Announcing BRAIN Research Awards 2022

The gut-brain axis in ASD presenting with gut inflammation

PROJECT PI: John-Paul Yu MD PhD, Assistant Professor, in Radiology (Neuroradiology), Psychiatry, and Biomedical Engineering at University of Wisconsin–Madison
PROJECT FOCUS: To identify how altered gut microbiome in IBD leads to increased risk for ASD by developing a novel human pediatric ASD/IBD microbiome model in mice.
PROJECT AIMS: We will identify altered gut-brain-behavior development in our model and directly test the ability of replacing altered microbiota-derived metabolites to rescue brain and behavior impairments relevant to ASD. Our work will provide the first test of human ASD/IBD microbiota to produce ASD-relevant brain and behavior phenotypes through altered metabolite and brain immune cell signaling. Lastly, we will employ state-of-the-art quantitative multi-compartment diffusion weighted imaging to develop a neuroimaging biomarker for both diagnostic accuracy and to track a microbiota-based therapeutic response.

CRE/FLP system in brain organoids as a tool for illuminating pathology mechanisms

PROJECT PI: Christopher Patzke PhD, John M. and Mary Jo Boler Assistant Professor, University of Notre Dame
PROJECT FOCUS: CRE/FLP system in brain organoids as a tool for acute mutation targeting and dissecting of autism disease pathology mechanism
PROJECT AIMS: This project has two goals: One goal is to study different types of human synapses in in vitro systems that come as close as possible to human brain in vivo situations. Current brain organoid systems are still very far away from being representative for any non-embryonic nervous system. The second goal is to establish a culture system that can be entirely and acutely switched from diseased to healthy genotype and vice versa. Advanced culture techniques paired with genetic engineering will be molecular tricks helping us to understand specific brain regions at any given time in development, in any given medical condition.

Evaluating clinical measures and and biomarkers in behavioural regression in ASD

PROJECT PI: Jennifer Frankovich MD MS, Clinical Professor, Dept of Pediatrics, Stanford University/Lucile Packard Children’s Hospital
PROJECT FOCUS: Illuminating biological underpinnings in behavioural regression in ASD compared to healthy controls and Pediatric Acute-onset Neuropsychiatric Syndrome (PANS).
PROJECT AIMS: Using our longitudinal clinical database and biobank, we aim to describe the clinical and immunological course of patients with autism (n=18) followed in our IBH Clinic through different states (flare, improved, chronic) and compare these data to findings in patients with PANS and to hospital/clinic controls. Immune studies will include monocyte profiles, single-cell RNA sequencing, the effects of plasma from autism patients on healthy monocytes, and blood-brain endothelial cells. Since these experiments will use only a fraction of the stored samples, the remaining will be reserved for cytokine/proteomic profiles, ATAC-seq, and functional assays, so that all these data can be correlated with the clinical data for informing biomarker discovery and clinical trials.

Neuroinflammation and brain development in Autism Spectrum Disorder

PROJECT PI: Paul Ashwood PhD, Associate Professor of immunology at the MIND Institute at the University of California Davis
PROJECT FOCUS: Mapping brain development in autism and correlating it to inflammatory/immune related disturbances.
PROJECT AIMS: Using RNAscope, immunohistochemistry (IHC) and protein arrays, we will measure inflammatory and immune regulatory cytokines in amygdala specimens from control and ASD individuals. Our overall hypothesis is that altered immune regulation maps to the lifelong trajectory of amygdala development in ASD. We will track cytokine levels in different cells to determine whether immune response correlates with brain growth trajectories. We will focus on the balance between regulatory cytokines such as transforming growth factor beta 1 (TGFb1), interleukin (IL)-10 and IL-35, and inflam-matory cytokines such as IL-1, IL-6, tumor necrosis factor alpha (TNFa) and IL-17. We will also attempt to investigate associations with ASD comorbidities and behavioral severity assessments.

