1
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Radulovic I, Schündeln MM, Müller L, Ptok J, Honisch E, Niederacher D, Wiek C, Scheckenbach K, Leblanc T, Larcher L, Soulier J, Reinhardt D, Schaal H, Andreassen PR, Hanenberg H. A novel cancer risk prediction score for the natural course of FA patients with biallelic BRCA2/FANCD1 mutations. Hum Mol Genet 2023; 32:1836-1849. [PMID: 36721989 DOI: 10.1093/hmg/ddad017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2022] [Revised: 11/01/2022] [Accepted: 01/20/2023] [Indexed: 02/02/2023] Open
Abstract
Biallelic germline mutations in BRCA2 occur in the FA-D1 subtype of the rare pediatric disorder, Fanconi anemia (FA), characterized clinically by congenital abnormalities and a high propensity to develop malignancies early in life. Clinical and genetic data from 96 FA-D1 patients with biallelic BRCA2 mutations were collected and used to develop a new cancer risk prediction score system based on the specific mutations in BRCA2. This score takes into account the location of frameshift/stop and missense mutations relative to exon 11 of BRCA2, which encodes the major sites for interaction with the RAD51 recombinase, and uses the MaxEnt and HBond splicing scores to analyze potential splice site pertubations. Among 75 FA-D1 patients with ascertained BRCA2 mutations, 66 patients developed 102 malignancies, ranging from one to three independent tumors per individual. The median age at the manifestation of peripheral embryonal tumors was 1.0, of hematologic malignancies 1.8, and of CNS tumors 2.7 years, respectively. Patients who received treatment lived longer than those without. Using our novel scoring system, we could distinguish three distinct cancer risk groups among FA-D1 patients: in the first, patients developed their initial malignancy at a median age of 1.3 years (n = 36, 95% CI 0.9-1.8), in the second group at 2.3 years (n = 17, 95% CI 1.4-4.4) and in the 3rd group at 23.0 years (n = 22, 95% CI 4.3-n/a). Therefore, this scoring system allows, for the first time, to predict the cancer manifestation of FA-D1 patients simply based on the type and position of the mutations in BRCA2.
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Affiliation(s)
- Ivana Radulovic
- Department of Pediatrics III, University Children's Hospital Essen, University of Duisburg-Essen, Essen, Germany
| | - Michael M Schündeln
- Department of Pediatrics III, University Children's Hospital Essen, University of Duisburg-Essen, Essen, Germany
| | - Lisa Müller
- Institute of Virology, Heinrich Heine University, Duesseldorf, Germany
| | - Johannes Ptok
- Institute of Virology, Heinrich Heine University, Duesseldorf, Germany
| | - Ellen Honisch
- Department of Gynecology & Obstetrics, Heinrich-Heine University, Düsseldorf, Germany
| | - Dieter Niederacher
- Department of Gynecology & Obstetrics, Heinrich-Heine University, Düsseldorf, Germany
| | - Constanze Wiek
- Department of Otorhinolaryngology & Head/Neck Surgery, Heinrich Heine University, Düsseldorf, Germany
| | - Kathrin Scheckenbach
- Department of Otorhinolaryngology & Head/Neck Surgery, Heinrich Heine University, Düsseldorf, Germany
| | - Thierry Leblanc
- Immunology and Hematology Department, Hôpital Robert-Debré, AP-HP, URP 35-18, Institut de Recherche Saint-Louis, Paris, France
| | - Lise Larcher
- Service Hématologie Biologique, AP-HP, Hôpital Saint-Louis, Paris, France
| | - Jean Soulier
- Immunology and Hematology Department, Hôpital Robert-Debré, AP-HP, URP 35-18, Institut de Recherche Saint-Louis, Paris, France.,Service Hématologie Biologique, AP-HP, Hôpital Saint-Louis, Paris, France.,Université Paris Cité, Inserm, CNRS GenCellDis, Paris, France
| | - Dirk Reinhardt
- Department of Pediatrics III, University Children's Hospital Essen, University of Duisburg-Essen, Essen, Germany
| | - Heiner Schaal
- Institute of Virology, Heinrich Heine University, Duesseldorf, Germany
| | - Paul R Andreassen
- Division of Experimental Hematology & Cancer Biology, Cancer & Blood Diseases Institute, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio, United States of America.,Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, Ohio, United States of America
| | - Helmut Hanenberg
- Department of Pediatrics III, University Children's Hospital Essen, University of Duisburg-Essen, Essen, Germany.,Department of Otorhinolaryngology & Head/Neck Surgery, Heinrich Heine University, Düsseldorf, Germany
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2
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Magvan B, Kloeble AA, Ptok J, Hoffmann D, Habermann D, Gantumur A, Paluschinski M, Enebish G, Balz V, Fischer JC, Chimeddorj B, Walker A, Timm J. Sequence diversity of hepatitis D virus in Mongolia. Front Med (Lausanne) 2023; 10:1108543. [PMID: 37035318 PMCID: PMC10077969 DOI: 10.3389/fmed.2023.1108543] [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] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2022] [Accepted: 02/06/2023] [Indexed: 04/11/2023] Open
Abstract
Introduction The Hepatitis Delta Virus (HDV) is a defective, single-stranded RNA virusoid encoding for a single protein, the Hepatitis Delta Antigen (HDAg), which requires the hepatitis B virus (HBV) envelope protein (HBsAg) for its transmission. Currently, hepatitis D is the most aggressive form of viral hepatitis and treatment options are limited. Worldwide 12 million people are chronically infected with HDV being at high risk for progression to cirrhosis and development of liver cancer. Objectives Although it is well established that Mongolia is the country with the highest prevalence of HDV infections, the information on the molecular epidemiology and factors contributing to HDV sequence diversity are largely unclear. The aim of the study was to characterize the sequence diversity of HDV in rural areas from Mongolia and to determine the extent of HLA class I-associated selection pressure. Patients and methods From the HepMongolia cohort from rural areas in Mongolia, 451 HBsAg-positive individuals were selected and anti-HDV, HDV-RNA and the sequence of the large HDAg was determined. For all individuals the HLA class I locus was genotyped. Residues under selection pressure in the presence of individual HLA class I types were identified with the recently published analysis tool HAMdetector. Results Of 431 HBsAg positive patients, 281 were anti-HDV positive (65%), and HDV-RNA could be detected in 207 of 281 (74%) of patients. The complete large HDAg was successfully sequenced from 131 samples. Phylogenetic analysis revealed that all Mongolian HDV isolates belong to genotype 1, however, they separate into several different clusters without clear regional association. In turn, from phylogeny there is strong evidence for recent local transmission events. Importantly, we found multiple residues with strong support for HLA class I-associated selection pressure consistent with a functional CD8+ T cell response directed against HDV. Conclusion HDV isolates from Mongolia are highly diverse. The molecular epidemiology suggests circulation of multiple subtypes and provides evidence for ongoing recent transmissions.
