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Article ; Online: Sensor and sensitivity: a screen for elite shRNAs.

Castanotto, Daniela

Molecular therapy : the journal of the American Society of Gene Therapy

2011 Volume 19, Issue 5, Page(s) 823–825

MeSH term(s)	Animals ; Base Composition ; Drug Discovery ; Gene Expression ; Gene Library ; Humans ; RNA Interference ; RNA, Small Interfering/therapeutic use
Chemical Substances	RNA, Small Interfering
Language	English
Publishing date	2011-05-02
Publishing country	United States
Document type	Journal Article
ZDB-ID	2010592-7
ISSN	1525-0024 ; 1525-0016
ISSN (online)	1525-0024
ISSN	1525-0016
DOI	10.1038/mt.2011.70
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Article ; Online: FDA-Approved Oligonucleotide Therapies in 2017.

Stein, Cy A / Castanotto, Daniela

Molecular therapy : the journal of the American Society of Gene Therapy

2017 Volume 25, Issue 5, Page(s) 1069–1075

Abstract: Oligonucleotides (oligos) have been under clinical development for approximately the past 30 years, beginning with antisense oligonucleotides (ASOs) and apatmers and followed about 15 years ago by siRNAs. During that lengthy period of time, numerous ... ...

Abstract	Oligonucleotides (oligos) have been under clinical development for approximately the past 30 years, beginning with antisense oligonucleotides (ASOs) and apatmers and followed about 15 years ago by siRNAs. During that lengthy period of time, numerous clinical trials have been performed and thousands of trial participants accrued onto studies. Of all the molecules evaluated as of January 2017, the regulatory authorities assessed that six provided clear clinical benefit in rigorously controlled trials. The story of these six is given in this review.
MeSH term(s)	Aptamers, Nucleotide/therapeutic use ; Clinical Trials as Topic ; Cytomegalovirus Retinitis/genetics ; Cytomegalovirus Retinitis/therapy ; Cytomegalovirus Retinitis/virology ; Drug Approval ; Hepatic Veno-Occlusive Disease/genetics ; Hepatic Veno-Occlusive Disease/pathology ; Hepatic Veno-Occlusive Disease/therapy ; Humans ; Hypercholesterolemia/genetics ; Hypercholesterolemia/pathology ; Hypercholesterolemia/therapy ; Macular Degeneration/genetics ; Macular Degeneration/pathology ; Macular Degeneration/therapy ; Morpholinos/therapeutic use ; Muscular Atrophy, Spinal/genetics ; Muscular Atrophy, Spinal/pathology ; Muscular Atrophy, Spinal/therapy ; Muscular Dystrophy, Duchenne/genetics ; Muscular Dystrophy, Duchenne/pathology ; Muscular Dystrophy, Duchenne/therapy ; Oligonucleotides/therapeutic use ; Oligonucleotides, Antisense/therapeutic use ; Polydeoxyribonucleotides/therapeutic use ; Thionucleotides/therapeutic use
Chemical Substances	Aptamers, Nucleotide ; Morpholinos ; Oligonucleotides ; Oligonucleotides, Antisense ; Polydeoxyribonucleotides ; Thionucleotides ; pegaptanib (2H1PA8H1EN) ; defibrotide (438HCF2X0M) ; nusinersen (5Z9SP3X666) ; mipomersen (9GJ8S4GU0M) ; eteplirsen (AIW6036FAS) ; fomivirsen (QX5LK7YCHV)
Language	English
Publishing date	2017-03-31
Publishing country	United States
Document type	Journal Article ; Review
ZDB-ID	2010592-7
ISSN	1525-0024 ; 1525-0016
ISSN (online)	1525-0024
ISSN	1525-0016
DOI	10.1016/j.ymthe.2017.03.023
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Article: Defibrotide (Defitelio): A New Addition to the Stockpile of Food and Drug Administration-approved Oligonucleotide Drugs.

Stein, Cy / Castanotto, Daniela / Krishnan, Amrita / Nikolaenko, Liana

Molecular therapy. Nucleic acids

2017 Volume 5, Page(s) e346

Language	English
Publishing date	2017-01-27
Publishing country	United States
Document type	Journal Article
ZDB-ID	2662631-7
ISSN	2162-2531
ISSN	2162-2531
DOI	10.1038/mtna.2016.42
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Article ; Online: Oligonucleotides to the (Gene) Rescue: FDA Approvals 2017-2019.

