7 research outputs found
Proteomic analysis of a compatible interaction between sugarcane and Sporisorium scitamineum
No full textSmut caused by Sporisorium scitamineum is one of the important diseases of sugarcane with global significance. Despite the intriguing nature of sugarcane - S. scitamineum interaction, several pertinent aspects remain unexplored. This study investigates the proteome level alterations occurring in the meristem of a S. scitamineum infected susceptible sugarcane cultivar at whip emergence stage. Differentially abundant proteins were identified by 2-DE coupled with MALDI-TOF/TOF-MS. Comprehensively, 53 sugarcane proteins identified were related to defense, stress, metabolism, protein folding, energy and cell division; in addition, a putative effector of S. scitamineum - chorismate mutase was identified. Transcript expression vis-à-vis the activity of phenylalanine ammonia lyase were relatively higher in the infected meristem. Abundance of seven candidate proteins in 2D gel profiles was in correlation with its corresponding transcript expression levels as validated by qRT-PCR. Furthermore, this study has opened up new perspectives on the interaction between sugarcane and S. scitamineum. This article is protected by copyright. All rights reserved
Expanding the genetic and phenotypic spectrum of skeletal dysplasias
No full textSkeletal dysplasias constitute a large and heterogeneous group of disorders, many causing disabilities with profound effects on the quality of life of the affected individuals and their families. Each individual skeletal dysplasia is rare, however, as more than 450 different disorders have been described, skeletal dysplasias as a group affect approximately three in 10 000 individuals. The age of onset for skeletal dysplasias ranges from prenatal to adult, but most of the affected individuals are diagnosed in childhood. Skeletal dysplasias mainly affect bone and cartilage, but symptoms may involve other organs, such as sensorineural hearing loss in Stickler syndrome, nephronophthisis in Sensenbrenner syndrome, and structural heart abnormalities in acromicric dysplasia. Therefore, most skeletal dysplasias can be defined as syndromes with a significant skeletal involvement.Clinical diagnosis of skeletal dysplasias is based on meticulous phenotypic characterization, skeletal radiography (for pattern recognition) and genetic testing. Molecular diagnostics has improved significantly by massively parallel sequencing (MPS) technologies, such as whole exome and genome sequencing. However, even after extensive clinical phenotyping and advanced molecular analyses, many patients with congenital skeletal disorders still lack molecular diagnoses and many clinical entities are not well-characterized regarding their natural course and complications. Molecular diagnosis is important since it gives information about prognosis and recurrence risk, as well as, in some cases possibilities to offer targeted treatment, participation in clinical trials, and tailored medical follow-up. This thesis focuses on gene discovery, studies of previously clinically defined skeletal dysplasias with unknown genetic background and aims to improve the molecular analyses for patients with diagnoses which are difficult to solve.In study I, we identify a novel pathogenic variant in ALG9, as the cause of a lethal skeletal syndrome in two families. In study II, we show that a variant in COL2A1 causes spondyloepiphyseal dysplasia type Stanescu. Study III shows that pathogenic variants in BMPER cause ischiospinal dysostosis (ISD), which is allelic to diaphanospondylodysostosis. In study IV, we describe a novel skeletal ciliopathy in four individuals with spondylometaphyseal dysplasia and thorax hypoplasia caused by pathogenic variants in KIAA0753. Finally, study V represents a cohort of 24 unrelated patients with skeletal ciliopathies, where we solve the genetic diagnoses in 83% of them. Here, we show two rare intronic variants and two exonic synonymous variants leading to aberrant splicing, which indicates that extended