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Agrawal K, Kang L, Ji S, Tena J, Jian W. Evaluating the use of locked nucleic acid capture probes in hybrid LC-MS/MS analysis of siRNA analytes. Bioanalysis 2023; 15:1129-1146. [PMID: 37638814 DOI: 10.4155/bio-2023-0079] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/29/2023] Open
Abstract
Background: Hybrid LC-MS assays for oligonucleotides rely on capture probes to develop assays with high sensitivity and specificity. Locked nucleic acid (LNA) probes are thermodynamically superior to existing capture probes, but are not currently used for hybrid LC-MS assays. Materials & methods: Using two lipid-conjugated double-stranded siRNA compounds as model analytes, hybrid LC-MS/MS assays using LNA probes were developed. Results: The workflows demonstrated the superiority of the LNA probes, optimized sample preparation conditions to maximize analyte recovery, evaluated the need for analyte-specific internal standards, and demonstrated that advanced mass spectrometric technology can increase assay sensitivity by up to 20-fold. Conclusion: The workflow can be used in future bioanalytical studies to develop effective hybrid LC-MS/MS methods for siRNA analytes.
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Affiliation(s)
- Karan Agrawal
- Bioanalysis Discovery & Development Sciences, Janssen Research & Development, Spring House, PA 19477, USA
| | - Lijuan Kang
- Bioanalysis Discovery & Development Sciences, Janssen Research & Development, Spring House, PA 19477, USA
| | - Shaofei Ji
- Translational PK/PD & Investigative Toxicology, Janssen Research & Development, Spring House, PA 19477, USA
| | - Jennyfer Tena
- Therapeutics Discovery, Janssen Research & Development, Brisbane, CA 94005, USA
| | - Wenying Jian
- Bioanalysis Discovery & Development Sciences, Janssen Research & Development, Spring House, PA 19477, USA
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Weidle UH, Sela T, Brinkmann U, Niewoehner J. Circular RNAs With Efficacy in Preclinical In Vitro and In Vivo Models of Esophageal Squamous Cell Carcinoma. Cancer Genomics Proteomics 2022; 19:283-298. [PMID: 35430563 DOI: 10.21873/cgp.20320] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2022] [Revised: 03/02/2022] [Accepted: 03/03/2022] [Indexed: 02/06/2023] Open
Abstract
Esophageal cancer is associated with a dismal prognosis. The armamentarium of approved drugs is focused on chemotherapy with modest therapeutic benefit. Recently, checkpoint inhibitory monoclonal antibody Pembrolizumab was approved. In order to identify new targets and modalities for the treatment of esophagus squamous cell carcinoma (ESCC) we searched the literature for circRNAs involved in the pathogenesis of ESCC. We identified two down-regulated and 17 up-regulated circRNAs as well as a synthetic circRNA with efficacy in preclinical in vivo systems. Down-regulated circRNAs sponge microRNAs directed against tumor suppressor genes. Up-regulated circRNAs sponge microRNAs directed against mRNAs, which encode proteins with pro-tumoral functions. We discuss issues such as reconstitution of down-regulated circRNAs and inhibition of up-regulated circRNAs with short interfering RNA (siRNA)- related entities. Also, we address druggability issues of the identified targets.
