It Takes Brains: Germline and Somatic Mutations in Neurodevelopmental Disorders
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CitationD'Gama, Alissa Maria. 2016. It Takes Brains: Germline and Somatic Mutations in Neurodevelopmental Disorders. Doctoral dissertation, Harvard University, Graduate School of Arts & Sciences.
AbstractThe human brain can be affected by many diseases during its development, and human genetics studies can illuminate the genetic etiology of these diseases, which is critical for understanding disease pathophysiology, improving diagnoses, and developing effective therapies. In this thesis, I study genetic factors underlying neurodevelopmental disorders, focusing on the intractable epilepsy syndromes focal cortical dysplasia (FCD) and hemimegalencephaly (HME) and on autism spectrum disorder (ASD). My work investigates the role of both germline mutations, which are present in all cells of an affected individual, and somatic, or post-zygotic, mutations, which are present in only a subset of cells of an affected individual and frequently are undetectable in blood DNA.
FCD and HME are associated with intractable epilepsy, and show a small cortical region (FCD) or an entire cortical hemisphere (HME) that is radiographically and histologically abnormal, suggesting causation by somatic mutations. Our work and others have implicated mammalian target of rapamycin (mTOR) pathway mutations in these disorders. Studying 83 patients with FCD or HME using deep sequencing, we show that FCD and HME are caused by mutations that activate the mTOR pathway, and we expand the allelic and locus heterogeneity of these disorders, implicating mutations in DEPDC5 in HME and sporadic FCD and in TSC2 in HME. Overall, we identify pathogenic mutations, mostly somatic, in 22 patients with FCD or HME, representing almost half for whom brain tissue was available. We show for both FCD and HME that indistinguishable radiologic and histologic lesions can be caused by multiple genetic mechanisms, including somatic activating point mutations in AKT3, MTOR, and PIK3CA and germline loss-of-function mutations in DEPDC5 and TSC2, usually with somatic loss-of-function mutations in the second allele of the same gene limited to the lesion. We also show that mutations in the same gene, and in some cases the same mutant allele, can cause a spectrum of phenotypes, from FCD to HME to bilateral brain overgrowth, likely reflecting both the developmental time window and progenitor cell type in which the mutation occurred. Single cell studies show that the mutations are enriched in specific cell types, and how the cell types involved reflect the progenitor cell type in which the mutation occurred.
Single nucleotide variants (SNVs), particularly loss-of-function mutations, are also significant contributors to the risk of autism spectrum disorder (ASD), which is characterized by deficits in social interaction and communication and restricted and repetitive behaviors, interests, or activities. Compared to FCD and HME, ASD is a relatively common neurodevelopmental disorder with greater genetic heterogeneity. We report the first deep sequencing study of 55 postmortem ASD brains for SNVs in 78 ASD candidate genes. Remarkably, even without parental samples, we find more ASD brains with mutations that are protein-altering, deleterious, or loss-of-function compared to controls, with recurrent deleterious mutations in well-known ASD genes like SCN2A, suggesting these mutations contribute to ASD risk. In six cases, the identified mutations and medical records suggest syndromic ASD diagnoses. Two ASD cases and one Fragile X premutation case show deleterious somatic point mutations in ASD genes, providing evidence that somatic mutations occur in ASD cases, and supporting a model in which a combination of germline and/or somatic mutations may contribute to ASD risk on a case-by-case basis. As for FCD and HME, our results suggest that ASD pathogenesis can involve interactions between somatic and germline mutations in some cases, emphasizing how the developmental history of the human brain modifies the germline genome.
Taken together, these studies show that different combinations of germline and somatic mutations contribute to both rare and common neurodevelopmental disorders, and that the time and place a mutation occurs is critical for determining its consequences in the human brain. We also demonstrate the utility of deep sequencing to discover somatic mutations, which may contribute to many other neurodevelopmental and neuropsychiatric diseases.
Citable link to this pagehttp://nrs.harvard.edu/urn-3:HUL.InstRepos:33493415
- FAS Theses and Dissertations 
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