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Cattaneo C, Enzo E, De Rosa L, Sercia L, Consiglio F, Forcato M, Bicciato S, Paiardini A, Basso G, Tagliafico E, Paganelli A, Fiorentini C, Magnoni C, Latella MC, De Luca M. Allele-specific CRISPR-Cas9 editing of dominant epidermolysis bullosa simplex in human epidermal stem cells. Mol Ther 2024; 32:372-383. [PMID: 38053334 PMCID: PMC10861943 DOI: 10.1016/j.ymthe.2023.11.027] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2023] [Revised: 10/28/2023] [Accepted: 11/30/2023] [Indexed: 12/07/2023] Open
Abstract
Epidermolysis bullosa simplex (EBS) is a rare skin disease inherited mostly in an autosomal dominant manner. Patients display a skin fragility that leads to blisters and erosions caused by minor mechanical trauma. EBS phenotypic and genotypic variants are caused by genetic defects in intracellular proteins whose function is to provide the attachment of basal keratinocytes to the basement membrane zone and most EBS cases display mutations in keratin 5 (KRT5) and keratin 14 (KRT14) genes. Besides palliative treatments, there is still no long-lasting effective cure to correct the mutant gene and abolish the dominant negative effect of the pathogenic protein over its wild-type counterpart. Here, we propose a molecular strategy for EBS01 patient's keratinocytes carrying a monoallelic c.475/495del21 mutation in KRT14 exon 1. Through the CRISPR-Cas9 system, we perform a specific cleavage only on the mutant allele and restore a normal cellular phenotype and a correct intermediate filament network, without affecting the epidermal stem cell, referred to as holoclones, which play a crucial role in epidermal regeneration.
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Affiliation(s)
- C Cattaneo
- Centre for Regenerative Medicine "Stefano Ferrari", Department of Life Sciences, University of Modena and Reggio Emilia, 41125 Modena, Italy
| | - E Enzo
- Centre for Regenerative Medicine "Stefano Ferrari", Department of Life Sciences, University of Modena and Reggio Emilia, 41125 Modena, Italy
| | - L De Rosa
- Centre for Regenerative Medicine "Stefano Ferrari", Department of Life Sciences, University of Modena and Reggio Emilia, 41125 Modena, Italy
| | - L Sercia
- Centre for Regenerative Medicine "Stefano Ferrari", Department of Life Sciences, University of Modena and Reggio Emilia, 41125 Modena, Italy
| | - F Consiglio
- Holostem Terapie Avanzate, s.r.l, 41125 Modena, Italy
| | - M Forcato
- Department of Life Sciences, University of Modena and Reggio Emilia, 41125 Modena, Italy
| | - S Bicciato
- Department of Life Sciences, University of Modena and Reggio Emilia, 41125 Modena, Italy
| | - A Paiardini
- Department of Biochemical Sciences 'A. Rossi Fanelli', Sapienza Università di Roma, 00185 Rome, Italy
| | - G Basso
- Genomic Units, IRCCS Humanitas Research Hospital, 20089 Rozzano, Milan, Italy
| | - E Tagliafico
- Department of Medical and Surgical Sciences, University of Modena and Reggio Emilia, 41124 Modena, Italy
| | - A Paganelli
- Regenerative and Oncological Dermatological Surgery Unit, Modena University Hospital, 41124 Modena, Italy
| | - C Fiorentini
- Regenerative and Oncological Dermatological Surgery Unit, Modena University Hospital, 41124 Modena, Italy
| | - C Magnoni
- Regenerative and Oncological Dermatological Surgery Unit, Modena University Hospital, 41124 Modena, Italy
| | - M C Latella
- Holostem Terapie Avanzate, s.r.l, 41125 Modena, Italy
| | - M De Luca
- Centre for Regenerative Medicine "Stefano Ferrari", Department of Life Sciences, University of Modena and Reggio Emilia, 41125 Modena, Italy.