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Affiliation(s)
- Battur Magvan
- Department of Microbiology and Infection Prevention and Control, Mongolian National University of Medical Sciences, Ulaanbaatar, Mongolia
| | - Anne Alina Kloeble
- Institute of Virology, University Hospital Düsseldorf, Düsseldorf, Germany
| | - Johannes Ptok
- Institute of Virology, University Hospital Düsseldorf, Düsseldorf, Germany
| | - Daniel Hoffmann
- Bioinformatics and Computational Biophysics, Faculty of Biology, University of Duisburg-Essen, Essen, Germany
| | - Daniel Habermann
- Bioinformatics and Computational Biophysics, Faculty of Biology, University of Duisburg-Essen, Essen, Germany
| | - Anuujin Gantumur
- Department of Microbiology and Infection Prevention and Control, Mongolian National University of Medical Sciences, Ulaanbaatar, Mongolia
| | | | - Gerelmaa Enebish
- Department of Microbiology and Infection Prevention and Control, Mongolian National University of Medical Sciences, Ulaanbaatar, Mongolia
| | - Vera Balz
- Institute for Transplant Diagnostics and Cell Therapeutics, University Hospital Dusseldorf, Dusseldorf, Germany
| | - Johannes C. Fischer
- Institute for Transplant Diagnostics and Cell Therapeutics, University Hospital Dusseldorf, Dusseldorf, Germany
| | - Battogtokh Chimeddorj
- Department of Microbiology and Infection Prevention and Control, Mongolian National University of Medical Sciences, Ulaanbaatar, Mongolia
- Institute of Biomedical Sciences, Mongolian National University of Medical Sciences, Ulaanbaatar, Mongolia
| | - Andreas Walker
- Institute of Virology, University Hospital Düsseldorf, Düsseldorf, Germany
- *Correspondence: Andreas Walker,
| | - Jörg Timm
- Institute of Virology, University Hospital Düsseldorf, Düsseldorf, Germany
- Jörg Timm,
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3
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Müller L, Andrée M, Moskorz W, Drexler I, Hauka S, Ptok J, Walotka L, Grothmann R, Hillebrandt J, Ritchie A, Peter L, Walker A, Timm J, Adams O, Schaal H. Adjusted COVID-19 booster schedules balance age-dependent differences in antibody titers benefitting risk populations. Front Aging 2022; 3:1027885. [PMID: 36313184 PMCID: PMC9596780 DOI: 10.3389/fragi.2022.1027885] [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] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/25/2022] [Accepted: 09/29/2022] [Indexed: 11/05/2022]
Abstract
We provide follow-up data on the humoral immune response after COVID-19 vaccinations of two distinct cohorts aged below 60 and over 80 years to screen for age-related differences in the longevity and magnitude of the induction of the antibody responses post booster-vaccinations. While anti-SARS-CoV-2 spike-specific IgG and neutralization capacity waned rapidly after the initial vaccination schedule, additional boosters highly benefitted the humoral immune responses especially in the elderly cohort, including the neutralization of Omikron variants. Thus, adjusted COVID-19 booster vaccination schedules are an appropriate tool to overcome limitations in the success of vaccinations.
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Affiliation(s)
- Lisa Müller
- Institute of Virology, Medical Faculty, University Hospital Düsseldorf, Heinrich-Heine University Düsseldorf, Düsseldorf, Germany,*Correspondence: Lisa Müller,
| | - Marcel Andrée
- Institute of Virology, Medical Faculty, University Hospital Düsseldorf, Heinrich-Heine University Düsseldorf, Düsseldorf, Germany
| | - Wiebke Moskorz
- Institute of Virology, Medical Faculty, University Hospital Düsseldorf, Heinrich-Heine University Düsseldorf, Düsseldorf, Germany
| | - Ingo Drexler
- Institute of Virology, Medical Faculty, University Hospital Düsseldorf, Heinrich-Heine University Düsseldorf, Düsseldorf, Germany
| | - Sandra Hauka
- Institute of Virology, Medical Faculty, University Hospital Düsseldorf, Heinrich-Heine University Düsseldorf, Düsseldorf, Germany
| | - Johannes Ptok
- Institute of Virology, Medical Faculty, University Hospital Düsseldorf, Heinrich-Heine University Düsseldorf, Düsseldorf, Germany
| | - Lara Walotka
- Institute of Virology, Medical Faculty, University Hospital Düsseldorf, Heinrich-Heine University Düsseldorf, Düsseldorf, Germany
| | - Ramona Grothmann
- Institute of Virology, Medical Faculty, University Hospital Düsseldorf, Heinrich-Heine University Düsseldorf, Düsseldorf, Germany
| | - Jonas Hillebrandt
- Institute of Virology, Medical Faculty, University Hospital Düsseldorf, Heinrich-Heine University Düsseldorf, Düsseldorf, Germany,Department of Nephrology, Medical Faculty, University Hospital Düsseldorf, Heinrich-Heine University Düsseldorf, Düsseldorf, Germany
| | - Anastasia Ritchie
- Institute of Virology, Medical Faculty, University Hospital Düsseldorf, Heinrich-Heine University Düsseldorf, Düsseldorf, Germany
| | - Laura Peter
- Institute of Virology, Medical Faculty, University Hospital Düsseldorf, Heinrich-Heine University Düsseldorf, Düsseldorf, Germany
| | - Andreas Walker
- Institute of Virology, Medical Faculty, University Hospital Düsseldorf, Heinrich-Heine University Düsseldorf, Düsseldorf, Germany
| | - Jörg Timm
- Institute of Virology, Medical Faculty, University Hospital Düsseldorf, Heinrich-Heine University Düsseldorf, Düsseldorf, Germany
| | - Ortwin Adams
- Institute of Virology, Medical Faculty, University Hospital Düsseldorf, Heinrich-Heine University Düsseldorf, Düsseldorf, Germany
| | - Heiner Schaal
- Institute of Virology, Medical Faculty, University Hospital Düsseldorf, Heinrich-Heine University Düsseldorf, Düsseldorf, Germany
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Müller L, Ptok J, Nisar A, Antemann J, Grothmann R, Hillebrand F, Brillen AL, Ritchie A, Theiss S, Schaal H. Modeling splicing outcome by combining 5'ss strength and splicing regulatory elements. Nucleic Acids Res 2022; 50:8834-8851. [PMID: 35947702 PMCID: PMC9410876 DOI: 10.1093/nar/gkac663] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Revised: 06/23/2022] [Accepted: 07/27/2022] [Indexed: 12/24/2022] Open
Abstract
