The Simons Foundation Autism Research Initiative (SFARI) is pleased to announce that it intends to fund five collaborative groups in response to the 2020 SFARI Collaboration on Sex Differences in Autism request for applications (RFA).

SFARI Collaborations are a new funding mechanism that provide substantive and stable funding support to multidisciplinary teams of investigators tackling critical issues in the autism research field. Collaborations are led by a director who oversees interdisciplinary, synergistic research efforts across multiple laboratories. Investigative groups within a Collaboration all focus on the same conceptually unified topic but incorporate different scientific disciplines, multiple levels of analysis and robust resource-sharing practices and data-sharing infrastructure.

The SFARI Collaboration on Sex Differences in Autism RFA opened to applicants in January 2020. The five collaborative groups who have been awarded funding were selected from a large competitive pool of applications and are expected to begin their studies in the summer and fall 2021. The projects are given funding for two to four years, with the opportunity of extending it based on the progress made.

The topic of sex-specific differences in autism spectrum disorder (ASD) was chosen for this SFARI Collaboration RFA because it poses important and fundamental questions about the biology of autism that will require large-scale, synergistic efforts to be answered. Although females may be underdiagnosed because of differences in presentation and/or diagnostic bias, there appears to be a substantial and consistent male bias in ASD prevalence that reflects differences between the sexes in susceptibility^1–4. Among many potential explanations, female resilience could reflect a genetic buffering effect^{2, 5–7} or differences in hormone exposure⁸. Either of these possibilities could result in differences in cellular and/or circuit function between the sexes^9–12. Considering the rapidly expanding knowledge of genetic and other risk factors in ASD, the stage seems set for significant advances in enhancing our understanding of the impact of sex on ASD risk and manifestations.

“There is growing recognition that many of the most pressing questions in autism research can only be addressed by taking a multidisciplinary approach,” says SFARI interim director John Spiro. “SFARI Collaborations provide the opportunity for leaders from different scientific disciplines, who use diverse methodologies and experimental systems, to work together on a common problem. Sharing data and insights early on in the research process will be key to accelerate progress towards the development of new therapies and support for individuals with autism and their families.

SFARI intends to provide approximately $28 million over the next four years to support these five collaborative groups. In total, more than 20 principal investigators and universities and research institutions are joining forces as part of these studies. The projects will use existing data and biospecimens from several autism cohorts and biobanks, including SPARK and Autism BrainNet, in addition to creating new datasets and resources that will be shared with the autism research community.

Diverse experimental approaches, including human genetic and phenotypic analyses, assays that involve a variety of model experimental systems (mice, voles, human stem cells and organoids), as well as molecular and hormonal studies that use human tissue (placental and postmortem brain tissue), will be used in an effort to identify key differences in gene, cell and circuit function, as well as prenatal factors, that account for the observed differential sensitivities of the two sexes to ASD.

“We are delighted to fund our first collaborative groups. We hope that findings from these large-scale studies will converge and allow us to gain robust insights into the question of sex differences in ASD, which has remained unanswered for quite some time now,” says Brigitta Gundersen, SFARI senior scientist who oversees this Collaboration funding mechanism.

The five collaborations that SFARI intends to fund are:

Project Title: The Autism Prenatal Sex Differences (APEX) study

Collaboration Director: Simon Baron-Cohen, Ph.D. (University of Cambridge)

Principal Investigators: Tal Biron-Shental, M.D. (Tel Aviv University), Lidia Gabis, M.D. (Sheba Medical Center), Daniel Geschwind, M.D., Ph.D. (University of California, Los Angeles), Alexander Heazell, M.B.ChB., Ph.D. (University of Manchester), Matthew Hurles, Ph.D. (Wellcome Sanger Institute), Madeline Lancaster, Ph.D. (Medical Research Council Laboratory of Molecular Biology), Hilary Martin, Ph.D.(Wellcome Sanger Institute), Jonathan Mill, Ph.D. (University of Exeter), David Rowitch, M.D., Ph.D.(University of Cambridge; University of California, San Francisco) and Deepak P. Srivastava, Ph.D. (King’s College London)

The overarching question that Simon Baron-Cohen and his collaborators are interested in is: How do genetics, prenatal sex steroids and the placenta contribute to sex differences in ASD? They plan to address this question by investigating how: (i) common and rare genetic variants contribute to ASD differently in males and females, (ii) prenatal sex steroid exposure and placental factors contribute to ASD differently in males and females, (iii) prenatal sex steroids and genetics interact to differentially affect gene regulation and brain development in males and females with ASD. Studies will be performed using cellular models (neurons and organoids derived from induced pluripotent stem cells, iPSC), genetic and phenotypic data from ASD cohorts, placental tissue from pregnancies with a family history of ASD and postmortem brain tissue.

