Papers by Carlo Colantuoni
ABSTRACTWe report the generation of a multimodal cell census and atlas of the mammalian primary m... more ABSTRACTWe report the generation of a multimodal cell census and atlas of the mammalian primary motor cortex (MOp or M1) as the initial product of the BRAIN Initiative Cell Census Network (BICCN). This was achieved by coordinated large-scale analyses of single-cell transcriptomes, chromatin accessibility, DNA methylomes, spatially resolved single-cell transcriptomes, morphological and electrophysiological properties, and cellular resolution input-output mapping, integrated through cross-modal computational analysis. Together, our results advance the collective knowledge and understanding of brain cell type organization: First, our study reveals a unified molecular genetic landscape of cortical cell types that congruently integrates their transcriptome, open chromatin and DNA methylation maps. Second, cross-species analysis achieves a unified taxonomy of transcriptomic types and their hierarchical organization that are conserved from mouse to marmoset and human. Third, cross-modal an...
ABSTRACTThe gEAR portal (gene Expression Analysis Resource, umgear.org) is an open access communi... more ABSTRACTThe gEAR portal (gene Expression Analysis Resource, umgear.org) is an open access community-driven tool for multi-omic and multi-species data visualization, analysis and sharing. The gEAR supports visualization of multiple RNA-seq data types (bulk, sorted, single cell/nucleus) and epigenomics data, from multiple species, time points and tissues in a single-page, user-friendly browsable format. An integrated scRNA-seq workbench provides access to raw data of scRNA-seq datasets for de novo analysis, as well as marker-gene and cluster comparisons of pre-assigned clusters. Users can upload, view, analyze and privately share their own data in the context of previously published datasets. Short, permanent URLs can be generated for dissemination of individual or collections of datasets in published manuscripts. While the gEAR is currently curated for auditory research with over 90 high-value datasets organized in thematic profiles, the gEAR also supports the BRAIN initiative (via n...
HIV-associated neurocognitive disorders (HAND) remain prevalent despite implementation of antiret... more HIV-associated neurocognitive disorders (HAND) remain prevalent despite implementation of antiretroviral therapy (ART). Development of HAND is linked to mitochondrial dysfunction and oxidative stress in the brain; therefore, upregulation of antioxidant defenses is critical to curtail neuronal damage. Superoxide dismutase 2 (SOD2) is a mitochondrial antioxidant enzyme essential for maintaining cellular viability. We hypothesized that SOD2 was upregulated during retroviral infection. Using a simian immunodeficiency virus (SIV)-infected macaque model of HIV, quantitative PCR showed elevated SOD2 mRNA in cortical gray (GM, 7.6-fold for SIV vs. uninfected) and white matter (WM, 77-fold for SIV vs. uninfected) during SIV infection. Further, SOD2 immunostaining was enhanced in GM and WM from SIV-infected animals. Double immunofluorescence labeling illustrated that SOD2 primarily co-localized with astrocyte marker glial fibrillary acidic protein (GFAP) in SIV-infected animals. Interestingly...
Single cell transcriptomics has transformed the characterization of brain cell identity by provid... more Single cell transcriptomics has transformed the characterization of brain cell identity by providing quantitative molecular signatures for large, unbiased samples of brain cell populations. With the proliferation of taxonomies based on individual datasets, a major challenge is to integrate and validate results toward defining biologically meaningful cell types. We used a battery of single-cell transcriptome and epigenome measurements generated by the BRAIN Initiative Cell Census Network (BICCN) to comprehensively assess the molecular signatures of cell types in the mouse primary motor cortex (MOp). We further developed computational and statistical methods to integrate these multimodal data and quantitatively validate the reproducibility of the cell types. The reference atlas, based on more than 600,000 high quality single-cell or -nucleus samples assayed by six molecular modalities, is a comprehensive molecular account of the diverse neuronal and non-neuronal cell types in MOp. Col...
