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Kumar A, Ahmed B, Kaur IP, Saha L. Exploring dose and downregulation dynamics in lipid nanoparticles based siRNA therapy: Systematic review and meta-analysis. Int J Biol Macromol 2024; 277:133984. [PMID: 39053830 DOI: 10.1016/j.ijbiomac.2024.133984] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2024] [Revised: 07/09/2024] [Accepted: 07/16/2024] [Indexed: 07/27/2024]
Abstract
Small interfering RNA (siRNA) holds promise as a therapeutic approach for various diseases, yet challenges persist in achieving efficient delivery, biodistribution, and minimizing off-target effects. Lipidic nanoformulations are being developed to address these hurdles, but the optimal dose for preclinical investigations remains unclear. This systematic review and meta-analysis aims to determine the optimal dose of nanoformulated siRNA and explore factors influencing dose and biodistribution, informing future research in this field. A comprehensive search across four electronic databases identified 25 potential studies, with 15 selected for meta-analysis after screening. Quality assessment was conducted using SYRCLE's risk of bias tool modified for animal studies based on research question. Study found an average siRNA dose of 1.513 ± 0.377 mg/kg with mean downregulation of 65.79 % achieved, with siRNA-LNPs mainly accumulating in the liver. While individual factors showed no significant correlation, a positive association between dose and downregulation was observed, alongside other influencing factors. Extrapolating intravenous doses to potential oral doses, we suggest an initial oral dose range of 1.5 to 8 mg/kg, considering siRNA-LNPs bioavailability. These findings contribute to advancing RNA interference research and encourage further exploration of siRNA-based treatments in personalized medicine.
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Affiliation(s)
- Anil Kumar
- Department of Pharmacology, Post Graduate Institute of Medical Education & Research (PGIMER), Chandigarh 160012, India
| | - Bakr Ahmed
- Department of Pharmaceutics, University Institute of Pharmaceutical Sciences, Panjab University, Chandigarh, Punjab, India
| | - Indu Pal Kaur
- Department of Pharmaceutics, University Institute of Pharmaceutical Sciences, Panjab University, Chandigarh, Punjab, India.
| | - Lekha Saha
- Department of Pharmacology, Post Graduate Institute of Medical Education & Research (PGIMER), Chandigarh 160012, India.
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2
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Schwich OD, Blümel N, Keller M, Wegener M, Setty ST, Brunstein ME, Poser I, Mozos IRDL, Suess B, Münch C, McNicoll F, Zarnack K, Müller-McNicoll M. SRSF3 and SRSF7 modulate 3'UTR length through suppression or activation of proximal polyadenylation sites and regulation of CFIm levels. Genome Biol 2021; 22:82. [PMID: 33706811 PMCID: PMC7948361 DOI: 10.1186/s13059-021-02298-y] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2020] [Accepted: 02/11/2021] [Indexed: 12/23/2022] Open
Abstract
Background Alternative polyadenylation (APA) refers to the regulated selection of polyadenylation sites (PASs) in transcripts, which determines the length of their 3′ untranslated regions (3′UTRs). We have recently shown that SRSF3 and SRSF7, two closely related SR proteins, connect APA with mRNA export. The mechanism underlying APA regulation by SRSF3 and SRSF7 remained unknown. Results Here we combine iCLIP and 3′-end sequencing and find that SRSF3 and SRSF7 bind upstream of proximal PASs (pPASs), but they exert opposite effects on 3′UTR length. SRSF7 enhances pPAS usage in a concentration-dependent but splicing-independent manner by recruiting the cleavage factor FIP1, generating short 3′UTRs. Protein domains unique to SRSF7, which are absent from SRSF3, contribute to FIP1 recruitment. In contrast, SRSF3 promotes distal PAS (dPAS) usage and hence long 3′UTRs directly by counteracting SRSF7, but also indirectly by maintaining high levels of cleavage factor Im (CFIm) via alternative splicing. Upon SRSF3 depletion, CFIm levels decrease and 3′UTRs are shortened. The indirect SRSF3 targets are particularly sensitive to low CFIm levels, because here CFIm serves a dual function; it enhances dPAS and inhibits pPAS usage by binding immediately downstream and assembling unproductive cleavage complexes, which together promotes long 3′UTRs. Conclusions We demonstrate that SRSF3 and SRSF7 are direct modulators of pPAS usage and show how small differences in the domain architecture of SR proteins can confer opposite effects on pPAS regulation. Supplementary Information The online version contains supplementary material available at 10.1186/s13059-021-02298-y.