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Badowski C, Tan TS, Aliev T, Trudil D, Larina M, Argentova V, Firdaus MJ, Benny P, Woo VS, Lane EB. Detrimental Effects of IFN-γ on an Epidermolysis Bullosa Simplex Cell Model and Protection by a Humanized Anti-IFN-γ Monoclonal Antibody. JID INNOVATIONS 2022; 2:100096. [PMID: 35265936 PMCID: PMC8899047 DOI: 10.1016/j.xjidi.2022.100096] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2021] [Revised: 10/14/2021] [Accepted: 11/17/2021] [Indexed: 12/12/2022] Open
Abstract
Epidermolysis bullosa is a group of severe skin blistering disorders, which currently have no cure. The pathology of epidermolysis bullosa is recognized as having an inflammatory component, but the role of inflammation in different epidermolysis bullosa disorders is unclear. Epidermolysis bullosa simplex (EBS) is primarily caused by sequence variants in keratin genes; its most severe form, EBS generalized severe, is characterized by aggregates of keratin proteins, and cell models of EBS generalized severe show constitutively elevated stress. IFN-γ is a major mediator of inflammation, and we show that the addition of IFN-γ alone to disease model keratinocytes promotes keratin aggregation, decreases cell-cell junctions, delays wound closure, and reduces cell proliferation. IFN-γ exposure weakens the intercellular cohesion of monolayers on mechanical stress, with IFN-γ-treated EBS monolayers more fragmented than IFN-γ-treated wild-type monolayers. A humanized monoclonal antibody to IFN-γ neutralized the detrimental effects on keratinocytes, restoring cell proliferation, increasing cell-cell adhesion, accelerating wound closure in the presence of IFN-γ, and reducing IFN-γ-mediated keratin aggregation in EBS cells. These suggest that treatment with IFN-γ blocking antibodies may constitute a promising new therapeutic strategy for patients with EBS and may also have ameliorating effects on other inflammatory skin diseases.
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Affiliation(s)
- Cedric Badowski
- Institute of Medical Biology, Agency for Science, Technology and Research (ASTAR), Singapore, Singapore
| | - Tong San Tan
- Institute of Medical Biology, Agency for Science, Technology and Research (ASTAR), Singapore, Singapore
- Skin Research Institute of Singapore (SRIS), Agency for Science, Technology and Research (ASTAR), Singapore, Singapore
| | - Teimur Aliev
- Faculty of Chemistry, Lomonosov Moscow State University, Moscow, Russia
| | - David Trudil
- NHDetect Corporation, Reisterstown, Maryland, USA
| | - Maria Larina
- Shemyakin–Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia
| | | | - Muhammad Jasrie Firdaus
- Institute of Medical Biology, Agency for Science, Technology and Research (ASTAR), Singapore, Singapore
- Skin Research Institute of Singapore (SRIS), Agency for Science, Technology and Research (ASTAR), Singapore, Singapore
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, Singapore
| | - Paula Benny
- Institute of Medical Biology, Agency for Science, Technology and Research (ASTAR), Singapore, Singapore
| | - Vivien S.T. Woo
- Institute of Medical Biology, Agency for Science, Technology and Research (ASTAR), Singapore, Singapore
- Department of Pathology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - E. Birgitte Lane
- Institute of Medical Biology, Agency for Science, Technology and Research (ASTAR), Singapore, Singapore
- Skin Research Institute of Singapore (SRIS), Agency for Science, Technology and Research (ASTAR), Singapore, Singapore
- Department of Pathology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
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3
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Logli E, Marzuolo E, D'Agostino M, Conti LA, Lena AM, Diociaiuti A, Dellambra E, Has C, Cianfanelli V, Zambruno G, El Hachem M, Magenta A, Candi E, Condorelli AG. Proteasome-mediated degradation of keratins 7, 8, 17 and 18 by mutant KLHL24 in a foetal keratinocyte model: Novel insight in congenital skin defects and fragility of epidermolysis bullosa simplex with cardiomyopathy. Hum Mol Genet 2021; 31:1308-1324. [PMID: 34740256 PMCID: PMC9029237 DOI: 10.1093/hmg/ddab318] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2021] [Revised: 10/05/2021] [Accepted: 10/21/2021] [Indexed: 01/18/2023] Open
