux L, Aronin N, Khvorova A. Hydrophobicity of Lipid-Conjugated siRNAs Predicts Productive Loading to Small Extracellular Vesicles. Mol Ther 2018; 26:1520-1528. [PMID: 29699940 DOI: 10.1016/j.ymthe.2018.03.019] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2018] [Revised: 03/28/2018] [Accepted: 03/28/2018] [Indexed: 12/28/2022] Open
Abstract
Small extracellular vesicles (sEVs) show promise as natural nano-devices for delivery of therapeutic RNA, but efficient loading of therapeutic RNA remains a challenge. We have recently shown that the attachment of cholesterol to small interfering RNAs (siRNAs) enables efficient and productive loading into sEVs. Here, we systematically explore the ability of lipid conjugates-fatty acids, sterols, and vitamins-to load siRNAs into sEVs and support gene silencing in primary neurons. Hydrophobicity of the conjugated siRNAs defined loading efficiency and the silencing activity of siRNA-sEVs complexes. Vitamin-E-conjugated siRNA supported the best loading into sEVs and productive RNA delivery to neurons.
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Affiliation(s)
- Annabelle Biscans
- RNA Therapeutics Institute, University of Massachusetts Medical School, Worcester, MA 01605, USA; Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Reka A Haraszti
- RNA Therapeutics Institute, University of Massachusetts Medical School, Worcester, MA 01605, USA; Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Dimas Echeverria
- RNA Therapeutics Institute, University of Massachusetts Medical School, Worcester, MA 01605, USA; Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Rachael Miller
- RNA Therapeutics Institute, University of Massachusetts Medical School, Worcester, MA 01605, USA; Department of Medicine, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Marie-Cecile Didiot
- RNA Therapeutics Institute, University of Massachusetts Medical School, Worcester, MA 01605, USA; Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | | | - Loic Roux
- RNA Therapeutics Institute, University of Massachusetts Medical School, Worcester, MA 01605, USA; Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Neil Aronin
- RNA Therapeutics Institute, University of Massachusetts Medical School, Worcester, MA 01605, USA; Department of Medicine, University of Massachusetts Medical School, Worcester, MA 01605, USA.
| | - Anastasia Khvorova
- RNA Therapeutics Institute, University of Massachusetts Medical School, Worcester, MA 01605, USA; Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA 01605, USA.
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85
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Hassler MR, Turanov AA, Alterman JF, Haraszti RA, Coles AH, Osborn MF, Echeverria D, Nikan M, Salomon WE, Roux L, Godinho BMDC, Davis SM, Morrissey DV, Zamore PD, Karumanchi SA, Moore MJ, Aronin N, Khvorova A. Comparison of partially and fully chemically-modified siRNA in conjugate-mediated delivery in vivo. Nucleic Acids Res 2018; 46:2185-2196. [PMID: 29432571 PMCID: PMC5861422 DOI: 10.1093/nar/gky037] [Citation(s) in RCA: 123] [Impact Index Per Article: 20.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2017] [Revised: 01/09/2018] [Accepted: 01/19/2018] [Indexed: 12/13/2022] Open
Abstract
Small interfering RNA (siRNA)-based drugs require chemical modifications or formulation to promote stability, minimize innate immunity, and enable delivery to target tissues. Partially modified siRNAs (up to 70% of the nucleotides) provide significant stabilization in vitro and are commercially available; thus are commonly used to evaluate efficacy of bio-conjugates for in vivo delivery. In contrast, most clinically-advanced non-formulated compounds, using conjugation as a delivery strategy, are fully chemically modified (100% of nucleotides). Here, we compare partially and fully chemically modified siRNAs in conjugate mediated delivery. We show that fully modified siRNAs are retained at 100x greater levels in various tissues, independently of the nature of the conjugate or siRNA sequence, and support productive mRNA silencing. Thus, fully chemically stabilized siRNAs may provide a better platform to identify novel moieties (peptides, aptamers, small molecules) for targeted RNAi delivery.
