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Obino D, Maurin M, Dingli F, Loew D, Lescure A, Terriac E, Goudot C, Malbec O, Lankar D, Yuseff MI, Lennon-Duménil AM, Moreau HD. Medium-throughput image-based phenotypic siRNA screen to unveil the molecular basis of B cell polarization. Sci Data 2023; 10:401. [PMID: 37353541 PMCID: PMC10290135 DOI: 10.1038/s41597-023-02301-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2022] [Accepted: 06/12/2023] [Indexed: 06/25/2023] Open
Abstract
Cell polarity is an essential and highly conserved process governing cell function. Cell polarization is generally triggered by an external signal that induces the relocation of the centrosome, thus defining the polarity axis of the cell. Here, we took advantage of B cells as a model to study cell polarity and perform a medium-throughput siRNA-based imaging screen to identify new molecular regulators of polarization. We first identified candidates based on a quantitative proteomic analysis of proteins differentially associated with the centrosome of resting non-polarized and stimulated polarized B cells. We then targeted 233 candidates in a siRNA screen and identified hits regulating the polarization of the centrosome and/or lysosomes in B cells upon stimulation. Our dataset of proteomics, images, and polarity indexes provides a valuable source of information for a broad community of scientists interested in the molecular mechanisms regulating cell polarity.
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Affiliation(s)
- Dorian Obino
- Institut Curie, PSL Research University, Inserm U932, Immunity and Cancer, 75005, Paris, France.
| | - Mathieu Maurin
- Institut Curie, PSL Research University, Inserm U932, Immunity and Cancer, 75005, Paris, France
| | - Florent Dingli
- Institut Curie, PSL Research University, CurieCoreTech Mass Spectrometry Proteomics, 75005, Paris, France
| | - Damarys Loew
- Institut Curie, PSL Research University, CurieCoreTech Mass Spectrometry Proteomics, 75005, Paris, France
| | - Aurianne Lescure
- Institut Curie, PSL Research University, Translational Research Department, BioPhenics Platform, PICT-IBISA, Paris, France
| | - Emmanuel Terriac
- Institut Curie, PSL Research University, CNRS UMR144, Paris, France
| | - Christel Goudot
- Institut Curie, PSL Research University, Inserm U932, Immunity and Cancer, 75005, Paris, France
| | - Odile Malbec
- Institut Curie, PSL Research University, Inserm U932, Immunity and Cancer, 75005, Paris, France
| | - Danielle Lankar
- Institut Curie, PSL Research University, Inserm U932, Immunity and Cancer, 75005, Paris, France
| | - Maria-Isabel Yuseff
- Institut Curie, PSL Research University, Inserm U932, Immunity and Cancer, 75005, Paris, France
- Department of Cellular and Molecular Biology, Faculty of Sciences, Pontificia Universidad Católica de Chile, Santiago, Chile
| | | | - Hélène D Moreau
- Institut Curie, PSL Research University, Inserm U932, Immunity and Cancer, 75005, Paris, France.
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Ramos-Alvarez I, Lee L, Jensen RT. Cofilin activation in pancreatic acinar cells plays a pivotal convergent role for mediating CCK-stimulated enzyme secretion and growth. Front Physiol 2023; 14:1147572. [PMID: 37138671 PMCID: PMC10149936 DOI: 10.3389/fphys.2023.1147572] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2023] [Accepted: 04/05/2023] [Indexed: 05/05/2023] Open
Abstract
Introduction: The actin regulatory protein, cofilin plays a key signaling role in many cells for numerous cellular responses including in proliferation, development, motility, migration, secretion and growth. In the pancreas it is important in islet insulin secretion, growth of pancreatic cancer cells and in pancreatitis. However, there are no studies on its role or activation in pancreatic acinar cells. Methods: To address this question, we studied the ability of CCK to activate cofilin in pancreatic acinar cells, AR42J cells and CCK1-R transfected Panc-1 cells, the signaling cascades involved and its effect on enzyme secretion and MAPK activation, a key mediator of pancreatic growth. Results: CCK (0.3 and 100 nM), TPA, carbachol, Bombesin, secretin and VIP decreased phospho-cofilin (i.e., activate cofilin) and both phospho-kinetic and inhibitor studies of cofilin, LIM kinase (LIMK) and Slingshot Protein Phosphatase (SSH1) demonstrated these conventional activators of cofilin were not involved. Serine phosphatases inhibitors (calyculin A and okadaic acid), however inhibited CCK/TPA-cofilin activation. Studies of various CCK-activated signaling cascades showed activation of PKC/PKD, Src, PAK4, JNK, ROCK mediated cofilin activation, but not PI3K, p38, or MEK. Furthermore, using both siRNA and cofilin inhibitors, cofilin activation was shown to be essential for CCK-mediated enzyme secretion and MAPK activation. Conclusion: These results support the conclusion that cofilin activation plays a pivotal convergent role for various cell signaling cascades in CCK mediated growth/enzyme secretion in pancreatic acini.