Project title: Genetic and molecular dissection of autism sex differences

Collaboration Director: Aravinda Chakravarti, Ph.D. (New York University School of Medicine)

Principal Investigators: Evan Eichler, Ph.D. (University of Washington; Howard Hughes Medical Institute), Tomasz Nowakowski, Ph.D. (University of California, San Francisco) and Huda Zoghbi, M.D. (Baylor College of Medicine; Texas Children’s Hospital; Howard Hughes Medical Institute)

Aravinda Chakravarti and his collaborators hypothesize that hormone-dependent gene regulation through enhancers can sex-bias the expression of ASD genes and early brain development. The experimental approach includes: (i) genome-wide tests of sequence variation with sex-biased frequency and/or transmission effects, with a focus on the X chromosome, (ii) the generation of transcriptional and open chromatin maps in the developing human cerebral cortex to identify sex-biased gene regulatory programs, (iii) the generation of transcriptional and open chromatin maps in male and female iPSC-derived neurons under hormonal challenge and (iv) functional assessments of candidate ASD variants in iPSC and mouse models. They plan to begin their work with a detailed case study of MECP2, the archetypal X-linked ASD risk gene, before performing more comprehensive analyses.

Project Title: Analysis of mechanisms underlying sex epistasis in autism

Collaboration Director: Joseph Dougherty, Ph.D. (Washington University in St. Louis)

Principal Investigators: Tychele Turner, Ph.D. (Washington University in St. Louis), Sven Sandin, Ph.D. (Icahn School of Medicine at Mount Sinai), Lauren Weiss, Ph.D. (University of California, San Francisco)

Joseph Dougherty and his collaborators propose an epistatic model whereby genetic risk and sex-based risk for ASD do not act independently of each other. To test this model, they plan to: (i) identify categories of genetic risk that interact with sex and models of epistasis that fit human data and (ii) comprehensively screen ASD-associated loci to identify functional alleles showing epistasis with sex. Studies will be performed using cellular models (iPSC-derived neurons), mouse models, genetic and phenotypic data from ASD cohorts, and postmortem brain tissue.

Project Title: Autism, sex differences and microglia

Collaboration Director: David C. Page, M.D. (Whitehead Institute; Massachusetts Institute of Technology; Howard Hughes Medical Institute)

Principal Investigators: Olivia Corradin, Ph.D. (Whitehead Institute), Nicole G. Coufal, M.D., Ph.D. (University of California, San Diego; Rady Children’s Hospital San Diego), and Christopher K. Glass, M.D., Ph.D. (University of California, San Diego)

David C. Page and his collaborators hypothesize that sex-biased and primate (or human)-specific expression of ASD-related genes in microglia will highlight pathways of pathogenic microglial dysfunction that contribute to ASD in both sexes. They plan to test this hypothesis by identifying sex differences in microglial gene expression, chromatin accessibility and enhancer activity across four species (human, macaque, marmoset and mouse).

Project Title: Anatomical, molecular and systems approaches to elucidate the mechanism of sex bias in autism

Collaboration Director: Stephan Sanders, B.M.B.S., Ph.D. (University of California, San Francisco)

Principal Investigators: David Anderson, Ph.D. (California Institute of Technology), Xin Jin, Ph.D. (Harvard University), Devanand Manoli, M.D., Ph.D. (University of California, San Francisco), Tomasz Nowakowski, Ph.D. (University of California, San Francisco), Nenad Sestan, M.D., Ph.D. (Yale University), Vikaas Sohal, M.D., Ph.D. (University of California, San Francisco), Jessica Tollkuhn, Ph.D. (Cold Spring Harbor Laboratory) and Donna Werling, Ph.D. (University of Wisconsin-Madison)

Stephan Sanders and his collaborators propose that interactions between robustly sex-differential cells in subcortical regions and neurons in the prefrontal cortex/striatum lead to ASD sex bias. To delineate this interaction, they plan to generate a map of sex-differential biology in the developing brain, use transcriptomic analyses to identify sex-differential and ASD-differential cell types in these regions and use systems neuroscience approaches to assess anatomical and functional relationships between sex-differential cell types and cortical/striatal neuronal activity. Studies will be performed using mice and prairie voles (both wildtype and ASD genetic models) and, where possible, postmortem brain tissue. Multiple developmental stages will be assessed.

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