Abstract
Epidermolysis bullosa simplex (EBS) with cardiomyopathy (EBS-KLHL24) is an EBS subtype caused by dominantly inherited, gain-of-function mutations in the gene encoding for the ubiquitin-ligase KLHL24, which addresses specific proteins to proteasomal degradation. EBS-KLHL24 patients are born with extensive denuded skin areas and skin fragility. Whilst skin fragility rapidly ameliorates, atrophy and scarring develop over time, accompanied by life-threatening cardiomyopathy. To date, pathogenetic mechanisms underlying such a unique disease phenotype are not fully characterized. The basal keratin 14 (K14) has been indicated as a KLHL24 substrate in keratinocytes. However, EBS-KLHL24 pathobiology cannot be determined by the mutation-enhanced disruption of K14 alone, as K14 is similarly expressed in foetal and postnatal epidermis and its protein levels are preserved both in vivo and in vitro disease models. In this study, we focused on foetal keratins as additional KLHL24 substrates. We showed that K7, K8, K17 and K18 protein levels are markedly reduced via proteasome degradation in normal foetal keratinocytes transduced with the mutant KLHL24 protein (ΔN28-KLHL24) as compared to control cells expressing the wild-type form. In addition, heat stress led to keratin network defects and decreased resilience in ΔN28-KLHL24 cells. The KLHL24-mediated degradation of foetal keratins could contribute to congenital skin defects in EBS-KLHL24. Furthermore, we observed that primary keratinocytes from EBS-KLHL24 patients undergo accelerated clonal conversion with reduced colony forming efficiency (CFE) and early replicative senescence. Finally, our findings pointed out a reduced CFE in ΔN28-KLHL24-transduced foetal keratinocytes as compared to controls, suggesting that mutant KLHL24 contributes to patients’ keratinocyte clonogenicity impairment.
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Affiliation(s)
- Elena Logli
- Genodermatosis Unit, Genetics and Rare Diseases Research Division, Bambino Gesù Children's Hospital, IRCCS, Piazza Sant'Onofrio 4, 00165, Rome, Italy
| | - Elisa Marzuolo
- Genodermatosis Unit, Genetics and Rare Diseases Research Division, Bambino Gesù Children's Hospital, IRCCS, Piazza Sant'Onofrio 4, 00165, Rome, Italy
| | - Marco D'Agostino
- Laboratory of Experimental Immunology, IDI-IRCCS, Via Monti di Creta 104, 00167, Rome, Italy
| | - Libenzio Adrian Conti
- Confocal Microscopy Core Facility, Bambino Gesù Children's Hospital, IRCCS, Viale di San Paolo 15, 00146, Rome, Italy
| | - Anna Maria Lena
- Department of Experimental Medicine, University of Rome "Tor Vergata", Via Montpellier 1, 00133, Rome, Italy
| | - Andrea Diociaiuti
- Dermatology Unit and Genodermatosis Unit, Genetics and Rare Diseases Research Division, Bambino Gesù Children's Hospital, IRCCS, Piazza Sant'Onofrio 4, 00165, Rome, Italy
| | | | - Cristina Has
- Department of Dermatology, Medical Faculty, Medical Center - University of Freiburg, Freiburg, Germany
| | - Valentina Cianfanelli
- Department of Pediatric Hemato-Oncology and Cell and Gene Therapy, Bambino Gesù Children's Hospital, IRCCS, Piazza Sant'Onofrio 4, 00165, Rome, Italy
| | - Giovanna Zambruno
- Genodermatosis Unit, Genetics and Rare Diseases Research Division, Bambino Gesù Children's Hospital, IRCCS, Piazza Sant'Onofrio 4, 00165, Rome, Italy
| | - May El Hachem
- Dermatology Unit and Genodermatosis Unit, Genetics and Rare Diseases Research Division, Bambino Gesù Children's Hospital, IRCCS, Piazza Sant'Onofrio 4, 00165, Rome, Italy
| | - Alessandra Magenta
- Institute of Translational Pharmacology (IFT), National Research Council of Italy (CNR), Via Fosso del Cavaliere 100, 00133, Rome, Italy
| | - Eleonora Candi
- Department of Experimental Medicine, University of Rome "Tor Vergata", Via Montpellier 1, 00133, Rome, Italy.,IDI-IRCCS, Via Monti di Creta 104, 00167, Rome, Italy
