Oleg Evgrafov, PhD

Genetics of Schizophrenia

The main project in our lab is a study of molecular mechanisms of schizophrenia. Schizophrenia (SCZ) is a highly heritable disease, and so far ~300 associated loci have been identified by genome wide association studies, each one with so small overall effect that all of them together account for only 10% of heritability. Most of these variants lie outside the coding regions, suggesting that they act by altering transcript expression levels. Ultimately all risks in the genome must pass through an RNA intermediate to be able to alter brain structure and function. Therefore, we decided to focus on expression profiling of SCZ.

We developed human cellular model, Cultured Neural progenitor cells derived from Olfactory Neuroepithelium (CNON), specifically to elucidate the causes of SCZ related to neurodevelopment (Evgrafov et al., 2011, Wrobel et al, 2013). We have evidence that these cells closely resemble neural progenitors of developing brain, kind of cells which divide, migrate and differentiate at the right place and the right time thus defining shape, size and structure of the brain. Effectively CNON provides an opportunity to “turn clock back” and study some specifics of fetal brain of an adult. We have collected biopsy samples from more than 300 individuals with schizophrenia or control group, develop CNON cultures and study gene expression profiles. We discovered a set of genes, differentially expressed between people with schizophrenia and control group, that overlap with loci found in other genetic studies of brain disorders (Evgrafov et al., 2020, Igolkina et al., 2018). A large number of these differentially expressed genes are involved in Wnt signaling, and the difference in gene expression comes from relatively small group of patients, ~20%, perhaps defining molecular subtype of the disorder.

What genomic variants cause these differences in gene expression? What exactly these differentially expressed genes do? How their products interact to each other? How they change cell’s functionality – ability to proliferate, migrate, differentiate, respond to critical signals? Do these changes in gene regulation of neural progenitors result in alterations in brain structure? We hope to answer these questions working further with this model.

Deciphering genetics of brain disorders is tremendous task, and it requires worldwide cooperation and development of common resources, tools and data sharing. We are a part of these global efforts. We were one of the pioneers of single cell transcriptomics (Qiu et al., 2012, Dueck et al., 2016, Kim et al., 2020), part of the team developing BrainSpan resources (Li et al., 2018) and participate in the ENCODE project (Rhie et al., 2018).

Our lab is also becoming a hub of multiple studies in collaboration with other SUNY DHSU investigators, involving sequencing technologies, including single cell and spatial transcriptomic sequencing and data analysis. We provide not only technical assistance, but bringing new ideas and directions to studies in different areas of cell biology and brain sciences such as memory consolidation project (PIs I. Hernandez, H.M.Alarcon), chronic obstructive pulmonary disease study (PI R. Foronjy) and others.

• Evgrafov OV, Wrobel BB, Kang X, Simpson G, Malaspina D, Knowles JA. (2011) Olfactory neuroepithelium-derived neural progenitor cells as a model system for investigating the molecular mechanisms of neuropsychiatric disorders. Psychiatr Genet. 21:217-28. PubMed PMID: 21451437.
• Evgrafov OV, Armoskus C, Wrobel BB, Spitsyna VN, Souaiaia T, Herstein JS, Walker CP, Nguyen JD, Camarena A, Weitz JR, Kim JMH, Lopez Duarte E, Wang K, Simpson GM, Sobell JL, Medeiros H, Pato MT, Pato CN, Knowles JA. (2020) Gene Expression in Patient-Derived Neural Progenitors Implicates WNT5A Signaling in the Etiology of Schizophrenia. Biol Psychiatry Jan 22;S0006-3223(20)30010-X. doi: 10.1016/j.biopsych.2020.01.005.
• Igolkina AA, Armoskus C, Newman JRB, Evgrafov OV, McIntyre LM, Nuzhdin SV, Samsonova MG. (2018) Analysis of Gene Expression Variance in Schizophrenia Using Structural Equation Modeling. Front Mol Neurosci. 11:192. doi: 10.3389/fnmol.2018.00192. eCollection 2018. PMID: 29942251
• Rhie SK, Schreiner S, Witt H, Armoskus C, Lay FD, Camarena A, Spitsyna VN, Guo Y, Berman BP, Evgrafov OV, Knowles JA, Farnham PJ. (2018) Using 3D epigenomic maps of primary olfactory neuronal cells from living individuals to understand gene regulation. Sci Adv. 2018 Dec 13;4(12):eaav8550. doi: 10.1126/sciadv.aav8550. eCollection 2018 Dec. PMID: 30555922
• Li M, Santpere G, Imamura Kawasawa Y, Evgrafov OV, Gulden FO, Pochareddy S, Sunkin SM, Li Z, Shin Y, Zhu Y, Sousa AMM, Werling DM, Kitchen RR, Kang HJ, Pletikos M, Choi J, Muchnik S, Xu X, Wang D, Lorente-Galdos B, Liu S, Giusti-Rodríguez P, Won H, de Leeuw CA, Pardiñas AF; BrainSpan Consortium; PsychENCODE Consortium; PsychENCODE Developmental Subgroup, Hu M, Jin F, Li Y, Owen MJ, O'Donovan MC, Walters JTR, Posthuma D, Reimers MA, Levitt P, Weinberger DR, Hyde TM, Kleinman JE, Geschwind DH, Hawrylycz MJ, State MW, Sanders SJ, Sullivan PF, Gerstein MB, Lein ES, Knowles JA, Sestan N. (2018) Integrative functional genomic analysis of human brain development and neuropsychiatric risks. Science. 2018 Dec 14;362(6420). pii: eaat7615. doi: 10.1126/science.aat7615. PMID: 30545854
• Qiu, S., Luo, S., Evgrafov, O., Li, R., Schroth, G.P., Levitt, P., Knowles, J.A., and Wang, K. (2012). Single-neuron RNA-Seq: technical feasibility and reproducibility. Frontiers in genetics 3, 124, PMID:22934102. PMCID: PMC3407998
• Dueck, H. R., Ai, R., Camarena, A., Ding, B., Dominguez, R., Evgrafov, O. V., … Weisberg, S. (2016). Assessing characteristics of RNA amplification methods for single cell RNA sequencing. BMC Genomics 2016 Nov 24;17(1):966. PMID: 27881084. PMCID: PMC5122016.
• Kim JMH, Camarena A, Walker C, Lin MY, Wolseley V, Souaiaia T, Thornton M, Grubbs B, Chow RH, Evgrafov OV, Knowles JA. (2020) Robust RNA-Seq of aRNA-amplified single cell material collected by patch clamp. Sci Rep. 2020;10(1):1979. Published 2020 Feb 6. doi:10.1038/s41598-020-58715-y
• Wrobel BB, Mazza JM, Evgrafov OV, Knowles JA. Assessing the efficacy of endoscopic office olfactory biopsy sites to produce neural progenitor cell cultures for the study of neuropsychiatric disorders. Int Forum Allergy Rhinol. 2013;3(2):133-138. doi:10.1002/alr.21080