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Autism Speaks Genetics Research Grants

Autism Speaks is committed to aggressively funding research that will accelerate the pace of discovery and, ultimately, improve the lives of all those who struggle with autism.

As part of this commitment, Autism Speaks, NAAR and CAN committed $11,533,722 to genetics research grants from 2005 and 2007.

From 1997 to 2004, the combined organizations spent $5,899,353 million on genetics grants.

Also, learn more about Autism Speaks’ current grants related to research on potential environmental factors in autism and grants releated to treatments for autism.

Current Autism Speaks Genetics Grants (2005-2007) 

Autism Genome Project (Autism Speaks Special Collaborative Project 2007) $5,000,000

Phase 2: Whole Genome Association, Copy Number Variations and Candidate Genes

The Autism Genome Project (AGP) is a public/private research partnership involving approximately 50 academic and research institutions that have pooled their DNA samples in a collaborative effort.

Building on findings from phase 1 or the genome scan, the coalition of researchers will now apply state-of-art ‘gene-chip‘ technologies to scan the genome for association with new genetic markers, as well as sub-microscopic copy number variations (CNVs) along chromosomes in autism. These findings will guide high-throughput DNA sequencing experiments designed to pinpoint underlying changes in DNA sequences in autism susceptibility genes.

The unprecedented statistical power generated by the AGP will ultimately allow researchers to confirm the role of these genes, in autism spectrum disorders.

Phase 2 of the project represents a $14.5 million dollar investment over three years by a consortium of funding partners, including including the British Medical Research Council, the Health Research Board of Ireland, Genome Canada and partners, Canadian Institutes for Health ResearchSouthwest Autism Research and Resource Center, and the Hilibrand Foundation.

Autism Genome Project (Autism Speaks Special Project 2007) $2,560,063

The Autism Simplex Collection (TASC)

Phase 2 of the Autism Genome Project (AGP) involves whole genome association, linkage follow up and candidate genes assessment, and additional interrogation of copy number variations (CNVs) across the genome. Consortium members plan to utilize 2,000 simplex families (i.e. parents plus one affected child, or 6,000 individuals) as an independent sample to help power the proposed analyses.

The TASC proposes to leverage its unique existing resource of >2,000 parent-child trio families previously ascertained by AGP member groups by updating phenotypic assessments to a common standard and providing fresh blood samples to central repository (i.e. AGRE) for DNA extraction and the generation of lymphoblastoid cell lines. These goals are important to provide a uniform resource for the forthcoming work proposed by the AGP to identify and characterize genetic risk factors in autism.

In addition, by agreeing to make the entire collection available to the wider scientific community within 24 months, the TASC will mobilize a valuable, high quality dataset that will complement existing autism DNA collections and to enable future studies.

Edward S. Brodkin, M.D., University of Pennsylvania School of Medicine (CAN Pilot Research Award 2006) $120,000

Genetic and Neurobiological Analysis of Sociability, an Autism Endophenotype, in a Mouse Model System

Impairments in social interactions are among the most prominent, disabling, and treatment-resistant symptoms of autism.

There is strong evidence for a major genetic component to these symptoms (Constantino and Todd 2000; Piven et al 1997). To elucidate the genetic and neurobiological basis of the social behavior symptoms in autism, it will be crucial to develop mouse model of sociability, because model organisms provide the high degree of experimental control necessary to analyze the complex effects of genes on brain and behavior.

We have recently developed such a mouse model of sociability, and have identified genetically-influenced differences in sociability among inbred mouse strains (Brodkin et al 2004).

The aims of the current proposal are

1) to further develop this mouse model system for autism research;

2) to assess the effects of particular autism candidate genes (the glutamate receptor subunit GluR6 gene and the gastrin releasing peptide receptor gene) on sociability by measuring the social behaviors of mice in which those genes have been deleted (gene “knockout” mice); and

3) in set of knockout and wildtype mice that differ greatly in sociability (see Aim 2), to identify a brain region(s) differentially activated by social behavior, and to compare expression of thousands of genes in that brain region in knockout vs. wildtype mice, using GeneChip technology.

These proposed studies are necessary steps towards elucidating the genetic and neurobiological basis of highly disabling symptoms of autism. Co-Sponsor: Christopher Camburn

Linda Brzustowicz, M.D., The State University of New Jersey at New Brunswick, James Millonig, Ph.D.,UMDNJ-RWJMS,Veronica Vieland, Ph.D., University of Iowa

Identification and Functional Assessment of Autism Susceptibility Genes 

Jonathan Sebat, Ph.D., Cold Spring Harbor Laboratory

Determining the Genetic Basis of Autism by High-Resolution Analysis of Copy Number

Michael Zwick, Ph.D., Emory University

Identifying Autism Susceptibility Genes by High-Throughput Chip Resequencing

(NIH Autism Susceptibility Gene Discovery RFA 2005) $1,500,000

The goal of the initiative is to advance knowledge of the relation between genetics and autism by examining existing dataset for genes and gene variants that confer susceptibility to autism. Researchers will also be assessing the functional significance of autism-associated genetic variants. This research may provide a means to subdivide autism spectrum disorders into identifiable, distinct disorders with different molecular mechanisms.

The National Institutes of Health (NIH) spearheaded the initiative, whose members include the National Institute of Mental Health (NIMH), National Institute for Neurological Disorders and Stroke (NINDS), the National Institute on Deafness and Other Communications Disorders (NIDCD), the National Institute of Child Health and Human Development (NICHD), and the National Institute of Environmental Health Sciences (NIEHS). The private nonprofit organizations that complete the partnership are Cure Autism Now (CAN), the National Alliance for Autism Research (NAAR) and the Southwest Autism Research & Resource Center (SARRC).

