Biology subjects

Morrow, A.

Publications and source records attributed to Morrow, A..

7 recordsLinked to original sources

bioRxiv2025

A single-cell genetic colocalization test improves power and resolves disease-mediating cell types

Statistical colocalization testing methods can determine if the same single-nucleotide polymorphism (SNP) underlies both a genome-wide association study (GWAS) locus as well as an expression quantitative trait (eQTL) locus. This can nominate potential mechanistic pathways from SNPs to genes to traits, while providing cell type or tissue context. Surprisingly, systematic colocalization testing with bulk-tissue eQTLs fails to link the majority of GWAS loci with gene expression changes. Mapping eQTLs with single-cell expression data has the potential to reveal the missing regulatory effects of GWAS variants. However, current pseudobulk cluster-based approaches may be underpowered when clustering accuracy is imperfect or with an incorrectly selected cluster resolution. To improve power of single-cell colocalization tests, we developed a cluster-free method, scJLIM. By modeling eQTL interactions with continuous cell states (e.g., principal components), scJLIM estimates eQTL significance and colocalization in individual cells. We benchmarked our method with simulated data, demonstrating improvements in power over pseudobulk methods. In our main applications, we used scJLIM to analyze blood and brain scRNA-seq datasets paired with autoimmune and neurological disease GWAS, respectively. We identified nearly twice as many total colocalizations compared with traditional pseudobulk analyses carried out within the major cell populations of these tissues. Aligning with a recent experimental study, we highlighted an example of the ETS2 gene colocalizing with an inflammatory bowel disease GWAS locus in a subset of myeloid cells. For Parkinsons disease (PD), our results pointed to TRPV2 as a potential gene of interest, corroborated by transcriptional changes in both post-mortem PD brains and iPSC-derived neuronal models of alpha-synucleinopathy.

genomics↗

bioRxiv2025

NERINE reveals rare variant associations in gene networks across multiple phenotypes and implicates an SNCA-PRL-LRRK2 subnetwork in Parkinson's disease

There are two primary approaches to study the genetic basis of human phenotypes. Experiments in model systems generate interpretable gene networks but, in isolation, do not establish relevance to the human condition. Statistical genetics identifies relevant association signals at the variant or gene level but lacks tools to test specific mechanistic models, as existing methods do not incorporate the topology of gene-gene interactions. We bridge these two strategies by introducing a method that competitively tests network hypotheses with rare variant associations. A hierarchical model-based association test NERINE for the first time incorporates gene network topology while remaining resilient to network inaccuracies. We demonstrate NERINEs ability to test network hypotheses derived from both canonical pathway databases and model system screens. Comprehensive database-wide search of pathway networks with NERINE uncovers compelling associations for breast cancer, cardiovascular diseases, and type II diabetes, which are undetected by single-gene tests. Testing bespoke networks from experimental screens targeting key PD pathologies: dopaminergic neuron survival and -synuclein pathobiology, NERINE highlights rare variant burden in gene modules related to autophagy, vesicle traiicking, and protein homeostasis. Genome-scale CRISPRi-screening of -synuclein toxicity modifiers in human neurons and NERINE converge on PRL, revealing an intraneuronal -synuclein/prolactin stress response that may impact resilience to PD pathologies.

genetics↗

bioRxiv2024

Individual Alpha Frequency Predicts the Sensitivity of Time Perception

A growing body of research links individual differences in the alpha-band frequency to temporal aspects of perception. However, whether the human alpha rhythm is a correlate of time perception itself has remained controversial. This study combined EEG with multiple duration perception tasks to evaluate whether individual alpha frequency (IAF) is associated with sensitivity or bias in judging visual durations across a range of peri-second durations (spanning 100-1200ms). In a temporal estimation task, participants (n = 55; 38 female, 13 male, 4 non-binary) reported the duration of a single stimulus between 300-1200ms. In a temporal discrimination task, participants reported which of two stimuli was longer: a standard (100, 600, or 1200ms) or comparison (50-150% of the standard). Stimuli also varied in whether their luminance was static or dynamically varying over time. We found that IAF was significantly related to the variance of duration estimates, a precision measure, but not average duration estimates, a bias measure. Further supporting this relationship, psychometric function slopes obtained from the independent duration discrimination tasks were positively correlated with IAF, particularly for the static stimulus conditions. These individual differences effects held when controlling for participant age. We also explored trial-level variability in alpha frequency and found it was predictive of shifts in the point of subjective equality (PSE) during discrimination of very short (100ms). Taken together, these results suggest that IAF plays a role in shaping individual differences in the sensitivity of time perception and that spontaneous variations around ones IAF can lead to a bias in temporal representations. Significance StatementBrain waves in the 8-13 Hz range, known as alpha waves, have long been hypothesized to modulate our perception of time, yet the evidence remains unclear. This study investigates the relationship between an individuals alpha frequency (IAF) and temporal sensitivity using a wide range of time perception tasks and stimulus durations to address gaps in the literature. We demonstrate that IAF is significantly associated with the precision of duration estimates and sensitivity in duration discrimination, particularly for static unchanging stimuli. These findings provide novel evidence that IAF shapes individual differences in time perception, emphasizing its role as a neural marker of temporal sensitivity.

neuroscience↗

bioRxiv2024

Deep sequencing of proteotoxicity modifier genes uncovers a Presenilin-2/beta-amyloid-actin genetic risk module shared among alpha-synucleinopathies