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Affiliation(s)
- Irene Ramos-Alvarez
- Digestive Diseases Branch, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, United States
| | - Lingaku Lee
- Digestive Diseases Branch, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, United States
- National Kyushu Cancer Center, Department of Hepato-Biliary-Pancreatology, Fukuoka, Japan
| | - Robert T. Jensen
- Digestive Diseases Branch, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, United States
- *Correspondence: Robert T. Jensen,
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Kleefeldt JM, Pozarska A, Nardiello C, Pfeffer T, Vadász I, Herold S, Seeger W, Morty RE. Commercially available transfection reagents and negative control siRNA are not inert. Anal Biochem 2020; 606:113828. [PMID: 32745542 DOI: 10.1016/j.ab.2020.113828] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2020] [Revised: 06/10/2020] [Accepted: 06/12/2020] [Indexed: 01/17/2023]
Abstract
The transfection of synthetic small interfering (si)RNA into cultured cells forms the basis of studies that use RNA interference (commonly referred to as "gene knockdown") to study the impact of loss of gene or protein expression on a biological pathway or process. In these studies, mock transfections (with transfection reagents alone), and the use of synthetic negative control (apparently inert) siRNA are both essential negative controls. This report reveals that three widely-used transfection reagents (X-tremeGENE™, HiPerFect, and Lipofectamine® 2000) and five commercially-available control siRNA (from Ambion, Sigma, Santa Cruz, Cell Signaling Technology, and Qiagen) are not inert in cell-culture studies. Both transfection reagents and control siRNA perturbed steady-state mRNA and protein levels in primary mouse lung fibroblasts and in NIH/3T3 cells (a widely-used mouse embryonic fibroblast cell-line), using components of the canonical transforming growth factor-β signaling machinery as a model system. Furthermore, transfection reagents and control siRNA reduced the viability and proliferation of both lung fibroblasts and NIH/3T3 cells. These data collectively provide a cautionary note to investigators to carefully consider the impact of control interventions, such as mock transfections and control siRNA, in RNA interference studies with synthetic siRNA.
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Affiliation(s)
- Jan M Kleefeldt
- Department of Lung Development and Remodelling, Max Planck Institute for Heart and Lung Research, Bad Nauheim, Member of the German Center for Lung Research (DZL), Parkstrasse 1, 60231, Bad Nauheim, Germany; Department of Internal Medicine (Pulmonology), University of Giessen and Marburg Lung Center (UGMLC), Member of the German Center for Lung Research (DZL), Justus Liebig University, Aulweg 123, 35392, Giessen, Germany
| | - Agnieszka Pozarska
- Department of Lung Development and Remodelling, Max Planck Institute for Heart and Lung Research, Bad Nauheim, Member of the German Center for Lung Research (DZL), Parkstrasse 1, 60231, Bad Nauheim, Germany; Department of Internal Medicine (Pulmonology), University of Giessen and Marburg Lung Center (UGMLC), Member of the German Center for Lung Research (DZL), Justus Liebig University, Aulweg 123, 35392, Giessen, Germany
| | - Claudio Nardiello
- Department of Lung Development and Remodelling, Max Planck Institute for Heart and Lung Research, Bad Nauheim, Member of the German Center for Lung Research (DZL), Parkstrasse 1, 60231, Bad Nauheim, Germany; Department of Internal Medicine (Pulmonology), University of Giessen and Marburg Lung Center (UGMLC), Member of the German Center for Lung Research (DZL), Justus Liebig University, Aulweg 123, 35392, Giessen, Germany
| | - Tilman Pfeffer
- Department of Lung Development and Remodelling, Max Planck Institute for Heart and Lung Research, Bad Nauheim, Member of the German Center for Lung Research (DZL), Parkstrasse 1, 60231, Bad Nauheim, Germany
| | - István Vadász
- Department of Internal Medicine (Pulmonology), University of Giessen and Marburg Lung Center (UGMLC), Member of the German Center for Lung Research (DZL), Justus Liebig University, Aulweg 123, 35392, Giessen, Germany
| | - Susanne Herold
- Department of Internal Medicine (Pulmonology), University of Giessen and Marburg Lung Center (UGMLC), Member of the German Center for Lung Research (DZL), Justus Liebig University, Aulweg 123, 35392, Giessen, Germany
| | - Werner Seeger
- Department of Lung Development and Remodelling, Max Planck Institute for Heart and Lung Research, Bad Nauheim, Member of the German Center for Lung Research (DZL), Parkstrasse 1, 60231, Bad Nauheim, Germany; Department of Internal Medicine (Pulmonology), University of Giessen and Marburg Lung Center (UGMLC), Member of the German Center for Lung Research (DZL), Justus Liebig University, Aulweg 123, 35392, Giessen, Germany
| | - Rory E Morty
- Department of Lung Development and Remodelling, Max Planck Institute for Heart and Lung Research, Bad Nauheim, Member of the German Center for Lung Research (DZL), Parkstrasse 1, 60231, Bad Nauheim, Germany; Department of Internal Medicine (Pulmonology), University of Giessen and Marburg Lung Center (UGMLC), Member of the German Center for Lung Research (DZL), Justus Liebig University, Aulweg 123, 35392, Giessen, Germany.