| | - Angelo Giuseppe Condorelli
- Genodermatosis Unit, Genetics and Rare Diseases Research Division, Bambino Gesù Children's Hospital, IRCCS, Piazza Sant'Onofrio 4, 00165, Rome, Italy
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Tan TS, Common JEA, Lim JSY, Badowski C, Firdaus MJ, Leonardi SS, Lane EB. A cell-based drug discovery assay identifies inhibition of cell stress responses as a new approach to treatment of epidermolysis bullosa simplex. J Cell Sci 2021; 134:272475. [PMID: 34643242 PMCID: PMC8542385 DOI: 10.1242/jcs.258409] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2021] [Accepted: 09/07/2021] [Indexed: 11/20/2022] Open
Abstract
In the skin fragility disorder epidermolysis bullosa simplex (EBS), mutations in keratin 14 (K14, also known as KRT14) or keratin 5 (K5, also known as KRT5) lead to keratinocyte rupture and skin blistering. Severe forms of EBS are associated with cytoplasmic protein aggregates, with elevated kinase activation of ERK1 and ERK2 (ERK1/2; also known as MAPK3 and MAPK1, respectively), suggesting intrinsic stress caused by misfolded keratin protein. Human keratinocyte EBS reporter cells stably expressing GFP-tagged EBS-mimetic mutant K14 were used to optimize a semi-automated system to quantify the effects of test compounds on keratin aggregates. Screening of a protein kinase inhibitor library identified several candidates that reduced aggregates and impacted on epidermal growth factor receptor (EGFR) signalling. EGF ligand exposure induced keratin aggregates in EBS reporter keratinocytes, which was reversible by EGFR inhibition. EBS keratinocytes treated with a known EGFR inhibitor, afatinib, were driven out of activation and towards quiescence with minimal cell death. Aggregate reduction was accompanied by denser keratin filament networks with enhanced intercellular cohesion and resilience, which when extrapolated to a whole tissue context would predict reduced epidermal fragility in EBS patients. This assay system provides a powerful tool for discovery and development of new pathway intervention therapeutic avenues for EBS.
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Affiliation(s)
- Tong San Tan
- Skin Research Institute of Singapore, A*STAR, Immunos Building, 8A Biomedical Grove, Singapore138648.,Institute of Medical Biology, A*STAR, Immunos Building, 8A Biomedical Grove, Singapore138648
| | - John E A Common
- Skin Research Institute of Singapore, A*STAR, Immunos Building, 8A Biomedical Grove, Singapore138648.,Institute of Medical Biology, A*STAR, Immunos Building, 8A Biomedical Grove, Singapore138648
| | - John S Y Lim
- A*STAR Microscopy Platform, Immunos Building, 8A Biomedical Grove, Singapore138648
| | - Cedric Badowski
- Institute of Medical Biology, A*STAR, Immunos Building, 8A Biomedical Grove, Singapore138648
| | - Muhammad Jasrie Firdaus
- Skin Research Institute of Singapore, A*STAR, Immunos Building, 8A Biomedical Grove, Singapore138648.,Institute of Medical Biology, A*STAR, Immunos Building, 8A Biomedical Grove, Singapore138648
| | - Steven S Leonardi
- Skin Research Institute of Singapore, A*STAR, Immunos Building, 8A Biomedical Grove, Singapore138648
| | - E Birgitte Lane
- Skin Research Institute of Singapore, A*STAR, Immunos Building, 8A Biomedical Grove, Singapore138648.,Institute of Medical Biology, A*STAR, Immunos Building, 8A Biomedical Grove, Singapore138648
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Xu Y, Wang Q, Meng G, Li D, Ma Z, Gao P, Zhang J, Zhang Q, Su Z. A rare cause of sudden chest pain and dyspnea: A CARE-compliant case report of Chilaiditi syndrome. Medicine (Baltimore) 2020; 99:e20220. [PMID: 32443352 PMCID: PMC7253721 DOI: 10.1097/md.0000000000020220] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
Abstract