Correct pre-mRNA processing in higher eukaryotes vastly depends on splice site recognition. Beyond conserved 5'ss and 3'ss motifs, splicing regulatory elements (SREs) play a pivotal role in this recognition process. Here, we present in silico designed sequences with arbitrary a priori prescribed splicing regulatory HEXplorer properties that can be concatenated to arbitrary length without changing their regulatory properties. We experimentally validated in silico predictions in a massively parallel splicing reporter assay on more than 3000 sequences and exemplarily identified some SRE binding proteins. Aiming at a unified 'functional splice site strength' encompassing both U1 snRNA complementarity and impact from neighboring SREs, we developed a novel RNA-seq based 5'ss usage landscape, mapping the competition of pairs of high confidence 5'ss and neighboring exonic GT sites along HBond and HEXplorer score coordinate axes on human fibroblast and endothelium transcriptome datasets. These RNA-seq data served as basis for a logistic 5'ss usage prediction model, which greatly improved discrimination between strong but unused exonic GT sites and annotated highly used 5'ss. Our 5'ss usage landscape offers a unified view on 5'ss and SRE neighborhood impact on splice site recognition, and may contribute to improved mutation assessment in human genetics.
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Affiliation(s)
| | | | - Azlan Nisar
- Institute of Virology, Medical Faculty, Heinrich-Heine-University Düsseldorf, Düsseldorf 40225, Germany,Institute for Bioinformatics and Chemoinformatics, Westphalian University of Applied Sciences, August-Schmidt-Ring 10, Recklinghausen 45665, Germany
| | - Jennifer Antemann
- Institute of Virology, Medical Faculty, Heinrich-Heine-University Düsseldorf, Düsseldorf 40225, Germany
| | - Ramona Grothmann
- Institute of Virology, Medical Faculty, Heinrich-Heine-University Düsseldorf, Düsseldorf 40225, Germany
| | - Frank Hillebrand
- Institute of Virology, Medical Faculty, Heinrich-Heine-University Düsseldorf, Düsseldorf 40225, Germany
| | - Anna-Lena Brillen
- Institute of Virology, Medical Faculty, Heinrich-Heine-University Düsseldorf, Düsseldorf 40225, Germany
| | - Anastasia Ritchie
- Institute of Virology, Medical Faculty, Heinrich-Heine-University Düsseldorf, Düsseldorf 40225, Germany
| | | | - Heiner Schaal
- To whom correspondence should be addressed. Tel: +49 211 81 12393; Fax: +49 211 81 10856;
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Müller L, Moskorz W, Brillen AL, Hillebrand F, Ostermann PN, Kiel N, Walotka L, Ptok J, Timm J, Lübke N, Schaal H. Altered HIV-1 mRNA Splicing Due to Drug-Resistance-Associated Mutations in Exon 2/2b. Int J Mol Sci 2021; 23:ijms23010156. [PMID: 35008581 PMCID: PMC8745674 DOI: 10.3390/ijms23010156] [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] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2021] [Revised: 12/18/2021] [Accepted: 12/22/2021] [Indexed: 12/02/2022] Open
Abstract
The underlying molecular mechanism and their general effect on the replication capacity of HIV 1 drug-resistance-associated mutations is often poorly understood. To elucidate the effect of two such mutations located in a region with a high density of spicing regulatory elements on the HIV-1-splicing outcome, bioinformatic predictions were combined with transfection and infection experiments. Results show that the previously described R263K drug-resistance-associated integrase mutation has additionally a severe effect on the ESE2b splicing regulatory element (SRE) in exon 2b, which causes loss of SD2b recognition. This was confirmed by an R263R silent mutation with a similar predicted effect on the exon 2b SRE. In contrast, a V260I mutation and its silent counterpart with a lower effect on ESS2b did not exhibit any differences in the splicing pattern. Since HIV-1 highly relies on a balanced splicing reaction, changes in the splicing outcome can contribute to changes in viral replication and might add to the effect of escape mutations toward antiviral drugs. Thus, a classification of mutations purely addressing proteins is insufficient.
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Müller L, Andrée M, Moskorz W, Drexler I, Walotka L, Grothmann R, Ptok J, Hillebrandt J, Ritchie A, Rabl D, Ostermann PN, Robitzsch R, Hauka S, Walker A, Menne C, Grutza R, Timm J, Adams O, Schaal H. Age-dependent Immune Response to the Biontech/Pfizer BNT162b2 Coronavirus Disease 2019 Vaccination. Clin Infect Dis 2021; 73:2065-2072. [PMID: 33906236 DOI: 10.1101/2021.03.03.21251066v1.abstract] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2021] [Indexed: 05/27/2023] Open
Abstract
BACKGROUND The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic has led to the development of various vaccines. Real-life data on immune responses elicited in the most vulnerable group of vaccinees older than age 80 years old are still underrepresented despite the prioritization of the elderly in vaccination campaigns. METHODS We conducted a cohort study with 2 age groups, young vaccinees below the age of 60 years and elderly vaccinees over the age of 80 years, to compare their antibody responses to the first and second dose of the BNT162b2 coronavirus disease 2019 vaccination. RESULTS Although the majority of participants in both groups produced specific immunoglobulin G antibody titers against SARS-CoV-2 spike protein, titers were significantly lower in elderly participants. Although the increment of antibody levels after the second immunization was higher in elderly participants, the absolute mean titer of this group remained lower than the <60 years of age group. After the second vaccination, 31.3% of the elderly had no detectable neutralizing antibodies in contrast to the younger group, in which only 2.2% had no detectable neutralizing antibodies. CONCLUSIONS Our data showed differences between the antibody responses raised after the first and second BNT162b2 vaccination, in particular lower frequencies of neutralizing antibodies in the elderly group. This suggests that this population needs to be closely monitored and may require earlier revaccination and/or an increased vaccine dose to ensure stronger long-lasting immunity and protection against infection.