Rüger, Jacqueline / Ioannou, Silvia / Castanotto, Daniela / Stein, Cy A

Trends in pharmacological sciences

2019 Volume 41, Issue 1, Page(s) 27–41

Abstract: Four decades have passed since oligonucleotides were first used to manipulate gene expression. There were few FDA approvals prior to 2016, mostly of drugs that eventually exhibited poor performance in the market. The aura of their younger siRNA relatives ...

Abstract	Four decades have passed since oligonucleotides were first used to manipulate gene expression. There were few FDA approvals prior to 2016, mostly of drugs that eventually exhibited poor performance in the market. The aura of their younger siRNA relatives had also faded during the past 15 years. However, several FDA approvals have occurred in the past 4 years, restoring hope that a new era has dawned in oligonucleotide/siRNA clinical therapeutics. Here, we review the field of oligonucleotide therapeutics and provide an update on FDA approvals of oligonucleotides from 2017 until the second quarter of 2019. We take into consideration the ethical issues looming over the still somewhat limited efficacy of these molecules, the toxicity of treatment, and the exorbitant cost of these therapeutic agents, which limits accessibility for many.
MeSH term(s)	Clinical Trials, Phase III as Topic ; Drug Approval ; Drug Costs ; Humans ; Oligonucleotides/administration & dosage ; Oligonucleotides/economics ; Oligonucleotides/genetics ; Oligonucleotides/pharmacology ; Randomized Controlled Trials as Topic ; United States ; United States Food and Drug Administration
Chemical Substances	Oligonucleotides
Language	English
Publishing date	2019-12-10
Publishing country	England
Document type	Journal Article ; Review
ZDB-ID	282846-7
ISSN	1873-3735 ; 0165-6147
ISSN (online)	1873-3735
ISSN	0165-6147
DOI	10.1016/j.tips.2019.10.009
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Zs.A 1513: Show issues			Location: Je nach Verfügbarkeit (siehe Angabe bei Bestand) bis Jg. 1994: Bestellungen von Artikeln über das Online-Bestellformular Jg. 1995 - 2021: Lesesall (1.OG) ab Jg. 2022: Lesesaal (EG)
Zs.MG 6: Show issues

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Article ; Online: Antisense oligonucleotides in cancer.

Castanotto, Daniela / Stein, Cy A

Current opinion in oncology

2014 Volume 26, Issue 6, Page(s) 584–589

Abstract: Purpose of review: Over the past several dozen years, regardless of the substantial effort directed toward developing rational oligonucleotide strategies to silence gene expression, antisense oligonucleotide-based cancer therapy has not been successful. ...

Abstract	Purpose of review: Over the past several dozen years, regardless of the substantial effort directed toward developing rational oligonucleotide strategies to silence gene expression, antisense oligonucleotide-based cancer therapy has not been successful. This review focuses on the most likely reasons for this lack of success, and on the barriers that still need to be overcome to make a clinical cancer treatment reality out of the promise of antisense therapy. Recent findings: Considerable progress has been made in the design and delivery of nucleic acid fragments. Chemical modifications have considerably improved oligonucleotide absorption, distribution and metabolism while at the same time reducing toxicity. Nevertheless, the delivery and the cellular uptake of these molecules are still not adequate to provide the desired therapeutic outcome. Recent therapeutic interventional phase III trials of antisense oligodeoxyribonucleotides for a cancer indication will be discussed, in addition to those studies that markedly improve the scientific understanding of the properties of these molecules. Summary: We still do not have a marketed antisense oligonucleotide for a cancer indication. This is because critical aspects of the cellular, tumor pharmacology and delivery properties of these agents are still not well understood.
MeSH term(s)	Animals ; Genetic Therapy/methods ; Humans ; Neoplasms/therapy ; Oligonucleotides, Antisense/therapeutic use
Chemical Substances	Oligonucleotides, Antisense
Language	English
Publishing date	2014-11
Publishing country	United States
Document type	Journal Article ; Review
ZDB-ID	1049384-0
ISSN	1531-703X ; 1040-8746
ISSN (online)	1531-703X
ISSN	1040-8746
DOI	10.1097/CCO.0000000000000127
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Article ; Online: 6BIO Enhances Oligonucleotide Activity in Cells: A Potential Combinatorial Anti-androgen Receptor Therapy in Prostate Cancer Cells.