Jia Chen, Sc.D., Mount Sinai School of Medicine (AS Biomedical Research Award 2006) $100,000

Testing the extreme male brain theory of autism 

Autism is a severe neurodevelopmental disorder, which has a complex genetic predisposition. The ratio of males to females affected by autism is approximately 4:1, suggesting that hormonal factors are involved in its development. One such sex difference lies in psychological behavior in which females have stronger empathizing (E) capability while males have stronger systemizing (S) capability. As an extension of the E-S theory, there has emerged an “extreme male brain” (EMB) theory for Autism.

This hypothesis proposes that individuals on the autistic spectrum are characterized by impairments in empathy alongside intact or even superior systemizing. The biological mechanism for the sex difference seen in autism has not been elucidated, but these findings suggest that endogenous hormone levels of parent and/or child may be important. The in utero window is likely to be a critical time for fetal exposure to sex hormones, and androgens in particular. Testosterone, the critical androgen, exerts its influence on a wide range of sex-differences including brain anatomy, sexually dimorphic behaviors, and cognitive abilities. Nevertheless, direct evidence of a testosterone-autism relationship is lacking in human populations.

The proposed study is designed to test the validity of the EMB theory. We will use functional polymorphisms in androgen-metabolizing genes as biomarkers for integrated hormone levels to elucidate relationships between androgen metabolism and autism risk. We will analyze “pro-androgenic” polymorphisms, which refer to functional polymorphisms that favor the production and accumulation of testosterone.

Genotyping will be performed on 260 complete case-parent triads (780 subjects) selected from the MSSM cohort of the Family Studies Program of the Seaver and NY Autism Center of Excellence. The androgen – autism relationship will then be confirmed by comparing the same genotype distribution in mothers and their offspring in the case-parent triad with those of population controls which consists of 300 healthy mother-child pairs from the MSSM Children’s Center for Environmental Health (CCEH).

This investigation will provide direct evidence on the validity of the EMB theory for autism. It will establish the utility of a new approach to understanding the hormonal basis of autism, which may lead to development of new preventive as well as treatment strategies.

John Constantino, M.D., Washington University School of Medicine (AS Biomedical Research Award 2005) $60,000

Replication of Quantitative Linkage Findings in a New Sample of Genotyped (but Not Yet Phenotyped) Autism Pedigrees

Although autism is largely an inherited disorder, the specific genes that cause most cases of the disorder remain unknown. Previous genetic studies of autism, which primarily involve affected pairs of siblings, have yielded only modest associations with specific chromosomal regions.

The affected sib pair design, however, has important limitations. Affected sib pairs are relatively rare, and this limits the sample size that can be used to search for genes for autism.

For complex diseases like autism, in which numerous genes may be acting in concert to cause the disorder, larger sample sizes may be needed to identify the genes (or combinations of genes) that are responsible. One way to increase both the size of a sample and its power to detect genes, is to adopt what is known as a quantitative approach, in which genetic markers are related not just to presence or absence of the disorder, but to the degree of symptom severity that each individual manifests.

Using information on all family members, including those with only subtle autistic-like traits, we have shown in an initial pilot sample of just over 100 families that the ability to identify genes for autism using a quantitative approach may be as powerful as using traditional affected sib pair methods in samples 4 times larger.

This is a proposal to replicate our original findings in a new sample of 150 families, by

1) obtaining quantitative assessments of autistic social impairment (the “phenotype” of interest) in all of the siblings in each family; and

2) studying the association between symptom severity (from very mild to very severe) with the available genotypic data on the subjects. If our findings hold true in this replication, they would directly narrow the search for genes in several chromosomal regions which are currently suspected of harboring autism susceptibility genes.

Furthermore, these quantitative methods could be applied to large numbers of extended autism pedigrees (including those involved in the NAAR Autism Genome Project), and could greatly enhance the power to identify other genes of major effect in autism.

Andrew Feinberg, M.D. and Joachim Hallmayer, M.D., John Hopkins-Stanford (AS Biomedical Research Award 2006) $100,000

Exploring the epigenetics of twins with autism 

We are testing the hypothesis that autism is caused in part by epigenetic alterations, i.e., hereditary information not involving the DNA sequence, such as DNA methylation, a covalent modification of the nucleotide cytosine that is inherited during cell division.

Epigenetics appears to be important in autism for several reasons, including linkage region overlap with known disorders associated with imprinting, existence of chromosomal abnormalities in regions known to be imprinted that lead to autism phenotypes, and maternal transmission of such abnormalities to children with such features, as well as parent of origin-specific linkage suggesting imprinting.

Furthermore, monozygotic (MZ) twins frequently show marked differences in phenotype for autism spectrum disorder. We will combine the expertise of Andrew Feinberg (Johns Hopkins), a pioneer in epigenetic analysis, with Joachim Hallmayer (Stanford), an expert in neurocognitive function in families, with an emphasis on twins. We will test the epigenetic hypothesis by performing genome-wide gene-specific DNA methylation analysis on oligonucleotide arrays, using DNA from fresh blood samples from monozygotic twins with autism, in order to identify genes that affect disease incidence or severity, that would be missed by conventional genetic analysis.

We will then validate targets by highly quantitative gene-specific methylation pyrosequencing analysis. If we can identify specific epigenetic alterations in autism, it will open a new and exciting avenue for diagnosis and treatment, such as carrier detection, prediction of clinical needs early in life to tailor appropriate intervention, and prenatal diagnosis.

Perhaps the most exciting application of an epigenetic discovery would be the possibility of treatment, since epigenetic alterations are inherently reversible, i.e. not involving mutations in the DNA sequence per se. Thus, new treatments for autism might eventually be developed for epigenetic targets more quickly than for genes showing conventional mutation.

Jozef Gecz, Ph.D., Women’s and Children’s Hospital, Australia (CAN Pilot Research Award 2005) $59,443

The Prevalence of Mutations in X-Chromosome Linked Genes 

Genes and the environment perform a delicate balancing act in the determination of the outcomes of many disorders, including autism. Research in other diseases has shown well-documented examples of patients and families where a defect in a given gene can be identified as the primary cause.

