Deciphering the molecular pathophysiology of muscular dystrophies facilitated by disease gene discovery using integrative next generation sequencing
Pediatric and Adolescent Medicine
Final Report Abstract
Congenital and limb-girdle muscular dystrophies are representing a clinical and genetically heterogeneous group of severe progressive disorders often fatally leading to death. At the start of the project, unfortunately, about 50% of the patients did not have a genetic diagnosis. A major obstacle for translational research was that unfortunately for many CMD and LGMD forms even the underlying disease genes and mechanisms have been unknown. The objective of my Emmy-Noether Group was to decipher the genetic basis of CMD/LGMD and clinically overlapping neuromuscular disorder. We aimed to achieve this via employing the latest sequencing technology and also aim to identify disturbed gene-specific biochemical pathways immediately downstream of the primary genetic defect (Aim1). Further, we aimed to use biophysical methods for understanding the impact of a missense variant/mutation on the protein structure and understand the biochemical function of the disease-related proteins (Aim2). To this end, we have established a pediatric neuromuscular outpatient clinic in the University Children's Hospital Cologne run by the PI. We have recruited, collected clinical data, and sequenced over 740 patients for this research study to date. In the first step, we have investigated the Mendeliome 276 patients and defined the genetic landscape for muscular dystrophies, dystroglycanopathies, congenital myopathies, and fetal akinesia. In the second step, we have performed whole-exome sequencing for 493 cases and about 40% of the WES cases (N=297) were solved. Of these sequenced patients, 244 were clinically diagnosed with primary muscle disease. In this subgroup, via targeted next-generation sequencing (NGS) the causative mutation was identified in 149 cases (61%). We have collected created a unique database and DNA resource of > 900 clinically well-defined rare neuromuscular cases the discovery of novel disease-related genes. We have discovered and published international impactful and visible journals on novel diseaserelated genes and also investigated in our laboratory the molecular disease mechanisms, as proven by first and corresponding authorships of our lab members. I would indicate here the novel glycosylation defects due to CCDC115 mutations or the severe pre-synaptic congenital myasthenic syndrome due to SLC5A7 mutations. Or a novel disease mechanism for neuropathy together with the treatment option by using PARP-inhibitors is novel and will expand our understanding of the role of PARylation in neurodegeneratio. While WES is currently very productive, for exomenegative cases we started to perform WGS. For the analysis of genomes, we focused first on introns and exons as well as promoter regions, the ExintromPro approach. The filtering of variants is ongoing, and we have acquired the stored muscle biopsies for RNA-Seq. In total, we have now 40 muscle biopsies from cases with negative Exome results. Importantly, the Cirak laboratory has been established from scratch and we can perform independently biophysical, biochemical, cell biological, and myology related experiments by using state-of-the-art molecular biological tools, which was defined as Aim 2 of this project. We have established an expression and purification pipeline for recombinant protein in E.coli. The work on 19 hISPD mutant proteins with their comprehensive biophysical analysis shows the efficiency and performance of our pipeline, providing a personalized treatment approach. Dr.Cirak and his group will work on the new hypothesis with 10 novel promising candidate genes and exploit the large genomic dataset as a professor at Ulm University.
Publications
- CCDC115 Deficiency Causes a Disorder of Golgi Homeostasis with Abnormal Protein Glycosylation. Am J Hum Genet. 2016 Feb 4;98(2):310-21