Schizophrenia Bulletin, 2018
profiles at the onset of psychosis can discern the likely trajectory symptoms over the subsequent... more profiles at the onset of psychosis can discern the likely trajectory symptoms over the subsequent 5 years of illness. Methods: The study sample consists of 200 first-episode psychosis cases (ICD-10 codes: F20-F29 or F30-F33) aged 18-65 years who presented to SLAM (South London and Maudsley NHS Trust) mental health services between the 1st of January 2010 and the 1st of January 2015. Patients were subsequently recruited to the GAP study. Patients were followed-up electronically for 5 years post recruitment using the CRIS research platform. RNA samples were collected at the baseline timepoint via PAXgene blood tubes and interrogates, using the Illumina HumanHT-12.v4 beadchip array. Samples were run at the National Institute for Health Research's (NIHR) Biomedical Research Centre for Mental Health (BRC-MH) at the Institute of Psychiatry, Psychology and Neuroscience. A total of 4756 probes passed a stringent quality control across the 200 samples. Results: CRIS data pertaining to the GAP cohort was interrogated for information on clinical symptoms over a 5-year period using text-mining and natural language processing apps that represent over 70 different dictionary definitions of psychotic and affective symptoms. Confirmatory factor analysis was used to reduce this to a much smaller set of orthogonal symptom dimensions which were then the subject of a genetic interrogation using gene expression data. The analysis was conducted using a statistical learning framework which combines Elastic net penalised regression methodology with K-fold cross-validation (via the GLMnet package in R). This identified gene transcripts that were predictive of longer term symptom trajectories in half of the available sample. The veracity of the model was further validated using the second withheld portion of the sample. Discussion: The results of this discovery phase may provide a rationale for subsequent multi-modal investigations whose aims will be to further enrich the biomarker signature and to also understand the molecular mechanisms that sustain them.
MotivationDimension reduction techniques are widely used to interpret high-dimensional biological... more MotivationDimension reduction techniques are widely used to interpret high-dimensional biological data. Features learned from these methods are used to discover both technical artifacts and novel biological phenomena. Such feature discovery is critically import to large single-cell datasets, where lack of a ground truth limits validation and interpretation. Transfer learning (TL) can be used to relate the features learned from one source dataset to a new target dataset to perform biologically-driven validation by evaluating their use in or association with additional sample annotations in that independent target dataset.ResultsWe developed an R/Bioconductor package, projectR, to perform TL for analyses of genomics data via TL of clustering, correlation, and factorization methods. We then demonstrate the utility TL for integrated data analysis with an example for spatial single-cell analysis.AvailabilityprojectR is available on Bioconductor and at https://github.com/genesofeve/projec...
PLOS ONE, 2019
Background Of the 108 Schizophrenia (SZ) risk-loci discovered through genome-wide association stu... more Background Of the 108 Schizophrenia (SZ) risk-loci discovered through genome-wide association studies (GWAS), 96 are not altering the sequence of any protein. Evidence linking non-coding risk-SNPs and genes may be established using expression quantitative trait loci (eQTL). However, other approaches such allelic expression quantitative trait loci (aeQTL) also may be of use. Methods We applied both the eQTL and aeQTL analysis to a biobank of deeply sequenced RNA from 680 dorso-lateral pre-frontal cortex (DLPFC) samples. For each of 340 genes proximal to the SZ risk-SNPs, we asked how much SNP-genotype affected total expression (eQTL), as well as how much the expression ratio between the two alleles differed from 1:1 as a consequence of the risk-SNP genotype (aeQTL). Results We analyzed overlap with comparable eQTL-findings: 16 of the 30 risk-SNPs known to have gene-level eQTL also had gene-level aeQTL effects. 6 of 21 risk-SNPs with known splice-eQTL had exon-aeQTL effects. 12 novel potential risk genes were identified with the aeQTL approach, while 55 tested SNP-pairs were found as eQTL but not aeQTL. Of the tested 108 loci we could find at least one gene to be associated with 21 of the risk-SNPs using gene-level aeQTL, and with an additional 18 risk-SNPs using exon-level aeQTL.