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Hibbitts AJ, Ramsey JM, Barlow J, MacLoughlin R, Cryan SA. In Vitro and In Vivo Assessment of PEGylated PEI for Anti-IL-8/CxCL-1 siRNA Delivery to the Lungs. NANOMATERIALS 2020; 10:nano10071248. [PMID: 32605011 PMCID: PMC7407419 DOI: 10.3390/nano10071248] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/06/2020] [Revised: 06/19/2020] [Accepted: 06/24/2020] [Indexed: 12/16/2022]
Abstract
Inhalation offers a means of rapid, local delivery of siRNA to treat a range of autoimmune or inflammatory respiratory conditions. This work investigated the potential of a linear 10 kDa Poly(ethylene glycol) (PEG)-modified 25 kDa branched polyethyleneimine (PEI) (PEI-LPEG) to effectively deliver siRNA to airway epithelial cells. Following optimization with anti- glyceraldehyde 3-phosphate dehydrogenase (GAPDH) siRNA, PEI and PEI-LPEG anti-IL8 siRNA nanoparticles were assessed for efficacy using polarised Calu-3 human airway epithelial cells and a twin stage impinger (TSI) in vitro lung model. Studies were then advanced to an in vivo lipopolysaccharide (LPS)-stimulated rodent model of inflammation. In parallel, the suitability of the siRNA-loaded nanoparticles for nebulization using a vibrating mesh nebuliser was assessed. The siRNA nanoparticles were nebulised using an Aerogen® Pro vibrating mesh nebuliser and characterised for aerosol output, droplet size and fine particle fraction. Only PEI anti-IL8 siRNA nanoparticles were capable of significant levels of IL-8 knockdown in vitro in non-nebulised samples. However, on nebulization through a TSI, only PEI-PEG siRNA nanoparticles demonstrated significant decreases in gene and protein expression in polarised Calu-3 cells. In vivo, both anti-CXCL-1 (rat IL-8 homologue) nanoparticles demonstrated a decreased CXCL-1 gene expression in lung tissue, but this was non-significant. However, PEI anti-CXCL-1 siRNA-treated rats were found to have significantly less infiltrating macrophages in their bronchoalveolar lavage (BAL) fluid. Overall, the in vivo gene and protein inhibition findings indicated a result more reminiscent of the in vitro bolus delivery rather than the in vitro nebulization data. This work demonstrates the potential of nebulised PEI-PEG siRNA nanoparticles in modulating pulmonary inflammation and highlights the need to move towards more relevant in vitro and in vivo models for respiratory drug development.
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Affiliation(s)
- Alan J. Hibbitts
- School of Pharmacy & Biomolecular Sciences, Royal College of Surgeons in Ireland, Dublin D02 YN77, Ireland; (A.J.H.); (J.M.R.); (R.M.)
- Trinity Centre for Biomedical Engineering, Trinity College, Dublin D02 R590, Ireland
| | - Joanne M. Ramsey
- School of Pharmacy & Biomolecular Sciences, Royal College of Surgeons in Ireland, Dublin D02 YN77, Ireland; (A.J.H.); (J.M.R.); (R.M.)
| | - James Barlow
- Department of Chemistry, Royal College of Surgeons in Ireland, Dublin D02 YN77, Ireland;
| | - Ronan MacLoughlin
- School of Pharmacy & Biomolecular Sciences, Royal College of Surgeons in Ireland, Dublin D02 YN77, Ireland; (A.J.H.); (J.M.R.); (R.M.)
- School of Pharmacy and Pharmaceutical Sciences, Trinity College, Dublin D02 PN40, Ireland
- Aerogen Ltd. Galway Business Park, Galway H91 HE94, Ireland
| | - Sally-Ann Cryan
- School of Pharmacy & Biomolecular Sciences, Royal College of Surgeons in Ireland, Dublin D02 YN77, Ireland; (A.J.H.); (J.M.R.); (R.M.)