RATIONALE Chilaiditi syndrome is a rare disorder characterized by a broad spectrum of (gastro-intestinal) symptoms caused by interposition of a segment of bowel between the liver and the diaphragm. Most cases present with abdominal symptoms and the morbidity tend to increase with age. PATIENT CONCERNS Here we present a rare case of Chilaiditi syndrome. An elderly postmenopausal woman developed unresolved postoperative respiratory symptoms and chest pain. Chest auscultation revealed considerable attenuation of respiratory sounds. She showed postoperative increase in D-dimer level and sudden onset of dyspnea. DIAGNOSES Considering the presence of atelectasis in the middle and lower lobes of the right lung, bedside fiberoptic bronchoscopy was performed immediately to rule out bronchial phlegm embolism. However, no phlegm embolism was found in the left lung, and a small amount of yellow-white mucus was seen in the upper lobe of the right lung. Due to external pressure, the lumen of the middle and lower lobes of the right lung was obviously narrowed. INTERVENTIONS The patient was placed in a semi-sitting position and a tube was passed through the anus to decompress the intestinal cavity; in addition, she received potassium supplementation. OUTCOMES The patient's symptoms improved markedly. Chest and semi-supine abdominal plain radiographs showed enhanced lung markings, shadows in the left lower lung lobes, elevation of the right diaphragm, and small amount of pneumoperitoneum. The patient recovered after 5 days of continuous treatment and was discharged. LESSONS Emergency computed tomographic pulmonary angiography may facilitate the diagnosis of Chilaiditi syndrome, especially in the postoperative setting. Occurrence of Chilaiditi syndrome in this patient was likely associated with surgical factors. Appropriate investigations and clear identification of etiology are essential for successful treatment.
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Affiliation(s)
- Yanling Xu
- Department of Respiratory Medicine
- Department of Geriatrics and General Medicine
| | - Qi Wang
- Department of Respiratory Medicine
| | | | - Dapeng Li
- Departments of Respiratory Medicine, Affiliated Hospital of Jilin Medical University, Jilin, Jilin 132000
| | - Zhiming Ma
- Department of Gastrointestinal Nutrition and Hernia Surgery
| | - Peng Gao
- Department of Respiratory Medicine
| | | | - Qun Zhang
- Department of Respiratory Medicine
- Department of Critical Care Medicine, The Second Affiliated Hospital of Jilin University, Changchun, Jilin 130041, China
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Spörrer M, Prochnicki A, Tölle RC, Nyström A, Esser PR, Homberg M, Athanasiou I, Zingkou E, Schilling A, Gerum R, Thievessen I, Winter L, Bruckner-Tuderman L, Fabry B, Magin TM, Dengjel J, Schröder R, Kiritsi D. Treatment of keratinocytes with 4-phenylbutyrate in epidermolysis bullosa: Lessons for therapies in keratin disorders. EBioMedicine 2019; 44:502-515. [PMID: 31078522 PMCID: PMC6603805 DOI: 10.1016/j.ebiom.2019.04.062] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2018] [Revised: 04/30/2019] [Accepted: 04/30/2019] [Indexed: 12/18/2022] Open
Abstract
Background Missense mutations in keratin 5 and 14 genes cause the severe skin fragility disorder epidermolysis bullosa simplex (EBS) by collapsing of the keratin cytoskeleton into cytoplasmic protein aggregates. Despite intense efforts, no molecular therapies are available, mostly due to the complex phenotype of EBS, comprising cell fragility, diminished adhesion, skin inflammation and itch. Methods We extensively characterized KRT5 and KRT14 mutant keratinocytes from patients with severe generalized EBS following exposure to the chemical chaperone 4-phenylbutyrate (4-PBA). Findings 4-PBA diminished keratin aggregates within EBS cells and ameliorated their inflammatory phenotype. Chemoproteomics of 4-PBA-treated and untreated EBS cells revealed reduced IL1β expression- but also showed activation of Wnt/β-catenin and NF-kB pathways. The abundance of extracellular matrix and cytoskeletal proteins was significantly altered, coinciding with diminished keratinocyte adhesion and migration in a 4-PBA dose-dependent manner. Interpretation Together, our study reveals a complex interplay of benefits and disadvantages that challenge the use of 4-PBA in skin fragility disorders.