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Affiliation(s)
- Ulrich H Weidle
- Roche Pharma Research and Early Development (pRED), Large Molecule Research, Roche Innovation Center Munich, Penzberg, Germany
| | - Tatjana Sela
- Roche Pharma Research and Early Development (pRED), Large Molecule Research, Roche Innovation Center Munich, Penzberg, Germany
| | - Ulrich Brinkmann
- Roche Pharma Research and Early Development (pRED), Large Molecule Research, Roche Innovation Center Munich, Penzberg, Germany
| | - Jens Niewoehner
- Roche Pharma Research and Early Development (pRED), Large Molecule Research, Roche Innovation Center Munich, Penzberg, Germany
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Miller AJ, Chang A, Cunningham PN. Chronic Microangiopathy Due to DCR-MYC, a Myc-Targeted Short Interfering RNA. Am J Kidney Dis 2019; 75:513-516. [PMID: 31866228 DOI: 10.1053/j.ajkd.2019.09.011] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2019] [Accepted: 09/16/2019] [Indexed: 12/25/2022]
Abstract
Thrombotic microangiopathy (TMA) is an emerging complication of oncologic therapy. Cancer-related causes of renal endothelial cell damage include cytotoxic chemotherapies, radiation given for myeloablation, and direct involvement of renal vasculature by tumor cells. Another class of therapeutic agents that has been implicated in TMA is the vascular endothelial growth factor (VEGF) pathway inhibitors, including the anti-VEGF monoclonal antibody bevacizumab and the VEGF receptor tyrosine kinase inhibitor sunitinib. These TMAs have been termed type II cancer drug-induced TMA and are distinguished from those associated with some cytotoxic chemotherapies (ie, type I) in that they are not dose dependent and patients are more likely to demonstrate some recovery of kidney function. Determination of the cause of TMA in oncologic patients often presents a significant challenge because patients frequently receive multiple chemotherapeutic agents simultaneously and clinicopathologic features often demonstrate substantial overlap, regardless of cause. We present a case of TMA with predominantly chronic features in a 70-year-old patient being treated for adenoid cystic carcinoma of the breast with a single agent, a short interfering RNA targeted against Myc (DCR-MYC).
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Affiliation(s)
- Aaron J Miller
- Department of Pathology, University of Chicago, Chicago, IL
| | - Anthony Chang
- Department of Pathology, University of Chicago, Chicago, IL
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Abstract
Nucleic acid-based therapeutics present huge potential in the treatment
of pulmonary diseases ranging from lung cancer to asthma and chronic pulmonary
diseases, which are often fatal and widely prevalent. The susceptibility of nucleic
acids to degradation and the complex structure of lungs retard the effective
pulmonary delivery of nucleic acid drug. To overcome these barriers, different
strategies have been exploited to increase the delivery efficiency using chemically
synthesized nucleic acids, vector encapsulation, proper formulation, and
administration route. However, several limitations regarding off-target effects and
immune stimulation of nucleic acid drugs hamper their translation into the clinical
practice. Therefore, their successful clinical application will ultimately rely on
well-developed carriers and methods to ensure safety and efficacy. In this review,
we provide a comprehensive overview of the nucleic acid application for pulmonary
diseases, covering action mechanism of the nucleic acid drugs, the novel delivery
systems, and the current formulation for the administration to lungs. The latest
advances of nucleic acid drugs under clinical evaluation to treat pulmonary
disorders will also be detailed.
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Qiu Y, Lam JK, Leung SW, Liang W. Delivery of RNAi Therapeutics to the Airways-From Bench to Bedside. Molecules 2016; 21:E1249. [PMID: 27657028 DOI: 10.3390/molecules21091249] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2016] [Revised: 09/05/2016] [Accepted: 09/13/2016] [Indexed: 12/12/2022] Open
Abstract
RNA interference (RNAi) is a potent and specific post-transcriptional gene silencing process. Since its discovery, tremendous efforts have been made to translate RNAi technology into therapeutic applications for the treatment of different human diseases including respiratory diseases, by manipulating the expression of disease-associated gene(s). Similar to other nucleic acid-based therapeutics, the major hurdle of RNAi therapy is delivery. Pulmonary delivery is a promising approach of delivering RNAi therapeutics directly to the airways for treating local conditions and minimizing systemic side effects. It is a non-invasive route of administration that is generally well accepted by patients. However, pulmonary drug delivery is a challenge as the lungs pose a series of anatomical, physiological and immunological barriers to drug delivery. Understanding these barriers is essential for the development an effective RNA delivery system. In this review, the different barriers to pulmonary drug delivery are introduced. The potential of RNAi molecules as new class of therapeutics, and the latest preclinical and clinical studies of using RNAi therapeutics in different respiratory conditions are discussed in details. We hope this review can provide some useful insights for moving inhaled RNAi therapeutics from bench to bedside.