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Affiliation(s)
- Lisa Müller
- Institute of Virology, Medical Faculty, University Hospital Düsseldorf, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Marcel Andrée
- Institute of Virology, Medical Faculty, University Hospital Düsseldorf, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Wiebke Moskorz
- Institute of Virology, Medical Faculty, University Hospital Düsseldorf, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Ingo Drexler
- Institute of Virology, Medical Faculty, University Hospital Düsseldorf, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Lara Walotka
- Institute of Virology, Medical Faculty, University Hospital Düsseldorf, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Ramona Grothmann
- Institute of Virology, Medical Faculty, University Hospital Düsseldorf, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Johannes Ptok
- Institute of Virology, Medical Faculty, University Hospital Düsseldorf, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Jonas Hillebrandt
- Institute of Virology, Medical Faculty, University Hospital Düsseldorf, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
- Department of Nephrology, Medical Faculty, University Hospital Düsseldorf, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Anastasia Ritchie
- Institute of Virology, Medical Faculty, University Hospital Düsseldorf, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Denise Rabl
- Institute of Virology, Medical Faculty, University Hospital Düsseldorf, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Philipp Niklas Ostermann
- Institute of Virology, Medical Faculty, University Hospital Düsseldorf, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Rebekka Robitzsch
- Institute of Virology, Medical Faculty, University Hospital Düsseldorf, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Sandra Hauka
- Institute of Virology, Medical Faculty, University Hospital Düsseldorf, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Andreas Walker
- Institute of Virology, Medical Faculty, University Hospital Düsseldorf, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Christopher Menne
- Institute of Virology, Medical Faculty, University Hospital Düsseldorf, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Ralf Grutza
- Institute of Virology, Medical Faculty, University Hospital Düsseldorf, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Jörg Timm
- Institute of Virology, Medical Faculty, University Hospital Düsseldorf, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Ortwin Adams
- Institute of Virology, Medical Faculty, University Hospital Düsseldorf, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Heiner Schaal
- Institute of Virology, Medical Faculty, University Hospital Düsseldorf, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
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7
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Goranci-Buzhala G, Mariappan A, Ricci-Vitiani L, Josipovic N, Pacioni S, Gottardo M, Ptok J, Schaal H, Callaini G, Rajalingam K, Dynlacht B, Hadian K, Papantonis A, Pallini R, Gopalakrishnan J. Cilium induction triggers differentiation of glioma stem cells. Cell Rep 2021; 36:109656. [PMID: 34496239 DOI: 10.1016/j.celrep.2021.109656] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2020] [Revised: 06/17/2021] [Accepted: 08/12/2021] [Indexed: 12/21/2022] Open
Abstract
Glioblastoma multiforme (GBM) possesses glioma stem cells (GSCs) that promote self-renewal, tumor propagation, and relapse. Understanding the mechanisms of GSCs self-renewal can offer targeted therapeutic interventions. However, insufficient knowledge of GSCs' fundamental biology is a significant bottleneck hindering these efforts. Here, we show that patient-derived GSCs recruit elevated levels of proteins that ensure the temporal cilium disassembly, leading to suppressed ciliogenesis. Depleting the cilia disassembly complex components is sufficient to induce ciliogenesis in a subset of GSCs via relocating platelet-derived growth factor receptor-alpha (PDGFR-α) to a newly induced cilium. Importantly, restoring ciliogenesis enabled GSCs to switch from self-renewal to differentiation. Finally, using an organoid-based glioma invasion assay and brain xenografts in mice, we establish that ciliogenesis-induced differentiation can prevent the infiltration of GSCs into the brain. Our findings illustrate a role for cilium as a molecular switch in determining GSCs' fate and suggest cilium induction as an attractive strategy to intervene in GSCs proliferation.
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Affiliation(s)
- Gladiola Goranci-Buzhala
- Institute of Human Genetics, University Hospital Düsseldorf, Heinrich-Heine-Universität, Universitätsstr. 1, 40225 Düsseldorf, Germany
| | - Aruljothi Mariappan
- Institute of Human Genetics, University Hospital Düsseldorf, Heinrich-Heine-Universität, Universitätsstr. 1, 40225 Düsseldorf, Germany
| | - Lucia Ricci-Vitiani
- Department of Oncology and Molecular Medicine, Istituto Superiore di Sanità, Rome 00161, Italy
| | - Natasa Josipovic
- Institute of Pathology, University Medicine Göttingen, Georg-August University Göttingen, Robert-Koch-Straße 40, 37075 Göttingen, and Center for Molecular Medicine, University of Cologne, 50931 Cologne, Germany
| | - Simone Pacioni
- Institute of Neurosurgery, Fondazione Policlinico Universitario A. Gemelli IRCCS-Università Cattolica del Sacro Cuore, Rome 00168, Italy
| | - Marco Gottardo
- Institute of Human Genetics, University Hospital Düsseldorf, Heinrich-Heine-Universität, Universitätsstr. 1, 40225 Düsseldorf, Germany
| | - Johannes Ptok
- Institute of Virology, Medical Faculty, University Hospital Düsseldorf, Heinrich-Heine-Universität, Universitätsstr. 1, 40225 Düsseldorf, Germany
| | - Heiner Schaal
- Institute of Virology, Medical Faculty, University Hospital Düsseldorf, Heinrich-Heine-Universität, Universitätsstr. 1, 40225 Düsseldorf, Germany
| | - Giuliano Callaini
- Department of Life Sciences University of Siena, Via Aldo Moro 2, Siena 53100, Italy
| | - Krishnaraj Rajalingam
- Cell Biology Unit, University Medical Center, Johannes Gutenberg University Mainz, Langenbeckstr. 1, 55131 Mainz, Germany
| | - Brian Dynlacht
- Department of Pathology and NYU Cancer Institute, NYU School of Medicine, New York, NY 10016, USA
| | - Kamyar Hadian
- Assay Development and Screening Platform, Institute of Molecular Toxicology and Pharmacology, Helmholtz Zentrum München, Ingolstädter Landstr.1, 85764 Neuherberg, Germany
| | - Argyris Papantonis
- Institute of Pathology, University Medicine Göttingen, Georg-August University Göttingen, Robert-Koch-Straße 40, 37075 Göttingen, and Center for Molecular Medicine, University of Cologne, 50931 Cologne, Germany
| | - Roberto Pallini
- Institute of Neurosurgery, Fondazione Policlinico Universitario A. Gemelli IRCCS-Università Cattolica del Sacro Cuore, Rome 00168, Italy
| | - Jay Gopalakrishnan
- Institute of Human Genetics, University Hospital Düsseldorf, Heinrich-Heine-Universität, Universitätsstr. 1, 40225 Düsseldorf, Germany.
