1
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Ansari M, Faour KNW, Shimamura A, Grimes G, Kao EM, Denhoff ER, Blatnik A, Ben-Isvy D, Wang L, Helm BM, Firth H, Breman AM, Bijlsma EK, Iwata-Otsubo A, de Ravel TJL, Fusaro V, Fryer A, Nykamp K, Stühn LG, Haack TB, Korenke GC, Constantinou P, Bujakowska KM, Low KJ, Place E, Humberson J, Napier MP, Hoffman J, Juusola J, Deardorff MA, Shao W, Rockowitz S, Krantz I, Kaur M, Raible S, Dortenzio V, Kliesch S, Singer-Berk M, Groopman E, DiTroia S, Ballal S, Srivastava S, Rothfelder K, Biskup S, Rzasa J, Kerkhof J, McConkey H, Sadikovic B, Hilton S, Banka S, Tüttelmann F, Conrad DF, O'Donnell-Luria A, Talkowski ME, FitzPatrick DR, Boone PM. Heterozygous loss-of-function SMC3 variants are associated with variable growth and developmental features. HGG Adv 2024; 5:100273. [PMID: 38297832 PMCID: PMC10876629 DOI: 10.1016/j.xhgg.2024.100273] [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] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2023] [Revised: 01/23/2024] [Accepted: 01/23/2024] [Indexed: 02/02/2024] Open
Abstract
Heterozygous missense variants and in-frame indels in SMC3 are a cause of Cornelia de Lange syndrome (CdLS), marked by intellectual disability, growth deficiency, and dysmorphism, via an apparent dominant-negative mechanism. However, the spectrum of manifestations associated with SMC3 loss-of-function variants has not been reported, leading to hypotheses of alternative phenotypes or even developmental lethality. We used matchmaking servers, patient registries, and other resources to identify individuals with heterozygous, predicted loss-of-function (pLoF) variants in SMC3, and analyzed population databases to characterize mutational intolerance in this gene. Here, we show that SMC3 behaves as an archetypal haploinsufficient gene: it is highly constrained against pLoF variants, strongly depleted for missense variants, and pLoF variants are associated with a range of developmental phenotypes. Among 14 individuals with SMC3 pLoF variants, phenotypes were variable but coalesced on low growth parameters, developmental delay/intellectual disability, and dysmorphism, reminiscent of atypical CdLS. Comparisons to individuals with SMC3 missense/in-frame indel variants demonstrated an overall milder presentation in pLoF carriers. Furthermore, several individuals harboring pLoF variants in SMC3 were nonpenetrant for growth, developmental, and/or dysmorphic features, and some had alternative symptomatologies with rational biological links to SMC3. Analyses of tumor and model system transcriptomic data and epigenetic data in a subset of cases suggest that SMC3 pLoF variants reduce SMC3 expression but do not strongly support clustering with functional genomic signatures of typical CdLS. Our finding of substantial population-scale LoF intolerance in concert with variable growth and developmental features in subjects with SMC3 pLoF variants expands the scope of cohesinopathies, informs on their allelic architecture, and suggests the existence of additional clearly LoF-constrained genes whose disease links will be confirmed only by multilayered genomic data paired with careful phenotyping.
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Affiliation(s)
- Morad Ansari
- South East Scotland Genetic Service, Western General Hospital, Edinburgh, UK; MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK
| | - Kamli N W Faour
- Division of Genetics and Genomics, Boston Children's Hospital, Boston, MA, USA; Cornelia de Lange Syndrome and Related Disorders Clinic, Boston Children's Hospital, Boston, MA, USA
| | - Akiko Shimamura
- Division of Hematology and Oncology, Boston Children's Hospital, Boston, MA, USA
| | - Graeme Grimes
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK
| | - Emeline M Kao
- Institutional Centers for Clinical and Translational Research, Boston Children's Hospital, Boston, MA, USA
| | - Erica R Denhoff
- Institutional Centers for Clinical and Translational Research, Boston Children's Hospital, Boston, MA, USA
| | - Ana Blatnik
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK; Department of Clinical Cancer Genetics, Institute of Oncology Ljubljana, Ljubljana, Slovenia
| | - Daniel Ben-Isvy
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA; Medical and Population Genetics, The Broad Institute of MIT and Harvard, Cambridge, MA, USA; Division of Medical Sciences, Harvard Medical School, Boston, MA, USA
| | - Lily Wang
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA; Medical and Population Genetics, The Broad Institute of MIT and Harvard, Cambridge, MA, USA; Division of Medical Sciences, Harvard Medical School, Boston, MA, USA
| | - Benjamin M Helm
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Helen Firth
- Clinical Genetics, Addenbrooke's Hospital, Cambridge University Hospitals, Cambridge, UK
| | - Amy M Breman
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Emilia K Bijlsma
- Department of Clinical Genetics, Leiden University Medical Centre, Leiden, the Netherlands
| | - Aiko Iwata-Otsubo
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Thomy J L de Ravel
- Centre for Human Genetics, UZ Leuven/Leuven University Hospitals, Leuven, Belgium
| | | | - Alan Fryer
- Department of Clinical Genetics, Alder Hey Children's Hospital Liverpool, Liverpool, UK
| | | | - Lara G Stühn
- Institute of Medical Genetics and Applied Genomics, University of Tübingen, Tübingen, Germany
| | - Tobias B Haack
- Institute of Medical Genetics and Applied Genomics, University of Tübingen, Tübingen, Germany
| | - G Christoph Korenke
- Department of Neuropaediatric and Metabolic Diseases, University Children's Hospital Oldenburg, Oldenburg, Germany
| | - Panayiotis Constantinou
- West of Scotland Centre for Genomic Medicine, Queen Elizabeth University Hospital, Glasgow, UK
| | | | - Karen J Low
- University Hospitals Bristol and Weston NHS Foundation Trust, Bristol, UK; University of Bristol, Bristol, UK
| | - Emily Place
- Massachusetts Eye and Ear Infirmary, Boston, MA, USA
| | | | | | | | | | - Matthew A Deardorff
- Departments of Pathology and Pediatrics, Children's Hospital Los Angeles and University of Southern California, Los Angeles, CA, USA
| | - Wanqing Shao
- Research Computing, Information Technology, Boston Children's Hospital, Boston, MA, USA
| | - Shira Rockowitz
- Division of Genetics and Genomics, Boston Children's Hospital, Boston, MA, USA; Research Computing, Information Technology, Boston Children's Hospital, Boston, MA, USA; The Manton Center for Orphan Disease Research, Boston Children's Hospital, Boston, MA, USA
| | - Ian Krantz
- Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Maninder Kaur
- Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Sarah Raible
- Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | | | - Sabine Kliesch
- Department of Clinical and Surgical Andrology, Centre of Reproductive Medicine and Andrology, University Hospital Münster, Münster, Germany
| | - Moriel Singer-Berk
- Medical and Population Genetics, The Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Emily Groopman
- Division of Genetics and Genomics, Boston Children's Hospital, Boston, MA, USA; Medical and Population Genetics, The Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Stephanie DiTroia
- Medical and Population Genetics, The Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Sonia Ballal
- Cornelia de Lange Syndrome and Related Disorders Clinic, Boston Children's Hospital, Boston, MA, USA; Division of Gastroenterology, Boston Children's Hospital, Boston, MA, USA
| | - Siddharth Srivastava
- Cornelia de Lange Syndrome and Related Disorders Clinic, Boston Children's Hospital, Boston, MA, USA; Divison of Neurology, Boston Children's Hospital, Boston, MA, USA
| | | | - Saskia Biskup
- Zentrum für Humangenetik, Tübingen, Germany; Center for Genomics and Transcriptomics (CeGaT), Tübingen, Germany
| | - Jessica Rzasa
- Molecular Diagnostics Program and Verspeeten Clinical Genome Centre, London Health Sciences Centre, London, ON, Canada
| | - Jennifer Kerkhof
- Molecular Diagnostics Program and Verspeeten Clinical Genome Centre, London Health Sciences Centre, London, ON, Canada
| | - Haley McConkey
- Molecular Diagnostics Program and Verspeeten Clinical Genome Centre, London Health Sciences Centre, London, ON, Canada
| | - Bekim Sadikovic
- Molecular Diagnostics Program and Verspeeten Clinical Genome Centre, London Health Sciences Centre, London, ON, Canada
| | - Sarah Hilton
- Manchester Centre for Genomic Medicine, Manchester University NHS Foundation Trust, Health Innovation Manchester, Manchester, UK
| | - Siddharth Banka
- Manchester Centre for Genomic Medicine, Manchester University NHS Foundation Trust, Health Innovation Manchester, Manchester, UK; Division of Evolution, Infection, and Genomics, School of Biological Sciences, Faculty of Biology, Medicine, and Health, University of Manchester, Manchester, UK
| | - Frank Tüttelmann
- Institute of Reproductive Genetics, University of Münster, Münster, Germany
| | - Donald F Conrad
- Division of Genetics, Oregon National Primate Research Center, Oregon Health and Science University, Portland, OR, USA; Center for Embryonic Cell and Gene Therapy, Oregon Health and Science University, Portland, OR, USA
| | - Anne O'Donnell-Luria
- Division of Genetics and Genomics, Boston Children's Hospital, Boston, MA, USA; Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA; Medical and Population Genetics, The Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Michael E Talkowski
- Medical and Population Genetics, The Broad Institute of MIT and Harvard, Cambridge, MA, USA; Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - David R FitzPatrick
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK
| | - Philip M Boone
- Cornelia de Lange Syndrome and Related Disorders Clinic, Boston Children's Hospital, Boston, MA, USA; Division of Genetics and Genomics, Boston Children's Hospital, Boston, MA, USA; Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA; Medical and Population Genetics, The Broad Institute of MIT and Harvard, Cambridge, MA, USA.
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2
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Sajan SA, Gradisch R, Vogel FD, Coffey AJ, Salyakina D, Soler D, Jayakar P, Jayakar A, Bianconi SE, Cooper AH, Liu S, William N, Benkel-Herrenbrück I, Maiwald R, Heller C, Biskup S, Leiz S, Westphal DS, Wagner M, Clarke A, Stockner T, Ernst M, Kesari A, Krenn M. De novo variants in GABRA4 are associated with a neurological phenotype including developmental delay, behavioral abnormalities and epilepsy. Eur J Hum Genet 2024:10.1038/s41431-024-01600-3. [PMID: 38565639 DOI: 10.1038/s41431-024-01600-3] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2023] [Revised: 02/03/2024] [Accepted: 03/19/2024] [Indexed: 04/04/2024] Open
Abstract
Nine out of 19 genes encoding GABAA receptor subunits have been linked to monogenic syndromes characterized by seizures and developmental disorders. Previously, we reported the de novo variant p.(Thr300Ile) in GABRA4 in a patient with epilepsy and neurodevelopmental abnormalities. However, no new cases have been reported since then. Through an international collaboration, we collected molecular and phenotype data of individuals carrying de novo variants in GABRA4. Patients and their parents were investigated either by exome or genome sequencing, followed by targeted Sanger sequencing in some cases. All variants within the transmembrane domain, including the previously reported p.(Thr300Ile) variant, were characterized in silico and analyzed by molecular dynamics (MD) simulation studies. We identified three novel de novo missense variants in GABRA4 (NM_000809.4): c.797 C > T, p.(Pro266Leu), c.899 C > A, p.(Thr300Asn), and c.634 G > A, p.(Val212Ile). The p.(Thr300Asn) variant impacts the same codon as the previously reported variant p.(Thr300Ile) and likely arose post-zygotically as evidenced by sequencing oral mucosal cells. Overlapping phenotypes among affected individuals included developmental delay (4/4), epileptiform EEG abnormalities (3/4), attention deficits (3/4), seizures (2/4), autistic features (2/4) and structural brain abnormalities (2/4). MD simulations of the three variants within the transmembrane domain of the receptor indicate that sub-microsecond scale dynamics differ between wild-type and mutated subunits. Taken together, our findings further corroborate an association between GABRA4 and a neurological phenotype including variable neurodevelopmental, behavioral and epileptic abnormalities.
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Affiliation(s)
- Samin A Sajan
- Department of Pediatrics, University of Wisconsin School of Medicine and Public Health, Madison, WI, USA
| | - Ralph Gradisch
- Center for Physiology and Pharmacology, Medical University of Vienna, Vienna, Austria
- Institute of Pharmacology and Toxicology, University of Zurich, Zurich, Switzerland
| | - Florian D Vogel
- Department of Pathobiology of the Nervous System, Center for Brain Research, Medical University of Vienna, Vienna, Austria
| | - Alison J Coffey
- lllumina Clinical Services Laboratory, Illumina Inc., San Diego, CA, USA
| | - Daria Salyakina
- Personalized Medicine and Health Outcomes Research, Nicklaus Children's Hospital, Miami, FL, USA
| | - Diana Soler
- Personalized Medicine and Health Outcomes Research, Nicklaus Children's Hospital, Miami, FL, USA
| | - Parul Jayakar
- Division of Genetics and Metabolism, Nicklaus Children's Hospital, Miami, FL, USA
| | - Anuj Jayakar
- Department of Neurology, Division of Epilepsy, Nicklaus Children's Hospital, Miami, FL, USA
| | | | | | | | | | | | - Robert Maiwald
- Medizinisches Versorgungszentrum für Gerinnungsdiagnostik und Medizinische Genetik Köln, Köln, Germany
| | | | - Saskia Biskup
- Zentrum für Humangenetik, Tübingen, Germany
- Center for Genomics and Transcriptomics (CeGaT), Tübingen, Germany
| | - Steffen Leiz
- Division of Neuropediatrics, Klinikum Dritter Orden, Munich, Germany
| | - Dominik S Westphal
- Institute of Human Genetics, School of Medicine, Klinikum rechts der Isar, Technical University of Munich, Munich, Germany
- Department of Internal Medicine I, School of Medicine & Klinikum rechts der Isar, Technical University of Munich, Munich, Germany
| | - Matias Wagner
- Institute of Human Genetics, School of Medicine, Klinikum rechts der Isar, Technical University of Munich, Munich, Germany
| | - Amy Clarke
- Center for Physiology and Pharmacology, Medical University of Vienna, Vienna, Austria
| | - Thomas Stockner
- Center for Physiology and Pharmacology, Medical University of Vienna, Vienna, Austria
| | - Margot Ernst
- Department of Pathobiology of the Nervous System, Center for Brain Research, Medical University of Vienna, Vienna, Austria
| | - Akanchha Kesari
- lllumina Clinical Services Laboratory, Illumina Inc., San Diego, CA, USA
| | - Martin Krenn
- Department of Neurology, Medical University of Vienna, Vienna, Austria.
- Comprehensive Center for Clinical Neurosciences & Mental Health, Medical University of Vienna, Vienna, Austria.
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3
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Zwirner S, Abu Rmilah AA, Klotz S, Pfaffenroth B, Kloevekorn P, Moschopoulou AA, Schuette S, Haag M, Selig R, Li K, Zhou W, Nelson E, Poso A, Chen H, Amiot B, Jia Y, Minshew A, Michalak G, Cui W, Rist E, Longerich T, Jung B, Felgendreff P, Trompak O, Premsrirut PK, Gries K, Muerdter TE, Heinkele G, Wuestefeld T, Shapiro D, Weissbach M, Koenigsrainer A, Sipos B, Ab E, Zacarias MO, Theisgen S, Gruenheit N, Biskup S, Schwab M, Albrecht W, Laufer S, Nyberg S, Zender L. First-in-class MKK4 inhibitors enhance liver regeneration and prevent liver failure. Cell 2024; 187:1666-1684.e26. [PMID: 38490194 PMCID: PMC11011246 DOI: 10.1016/j.cell.2024.02.023] [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] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2023] [Revised: 11/20/2023] [Accepted: 02/20/2024] [Indexed: 03/17/2024]
Abstract
Diminished hepatocyte regeneration is a key feature of acute and chronic liver diseases and after extended liver resections, resulting in the inability to maintain or restore a sufficient functional liver mass. Therapies to restore hepatocyte regeneration are lacking, making liver transplantation the only curative option for end-stage liver disease. Here, we report on the structure-based development and characterization (nuclear magnetic resonance [NMR] spectroscopy) of first-in-class small molecule inhibitors of the dual-specificity kinase MKK4 (MKK4i). MKK4i increased liver regeneration upon hepatectomy in murine and porcine models, allowed for survival of pigs in a lethal 85% hepatectomy model, and showed antisteatotic and antifibrotic effects in liver disease mouse models. A first-in-human phase I trial (European Union Drug Regulating Authorities Clinical Trials [EudraCT] 2021-000193-28) with the clinical candidate HRX215 was conducted and revealed excellent safety and pharmacokinetics. Clinical trials to probe HRX215 for prevention/treatment of liver failure after extensive oncological liver resections or after transplantation of small grafts are warranted.
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Affiliation(s)
- Stefan Zwirner
- Department of Medical Oncology and Pneumology (Internal Medicine VIII), University Hospital Tübingen, Tübingen 72076, Germany; HepaRegeniX GmbH, Tübingen 72072, Germany
| | - Anan A Abu Rmilah
- William J. von Liebig Center for Transplantation and Clinical Regeneration, Mayo Clinic, Rochester, MN 55905, USA
| | - Sabrina Klotz
- Department of Medical Oncology and Pneumology (Internal Medicine VIII), University Hospital Tübingen, Tübingen 72076, Germany
| | - Bent Pfaffenroth
- Department of Pharmaceutical Chemistry, University of Tübingen, Tübingen 72076, Germany
| | - Philip Kloevekorn
- Department of Pharmaceutical Chemistry, University of Tübingen, Tübingen 72076, Germany
| | - Athina A Moschopoulou
- Department of Medical Oncology and Pneumology (Internal Medicine VIII), University Hospital Tübingen, Tübingen 72076, Germany
| | - Svenja Schuette
- Department of Medical Oncology and Pneumology (Internal Medicine VIII), University Hospital Tübingen, Tübingen 72076, Germany
| | - Mathias Haag
- Dr. Margarete Fischer-Bosch Institute of Clinical Pharmacology, Stuttgart 70376, Germany
| | - Roland Selig
- HepaRegeniX GmbH, Tübingen 72072, Germany; Department of Pharmaceutical Chemistry, University of Tübingen, Tübingen 72076, Germany
| | - Kewei Li
- William J. von Liebig Center for Transplantation and Clinical Regeneration, Mayo Clinic, Rochester, MN 55905, USA
| | - Wei Zhou
- William J. von Liebig Center for Transplantation and Clinical Regeneration, Mayo Clinic, Rochester, MN 55905, USA
| | - Erek Nelson
- William J. von Liebig Center for Transplantation and Clinical Regeneration, Mayo Clinic, Rochester, MN 55905, USA
| | - Antti Poso
- Department of Medical Oncology and Pneumology (Internal Medicine VIII), University Hospital Tübingen, Tübingen 72076, Germany; School of Pharmacy, University of Eastern Finland, Kuopio 70211, Finland; iFIT Cluster of Excellence (EXC 2180) "Image-guided and Functionally Instructed Tumor Therapies", University of Tübingen, Tübingen 72076, Germany
| | - Harvey Chen
- William J. von Liebig Center for Transplantation and Clinical Regeneration, Mayo Clinic, Rochester, MN 55905, USA
| | - Bruce Amiot
- William J. von Liebig Center for Transplantation and Clinical Regeneration, Mayo Clinic, Rochester, MN 55905, USA
| | - Yao Jia
- William J. von Liebig Center for Transplantation and Clinical Regeneration, Mayo Clinic, Rochester, MN 55905, USA
| | - Anna Minshew
- William J. von Liebig Center for Transplantation and Clinical Regeneration, Mayo Clinic, Rochester, MN 55905, USA
| | - Gregory Michalak
- William J. von Liebig Center for Transplantation and Clinical Regeneration, Mayo Clinic, Rochester, MN 55905, USA
| | - Wei Cui
- Department of Medical Oncology and Pneumology (Internal Medicine VIII), University Hospital Tübingen, Tübingen 72076, Germany
| | - Elke Rist
- Department of Medical Oncology and Pneumology (Internal Medicine VIII), University Hospital Tübingen, Tübingen 72076, Germany
| | - Thomas Longerich
- Institute of Pathology, University Hospital Heidelberg, Heidelberg 69120, Germany
| | | | - Philipp Felgendreff
- William J. von Liebig Center for Transplantation and Clinical Regeneration, Mayo Clinic, Rochester, MN 55905, USA
| | - Omelyan Trompak
- Department of Medical Oncology and Pneumology (Internal Medicine VIII), University Hospital Tübingen, Tübingen 72076, Germany
| | | | - Katharina Gries
- Department of Medical Oncology and Pneumology (Internal Medicine VIII), University Hospital Tübingen, Tübingen 72076, Germany
| | - Thomas E Muerdter
- Dr. Margarete Fischer-Bosch Institute of Clinical Pharmacology, Stuttgart 70376, Germany
| | - Georg Heinkele
- Dr. Margarete Fischer-Bosch Institute of Clinical Pharmacology, Stuttgart 70376, Germany
| | - Torsten Wuestefeld
- Laboratory for In Vivo Genetics & Gene Therapy, Genome Institute of Singapore, Agency for Science, Technology and Research (A(∗)STAR), Singapore 138672, Singapore; School of Biological Sciences, Nanyang Technological University of Singapore, Singapore 637551, Singapore
| | | | | | - Alfred Koenigsrainer
- iFIT Cluster of Excellence (EXC 2180) "Image-guided and Functionally Instructed Tumor Therapies", University of Tübingen, Tübingen 72076, Germany; German Cancer Research Consortium (DKTK), German Cancer Research Center (DKFZ), Heidelberg 69120, Germany; Department of General-, Visceral, and Transplant Surgery, University Hospital Tübingen, Tübingen 72076, Germany
| | - Bence Sipos
- Department of Medical Oncology and Pneumology (Internal Medicine VIII), University Hospital Tübingen, Tübingen 72076, Germany
| | - Eiso Ab
- ZoBio B.V., Leiden 2333 CH, the Netherlands
| | | | | | | | | | - Matthias Schwab
- Dr. Margarete Fischer-Bosch Institute of Clinical Pharmacology, Stuttgart 70376, Germany; iFIT Cluster of Excellence (EXC 2180) "Image-guided and Functionally Instructed Tumor Therapies", University of Tübingen, Tübingen 72076, Germany; Department of Clinical Pharmacology, Pharmacy and Biochemistry, University of Tübingen, Tübingen 72076, Germany
| | | | - Stefan Laufer
- Department of Pharmaceutical Chemistry, University of Tübingen, Tübingen 72076, Germany; Tübingen Center for Academic Drug Discovery & Development (TüCAD(2)), Tübingen 72076, Germany.
| | - Scott Nyberg
- William J. von Liebig Center for Transplantation and Clinical Regeneration, Mayo Clinic, Rochester, MN 55905, USA.
| | - Lars Zender
- Department of Medical Oncology and Pneumology (Internal Medicine VIII), University Hospital Tübingen, Tübingen 72076, Germany; iFIT Cluster of Excellence (EXC 2180) "Image-guided and Functionally Instructed Tumor Therapies", University of Tübingen, Tübingen 72076, Germany; German Cancer Research Consortium (DKTK), German Cancer Research Center (DKFZ), Heidelberg 69120, Germany; Tübingen Center for Academic Drug Discovery & Development (TüCAD(2)), Tübingen 72076, Germany.
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4
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Schoch K, Ruegg MSG, Fellows BJ, Cao J, Uhrig S, Einsele-Scholz S, Biskup S, Hawarden SRA, Salpietro V, Capra V, Brown CM, Accogli A, Shashi V, Bicknell LS. A second hotspot for pathogenic exon-skipping variants in CDC45. Eur J Hum Genet 2024:10.1038/s41431-024-01583-1. [PMID: 38467731 DOI: 10.1038/s41431-024-01583-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2023] [Revised: 02/13/2024] [Accepted: 02/26/2024] [Indexed: 03/13/2024] Open
Abstract
Biallelic pathogenic variants in CDC45 are associated with Meier-Gorlin syndrome with craniosynostosis (MGORS type 7), which also includes short stature and absent/hypoplastic patellae. Identified variants act through a hypomorphic loss of function mechanism, to reduce CDC45 activity and impact DNA replication initiation. In addition to missense and premature termination variants, several pathogenic synonymous variants have been identified, most of which cause increased exon skipping of exon 4, which encodes an essential part of the RecJ-orthologue's DHH domain. Here we have identified a second cohort of families segregating CDC45 variants, where patients have craniosynostosis and a reduction in height, alongside common facial dysmorphisms, including thin eyebrows, consistent with MGORS7. Skipping of exon 15 is a consequence of two different variants, including a shared synonymous variant that is enriched in individuals of East Asian ancestry, while other variants in trans are predicted to alter key intramolecular interactions in α/β domain II, or cause retention of an intron within the 3'UTR. Our cohort and functional data confirm exon skipping is a relatively common pathogenic mechanism in CDC45, and highlights the need for alternative splicing events, such as exon skipping, to be especially considered for variants initially predicted to be less likely to cause the phenotype, particularly synonymous variants.
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Affiliation(s)
- Kelly Schoch
- Division of Medical Genetics, Department of Pediatrics, Duke University School of Medicine, Durham, NC, USA
| | - Mischa S G Ruegg
- Department of Biochemistry, University of Otago, Dunedin, New Zealand
| | - Bridget J Fellows
- Department of Biochemistry, University of Otago, Dunedin, New Zealand
| | - Joseph Cao
- Division of Pediatric Radiology, Department of Radiology Duke University School of Medicine, Durham, NC, USA
| | - Sabine Uhrig
- Institute of Clinical Genetics, Klinikum Stuttgart, Stuttgart, Germany
| | | | - Saskia Biskup
- Center for Human Genetics Tuebingen and CeGaT GmbH, Tuebingen, Germany
| | - Samuel R A Hawarden
- Department of Pathology, Dunedin School of Medicine, University of Otago, Dunedin, New Zealand
| | - Vincenzo Salpietro
- Department of Biotechnological and Applied Clinical Sciences, University of L'Aquila, L'Aquila, Italy
| | - Valeria Capra
- Genomics and Clinical Genetics, IRCCS Istituto Giannina Gaslini, Genoa, Italy
| | - Chris M Brown
- Department of Biochemistry, University of Otago, Dunedin, New Zealand
| | - Andrea Accogli
- Department of Specialized Medicine, Division of Medical Genetics, McGill University Health Centre, Montreal, QC, Canada
- Department of Human Genetics, Faculty of Medicine, McGill University, Montreal, QC, Canada
| | - Vandana Shashi
- Division of Medical Genetics, Department of Pediatrics, Duke University School of Medicine, Durham, NC, USA
| | - Louise S Bicknell
- Department of Biochemistry, University of Otago, Dunedin, New Zealand.
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5
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Park JH, Och U, Braun T, Kriegel MF, Biskup S, Korall H, Uhlig CE, Marquardt T. Treatment of AICA ribosiduria by suppression of de novo purine synthesis. Mol Genet Metab 2024; 141:108124. [PMID: 38244287 DOI: 10.1016/j.ymgme.2023.108124] [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] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/24/2023] [Revised: 12/29/2023] [Accepted: 12/30/2023] [Indexed: 01/22/2024]
Abstract
AICA ribosiduria is an ultra-rare disorder of de novo purine biosynthesis associated with developmental delay of varying severity, seizures, and varying degrees of visual impairment due to chorioretinal atrophy. Caused by biallelic pathogenic variants in ATIC, accumulation of AICA-riboside is the biochemical hallmark and presumed pathomechanism of the condition. In this study, we report the case of a teenage patient compound-heterozygous for the variants c.1277 A > G (p.K426R) and c.642G > C (p.Q214H) in ATIC, with the latter not previously reported. Excessive secretion of AICA-riboside and succinyladenosine was significantly reduced following the introduction of a purine-enriched diet. By suppressing de novo purine biosynthesis in favour of purine salvage, exogenous purine substitution represents a promising treatment approach for AICA ribosiduria. SYNOPSIS: Suppression of de novo purine biosynthesis by increased exogeneous purine supply leads to decreased accumulation of AICA-riboside and succinyl-adenosine and thus is a promising treatment approach for AICA ribosiduria.
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Affiliation(s)
- Julien H Park
- Department of General Pediatrics, University of Münster, Münster, Germany
| | - Ulrike Och
- Department of General Pediatrics, University of Münster, Münster, Germany
| | - Tim Braun
- Zentrum für Stoffwechseldiagnostik GmbH, Reutlingen, Germany
| | - Matthias F Kriegel
- Department of Ophthalmology, University of Münster Medical Centre, Münster, Germany
| | - Saskia Biskup
- Center for Genomics and Transcriptomics CeGaT GmbH and Praxis für Humangenetik Tübingen, Tübingen, Germany
| | - Herbert Korall
- Zentrum für Stoffwechseldiagnostik GmbH, Reutlingen, Germany
| | - Constantin E Uhlig
- Department of Ophthalmology, University of Münster Medical Centre, Münster, Germany
| | - Thorsten Marquardt
- Department of General Pediatrics, University of Münster, Münster, Germany.