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Affiliation(s)
- Oliver Daniel Schwich
- Institute for Molecular Bio Science, Goethe University Frankfurt, Max-von-Laue-Str. 13, 60438, Frankfurt, Germany.,Buchmann Institute for Molecular Life Sciences, Goethe University Frankfurt, Max-von-Laue-Str. 15, 60438, Frankfurt, Germany
| | - Nicole Blümel
- Institute for Molecular Bio Science, Goethe University Frankfurt, Max-von-Laue-Str. 13, 60438, Frankfurt, Germany
| | - Mario Keller
- Buchmann Institute for Molecular Life Sciences, Goethe University Frankfurt, Max-von-Laue-Str. 15, 60438, Frankfurt, Germany.,Faculty of Biological Sciences, Goethe University Frankfurt, 60438, Frankfurt am Main, Germany
| | - Marius Wegener
- Institute for Molecular Bio Science, Goethe University Frankfurt, Max-von-Laue-Str. 13, 60438, Frankfurt, Germany.,Buchmann Institute for Molecular Life Sciences, Goethe University Frankfurt, Max-von-Laue-Str. 15, 60438, Frankfurt, Germany
| | - Samarth Thonta Setty
- Buchmann Institute for Molecular Life Sciences, Goethe University Frankfurt, Max-von-Laue-Str. 15, 60438, Frankfurt, Germany
| | - Melinda Elaine Brunstein
- Institute of Biochemistry II, Medical School, Goethe University Frankfurt, Sandhofstr. 2-4, 60528, Frankfurt am Main, Germany
| | - Ina Poser
- Max Planck Institute of Molecular Cell Biology and Genetics, Pfotenhauerstr. 108, 01307, Dresden, Germany
| | | | - Beatrix Suess
- Department of Biology, Technical University Darmstadt, Schnittspahnstr. 10, 64287, Darmstadt, Germany
| | - Christian Münch
- Institute of Biochemistry II, Medical School, Goethe University Frankfurt, Sandhofstr. 2-4, 60528, Frankfurt am Main, Germany
| | - François McNicoll
- Institute for Molecular Bio Science, Goethe University Frankfurt, Max-von-Laue-Str. 13, 60438, Frankfurt, Germany
| | - Kathi Zarnack
- Buchmann Institute for Molecular Life Sciences, Goethe University Frankfurt, Max-von-Laue-Str. 15, 60438, Frankfurt, Germany. .,Faculty of Biological Sciences, Goethe University Frankfurt, 60438, Frankfurt am Main, Germany.
| | - Michaela Müller-McNicoll
- Institute for Molecular Bio Science, Goethe University Frankfurt, Max-von-Laue-Str. 13, 60438, Frankfurt, Germany.
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3
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SRSF7 maintains its homeostasis through the expression of Split-ORFs and nuclear body assembly. Nat Struct Mol Biol 2020; 27:260-273. [PMID: 32123389 PMCID: PMC7096898 DOI: 10.1038/s41594-020-0385-9] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2019] [Accepted: 01/23/2020] [Indexed: 02/08/2023]
Abstract
SRSF7 is an essential RNA-binding protein whose misexpression promotes cancer. Here, we describe how SRSF7 maintains its protein homeostasis in murine P19 cells using an intricate negative feedback mechanism. SRSF7 binding to its premessenger RNA promotes inclusion of a poison cassette exon and transcript degradation via nonsense-mediated decay (NMD). However, elevated SRSF7 levels inhibit NMD and promote translation of two protein halves, termed Split-ORFs, from the bicistronic SRSF7-PCE transcript. The first half acts as dominant-negative isoform suppressing poison cassette exon inclusion and instead promoting the retention of flanking introns containing repeated SRSF7 binding sites. Massive SRSF7 binding to these sites and its oligomerization promote the assembly of large nuclear bodies, which sequester SRSF7 transcripts at their transcription site, preventing their export and restoring normal SRSF7 protein levels. We further show that hundreds of human and mouse NMD targets, especially RNA-binding proteins, encode potential Split-ORFs, some of which are expressed under specific cellular conditions.
