Genetic Variation; Genetic Predisposition to Disease; Gene Silencing; Neurogenesis
My research interest focuses on how genes and genetic mechanisms contribute to childhood developmental or late-onset disorders of the human nervous system. State-of-the art technologies are used to investigate global molecular changes that arise during neuronal fate specification and differentiation from pluripotent embryonic stem (ES) cells. To gain new insights into pathogenesis of specific neurological and neurodevelopmental disorders, such as autism, pluripotent stem cells are derived by reprogramming of differentiated, mature cells of affected patients. Exploring the genetic, molecular and biological features of neural differentiation process from embryonic and patient-specific stem cells may offer an unprecedented chance to understand normal and abnormal human brain development and diseases, with implications for drug development and potential cellular replacement therapy.
Extensive Research Description
A deep commitment to academic medicine has fundamentally influenced my research interests, from years of basic molecular neuroscience research to becoming a double-boarded physician in Adult Neurology and Clinical Genetics with a continuing involvement in basic and translational research. My early studies focused on how conserved genetic programs can change in mature neurons in response to specific, transmitter-receptor mediated signals. The realization, that dynamic alteration of genetic programs may also play a fundamental role in pathological processes, led to my focus on how various layers of genomic architecture are influencing a phenotype in health and disease.
1. Exploitation of rare genetic disorders with Mendelian trait may provide novel insights into mechanisms of common disorders and complex biological processes, such as dementia, diabetes or aging, and recognized disease pathways can offer strategies for prevention, diagnosis, and therapy.
Among the simple Mendelian disorders of humans, Werner syndrome most closely resembles an acceleration of normal aging. In prior studies I demonstrated that WRN protein directly interacts with the DNA replication machinery. To define better cellular events that are specifically vulnerable to WRN deficiency, I used RNA interference (RNAi) to silence the expression of Wrn gene and other RecQ helicases, linked to different clinical phenotypes, in primary human fibroblasts. The series of investigations strongly suggest that defects in DNA repair of specific lesions produced by oxidative damage in slowly dividing or non-dividing cells account for those unique aspects of Werner syndrome that mimic normal aging. We also propose that over time these DNA lesions would also accumulate in stem/precursor cells impairing their replicative capacity, thereby contributing to the complex aging phenotype. Our observations attest to the concept that in metazoan models of aging most pathology occurs in organs made up of slowly dividing or non-dividing cells and that impaired DNA repair and genomic instability, driven by oxidative damage, may underlie normal human aging. These studies further fostered some of the current projects to understand the role of oxygen environment on stem cell pluripotency, stem cell aging and neural lineage specification.
2. Genetic mapping, identifying contributing gene mutations and variants, is only an initial step toward biological understanding of rare or common diseases. Creation of disease models, both in human cell culture and animals, is crucial. Human embryonic stem (hES) cells offer an unprecedented access to the earliest stage of development and modeling cell fate and function. In particular, molecular changes that arise during neuronal differentiation and fate specification can be elucidated that may offer key understanding of normal and abnormal human neural development and disease processes.
We are using a multifaceted approach with investigators of the Yale Stem Cell Center, integrating genomic, proteomic, and genetic experiments to elucidate the molecular events that control neural cell differentiation using hES cells as model system. We have analyzed global transcriptome changes that occur during the early differentiation of human embryonic stem cells (hESCs) into the neural lineage. Next generation, state-of-the-art sequencing analysis revealed a remarkable complexity in gene transcription and splicing dynamics during neural cell differentiation with a wealth of previously unannotated novel transcripts and spliced isoforms specific for each stage of differentiation. My current efforts are focused on a novel type of unbiased, genome-wide functional screen to identify genetic mechanisms that control the steps of the neural differentiation in hES cells. These studies and the platform would offer targets for more downstream goals, including mechanistic investigations or drug discovery.
Further, in a collaborative project within Yale, we investigate the effect of hypoxia in neural stem cell function to identify key genes and their networks that enable neuronal stem cells to repair the injured brain in mouse model of perinatal hypoxia and elucidate the role of these genes for human neuronal stem cell function. The project may provide clues how to promote neuronal stem cell regenerative potential in traumatic, vascular and degenerative disorders of the human brain.
