1
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Botta S, de Prisco N, Chemiakine A, Brandt V, Cabaj M, Patel P, Doron-Mandel E, Treadway CJ, Jovanovic M, Brown NG, Soni RK, Gennarino VA. Dosage sensitivity to Pumilio1 variants in the mouse brain reflects distinct molecular mechanisms. EMBO J 2023:e112721. [PMID: 37070548 DOI: 10.15252/embj.2022112721] [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] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2022] [Revised: 03/01/2023] [Accepted: 03/14/2023] [Indexed: 04/19/2023] Open
Abstract
Different mutations in the RNA-binding protein Pumilio1 (PUM1) cause divergent phenotypes whose severity tracks with dosage: a mutation that reduces PUM1 levels by 25% causes late-onset ataxia, whereas haploinsufficiency causes developmental delay and seizures. Yet PUM1 targets are derepressed to equal degrees in both cases, and the more severe mutation does not hinder PUM1's RNA-binding ability. We therefore considered the possibility that the severe mutation might disrupt PUM1 interactions, and identified PUM1 interactors in the murine brain. We find that mild PUM1 loss derepresses PUM1-specific targets, but the severe mutation disrupts interactions with several RNA-binding proteins and the regulation of their targets. In patient-derived cell lines, restoring PUM1 levels restores these interactors and their targets to normal levels. Our results demonstrate that dosage sensitivity does not always signify a linear relationship with protein abundance but can involve distinct mechanisms. We propose that to understand the functions of RNA-binding proteins in a physiological context will require studying their interactions as well as their targets.
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Affiliation(s)
- Salvatore Botta
- Department of Genetics and Development, Columbia University Irving Medical Center, New York, NY, USA
- Department of Translational Medical Science, University of Campania Luigi Vanvitelli, Caserta, Italy
| | - Nicola de Prisco
- Department of Genetics and Development, Columbia University Irving Medical Center, New York, NY, USA
| | - Alexei Chemiakine
- Department of Genetics and Development, Columbia University Irving Medical Center, New York, NY, USA
| | - Vicky Brandt
- Department of Genetics and Development, Columbia University Irving Medical Center, New York, NY, USA
| | - Maximilian Cabaj
- Department of Genetics and Development, Columbia University Irving Medical Center, New York, NY, USA
| | - Purvi Patel
- Proteomics and Macromolecular Crystallography Shared Resource, Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY, USA
| | - Ella Doron-Mandel
- Department of Biological Sciences, Columbia University, New York, NY, USA
| | - Colton J Treadway
- Department of Pharmacology and Lineberger Comprehensive Cancer Center, University of North Carolina School of Medicine, Chapel Hill, NC, USA
| | - Marko Jovanovic
- Department of Biological Sciences, Columbia University, New York, NY, USA
| | - Nicholas G Brown
- Department of Pharmacology and Lineberger Comprehensive Cancer Center, University of North Carolina School of Medicine, Chapel Hill, NC, USA
| | - Rajesh K Soni
- Proteomics and Macromolecular Crystallography Shared Resource, Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY, USA
| | - Vincenzo A Gennarino
- Department of Genetics and Development, Columbia University Irving Medical Center, New York, NY, USA
- Departments of Neurology, Columbia University Irving Medical Center, New York, NY, USA
- Columbia Stem Cell Initiative, Columbia University Irving Medical Center, New York, NY, USA
- Initiative for Columbia Ataxia and Tremor, Columbia University Irving Medical Center, New York, NY, USA
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2
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de Prisco N, Ford C, Elrod ND, Lee W, Tang LC, Huang KL, Lin A, Ji P, Jonnakuti VS, Boyle L, Cabaj M, Botta S, Õunap K, Reinson K, Wojcik MH, Rosenfeld JA, Bi W, Tveten K, Prescott T, Gerstner T, Schroeder A, Fong CT, George-Abraham JK, Buchanan CA, Hanson-Khan A, Bernstein JA, Nella AA, Chung WK, Brandt V, Jovanovic M, Targoff KL, Yalamanchili HK, Wagner EJ, Gennarino VA. Alternative polyadenylation alters protein dosage by switching between intronic and 3'UTR sites. Sci Adv 2023; 9:eade4814. [PMID: 36800428 PMCID: PMC9937581 DOI: 10.1126/sciadv.ade4814] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/18/2022] [Accepted: 01/19/2023] [Indexed: 06/18/2023]
Abstract
Alternative polyadenylation (APA) creates distinct transcripts from the same gene by cleaving the pre-mRNA at poly(A) sites that can lie within the 3' untranslated region (3'UTR), introns, or exons. Most studies focus on APA within the 3'UTR; however, here, we show that CPSF6 insufficiency alters protein levels and causes a developmental syndrome by deregulating APA throughout the transcript. In neonatal humans and zebrafish larvae, CPSF6 insufficiency shifts poly(A) site usage between the 3'UTR and internal sites in a pathway-specific manner. Genes associated with neuronal function undergo mostly intronic APA, reducing their expression, while genes associated with heart and skeletal function mostly undergo 3'UTR APA and are up-regulated. This suggests that, under healthy conditions, cells toggle between internal and 3'UTR APA to modulate protein expression.