Autism is a complex genetic disorder, with many genes contributing. This study will look at genes on the human X-chromosome, which has been linked to various developmental issues (including autism).

Dr. Gecz will be using samples from Cure Autism Now’s AGRE gene bank to study two genes (ARX and STK9) his lab had previously tied to another disorder, X-linked mental retardation Because many patients with X-linked mental retardation also have autism, Dr. Gecz will now be screening autism patients for mutations in the ARX and STK9 genes.

Daniel Geschwind, M.D., Ph.D., University of California, Los Angeles (CAN Genetic Initiative Award 2005) $188,000

Identification of the Factors Underlying Chromosome 17q Autism Genetic Risk by Dense SNP Genotyping 

Recently Dr. Geschwind and collaborators have identified an autism locus on chromosome 17q. Strikingly, this locus appears to be specifically related to male susceptibility to autism; females do not contribute to the linkage signal.

They have now used an independent sample from Cure Autism Now’s AGRE biomaterial bank to confirm this locus at a level considered highly significant–a first in autism research.

To find the actual gene or genes, it is necessary to interrogate all genes within this region using a process called SNP genotyping. They will use this method to test SNPs at high density in every gene in the region, allowing them to screen every single gene and hopefully, identify the causal risk gene.

Dr. Geschwind’s laboratory has the most efficient technology for performing this study, and by partnering with Cure Autism Now will perform this work at a significantly reduced timescale. This will provide a major advance for the field, and identify a gene or genes related to male-specific autism risk.

Randi Hagerman, M.D., M.I.N.D. Institute (AS Augmentation and Bridge Award 2007) $50,000

Genotype-Phenotype Relationships in Fragile X Families 

This proposal focuses on understanding the characteristics and molecular aspects of autism and attention deficit hyperactivity disorder (ADHD) in young males with the fragile X premutation.

Fragile X syndrome (FXS) is the most common heritable form of mental retardation and is a frequent cause of autism. Between 2% to 8% of children with autism have fragile X and approximately 30% of children with fragile X have autism. Individuals with the premutation (55-200 repeats) have elevated fragile X mental retardation 1 (FMR1) mRNA and are at risk to develop the fragile X-associated tremor/ataxia syndrome (FXTAS) with aging.

We have recently reported a high rate of autism and ADHD in boys with the premutation, suggesting a developmental RNA toxicity effect of the premutation. Twenty young males with the premutation and 20 young males without the premutation, between the ages of 8-16 years, will be recruited for this study.

Each subject will undergo a thorough evaluation for autism and ADHD, in addition to a molecular analysis for fragile X. This project will assess whether autism in young males with the premutation is related to a FMR1 protein (FMRP) deficit or elevated FMR1 mRNA toxicity and will provide insight on the molecular aspects of autism.

Joachim Hallmayer, M.D., Stanford University (AS Augmentation and Bridge Award 2007) $99,913

A California population-based twin study of autism 

Of all multifactorial child psychiatric disorders, autism is the most strongly genetically influenced. The inherited liability is not restricted to the full clinical syndrome of autism but encompasses a range of behavioral and cognitive characteristics. Family studies have failed to distinguish whether the genetic liability to autism falls on a continuous spectrum of severity or whether it may be better subdivided into distinct categorical subtypes. From a genetic standpoint this raises the question, whether different aspects of the autism phenotype are influenced by different loci.

This study is the largest, population-based study of twins with autism. With this unique sample Dr. Hallmayer and colleagues will attempt to unravel the relationship between genes and environment as it pertains to the cognitive impairments and the clinical symptoms.

Twin pairs are assessed using (a) clinical measures of autistic-like behaviors (b) more specific measures for repetitive and stereotyped behaviors, (c) measures of general cognitive ability d) measures of more specific neurocognitive abilities .

The information will allow the scientists to address several fundamental questions:

(1) what is the heritability of autism

(2) what is the contribution of genetic factors to variation in symptom dimensions?

(3) is there a continuum between the quantitative neurocognitive traits and clinical disorder?

(4) what proportion of the variance in the neurocognitive traits is accounted for by genetic and non-genetic factors.

We are proposing to augment the ongoing project by:

1) Increasing the number of twin pairs by including additional regional centers, which had been previously excluded because of budget cuts by NIMH,

2) Evaluate additional non-twin siblings with the Social Reciprocity Scales (SRS)

, 3) Screen additional non-twin siblings for autism symptoms and assess; siblings with a clinical diagnosis of autism or above a pre-specified cut-off will be assessed using standardized instruments

4) Obtain blood samples on all family members including non-affected siblings.

James Millonig, Ph.D., UMDNJ-RWJMS (AS Biomedical Research Award 2005) $120,000

Genetic and functional analysis of ENGRAILED 2, a cerebellar patterning gene 

Cerebellar defects are the most prevalent morphological abnormality associated with autism. Autopsy and neuroimaging studies indicate that these defects are due to abnormal cerebellar development. This result means that genes, which control cerebellar development, might be defective in autism.

Fortunately, the genetic pathways that regulate cerebellar development have been investigated in detail in the mouse. We have generated a list of candidate genes that perform essential functions during mouse cerebellar development and have placed them on the human genome map. Several of these genes map to chromosomal regions that segregate with autism.

One of these genes, ENGRAILED2 (EN2) – a transcription factor important for cerebellar development, was of particular interest because mouse mutants in this gene exhibited cerebellar abnormalities that were remarkably similar to those described for autistic individuals. In collaboration with Linda Brzustowicz’s group (Department of Genetics, Rutgers University), we have demonstrated that certain variants of EN2 are inherited more frequently in autistic individuals than unaffected siblings.

This result has now been replicated in a second dataset and is maintained in a very large sample of 532 families, indicating that EN2 is likely to contribute to ASD genetic susceptibility in the general population. However, final genetic proof will require identifying a “mutation” in EN2 that increases risk to ASD.