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4
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Bäumer N, Rehkämper J, Appel N, Terheyden L, Hartmann W, Wardelmann E, Buchholz F, Müller-Tidow C, Berdel WE, Bäumer S. Downregulation of PIK3CA via antibody-esiRNA-complexes suppresses human xenograft tumor growth. PLoS One 2018; 13:e0200163. [PMID: 30001368 PMCID: PMC6042707 DOI: 10.1371/journal.pone.0200163] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2018] [Accepted: 06/20/2018] [Indexed: 11/25/2022] Open
Abstract
Precision cancer therapy requires on the one hand detailed knowledge about a tumor’s driver oncogenes and on the other hand an effective targeted therapy that specifically inhibits these oncogenes. While the determination of genomic landscape of a tumor has reached a very precise level, the respective therapy options are scarce. The application of small inhibitory (si) RNAs is a promising field of investigation. Here, we present the effective in vivo-treatment of colorectal cancer (CRC) xenograft tumors with antibody-complexed, endoribonuclease-prepared small inhibitory (esi)RNAs. We chose heterogeneous endoribonuclease-prepared siRNA pools (esiRNAs) against the frequently mutated genes PIK3CA and KRAS and coupled them to the anti-EGFR antibody cetuximab, which was internalized specifically into the tumor cells. esiRNA pools have been shown to exhibit superior specificity in target gene knockdown compared to classic siRNAs. We identified a significant decrease in tumor growth upon this treatment due to decreased tumor cell proliferation. The ex vivo-analysis of the xenograft CRC tumors revealed the expected downregulation of the intended direct targets PIK3CA and KRAS on protein level. Moreover, known downstream targets for EGFR signaling such as p-ERK, p-AKT, and c-MYC were decreased as well. We therefore propose the use of antibody-esiRNA complexes as a novel experimental treatment option against key components of the EGFR signaling cascade.
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Affiliation(s)
- Nicole Bäumer
- Department of Medicine A, Hematology/Oncology, University of Muenster, Muenster, Germany
| | - Jan Rehkämper
- Gerhard-Domagk Institute for Pathology, University of Muenster, Muenster, Germany
| | - Neele Appel
- Department of Medicine A, Hematology/Oncology, University of Muenster, Muenster, Germany
| | - Lisa Terheyden
- Department of Medicine A, Hematology/Oncology, University of Muenster, Muenster, Germany
| | - Wolfgang Hartmann
- Gerhard-Domagk Institute for Pathology, University of Muenster, Muenster, Germany
| | - Eva Wardelmann
- Gerhard-Domagk Institute for Pathology, University of Muenster, Muenster, Germany
| | - Frank Buchholz
- Universitäts KrebsCentrum (UCC), Medical Systems Biology, Medical Faculty, Technische Universität Dresden, Dresden, Germany
- German Cancer Research Center (DKFZ), Heidelberg and German Cancer Consortium (DKTK) Partner Site, Dresden, Germany
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
- National Center for Tumor Diseases (NCT), University Hospital Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany
| | - Carsten Müller-Tidow
- Department of Medicine A, Hematology/Oncology, University of Muenster, Muenster, Germany
- Department of Medicine V, University of Heidelberg, Heidelberg, Germany
| | - Wolfgang E. Berdel
- Department of Medicine A, Hematology/Oncology, University of Muenster, Muenster, Germany
| | - Sebastian Bäumer
- Department of Medicine A, Hematology/Oncology, University of Muenster, Muenster, Germany
- * E-mail:
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5
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Toyoda Y, Cattin CJ, Stewart MP, Poser I, Theis M, Kurzchalia TV, Buchholz F, Hyman AA, Müller DJ. Genome-scale single-cell mechanical phenotyping reveals disease-related genes involved in mitotic rounding. Nat Commun 2017; 8:1266. [PMID: 29097687 PMCID: PMC5668354 DOI: 10.1038/s41467-017-01147-6] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2017] [Accepted: 08/22/2017] [Indexed: 01/01/2023] Open
Abstract
To divide, most animal cells drastically change shape and round up against extracellular confinement. Mitotic cells facilitate this process by generating intracellular pressure, which the contractile actomyosin cortex directs into shape. Here, we introduce a genome-scale microcantilever- and RNAi-based approach to phenotype the contribution of > 1000 genes to the rounding of single mitotic cells against confinement. Our screen analyzes the rounding force, pressure and volume of mitotic cells and localizes selected proteins. We identify 49 genes relevant for mitotic rounding, a large portion of which have not previously been linked to mitosis or cell mechanics. Among these, depleting the endoplasmic reticulum-localized protein FAM134A impairs mitotic progression by affecting metaphase plate alignment and pressure generation by delocalizing cortical myosin II. Furthermore, silencing the DJ-1 gene uncovers a link between mitochondria-associated Parkinson's disease and mitotic pressure. We conclude that mechanical phenotyping is a powerful approach to study the mechanisms governing cell shape.