Zhang, Xiaowei / Castanotto, Daniela / Nam, Sangkil / Horne, David / Stein, Cy

Molecular therapy : the journal of the American Society of Gene Therapy

2017 Volume 25, Issue 1, Page(s) 79–91

Abstract: Approximately 15%-25% of men diagnosed with prostate cancer do not survive their disease. The American Cancer Society estimated that for the year 2016 the number of prostate cancer deaths will be 26,120. Thus, there is a critical need for novel ... ...

Abstract	Approximately 15%-25% of men diagnosed with prostate cancer do not survive their disease. The American Cancer Society estimated that for the year 2016 the number of prostate cancer deaths will be 26,120. Thus, there is a critical need for novel approaches to treat this deadly disease. Using high-throughput small-molecule screening, we found that the small molecule 6-bromo-indirubin-3'-oxime (6BIO) significantly improves the targeting of antisense oligonucleotides (ASOs) delivered by gymnosis (i.e., in the absence of any transfection reagents) in both the cell cytoplasm and the nucleus. Furthermore, as a single agent, 6BIO had the unexpected ability to simultaneously downregulate androgen receptor (AR) expression and AR signaling in prostate cancer cells. This includes downregulating levels of the AR-V7, a drug-resistance-related AR splice variant that is important in the progression of prostate cancer. Combining 6BIO and an anti-AR oligonucleotide (AR-ASO) can augment the downregulation of AR expression. We also demonstrated that 6BIO enhances ASO function and represses AR expression through the inhibition of the two main glycogen synthase kinase 3 (GSK-3) isoforms: GSK-3α and GSK-3β activity. Our findings provide a rationale for the use of 6BIO as a single agent or as part of a combinatorial ASO-based therapy in the treatment of human prostate cancer.
MeSH term(s)	Androgen Receptor Antagonists/pharmacology ; Antineoplastic Agents/pharmacology ; Cell Line, Tumor ; Cytoplasm ; Drug Synergism ; Glycogen Synthase Kinase 3/metabolism ; Glycogen Synthase Kinase 3 beta/metabolism ; Humans ; Indoles/pharmacology ; Male ; MicroRNAs/genetics ; MicroRNAs/pharmacology ; Oligonucleotides/genetics ; Oligonucleotides/pharmacology ; Oncogenes/genetics ; Oximes/pharmacology ; Prostatic Neoplasms/genetics ; Prostatic Neoplasms/metabolism ; RNA Splicing ; Receptors, Androgen/genetics ; Receptors, Androgen/metabolism ; Signal Transduction
Chemical Substances	6-bromoindirubin-3'-oxime ; Androgen Receptor Antagonists ; Antineoplastic Agents ; Indoles ; MIRN21 microRNA, human ; MicroRNAs ; Oligonucleotides ; Oximes ; Receptors, Androgen ; Glycogen Synthase Kinase 3 beta (EC 2.7.11.1) ; Glycogen Synthase Kinase 3 (EC 2.7.11.26) ; glycogen synthase kinase 3 alpha (EC 2.7.11.26)
Language	English
Publishing date	2017-01-04
Publishing country	United States
Document type	Journal Article
ZDB-ID	2010592-7
ISSN	1525-0024 ; 1525-0016
ISSN (online)	1525-0024
ISSN	1525-0016
DOI	10.1016/j.ymthe.2016.10.017
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Article ; Online: Ammonium and arsenic trioxide are potent facilitators of oligonucleotide function when delivered by gymnosis.

Zhang, Xiaowei / Castanotto, Daniela / Liu, Xueli / Shemi, Amotz / Stein, Cy A

Nucleic acids research

2018 Volume 46, Issue 7, Page(s) 3612–3624

Abstract: Oligonucleotide (ON) concentrations employed for therapeutic applications vary widely, but in general are high enough to raise significant concerns for off target effects and cellular toxicity. However, lowering ON concentrations reduces the chances of a ...