RNA studies are necessary to improve molecular diagnostics in some cases.Altogether, the results of these studies expand the genetic and phenotypic spectrum of skeletal dysplasias and demonstrate that MPS technology in combination with meticulous phenotyping is a powerful method to discover disease-causing variants in patients with congenital skeletal disorders.List of scientific papersI. A novel phenotype in N-glycosylation disorders: Gillessen-Kaesbach-Nishimura skeletal dysplasia due to pathogenic variants in ALG9. Tham E, Eklund EA, Hammarsjö A, Bengtson P, Geiberger S, Lagerstedt-Robinson K, Malmgren H, Nilsson D, Grigelionis G, Conner P, Lindgren P, Lindstrand A, Wedell A, Albåge M, Zielinska K, Nordgren A, Papadogiannakis N, Nishimura G, Grigelioniene G. Eur J Hum Genet. 2016 Feb;24(2):198-207. https://doi.org/10.1038/ejhg.2015.91 II. Pathogenic variant in the COL2A1 gene is associated with Spondyloepiphyseal dysplasia type Stanescu. Hammarsjö A, Nordgren A, Lagerstedt-Robinson K, Malmgren H, Nilsson D, Wedrén S, Nordenskjöld M, Nishimura G, Grigelioniene G. Am J Med Genet A. 2016 Jan;170A(1):266-9. https://doi.org/10.1002/ajmg.a.37387 III. Extending the phenotype of BMPER-related skeletal dysplasias to ischiospinal dysostosis. Kuchinskaya E, Grigelioniene G, Hammarsjö A, Lee HR, Högberg L, Grigelionis G, Kim OH, Nishimura G, Cho TJ. Orphanet J Rare Dis. 2016 Jan 4;11:1. https://doi.org/10.1186/s13023-015-0380-0 IV. Novel KIAA0753 mutations extend the phenotype of skeletal ciliopathies. Hammarsjö A, Wang Z, Vaz R, Taylan F, Sedghi M, Girisha KM, Chitayat D, Neethukrishna K, Shannon P, Godoy R, Gowrishankar K, Lindstrand A, Nasiri J, Baktashian M, Newton PT, Guo L, Hofmeister W, Pettersson M, Chagin AS, Nishimura G, Yan L, Matsumoto N, Nordgren A, Miyake N, Grigelioniene G, Ikegawa S. Sci Rep. 2017 Nov 14;7(1):15585. https://doi.org/10.1038/s41598-017-15442-1 V. Increased yield of genetic diagnoses in skeletal ciliopathies using massively parallel sequencing, structural variant and RNA analyses. Hammarsjö A, Pettersson M, Chitayat D, Handa A, Taylan F, Eisfeldt J, Lagerstedt-Robinson K, Nilsson D, Girisha KM, Conner P, Papadogiannakis N, Anderlid BM, Basel D, Furuya S, Ohashi H, Nayak SS, Horemuzova E, Millar K, Godoy R, Lin A, Fukuda N, Hyodo H, Korņejeva L, Shimizu K, Beleza- Meireles A, Chung B, Wirta V, Stranneheim H, Magnusson M, Wedell A, Nordgren A, Nishimura G, Lindstrand A, Grigelioniene G. [Submitted]</p
Novel KIAA0753 mutations extend the phenotype of skeletal ciliopathies
No full textAbstractThe skeletal ciliopathies are a heterogeneous group of disorders with a significant clinical and genetic variability and the main clinical features are thoracic hypoplasia and short tubular bones. To date, 25 genes have been identified in association with skeletal ciliopathies. Mutations in the KIAA0753 gene have recently been associated with Joubert syndrome (JBTS) and orofaciodigital (OFD) syndrome. We report biallelic pathogenic variants in KIAA0753 in four patients with short-rib type skeletal dysplasia. The manifestations in our patients are variable and ranging from fetal lethal to viable and moderate skeletal dysplasia with narrow thorax and abnormal metaphyses. We demonstrate that KIAA0753 is expressed in normal fetal human growth plate and show that the affected fetus, with a compound heterozygous frameshift and a nonsense mutation in KIAA0753, has an abnormal proliferative zone and a broad hypertrophic zone. The importance of KIAA0753 for normal skeletal development is further confirmed by our findings that zebrafish embryos homozygous for a nonsense mutation in kiaa0753 display altered cartilage patterning.</jats:p
Clinically relevant variants in a large cohort of Indian patients with Marfan syndrome and related disorders identified by next-generation sequencing