Jansen JC, Cirak S, van Scherpenzeel M, Timal S, Reunert J, Rust S, Pérez B, Vicogne D, Krawitz P, Wada Y, Ashikov A, Pérez-Cerdá C, Medrano C, Arnoldy A, Hoischen A, Huijben K, Steenbergen G, Quelhas D, Diogo L, Rymen D, Jaeken J, Guffon N, Cheillan D, van den Heuvel LP, Maeda Y, Kaiser O, Schara U, Gerner P, van den Boogert MA, Holleboom AG, Nassogne MC, Sokal E, Salomon J, van den Bogaart G, Drenth JP, Huynen MA, Veltman JA, Wevers RA, Morava E, Matthijs G, Foulquier F, Marquardt T, Lefeber DJ
(See online at https://doi.org/10.1016/j.ajhg.2015.12.010) - Homozygous mutation in Atlastin GTPase 1 causes recessive hereditary spastic paraplegia. J Hum Genet. 2016 Jun;61(6):571-3
Willkomm L, Heredia R, Hoffmann K, Wang H, Voit T, Hoffman EP, Cirak S
(See online at https://doi.org/10.1038/jhg.2016.6) - Choline transporter mutations in severe congenital myasthenic syndrome disrupt transporter localization. Brain. 2017 Nov 1;140(11):2838-2850
Wang H, Salter CG, Refai O, Hardy H, Barwick KES, Akpulat U, Kvarnung M, Chioza BA, Harlalka G, Taylan F, Sejersen T, Wright J, Zimmerman HH, Karakaya M, Stüve B, Weis J, Schara U, Russell MA, Abdul-Rahman OA, Chilton J, Blakely RD, Baple EL, Cirak S, Crosby AH
(See online at https://doi.org/10.1093/brain/awx249) - Recessive PIEZO2 stop mutation causes distal arthrogryposis with distal muscle weakness, scoliosis and proprioception defects. J Hum Genet. 2017 Apr;62(4):497-501
Haliloglu G, Becker K, Temucin C, Talim B, Küçükşahin N, Pergande M, Motameny S, Nürnberg P, Aydingoz U, Topaloglu H, Cirak S
(See online at https://doi.org/10.1038/jhg.2016.153) - A novel SPEG mutation causes non-compaction cardiomyopathy and neuropathy in a floppy infant with centronuclear myopathy. Acta Neuropathol Commun. 2018 Aug 29;6(1):83
Wang H, Schänzer A, Kampschulte B, Daimagüler HS, Logeswaran T, Schlierbach H, Petzinger J, Ehrhardt H, Hahn A, Cirak S
(See online at https://doi.org/10.1186/s40478-018-0589-y) - Biallelic Mutations in ADPRHL2, Encoding ADP-Ribosylhydrolase 3, Lead to a Degenerative Pediatric Stress-Induced Epileptic Ataxia Syndrome. Am J Hum Genet. 2018 Sep 6;103(3):431-439
Ghosh SG, Becker K, Huang H, Dixon-Salazar T, Chai G, Salpietro V, Al-Gazali L, Waisfisz Q, Wang H, Vaux KK, Stanley V, Manole A, Akpulat U, Weiss MM, Efthymiou S, Hanna MG, Minetti C, Striano P, Pisciotta L, De Grandis E, Altmüller J, Nürnberg P, Thiele H, Yis U, Okur TD, Polat AI, Amiri N, Doosti M, Karimani EG, Toosi MB, Haddad G, Karakaya M, Wirth B, van Hagen JM, Wolf NI, Maroofian R, Houlden H, Cirak S, Gleeson JG
(See online at https://doi.org/10.1016/j.ajhg.2018.10.002) - Bi-allelic mutations in uncoordinated mutant number-45 myosin chaperone B are a cause for congenital myopathy. Acta Neuropathol Commun. 2019 Dec 18;7(1):211
Dafsari HS, Kocaturk NM, Daimagüler HS, Brunn A, Dötsch J, Weis J, Deckert M, Cirak S
(See online at https://doi.org/10.1186/s40478-019-0869-1) - Genotype-Phenotype Correlations in Charcot-Marie-Tooth Disease Due to MTMR2 Mutations and Implications in Membrane Trafficking. Front Neurosci. 2019 Oct 14;13:974
Wang H, Kaçar Bayram A, Sprute R, Ozdemir O, Cooper E, Pergande M, Efthymiou S, Nedic I, Mazaheri N, Stumpfe K, Azizi Malamiri R, Shariati G, Zeighami J, Bayram N, Naghibzadeh SK, Tajik M, Yaşar M, Sami Güven A, Bibi F, Sultan T, Salpietro V, Houlden H, Per H, Galehdari H, Shalbafan B, Jamshidi Y, Cirak S
(See online at https://doi.org/10.3389/fnins.2019.00974) - The clinical-phenotype continuum in DYNC1H1-related disordersgenomic profiling and proposal for a novel classification. J Hum Genet. 2020 Nov;65(11):1003-1017
Becker LL, Dafsari HS, Schallner J, Abdin D, Seifert M, Petit F, Smol T, Bok L, Rodan L, Krapels I, Sprangers S, Weschke B, Johnson K, Straub V, Kaindl AM, Di Donato N, von der Hagen M, Cirak S
(See online at https://doi.org/10.1038/s10038-020-0803-1) - The genomic and clinical landscape of fetal akinesia. Genet Med. 2020 Mar;22(3):511-523
Pergande M, Motameny S, Özdemir Ö, Kreutzer M, Wang H, Daimagüler HS, Becker K, Karakaya M, Ehrhardt H, Elcioglu N, Ostojic S, Chao CM, Kawalia A, Duman Ö, Koy A, Hahn A, Reimann J, Schoner K, Schänzer A, Westhoff JH, Schwaibold EMC, Cossee M, Imbert-Bouteille M, von Pein H, Haliloglu G, Topaloglu H, Altmüller J, Nürnberg P, Thiele H, Heller R, Cirak S
(See online at https://doi.org/10.1038/s41436-019-0680-1)
