Transcriptome analysis of MBD5-associated neurodevelopmental disorder (MAND) neural progenitor cells reveals dysregulation of autism-associated genes

Sureni V Mullegama,Toshihiko Ezashi,Sarah H Elsea,Yuchen Tian,Stephen R Williams,Jeffrey W Innis,Ying Yang,Steven D Klein,Julian A Martinez-Agosto,Chad Haldeman-Englert,Frank J Probst

doi:10.1038/s41598-021-90798-z

Abstract

MBD5-associated neurodevelopmental disorder (MAND) is an autism spectrum disorder (ASD) characterized by intellectual disability, motor delay, speech impairment and behavioral problems; however, the biological role of methyl-CpG-binding domain 5, MBD5, in neurodevelopment and ASD remains largely undefined. Hence, we created neural progenitor cells (NPC) derived from individuals with chromosome 2q23.1 deletion and conducted RNA-seq to identify differentially expressed genes (DEGs) and the biological processes and pathways altered in MAND. Primary skin fibroblasts from three unrelated individuals with MAND and four unrelated controls were converted into induced pluripotent stem cell (iPSC) lines, followed by directed differentiation of iPSC to NPC. Transcriptome analysis of MAND NPC revealed 468 DEGs (q < 0.05), including 20 ASD-associated genes. Comparison of DEGs in MAND with SFARI syndromic autism genes revealed a striking significant overlap in biological processes commonly altered in neurodevelopmental phenotypes, with TGFβ, Hippo signaling, DNA replication, and cell cycle among the top enriched pathways. Overall, these transcriptome deviations provide potential connections to the overlapping neurocognitive and neuropsychiatric phenotypes associated with key high-risk ASD genes, including chromatin modifiers and epigenetic modulators, that play significant roles in these disease states.

Highlights

Autism spectrum disorder (ASD) is an encompassing term that describes neurodevelopmental disorders that have common deficits in communication and social interactions, accompanied by stereotyped behaviors and restricted interest
The utilization of chromosomal microarray (CMA) led to the identification of MBD5-associated neurodevelopmental disorder (MAND, MIM 156200), which is an autism spectrum disorder (ASD) characterized by intellectual disability, motor delay, severe speech impairment, and behavioral p roblems[5]
We generated and characterized induced pluripotent stem cell (iPSC) and neural progenitor cells (NPC) that were derived from MAND (2q23.1 deletion syndrome) patients with overlapping phenotypes of ID and autism

Summary

Introduction

Autism spectrum disorder (ASD) is an encompassing term that describes neurodevelopmental disorders that have common deficits in communication and social interactions, accompanied by stereotyped behaviors and restricted interest. MAND serves as an umbrella term that encompasses 2q23.1 deletion syndrome, MBD5 variant cases, and 2q23.1 duplications[5] The conditions in this group of disorders have copy number variations or pathogenic sequence variants in the methyl-binding domain 5 gene (MBD5, MIM 611472), which is responsible for the majority of the phenotypes present in MAND6,7. Next-generation RNA-sequencing (RNA-seq) has been utilized in numerous studies and is a valid tool to identify therapeutic targets, biomarkers, pathways, and genes associated with ASD modeled by stem cell-derived human neurons[16,17,18,19]. We explore the underpinnings of the neurodevelopmental phenotype of MAND by creating neural progenitor cells (NPC) derived from patients with 2q23.1 deletion syndrome, followed by RNA-seq to identify the contributing molecular pathways. Altered genes significantly overlap with ASD-associated genes, providing further insight into mechanisms underlying ASD by identifying shared network perturbances caused by the genetically penetrant MAND-associated 2q23.1 deletion

Methods

Results

Conclusion