No full textAbstract: Marfan syndrome and related disorders are a group of heritable connective tissue disorders and share many clinical features that involve cardiovascular, skeletal, craniofacial, ocular, and cutaneous abnormalities. The majority of affected individuals have aortopathies associated with early mortality and morbidity. Implementation of targeted gene panel next-generation sequencing in these individuals is a powerful tool to obtain a genetic diagnosis. Here, we report on clinical and genetic spectrum of 53 families from India with a total of 83 patients who had a clinical diagnosis suggestive of Marfan syndrome or related disorders. We obtained a molecular diagnosis in 45/53 (85%) index patients, in which 36/53 (68%) had rare variants in FBN1 (Marfan syndrome; 63 patients in total), seven (13.3%) in TGFBR1/TGFBR2 (Loeys-Dietz syndrome; nine patients in total) and two patients (3.7%) in SKI (Shprintzen-Goldberg syndrome). 21 of 41 rare variants (51.2%) were novel. We did not detect a disease-associated variant in 8 (15%) index patients, and none of them met the Ghent Marfan diagnostic criteria. We found the homozygous FBN1 variant p.(Arg954His) in a boy with typical features of Marfan syndrome. Our study is the first reporting on the spectrum of variants in FBN1, TGFBR1, TGFBR2, and SKI in Indian individuals
Hypomorphic Mutations in TONSL Cause SPONASTRIME Dysplasia
No full textSPONASTRIME dysplasia is a rare, recessive skeletal dysplasia characterized by short stature, facial dysmorphism, and aberrant radiographic findings of the spine and long bone metaphysis. No causative genetic alterations for SPONASTRIME dysplasia have yet been determined. Using whole-exome sequencing (WES), we identified bi-allelic TONSL mutations in 10 of 13 individuals with SPONASTRIME dysplasia. TONSL is a multi-domain scaffold protein that interacts with DNA replication and repair factors and which plays critical roles in resistance to replication stress and the maintenance of genome integrity. We show here that cellular defects in dermal fibroblasts from affected individuals are complemented by the expression of wild-type TONSL. In addition, in vitro cell-based assays and in silico analyses of TONSL structure support the pathogenicity of those TONSL variants. Intriguingly, a knock-in (KI) Tonsl mouse model leads to embryonic lethality, implying the physiological importance of TONSL. Overall, these findings indicate that genetic variants resulting in reduced function of TONSL cause SPONASTRIME dysplasia and highlight the importance of TONSL in embryonic development and postnatal growth. © 2019 American Society of Human Genetic11Nsciescopu
Clinical and genetic spectrum of 104 Indian families with central nervous system white matter abnormalities
No full textGenetic disorders with predominant central nervous system white matter abnormalities (CNS WMAs), also called leukodystrophies, are heterogeneous entities. We ascertained 117 individuals with CNS WMAs from 104 unrelated families. Targeted genetic testing was carried out in 16 families and 13 of them received a diagnosis. Chromosomal microarray (CMA) was performed for three families and one received a diagnosis. Mendeliome sequencing was used for testing 11 families and all received a diagnosis. Whole exome sequencing (WES) was performed in 80 families and was diagnostic in 52 (65%). Singleton WES was diagnostic for 50/75 (66.67%) families. Overall, genetic diagnoses were obtained in 77 families (74.03%). Twenty‐two of 47 distinct disorders observed in this cohort have not been reported in Indian individuals previously. Notably, disorders of nuclear mitochondrial pathology were most frequent (9 disorders in 20 families). Thirty‐seven of 75 (49.33%) disease‐causing variants are novel. To sum up, the present cohort describes the phenotypic and genotypic spectrum of genetic disorders with CNS WMAs in our population. It demonstrates WES, especially singleton WES, as an efficient tool in the diagnosis of these heterogeneous entities. It also highlights possible founder events and recurrent disease‐causing variants in our population and their implications on the testing strategy.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/170794/1/cge14037.pdfhttp://deepblue.lib.umich.edu/bitstream/2027.42/170794/2/cge14037_am.pd
