Biology subjects

Calderon, D.

Publications and source records attributed to Calderon, D..

At least 19 recordsLinked to original sources

bioRxiv2025

Large-scale discovery of neural enhancers for cis-regulation therapies

CRISPR-based gene activation (CRISPRa) has emerged as a promising therapeutic approach for neurodevelopmental disorders (NDD) caused by haploinsufficiency. However, scaling this cis-regulatory therapy (CRT) paradigm requires pinpointing which candidate cis-regulatory elements (cCREs) are active in human neurons, and which can be targeted with CRISPRa to yield specific and therapeutic levels of target gene upregulation. Here, we combine Massively Parallel Reporter Assays (MPRAs) and a multiplex single cell CRISPRa screen to discover functional human neural enhancers whose CRISPRa targeting yields specific upregulation of NDD risk genes. First, we tested 5,425 candidate neuronal enhancers with MPRA, identifying 2,422 that are active in human neurons. Selected cCREs also displayed specific, autonomous in vivo activity in the developing mouse central nervous system. Next, we applied multiplex single-cell CRISPRa screening with 15,643 gRNAs to test all MPRA-prioritized cCREs and 761 promoters of NDD genes in their endogenous genomic contexts. We identified hundreds of promoter- and enhancer-targeting CRISPRa gRNAs that upregulated 200 of the 337 NDD genes in human neurons, including 91 novel enhancer-gene pairs. Finally, we confirmed that several of the CRISPRa gRNAs identified here demonstrated selective and therapeutically relevant upregulation of SCN2A, CHD8, CTNND2 and TCF4 when delivered virally to patient cell lines, human cerebral organoids, and a humanized mouse model of hTcf4. Our results provide a comprehensive resource of active, target-linked human neural enhancers for NDD genes and corresponding gRNA reagents for CRT development. More broadly, this work advances understanding of neural gene regulation and establishes a generalizable strategy for discovering CRT gRNA candidates across cell types and haploinsufficient disorders.

genomics↗

bioRxiv2025

Single-cell, multi-region profiling of the macaque brain across the lifespan

Brain aging is a complex process with profound health and societal consequences. However, the molecular and cellular pathways that govern its temporal progression-along with any cell type-, region-, and sex-specific heterogeneity in such progression-remain poorly defined. Here, we present a transcriptomic atlas of 5.3 million cells from 582 samples spanning 11 brain regions of 55 rhesus macaques (29 female, 26 male), aged 5 months (early life) to 21 years (late adulthood). We annotate 12 major cell classes and 225 subclusters, including region-specific subtypes of excitatory and inhibitory neurons, astrocytes, and ependymal cells. We identify a vulnerable excitatory neuron population in the superficial cortical lamina and a cortical interneuron population that are less abundant later in life, along with subtle, region-specific, age-associated compositional differences in subpopulations of microglia and oligodendrocytes, whose detection required single-cell resolution. Finally, we chart convergent and divergent age-associated molecular signatures across brain regions and cell classes-where some of these signatures are sex-specific and could underlie sex biases in neurological disorders. We find that age-associated transcriptional programs not only overlap substantially with those seen in Alzheimers disease (AD), but also unfold along distinct temporal trajectories across brain regions, suggesting that aging and AD may share molecular roots that emerge at different life stages and in region-specific, sex-specific windows of vulnerability. This work provides a temporal, regional, and sex-stratified atlas of the aging primate brain, offering insights into cell type-specific vulnerabilities and regional heterogeneity with translational human relevance.

neuroscience↗

bioRxiv2024

Genic and phylogenomic discordances reveal conflicting hybridization episodes in temperate Loliinae grasses