3. To understand the genetic and molecular underpinnings of neurological and neurodevelopmental disorders, we capitalize on the recent technical development of reprogramming adult, differentiated somatic cells to pluripotent stem cells. These induced pluripotent stem (iPS) cells can be derived with a specific genetic and disease background and can differentiate into essentially any cell types of the body. Thus, by using patient-specific cells one may gain knowledge of key molecular players and abnormalities of neural fate determination and function to understand monogenic or complex developmental and degenerative brain disorders. This would not be otherwise possible to do in living CNS.
With other Yale investigators with interest in neurogenetics, we have recently launched the Program in Neurodevelopment and Regeneration and began to generate iPS cell lines derived directly from patients with various neurodevelopmental disorders with notable genetic component, such as autism spectrum disorders (ASD). We are particularly interested to understand if macrocephaly, a well replicated phenotype in ASD, may be related to intrinsic alterations neuronal stem cell properties governing cell proliferation and/or neural and glial differentiation and how these processes align with the patient-specific genomic architecture. Advanced technologies are used to reprogram skin cells, obtain data on patient-specific DNA variations and integrate with quantitative gene expression information and correlative epigenetic regulatory marks along with phenotypic analysis of neural differentiation. These projects may provide an exceptional chance to understand the genetic and cellular mechanisms underlying this complex disorder and also to correlate with the clinical phenotype. As a model in general, iPS cells provide an invaluable resource for in vitro disease modeling, pharmaceutical screening (drugs/small molecules) and potential for cell-replacement therapy.
4. Having the opportunity to clinically evaluate patients with rare neurogenetic conditions, I interact regularly with scientists of the field to pursue molecular studies. I am particularly interested to contribute to the ongoing gene discovery efforts at Yale for autism, mental retardation and disorders of brain malformations, among others.
- Integrated approach to neural differentiation of human embryonic stem (hES) cells - use the latest advances in large-scale genomic and proteomic approaches to decipher critical elements of neuronal differentiation from human embryonic stem (ES) cells. Genes and pathways identified by these studies provide a basis for mechanistic investigations, construction of model biological networks and drug discovery.
- Cellular and genetic determinants of increased head size in autism - novel genetic, genomic and morphological approaches are used in this collaborative project to study neuronal differentiation of induced pluripotent stem (iPS) cells derived from patients with autism spectrum disorder. The project provides an unprecedented chance to understand the biological mechanisms of this disease.
- Effect of hypoxia on neural stem cell function in mouse and human - this collaborative project aims to identify key genes and their networks that enable neuronal stem cells to repair the injured brain in mouse model of perinatal hypoxia and elucidate their role for human neuronal stem cell function. The project may uncover how to promote neuronal stem cell regenerative potential in traumatic, vascular and degenerative disorders of the human brain.
FOXG1-Dependent Dysregulation of GABA/Glutamate Neuron Differentiation in Autism Spectrum Disorders.
Cell. 2015 Jul 16;162(2):375-90. doi: 10.1016/j.cell.2015.06.034.
Primary dystonias and genetic disorders with dystonia as clinical feature of the disease.
Narges Moghimi, Bahman Jabbari and Anna M. Szekely (2013): Primary dystonias and genetic disorders with dystonia as clinical feature of the disease. European Journal of Paediatric Neurology (2013), http://dx.doi.org/10.1016/j.ejpn.2013.05.015
- Ying Zhang, Vincent P. Schulz, Brian D. Reed, Zheng Wang, Xinghua Pan, Jessica Mariani, Ghia Euskirchen, Michael P. Snyder, Flora M. Vaccarino, Natalia Ivanova, Sherman M. Weissman and Anna M. Szekely (2013): Functional genomic screen of human stem cell differentiation reveals pathways involved inneurodevelopment and neurodegeneration. Proc.Natl.Acad.Sci.USA, www.pnas.org/cgi/doi/10.1073/pnas.1309725110
- Alexej Abyzov, Dean Palejev, Lior Rosenberg Belmaker, Ying Zhang, Jessica Mariani, Livia Tomasini, Anthony Ferrandino, Anna Szekely, Michael Wilson, Michael Seamus Haney, Elena L. Grigorenko, Anita Huttner, Sherman Weissman, Alexander Eckehart Urban, Mark Gerstein, Flora M. Vaccarino (2012). Detection and analysis of origin of genomic CNV in human induced pluripotent stem cells using whole genome sequencing Nature, 2012 Nov 18. doi: 10.1038/nature11629.