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6
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Spahn S, Kleinhenz F, Shevchenko E, Stahl A, Rasen Y, Geisler C, Ruhm K, Klaumuenzer M, Kronenberger T, Laufer SA, Sundberg-Malek H, Bui KC, Horger M, Biskup S, Schulze-Osthoff K, Templin M, Malek NP, Poso A, Bitzer M. The molecular interaction pattern of lenvatinib enables inhibition of wild-type or kinase-mutated FGFR2-driven cholangiocarcinoma. Nat Commun 2024; 15:1287. [PMID: 38346946 PMCID: PMC10861557 DOI: 10.1038/s41467-024-45247-6] [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] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2023] [Accepted: 01/18/2024] [Indexed: 02/15/2024] Open
Abstract
Fibroblast growth factor receptor (FGFR)-2 can be inhibited by FGFR-selective or non-selective tyrosine kinase inhibitors (TKIs). Selective TKIs are approved for cholangiocarcinoma (CCA) with FGFR2 fusions; however, their application is limited by a characteristic pattern of adverse events or evocation of kinase domain mutations. A comprehensive characterization of a patient cohort treated with the non-selective TKI lenvatinib reveals promising efficacy in FGFR2-driven CCA. In a bed-to-bench approach, we investigate FGFR2 fusion proteins bearing critical tumor-relevant point mutations. These mutations confer growth advantage of tumor cells and increased resistance to selective TKIs but remain intriguingly sensitive to lenvatinib. In line with clinical observations, in-silico analyses reveal a more favorable interaction pattern of lenvatinib with FGFR2, including an increased flexibility and ligand efficacy, compared to FGFR-selective TKIs. Finally, the treatment of a patient with progressive disease and a newly developed kinase mutation during therapy with a selective inhibitor results in a striking response to lenvatinib. Our in vitro, in silico, and clinical data suggest that lenvatinib is a promising treatment option for FGFR2-driven CCA, especially when insurmountable adverse reactions of selective TKIs or acquired kinase mutations occur.
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Affiliation(s)
- Stephan Spahn
- Department of Internal Medicine I, University Hospital Tuebingen, 72076, Tuebingen, Germany.
| | - Fabian Kleinhenz
- Department of Internal Medicine I, University Hospital Tuebingen, 72076, Tuebingen, Germany
| | - Ekaterina Shevchenko
- Department of Pharmaceutical and Medicinal Chemistry, Institute of Pharmaceutical Sciences, Eberhard-Karls-University, 72076, Tuebingen, Germany
- Tuebingen Center for Academic Drug Discovery & Development (TüCAD2), 72076, Tuebingen, Germany
| | - Aaron Stahl
- NMI Natural and Medical Sciences Institute at the University of Tuebingen, 72770, Reutlingen, Germany
| | - Yvonne Rasen
- Department of Internal Medicine I, University Hospital Tuebingen, 72076, Tuebingen, Germany
| | - Christine Geisler
- Department of Internal Medicine I, University Hospital Tuebingen, 72076, Tuebingen, Germany
| | - Kristina Ruhm
- Center for Personalized Medicine, Eberhard-Karls University, 72076, Tuebingen, Germany
| | | | - Thales Kronenberger
- Department of Pharmaceutical and Medicinal Chemistry, Institute of Pharmaceutical Sciences, Eberhard-Karls-University, 72076, Tuebingen, Germany
- Tuebingen Center for Academic Drug Discovery & Development (TüCAD2), 72076, Tuebingen, Germany
| | - Stefan A Laufer
- Department of Pharmaceutical and Medicinal Chemistry, Institute of Pharmaceutical Sciences, Eberhard-Karls-University, 72076, Tuebingen, Germany
- Tuebingen Center for Academic Drug Discovery & Development (TüCAD2), 72076, Tuebingen, Germany
- Cluster of Excellence, Image Guided and Functionally Instructed Tumor Therapies, Eberhard-Karls University, 72076, Tuebingen, Germany
| | - Holly Sundberg-Malek
- Center for Personalized Medicine, Eberhard-Karls University, 72076, Tuebingen, Germany
| | - Khac Cuong Bui
- Department of Internal Medicine I, University Hospital Tuebingen, 72076, Tuebingen, Germany
| | - Marius Horger
- Department of Diagnostic and Interventional Radiology, Eberhard-Karls University, 72076, Tuebingen, Germany
| | - Saskia Biskup
- CeGaT GmbH and Praxis für Humangenetik, 72076, Tuebingen, Germany
| | - Klaus Schulze-Osthoff
- Cluster of Excellence, Image Guided and Functionally Instructed Tumor Therapies, Eberhard-Karls University, 72076, Tuebingen, Germany
- Department of Molecular Medicine, Interfaculty Institute for Biochemistry, Eberhard-Karls University, 72076, Tuebingen, Germany
- German Cancer Consortium (DKTK) and German Cancer Research Center (DKFZ), 69120, Heidelberg, Germany
| | - Markus Templin
- NMI Natural and Medical Sciences Institute at the University of Tuebingen, 72770, Reutlingen, Germany
| | - Nisar P Malek
- Department of Internal Medicine I, University Hospital Tuebingen, 72076, Tuebingen, Germany
- Center for Personalized Medicine, Eberhard-Karls University, 72076, Tuebingen, Germany
- Cluster of Excellence, Image Guided and Functionally Instructed Tumor Therapies, Eberhard-Karls University, 72076, Tuebingen, Germany
- German Cancer Consortium (DKTK) and German Cancer Research Center (DKFZ), 69120, Heidelberg, Germany
- M3-Research Center for Malignome, Metabolome and Microbiome, Eberhard-Karls University, 72076, Tuebingen, Germany
| | - Antti Poso
- Department of Pharmaceutical and Medicinal Chemistry, Institute of Pharmaceutical Sciences, Eberhard-Karls-University, 72076, Tuebingen, Germany
- Tuebingen Center for Academic Drug Discovery & Development (TüCAD2), 72076, Tuebingen, Germany
- Cluster of Excellence, Image Guided and Functionally Instructed Tumor Therapies, Eberhard-Karls University, 72076, Tuebingen, Germany
- School of Pharmacy, University of Eastern Finland, 70210, Kuopio, Finland
| | - Michael Bitzer
- Department of Internal Medicine I, University Hospital Tuebingen, 72076, Tuebingen, Germany.
- Center for Personalized Medicine, Eberhard-Karls University, 72076, Tuebingen, Germany.
- Cluster of Excellence, Image Guided and Functionally Instructed Tumor Therapies, Eberhard-Karls University, 72076, Tuebingen, Germany.
- M3-Research Center for Malignome, Metabolome and Microbiome, Eberhard-Karls University, 72076, Tuebingen, Germany.
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7
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Harter J, Buth E, Johaenning J, Battke F, Kopp M, Zelba H, Schulze M, Koedding J, Biskup S. Analytical Performance Evaluation of a 523-Gene Circulating Tumor DNA Assay for Next-Generation Sequencing-Based Comprehensive Tumor Profiling in Liquid Biopsy Samples. J Mol Diagn 2024; 26:61-72. [PMID: 37865292 DOI: 10.1016/j.jmoldx.2023.10.001] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2023] [Revised: 09/21/2023] [Accepted: 10/02/2023] [Indexed: 10/23/2023] Open
Abstract
Next-generation sequencing (NGS)-based comprehensive tumor profiling from liquid biopsy samples can significantly improve diagnosis and monitoring of tumors when high-quality tissue material is difficult to obtain. In addition, it offers the potential to capture the entire complexity of the tumor, which is particularly important for highly heterogeneous or metastatic tumors. Here, we report the findings of an analytical performance evaluation of the TruSight Oncology 500 circulating tumor DNA (ctDNA) assay, a 523-gene NGS panel developed for ctDNA-based comprehensive genomic profiling of tumors, using reference and patient samples. Using 30 ng cell-free DNA, the assay showed high sensitivity and low variant detection variability for single-nucleotide variants, insertions and deletions, and fusions down to a variant allele frequency (VAF) of 0.5% in the reference samples and VAFs that were highly concordant with previous digital droplet PCR results in the patient samples. At reduced input amounts (20, 15, and 5 ng) and below VAFs of 0.5%, sensitivity was considerably lower and variant detection variability increased. Covering 523 tumor-associated genes, the assay demonstrated a convincing performance comparable to NGS-based ctDNA assays with smaller gene panels, highlighting its value to screen large numbers of different genes.
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Affiliation(s)
| | | | | | | | | | - Henning Zelba
- Center for Human Genetics Tuebingen, Tuebingen, Germany
| | | | | | - Saskia Biskup
- CeGaT GmbH, Tuebingen, Germany; Center for Human Genetics Tuebingen, Tuebingen, Germany
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8
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Rensing-Ehl A, Lorenz MR, Führer M, Willenbacher W, Willenbacher E, Sopper S, Abinun M, Maccari ME, König C, Haegele P, Fuchs S, Castro C, Kury P, Pelle O, Klemann C, Heeg M, Thalhammer J, Wegehaupt O, Fischer M, Goldacker S, Schulte B, Biskup S, Chatelain P, Schuster V, Warnatz K, Grimbacher B, Meinhardt A, Holzinger D, Oommen PT, Hinze T, Hebart H, Seeger K, Lehmberg K, Leahy TR, Claviez A, Vieth S, Schilling FH, Fuchs I, Groß M, Rieux-Laucat F, Magerus A, Speckmann C, Schwarz K, Ehl S. Abnormal biomarkers predict complex FAS or FADD defects missed by exome sequencing. J Allergy Clin Immunol 2024; 153:297-308.e12. [PMID: 37979702 DOI: 10.1016/j.jaci.2023.11.006] [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] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2023] [Revised: 11/06/2023] [Accepted: 11/09/2023] [Indexed: 11/20/2023]
Abstract
BACKGROUND Elevated TCRαβ+CD4-CD8- double-negative T cells (DNT) and serum biomarkers help identify FAS mutant patients with autoimmune lymphoproliferative syndrome (ALPS). However, in some patients with clinical features and biomarkers consistent with ALPS, germline or somatic FAS mutations cannot be identified on standard exon sequencing (ALPS-undetermined: ALPS-U). OBJECTIVE We sought to explore whether complex genetic alterations in the FAS gene escaping standard sequencing or mutations in other FAS pathway-related genes could explain these cases. METHODS Genetic analysis included whole FAS gene sequencing, copy number variation analysis, and sequencing of FAS cDNA and other FAS pathway-related genes. It was guided by FAS expression analysis on CD57+DNT, which can predict somatic loss of heterozygosity (sLOH). RESULTS Nine of 16 patients with ALPS-U lacked FAS expression on CD57+DNT predicting heterozygous "loss-of-expression" FAS mutations plus acquired somatic second hits in the FAS gene, enriched in DNT. Indeed, 7 of 9 analyzed patients carried deep intronic mutations or large deletions in the FAS gene combined with sLOH detectable in DNT; 1 patient showed a FAS exon duplication. Three patients had reduced FAS expression, and 2 of them harbored mutations in the FAS promoter, which reduced FAS expression in reporter assays. Three of the 4 ALPS-U patients with normal FAS expression carried heterozygous FADD mutations with sLOH. CONCLUSION A combination of serum biomarkers and DNT phenotyping is an accurate means to identify patients with ALPS who are missed by routine exome sequencing.
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Affiliation(s)
- Anne Rensing-Ehl
- Institute for Immunodeficiency, Center for Chronic Immunodeficiency (CCI), Medical Center - University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany.
| | | | - Marita Führer
- Institute for Clinical Transfusion Medicine and Immunogenetics Ulm, German Red Cross Blood Service Baden-Wuerttemberg - Hessen, Ulm, Germany
| | - Wolfgang Willenbacher
- Clinic for Internal Medicine V, Hematology and Oncology, Medical University Innsbruck, Innsbruck, Austria; Syndena GmbH, Connect to cure, Innsbruck, Austria
| | - Ella Willenbacher
- Clinic for Internal Medicine V, Hematology and Oncology, Medical University Innsbruck, Innsbruck, Austria
| | - Sieghart Sopper
- Clinic for Internal Medicine V, Hematology and Oncology, Medical University Innsbruck, Innsbruck, Austria; Tyrolean Cancer Research Institute, Innsbruck, Austria
| | - Mario Abinun
- Paediatric Immunology, Great North Children's Hospital, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Maria Elena Maccari
- Institute for Immunodeficiency, Center for Chronic Immunodeficiency (CCI), Medical Center - University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany; Division of Pediatric Hematology and Oncology, Department of Pediatrics and Adolescent Medicine, Medical Center - University of Freiburg, Faculty of Medicine, University of Freiburg, Mathildenstr. 1, Freiburg, Germany
| | - Christoph König
- Institute for Immunodeficiency, Center for Chronic Immunodeficiency (CCI), Medical Center - University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany; Faculty of Biology, University of Freiburg, Schaenzlestrasse 1, Freiburg, Germany
| | - Pauline Haegele
- Institute for Immunodeficiency, Center for Chronic Immunodeficiency (CCI), Medical Center - University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Sebastian Fuchs
- Institute for Immunodeficiency, Center for Chronic Immunodeficiency (CCI), Medical Center - University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Carla Castro
- Institute for Immunodeficiency, Center for Chronic Immunodeficiency (CCI), Medical Center - University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Patrick Kury
- Institute for Immunodeficiency, Center for Chronic Immunodeficiency (CCI), Medical Center - University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Olivier Pelle
- Laboratory of Immunogenetics of Pediatric Autoimmune Diseases, Université Paris Cité, INSERM UMR 1163, Imagine Institute, Paris, France
| | - Christian Klemann
- Institute for Immunodeficiency, Center for Chronic Immunodeficiency (CCI), Medical Center - University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Maximilian Heeg
- Institute for Immunodeficiency, Center for Chronic Immunodeficiency (CCI), Medical Center - University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Julian Thalhammer
- Institute for Immunodeficiency, Center for Chronic Immunodeficiency (CCI), Medical Center - University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany; Paediatric Immunology, Great North Children's Hospital, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Oliver Wegehaupt
- Institute for Immunodeficiency, Center for Chronic Immunodeficiency (CCI), Medical Center - University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany; Division of Pediatric Hematology and Oncology, Department of Pediatrics and Adolescent Medicine, Medical Center - University of Freiburg, Faculty of Medicine, University of Freiburg, Mathildenstr. 1, Freiburg, Germany
| | - Marco Fischer
- Institute for Immunodeficiency, Center for Chronic Immunodeficiency (CCI), Medical Center - University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany; Division of Pediatric Hematology and Oncology, Department of Pediatrics and Adolescent Medicine, Medical Center - University of Freiburg, Faculty of Medicine, University of Freiburg, Mathildenstr. 1, Freiburg, Germany
| | - Sigune Goldacker
- Institute for Immunodeficiency, Center for Chronic Immunodeficiency (CCI), Medical Center - University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Björn Schulte
- Center for Human Genetics, Paul-Ehrlich-Str. 23, Tuebingen, Germany
| | - Saskia Biskup
- Center for Human Genetics, Paul-Ehrlich-Str. 23, Tuebingen, Germany
| | | | - Volker Schuster
- Children's Hospital, Faculty of Medicine, University of Leipzig, Leipzig, Germany
| | - Klaus Warnatz
- Institute for Immunodeficiency, Center for Chronic Immunodeficiency (CCI), Medical Center - University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany; Clinic for Rheumatolgy and Clinical Immunology, Medical Center - University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Bodo Grimbacher
- Institute for Immunodeficiency, Center for Chronic Immunodeficiency (CCI), Medical Center - University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany; Clinic for Rheumatolgy and Clinical Immunology, Medical Center - University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany; DZIF - German Center for Infection Research, Satellite Center Freiburg, Freiburg, Germany; CIBSS - Centre for Integrative Biological Signalling Studies, Albert-Ludwigs University, Freiburg, Germany; RESIST - Cluster of Excellence 2155 to Hannover Medical School, Satellite Center Freiburg, Freiburg, Germany
| | - Andrea Meinhardt
- Center for Pediatrics and Adolescent Medicine, Department of Pediatric Oncology, Hematology and Immunodeficiencies, University Hospital Giessen, Giessen, Germany
| | - Dirk Holzinger
- Department of Pediatric Hematology-Oncology, University of Duisburg-Essen, Essen, Germany; Department of Applied Health Sciences, University of Applied Sciences Bochum, Bochum, Germany
| | - Prasad Thomas Oommen
- Department of Pediatric Oncology, Hematology and Clinical Immunology, University Hospital, Medical Faculty, Heinrich Heine University, Düsseldorf, Germany
| | - Tanja Hinze
- Department of Pediatric Rheumatology and Immunology, University Hospital Münster, Münster, Germany
| | - Holger Hebart
- Department of Internal Medicine, Kliniken Ostalb, Stauferklinikum, Mutlangen, Germany
| | - Karlheinz Seeger
- Charité Universitätsmedizin Berlin, Department of Pediatric Oncology/Hematology, Augustenburger Pl. 1, Berlin, Germany
| | - Kai Lehmberg
- Department of Paediatric Immunology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Timothy Ronan Leahy
- Department of Paediatric Immunology/ID, Children's Health Ireland (CHI) at Crumlin, Dublin; University of Dublin, Trinity College, Dublin, Ireland
| | - Alexander Claviez
- Department of Pediatrics, University Medical Center, UKSH Campus Kiel, Kiel, Germany
| | - Simon Vieth
- Department of Pediatrics, University Medical Center, UKSH Campus Kiel, Kiel, Germany
| | - Freimut H Schilling
- Department of Pediatric Oncology-Hematology-Immunology, Children's Hospital Lucerne, Lucerne, Switzerland
| | - Ilka Fuchs
- Institute for Immunodeficiency, Center for Chronic Immunodeficiency (CCI), Medical Center - University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Miriam Groß
- Institute for Immunodeficiency, Center for Chronic Immunodeficiency (CCI), Medical Center - University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Frederic Rieux-Laucat
- Laboratory of Immunogenetics of Pediatric Autoimmune Diseases, Université Paris Cité, INSERM UMR 1163, Imagine Institute, Paris, France
| | - Aude Magerus
- Laboratory of Immunogenetics of Pediatric Autoimmune Diseases, Université Paris Cité, INSERM UMR 1163, Imagine Institute, Paris, France
| | - Carsten Speckmann
- Institute for Immunodeficiency, Center for Chronic Immunodeficiency (CCI), Medical Center - University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany; Division of Pediatric Hematology and Oncology, Department of Pediatrics and Adolescent Medicine, Medical Center - University of Freiburg, Faculty of Medicine, University of Freiburg, Mathildenstr. 1, Freiburg, Germany
| | - Klaus Schwarz
- Institute for Transfusion Medicine, University of Ulm, Ulm, Germany; Institute for Clinical Transfusion Medicine and Immunogenetics Ulm, German Red Cross Blood Service Baden-Wuerttemberg - Hessen, Ulm, Germany
| | - Stephan Ehl
- Institute for Immunodeficiency, Center for Chronic Immunodeficiency (CCI), Medical Center - University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
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9
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Accogli A, Lin SJ, Severino M, Kim SH, Huang K, Rocca C, Landsverk M, Zaki MS, Al-Maawali A, Srinivasan VM, Al-Thihli K, Schaefer GB, Davis M, Tonduti D, Doneda C, Marten LM, Mühlhausen C, Gomez M, Lamantea E, Mena R, Nizon M, Procaccio V, Begtrup A, Telegrafi A, Cui H, Schulz HL, Mohr J, Biskup S, Loos MA, Aráoz HV, Salpietro V, Keppen LD, Chitre M, Petree C, Raymond L, Vogt J, Sawyer LB, Basinger AA, Pedersen SV, Pearson TS, Grange DK, Lingappa L, McDunnah P, Horvath R, Cognè B, Isidor B, Hahn A, Gripp KW, Jafarnejad SM, Østergaard E, Prada CE, Ghezzi D, Gowda VK, Taylor RW, Sonenberg N, Houlden H, Sissler M, Varshney GK, Maroofian R. Clinical, neuroradiological, and molecular characterization of mitochondrial threonyl-tRNA-synthetase (TARS2)-related disorder. Genet Med 2023; 25:100938. [PMID: 37454282 DOI: 10.1016/j.gim.2023.100938] [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] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2023] [Revised: 07/11/2023] [Accepted: 07/11/2023] [Indexed: 07/18/2023] Open
Abstract
PURPOSE Biallelic variants in TARS2, encoding the mitochondrial threonyl-tRNA-synthetase, have been reported in a small group of individuals displaying a neurodevelopmental phenotype but with limited neuroradiological data and insufficient evidence for causality of the variants. METHODS Exome or genome sequencing was carried out in 15 families. Clinical and neuroradiological evaluation was performed for all affected individuals, including review of 10 previously reported individuals. The pathogenicity of TARS2 variants was evaluated using in vitro assays and a zebrafish model. RESULTS We report 18 new individuals harboring biallelic TARS2 variants. Phenotypically, these individuals show developmental delay/intellectual disability, regression, cerebellar and cerebral atrophy, basal ganglia signal alterations, hypotonia, cerebellar signs, and increased blood lactate. In vitro studies showed that variants within the TARS2301-381 region had decreased binding to Rag GTPases, likely impairing mTORC1 activity. The zebrafish model recapitulated key features of the human phenotype and unraveled dysregulation of downstream targets of mTORC1 signaling. Functional testing of the variants confirmed the pathogenicity in a zebrafish model. CONCLUSION We define the clinico-radiological spectrum of TARS2-related mitochondrial disease, unveil the likely involvement of the mTORC1 signaling pathway as a distinct molecular mechanism, and establish a TARS2 zebrafish model as an important tool to study variant pathogenicity.
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Affiliation(s)
- Andrea Accogli
- Division of Medical Genetics, Department of Specialized Medicine, Montreal Children's Hospital, McGill University Health Centre (MUHC), Montreal, Canada; Department of Human Genetics, McGill University, Montreal, QC, Canada
| | - Sheng-Jia Lin
- Genes & Human Disease Research Program, Oklahoma Medical Research Foundation, Oklahoma City, OK
| | | | - Sung-Hoon Kim
- Goodman Cancer Institute, McGill University, Montreal, Canada; Department of Biochemistry, McGill University, Montreal, Canada
| | - Kevin Huang
- Genes & Human Disease Research Program, Oklahoma Medical Research Foundation, Oklahoma City, OK
| | - Clarissa Rocca
- Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, London, United Kingdom
| | - Megan Landsverk
- University of South Dakota Sanford School of Medicine Sioux Falls, SD; Sanford Research, Pediatrics and Rare Diseases Group, Sioux Falls, SD
| | - Maha S Zaki
- Human Genetics and Genome Research Institute, Clinical Genetics Department, National Research Centre, Cairo, Egypt
| | - Almundher Al-Maawali
- Department of Genetics, College of Medicine and Health Sciences, Sultan Qaboos University, Muscat, Oman; Genetic and Developmental Medicine Clinic, Sultan Qaboos University Hospital, Muscat, Oman
| | | | - Khalid Al-Thihli
- Department of Genetics, College of Medicine and Health Sciences, Sultan Qaboos University, Muscat, Oman; Genetic and Developmental Medicine Clinic, Sultan Qaboos University Hospital, Muscat, Oman
| | - G Bradly Schaefer
- Department of Pediatrics, University of Arkansas for Medical Sciences, Little Rock, AR
| | - Monica Davis
- Department of Pediatrics, University of Arkansas for Medical Sciences, Little Rock, AR
| | - Davide Tonduti
- Unit of Pediatric Neurology, COALA (Center for Diagnosis and Treatment of Leukodystrophies), V. Buzzi Children's Hospital, Milan, Italy; Department of Biomedical and Clinical Sciences, University of Milan, Milan, Italy
| | - Chiara Doneda
- Pediatric Radiology and Neuroradiology Department, Children's Hospital Vittore Buzzi, Milan, Italy
| | - Lara M Marten
- Department of Pediatrics and Adolescent Medicine, University Medical Center Göttingen, Germany
| | - Chris Mühlhausen
- Department of Pediatrics and Adolescent Medicine, University Medical Center Göttingen, Germany
| | - Maria Gomez
- Centro de Obsetricia y Ginecologia & Centro Medico Moderno, Santo Domingo, Dominican Republic
| | - Eleonora Lamantea
- Unit of Medical Genetics and Neurogenetics, Fondazione IRCCS Istituto Neurologico Carlo Besta, Milan, Italy
| | - Rafael Mena
- Division of Neonatology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH; Centro de Obsetricia y Ginecologia, Santo Domingo, Dominican Republic
| | - Mathilde Nizon
- Service de Génétique Médicale, CHU de Nantes, Nantes Université, Nantes, France; Nantes Université, CNRS, INSERM, l'Institut du Thorax, Nantes, France
| | - Vincent Procaccio
- University of Angers, MitoLab Team, Unité MitoVasc, UMR CNRS 6015, INSERM U1083, SFR ICAT, Angers, France; Department of Genetics, CHU Angers, Angers, France
| | | | | | | | - Heidi L Schulz
- Human Genetic center Tübingen, Baden-Württemberg, Germany
| | - Julia Mohr
- Human Genetic center Tübingen, Baden-Württemberg, Germany
| | - Saskia Biskup
- Human Genetic center Tübingen, Baden-Württemberg, Germany; CeGaT GmbH, Germany
| | - Mariana Amina Loos
- Department of Neurology, Hospital de Pediatría Juan P. Garrahan, Buenos Aires, Argentina
| | - Hilda Verónica Aráoz
- Genomics Laboratory, Hospital de Pediatría Juan P. Garrahan, Buenos Aires, Argentina
| | - Vincenzo Salpietro
- Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, London, United Kingdom; Department of Biotechnological and Applied Clinical Sciences, University of L'Aquila, L'Aquila, Italy
| | - Laura Davis Keppen
- University of South Dakota Sanford School of Medicine Sioux Falls, SD; Sanford Research, Pediatrics and Rare Diseases Group, Sioux Falls, SD
| | - Manali Chitre
- Cambridge University Hospitals NHS Foundation Trust, Cambridge, United Kingdom
| | - Cassidy Petree
- Genes & Human Disease Research Program, Oklahoma Medical Research Foundation, Oklahoma City, OK
| | - Lucy Raymond
- Cambridge University Hospitals NHS Foundation Trust, Cambridge, United Kingdom
| | - Julie Vogt
- West Midlands Regional Genetics Service, Birmingham Women and Children's Hospital NHS Foundation Trust, Birmingham, United Kingdom
| | - Lindsey B Sawyer
- Children's Hospital of the King's Daughters, Norfolk, Virginia, VA
| | - Alice A Basinger
- Children's Hospital of the King's Daughters, Norfolk, Virginia, VA
| | - Signe Vandal Pedersen
- Department of Genetics, Copenhagen University Hospital Rigshospitalet, Copenhagen, Denmark
| | - Toni S Pearson
- Department of Neurology, Washington University School of Medicine, St. Louis, MO
| | - Dorothy K Grange
- Division of Genetics and Genomic Medicine, Department of Pediatrics, Washington University School of Medicine, St. Louis, MO; Center for the Investigation of Membrane Excitability Diseases (CIMED), St. Louis, MO
| | | | - Paige McDunnah
- Division of Medical Genetics, Nemours/A I duPont Hospital for Children, Wilmington, DE
| | - Rita Horvath
- Department of Clinical Neurosciences, University of Cambridge, Cambridge, United Kingdom
| | - Benjamin Cognè
- Service de Génétique Médicale, CHU de Nantes, Nantes Université, Nantes, France; Nantes Université, CNRS, INSERM, l'Institut du Thorax, Nantes, France
| | - Bertrand Isidor
- Service de Génétique Médicale, CHU de Nantes, Nantes Université, Nantes, France
| | - Andreas Hahn
- Department of Child Neurology, University Hospital, Gießen, Germany
| | - Karen W Gripp
- Division of Medical Genetics, Nemours/A I duPont Hospital for Children, Wilmington, DE
| | - Seyed Mehdi Jafarnejad
- Patrick G. Johnston Centre for Cancer Research, Queen's University Belfast, Belfast, United Kingdom
| | - Elsebet Østergaard
- Department of Genetics, Copenhagen University Hospital Rigshospitalet, Copenhagen, Denmark; Department of Clinical Medicine, University of Copenhagen, Copenhagen, Denmark
| | - Carlos E Prada
- Division of Genetics, Genomics, and Metabolism, Ann & Robert Lurie Children's Hospital of Chicago, Chicago; Department of Pediatrics, Feinberg School of Medicine, Northwestern University, Chicago; Fundacion Cardiovascular de Colombia, Floridablanca, Colombia
| | - Daniele Ghezzi
- Unit of Medical Genetics and Neurogenetics, Fondazione IRCCS Istituto Neurologico Carlo Besta, Milan, Italy; Department of Pathophysiology and Transplantation, University of Milan, Milan, Italy
| | | | - Robert W Taylor
- Wellcome Centre for Mitochondrial Research, Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne, United Kingdom; NHS Highly Specialized Service for Rare Mitochondrial Disorders of Adults and Children, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Nahum Sonenberg
- Goodman Cancer Institute, McGill University, Montreal, Canada; Department of Biochemistry, McGill University, Montreal, Canada
| | - Henry Houlden
- Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, London, United Kingdom
| | - Marie Sissler
- ARNA - UMR5320 CNRS - U1212 INSERM, Université de Bordeaux, IECB, Pessac, France
| | - Gaurav K Varshney
- Genes & Human Disease Research Program, Oklahoma Medical Research Foundation, Oklahoma City, OK.
| | - Reza Maroofian
- Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, London, United Kingdom.