- Trinity Centre for Biomedical Engineering, Trinity College, Dublin D02 R590, Ireland
- Correspondence: ; Tel.: +353-14022741
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Collins M, Li Y, Bowser R. RBM45 associates with nuclear stress bodies and forms nuclear inclusions during chronic cellular stress and in neurodegenerative diseases. Acta Neuropathol Commun 2020; 8:91. [PMID: 32586379 PMCID: PMC7318465 DOI: 10.1186/s40478-020-00965-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2020] [Accepted: 06/11/2020] [Indexed: 12/12/2022] Open
Abstract
The RNA binding protein (RBP) RBM45 forms nuclear and cytoplasmic inclusions in neurons and glia in amyotrophic lateral sclerosis (ALS), frontotemporal lobar degeneration with TDP-43 proteinopathy (FTLD-TDP), and Alzheimer's disease (AD). The normal functions of RBM45 are poorly understood, as are the mechanisms by which it forms inclusions in disease. To better understand the normal and pathological functions of RBM45, we evaluated whether the protein functions via association with several membraneless organelles and whether such an association could promote the formation of nuclear RBM45 inclusions. Under basal conditions, RBM45 is diffusely distributed throughout the nucleus and does not localize to membraneless organelles, including nuclear speckles, Cajal bodies, or nuclear gems. During cellular stress, however, nuclear RBM45 undergoes a reversible, RNA-binding dependent incorporation into nuclear stress bodies (NSBs). Chronic stress leads to the persistent association of RBM45 with NSBs and the irreversible accumulation of nuclear RBM45 inclusions. We also quantified the cell type- and disease-specific patterns of RBM45 pathology in ALS, FTLD-TDP, and AD. RBM45 nuclear and cytoplasmic inclusions are found in both neurons and glia in ALS, FTLD-TDP, and AD but are absent in non-neurologic disease controls. Across neurodegenerative diseases, RBM45 nuclear inclusion pathology occurs more frequently than cytoplasmic RBM45 inclusion pathology and exhibits cell type-specific variation. Collectively, our results define new stress-associated functions of RBM45, a mechanism for nuclear RBM45 inclusion formation, a role for NSBs in the pathogenesis of ALS, FTLD-TDP, and AD, and further underscore the importance of protein self-association to both the normal and pathological functions of RBPs in these diseases.
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Abstract
Coxiella burnetii is a unique bacterial pathogen that replicates to high numbers in a lysosome-like intracellular niche. This study identified host proteins that contribute to the pathogen’s capacity to establish this niche and activate the Dot/Icm secretion system required for intracellular replication. Many host proteins were found to contribute to the establishment of C. burnetii virulence by aiding trafficking of the pathogen to the lysosome and creating the degradative lysosome environment. Pathogenic bacteria are able to sense and adapt to their environment by altering their gene expression profile. Here we demonstrated that C. burnetii detects specific amino acids present in the lysosome using a two-component system that up-regulates expression of genes required for Dot/Icm activity. Coxiella burnetii is an intracellular pathogen that replicates in a lysosome-like vacuole through activation of a Dot/Icm-type IVB secretion system and subsequent translocation of effectors that remodel the host cell. Here a genome-wide small interfering RNA screen and reporter assay were used to identify host proteins required for Dot/Icm effector translocation. Significant, and independently validated, hits demonstrated the importance of multiple protein families required for endocytic trafficking of the C. burnetii-containing vacuole to the lysosome. Further analysis demonstrated that the degradative activity of the lysosome created by proteases, such as TPP1, which are transported to the lysosome by receptors, such as M6PR and LRP1, are critical for C. burnetii virulence. Indeed, the C. burnetii PmrA/B regulon, responsible for transcriptional up-regulation of genes encoding the Dot/Icm apparatus and a subset of effectors, induced expression of a virulence-associated transcriptome in response to degradative products of the lysosome. Luciferase reporter strains, and subsequent RNA-sequencing analysis, demonstrated that particular amino acids activate the C. burnetii PmrA/B two-component system. This study has further enhanced our understanding of C. burnetii pathogenesis, the host–pathogen interactions that contribute to bacterial virulence, and the different environmental triggers pathogens can sense to facilitate virulence.
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Abstract
Functional genomics is the study of the function of genes on a genome-wide level. Reporter gene assays can be utilized in this context to dissect signaling cascades, find new drug targets, or decipher the function of gene expression. The genome-wide scale of these experiments necessitates a different approach toward science than traditional single hypothesis driven research. High-throughput experimentation requires large project teams, automation, and discrete validation of each step in the automation and assay process. The purpose of this chapter is to provide a general outline of a standard functional genomics project with a reporter gene assay as readout, give an overview of the methodologies employed and familiarize the reader with the subsequent data analysis. The advantages of such high throughput experimentation are speed, quantitative results, and insights into biology on a genome-wide scale all of which enable a more rapid progress of science.
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Affiliation(s)
- Genevieve Welch
- Department of Genomics, The Genomics Institute of the Novartis Research Foundation, San Diego, CA, USA
- Functional Genomics Screening Team, The Genomics Institute of the Novartis Research Foundation, San Diego, CA, USA
| | - Robert Damoiseaux
- Department of Molecular and Medical Pharmacology, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, USA
- California NanoSystems Institute, University of California Los Angeles, Los Angeles, CA, USA
- Johnsson Comprehensive Cancer Center, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, USA
| | - Loren Miraglia
- Department of Genomics, The Genomics Institute of the Novartis Research Foundation, San Diego, CA, USA.
- Functional Genomics Screening Team, The Genomics Institute of the Novartis Research Foundation, San Diego, CA, USA.