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Jangravi Z, Tabar MS, Mirzaei M, Parsamatin P, Vakilian H, Alikhani M, Shabani M, Haynes PA, Goodchild AK, Gourabi H, Baharvand H, Salekdeh GH. Two Splice Variants of Y Chromosome-Located Lysine-Specific Demethylase 5D Have Distinct Function in Prostate Cancer Cell Line (DU-145). J Proteome Res 2015. [PMID: 26215926 DOI: 10.1021/acs.jproteome.5b00333] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
One of the major objectives of the Human Y Chromosome Proteome Project is to characterize sets of proteins encoded from the human Y chromosome. Lysine (K)-specific demethylase 5D (KDM5D) is located on the AZFb region of the Y chromosome and encodes a JmjC-domain-containing protein. KDM5D, the least well-documented member of the KDM5 family, is capable of demethylating di- and trimethyl H3K4. In this study, we detected two novel splice variants of KDM5D with lengths of 2650bp and 2400bp that correspond to the 100 and 80 kDa proteins in the human prostate cancer cell line, DU-145. The knockdown of two variants using the short interfering RNA (siRNA) approach increased the growth rate of prostate cancer cells and reduced cell apoptosis. To explore the proteome pattern of the cells after KDM5D downregulation, we applied a shotgun label-free quantitative proteomics approach. Of 820 proteins present in all four replicates of two treatments, the abundance of 209 proteins changed significantly in response to KDM5D suppression. Of these, there were 102 proteins observed to be less abundant and 107 more abundant in KDM5D knockdown cells compared with control cells. The results revealed that KDM5D knockdown altered the abundance of proteins involved in RNA processing, protein synthesis, apoptosis, the cell cycle, and growth and proliferation. In conjunction, these results provided new insights into the function of KDM5D and its splice variants. The proteomics data are available at PRIDE with ProteomeXchange identifier PXD000416.
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Affiliation(s)
- Zohreh Jangravi
- Molecular Systems Biology Department at Cell Science Research Center, Royan Institute for Stem Cell Biology and Technology, ACECR , Tehran, Iran.,Biochemistry Department, Iran University of Medical Sciences , Tehran, Iran
| | - Mehdi Sharif Tabar
- Molecular Systems Biology Department at Cell Science Research Center, Royan Institute for Stem Cell Biology and Technology, ACECR , Tehran, Iran
| | - Mehdi Mirzaei
- The Australian School of Advanced Medicine, Faculty of Human Sciences, Macquarie University , Sydney, New South Wales 2109, Australia
| | - Pouria Parsamatin
- Molecular Systems Biology Department at Cell Science Research Center, Royan Institute for Stem Cell Biology and Technology, ACECR , Tehran, Iran
| | - Haghighat Vakilian
- Molecular Systems Biology Department at Cell Science Research Center, Royan Institute for Stem Cell Biology and Technology, ACECR , Tehran, Iran
| | - Mehdi Alikhani
- Molecular Systems Biology Department at Cell Science Research Center, Royan Institute for Stem Cell Biology and Technology, ACECR , Tehran, Iran
| | - Mohammad Shabani
- Biochemistry Department, Iran University of Medical Sciences , Tehran, Iran
| | - Paul A Haynes
- Department of Chemistry and Biomolecular Sciences, Macquarie University , Sydney, New South Wales 2109, Australia
| | - Ann K Goodchild
- The Australian School of Advanced Medicine, Faculty of Human Sciences, Macquarie University , Sydney, New South Wales 2109, Australia
| | - Hamid Gourabi
- Department of Genetics at Reproductive Biomedicine Research Center, Royan Institute for Reproductive Biomedicine, ACECR , Tehran, Iran
| | - Hossein Baharvand
- Department of Developmental Biology, University of Science and Culture, ACECR , Tehran, Iran.,Department of Stem Cells and Developmental Biology at Cell Science Research Center, Royan Institute for Stem Cell Biology and Technology, ACECR , Tehran, Iran
| | - Ghasem Hosseini Salekdeh
- Molecular Systems Biology Department at Cell Science Research Center, Royan Institute for Stem Cell Biology and Technology, ACECR , Tehran, Iran.,Department of Systems Biology, Agricultural Biotechnology Research Institute of Iran , Karaj, Iran
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