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Affiliation(s)
- Yusuke Toyoda
- Max Planck Institute of Molecular Cell Biology and Genetics, Pfotenhauerstrasse 108, 01307, Dresden, Germany.,Division of Cell Biology, Life Science Institute, Kurume University, Hyakunen-Kohen 1-1, Kurume, Fukuoka, 839-0864, Japan
| | - Cedric J Cattin
- Department of Biosystems Science and Engineering (D-BSSE), Eidgenössische Technische Hochschule (ETH) Zurich, Mattenstrasse 26, 4058, Basel, Switzerland
| | - Martin P Stewart
- Department of Biosystems Science and Engineering (D-BSSE), Eidgenössische Technische Hochschule (ETH) Zurich, Mattenstrasse 26, 4058, Basel, Switzerland.,Department of Chemical Engineering, Massachusetts Institute of Technology, 500 Main Street, Cambridge, MA, 02139-4307, USA.,The Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, 500 Main Street, Cambridge, MA, 02139-4307, USA
| | - Ina Poser
- Max Planck Institute of Molecular Cell Biology and Genetics, Pfotenhauerstrasse 108, 01307, Dresden, Germany
| | - Mirko Theis
- UCC, Medical System biology, Medical Faculty Carl Gustav Carus, University of Technology Dresden, Am Tatzberg 47/49, 01307, Dresden, Germany
| | - Teymuras V Kurzchalia
- Max Planck Institute of Molecular Cell Biology and Genetics, Pfotenhauerstrasse 108, 01307, Dresden, Germany
| | - Frank Buchholz
- Max Planck Institute of Molecular Cell Biology and Genetics, Pfotenhauerstrasse 108, 01307, Dresden, Germany.,UCC, Medical System biology, Medical Faculty Carl Gustav Carus, University of Technology Dresden, Am Tatzberg 47/49, 01307, Dresden, Germany
| | - Anthony A Hyman
- Max Planck Institute of Molecular Cell Biology and Genetics, Pfotenhauerstrasse 108, 01307, Dresden, Germany.
| | - Daniel J Müller
- Department of Biosystems Science and Engineering (D-BSSE), Eidgenössische Technische Hochschule (ETH) Zurich, Mattenstrasse 26, 4058, Basel, Switzerland.
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6
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Botti V, McNicoll F, Steiner MC, Richter FM, Solovyeva A, Wegener M, Schwich OD, Poser I, Zarnack K, Wittig I, Neugebauer KM, Müller-McNicoll M. Cellular differentiation state modulates the mRNA export activity of SR proteins. J Cell Biol 2017; 216:1993-2009. [PMID: 28592444 PMCID: PMC5496613 DOI: 10.1083/jcb.201610051] [Citation(s) in RCA: 49] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2016] [Revised: 03/22/2017] [Accepted: 04/24/2017] [Indexed: 01/22/2023] Open
Abstract
SR proteins connect nuclear pre-mRNA processing to mRNA export and translation. Botti et al. develop a quantitative nucleocytoplasmic shuttling assay and show that SR proteins are differentially modified and active in differentiated and pluripotent cells. SR proteins function in nuclear pre-mRNA processing, mRNA export, and translation. To investigate their cellular dynamics, we developed a quantitative assay, which detects differences in nucleocytoplasmic shuttling among seven canonical SR protein family members. As expected, SRSF2 and SRSF5 shuttle poorly in HeLa cells but surprisingly display considerable shuttling in pluripotent murine P19 cells. Combining individual-resolution cross-linking and immunoprecipitation (iCLIP) and mass spectrometry, we show that elevated arginine methylation of SRSF5 and lower phosphorylation levels of cobound SRSF2 enhance shuttling of SRSF5 in P19 cells by modulating protein–protein and protein–RNA interactions. Moreover, SRSF5 is bound to pluripotency-specific transcripts such as Lin28a and Pou5f1/Oct4 in the cytoplasm. SRSF5 depletion reduces and overexpression increases their cytoplasmic mRNA levels, suggesting that enhanced mRNA export by SRSF5 is required for the expression of pluripotency factors. Remarkably, neural differentiation of P19 cells leads to dramatically reduced SRSF5 shuttling. Our findings indicate that posttranslational modification of SR proteins underlies the regulation of their mRNA export activities and distinguishes pluripotent from differentiated cells.