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10
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Tropitzsch A, Schade-Mann T, Gamerdinger P, Dofek S, Schulte B, Schulze M, Fehr S, Biskup S, Haack TB, Stöbe P, Heyd A, Harre J, Lesinski-Schiedat A, Büchner A, Lenarz T, Warnecke A, Müller M, Vona B, Dahlhoff E, Löwenheim H, Holderried M. Variability in Cochlear Implantation Outcomes in a Large German Cohort With a Genetic Etiology of Hearing Loss. Ear Hear 2023; 44:1464-1484. [PMID: 37438890 PMCID: PMC10583923 DOI: 10.1097/aud.0000000000001386] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2022] [Accepted: 04/04/2023] [Indexed: 07/14/2023]
Abstract
OBJECTIVES The variability in outcomes of cochlear implantation is largely unexplained, and clinical factors are not sufficient for predicting performance. Genetic factors have been suggested to impact outcomes, but the clinical and genetic heterogeneity of hereditary hearing loss makes it difficult to determine and interpret postoperative performance. It is hypothesized that genetic mutations that affect the neuronal components of the cochlea and auditory pathway, targeted by the cochlear implant (CI), may lead to poor performance. A large cohort of CI recipients was studied to verify this hypothesis. DESIGN This study included a large German cohort of CI recipients (n = 123 implanted ears; n = 76 probands) with a definitive genetic etiology of hearing loss according to the American College of Medical Genetics (ACMG)/Association for Molecular Pathology (AMP) guidelines and documented postoperative audiological outcomes. All patients underwent preoperative clinical and audiological examinations. Postoperative CI outcome measures were based on at least 1 year of postoperative audiological follow-up for patients with postlingual hearing loss onset (>6 years) and 5 years for children with congenital or pre/perilingual hearing loss onset (≤6 years). Genetic analysis was performed based on three different methods that included single-gene screening, custom-designed hearing loss gene panel sequencing, targeting known syndromic and nonsyndromic hearing loss genes, and whole-genome sequencing. RESULTS The genetic diagnosis of the 76 probands in the genetic cohort involved 35 genes and 61 different clinically relevant (pathogenic, likely pathogenic) variants. With regard to implanted ears (n = 123), the six most frequently affected genes affecting nearly one-half of implanted ears were GJB2 (21%; n = 26), TMPRSS3 (7%; n = 9), MYO15A (7%; n = 8), SLC26A4 (5%; n = 6), and LOXHD1 and USH2A (each 4%; n = 5). CI recipients with pathogenic variants that influence the sensory nonneural structures performed at or above the median level of speech performance of all ears at 70% [monosyllable word recognition score in quiet at 65 decibels sound pressure level (SPL)]. When gene expression categories were compared to demographic and clinical categories (total number of compared categories: n = 30), mutations in genes expressed in the spiral ganglion emerged as a significant factor more negatively affecting cochlear implantation outcomes than all clinical parameters. An ANOVA of a reduced set of genetic and clinical categories (n = 10) identified five detrimental factors leading to poorer performance with highly significant effects ( p < 0.001), accounting for a total of 11.8% of the observed variance. The single strongest category was neural gene expression accounting for 3.1% of the variance. CONCLUSIONS The analysis of the relationship between the molecular genetic diagnoses of a hereditary etiology of hearing loss and cochlear implantation outcomes in a large German cohort of CI recipients revealed significant variabilities. Poor performance was observed with genetic mutations that affected the neural components of the cochlea, supporting the "spiral ganglion hypothesis."
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Affiliation(s)
- Anke Tropitzsch
- Department of Otolaryngology—Head & Neck Surgery, University of Tübingen Medical Center, Tübingen, Germany
- Hearing Center, Department of Otolaryngology—Head & Neck Surgery, University of Tübingen Medical Center, Tübingen, Germany
- Center for Rare Hearing Disorders, Centre for Rare Diseases, University of Tübingen, Tübingen, Germany
- Neurosensory Center, Departments of Otolaryngology—Head & Neck Surgery and Ophthalmology, University of Tübingen Medical Center, Tübingen, Germany
| | - Thore Schade-Mann
- Department of Otolaryngology—Head & Neck Surgery, University of Tübingen Medical Center, Tübingen, Germany
- Hearing Center, Department of Otolaryngology—Head & Neck Surgery, University of Tübingen Medical Center, Tübingen, Germany
| | - Philipp Gamerdinger
- Department of Otolaryngology—Head & Neck Surgery, University of Tübingen Medical Center, Tübingen, Germany
- Hearing Center, Department of Otolaryngology—Head & Neck Surgery, University of Tübingen Medical Center, Tübingen, Germany
| | - Saskia Dofek
- Department of Otolaryngology—Head & Neck Surgery, University of Tübingen Medical Center, Tübingen, Germany
| | - Björn Schulte
- CeGaT GmbH und Praxis für Humangenetik Tübingen, Tübingen, Germany
| | - Martin Schulze
- CeGaT GmbH und Praxis für Humangenetik Tübingen, Tübingen, Germany
| | - Sarah Fehr
- CeGaT GmbH und Praxis für Humangenetik Tübingen, Tübingen, Germany
| | - Saskia Biskup
- CeGaT GmbH und Praxis für Humangenetik Tübingen, Tübingen, Germany
| | - Tobias B. Haack
- Institute of Medical Genetics and Applied Genomics, University of Tübingen, Tübingen, Germany
| | - Petra Stöbe
- Institute of Medical Genetics and Applied Genomics, University of Tübingen, Tübingen, Germany
| | - Andreas Heyd
- Department of Otolaryngology—Head & Neck Surgery, University of Tübingen Medical Center, Tübingen, Germany
| | - Jennifer Harre
- Department of Otorhinolaryngology—Head & Neck Surgery, Hannover Medical School, Hannover, Germany
- Cluster of Excellence “Hearing4all” of the German Research Foundation, Hannover, Germany
| | - Anke Lesinski-Schiedat
- Department of Otorhinolaryngology—Head & Neck Surgery, Hannover Medical School, Hannover, Germany
- Cluster of Excellence “Hearing4all” of the German Research Foundation, Hannover, Germany
| | - Andreas Büchner
- Department of Otorhinolaryngology—Head & Neck Surgery, Hannover Medical School, Hannover, Germany
- Cluster of Excellence “Hearing4all” of the German Research Foundation, Hannover, Germany
| | - Thomas Lenarz
- Department of Otorhinolaryngology—Head & Neck Surgery, Hannover Medical School, Hannover, Germany
- Cluster of Excellence “Hearing4all” of the German Research Foundation, Hannover, Germany
| | - Athanasia Warnecke
- Department of Otorhinolaryngology—Head & Neck Surgery, Hannover Medical School, Hannover, Germany
- Cluster of Excellence “Hearing4all” of the German Research Foundation, Hannover, Germany
| | - Marcus Müller
- Department of Otolaryngology—Head & Neck Surgery, University of Tübingen Medical Center, Tübingen, Germany
- Neurosensory Center, Departments of Otolaryngology—Head & Neck Surgery and Ophthalmology, University of Tübingen Medical Center, Tübingen, Germany
| | - Barbara Vona
- Department of Otolaryngology—Head & Neck Surgery, University of Tübingen Medical Center, Tübingen, Germany
- Neurosensory Center, Departments of Otolaryngology—Head & Neck Surgery and Ophthalmology, University of Tübingen Medical Center, Tübingen, Germany
| | - Ernst Dahlhoff
- Department of Otolaryngology—Head & Neck Surgery, University of Tübingen Medical Center, Tübingen, Germany
- Neurosensory Center, Departments of Otolaryngology—Head & Neck Surgery and Ophthalmology, University of Tübingen Medical Center, Tübingen, Germany
| | - Hubert Löwenheim
- Department of Otolaryngology—Head & Neck Surgery, University of Tübingen Medical Center, Tübingen, Germany
- Neurosensory Center, Departments of Otolaryngology—Head & Neck Surgery and Ophthalmology, University of Tübingen Medical Center, Tübingen, Germany
| | - Martin Holderried
- Department of Otolaryngology—Head & Neck Surgery, University of Tübingen Medical Center, Tübingen, Germany
- Department of Medical Development and Quality Management, University Hospital Tübingen, Tübingen, Germany
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11
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Castro MP, Sipos B, Biskup S, Kahn N. Network-targeting combination therapy of leptomeningeal glioblastoma using multiple synthetic lethal strategies: a case report. Front Oncol 2023; 13:1210224. [PMID: 38023264 PMCID: PMC10644375 DOI: 10.3389/fonc.2023.1210224] [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] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2023] [Accepted: 09/20/2023] [Indexed: 12/01/2023] Open
Abstract
Network targeting of disease-specific nodes represents a useful principle for designing combination cancer therapy. In this case of a patient with relapsed leptomeningeal glioblastoma, comprehensive molecular diagnosis led to the identification of a disease network characterized by multiple disease-specific synthetic lethal vulnerabilities involving DNA repair, REDOX homeostasis, and impaired autophagy which suggested a novel network-targeting combination therapy (NTCT). A treatment regimen consisting of lomustine, olaparib, digoxin, metformin, and high dose intravenous ascorbate was employed using the principle of intra-patient dose escalation to deliver the treatment with adequate safety measures to achieve a definitive clinical result.
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Affiliation(s)
- Michael P. Castro
- Personalized Cancer Medicine, PLLC, Santa Monica, CA, United States
- Beverly Hills Cancer Center, Beverly Hills, CA, United States
- Cellworks Group, Inc, San Francisco, CA, United States
| | - Bence Sipos
- Department of Pathology, Molekularpathologie Baden-Württemberg GbR, Tuebingen, Germany
| | - Saskia Biskup
- Center for Genomics & Transcriptomics, GmbH, Tuebingen, Germany
| | - Nina Kahn
- Independent Researcher, Amsterdam, Netherlands
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12
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Zelba H, Rabsteyn A, Bartsch O, Kyzirakos C, Kayser S, Seibold M, Harter J, Latzer P, Hadaschik D, Battke F, Golf A, Rettig MB, Biskup S. Case Report: Targeting of individual somatic tumor mutations by multipeptide vaccination tailored for HLA class I and II presentation induces strong CD4 and CD8 T-cell responses in a patient with metastatic castration sensitive prostate cancer. Front Immunol 2023; 14:1271449. [PMID: 37920460 PMCID: PMC10619716 DOI: 10.3389/fimmu.2023.1271449] [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] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2023] [Accepted: 10/02/2023] [Indexed: 11/04/2023] Open
Abstract
Localized prostate cancer is curable, but metastatic castration sensitive prostate cancer has a low 5-year survival rate, while broad treatment options are lacking. Here we present an mCSPC patient under remission receiving individualized neoantigen-derived peptide vaccination as recurrence prophylaxis in the setting of an individual treatment attempt. The patient was initially analyzed for somatic tumor mutations and then consecutively treated with two different peptide vaccines over a period of 33 months. The first vaccine contained predicted HLA class I binding peptides only whereas the second vaccine contained both predicted HLA class I and II binding peptides. Intracellular cytokine staining after 12 day in-vitro expansion measuring four T-cell activation markers (IFNg, TNF-α, IL-2, CD154) was used to determine vaccine-induced T-cell responses. While the first vaccine induced only one robust CD4+ T-cell response after 21 vaccinations, co-vaccination of HLA class I and II peptides induced multiple strong and durable CD4+ and CD8+ T-cell responses already after sixth vaccinations. The vaccine-induced immune responses were robust and polyfunctional. PSA remained undetectable for 51 months. The results presented here implicate that neoantigen-targeting vaccines might be considered for those cancer subtypes where therapeutic options are limited. Furthermore, our findings suggest that both HLA class I and II restricted peptides should be considered for future peptide vaccination trials.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | - Alexander Golf
- MVZ Zentrum für ambulante Onkologie GmbH, Tuebingen, Germany
| | - Matthew B. Rettig
- Departments of Medicine and Urology, University of California, Los Angeles, Los Angeles, CA, United States
- Department of Medicine, VA Greater Los Angeles Healthcare System, Los Angeles, CA, United States
| | - Saskia Biskup
- Zentrum für Humangenetik, Tuebingen, Germany
- CeGaT GmbH, Tuebingen, Germany
- MVZ Zentrum für ambulante Onkologie GmbH, Tuebingen, Germany
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13
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Ansari M, Faour KNW, Shimamura A, Grimes G, Kao EM, Denhoff ER, Blatnik A, Ben-Isvy D, Wang L, Helm BM, Firth H, Breman AM, Bijlsma EK, Iwata-Otsubo A, de Ravel TJL, Fusaro V, Fryer A, Nykamp K, Stühn LG, Haack TB, Korenke GC, Constantinou P, Bujakowska KM, Low KJ, Place E, Humberson J, Napier MP, Hoffman J, Juusola J, Deardorff MA, Shao W, Rockowitz S, Krantz I, Kaur M, Raible S, Kliesch S, Singer-Berk M, Groopman E, DiTroia S, Ballal S, Srivastava S, Rothfelder K, Biskup S, Rzasa J, Kerkhof J, McConkey H, O'Donnell-Luria A, Sadikovic B, Hilton S, Banka S, Tüttelmann F, Conrad D, Talkowski ME, FitzPatrick DR, Boone PM. Heterozygous loss-of-function SMC3 variants are associated with variable and incompletely penetrant growth and developmental features. medRxiv 2023:2023.09.27.23294269. [PMID: 37808847 PMCID: PMC10557843 DOI: 10.1101/2023.09.27.23294269] [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] [Subscribe] [Scholar Register] [Indexed: 10/10/2023]
Abstract
Heterozygous missense variants and in-frame indels in SMC3 are a cause of Cornelia de Lange syndrome (CdLS), marked by intellectual disability, growth deficiency, and dysmorphism, via an apparent dominant-negative mechanism. However, the spectrum of manifestations associated with SMC3 loss-of-function variants has not been reported, leading to hypotheses of alternative phenotypes or even developmental lethality. We used matchmaking servers, patient registries, and other resources to identify individuals with heterozygous, predicted loss-of-function (pLoF) variants in SMC3, and analyzed population databases to characterize mutational intolerance in this gene. Here, we show that SMC3 behaves as an archetypal haploinsufficient gene: it is highly constrained against pLoF variants, strongly depleted for missense variants, and pLoF variants are associated with a range of developmental phenotypes. Among 13 individuals with SMC3 pLoF variants, phenotypes were variable but coalesced on low growth parameters, developmental delay/intellectual disability, and dysmorphism reminiscent of atypical CdLS. Comparisons to individuals with SMC3 missense/in-frame indel variants demonstrated a milder presentation in pLoF carriers. Furthermore, several individuals harboring pLoF variants in SMC3 were nonpenetrant for growth, developmental, and/or dysmorphic features, some instead having intriguing symptomatologies with rational biological links to SMC3 including bone marrow failure, acute myeloid leukemia, and Coats retinal vasculopathy. Analyses of transcriptomic and epigenetic data suggest that SMC3 pLoF variants reduce SMC3 expression but do not result in a blood DNA methylation signature clustering with that of CdLS, and that the global transcriptional signature of SMC3 loss is model-dependent. Our finding of substantial population-scale LoF intolerance in concert with variable penetrance in subjects with SMC3 pLoF variants expands the scope of cohesinopathies, informs on their allelic architecture, and suggests the existence of additional clearly LoF-constrained genes whose disease links will be confirmed only by multi-layered genomic data paired with careful phenotyping.
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Affiliation(s)
- Morad Ansari
- South East Scotland Genetic Service, Western General Hospital, Edinburgh, UK
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK
- These authors contributed equally
| | - Kamli N W Faour
- Division of Genetics and Genomics, Boston Children's Hospital, Boston, MA, US
- Cornelia de Lange Syndrome and Related Disorders Clinic, Boston Children's Hospital, Boston, MA, US
- These authors contributed equally
| | - Akiko Shimamura
- Division of Hematology and Oncology, Boston Children's Hospital, Boston, MA, US
| | - Graeme Grimes
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK
| | - Emeline M Kao
- Institutional Centers for Clinical and Translational Research, Boston Children's Hospital, Boston, MA, US
| | - Erica R Denhoff
- Institutional Centers for Clinical and Translational Research, Boston Children's Hospital, Boston, MA, US
| | - Ana Blatnik
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK
- Department of Clinical Cancer Genetics, Institute of Oncology Ljubljana, Ljubljana, SI
| | - Daniel Ben-Isvy
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, US
- Medical and Population Genetics, The Broad Institute of MIT and Harvard, Cambridge, MA, US
- Division of Medical Sciences, Harvard Medical School, Boston, MA, US
| | - Lily Wang
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, US
- Medical and Population Genetics, The Broad Institute of MIT and Harvard, Cambridge, MA, US
- Division of Medical Sciences, Harvard Medical School, Boston, MA, US
| | - Benjamin M Helm
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN, US
| | - Helen Firth
- Clinical Genetics, Addenbrooke's Hospital, Cambridge University Hospitals, Cambridge, UK
| | - Amy M Breman
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN, US
| | - Emilia K Bijlsma
- Department of Clinical Genetics, Leiden University Medical Centre, Leiden, NL
| | - Aiko Iwata-Otsubo
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN, US
| | - Thomy J L de Ravel
- Centre for Human Genetics, UZ Leuven/ Leuven University Hospitals, Leuven, BE
| | | | - Alan Fryer
- Department of Clinical Genetics, Alder Hey Children's Hospital Liverpool, Liverpool, UK
| | | | - Lara G Stühn
- Institute of Medical Genetics and Applied Genomics, University of Tuebingen, Tuebingen, DE
| | - Tobias B Haack
- Institute of Medical Genetics and Applied Genomics, University of Tuebingen, Tuebingen, DE
| | - G Christoph Korenke
- University Children's Hospital Oldenburg, Department of Neuropaediatric and Metabolic Diseases, University Children's Hospital Oldenburg, Oldenburg, DE
| | - Panayiotis Constantinou
- West of Scotland Centre for Genomic Medicine, Queen Elizabeth University Hospital, Glasgow, UK
| | | | - Karen J Low
- University Hospitals Bristol and Weston NHS Foundation Trust, Bristol, UK
- University of Bristol, Bristol, UK
| | - Emily Place
- Massachusetts Eye and Ear Infirmary, Boston, MA, US
| | | | | | | | | | - Matthew A Deardorff
- Departments of Pathology and Pediatrics, Children's Hospital Los Angeles and University of Southern California, Los Angeles, CA, US
| | - Wanqing Shao
- Research Computing, Information Technology, Boston Children's Hospital, Boston, MA, US
| | - Shira Rockowitz
- Research Computing, Information Technology, Boston Children's Hospital, Boston, MA, US
- The Manton Center for Orphan Disease Research, Boston Children's Hospital, Boston, MA, US
- Division of Genetics and Genomics, Boston Children's Hospital, Boston, MA, US
| | - Ian Krantz
- Children's Hospital of Philadelphia, Philadelphia, PA, US
| | - Maninder Kaur
- Children's Hospital of Philadelphia, Philadelphia, PA, US
| | - Sarah Raible
- Children's Hospital of Philadelphia, Philadelphia, PA, US
| | - Sabine Kliesch
- Department of Clinical and Surgical Andrology, Centre of Reproductive Medicine and Andrology, University Hospital Münster, Münster, DE
| | - Moriel Singer-Berk
- Medical and Population Genetics, The Broad Institute of MIT and Harvard, Cambridge, MA, US
| | - Emily Groopman
- Division of Genetics and Genomics, Boston Children's Hospital, Boston, MA, US
- Medical and Population Genetics, The Broad Institute of MIT and Harvard, Cambridge, MA, US
| | - Stephanie DiTroia
- Medical and Population Genetics, The Broad Institute of MIT and Harvard, Cambridge, MA, US
| | - Sonia Ballal
- Cornelia de Lange Syndrome and Related Disorders Clinic, Boston Children's Hospital, Boston, MA, US
- Division of Gastroenterology, Boston Children's Hospital, Boston, MA, US
| | - Siddharth Srivastava
- Cornelia de Lange Syndrome and Related Disorders Clinic, Boston Children's Hospital, Boston, MA, US
- Divison of Neurology, Boston Children's Hospital, Boston, MA, US
| | | | - Saskia Biskup
- Zentrum für Humangenetik, Tübingen, DE
- Center for Genomics and Transcriptomics (CeGaT), Tübingen, DE
| | - Jessica Rzasa
- Molecular Diagnostics Program and Verspeeten Clinical Genome Centre, LHSC, London, CA
| | - Jennifer Kerkhof
- Molecular Diagnostics Program and Verspeeten Clinical Genome Centre, LHSC, London, CA
| | - Haley McConkey
- Molecular Diagnostics Program and Verspeeten Clinical Genome Centre, LHSC, London, CA
| | - Anne O'Donnell-Luria
- Division of Genetics and Genomics, Boston Children's Hospital, Boston, MA, US
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, US
- Medical and Population Genetics, The Broad Institute of MIT and Harvard, Cambridge, MA, US
| | - Bekim Sadikovic
- Molecular Diagnostics Program and Verspeeten Clinical Genome Centre, LHSC, London, CA
| | | | | | - Frank Tüttelmann
- Institute of Reproductive Genetics, University of Münster, Münster, DE
| | - Donald Conrad
- Division of Genetics, Oregon National Primate Research Center, Oregon Health and Science University, Portland, OR, US
- Center for Embryonic Cell and Gene Therapy, Oregon Health and Science University, Portland, OR, US
| | - Michael E Talkowski
- Medical and Population Genetics, The Broad Institute of MIT and Harvard, Cambridge, MA, US
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, US
| | - David R FitzPatrick
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK
- These authors contributed equally
| | - Philip M Boone
- Cornelia de Lange Syndrome and Related Disorders Clinic, Boston Children's Hospital, Boston, MA, US
- Division of Genetics and Genomics, Boston Children's Hospital, Boston, MA, US
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, US
- Medical and Population Genetics, The Broad Institute of MIT and Harvard, Cambridge, MA, US
- These authors contributed equally
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14
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Calame DG, Moreno Vadillo C, Berger S, Lotze T, Shinawi M, Poupak J, Heller C, Cohen J, Person R, Telegrafi A, Phitsanuwong C, Fiala K, Thiffault I, Del Viso F, Zhou D, Fleming EA, Pastinen T, Fatemi A, Thomas S, Pascual SI, Torres RJ, Prior C, Gómez-González C, Biskup S, Lupski JR, Maric D, Holmgren M, Regier D, Yano ST. Cation leak through the ATP1A3 pump causes spasticity and intellectual disability. Brain 2023; 146:3162-3171. [PMID: 37043503 PMCID: PMC10393399 DOI: 10.1093/brain/awad124] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2022] [Revised: 02/09/2023] [Accepted: 02/28/2023] [Indexed: 04/13/2023] Open
Abstract
ATP1A3 encodes the α3 subunit of the sodium-potassium ATPase, one of two isoforms responsible for powering electrochemical gradients in neurons. Heterozygous pathogenic ATP1A3 variants produce several distinct neurological syndromes, yet the molecular basis for phenotypic variability is unclear. We report a novel recurrent variant, ATP1A3(NM_152296.5):c.2324C>T; p.(Pro775Leu), in nine individuals associated with the primary clinical features of progressive or non-progressive spasticity and developmental delay/intellectual disability. No patients fulfil diagnostic criteria for ATP1A3-associated syndromes, including alternating hemiplegia of childhood, rapid-onset dystonia-parkinsonism or cerebellar ataxia-areflexia-pes cavus-optic atrophy-sensorineural hearing loss (CAPOS), and none were suspected of having an ATP1A3-related disorder. Uniquely among known ATP1A3 variants, P775L causes leakage of sodium ions and protons into the cell, associated with impaired sodium binding/occlusion kinetics favouring states with fewer bound ions. These phenotypic and electrophysiologic studies demonstrate that ATP1A3:c.2324C>T; p.(Pro775Leu) results in mild ATP1A3-related phenotypes resembling complex hereditary spastic paraplegia or idiopathic spastic cerebral palsy. Cation leak provides a molecular explanation for this genotype-phenotype correlation, adding another mechanism to further explain phenotypic variability and highlighting the importance of biophysical properties beyond ion transport rate in ion transport diseases.
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Affiliation(s)
- Daniel G Calame
- Section of Pediatric Neurology and Developmental Neuroscience, Department of Pediatrics, Baylor College of Medicine, Houston, TX 77030, USA
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
- Texas Children’s Hospital, Houston, TX 77030, USA
| | - Cristina Moreno Vadillo
- National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD 20892, USA
| | - Seth Berger
- Children’s National Rare Disease Institute, Children’s National Hospital, Washington, DC 20012, USA
| | - Timothy Lotze
- Section of Pediatric Neurology and Developmental Neuroscience, Department of Pediatrics, Baylor College of Medicine, Houston, TX 77030, USA
- Texas Children’s Hospital, Houston, TX 77030, USA
| | - Marwan Shinawi
- Department of Pediatrics, Division of Genetics and Genomic Medicine, Washington University School of Medicine, St. Louis, MO 63110, USA
| | | | - Corina Heller
- Praxis Für Humangenetik Tübingen, Tuebingen 72076, Germany
- CeGaT GmbH, Tuebingen 72076, Germany
| | - Julie Cohen
- Department of Neurology and Developmental Medicine, Kennedy Krieger Institute, Baltimore, MD 21205, USA
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | | | | | - Chalongchai Phitsanuwong
- Section of Pediatric Neurology, Department of Pediatrics, Comer Children’s Hospital, University of Chicago, Chicago, IL 60637, USA
| | - Kaylene Fiala
- Section of Pediatric Neurology, Department of Pediatrics, Comer Children’s Hospital, University of Chicago, Chicago, IL 60637, USA
| | - Isabelle Thiffault
- Genomic Medicine Center, Children's Mercy Research Institute, Kansas City, MO 64108, USA
- School of Medicine, University of Missouri Kansas City, Kansas City, MO 64108, USA
- Department of Pathology and Laboratory Medicine, Children's Mercy Hospital, Kansas City, MO 64108, USA
| | - Florencia Del Viso
- Genomic Medicine Center, Children's Mercy Research Institute, Kansas City, MO 64108, USA
- Department of Pathology and Laboratory Medicine, Children's Mercy Hospital, Kansas City, MO 64108, USA
| | - Dihong Zhou
- School of Medicine, University of Missouri Kansas City, Kansas City, MO 64108, USA
- Department of Genetics, Children's Mercy Hospital, Kansas City, MO 64108, USA
| | - Emily A Fleming
- Department of Genetics, Children's Mercy Hospital, Kansas City, MO 64108, USA
| | - Tomi Pastinen
- Genomic Medicine Center, Children's Mercy Research Institute, Kansas City, MO 64108, USA
- School of Medicine, University of Missouri Kansas City, Kansas City, MO 64108, USA
| | - Ali Fatemi
- Department of Neurology and Developmental Medicine, Kennedy Krieger Institute, Baltimore, MD 21205, USA
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
- Department of Pediatrics, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | - Sruthi Thomas
- Departments of Physical Medicine & Rehabilitation and Neurosurgery, Baylor College of Medicine, Houston, TX 77030, USA
| | - Samuel I Pascual
- Department of Pediatric Neurology, La Paz University Hospital, Madrid, Spain
| | - Rosa J Torres
- La Paz University Hospital Health Research Institute (FIBHULP), IdiPaz, Madrid, Spain
- Center for Biomedical Network Research on Rare Diseases (CIBERER), Instituto de Salud Carlos III, 20829 Madrid, Spain
| | - Carmen Prior
- Department of Genetics, Genetic Service, La Paz University Hospital, Madrid, Spain
| | - Clara Gómez-González
- Department of Genetics, Genetic Service, La Paz University Hospital, Madrid, Spain
| | - Saskia Biskup
- Praxis Für Humangenetik Tübingen, Tuebingen 72076, Germany
- CeGaT GmbH, Tuebingen 72076, Germany
| | - James R Lupski
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
- Texas Children’s Hospital, Houston, TX 77030, USA
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA
- Department of Pediatrics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Dragan Maric
- Flow and Imaging Cytometry Core Facility, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD 20892, USA
| | - Miguel Holmgren
- National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD 20892, USA
| | - Debra Regier
- Children’s National Rare Disease Institute, Children’s National Hospital, Washington, DC 20012, USA
| | - Sho T Yano
- National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
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15
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Schmidt M, Mattern S, Singer S, Schulze M, Biskup S, Krumm P, Lauer UM, Zender L, Hinterleitner C, Hinterleitner M. NOTCH3 missense mutations as predictor of long-term response to gemcitabine in a patient with epithelioid hemangioendothelioma. J Cancer Res Clin Oncol 2023; 149:6753-6757. [PMID: 36749424 PMCID: PMC10356887 DOI: 10.1007/s00432-023-04598-1] [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] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2023] [Accepted: 01/24/2023] [Indexed: 02/08/2023]
Abstract
PURPOSE Epithelioid hemangioendothelioma (EHE) as a very rare malignant vascular tumor belongs to the heterogenous group of soft-tissue sarcomas. Depending on the clinical course of the disease, interdisciplinary treatment concepts are required, including surgery, radiotherapy and systemic cancer therapy. However, due to its uncommonness, standard treatment options are lacking so far, especially in advanced disease with distant metastases. METHODS AND RESULTS Here we report on an unusual case of a patient with metastasized EHE showing long-term response to second line treatment with gemcitabine over almost 2 decades. Cancer genome sequencing of the patient's tumor tissue detected a NOTCH3 missense mutation which could provide an explanation for these clinical findings. NOTCH3 is known to be a mediator of resistance towards gemcitabine-based cancer treatment, at least in pancreatic cancer and non-small cell lung cancer. CONCLUSION The observation that this missense mutation of NOTCH3 is associated with an increased response to treatment with gemcitabine in EHE can be used prospectively to assess NOTCH3 as potential biomarker for predicting therapy response to gemcitabine.