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Affiliation(s)
- Marina Spörrer
- Department of Physics, Friedrich-Alexander-University Erlangen-Nuremberg, Erlangen, Germany
| | - Ania Prochnicki
- Institute of Neuropathology, Friedrich-Alexander-University Erlangen-Nuremberg, Erlangen, Germany
| | - Regine C Tölle
- Department of Biology, University of Fribourg, Switzerland
| | - Alexander Nyström
- Department of Dermatology, Medical Center - University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Philipp R Esser
- Department of Dermatology, Medical Center - University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Melanie Homberg
- Institute of Biology and SIKT, University of Leipzig, Leipzig, Germany
| | - Ioannis Athanasiou
- Department of Dermatology, Medical Center - University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Eleni Zingkou
- Department of Dermatology, Medical Center - University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Achim Schilling
- Department of Physics, Friedrich-Alexander-University Erlangen-Nuremberg, Erlangen, Germany; Experimental Otolaryngology, ENT Hospital, Head and Neck Surgery, Friedrich-Alexander University Erlangen-Nuremberg, Erlangen, Germany
| | - Richard Gerum
- Department of Physics, Friedrich-Alexander-University Erlangen-Nuremberg, Erlangen, Germany
| | - Ingo Thievessen
- Department of Physics, Friedrich-Alexander-University Erlangen-Nuremberg, Erlangen, Germany
| | - Lilli Winter
- Institute of Neuropathology, Friedrich-Alexander-University Erlangen-Nuremberg, Erlangen, Germany
| | - Leena Bruckner-Tuderman
- Department of Dermatology, Medical Center - University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Ben Fabry
- Department of Physics, Friedrich-Alexander-University Erlangen-Nuremberg, Erlangen, Germany
| | - Thomas M Magin
- Institute of Biology and SIKT, University of Leipzig, Leipzig, Germany
| | - Jörn Dengjel
- Department of Biology, University of Fribourg, Switzerland; Department of Dermatology, Medical Center - University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Rolf Schröder
- Institute of Neuropathology, Friedrich-Alexander-University Erlangen-Nuremberg, Erlangen, Germany
| | - Dimitra Kiritsi
- Department of Dermatology, Medical Center - University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany.
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7
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Ran D, Daye ZJ. Gene expression variability and the analysis of large-scale RNA-seq studies with the MDSeq. Nucleic Acids Res 2017; 45:e127. [PMID: 28535263 PMCID: PMC5737414 DOI: 10.1093/nar/gkx456] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2016] [Revised: 04/10/2017] [Accepted: 05/19/2017] [Indexed: 12/21/2022] Open
Abstract
Rapidly decreasing cost of next-generation sequencing has led to the recent availability of large-scale RNA-seq data, that empowers the analysis of gene expression variability, in addition to gene expression means. In this paper, we present the MDSeq, based on the coefficient of dispersion, to provide robust and computationally efficient analysis of both gene expression means and variability on RNA-seq counts. The MDSeq utilizes a novel reparametrization of the negative binomial to provide flexible generalized linear models (GLMs) on both the mean and dispersion. We address challenges of analyzing large-scale RNA-seq data via several new developments to provide a comprehensive toolset that models technical excess zeros, identifies outliers efficiently, and evaluates differential expressions at biologically interesting levels. We evaluated performances of the MDSeq using simulated data when the ground truths are known. Results suggest that the MDSeq often outperforms current methods for the analysis of gene expression mean and variability. Moreover, the MDSeq is applied in two real RNA-seq studies, in which we identified functionally relevant genes and gene pathways. Specifically, the analysis of gene expression variability with the MDSeq on the GTEx human brain tissue data has identified pathways associated with common neurodegenerative disorders when gene expression means were conserved.
