Autism Tissue Program (ATP)
Brain Resources and Data Monthly Report
Program. Daniel Lightfoot, Ph.D., Program Director
Jane Pickett, Ph.D., Director of Brain Resources and Data
Carolyn Komich Hare, M.S., Clinical Coordinator, ADI-R Certified Trainer
Ellen Xiu, M.S., Data Coordinator
Donor lists/phenotype and genotype data are available on the ATP informatics portal at
www.atpportal.org. Daniel Lightfoot and Rich Pickett, the portal architect, are collaborating on graphical
illustrations of the resource. This is an overview of donors tracked in the portal as a service to
investigators. The ATP tissue board approves tissue distributions from Harvard-ATP, Harvard, IBR and
Oxford [collaborating brain banks]. These are ‘primary’ brain tissue collections; ‘secondary’
distributions are stained slides, floating sections, and DNA (RNA soon) processed by investigators using
the primary resource. All distributions, and results as published, or submitted, are tracked in the portal.
Tissue Advisory Board (TAB)
The TAB responsibilities and a membership list are appended to this report. Guidelines for proposals to
obtain tissue are on www.atpportal.org. The deadline for tissue applications is July 15th and the next
TAB meeting will be in August. Investigators interested in applying for DNA derived from brain
cortical (BA19) tissue, or cell cultures derived from skin fibroblasts of individuals with autism with and
without fragile X, please contact firstname.lastname@example.org for the application form and access to the portal
genotype data. RNA array data, both raw and normalized data with thresholding for brain-expressed
genes, is deposited in GEO: accession number GSE28521, for three brain areas – see Geschwind project
for details or contact email@example.com.
Project statistics for this month:
This Month: Cumulative Total
TISSUE INQUIRES: 4 394
TISSUE PROPOSALS: 2 196
New PROJECTS APPROVED: 1 117
Xuegun Li, Emory University School of Medicine; #2619; DNA Application approved.
Genome-wide DNA Methylation Profiling in Autism Spectrum Disorders
Autism is comprised of a clinically heterogeneous group of disorders, collectively termed autism
spectrum disorders (ASD), that share common features of impaired social relationship, impaired
language and communication, and limited range of interests and behavior. Autism is among the most
heritable neuropsychiatric disorders, and accumulating evidence suggests a complex etiology for ASD
that may include epigenetic and environmental factors. Methylation of the C5 position of cytosine (5-
meC) residues in DNA has long been recognized as an epigenetic silencing mechanism of fundamental
importance. The methylation of CpG sites within the human genome is maintained by a number of DNA
methyltransferases (DNMTs) and has multifaceted roles for the silencing of transposable elements, for
the defense against viral sequences and for the transcriptional modulation of certain genes. Very recently
a previously unrecognized modified DNA base, 5-hydroxymethylcytosine (5-hmC), was found in
mammalian DNA. 5-hmC constitutes a significant portion of nucleotides in the brain cells (~0.6% of
total nucleotides in Purkinje cells and ~0.2% in granule cells) and embryonic stem cells (~0.032%). The
surprising abundance of 5-hmC discovered in brain and stem cells suggests important roles for this
modification. These findings have fostered wide speculation that this 5-hmC modification might also be
an important epigenetic modification. Understanding the role of 5-hmC in development is difficult
because neither of the methodologies currently available that can distinguish 5-hmC from 5-meC, thin
layer chromatography and mass spectrometry, can provide information about the genomic location of 5-
hmC. Bisulfite sequencing can provide sequence information but cannot distinguish 5-hmC from 5-meC.
To overcome these technical problems, we have established the technology to profile the genome-wide
distribution of 5-hmC. Our study will reveal the function of 5-hmCs during postnatal brain development
and its roles in the etiology of and pathogenesis of autism
June 22. Daniel Lightfoot participated in the annual IDEAS conference held in Philadelphia and
provided an update on the ATP involvement in brain donation of individuals with chromosome 15q
Published Papers/Abstracts on research supported, all or in part, by brain donations
1. Scherer SW, Dawson G. Risk factors for autism: translating genomic discoveries into
diagnostics. Hum Genet. 2011 Jun 24. [Epub ahead of print]
Autism spectrum disorders (ASDs) are a group of conditions characterized by impairments in
communication and reciprocal social interaction, and the presence of restricted and repetitive behaviors.