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Affiliation(s)
- Moritz Schmidt
- Department of Medical Oncology and Pneumology (Internal Medicine VIII), University Hospital Tuebingen, 72076, Tuebingen, Germany
- DFG Cluster of Excellence 2180 'Image-Guided and Functional Instructed Tumor Therapy' (iFIT), University of Tuebingen, 72076, Tuebingen, Germany
| | - Sven Mattern
- Department of Pathology, University Hospital Tuebingen, Tuebingen, Germany
| | - Stephan Singer
- Department of Pathology, University Hospital Tuebingen, Tuebingen, Germany
| | | | - Saskia Biskup
- Praxis Für Humangenetik Tübingen, Tuebingen, Germany
- CeGaT GmbH, Center for Genomics and Transcriptomics, Tuebingen, Germany
| | - Patrick Krumm
- Department of Radiology, University Hospital Tuebingen, Tuebingen, Germany
| | - Ulrich M Lauer
- Department of Medical Oncology and Pneumology (Internal Medicine VIII), University Hospital Tuebingen, 72076, Tuebingen, Germany
- DFG Cluster of Excellence 2180 'Image-Guided and Functional Instructed Tumor Therapy' (iFIT), University of Tuebingen, 72076, Tuebingen, Germany
- German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Tuebingen, Germany
| | - Lars Zender
- Department of Medical Oncology and Pneumology (Internal Medicine VIII), University Hospital Tuebingen, 72076, Tuebingen, Germany
- DFG Cluster of Excellence 2180 'Image-Guided and Functional Instructed Tumor Therapy' (iFIT), University of Tuebingen, 72076, Tuebingen, Germany
- German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Tuebingen, Germany
| | - Clemens Hinterleitner
- Department of Medical Oncology and Pneumology (Internal Medicine VIII), University Hospital Tuebingen, 72076, Tuebingen, Germany
- DFG Cluster of Excellence 2180 'Image-Guided and Functional Instructed Tumor Therapy' (iFIT), University of Tuebingen, 72076, Tuebingen, Germany
- Cancer Biology and Genetics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Martina Hinterleitner
- Department of Medical Oncology and Pneumology (Internal Medicine VIII), University Hospital Tuebingen, 72076, Tuebingen, Germany.
- DFG Cluster of Excellence 2180 'Image-Guided and Functional Instructed Tumor Therapy' (iFIT), University of Tuebingen, 72076, Tuebingen, Germany.
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16
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Bundalian L, Su YY, Chen S, Velluva A, Kirstein AS, Garten A, Biskup S, Battke F, Lal D, Heyne HO, Platzer K, Lin CC, Lemke JR, Le Duc D. Epilepsies of presumed genetic etiology show enrichment of rare variants that occur in the general population. Am J Hum Genet 2023; 110:1110-1122. [PMID: 37369202 PMCID: PMC10357498 DOI: 10.1016/j.ajhg.2023.06.004] [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] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2023] [Revised: 06/05/2023] [Accepted: 06/06/2023] [Indexed: 06/29/2023] Open
Abstract
Previous studies suggested that severe epilepsies, e.g., developmental and epileptic encephalopathies (DEEs), are mainly caused by ultra-rare de novo genetic variants. For milder disease, rare genetic variants could contribute to the phenotype. To determine the importance of rare variants for different epilepsy types, we analyzed a whole-exome sequencing cohort of 9,170 epilepsy-affected individuals and 8,436 control individuals. Here, we separately analyzed three different groups of epilepsies: severe DEEs, genetic generalized epilepsy (GGE), and non-acquired focal epilepsy (NAFE). We required qualifying rare variants (QRVs) to occur in control individuals with an allele count ≥ 1 and a minor allele frequency ≤ 1:1,000, to be predicted as deleterious (CADD ≥ 20), and to have an odds ratio in individuals with epilepsy ≥ 2. We identified genes enriched with QRVs primarily in NAFE (n = 72), followed by GGE (n = 32) and DEE (n = 21). This suggests that rare variants may play a more important role for causality of NAFE than for DEE. Moreover, we found that genes harboring QRVs, e.g., HSGP2, FLNA, or TNC, encode proteins that are involved in structuring the brain extracellular matrix. The present study confirms an involvement of rare variants for NAFE that occur also in the general population, while in DEE and GGE, the contribution of such variants appears more limited.
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Affiliation(s)
- Linnaeus Bundalian
- Institute of Human Genetics, University of Leipzig Medical Center, 04103 Leipzig, Germany.
| | - Yin-Yuan Su
- Institute of Biomedical Informatics, National Yang Ming Chiao Tung University, Taipei, Taiwan
| | - Siwei Chen
- Analytic and Translational Genetics Unit, Department of Medicine, Boston, MA, USA; Massachusetts General Hospital, Boston, MA 02114, USA; Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Akhil Velluva
- Division of General Biochemistry, Rudolf Schönheimer Institute of Biochemistry, Medical Faculty, Leipzig University, 04103 Leipzig, Germany; Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany
| | - Anna Sophia Kirstein
- Pediatric Research Center, University Hospital for Children and Adolescents, Leipzig University, 04103 Leipzig, Germany
| | - Antje Garten
- Pediatric Research Center, University Hospital for Children and Adolescents, Leipzig University, 04103 Leipzig, Germany
| | - Saskia Biskup
- CeGaT GmbH, 72076 Tuebingen, Germany; Hertie-Institute for Clinical Brain Research, 72070 Tubingen, Germany
| | | | - Dennis Lal
- Analytic and Translational Genetics Unit, Department of Medicine, Boston, MA, USA; Massachusetts General Hospital, Boston, MA 02114, USA; Cologne Center for Genomics, University of Cologne, 50937 Cologne, Germany
| | - Henrike O Heyne
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA; Hasso-Plattner-Institut for Digital Engineering, University of Potsdam, Potsdam, Germany; Hasso Plattner Institute at Mount Sinai, Mount Sinai School of Medicine, New York, NY, USA; Institute for Molecular Medicine Finland: FIMM, University of Helsinki, Helsinki, Finland
| | - Konrad Platzer
- Institute of Human Genetics, University of Leipzig Medical Center, 04103 Leipzig, Germany
| | - Chen-Ching Lin
- Institute of Biomedical Informatics, National Yang Ming Chiao Tung University, Taipei, Taiwan
| | - Johannes R Lemke
- Institute of Human Genetics, University of Leipzig Medical Center, 04103 Leipzig, Germany; Center for Rare Diseases, University of Leipzig Medical Center, 04103 Leipzig, Germany
| | - Diana Le Duc
- Institute of Human Genetics, University of Leipzig Medical Center, 04103 Leipzig, Germany; Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany.
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17
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Szczawińska-Popłonyk A, Popłonyk N, Badura-Stronka M, Juengling J, Huhn K, Biskup S, Bancerz B, Walkowiak J. The clinical phenotype with gastrostomy and abdominal wall infection in a pediatric patient with Takenouchi-Kosaki syndrome due to a heterozygous c.191A > G (p.Tyr64Cys) variant in CDC42: a case report. Front Genet 2023; 14:1108852. [PMID: 37347054 PMCID: PMC10280004 DOI: 10.3389/fgene.2023.1108852] [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] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2022] [Accepted: 05/23/2023] [Indexed: 06/23/2023] Open
Abstract
The CDC42 (cell division cycle homolog 42) gene product, Cdc42 belongs to the Rho GTPase family which plays a pivotal role in the regulation of multiple cellular functions, including cell cycle progression, motility, migration, proliferation, transcription activation, and reactive oxygen species production. The Cdc42 molecule controls various tissue-specific functional pathways underpinning organogenesis as well as developmental integration of the hematopoietic and immune systems. Heterozygous c.191A>G (p.Tyr64Cys) pathogenic variants in CDC42 cause Takenouchi-Kosaki syndrome characterized by a spectrum of phenotypic features comprising psychomotor developmental delay, sensorineural hearing loss, growth retardation, facial dysmorphism, cardiovascular and urinary tract malformations, camptodactyly, accompanied by thrombocytopenia and immunodeficiency of variable degree. Herein, we report a pediatric patient with the Takenouchi-Kosaki syndrome due to a heterozygous p.Tyr64Cys variant in CDC42 manifesting as a congenital malformation complex accompanied by macrothrombocytopenia, poor specific antibody response, B and T cell immunodeficiency, and low serum immunoglobulin A level. We also suggst that feeding disorders, malnutrition, and a gastrointestinal infection could be a part of the phenotypic characteristics of Takenouchi-Kosaki syndrome supporting the hypothesis of immune dysregulation and systemic inflammation occurring in the p.Tyr64Cys variant in CDC42.
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Affiliation(s)
- Aleksandra Szczawińska-Popłonyk
- Department of Pediatric Pneumonology, Allergy and Clinical Immunology, Institute of Pediatrics, Karol Jonscher University Hospital, Poznań University of Medical Sciences, Poznań, Poland
| | - Natalia Popłonyk
- Student Scientific Society, Poznań University of Medical Sciences, Poznań, Poland
| | - Magdalena Badura-Stronka
- Centers for Medical Genetics Genesis, Poznań, Poland
- Chair and Department of Medical Genetics, Poznań University of Medical Sciences, Poznań, Poland
| | | | - Kerstin Huhn
- Zentrum Fur Humangenetik Tübingen, Tübingen, Germany
| | - Saskia Biskup
- Zentrum Fur Humangenetik Tübingen, Tübingen, Germany
- CeGaT GmbH, Tübingen, Germany
| | - Bartłomiej Bancerz
- Department of Pediatric Gastroenterology and Metabolic Diseases, Institute of Pediatrics, Karol Jonscher University Hospital, Poznań University of Medical Sciences, Poznań, Poland
| | - Jarosław Walkowiak
- Department of Pediatric Gastroenterology and Metabolic Diseases, Institute of Pediatrics, Karol Jonscher University Hospital, Poznań University of Medical Sciences, Poznań, Poland
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18
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Mao K, Borel C, Ansar M, Jolly A, Makrythanasis P, Froehlich C, Iwaszkiewicz J, Wang B, Xu X, Li Q, Blanc X, Zhu H, Chen Q, Jin F, Ankamreddy H, Singh S, Zhang H, Wang X, Chen P, Ranza E, Paracha SA, Shah SF, Guida V, Piceci-Sparascio F, Melis D, Dallapiccola B, Digilio MC, Novelli A, Magliozzi M, Fadda MT, Streff H, Machol K, Lewis RA, Zoete V, Squeo GM, Prontera P, Mancano G, Gori G, Mariani M, Selicorni A, Psoni S, Fryssira H, Douzgou S, Marlin S, Biskup S, De Luca A, Merla G, Zhao S, Cox TC, Groves AK, Lupski JR, Zhang Q, Zhang YB, Antonarakis SE. FOXI3 pathogenic variants cause one form of craniofacial microsomia. Nat Commun 2023; 14:2026. [PMID: 37041148 PMCID: PMC10090152 DOI: 10.1038/s41467-023-37703-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2022] [Accepted: 03/28/2023] [Indexed: 04/13/2023] Open
Abstract
Craniofacial microsomia (CFM; also known as Goldenhar syndrome), is a craniofacial developmental disorder of variable expressivity and severity with a recognizable set of abnormalities. These birth defects are associated with structures derived from the first and second pharyngeal arches, can occur unilaterally and include ear dysplasia, microtia, preauricular tags and pits, facial asymmetry and other malformations. The inheritance pattern is controversial, and the molecular etiology of this syndrome is largely unknown. A total of 670 patients belonging to unrelated pedigrees with European and Chinese ancestry with CFM, are investigated. We identify 18 likely pathogenic variants in 21 probands (3.1%) in FOXI3. Biochemical experiments on transcriptional activity and subcellular localization of the likely pathogenic FOXI3 variants, and knock-in mouse studies strongly support the involvement of FOXI3 in CFM. Our findings indicate autosomal dominant inheritance with reduced penetrance, and/or autosomal recessive inheritance. The phenotypic expression of the FOXI3 variants is variable. The penetrance of the likely pathogenic variants in the seemingly dominant form is reduced, since a considerable number of such variants in affected individuals were inherited from non-affected parents. Here we provide suggestive evidence that common variation in the FOXI3 allele in trans with the pathogenic variant could modify the phenotypic severity and accounts for the incomplete penetrance.
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Affiliation(s)
- Ke Mao
- School of Engineering Medicine, Beihang University, Beijing, 100191, China
| | - Christelle Borel
- Department of Genetic Medicine and Development, University of Geneva Medical Faculty, Geneva, 1211, Switzerland
| | - Muhammad Ansar
- Department of Genetic Medicine and Development, University of Geneva Medical Faculty, Geneva, 1211, Switzerland
- Jules-Gonin Eye Hospital, Department of Ophthalmology, University of Lausanne, 1004, Lausanne, Switzerland
| | - Angad Jolly
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Periklis Makrythanasis
- Department of Genetic Medicine and Development, University of Geneva Medical Faculty, Geneva, 1211, Switzerland
- Laboratory of Medical Genetics, Medical School, University of Athens, Athens, Greece
- Biomedical Research Foundation of the Academy of Athens, Athens, Greece
| | | | - Justyna Iwaszkiewicz
- Molecular Modeling Group, Swiss Institute of Bioinformatics, Lausanne, 1015, Switzerland
| | - Bingqing Wang
- Plastic Surgery Hospital, Chinese Academy of Medical Sciences, Beijing, 100144, China
| | - Xiaopeng Xu
- School of Engineering Medicine, Beihang University, Beijing, 100191, China
- Key Laboratory of Big Data-Based Precision Medicine (Beihang University), Ministry of Industry and Information Technology, Beijing, China
| | - Qiang Li
- Department of Plastic Surgery, Affiliated Hospital of Xuzhou Medical University, Xuzhou, 221000, China
| | - Xavier Blanc
- Medigenome, Swiss Institute of Genomic Medicine, 1207, Geneva, Switzerland
| | - Hao Zhu
- School of Engineering Medicine, Beihang University, Beijing, 100191, China
| | - Qi Chen
- Plastic Surgery Hospital, Chinese Academy of Medical Sciences, Beijing, 100144, China
| | - Fujun Jin
- School of Engineering Medicine, Beihang University, Beijing, 100191, China
- Key Laboratory of Big Data-Based Precision Medicine (Beihang University), Ministry of Industry and Information Technology, Beijing, China
| | - Harinarayana Ankamreddy
- Department of Biotechnology, School of Bioengineering, SRMIST, Kattankulathur, Tamilnadu, 603203, India
| | - Sunita Singh
- Department of Neuroscience, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Hongyuan Zhang
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
- Department of Neuroscience, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Xiaogang Wang
- School of Engineering Medicine, Beihang University, Beijing, 100191, China
- Key Laboratory of Big Data-Based Precision Medicine (Beihang University), Ministry of Industry and Information Technology, Beijing, China
| | - Peiwei Chen
- Department of Otolaryngology-Head and Neck Surgery, Beijing Tongren Hospital, Capital Medical University, Beijing, China
| | - Emmanuelle Ranza
- Medigenome, Swiss Institute of Genomic Medicine, 1207, Geneva, Switzerland
| | - Sohail Aziz Paracha
- Anatomy Department, Khyber Medical University Institute of Medical Sciences (KIMS), Kohat, Pakistan
| | - Syed Fahim Shah
- Department of Medicine, KMU Institute of Medical Sciences (KIMS), DHQ Hospital KDA, Kohat, Pakistan
| | - Valentina Guida
- Medical Genetics Division, Fondazione IRCCS Casa Sollievo della Sofferenza, San Giovanni Rotondo, Italy
| | | | - Daniela Melis
- Department of Medicine, Surgery, and Dentistry, Università University degli of Studi di Salerno, Salerno, Italy
| | - Bruno Dallapiccola
- Medical Genetics and Rare Disease Research Division, Pediatric Cardiology, Medical Genetics Laboratory, Neuropsychiatry, Scientific Rectorate, Bambino Gesù Children Hospital, IRCCS, Rome, Italy
| | | | - Antonio Novelli
- Sezione di Genetica Medica, Ospedale 'Bambino Gesù', Rome, Italy
| | - Monia Magliozzi
- Sezione di Genetica Medica, Ospedale 'Bambino Gesù', Rome, Italy
| | - Maria Teresa Fadda
- Department of Maxillo-Facial Surgery, Policlinico Umberto I, Rome, Italy
| | - Haley Streff
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Keren Machol
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Richard A Lewis
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Vincent Zoete
- Molecular Modeling Group, Swiss Institute of Bioinformatics, Lausanne, 1015, Switzerland
- Department of Fundamental Oncology, Ludwig Institute for Cancer Research, Lausanne University, Epalinges, 1066, Switzerland
| | - Gabriella Maria Squeo
- Laboratory of Regulatory & Functional Genomics, Fondazione IRCCS Casa Sollievo della Sofferenza, San Giovanni Rotondo, Italy
| | - Paolo Prontera
- Medical Genetics Unit, Hospital Santa Maria della Misericordia, Perugia, Italy
| | - Giorgia Mancano
- Medical Genetics Unit, University of Perugia Hospital SM della Misericordia, Perugia, Italy
| | - Giulia Gori
- Medical Genetics Unit, Meyer Children's University Hospital, Florence, Italy
| | - Milena Mariani
- Pediatric Department, ASST Lariana, Santa Anna General Hospital, Como, Italy
| | - Angelo Selicorni
- Pediatric Department, ASST Lariana, Santa Anna General Hospital, Como, Italy
| | - Stavroula Psoni
- Laboratory of Medical Genetics, Medical School, University of Athens, Athens, Greece
| | - Helen Fryssira
- Laboratory of Medical Genetics, Medical School, University of Athens, Athens, Greece
| | - Sofia Douzgou
- Division of Evolution, Infection and Genomics, School of Biological Sciences, University of Manchester, Manchester, UK
- Department of Medical Genetics, Haukeland University Hospital, Bergen, Norway
| | - Sandrine Marlin
- Centre de Référence Surdités Génétiques, Hôpital Necker, Institut Imagine, Paris, France
| | - Saskia Biskup
- CeGaT GmbH and Praxis für Humangenetik Tuebingen, Tuebingen, 72076, Germany
| | - Alessandro De Luca
- Medical Genetics Division, Fondazione IRCCS Casa Sollievo della Sofferenza, San Giovanni Rotondo, Italy
| | - Giuseppe Merla
- Laboratory of Regulatory & Functional Genomics, Fondazione IRCCS Casa Sollievo della Sofferenza, San Giovanni Rotondo, Italy
- Department of Molecular Medicine and Medical Biotechnology, University of Naples Federico II, Via S. Pansini 5, 80131, Naples, Italy
| | - Shouqin Zhao
- Department of Otolaryngology-Head and Neck Surgery, Beijing Tongren Hospital, Capital Medical University, Beijing, China
| | - Timothy C Cox
- Departments of Oral & Craniofacial Sciences and Pediatrics, University of Missouri-Kansas City, Kansas City, MO, 64108, USA
| | - Andrew K Groves
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
- Department of Neuroscience, Baylor College of Medicine, Houston, TX, 77030, USA
| | - James R Lupski
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
- Department of Pediatrics, Baylor College of Medicine, Houston, TX, 77030, USA
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Qingguo Zhang
- Plastic Surgery Hospital, Chinese Academy of Medical Sciences, Beijing, 100144, China.
| | - Yong-Biao Zhang
- School of Engineering Medicine, Beihang University, Beijing, 100191, China.
- Key Laboratory of Big Data-Based Precision Medicine (Beihang University), Ministry of Industry and Information Technology, Beijing, China.
| | - Stylianos E Antonarakis
- Department of Genetic Medicine and Development, University of Geneva Medical Faculty, Geneva, 1211, Switzerland.
- Medigenome, Swiss Institute of Genomic Medicine, 1207, Geneva, Switzerland.
- iGE3 Institute of Genetics and Genomes in Geneva, Geneva, Switzerland.
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19
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Cannet C, Frauendienst-Egger G, Freisinger P, Götz H, Götz M, Himmelreich N, Kock V, Spraul M, Bus C, Biskup S, Trefz F. Ex vivo proton spectroscopy ( 1 H-NMR) analysis of inborn errors of metabolism: Automatic and computer-assisted analyses. NMR Biomed 2023; 36:e4853. [PMID: 36264537 DOI: 10.1002/nbm.4853] [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] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/21/2021] [Revised: 07/29/2022] [Accepted: 10/05/2022] [Indexed: 06/16/2023]
Abstract
There are about 1500 genetic metabolic diseases. A small number of treatable diseases are diagnosed by newborn screening programs, which are continually being developed. However, most diseases can only be diagnosed based on clinical symptoms or metabolic findings. The main biological fluids used are urine, plasma and, in special situations, cerebrospinal fluid. In contrast to commonly used methods such as gas chromatography and high performance liquid chromatography mass spectrometry, ex vivo proton spectroscopy (1 H-NMR) is not yet used in routine clinical practice, although it has been recommended for more than 30 years. Automatic analysis and improved NMR technology have also expanded the applications used for the diagnosis of inborn errors of metabolism. We provide a mini-overview of typical applications, especially in urine but also in plasma, used to diagnose common but also rare genetic metabolic diseases with 1 H-NMR. The use of computer-assisted diagnostic suggestions can facilitate interpretation of the profiles. In a proof of principle, to date, 182 reports of 59 different diseases and 500 reports of healthy children are stored. The percentage of correct automatic diagnoses was 74%. Using the same 1 H-NMR profile-targeted analysis, it is possible to apply an untargeted approach that distinguishes profile differences from healthy individuals. Thus, additional conditions such as lysosomal storage diseases or drug interferences are detectable. Furthermore, because 1 H-NMR is highly reproducible and can detect a variety of different substance categories, the metabolomic approach is suitable for monitoring patient treatment and revealing additional factors such as nutrition and microbiome metabolism. Besides the progress in analytical techniques, a multiomics approach is most effective to combine metabolomics with, for example, whole exome sequencing, to also diagnose patients with nondetectable metabolic abnormalities in biological fluids. In this mini review we also provide our own data to demonstrate the role of NMR in a multiomics platform in the field of inborn errors of metabolism.
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Affiliation(s)
| | - Georg Frauendienst-Egger
- Department of Pediatrics, Reutlingen, Klinikum Reutlingen, School of Medicine, University of Tuebingen, Reutlingen, Germany
| | - Peter Freisinger
- Department of Pediatrics, Reutlingen, Klinikum Reutlingen, School of Medicine, University of Tuebingen, Reutlingen, Germany
| | | | | | | | - Vanessa Kock
- Department of Pediatrics, Reutlingen, Klinikum Reutlingen, School of Medicine, University of Tuebingen, Reutlingen, Germany
| | | | - Christine Bus
- CEGAT, Tübingen, Germany and Human Genetics Institute, Tübingen, Germany
| | - Saskia Biskup
- CEGAT, Tübingen, Germany and Human Genetics Institute, Tübingen, Germany
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20
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Bundalian L, Su YY, Chen S, Velluva A, Kirstein AS, Garten A, Biskup S, Battke F, Lal D, Heyne HO, Platzer K, Lin CC, Lemke JR, Le Duc D. The role of rare genetic variants enrichment in epilepsies of presumed genetic etiology. medRxiv 2023:2023.01.17.23284702. [PMID: 36974069 PMCID: PMC10041669 DOI: 10.1101/2023.01.17.23284702] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
Previous studies suggested that severe epilepsies e.g., developmental and epileptic encephalopathies (DEE) are mainly caused by ultra-rare de novo genetic variants. For milder phenotypes, rare genetic variants could contribute to the phenotype. To determine the importance of rare variants for different epilepsy types, we analyzed a whole-exome sequencing cohort of 9,170 epilepsy-affected individuals and 8,436 controls. Here, we separately analyzed three different groups of epilepsies : severe DEEs, genetic generalized epilepsy (GGE), and non-acquired focal epilepsy (NAFE). We required qualifying rare variants (QRVs) to occur in controls at a minor allele frequency ≤ 1:1,000, to be predicted as deleterious (CADD≥20), and to have an odds ratio in epilepsy cases ≥2. We identified genes enriched with QRVs in DEE (n=21), NAFE (n=72), and GGE (n=32) - the number of enriched genes are found greatest in NAFE and least in DEE. This suggests that rare variants may play a more important role for causality of NAFE than in DEE. Moreover, we found that QRV-carrying genes e.g., HSGP2, FLNA or TNC are involved in structuring the brain extracellular matrix. The present study confirms an involvement of rare variants for NAFE, while in DEE and GGE, the contribution of such variants appears more limited.
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Affiliation(s)
- Linnaeus Bundalian
- Institute of Human Genetics, University of Leipzig Medical Center, 4103 Leipzig, Germany
| | - Yin-Yuan Su
- Institute of Biomedical Informatics, National Yang Ming Chiao Tung University, Taipei, Taiwan
| | - Siwei Chen
- Analytic and Translational Genetics Unit, Department of Medicine, Massachusetts General Hospital, Boston, MA 02114, USA
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Akhil Velluva
- Division of General Biochemistry, Rudolf Schönheimer Institute of Biochemistry, Medical Faculty, Leipzig University, 04103, Leipzig, Germany
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, 04103, Leipzig, Germany
| | - Anna Sophia Kirstein
- Pediatric Research Center, University Hospital for Children and Adolescents, Leipzig University, 04103, Leipzig, Germany
| | - Antje Garten
- Pediatric Research Center, University Hospital for Children and Adolescents, Leipzig University, 04103, Leipzig, Germany
| | - Saskia Biskup
- CeGaT GmbH, 72076, Tuebingen, Germany
- Hertie-Institute for Clinical Brain Research, 72070, Tubingen, Germany
| | | | - Dennis Lal
- Analytic and Translational Genetics Unit, Department of Medicine, Massachusetts General Hospital, Boston, MA 02114, USA
- Cologne Center for Genomics, University of Cologne, 50937 Cologne, Germany
| | - Henrike O Heyne
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Hasso-Plattner-Institut for Digital Engineering, University of Potsdam, Potsdam, Germany
- Hasso Plattner Institute at Mount Sinai, Mount Sinai School of Medicine, NY, US
- Institute for Molecular Medicine Finland: FIMM, University of Helsinki, Helsinki, Finland
| | - Konrad Platzer
- Institute of Human Genetics, University of Leipzig Medical Center, 4103 Leipzig, Germany
| | - Chen-Ching Lin
- Institute of Biomedical Informatics, National Yang Ming Chiao Tung University, Taipei, Taiwan
| | - Johannes R Lemke
- Institute of Human Genetics, University of Leipzig Medical Center, 4103 Leipzig, Germany
- Center for Rare Diseases, University of Leipzig Medical Center, 4103 Leipzig, Germany
| | - Diana Le Duc
- Institute of Human Genetics, University of Leipzig Medical Center, 4103 Leipzig, Germany
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, 04103, Leipzig, Germany
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21
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Maass F, Jamous A, Biskup S, Eisenberg H, D' Hedouville Z, Bähr M, van Riesen C. Spinocerebellar ataxia type 35 caused by a new
TGM6
variant: video documentation of a German family. Mov Disord Clin Pract 2023. [DOI: 10.1002/mdc3.13717] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/12/2023] Open
Affiliation(s)
- Fabian Maass
- Dept. of Neurology University Medical Center Göttingen Germany
| | - Ala Jamous
- Department of Neuroradiology University Medical Center Göttingen Germany
| | - Saskia Biskup
- CeGaT, Center for Genomics and Transcriptomics Tübingen Germany
| | - Hanna Eisenberg
- Dept. of Neurology University Medical Center Göttingen Germany
| | | | - Mathias Bähr
- Dept. of Neurology University Medical Center Göttingen Germany
| | - Christoph van Riesen
- Dept. of Neurology University Medical Center Göttingen Germany
- Germany Center for Neurodegenerative Diseases (DZNE) Göttingen Germany
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22
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Roessler F, Beck AE, Susie B, Tobias B, Begtrup A, Biskup S, Caluseriu O, Delanty N, Fröhlich C, Greally MT, Karnstedt M, Klöckner C, Kurtzberg J, Schubert S, Schulze M, Weidenbach M, Westphal DS, White M, Wolf CM, Zyskind J, Popp B, Strehlow V. Genetic and phenotypic spectrum in the NONO-associated syndromic disorder. Am J Med Genet A 2023; 191:469-478. [PMID: 36426740 DOI: 10.1002/ajmg.a.63044] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [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: 05/23/2022] [Revised: 09/23/2022] [Accepted: 09/30/2022] [Indexed: 11/26/2022]
Abstract
The non-POU domain-containing octamer-binding (NONO) protein is involved in multiple steps of gene regulation such as RNA metabolism and DNA repair. Hemizygous pathogenic variants in the NONO gene were confirmed to cause a rare X-linked syndromic disorder. Through our in-house diagnostics and subsequent matchmaking, we identified six unrelated male individuals with pathogenic or likely pathogenic NONO variants. For a detailed comparison, we reviewed all published characterizations of the NONO-associated disorder. The combined cohort consists of 16 live-born males showing developmental delay, corpus callosum anomalies, non-compaction cardiomyopathy and relative macrocephaly as leading symptoms. Seven prenatal literature cases were characterized by cardiac malformations. In this study, we extend the phenotypic spectrum through two more cases with epilepsy as well as two more cases with hematologic anomalies. By RNA expression analysis and structural modeling of a new in-frame splice deletion, we reinforce loss-of-function as the pathomechanism for the NONO-associated syndromic disorder.