ABSTRACTNew approaches are urgently needed to glean biological insights from the vast amounts of ... more ABSTRACTNew approaches are urgently needed to glean biological insights from the vast amounts of single cell RNA sequencing (scRNA-Seq) data now being generated. To this end, we propose that cell identity should map to a reduced set of factors which will describe both exclusive and shared biology of individual cells, and that the dimensions which contain these factors reflect biologically meaningful relationships across different platforms, tissues and species. To find a robust set of dependent factors in large-scale scRNA- Seq data, we developed a Bayesian non-negative matrix factorization (NMF) algorithm, scCoGAPS. Application of scCoGAPS to scRNA-Seq data obtained over the course of mouse retinal development identified gene expression signatures for factors associated with specific cell types and continuous biological processes. To test whether these signatures are shared across diverse cellular contexts, we developed projectR to map biologically disparate datasets into the facto...
Defining the environmental context in which genes enhance susceptibility can provide insight into... more Defining the environmental context in which genes enhance susceptibility can provide insight into the pathogenesis of complex disorders, like schizophrenia. Here we show that the intrauterine and perinatal environment modulates the association of schizophrenia with genomic risk, as measured with polygenic risk scores (PRS) based primarily on GWAS significant variants. Genomic risk interacts with intrauterine and perinatal complications (Early Life Complications, ELCs) in each of three independent samples from USA, Italy and Germany (overall n=1693, p=6e-05). In each sample, the liability of schizophrenia explained by PRS is nominally more than five times greater in the presence of a history of ELCs compared with its absence. In each sample, patients with positive ELC histories have higher PRS than patients without ELCs, which is further confirmed in two additional patient samples from Germany and Japan (overall n=2038, p=1e-04). The gene set based on the schizophrenia loci interacti...
Genetic and genomic studies suggest an important role for transcriptional regulatory changes in b... more Genetic and genomic studies suggest an important role for transcriptional regulatory changes in brain diseases, but roles for specific transcription factors (TFs) remain poorly understood. We integrated human brain-specific DNase I footprinting and TF-gene co-expression to reconstruct a transcriptional regulatory network (TRN) model for the human brain, predicting the brain-specific binding sites and target genes for 741 TFs. We used this model to predict core TFs involved in psychiatric and neurodegenerative diseases. Our results suggest that disease-related transcriptomic and genetic changes converge on small sets of disease-specific regulators, with distinct networks underlying neurodegenerative vs. psychiatric diseases. Core TFs were frequently implicated in a disease through multiple mechanisms, including differential expression of their target genes, disruption of their binding sites by disease-associated SNPs, and associations of the genetic loci encoding these TFs with disea...
BMC bioinformatics, Jan 6, 2015
Genomic data production is at its highest level and continues to increase, making available novel... more Genomic data production is at its highest level and continues to increase, making available novel primary data and existing public data to researchers for exploration. Here we explore the consequences of "batch" correction for biological discovery in two publicly available expression datasets. We consider this to include the estimation of and adjustment for wide-spread systematic heterogeneity in genomic measurements that is unrelated to the effects under study, whether it be technical or biological in nature. We present three illustrative data analyses using surrogate variable analysis (SVA) and describe how to perform artifact discovery in light of natural heterogeneity within biological groups, secondary biological questions of interest, and non-linear treatment effects in a dataset profiling differentiating pluripotent cells (GSE32923) and another from human brain tissue (GSE30272). Careful specification of biological effects of interest is very important to factor-bas...
Journal of nuclear medicine : official publication, Society of Nuclear Medicine, 2005
The endogenous opioid system of the brain has been implicated in feeding behavior. Abnormal repea... more The endogenous opioid system of the brain has been implicated in feeding behavior. Abnormal repeated activation of this system may constitute a neural substrate for the compulsive eating behavior observed in bulimia nervosa. This study examined the binding potential of the brain mu-opioid receptor (mu-OR) in bulimia nervosa. Eight women with bulimia nervosa and 8 female controls underwent brain MRI followed by (11)C-carfentanil PET. Voxel-based methods were used to assess group differences in mu-OR binding between controls and bulimic subjects and to correlate mu-OR binding with the frequency of recent self-reported abnormal eating behaviors in bulimic subjects. mu-OR binding in the left insular cortex was less in bulimic subjects than in controls and correlated negatively with recent fasting behavior. Changes in mu-OR binding in the insula may be important in the pathogenesis or maintenance of the self-perpetuating behavioral cycle of bulimic subjects because the insula is the prim...