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Affiliation(s)
- Nicola de Prisco
- Department of Genetics and Development, Columbia University Irving Medical Center, New York, NY, USA
- Columbia Stem Cell Initiative, Columbia University Irving Medical Center, New York, NY, USA
| | - Caitlin Ford
- Department of Genetics and Development, Columbia University Irving Medical Center, New York, NY, USA
- Department of Pediatrics, College of Physicians and Surgeons, Columbia University Irving Medical Center, New York, NY, USA
| | - Nathan D. Elrod
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch at Galveston, Galveston, TX, USA
| | - Winston Lee
- Department of Genetics and Development, Columbia University Irving Medical Center, New York, NY, USA
- Department Ophthalmology, Columbia University Irving Medical Center, New York, NY, USA
| | - Lauren C. Tang
- Department of Biological Sciences, Columbia University, New York, NY, USA
| | - Kai-Lieh Huang
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch at Galveston, Galveston, TX, USA
- Department of Biochemistry and Biophysics, University of Rochester School of Medicine and Dentistry, Rochester, NY, USA
| | - Ai Lin
- Department of Etiology and Carcinogenesis, National Cancer Center/National Clinical Research Center/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, WC67+HC Dongcheng, Beijing, China
| | - Ping Ji
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch at Galveston, Galveston, TX, USA
| | - Venkata S. Jonnakuti
- Department of Pediatrics, Baylor College of Medicine and Texas Children’s Hospital, Houston, TX, USA
- Jan and Dan Duncan Neurological Research Institute, Texas Children’s Hospital, Houston, TX, USA
- Program in Quantitative and Computational Biology, Baylor College of Medicine, Houston, TX, USA
- Medical Scientist Training Program, Baylor College of Medicine, Houston, TX, USA
| | - Lia Boyle
- Department of Genetics and Development, Columbia University Irving Medical Center, New York, NY, USA
- Department of Pediatrics, College of Physicians and Surgeons, Columbia University Irving Medical Center, New York, NY, USA
| | - Maximilian Cabaj
- Department of Genetics and Development, Columbia University Irving Medical Center, New York, NY, USA
| | - Salvatore Botta
- Department of Genetics and Development, Columbia University Irving Medical Center, New York, NY, USA
- Department of Translational Medical Science, University of Campania Luigi Vanvitelli, Caserta, Italy
| | - Katrin Õunap
- Department of Clinical Genetics, Genetics and Personalized Medicine Clinic, Tartu University Hospital, Tartu, Estonia
- Institute of Clinical Medicine, University of Tartu, Tartu, Estonia
| | - Karit Reinson
- Department of Clinical Genetics, Genetics and Personalized Medicine Clinic, Tartu University Hospital, Tartu, Estonia
- Institute of Clinical Medicine, University of Tartu, Tartu, Estonia
| | - Monica H. Wojcik
- Broad Center for Mendelian Genomics, Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Jill A. Rosenfeld
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
- Baylor Genetics Laboratories, Houston, TX, USA
| | - Weimin Bi
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
- Baylor Genetics Laboratories, Houston, TX, USA
| | - Kristian Tveten
- Department of Medical Genetics, Telemark Hospital Trust, 3710 Skien, Norway
| | - Trine Prescott
- Department of Medical Genetics, Telemark Hospital Trust, 3710 Skien, Norway
| | - Thorsten Gerstner
- Department of Child Neurology and Rehabilitation and Department of Pediatrics, Hospital of Southern Norway, Arendal, Norway
| | - Audrey Schroeder
- Division of Medical Genetics, University of Rochester Medical Center, Rochester, NY, USA
| | - Chin-To Fong
- Department of Pediatrics and of Medicine, University of Rochester Medical Center, Rochester, NY, USA
| | - Jaya K. George-Abraham
- Dell Children’s Medical Group, Austin, TX, USA
- Department of Pediatrics, The University of Texas at Austin Dell Medical School, Austin, TX, USA
| | | | - Andrea Hanson-Khan
- Department of Pediatrics, Division of Medical Genetics, Stanford School of Medicine, Palo Alto, CA, USA