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Affiliation(s)
- Matthew R Hassler
- RNA Therapeutics Institute, University of Massachusetts Medical School, USA
| | - Anton A Turanov
- RNA Therapeutics Institute, University of Massachusetts Medical School, USA
| | - Julia F Alterman
- RNA Therapeutics Institute, University of Massachusetts Medical School, USA
| | - Reka A Haraszti
- RNA Therapeutics Institute, University of Massachusetts Medical School, USA
| | - Andrew H Coles
- RNA Therapeutics Institute, University of Massachusetts Medical School, USA
| | - Maire F Osborn
- RNA Therapeutics Institute, University of Massachusetts Medical School, USA
| | - Dimas Echeverria
- RNA Therapeutics Institute, University of Massachusetts Medical School, USA
| | - Mehran Nikan
- RNA Therapeutics Institute, University of Massachusetts Medical School, USA
| | - William E Salomon
- RNA Therapeutics Institute, University of Massachusetts Medical School, USA
| | - Loïc Roux
- RNA Therapeutics Institute, University of Massachusetts Medical School, USA
| | | | - Sarah M Davis
- RNA Therapeutics Institute, University of Massachusetts Medical School, USA
| | | | - Phillip D Zamore
- RNA Therapeutics Institute, University of Massachusetts Medical School, USA
| | | | - Melissa J Moore
- RNA Therapeutics Institute, University of Massachusetts Medical School, USA
| | - Neil Aronin
- RNA Therapeutics Institute, University of Massachusetts Medical School, USA
- Department of Medicine, University of Massachusetts Medical School, USA
| | - Anastasia Khvorova
- RNA Therapeutics Institute, University of Massachusetts Medical School, USA
- Department of Molecular Medicine, University of Massachusetts Medical School, USA
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86
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Wu S, Zhang A, Li S, Chatterjee S, Qi R, Segura‐Ibarra V, Ferrari M, Gupte A, Blanco E, Hamilton DJ. Polymer Functionalization of Isolated Mitochondria for Cellular Transplantation and Metabolic Phenotype Alteration. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2018; 5:1700530. [PMID: 29593955 PMCID: PMC5867055 DOI: 10.1002/advs.201700530] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/24/2017] [Revised: 10/26/2017] [Indexed: 05/31/2023]
Abstract
Aberrant mitochondrial energy transfer underlies prevalent chronic health conditions, including cancer, cardiovascular, and neurodegenerative diseases. Mitochondrial transplantation represents an innovative strategy aimed at restoring favorable metabolic phenotypes in cells with dysfunctional energy metabolism. While promising, significant barriers to in vivo translation of this approach abound, including limited cellular uptake and recognition of mitochondria as foreign. The objective is to functionalize isolated mitochondria with a biocompatible polymer to enhance cellular transplantation and eventual in vivo applications. Herein, it is demonstrated that grafting of a polymer conjugate composed of dextran with triphenylphosphonium onto isolated mitochondria protects the organelles and facilitates cellular internalization compared with uncoated mitochondria. Importantly, mitochondrial transplantation into cancer and cardiovascular cells has profound effects on respiration, mediating a shift toward improved oxidative phosphorylation, and reduced glycolysis. These findings represent the first demonstration of polymer functionalization of isolated mitochondria, highlighting a viable strategy for enabling clinical applications of mitochondrial transplantation.