Abstract	Oligonucleotide (ON) concentrations employed for therapeutic applications vary widely, but in general are high enough to raise significant concerns for off target effects and cellular toxicity. However, lowering ON concentrations reduces the chances of a therapeutic response, since typically relatively small amounts of ON are taken up by targeted cells in tissue culture. It is therefore imperative to identify new strategies to improve the concentration dependence of ON function. In this work, we have identified ammonium ion (NH4+) as a non-toxic potent enhancer of ON activity in the nucleus and cytoplasm following delivery by gymnosis. NH4+ is a metabolite that has been extensively employed as diuretic, expectorant, for the treatment of renal calculi and in a variety of other diseases. Enhancement of function can be found in attached and suspension cells, including in difficult-to-transfect Jurkat T and CEM T cells. We have also demonstrated that NH4+ can synergistically interact with arsenic trioxide (arsenite) to further promote ON function without producing any apparent increased cellular toxicity. These small, inexpensive, widely distributed molecules could be useful not only in laboratory experiments but potentially in therapeutic ON-based combinatorial strategy for clinical applications.
MeSH term(s)	Ammonium Compounds/pharmacology ; Apoptosis/drug effects ; Arsenic Trioxide/pharmacology ; Cell Nucleus/drug effects ; Cell Proliferation/drug effects ; Humans ; Jurkat Cells ; Oligonucleotides/biosynthesis ; Oligonucleotides/genetics
Chemical Substances	Ammonium Compounds ; Oligonucleotides ; Arsenic Trioxide (S7V92P67HO)
Language	English
Publishing date	2018-03-01
Publishing country	England
Document type	Journal Article ; Research Support, N.I.H., Extramural
ZDB-ID	186809-3
ISSN	1362-4962 ; 1362-4954 ; 0301-5610 ; 0305-1048
ISSN (online)	1362-4962 ; 1362-4954
ISSN	0301-5610 ; 0305-1048
DOI	10.1093/nar/gky150
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Article ; Online: Incorporation of aptamers in the terminal loop of shRNAs yields an effective and novel combinatorial targeting strategy.

Pang, Ka Ming / Castanotto, Daniela / Li, Haitang / Scherer, Lisa / Rossi, John J

Nucleic acids research

2017 Volume 46, Issue 1, Page(s) e6

Abstract: Gene therapy by engineering patient's own blood cells to confer HIV resistance can potentially lead to a functional cure for AIDS. Toward this goal, we have previously developed an anti-HIV lentivirus vector that deploys a combination of shRNA, ribozyme ... ...

Abstract	Gene therapy by engineering patient's own blood cells to confer HIV resistance can potentially lead to a functional cure for AIDS. Toward this goal, we have previously developed an anti-HIV lentivirus vector that deploys a combination of shRNA, ribozyme and RNA decoy. To further improve this therapeutic vector against viral escape, we sought an additional reagent to target HIV integrase. Here, we report the development of a new strategy for selection and expression of aptamer for gene therapy. We developed a SELEX protocol (multi-tag SELEX) for selecting RNA aptamers against proteins with low solubility or stability, such as integrase. More importantly, we expressed these aptamers in vivo by incorporating them in the terminal loop of shRNAs. This novel strategy allowed efficient expression of the shRNA-aptamer fusions that targeted RNAs and proteins simultaneously. Expressed shRNA-aptamer fusions targeting HIV integrase or reverse transcriptase inhibited HIV replication in cell cultures. Viral inhibition was further enhanced by combining an anti-integrase aptamer with an anti-HIV Tat-Rev shRNA. This construct exhibited efficacy comparable to that of integrase inhibitor Raltegravir. Our strategy for the selection and expression of RNA aptamers can potentially extend to other gene therapy applications.
MeSH term(s)	Acquired Immunodeficiency Syndrome/genetics ; Acquired Immunodeficiency Syndrome/therapy ; Acquired Immunodeficiency Syndrome/virology ; Aptamers, Nucleotide/chemistry ; Aptamers, Nucleotide/genetics ; Aptamers, Nucleotide/metabolism ; Base Sequence ; Gene Expression Regulation, Viral ; Genetic Therapy/methods ; HIV Infections/genetics ; HIV Infections/therapy ; HIV Infections/virology ; HIV Integrase/genetics ; HIV-1/genetics ; HIV-1/metabolism ; Humans ; Nucleic Acid Conformation ; Protein Binding ; RNA, Small Interfering/chemistry ; RNA, Small Interfering/genetics ; RNA, Small Interfering/metabolism ; RNA, Viral/chemistry ; RNA, Viral/genetics ; RNA, Viral/metabolism ; RNA-Directed DNA Polymerase/genetics ; Virus Replication/genetics
Chemical Substances	Aptamers, Nucleotide ; RNA, Small Interfering ; RNA, Viral ; HIV Integrase (EC 2.7.7.-) ; RNA-Directed DNA Polymerase (EC 2.7.7.49)
Language	English
Publishing date	2017-10-26
Publishing country	England
Document type	Journal Article ; Research Support, N.I.H., Extramural
ZDB-ID	186809-3
ISSN	1362-4962 ; 1362-4954 ; 0301-5610 ; 0305-1048
ISSN (online)	1362-4962 ; 1362-4954
ISSN	0301-5610 ; 0305-1048
DOI	10.1093/nar/gkx980
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Article ; Online: The promises and pitfalls of RNA-interference-based therapeutics.