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Malcolm DW, Sorrells JE, Van Twisk D, Thakar J, Benoit DSW. Evaluating side effects of nanoparticle-mediated siRNA delivery to mesenchymal stem cells using next generation sequencing and enrichment analysis. Bioeng Transl Med 2016; 1:193-206. [PMID: 27981244 PMCID: PMC5125403 DOI: 10.1002/btm2.10035] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2016] [Revised: 09/06/2016] [Accepted: 09/13/2016] [Indexed: 12/11/2022] Open
Abstract
RNA interference has immense potential to modulate cell functions. However, effective delivery of small interfering RNA (siRNA) while avoiding deleterious side effects has proven challenging. This study investigates both intended and unintended effects of diblock copolymer nanoparticle (NP) delivery of siRNA delivery to human mesenchymal stem cells (hMSC). Specifically, siRNA delivery was investigated at a range of NP‐siRNA:hMSC ratios with a focus on the effects of NP‐siRNA treatment on hMSC functions. Additionally, next generation RNA sequencing (RNAseq) was used with enrichment analysis to observe side effects in hMSC gene expression. Results show NP‐siRNA delivery is negatively correlated with hMSC density. However, higher NP‐siRNA:hMSC ratios increased cytotoxicity and decreased metabolic activity. hMSC proliferation was largely unaffected by NP‐siRNA treatment, except for a threefold reduction in hMSCs seeded at 4,000 cells/cm2. Flow cytometry reveals that apoptosis is a function of NP‐siRNA treatment time and seeding density; ∼14% of the treated hMSCs seeded at 8,000 cells/cm2 were annexin V+‐siRNA+ 24 hr after treatment, while 11% of the treated population was annexin V+‐siRNA−. RNAseq shows that NP‐siRNA treatment results in transcriptomic changes in hMSCs, while pathway analysis shows upregulation of apoptosis signaling and downregulation of metabolism, cell cycle, and DNA replication pathways, as corroborated by apoptosis, metabolism, and proliferation assays. Additionally, multiple innate immune signaling pathways such as toll‐like receptor, RIG‐I‐like receptor, and nuclear factor‐κB signaling pathways are upregulated. Furthermore, and consistent with traditional siRNA immune activation, cytokine–cytokine receptor signaling was also upregulated. Overall, this study provides insight into NP‐siRNA:hMSC ratios that are favorable for siRNA delivery. Moreover, NP‐siRNA delivery results in side effects across the hMSC transcriptome that suggest activation of the innate immunity that could alter MSC functions associated with their therapeutic potential.
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Affiliation(s)
- Dominic W Malcolm
- Dept. of Biomedical Engineering University of Rochester Rochester NY 14627; Center for Musculoskeletal Research, University of Rochester Rochester NY14642
| | - Janet E Sorrells
- Dept. of Biomedical Engineering University of Rochester Rochester NY 14627
| | - Daniel Van Twisk
- Dept. of Microbiology and Immunology University of Rochester Rochester NY 14627
| | - Juilee Thakar
- Dept. of Microbiology and Immunology University of Rochester Rochester NY 14627; Dept. of Biostatistics and Computational Biology University of Rochester Rochester NY 14642
| | - Danielle S W Benoit
- Dept. of Biomedical Engineering University of Rochester Rochester NY 14627; Center for Musculoskeletal Research, University of Rochester Rochester NY 14642; Dept. of Chemical Engineering University of Rochester Rochester NY 14627
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Raof NA, Rajamani D, Chu HC, Gurav A, Johnson JM, LoGerfo FW, Pradhan-Nabzdyk L, Bhasin M. The effects of transfection reagent polyethyleneimine (PEI) and non-targeting control siRNAs on global gene expression in human aortic smooth muscle cells. BMC Genomics 2016; 17:20. [PMID: 26728506 PMCID: PMC4700750 DOI: 10.1186/s12864-015-2267-9] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2015] [Accepted: 12/01/2015] [Indexed: 12/21/2022] Open
Abstract
BACKGROUND RNA interference (RNAi) is a powerful platform utilized to target transcription of specific genes and downregulate the protein product. To achieve effective silencing, RNAi is usually applied to cells or tissue with a transfection reagent to enhance entry into cells. A commonly used control is the same transfection reagent plus a "noncoding RNAi". However, this does not control for the genomic response to the transfection reagent alone or in combination with the noncoding RNAi. These control effects while not directly targeting the gene in question may influence expression of other genes that in turn alter expression of the target. The current study was prompted by our work focused on prevention of vascular bypass graft failure and our experience with gene silencing in human aortic smooth muscle cells (HAoSMCs) where we suspected that off target effects through this mechanism might be substantial. We have used Next Generation Sequencing (NGS) technology and bioinformatics analysis to examine the genomic response of HAoSMCs to the transfection reagent alone (polyethyleneimine (PEI)) or in combination with commercially obtained control small interfering RNA (siRNAs) (Dharmacon and Invitrogen). RESULTS Compared to untreated cells, global gene expression of HAoSMcs after transfection either with PEI or in combination with control siRNAs displayed significant alterations in gene transcriptome after 24 h. HAoSMCs transfected by PEI alone revealed alterations of 213 genes mainly involved in inflammatory and immune responses. HAoSMCs transfected by PEI complexed with siRNA from either Dharmacon or Invitrogen showed substantial gene variation of 113 and 85 genes respectively. Transfection of cells with only PEI or with PEI and control siRNAs resulted in identification of 20 set of overlapping altered genes. Further, systems biology analysis revealed key master regulators in cells transfected with control siRNAs including the cytokine, Interleukin (IL)-1, transcription factor GATA Binding Protein (GATA)-4 and the methylation enzyme, Enhancer of zeste homolog 2 (EZH-2) a cytokine with an apical role in initiating the inflammatory response. CONCLUSIONS Significant off-target effects in HAoSMCs transfected with PEI alone or in combination with control siRNAs may lead to misleading conclusions concerning the effectiveness of a targeted siRNA strategy. The lack of structural information about transfection reagents and "non coding" siRNA is a hindrance in the development of siRNA based therapeutics.
