A chromosomal connectome for psychiatric and metabolic risk variants in adult dopaminergic neurons

BACKGROUND: Midbrain dopaminergic neurons (MDN) represent 0.0005% of the brain\u27s 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\u27s 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

Machine learning combining multi-omics data and network algorithms identifies adrenocortical carcinoma prognostic biomarkers

Background: Rare endocrine cancers such as Adrenocortical Carcinoma (ACC) present a serious diagnostic and prognostication challenge. The knowledge about ACC pathogenesis is incomplete, and patients have limited therapeutic options. Identification of molecular drivers and effective biomarkers is required for timely diagnosis of the disease and stratify patients to offer the most beneficial treatments. In this study we demonstrate how machine learning methods integrating multi-omics data, in combination with system biology tools, can contribute to the identification of new prognostic biomarkers for ACC.Methods: ACC gene expression and DNA methylation datasets were downloaded from the Xena Browser (GDC TCGA Adrenocortical Carcinoma cohort). A highly correlated multi-omics signature discriminating groups of samples was identified with the data integration analysis for biomarker discovery using latent components (DIABLO) method. Additional regulators of the identified signature were discovered using Clarivate CBDD (Computational Biology for Drug Discovery) network propagation and hidden nodes algorithms on a curated network of molecular interactions (MetaBase™). The discriminative power of the multi-omics signature and their regulators was delineated by training a random forest classifier using 55 samples, by employing a 10-fold cross validation with five iterations. The prognostic value of the identified biomarkers was further assessed on an external ACC dataset obtained from GEO (GSE49280) using the Kaplan-Meier estimator method. An optimal prognostic signature was finally derived using the stepwise Akaike Information Criterion (AIC) that allowed categorization of samples into high and low-risk groups.Results: A multi-omics signature including genes, micro RNA's and methylation sites was generated. Systems biology tools identified additional genes regulating the features included in the multi-omics signature. RNA-seq, miRNA-seq and DNA methylation sets of features revealed a high power to classify patients from stages I-II and stages III-IV, outperforming previously identified prognostic biomarkers. Using an independent dataset, associations of the genes included in the signature with Overall Survival (OS) data demonstrated that patients with differential expression levels of 8 genes and 4 micro RNA's showed a statistically significant decrease in OS. We also found an independent prognostic signature for ACC with potential use in clinical practice, combining 9-gene/micro RNA features, that successfully predicted high-risk ACC cancer patients.Conclusion: Machine learning and integrative analysis of multi-omics data, in combination with Clarivate CBDD systems biology tools, identified a set of biomarkers with high prognostic value for ACC disease. Multi-omics data is a promising resource for the identification of drivers and new prognostic biomarkers in rare diseases that could be used in clinical practice

The mouse cortex regulome. Effects of environmental enrichment on postnatal brain development

El reguloma està constituït per un sistema complex de factors que controlen el fenotip molecular de la cèl·lula, que al seu torn està influenciada pel medi ambient. Qualsevol pertorbació pot desencadenar canvis que poden implicar una regulació disfuncional. El cervell integra constantment una quantitat considerable d’informació motora, sensorial i cognitiva. Aquesta integració és particularment important en el desenvolupament postnatal, en què el cervell ha d'establir els compromisos moleculars necessaris per adaptar-se a un entorn canviant. L'objectiu d'aquest estudi és investigar com els factors ambientals poden influenciar en el reguloma de l'escorça cerebral durant el desenvolupament postnatal. Per tal d'estudiar la interacció entre el reguloma i el medi ambient, s’ha utilitzat el paradigma d'enriquiment ambiental en què s’exposa els ratolins a estímuls freqüentment canviants de manera constant durant un mes. En aquest estudi s'ha emprat seqüenciació d'última generació per poder analitzar l'epigenoma, regions obertes de la cromatina, interaccions cromosòmiques, el transcriptoma i el proteoma. En particular, s’observen canvis dinàmics en la cobertura de la modificació H3K79me2 neuronal, juntament amb un augment general d'accessibilitat en regions promotores i enhancers associats a gens importants per a l'aprenentatge. Complementàriament, les dades de transcriptòmica i proteòmica recolzen aquests resultats. Així mateix, s’ha implementat una estratègia particular en citometria de flux que ha permès esbrinar quines són les majors diferències en els canvis induïts per l'enriquiment ambiental en l'escorça cerebral i neurones corticals. En conjunt, i per primer cop, aquests estudis apunten que l'enriquiment ambiental indueix una sèrie de canvis en els mecanismes de regulació de les neurones corticals, relacionats amb un minuciós ajust sinàptic durant el desenvolupament postnatal.The regulome constitutes a complex system of factors that control the molecular phenotype of the cell, which is influenced by the environment. Any disturbance can trigger a set of changes involving dysfunctional regulation. The brain constantly integrates a multitude of motor, sensory and cognitive information. This engagement is particularly important in postnatal development when the brain must establish the molecular commitments needed to adapt to a changing environment. The aim of this study is to investigate how environmental factors influence the cerebral cortex regulome during postnatal development. In order to study the interaction between the regulome and the environment, we used the paradigm of environmental enrichment (EE) in which mice received constant and novel stimulation during a month. Next Generation Sequencing (NGS) –based techniques were employed to analyze the epigenome, gene accessibility, chromosomal interactions, the transcriptome and the proteome. Notably, dynamic changes in neuronal H3K79me2 coverage were observed, together with a general gain of promoter and enhancer accessibility of learning-associated genes. These changes were also supported by transcriptomic and proteomic data. We followed a flow cytometry strategy that allowed us to highlight differences in EE-induced changes in the cerebral cortex and cortical neurons. Our research reveals for the first time that EE induces changes in the regulatory mechanisms related with synaptic fine-tuning in cortical neurons during postnatal development