The spectrum of autistic features is variable, with severity of symptoms ranging from mild to severe,
sometimes with poor clinical outcomes. Twin and family studies indicate a strong genetic basis for ASD
susceptibility. Recent progress in defining rare highly penetrant mutations and copy number variations
as ASD risk factors has prompted early uptake of these research findings into clinical diagnostics, with
microarrays becoming a 'standard of care' test for any ASD diagnostic work-up. The ever-changing
landscape of the generation of genomic data coupled with the vast heterogeneity in cause and expression
of ASDs (further influenced by issues of penetrance, variable expressivity, multigenic inheritance and
ascertainment) creates complexity that demands careful consideration of how to apply this knowledge.
Here, we discuss the scientific, ethical, policy and communication aspects of translating the new
discoveries into clinical and diagnostic tools for promoting the well-being of individuals and families
2. Oblak AL, Rosene DL, Kemper TL, Bauman ML, Blatt GJ. Altered posterior cingulate cortical
cyctoarchitecture, but normal density of neurons and interneurons in the posterior cingulate cortex and
fusiform gyrus in autism. Autism Res. 2011 Jun;4(3):200-11. doi: 10.1002/aur.188. Epub 2011 Feb 28
Autism is a developmental disorder with prenatal origins, currently estimated to affect 1 in 91 children
in the United States. Social-emotional deficits are a hallmark of autism and early neuropathology studies
have indicated involvement of the limbic system. Imaging studies demonstrate abnormal activation of
the posterior cingulate cortex (PCC), a component of the limbic system. Abnormal activation has also
been noted in the fusiform gyrus (FFG), a region important for facial recognition and a key element in
social interaction. A potential imbalance between excitatory and inhibitory interneurons in the cortex
may contribute to altered information processing in autism. Furthermore, reduced numbers of GABA
receptors have previously been reported in the autistic brain. Thionin-stained sections were used to
qualitatively assess cytoarchitectonic patterning and quantitatively determine the density of neurons and
immunohistochemistry was used to determine the densities of a subset of GABAergic interneurons
utilizing parvalbumin-and calbindin-immunoreactivity. In autism, the PCC displayed altered
cytoarchitecture with irregularly distributed neurons, poorly demarcated layers IV and V, and increased
presence of white matter neurons. In contrast, no neuropathology was observed in the FFG. There was
no significant difference in the density of thionin, parvalbumin, or calbindin interneurons in either
region and there was a trend towards a reduced density of calbindin neurons in the PCC. This study
highlights the presence of abnormal findings in the PCC, which appear to be developmental in nature
and could affect the local processing of social-emotional behaviors as well as functioning of interrelated
3. Greco CM, Navarro CS, Hunsaker MR, Maezawa I, Shuler JF, Tassone F, Delany M, Au JW,
Berman RF, Jin LW, Schumann C, Hagerman PJ, Hagerman RJ. Neuropathologic features in the
hippocampus and cerebellum of three older men with fragile X syndrome. Mol Autism. 2011 Feb
The FMR1 gene is polymorphic for the length of CGG trinucleotide repeat expansions in the 5'
untranslated region. Premutation (55-200 CGG repeats) and full-mutation (>200 CGG repeats) alleles
give rise to their respective disorders by different pathogenic mechanisms: RNA gain-of-function
toxicity leads to fragile X-associated tremor/ataxia syndrome in the premutation range, and
transcriptional silencing and absence of fragile X mental retardation protein (FMRP) lead to fragile X
syndrome in the full-mutation range. However, for the latter, incomplete silencing and/or sizemosaicism
might result in some contribution to the disease process from residual messenger RNA
production. To address this possibility, we examined the brains of 3 cases of fragile X syndrome for the
presence of intranuclear inclusions in the hippocampal dentate gyrus. We identified low levels (0.1%-
1.3%) of intranuclear inclusions in all 3 cases. Quantitative reverse transcription-polymerase chain
reaction for FMR1 messenger RNA and immunofluorescence for FMRP revealed low but detectable
levels of both RNA and protein in the 3 cases, consistent with the presence of small numbers of
inclusions. The intranuclear inclusions were only present in FMRP-immunoreactive cells. The small
numbers of inclusions and very low levels of both FMR1 RNA and protein suggest that the clinical
course in these 3 subjects would not have been influenced by contributions from RNA toxicity.
