Browsing by Author "Zhu, Bohan"

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    Epigenomic tomography for probing spatially defined chromatin state in the brain
    Liu, Zhengzhi; Deng, Chengyu; Zhou, Zirui; Ya, Xiao; Jiang, Shan; Zhu, Bohan; Naler, Lynette B.; Jia, Xiaoting; Yao, Danfeng (Daphne); Lu, Chang (Cell Press, 2024-03-25)
    Spatially resolved epigenomic profiling is critical for understanding biology in the mammalian brain. Singlecell spatial epigenomic assays were developed recently for this purpose, but they remain costly and labor intensive for examining brain tissues across substantial dimensions and surveying a collection of brain samples. Here, we demonstrate an approach, epigenomic tomography, that maps spatial epigenomes of mouse brain at the scale of centimeters. We individually profiled neuronal and glial fractions of mouse neocortex slices with 0.5 mm thickness. Tri-methylation of histone 3 at lysine 27 (H3K27me3) or acetylation of histone 3 at lysine 27 (H3K27ac) features across these slices were grouped into clusters based on their spatial variation patterns to form epigenomic brain maps. As a proof of principle, our approach reveals striking dynamics in the frontal cortex due to kainic-acid-induced seizure, linked with transmembrane ion transporters, exocytosis of synaptic vesicles, and secretion of neurotransmitters. Epigenomic tomography provides a powerful and cost-effective tool for characterizing brain disorders based on the spatial epigenome.
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    Low-Input Multi-Omic Studies of Brain Neuroscience Involved in Mental Diseases
    Zhu, Bohan (Virginia Tech, 2022-09-13)
    Psychiatric disorders are believed to result from the combination of genetic predisposition and many environmental triggers. While the large number of disease-associated genetic variations have been recognized by previous genome-wide association studies (GWAS), the role of epigenetic mechanisms that mediate the effects of environmental factors on CNS gene activity in the etiology of most mental illnesses is still largely unclear. A growing body of evidence suggested that the abnormalities (changes in gene expression, formation of neural circuits, and behavior) involved in most psychiatric syndromes are preserved by epigenetic modifications identified in several specific brain regions. In this thesis, we developed the second generation of one of our microfluidic technologies (MOWChIP-seq) and used it to profile genome-wide histone modifications in three mental illness-related biological studies: the effect of psychedelics in mice, schizophrenia, and the effect of maternal immune activation in mice offspring. The second generation of MOWChIP-seq was designed to generate histone modification profiles from as few as 100 cells per assay with a throughput as high as eight assays in each run. Then, we applied the new MOWChIP-seq and SMART-seq2 to profile the histone modification H3K27ac and transcriptome, respectively, using NeuN+ neuronal nuclei from the mouse frontal cortex after a single dose of psychedelic administration. The epigenomic and transcriptomic changes induced by 2,5-Dimethoxy-4-iodoamphetamine (DOI), a subtype of psychedelics, in mouse neuronal nuclei at various time points suggest that the long-lasting effects of the psychedelic are more closely related to epigenomic alterations than the changes in transcriptomic patterns. Next, we comprehensively characterized epigenomic and transcriptomic features from the frontal cortex of 29 individuals with schizophrenia and 29 individually matched controls (gender and age). We found that schizophrenia subjects exhibited thousands of neuronal vs. glial epigenetic differences at regions that included several susceptibility genetic loci, such as NRXN1, RGS4 and GRIN3A. Finally, we investigated the epigenetic and transcriptomic alterations induced by the maternal immune activation (MIA) in mice offspring's frontal cortex. Pregnant mice were injected with influenza virus at GD 9.5 and the frontal cortex from mice pups (10 weeks old) were examined later. The results offered us some insights into the contribution of MIA to the etiology of some mental disorders, like schizophrenia and autism.
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    Prolonged epigenomic and synaptic plasticity alterations following single exposure to a psychedelic in mice
    de la Fuente Revenga, Mario; Zhu, Bohan; Guevara, Christopher A.; Naler, Lynette B.; Saunders, Justin M.; Zhou, Zirui; Toneatti, Rudy; Sierra, Salvador; Wolstenholme, Jennifer T.; Beardsley, Patrick M.; Huntley, George W.; Lu, Chang; González-Maso, Javier (Cell Press, 2021-10-19)
    Clinical evidence suggests that rapid and sustained antidepressant action can be attained with a single exposure to psychedelics. However, the biological substrates and key mediators of psychedelics’ enduring action remain unknown. Here, we show that a single administration of the psychedelic DOI produces fast-acting effects on frontal cortex dendritic spine structure and acceleration of fear extinction via the 5-HT2A receptor. Additionally, a single dose of DOI leads to changes in chromatin organization, particularly at enhancer regions of genes involved in synaptic assembly that stretch for days after the psychedelic exposure. These DOI-induced alterations in the neuronal epigenome overlap with genetic loci associated with schizophrenia, depression, and attention deficit hyperactivity disorder. Together, these data support that epigenomic-driven changes in synaptic plasticity sustain psychedelics’ long-lasting antidepressant action but also warn about potential substrate overlap with genetic risks for certain psychiatric conditions.