run_metadata: 19491
This data as json
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| 19491 | ERR14208825 | ERX13611045 | ERS22979757 | ERP167299 | PRJEB83709 | YTHDF2 and ASD DM | 3296f78e-e1c0-43ea-968c-53fe04e67615 | Other | Among autistic individuals a subphenotype of disproportionate megalencephaly ASD DM seen at three years of age is associated with co occurring intellectual disability and poorer prognoses later in life. However many of the genes contributing to ASD DM have yet to be delineated. In this study we identified additional ASD DM candidate genes with the aim to better define the genetic etiology of this subphenotype of autism. We expanded the previously studied sample size of ASD DM individuals ten fold by including probands from the Autism Phenome Project and Simons Simplex Collection totaling 766 autistic individuals meeting the criteria for megalencephaly or macrocephaly and revealing 154 candidate ASD DM genes harboring de novo protein impacting variants. Our findings include fourteen high confidence autism genes and seven genes previously associated with DM. Five impacted genes have previously been associated with both autism and DM including CHD8 and PTEN. By performing functional network analysis we expanded to additional candidate genes including one previously implicated in ASD DM PIK3CA as well as 184 additional genes previously implicated in ASD or DM alone. Using zebrafish we modeled a de novo tandem duplication impacting YTHDF2 encoding an N6 methyladenosine m6A mRNA reader in an ASD DM proband. Testing zebrafish CRISPR knockdown led to reduced head/brain size while overexpressing YTHDF2 resulted in increased head and brain size matching that of the proband. Single cell transcriptomes of YTHDF2 gain of function larvae point to reduced expression of Fragile X syndrome associated FMRP target genes globally and in the developing brain providing insight into the mechanism underlying autistic phenotypes. We additionally discovered a variant impacting a different gene encoding an m6A reader YTHDC1 in our ASD DM cohort. Though we highlight only two cases to date our study provides support for the m6A RNA modification pathway as potentially contributing to this severe form of autism. | ENA FIRST PUBLIC:2025 02 01|ENA LAST UPDATE:2025 02 01 | Single cell RNA sequencing of zebrafish heads | YTHDF2 2 sample | SAMEA117628619 | UNIVERSITY OF CALIFORNIA - DAVIS | ENA first public:2025 02 01|INSDC center name:UNIVERSITY OF CALIFORNIA DAVIS|INSDC status:public|Submitter Id:Sample 016|collection date:2022 08 07|common name:zebrafish|dev stage:72 hpf|geographic location country and/or sea:USA|sample name:Sample 016|scientific name:Danio rerio | Raw reads: YTHDF2 2 sample | webin reads YTHDF2 2 sample | unspecified | RNA-Seq | TRANSCRIPTOMIC SINGLE CELL | cDNA | SINGLE | ILLUMINA | Illumina NovaSeq 6000 | ERP167299 | Raw reads: YTHDF2 2 sample | ENA FIRST PUBLIC:2025 02 01|ENA LAST UPDATE:2025 02 01 | D12.bam | bam | 626993184.0 | 7599502.0 | webin reads YTHDF2 2 sample | 0:82.50 | A:182701108;C:91008174;G:172822143;T:180459253;N:2506 | 82 | 182701108 | 91008174 | 172822143 | 180459253 | 2506 | ERX13611045 | ERS22979757 | ERA31123307 | UNIVERSITY OF CALIFORNIA - DAVIS|European Nucleotide Archive | UNIVERSITY OF CALIFORNIA - DAVIS | B | usable mapping rate | illumina | novaseq_era | unknown | cdna_unspecified | unknown | sc | single_cell_generic | generic-scrnaseq-only | United States | 2025-02-01 | Larval | Larval | Head | Nervous System |