The grass subtribe Loliinae has great ecological and economic importance, as it includes community-dominant species of world mountain grasslands and the most extensively cultivated pasture, fodder and lawn grasses (fescues, ryegrasses). Resolving the phylogeny of recently evolved Loliinae lineages has proven challenging due to frequent introgressions and polyploidizations that occurred throughout their history. Evolutionary reconstruction based on genome-wide data sets is useful for large groups of species, enabling recovering phylogenetic trees, contrasting their topologies, unraveling the origins of the discordances, and testing hypotheses on their reticulate history. Here we present the first target-capture phylogeny of Loliinae using 234 single-copy nuclear coding loci for a large sample of 132 representative taxa, covering all its 29 evolutionary lineages. Additionally, we have completed organelle (plastome) sequences to elucidate the hybridogenic speciation history of the Loliinae from complementary genome sources. Concatenated maximum likelihood and multispecies coalescent trees of single-copy genes showed well-supported relationships for major lineages, which were generally consistent across analyses and genomes, and with previous taxonomic and phylogenetic findings. However, they also revealed high levels of both nuclear and cyto-nuclear discordances. The time-calibrated phylogeny of target-capture data supports an early Miocene origin for Loliinae and Mid-Late Miocene splits for its main broad-leaved and fine-leaved lineages, while current species-rich groups radiated in Plio-Pleistocene times. Hybridization and topological incongruence tests between the nuclear single-copy genes and plastome-based trees using multiple approaches and different sampling subsets confirmed the rampant introgression experienced by Loliinae at deep and shallow nodes. However, hybridization rates differed from lineage to lineage within the major clades and were not correlated with time or ploidy but rather depended on the "hybridogenous" nature of particular lineages. Our analyses detected high hybridization rates in four broad-leaved (Subulatae-Hawaiian, Tropical-South African, Mexico-Central-South American and Leucopoa p.p.) and five fine-leaved Loliinae lineages (American II, Aulaxyper, Afroalpine, American-Neozeylandic) containing rogue species that probably originated from trans-clade crosses and are more likely to hybridize greatly. In contrast, they recovered low hybridization rates in four broad-leaved (Schedonorus-Lolium, Subbulbosae, Drymanthele-Pseudoscariosae-Lojaconoa, Leucopoa pp) and six fine-leaved lineages (Festuca, Psilurus-Vulpia, American I, Exaratae-Loretia, American-Vulpia-Pampas, Eskia), with species derived from single ancestors that hybridize only with close congeners. The levels of intragenomic nuclear discordance could have been magnified by the prevalence of allopolyploids in the Loliinae and by methodological bias in the selection of orthologs; however, our nuclear and plastome trees have revealed key hybrid origins in these grasses. [allopolyploidization, lineage-specific hybridization rates, nuclear and cyto-nuclear discordances, Festuca and related genera, phylogenomics, nuclear single-copy genes, plastome].

evolutionary biology↗

bioRxiv2024

Sensorimotor integration enhances temperature stimulus processing

Animals optimize behavior by integrating sensory input with motor actions. We hypothe-sized that coupling thermosensory information with motor output enhances the brains capacity to process temperature changes, leading to more precise and adaptive behaviors. To test this, we developed a virtual "thermal plaid" environment where zebrafish either actively controlled temperature changes (sensorimotor feedback) or passively experienced the same thermal fluctuations. Our findings demonstrate that sensorimotor feedback amplifies the influence of thermal stimuli on swim initiation, resulting in more structured and organized motor output. We show that previously identified mixed-selectivity neurons that simultaneously encode thermal cues and motor activity enable the integration of sensory and motor feedback to optimize behavior. These results highlight the role of sensorimotor integration in refining thermosensory processing, revealing critical neural mechanisms underlying flexible thermoregulatory behavior. Our study offers new insights into how animals adaptively process environmental stimuli and adjust their actions, contributing to a deeper understanding of the neural circuits driving goal-directed behavior in dynamic environments.