Biomarker discovery for autism detection and treatment

PROJECT PI: Karen Parker PhD, Associate Professor (Research) of Psychiatry & Behavioral Sciences, Stanford University
PROJECT FOCUS: Discovery of clinical biomarkers for improved detection and treatment of autism
PROJECT AIMS: To identify robust protein markers of ASD for novel therapeutic target identification and diagnostic test development using an innovative CSF-first strategy. This project is based on promising preliminary data and is statistically well-powered to detect effects. Our specific aims are two-fold: Aim 1: Use the full power of Olink’s state-of-the-art proteomic platform to identify proteins in banked CSF samples that enable accurate differentiation of children with ASD from unrelated child controls. Aim 2: Assess whether the multiplex CSF protein profile is evident in banked blood samples from children with ASD and unrelated child controls

Bio behavioral study of arousal in nonspeaking children with autism

PROJECT PI: Sarah A. Schoen, PhD, OTR, Director of Research, STAR Institute for Sensory Processing
PROJECT FOCUS: Assess the presence of stress patterns impacting functioning in autism
PROJECT AIMS: The over arching goal of this study is to better understand and treat the unique arousal/ stress responses of non-speaking autistic children. Specifically this project will employ novel tools to assess the presence of stress patterns impacting function as well as determine the role of arousal mechanisms in treatment. We will employ a bio behavioral approach for the examination of arousal, and provide intervention that is informed by these tools. We will measure the effectiveness of a unique short term, intensive intervention that focuses on autonomic, sensory, motor and emotional components of arousal with the ultimate goal of increasing client well-being, sense of agency and autonomy.

Autism spectrum disorder inflammatory subtype and long COVID

PROJECT PI: Harumi Jyonouchi MD, Board Certified Allergist/Immunologist, Saint Peter’s University Hospital, Rutgers-Robert Wood Johnson Medical School
PROJECT FOCUS: Immune mediated inflammation in long COVID patients with or without ASD
PROJECT AIMS: The long-term goal of our research is to determine the underlying mechanisms of immune
mediated inflammation in long COVID patients with or without ASD. The immediate goals of this proposal are to assess how COVID infection triggered long-term changes in the innate immune system affect ASD subjects in comparison with non-ASD long COVID subjects. Completion of this project will help identify 1) key pathological changes in long COVID symptoms in ASD subjects, and 2) how these changes affect clinical features of ASD and assess treatment options in these subjects.

Profiling auditory sensitivity in Autism Spectrum Disorder

PROJECT PI: Adam Naples, PhD, Assistant Professor in the Child Study Center at the Yale School of Medicine
PROJECT FOCUS: Specifying the exact nature of auditory processing disturbances in autism
PROJECT AIMS: To determine whether measures of fluctuations in PD and EEG differ between participants with ASD and NT controls. Second, we will determine how measures of fluctuations in PD and EEG affect the day-to-day
experience of auditory sensitivity.

Defining comorbidities in Autism Spectrum Disorder

PROJECT PI: Chandra Menendez PhD, Postdoctoral Fellow in the Department of Microbiology and Immunology at the University of Oklahoma Health Sciences Center
PROJECT FOCUS: The human translational study will identify biomarkers and advance the identification and treatment of basal ganglia comorbidities in ASD
PROJECT AIMS: To investigate the hypothesis that infections and basal ganglia autoimmunity are risk factors in ASD comorbidities. The project will attempt to determine putative AAb biomarkers (including AAbs that activate the dopamine receptors) and immunophenotypic signatures in ASD and correlate them with ASD comorbidities or immune dysregulation. It will also investigate immunophenotypic signatures in ASD subtypes with and without comorbidities.

BRAIN Funded Research 2021

Using a Humanized Mouse Model And Human Intestinal Tissue to Evaluate the Zonulin Pathway For Personalized Treatment of Autism

PROJECT PI: Dr Alessio Fasano, Professor of Pediatrics & Vice Chair of Research at Mass. General Hospital, Professor of Nutrition at Harvard T.H. Chan School of Public Health.
PROJECT FOCUS: gut permeability/microbiome /immune response interplay in autism
PROJECT AIMS: advance our understanding of ASD pathogenesis and the mechanisms behind increased gut permeability; identify biomarkers to stratify the ASD population in specific subgroups; validate the zonulin inhibitor AT1001 (already showing robust safety profiles in phase 3 human trials with the name Larazotide acetate) as a possible personalized therapeutic strategic treatment, so posing foundations for future clinical trials in ASD.

Evaluation of Transcranial Photobiomodulation in Autism: Double-Blind, Placebo-Controlled, Randomized Study

PROJECT PI: Tolga Atilla Ceranoglu, MD, Assistant Professor in Psychiatry, Harvard Medical School and Mass. General Hospital.
PROJECT FOCUS: transcranial photobiomodulation (t-PBM) is a novel form of neuromodulation that is based on non-retinal exposure to light at specific wavelengths. So far it has yielded very promising early results for the treatment of several neuropsychiatric disorders. Its mechanisms of action include increasing mitochondrial energy production, lowering inflammation and increasing regional blood flow in the brain. The treatment has a low cost, good safety profile, and it is easy to self-administer.
PROJECT AIMS: evaluate efficacy and safety of t-PBM treatment of autism and provide the first step towards FDA approval.