- Department of Genetics, Stanford School of Medicine, Palo Alto, CA, USA
| | - Jonathan A. Bernstein
- Department of Pediatrics, Division of Medical Genetics, Stanford School of Medicine, Palo Alto, CA, USA
| | - Aikaterini A. Nella
- Jan and Dan Duncan Neurological Research Institute, Texas Children’s Hospital, Houston, TX, USA
| | - Wendy K. Chung
- Department of Pediatrics, College of Physicians and Surgeons, Columbia University Irving Medical Center, New York, NY, USA
- Department of Medicine, Columbia University Irving Medical Center, New York, NY, USA
| | - Vicky Brandt
- Department of Genetics and Development, Columbia University Irving Medical Center, New York, NY, USA
| | - Marko Jovanovic
- Department of Biological Sciences, Columbia University, New York, NY, USA
| | - Kimara L. Targoff
- Columbia Stem Cell Initiative, Columbia University Irving Medical Center, New York, NY, USA
- Department of Pediatrics, College of Physicians and Surgeons, Columbia University Irving Medical Center, New York, NY, USA
| | - Hari Krishna Yalamanchili
- Jan and Dan Duncan Neurological Research Institute, Texas Children’s Hospital, Houston, TX, USA
- USDA/ARS Children’s Nutrition Research Center, Department of Pediatrics, Baylor College of Medicine, Houston, TX, USA
| | - Eric J. Wagner
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch at Galveston, Galveston, TX, USA
- Department of Biochemistry and Biophysics, University of Rochester School of Medicine and Dentistry, Rochester, NY, USA
| | - Vincenzo A. Gennarino
- Department of Genetics and Development, Columbia University Irving Medical Center, New York, NY, USA
- Columbia Stem Cell Initiative, Columbia University Irving Medical Center, New York, NY, USA
- Department of Pediatrics, College of Physicians and Surgeons, Columbia University Irving Medical Center, New York, NY, USA
- Department of Neurology, Columbia University Irving Medical Center, New York, NY, USA
- Initiative for Columbia Ataxia and Tremor, Columbia University Irving Medical Center, New York, NY, USA
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Lee W, de Prisco N, Gennarino VA, Buttery S. How to expand the method details in your Cell Press paper with step-by-step STAR Protocols. STAR Protoc 2022; 3:101550. [PMID: 35809237 PMCID: PMC9284439 DOI: 10.1016/j.xpro.2022.101550] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022] Open
Abstract
Publishing a primary research article is typically the result of a collaborative effort between a variety of researchers across differing career stages. STAR Protocols can complement a research article and empower authors to share the expertise they contributed to the larger study. In this Backstory, we interview members of the Gennarino lab, who published a Cell paper and four protocols, covering bioinformatics, culturing of patient-derived cell lines, neuroimaging from mouse brain sections and primary neurons, and mouse seizure recordings. For more information on the protocols related to this backstory, please refer to (Gennarino et al., 2018).
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Affiliation(s)
- Winston Lee
- Department of Genetics & Development, Columbia University Irving Medical Center, New York, NY, USA; Department Ophthalmology, Columbia University Irving Medical Center, New York, NY, USA
| | - Nicola de Prisco
- Department of Genetics & Development, Columbia University Irving Medical Center, New York, NY, USA
| | - Vincenzo A Gennarino
- Department of Genetics & Development, Columbia University Irving Medical Center, New York, NY, USA; Department of Pediatrics, College of Physicians & Surgeons, Columbia University Irving Medical Center, New York, NY, USA; Columbia Stem Cell Initiative, Columbia University Irving Medical Center, New York, NY, USA; Department of Neurology, Columbia University Irving Medical Center, New York, NY, USA; Initiative for Columbia Ataxia and Tremor, Columbia University Irving Medical Center, New York, NY, USA
| | - Shawnna Buttery
- Lead Editor, STAR Protocols, Cell Press, Cambridge, MA 02139, USA.