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Affiliation(s)
- Nurazhani A Raof
- The Frank W. LoGerfo Division of Vascular and Endovascular Surgery, Beth Israel Deaconess Medical Center, Harvard Medical School, 330 Brookline Ave, Stoneman 8 M-10E, Boston, 02215, MA, USA.
| | - Deepa Rajamani
- Division of Interdisciplinary Medicine and Biotechnology, Genomics and Proteomics Center, Beth Israel Deaconess Medical Center, Harvard Medical School, 99 Brookline Avenue, Boston, MA, 02215, USA.
| | - Hsun-Chieh Chu
- The Frank W. LoGerfo Division of Vascular and Endovascular Surgery, Beth Israel Deaconess Medical Center, Harvard Medical School, 330 Brookline Ave, Stoneman 8 M-10E, Boston, 02215, MA, USA. .,Department of Medicine, National Yang-Ming University, School of Medicine, Taipei City, Taiwan.
| | - Aniket Gurav
- The Frank W. LoGerfo Division of Vascular and Endovascular Surgery, Beth Israel Deaconess Medical Center, Harvard Medical School, 330 Brookline Ave, Stoneman 8 M-10E, Boston, 02215, MA, USA.
| | - Joel M Johnson
- The Frank W. LoGerfo Division of Vascular and Endovascular Surgery, Beth Israel Deaconess Medical Center, Harvard Medical School, 330 Brookline Ave, Stoneman 8 M-10E, Boston, 02215, MA, USA.
| | - Frank W LoGerfo
- The Frank W. LoGerfo Division of Vascular and Endovascular Surgery, Beth Israel Deaconess Medical Center, Harvard Medical School, 330 Brookline Ave, Stoneman 8 M-10E, Boston, 02215, MA, USA.
| | - Leena Pradhan-Nabzdyk
- The Frank W. LoGerfo Division of Vascular and Endovascular Surgery, Beth Israel Deaconess Medical Center, Harvard Medical School, 330 Brookline Ave, Stoneman 8 M-10E, Boston, 02215, MA, USA.
| | - Manoj Bhasin
- Division of Interdisciplinary Medicine and Biotechnology, Genomics and Proteomics Center, Beth Israel Deaconess Medical Center, Harvard Medical School, 99 Brookline Avenue, Boston, MA, 02215, USA.
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Fennell M, Commisso C, Ramirez C, Garippa R, Bar-Sagi D. High-content, full genome siRNA screen for regulators of oncogenic HRAS-driven macropinocytosis. Assay Drug Dev Technol 2015; 13:347-55. [PMID: 26267765 PMCID: PMC4554932 DOI: 10.1089/adt.2015.660] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Uptake of nutrients, such as glucose and amino acids, is critical to support cell growth and is typically mediated by cell surface transporters. An alternative mechanism for the bulk uptake of nutrients from the extracellular space is macropinocytosis, a nonclathrin, and nonreceptor-mediated endocytic process, in which extracellular fluid is taken up into large intracellular vesicles called macropinosomes. Oncogenic transformation leads to the increased metabolic activity of tumor cells, and in the Ras-driven tumor part of this enhanced activity is the stimulation of macropinocytosis. To measure oncogene-dependent macropinocytosis, we used HeLa cells expressing oncogenic HRAS(G12D) driven from a Tet-regulated promoter. Upon oncogenic HRAS expression, the cells undergo metabolic changes that include the elevation of macropinocytosis. We detected macropinocytosis through the uptake of lysine-fixable tetramethyl rhodamine (TMR)-Dextran (70 kDa) from the cell media into nascent intracellular macropinosomes. These macropinosomes were quantified by image-based high-content analysis, with the size, intensity, and position of macropinosomes measured. Using this model system, we ran a full genome-wide siRNA screen (siGenome™; GE) to identify genes involved in controlling oncogenic HRAS-dependent macropinocytosis. Hits from the primary screen were confirmed with siRNA reagents from a different library (GE, OTP), which allowed us to mitigate potential off-target effects. Candidate genes from this screen include known regulators of macropinocytosis as well as novel targets.