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Affiliation(s)
- Di Ran
- Mel and Enid Zuckerman College of Public Health, The University of Arizona, Tucson, AZ 85724, USA
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8
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Rice RH, Durbin-Johnson BP, Salemi M, Schwartz ME, Rocke DM, Phinney BS. Proteomic profiling of Pachyonychia congenita plantar callus. J Proteomics 2017. [PMID: 28648685 DOI: 10.1016/j.jprot.2017.06.017] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
Callus samples from the ball and the arch of the foot, collected on tape circles, were compared by shotgun proteomic profiling. Pachyonychia congenita subjects were sampled who exhibited a mutation in KRT6A, KRT6B, KRT6C, KRT16 or KRT17, and the proteins were digested and analyzed by tandem mass spectrometry. In comparison with samples from unaffected control subjects, those from subjects with KRT6A or KRT16 mutations displayed the most differences in profile from normal, while those from subjects with KRT6C or KRT17 mutations showed few differences from normal. The profiles from subjects with KRT6B mutations were intermediate in protein profile differences. Degree of departure from the normal profile could be estimated by expression of numerous proteins in callus from the ball of the foot that were consistently different. By contrast, the protein profile from the arch of the foot was hardly affected. The results provide a foundation for noninvasive monitoring of the efficacy of treatments with quantitative assessment of departure from the normal phenotype. SIGNIFICANCE Pachyonychia congenita is an orphan disease in which the connection between the basic defect (keratin mutation) and debilitating symptoms (severe plantar pain) is poorly understood. Present work addresses the degree to which the protein profile is altered in the epidermis where the severe pain originates. The results indicate that the mutated keratins differ greatly in the degree to which they elicit perturbations in protein profile. In those cases with markedly altered protein levels, monitoring the callus profile may provide an objective measure of treatment efficacy.
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Affiliation(s)
- Robert H Rice
- Department of Environmental Toxicology, University of California, Davis, CA.
| | - Blythe P Durbin-Johnson
- Division of Biostatistics, Department of Public Health Sciences, Clinical and Translational Science Center Biostatistics Core, University of California, Davis, CA
| | - Michelle Salemi
- Proteomics Core Facility, University of California, Davis, CA
| | | | - David M Rocke
- Division of Biostatistics, Department of Public Health Sciences, Clinical and Translational Science Center Biostatistics Core, University of California, Davis, CA
| | - Brett S Phinney
- Proteomics Core Facility, University of California, Davis, CA
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9
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He Y, Maier K, Leppert J, Hausser I, Schwieger-Briel A, Weibel L, Theiler M, Kiritsi D, Busch H, Boerries M, Hannula-Jouppi K, Heikkilä H, Tasanen K, Castiglia D, Zambruno G, Has C. Monoallelic Mutations in the Translation Initiation Codon of KLHL24 Cause Skin Fragility. Am J Hum Genet 2016; 99:1395-1404. [PMID: 27889062 DOI: 10.1016/j.ajhg.2016.11.005] [Citation(s) in RCA: 61] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2016] [Accepted: 11/07/2016] [Indexed: 11/28/2022] Open
Abstract
The genetic basis of epidermolysis bullosa, a group of genetic disorders characterized by the mechanically induced formation of skin blisters, is largely known, but a number of cases still remain genetically unsolved. Here, we used whole-exome and targeted sequencing to identify monoallelic mutations, c.1A>G and c.2T>C, in the translation initiation codon of the gene encoding kelch-like protein 24 (KLHL24) in 14 individuals with a distinct skin-fragility phenotype and skin cleavage within basal keratinocytes. Remarkably, mutation c.1A>G occurred de novo and was recurrent in families originating from different countries. The striking similarities of the clinical features of the affected individuals point to a unique and very specific pathomechanism. We showed that mutations in the translation initiation codon of KLHL24 lead to the usage of a downstream translation initiation site with the same reading frame and formation of a truncated polypeptide. The pathobiology was examined in keratinocytes and fibroblasts of the affected individuals and via expression of mutant KLHL24, and we found mutant KLHL24 to be associated with abnormalities of intermediate filaments in keratinocytes and fibroblasts. In particular, KLHL24 mutations were associated with irregular and fragmented keratin 14. Recombinant overexpression of normal KLHL24 promoted keratin 14 degradation, whereas mutant KLHL24 showed less activity than the normal molecule. These findings identify KLHL24 mutations as a cause of skin fragility and identify a role for KLHL24 in maintaining the balance between intermediate filament stability and degradation required for skin integrity.