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4
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de Prisco N, Chemiakine A, Lee W, Botta S, Gennarino VA. Protocol to assess the effect of disease-driving variants on mouse brain morphology and primary hippocampal neurons. STAR Protoc 2022; 3:101244. [PMID: 35310074 PMCID: PMC8931472 DOI: 10.1016/j.xpro.2022.101244] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
Genetic variants that affect neurological function will often produce changes visible at the level of gross morphology, either of the whole brain or of specific neuronal types. Here we describe how to perfuse and dissect the brain in preparation for Nissl staining. Then we outline steps for culturing mouse primary hippocampal neurons to evaluate dendritic arborization (Sholl analysis). For complete details on the use and execution of this protocol, please refer to Gennarino et al. (2018).
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Affiliation(s)
- Nicola de Prisco
- Department of Genetics and Development, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Alexei Chemiakine
- Department of Genetics and Development, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Winston Lee
- Department of Genetics and Development, Columbia University Irving Medical Center, New York, NY 10032, USA
- Department of Ophthalmology, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Salvatore Botta
- Department of Genetics and Development, Columbia University Irving Medical Center, New York, NY 10032, USA
- Department of Translational Medical Science, University of Campania Luigi Vanvitelli, 81100 Caserta, Italy
| | - Vincenzo A. Gennarino
- Department of Genetics and Development, Columbia University Irving Medical Center, New York, NY 10032, USA
- Departments of Pediatrics and Neurology, Columbia University Irving Medical Center, New York, NY 10032, USA
- Columbia Stem Cell Initiative, Columbia University Irving Medical Center, New York, NY 10032, USA
- Initiative for Columbia Ataxia and Tremor, Columbia University Irving Medical Center, New York, NY 10032, USA
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5
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Abstract
Quantifying differences in the amount of protein and mRNA caused by missense mutations in a gene of interest can be challenging, especially when using patient-derived primary cells, which are intrinsically variable. In this protocol, we describe how to culture patient-derived lymphoblast and fibroblast cell lines for later mRNA and protein quantification. We also describe the steps to examine variants of PUM1 in HEK293T cells, but the protocol can be applied to other proteins of interest. For complete details on the use and execution of this protocol, please refer to Gennarino et al. (2018).
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Affiliation(s)
- Nicola de Prisco
- Department of Genetics and Development, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Salvatore Botta
- Department of Genetics and Development, Columbia University Irving Medical Center, New York, NY 10032, USA
- Department of Translational Medical Science, University of Campania Luigi Vanvitelli, Caserta, 81100, Italy
| | - Winston Lee
- Department of Genetics and Development, Columbia University Irving Medical Center, New York, NY 10032, USA
- Department of Ophthalmology, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Sarallah Rezazadeh
- Department of Genetics and Development, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Alexei Chemiakine
- Department of Genetics and Development, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Vincenzo A. Gennarino
- Department of Genetics and Development, Columbia University Irving Medical Center, New York, NY 10032, USA
- Departments of Pediatrics and Neurology, Columbia University Irving Medical Center, New York, NY 10032, USA
- Columbia Stem Cell Initiative, Columbia University Irving Medical Center, New York, NY 10032, USA
- Initiative for Columbia Ataxia and Tremor, Columbia University Irving Medical Center, New York, NY 10032, USA
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Abstract
Identifying a disease gene and determining its causality in patients can be challenging. Here, we present an approach to predicting the pathogenicity of deletions and missense variants for an autosomal dominant gene. We provide online resources for identifying patients and determining constraint metrics to isolate the causal gene among several candidates encompassed in a shared region of deletion. We also provide instructions for optimizing functional annotation programs that may be otherwise inaccessible to a nonexpert or novice in computational approaches. For complete details on the use and execution of this protocol, please refer to Gennarino et al. (2018).