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Affiliation(s)
- Suhong Wu
- Department of NanomedicineHouston Methodist Research InstituteHoustonTX77030USA
| | - Aijun Zhang
- Center for BioenergeticsHouston Methodist Research InstituteHoustonTX77030USA
| | - Shumin Li
- Center for BioenergeticsHouston Methodist Research InstituteHoustonTX77030USA
| | - Somik Chatterjee
- Center for BioenergeticsHouston Methodist Research InstituteHoustonTX77030USA
| | - Ruogu Qi
- Department of NanomedicineHouston Methodist Research InstituteHoustonTX77030USA
| | | | - Mauro Ferrari
- Department of NanomedicineHouston Methodist Research InstituteHoustonTX77030USA
- Department of MedicineWeill Cornell MedicineNew YorkNY10065USA
| | - Anisha Gupte
- Center for BioenergeticsHouston Methodist Research InstituteHoustonTX77030USA
- Department of PhysiologyWeill Cornell MedicineNew YorkNY10065USA
| | - Elvin Blanco
- Department of NanomedicineHouston Methodist Research InstituteHoustonTX77030USA
| | - Dale J. Hamilton
- Center for BioenergeticsHouston Methodist Research InstituteHoustonTX77030USA
- Department of MedicineWeill Cornell MedicineNew YorkNY10065USA
- Division EndocrinologyDiabetes, and MetabolismDepartment of MedicineHouston Methodist HospitalHoustonTX77030USA
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87
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Tai W, Gao X. Noncovalent tagging of siRNA with steroids for transmembrane delivery. Biomaterials 2018; 178:720-727. [PMID: 29433754 DOI: 10.1016/j.biomaterials.2018.02.007] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2017] [Revised: 02/02/2018] [Accepted: 02/02/2018] [Indexed: 01/30/2023]
Abstract
Short interfering RNA (siRNA) has broad applications in biology and medicine, and holds tremendous potential to become a new class of therapeutics for many diseases. As a highly anionic macrobiomolecule, its cytosolic delivery, however, has been a major roadblock in translation. Here, we report the development of small, bifunctional chemical tags capable of transporting siRNA directly into the cytosol. The bifunctional tags consist of a siRNA-binding moiety that interacts with siRNA non-covalently, and a steroid domain that readily fuses with the mammalian cell membrane. In contrast to the conventional covalently conjugated siRNA-steroid that enters cells largely via endocytosis which substantially limits siRNA bioavailability, the non-covalently tagged siRNA is cell membrane-permeant, avoiding the endocytic pathway. This new methodology enables effective RNA interference (RNAi) without the need of cationic transfection or endosomolytic agents, opening a new avenue for intracellular delivery of native biologics.
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Affiliation(s)
- Wanyi Tai
- Department of Bioengineering, University of Washington, Seattle, WA 98195, USA
| | - Xiaohu Gao
- Department of Bioengineering, University of Washington, Seattle, WA 98195, USA.
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88
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Didiot MC, Haraszti RA, Aronin N, Khvorova A. Loading of Extracellular Vesicles with Hydrophobically Modified siRNAs. Methods Mol Biol 2018; 1740:199-214. [PMID: 29388146 DOI: 10.1007/978-1-4939-7652-2_16] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Delivery represents a significant barrier to the clinical advancement of oligonucleotide therapeutics. Small, endogenous extracellular vesicles (EVs) have the potential to act as oligonucleotide delivery vehicles, but robust and scalable methods for loading RNA therapeutic cargo into vesicles are lacking. Here we describe the efficient loading of hydrophobically modified siRNAs (hsiRNAs) into EVs upon co-incubation, without altering vesicle size distribution or integrity. This method is expected to advance the development of EV-based therapies for the treatment of a broad range of disorders.
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Affiliation(s)
- Marie-Cecile Didiot
- RNA Therapeutics Institute, University of Massachusetts Medical School, Worcester, MA, USA
- Department of Molecular Medicine, University of Massachusetts Medical School, Worcester, MA, USA
| | - Reka A Haraszti
- RNA Therapeutics Institute, University of Massachusetts Medical School, Worcester, MA, USA
- Department of Molecular Medicine, University of Massachusetts Medical School, Worcester, MA, USA
| | - Neil Aronin
- RNA Therapeutics Institute, University of Massachusetts Medical School, Worcester, MA, USA
- Department of Medicine, University of Massachusetts Medical School, Worcester, MA, USA
| | - Anastasia Khvorova
- RNA Therapeutics Institute, University of Massachusetts Medical School, Worcester, MA, USA.
- Department of Molecular Medicine, University of Massachusetts Medical School, Worcester, MA, USA.