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Affiliation(s)
- Valentina Botti
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT
| | - François McNicoll
- Cluster of Excellence Macromolecular Complexes, Institute of Cell Biology and Neuroscience, Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Michaela C Steiner
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
| | - Florian M Richter
- Functional Proteomics Group, Institute for Biochemistry I, Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Anfisa Solovyeva
- Cluster of Excellence Macromolecular Complexes, Institute of Cell Biology and Neuroscience, Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Marius Wegener
- Cluster of Excellence Macromolecular Complexes, Institute of Cell Biology and Neuroscience, Goethe University Frankfurt, Frankfurt am Main, Germany.,Buchmann Institute for Molecular Life Sciences, Frankfurt am Main, Germany
| | - Oliver D Schwich
- Cluster of Excellence Macromolecular Complexes, Institute of Cell Biology and Neuroscience, Goethe University Frankfurt, Frankfurt am Main, Germany.,Buchmann Institute for Molecular Life Sciences, Frankfurt am Main, Germany
| | - Ina Poser
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
| | - Kathi Zarnack
- Buchmann Institute for Molecular Life Sciences, Frankfurt am Main, Germany
| | - Ilka Wittig
- Functional Proteomics Group, Institute for Biochemistry I, Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Karla M Neugebauer
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT
| | - Michaela Müller-McNicoll
- Cluster of Excellence Macromolecular Complexes, Institute of Cell Biology and Neuroscience, Goethe University Frankfurt, Frankfurt am Main, Germany
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7
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Affiliation(s)
- Nicole Bäumer
- Deparment of Medicine A, Hematology and
Oncology, University Hospital Muenster, Albert-Schweitzer Campus 1, Muenster, DE 48149, Germany
| | - Wolfgang E. Berdel
- Deparment of Medicine A, Hematology and
Oncology, University Hospital Muenster, Albert-Schweitzer Campus 1, Muenster, DE 48149, Germany
| | - Sebastian Bäumer
- Deparment of Medicine A, Hematology and
Oncology, University Hospital Muenster, Albert-Schweitzer Campus 1, Muenster, DE 48149, Germany
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8
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Abstract
RNAi technologies enable the testing of gene function in a cell-type- and stage-specific manner in Drosophila. The development of genome-wide RNAi libraries has allowed expansion of this approach to the genome scale and supports identification of most genes required for a given process in a cell type of choice. However, a large-scale RNAi approach also harbors many potential pitfalls that can complicate interpretation of the results. Here, we summarize published screens and provide a guide on how to optimally plan and perform a large-scale, in vivo RNAi screen. We highlight the importance of assay design and give suggestions on how to optimize the assay conditions by testing positive and negative control genes. These genes are used to estimate false-negative and false-positive rates of the screen data. We discuss the planning and logistics of a large-scale screen in detail and suggest bioinformatics platforms to identify and select gene groups of interest for secondary assays. Finally, we review various options to confirm RNAi knock-down specificity and thus identify high confidence genes for more detailed case-by-case studies in the future.
