Genetic studies of rare skeletal disorders : to solve the unsolved

Congenital skeletal disorders, also called skeletal dysplasias, constitute a diverse group of rare genetic conditions that occur in approximately 1 per 3000-5000 births. Skeletal dysplasias exhibit both clinical and molecular heterogeneity, with the phenotype of the affected individuals varying based on the severity of the disease. While skeletal dysplasias primarily affect cartilage and bone, they often include extraskeletal manifestations, including internal organ abnormalities. Diagnosis of skeletal disorders includes clinical characterization, radiographic pattern recognition, and genetic testing. Despite the advancements in genome sequencing technologies, there remains a gap in understanding the genetic and phenotypic characteristics of some of the skeletal disorders, and new types of skeletal dysplasias continue to be identified.

The work in this thesis focused on identifying genetic causes and molecular mechanisms of rare skeletal disorders. Using genome sequencing the objective was to identify new genes or novel variants and improve the clinical and genetic characterization in the individuals with skeletal disease of unknown genetic background. The research goals were achieved through four constituent studies included in this thesis.

Study I identified TOMM7 as a novel disease-causing gene in a patient with syndromic short stature and developmental delay. The molecular pathogenesis of TOMM7 (c.73T>C, p.Trp25Arg) variant was studied in a mouse model. Tomm7 mutant mice showed growth restriction, reduced chondrocyte proliferation, and lipoatrophy caused by mitochondrial dysfunction. Study II identified ADAMTSL2 as a genetic cause of previously genetically uncharacterized skeletal dysplasia cortical dysostosis Al-Gazali type and connected it to the spectrum of ADAMTSL2-related disorders. This study included a cohort of nine individuals characterized by intrauterine growth restriction, distinct radiological patterns, and early mortality. Using primary dermal fibroblasts from the affected individual, we showed abnormal organization of the fibrillin-1 microfibrils. Study III identified disease-causing variants in the RAB34 gene in a fetus with complex malformations, including skeletal abnormalities consistent with shortrib thoracic dysplasia, and a combination of rarely occurring pre- and postaxial polydactyly. Study IV focused on investigating gene dosage abnormalities in type I collagen genes COL1A1 and COL1A2 in eight patients from five unrelated families with Osteogenesis Imperfecta (OI). A complex structural variant, including deletion and duplication in COL1A2, was resolved by long-read genome sequencing in a patient with progressively deforming OI, characterized by multiple fractures and short stature.

This thesis has contributed to the field by broadening the genetic and phenotypic understanding of several congenital skeletal disorders. Two genes previously not associated with human phenotype, TOMM7 and RAB34, were described. Furthermore, a genetic cause was identified for the previously unresolved Al-Gazali skeletal dysplasia. Genome sequencing serves as a first-tier research tool for identifying novel candidate genes and variants; however, linking these variants to specific diseases depends on a range of factors, including knowledge of gene and protein function and detailed phenotypic characterization of patient groups.

List of scientific papers

I. A hypomorphic variant in the translocase of the outer mitochondrial membrane complex subunit TOMM7 causes short stature and developmental delay. Young C, Batkovskyte D, Kitamura M, Shvedova M, Mihara Y, Akiba J, Zhou W, Hammarsjö A, Nishimura G, Yatsuga S, Grigelioniene G, Kobayashi T. HGG Advances. 2022 Oct 4;4(1):100148. doi: 10.1016/j.xhgg.2022.100148. PMID: 36299998.
https://doi.org/10.1016/j.xhgg.2022.100148

II. Al-Gazali skeletal dysplasia constitutes the lethal end of ADAMTSL2-related disorders. Batkovskyte D, McKenzie F, Taylan F, Simsek-Kiper PO, Nikkel SM, Ohashi H, Stevenson RE, Ha T, Cavalcanti DP, Miyahara H, Skinner SA, Aguirre MA, Akçören Z, Utine GE, Chiu T, Shimizu K, Hammarsjö A, Boduroglu K, Moore HW, Louie RJ, Arts P, Merrihew AN, Babic M, Jackson MR, Papadogiannakis N, Lindstrand A, Nordgren A, Barnett CP, Scott HS, Chagin AS, Nishimura G, Grigelioniene G. Journal of Bone and Mineral Research. 2023 May;38(5):692-706. doi: 10.1002/jbmr.4799. Epub 2023 Mar 27. PMID: 36896612.
https://doi.org/10.1002/jbmr.4799

III. Compound heterozygous variants in RAB34 in a rare skeletal ciliopathy syndrome. Batkovskyte D, Komatsu M, Hammarsjö A, Pooh R, Shimokawa O, Ikegawa S, Grigelioniene G, Nishimura G, Yamada T. Clinical Genetics. 2024 Jan;105(1):87-91. doi: 10.1111/cge.14419. Epub 2023 Aug 24. PMID: 37619988.
https://doi.org/10.1111/cge.14419

IV. Structural variants in COL1A1 and COL1A2 in Osteogenesis Imperfecta. Batkovskyte D, Swolin-Eide D, Hammarsjö A, Bilgrav Sæther K, Thunström S, Lundin J, Eisfeldt J, Lindstrand A, Nordgren A, Åström E, Grigelioniene G. 2024. [Manuscript]