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Affiliation(s)
- Winston Lee
- Department of Genetics and Development, Columbia University Irving Medical Center, New York, NY 10032, USA
- Department of Ophthalmology, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Nicola de Prisco
- Department of Genetics and Development, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Vincenzo A. Gennarino
- Department of Genetics and Development, Columbia University Irving Medical Center, New York, NY 10032, USA
- Departments of Pediatrics and Neurology, Columbia University Irving Medical Center, New York, NY 10032, USA
- Columbia Stem Cell Initiative, Columbia University Irving Medical Center, New York, NY 10032, USA
- Initiative for Columbia Ataxia and Tremor, Columbia University Irving Medical Center, New York, NY 10032, USA
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7
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Matrood S, de Prisco N, Wissniowski TT, Wiese D, Jabari S, Griesmann H, Wanzel M, Stiewe T, Neureiter D, Klieser E, Mintziras I, Buchholz M, Bartsch DK, Gennarino VA, Di Fazio P. Modulation of Pancreatic Neuroendocrine Neoplastic Cell Fate by Autophagy-Mediated Death. Neuroendocrinology 2021; 111:965-985. [PMID: 33108790 DOI: 10.1159/000512567] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/28/2020] [Accepted: 10/02/2020] [Indexed: 02/05/2023]
Abstract
INTRODUCTION Autophagic cell death in cancer cells can be mediated by inhibition of deacetylases. Although extensive studies have focused on the autophagic process in cancer, little is known about the role of autophagy in degrading cytosolic and nuclear components of pancreatic neuroendocrine neoplastic (pNEN) cells leading to cell death, thus improving the therapy of patients affected by pNEN. METHODS 2D and 3D human pNEN and pancreatic stellate cells were treated with panobinostat and bafilomycin. Autophagy markers were detected by RT-qPCR, immunofluorescence, and Western blot. Autophagosomes were detected by electron microscopy and their maturation by real-time fluorescence of LC3B stable transfected cells. ChIP was performed at the cAMP responsive element. Immunofluorescence was performed in murine pancreatic tissue. RESULTS We observed that pan-deacetylase inhibitor panobinostat treatment causes autophagic cell death in pNEN cells. We also found that although AMPK-α phosphorylation is counterbalanced by phosphorylated AKT, it is not capable to inhibiting autophagic cell death. However, the binding activity of the cAMP responsive element is prompted by panobinostat. Although autophagy inhibition prevented autophagosome synthesis, maturation, and cell death, panobinostat treatment induced the accumulation of mature autophagosomes in the cytosol and the nucleus, leading to disruption of the organelles, cellular digestion, and decay. Observation of autophagosome membrane proteins Beclin1 and LC3B aggregation in murine pancreatic islets indicates that autophagy restoration may also lead to autophagosome aggregation in murine insulinoma cells. A basal low expression of autophagy markers was detectable in patients affected by pNEN, and, interestingly, the expression of these markers was significantly lower in metastatic pNEN. DISCUSSION/CONCLUSION Our study highlights that the autophagy functional restoration and prolongation of this catabolic process, mediated by inhibition of deacetylase, is responsible for the reduction of pNEN cells. Prompting of autophagy cell death could be a promising strategy for the therapy of pNEN.
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Affiliation(s)
- Sami Matrood
- Department of Visceral Thoracic and Vascular Surgery, Philipps University Marburg, Marburg, Germany
| | - Nicola de Prisco
- Departments of Genetics and Development, Pediatrics and Neurology, Columbia University Irving Medical Center, New York, New York, USA
- Columbia Stem Cell Initiative, Columbia University Irving Medical Center, New York, New York, USA
| | | | - Dominik Wiese
- Department of Visceral Thoracic and Vascular Surgery, Philipps University Marburg, Marburg, Germany
| | - Samir Jabari
- Institute of Anatomy I, University of Erlangen-Nuremberg, Erlangen, Germany
| | - Heidi Griesmann
- Department of Internal Medicine I, University Hospital Halle (Saale), Halle (Saale), Germany
| | - Michael Wanzel
- Institute for Molecular Oncology, Member of the German Center for Lung Research, Philipps University Marburg, Marburg, Germany
| | - Thorsten Stiewe
- Institute for Molecular Oncology, Member of the German Center for Lung Research, Philipps University Marburg, Marburg, Germany
| | - Daniel Neureiter
- Institute of Pathology, Paracelsus Medical University/Salzburger Landeskliniken (SALK), Salzburg, Austria
| | - Eckhard Klieser
- Institute of Pathology, Paracelsus Medical University/Salzburger Landeskliniken (SALK), Salzburg, Austria
| | - Ioannis Mintziras
- Department of Visceral Thoracic and Vascular Surgery, Philipps University Marburg, Marburg, Germany
| | - Malte Buchholz
- Department of Gastroenterology, Philipps University Marburg, Marburg, Germany
| | - Detlef K Bartsch
- Department of Visceral Thoracic and Vascular Surgery, Philipps University Marburg, Marburg, Germany
| | - Vincenzo A Gennarino
- Departments of Genetics and Development, Pediatrics and Neurology, Columbia University Irving Medical Center, New York, New York, USA
- Columbia Stem Cell Initiative, Columbia University Irving Medical Center, New York, New York, USA
| | - Pietro Di Fazio
- Department of Visceral Thoracic and Vascular Surgery, Philipps University Marburg, Marburg, Germany,
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Marty R, de Prisco N, Carter H, Font-Burgada J. MHC-I genotype drives early immune selection of oncogenic mutations. Mol Cell Oncol 2018; 5:e1409863. [PMID: 29487895 PMCID: PMC5821412 DOI: 10.1080/23723556.2017.1409863] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2017] [Revised: 11/20/2017] [Accepted: 11/22/2017] [Indexed: 11/24/2022]
Abstract
MHC-I exposes the intracellular contents to immune cells for surveillance of cellular health. Due to high genomic variation, individuals' immune systems differ in their ability to expose and eliminate cancer-causing mutations. These personalized immune blind spots create specific oncogenic mutation predispositions within patients and influence their prevalence across populations.
