About
Titles
Harris Professor in the Child Study Center
Director, Program in Neurodevelopment and Regeneration, Child Study Center; Professor in the Department of Neuroscience
Biography
Flora Vaccarino is the Harris Professor at the Child Study Center and Professor in the Department of Neuroscience at Yale University. She received her MD from the University of Padova in Italy. She spent few years as Neuropharmacology Fellow at NIH, trained in clinical psychiatry at Yale, and then was a Research Fellow in developmental genetics at the Yale School of Medicine, where she raised through the ranks to Assistant, Associate and full Professor. Vaccarino leads a multidisciplinary research group working towards new directions for the study of mammalian brain development, particularly human, using stem cell biology and genomics as tools. She has been studying brain development in animal models for over 20 years, focusing on the role of growth factor receptor signaling in the regulation of stem cell behavior and cerebral cortex morphogenesis. Inspired by Sasai’s work, Vaccarino and her lab pioneered the generation of 3D brain organoids from induced pluripotent stem cells (iPSCs) in 2012, and showed that they recapitulate early fetal development of the human cerebral cortex. They then performed an extensive comparison of the organoid’s transcriptome and noncoding elements with isogenic postmortem human fetal cortex and characterized gene regulatory mechanisms that shape the earliest cell fate decisions in human cortical development. Her lab has generated an extensive collection of patient-derived iPSC lines to study altered gene regulatory mechanisms in Autism Spectrum Disorders. Her interests include human somatic genomic variation as a tool to study lineage specification in human embryonic development. She was one of the fiunding members of the Brain Somatic Mosaicism Network (BSMN), a multi-site consortium that studied somatic mosaicism and its implication for neuropsychiatric diseases. Vaccarino is a Fellow of American Association for the Advancement of Science and a member of the PsychENCODE the Somatic Mosaicism across Human Tissues ( SMaHT) Consortia.
Appointments
Child Study Center
ProfessorPrimaryNeuroscience
ProfessorSecondary
Other Departments & Organizations
- Center for Brain & Mind Health
- Child & Adolescent Psychiatry Training Program
- Child Study Center
- Embryonic Stem Cell Research Oversight
- Interdepartmental Neuroscience Program
- Kavli Institute for Neuroscience
- Neuroscience
- Neuroscience Track
- Program in Neurodevelopment and Regeneration
- Tic Disorder & Obsessive Compulsive Disorder Program
- Vaccarino Lab
- WHRY Pilot Project Program Investigators
- Women's Health Research at Yale
- Wu Tsai Institute
- Yale Center for Genomic Health
- Yale Combined Program in the Biological and Biomedical Sciences (BBS)
- Yale Stem Cell Center
- Yale Ventures
Education & Training
- Resident
- Yale University, School of Medicine, Psychiatry (1991)
- Visiting Assistant Professor
- FIDIA-Georgetown Institute for the Neurosciences (1987)
- Research Fellow
- NIMH-Laboratory of Preclinical Pharmacology (1985)
- MD
- Padua University Medical University (1979)
Research
Overview
The Vaccarino laboratory has elucidated crucial mechanisms that regulate neural stem cell self-renewal, survival and differentiation. The lab has been examining conserved mechanisms of forebrain development using mouse models, and human-specific mechanisms by examining human stem and progenitor cells. Using induced pluripotent cells (iPSC) derived from living individuals, the Vaccarino group is now examining how human stem cell differentiation varies across different genetic backgrounds, sex, and clinical phenotypes.