Blog on the importance of brain donation from ATP founder, Eric London.
Researchers and interested person are invited to contribute to the Science Blogs at any time. If
interested, please contact Jane Pickett or firstname.lastname@example.org for July blogs.
UK Brain Donation Programme. The portal also houses medico-clinical information on 12
donors to the UK Brain Bank for Autism and Related Developmental Research. There is an
excellent video on the site – please see at: http://www.brainbankforautism.org.uk .
In new news from the UK BBA, Professor Margaret Esiri, Director of the brain bank at Oxford
received an award from the MRC (like NIH) to carry out a pilot project to collect control brains.
The brain tissue from unaffected individuals is very important.
UK BBA activity as of May 1, 2011
15 brains have been donated (4 additional to be transferred to Oxford)= 19
18 of these donors had an ASD
3 had an associated condition ( 2 had epilepsy and one had chromosome 15q duplication
1 had epilepsy but not an ASD (so this is the only control tissue donated so far)
IDEAS. Please note that the ATP works with IDEAS, a support group for chromosome 15q
duplications, www.dup15q.org. The donor list can be found under 'Disorders' in 'Case Data'.
Use of these specimens is contingent on approval by the IDEAS science advisers; therefore,
applications including these donors need to clearly justify their use.
Diagnostic terms used in portal. The diagnosis of autism is most often made after a home
visit with the legal next of kin or by review of all written or video records. Autism-Suspected
is still used for donors not evaluated by ATP staff, unless ADI-R raw data is available to make a
diagnosis. Donors with a history of autism, and evaluated by the ATP clinical staff, have been
given one of four descriptions after evaluation; these are updated as more information is
Autism - confirmed by ADI-R [domain scores n portal; raw data in ISAAC)
Autism - supported by records [supporting documents and summary available]
Autism - suspected; seeking records [evaluation not complete]
Autism - suspected; no confirmation [no records or family to support diagnosis]
Clinical documentation is based on interviews with parents and home visits to do the ADI-R
and SCQ (Autism Diagnositc Interview – Revised and Social Communication Questionniare).
ADI-R domain and SCQ scores are posted to the ATP Informatics Portal (www.atpportal.org)
with other phenotypic records. Raw ADI-R and SCQ data are entered into the Autism Genetic
Resource Exchange database called (ISAAC). It has been brought to ATP attention that grant
reviewers are expecting to see quantatitive behavioral data that represents the subject at the time
of testing, or in the case of a brain donor, at the age of death. ATP staff can provide this
information for HBTRC donors as well as indicators of regression or aggression.
Data. ATP Informatics Portal. Since its inception, a goal of the portal is to track all known donated
brains available for and/or used in ASD research, and to capture results. To date, 491 donated
brain specimens are listed in the portal; these reside in various banks and private collections.
The ATP is authorized to approve of distribution of brain tissue collected for the program by
Harvard; therefore, ‘Harvard-ATP’ in the Source column on the Case Data page will sort out the
tissues ATP can distribute upon approval by the Tissue Advisory Board (TAB). Abstracts,
published reports and datasets from projects supported by tissue donation may be found on the
ATP Informatics Portal. For login access please see information at www.atpportal.org or write
Jane Pickett, Ph.D.