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Affiliation(s)
- Rachel Marty
- Department of Medicine, Division of Medical Genetics, University of California San Diego, La Jolla, CA, USA.,Bioinformatics and Systems Biology Program, University of California San Diego, La Jolla, CA, USA
| | - Nicola de Prisco
- Cancer Biology Program, Fox Chase Cancer Center, 333 Cottman Avenue, Philadelphia, PA, USA
| | - Hannah Carter
- Department of Medicine, Division of Medical Genetics, University of California San Diego, La Jolla, CA, USA.,Bioinformatics and Systems Biology Program, University of California San Diego, La Jolla, CA, USA.,Moores Cancer Center, University of California San Diego, La Jolla, CA, USA.,Cancer Cell Map Initiative (CCMI), University of California San Diego, La Jolla, CA, USA
| | - Joan Font-Burgada
- Cancer Biology Program, Fox Chase Cancer Center, 333 Cottman Avenue, Philadelphia, PA, USA
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Botta S, de Prisco N, Marrocco E, Renda M, Sofia M, Curion F, Bacci ML, Ventrella D, Wilson C, Gesualdo C, Rossi S, Simonelli F, Surace EM. Targeting and silencing of rhodopsin by ectopic expression of the transcription factor KLF15. JCI Insight 2017; 2:96560. [PMID: 29263295 DOI: 10.1172/jci.insight.96560] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [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: 07/27/2017] [Accepted: 11/15/2017] [Indexed: 12/20/2022] Open
Abstract
The genome-wide activity of transcription factors (TFs) on multiple regulatory elements precludes their use as gene-specific regulators. Here we show that ectopic expression of a TF in a cell-specific context can be used to silence the expression of a specific gene as a therapeutic approach to regulate gene expression in human disease. We selected the TF Krüppel-like factor 15 (KLF15) based on its putative ability to recognize a specific DNA sequence motif present in the rhodopsin (RHO) promoter and its lack of expression in terminally differentiated rod photoreceptors (the RHO-expressing cells). Adeno-associated virus (AAV) vector-mediated ectopic expression of KLF15 in rod photoreceptors of pigs enables Rho silencing with limited genome-wide transcriptional perturbations. Suppression of a RHO mutant allele by KLF15 corrects the phenotype of a mouse model of retinitis pigmentosa with no observed toxicity. Cell-specific-context conditioning of TF activity may prove a novel mode for somatic gene-targeted manipulation.
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Affiliation(s)
| | | | - Elena Marrocco
- Telethon Institute of Genetics and Medicine, Napoli, Italy
| | - Mario Renda
- Telethon Institute of Genetics and Medicine, Napoli, Italy
| | - Martina Sofia
- Telethon Institute of Genetics and Medicine, Napoli, Italy
| | - Fabiola Curion
- Telethon Institute of Genetics and Medicine, Napoli, Italy
| | - Maria Laura Bacci
- Department of Veterinary Medical Sciences, University of Bologna, Bologna, Italy
| | - Domenico Ventrella
- Department of Veterinary Medical Sciences, University of Bologna, Bologna, Italy
| | - Cathal Wilson
- Telethon Institute of Genetics and Medicine, Napoli, Italy
| | - Carlo Gesualdo
- Multidisciplinary Department of Medical, Surgical and Dental Sciences, Eye Clinic, Second University of Naples, Naples, Italy
| | - Settimio Rossi
- Multidisciplinary Department of Medical, Surgical and Dental Sciences, Eye Clinic, Second University of Naples, Naples, Italy
| | - Francesca Simonelli
- Multidisciplinary Department of Medical, Surgical and Dental Sciences, Eye Clinic, Second University of Naples, Naples, Italy
| | - Enrico Maria Surace
- Telethon Institute of Genetics and Medicine, Napoli, Italy.,Department of Translational Medicine, University of Naples Federico II, Naples, Italy