A highly integrated and complex PPARGC1A transcription factor binding network in HepG2 cells.
Alexandra E. Charos, Brian D. Reed, Debasish Raha, Anna M. Szekely, Sherman M. Weissman and Michael Snyder (2012): A highly integrated and complex PPARGC1A transcription factor binding network in HepG2 cells. Genome Research 22, 1668-1679.
Modeling Human Cortical Development in vitro using induced Pluripotent Stem Cells.
Jessica Mariani, Maria Vittoria Simonini, Dean Palejev, Livia Tomasini, Gianfilippo Coppola, Anna Szekely, Tamas Horvath, and Flora M. Vaccarino (2012): Modeling Human Cortical Development in vitro using induced Pluripotent Stem Cells. Proc.Natl.Acad.Sci. USA, 109, 12770-12775. Epub 2012 Jul 3.
Induced pluripotent stem cells: a new tool to confront the challenge of neuropsychiatric disorders.
Flora Vaccarino, Hanna E Stevens, Arif Kocabas, Anna Szekely, Elena L Grigorenko, Sherman Weissman (2011): Induced pluripotent stem cells: a new tool to confront the challenge of neuropsychiatric disorders. Neuropharmacology 60(7-8), 1355-1363. [Epub Mar 1, 2011]
Annual Research Review: The promise of stem cell research for neuropsychiatric disorders.
Flora M. Vaccarino, Alexander Eckehart Urban, Hanna Stevens, Anna Szekely, Alexej Abyzov, Elena Grigorenko, Mark Gerstein, Sherman Weissman (2011): The promise of stem cell research for neuropsychiatric disorders. The Journal of Child Psychology and Psychiatry 52(4) 504-516. [Epub January 4, 2011]
- Jia Qian Wu*, Lukas Habegger*, Parinya Noisa, Anna Szekely, Caihong Qiu, Stephen Hutchison, Debasish Raha, Haifan Lin, Michael Egholm, Sherman Weissman, Wei Cui, Mark Gerstein, and Michael Snyder (2010): Dynamic Transcriptomes during Neural Differentiation of Human Embryonic Stem Cells Revealed by Integrating Short, Long, and Paired-end Sequencing. Proc.Natl.Acad.Sci. USA, 107, 5254-5259.
Genome-wide occupancy of SREBP1 and its partners NFY and SP1 reveals novel functional roles and combinatorial regulation of distinct classes of genes.
Reed, B.D., Charos, A.E, Szekely, A.M., Weissman, S.M. and Snyder, M. (2008): Genome-wide occupancy of SREBP1 and its partners, NFY and SP1 reveals novel functional roles and combinatorial regulation of distinct classes of genes. PLoS Genetics 4, e1000133.
Karyotype-phenotype insights from 11q14.1-q23.2 interstitial deletions: FZD4 haploinsufficiency and exudative vitreoretinopathy in a patient with a complex chromosome rearrangement.
Li, P., Zhang, H., Huff, S., Nimmakayalu, M., Qumsiyeh, M., Yu, J., Szekely, A., Xu, T. and Pober, B.R. (2006): Karyotype-Phenotype Insights from 11q14.1-q23.2 Interstitial Deletions: FZD4 Haploinsufficiency and Exudative Vitreoretinopathy in a Patient
Werner protein protects non-proliferating cells from oxidative DNA damage.
Szekely, A.M., Bleichert, F., Nümann, A., Van Komen, S., Manasanch, E., Ben Nasr, A.,Canaan,A. and Weissman, S.M. (2005): Werner protein protects non-proliferating cells from oxidative DNA damage. Molecular Cell Biology 25, 10492-10506.
Werner protein recruits DNA polymerase delta to the nucleolus.
Szekely, A.M., Chen, Y.H., Zhang, C.Y, Oshima, J. and Weissman, S.M. (2000): Werner protein recruits DNA polymerase ? to the nucleolus. Proc.Natl.Acad.Sci. USA 97, 11365-11370.