In the 1990’s Vaccarino and colleagues reported that an extracellular protein called Basic Fibroblast Growth Factor 2 (FGF2) increases the number of progenitors for excitatory cortical neurons in vitro (Vaccarino et al., 1995) and in vivo, by microinjection of FGF2 into the cerebral ventricles of rat embryos, producing an increase in cortical surface area (Vaccarino et al., 1999). This was the first evidence that a single factor can elicit a permanent increase in pyramidal neuron number and cerebral cortical size in a mammalian species. Subsequent work demonstrated that the FGF ligands (Vaccarino et al., 1999; Raballo et al., 2000; Korada et al., 2002) and FGF receptors are essential for normal telencephalic development in a region-specific fashion. The Fgfr1 gene knockout alone thwarts cell proliferation within the hippocampal primordium, causing lifelong hippocampal atrophy (Ohkubo et al., 2004), and the double knockout of Fgfr1 and Fgfr2 causes prefrontal cortex volume loss with fewer pyramidal cells (Stevens et al, 2010). Finally, the combined knockout of Fgfr1, Fgfr2 and Fgfr3 in early neurogenesis depletes the cortical stem cell pool globally, resulting in premature ending of neurogenesis and decreased cortical surface area (Rash et al, 2011). Conversely, a microinjection of FGF2 in the lateral ventricles at pre-neurogenic stages of cortical development generates a massive enlargement of frontal cortical surface and the appearance of gyrus-like convolutions in stereotypic bilateral locations (Rash et al, 2013).
In summary, our studies have shown that FGFs establish the primary structure and the surface area of the cerebral cortex by promoting the self-renewal of neural stem cells and the differentiation of projection neurons from neuroepithelial precursors.
The lab has also examined the roles of FGFs in astroglial cells—diverse cellular elements that evolve from a primary role of neural progenitors during embryonic development, to essential partners in neuronal migration, maturation, and metabolic support in the adult brain. To study astroglial cells, the lab has generated the GFAP-CreERT2 transgenic line, in which the Cre recombinase can be transiently induced by a tamoxifen injection in GFAP+ astroglial cells (Ganat et al, 2006). By marking GFAP+ astroglial cells via recombination of genetic reporters, we found that astrocytes can produce neurons in the immature brain, a process that is enhanced by hypoxic injury (Fagel et al., 2006, and Fagel et al, 2009; Bi et al, 2011) and dependent in part upon FGF receptor function (Fagel et al, 2009; Stevens et al, 2102). Furthermore, FGF receptors are required in astroglia to indirectly promote the maturation of cortical inhibitory interneurons during early postnatal development (Müller Smith et al, 2014). Induced loss of FGF signaling only in postnatal astrocytes generates stereotypic locomotor hyperactivity and learning and memory defects that correlate with deficit in specific cell populations in the postnatal brain (Müller Smith et al, 2008, Stevens et al, 2012).
Conscious of the profound differences between brain development in rodents and primates, the Vaccarino lab has been pursuing parallel studies of the human brain. A major theme is whether an excitatory/inhibitory neuron imbalance in specific forebrain systems due to disparate etiologies (i.e., gene mutations; prenatal factors; environmental noxae) may predispose to neuropsychiatric disorders such as autism and Tourette syndrome.
Through postmortem studies of patient and control brains, the lab has discovered in landmark studies that individuals with Tourette’s syndrome (TS) have losses of GABAergic and cholinergic interneurons in the striatum. TS is a developmental disorder of childhood characterized by motor and vocal tics. We demonstrated a large decrease in three classes of interneurons in the striatum of TS: Parvalbumin+; NOS+/NPY+/SST+; and cholinergic (Kalanithi et al, 2005; Kataoka et al, 2010). RNA sequencing confirmed the decreased in interneuron transcripts, and also revealed an up-regulation of inflammatory response- and immune system-related genes (Lennington et al., 2014). The hypothesis is that altered development of subsets of inhibitory neurons in cortico-basal ganglia circuits causes specific alterations in neuronal firing that may cause disorders of the TS spectrum. Current studies using iPSC-derived basal ganglia organoids confirm thwarted development of inhibitory and cholinergic interneurons in TS and suggest potential pathophysiological mechanisms (see below).
To model disorders of brain development in a human system, the Vaccarino lab has adopted the induced pluripotent stem cell (iPSC) model and over the last several years has derived over 600 iPSC lines from patients with developmental disorders. Vaccarino and colleagues pioneered the generation of cortical organoids from iPSC lines (Mariani et al, 2012) and contributed fundamental work on neurodevelopmental alterations in severe, idiopathic ASD using this tool. Transcriptome and cell fate studies in organoids from individuals affected with ASD as compared to unaffected family members indicated alterations in cell proliferation, overproduction of synapses and a striking imbalance between inhibitory and excitatory neurons and their precursors (Mariani et al, Cell, 2015). The work has also revealed an important role of the transcription factor FOXG1 in the overproduction of GABAegic precursor cells (Mariani et al, 2015).