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10
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Marty R, Kaabinejadian S, Rossell D, Slifker MJ, van de Haar J, Engin HB, de Prisco N, Ideker T, Hildebrand WH, Font-Burgada J, Carter H. MHC-I Genotype Restricts the Oncogenic Mutational Landscape. Cell 2017; 171:1272-1283.e15. [PMID: 29107334 DOI: 10.1016/j.cell.2017.09.050] [Citation(s) in RCA: 258] [Impact Index Per Article: 36.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2017] [Revised: 07/14/2017] [Accepted: 09/27/2017] [Indexed: 12/21/2022]
Abstract
MHC-I molecules expose the intracellular protein content on the cell surface, allowing T cells to detect foreign or mutated peptides. The combination of six MHC-I alleles each individual carries defines the sub-peptidome that can be effectively presented. We applied this concept to human cancer, hypothesizing that oncogenic mutations could arise in gaps in personal MHC-I presentation. To validate this hypothesis, we developed and applied a residue-centric patient presentation score to 9,176 cancer patients across 1,018 recurrent oncogenic mutations. We found that patient MHC-I genotype-based scores could predict which mutations were more likely to emerge in their tumor. Accordingly, poor presentation of a mutation across patients was correlated with higher frequency among tumors. These results support that MHC-I genotype-restricted immunoediting during tumor formation shapes the landscape of oncogenic mutations observed in clinically diagnosed tumors and paves the way for predicting personal cancer susceptibilities from knowledge of MHC-I genotype.
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Affiliation(s)
- Rachel Marty
- Department of Medicine, Division of Medical Genetics, University of California San Diego, La Jolla, CA 92093, USA; Bioinformatics and Systems Biology Program, University of California San Diego, La Jolla, CA 92093, USA
| | - Saghar Kaabinejadian
- Department of Microbiology and Immunology, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104, USA
| | - David Rossell
- Department of Economics & Business, Universitat Pompeu Fabra, 08002 Barcelona, Spain
| | - Michael J Slifker
- Biostatistics and Bioinformatics Facility, Fox Chase Cancer Center, 333 Cottman Avenue, Philadelphia, PA 19111, USA
| | - Joris van de Haar
- Department of Medicine, Division of Medical Genetics, University of California San Diego, La Jolla, CA 92093, USA; Division of Molecular Oncology & Immunology, the Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, the Netherlands
| | - Hatice Billur Engin
- Department of Medicine, Division of Medical Genetics, University of California San Diego, La Jolla, CA 92093, USA
| | - Nicola de Prisco
- Cancer Biology Program, Fox Chase Cancer Center, 333 Cottman Avenue, Philadelphia, PA 19111, USA
| | - Trey Ideker
- Department of Medicine, Division of Medical Genetics, University of California San Diego, La Jolla, CA 92093, USA; Bioinformatics and Systems Biology Program, University of California San Diego, La Jolla, CA 92093, USA; Moores Cancer Center, University of California San Diego, La Jolla, CA 92093, USA; Cancer Cell Map Initiative (CCMI), University of California San Diego, La Jolla, CA 92093, USA; Department of Computer Science, University of California San Diego, La Jolla, CA 92093, USA
| | - William H Hildebrand
- Department of Microbiology and Immunology, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104, USA
| | - Joan Font-Burgada
- Department of Pharmacology, School of Medicine, University of California San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA; Cancer Biology Program, Fox Chase Cancer Center, 333 Cottman Avenue, Philadelphia, PA 19111, USA.