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9
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Bäumer N, Appel N, Terheyden L, Buchholz F, Rossig C, Müller-Tidow C, Berdel WE, Bäumer S. Antibody-coupled siRNA as an efficient method for in vivo mRNA knockdown. Nat Protoc 2015; 11:22-36. [PMID: 26633129 DOI: 10.1038/nprot.2015.137] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Knockdown of genes by RNA interference (RNAi) in vitro requires methods of transfection or transduction, both of which have limited impact in vivo. As a virus-free approach, we chemically coupled cell surface receptors internalizing antibodies to the short interfering RNA (siRNA) carrier peptide protamine using the bispecific cross-linker sulfo-SMCC (sulfosuccinimidyl 4-(N-maleimidomethyl)cyclohexane-1-carboxylate). First, protamine was conjugated amino-terminally to sulfo-SMCC, and then this conjugate was coupled via cysteine residues to the IgG backbone to carry siRNA. This complex can efficiently find, bind and internalize into receptor-positive cells in vitro and in vivo, which can be checked by flow cytometry, fluorescence microscopy and western blotting. This method obtains results similar to those of siRNA targeting molecules engineered by genetic fusions between receptor-binding and siRNA carrier units, with the advantage of using readily available purified proteins without the need for engineering, expression and purification of respective constructs. The procedure for coupling the complex takes ∼ 2 d, and the functional assays take ∼ 2 weeks.
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Affiliation(s)
- Nicole Bäumer
- Department of Medicine A, Hematology and Oncology, University Hospital Muenster, Muenster, Germany
| | - Neele Appel
- Department of Medicine A, Hematology and Oncology, University Hospital Muenster, Muenster, Germany
| | - Lisa Terheyden
- Department of Medicine A, Hematology and Oncology, University Hospital Muenster, Muenster, Germany
| | - Frank Buchholz
- University Cancer Center (UCC), Medical Systems Biology, Medical Faculty, Technische Universität (TU) Dresden, Germany
| | - Claudia Rossig
- Department of Pediatric Hematology and Oncology, University Children's Hospital Muenster, Muenster, Germany
| | - Carsten Müller-Tidow
- Department of Medicine A, Hematology and Oncology, University Hospital Muenster, Muenster, Germany.,Department of Medicine IV, Hematology and Oncology, University Hospital Halle, Halle, Germany
| | - Wolfgang E Berdel
- Department of Medicine A, Hematology and Oncology, University Hospital Muenster, Muenster, Germany
| | - Sebastian Bäumer
- Department of Medicine A, Hematology and Oncology, University Hospital Muenster, Muenster, Germany
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10
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Systems Analyses Reveal Shared and Diverse Attributes of Oct4 Regulation in Pluripotent Cells. Cell Syst 2015; 1:141-51. [PMID: 27135800 DOI: 10.1016/j.cels.2015.08.002] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2015] [Revised: 07/07/2015] [Accepted: 08/04/2015] [Indexed: 11/23/2022]
Abstract
We combine a genome-scale RNAi screen in mouse epiblast stem cells (EpiSCs) with genetic interaction, protein localization, and "protein-level dependency" studies-a systematic technique that uncovers post-transcriptional regulation-to delineate the network of factors that control the expression of Oct4, a key regulator of pluripotency. Our data signify that there are similarities, but also fundamental differences in Oct4 regulation in EpiSCs versus embryonic stem cells (ESCs). Through multiparametric data analyses, we predict that Tox4 is associating with the Paf1C complex, which maintains cell identity in both cell types, and validate that this protein-protein interaction exists in ESCs and EpiSCs. We also identify numerous knockdowns that increase Oct4 expression in EpiSCs, indicating that, in stark contrast to ESCs, Oct4 is under active repressive control in EpiSCs. These studies provide a framework for better understanding pluripotency and for dissecting the molecular events that govern the transition from the pre-implantation to the post-implantation state.