The goal of this proposal is two-fold: 1) to identify genetic polymorphisms that are inherited in a manner consistent with them being “mutations” and 2) to determine whether these polymorphisms affect the expression or function of EN2.

These experiments will help us determine whether EN2 acts a autism susceptibility locus, which could provide important insight into the genetic and developmental basis of autism.

Yuhei Nishimura, Ph.D., University of California, Los Angeles (CAN Young Investigator Award 2006) $80,000

Identification of Candidate Genes for Autism Spectrum Disorders 

Autism is a heterogeneous condition that is likely to result from the combined effects of multiple, genetic factors interacting with environmental factors.

Classification of autism patients based on genotypic information is one effective way to identify more homogeneous subgroups and hasten the identification of genes underlying autism. About 3% of typical autistic children have Fragile X syndrome (FRAX, 1-2%) or maternally inherited 15q11-q13 duplications (15qDup, 1-2%), comprising homogeneous populations with mendelian autism.

We have preliminarly analyzed the whole-genome mRNA expression profile in lymphoblastoid cells from individuals with autism and FRAX or 15qDup and compared the expression profile with those of individuals without autism.

We reasoned that known subgroups of autistic patients would allow us to provide a proof principle of the utility of microarrays to distinguish autistic subgroups among those with idiopathic autism.

Our preliminary results suggest that an approach based on lymphoblast gene expression profiling could be widely used to subgroup autistic subjects and to identify candidate genes for autism. In this proposal, we will analyze gene expression profiles in lymphoblastoid cells from more individuals in AGRE to identify genes differentially expressed in individuals with autism compared to those without autism and to provide more conclusive evidence that lymphoblast gene expression can be used to subgroup autism by etiology.

Three groups will be used, a) individuals with FRAX or 15qDup, b) MZ twins with autism discordant for repetitive behavior and c) DZ twins discordant for autism.

Co-Sponsors: The Boler Company Foundation and The Gassin Family Foundation

Antonio Persico, Ph.D., Univ. Campus Bio-Medico, Lab of Mol Psychiatry & Neurogenetics (Autism Speaks Biomedical Research Award 2005) $60,000

Addressing the Pathophysiology of Endophenotypes in Autism: Megalencephaly, Hyperserotoninemia, and Peptiduria

Autism represents the most “genetic” neuropsychiatric disorder but, contrary to initial expectations, its genetic underpinnings are heterogeneous and complex, certainly not as straightforward as those of single-gene disorders like haemophilia and Duchenne muscular dystrophy.

To study this complex disease, we have set up a long-standing network of nine clinical groups and four laboratories with expertise in human genetics, biochemistry, animal behavior, and child neuropsychiatry. Importantly, since the very beginning of our project we have collected not only DNA, but also plasma and urines in order to measure serotonin blood levels and urinary amounts of small peptides.

In fact, according to prior studies, specific subgroups of autistic patients are characterized by “markers of disease” or “endophenotypes”, especially elevated serotonin blood levels, loss of oligopeptides with the urines, and enlarged head circumference. These markers are currently believed to be more closely related to underlying genetic variants than the complex clinical symptomatology of autism.

Our sample currently encompasses 238 simplex and 27 multiplex families, including 293 primary autistic patients. We already have assessed serotonin blood levels, and urinary peptide excretion rates in 152, and 180 autistic patients, and in 325 and 400 first-degree relatives, respectively. Fronto-occipital cranial circumference has been recorded in 212 patients and 54 unaffected siblings.

This application seeks funding to (a) recruit another 190 families, and assess them at the clinical (ADOS and ADI), biochemical (serotonin blood levels and urinary peptide excretion rates) and morphological level (head circumference); (b) perform genetic linkage/association studies in strong candidate genes likely involved in the biological processes underlying elevated serotonin blood levels, enlarged head circumference, and urinary loss of small peptides.

The identification and characterization of alterations at the DNA level either causing autism, conferring vulnerability, or explaining “marker” features associated with this disease, will undoubtedly enhance our understanding of the neurobiological bases of autism, and likely pave the path to earlier and more reliable diagnoses, and possibly to novel treatment strategies.

Douglas Portman, Ph.D., University of Rochester School of Medicine and Dentistry (AS Biomedical Research Award 2005) $110,649

Genetic control of sexual dimorphism in the nervous system: a nematode model for genetic mechanisms in autism 

One of the many mysteries about autism is its highly biased sex ratio: approximately 75-80% of individuals with autism are male.

Though the development of autism is strongly influenced by genetic factors, no obvious linkage of autism susceptibility genes to sex chromosomes has been found that might explain this biased ratio.

We therefore hypothesize that there exist underlying sexual dimorphisms in the central nervous system that predispose the male brain to autism. Interestingly, recent evidence has demonstrated that the masculinization of the CNS depends not only on circulating sex hormones, but also on cell-intrinsic genetic pathways that function directly downstream of sex chromosome content. It therefore seems quite likely that the normal function of these pathways themselves may explain the predisposition of the male brain to autism.

Moreover, mutations in these genes could contribute to autism by hypermasculinizing specific areas of the brain as predicted by Baron-Cohen’s “extreme male brain” theory of autism. Very little is known about cell-intrinsic, non-hormonal sex-determination pathways in the vertebrate nervous system.

However, invertebrates such as the nematode C. elegans provide an ideal opportunity to dissect the conserved mechanisms that control genetic, non-hormonal sexual dimorphisms in the nervous system. Recent evidence indicates that conserved factors may act in sex-determination pathways in all animals, making C. elegans an excellent and unique system in which to identify and characterize the genetic factors that masculinize the animal nervous system.

Human orthologs of these factors may account for the male predisposition to autism; moreover, genetic mutations in these genes may directly confer increased autism susceptibility. Our work represents and innovative and novel approach to understanding the genetic and sex-specific components of the development of autism, ultimately providing potential opportunities for novel diagnostic and therapeutic tools.