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8
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Ptok J, Müller L, Ostermann PN, Ritchie A, Dilthey AT, Theiss S, Schaal H. Modifying splice site usage with ModCon: Maintaining the genetic code while changing the underlying mRNP code. Comput Struct Biotechnol J 2021; 19:3069-3076. [PMID: 34136105 PMCID: PMC8178101 DOI: 10.1016/j.csbj.2021.05.033] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2021] [Revised: 05/14/2021] [Accepted: 05/20/2021] [Indexed: 11/22/2022] Open
Abstract
Codon degeneracy of amino acid sequences permits an additional “mRNP code” layer underlying the genetic code that is related to RNA processing. In pre-mRNA splicing, splice site usage is determined by both intrinsic strength and sequence context providing RNA binding sites for splicing regulatory proteins. In this study, we systematically examined modification of splicing regulatory properties in the neighborhood of a GT site, i.e. potential splice site, without altering the encoded amino acids. We quantified the splicing regulatory properties of the neighborhood around a potential splice site by its Splice Site HEXplorer Weight (SSHW) based on the HEXplorer score algorithm. To systematically modify GT site neighborhoods, either minimizing or maximizing their SSHW, we designed the novel stochastic optimization algorithm ModCon that applies a genetic algorithm with stochastic crossover, insertion and random mutation elements supplemented by a heuristic sliding window approach. To assess the achievable range in SSHW in human splice donors without altering the encoded amino acids, we applied ModCon to a set of 1000 randomly selected Ensembl annotated human splice donor sites, achieving substantial and accurate changes in SSHW. Using ModCon optimization, we successfully switched splice donor usage in a splice site competition reporter containing coding sequences from FANCA, FANCB or BRCA2, while retaining their amino acid coding information. The ModCon algorithm and its R package implementation can assist in reporter design by either introducing novel splice sites, silencing accidental, undesired splice sites, and by generally modifying the entire mRNP code while maintaining the genetic code.
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Key Words
- A, adenine
- F1, filial sequence 1
- G, guanine
- GA, genetic algorithm
- HBS, HBond score
- HBond score
- HEXplorer score
- HZEI, HEXplorer score
- P1, parental sequence 1
- SA, splice acceptor
- SD, splice donor
- SR proteins, serine- and arginine-rich proteins
- SRP, splicing regulatory protein
- SSHW, splice site HEXplorer weight
- SW, sliding window
- Splice donor
- Splicing regulatory proteins
- Splicing reporter
- T, thymine
- eGFP, enhanced green fluorescent protein
- hnRNP, heterogeneous nuclear ribonucleoproteins
- nt, nucleotides
- pre-mRNA splicing
- pre-mRNA, precursor messenger RNA
- snRNA, small nuclear RNA
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Affiliation(s)
- Johannes Ptok
- Institute of Virology, Medical Faculty, Heinrich Heine University Düsseldorf, D-40225 Düsseldorf, Germany
| | - Lisa Müller
- Institute of Virology, Medical Faculty, Heinrich Heine University Düsseldorf, D-40225 Düsseldorf, Germany
| | - Philipp Niklas Ostermann
- Institute of Virology, Medical Faculty, Heinrich Heine University Düsseldorf, D-40225 Düsseldorf, Germany
| | - Anastasia Ritchie
- Institute of Virology, Medical Faculty, Heinrich Heine University Düsseldorf, D-40225 Düsseldorf, Germany
| | - Alexander T Dilthey
- Institute of Medical Statistics and Computational Biology, University of Cologne, Cologne, Germany
- Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, Cologne, Germany
- Institute of Medical Microbiology and Hospital Hygiene, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Stephan Theiss
- Institute of Virology, Medical Faculty, Heinrich Heine University Düsseldorf, D-40225 Düsseldorf, Germany
| | - Heiner Schaal
- Institute of Virology, Medical Faculty, Heinrich Heine University Düsseldorf, D-40225 Düsseldorf, Germany
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9
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Müller L, Andrée M, Moskorz W, Drexler I, Walotka L, Grothmann R, Ptok J, Hillebrandt J, Ritchie A, Rabl D, Ostermann PN, Robitzsch R, Hauka S, Walker A, Menne C, Grutza R, Timm J, Adams O, Schaal H. Age-dependent immune response to the Biontech/Pfizer BNT162b2 COVID-19 vaccination. Clin Infect Dis 2021; 73:2065-2072. [PMID: 33906236 PMCID: PMC8135422 DOI: 10.1093/cid/ciab381] [Citation(s) in RCA: 315] [Impact Index Per Article: 105.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2021] [Indexed: 12/20/2022] Open
Abstract
Background The SARS-CoV-2 pandemic has led to the development of various vaccines. Real-life data on immune responses elicited in the most vulnerable group of vaccinees over 80 years old is still underrepresented despite the prioritization of the elderly in vaccination campaigns. Methods We conducted a cohort study with two age groups, young vaccinees below the age of 60 and elderly vaccinees over the age of 80, to compare their antibody responses to the first and second dose of the BNT162b2 COVID-19 vaccination. Results While the majority of participants in both groups produced specific IgG antibody titers against SARS-CoV-2 spike protein, titers were significantly lower in elderly participants. Although the increment of antibody levels after the second immunization was higher in elderly participants, the absolute mean titer of this group remained lower than the <60 group. After the second vaccination, 31.3 % of the elderly had no detectable neutralizing antibodies in contrast to the younger group, in which only 2.2% had no detectable neutralizing antibodies. Conclusion Our data showed differences between the antibody responses raised after the first and second BNT162b2 vaccination, in particular lower frequencies of neutralizing antibodies in the elderly group. This suggests that this population needs to be closely monitored and may require earlier revaccination or/and an increased vaccine dose to ensure stronger long lasting immunity and protection against infection.
