Non-autonomous regulation of interneuron fate, position, and survival by excitatory neurons during cortical development

The National Institute of Neurological Disorders and Stroke (NINDS), part of the Department of Health and Human Services National Institutes of Health, awarded $153,560 to the Broad Institute, Inc. (doing business as Broad Institute of MIT and Harvard) on December 1, 2026, under the Extramural Research Programs in the Neurosciences and Neurological Disorders program (CFDA 93.853).

The award funds research examining how excitatory neurons regulate interneuron fate, position, and survival during cortical development. The work tests the hypothesis that distinct excitatory neuron populations influence interneuron development at discrete developmental stages using cre-conditional knockout approaches, single-nucleus RNA-seq, and spatial transcriptomics. In Aim 1, the research knocks out TBR1 or SATB2 transcription factors in early-born transient excitatory populations—Cajal-Retzius and subplate neurons—to assess their role in regulating interneuron fate and positioning during migration. In Aim 2, the work knocks out TBR1 or SATB2 in layer-specific pyramidal neurons to test how changes in pyramidal neuron identity affect interneuron subtype fate and position, with investigation of whether changes in subtype proportions relate to changes in cell survival.

The research addresses how disruptions in excitatory-inhibitory balance contribute to neurodevelopmental disorders such as autism spectrum disorder.

Period of performance runs from December 1, 2026, through January 31, 2029. Work is performed in Cambridge, Massachusetts.

Abstract

Excitatory and inhibitory neurons establish precise patterns of connectivity during cortical development, and disruptions in excitatory-inhibitory balance are a hallmark of neurodevelopmental disorders such as autism spectrum disorder (ASD). Interneurons, which mediate inhibition in the cortex, are initially specified into a few cardinal classes during embryogenesis and are subsequently refined into dozens of transcriptionally distinct 'definitive' subtypes postnatally through a poorly understood process of fate refinement. Recent evidence suggests that non-autonomous cues from excitatory neurons play a key role in shaping cortical interneuron fate, position, and survival during embryonic and postnatal development-highlighting a critical window in which local interactions may influence long-term circuit organization. The primary goal of this nrsa F32 proposal is to define the spatial and temporal contributions of distinct excitatory neuron populations to interneuron development. I will focus on TBR1 and SATB2, two transcription factors associated with ASD that regulate excitatory neuron identity in the cortex. Using CRE-conditional knockout approaches, i will test the hypothesis that excitatory neuron subtypes influence interneurons at discrete developmental stages leveraging single-nucleus RNA-SEQ and spatial transcriptomics. In aim 1, i will knock out TBR1 or SATB2 in early-born transient excitatory populations-cajal-retzius and subplate neurons- to assess their role in regulating interneuron fate and positioning during their migration. In aim 2, i will knock out TBR1 or SATB2 in layer-specific pyramidal neurons to test how changes in pyramidal neuron identity affects interneuron subtype fate and position. I will determine whether changes in subtype proportions relate to changes in cell survival by repeating key experiments under a BAX loss-of-function background, or cell fate, leveraging waddington optimal transport and RNA velocity analysis to assess shifts in developmental trajectories. This work will be carried out in the laboratory of DR. Gord fishell at the broad institute-an outstanding training environment with deep expertise in developmental neuroscience. By linking subtype- and stage-specific excitatory-inhibitory interactions to genes implicated in ASD and ID, this work will advance our understanding of how early developmental perturbations alter circuit assembly and potentially contribute to neurodevelopmental disorders.