Vijaya Ramesh, Ph.D., and Susan Santangelo, Ph.D. Massachusetts General Hospital (CAN Pilot Research Award 2007) $60,000

PTEN as a Candidate Gene for Autism Spectrum Disorders 

The root causes of autism spectrum disorders (ASD) remain almost entirely unknown. Despite strong evidence for genetic involvement, no specific genes have yet been identified.

The co-occurrence of ASD and Tuberous Sclerosis Complex (TSC) has been recognized for many years. Features of ASD are present in 25-50% of individuals with TSC, a neurodevelopmental disorder caused by mutations in tumor suppressor genes TSC1 and TSC2, encoding hamartin and tuberin respectively.

Tuberin and hamartin function together to inhibit mTOR signaling. In addition to being a critical regulator of cell growth, mTOR signaling plays an essential role in neural plasticity and synapse function. Naturally occurring mutations resulting in inactivation, or downregulation of the tuberin-hamartin complex through phosphorylation, lead to aberrant activation of mTOR signaling.

One of the key upstream regulators of PI3K/Akt/mTOR signaling is the phosphatase PTEN. Mutations in PTEN result in Akt activation, with consequential tuberin phosphorylation and mTOR activation. Intriguingly, PTEN mutations have been reported in a few autistic individuals with macrocephaly. Furthermore a very recent study has reported behavioral abnormalities resembling human ASD in mice where Pten deficiency is confined to discrete mature neuronal populations.

We hypothesize that inherited variations in PTEN, which influence mTOR signaling, will be associated with genetic risk for ASD. We will test this hypothesis by scanning the entire coding region of PTEN gene first in 156 parent-offspring trios affected with ASD. In collaboration with Dr. Rudy Tanzi, this analysis will be extended to at least another 250 parent-offspring trios available through AGRE.

Our hypothesis, if proven, would break new ground in understanding the pathogenesis of ASD. Co-Sponsor: The Gassin Family Foundation.

Vijaya Ramesh, Ph.D., Massachusetts General Hospital (AS Biomedical Research Award 2005) $120,000

Pam as a Candidate Gene for Autism 

Tuberous sclerosis complex, commonly known as TSC, is an inherited disease affecting many organs with brain being one of the most severely affected organ. Neurological complications in TSC include seizures, mental retardation and autism.

Features of autism spectrum disorders are reported to be present in 25-50% of individuals with TSC. Two TSC genes TSC1, and TSC2, are responsible for the disease. TSC1 encodes a protein known as hamartin, and TSC2 encodes a protein known as tuberin. Mutations in either the TSC1 gene or TSC2 gene disrupt the functions of hamartin and tuberin resulting in TSC and the associated neurological symptoms including autism.

The precise mechanism by which mutations in the TSC genes result in neurological manifestations is currently under investigation in a few laboratories including our own. Many proteins exert their function in partnership with other proteins, and our laboratory research interests include isolating such proteins that partner with hamartin and tuberin in the brain.

We recently identified a protein known as Pam as a partner of tuberin and hamartin. Pam is known to have distinct functions in the nervous system. In our ongoing studies we have observed that Pam can regulate the activities of hamartin and tuberin. Pam family members in other systems play an important role in neurons.

Pam is also expected to have a crucial role in brain development and neuronal connectivity. Furthermore, Pam maps to a region of a human chromosome where an autism locus has been implicated in some families.

We predict that Pam could play a role in autism through its interaction with hamartin and tuberin, and through its critical function in neurons. In this proposal we plan to examine the involvement of Pam in autism, which could provide new clues for understanding autism in TSC as well as autism in general.

James Rand, Ph.D., Oklahoma Medical Research Foundation (AS Biomedical Research Award 2006) $120,000

Molecular and Cellular Mechanisms of Neuroligin-Mediated Synaptogenesis

One of the most striking results emerging from the intensive international effort to identify “autism-related” genes has been the recent demonstration of an association with autism (in some families) of mutations in genes encoding a family of proteins called neuroligins.

Neuroligins are synaptic proteins present on post-synaptic cell membranes, and they bind specifically to a set of presynaptic membrane proteins called neurexins. Recent studies have shown that the binding of neuroligin to neurexin can be sufficient to mediate the assembly of the presynaptic components of a synapse (Dean et al. 2003;Scheiffele et al. 2000).

There are 4 neuroligin-encoding genes in humans, and mutations disrupting the NLGN3 and NLGN4 genes (both of which are on the X-chromosome) seem to be associated with autism (Chih et al. 2004;Jamain et al. 2003;Laumonnier et al. 2004).

The association of autism with a disruption in components involved in synapse assembly provides a point of entry for investigating the altered development and “miswiring” of the brain in autistic individuals. However, what is still needed is a more precise understanding of the molecular and temporal details of neuroligin expression, neuroligin trafficking, and neuroligin-mediated synaptogenesis.

Although much can be learned from tissue culture, cell culture and studies of knock-out mice, we believe that, as has been true of so may other areas of biological research, an important contribution can be made through the use of simple model systems. We are therefore proposing to analyze the molecular genetics and cell biology of neuroligin and the interactions between neuroligin and neurexin in the nematode C. elegans.

We will use C. elegans for these studies because of its simple nervous system and its ease of genetic and molecular analysis; all such studies are far easier, quicker, and less expensive in C. elegans than in mice.

We will be addressing 2 basic issues:

(1) what are the proteins or factors required for proper expression and localization of neuroligins; and

(2) if neuroligin is absent during nervous system development, might there be some remedial effect from expressing it in mature neurons. 

Lawrence T. Reiter, Ph.D., University of Tennessee Medical School (CAN Pilot Research Award 2006) $120,000

A Proteomics Approach to the Identification and Characterization of Protein Targets Regulated by UBE3A 

Autism spectrum disorders include the severely debilitating Rett syndrome (RTT) and Angelman syndrome (AS). These disorders are interrelated at the molecular level and mutations in the gene that causes RTT can also cause AS. In addition, approximately 3% of all inherited autism cases may result from maternally inherited duplications of the region containing the gene that causes AS, UBE3A.