Immunoregulation and Gastrointestinal Issues in Autism Spectrum Disorder

PROJECT PI: Paul Ashwood, PhD, Professor of Microbiology and Immunology, MIND Institute, University of California Davis.
PROJECT FOCUS: understand underlying pathological pathways in gastrointestinal (GI) issues in autism and develop treatment strategies.
PROJECT AIMS: determine the mechanisms of increased innate immune activation. The project will examine the hypothesis is that macrophage dysfunction in autism is due to epigenetic changes that cause increased immune activation, decreased endotoxin/bacterial tolerance, and lead to inflammation. The researchers will aim to identify a panel of biomarkers, or biological signatures, that could be used for patient stratification, development of new therapeutic targets, or to monitor treatment responses.

High-Frequency Oscillation as a Biomarker of Mitochondrial Dysfunction Associated with Epilepsy in Autism

PROJECT PI: Richard Frye, MD PhD, Pediatric Neurologist, Phoenix Children’s Hospital.
PROJECT FOCUS: studying mitochondrial dysfunction as a cause of epilepsy in individuals with and without autism as well as the correlation with these areas of mitochondrial dysfunction with high frequency oscillations (HFO) that can be recorded non-invasively as a biomarker of mitochondrial associated epilepsy. Individuals with autism are at an increased risk for epilepsy and seizures. Epilepsy is the leading cause of death in autism.
PROJECT AIMS: deepen our understanding of the biological mechanisms that underlie epilepsy, including treatment-resistant epilepsy, and to open a path to novel biomarkers, assessment methods and treatments.

Autism with Neurodevelopmental Regression Associated Mitochondrial Dysfunction: Further Development of In Vitro Models and Pathways to Treatment

PROJECT PI: Richard Frye, MD PhD, Pediatric Neurologist, Phoenix Children’s Hospital.
PROJECT FOCUS: mitochondrial dysfunction in regressive autism. About one-third of children with autism spectrum disorder demonstrate a major neurodevelopmental regression – loss of previously acquired language and social interaction skills, as well as emergence of restricted and repetitive behaviors.
PROJECT AIMS: The overall goal of this study is to develop better treatments for children with autism. In order to reach this aim, the investigators will further characterize mitochondrial dysfunction in their in vitro models and test agents that potentially modulate mitochondrial function in order to discover novel targeted treatments for this subset of autism.

Early Biomarkers in Autism Spectrum Disorders: Birth Folate Autoantibody Receptor Status

PROJECT PI: Harris Huberman, MD, Pediatrician, SUNY Downstate Medical Center.
PROJECT FOCUS: examine the role of folate receptor auto-antibodies (FRAA) in the development and manifestations of autism. Folate in the central nervous system plays a role in a myriad of metabolic, genomic and brain architectonic processes. FRAAs have been clearly correlated with autism and appear to constitute a significant contributing factor.
PROJECT AIMS: improve understanding of central folate deficiency on infant development; improve understanding how measures of brain activity and social behavior correlate with FRAA status, and later ASD diagnosis; improve early identification of ASD and lay the groundwork for future treatment interventions of high-risk infants with leucovorin.

Biomarkers of Innate Immune Memory in Autism Spectrum Disorders

PROJECT PI: Harumi Jyonouchi, MD, Board-certified Allergist/Immunologist, Saint Peter’s Hospital, Professor of Pediatrics at Rutgers Robert Wood Johnson Medical School.
PROJECT FOCUS: immune mediated inflammation that affects not only the brain but also other organs has been implicated in many of the observed clinical features in autism. However, inflammation in autism appears not associated with specific environmental factors, but appears to be driven by innate immune memory (IIM) responses that are generated by metabolic and epigenetic changes triggered by an initial stimulus.
PROJECT AIMS: determine the underlying mechanisms of immune mediated inflammation and their effects on the development and progress of autism.