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Affiliation(s)
- Franziska Roessler
- Institute of Human Genetics, University of Leipzig Medical Center, Leipzig, Germany
| | - Anita E Beck
- Division of Genetic Medicine, Department of Pediatrics, University of Washington, Seattle, Washington, USA.,Seattle Children's Hospital, Seattle, Washington, USA
| | - Ball Susie
- Central Washington Genetics Program, Yakima Valley Memorial, Yakima, Washington, USA
| | - Bartolomaeus Tobias
- Institute of Human Genetics, University of Leipzig Medical Center, Leipzig, Germany
| | | | | | - Oana Caluseriu
- Department of Medical Genetics, University of Alberta, Edmonton, Alberta, Canada
| | - Norman Delanty
- FutureNeuro SFI Research Centre, The Royal College of Surgeons in Ireland, Dublin, Ireland.,Department of Neurology, Beaumont Hospital, Dublin, Ireland
| | | | - Marie T Greally
- FutureNeuro SFI Research Centre, The Royal College of Surgeons in Ireland, Dublin, Ireland.,School of Pharmacy and Biomolecular Sciences, The Royal College of Surgeons in Ireland, Dublin, Ireland
| | - Maike Karnstedt
- Institute of Human Genetics, University of Leipzig Medical Center, Leipzig, Germany
| | - Chiara Klöckner
- Institute of Human Genetics, University of Leipzig Medical Center, Leipzig, Germany
| | - Joanne Kurtzberg
- Marcus Center for Cellular Cures, Duke University School of Medicine, Durham, North Carolina, USA
| | - Susanna Schubert
- Institute of Human Genetics, University of Leipzig Medical Center, Leipzig, Germany
| | | | - Michael Weidenbach
- Department for Pediatric Cardiology, Heart Center Leipzig, University of Leipzig, Leipzig, Germany
| | - Dominik S Westphal
- Institute of Human Genetics, Klinikum Rechts der Isar, School of Medicine, Technical University Munich, Germany.,Department of Internal Medicine I, Klinikum Rechts der Isar, School of Medicine, Technical University Munich, Munich, Germany
| | - Maire White
- FutureNeuro SFI Research Centre, The Royal College of Surgeons in Ireland, Dublin, Ireland.,School of Pharmacy and Biomolecular Sciences, The Royal College of Surgeons in Ireland, Dublin, Ireland
| | - Cordula M Wolf
- Department of Congenital Heart Defects and Pediatric Cardiology, German Heart Center Munich, Technical University of Munich, School of Medicine and Health, DZHK (German Centre for Cardiovascular Research), Munich Heart Alliance, Munich, Germany
| | | | - Bernt Popp
- Institute of Human Genetics, University of Leipzig Medical Center, Leipzig, Germany
| | - Vincent Strehlow
- Institute of Human Genetics, University of Leipzig Medical Center, Leipzig, Germany
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23
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Bodenbender JP, Marino V, Bethge L, Stingl K, Haack TB, Biskup S, Kohl S, Kühlewein L, Dell’Orco D, Weisschuh N. Biallelic Variants in TULP1 Are Associated with Heterogeneous Phenotypes of Retinal Dystrophy. Int J Mol Sci 2023; 24:ijms24032709. [PMID: 36769033 PMCID: PMC9916573 DOI: 10.3390/ijms24032709] [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] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2023] [Revised: 01/24/2023] [Accepted: 01/27/2023] [Indexed: 02/04/2023] Open
Abstract
Biallelic pathogenic variants in TULP1 are mostly associated with severe rod-driven inherited retinal degeneration. In this study, we analyzed clinical heterogeneity in 17 patients and characterized the underlying biallelic variants in TULP1. All patients underwent thorough ophthalmological examinations. Minigene assays and structural analyses were performed to assess the consequences of splice variants and missense variants. Three patients were diagnosed with Leber congenital amaurosis, nine with early onset retinitis pigmentosa, two with retinitis pigmentosa with an onset in adulthood, one with cone dystrophy, and two with cone-rod dystrophy. Seventeen different alleles were identified, namely eight missense variants, six nonsense variants, one in-frame deletion variant, and two splice site variants. For the latter two, minigene assays revealed aberrant transcripts containing frameshifts and premature termination codons. Structural analysis and molecular modeling suggested different degrees of structural destabilization for the missense variants. In conclusion, we report the largest cohort of patients with TULP1-associated IRD published to date. Most of the patients exhibited rod-driven disease, yet a fraction of the patients exhibited cone-driven disease. Our data support the hypothesis that TULP1 variants do not fold properly and thus trigger unfolded protein response, resulting in photoreceptor death.
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Affiliation(s)
- Jan-Philipp Bodenbender
- Department for Ophthalmology, University Eye Hospital, University of Tübingen, 72076 Tübingen, Germany
- Correspondence: (J.-P.B.); (N.W.)
| | - Valerio Marino
- Section of Biological Chemistry, Department of Neurosciences, Biomedicine and Movement Sciences, University of Verona, 37124 Verona, Italy
| | - Leon Bethge
- Department for Ophthalmology, University Eye Hospital, University of Tübingen, 72076 Tübingen, Germany
| | - Katarina Stingl
- Department for Ophthalmology, University Eye Hospital, University of Tübingen, 72076 Tübingen, Germany
| | - Tobias B. Haack
- Institute of Medical Genetics and Applied Genomics, University of Tübingen, 72076 Tübingen, Germany
- Centre for Rare Diseases, University of Tübingen, 72076 Tübingen, Germany
| | - Saskia Biskup
- Praxis für Humangenetik, 72076 Tübingen, Germany
- CeGaT GmbH, 72076 Tübingen, Germany
| | - Susanne Kohl
- Department for Ophthalmology, Institute for Ophthalmic Research, University of Tübingen, 72076 Tübingen, Germany
| | - Laura Kühlewein
- Department for Ophthalmology, University Eye Hospital, University of Tübingen, 72076 Tübingen, Germany
| | - Daniele Dell’Orco
- Section of Biological Chemistry, Department of Neurosciences, Biomedicine and Movement Sciences, University of Verona, 37124 Verona, Italy
| | - Nicole Weisschuh
- Department for Ophthalmology, Institute for Ophthalmic Research, University of Tübingen, 72076 Tübingen, Germany
- Correspondence: (J.-P.B.); (N.W.)
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24
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Park JH, Nordström U, Tsiakas K, Keskin I, Elpers C, Mannil M, Heller R, Nolan M, Alburaiky S, Zetterström P, Hempel M, Schara-Schmidt U, Biskup S, Steinacker P, Otto M, Weishaupt J, Hahn A, Santer R, Marquardt T, Marklund SL, Andersen PM. The motor system is exceptionally vulnerable to absence of the ubiquitously expressed superoxide dismutase-1. Brain Commun 2023; 5:fcad017. [PMID: 36793789 PMCID: PMC9924500 DOI: 10.1093/braincomms/fcad017] [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] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2022] [Revised: 10/21/2022] [Accepted: 01/24/2023] [Indexed: 01/30/2023] Open
Abstract
Superoxide dismutase-1 is a ubiquitously expressed antioxidant enzyme. Mutations in SOD1 can cause amyotrophic lateral sclerosis, probably via a toxic gain-of-function involving protein aggregation and prion-like mechanisms. Recently, homozygosity for loss-of-function mutations in SOD1 has been reported in patients presenting with infantile-onset motor neuron disease. We explored the bodily effects of superoxide dismutase-1 enzymatic deficiency in eight children homozygous for the p.C112Wfs*11 truncating mutation. In addition to physical and imaging examinations, we collected blood, urine and skin fibroblast samples. We used a comprehensive panel of clinically established analyses to assess organ function and analysed oxidative stress markers, antioxidant compounds, and the characteristics of the mutant Superoxide dismutase-1. From around 8 months of age, all patients exhibited progressive signs of both upper and lower motor neuron dysfunction, cerebellar, brain stem, and frontal lobe atrophy and elevated plasma neurofilament concentration indicating ongoing axonal damage. The disease progression seemed to slow down over the following years. The p.C112Wfs*11 gene product is unstable, rapidly degraded and no aggregates were found in fibroblast. Most laboratory tests indicated normal organ integrity and only a few modest deviations were found. The patients displayed anaemia with shortened survival of erythrocytes containing decreased levels of reduced glutathione. A variety of other antioxidants and oxidant damage markers were within normal range. In conclusion, non-neuronal organs in humans show a remarkable tolerance to absence of Superoxide dismutase-1 enzymatic activity. The study highlights the enigmatic specific vulnerability of the motor system to both gain-of-function mutations in SOD1 and loss of the enzyme as in the here depicted infantile superoxide dismutase-1 deficiency syndrome.
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Affiliation(s)
- Julien H Park
- Department of Clinical Sciences, Neurosciences, Umeå University, 901 87 Umeå, Sweden,Department of General Paediatrics, University of Münster, 48149 Münster, Germany
| | - Ulrika Nordström
- Department of Clinical Sciences, Neurosciences, Umeå University, 901 87 Umeå, Sweden
| | - Konstantinos Tsiakas
- Department of Paediatrics, University Medical Centre Hamburg-Eppendorf, 20251 Hamburg, Germany
| | - Isil Keskin
- Department of Medical Biosciences, Pathology, Umeå University, 901 85 Umeå, Sweden
| | - Christiane Elpers
- Department of General Paediatrics, University of Münster, 48149 Münster, Germany
| | - Manoj Mannil
- Clinic for Radiology, University Hospital Münster, WWU University of Münster, 48149 Münster, Germany
| | - Raoul Heller
- Starship Children’s Health, Auckland City Hospital, Auckland 1142, New Zealand
| | - Melinda Nolan
- Starship Children’s Health, Auckland City Hospital, Auckland 1142, New Zealand
| | - Salam Alburaiky
- Starship Children’s Health, Auckland City Hospital, Auckland 1142, New Zealand
| | - Per Zetterström
- Department of Medical Biosciences, Clinical Chemistry, Umeå University, 901 87 Umeå, Sweden
| | - Maja Hempel
- Department of Paediatrics, University Medical Centre Hamburg-Eppendorf, 20251 Hamburg, Germany,Current address: Institute of Human Genetics, University Hospital Heidelberg, 69120 Heidelberg, Germany
| | | | - Saskia Biskup
- CeGAT GmbH and Praxis für Humangenetik Tübingen, 72076 Tübingen, Germany
| | - Petra Steinacker
- Department of Neurology, Martin-Luther-University Halle-Wittenberg, 06120 Halle (Saale), Germany
| | - Markus Otto
- Department of Neurology, Martin-Luther-University Halle-Wittenberg, 06120 Halle (Saale), Germany
| | - Jochen Weishaupt
- Division for Neurodegenerative Diseases, Department of Neurology, Medical Faculty Mannheim, University of Heidelberg, 68167 Mannheim, Germany
| | - Andreas Hahn
- Department of Child Neurology, Justus Liebig University, 35392 Giessen, Germany
| | - René Santer
- Department of Paediatrics, University Medical Centre Hamburg-Eppendorf, 20251 Hamburg, Germany
| | - Thorsten Marquardt
- Department of General Paediatrics, University of Münster, 48149 Münster, Germany
| | - Stefan L Marklund
- Department of Medical Biosciences, Clinical Chemistry, Umeå University, 901 87 Umeå, Sweden
| | - Peter M Andersen
- Correspondence to: Peter Munch Andersen Department of Clinical Science, Neurosciences Umeå University, SE-901 85 Umeå, Sweden E-mail:
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25
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Horn S, Danyel M, Erdmann N, Boschann F, Gunnarsson C, Biskup S, Juengling J, Potratz C, Prager C, Kaindl AM. Case report: KPTN gene-related syndrome associated with a spectrum of neurodevelopmental anomalies including severe epilepsy. Front Neurol 2023; 13:1113811. [PMID: 36703628 PMCID: PMC9871926 DOI: 10.3389/fneur.2022.1113811] [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] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Accepted: 12/15/2022] [Indexed: 01/11/2023] Open
Abstract
Biallelic variants in the kaptin gene KPTN were identified recently in individuals with a novel syndrome referred to as autosomal recessive intellectual developmental disorder 41 (MRT41). MRT41 is characterized by developmental delay, predominantly in language development, behavioral abnormalities, and epilepsy. Only about 15 affected individuals have been described in the literature, all with primary or secondary macrocephaly. Using exome sequencing, we identified three different biallelic variants in KPTN in five affected individuals from three unrelated families. In total, two KPTN variants were already reported as a loss of function variants. A novel splice site variant in KPTN was detected in two unrelated families of this study. The core phenotype with neurodevelopment delay was present in all patients. However, macrocephaly was not present in at least one patient. In total, two patients exhibited developmental and epileptic encephalopathies with generalized tonic-clonic seizures that were drug-resistant in one of them. Thus, we further delineate the KPTN-related syndrome, especially emphasizing the severity of epilepsy phenotypes and difficulties in treatment in patients of our cohort.
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Affiliation(s)
- Svea Horn
- Department of Pediatric Neurology, Charité–Universitätsmedizin Berlin, Berlin, Germany,Center for Chronically Sick Children, Charité–Universitätsmedizin Berlin, Berlin, Germany
| | - Magdalena Danyel
- Institute of Medical Genetics and Human Genetics, Charité–Universitätsmedizin Berlin, Berlin, Germany,BIH Biomedical Innovation Academy, BIH Charité Clinician Scientist Program, Berlin Institute of Health at Charité–Universitätsmedizin Berlin, Berlin, Germany
| | - Nina Erdmann
- Department of Pediatric Neurology, Charité–Universitätsmedizin Berlin, Berlin, Germany,Center for Chronically Sick Children, Charité–Universitätsmedizin Berlin, Berlin, Germany
| | - Felix Boschann
- Institute of Medical Genetics and Human Genetics, Charité–Universitätsmedizin Berlin, Berlin, Germany,BIH Biomedical Innovation Academy, BIH Charité Clinician Scientist Program, Berlin Institute of Health at Charité–Universitätsmedizin Berlin, Berlin, Germany
| | - Cecilia Gunnarsson
- Department of Clinical Genetics, Linköping University, Linköping, Sweden,Department of Biomedical and Clinical Sciences, Linköping University, Linköping, Sweden,Centre for Rare Diseases in South East Region of Sweden, Linköping University, Linköping, Sweden
| | | | | | - Cornelia Potratz
- Department of Pediatric Neurology, Charité–Universitätsmedizin Berlin, Berlin, Germany,Center for Chronically Sick Children, Charité–Universitätsmedizin Berlin, Berlin, Germany
| | - Christine Prager
- Department of Pediatric Neurology, Charité–Universitätsmedizin Berlin, Berlin, Germany,Center for Chronically Sick Children, Charité–Universitätsmedizin Berlin, Berlin, Germany
| | - Angela M. Kaindl
- Department of Pediatric Neurology, Charité–Universitätsmedizin Berlin, Berlin, Germany,Center for Chronically Sick Children, Charité–Universitätsmedizin Berlin, Berlin, Germany,Institute for Cell Biology and Neurobiology, Charité–Universitätsmedizin Berlin, Berlin, Germany,*Correspondence: Angela M. Kaindl ✉
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26
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Mensah MA, Niskanen H, Magalhaes AP, Basu S, Kircher M, Sczakiel HL, Reiter AMV, Elsner J, Meinecke P, Biskup S, Chung BHY, Dombrowsky G, Eckmann-Scholz C, Hitz MP, Hoischen A, Holterhus PM, Hülsemann W, Kahrizi K, Kalscheuer VM, Kan A, Krumbiegel M, Kurth I, Leubner J, Longardt AC, Moritz JD, Najmabadi H, Skipalova K, Snijders Blok L, Tzschach A, Wiedersberg E, Zenker M, Garcia-Cabau C, Buschow R, Salvatella X, Kraushar ML, Mundlos S, Caliebe A, Spielmann M, Horn D, Hnisz D. Aberrant phase separation and nucleolar dysfunction in rare genetic diseases. Nature 2023; 614:564-571. [PMID: 36755093 PMCID: PMC9931588 DOI: 10.1038/s41586-022-05682-1] [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] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2021] [Accepted: 12/22/2022] [Indexed: 02/10/2023]
Abstract
Thousands of genetic variants in protein-coding genes have been linked to disease. However, the functional impact of most variants is unknown as they occur within intrinsically disordered protein regions that have poorly defined functions1-3. Intrinsically disordered regions can mediate phase separation and the formation of biomolecular condensates, such as the nucleolus4,5. This suggests that mutations in disordered proteins may alter condensate properties and function6-8. Here we show that a subset of disease-associated variants in disordered regions alter phase separation, cause mispartitioning into the nucleolus and disrupt nucleolar function. We discover de novo frameshift variants in HMGB1 that cause brachyphalangy, polydactyly and tibial aplasia syndrome, a rare complex malformation syndrome. The frameshifts replace the intrinsically disordered acidic tail of HMGB1 with an arginine-rich basic tail. The mutant tail alters HMGB1 phase separation, enhances its partitioning into the nucleolus and causes nucleolar dysfunction. We built a catalogue of more than 200,000 variants in disordered carboxy-terminal tails and identified more than 600 frameshifts that create arginine-rich basic tails in transcription factors and other proteins. For 12 out of the 13 disease-associated variants tested, the mutation enhanced partitioning into the nucleolus, and several variants altered rRNA biogenesis. These data identify the cause of a rare complex syndrome and suggest that a large number of genetic variants may dysregulate nucleoli and other biomolecular condensates in humans.
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Affiliation(s)
- Martin A. Mensah
- grid.6363.00000 0001 2218 4662Institute of Medical Genetics and Human Genetics, Charité–Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany ,grid.484013.a0000 0004 6879 971XBIH Biomedical Innovation Academy, Berlin Institute of Health at Charité–Universitätsmedizin Berlin, Berlin, Germany ,grid.419538.20000 0000 9071 0620RG Development and Disease, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Henri Niskanen
- grid.419538.20000 0000 9071 0620Department of Genome Regulation, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Alexandre P. Magalhaes
- grid.419538.20000 0000 9071 0620Department of Genome Regulation, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Shaon Basu
- grid.419538.20000 0000 9071 0620Department of Genome Regulation, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Martin Kircher
- grid.484013.a0000 0004 6879 971XExploratory Diagnostic Sciences, Berlin Institute of Health at Charité–Universitätsmedizin Berlin, Berlin, Germany ,grid.4562.50000 0001 0057 2672Institute of Human Genetics, University Hospitals Schleswig-Holstein, University of Lübeck and Kiel University, Lübeck, Kiel Germany
| | - Henrike L. Sczakiel
- grid.6363.00000 0001 2218 4662Institute of Medical Genetics and Human Genetics, Charité–Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany ,grid.484013.a0000 0004 6879 971XBIH Biomedical Innovation Academy, Berlin Institute of Health at Charité–Universitätsmedizin Berlin, Berlin, Germany ,grid.419538.20000 0000 9071 0620RG Development and Disease, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Alisa M. V. Reiter
- grid.6363.00000 0001 2218 4662Institute of Medical Genetics and Human Genetics, Charité–Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
| | - Jonas Elsner
- grid.6363.00000 0001 2218 4662Institute of Medical Genetics and Human Genetics, Charité–Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
| | - Peter Meinecke
- grid.13648.380000 0001 2180 3484Institute of Human Genetics, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Saskia Biskup
- grid.498061.20000 0004 6008 5552Center for Genomics and Transcriptomics (CeGaT), Tübingen, Germany
| | - Brian H. Y. Chung
- grid.194645.b0000000121742757Department of Pediatrics and Adolescent Medicine, School of Clinical Medicine, LKS Faculty of Medicine, The University of Hong Kong, Pok Fu Lam, Hong Kong
| | - Gregor Dombrowsky
- grid.412468.d0000 0004 0646 2097Department of Congenital Heart Disease and Pediatric Cardiology, University Hospital Schleswig-Holstein, Kiel, Germany ,grid.5560.60000 0001 1009 3608Department of Medical Genetics, Carl von Ossietzky University, Oldenburg, Germany
| | - Christel Eckmann-Scholz
- grid.412468.d0000 0004 0646 2097Department of Obstetrics and Gynecology, University Hospital Schleswig-Holstein, Kiel, Germany
| | - Marc Phillip Hitz
- grid.412468.d0000 0004 0646 2097Department of Congenital Heart Disease and Pediatric Cardiology, University Hospital Schleswig-Holstein, Kiel, Germany ,grid.5560.60000 0001 1009 3608Department of Medical Genetics, Carl von Ossietzky University, Oldenburg, Germany
| | - Alexander Hoischen
- grid.10417.330000 0004 0444 9382Department of Internal Medicine, Radboud Institute for Molecular Life Sciences, Radboud Expertise Center for Immunodeficiency and Autoinflammation and Radboud Center for Infectious Disease (RCI), Radboud University Medical Center, Nijmegen, The Netherlands ,grid.10417.330000 0004 0444 9382Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Paul-Martin Holterhus
- grid.412468.d0000 0004 0646 2097Department of Pediatrics, Pediatric Endocrinology and Diabetes, University Hospital Schleswig-Holstein, Schleswig-Holstein, Germany
| | - Wiebke Hülsemann
- grid.440182.b0000 0004 0580 3398Handchirurgie, Katholisches Kinderkrankenhaus Wilhelmstift, Hamburg, Germany
| | - Kimia Kahrizi
- grid.472458.80000 0004 0612 774XGenetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
| | - Vera M. Kalscheuer
- grid.419538.20000 0000 9071 0620RG Development and Disease, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Anita Kan
- grid.415550.00000 0004 1764 4144Department of Obstetrics and Gynaecology, Queen Mary Hospital, Pok Fu Lam, Hong Kong
| | - Mandy Krumbiegel
- grid.5330.50000 0001 2107 3311Institute of Human Genetics, Universitätsklinikum Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), Erlangen, Germany
| | - Ingo Kurth
- grid.412301.50000 0000 8653 1507Institute for Human Genetics and Genomic Medicine, Medical Faculty, RWTH Aachen University Hospital, Aachen, Germany
| | - Jonas Leubner
- grid.6363.00000 0001 2218 4662Department of Pediatric Neurology, Charité–Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
| | - Ann Carolin Longardt
- grid.412468.d0000 0004 0646 2097Department of Pediatrics, University Hospital Center Schleswig‐Holstein, Kiel, Germany
| | - Jörg D. Moritz
- grid.412468.d0000 0004 0646 2097Department of Radiology and Neuroradiology, Pediatric Radiology, University Hospital Schleswig-Holstein, Kiel, Germany
| | - Hossein Najmabadi
- grid.472458.80000 0004 0612 774XGenetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
| | - Karolina Skipalova
- grid.6363.00000 0001 2218 4662Institute of Medical Genetics and Human Genetics, Charité–Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
| | - Lot Snijders Blok
- grid.10417.330000 0004 0444 9382Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Andreas Tzschach
- grid.5963.9Institute of Human Genetics, Medical Center, University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Eberhard Wiedersberg
- grid.491868.a0000 0000 9601 2399Zentrum für Kinder-und Jugendmedizin, Helios Kliniken Schwerin, Schwerin, Germany
| | - Martin Zenker
- grid.5807.a0000 0001 1018 4307Institute of Human Genetics, University Hospital, Otto-von-Guericke University, Magdeburg, Germany
| | - Carla Garcia-Cabau
- grid.473715.30000 0004 6475 7299Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - René Buschow
- grid.419538.20000 0000 9071 0620Microscopy Core Facility, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Xavier Salvatella
- grid.473715.30000 0004 6475 7299Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona, Spain ,grid.425902.80000 0000 9601 989XICREA, Passeig Lluís Companys 23, Barcelona, Spain
| | - Matthew L. Kraushar
- grid.419538.20000 0000 9071 0620Department of Genome Regulation, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Stefan Mundlos
- grid.6363.00000 0001 2218 4662Institute of Medical Genetics and Human Genetics, Charité–Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany ,grid.484013.a0000 0004 6879 971XBIH Biomedical Innovation Academy, Berlin Institute of Health at Charité–Universitätsmedizin Berlin, Berlin, Germany ,grid.419538.20000 0000 9071 0620RG Development and Disease, Max Planck Institute for Molecular Genetics, Berlin, Germany ,grid.506128.8BCRT-Berlin Institute of Health Center for Regenerative Therapies, Berlin, Germany
| | - Almuth Caliebe
- grid.4562.50000 0001 0057 2672Institute of Human Genetics, University Hospitals Schleswig-Holstein, University of Lübeck and Kiel University, Lübeck, Kiel Germany
| | - Malte Spielmann
- RG Development and Disease, Max Planck Institute for Molecular Genetics, Berlin, Germany. .,Institute of Human Genetics, University Hospitals Schleswig-Holstein, University of Lübeck and Kiel University, Lübeck, Kiel, Germany. .,DZHK (German Centre for Cardiovascular Research), partner site Hamburg, Lübeck, Kiel, Lübeck, Germany.
| | - Denise Horn
- Institute of Medical Genetics and Human Genetics, Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany.
| | - Denes Hnisz
- Department of Genome Regulation, Max Planck Institute for Molecular Genetics, Berlin, Germany.
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27
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Renovanz M, Kurz SC, Rieger J, Walter B, Becker H, Hille H, Bombach P, Rieger D, Grosse L, Häusser L, Skardelly M, Merk DJ, Paulsen F, Hoffmann E, Gani C, Neumann M, Beschorner R, Rieß O, Roggia C, Schroeder C, Ossowski S, Armeanu-Ebinger S, Gschwind A, Biskup S, Schulze M, Fend F, Singer S, Zender L, Lengerke C, Brucker SY, Engler T, Forschner A, Stenzl A, Kohlbacher O, Nahnsen S, Gabernet G, Fillinger S, Bender B, Ernemann U, Öner Ö, Beha J, Malek HS, Möller Y, Ruhm K, Tatagiba M, Schittenhelm J, Bitzer M, Malek N, Zips D, Tabatabai G. Clinical outcome of biomarker-guided therapies in adult patients with tumors of the nervous system. Neurooncol Adv 2023; 5:vdad012. [PMID: 36915613 PMCID: PMC10007909 DOI: 10.1093/noajnl/vdad012] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/16/2023] Open
Abstract
Background The clinical utility of molecular profiling and targeted therapies for neuro-oncology patients outside of clinical trials is not established. We aimed at investigating feasibility and clinical utility of molecular profiling and targeted therapy in adult patients with advanced tumors in the nervous system within a prospective observational study. Methods molecular tumor board (MTB)@ZPM (NCT03503149) is a prospective observational precision medicine study for patients with advanced tumors. After inclusion of patients, we performed comprehensive molecular profiling, formulated ranked biomarker-guided therapy recommendations based on consensus by the MTB, and collected prospective clinical outcome data. Results Here, we present initial data of 661 adult patients with tumors of the nervous system enrolled by December 31, 2021. Of these, 408 patients were presented at the MTB. Molecular-instructed therapy recommendations could be made in 380/408 (93.1%) cases and were prioritized by evidence levels. Therapies were initiated in 86/380 (22.6%) cases until data cutoff. We observed a progression-free survival ratio >1.3 in 31.3% of patients. Conclusions Our study supports the clinical utility of biomarker-guided therapies for neuro-oncology patients and indicates clinical benefit in a subset of patients. Our data might inform future clinical trials, translational studies, and even clinical care.
