Investigation of de novo variants and copy number variantions in autism spectrum disorder etiology

Author(s)

Eduarda Morgana da Silva Montenegro Malaguti de Souza

• Document type: Doctoral Thesis
• Press: São Paulo.
• Institution: Universidade de São Paulo (USP). Instituto de Biociências (IBIOC/SB)
• Defense date: 2020-08-21

Examining board members

Maria Rita dos Santos e Passos Bueno; Alexander Augusto de Lima Jorge; Taiza Stumpp Teixeira; Maria Dulcetti Vibranovski

• Advisor: Maria Rita dos Santos e Passos Bueno

Abstract

Autism Spectrum Disorder (ASD) is a heterogeneous and complex genetic disorder that includes conditions with clinical manifestation in early childhood, characterized by persistent difficult in social/communication skills, besides restricted interests, and repetitive behavior. Large genomic studies inferred the relevance of single nucleotide variants (SNVs), small insertions and deletions (Indels), and copy number variants (CNVs) to ASD etiology. Additionally, ASD patients are enhanced for de novo mutations (DNMs) compared to control populations, for both SNVs/Indels and CNVs, being these alterations analyses powerful approaches to gene discovery and validation, together with analysis of large genomic databases of neurodevelopmental disorders (NDD). Therefore, our first main goal was to characterize rare copy number variations (CNVs) and exonic de novo variants (DNVs) in ASD Brazilian cohorts, the first composed by 30 trios (chapter II), and the second wherein only CNVs were analyzed, composed by 144 ASD individuals (chapter III). Also, aiming to elucidate these findings role to ASD etiology, we evaluated them in two large databases analysis of more than 20,000 and 10,000 NDD individuals, respectively. The first cohort analysis supported three pathogenic CNVs: 1q21.1, 4q35, and 17p13.3; and four pathogenic DNVS, being one of them identified in a novel ASD candidate gene: PRPF8. Regarding the second cohort of 144 individuals, we identified three deletions and one duplication in ASD candidate genes highly intolerant to loss of function: NR3C2, DPP6, CDH8/CDH11, and CSMD1. Besides CNVs affecting two potential ASD candidate genes: FGF2 and PTPRN2. Finally, 18% of individuals carrying a likely pathogenic or pathogenic CNV, also carried a second rare CNV, reinforcing the oligogenic model relevance for ASD. Our second main goal was to evaluate DNVs in 33 multigenerational families (231 individuals; chapter IV), to provide new insights into potential DNVs pathogenicity across generations. We determined for the first time, DNVs rate in parents, which was lower than probands and similar to controls. We observed a higher proportion of parents over 30 years old compared to grandparents, a positive correlation between DNVs and fathers age, and a predominantly paternal origin of DNVs in both generations. Intriguingly, besides the small cohort, we observed a segregation bias in the paternal transmission of pathogenic DNVs, which was not observed in the transmission of the maternal DNV, suggesting the selection of these variants in paternal gametes. Also, we evidenced ZNF536, MSL2 and HDAC9, as possible candidate genes to ASD. Our unexplored Brazilian population with tetra-hybrid composition was valuable to validate previous candidate genes and to identify novel ones. As we have shown, this was possible due the availability of genomic data from large cohorts, such as MSSNG, SSC, DDD and NDD big cohort\'s papers. To our knowledge, this is the first study showing DNVs in parents, and despite our small sample, we were able to observe DNVs rates difference, as well as the segregation bias in the paternal transmission of pathogenic DNVs. Finally, the study delineation led us to support potential novel candidate genes to ASD: PRPF8, FGF2, PTPRN2, ZNF536, MSL2, e HDAC9. (AU)

• FAPESP's process: 17/05824-2 - Investigation of parents de novo risk variants in Autism Spectrum Disorder (ASD)
• Grantee: Eduarda Morgana da Silva Montenegro Malaguti de Souza
• Support Opportunities: Scholarships in Brazil - Doctorate