The mouse cortex regulome. Effects of environmental enrichment on postnatal brain development

El reguloma està constituït per un sistema complex de factors que controlen el fenotip molecular de la cèl·lula, que al seu torn està influenciada pel medi ambient. Qualsevol pertorbació pot desencadenar canvis que poden implicar una regulació disfuncional. El cervell integra constantment una quantitat considerable d’informació motora, sensorial i cognitiva. Aquesta integració és particularment important en el desenvolupament postnatal, en què el cervell ha d'establir els compromisos moleculars necessaris per adaptar-se a un entorn canviant. L'objectiu d'aquest estudi és investigar com els factors ambientals poden influenciar en el reguloma de l'escorça cerebral durant el desenvolupament postnatal. Per tal d'estudiar la interacció entre el reguloma i el medi ambient, s’ha utilitzat el paradigma d'enriquiment ambiental en què s’exposa els ratolins a estímuls freqüentment canviants de manera constant durant un mes. En aquest estudi s'ha emprat seqüenciació d'última generació per poder analitzar l'epigenoma, regions obertes de la cromatina, interaccions cromosòmiques, el transcriptoma i el proteoma. En particular, s’observen canvis dinàmics en la cobertura de la modificació H3K79me2 neuronal, juntament amb un augment general d'accessibilitat en regions promotores i enhancers associats a gens importants per a l'aprenentatge. Complementàriament, les dades de transcriptòmica i proteòmica recolzen aquests resultats. Així mateix, s’ha implementat una estratègia particular en citometria de flux que ha permès esbrinar quines són les majors diferències en els canvis induïts per l'enriquiment ambiental en l'escorça cerebral i neurones corticals. En conjunt, i per primer cop, aquests estudis apunten que l'enriquiment ambiental indueix una sèrie de canvis en els mecanismes de regulació de les neurones corticals, relacionats amb un minuciós ajust sinàptic durant el desenvolupament postnatal.The regulome constitutes a complex system of factors that control the molecular phenotype of the cell, which is influenced by the environment. Any disturbance can trigger a set of changes involving dysfunctional regulation. The brain constantly integrates a multitude of motor, sensory and cognitive information. This engagement is particularly important in postnatal development when the brain must establish the molecular commitments needed to adapt to a changing environment. The aim of this study is to investigate how environmental factors influence the cerebral cortex regulome during postnatal development. In order to study the interaction between the regulome and the environment, we used the paradigm of environmental enrichment (EE) in which mice received constant and novel stimulation during a month. Next Generation Sequencing (NGS) –based techniques were employed to analyze the epigenome, gene accessibility, chromosomal interactions, the transcriptome and the proteome. Notably, dynamic changes in neuronal H3K79me2 coverage were observed, together with a general gain of promoter and enhancer accessibility of learning-associated genes. These changes were also supported by transcriptomic and proteomic data. We followed a flow cytometry strategy that allowed us to highlight differences in EE-induced changes in the cerebral cortex and cortical neurons. Our research reveals for the first time that EE induces changes in the regulatory mechanisms related with synaptic fine-tuning in cortical neurons during postnatal development