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Affiliation(s)
- Mirjam Renovanz
- Department of Neurology and Interdisciplinary Neuro-Oncology, Hertie Institute for Clinical Brain Research, Eberhard Karls University Tübingen, Germany.,Center for Neuro-Oncology, Comprehensive Cancer Center Tübingen-Stuttgart, University Hospital Tübingen, Germany.,Department of Neurosurgery, Eberhard Karls University Tübingen, Germany
| | - Sylvia C Kurz
- Department of Neurology and Interdisciplinary Neuro-Oncology, Hertie Institute for Clinical Brain Research, Eberhard Karls University Tübingen, Germany.,Center for Neuro-Oncology, Comprehensive Cancer Center Tübingen-Stuttgart, University Hospital Tübingen, Germany
| | - Johannes Rieger
- Department of Neurology and Interdisciplinary Neuro-Oncology, Hertie Institute for Clinical Brain Research, Eberhard Karls University Tübingen, Germany.,Center for Neuro-Oncology, Comprehensive Cancer Center Tübingen-Stuttgart, University Hospital Tübingen, Germany
| | - Bianca Walter
- Department of Neurology and Interdisciplinary Neuro-Oncology, Hertie Institute for Clinical Brain Research, Eberhard Karls University Tübingen, Germany
| | - Hannes Becker
- Department of Neurology and Interdisciplinary Neuro-Oncology, Hertie Institute for Clinical Brain Research, Eberhard Karls University Tübingen, Germany.,Center for Neuro-Oncology, Comprehensive Cancer Center Tübingen-Stuttgart, University Hospital Tübingen, Germany.,Department of Neurosurgery, Eberhard Karls University Tübingen, Germany
| | - Hanni Hille
- Department of Neurology and Interdisciplinary Neuro-Oncology, Hertie Institute for Clinical Brain Research, Eberhard Karls University Tübingen, Germany
| | - Paula Bombach
- Department of Neurology and Interdisciplinary Neuro-Oncology, Hertie Institute for Clinical Brain Research, Eberhard Karls University Tübingen, Germany.,Center for Neuro-Oncology, Comprehensive Cancer Center Tübingen-Stuttgart, University Hospital Tübingen, Germany.,Center for Personalized Medicine Tübingen, Eberhard Karls University Tübingen, Germany
| | - David Rieger
- Department of Neurology and Interdisciplinary Neuro-Oncology, Hertie Institute for Clinical Brain Research, Eberhard Karls University Tübingen, Germany.,Center for Neuro-Oncology, Comprehensive Cancer Center Tübingen-Stuttgart, University Hospital Tübingen, Germany
| | - Lucia Grosse
- Department of Neurology and Interdisciplinary Neuro-Oncology, Hertie Institute for Clinical Brain Research, Eberhard Karls University Tübingen, Germany.,Center for Neuro-Oncology, Comprehensive Cancer Center Tübingen-Stuttgart, University Hospital Tübingen, Germany
| | - Lara Häusser
- Department of Neurology and Interdisciplinary Neuro-Oncology, Hertie Institute for Clinical Brain Research, Eberhard Karls University Tübingen, Germany.,German Cancer Consortium (DKTK), DKFZ partner site Tübingen, Eberhard Karls University of Tübingen, Germany
| | - Marco Skardelly
- Department of Neurology and Interdisciplinary Neuro-Oncology, Hertie Institute for Clinical Brain Research, Eberhard Karls University Tübingen, Germany.,Center for Neuro-Oncology, Comprehensive Cancer Center Tübingen-Stuttgart, University Hospital Tübingen, Germany
| | - Daniel J Merk
- Department of Neurology and Interdisciplinary Neuro-Oncology, Hertie Institute for Clinical Brain Research, Eberhard Karls University Tübingen, Germany
| | - Frank Paulsen
- Center for Neuro-Oncology, Comprehensive Cancer Center Tübingen-Stuttgart, University Hospital Tübingen, Germany.,Center for Personalized Medicine Tübingen, Eberhard Karls University Tübingen, Germany.,Department of Radiation Oncology, Eberhard Karls University Tübingen, Germany
| | - Elgin Hoffmann
- Center for Neuro-Oncology, Comprehensive Cancer Center Tübingen-Stuttgart, University Hospital Tübingen, Germany.,Center for Personalized Medicine Tübingen, Eberhard Karls University Tübingen, Germany.,Department of Radiation Oncology, Eberhard Karls University Tübingen, Germany
| | - Cihan Gani
- Center for Neuro-Oncology, Comprehensive Cancer Center Tübingen-Stuttgart, University Hospital Tübingen, Germany.,Center for Personalized Medicine Tübingen, Eberhard Karls University Tübingen, Germany.,Department of Radiation Oncology, Eberhard Karls University Tübingen, Germany.,German Cancer Consortium (DKTK), DKFZ partner site Tübingen, Eberhard Karls University of Tübingen, Germany
| | - Manuela Neumann
- Center for Neuro-Oncology, Comprehensive Cancer Center Tübingen-Stuttgart, University Hospital Tübingen, Germany.,Center for Personalized Medicine Tübingen, Eberhard Karls University Tübingen, Germany.,Institute of Pathology and Neuropathology, Department of Neuropathology, Eberhard Karls University Tübingen, Germany.,German Cancer Consortium (DKTK), DKFZ partner site Tübingen, Eberhard Karls University of Tübingen, Germany
| | - Rudi Beschorner
- Center for Neuro-Oncology, Comprehensive Cancer Center Tübingen-Stuttgart, University Hospital Tübingen, Germany.,Center for Personalized Medicine Tübingen, Eberhard Karls University Tübingen, Germany.,Institute of Pathology and Neuropathology, Department of Neuropathology, Eberhard Karls University Tübingen, Germany.,German Cancer Consortium (DKTK), DKFZ partner site Tübingen, Eberhard Karls University of Tübingen, Germany
| | - Olaf Rieß
- Center for Personalized Medicine Tübingen, Eberhard Karls University Tübingen, Germany.,Institute of Medical Genetics and Applied Genomics, Eberhard Karls University Tübingen, Germany.,Cluster of Excellence (EXC 2180) "Image Guided and Functionally Instructed Tumor Therapies", Eberhard Karls University of Tübingen, Germany.,German Cancer Consortium (DKTK), DKFZ partner site Tübingen, Eberhard Karls University of Tübingen, Germany
| | - Cristiana Roggia
- Center for Personalized Medicine Tübingen, Eberhard Karls University Tübingen, Germany.,Institute of Medical Genetics and Applied Genomics, Eberhard Karls University Tübingen, Germany
| | - Christopher Schroeder
- Center for Personalized Medicine Tübingen, Eberhard Karls University Tübingen, Germany.,Institute of Medical Genetics and Applied Genomics, Eberhard Karls University Tübingen, Germany
| | - Stephan Ossowski
- Center for Personalized Medicine Tübingen, Eberhard Karls University Tübingen, Germany.,Institute of Medical Genetics and Applied Genomics, Eberhard Karls University Tübingen, Germany
| | - Sorin Armeanu-Ebinger
- Center for Personalized Medicine Tübingen, Eberhard Karls University Tübingen, Germany.,Institute of Medical Genetics and Applied Genomics, Eberhard Karls University Tübingen, Germany
| | - Axel Gschwind
- Center for Personalized Medicine Tübingen, Eberhard Karls University Tübingen, Germany.,Institute of Medical Genetics and Applied Genomics, Eberhard Karls University Tübingen, Germany
| | - Saskia Biskup
- Center for Genomics and Transcriptomics (CeGaT) & Center for Human Genetics Tübingen, Germany.,Cluster of Excellence (EXC 2180) "Image Guided and Functionally Instructed Tumor Therapies", Eberhard Karls University of Tübingen, Germany
| | - Martin Schulze
- Center for Genomics and Transcriptomics (CeGaT) & Center for Human Genetics Tübingen, Germany
| | - Falko Fend
- Center for Personalized Medicine Tübingen, Eberhard Karls University Tübingen, Germany.,Department of Pathology and Neuropathology, Institute of Pathology and Molecular Pathology, Eberhard Karls University Tübingen, Germany.,Cluster of Excellence (EXC 2180) "Image Guided and Functionally Instructed Tumor Therapies", Eberhard Karls University of Tübingen, Germany.,German Cancer Consortium (DKTK), DKFZ partner site Tübingen, Eberhard Karls University of Tübingen, Germany
| | - Stephan Singer
- Center for Personalized Medicine Tübingen, Eberhard Karls University Tübingen, Germany.,Department of Pathology and Neuropathology, Institute of Pathology and Molecular Pathology, Eberhard Karls University Tübingen, Germany.,Cluster of Excellence (EXC 2180) "Image Guided and Functionally Instructed Tumor Therapies", Eberhard Karls University of Tübingen, Germany.,German Cancer Consortium (DKTK), DKFZ partner site Tübingen, Eberhard Karls University of Tübingen, Germany
| | - Lars Zender
- Center for Personalized Medicine Tübingen, Eberhard Karls University Tübingen, Germany.,Department of Medical Oncology and Pneumology (Internal Medicine VIII), Eberhard Karls University Tübingen, Germany.,Cluster of Excellence (EXC 2180) "Image Guided and Functionally Instructed Tumor Therapies", Eberhard Karls University of Tübingen, Germany.,German Cancer Consortium (DKTK), DKFZ partner site Tübingen, Eberhard Karls University of Tübingen, Germany
| | - Claudia Lengerke
- Department of Internal Medicine II, Eberhard Karls University Tübingen, Germany.,German Cancer Consortium (DKTK), DKFZ partner site Tübingen, Eberhard Karls University of Tübingen, Germany
| | - Sara Yvonne Brucker
- Department of Gynecology and Obstetrics, Eberhard Karls University Tübingen, Germany.,German Cancer Consortium (DKTK), DKFZ partner site Tübingen, Eberhard Karls University of Tübingen, Germany
| | - Tobias Engler
- Department of Gynecology and Obstetrics, Eberhard Karls University Tübingen, Germany.,German Cancer Consortium (DKTK), DKFZ partner site Tübingen, Eberhard Karls University of Tübingen, Germany
| | - Andrea Forschner
- Department of Dermatology and Center for Dermato-Oncology, Eberhard Karls University Tübingen, Germany.,German Cancer Consortium (DKTK), DKFZ partner site Tübingen, Eberhard Karls University of Tübingen, Germany
| | - Arnulf Stenzl
- Department of Urology, Eberhard Karls University Tübingen, Germany.,German Cancer Consortium (DKTK), DKFZ partner site Tübingen, Eberhard Karls University of Tübingen, Germany
| | - Oliver Kohlbacher
- Center for Personalized Medicine Tübingen, Eberhard Karls University Tübingen, Germany.,Institute for Translational Bioinformatics, Eberhard Karls University Tübingen, Germany.,German Cancer Consortium (DKTK), DKFZ partner site Tübingen, Eberhard Karls University of Tübingen, Germany
| | - Sven Nahnsen
- Center for Personalized Medicine Tübingen, Eberhard Karls University Tübingen, Germany.,Quantitative Biology Center (QBiC), Eberhard Karls University Tübingen, Germany.,Department of Medical Oncology and Pneumology (Internal Medicine VIII), Eberhard Karls University Tübingen, Germany.,Cluster of Excellence (EXC 2180) "Image Guided and Functionally Instructed Tumor Therapies", Eberhard Karls University of Tübingen, Germany.,German Cancer Consortium (DKTK), DKFZ partner site Tübingen, Eberhard Karls University of Tübingen, Germany
| | - Gisela Gabernet
- Quantitative Biology Center (QBiC), Eberhard Karls University Tübingen, Germany
| | - Sven Fillinger
- Quantitative Biology Center (QBiC), Eberhard Karls University Tübingen, Germany
| | - Benjamin Bender
- Center for Neuro-Oncology, Comprehensive Cancer Center Tübingen-Stuttgart, University Hospital Tübingen, Germany.,Center for Personalized Medicine Tübingen, Eberhard Karls University Tübingen, Germany.,Department of Diagnostic and Interventional Neuroradiology, Department of Radiology, Eberhard Karls University Tübingen, Germany
| | - Ulrike Ernemann
- Center for Neuro-Oncology, Comprehensive Cancer Center Tübingen-Stuttgart, University Hospital Tübingen, Germany.,Center for Personalized Medicine Tübingen, Eberhard Karls University Tübingen, Germany.,Department of Diagnostic and Interventional Neuroradiology, Department of Radiology, Eberhard Karls University Tübingen, Germany
| | - Öznur Öner
- Center for Personalized Medicine Tübingen, Eberhard Karls University Tübingen, Germany
| | - Janina Beha
- Center for Personalized Medicine Tübingen, Eberhard Karls University Tübingen, Germany
| | - Holly Sundberg Malek
- Center for Personalized Medicine Tübingen, Eberhard Karls University Tübingen, Germany
| | - Yvonne Möller
- Center for Personalized Medicine Tübingen, Eberhard Karls University Tübingen, Germany
| | - Kristina Ruhm
- Center for Personalized Medicine Tübingen, Eberhard Karls University Tübingen, Germany
| | - Marcos Tatagiba
- Center for Neuro-Oncology, Comprehensive Cancer Center Tübingen-Stuttgart, University Hospital Tübingen, Germany.,Center for Personalized Medicine Tübingen, Eberhard Karls University Tübingen, Germany.,Department of Neurosurgery, Eberhard Karls University Tübingen, Germany
| | - Jens Schittenhelm
- Center for Neuro-Oncology, Comprehensive Cancer Center Tübingen-Stuttgart, University Hospital Tübingen, Germany.,Center for Personalized Medicine Tübingen, Eberhard Karls University Tübingen, Germany.,Institute of Pathology and Neuropathology, Department of Neuropathology, Eberhard Karls University Tübingen, Germany.,German Cancer Consortium (DKTK), DKFZ partner site Tübingen, Eberhard Karls University of Tübingen, Germany
| | - Michael Bitzer
- Center for Personalized Medicine Tübingen, Eberhard Karls University Tübingen, Germany.,Department of Internal Medicine I, Eberhard Karls University Tübingen, Germany.,Cluster of Excellence (EXC 2180) "Image Guided and Functionally Instructed Tumor Therapies", Eberhard Karls University of Tübingen, Germany.,German Cancer Consortium (DKTK), DKFZ partner site Tübingen, Eberhard Karls University of Tübingen, Germany
| | - Nisar Malek
- Center for Personalized Medicine Tübingen, Eberhard Karls University Tübingen, Germany.,Department of Internal Medicine I, Eberhard Karls University Tübingen, Germany.,Cluster of Excellence (EXC 2180) "Image Guided and Functionally Instructed Tumor Therapies", Eberhard Karls University of Tübingen, Germany.,German Cancer Consortium (DKTK), DKFZ partner site Tübingen, Eberhard Karls University of Tübingen, Germany
| | - Daniel Zips
- Center for Neuro-Oncology, Comprehensive Cancer Center Tübingen-Stuttgart, University Hospital Tübingen, Germany.,Center for Personalized Medicine Tübingen, Eberhard Karls University Tübingen, Germany.,Department of Radiation Oncology, Eberhard Karls University Tübingen, Germany.,German Cancer Consortium (DKTK), DKFZ partner site Tübingen, Eberhard Karls University of Tübingen, Germany
| | - Ghazaleh Tabatabai
- Department of Neurology and Interdisciplinary Neuro-Oncology, Hertie Institute for Clinical Brain Research, Eberhard Karls University Tübingen, Germany.,Center for Neuro-Oncology, Comprehensive Cancer Center Tübingen-Stuttgart, University Hospital Tübingen, Germany.,Center for Personalized Medicine Tübingen, Eberhard Karls University Tübingen, Germany.,Cluster of Excellence (EXC 2180) "Image Guided and Functionally Instructed Tumor Therapies", Eberhard Karls University of Tübingen, Germany.,German Cancer Consortium (DKTK), DKFZ partner site Tübingen, Eberhard Karls University of Tübingen, Germany
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28
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Waibel AM, Stoye JM, Villavicencio-Lorini P, Hoffmann K, Obermaier C, Biskup S, Grünauer-Kloevekorn C. Specific Changes in OCT Imaging Associated with a Novel Mutation of the RS1 Gene in X-Linked Retinoschisis. Klin Monbl Augenheilkd 2022; 239:1473-1477. [PMID: 36493766 DOI: 10.1055/a-1901-1011] [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] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
X-linked retinoschisis (XLRS) is a rare vitreoretinal dystrophy caused by molecular genetic changes in the RS1 gene. It usually manifests itself at a young age with symmetrical splitting within different layers of the retina and leads to a significant reduction in visual acuity. Correct diagnosis at older ages is difficult due to nonspecific changes in OCT scans. We report the morphological changes in OCT scans at different stages of life in a family with XLRS and a novel mutation in the RS1 gene. Our 78-year-old index patient presented with visual disturbances that he had experienced since his childhood. After a detailed anamnesis, complete clinical examination and measurement with SD-OCT, we performed germline genetic testing using whole blood DNA on the index patient, his clinically unaffected daughter and her clinically affected son. The OCT examination of the index patient showed nonspecific atrophic macular changes on both sides. A fundoscopy of the 8-year-old grandson showed the typical macular star pattern. The OCT scan showed the typical retinoschisis of the macula. The genetic analysis revealed the previously undescribed pathogenic variant c.487T>G; p.Trp163Gly in the RS1 gene in all 3 patients. The typical fundus image and OCT pattern, which are absent in the 78-year-old patient, are also present in childhood with the novel RS1 mutation. Our case shows that even with nonspecific changes in the OCT scans, a detailed family history can provide important information on X-linked recessive inheritance and thus for an appropriate molecular genetic diagnosis, so that rare retinal diseases can be diagnosed even at an advanced age.
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Affiliation(s)
| | | | | | - Katrin Hoffmann
- Institut für Humangenetik, Martin-Luther-Universität Halle-Wittenberg, Halle/Saale, Deutschland
| | | | - Saskia Biskup
- Humangenetik, Praxis für Humangenetik Tübingen, Deutschland
| | - Claudia Grünauer-Kloevekorn
- Augenheilkunde, PraxisKlinik Augenärzte am Markt, Halle/Saale, Deutschland.,Medizinische Fakultät, Martin-Luther-Universität Halle-Wittenberg, Halle/Saale, Deutschland
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29
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Daghagh H, Rahbar Kafshboran H, Daneshmandpour Y, Nasiri Aghdam M, Talebian S, Nouri Nojadeh J, Hamzeiy H, Biskup S, Sakhinia E. Homozygous mutation in CSF1R causes brain abnormalities, neurodegeneration, and dysosteosclerosis (BANDDOS). Bioimpacts 2022. [DOI: 10.34172/bi.2022.23528] [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] [Subscribe] [Scholar Register] [Indexed: 02/22/2023]
Abstract
Introduction: The CSF1R gene encodes the receptor for colony-stimulating factor-1, the macrophage, and monocyte-specific growth factor. Mutations in this gene cause hereditary diffuse leukoencephalopathy with spheroids (HDLS) with autosomal dominant inheritance and BANDDOS (Brain Abnormalities, Neurodegeneration, and Dysosteosclerosis) with autosomal recessive inheritance. Methods: Targeted gene sequencing was performed on the genomic DNA samples of the deceased patient and a fetus along with ten healthy members of his family to identify the disease-causing mutation. Bioinformatics tools were used to study the mutation effect on protein function and structure. To predict the effect of the mutation on the protein, various bioinformatics tools were applied. Results: A novel homozygous variant was identified in the gene CSF1R, c.2498C>T; p.T833M in exon 19, in the index patient and the fetus. Furthermore, some family members were heterozygous for this variant, while they had not any symptoms of the disease. In silico analysis indicated this variant has a detrimental effect on CSF1R. It is conserved among humans and other similar species. The variant is located within the functionally essential PTK domain of the receptor. However, no structural damage was introduced by this substitution. Conclusion: In conclusion, regarding the inheritance pattern in the family and clinical manifestations in the index patient, we propose that the mentioned variant in the CSF1R gene may cause BANDDOS.
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Affiliation(s)
- Hossein Daghagh
- Department of Medical Genetics, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran
- Tabriz Genetic Analysis Centre (TGAC), Tabriz University of Medical Sciences, Tabriz, Iran
| | | | - Yousef Daneshmandpour
- Department of Medical Genetics, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran
- Tabriz Genetic Analysis Centre (TGAC), Tabriz University of Medical Sciences, Tabriz, Iran
| | - Maryam Nasiri Aghdam
- Tabriz Genetic Analysis Centre (TGAC), Tabriz University of Medical Sciences, Tabriz, Iran
| | - Shahrzad Talebian
- Department of Medical Genetics, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Jafar Nouri Nojadeh
- Department of Medical Genetics, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Hamid Hamzeiy
- Tabriz Genetic Analysis Centre (TGAC), Tabriz University of Medical Sciences, Tabriz, Iran
| | | | - Ebrahim Sakhinia
- Department of Medical Genetics, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran
- Tabriz Genetic Analysis Centre (TGAC), Tabriz University of Medical Sciences, Tabriz, Iran
- Connective Tissue Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
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30
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Schmidt J, Dreha-Kulaczewski S, Zafeiriou MP, Schreiber MK, Wilken B, Funke R, Neuhofer CM, Altmüller J, Thiele H, Nürnberg P, Biskup S, Li Y, Zimmermann WH, Kaulfuß S, Yigit G, Wollnik B. Somatic mosaicism in STAG2-associated cohesinopathies: Expansion of the genotypic and phenotypic spectrum. Front Cell Dev Biol 2022; 10:1025332. [DOI: 10.3389/fcell.2022.1025332] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2022] [Accepted: 10/26/2022] [Indexed: 11/17/2022] Open
Abstract
STAG2 is a component of the large, evolutionarily highly conserved cohesin complex, which has been linked to various cellular processes like genome organization, DNA replication, gene expression, heterochromatin formation, sister chromatid cohesion, and DNA repair. A wide spectrum of germline variants in genes encoding subunits or regulators of the cohesin complex have previously been identified to cause distinct but phenotypically overlapping multisystem developmental disorders belonging to the group of cohesinopathies. Pathogenic variants in STAG2 have rarely been implicated in an X-linked cohesinopathy associated with undergrowth, developmental delay, and dysmorphic features. Here, we describe for the first time a mosaic STAG2 variant in an individual with developmental delay, microcephaly, and hemihypotrophy of the right side. We characterized the grade of mosaicism by deep sequencing analysis on DNA extracted from EDTA blood, urine and buccal swabs. Furthermore, we report an additional female with a novel de novo splice variant in STAG2. Interestingly, both individuals show supernumerary nipples, a feature that has not been reported associated to STAG2 before. Remarkably, additional analysis of STAG2 transcripts in both individuals showed only wildtype transcripts, even after blockage of nonsense-mediated decay using puromycin in blood lymphocytes. As the phenotype of STAG2-associated cohesinopathies is dominated by global developmental delay, severe microcephaly, and brain abnormalities, we investigated the expression of STAG2 and other related components of the cohesin complex during Bioengineered Neuronal Organoids (BENOs) generation by RNA sequencing. Interestingly, we observed a prominent expression of STAG2, especially between culture days 0 and 15, indicating an essential function of STAG2 in early brain development. In summary, we expand the genotypic and phenotypic spectrum of STAG2-associated cohesinopathies and show that BENOs represent a promising model to gain further insights into the critical role of STAG2 in the complex process of nervous system development.
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31
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Zelba H, McQueeney A, Rabsteyn A, Bartsch O, Kyzirakos C, Kayser S, Harter J, Latzer P, Hadaschik D, Battke F, Hartkopf AD, Biskup S. Adjuvant Treatment for Breast Cancer Patients Using Individualized Neoantigen Peptide Vaccination-A Retrospective Observation. Vaccines (Basel) 2022; 10:1882. [PMID: 36366390 PMCID: PMC9698403 DOI: 10.3390/vaccines10111882] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2022] [Revised: 10/27/2022] [Accepted: 11/03/2022] [Indexed: 08/16/2023] Open
Abstract
Breast cancer is a tumor entity that is one of the leading causes of mortality among women worldwide. Although numerous treatment options are available, current explorations of personalized vaccines have shown potential as promising new treatment options to prevent the recurrence of cancer. Here we present a small proof of concept study using a prophylactic peptide vaccination approach in four female breast cancer patients who achieved remission after standard treatment. The patients were initially analyzed for somatic tumor mutations and then treated with personalized neoantigen-derived peptide vaccines. These vaccines consisted of HLA class I and class II peptides and were administered intracutaneously followed by subcutaneous application of sargramostim and/or topical imiquimod as an immunological adjuvant. After an initial priming phase of four vaccinations within two weeks, patients received monthly boosting/maintenance vaccinations. Chemotherapy or checkpoint inhibition was not performed during vaccination. One patient received hormone therapy. The vaccines were well tolerated with no serious adverse events. All patients displayed vaccine-induced CD4+ and/or CD8+ T-cell responses against various neoantigens. Furthermore, all patients remained tumor-free and had persistent T-cell responses, even several months after the last vaccination, suggesting the potential of peptide vaccines as an immunosurveillance and long term prophylaxis option.
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Affiliation(s)
- Henning Zelba
- Zentrum für Humangenetik Tübingen, 72076 Tuebingen, Germany
| | - Alex McQueeney
- Zentrum für Humangenetik Tübingen, 72076 Tuebingen, Germany
| | - Armin Rabsteyn
- Zentrum für Humangenetik Tübingen, 72076 Tuebingen, Germany
| | - Oliver Bartsch
- Zentrum für Humangenetik Tübingen, 72076 Tuebingen, Germany
| | | | - Simone Kayser
- Zentrum für Humangenetik Tübingen, 72076 Tuebingen, Germany
| | | | - Pauline Latzer
- Zentrum für Humangenetik Tübingen, 72076 Tuebingen, Germany
| | | | | | - Andreas D. Hartkopf
- Department of Obstetrics and Gynaecology University of Tuebingen, 72074 Tuebingen, Germany
| | - Saskia Biskup
- Zentrum für Humangenetik Tübingen, 72076 Tuebingen, Germany
- CeGaT GmbH, 72076 Tuebingen, Germany
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32
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Guo L, Park J, Yi E, Marchi E, Hsieh TC, Kibalnyk Y, Moreno-Sáez Y, Biskup S, Puk O, Beger C, Li Q, Wang K, Voronova A, Krawitz PM, Lyon GJ. KBG syndrome: videoconferencing and use of artificial intelligence driven facial phenotyping in 25 new patients. Eur J Hum Genet 2022; 30:1244-1254. [PMID: 35970914 PMCID: PMC9626563 DOI: 10.1038/s41431-022-01171-1] [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] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2022] [Revised: 05/26/2022] [Accepted: 07/26/2022] [Indexed: 02/04/2023] Open
Abstract
Genetic variants in Ankyrin Repeat Domain 11 (ANKRD11) and deletions in 16q24.3 are known to cause KBG syndrome, a rare syndrome associated with craniofacial, intellectual, and neurobehavioral anomalies. We report 25 unpublished individuals from 22 families with molecularly confirmed diagnoses. Twelve individuals have de novo variants, three have inherited variants, and one is inherited from a parent with low-level mosaicism. The mode of inheritance was unknown for nine individuals. Twenty are truncating variants, and the remaining five are missense (three of which are found in one family). We present a protocol emphasizing the use of videoconference and artificial intelligence (AI) in collecting and analyzing data for this rare syndrome. A single clinician interviewed 25 individuals throughout eight countries. Participants' medical records were reviewed, and data was uploaded to the Human Disease Gene website using Human Phenotype Ontology (HPO) terms. Photos of the participants were analyzed by the GestaltMatcher and DeepGestalt, Face2Gene platform (FDNA Inc, USA) algorithms. Within our cohort, common traits included short stature, macrodontia, anteverted nares, wide nasal bridge, wide nasal base, thick eyebrows, synophrys and hypertelorism. Behavioral issues and global developmental delays were widely present. Neurologic abnormalities including seizures and/or EEG abnormalities were common (44%), suggesting that early detection and seizure prophylaxis could be an important point of intervention. Almost a quarter (24%) were diagnosed with attention deficit hyperactivity disorder and 28% were diagnosed with autism spectrum disorder. Based on the data, we provide a set of recommendations regarding diagnostic and treatment approaches for KBG syndrome.
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Affiliation(s)
- Lily Guo
- grid.420001.70000 0000 9813 9625Department of Human Genetics, NYS Institute for Basic Research in Developmental Disabilities, 1050 Forest Hill Road, Staten Island, NY 10314 USA
| | - Jiyeon Park
- grid.420001.70000 0000 9813 9625Department of Human Genetics, NYS Institute for Basic Research in Developmental Disabilities, 1050 Forest Hill Road, Staten Island, NY 10314 USA
| | - Edward Yi
- grid.420001.70000 0000 9813 9625Department of Human Genetics, NYS Institute for Basic Research in Developmental Disabilities, 1050 Forest Hill Road, Staten Island, NY 10314 USA
| | - Elaine Marchi
- grid.420001.70000 0000 9813 9625Department of Human Genetics, NYS Institute for Basic Research in Developmental Disabilities, 1050 Forest Hill Road, Staten Island, NY 10314 USA
| | - Tzung-Chien Hsieh
- grid.10388.320000 0001 2240 3300Institute for Genomic Statistics and Bioinformatics, University Hospital Bonn, Rheinische Friedrich-Wilhelms-Universität Bonn, Bonn, Germany
| | - Yana Kibalnyk
- grid.17089.370000 0001 2190 316XDepartment of Medical Genetics, Faculty of Medicine & Dentistry, University of Alberta, Edmonton, AB Canada ,grid.17089.370000 0001 2190 316XDepartment of Cell Biology, Faculty of Medicine & Dentistry, University of Alberta, Edmonton, AB Canada
| | | | - Saskia Biskup
- CeGaT GmbH, Praxis für Humangenetik Tübingen, Tübingen, Germany
| | - Oliver Puk
- CeGaT GmbH, Praxis für Humangenetik Tübingen, Tübingen, Germany
| | - Carmela Beger
- grid.512442.40000 0004 0553 6293MVZ Labor Krone GbR, Filialpraxis für Humangenetik, Bielefeld, Germany
| | - Quan Li
- grid.17063.330000 0001 2157 2938Princess Margaret Cancer Centre, University Health Network, University of Toronto, Toronto, ON M5G2C1 Canada
| | - Kai Wang
- grid.239552.a0000 0001 0680 8770Raymond G. Perelman Center for Cellular and Molecular Therapeutics, Children’s Hospital of Philadelphia, Philadelphia, PA 19104 USA
| | - Anastassia Voronova
- grid.17089.370000 0001 2190 316XDepartment of Medical Genetics, Faculty of Medicine & Dentistry, University of Alberta, Edmonton, AB Canada ,grid.17089.370000 0001 2190 316XDepartment of Cell Biology, Faculty of Medicine & Dentistry, University of Alberta, Edmonton, AB Canada
| | - Peter M. Krawitz
- grid.10388.320000 0001 2240 3300Institute for Genomic Statistics and Bioinformatics, University Hospital Bonn, Rheinische Friedrich-Wilhelms-Universität Bonn, Bonn, Germany
| | - Gholson J. Lyon
- grid.420001.70000 0000 9813 9625Department of Human Genetics, NYS Institute for Basic Research in Developmental Disabilities, 1050 Forest Hill Road, Staten Island, NY 10314 USA ,grid.420001.70000 0000 9813 9625George A. Jervis Clinic, NYS Institute for Basic Research in Developmental Disabilities, 1050 Forest Hill Road, Staten Island, NY 10314 USA ,grid.212340.60000000122985718Biology PhD Program, The Graduate Center, The City University of New York, New York, NY USA
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Bögershausen N, Krawczyk HE, Jamra RA, Lin SJ, Yigit G, Hüning I, Polo AM, Vona B, Huang K, Schmidt J, Altmüller J, Luppe J, Platzer K, Dörgeloh BB, Busche A, Biskup S, Mendes MI, Smith DEC, Salomons GS, Zibat A, Bültmann E, Nürnberg P, Spielmann M, Lemke JR, Li Y, Zenker M, Varshney GK, Hillen HS, Kratz CP, Wollnik B. WARS1 and SARS1: Two tRNA synthetases implicated in autosomal recessive microcephaly. Hum Mutat 2022; 43:1454-1471. [PMID: 35790048 DOI: 10.1002/humu.24430] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [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: 06/03/2021] [Revised: 06/10/2022] [Accepted: 07/01/2022] [Indexed: 02/04/2023]
Abstract
Aminoacylation of transfer RNA (tRNA) is a key step in protein biosynthesis, carried out by highly specific aminoacyl-tRNA synthetases (ARSs). ARSs have been implicated in autosomal dominant and autosomal recessive human disorders. Autosomal dominant variants in tryptophanyl-tRNA synthetase 1 (WARS1) are known to cause distal hereditary motor neuropathy and Charcot-Marie-Tooth disease, but a recessively inherited phenotype is yet to be clearly defined. Seryl-tRNA synthetase 1 (SARS1) has rarely been implicated in an autosomal recessive developmental disorder. Here, we report five individuals with biallelic missense variants in WARS1 or SARS1, who presented with an overlapping phenotype of microcephaly, developmental delay, intellectual disability, and brain anomalies. Structural mapping showed that the SARS1 variant is located directly within the enzyme's active site, most likely diminishing activity, while the WARS1 variant is located in the N-terminal domain. We further characterize the identified WARS1 variant by showing that it negatively impacts protein abundance and is unable to rescue the phenotype of a CRISPR/Cas9 wars1 knockout zebrafish model. In summary, we describe two overlapping autosomal recessive syndromes caused by variants in WARS1 and SARS1, present functional insights into the pathogenesis of the WARS1-related syndrome and define an emerging disease spectrum: ARS-related developmental disorders with or without microcephaly.
