title: Molecular dissection of germline chromothripsis in a developmental context using patient-derived iPS cells.
abstract: Germline chromothripsis causes complex genomic rearrangements that are likely to affect multiple genes and their regulatory contexts. The contribution of individual rearrangements and affected genes to the phenotypes of patients with complex germline genomic rearrangements is generally unknown.
  
  
  
  To dissect the impact of germline chromothripsis in a relevant developmental context, we performed trio-based RNA expression analysis on blood cells, induced pluripotent stem cells (iPSCs), and iPSC-derived neuronal cells from a patient with de novo germline chromothripsis and both healthy parents. In addition, Hi-C and 4C-seq experiments were performed to determine the effects of the genomic rearrangements on transcription regulation of genes in the proximity of the breakpoint junctions.
  
  
  
  Sixty-seven genes are located within 1 Mb of the complex chromothripsis rearrangements involving 17 breakpoints on four chromosomes. We find that three of these genes (FOXP1, DPYD, and TWIST1) are both associated with developmental disorders and differentially expressed in the patient. Interestingly, the effect on TWIST1 expression was exclusively detectable in the patient's iPSC-derived neuronal cells, stressing the need for studying developmental disorders in the biologically relevant context. Chromosome conformation capture analyses show that TWIST1 lost genomic interactions with several enhancers due to the chromothripsis event, which likely led to deregulation of TWIST1 expression and contributed to the patient's craniosynostosis phenotype.
  
  
  