Mutations in the protein targets of the ubiquitin ligase UBE3A may, therefore, account for a significant percentage of inherited autism cases as well. Herein we describe a proteomics approach utilizing the powerful genetic model organism Drosophila melanogaster to identify the protein targets of fly dube3a. Wild type, dominant negative and epitope tagged forms of dube3a will be over-expressed in the brains of flies using the GAL4/UAS system in order to increase or decrease the levels of dube3a protein targets.

We will then identify these targets by 2D gel electrophoresis and mass spectrometry. Potential targets will be validated though genetic suppressor/enhancer screens, immunoprecipitation binding assays in 293T cells and immunohistochemistry in the brains of Ube3a-null mice. Finally, we will screen the human orthologs of these validated target genets in the AGRE sample collection for evidence of involvement in genetic risk for development of autism.

John Rubenstein, M.D., Ph.D., University of California, San Francisco (CAN Pilot Research Award 2005) $120,000

DLX Genes and Autism 

Autism is frequently associated with epilepsy. This and other aspects of Autism have led to a multifactorial model postulating that some cases of Autism are due to an increase in the ratio of excitation/inhibition in key neural circuits (Rubenstein and Merzenich, 2003).

GABAergic local circuit neurons have the central role in inhibiting the activity of cortical and hippocampal glutamatergic neurons. Therefore, defects in the development and/or function of these GABAergic neurons could underlie some forms of Autism.

Recent discoveries have begun to elucidate the genetic mechanisms that control forebrain GABAergic neuronal development. The DLX1, 2, 5 and 6 homeobox genes have a central role in these processes. Furthermore, these genes are located in regions of chromosomes 2 and 7 that are linked to Autism.

This led us to begin sequencing the exons and known regulatory elements of these DLX genes in patients with Autism. Our initial studies have identified 5 types of non-synonymous mutations in DLX2 and DLX5 that are present in Autistic probands roughly 10-times more frequently than in a control population. We propose to expand our sequencing effort and to study the biochemical ramifications of these mutations. 

Scott B. Selleck, M.D., Ph.D., University of Minnesota (CAN Pilot Research Award 2007) $120,000

Genomic Instability of an Interval on Chromosome 10q and its Contribution to Autism Spectrum Disorder 

We have identified a region of chromosome 10q that bears a number of large segmental duplications or low copy repeats.

Our analysis of this region began with the identification of a large kindred with developmental delay and autism associated with a 7 Mb deletion involving two segmental duplicons. We have since identified three other families with rearrangements involving these segmental duplicons.

Further studies showed the rearrangements to be complex, with noncontiguous deletions and some breakpoints mapping outside, but near, the segmental duplicons. These finding suggested this region is genetically unstable and smaller rearrangements not detectable with traditional cytogenetic methods might contribute to autism spectrum disorder.

We therefore examined the inheritance of simple tandem repeat polymorphisms (STRPs) in the 10q region in a set of 119 autism families compared to 173 non-autistic control families. We found significantly higher rates of loss-of-heterozygosity for these 10q markers in autistic families compared to controls.

Markers on other chromosomes do not show this elevated rate of mutation in these same autism families. Our proposed work aims to examine DNA copy number changes in the 10q interval in autistic children compared to normal controls, and determine if another independently ascertained set of autism families (autism genetics research exchange, AGRE) shows an elevated frequency of STRP mutations.

Our long-term goals are to understand the degree to which genomic instability mediated by segmental duplications contributes to autism spectrum disorder generally and what genes in the 10q interval might be affecting the development of autism.

Frank R. Sharp, M.D., University of California, Davis (CAN Pilot Research Award 2007) $120,000

Blood Genomic Studies of Children with Idiopathic Autism

Autism appears to be a complex neurodevelopmental disease that may be caused by the interaction of a genetic predisposition combined with environmental influences. We have demonstrated that blood genomic profiling in humans can reliably detect the effects of genetic diseases on blood gene expression, and environmental agents like medications or infections also produce characteristic blood genomic profiles.

We have applied this approach to children with autism ages 2 to 5, and discovered genomic profiles in blood that correlate with the age of onset of children with autism, and correlate with high expression of genes associated with Natural Killer (NK) cells and cytotoxic T lymphocytes, CD8+ cells.

In this project we propose to study 100 children with autism compared to controls, and test whether the genes found to be regulated in children 2-5 years old are also regulated in children 5 to 18 years old. We will confirm that age at onset produces characteristic blood genomic profiles in children with autism at all ages, and that the genes regulated in Natural Killer cells – that normally kill viruses when they enter the blood stream – are also upregulated in a large subgroup of children with autism.

Finally, the results of the first half of the patients will be used to predict the subgroups in the second half of the patients. This study should help identify endophenotypes of autism, and possibly point to abnormalities of NK and/or CD8 cells that might affect the ability of a fetus or child to deal with certain types of viruses.

Marwan Shinawi, M.D., Baylor College of Medicine (CAN Young Investigator Award 2005) $80,000

Search for an Autism Gene on the Y chromosome

This study will attempt to identify the biological and molecular basis of autism. Specifically, the intent is to try to discover the cause of autism and develop a laboratory test that would be used to diagnose patients with autism.

The study will also attempt to explain the higher male predisposition to autism. The fact that the methods used till now have failed to provide strong evidence for a major causative gene for autism suggests that many genes might contribute to autism or other genetic mechanisms may be involved. Dr. Shinawi will test whether changes that do not involve nucleotide sequence such as changes in chromatin structure and nucleotide sequence methylation can alter gene expression and eventually cause autism.

The heritable changes in gene function that occur without a change in the DNA sequence are called epigenetic changes. The DNA methylation is a chemical modification of the nucleotide sequence itself that can change the expression of different genes. The emphasis will be on genes that are located on the Y chromosome, an area that has been under investigated.