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Affiliation(s)
- Nina Bögershausen
- Institute of Human Genetics, University Medical Center Göttingen, Göttingen, Germany
| | - Hannah E Krawczyk
- Institute of Human Genetics, University Medical Center Göttingen, Göttingen, Germany
| | - Rami A Jamra
- Institute of Human Genetics, University of Leipzig Medical Center, Leipzig, Germany
| | - Sheng-Jia Lin
- Genes & Human Disease Research Program, Oklahoma Medical Research Foundation, Oklahoma City, Oklahoma, USA
| | - Gökhan Yigit
- Institute of Human Genetics, University Medical Center Göttingen, Göttingen, Germany
| | - Irina Hüning
- Institut für Humangenetik, Universitätsklinikum Schleswig-Holstein, Lübeck, Germany
| | - Anna M Polo
- MVZ Labor Krone, Filialpraxis für Humangenetik, Bielefeld, Germany
| | - Barbara Vona
- Institute of Human Genetics, University Medical Center Göttingen, Göttingen, Germany.,Institute for Auditory Neuroscience and InnerEarLab, University Medical Center Göttingen, Göttingen, Germany
| | - Kevin Huang
- Genes & Human Disease Research Program, Oklahoma Medical Research Foundation, Oklahoma City, Oklahoma, USA
| | - Julia Schmidt
- Institute of Human Genetics, University Medical Center Göttingen, Göttingen, Germany
| | - Janine Altmüller
- Cologne Center for Genomics (CCG), Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany.,Core Facility Genomics, Berlin Institute of Health at Charité - Universitätsmedizin Berlin, Berlin, Germany.,Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin, Germany
| | - Johannes Luppe
- Institute of Human Genetics, University of Leipzig Medical Center, Leipzig, Germany
| | - Konrad Platzer
- Institute of Human Genetics, University of Leipzig Medical Center, Leipzig, Germany
| | - Beate B Dörgeloh
- Department of Pediatric Hematology and Oncology, Hannover Medical School, Hannover, Germany
| | - Andreas Busche
- Institut für Humangenetik, Westfälische Wilhelms-Universität Münster, Münster, Germany
| | - Saskia Biskup
- CeGaT GmbH, Center for Genomics and Transcriptomics, Tübingen, Germany
| | - Marisa I Mendes
- Laboratory Genetic Metabolic Diseases, Amsterdam Gastroenterology and Metabolism, Amsterdam Neuroscience, Amsterdam UMC, Amsterdam, Netherlands
| | - Desiree E C Smith
- Laboratory Genetic Metabolic Diseases, Amsterdam Gastroenterology and Metabolism, Amsterdam Neuroscience, Amsterdam UMC, Amsterdam, Netherlands
| | - Gajja S Salomons
- Laboratory Genetic Metabolic Diseases, Amsterdam Gastroenterology and Metabolism, Amsterdam Neuroscience, Amsterdam UMC, Amsterdam, Netherlands
| | - Arne Zibat
- Institute of Human Genetics, University Medical Center Göttingen, Göttingen, Germany
| | - Eva Bültmann
- Institute of Diagnostic and Interventional Neuroradiology, Hannover Medical School, Hannover, Germany
| | - Peter Nürnberg
- Cologne Center for Genomics (CCG), Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany.,Center for Molecular Medicine Cologne (CMMC), Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany
| | - Malte Spielmann
- Institut für Humangenetik, Universitätsklinikum Schleswig-Holstein, Lübeck, Germany
| | - Johannes R Lemke
- Institute of Human Genetics, University of Leipzig Medical Center, Leipzig, Germany
| | - Yun Li
- Institute of Human Genetics, University Medical Center Göttingen, Göttingen, Germany
| | - Martin Zenker
- Institute of Human Genetics, Otto-von-Guericke University Magdeburg, Magdeburg, Germany
| | - Gaurav K Varshney
- Genes & Human Disease Research Program, Oklahoma Medical Research Foundation, Oklahoma City, Oklahoma, USA
| | - Hauke S Hillen
- Research Group Structure and Function of Molecular Machines, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany.,Department of Cellular Biochemistry, University Medical Center Göttingen, Göttingen, Germany.,Cluster of Excellence "Multiscale Bioimaging: From Molecular Machines to Networks of Excitable cells" (MBExC), University of Göttingen, Göttingen, Germany
| | - Christian P Kratz
- Department of Pediatric Hematology and Oncology, Hannover Medical School, Hannover, Germany
| | - Bernd Wollnik
- Institute of Human Genetics, University Medical Center Göttingen, Göttingen, Germany.,Cluster of Excellence "Multiscale Bioimaging: From Molecular Machines to Networks of Excitable cells" (MBExC), University of Göttingen, Göttingen, Germany.,DZHK (German Centre for Cardiovascular Research), Partner Site Göttingen, Göttingen, Germany
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34
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Schneider SA, Mueller C, Biskup S, Fietzek UM, Schroeder AS. Neurodevelopmental disorder with dystonia due to SOX6 mutations. Mol Genet Genomic Med 2022; 10:e2051. [PMID: 36069193 PMCID: PMC9747553 DOI: 10.1002/mgg3.2051] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2022] [Revised: 06/30/2022] [Accepted: 08/18/2022] [Indexed: 01/11/2023] Open
Abstract
BACKGROUND Mutations in SOX6 have recently been recognized as a new molecular cause of neurodevelopmental disorders characterized by intellectual disability, behavioral changes, and nonspecific facial and digital skeletal abnormalities. To date, <25 cases have been reported in the literature. METHODS AND FINDINGS Here we report a new case of SOX6-associated neurodegeneration and expand the phenotype to include ceratoconus. The clinical picture consisted of early onset mildly reduced intellectual function, facial asymmetry, and dystonic tremor of hands and neck, substantially improved by levodopa. Skeletal abnormalities included scoliosis and hypertrophy of the mandibular coronoid process. A heterozygous de novo loss-of-function variant in SOX6 (c.277 C>T. p.Arg93*) was molecularly confirmed which leads to truncation of the SOX6 protein in its N-terminus, upstream of any known functional domain. CONCLUSION SOX6-associated neurodevelopmental delayis ultrarare with less than 25 cases described in the literature. We report a new case who presented with early-onset mildly reduced intellectual function, facial asymmetry, skeletal abnormalities and dystonic tremor of hands and neck, substantially improved by levodopa. Given the therapeutic implications, SOX6 mutations should be considered in patients with complex dystonia parkinsonism.
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Affiliation(s)
- Susanne A. Schneider
- Department of NeurologyUniversity Hospital, Ludwig Maximilians UniversitätMunichGermany
| | - Christine Mueller
- Department of Pediatric Neurology, Developmental Medicine, Social Pediatrics, Dr. von Hauner Children's HospitalLMU ‐ University Hospital, Ludwig Maximilians UniversitätMunichGermany
| | - Saskia Biskup
- Center for Genomics and Transcriptomics CeGaT GmbH and Praxis für Humangenetik TübingenTübingenGermany
| | - Urban M. Fietzek
- Department of NeurologyUniversity Hospital, Ludwig Maximilians UniversitätMunichGermany,Department of Neurology and Clinical NeurophysiologySchön Klinik München SchwabingMunichGermany
| | - Andreas Sebastian Schroeder
- Department of Pediatric Neurology, Developmental Medicine, Social Pediatrics, Dr. von Hauner Children's HospitalLMU ‐ University Hospital, Ludwig Maximilians UniversitätMunichGermany
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35
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Maurer MH, Kohler A, Hudemann M, Jüngling J, Biskup S, Menzel M. Case Report of a Juvenile Patient with Autism Spectrum Disorder with a Novel Combination of Copy Number Variants in ADGRL3 (LPHN3) and Two Pseudogenes. Appl Clin Genet 2022; 15:125-131. [PMID: 36082049 PMCID: PMC9447451 DOI: 10.2147/tacg.s361239] [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: 02/05/2022] [Accepted: 08/25/2022] [Indexed: 11/23/2022] Open
Abstract
We report the finding of two copy number variants (CNVs) in a 12-year-old boy presenting both with autism spectrum disorder (ASD) and attention deficit/hyperactivity disorder (ADHD). Clinical features included aggressive behavior, mood instability, suicidal statements, repetitive and restrictive behavior, sensitivity to noise, learning problems and dyslexia, though no intellectual disability was present. Using array-based comparative genomic hybridization (array-CGH), we identified two CNVs, both triplex duplications of 324 kb on 3p26.3, and 284 kb on 4q13.1, respectively. One of the CNVs is located on chromosome 4q13.1 in the region of the gene encoding for adhesion G protein-coupled receptor L3 (ADGRL3, former name: latrophilin-3, LPHN3), the other on chromosome 3p26.3 in the region of the two pseudogenes AC090043.1 and RPL23AP39. The patient described in the present study showed increased symptoms under methylphenidate treatment but responded positively to 3 mg per day of the atypical neuroleptic drug aripiprazole. To our knowledge, this is the first report of a CNV in the ADGRL3 gene and its first association with ASD in humans.
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Affiliation(s)
- Martin H Maurer
- Mariaberg Hospital for Child and Adolescent Psychiatry, Gammertingen, Germany
- Correspondence: Martin H Maurer, Mariaberg Hospital for Child and Adolescent Psychiatry, Burghaldenstraße 12, Gammertingen, 72501, Germany, Tel +49 7124 9237200, Fax +49 7124 923555, Email
| | - Anja Kohler
- Mariaberg Hospital for Child and Adolescent Psychiatry, Gammertingen, Germany
| | - Melanie Hudemann
- Mariaberg Hospital for Child and Adolescent Psychiatry, Gammertingen, Germany
| | | | - Saskia Biskup
- Zentrum für Humangenetik, Tübingen, Germany
- Center for Genomics and Transcriptomics, CeGaT GmbH, Tübingen, Germany
| | - Martin Menzel
- Mariaberg Hospital for Child and Adolescent Psychiatry, Gammertingen, Germany
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Becker LL, Ebstein F, Horn D, Zouboulis CC, Krüger E, Kaindl AM, Eger A, Kallinich T, Biskup S, Schmid S, Stenzel W, Münzfeld H, Blume-Peytavi U. Interferon receptor dysfunction in a child with malignant atrophic papulosis and CNS involvement. Lancet Neurol 2022; 21:682-686. [PMID: 35841902 DOI: 10.1016/s1474-4422(22)00167-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2021] [Revised: 02/14/2022] [Accepted: 04/07/2022] [Indexed: 11/29/2022]
Affiliation(s)
- Lena-Luise Becker
- Department of Pediatric Neurology, Charité-Universitätsmedizin Berlin, 13353 Berlin, Germany; Center for Chronically Sick Children, Charité-Universitätsmedizin Berlin, 13353 Berlin, Germany; Institute for Cell Biology and Neurobiology, Charité-Universitätsmedizin Berlin, 13353 Berlin, Germany.
| | - Frédéric Ebstein
- Institute of Medical Biochemistry and Molecular Biology, Greifswald University Medicine, Greifswald, Germany
| | - Denise Horn
- Institute of Medical Genetics and Human Genetics, Charité-Universitätsmedizin Berlin, 13353 Berlin, Germany
| | - Christos C Zouboulis
- Faculty of Health Sciences, Brandenburg Medical School Theodor Fontane, Dessau, Germany; Departments of Dermatology, Venerology, Allergology, and Immunology, Dessau Medical Center, Dessau, Germany
| | - Elke Krüger
- Institute of Medical Biochemistry and Molecular Biology, Greifswald University Medicine, Greifswald, Germany
| | - Angela M Kaindl
- Department of Pediatric Neurology, Charité-Universitätsmedizin Berlin, 13353 Berlin, Germany; Center for Chronically Sick Children, Charité-Universitätsmedizin Berlin, 13353 Berlin, Germany; Institute for Cell Biology and Neurobiology, Charité-Universitätsmedizin Berlin, 13353 Berlin, Germany
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37
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Nasser F, Kohl S, Kurtenbach A, Kempf M, Biskup S, Zuleger T, Haack TB, Weisschuh N, Stingl K, Zrenner E. Ophthalmic and Genetic Features of Bardet Biedl Syndrome in a German Cohort. Genes (Basel) 2022; 13:genes13071218. [PMID: 35886001 PMCID: PMC9322102 DOI: 10.3390/genes13071218] [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] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2022] [Revised: 06/29/2022] [Accepted: 07/02/2022] [Indexed: 12/04/2022] Open
Abstract
The aim of this study was to characterize the ophthalmic and genetic features of Bardet Biedl (BBS) syndrome in a cohort of patients from a German specialized ophthalmic care center. Sixty-one patients, aged 5−56 years, underwent a detailed ophthalmic examination including visual acuity and color vision testing, electroretinography (ERG), visually evoked potential recording (VEP), fundus examination, and spectral domain optical coherence tomography (SD-OCT). Adaptive optics flood illumination ophthalmoscopy was performed in five patients. All patients had received diagnostic genetic testing and were selected upon the presence of apparent biallelic variants in known BBS-associated genes. All patients had retinal dystrophy with morphologic changes of the retina. Visual acuity decreased from ~0.2 (decimal) at age 5 to blindness 0 at 50 years. Visual field examination could be performed in only half of the patients and showed a concentric constriction with remaining islands of function in the periphery. ERG recordings were mostly extinguished whereas VEP recordings were reduced in about half of the patients. The cohort of patients showed 51 different likely biallelic mutations—of which 11 are novel—in 12 different BBS-associated genes. The most common associated genes were BBS10 (32.8%) and BBS1 (24.6%), and by far the most commonly observed variants were BBS10 c.271dup;p.C91Lfs*5 (21 alleles) and BBS1 c.1169T>G;p.M390R (18 alleles). The phenotype associated with the different BBS-associated genes and genotypes in our cohort is heterogeneous, with diverse features without genotype−phenotype correlation. The results confirm and expand our knowledge of this rare disease.
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Affiliation(s)
- Fadi Nasser
- Centre for Ophthalmology, University of Tübingen, 72076 Tuebingen, Germany; (S.K.); (A.K.); (M.K.); (N.W.); (K.S.); (E.Z.)
- Department of Ophthalmology, University of Leipzig, 04103 Leipzig, Germany
- Correspondence:
| | - Susanne Kohl
- Centre for Ophthalmology, University of Tübingen, 72076 Tuebingen, Germany; (S.K.); (A.K.); (M.K.); (N.W.); (K.S.); (E.Z.)
| | - Anne Kurtenbach
- Centre for Ophthalmology, University of Tübingen, 72076 Tuebingen, Germany; (S.K.); (A.K.); (M.K.); (N.W.); (K.S.); (E.Z.)
| | - Melanie Kempf
- Centre for Ophthalmology, University of Tübingen, 72076 Tuebingen, Germany; (S.K.); (A.K.); (M.K.); (N.W.); (K.S.); (E.Z.)
- Center for Rare Eye Diseases, University of Tübingen, 72076 Tuebingen, Germany
| | | | - Theresia Zuleger
- Institute of Medical Genetics and Applied Genomics, University of Tübingen, 72076 Tuebingen, Germany; (T.Z.); (T.B.H.)
| | - Tobias B. Haack
- Institute of Medical Genetics and Applied Genomics, University of Tübingen, 72076 Tuebingen, Germany; (T.Z.); (T.B.H.)
| | - Nicole Weisschuh
- Centre for Ophthalmology, University of Tübingen, 72076 Tuebingen, Germany; (S.K.); (A.K.); (M.K.); (N.W.); (K.S.); (E.Z.)
| | - Katarina Stingl
- Centre for Ophthalmology, University of Tübingen, 72076 Tuebingen, Germany; (S.K.); (A.K.); (M.K.); (N.W.); (K.S.); (E.Z.)
- Center for Rare Eye Diseases, University of Tübingen, 72076 Tuebingen, Germany
| | - Eberhart Zrenner
- Centre for Ophthalmology, University of Tübingen, 72076 Tuebingen, Germany; (S.K.); (A.K.); (M.K.); (N.W.); (K.S.); (E.Z.)
- Werner Reichardt Centre for Integrative Neuroscience (CIN), University of Tübingen, 72076 Tuebingen, Germany
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38
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Scala M, Nishikawa M, Ito H, Tabata H, Khan T, Accogli A, Davids L, Ruiz A, Chiurazzi P, Cericola G, Schulte B, Monaghan KG, Begtrup A, Torella A, Pinelli M, Denommé-Pichon AS, Vitobello A, Racine C, Mancardi MM, Kiss C, Guerin A, Wu W, Gabau Vila E, Mak BC, Martinez-Agosto JA, Gorin MB, Duz B, Bayram Y, Carvalho CMB, Vengoechea JE, Chitayat D, Tan TY, Callewaert B, Kruse B, Bird LM, Faivre L, Zollino M, Biskup S, Striano P, Nigro V, Severino M, Capra V, Costain G, Nagata KI. Variant-specific changes in RAC3 function disrupt corticogenesis in neurodevelopmental phenotypes. Brain 2022; 145:3308-3327. [PMID: 35851598 PMCID: PMC9473360 DOI: 10.1093/brain/awac106] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [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: 08/05/2021] [Revised: 02/01/2022] [Accepted: 03/13/2022] [Indexed: 01/17/2023] Open
Abstract
Variants in RAC3, encoding a small GTPase RAC3 which is critical for the regulation of actin cytoskeleton and intracellular signal transduction, are associated with a rare neurodevelopmental disorder with structural brain anomalies and facial dysmorphism. We investigated a cohort of 10 unrelated participants presenting with global psychomotor delay, hypotonia, behavioural disturbances, stereotyped movements, dysmorphic features, seizures and musculoskeletal abnormalities. MRI of brain revealed a complex pattern of variable brain malformations, including callosal abnormalities, white matter thinning, grey matter heterotopia, polymicrogyria/dysgyria, brainstem anomalies and cerebellar dysplasia. These patients harboured eight distinct de novo RAC3 variants, including six novel variants (NM_005052.3): c.34G > C p.G12R, c.179G > A p.G60D, c.186_188delGGA p.E62del, c.187G > A p.D63N, c.191A > G p.Y64C and c.348G > C p.K116N. We then examined the pathophysiological significance of these novel and previously reported pathogenic variants p.P29L, p.P34R, p.A59G, p.Q61L and p.E62K. In vitro analyses revealed that all tested RAC3 variants were biochemically and biologically active to variable extent, and exhibited a spectrum of different affinities to downstream effectors including p21-activated kinase 1. We then focused on the four variants p.Q61L, p.E62del, p.D63N and p.Y64C in the Switch II region, which is essential for the biochemical activity of small GTPases and also a variation hot spot common to other Rho family genes, RAC1 and CDC42. Acute expression of the four variants in embryonic mouse brain using in utero electroporation caused defects in cortical neuron morphology and migration ending up with cluster formation during corticogenesis. Notably, defective migration by p.E62del, p.D63N and p.Y64C were rescued by a dominant negative version of p21-activated kinase 1. Our results indicate that RAC3 variants result in morphological and functional defects in cortical neurons during brain development through variant-specific mechanisms, eventually leading to heterogeneous neurodevelopmental phenotypes.
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Affiliation(s)
| | | | | | - Hidenori Tabata
- Department of Molecular Neurobiology, Institute for Developmental Research, Aichi Developmental Disability Center, 713-8 Kamiya, Kasugai 480-0392, Japan
| | - Tayyaba Khan
- Genetics and Genome Biology, Research Institute, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Andrea Accogli
- Department of Neurosciences, Rehabilitation, Ophthalmology, Genetics, Maternal and Child Health, University of Genoa, Genoa, Italy
| | - Laura Davids
- Department of Human Genetics, Emory Healthcare, Atlanta, GA 30322, USA
| | - Anna Ruiz
- Genetics Laboratory, UDIAT-Centre Diagnòstic, Parc Taulí Hospital Universitari, Institut d'Investigació i Innovació Parc Taulí I3PT, Universitat Autònoma de, Barcelona, Sabadell, Spain
| | - Pietro Chiurazzi
- Dipartimento Universitario Scienze della Vita e Sanità Pubblica, Sezione di Medicina Genomica, Università Cattolica Sacro Cuore, Rome, Italy,Genetica Medica, Fondazione Policlinico Universitario A. Gemelli IRCCS, Rome, Italy
| | - Gabriella Cericola
- Neuropediatric Department, Helios-Klinikum Hildesheim, Hildesheim, Germany
| | | | | | | | - Annalaura Torella
- Telethon Institute of Genetics and Medicine, Pozzuoli, Naples, Italy,Department of Precision Medicine, University of Campania Luigi Vanvitelli, Naples, Italy
| | - Michele Pinelli
- Telethon Institute of Genetics and Medicine, Pozzuoli, Naples, Italy
| | - Anne Sophie Denommé-Pichon
- INSERM UMR1231 Génétique des Anomalies du Développement, Université de Bourgogne Franche-Comté, Dijon, France,Laboratoire de Génétique Moléculaire, UF Innovation en diagnostic génomique des maladies rares, Plateau Technique de Biologie, CHU de Dijon Bourgogne, Dijon, France,Centre de Génétique et Centre de Référence Anomalies du Développement et Syndromes Malformatifs de l'interrégion Est, FHU TRANSLAD, Hôpital d'Enfants, CHU de Dijon Bourgogne, Dijon, France
| | - Antonio Vitobello
- INSERM UMR1231 Génétique des Anomalies du Développement, Université de Bourgogne Franche-Comté, Dijon, France,Laboratoire de Génétique Moléculaire, UF Innovation en diagnostic génomique des maladies rares, Plateau Technique de Biologie, CHU de Dijon Bourgogne, Dijon, France
| | - Caroline Racine
- Laboratoire de Génétique Moléculaire, UF Innovation en diagnostic génomique des maladies rares, Plateau Technique de Biologie, CHU de Dijon Bourgogne, Dijon, France,Centre de Génétique et Centre de Référence Anomalies du Développement et Syndromes Malformatifs de l'interrégion Est, FHU TRANSLAD, Hôpital d'Enfants, CHU de Dijon Bourgogne, Dijon, France
| | - Maria Margherita Mancardi
- Unit of Child Neuropsychiatry, Department of Medical and Surgical Neuroscience and Rehabilitation, IRCCS Istituto Giannina Gaslini, Genova, Italy
| | - Courtney Kiss
- Division of Medical Genetics, Department of Pediatrics, Queen’s University, Kingston, ON K7L 2V7, Canada
| | - Andrea Guerin
- Division of Medical Genetics, Department of Pediatrics, Queen’s University, Kingston, ON K7L 2V7, Canada
| | - Wendy Wu
- Genetics and Genome Biology, Research Institute, The Hospital for Sick Children, Toronto, Ontario, Canada,Queen’s University, Kingston, ON, Canada
| | - Elisabeth Gabau Vila
- Paediatric Unit, Parc Taulí Hospital Universitari, Institut d'Investigació i Innovació Parc Taulí I3PT, Universitat Autònoma de, Barcelona, Sabadell, Spain
| | - Bryan C Mak
- Department of Human Genetics, David Geffen School of Medicine, University of California-Los Angeles, Los Angeles, CA, USA
| | - Julian A Martinez-Agosto
- Department of Human Genetics, David Geffen School of Medicine, University of California-Los Angeles, Los Angeles, CA, USA,Department of Pediatrics, David Geffen School of Medicine, University of California-Los Angeles, Los Angeles, CA, USA,Department of Psychiatry and Biobehavioral Sciences, David Geffen School of Medicine, University of California-Los Angeles, Los Angeles, CA, USA
| | - Michael B Gorin
- Department of Human Genetics, David Geffen School of Medicine, University of California-Los Angeles, Los Angeles, CA, USA,Department of Ophthalmology, Jules Stein Eye Institute, David Geffen School of Medicine, UCLA, Los Angeles 90095, CA, USA,Brain Research Institute, UCLA, Los Angeles 90095, CA, USA
| | - Bugrahan Duz
- Haseki Training and Research Hospital, Istanbul, Turkey
| | - Yavuz Bayram
- Division of Genomic Diagnostics, Department of Pathology and Laboratory Medicine, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA,Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Claudia M B Carvalho
- Pacific Northwest Research Institute, Seattle, WA 98122, USA,Baylor College of Medicine, Houston, TX 77030, USA
| | | | - David Chitayat
- The Prenatal Diagnosis and Medical Genetics Program, Department of Obstetrics and Gynecology, Mount Sinai Hospital, University of Toronto, Toronto, Ontario, Canada,Division of Clinical and Metabolic Genetics, Department of Paediatrics, The Hospital for Sick Children, Toronto, Ontario, Canada,Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | - Tiong Yang Tan
- Victorian Clinical Genetics Services, Murdoch Children’s Research Institute, and Department of Paediatrics, University of Melbourne, Melbourne, VIC 3052, Australia
| | - Bert Callewaert
- Center for Medical Genetics, Ghent University Hospital, Gent, Belgium
| | - Bernd Kruse
- Neuropediatric Department, Helios-Klinikum Hildesheim, Hildesheim, Germany
| | - Lynne M Bird
- Department of Pediatrics, University of California San Diego, San Diego, CA, USA,Genetics/Dysmorphology, Rady Children’s Hospital San Diego, San Diego, CA, USA
| | - Laurence Faivre
- INSERM UMR1231 Génétique des Anomalies du Développement, Université de Bourgogne Franche-Comté, Dijon, France,Centre de Génétique et Centre de Référence Anomalies du Développement et Syndromes Malformatifs de l'interrégion Est, FHU TRANSLAD, Hôpital d'Enfants, CHU de Dijon Bourgogne, Dijon, France
| | - Marcella Zollino
- Dipartimento Universitario Scienze della Vita e Sanità Pubblica, Sezione di Medicina Genomica, Università Cattolica Sacro Cuore, Rome, Italy,Genetica Medica, Fondazione Policlinico Universitario A. Gemelli IRCCS, Rome, Italy
| | - Saskia Biskup
- Praxis für Humangenetik, Tübingen, Germany,CeGaT GmbH, Tübingen, Germany
| | | | | | - Pasquale Striano
- Department of Neurosciences, Rehabilitation, Ophthalmology, Genetics, Maternal and Child Health, University of Genoa, Genoa, Italy,Pediatric Neurology and Muscular Diseases Unit, IRCCS Istituto Giannina Gaslini, Genoa, Italy
| | - Vincenzo Nigro
- Telethon Institute of Genetics and Medicine, Pozzuoli, Naples, Italy,Department of Precision Medicine, University of Campania Luigi Vanvitelli, Naples, Italy
| | | | - Valeria Capra
- Correspondence may also be addressed to: Valeria Capra Medical Genetics Unit, IRCCS Istituto Giannina Gaslini, Genoa, Italy E-mail:
| | - Gregory Costain
- Correspondence may also be addressed to: Gregory Costain Division of Clinical and Metabolic Genetics Department of Pediatrics The Hospital for Sick Children Toronto, Ontario, Canada E-mail:
| | - Koh ichi Nagata
- Correspondence to: Koh-ichi Nagata Department of Molecular Neurobiology Institute for Developmental Research Aichi Human Service Center, 713-8 Kamiya Kasugai, Aichi 480-0392, Japan E-mail:
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Cordts I, Önder D, Traschütz A, Kobeleva X, Karin I, Minnerop M, Koertvelyessy P, Biskup S, Forchhammer S, Binder J, Tzschach A, Meiss F, Schmidt A, Kreiß M, Cremer K, Mensah MA, Park J, Rautenberg M, Deininger N, Sturm M, Lingor P, Klopstock T, Weiler M, Marxreiter F, Synofzik M, Posch C, Sirokay J, Klockgether T, Haack TB, Deschauer M. Adult-Onset Neurodegeneration in Nucleotide Excision Repair Disorders (NERD ND ): Time to Move Beyond the Skin. Mov Disord 2022; 37:1707-1718. [PMID: 35699229 DOI: 10.1002/mds.29071] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [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: 01/05/2022] [Revised: 03/06/2022] [Accepted: 03/21/2022] [Indexed: 12/21/2022] Open
Abstract
BACKGROUND Variants in genes of the nucleotide excision repair (NER) pathway have been associated with heterogeneous clinical presentations ranging from xeroderma pigmentosum to Cockayne syndrome and trichothiodystrophy. NER deficiencies manifest with photosensitivity and skin cancer, but also developmental delay and early-onset neurological degeneration. Adult-onset neurological features have been reported in only a few xeroderma pigmentosum cases, all showing at least mild skin manifestations. OBJECTIVE The aim of this multicenter study was to investigate the frequency and clinical features of patients with biallelic variants in NER genes who are predominantly presenting with neurological signs. METHODS In-house exome and genome datasets of 14,303 patients, including 3543 neurological cases, were screened for deleterious variants in NER-related genes. Clinical workup included in-depth neurological and dermatological assessments. RESULTS We identified 13 patients with variants in ERCC4 (n = 8), ERCC2 (n = 4), or XPA (n = 1), mostly proven biallelic, including five different recurrent and six novel variants. All individuals had adult-onset progressive neurological deterioration with ataxia, dementia, and frequently chorea, neuropathy, and spasticity. Brain magnetic resonance imaging showed profound global brain atrophy in all patients. Dermatological examination did not show any skin cancer or pronounced ultraviolet damage. CONCLUSIONS We introduce NERDND as adult-onset neurodegeneration (ND ) within the spectrum of autosomal recessive NER disorders (NERD). Our study demonstrates that NERDND is probably an underdiagnosed cause of neurodegeneration in adulthood and should be considered in patients with overlapping cognitive and movement abnormalities. © 2022 The Authors. Movement Disorders published by Wiley Periodicals LLC on behalf of International Parkinson and Movement Disorder Society.