Whether neurodegenerative diseases linked to misfolding of the same protein share genetic risk drivers or whether different protein-aggregation pathologies in neurodegeneration are mechanistically related remains uncertain. Conventional genetic analyses are underpowered to address these questions. Through careful selection of patients based on protein aggregation phenotype (rather than clinical diagnosis) we can increase statistical power to detect associated variants in a targeted set of genes that modify proteotoxicities. Genetic modifiers of alpha-synuclein ([a]S) and beta-amyloid (A{beta}) cytotoxicity in yeast are enriched in risk factors for Parkinsons disease (PD) and Alzheimers disease (AD), respectively. Here, along with known AD/PD risk genes, we deeply sequenced exomes of 430 [a]S/A{beta} modifier genes in patients across alpha-synucleinopathies (PD, Lewy body dementia and multiple system atrophy). Beyond known PD genes GBA1 and LRRK2, rare variants AD genes (CD33, CR1 and PSEN2) and A{beta} toxicity modifiers involved in RhoA/actin cytoskeleton regulation (ARGHEF1, ARHGEF28, MICAL3, PASK, PKN2, PSEN2) were shared risk factors across synucleinopathies. Actin pathology occurred in iPSC synucleinopathy models and RhoA downregulation exacerbated [a]S pathology. Even in sporadic PD, the expression of these genes was altered across CNS cell types. Genome-wide CRISPR screens revealed the essentiality of PSEN2 in both human cortical and dopaminergic neurons, and PSEN2 mutation carriers exhibited diffuse brainstem and cortical synucleinopathy independent of AD pathology. PSEN2 contributes to a common-risk signal in PD GWAS and regulates [a]S expression in neurons. Our results identify convergent mechanisms across synucleinopathies, some shared with AD.

genomics↗

bioRxiv2021

Pre-Stimulus Alpha-Band Phase Gates Afferent Visual Cortex Responses

The neurogenesis of alpha-band (8-13 Hz) activity has been characterized across many different animal experiments. However, the functional role that alpha oscillations play in perception and behavior has largely been attributed to two contrasting hypotheses, with human evidence in favor of either (or both or neither) remaining sparse. On the one hand, alpha generators have been observed in relay sectors of the visual thalamus and are postulated to phasically inhibit afferent visual input in a feedforward manner 1-4. On the other hand, evidence also suggests that the direction of influence of alpha activity propagates backwards along the visual hierarchy, reflecting a feedback influence upon the visual cortex 5-9. The primary source of human evidence regarding the role of alpha phase in visual processing has been on perceptual reports 10-16, which could be modulated either by feedforward or feedback alpha activity. Thus, although these two hypotheses are not mutually exclusive, human evidence clearly supporting either one is lacking. Here, we present human subjects with large, high-contrast visual stimuli that elicit robust C1 event-related potentials (ERP), which peak between 70-80 milliseconds post-stimulus and are thought to reflect afferent primary visual cortex (V1) input17-20. We find that the phase of ongoing alpha oscillations modulates the global field power (GFP) of the EEG during this first volley of stimulus processing (the C1 time-window). On the standard assumption21-23 that this early activity reflects postsynaptic potentials being relayed to visual cortex from the thalamus, our results suggest that alpha phase gates visual responses during the first feed-forward sweep of processing.

neuroscience↗

bioRxiv2021

No Evidence for a Single Oscillator Underlying Discrete Visual Percepts

Theories of perception based on discrete sampling posit that visual consciousness is reconstructed based on snapshot-like perceptual moments, as opposed to being updated continuously. According to a model proposed by Schneider (2018), discrete sampling can explain both the flash-lag and the Frohlich illusion, whereby a lag in the conscious updating of a moving stimulus alters its perceived spatial location in comparison to a stationary stimulus. The alpha-band frequency, which is associated with phasic modulation of stimulus detection and the temporal resolution of perception, has been proposed to reflect the duration of perceptual moments. The goal of this study was to determine whether a single oscillator (e.g., alpha) is underlying the duration of perceptual moments, which would predict that the point of subjective equality (PSE) in the flash-lag and Frohlich illusions are positively correlated across individuals. Although our displays induced robust flash-lag and Frohlich effects, virtually zero correlation was seen between the PSE in the two illusions, indicating that the illusion magnitudes are unrelated across observers. These findings suggest that, if discrete sampling theory is true, these illusory percepts either rely on different oscillatory frequencies or not on oscillations at all. Alternatively, discrete sampling may not be the mechanism underlying these two motion illusions or our methods were ill-suited to test the theory.

neuroscience↗

bioRxiv2019

Regulated spindle orientation buffers tissue growth in the epidermis

Tissue homeostasis requires a balance between progenitor cell proliferation and loss. Mechanisms that maintain this robust balance are needed to avoid tissue loss or overgrowth. Here we demonstrate that regulation of spindle orientation/asymmetric cell divisions is one mechanism that is used to buffer changes in proliferation and tissue turnover in mammalian skin. Genetic and pharmacologic experiments demonstrate that asymmetric cell divisions were increased in hyperproliferative conditions and decreased under hypoproliferative conditions. Further, active K-Ras also increased the frequency of asymmetric cell divisions. Disruption of spindle orientation in combination with constitutively active K-Ras resulted in massive tissue overgrowth. Together, these data highlight the essential roles of spindle orientation in buffering tissue homeostasis in response to perturbations.

cell biology↗