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89
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Jeong EH, Jeong H, Jang B, Kim B, Kim M, Kwon H, Lee K, Lee H. Aptamer-incorporated DNA Holliday junction for the targeted delivery of siRNA. J IND ENG CHEM 2017. [DOI: 10.1016/j.jiec.2017.07.025] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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90
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Godinho BMDC, Gilbert JW, Haraszti RA, Coles AH, Biscans A, Roux L, Nikan M, Echeverria D, Hassler M, Khvorova A. Pharmacokinetic Profiling of Conjugated Therapeutic Oligonucleotides: A High-Throughput Method Based Upon Serial Blood Microsampling Coupled to Peptide Nucleic Acid Hybridization Assay. Nucleic Acid Ther 2017; 27:323-334. [PMID: 29022758 DOI: 10.1089/nat.2017.0690] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Therapeutic oligonucleotides, such as small interfering RNAs (siRNAs), hold great promise for the treatment of incurable genetically defined disorders by targeting cognate toxic gene products for degradation. To achieve meaningful tissue distribution and efficacy in vivo, siRNAs must be conjugated or formulated. Clear understanding of the pharmacokinetic (PK)/pharmacodynamic behavior of these compounds is necessary to optimize and characterize the performance of therapeutic oligonucleotides in vivo. In this study, we describe a simple and reproducible methodology for the evaluation of in vivo blood/plasma PK profiles and tissue distribution of oligonucleotides. The method is based on serial blood microsampling from the saphenous vein, coupled to peptide nucleic acid hybridization assay for quantification of guide strands. Performed with minimal number of animals, this method allowed unequivocal detection and sensitive quantification without the need for amplification, or further modification of the oligonucleotides. Using this methodology, we compared plasma clearances and tissue distribution profiles of two different hydrophobically modified siRNAs (hsiRNAs). Notably, cholesterol-hsiRNA presented slow plasma clearances and mainly accumulated in the liver, whereas, phosphocholine-docosahexaenoic acid-hsiRNA was rapidly cleared from the plasma and preferably accumulated in the kidney. These data suggest that the PK/biodistribution profiles of modified hsiRNAs are determined by the chemical nature of the conjugate. Importantly, the method described in this study constitutes a simple platform to conduct pilot assessments of the basic clearance and tissue distribution profiles, which can be broadly applied for evaluation of new chemical variants of siRNAs and micro-RNAs.
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Affiliation(s)
- Bruno M D C Godinho
- 1 RNA Therapeutics Institute, University of Massachusetts Medical School , Worcester, Massachusetts.,2 Department of Molecular Medicine, University of Massachusetts Medical School , Worcester, Massachusetts
| | - James W Gilbert
- 1 RNA Therapeutics Institute, University of Massachusetts Medical School , Worcester, Massachusetts.,2 Department of Molecular Medicine, University of Massachusetts Medical School , Worcester, Massachusetts
| | - Reka A Haraszti
- 1 RNA Therapeutics Institute, University of Massachusetts Medical School , Worcester, Massachusetts.,2 Department of Molecular Medicine, University of Massachusetts Medical School , Worcester, Massachusetts
| | - Andrew H Coles
- 1 RNA Therapeutics Institute, University of Massachusetts Medical School , Worcester, Massachusetts.,2 Department of Molecular Medicine, University of Massachusetts Medical School , Worcester, Massachusetts
| | - Annabelle Biscans
- 1 RNA Therapeutics Institute, University of Massachusetts Medical School , Worcester, Massachusetts.,2 Department of Molecular Medicine, University of Massachusetts Medical School , Worcester, Massachusetts
| | - Loic Roux
- 1 RNA Therapeutics Institute, University of Massachusetts Medical School , Worcester, Massachusetts.,2 Department of Molecular Medicine, University of Massachusetts Medical School , Worcester, Massachusetts
| | - Mehran Nikan
- 1 RNA Therapeutics Institute, University of Massachusetts Medical School , Worcester, Massachusetts.,2 Department of Molecular Medicine, University of Massachusetts Medical School , Worcester, Massachusetts
| | - Dimas Echeverria
- 1 RNA Therapeutics Institute, University of Massachusetts Medical School , Worcester, Massachusetts.,2 Department of Molecular Medicine, University of Massachusetts Medical School , Worcester, Massachusetts
| | - Matthew Hassler
- 1 RNA Therapeutics Institute, University of Massachusetts Medical School , Worcester, Massachusetts.,2 Department of Molecular Medicine, University of Massachusetts Medical School , Worcester, Massachusetts
| | - Anastasia Khvorova
- 1 RNA Therapeutics Institute, University of Massachusetts Medical School , Worcester, Massachusetts.,2 Department of Molecular Medicine, University of Massachusetts Medical School , Worcester, Massachusetts