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Affiliation(s)
- Isabell Cordts
- Department of Neurology, Klinikum rechts der Isar, Technical University Munich, Munich, Germany
| | - Demet Önder
- Department of Neurology, University Hospital Bonn, Bonn, Germany.,German Center for Neurodegenerative Diseases, Bonn, Germany
| | - Andreas Traschütz
- Department of Neurodegeneration, Hertie Institute for Clinical Brain Research, University of Tübingen, Tübingen, Germany.,German Center for Neurodegenerative Diseases, Tübingen, Germany
| | - Xenia Kobeleva
- Department of Neurology, University Hospital Bonn, Bonn, Germany.,German Center for Neurodegenerative Diseases, Bonn, Germany
| | - Ivan Karin
- Friedrich-Baur-Institute, Department of Neurology, University Hospital of the Ludwig-Maximilians-University (LMU) Munich, Munich, Germany
| | - Martina Minnerop
- Institute of Neuroscience and Medicine, Research Centre Jülich, Jülich, Germany.,Department of Neurology, Center for Movement Disorders and Neuromodulation, Medical Faculty, Heinrich-Heine University Düsseldorf, Düsseldorf, Germany.,Institute of Clinical Neuroscience and Medical Psychology, Medical Faculty, Heinrich-Heine University Düsseldorf, Düsseldorf, Germany
| | - Peter Koertvelyessy
- Department of Neurology, Campus Benjamin Franklin, Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
| | - Saskia Biskup
- CeGaT GmbH und Praxis für Humangenetik Tübingen, Tübingen, Germany
| | - Stephan Forchhammer
- Division of Dermatooncology, Department of Dermatology, University of Tübingen, Tübingen, Germany
| | | | - Andreas Tzschach
- Institute of Human Genetics, Medical Center-University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Frank Meiss
- Department of Dermatology and Venereology, Medical Center-University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Axel Schmidt
- Institute of Human Genetics, University of Bonn, School of Medicine and University Hospital Bonn, Bonn, Germany
| | - Martina Kreiß
- Institute of Human Genetics, University of Bonn, School of Medicine and University Hospital Bonn, Bonn, Germany
| | - Kirsten Cremer
- Institute of Human Genetics, University of Bonn, School of Medicine and University Hospital Bonn, Bonn, Germany
| | - Martin A Mensah
- Institute of Medical Genetics and Human Genetics, Charité-Universitätsmedizin Berlin, Berlin, Germany.,BIH Biomedical Innovation Academy, Digital Clinician Scientist Program, Berlin Institute of Health at Charité-Universitätsmedizin Berlin, Germany
| | - Joohyun Park
- Institute of Medical Genetics and Applied Genomics, University of Tübingen, Tübingen, Germany
| | - Maren Rautenberg
- Institute of Medical Genetics and Applied Genomics, University of Tübingen, Tübingen, Germany
| | - Natalie Deininger
- Institute of Medical Genetics and Applied Genomics, University of Tübingen, Tübingen, Germany
| | - Marc Sturm
- Institute of Medical Genetics and Applied Genomics, University of Tübingen, Tübingen, Germany
| | - Paul Lingor
- Department of Neurology, Klinikum rechts der Isar, Technical University Munich, Munich, Germany
| | - Thomas Klopstock
- Friedrich-Baur-Institute, Department of Neurology, University Hospital of the Ludwig-Maximilians-University (LMU) Munich, Munich, Germany.,Munich Cluster for Systems Neurology (SyNergy), Munich, Germany.,German Center for Neurodegenerative Diseases, Munich, Germany
| | - Markus Weiler
- Department of Neurology, Heidelberg University Hospital, Heidelberg, Germany
| | - Franz Marxreiter
- Department of Molecular Neurology, University Hospital Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany.,Center for Rare Diseases (ZSEER), University Hospital Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
| | - Matthis Synofzik
- Department of Neurodegeneration, Hertie Institute for Clinical Brain Research, University of Tübingen, Tübingen, Germany.,German Center for Neurodegenerative Diseases, Tübingen, Germany
| | - Christian Posch
- Department of Dermatology and Allergy, School of Medicine, German Cancer Consortium, Technical University of Munich, Munich, Germany.,Faculty of Medicine, Sigmund Freud University Vienna, Vienna, Austria
| | - Judith Sirokay
- Department of Dermatology and Allergy, University Hospital Bonn, Bonn, Germany
| | - Thomas Klockgether
- Department of Neurology, University Hospital Bonn, Bonn, Germany.,German Center for Neurodegenerative Diseases, Bonn, Germany
| | - Tobias B Haack
- Institute of Medical Genetics and Applied Genomics, University of Tübingen, Tübingen, Germany.,Centre for Rare Diseases, University of Tübingen, Tübingen, Germany
| | - Marcus Deschauer
- Department of Neurology, Klinikum rechts der Isar, Technical University Munich, Munich, Germany
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Forschner A, Niessner H, Sinnberg T, Eigentler T, Amaral T, Seith F, Garbe C, Biskup S, Battke F. Zirkulierende Tumor-DNA (ctDNA) bei der Entdeckung von Rezidiven bei Melanompatienten mit adjuvanter Anti-PD-1-Therapie. J Dtsch Dermatol Ges 2022; 20:867-871. [PMID: 35711040 DOI: 10.1111/ddg.14766_g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
| | | | - Tobias Sinnberg
- Dermatoonkologie, Universitäts-Hautklinik Tübingen.,iFIT Exzellenzcluster (EXC 2180), Universität Tübingen
| | | | - Teresa Amaral
- Dermatoonkologie, Universitäts-Hautklinik Tübingen.,Portuguese Air Force Health Care Direction, Lissabon, Portugal
| | - Ferdinand Seith
- Abteilung für diagnostische und interventionelle Radiologie, Universitäts-Klinikum Tübingen
| | - Claus Garbe
- Dermatoonkologie, Universitäts-Hautklinik Tübingen
| | - Saskia Biskup
- Center for Genomics and Transcriptomics (CeGaT) GmbH, Tübingen
| | - Florian Battke
- Center for Genomics and Transcriptomics (CeGaT) GmbH, Tübingen
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Forschner A, Niessner H, Sinnberg T, Eigentler T, Amaral T, Seith F, Garbe C, Biskup S, Battke F. Circulating tumor DNA (ctDNA) in the detection of relapse in melanoma patients with adjuvant anti-PD-1 therapy. J Dtsch Dermatol Ges 2022; 20:867-871. [PMID: 35555861 DOI: 10.1111/ddg.14766] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Andrea Forschner
- Department of Dermatology, University Hospital Tuebingen, Tübingen, Germany
| | - Heike Niessner
- Department of Dermatology, University Hospital Tuebingen, Tübingen, Germany
| | - Tobias Sinnberg
- Department of Dermatology, University Hospital Tuebingen, Tübingen, Germany.,iFIT cluster of excellence (EXC 2180), University of Tuebingen, Germany
| | - Thomas Eigentler
- Department of Dermatology, University Hospital Tuebingen, Tübingen, Germany
| | - Teresa Amaral
- Department of Dermatology, University Hospital Tuebingen, Tübingen, Germany.,Portuguese Air Force Health Care Direction, Lisbon, Portugal
| | - Ferdinand Seith
- Department of Diagnostic and Interventional Radiology, University Hospital Tuebingen, Tuebingen, Germany
| | - Claus Garbe
- Department of Dermatology, University Hospital Tuebingen, Tübingen, Germany
| | - Saskia Biskup
- Center for Genomics and Transcriptomics (CeGaT) GmbH, Tuebingen, Germany
| | - Florian Battke
- Center for Genomics and Transcriptomics (CeGaT) GmbH, Tuebingen, Germany
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Nowomiejska K, Nasser F, Stingl K, Schimpf‐Linzenbold S, Biskup S, Brzozowska A, Rejdak R, Kohl S, Zrenner E. Disease expression caused by different variants in the BEST1 gene: genotype and phenotype findings in bestrophinopathies. Acta Ophthalmol 2022; 100:e847-e858. [PMID: 34327816 PMCID: PMC9328113 DOI: 10.1111/aos.14958] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [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: 12/13/2020] [Accepted: 06/17/2021] [Indexed: 12/30/2022]
Abstract
Purpose: To analyse the spectrum of clinical features and molecular genetic data in a series of patients carrying likely disease-associated variants in the BEST1 gene. Methods: Retrospective observational analysis of clinical data extracted from the medical records of visual function, multimodal imaging and electrophysiology of 62 eyes of 31 patients. Molecular genetic analysis was performed by means of panel-based NGS or Sanger sequencing. Results: The spectrum of variants in the BEST1 gene comprised 19 different variants and three of which are novel. Fundus photographs and OCT images allowed categorization of 52 eyes as Best vitelliform macular dystrophy (BVMD) with stages 1 to 5 and 10 eyes with autosomal recessive bestrophinopathy (ARB), with more severe phenotype. One patient was shown to be heterozygous for a variant, which has so far been described only in ARB, but this patient had the BVMD phenotype. There was no significant progression of the visual acuity during the follow-up period of 5 years both in BVMD and ARB. The most prevalent pattern of fundus autofluorescence (FAF) in BVMD was ‘patchy’. There were diverse visual field defects in static automated perimetry (SAP) depending on the stage. The Arden ratio was significantly lower in ARB patients and in eyes with stage 5 of BVMD. Conclusions: The genotype does not always predict the phenotype in patients with BVMD and ARB; however, having two mutations in the BEST1 gene causes a more severephenotype. FAFhelped to distinguish ARB from BVMD. Most of the observed eyesdidnotprogressfunctionallyduringthefollow-up.ARBandtheatrophicstageof BVMD as the disease end-stage had the worst visual functions and EOG results.
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Affiliation(s)
- Katarzyna Nowomiejska
- Chair and Department of General and Pediatric Ophthalmology Medical University of Lublin Lublin Poland
- Institute for Ophthalmic Research Center for Ophthalmology University of Tübingen Tübingen Germany
| | - Fadi Nasser
- Institute for Ophthalmic Research Center for Ophthalmology University of Tübingen Tübingen Germany
| | - Katarina Stingl
- University Eye Hospital Center for Ophthalmology University of Tübingen Tübingen Germany
- Center for Rare Eye Diseases University of Tübingen Tübingen Germany
| | | | | | - Agnieszka Brzozowska
- Department of Mathematics and Medical Biostatistics Medical University of Lublin Lublin Poland
| | - Robert Rejdak
- Chair and Department of General and Pediatric Ophthalmology Medical University of Lublin Lublin Poland
| | - Susanne Kohl
- Institute for Ophthalmic Research Center for Ophthalmology University of Tübingen Tübingen Germany
| | - Eberhart Zrenner
- Institute for Ophthalmic Research Center for Ophthalmology University of Tübingen Tübingen Germany
- Werner Reichardt Centre for Integrative Neuroscience University of Tübingen Tübingen Germany
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Dohrn MF, Heller C, Zengeler D, Obermaier CD, Biskup S, Weis J, Nikolin S, Claeys KG, Schöne U, Beijer D, Winter N, Achenbach P, Gess B, Schulz JB, Mulahasanovic L. Heterozygous POLG variant Ser1181Asn co-segregating in a family with autosomal dominant axonal neuropathy, proximal muscle fatigability, ptosis, and ragged red fibers. Neurol Res Pract 2022; 4:5. [PMID: 35101151 PMCID: PMC8805222 DOI: 10.1186/s42466-022-00169-w] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2021] [Accepted: 12/30/2021] [Indexed: 11/25/2022] Open
Abstract
By whole-exome sequencing, we found the heterozygous POLG variant c.3542G>A; p.Ser1181Asn in a family of four affected individuals, presenting with a mixed neuro-myopathic phenotype. The variant is located within the active site of polymerase gamma, in a cluster region associated with an autosomal dominant inheritance. In adolescence, the index developed distal atrophies and weakness, sensory loss, afferent ataxia, double vision, and bilateral ptosis. One older sister presented with Charcot-Marie-Tooth-like symptoms, while the youngest sister and father reported exercise-induced muscle pain and proximal weakness. In none of the individuals, we observed any involvement of the central nervous system. Muscle biopsies obtained from the father and the older sister showed ragged-red fibers, and electron microscopy confirmed mitochondrial damage. We conclude that this novel POLG variant explains this family’s phenotype.
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Nikonishyna YV, Ortner NJ, Kaserer T, Hoffmann J, Biskup S, Dafotakis M, Reetz K, Schulz JB, Striessnig J, Dohrn MF. Novel CACNA1A Variant p.Cys256Phe Disrupts Disulfide Bonds and Causes Spinocerebellar Ataxia. Mov Disord 2022; 37:401-404. [PMID: 34647648 DOI: 10.1002/mds.28835] [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] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2021] [Revised: 08/25/2021] [Accepted: 09/21/2021] [Indexed: 11/09/2022] Open
Abstract
BACKGROUND Spinocerebellar ataxia (SCA) is a progressive, autosomal dominant neurodegenerative disorder typically associated with CAG repeat expansions. OBJECTIVE We assessed the pathogenicity of the novel, heterozygous missense variant p.Cys256Phe (C256F) in the pore-forming α1-subunit of the Cav2.1 Ca2+ channel found in a 63-year-old woman with SCA with no CAG repeat expansion. METHODS We examined the effect of the C256F variant on channel function using whole-cell patch-clamp recordings in transfected tsA-201 cells. RESULTS The maximum Ca2+ current density was significantly reduced in the mutant compared to wild-type, which could not be explained by lower expression levels of mutant Cav2.1 α1- protein. Together with a significant increase in current inactivation, this is consistent with a loss of channel function. Molecular modeling predicted disruption of a conserved disulfide bond through the C256F variant. CONCLUSIONS Our results support the pathogenicity of the C256F variant for the SCA phenotype and provide further insight into Cav2.1 structure and function.
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Affiliation(s)
- Yuliia V Nikonishyna
- Department of Pharmacology and Toxicology, Institute of Pharmacy, Center for Molecular Biosciences Innsbruck, University of Innsbruck, Innsbruck, Austria
| | - Nadine J Ortner
- Department of Pharmacology and Toxicology, Institute of Pharmacy, Center for Molecular Biosciences Innsbruck, University of Innsbruck, Innsbruck, Austria
| | - Teresa Kaserer
- Department of Pharmaceutical Chemistry, Institute of Pharmacy, Center for Molecular Biosciences Innsbruck, University of Innsbruck, Innsbruck, Austria
| | - Jessica Hoffmann
- Center for Genomics and Transcriptomics and Praxis für Humangenetik Tübingen, Tübingen, Germany
| | - Saskia Biskup
- Center for Genomics and Transcriptomics and Praxis für Humangenetik Tübingen, Tübingen, Germany
| | - Manuel Dafotakis
- Department of Neurology, Medical Faculty of the RWTH Aachen University, Aachen, Germany
| | - Kathrin Reetz
- Department of Neurology, Medical Faculty of the RWTH Aachen University, Aachen, Germany
- JARA-BRAIN Institute Molecular Neuroscience and Neuroimaging, Forschungszentrum Jülich GmbH and RWTH Aachen University, Aachen, Germany
| | - Jörg B Schulz
- Department of Neurology, Medical Faculty of the RWTH Aachen University, Aachen, Germany
- JARA-BRAIN Institute Molecular Neuroscience and Neuroimaging, Forschungszentrum Jülich GmbH and RWTH Aachen University, Aachen, Germany
| | - Jörg Striessnig
- Department of Pharmacology and Toxicology, Institute of Pharmacy, Center for Molecular Biosciences Innsbruck, University of Innsbruck, Innsbruck, Austria
| | - Maike F Dohrn
- Department of Neurology, Medical Faculty of the RWTH Aachen University, Aachen, Germany
- Dr. John T. Macdonald Foundation, Department of Human Genetics and John P. Hussman Institute for Human Genomics, University of Miami, Miller School of Medicine, Miami, Florida, USA
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45
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Nikonishyna YV, Hofer NT, Ortner NJ, Kaserer T, Hoffman J, Biskup S, Dafotakis M, Schulz JB, Dohrn MF, Striessnig J. Missense mutations in voltage-gated calcium channels associated with neurodevelopmental and neurodegenerative disorders. Biophys J 2022. [DOI: 10.1016/j.bpj.2021.11.2235] [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: 12/01/2022] Open
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46
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Michaeli O, Ladany H, Erez A, Shachar SB, Izraeli S, Lidzbarsky G, Basel-Salmon L, Biskup S, Maruvka YE, Toledano H, Goldberg Y. Di-genic inheritance of germline POLE and PMS2 pathogenic variants causes a unique condition associated with pediatric cancer predisposition. Clin Genet 2021; 101:442-447. [PMID: 34967012 DOI: 10.1111/cge.14106] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [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: 10/16/2021] [Revised: 12/12/2021] [Accepted: 12/25/2021] [Indexed: 11/25/2022]
Abstract
Polymerase proofreading-associated polyposis (PPAP) and Lynch syndrome, caused by mutated POLE and mismatch repair (MMR) genes, respectively, are associated with adult-onset cancer. PPAP and MMR-deficient tumors are both hypermutated, and each has a unique mutational signature. We describe a 4.5-year-old boy with multiple café au lait spots who presented with metastatic Sonic Hedgehog-activated medulloblastoma, with partial response to intensive chemotherapy and immunotherapy. Tumor showed microsatellite stability, loss of PMS2 nuclear expression, and an exceptionally high tumor mutational burden of 276 Mut/Mb. Germline molecular analysis revealed an inherited heterozygous pathogenic POLE variant and a de novo heterozygous PMS2 pathogenic variant. The tumor featured the MMR, POLE, and POLE+MMR mutational signatures. This is the first description of a di-genic condition, which we named "POL-LYNCH syndrome", manifested by an aggressive ultra-mutant pediatric medulloblastoma with a unique genomic signature. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Orli Michaeli
- Department of Pediatric Hematology and Oncology, Schneider Children's Medical Center of Israel, Petach Tikva, Israel
| | - Hagay Ladany
- Biotechnology and Food Engineering, Technion - Israel Institute of Technology, Haifa, Israel
| | - Ayelet Erez
- Department of Biological Regulation, Weizmann Institute of Science, Rehovot, Israel
| | - Shay Ben Shachar
- Clalit Research Institute & Department of Genetics, Schneider Children's Medical Center of Israel, Petach Tikva, Israel
| | - Shai Izraeli
- Department of Pediatric Hematology and Oncology, Schneider Children's Medical Center of Israel, Petach Tikva, Israel.,Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Gabriel Lidzbarsky
- Raphael Recanati Genetic Institute, Rabin Medical Center-Beilinson Hospital, Petach Tikva, Israel
| | - Lina Basel-Salmon
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel.,Raphael Recanati Genetic Institute, Rabin Medical Center-Beilinson Hospital, Petach Tikva, Israel
| | - Saskia Biskup
- CeGaT Center for Genomics and Transcriptomics, Tuebingen, Germany
| | - Yosef E Maruvka
- Biotechnology and Food Engineering, Technion - Israel Institute of Technology, Haifa, Israel
| | - Helen Toledano
- Department of Pediatric Hematology and Oncology, Schneider Children's Medical Center of Israel, Petach Tikva, Israel.,Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Yael Goldberg
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel.,Raphael Recanati Genetic Institute, Rabin Medical Center-Beilinson Hospital, Petach Tikva, Israel
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47
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Gabriel H, Korinth D, Ritthaler M, Schulte B, Battke F, von Kaisenberg C, Wüstemann M, Schulze B, Friedrich-Freksa A, Pfeiffer L, Entezami M, Schröer A, Bürger J, Schwaibold EMC, Lebek H, Biskup S. Trio exome sequencing is highly relevant in prenatal diagnostics. Prenat Diagn 2021; 42:845-851. [PMID: 34958143 PMCID: PMC9305182 DOI: 10.1002/pd.6081] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [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: 09/14/2021] [Revised: 12/13/2021] [Accepted: 12/14/2021] [Indexed: 12/26/2022]
Abstract
Objective About 3% of newborns show malformations, with about 20% of the affected having genetic causes. Clarification of genetic diseases in postnatal diagnostics was significantly improved with high‐throughput sequencing, in particular through whole exome sequencing covering all protein‐coding regions. Here, we aim to extend the use of this technology to prenatal diagnostics. Method Between 07/2018 and 10/2020, 500 pregnancies with fetal ultrasound abnormalities were analyzed after genetic counseling as part of prenatal diagnostics using WES of the fetus and parents. Results Molecular genetic findings could explain ultrasound abnormalities in 38% of affected fetuses. In 47% of these, disease‐causing de novo variants were found. Pathogenic variants in genes with autosomal recessive or X‐linked inheritance were detected in more than one‐third (70/189 = 37%). The latter are associated with increased probability of recurrence, making their detection important for further pregnancies. Average time from sample receipt to report was 12 days in the recent cases. Conclusion Trio exome sequencing is a useful addition to prenatal diagnostics due to its high diagnostic yield and short processing time (comparable to chromosome analysis). It covers a wide spectrum of genetic changes. Comprehensive interdisciplinary counseling before and after diagnostics is indispensable.
What's already known about this topic?
It is known that about 20% of malformations in newborns can be associated with genetic causes. Whole‐exome sequencing, and especially trio exome sequencing, is an established and successful method in postnatal genetic diagnostics. Diagnostic yield for trio exome sequencing is around 37%.
What does this study add?
We show that trio exome sequencing is a fast and comprehensive method in prenatal diagnostics with diagnostic yield similar to that of postnatal trio exome sequencing. We provide case solution rates for different phenotypic observations from 19% for abnormalities of internal organs up to 52% for skeletal malformations.
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Affiliation(s)
| | - Dirk Korinth
- Praxis für Humangenetik Tübingen, Tübingen, Germany
| | | | | | | | | | - Max Wüstemann
- Zentrum für Pränatalmedizin Hannover, Hannover, Germany
| | | | | | - Lutz Pfeiffer
- Medicover Humangenetik Berlin-Lichtenberg, Berlin, Germany
| | | | | | | | | | - Holger Lebek
- Pränatale Diagnostik Berlin-Lichtenberg, Berlin, Germany
| | - Saskia Biskup
- Praxis für Humangenetik Tübingen, Tübingen, Germany.,CeGaT GmbH, Tübingen, Germany
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48
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Kovacs B, Winnik S, Medeiros-Domingo A, Costa S, Fu G, Biskup S, Ruschitzka F, Flammer AJ, Tanner FC, Duru F, Saguner AM. The novel TRPM4 c.448G>T variant is associated with familial conduction disorders, cardiomyopathy, and sudden cardiac death. Cardiol J 2021; 29:514-516. [PMID: 34897640 PMCID: PMC9170332 DOI: 10.5603/cj.a2021.0157] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2021] [Revised: 10/14/2021] [Accepted: 11/20/2021] [Indexed: 11/25/2022] Open
Affiliation(s)
- Boldizsar Kovacs
- Department of Cardiology, Division of Electrophysiology and Pacing, University Heart Center Zurich, Switzerland
| | - Stephan Winnik
- Department of Cardiology, Division of Electrophysiology and Pacing, University Heart Center Zurich, Switzerland
| | | | - Sarah Costa
- Department of Cardiology, Division of Electrophysiology and Pacing, University Heart Center Zurich, Switzerland
| | - Guan Fu
- Department of Cardiology, Division of Electrophysiology and Pacing, University Heart Center Zurich, Switzerland
| | - Saskia Biskup
- Praxis für Humangenetik, Tübingen, Germany & CeGaT GmbH, Tübingen, Germany
| | | | | | - Felix C Tanner
- Department of Cardiology, University Heart Center, Switzerland
| | - Firat Duru
- Department of Cardiology, Division of Electrophysiology and Pacing, University Heart Center Zurich, Switzerland
| | - Ardan M Saguner
- Department of Cardiology, Division of Electrophysiology and Pacing, University Heart Center Zurich, Switzerland.
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49
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Gilbert S, Gabriel H, Pankow A, Biskup S, Wagner AD. [What is confirmed in the diagnostics of autoinflammatory fever diseases?]. Internist (Berl) 2021; 62:1290-1294. [PMID: 34878559 DOI: 10.1007/s00108-021-01221-8] [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] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/09/2021] [Indexed: 11/29/2022]
Abstract
Periodic fever syndromes (PFS) are a group of rare autoinflammatory diseases, which are characterized by disorders of the innate immune reaction and life-long recurrent episodes of inflammatory symptoms. This article describes the diagnostic approach. In addition to the patient medical history, physical examination and laboratory determinations, gene tests are becoming increasingly more important. The panel diagnostics using high throughput sequencing or next generation sequencing (NGS) is the method of choice for the detection of a genetic cause of PFS. This article discusses the diagnostic decision support systems (DDSS) that can play a future role in the diagnosis of rare diseases, especially those with complex patterns of symptoms.
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Affiliation(s)
- Stephen Gilbert
- Ada Health GmbH, Karl-Liebknecht-Str. 1, 10178, Berlin, Deutschland.,Else Kröner-Fresenius Center for Digital Health, Faculty of Medicine Carl Gustav Carus, Louisenstr. 120, 61348, Bad Homburg, Deutschland.,Technische Universität Dresden, Dresden, Deutschland
| | - Heinz Gabriel
- Praxis für Humangenetik Tübingen, Paul-Ehrlich-Str. 23, 72076, Tübingen, Deutschland
| | - Anne Pankow
- Abt. für Nieren- und Hochdruckerkrankungen, Ambulanz für seltene entzündliche, Systemerkrankungen mit Nierenbeteiligung, Medizinische Hochschule Hannover, Carl-Neuberg-Str. 1, 30625, Hannover, Deutschland.,Klinik für Rheumatologie und Immunologie, Berlin, Charité, Charitéplatz 1, 10117, Berlin, Deutschland
| | - Saskia Biskup
- Praxis für Humangenetik Tübingen, Paul-Ehrlich-Str. 23, 72076, Tübingen, Deutschland
| | - Annette Doris Wagner
- Abt. für Nieren- und Hochdruckerkrankungen, Ambulanz für seltene entzündliche, Systemerkrankungen mit Nierenbeteiligung, Medizinische Hochschule Hannover, Carl-Neuberg-Str. 1, 30625, Hannover, Deutschland.
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50
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Meyer M, Hollenbeck JC, Reunert J, Seelhöfer A, Rust S, Fobker M, Biskup S, Och U, Linden M, Sass JO, Marquardt T. 3-Hydroxyisobutyrate dehydrogenase (HIBADH) deficiency-A novel disorder of valine metabolism. J Inherit Metab Dis 2021; 44:1323-1329. [PMID: 34176136 DOI: 10.1002/jimd.12410] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/30/2020] [Revised: 06/04/2021] [Accepted: 06/14/2021] [Indexed: 11/08/2022]
Abstract
3-Hydroxyisobutyric acid (3HiB) is an intermediate in the degradation of the branched-chain amino acid valine. Disorders in valine degradation can lead to 3HiB accumulation and its excretion in the urine. This article describes the first two patients with a new metabolic disorder, 3-hydroxyisobutyrate dehydrogenase (HIBADH) deficiency, its phenotype and its treatment with a low-valine diet. The detected mutation in the HIBADH gene leads to nonsense-mediated mRNA decay of the mutant allele and to a complete loss-of-function of the enzyme. Under strict adherence to a low-valine diet a rapid decrease of 3HiB excretion in the urine was observed. Due to limited patient numbers and intrafamilial differences in phenotype with one affected and one unaffected individual, the clinical phenotype of HIBADH deficiency needs further evaluation.
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Affiliation(s)
- Melanie Meyer
- Department of General Pediatrics, University Hospital, Münster, Germany
| | - Jana C Hollenbeck
- Bonn-Rhein-Sieg University of Applied Sciences, Department of Natural Sciences & Institute for Functional Gene Analytics (IFGA), RG Inborn Errors of Metabolism, Rheinbach, Germany
| | - Janine Reunert
- Department of General Pediatrics, University Hospital, Münster, Germany
| | - Anja Seelhöfer
- Department of General Pediatrics, University Hospital, Münster, Germany
| | - Stephan Rust
- Department of General Pediatrics, University Hospital, Münster, Germany
| | - Manfred Fobker
- Center for Laboratory Medicine, University Hospital, Münster, Germany
| | - Saskia Biskup
- CeGaT GmbH und Praxis für Humangenetik Tübingen, Tübingen, Germany
| | - Ulrike Och
- Department of General Pediatrics, University Hospital, Münster, Germany
| | | | - Jörn Oliver Sass
- Bonn-Rhein-Sieg University of Applied Sciences, Department of Natural Sciences & Institute for Functional Gene Analytics (IFGA), RG Inborn Errors of Metabolism, Rheinbach, Germany
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