If an epigenetic basis is identified for autism, there might be the potential for therapeutic intervention using compounds such as folic acid, which are known to alter the regulation of genes that are subject to regulation by DNA methylation. Jonathan Pettigrew Memorial Award 

Patrick Sullivan, M.D., University of North Carolina (AS Biomedical Research Award 2006) $100,000

Fragile X syndrome may yield clues to the genetics of autism 

With occasional exceptions, the genetic dissection of complex traits has proven more difficult than many researchers anticipated.

This is particularly the case for neuropsychiatric disorders like autism where proof “beyond a reasonable doubt” remains elusive despite intensive efforts by a large number of groups. A key issue is that positive findings from genomewide searches by linkage or association have an overwhelming probability of being false positives unless the a priori probability of association is substantially elevated. At present, there are few ways to estimate a priori probabilities. We propose here a proof-of-concept pilot study. This proposal will provide data that will strongly support an eventual, full-scale effort.

If the genetic effect sizes are conspicuously large, it is possible that this pilot study will itself be informative. In the full study, we are pursuing an achievable and potentially highly informative way to identify candidate genes for autism with high a posteriori probabilities via multiple strategies. To do this, we will capitalize on the fact that individuals with Fragile X Syndrome have similar mutations in FMR1 and yet vary dramatically in their degree of autism with about a third of Fragile X Syndrome probands unaffected, intermediately affected, and affected with autism.

The presence of genetic modifier loci is strongly supported by the observation that Fmr1 knockout mice have marked behavioral differences depending on genetic background. Therefore, using FMR1 as a “toehold”, the full study will apply twostage genomewide association to 500 individuals with proven expansion of the FMR1 CGG 5′ UTR repeat to >200 copies.

Multistage designs have become standard in the field as they preserve statistical power while minimizing cost. In Stage 1, we will conduct genomewide association in half the sample using the Illumina 500K SNP platform. In Stage 2, we will prioritize ~7,500 SNPs for genotyping in the whole sample based on findings from Stage 1, the genomic locations of transcripts and proteins known to interact with FMRP (the RNA binding protein product of FMR1), and convergent findings from external genomewide linkage and association studies for autism.

Following limited resequencing, in Stage 3, we will investigate whether the most compelling findings replicate in an independent sample of 700 cases with autism and 700 matched controls. In this pilot study, we request funding to establish a sample of 150 males with Fragile X Syndrome. All individuals will have confirmed FMR1 mutation status and will have validated assessments of autistic behavior via inexpensive methods (telephone and questionnaire – expensive home assessments are planned in the full study).

We will then genotype 768 carefully selected genetic markers (SNPs) in genes whose products are known to interact with FMRP. Statistical analyses will investigate associations between genotypes and haplotypes with the degree of autism. We note that this work is highly synergistic with the NIH-funded Autism and Fragile X centers at UNCChapel Hill.

Although we request no funds for these efforts, our co-investigators at UNC-CH are wellpositioned quickly to explore the molecular neurobiology of the best findings. Finally, as autistic features are correlated with worse outcome in Fragile X syndrome, our results could lead to improved treatments for important subsets of individuals with Fragile X syndrome.

Zohreh Talebizadeh, Ph.D., Children’s Mercy Hospital & University of Missouri, Kansas City (CAN Young Investigator Award 2005) $79,636

X Chromosome Inactivation and Candidate Gene Studies in Females with Autism 

Autism is genetically and phenotypically heterogeneous disorder. Thus, traditional gene identification methods such as linkage analysis are not sufficiently powerful to identify responsible gene(s). Therefore, studying a more homogeneous group of autistic subjects should provide more power in identification of the underlying genetic factors. A

four fold increased prevalence of autism in males than in females suggests a role of the X chromosome. We previously studied X chromosome inactivation in 30 females with classical autism. A significantly higher (p=0.04) prevalence of X chromosome skewness was detected in autistic females (33%) compared with controls (11%). X chromosome skewness was also seen in 50% of the mothers with autistic daughters. Such a consistency of X inactivation pattern in mother/daughter pairs is rare in the normal population.

We hypothesized that X chromosome skewness may predispose a subset of females to autism. To evaluate our hypothesis, in the current project we will: 1) perform X chromosome inactivation in 100 autistic females from AGRE; 2) examine clinical differences between individuals with significant X inactivation skewness and random X inactivation pattern 3) screen three X-linked candidate genes (e.g., NLGN3, NLGN4 and MECP2) in autistic females with significant X inactivation skewness using both direct DNA sequencing and quantitative gene expression analysis.

These screening methods will enable us to search for sequence changes in the coding region of these candidate genes as well as up or down differences at the expression level. These changes may also reflect other alterations (e.g., change at the promoter regions or regulatory factors).

John B. Vincent, Ph.D., Center for Addiction and Mental Health

(CAN Pilot Research Award 2005) $29,998

Investigation of the Involvement of the MECP2 Gene Exon 1 and the Encoded Protein MeCP2B in Autism 

Both autism and Rett syndrome are forms of pervasive developmental disorder with a number of similarities in clinical features. Mutations in a gene called MECP2 are responsible for 80% of Rett syndrome cases. Importantly, mutations in the MECP2 gene occasionally cause symptoms that are indistinguishable from autism. Dr. Vincent has just identified a previously unknown portion of the MECP2 gene, which may help divulge more information about how this gene functions.

The investigators have already found a mutation within this new region in one girl with Rett syndrome. This finding suggests that the protein made by the new version of the gene may be the disease-relevant form. This study will be exploring the link between autism and the new form of the MECP2 gene, and hopes to elucidate its role in brain development by making animal models.