Nature Genetics, 1999
Motorola is developing a high-throughput, single nucleotide polymorphism (SNP) analysis system wh... more Motorola is developing a high-throughput, single nucleotide polymorphism (SNP) analysis system which is based on microarrays of raised, hydrophilic gel pads. This three-dimensional microarray system offers distinct advantages over flat microarrays, including a well-characterized, covalent linkage of probes to the gel polymer and a diversity of functional groups available for biomolecule attachment, within an aqueous microenvironment, which is conducive to enzymatic activity. The SNP analysis system assays the DNA polymerase-mediated extension of an anchored oligonucleotide probe which is hybridized to a polymorphic site in an amplified target DNA sample. Assays are analysed for fluorescence signal in a confocal laser slide scanner. This SNP scoring system is currently being used to genotype a population of 1,000 individuals within a larger effort to identify genetic determinants of obesity-related phenotypes in humans. We will presented data to illustrate both the overall performance of this SNP genotyping system, as well as specific results from this pilot study.
The endogenous opioid system of the brain has been implicated in feeding behavior. Abnormal repea... more The endogenous opioid system of the brain has been implicated in feeding behavior. Abnormal repeated activation of this system may constitute a neural substrate for the compulsive eating behavior observed in bulimia nervosa. This study examined the binding potential of the brain -opioid receptor (-OR) in bulimia nervosa. Methods: Eight women with bulimia nervosa and 8 female con- trols underwent brain MRI followed by 11C-carfentanil PET. Voxel- based methods were used to assess group differences in -OR binding between controls and bulimic subjects and to correlate -OR binding with the frequency of recent self-reported abnormal eating behaviors in bulimic subjects. Results: -OR binding in the left insular cortex was less in bulimic subjects than in controls and correlated negatively with recent fasting behavior. Conclusion: Changes in -OR binding in the insula may be important in the pathogenesis or maintenance of the self-perpetuating behavioral cycle of bulimic subjects because the...
PLoS ONE, 2013
Aging is often associated with cognitive decline, but many elderly individuals maintain a high le... more Aging is often associated with cognitive decline, but many elderly individuals maintain a high level of function throughout life. Here we studied outbred rats, which also exhibit individual differences across a spectrum of outcomes that includes both preserved and impaired spatial memory. Previous work in this model identified the CA3 subfield of the hippocampus as a region critically affected by age and integral to differing cognitive outcomes. Earlier microarray profiling revealed distinct gene expression profiles in the CA3 region, under basal conditions, for aged rats with intact memory and those with impairment. Because prominent age-related deficits within the CA3 occur during neural encoding of new information, here we used microarray analysis to gain a broad perspective of the aged CA3 transcriptome under activated conditions. Behaviorally-induced CA3 expression profiles differentiated aged rats with intact memory from those with impaired memory. In the activated profile, we observed substantial numbers of genes (greater than 1000) exhibiting increased expression in aged unimpaired rats relative to aged impaired, including many involved in synaptic plasticity and memory mechanisms. This unimpaired aged profile also overlapped significantly with a learning induced gene profile previously acquired in young adults. Alongside the increased transcripts common to both young learning and aged rats with preserved memory, many transcripts behaviorallyactivated in the current study had previously been identified as repressed in the aged unimpaired phenotype in basal expression. A further distinct feature of the activated profile of aged rats with intact memory is the increased expression of an ensemble of genes involved in inhibitory synapse function, which could control the phenotype of neural hyperexcitability found in the CA3 region of aged impaired rats. These data support the conclusion that aged subjects with preserved memory recruit adaptive mechanisms to retain tight control over excitability under both basal and activated conditions.
