Our long-term goal is to understand the etiology and the molecular mechanisms underlying the pathophysiology of ASD and to define molecular and cellular components that could be targeted for developing therapeutic compounds for the disorder. The approaches we are taking towards achieving these goals include genetic analyses, animal models, and induced pluripotent stem cells.

Genetic Analyses

For over 30 years, studies of families and twins have indicated that genetic factors account for a large portion of ASD risk. However, to date, less than 20% of ASD cases can be identified with a molecular genetic cause. Our research efforts aim to uncover the genetic variation in the remaining cases (idiopathic ASD), and thus identify novel genes and mutations conferring risk for ASD. Since the statistical power for gene discovery increases with the sample size, we collaborate with other research teams to collect large ASD cohorts.

We are co-leaders of the Autism Sequencing Consortium (ASC), a collaboration of over 40 international research groups founded in 2010 with the immediate goal of analyzing the exomes of over 40,000 individuals. As part of the ASC, we apply cutting-edge genomics technologies, including whole-exome sequencing, to large populations comprising ASD families, ASD cases and healthy controls. We investigate genetic variation at all scales, including single-nucleotide variation (SNV), small deletions and duplication (indels), and copy number variants (CNV). Data emerging from our research are being intersected with findings from genetic studies on schizophrenia, epilepsy, and intellectual disability, to better understand the bases of the ASD comorbidities.

As part of the translational approach that characterizes our research, the genetic data are used to create increasingly sophisticated pre-clinical cell and animal models for basic studies, drug design and testing (see below). Also, we work closely with the clinical team at the Seaver Autism Center to use the genetic findings to ameliorate patient care. Genetic discoveries can help with accurate diagnosis, and can provide information for the prediction of the clinical course of the disease and opportunities for genetic counseling. Genetic studies will also constitute the first step of pioneering personalized clinical care by integrating personal genomics data with specific therapeutics.

Animal Models

A major goal of our group is to understand the role of the SHANK3 gene in ASD and in Phelan-McDermid syndrome (PMS)/22q13 deletion syndrome, which is one of the more common causes of ASD. The SHANK3 gene product, known as the SHANK3 protein, is an important structural component of our neurons, particularly at the postsynaptic density compartment of the synapse. Our aim is to better understand how mutations in the SHANK3 gene lead to the manifestation of the PMS phenotype, including ASD. Once we uncover the synaptic biological mechanisms and pathways affected by the SHANK3 mutations, we can target these pathways with therapeutic compounds aimed at improving the symptomatology of the disorder.

One of the most powerful strategies to study mechanisms of diseases/disorders is by modeling them in experimental animals. To model PMS and further study the pathophysiology of the disorder, our team is using both mice and rats that have a mutation in the Shank3 gene, and is applying multidisciplinary approaches including molecular biology, electrophysiology, behavior, neuroimaging, among others, to identify alterations at all levels. Compared to mice, rats have additional advantages such as more complex and humanlike neural circuitry and behavioral repertoire. Rats also remain a primary choice of the pharmaceutical industry for studying pharmacokinetic properties of novel drugs, which is an ultimate goal of our group. Hence, emerging findings from our preclinical studies in the Shank3 models will form a basis for experimental therapeutic studies in subjects with PMS by our clinical team at the Seaver Autism Center.

Induced Pluripotent Stem Cells

Because of their pluripotency and ability to differentiate into neural cell types, induced pluripotent stem cells (iPSCs) derived from patients represent an experimental system of choice for the study of complex neuropsychiatric disorders such as autism and schizophrenia. To determine the impact of Shank3 mutations on neuronal mechanisms and pathways, we are generating iPSCs from blood samples collected from PMS patients and their siblings (as a control) and are reprogramming them into neural progenitor cells (NPCs) and differentiating them into mature neurons. These cells can be used to mimic the pathology of the disorder and to thoroughly understand the physiology of neuronal populations that would otherwise not be accessible for investigation. Similarly we are collecting blood samples from patients with idiopathic autism or other monogenic forms of autism.

Another strategy used in our laboratory consists of creating and phenotyping a series of isogenic NPC lines using gene-targeting methods (shRNA gene silencing and/or targeted knockout by TALENs or CRISPR) in healthy control cells. We selected over 100 genes associated with ASD from our genetic analyses to be investigated.

Both patient-derived cells and engineered cells are tested through a battery of high-throughput phenotypic and molecular assays at both the progenitor and mature neuron stage designed to assess genome wide expression changes and a range of phenotypes including cell replication, survival, migration, connectivity, electrophysiological properties, dendritic arborization and synaptic structure. This work will provide insight into the neuronal pathways disrupted in ASD and, ultimately, those cell lines will provide a unique platform for drug discovery, allowing high-throughput screening of large compounds libraries for their effect on modulating the human neural phenotype of ASD.