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11
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Bäumer S, Bäumer N, Appel N, Terheyden L, Fremerey J, Schelhaas S, Wardelmann E, Buchholz F, Berdel WE, Müller-Tidow C. Antibody-mediated delivery of anti-KRAS-siRNA in vivo overcomes therapy resistance in colon cancer. Clin Cancer Res 2015; 21:1383-94. [PMID: 25589625 DOI: 10.1158/1078-0432.ccr-13-2017] [Citation(s) in RCA: 82] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
PURPOSE KRAS mutations are frequent driver mutations in multiple cancers. KRAS mutations also induce anti-EGFR antibody resistance in adenocarcinoma such as colon cancer. The aim of this study was to overcome anti-EGFR antibody resistance by coupling the antibody to KRAS-specific siRNA. EXPERIMENTAL DESIGN The anti-EGFR antibody was chemically coupled to siRNA. The resulting complex was tested for antibody binding efficiency, serum stability and ability to deliver siRNA to EGFR-expressing cells. Western blotting, viability, apoptosis, and colony formation assays were performed for efficacy evaluation in vitro. Furthermore, therapeutic activity of the antibody-KRAS-siRNA complexes was examined in in vivo xenograft mouse tumor models. RESULTS Antibody-siRNA complexes were targeted and internalized via the EGFR receptor. Upon internalization, target gene expression was strongly and specifically repressed, followed by a reduced proliferation and viability, and induced apoptosis of the cells in vitro. Clonogenic growth of mutant KRAS-bearing cells was suppressed by KRAS-siRNA-anti-EGFR antibody complexes. In xenograft mouse models, anti-EGFR antibody-KRAS-siRNA complexes significantly slowed tumor growth in anti-EGFR-resistant cells. CONCLUSIONS The coupling of siRNA against KRAS to anti-EGFR antibodies provides a novel therapy approach for KRAS-mutated EGFR-positive cancer cells in vitro and in vivo. These findings provide an innovative approach for cancer-specific siRNA application and for enhanced therapeutic potential of monoclonal antibody therapy and personalized treatment of cancer entities.
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Affiliation(s)
- Sebastian Bäumer
- Department of Medicine A, Hematology/Oncology, University of Muenster, Muenster, Germany.
| | - Nicole Bäumer
- Department of Medicine A, Hematology/Oncology, University of Muenster, Muenster, Germany
| | - Neele Appel
- Department of Medicine A, Hematology/Oncology, University of Muenster, Muenster, Germany
| | - Lisa Terheyden
- Department of Medicine A, Hematology/Oncology, University of Muenster, Muenster, Germany
| | - Julia Fremerey
- Department of Medicine A, Hematology/Oncology, University of Muenster, Muenster, Germany
| | - Sonja Schelhaas
- European Institute for Molecular Imaging (EIMI), University of Muenster, Muenster, Germany
| | - Eva Wardelmann
- Gerhard-Domagk Institute for Pathology, University of Muenster, Muenster, Germany
| | - Frank Buchholz
- UCC, Medical Systems Biology, Medical Faculty, TU Dresden, Dresden, Germany
| | - Wolfgang E Berdel
- Department of Medicine A, Hematology/Oncology, University of Muenster, Muenster, Germany
| | - Carsten Müller-Tidow
- Department of Medicine A, Hematology/Oncology, University of Muenster, Muenster, Germany. Department of Medicine IV, Hematology and Oncology, University of Halle, Halle, Germany.
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12
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Abstract
Targeted therapies in personalized medicine require the knowledge about the molecular changes within the patient that cause the disease. With the beginning of the new century, a plethora of new technologies became available to detect these changes and use this information as starting point for drug development. Next-generation genome sequencing and sophisticated genome-wide functional genomics' methods have led to a significant increase in the identification of novel drug target candidates and understanding of the relevance of these genomic and molecular changes for the diseases. As functional genomic tool for target identification, high-throughput gene silencing through RNA interference screening has become the established method. RNAi is discussed with its advantages and challenges in this chapter. Furthermore the potential of CRISPR/Cas9, a gene-editing method that has recently been adapted for use as functional screening tool, will be briefly reviewed.
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13
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Mohr SE, Smith JA, Shamu CE, Neumüller RA, Perrimon N. RNAi screening comes of age: improved techniques and complementary approaches. Nat Rev Mol Cell Biol 2014; 15:591-600. [PMID: 25145850 PMCID: PMC4204798 DOI: 10.1038/nrm3860] [Citation(s) in RCA: 231] [Impact Index Per Article: 23.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Gene silencing through sequence-specific targeting of mRNAs by RNAi has enabled genome-wide functional screens in cultured cells and in vivo in model organisms. These screens have resulted in the identification of new cellular pathways and potential drug targets. Considerable progress has been made to improve the quality of RNAi screen data through the development of new experimental and bioinformatics approaches. The recent availability of genome-editing strategies, such as the CRISPR (clustered regularly interspaced short palindromic repeats)-Cas9 system, when combined with RNAi, could lead to further improvements in screen data quality and follow-up experiments, thus promoting our understanding of gene function and gene regulatory networks.