ATP Director of Brain Resources and Data
Appendix. ATP Tissue Advisory Board; ATP Initiative; Celloidin Library; Neural and Skin Stem Cells
Tissue Advisory Board (TAB)
The TAB is an external board comprised of 12 members with expertise ranging from psychiatry to
imaging to genetics to brain bank directors and neuropathologists. Reviewers from the TAB are
selected to post written reviews and scores of proposals then the full board meets quarterly for a
discussion and final scoring of each application. A score of 2.5 or better (lower) is required to obtain
tissue, as well as adequate funding. PIs are either approved or given recommendations to improve their
proposals should they want to reapply. Members serve 5 year terms; nominations for TAB membership
Keith A. Young, Ph.D. Associate Professor and Vice-Chair for Research, Psychiatry and Behavioral Science, Texas A&M
Health Science Center and Central Texas VA. Major Fields of Interest; Neuropathology, genetics, animal models and
translational therapeutics. Dr Young studies the role of the thalamus in mental illness and behavior. 2005; Chair 2009-2013.
David S. Baskin, M.D., F.A.C.S. Professor Neurological Surgery and Residency Program Director, Director of Research,
Department of Neurosurgery at The Methodist Neurological Institute, and co-chair of the Cure Autism Now Scientific
Review Council. Major Research Interests: immune alterations in autism, molecular biology and new treatments for stroke;
apoptotic cell death, spinal cord injury, brain tumors, imaging, nanotechnology, and microsurgery.
William M. Byne, M.D., Ph.D. Associate Professor, Department of Psychiatry, Mount Sinai School of Medicine, New
York, NY. Major Fields of Interest: Neuropathology of schizophrenia, quantitative postmortem neuroanatomy and
neuroimaging, neuroendocrinology and brain development.
Emanuel DiCicco-Bloom, M.D. Professor of Neuroscience & Cell Biology, and also Professor of Pediatrics (Neurology)
NJ’s University of Medicine and Dentistry at Robert Wood Johnson Medical School.
Margaret Esiri, Professor in Neuropathology, John Radcliffe Hospital, Oxford, London. Director of the Thomas Willis
Oxford Brain Collection, one of the largest repositories of such tissue in the UK and author of 2008 “Oppenheimer’s Diagnostic
Neuropathology: a Practice Manual” with Daniel Perl. Prof. Esiri has a longstanding interest in the neuropathology of multiple sclerosis
and diseases that cause dementia, particularly Alzheimer's disease and vascular causes of dementia. She was responsible for completion of
ethics application in the UK that is the foundation of the Brain Bank for Autism and Developmental Disorders at Oxford.
Antonio Y. Hardan, M.D. Assistant Professor of Psychiatry and Behavioral Sciences, Stanford University. Dr. Hardan is the
Director of the Autism and Developmental Disabilities Clinic. He has over 15 years of clinical experience evaluating and
treating children, adolescent and adults with autism. His research interests include the following areas: neuroimaging
(anatomical MRI and Spectroscopy) and psychopharmacology.
Christine M. Hulette, M.D. Professor of Pathology, Duke University Medical Center and Director of the Kathleen Price
Bryan brain bank. Her expertise includes neuroanatomy, neurophysiology and neuropathology of aging, gene expression
profiles in anatomically and functionally distinct regions of the normal aged human brain and quality control of human
donated tissue: legal, ethical and technical issues.
James W. Ironside, CBE, FRCPath. Professor of Clinical Neuropathology, University of Edinburgh. Scotland, president of
the British Neuropathology Society and the director of the MRC Network of UK Brain Banks. His main focus of research is
the pathology of human prion disease, with attention to CJD medicine and healthcare in the UK and Europe. An interest in
diagnostic neuro-onncology led to the development of molecular diagnostic facilities for brain tumors in Edinburgh.
Nicholas T. Lange, Sc.D. Associate Professor of Psychiatry at Harvard Medical School and of Biostatistics, Harvard
School of Public Health. Dr. Lange is also director of the Neurostatistics Laboratory (NSL) at McLean Hospital. His
research interests include functional and anatomical magnetic resonance imaging (fMRI, MRI), diffusion tensor imaging
(DT-MRI) and specialized microscopy for brain tissue analysis of gene expression.
