Elucidating the pathogenic mechanisms by which KAT6A mutations alter human in vitro neurodevelopment

About This Grant

PROJECT SUMMARY/ABSTRACT (Limit: 30 lines of text) Chromatinopathies, defined as developmental disorders caused by germline mutations in epigenetic genes, present a significant challenge for millions of Americans affected by these 179 rare diseases since ~94% of all rare diseases do not have treatments available -- highlighting a huge patient population with unmet needs. Our lab found heterozygous nonsense mutations (i.e. truncating) in the KAT6A gene cause a Chromatinopathy called Arboleda-Tham Syndrome (ARTHS) that is also referred to as a rare neurodevelopmental disorder. Although neurological deficits are always observed in ARTHS, the pathogenic mechanisms underlying these phenotypes are not understood and nothing is known about KAT6A’s functions in human neurodevelopment (ND). KAT6A is the catalytic subunit of a histone acetyltransferase (HAT) complex that acetylates histones. My preprint study of ARTHS Cerebral Organoids (COs) describes the consequences of KAT6A deficiency during in vitro human ND. We show ARTHS COs are delayed in repressing the expression of pluripotency/cell cycle transcription factors (TFs) during neural differentiation compared to controls -- leading to an overabundance of cycling neural progenitor cell (NPC) markers in genes upregulated in ARTHS COs. My preliminary data also shows ARTHS neurons suffer from phenotypic defects like aberrant synapse morphology and metabolic dysfunction compared to controls. We propose a research strategy to uncover the mechanisms underpinning our observations in neural models derived from ARTHS patients to elucidate the functional consequences of KAT6A deficiency during human in vitro ND. I hypothesize during neuronal differentiation, truncating KAT6A mutations cause reduced KAT6A protein or HAT activity -- leading to altered gene regulation at cell cycle and ND-related genes via remodeling of histone acetylation and TF binding. I also hypothesize, independent of these gene regulatory consequences, the loss of KAT6A function negatively affects NPC cell fate & neuron health through altered proliferation and mitochondrial dynamics, respectively. I will differentiate rare induced pluripotent stem cells harboring truncating KAT6A mutations and matched controls into NPCs and neurons. In Aim 1, I will apply complementary functional genomics assays to these cells & perform vertical data integration to identify the precise mechanisms by which KAT6A deficiency causes aberrant changes in transcription and chromatin remodeling via perturbations to the histone acetylation and TF landscape. In Aim 2, using these cells and KAT6A inhibitors, I will quantify changes in select cellular phenotypes using high throughput methods to deconvolute the negative phenotypic consequences of losing KAT6A function during neuronal differentiation. Together, these aims utilize orthogonal approaches in human stem cells to identify the molecular and cellular mechanisms underpinning KAT6A’s function in human in vitro ND and ARTHS neuropathology.