neuroscience↗

bioRxiv2024

A DIFFERENTIAL REQUIREMENT FOR THE CILIOPATHY GENE RPGRIP1L IN HUMAN AND MOUSE SPINAL PROGENITOR FATE SPECIFICATION

Studying developmental processes in the context of the human central nervous system is essential to understand neurodevelopmental diseases. In this paper we perform a comparative functional study of the ciliopathy gene RPGRIP1L in human and mouse spinal development using in vitro 3D differentiation of pluripotent stem cells. RPGRIP1L, a causal gene of severe neurodevelopmental ciliopathies such as Joubert and Meckel syndromes, encodes a scaffolding protein of the ciliary transition zone involved in ciliary gating. Previous work has identified a major role for Rpgrip1l in mouse brain and spinal cord development, via controlling the Sonic Hedgehog (SHH)/GLI pathway. We show that spinal organoids derived from Rpgrip1l mutant mouse embryonic stem cells faithfully recapitulate the loss of motoneurons and the strong reduction of SHH signaling observed in the mutant mice. In contrast, human induced pluripotent stem cells mutant for RPGRIP1L produce motoneurons and activate the SHH pathway at levels similar to wild types, a property shared by human iPSCs mutant for another ciliopathy gene TMEM67. Moreover, we show that, in human RPGRIP1L mutant organoids, motoneurons acquire a more anterior identity, expressing HOX genes and other proteins normally present in the hindbrain and cervical spinal cord while motoneurons from wild type organoids strictly display a caudal brachial identity. By performing a temporal transcriptome analysis throughout the differentiation process, we find that the antero-posterior specification defect arises in early axial progenitors and correlates with the loss of cilia in these cells. Thus, this study uncovers distinct functions in humans and mice for ciliopathy proteins and a novel role for RPGRIP1L in human spinal antero-posterior patterning. These findings have important implications for understanding the role of cilia in human spinal cord development and the pathogenic mechanisms of neurodevelopmental ciliopathies.

developmental biology↗

bioRxiv2023

A multiplex, prime editing framework for identifying drug resistance variants at scale

CRISPR-based genome editing has revolutionized functional genomics, enabling screens in which thousands of perturbations of either gene expression or primary genome sequence can be competitively assayed in single experiments. However, for libraries of specific mutations, a challenge of CRISPR-based screening methods such as saturation genome editing is that only one region (e.g. one exon) can be studied per experiment. Here we describe prime-SGE ("prime saturation genome editing"), a new framework based on prime editing, in which libraries of specific mutations can be installed into genes throughout the genome and functionally assessed in a single, multiplex experiment. Prime-SGE is based on quantifying the abundance of prime editing guide RNAs (pegRNAs) in the context of a functional selection, rather than quantifying the mutations themselves. We apply prime-SGE to assay thousands of single nucleotide changes in eight oncogenes for their ability to confer drug resistance to three EGFR tyrosine kinase inhibitors. Although currently restricted to positive selection screens by the limited efficiency of prime editing, our strategy opens the door to the possibility of functionally assaying vast numbers of precise mutations at locations throughout the genome.

genomics↗

bioRxiv2023

Chromatin context-dependent regulation and epigenetic manipulation of prime editing

Prime editing is a powerful means of introducing precise changes to specific locations in mammalian genomes. However, the widely varying efficiency of prime editing across target sites of interest has limited its adoption in the context of both basic research and clinical settings. Here, we set out to exhaustively characterize the impact of the cis-chromatin environment on prime editing efficiency. Using a newly developed and highly sensitive method for mapping the genomic locations of a randomly integrated "sensor", we identify specific epigenetic features that strongly correlate with the highly variable efficiency of prime editing across different genomic locations. Next, to assess the interaction of trans-acting factors with the cis-chromatin environment, we develop and apply a pooled genetic screening approach with which the impact of knocking down various DNA repair factors on prime editing efficiency can be stratified by cis-chromatin context. Finally, we demonstrate that we can dramatically modulate the efficiency of prime editing through epigenome editing, i.e. altering chromatin state in a locus-specific manner in order to increase or decrease the efficiency of prime editing at a target site. Looking forward, we envision that the insights and tools described here will broaden the range of both basic research and therapeutic contexts in which prime editing is useful.