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Affiliation(s)
- Myles Fennell
- RNAi and Gene Editing Core Facility, Memorial Sloan-Kettering Cancer Center, New York, New York
| | - Cosimo Commisso
- NCI-Designated Cancer Center Cell Death and Survival Networks Program, Sanford-Burnham Medical Research Institute, La Jolla, California
| | - Craig Ramirez
- Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, New York, New York
| | - Ralph Garippa
- RNAi and Gene Editing Core Facility, Memorial Sloan-Kettering Cancer Center, New York, New York
| | - Dafna Bar-Sagi
- Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, New York, New York
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Beppu LY, Anilkumar AA, Newbury RO, Dohil R, Broide DH, Aceves SS. TGF-β1-induced phospholamban expression alters esophageal smooth muscle cell contraction in patients with eosinophilic esophagitis. J Allergy Clin Immunol 2014; 134:1100-1107.e4. [PMID: 24835503 PMCID: PMC4231011 DOI: 10.1016/j.jaci.2014.04.004] [Citation(s) in RCA: 60] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2013] [Revised: 03/18/2014] [Accepted: 04/04/2014] [Indexed: 12/21/2022]
Abstract
BACKGROUND Eosinophilic esophagitis (EoE) is a chronic antigen-mediated disease characterized by esophageal eosinophilia, remodeling, and fibrosis. TGF-β1 is a central regulator of EoE remodeling and increases esophageal smooth muscle (ESM) cell contraction. OBJECTIVE In this study we aimed to understand the molecular mechanisms by which TGF-β1 could induce ESM cell contraction. METHODS We used primary human ESM cells and esophageal myofibroblasts (EMFs) to assess the mechanisms of TGF-β1-induced contraction. We analyzed the expression, phosphorylation, and function of phospholamban (PLN), a sarcoendoplasmic reticulum regulatory protein induced by TGF-β1. Expression of PLN, phospho-PLN, and its regulatory pathway was analyzed in the ESM of biopsy specimens from patients with EoE and control subjects. Gene silencing in EMFs from patients with EoE was used to understand the role of PLN in contraction. RESULTS TGF-β1 induced and phosphorylated PLN in primary human ESM cells and EMFs from patients with EoE. PLN and phospho-PLN levels were increased in smooth muscle from patients with EoE compared with that seen in smooth muscle from control subjects in vivo. PLN inhibition significantly diminished TGF-β1-induced EMF contraction in patients with EoE. PLN expression and ESM/EMF contraction depended on TGF-β receptor I signals. CONCLUSION We describe a previously unrecognized mechanism for ESM cell contraction that depends on TGF-β1, its receptors, and PLN. Because PLN levels are increased in smooth muscle from patients with EoE and PLN silencing diminishes contraction, we provide a novel potential mechanistic framework and therapeutic target for ESM dysfunction in patients with EoE.
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Affiliation(s)
- Lisa Y Beppu
- Division of Allergy and Immunology, University of California, San Diego, Calif; Department of Pediatrics, University of California, San Diego, Calif
| | - Arjun A Anilkumar
- Division of Allergy and Immunology, University of California, San Diego, Calif; Department of Medicine, University of California, San Diego, Calif
| | - Robert O Newbury
- Department of Pediatrics, University of California, San Diego, Calif; Division of Pathology, University of California, San Diego, Calif
| | - Ranjan Dohil
- Department of Pediatrics, University of California, San Diego, Calif; Division of Gastroenterology, University of California, San Diego, Calif
| | - David H Broide
- Division of Allergy and Immunology, University of California, San Diego, Calif; Department of Medicine, University of California, San Diego, Calif
| | - Seema S Aceves
- Division of Allergy and Immunology, University of California, San Diego, Calif; Department of Pediatrics, University of California, San Diego, Calif; Department of Medicine, University of California, San Diego, Calif.