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Affiliation(s)
- Stephanie E Mohr
- 1] Drosophila RNAi Screening Center, Harvard Medical School, Boston, Massachusetts MA 02115, USA. [2] Department of Genetics, Harvard Medical School, Boston, Massachusetts MA 02115, USA
| | - Jennifer A Smith
- ICCB-Longwood Screening Facility, Harvard Medical School, Boston, Massachusetts MA 02115, USA
| | - Caroline E Shamu
- ICCB-Longwood Screening Facility, Harvard Medical School, Boston, Massachusetts MA 02115, USA
| | - Ralph A Neumüller
- Department of Genetics, Harvard Medical School, Boston, Massachusetts MA 02115, USA
| | - Norbert Perrimon
- 1] Drosophila RNAi Screening Center, Harvard Medical School, Boston, Massachusetts MA 02115, USA. [2] Department of Genetics, Harvard Medical School, Boston, Massachusetts MA 02115, USA. [3] Howard Hughes Medical Institute, Boston, Massachusetts MA 02115, USA
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14
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Smith CL, Matheson TD, Trombly DJ, Sun X, Campeau E, Han X, Yates JR, Kaufman PD. A separable domain of the p150 subunit of human chromatin assembly factor-1 promotes protein and chromosome associations with nucleoli. Mol Biol Cell 2014; 25:2866-81. [PMID: 25057015 PMCID: PMC4161520 DOI: 10.1091/mbc.e14-05-1029] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Chromatin assembly factor-1 contains a separable domain unrelated to histone deposition, which provides a previously unrecognized ability to maintain nucleolar protein and chromosome associations. Chromatin assembly factor-1 (CAF-1) is a three-subunit protein complex conserved throughout eukaryotes that deposits histones during DNA synthesis. Here we present a novel role for the human p150 subunit in regulating nucleolar macromolecular interactions. Acute depletion of p150 causes redistribution of multiple nucleolar proteins and reduces nucleolar association with several repetitive element–containing loci. Of note, a point mutation in a SUMO-interacting motif (SIM) within p150 abolishes nucleolar associations, whereas PCNA or HP1 interaction sites within p150 are not required for these interactions. In addition, acute depletion of SUMO-2 or the SUMO E2 ligase Ubc9 reduces α-satellite DNA association with nucleoli. The nucleolar functions of p150 are separable from its interactions with the other subunits of the CAF-1 complex because an N-terminal fragment of p150 (p150N) that cannot interact with other CAF-1 subunits is sufficient for maintaining nucleolar chromosome and protein associations. Therefore these data define novel functions for a separable domain of the p150 protein, regulating protein and DNA interactions at the nucleolus.
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Affiliation(s)
- Corey L Smith
- Program in Gene Function and Expression, Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA 01605
| | - Timothy D Matheson
- Program in Gene Function and Expression, Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA 01605
| | - Daniel J Trombly
- Program in Gene Function and Expression, Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA 01605
| | - Xiaoming Sun
- Program in Gene Function and Expression, Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA 01605
| | - Eric Campeau
- Program in Gene Function and Expression, Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA 01605
| | - Xuemei Han
- Department of Chemical Physiology, Scripps Research Institute, La Jolla, CA 92037
| | - John R Yates
- Department of Chemical Physiology, Scripps Research Institute, La Jolla, CA 92037
| | - Paul D Kaufman
- Program in Gene Function and Expression, Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA 01605
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15
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Abstract
We recently invented a method to produce highly potent siRNAs in Escherichia coli, based on the serendipitous discovery that ectopic expression of p19, a plant viral siRNA-binding protein, stabilizes otherwise unstable bacterial siRNAs, which we named pro-siRNAs for prokaryotic siRNAs. We present a detailed protocol describing how to produce pro-siRNAs for efficiently knocking down any gene, beginning with the design of a pro-siRNA expression plasmid and ending with siRNA purification. This protocol uses one plasmid to co-express a recombinant His-tagged p19 protein and a long hairpin RNA containing sense and antisense sequences of the target gene. pro-siRNAs are isolated and purified using nickel beads and HPLC, using methods used to produce recombinant proteins. Once a pro-siRNA plasmid is obtained, production of purified pro-siRNAs takes a few days. The pro-siRNA technique provides a reliable and renewable source of siRNAs, and it can be implemented in any laboratory whose members are skilled in routine molecular biology techniques.
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