molecular biology↗

bioRxiv2023

Multiplex, single-cell CRISPRa screening for cell type specific regulatory elements

CRISPR-based gene activation (CRISPRa) is a promising therapeutic approach for gene therapy, upregulating gene expression by targeting promoters or enhancers in a tissue/cell-type specific manner. Here, we describe an experimental framework that combines highly multiplexed perturbations with single-cell RNA sequencing (sc-RNA-seq) to identify cell-type-specific, CRISPRa-responsive cis-regulatory elements and the gene(s) they regulate. Random combinations of many gRNAs are introduced to each of many cells, which are then profiled and partitioned into test and control groups to test for effect(s) of CRISPRa perturbations of both enhancers and promoters on the expression of neighboring genes. Applying this method to a library of 493 gRNAs targeting candidate cis-regulatory elements in both K562 cells and iPSC-derived excitatory neurons, we identify gRNAs capable of specifically upregulating intended target genes and no other neighboring genes within 1 Mb, including gRNAs yielding upregulation of six autism spectrum disorder (ASD) and neurodevelopmental disorder (NDD) risk genes in neurons. A consistent pattern is that the responsiveness of individual enhancers to CRISPRa is restricted by cell type, implying a dependency on either chromatin landscape and/or additional trans-acting factors for successful gene activation. The approach outlined here may facilitate large-scale screens for gRNAs that activate therapeutically relevant genes in a cell type-specific manner.

genomics↗

bioRxiv2022

Multiplex profiling of developmental enhancers with quantitative, single-cell expression reporters

The inability to scalably and precisely measure the activity of developmental enhancers in multicellular systems is a bottleneck in genomics. Here, we develop a dual RNA cassette that decouples the detection and quantification tasks inherent to multiplex single-cell reporter assays, resulting in accurate measurement of reporter expression over a >10,000-fold range of activity with a precision approaching the limit set by Poisson counting noise. Together with RNA barcode circularization, these single-cell quantitative expression reporters (scQers) provide high-contrast readouts analogous to classic in situ assays, but entirely from sequencing. Screening >200 enhancers in a multicellular in vitro model of early mammalian development, we identified numerous autonomous and cell-type-specific elements, including constituents of the Sox2 control region exclusively active in pluripotent cells, endoderm-specific enhancers, including near Foxa2 and Gata4, and a compact pleiotropic enhancer at the Lamc1 locus. scQers can be mobilized in developmental systems to quantitatively characterize native, perturbed, and synthetic enhancers at scale, with high sensitivity and at single-cell resolution.

genomics↗

bioRxiv2022

Zebrafish her3 knockout impacts developmental and cancer-related gene signatures

HES3 is a basic helix-loop-helix transcription factor that regulates neural stem cell renewal during development. HES3 overexpression is predictive of reduced overall survival in patients with fusion-positive rhabdomyosarcoma, a pediatric cancer that resembles immature and undifferentiated skeletal muscle. However, the mechanisms of HES3 cooperation in fusion-positive rhabdomyosarcoma are unclear and are likely related to her3/HES3s role in neurogenesis. To investigate HES3s function during development, we generated a zebrafish CRISPR/Cas9 knockout of her3, the zebrafish ortholog of HES3. Loss of her3 is not embryonic lethal and adults exhibit expected Mendelian ratios. Embryonic her3 zebrafish mutants are significantly smaller than wildtype and a subset present with lens defects as adults. Transcriptomic analysis of her3 mutant embryos indicates that genes involved in organ development, such as pctp and grinab, are significantly downregulated. Further, differentially expressed genes in her3 knockout embryos are enriched for HOX and SOX10 motifs. Several cancer-related gene pathways are impacted, including the inhibition of matrix metalloproteinases. Altogether, this new model is a powerful system to study her3/HES3-mediated neural development and its misappropriation in cancer contexts. Summary StatementHere, we generate and characterize a zebrafish her3/HES3 knockout to elucidate the functional role of her3/HES3, a transcriptional repressor, in neural development and tumorigenic processes.