Castanotto, Daniela / Rossi, John J

Nature

2009 Volume 457, Issue 7228, Page(s) 426–433

Abstract: The discovery that gene expression can be controlled by the Watson-Crick base-pairing of small RNAs with messenger RNAs containing complementary sequence - a process known as RNA interference - has markedly advanced our understanding of eukaryotic gene ... ...

Abstract	The discovery that gene expression can be controlled by the Watson-Crick base-pairing of small RNAs with messenger RNAs containing complementary sequence - a process known as RNA interference - has markedly advanced our understanding of eukaryotic gene regulation and function. The ability of short RNA sequences to modulate gene expression has provided a powerful tool with which to study gene function and is set to revolutionize the treatment of disease. Remarkably, despite being just one decade from its discovery, the phenomenon is already being used therapeutically in human clinical trials, and biotechnology companies that focus on RNA-interference-based therapeutics are already publicly traded.
MeSH term(s)	Animals ; Clinical Trials as Topic ; Gene Knockdown Techniques ; Genetic Therapy/adverse effects ; Genetic Therapy/trends ; Humans ; RNA Interference ; RNA, Small Interfering/administration & dosage ; RNA, Small Interfering/adverse effects ; RNA, Small Interfering/genetics ; RNA, Small Interfering/therapeutic use
Chemical Substances	RNA, Small Interfering
Keywords	covid19
Language	English
Publishing date	2009-01-21
Publishing country	England
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Review
ZDB-ID	120714-3
ISSN	1476-4687 ; 0028-0836
ISSN (online)	1476-4687
ISSN	0028-0836
DOI	10.1038/nature07758
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Article ; Online: A stress-induced response complex (SIRC) shuttles miRNAs, siRNAs, and oligonucleotides to the nucleus.

Castanotto, Daniela / Zhang, Xiaowei / Alluin, Jessica / Zhang, Xizhe / Rüger, Jacqueline / Armstrong, Brian / Rossi, John / Riggs, Arthur / Stein, C A

Proceedings of the National Academy of Sciences of the United States of America

2018 Volume 115, Issue 25, Page(s) E5756–E5765

Abstract: Although some information is available for specific subsets of miRNAs and several factors have been shown to bind oligonucleotides (ONs), no general transport mechanism for these molecules has been identified to date. In this work, we demonstrate that ... ...

Abstract	Although some information is available for specific subsets of miRNAs and several factors have been shown to bind oligonucleotides (ONs), no general transport mechanism for these molecules has been identified to date. In this work, we demonstrate that the nuclear transport of ONs, siRNAs, and miRNAs responds to cellular stress. Furthermore, we have identified a stress-induced response complex (SIRC), which includes Ago-1 and Ago-2 in addition to the transcription and splicing regulators YB1, CTCF, FUS, Smad1, Smad3, and Smad4. The SIRC transports endogenous miRNAs, siRNAs, and ONs to the nucleus. We show that cellular stress can significantly increase ON- or siRNA-directed splicing switch events and endogenous miRNA targeting of nuclear RNAs.
MeSH term(s)	Active Transport, Cell Nucleus/physiology ; Cell Line ; Cell Line, Tumor ; Cell Nucleus/metabolism ; HEK293 Cells ; HeLa Cells ; Humans ; MicroRNAs/metabolism ; Oligonucleotides/metabolism ; RNA, Small Interfering/metabolism ; Transcription, Genetic/physiology
Chemical Substances	MicroRNAs ; Oligonucleotides ; RNA, Small Interfering
Language	English
Publishing date	2018-06-04
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural
ZDB-ID	209104-5
ISSN	1091-6490 ; 0027-8424
ISSN (online)	1091-6490
ISSN	0027-8424
DOI	10.1073/pnas.1721346115
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