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Program in Bioinformatics and Integrative Biology

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Biochemical Phenomena, Metabolism, and Nutrition | Bioinformatics | Computational Biology | Genomics | Integrative Biology | Molecular and Cellular Neuroscience | Psychiatry and Psychology


BACKGROUND: Midbrain dopaminergic neurons (MDN) represent 0.0005% of the brain's neuronal population and mediate cognition, food intake, and metabolism. MDN are also posited to underlay the neurobiological dysfunction of schizophrenia (SCZ), a severe neuropsychiatric disorder that is characterized by psychosis as well as multifactorial medical co-morbidities, including metabolic disease, contributing to markedly increased morbidity and mortality. Paradoxically, however, the genetic risk sequences of psychosis and traits associated with metabolic disease, such as body mass, show very limited overlap.

METHODS: We investigated the genomic interaction of SCZ with medical conditions and traits, including body mass index (BMI), by exploring the MDN's "spatial genome," including chromosomal contact landscapes as a critical layer of cell type-specific epigenomic regulation. Low-input Hi-C protocols were applied to 5-10 x 10(3) dopaminergic and other cell-specific nuclei collected by fluorescence-activated nuclei sorting from the adult human midbrain.

RESULTS: The Hi-C-reconstructed MDN spatial genome revealed 11 "Euclidean hot spots" of clustered chromatin domains harboring risk sequences for SCZ and elevated BMI. Inter- and intra-chromosomal contacts interconnecting SCZ and BMI risk sequences showed massive enrichment for brain-specific expression quantitative trait loci (eQTL), with gene ontologies, regulatory motifs and proteomic interactions related to adipogenesis and lipid regulation, dopaminergic neurogenesis and neuronal connectivity, and reward- and addiction-related pathways.

CONCLUSIONS: We uncovered shared nuclear topographies of cognitive and metabolic risk variants. More broadly, our PsychENCODE sponsored Hi-C study offers a novel genomic approach for the study of psychiatric and medical co-morbidities constrained by limited overlap of their respective genetic risk architectures on the linear genome.


BMI GWAS, Dopamine, Euclidean hot spots, Metabolic syndrome, Neurons, Obesity, Schizophrenia, Schizophrenia GWAS, Shared nuclear territories, Spatial genome, chrom3D

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© The Author(s). 2020 Open Access: This article is distributed under the terms of the Creative Commons Attribution 4.0 International License (, which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver ( applies to the data made available in this article, unless otherwise stated.

DOI of Published Version



Espeso-Gil S, Halene T, Bendl J, Kassim B, Ben Hutta G, Iskhakova M, Shokrian N, Auluck P, Javidfar B, Rajarajan P, Chandrasekaran S, Peter CJ, Cote A, Birnbaum R, Liao W, Borrman T, Wiseman J, Bell A, Bannon MJ, Roussos P, Crary JF, Weng Z, Marenco S, Lipska B, Tsankova NM, Huckins L, Jiang Y, Akbarian S. A chromosomal connectome for psychiatric and metabolic risk variants in adult dopaminergic neurons. Genome Med. 2020 Feb 19;12(1):19. doi: 10.1186/s13073-020-0715-x. PMID: 32075678; PMCID: PMC7031924. Link to article on publisher's site

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Genome medicine


Full author list omitted for brevity. For the full list of authors, see article.

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Creative Commons License

Creative Commons Attribution 4.0 License
This work is licensed under a Creative Commons Attribution 4.0 License.