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Affiliation(s)
- Lisa Müller
- Institute of Virology, Medical Faculty, University Hospital Düsseldorf, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Marcel Andrée
- Institute of Virology, Medical Faculty, University Hospital Düsseldorf, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Wiebke Moskorz
- Institute of Virology, Medical Faculty, University Hospital Düsseldorf, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Ingo Drexler
- Institute of Virology, Medical Faculty, University Hospital Düsseldorf, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Lara Walotka
- Institute of Virology, Medical Faculty, University Hospital Düsseldorf, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Ramona Grothmann
- Institute of Virology, Medical Faculty, University Hospital Düsseldorf, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Johannes Ptok
- Institute of Virology, Medical Faculty, University Hospital Düsseldorf, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Jonas Hillebrandt
- Institute of Virology, Medical Faculty, University Hospital Düsseldorf, Heinrich Heine University Düsseldorf, Düsseldorf, Germany.,Department of Nephrology, Medical Faculty, University Hospital Düsseldorf, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Anastasia Ritchie
- Institute of Virology, Medical Faculty, University Hospital Düsseldorf, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Denise Rabl
- Institute of Virology, Medical Faculty, University Hospital Düsseldorf, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Philipp Niklas Ostermann
- Institute of Virology, Medical Faculty, University Hospital Düsseldorf, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Rebekka Robitzsch
- Institute of Virology, Medical Faculty, University Hospital Düsseldorf, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Sandra Hauka
- Institute of Virology, Medical Faculty, University Hospital Düsseldorf, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Andreas Walker
- Institute of Virology, Medical Faculty, University Hospital Düsseldorf, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Christopher Menne
- Institute of Virology, Medical Faculty, University Hospital Düsseldorf, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Ralf Grutza
- Institute of Virology, Medical Faculty, University Hospital Düsseldorf, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Jörg Timm
- Institute of Virology, Medical Faculty, University Hospital Düsseldorf, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Ortwin Adams
- Institute of Virology, Medical Faculty, University Hospital Düsseldorf, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Heiner Schaal
- Institute of Virology, Medical Faculty, University Hospital Düsseldorf, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
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10
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Ptok J, Theiss S, Schaal H. VarCon: An R Package for Retrieving Neighboring Nucleotides of an SNV. Cancer Inform 2020; 19:1176935120976399. [PMID: 33281441 PMCID: PMC7691889 DOI: 10.1177/1176935120976399] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2020] [Accepted: 11/01/2020] [Indexed: 11/24/2022] Open
Abstract
Reporting of a single nucleotide variant (SNV) follows the Sequence Variant Nomenclature
(http://varnomen.hgvs.org/), using an unambiguous numbering scheme specific
for coding and noncoding DNA. However, the corresponding sequence neighborhood of a given
SNV, which is required to assess its impact on splicing regulation, is not easily
accessible from this nomenclature. Providing fast and easy access to this neighborhood
just from a given SNV reference, the novel tool VarCon combines information of the Ensembl
human reference genome and the corresponding transcript table for accurate retrieval.
VarCon also displays splice site scores (HBond and MaxEnt scores) and HEXplorer profiles
of an SNV neighborhood, reflecting position-dependent splice enhancing and silencing
properties.
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Affiliation(s)
- Johannes Ptok
- Institute of Virology, Medical Faculty, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Stephan Theiss
- Institute of Virology, Medical Faculty, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Heiner Schaal
- Institute of Virology, Medical Faculty, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
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11
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Erkelenz S, Poschmann G, Ptok J, Müller L, Schaal H. Profiling of cis- and trans-acting factors supporting noncanonical splice site activation. RNA Biol 2020; 18:118-130. [PMID: 32693676 DOI: 10.1080/15476286.2020.1798111] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022] Open
Abstract
Recently, by combining transcriptomics with functional splicing reporter assays we were able to identify GT > GC > TT as the three highest ranked dinucleotides of human 5' splice sites (5'ss). Here, we have extended our investigations to the proteomic characterization of nuclear proteins that bind to canonical and noncanonical 5'ss. Surprisingly, we found that U1 snRNP binding to functional 5'ss sequences prevented components of the DNA damage response (DDR) from binding to the RNA, suggesting a close link between spliceosome arrangement and genome stability. We demonstrate that all tested noncanonical 5'ss sequences are bona-fide targets of the U2-type spliceosome and are bound by U1 snRNP, including U1-C, in the presence of splicing enhancers. The quantity of precipitated U1-C protein was similar for all noncanonical 5'ss dinucleotides, so that the highly different 5'ss usage was likely due to a later step after early U1 snRNP binding. In addition, we show that an internal GT at positions +5/+6 can be advantageous for splicing at position +1 of noncanonical splice sites. Likewise, and in agreement with previous observations, splicing inactive U1 snRNP binding sites could serve as splicing enhancers, which may also explain the higher abundance of U1 snRNPs compared to other U snRNPs. Finally, we observe that an arginine-serine (RS)-rich domain recruitment to stem loop I of the U1 snRNA is functionally sufficient to promote exon-definition and upstream 3'ss activation.