developmental biology↗

bioRxiv2022

A Longitudinal Study of Dominant E. coli Lineages and Antimicrobial Resistance in the Gut of Children Living in an Upper Middle-income Country

The gastrointestinal tract constitutes a complex and diverse ecosystem. Escherichia coli is one of the most frequently studied and characterized species in the gut ecosystem, nevertheless, there has been little research to determine their diversity and population dynamics in the intestines of children over time. In this prospective study, a fresh fecal sample was obtained from children longitudinally over one year (30 fecal samples at sampling period 1 and 22 fecal samples at sampling periods 2 and 3). From each stool sample, five E. coli colonies were randomly selected (n = 405 E. coli isolates total) in order to characterize the genotype and phenotypic antimicrobial resistance patterns. We found that all numerically dominant E. coli lineages in childrens intestines were transient colonizers, and antimicrobial resistance phenotypes of these strains varied significantly over time without any apparent selective force. Whole-genome sequencing of 3 isolates belonging to ST131 found in one child during the sampling period I and II indicated that isolates were three different ST 131 clones that carried extended-spectrum {beta}-lactamase (ESBL) genes. IMPORTANCEThe length of residency and numeric dominance of antimicrobial-resistant E. coli may affect the extent to which an isolate contributes to the dissemination of antimicrobial resistance in a community. We studied the persistence of numerically dominant and antimicrobial-resistant lineages of E. coli in the human intestine. We found that E. coli lineages in the children's gut change considerably and rapidly over time. This study suggests that some phenotypic resistance patterns may result from the random distribution of genes in E. coli populations over time and may not be associated with differential exposure to antimicrobials.

microbiology↗

bioRxiv2021

Identification and characterization of hPSC-derived FOXA2+ progenitor cells with ventricular cardiac differentiation potential

While much progress has been made in understanding early cardiac development, the precise mechanisms that specify the different cardiomyocyte subtypes remain poorly understood. Recent data from our lab have shown that transient Foxa2 expression identifies a progenitor population with exclusive ventricular differentiation potential in the mouse heart. Here we have translated this concept to the human pluripotent stem cell (hPSC) system. Using a FOXA2-GFP reporter cell line we characterized expression of FOXA2 during hPSC cardiac differentiation and found that a subset of cardiac mesoderm precursors transiently expresses FOXA2. Gene expression analysis of FOXA2+ and FOXA2- cardiac mesoderm revealed that both populations similarly express early cardiac specification markers such as PDGFRA, TBX5, and ISL1, while other key candidates including TBX20 and GATA4 are significantly upregulated in the FOXA2+ population. Isolation and subsequent differentiation of FOXA2+ and FOXA2- populations demonstrates their comparable differentiation potential to both cardiomyocytes and epicardial cells. However, cardiomyocytes derived from FOXA2+ precursors showed enhanced differentiation efficiency toward ventricular cardiomyocytes compared to cardiomyocytes derived from FOXA2- precursors. To identify new mechanisms that regulate ventricular specification, we performed small molecule screening and found that inhibition of the EGFR pathway strongly increased the cardiac mesoderm population in general, and the FOXA2+ precursors in particular. Finally, we have identified a combination of cell surface markers to specifically isolate FOXA2+ cardiac precursors. In summary, our results suggest that FOXA2+ cardiac mesoderm harbors ventricular-specific differentiation potential and isolation of these cells permits the generation of cultures enriched for ventricular cardiomyocytes. Generating such enriched cardiac populations will be relevant for regenerative medicine approaches, as well as for disease modeling from induced pluripotent stem cells.