| | - Hannah Carter
- Department of Medicine, Division of Medical Genetics, University of California San Diego, La Jolla, CA 92093, USA; Bioinformatics and Systems Biology Program, University of California San Diego, La Jolla, CA 92093, USA; Moores Cancer Center, University of California San Diego, La Jolla, CA 92093, USA; Cancer Cell Map Initiative (CCMI), University of California San Diego, La Jolla, CA 92093, USA
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Botta S, Marrocco E, de Prisco N, Curion F, Renda M, Sofia M, Lupo M, Bacci ML, Gesualdo C, Rossi S, Simonelli F, Surace EM. 320. Transcriptional Silencing via Synthetic DNA Binding Protein Lacking Canonical Repressor Domains as a Potent Tool to Generate Therapeutics. Mol Ther 2016. [DOI: 10.1016/s1525-0016(16)33129-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022] Open
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Botta S, Marrocco E, de Prisco N, Curion F, Renda M, Sofia M, Lupo M, Carissimo A, Bacci ML, Gesualdo C, Rossi S, Simonelli F, Surace EM. Rhodopsin targeted transcriptional silencing by DNA-binding. eLife 2016; 5:e12242. [PMID: 26974343 PMCID: PMC4805542 DOI: 10.7554/elife.12242] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2015] [Accepted: 02/19/2016] [Indexed: 01/22/2023] Open
Abstract
Transcription factors (TFs) operate by the combined activity of their DNA-binding domains (DBDs) and effector domains (EDs) enabling the coordination of gene expression on a genomic scale. Here we show that in vivo delivery of an engineered DNA-binding protein uncoupled from the repressor domain can produce efficient and gene-specific transcriptional silencing. To interfere with RHODOPSIN (RHO) gain-of-function mutations we engineered the ZF6-DNA-binding protein (ZF6-DB) that targets 20 base pairs (bp) of a RHOcis-regulatory element (CRE) and demonstrate Rho specific transcriptional silencing upon adeno-associated viral (AAV) vector-mediated expression in photoreceptors. The data show that the 20 bp-long genomic DNA sequence is necessary for RHO expression and that photoreceptor delivery of the corresponding cognate synthetic trans-acting factor ZF6-DB without the intrinsic transcriptional repression properties of the canonical ED blocks Rho expression with negligible genome-wide transcript perturbations. The data support DNA-binding-mediated silencing as a novel mode to treat gain-of-function mutations. DOI:http://dx.doi.org/10.7554/eLife.12242.001 Proteins called transcription factors bind to sections of DNA known as regulatory elements to activate or deactivate nearby genes. In animals, transcription factors typically have two sections: a “DNA-binding domain” that attaches to DNA, and an “effector domain” that is responsible for interacting with other proteins to regulate the gene’s expression. Rhodopsin is a gene that encodes the instructions needed to make a light-sensitive protein in the eyes of humans and other animals. Botta et al. have now used this gene as an example to investigate whether proteins that contain a DNA-binding domain – but not an effector domain – can repress gene expression. The experiments show that only a small section of the regulatory elements in the human Rhodopsin gene is actually required for the gene to be expressed. Botta et al. designed an artificial protein – referred to as ZF6-DB – that is able to bind to this section of DNA. The binding of ZF6-DB to this short DNA section was sufficient to switch off a Rhodopsin gene in living pig cells, and, unlike conventional transcription factors, seemed to have minimal impact other genes. Next, Botta et al. used a virus to insert both the gene that encodes ZF6-DB and a normal copy of Rhodopsin into pigs. In these animals, ZF6-DB switched off the existing copy of Rhodopsin, but not the inserted copy so the cells produced a working form of the light-sensitive protein. Further experiments were carried out in mice that have both a faulty version and a normal copy of the Rhodopsin gene. ZF6-DB switched off the faulty Rhodopsin gene, which allowed the normal Rhodopsin gene to work without any interference from the faulty copy. Mutations in Rhodopsin can cause an eye disease that leads to severe loss of vision in humans. These new findings could now guide future efforts to develop treatments for people with this condition. It will also be important to investigate how ZF6-DB binds to the regulatory elements in the Rhodopsin gene and whether a similar strategy could be used to alter the expression of other genes. DOI:http://dx.doi.org/10.7554/eLife.12242.002
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Affiliation(s)
| | - Elena Marrocco
- Telethon Institute of Genetics and Medicine, Napoli, Italy
| | | | - Fabiola Curion
- Telethon Institute of Genetics and Medicine, Napoli, Italy
| | - Mario Renda
- Telethon Institute of Genetics and Medicine, Napoli, Italy
| | - Martina Sofia
- Telethon Institute of Genetics and Medicine, Napoli, Italy
| | | | | | - Maria Laura Bacci
- Department of Veterinary Medical Sciences, University of Bologna, Bologna, Italy
| | - Carlo Gesualdo
- Multidisciplinary Department of Medical, Surgical and Dental Sciences, Eye Clinic, Second University of Naples, Naples, Italy
| | - Settimio Rossi
- Multidisciplinary Department of Medical, Surgical and Dental Sciences, Eye Clinic, Second University of Naples, Naples, Italy
| | - Francesca Simonelli
- Multidisciplinary Department of Medical, Surgical and Dental Sciences, Eye Clinic, Second University of Naples, Naples, Italy
| | - Enrico Maria Surace
- Telethon Institute of Genetics and Medicine, Napoli, Italy.,Department of Translational Medicine, University of Naples Federico II, Naples, Italy
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