Other studies integrated genomes, transcriptomes and cellular phenotypes to better characterize the organoids as a model for brain development. As part of the PsychENCODE collaborative multi-site project, the lab generated a genome-scale catalog of transcripts and regulatory DNA elements, primarily enhancers, in iPSC-derived organoids and human brain specimens of the same genetic background. The work established that cortical organoids reflect the human cerebral cortex at embryonic to early fetal stages of human brain development, and display a large repertoire of active enhancers that control early neuronal fate and differentiation (Amiri et al, 2018).
Current studies are using single cell approaches to characterize brain organoids in people with different genetic background and in patients with ASD and Tourette syndrome, integrating gene expression with gene regulatory elements and chromatin architecture.
In recent years, somatic mosaicism has emerged as a potential source of differences in developmental trajectories among individuals. Somatic mosaicism is the accumulation of mutations in cellular genomes after fertilization. These can be variations in DNA sequence, including single nucleotide variations (SNVs) and small insertions/deletions (Indels), or variations in DNA copy number (CNVs), in the form of large duplication/deletions. The notion that cells in an individual organism do not share the same genome is not new, but only in the last decade the scientific community has begun to use emerging deep sequencing technologies to understand the scale of this phenomenon. Somatic mutations are present in both normal cells and in various diseases (Jourdon et al, 2020) and somatic variation has been suggested to play a role in driving neuronal diversity and genome evolution. We collaborate closely with the computational genomics laboratory of Alexej Abyzov at the Mayo Clinic. Together, we have demonstrated and quantified widespread somatic mosaicism in many human cell types and tissues, including human skin fibrolasts (Abyzov et al, Nature, 2012; Abyzov et al, Genome Research, 2017; Fasching et al, Science, 2021) and the human developing brain (Bae et al, Science, 2018).
We were founding members of the Brain Somatic Mosaicism (BSMN) network, sponsored by the National Institute of Mental Health (NIMH) and encompassing laboratories from several major centers in the US. We are active members of the Somatic Mosaisism across Human Tissues (SMaHT) consortium, which aims at generating a catalog of somatic genomic variants in several tissue across the human body and brain.
Using postmortem tissue, our group was the first to use retrospective somatic mutations to delineate a lineage map for the early human embryo, which suggested that a mosaic single nucleotide variant (SNV) is generated at each cell division (rate: 1.3 SNVs/cell/mitosis) (Bae et al, Science, 2018). Since then, we determined that lineage reconstruction can be done in living persons, opening the possibility of using routine lineage reconstruction for understanding individual differences in development, as well as early diagnosis of many medical conditions involving lineage asymmetry and clonal expansion due to MM, including cancer and epilepsy (Fasching et al, Science, 2021).
Our current work seeks to develop a comprehensive yet minimally invasive approach, including experimental procedures and computational methods, for generating individualized lineage and mosaicism maps. If successful, it could provide a fundamental shift in clinical practice from considering just the individual germline genome to considering the germline genome along with the individual lineage and mosaicism maps and, perhaps, updating these maps over an individual’s lifetime.
Medical Subject Headings (MeSH)
Academic Achievements and Community Involvement
Links & Media
Media
- The tree is based on mosaic single nucleotide variants (black) and indels (green) discovered in 25 fibroblast-derived iPSC lines from 4 skin biopsies and also present in blood, saliva and urine. Note that the first division is drastically asymmetric, with one daughter generating 90-70% of tissues and the other only 10-30%. For details see Fasching et al, Science 2021.
- Telencephalic organoid derived from human iPSC and grown in 3D culture. Red, progenitor cells stained for SOX1; green, immature neurons stinaed for bIII tubulin.
News
- March 20, 2024
The power of collaboration
- March 12, 2024
Five From Yale School of Medicine Elected to Association of American Physicians
- January 05, 2024Source: AUTISM ADVOCATE Parenting Magazine
Researchers Investigate Head Size and Autism
- September 07, 2023Source: Connecticut Public Radio
Yale researchers find 2 types of autism, underscoring the need for different treatments