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91
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Metelev V, Zhang S, Zheng S, Kumar AT, Bogdanov A. Fluorocarbons Enhance Intracellular Delivery of Short STAT3-sensors and Enable Specific Imaging. Am J Cancer Res 2017; 7:3354-3368. [PMID: 28900515 PMCID: PMC5595137 DOI: 10.7150/thno.19704] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2017] [Accepted: 07/12/2017] [Indexed: 02/06/2023] Open
Abstract
Short oligonucleotide sequences are now being widely investigated for their potential therapeutic properties. The modification of oligonucleotide termini with short fluorinated residues is capable of drastically altering their behavior in complex in vitro and in vivo systems, and thus may serve to greatly enhance their therapeutic potential. The main goals of our work were to explore: 1) how modification of STAT3 transcription factor-binding oligodeoxynucleotide (ODN) duplexes (ODND) with one or two short fluorocarbon (FC)-based residues would change their properties in vitro and in vivo, and if so, how this would affect their intracellular uptake by cancer cells, and 2) the ability of such modified ODND to form non-covalent complexes with FC-modified carrier macromolecule. The latter has an inherent advantage of producing a 19F-specific magnetic resonance (MR) imaging signature. Thus, we also tested the ability of such copolymers to generate 19F-MR signals. Materials and Methods. Fluorinated nucleic acid residues were incorporated into ODN by using automated synthesis or via activated esters on ODN 5'-ends. To quantify ODND uptake by the cells and to track their stability, we covalently labeled ODN with fluorophores using internucleoside linker technology; the FC-modified carrier was synthesized by acylation of pegylated polylysine graft copolymer with perfluoroundecanoic acid (M5-gPLL-PFUDA). Results. ODN with a single FC group exhibited a tendency to form duplexes with higher melting points and with increased stability against degradation when compared to control non-modified ODNs. ODND carrying fluorinated residues showed complex formation with M5-gPLL-PFUDA as predicted by molecular dynamics simulations. Moreover, FC groups modulated the specificity of ODND binding to the STAT3 target. Finally, FC modification resulted in greater cell uptake (2 to 4 fold higher) when compared to the uptake of non-modified ODND as determined by quantitative confocal fluorescence imaging of A431 and INS-1 cells. Conclusion. ODND modification with FC residues enables fine-tuning of protein binding specificity to double-strand binding motifs and results in an increased internalization by A431 and INS-1 cells in culture. Our results show that modification of ODN termini with FC residues is both a feasible and powerful strategy for developing more efficient nucleic acid-based therapies with the added benefit of allowing for non-invasive MR imaging of ODND therapeutic targeting and response.
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92
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Haraszti RA, Roux L, Coles AH, Turanov AA, Alterman JF, Echeverria D, Godinho BM, Aronin N, Khvorova A. 5΄-Vinylphosphonate improves tissue accumulation and efficacy of conjugated siRNAs in vivo. Nucleic Acids Res 2017; 45:7581-7592. [PMID: 28591791 PMCID: PMC5570069 DOI: 10.1093/nar/gkx507] [Citation(s) in RCA: 78] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2017] [Revised: 05/23/2017] [Accepted: 05/31/2017] [Indexed: 12/20/2022] Open
Abstract
5΄-Vinylphosphonate modification of siRNAs protects them from phosphatases, and improves silencing activity. Here, we show that 5΄-vinylphosphonate confers novel properties to siRNAs. Specifically, 5΄-vinylphosphonate (i) increases siRNA accumulation in tissues, (ii) extends duration of silencing in multiple organs and (iii) protects siRNAs from 5΄-to-3΄ exonucleases. Delivery of conjugated siRNAs requires extensive chemical modifications to achieve stability in vivo. Because chemically modified siRNAs are poor substrates for phosphorylation by kinases, and 5΄-phosphate is required for loading into RNA-induced silencing complex, the synthetic addition of a 5΄-phosphate on a fully modified siRNA guide strand is expected to be beneficial. Here, we show that synthetic phosphorylation of fully modified cholesterol-conjugated siRNAs increases their potency and efficacy in vitro, but when delivered systemically to mice, the 5΄-phosphate is removed within 2 hours. The 5΄-phosphate mimic 5΄-(E)-vinylphosphonate stabilizes the 5΄ end of the guide strand by protecting it from phosphatases and 5΄-to-3΄ exonucleases. The improved stability increases guide strand accumulation and retention in tissues, which significantly enhances the efficacy of cholesterol-conjugated siRNAs and the duration of silencing in vivo. Moreover, we show that 5΄-(E)-vinylphosphonate stabilizes 5΄ phosphate, thereby enabling systemic delivery to and silencing in kidney and heart.