developmental biology↗

bioRxiv2021

Systematic reconstruction of the cellular trajectories of mammalian embryogenesis

Mammalian embryogenesis is characterized by rapid cellular proliferation and diversification. Within a few weeks, a single cell zygote gives rise to millions of cells expressing a panoply of molecular programs, including much of the diversity that will subsequently be present in adult tissues. Although intensively studied, a comprehensive delineation of the major cellular trajectories that comprise mammalian development in vivo remains elusive. Here we set out to integrate several single cell RNA-seq datasets (scRNA-seq) that collectively span mouse gastrulation and organogenesis. We define cell states at each of 19 successive stages spanning E3.5 to E13.5, heuristically connect them with their pseudo-ancestors and pseudo-descendants, and for a subset of stages, deconvolve their approximate spatial distributions. Despite being constructed through automated procedures, the resulting trajectories of mammalian embryogenesis (TOME) are largely consistent with our contemporary understanding of mammalian development. We leverage TOME to nominate transcription factors (TF) and TF motifs as key regulators of each branch point at which a new cell type emerges. Finally, to facilitate comparisons across vertebrates, we apply the same procedures to single cell datasets of zebrafish and frog embryogenesis, and nominate "cell type homologs" based on shared regulators and transcriptional states.

developmental biology↗

bioRxiv2020

A longitudinal study of E. coli lineages and antimicrobial resistance in Ecuadorian children

The gastrointestinal tract (GIT) constitutes a complex and diverse ecosystem. Escherichia coli is one of the most frequently studied and characterized species in the gut ecosystem. Nevertheless, there has been little research to determine their diversity and population dynamics in the intestines of children over time. Many intestinal E. coli lineages carry antimicrobial resistance and virulence genes, which have implications in disease and public health. In this one-year prospective study, a fresh fecal sample was obtained from 30 children longitudinally for one year (n = 82 fecal samples). From each stool sample, five Escherichia coli colonies were randomly selected to characterize their genotype and phenotypic antimicrobial resistance pattern (n = 405 E. coli isolates). We found that the most numerically dominant E. coli lineages in childrens intestines were transient colonizers, and phenotypic antimicrobial resistance varied significantly over time, however, ST131 a multi-drug resistant pathogen, and 3 additional STs persisted in a childs intestine for 3 months or more. IMPORTANCEThe length of residency and numeric dominance of antimicrobial-resistant E. coli may affect the extent to which an isolate contributes to the dissemination of antimicrobial resistance. We studied the persistence of numerically dominant and antimicrobial-resistant lineages of E. coli in the human intestine and found that E. coli lineages in the gut of children change rapidly over time.

microbiology↗

bioRxiv2020

TransMPRA: A framework for assaying the role of many trans-acting factors at many enhancers

Gene regulation occurs through trans-acting factors (e.g. transcription factors) acting on cis-regulatory elements (e.g. enhancers). Massively parallel reporter assays (MPRAs) functionally survey large numbers of cis-regulatory elements for regulatory potential, but do not identify the trans-acting factors that mediate any observed effects. Here we describe transMPRA -- a reporter assay that efficiently combines multiplex CRISPR-mediated perturbation and MPRAs to identify trans-acting factors that modulate the regulatory activity of specific enhancers.

genomics↗

bioRxiv2019

Sporadic activation of an oxidative stress-dependent NRF2-p53 signaling network in breast epithelial spheroids and premalignancies