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Affiliation(s)
- Yinghong He
- Department of Dermatology, University Medical Center Freiburg, Freiburg 79104, Germany
| | - Kristin Maier
- Department of Dermatology, University Medical Center Freiburg, Freiburg 79104, Germany
| | - Juna Leppert
- Department of Dermatology, University Medical Center Freiburg, Freiburg 79104, Germany
| | - Ingrid Hausser
- Department of Pathology, University of Heidelberg, Heidelberg 69120, Germany
| | - Agnes Schwieger-Briel
- Department of Paediatric Dermatology, University Children's Hospital Zurich, Zurich 8091, Switzerland; Department of Dermatology, University Hospital Zurich, Zurich 8091, Switzerland
| | - Lisa Weibel
- Department of Paediatric Dermatology, University Children's Hospital Zurich, Zurich 8091, Switzerland; Department of Dermatology, University Hospital Zurich, Zurich 8091, Switzerland
| | - Martin Theiler
- Department of Paediatric Dermatology, University Children's Hospital Zurich, Zurich 8091, Switzerland; Department of Dermatology, University Hospital Zurich, Zurich 8091, Switzerland
| | - Dimitra Kiritsi
- Department of Dermatology, University Medical Center Freiburg, Freiburg 79104, Germany
| | - Hauke Busch
- Systems Biology of the Cellular Microenvironment Group, Institute of Molecular Medicine and Cell Research, Albert-Ludwigs-University Freiburg, Freiburg 79104, Germany; German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Heidelberg 69120, Germany; Comprehensive Cancer Center Freiburg, Freiburg 79106, Germany
| | - Melanie Boerries
- Systems Biology of the Cellular Microenvironment Group, Institute of Molecular Medicine and Cell Research, Albert-Ludwigs-University Freiburg, Freiburg 79104, Germany; German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Heidelberg 69120, Germany; Comprehensive Cancer Center Freiburg, Freiburg 79106, Germany
| | - Katariina Hannula-Jouppi
- Department of Dermatology and Allergology, University of Helsinki and Helsinki University Hospital, Helsinki 00014, Finland; Folkhälsan Institute of Genetics, University of Helsinki, Helsinki 00014, Finland
| | - Hannele Heikkilä
- Department of Dermatology and Allergology, University of Helsinki and Helsinki University Hospital, Helsinki 00014, Finland
| | - Kaisa Tasanen
- Department of Dermatology, PEDEGO Research Unit, Medical Research Center Oulu, Oulu University Hospital and University of Oulu, Oulu 90014, Finland
| | - Daniele Castiglia
- Laboratory of Molecular and Cell Biology, Istituto Dermopatico dell'Immacolata, Istituto di Ricovero e Cura a Carattere Scientifico, Rome 00167, Italy
| | - Giovanna Zambruno
- Genetic and Rare Diseases Research Area, Bambino Gesù Children's Hospital, Istituto di Ricovero e Cura a Carattere Scientifico, Rome 00165, Italy
| | - Cristina Has
- Department of Dermatology, University Medical Center Freiburg, Freiburg 79104, Germany.
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