Oncogene, 2004
Receptor tyrosine kinases (RTK) and the tumor suppressor PTEN co-regulate oncogenic cell signalin... more Receptor tyrosine kinases (RTK) and the tumor suppressor PTEN co-regulate oncogenic cell signaling pathways. How these interactions influence gene transcription is inadequately understood. We used expression microarrays to investigate the effects of PTEN on gene expression changes caused by activating c-Met in human glioblastoma cells. c-Met activation by scatter factor/hepatocyte growth factor (SF/HGF) altered the expression of 27-fold more genes in PTEN-null U-373MG cells than in PTEN homozygous primary normal human astrocytes (523 vs 19 genes). Restoring wt-PTEN in U-373MG cells dramatically altered patterns of c-Met regulated gene expression. This effect was varied depending on the specific gene in question. PTEN reduced the number of c-Met regulated transcripts from 931 to 502, decreased the relative number of genes upregulated by c-Met from 46 to 25%, and increased the relative number of downregulated genes from 54 to 75%. PTEN and c-Met co-regulated many genes involved in cell growth regulation such as oncogenes, growth factors, transcription factors, and constituents of the ubiquitin pathway. c-Met activation in PTEN-null (but not PTEN reconstituted) cells led to upregulation of the EGFR agonist TGFa and subsequently to EGFR activation. Using PTEN mutants, we found that PTEN's transcriptional effects were either lipid-phosphatase dependent, protein-phosphatase dependent, or phosphataseindependent. These results show that PTEN has critical and mechanistically complex effects on RTK-regulated gene transcription. These findings expand our understanding of tumor promoter/suppressor interrelationships and downstream transcriptional effects of PTEN loss and c-Met overexpression in malignant gliomas.
Neuroscience Research, 2010
Deficits in odor identification have been the most frequently described in schizophrenia (SZ). A ... more Deficits in odor identification have been the most frequently described in schizophrenia (SZ). A relationship between dysfunction in odor identification and negative symptoms of SZ has also been reported. Furthermore, deficit SZ (a subtype of the illness with primary, enduring negative symptoms) has been found to be associated with a particularly poor performance on odor identification tests indicating that deficits in smell identification could be differentially expressed in some subtypes of SZ. We describe correlations of performance on smell identification with positive and negative symptoms of SZ. Patients with SZ (n=15) and normal controls (n=19) were tested by the University of Pennsylvania Smell Identification Test (UPSIT). Psychopathology was assessed with the Scales for the Assessment of Positive and Negative Symptoms (SAPS and SANS). SZ patients performed more poorly on the UPSIT test than did normal controls. Consistent with previous findings, we observed a correlation of SANS with UPSIT performance. In particular, specific subdomains of SANS, such as blunted affect, apathy and anhedonia, were associated with odor identification deficits. Furthermore, UPSIT score predict these subdomains of negative symptoms. No correlation was observed between positive symptom and odor identification deficits. Our study further reinforces a relation between olfactory identification deficit and negative symptoms in SZ and suggests that smell identification could be a candidate endophenotype relevant to negative symptoms of SZ.
Neuroscience Research, 2010
Neurobiology of Disease, 2001
The identification of mutations in the transcriptional repressor methyl-CpG-binding protein 2 (ME... more The identification of mutations in the transcriptional repressor methyl-CpG-binding protein 2 (MECP2) gene in Rett Syndrome (RTT) suggests that an inappropriate release of transcriptional silencing may give rise to RTT neuropathology. Despite this progress, the molecular basis of RTT neuropathogenesis remains unclear. Using multiple cDNA microarray technologies, subtractive hybridization, and conventional biochemistry, we generated comprehensive gene expression profiles of postmortem brain tissue from RTT patients and matched controls. Many glial transcripts involved in known neuropathological mechanisms were found to have increased expression in RTT brain, while decreases were observed in the expression of multiple neuron-specific mRNAs. Dramatic and consistent decreases in transcripts encoding presynaptic markers indicated a specific deficit in presynaptic development. Employing multiple clustering algorithms, it was possible to accurately segregate RTT from control brain tissue samples based solely on gene expression profile. Although previously achieved in cancers, our results constitute the first report of human disease classification using gene expression profiling in a complex tissue source such as brain.
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Papers by Carlo Colantuoni