Connecting Rare Genetic Mutations in Autism to Common Biological Pathways

PROJECT PI: Joseph D. Buxbaum, PhD, Professor of Psychiatry, Genetics and Neuroscience, Icahn School of Medicine at Mount Sinai. Director of the Seaver Autism Center.
PROJECT FOCUS: study the function of many autism-linked genes simultaneously, in order to identifying a smaller number of common pathways shared by those genes. Apply a computational drug repurposing approach to search for already existing compounds that would be predicted to revert altered ASD pathways to a healthy state.
PROJECT AIMS: improve our understand of how changes in nerve and brain development lead to autism disorder in order to develop effective new treatments for ASD we need to

Using AI & Machine Learning to Develop Metabolic Biomarkers in Autism Spectrum Disorders

PROJECT PI: Dr. Juergen Hahn, Professor & Department Head, Biomedical Engineering, Rensselaer Polytechnic Institute.
PROJECT FOCUS: analyzing measurements of metabolite concentrations of the folate-dependent one-carbon metabolism and transsulfuration pathways to distinguish children diagnosed with autism from their typically-developing peers.
PROJECT AIMS: replicate the results on a new, large cohort of children using state-of-the-art technologies appropriate for a commercial lab test; develop the foundation for autism biomarkers to be used for diagnosing autism and for assessing efficacy of treatments.

Study the Pathological Status in Gastrointestinal Tissue in GI Symptomatic Children with and without Autism

PROJECT PI: Stephen Walker, PhD, Professor of Regenerative Medicine, Wake Forest School of Medicine, and Arthur Krigsman MD, Board-certified Pediatric Gastroenterologist
PROJECT FOCUS: significant molecular pathology is often lurking in the normal or near normal light microscopic images of intestinal biopsy tissue of GI symptomatic children with ASD.
PROJECT AIMS: replicate the existing findings in order to provide support for a change in prevailing clinical practice of the evaluation of GI symptomatic ASD children to include a more thorough evaluation of biopsy tissue when the presenting symptoms are suggestive of an inflammatory phenotype.

MEF2C Haploinsufficiency Drug Discovery - Potential to Improve ASD Phenotypes

PROJECT PI: Stuart Lipton, MD, PhD, Professor of Molecular Medicine, Scripps Research.
PROJECT FOCUS: partial loss of MEF2C activity is known to lead to ASD, intellectual disability, epilepsy and other neurological symptoms. Since MEF2C is a major regulator of the expression of various other proteins known to be involved in various forms of ASD, such a drug may be an effective treatment for a wide variety of ASDs.
PROJECT AIMS: optimize lead compounds discovered by Lipton’s lab in order to develop drug candidates to treat a specific type of autism by increasing the activity of MEF2C neuronal transcription factor.

Pharmacologically Remediable Traits of ASD in a Mouse Model Implicate a Serotonin – Neuroinflammatory Connection

PROJECT PI: Randy Blakely, PhD, Professor of Biomedical Science, Florida Atlantic University.

BRAIN Funded Research 2020

Characterizing Altered Innate Immune Memory in Autism & Exploring Select MicroRNAs as Biomarkers

PROJECT PI: Harumi Jyonouchi, MD, Board-certified Allergist/Immunologist, Saint Peter’s Hospital. Professor of Pediatrics, Rutgers Robert Wood Johnson Medical School.

Understanding Differences in Intestinal Epithelium in Autism and Controls & Constructing a Biobank of Intestinal Organoids

PROJECT PI: Paul Ashwood, PhD, Professor of Microbiology and Immunology at the MIND Institute, University of California Davis.

Microbiota Transfer Therapy for Individuals with Autism Spectrum Disorder, with Extensive Testing

PROJECT PI: James Adams, PhD, President’s Professor, Arizona State University.

Gene-Microbiome Interactions in ASD: the Effects on Neurotransmitter Release, Immune Responses & GI Function

PROJECT PI: Sarkis Mazmanian PhD, Luis & Nelly Soux Professor of Microbiology in the Division of Biology & Biological Engineering, Caltech.

Investigating Chemical Exposures and Crosstalk between the Metabolome and Exposome in Autism

PROJECT PI: Robert Naviaux, MD, PhD, UC San Diego

Explore if Treatments Targeting Mitochondrial Function in Autism Will Improve the Core Symptoms

PROJECT PI: Richard Frye, MD PhD, Pediatric Neurologist, Phoenix Children’s Hospital.


Establish a Rat Model of ASD to Study Genetic & Epigenetic Changes and Associated Behavioural Deficits

PROJECT PI: Edward Quadros, PhD, SUNY Downstate.

Symptom Improvement ASD Children Following Treatment for their Chronic GI Inflammation

PROJECT PI: Arthur Krigsman, MD, Board-certified Pediatric Gastroenterologist.

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