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Affiliation(s)
- Steffen Erkelenz
- Institute of Virology, Medical Faculty, Heinrich Heine University Düsseldorf , Düsseldorf, Germany.,Institute for Genetics and Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne , Cologne, Germany
| | - Gereon Poschmann
- Molecular Proteomics Laboratory, BMFZ, Universitätsklinikum Düsseldorf , Düsseldorf, Germany
| | - Johannes Ptok
- Institute of Virology, Medical Faculty, Heinrich Heine University Düsseldorf , Düsseldorf, Germany
| | - Lisa Müller
- Institute of Virology, Medical Faculty, Heinrich Heine University Düsseldorf , Düsseldorf, Germany
| | - Heiner Schaal
- Institute of Virology, Medical Faculty, Heinrich Heine University Düsseldorf , Düsseldorf, Germany
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12
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Ptok J, Müller L, Theiss S, Schaal H. Context matters: Regulation of splice donor usage. Biochim Biophys Acta Gene Regul Mech 2019; 1862:194391. [PMID: 31202784 DOI: 10.1016/j.bbagrm.2019.06.002] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/26/2019] [Revised: 06/07/2019] [Accepted: 06/09/2019] [Indexed: 11/16/2022]
Abstract
Elaborate research on splicing, starting in the late seventies, evolved from the discovery that 5' splice sites are recognized by their complementarity to U1 snRNA towards the realization that RNA duplex formation cannot be the sole basis for 5'ss selection. Rather, their recognition is highly influenced by a number of context factors including transcript architecture as well as splicing regulatory elements (SREs) in the splice site neighborhood. In particular, proximal binding of splicing regulatory proteins highly influences splicing outcome. The importance of SRE integrity especially becomes evident in the light of human pathogenic mutations where single nucleotide changes in SREs can severely affect the resulting transcripts. Bioinformatics tools nowadays greatly assist in the computational evaluation of 5'ss, their neighborhood and the impact of pathogenic mutations. Although predictions are already quite robust, computational evaluation of the splicing regulatory landscape still faces challenges to increase future reliability. This article is part of a Special Issue entitled: RNA structure and splicing regulation edited by Francisco Baralle, Ravindra Singh and Stefan Stamm.
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Affiliation(s)
- Johannes Ptok
- Institute of Virology, Medical Faculty, Heinrich Heine University Düsseldorf, D-40225 Düsseldorf, Germany
| | - Lisa Müller
- Institute of Virology, Medical Faculty, Heinrich Heine University Düsseldorf, D-40225 Düsseldorf, Germany
| | - Stephan Theiss
- Institute of Clinical Neuroscience and Medical Psychology, Medical Faculty, Heinrich Heine University Düsseldorf, D-40225 Düsseldorf, Germany
| | - Heiner Schaal
- Institute of Virology, Medical Faculty, Heinrich Heine University Düsseldorf, D-40225 Düsseldorf, Germany.
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13
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Erkelenz S, Theiss S, Kaisers W, Ptok J, Walotka L, Müller L, Hillebrand F, Brillen AL, Sladek M, Schaal H. Ranking noncanonical 5' splice site usage by genome-wide RNA-seq analysis and splicing reporter assays. Genome Res 2018; 28:1826-1840. [PMID: 30355602 PMCID: PMC6280755 DOI: 10.1101/gr.235861.118] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [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] [Received: 02/08/2018] [Accepted: 10/20/2018] [Indexed: 01/01/2023]
Abstract
Most human pathogenic mutations in 5' splice sites affect the canonical GT in positions +1 and +2, leading to noncanonical dinucleotides. On the other hand, noncanonical dinucleotides are observed under physiological conditions in ∼1% of all human 5'ss. It is therefore a challenging task to understand the pathogenic mutation mechanisms underlying the conditions under which noncanonical 5'ss are used. In this work, we systematically examined noncanonical 5' splice site selection, both experimentally using splicing competition reporters and by analyzing a large RNA-seq data set of 54 fibroblast samples from 27 subjects containing a total of 2.4 billion gapped reads covering 269,375 exon junctions. From both approaches, we consistently derived a noncanonical 5'ss usage ranking GC > TT > AT > GA > GG > CT. In our competition splicing reporter assay, noncanonical splicing was strictly dependent on the presence of upstream or downstream splicing regulatory elements (SREs), and changes in SREs could be compensated by variation of U1 snRNA complementarity in the competing 5'ss. In particular, we could confirm splicing at different positions (i.e., -1, +1, +5) of a splice site for all noncanonical dinucleotides "weaker" than GC. In our comprehensive RNA-seq data set analysis, noncanonical 5'ss were preferentially detected in weakly used exon junctions of highly expressed genes. Among high-confidence splice sites, they were 10-fold overrepresented in clusters with a neighboring, more frequently used 5'ss. Conversely, these more frequently used neighbors contained only the dinucleotides GT, GC, and TT, in accordance with the above ranking.
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Affiliation(s)
- Steffen Erkelenz
- Institute of Virology, Medical Faculty, Heinrich Heine University Düsseldorf, D-40225 Düsseldorf, Germany
| | - Stephan Theiss
- Institute of Clinical Neuroscience and Medical Psychology, Medical Faculty, Heinrich Heine University Düsseldorf, D-40225 Düsseldorf, Germany
| | - Wolfgang Kaisers
- Center for Biological and Medical Research (BMFZ), Center of Bioinformatics and Biostatistics (CBiBs), Heinrich Heine University Düsseldorf, D-40225 Düsseldorf, Germany
| | - Johannes Ptok
- Institute of Virology, Medical Faculty, Heinrich Heine University Düsseldorf, D-40225 Düsseldorf, Germany
| | - Lara Walotka
- Institute of Virology, Medical Faculty, Heinrich Heine University Düsseldorf, D-40225 Düsseldorf, Germany
| | - Lisa Müller
- Institute of Virology, Medical Faculty, Heinrich Heine University Düsseldorf, D-40225 Düsseldorf, Germany
| | - Frank Hillebrand
- Institute of Virology, Medical Faculty, Heinrich Heine University Düsseldorf, D-40225 Düsseldorf, Germany
| | - Anna-Lena Brillen
- Institute of Virology, Medical Faculty, Heinrich Heine University Düsseldorf, D-40225 Düsseldorf, Germany
| | - Michael Sladek
- Institute of Virology, Medical Faculty, Heinrich Heine University Düsseldorf, D-40225 Düsseldorf, Germany
| | - Heiner Schaal
- Institute of Virology, Medical Faculty, Heinrich Heine University Düsseldorf, D-40225 Düsseldorf, Germany
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14
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Brillen AL, Schöneweis K, Walotka L, Hartmann L, Müller L, Ptok J, Kaisers W, Poschmann G, Stühler K, Buratti E, Theiss S, Schaal H. Succession of splicing regulatory elements determines cryptic 5΄ss functionality. Nucleic Acids Res 2017; 45:4202-4216. [PMID: 28039323 PMCID: PMC5397162 DOI: 10.1093/nar/gkw1317] [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] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2016] [Accepted: 12/19/2016] [Indexed: 12/25/2022] Open
Abstract
A critical step in exon definition is the recognition of a proper splice donor (5΄ss) by the 5’ end of U1 snRNA. In the selection of appropriate 5΄ss, cis-acting splicing regulatory elements (SREs) are indispensable. As a model for 5΄ss recognition, we investigated cryptic 5΄ss selection within the human fibrinogen Bβ-chain gene (FGB) exon 7, where we identified several exonic SREs that simultaneously acted on up- and downstream cryptic 5΄ss. In the FGB exon 7 model system, 5΄ss selection iteratively proceeded along an alternating sequence of U1 snRNA binding sites and interleaved SREs which in principle supported different 3’ exon ends. Like in a relay race, SREs either suppressed a potential 5΄ss and passed the splicing baton on or splicing actually occurred. From RNA-Seq data, we systematically selected 19 genes containing exons with silent U1 snRNA binding sites competing with nearby highly used 5΄ss. Extensive SRE analysis by different algorithms found authentic 5΄ss significantly more supported by SREs than silent U1 snRNA binding sites, indicating that our concept may permit generalization to a model for 5΄ss selection and 3’ exon end definition.
