Topology of cortical and thalamic gene expression changes in autism

  • Awarded: 2022
  • Award Type: Targeted: Autism BrainNet Analysis
  • Award #: 957585

In work that began nearly 15 years ago, Daniel Geschwind and collaborators identified a shared pattern of transcriptomic and epigenetic dysregulation in postmortem brain tissue of people with autism spectrum disorder (ASD)1. This was observed in approximately two-thirds to three-fourths of ASD samples, and such findings have been validated and refined over the ensuing decade2-6. Thus, there is a convergent molecular pathology in the cortex of people with ASD reflected by transcriptomic and epigenetic dysregulation7 that in turn reflects decreases in neuronal and synaptic signaling genes, particularly within superficial layer neurons within the cortex, as well as increases in activated microglia and reactive astrocytes.

Geschwind, in collaboration with Michael Gandal and Dorothy Schafer’s laboratories, propose to substantially extend and refine these observations. In particular, they plan to analyze the topology of molecular changes across cortical regions within different neuronal subtypes that compose local and long-distance intracortical circuits and their respective thalamic nuclei. It is remarkable that it is currently unknown whether there are any transcriptomic or cellular changes in the thalamus in people with ASD — the current project proposes to begin to fill this gap. Moreover, the mechanisms and anatomical relationships linking activated glia and neuronal dysregulation are unknown.

The investigators plan to rigorously apply bulk RNAseq and multiple single-cell genomic technologies in several cortical and thalamic regions from 30 postmortem samples from individuals with ASD and 30 samples from neurotypical individuals (donated to the Autism BrainNet collection). The methodologies that will be used include snMulti-omics (single nuclei RNA sequencing and Assay for Transposase-Accessible Chromatin using Sequencing [ATAC-seq]), long-read PacBio sequencing to differentiate isoforms (IsoSeq) and MERFISH (multiplexed error-robust fluorescence in situ hybridization) in order to interrogate: (1) the correspondence in transcriptomic changes within connected thalamo-cortical circuits, (2) the transcription factor regulatory networks that lead to cell-type specific disease-associated signatures, (3) the disease-associated changes in isoform expression and usage, which carries a significant proportion of disease signature, and (4) the spatial topology linking activated glial states with disrupted neuronal signatures within specific laminae.

These studies will have broad implications for understanding pathophysiological mechanisms underlying ASD and will generate high-quality, large data sets for harmonization with others to help create more comprehensive maps of molecular, cellular and circuit dysfunction in ASD.


  1. Voineagu I. et al. Nature. 474, 380-384 (2011) PubMed
  2. Parikshak N.N. et al. Nature 540, 423-427 (2016) PubMed
  3. Wong C.C.Y. et al. Hum. Mol. Genet. 28, 2201-2211 (2019) PubMed
  4. Gandal M.J. et al. Science 362, eaat8127 (2018) PubMed
  5. Gandal M.J. et al. Nature 611, 532-539 (2022) PubMed
  6. Gandal M.J. et al. Science 359, 693-697 (2018) PubMed
  7. Ramaswami G. et al. Nat. Commun. 11, 4873 (2020) PubMed
Subscribe to our newsletter and receive SFARI funding announcements and news