  We demonstrate that a combination of patient-derived iPSC differentiation and trio-based molecular profiling is a powerful approach to improve the interpretation of pathogenic complex genomic rearrangements. Here we have applied this approach to identify misexpression of TWIST1, FOXP1, and DPYD as key contributors to the complex congenital phenotype resulting from germline chromothripsis rearrangements.
authors.affiliation: Center for Molecular Medicine and Cancer Genomics Netherlands, Division Biomedical Genetics, University Medical Center Utrecht, Universiteitsweg 100, Utrecht, 3584CG, The Netherlands.
authors.forename: Sjors
authors.initials: S
authors.lastname: Middelkamp
authors.affiliation: Center for Molecular Medicine and Cancer Genomics Netherlands, Division Biomedical Genetics, University Medical Center Utrecht, Universiteitsweg 100, Utrecht, 3584CG, The Netherlands.|Cardiovascular and Metabolic Sciences, Max-Delbrück-Center for Molecular Medicine (MDC) in the Helmholtz Association, Robert-Rössle-Strasse 10, Berlin, 13125, Germany.
authors.forename: Sebastiaan
authors.initials: S
authors.lastname: van Heesch
authors.affiliation: Department of Cell Biology, Center for Molecular Medicine and Regenerative Medicine Center, University Medical Center Utrecht, Uppsalalaan 6, Utrecht, 3584CT, The Netherlands.
authors.forename: A Koen
authors.initials: AK
authors.lastname: Braat
authors.affiliation: Center for Molecular Medicine and Cancer Genomics Netherlands, Division Biomedical Genetics, University Medical Center Utrecht, Universiteitsweg 100, Utrecht, 3584CG, The Netherlands.
authors.forename: Joep
authors.initials: J
authors.lastname: de Ligt
authors.affiliation: Department of Molecular Epidemiology, Leiden University Medical Center, Einthovenweg 20, Leiden, 2333ZC, The Netherlands.
authors.forename: Maarten
authors.initials: M
authors.lastname: van Iterson
authors.affiliation: Cergentis B.V., Yalelaan 62, Utrecht, 3584CM, The Netherlands.
authors.forename: Marieke
authors.initials: M
authors.lastname: Simonis
authors.affiliation: Center for Molecular Medicine and Cancer Genomics Netherlands, Division Biomedical Genetics, University Medical Center Utrecht, Universiteitsweg 100, Utrecht, 3584CG, The Netherlands.
authors.forename: Markus J
authors.initials: MJ
authors.lastname: van Roosmalen
authors.affiliation: MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Crewe Road, Edinburgh, EH4 2XU, UK.
authors.forename: Martijn J E
authors.initials: MJ
authors.lastname: Kelder
authors.affiliation: Department of Pediatric Pulmonology & Laboratory of Translational Immunology, Wilhelmina Children's Hospital, University Medical Centre, Lundlaan 6, Utrecht, 3584EA, The Netherlands.
authors.forename: Evelien
authors.initials: E
authors.lastname: Kruisselbrink
authors.affiliation: Center for Molecular Medicine and Cancer Genomics Netherlands, Division Biomedical Genetics, University Medical Center Utrecht, Universiteitsweg 100, Utrecht, 3584CG, The Netherlands.
authors.forename: Ron
authors.initials: R
authors.lastname: Hochstenbach
authors.affiliation: Department of Genetics, University Medical Center Utrecht, Lundlaan 6, Utrecht, 3584EA, The Netherlands.
authors.forename: Nienke E
authors.initials: NE
authors.lastname: Verbeek
authors.affiliation: Department of Genetics, University Medical Center Utrecht, Lundlaan 6, Utrecht, 3584EA, The Netherlands.
authors.forename: Elly F
authors.initials: EF
authors.lastname: Ippel
authors.affiliation: Department of Translational Neuroscience, Brain Center Rudolf Magnus, University Medical Center Utrecht, Universiteitsweg 100, Utrecht, 3584CG, The Netherlands.
authors.forename: Youri
authors.initials: Y
authors.lastname: Adolfs
authors.affiliation: Department of Translational Neuroscience, Brain Center Rudolf Magnus, University Medical Center Utrecht, Universiteitsweg 100, Utrecht, 3584CG, The Netherlands.
authors.forename: R Jeroen
authors.initials: RJ
authors.lastname: Pasterkamp
authors.affiliation: Center for Molecular Medicine and Cancer Genomics Netherlands, Division Biomedical Genetics, University Medical Center Utrecht, Universiteitsweg 100, Utrecht, 3584CG, The Netherlands.
authors.forename: Wigard P
authors.initials: WP
authors.lastname: Kloosterman
authors.affiliation: Center for Molecular Medicine and Cancer Genomics Netherlands, Division Biomedical Genetics, University Medical Center Utrecht, Universiteitsweg 100, Utrecht, 3584CG, The Netherlands. E.W.Kuijk-3@umcutrecht.nl.
authors.forename: Ewart W
authors.initials: EW
authors.lastname: Kuijk
authors.affiliation: Center for Molecular Medicine and Cancer Genomics Netherlands, Division Biomedical Genetics, University Medical Center Utrecht, Universiteitsweg 100, Utrecht, 3584CG, The Netherlands. ecuppen@umcutrecht.nl.
authors.forename: Edwin
authors.initials: E
authors.lastname: Cuppen
mesh_terms: D000072837:Chromothripsis; D042943:Dihydrouracil Dehydrogenase (NADP) / Q000235:genetics; D051858:Forkhead Transcription Factors / Q000235:genetics; D005786:Gene Expression Regulation; D018095:Germ-Line Mutation; D006801:Humans; D057026:Induced Pluripotent Stem Cells / Q000378:metabolism; D007962:Leukocytes / Q000378:metabolism; D009474:Neurons / Q000378:metabolism; D009687:Nuclear Proteins / Q000235:genetics; D012097:Repressor Proteins / Q000235:genetics; D059467:Transcriptome; D051879:Twist-Related Protein 1 / Q000235:genetics
chemical_list: C486626:FOXP1 protein, human; D051858:Forkhead Transcription Factors; D009687:Nuclear Proteins; D012097:Repressor Proteins; C103173:TWIST1 protein, human; D051879:Twist-Related Protein 1; D042943:Dihydrouracil Dehydrogenase (NADP)
keywords: Chromosome conformation capture; Chromothripsis; Complex genomic rearrangements; Congenital disorders; Craniosynostosis; Induced pluripotent stem cells; Neuronal differentiation; Personal genomics; RNA-sequencing; TWIST1