Breast-mammary epithelial cells experience different local environments during tissue development and tumorigenesis. Microenvironmental heterogeneity gives rise to distinct cell-regulatory states whose identity and importance are just beginning to be appreciated. Cellular states diversify when clonal 3D spheroids are cultured in basement membrane, and prior transcriptomic analyses identified a state associated with stress tolerance and poor response to anticancer therapeutics. Here, we examined the regulation of this state and found that it is jointly coordinated by the NRF2 and p53 pathways, which are co-stabilized by spontaneous oxidative stress within the 3D cultures. Inhibition of NRF2 or p53 individually disrupts some of the transcripts defining the regulatory state but does not yield a notable phenotype in nontransformed breast epithelial cells. In contrast, combined perturbation prevents 3D growth in an oxidative stress-dependent manner. By integrating systems models of NRF2 and p53 signaling together as a single oxidative-stress network, we recapitulate these observations and make predictions about oxidative stress profiles during 3D growth. Similar coordination of NRF2 and p53 signaling is observed in normal breast epithelial tissue and hormone-negative ductal carcinoma in situ lesions. However, the pathways are uncoupled in triple-negative breast cancer, a subtype in which p53 is usually mutated. Using the integrated model, we reconcile the different NRF2-knockdown phenotypes of triple-negative cancer lines with their inferred handling of oxidative stress. Our results point to an oxidative stress-tolerance network that is important for single cells during glandular development and the early stages of breast cancer. One Sentence SummaryReactive oxygen species co-stabilize a non-oncogene and a tumor suppressor for triple-negative breast cancer when cells are surrounded by basement-membrane ECM.

cancer biology↗

bioRxiv2018

Landscape of stimulation-responsive chromatin across diverse human immune cells

The immune system is controlled by a balanced interplay among specialized cell types transitioning between resting and stimulated states. Despite its importance, the regulatory landscape of this system has not yet been fully characterized. To address this gap, we collected ATAC-seq and RNA-seq data under resting and stimulated conditions for 25 immune cell types from peripheral blood of four healthy individuals, and seven cell types from three fetal thymus samples. We found that stimulation caused widespread chromatin remodeling, including a large class of response elements shared between stimulated B and T cells. Furthermore, several autoimmune traits showed significant heritability in stimulation-responsive elements from distinct cell types, highlighting the critical importance of these cell states in autoimmunity. Use of allele-specific read-mapping identified thousands of variants that alter chromatin accessibility in particular conditions. Notably, variants associated with changes in stimulation-specific chromatin accessibility were not enriched for associations with gene expression regulation in whole blood - a tissue commonly used in eQTL studies. Thus, large-scale maps of variants associated with gene regulation lack a condition important for understanding autoimmunity. As a proof-of-principle we identified variant rs6927172, which links stimulated T cell-specific chromatin dysregulation in the TNFAIP3 locus to ulcerative colitis and rheumatoid arthritis. Overall, our results provide a broad resource of chromatin landscape dynamics and highlight the need for large-scale characterization of effects of genetic variation in stimulated cells.

genomics↗

bioRxiv2017

Inferring Relevant Cell Types For Complex Traits Using Single-Cell Gene Expression

Previous studies have prioritized trait-relevant cell types by looking for an enrichment of GWAS signal within functional regions. However, these studies are limited in cell resolution by the lack of functional annotations from difficult-to-characterize or rare cell populations. Measurement of single-cell gene expression has become a popular method for characterizing novel cell types, and yet, hardly any work exists linking single-cell RNA-seq to phenotypes of interest. To address this deficiency, we present RolyPoly, a regression-based polygenic model that can prioritize trait-relevant cell types and genes from GWAS summary statistics and single-cell RNA-seq. We demonstrate RolyPolys accuracy through simulation and validate previously known tissue-trait associations. We discover a significant association between microglia and late-onset Alzheimers disease, and an association between oligodendrocytes and replicating fetal cortical cells with schizophrenia. Additionally, RolyPoly computes a trait-relevance score for each gene which reflects the importance of expression specific to a cell type. We found that differentially expressed genes in the prefrontal cortex of Alzheimers patients were significantly enriched for highly ranked genes by RolyPoly gene scores. Overall, our method represents a powerful framework for understanding the effect of common variants on cell types contributing to complex traits.

genomics↗