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Type I interferon upregulates Bak and contributes to T cell loss during human immunodeficiency virus (HIV) infection. PLoS Pathog 2013; 9:e1003658. [PMID: 24130482 PMCID: PMC3795023 DOI: 10.1371/journal.ppat.1003658] [Citation(s) in RCA: 70] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2013] [Accepted: 08/12/2013] [Indexed: 11/19/2022] Open
Abstract
The role of Type I interferon (IFN) during pathogenic HIV and SIV infections remains unclear, with conflicting observations suggesting protective versus immunopathological effects. We therefore examined the effect of IFNα/β on T cell death and viremia in HIV infection. Ex vivo analysis of eight pro- and anti-apoptotic molecules in chronic HIV-1 infection revealed that pro-apoptotic Bak was increased in CD4+ T cells and correlated directly with sensitivity to CD95/Fas-mediated apoptosis and inversely with CD4+ T cell counts. Apoptosis sensitivity and Bak expression were primarily increased in effector memory T cells. Knockdown of Bak by RNA interference inhibited CD95/Fas-induced death of T cells from HIV-1-infected individuals. In HIV-1-infected patients, IFNα-stimulated gene expression correlated positively with ex vivo T cell Bak levels, CD95/Fas-mediated apoptosis and viremia and negatively with CD4+ T cell counts. In vitro IFNα/β stimulation enhanced Bak expression, CD95/Fas expression and CD95/Fas-mediated apoptosis in healthy donor T cells and induced death of HIV-specific CD8+ T cells from HIV-1-infected patients. HIV-1 in vitro sensitized T cells to CD95/Fas-induced apoptosis and this was Toll-like receptor (TLR)7/9- and Type I IFN-dependent. This sensitization by HIV-1 was due to an indirect effect on T cells, as it occurred in peripheral blood mononuclear cell cultures but not purified CD4+ T cells. Finally, peak IFNα levels and viral loads correlated negatively during acute SIV infection suggesting a potential antiviral effect, but positively during chronic SIV infection indicating that either the virus drives IFNα production or IFNα may facilitate loss of viral control. The above findings indicate stage-specific opposing effects of Type I IFNs during HIV-1 infection and suggest a novel mechanism by which these cytokines contribute to T cell depletion, dysregulation of cellular immunity and disease progression.
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Dicke T, Pali-Schöll I, Kaufmann A, Bauer S, Renz H, Garn H. Absence of unspecific innate immune cell activation by GATA-3-specific DNAzymes. Nucleic Acid Ther 2012; 22:117-26. [PMID: 22428550 DOI: 10.1089/nat.2011.0294] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023] Open
Abstract
DNAzymes of the 10-23 family represent an important class of antisense molecules with implications for therapeutic treatment of diseases. These molecules are single-stranded oligodeoxynucleotides combining the high specificity of oligonucleotide base pairing with an inherent RNA-cleaving enzymatic activity. However, like other oligonucleotide-based molecules these substances might exert so-called off-target effects, which have not been investigated so far for this molecule class. Therefore, the present study investigates putative off-target effects of DNAzymes on innate immune mechanisms using GATA-3-specific DNAzymes that have recently been developed as novel therapeutic approach for the treatment of allergic diseases including allergic asthma. The conserved catalytic domain of 10-23 DNAzymes contains a CpG motif that may stimulate innate immune cells via Toll-like receptor 9 (TLR-9). Therefore, potential TLR-9-mediated as well as TLR-9 independent cell activation was investigated using TLR-9-transfected HEK293 cells, macrophage cell lines and primary innate immune cells. Furthermore, putative effects of GATA-3-specific DNAzymes on the activation of neutrophil granulocytes and degranulation of mast cells/basophils were analyzed. In summary, no innate immune cell-stimulating activities of the tested DNAzymes were observed in any of the systems. Consequently, use of GATA-3-specific DNAzymes may represent a novel and highly specific approach for the treatment of allergic diseases.
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Affiliation(s)
- Tanja Dicke
- Sterna Biologicals GmbH & Co. KG, Marburg, Germany
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Control of transient, resurgent, and persistent current by open-channel block by Na channel beta4 in cultured cerebellar granule neurons. Proc Natl Acad Sci U S A 2010; 107:12357-62. [PMID: 20566860 DOI: 10.1073/pnas.1005633107] [Citation(s) in RCA: 98] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Voltage-gated Na channels in several classes of neurons, including cells of the cerebellum, are subject to an open-channel block and unblock by an endogenous protein. The Na(V)beta4 (Scn4b) subunit is a candidate blocking protein because a free peptide from its cytoplasmic tail, the beta4 peptide, can block open Na channels and induce resurgent current as channels unblock upon repolarization. In heterologous expression systems, however, Na(V)beta4 fails to produce resurgent current. We therefore tested the necessity of this subunit in generating resurgent current, as well as its influence on Na channel gating and action potential firing, by studying cultured cerebellar granule neurons treated with siRNA targeted against Scn4b. Knockdown of Scn4b, confirmed with quantitative RT-PCR, led to five electrophysiological phenotypes: a loss of resurgent current, a reduction of persistent current, a hyperpolarized half-inactivation voltage of transient current, a higher rheobase, and a decrease in repetitive firing. All disruptions of Na currents and firing were rescued by the beta4 peptide. The simplest interpretation is that Na(V)beta4 itself blocks Na channels of granule cells, making this subunit the first blocking protein that is responsible for resurgent current. The results also demonstrate that a known open-channel blocking peptide not only permits a rapid recovery from nonconducting states upon repolarization from positive voltages but also increases Na channel availability at negative potentials by antagonizing fast inactivation. Thus, Na(V)beta4 expression determines multiple aspects of Na channel gating, thereby regulating excitability in cultured cerebellar granule cells.
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