Christopher A. Walsh, M.D., Ph.D., Beth Israel Deconess Medical Center(CAN Pilot Research Award 2005) 119,988

Recessive Genes for Autism Spectrum Disorders 

Studies suggest that autism often has a genetic cause but, to date, only two possible autism genes have been identified. We do not yet know what proportion of autism is caused by the action of either of these genes. This study involves the search for additional genes that may be involved in causing autism. By taking the unique approach of focusing our research on families with equal numbers of males and females affected, as well as families in which the parents may be related to one another, we plan to identify genes that can lead to autism only when inherited from both sides of the family. These so-called recessive genes may be individually rare, but collectively cause a substantial proportion of autism. Co-Sponsor: The Galli Family in honor of David Duber

Stephanie White, Ph.D., UCLA (AS Post-Doctoral Fellowship Award 2005) $56,032.10

Molecular targets for socially-learned vocalization

Autism can be clinically diagnosed by two deficits: an inability to participate in joint attention, and poor language development with abnormal social use. In order to understand the mechanisms of this disorder and to develop treatments to compensate for these deficits, the basic neural mechanisms for speech development and for social influences on this learning must be known.

However, to date, we have little understanding of the basic cellular and molecular processes underlying human speech nor do we know how social interactions influence vocal-learning mechanisms.

Many confounding factors make identification of the neural mechanisms that underlie vocal learning currently intractable in humans. Fortunately, songbirds offer the potential to identify socially-sensitive neural mechanisms for vocal-learning, including human speech. Songbirds, like humans –but not other primates nor rodents– learn their vocalizations.

Vocal-learning in songbirds shares key aspects with human speech. In both songbirds and humans:

1) Vocal-learning happens during critical developmental phases;

2) It occurs within discrete regions of the brain that are dedicated to the development and production of learned vocalizations;

3) Social influences have a significant impact on vocal-learning. Importantly, songbirds alone are open to direct physiological, molecular, and behavioral analyses. 

The proposed studies use songbirds for their unparalleled potential to reveal the basic neural mechanisms that underlie vocal learning. We will use cell and slice cultures of songbird brain obtained during the formation and the function of song structures, and songbird cDNA microarrays, to identify gene targets for vocal learning.

In further studies, conducted alongside or directly following the proposed research, molecules identified in the songbird will be compared to those identified in human brains to assess their role in human speech and language.

Tero Ylisaukko-oja, Ph.D., National Public Health Institute, Finland (CAN Young Investigator Award 2005) $80,000

Genome-wide Linkage Disequilibrium and Expression Analysis of Autism in a Large Isolated Pedigree 

Autism is a strongly genetic disorder with complex etiology. Several genome-wide screens have been performed in autism, including two in the Finnish population, resulting in identification of multiple putative susceptibility loci.

As a part of the study of autism spectrum disorders in the Finnish population, we have performed extensive genealogical searches and attempted toidentify common ancestors for the participating families. As a result, we have been able to connect 21 Finnish autism families by genealogical links extending to 17th century.

Although the earlier work in the Finnish population has revealed some interesting loci, the benefits of this isolated pedigree have not been maximally utilized so far. In this study, we aim to exploit this exceptional family resource by using the latest techniques in molecular genetics and biocomputing. We hypothesize that the families in the isolated pedigree have inherited the same predisposing allele(s) from the common ancestor. We will use a dense set of microsatellite and SNP markers to reveal the shared haplotypes around the predisposing variant.

We will also monitor the gene expression profiles in the lymphocytes of autistic individuals in these families, which could give clues about the functional candidate genes and relevant pathways. Several methods, including biocomputing, haplotype block characterization, extensive sequencing, and analyses with larger Finnish autism sample, will be used for identification of the predisposing variant.

This data could pave the way towards identification of novel metabolic pathways underlying autism, and thus provide new insights into etiopathogenesis of autism and related disorders.


Autistic people have fought the inclusion of ABA in therapy for us since before Autism Speaks, and other non-Autistic-led autism organizations, started lobbying legislation to get it covered by insurances and Medicaid. 

ABA is a myth originally sold to parents that it would keep their Autistic child out of an institution. Today, parents are told that with early intervention therapy their child will either be less Autistic or no longer Autistic by elementary school, and can be mainstreamed in typical education classes. ABA is very expensive to pay out of pocket. Essentially, Autism Speaks has justified the big price tag up front will offset the overall burden on resources for an Autistic’s lifetime. The recommendation for this therapy is 40 hours a week for children and toddlers.

The original study that showed the success rate of ABA to be at 50% has never been replicated. In fact, the study of ABA by United States Department of Defense was denounced as a failure. Not just once, but multiple times. Simply stated: ABA doesn’t workIn study after repeated study: ABA (conversion therapy) doesn’t work. 

What more recent studies do show: Autistics who experienced ABA therapy are at high risk to develop PTSD and other lifelong trauma-related conditions. Historically, the autism organizations promoting ABA as a cure or solution have silenced Autistic advocates’ opposition. ABA is also known as gay conversion therapy.

The ‘cure’ for Autistics not born yet is the prevention of birth. 

The ‘cure’ is a choice to terminate a pregnancy based on ‘autism risk.’ The cure is abortion. This is the same ‘cure’ society has for Down Syndrome. 

This is eugenics 2021. Instead of killing Autistics and disabled children in gas chambers or ‘mercy killings’ like in Aktion T4, it’ll happen at the doctor’s office, quietly, one Autistic baby at a time. Different approaches yes, but still eugenics and the extinction of an entire minority group of people.

Fact: You can’t cure Autistics from being Autistic.

Fact: You can’t recover an Autistic from being Autistic.

Fact: You can groom an Autistic to mask and hide their traits. Somewhat. … however, this comes at the expense of the Autistic child, promotes Autistic Burnout (this should not be confused with typical burnout, Autistic Burnout can kill Autistics), and places the Autistic child at high risk for PTSD and other lifelong trauma-related conditions.

[Note: Autism is NOT a disease, but a neurodevelopmental difference and disability.]

Fact: Vaccines Do Not Cause Autism.

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