Spatial genome exploration in the context of cognitive and neurological disease

The \u27non-linear\u27 genome, or the spatial proximity of non-contiguous sequences, emerges as an important regulatory layer for genome organization and function, including transcriptional regulation. Here, we review recent genome-scale chromosome conformation mappings (\u27Hi-C\u27) in developing and adult human and mouse brain. Neural differentiation is associated with widespread remodeling of the chromosomal contact map, reflecting dynamic changes in cell-type-specific gene expression programs, with a massive (estimated 20-50%) net loss of chromosomal contacts that is specific for the neuronal lineage. Hi-C datasets provided an unexpected link between locus-specific abnormal expansion of repeat sequences positioned at the boundaries of self-associating topological chromatin domains, and monogenic neurodevelopmental and neurodegenerative disease. Furthermore, integrative cell-type-specific Hi-C and transcriptomic analysis uncovered an expanded genomic risk space for sequences conferring liability for schizophrenia and other cognitive disease. We predict that spatial genome exploration will deliver radically new insights into the brain nucleome in health and disease

Environmental enrichment induces epigenomic and genome organization changes relevant for cognition

In early development, the environment triggers mnemonic epigenomic programs resulting in memory and learning experiences to confer cognitive phenotypes into adulthood. To uncover how environmental stimulation impacts the epigenome and genome organization, we used the paradigm of environmental enrichment (EE) in young mice constantly receiving novel stimulation. We profiled epigenome and chromatin architecture in whole cortex and sorted neurons by deep-sequencing techniques. Specifically, we studied chromatin accessibility, gene and protein regulation, and 3D genome conformation, combined with predicted enhancer and chromatin interactions. We identified increased chromatin accessibility, transcription factor binding including CTCF-mediated insulation, differential occupancy of H3K36me3 and H3K79me2, and changes in transcriptional programs required for neuronal development. EE stimuli led to local genome re-organization by inducing increased contacts between chromosomes 7 and 17 (inter-chromosomal). Our findings support the notion that EE-induced learning and memory processes are directly associated with the epigenome and genome organization.We acknowledge support of the Spanish Ministry of Economy and Competitiveness (SAF2011-26216), “Centro de Excelencia Severo Ochoa 2017-2021,” SEV-2016-0571, the CERCA Programme/Generalitat de Catalunya and Jerome Lejeune Foundation, Swiss National Science Foundation Fellowship (PBLAP3_136878) and Co-funded by Marie Curie Actions to CNH. Resources for analyses conducted by SE-G were partially supported by the U.S. National Institutes of Mental Health Funds R01MH104341 and R01MH117790 and by the Social Sciences and Humanities Research Council of Canada (NFRFE-2018-01305). We acknowledge support of the Spanish Ministry of Science and Innovation to the EMBL partnership, Agencia Estatal de Investigaci n (PID2019-110755RB-I00/AEI / 10.13039/501100011033), the European Union’s Horizon 2020 Research and Innovation programme under grant agreement No 848077, Jerôme Lejeune Foundation, NIH (Grant Number: 1R01EB 028159-01), Marató TV3 (#2016/20-30). RP-R resources were supported by R01GM109215. We thank the support of the University of Tübingen for the Open Access Publication Funds contribution

Neuron-specific signatures in the chromosomal connectome associated with schizophrenia risk.

To explore the developmental reorganization of the three-dimensional genome of the brain in the context of neuropsychiatric disease, we monitored chromosomal conformations in differentiating neural progenitor cells. Neuronal and glial differentiation was associated with widespread developmental remodeling of the chromosomal contact map and included interactions anchored in common variant sequences that confer heritable risk for schizophrenia. We describe cell type-specific chromosomal connectomes composed of schizophrenia risk variants and their distal targets, which altogether show enrichment for genes that regulate neuronal connectivity and chromatin remodeling, and evidence for coordinated transcriptional regulation and proteomic interaction of the participating genes. Developmentally regulated chromosomal conformation changes at schizophrenia-relevant sequences disproportionally occurred in neurons, highlighting the existence of cell type-specific disease risk vulnerabilities in spatial genome organization