Deborah A. Lee, M.D., Ph.D. Global Medical Director-Neurology at Baxter Healthcare Corporation, Deerfield, IL. Her
past experience has been in clinical work and neuropathology research of autism.
Stephen D. Ginsberg, Ph.D., Associate Professor in Psychiatry & Neuroscience at the New York University School of
Medicine with expertise on molecular mechanisms using state-of-the-art molecular biology, immunohistochemical, and
imaging techniques in the study of human port mortem brain tissue. The principal focus is to delineate cellular and molecular
mechanisms underlying synaptic and dendritic reorganization following various brain injuries, including excitotoxicity,
specific lesions, and neurodegeneration using human brain tissue and animal models.
Richard S. Nowakowski, Ph.D. Transitioning this spring to Randolph L. Rill Professor and Chair in the Department of
Biomedical Sciences, College of Medicine at Florida State University from UMDNJ-Robert Wood Johnson Medical School,
New Jersey. Major Research Interests: Cell cycle and cell cycle control of neurostem cells during development and during
adult neurogenesis; genetic and genome wide approaches to CNS development. He serves on the editorial boards of Cerebral
Cortex, Journal of Comparative Neurology and Developmental Neuroscience.
The Autism Celloidin Library (ACL) – The ACL is an ATP established collection of age- and sexmatched
whole hemispheres from both unaffected (control) and autistic individuals representing much
of the human lifespan. The globally limited availability of brain tissue severely limited a key scientific
field of comparative (autism and unaffected) tissue analysis. To address this significant crisis in autism
research, the ATP created the ACL - the largest permanent brain tissue resource for basic neurological
studies in autism. To maximize the scientific potential of this resource, the collection was allocated into
three distinct series, each with their own unique experimental attributes. Each whole hemisphere has
been hardened (fixed in celloidin), carefully sectioned at 200 μm intervals and serially allocated into 3
separate series, by sequentially placing each cut section into one of the three successive groups (i.e. –
1,2,3…1,2,3…). Each series was then allocated to a separate scientific fate:
• Series 1 – Tissue was stained with Cresyl Violet (CV), permanently mounted on glass slides and
resides at the Department of Neurobiology, New York State Institute for Basic Research in
Developmental Disabilities (IBR) for experimental research, under the stewardship of Jerzy
• Series 2 – Tissue was stained with Gallocyanin, permanently mounted on glass slides and resides
at the Department of Neuroscience, Mount Sinai School of Medicine in New York for
experimental research, under the stewardship of Patrick Hof, MD.
• Series 3 – Tissue has been placed in reserve at IBR as floating sections in EtOH and is an
invaluable resource for future research.
Working collaboratively with both stewards of the ACL series above are Eric Courchesne, Ph.D.,
UCSD, and Cynthia Schumann, Ph.D. with David Amaral, Ph.D. at the UC Davis M.I.N.D. Institute,
and Manuel Casanova, MD., who contribute their unique approaches, the ATP is not only able to greatly
stimulate the research efforts of these scientists, but is also able to pool all resulting research data by
these researchers and leverage the greatest scientific value from this exceptional collection.
Neural and skin fibroblast stem cells
The National Human Neural Stem Cell Resource (NHNSCR) has created an Autism induced pluripotent
stem cell (iPSC) Biorepository and now has available dozens of fibroblast lines taken from patients with
idiopathic autism as well as patients with FMR1 gene mutations (both full- and pre-mutations), with and
without an accompanying autism spectrum disorder. More information on these lines will be posted
soon; applications will be screened by the ATP TAB. All of the cultures are established under an NIH
grant (R01HD059967), entitled “An Open Repository of Autism iPSCs and their derivatives”. This
effort is in close collaboration with Dr. Randi Hagerman of the UC Davis MIND Institute.
For more information, please e-mail Dr. Phil Schwartz at email@example.com. URL www.nhnscr.org
Philip H. Schwartz, PhD
Director, National Human Neural Stem Cell Resource Director, Autism iPSC Biorepository Children's
Hospital of Orange County Research Institute
455 South Main Street Orange, CA 92868-3874 (714) 516-4310 (Tel) (714) 289-4531 FAX