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Affiliation(s)
- Reka A. Haraszti
- RNA Therapeutics Institute, University of Massachusetts Medical School, 01605 Worcester, MA, USA
- Program in Molecular Medicine, University of Massachusetts Medical School, 01605 Worcester, MA, USA
| | - Loic Roux
- RNA Therapeutics Institute, University of Massachusetts Medical School, 01605 Worcester, MA, USA
- Program in Molecular Medicine, University of Massachusetts Medical School, 01605 Worcester, MA, USA
| | - Andrew H. Coles
- RNA Therapeutics Institute, University of Massachusetts Medical School, 01605 Worcester, MA, USA
- Program in Molecular Medicine, University of Massachusetts Medical School, 01605 Worcester, MA, USA
| | - Anton A. Turanov
- RNA Therapeutics Institute, University of Massachusetts Medical School, 01605 Worcester, MA, USA
- Program in Molecular Medicine, University of Massachusetts Medical School, 01605 Worcester, MA, USA
| | - Julia F. Alterman
- RNA Therapeutics Institute, University of Massachusetts Medical School, 01605 Worcester, MA, USA
- Program in Molecular Medicine, University of Massachusetts Medical School, 01605 Worcester, MA, USA
| | - Dimas Echeverria
- RNA Therapeutics Institute, University of Massachusetts Medical School, 01605 Worcester, MA, USA
- Program in Molecular Medicine, University of Massachusetts Medical School, 01605 Worcester, MA, USA
| | - Bruno M.D.C. Godinho
- RNA Therapeutics Institute, University of Massachusetts Medical School, 01605 Worcester, MA, USA
- Program in Molecular Medicine, University of Massachusetts Medical School, 01605 Worcester, MA, USA
| | - Neil Aronin
- RNA Therapeutics Institute, University of Massachusetts Medical School, 01605 Worcester, MA, USA
- Department of Medicine, University of Massachusetts Medical School, 01605 Worcester, MA, USA
| | - Anastasia Khvorova
- RNA Therapeutics Institute, University of Massachusetts Medical School, 01605 Worcester, MA, USA
- Program in Molecular Medicine, University of Massachusetts Medical School, 01605 Worcester, MA, USA
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93
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Alterman JF, Coles AH, Hall LM, Aronin N, Khvorova A, Didiot MC. A High-throughput Assay for mRNA Silencing in Primary Cortical Neurons in vitro with Oligonucleotide Therapeutics. Bio Protoc 2017; 7:e2501. [PMID: 28966945 DOI: 10.21769/bioprotoc.2501] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022] Open
Abstract
Primary neurons represent an ideal cellular system for the identification of therapeutic oligonucleotides for the treatment of neurodegenerative diseases. However, due to the sensitive nature of primary cells, the transfection of small interfering RNAs (siRNA) using classical methods is laborious and often shows low efficiency. Recent progress in oligonucleotide chemistry has enabled the development of stabilized and hydrophobically modified small interfering RNAs (hsiRNAs). This new class of oligonucleotide therapeutics shows extremely efficient self-delivery properties and supports potent and durable effects in vitro and in vivo. We have developed a high-throughput in vitro assay to identify and test hsiRNAs in primary neuronal cultures. To simply, rapidly, and accurately quantify the mRNA silencing of hundreds of hsiRNAs, we use the QuantiGene 2.0 quantitative gene expression assay. This high-throughput, 96-well plate-based assay can quantify mRNA levels directly from sample lysate. Here, we describe a method to prepare short-term cultures of mouse primary cortical neurons in a 96-well plate format for high-throughput testing of oligonucleotide therapeutics. This method supports the testing of hsiRNA libraries and the identification of potential therapeutics within just two weeks. We detail methodologies of our high throughput assay workflow from primary neuron preparation to data analysis. This method can help identify oligonucleotide therapeutics for treatment of various neurological diseases.