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Affiliation(s)
- Anna-Lena Brillen
- Institute for Virology, Heinrich-Heine-University Düsseldorf, 40225 Düsseldorf, Germany
| | - Katrin Schöneweis
- Department of Infectious Diseases, Molecular Virology, University Hospital Heidelberg, 69120 Heidelberg, Germany
| | - Lara Walotka
- Institute for Virology, Heinrich-Heine-University Düsseldorf, 40225 Düsseldorf, Germany
| | - Linda Hartmann
- Institute for Virology, Heinrich-Heine-University Düsseldorf, 40225 Düsseldorf, Germany
| | - Lisa Müller
- Institute for Virology, Heinrich-Heine-University Düsseldorf, 40225 Düsseldorf, Germany
| | - Johannes Ptok
- Institute for Virology, Heinrich-Heine-University Düsseldorf, 40225 Düsseldorf, Germany
| | - Wolfgang Kaisers
- Department of Anesthesiology, University Hospital Düsseldorf, Heinrich-Heine-University Düsseldorf, 40225 Düsseldorf, Germany
| | - Gereon Poschmann
- Molecular Proteomics Laboratory, BMFZ, Heinrich-Heine-University Düsseldorf, 40225 Düsseldorf, Germany
| | - Kai Stühler
- Molecular Proteomics Laboratory, BMFZ, Heinrich-Heine-University Düsseldorf, 40225 Düsseldorf, Germany.,Institute for Molecular Medicine, University Hospital Düsseldorf, Heinrich-Heine-University Düsseldorf, 40225 Düsseldorf, Germany
| | - Emanuele Buratti
- International Centre for Genetic Engineering and Biotechnology (ICGEB), Area Science Park, 34149 Trieste, Italy
| | - Stephan Theiss
- Institute of Clinical Neuroscience and Medical Psychology, Heinrich-Heine-University Düsseldorf, 40225
| | - Heiner Schaal
- Institute for Virology, Heinrich-Heine-University Düsseldorf, 40225 Düsseldorf, Germany
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15
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Kaisers W, Ptok J, Schwender H, Schaal H. Validation of Splicing Events in Transcriptome Sequencing Data. Int J Mol Sci 2017; 18:ijms18061110. [PMID: 28545234 PMCID: PMC5485934 DOI: 10.3390/ijms18061110] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2017] [Revised: 04/26/2017] [Accepted: 04/28/2017] [Indexed: 11/16/2022] Open
Abstract
Genomic alignments of sequenced cellular messenger RNA contain gapped alignments which are interpreted as consequence of intron removal. The resulting gap-sites, genomic locations of alignment gaps, are landmarks representing potential splice-sites. As alignment algorithms report gap-sites with a considerable false discovery rate, validations are required. We describe two quality scores, gap quality score (gqs) and weighted gap information score (wgis), developed for validation of putative splicing events: While gqs solely relies on alignment data wgis additionally considers information from the genomic sequence. FASTQ files obtained from 54 human dermal fibroblast samples were aligned against the human genome (GRCh38) using TopHat and STAR aligner. Statistical properties of gap-sites validated by gqs and wgis were evaluated by their sequence similarity to known exon-intron borders. Within the 54 samples, TopHat identifies 1,000,380 and STAR reports 6,487,577 gap-sites. Due to the lack of strand information, however, the percentage of identified GT-AG gap-sites is rather low. While gap-sites from TopHat contain ≈89% GT-AG, gap-sites from STAR only contain ≈42% GT-AG dinucleotide pairs in merged data from 54 fibroblast samples. Validation with gqs yields 156,251 gap-sites from TopHat alignments and 166,294 from STAR alignments. Validation with wgis yields 770,327 gap-sites from TopHat alignments and 1,065,596 from STAR alignments. Both alignment algorithms, TopHat and STAR, report gap-sites with considerable false discovery rate, which can drastically be reduced by validation with gqs and wgis.
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Affiliation(s)
- Wolfgang Kaisers
- Department for Anaesthesiology, University Hospital Düsseldorf, Heinrich Heine University, 40225 Düsseldorf, Germany.
- BMFZ (Biologisch-Medizinisches Forschungszentrum), Heinrich Heine University, 40225 Düsseldorf, Germany.
| | - Johannes Ptok
- Institute of Virology, University Hospital Düsseldorf, Heinrich Heine University, 40225 Düsseldorf, Germany.
| | - Holger Schwender
- BMFZ (Biologisch-Medizinisches Forschungszentrum), Heinrich Heine University, 40225 Düsseldorf, Germany.
- Mathematical Institute, Heinrich Heine University, 40225 Düsseldorf, Germany.
| | - Heiner Schaal
- BMFZ (Biologisch-Medizinisches Forschungszentrum), Heinrich Heine University, 40225 Düsseldorf, Germany.
- Institute of Virology, University Hospital Düsseldorf, Heinrich Heine University, 40225 Düsseldorf, Germany.
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