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Affiliation(s)
- Julia F Alterman
- RNA Therapeutics Institute, University of Massachusetts Medical School, Worcester, MA, USA.,Department of Molecular Medicine, University of Massachusetts Medical School, Worcester, MA, USA
| | - Andrew H Coles
- RNA Therapeutics Institute, University of Massachusetts Medical School, Worcester, MA, USA.,Department of Molecular Medicine, University of Massachusetts Medical School, Worcester, MA, USA
| | - Lauren M Hall
- RNA Therapeutics Institute, University of Massachusetts Medical School, Worcester, MA, USA.,Department of Medicine, University of Massachusetts Medical School, Worcester, MA, USA
| | - Neil Aronin
- RNA Therapeutics Institute, University of Massachusetts Medical School, Worcester, MA, USA.,Department of Medicine, University of Massachusetts Medical School, Worcester, MA, USA
| | - Anastasia Khvorova
- RNA Therapeutics Institute, University of Massachusetts Medical School, Worcester, MA, USA.,Department of Molecular Medicine, University of Massachusetts Medical School, Worcester, MA, USA
| | - Marie-Cécile Didiot
- RNA Therapeutics Institute, University of Massachusetts Medical School, Worcester, MA, USA.,Department of Molecular Medicine, University of Massachusetts Medical School, Worcester, MA, USA
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94
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Fumoto S, Nishida K. Methods for Evaluating the Stimuli-Responsive Delivery of Nucleic Acid and Gene Medicines. Chem Pharm Bull (Tokyo) 2017; 65:642-648. [DOI: 10.1248/cpb.c17-00096] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Affiliation(s)
| | - Koyo Nishida
- Graduate School of Biomedical Sciences, Nagasaki University
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95
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Haraszti RA, Coles A, Aronin N, Khvorova A, Didiot MC. Loading of Extracellular Vesicles with Chemically Stabilized Hydrophobic siRNAs for the Treatment of Disease in the Central Nervous System. Bio Protoc 2017; 7:e2338. [PMID: 28868334 DOI: 10.21769/bioprotoc.2338] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022] Open
Abstract
Efficient delivery of oligonucleotide therapeutics, i.e., siRNAs, to the central nervous system represents a significant barrier to their clinical advancement for the treatment of neurological disorders. Small, endogenous extracellular vesicles were shown to be able to transport lipids, proteins and RNA between cells, including neurons. This natural trafficking ability gives extracellular vesicles the potential to be used as delivery vehicles for oligonucleotides, i.e., siRNAs. However, robust and scalable methods for loading of extracellular vesicles with oligonucleotide cargo are lacking. We describe a detailed protocol for the loading of hydrophobically modified siRNAs into extracellular vesicles upon simple co-incubation. We detail methods of the workflow from purification of extracellular vesicles to data analysis. This method may advance extracellular vesicles-based therapies for the treatment of a broad range of neurological disorders.
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Affiliation(s)
- Reka A Haraszti
- RNA Therapeutics Institute, University of Massachusetts Medical School, Worcester, MA, USA.,Department of Molecular Medicine, University of Massachusetts Medical School, Worcester, MA, USA
| | - Andrew Coles
- RNA Therapeutics Institute, University of Massachusetts Medical School, Worcester, MA, USA.,Department of Molecular Medicine, University of Massachusetts Medical School, Worcester, MA, USA
| | - Neil Aronin
- RNA Therapeutics Institute, University of Massachusetts Medical School, Worcester, MA, USA.,Department of Medicine, University of Massachusetts Medical School, Worcester, MA, USA
| | - Anastasia Khvorova
- RNA Therapeutics Institute, University of Massachusetts Medical School, Worcester, MA, USA.,Department of Molecular Medicine, University of Massachusetts Medical School, Worcester, MA, USA
| | - Marie-Cécile Didiot
- RNA Therapeutics Institute, University of Massachusetts Medical School, Worcester, MA, USA.,Department of Molecular Medicine, University of Massachusetts Medical School, Worcester, MA, USA
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