Biology subjects

Del Rosario, J.

Publications and source records attributed to Del Rosario, J..

10 recordsLinked to original sources

bioRxiv2025

A standardized and reproducible behavioral protocol to elicit visual spatial attention in mice

Understanding how neural activity gives rise to cognitive processes such as selective attention is a fundamental goal of neuroscience. An important but often overlooked advance towards this goal requires the development and sharing of rigorous and reproducible behavioral tasks across labs; this is particularly important given the recent surge in studies of cognition and perception in mice. Here, we developed a standardized training protocol for head-fixed mice to become experts in a psychometric visual contrast detection task in just 17 days. Experts detected stimuli at two distinct spatial locations for several hundred trials per day. As consecutive trials elapsed at either location, the speed, accuracy, and contrast sensitivity of visual perception improved - all hallmarks of spatial attention improving performance, as seen in primates. These findings validate the efficacy of this protocol to reveal multiple aspects of selective spatial attention in mice, establishing a rigorous and reproducible tool for the community.

neuroscience↗

bioRxiv2025

Reproducible autosomal gene expression changes with loss of typical X and Y complement across tumor types

Although there are known sex differences in cancer incidence, severity, and treatment, the sex chromosomes are typically excluded from genomic analyses because of the unique technical challenges associated with assessing their copy number, sequence variation, and expression. Here we assess sex chromosome complement in three widely-used human genomics datasets from normal (non-cancerous) tissues, primary tumors, and cancer cell lines and study the effects on genome-wide gene expression. Expected sex chromosome complements based on reported patient sex were observed in non-cancerous tissues, but about half of tumors and cancer cell lines showed loss of typical sex chromosome gene expression across tissue types with three categories: loss of chromosome Y (LOY), loss of chromosome X (LOX) and reactivation of the inactive X chromosome (XaXa). Genes consistently differentially expressed in tumors with loss of chromosome X, loss of chromosome Y, or loss of X chromosome inactivation are associated with the hallmarks of cancer and include both sex-linked and autosomal genes from nearly all chromosomes, druggable genes, and genes with molecular functions relevant to cancer signaling, such as kinase activity. Strikingly, tumors that are X0, including tumors from female patients that have lost an X chromosome and tumors from male patients that have lost a Y chromosome, cluster together by gene expression profile. Patients with tumors that have LOX or LOY had poorer survival outcomes compared to those with tumors that had maintained their sex chromosome complement. Further, LOX and LOY eliminates nearly all of the differential gene expression between tumors from different patient sexes, affecting sex chromosomal and autosomal gene expression. Going forward, considering patient sex as well as the entire genome, including assessment of the sex chromosome complement, will provide additional insights into personalized tumor etiology, progression, treatment, and patient outcome. TeaserLoss of typical sex chromosome complement is present in primary tumors and cancer cell lines across tissue types. We identify consistent autosomal gene expression changes across multiple cancers when the sex chromosome complement is altered, and show that loss of sex chromosomes reduces tumor gene expression differences between patient sexes. We show that loss of sex chromosomes is also associated with poorer patient survival.

cancer biology↗

bioRxiv2025

Single nucleus multiomic atlas of human dorsal root ganglia reveals the contribution of non-neuronal cell types to pain

Sensory neurons residing in dorsal root ganglia (DRG) transmit sensory information such as pain, itch, touch, pressure and bodily position to the central nervous system. The activity of sensory neurons is regulated by non-neuronal cell types in the DRG, including satellite glial cells (SGCs), immune cells and fibroblasts. Dysregulated gene expression in DRG cells contributes to sensory nervous system disorders such as chronic pain. Understanding the genetic underpinnings of these conditions requires dissecting transcriptional regulation in human tissue. In this study, we profiled transcriptomic and chromatin accessibility landscapes from postmortem human DRG (hDRG) samples at single-nucleus level. We demonstrate that sequencing depth significantly impacts downstream analysis, with deeper sequencing yielding more detected cells and features, improved data integration, refined clustering and annotation, and more accurate scientific interpretations. We identified nine major cell types, defined their molecular signatures, and mapped cis-regulatory landscapes. Integration of gene expression with chromatin accessibility enabled peak-gene association and transcriptional network analyses, revealing transcription factors, their target genes, regulatory elements and potential partners that cooperatively drive cell-type-specific gene expression programs. This integrative approach identified cell types, genes, and cis-regulatory regions potentially driving pain conditions. Our unbiased genome-wide analysis not only recovered known pain-related genes but also highlighted novel candidate genes and regulatory regions implicated in pain mechanisms. Importantly, our results demonstrate that non-neuronal cells, including endothelial cells, fibroblasts, macrophages, and SGCs, play critical roles in pain pathogenesis and should be investigated as therapeutic targets. One Sentence SummaryOur work provides a comprehensive single-nucleus multi-omic atlas of human dorsal root ganglia, uncovering novel cell-type-specific regulatory mechanisms and candidate therapeutic targets for pain, thereby directly advancing translational insights into human sensory disorders and chronic pain pathogenesis.

neuroscience↗

bioRxiv2025

A multi-omic atlas of human autonomic and sensory ganglia implicates cell types in peripheral neuropathies

The human peripheral nervous system (PNS) consists of many ganglia including sympathetic ganglia (SG) and dorsal root ganglia (DRG). These ganglia house the cell bodies of diverse PNS neurons that transmit autonomic and sensory signals, as well as a much larger number of non-neuronal cells. However, the molecular and cellular diversity of these human PNS cell types and their implications in human disease remain elusive. By generating an integrated single-cell multi-omic atlas of human SG and DRG, we provide comprehensive transcriptional and epigenomic landscapes of various cell types in these peripheral ganglia. While the major cell types and their cell-type-specific transcriptional and epigenomic features are similar between human SG and DRG, we identify key differences between SG and DRG cell types. These differences highlight the distinct molecular and cellular mechanisms underlying their specific functions. We also profiled key genomic regulatory networks that govern cell-type-specific gene expression in these peripheral ganglia. Moreover, by mapping the expression and chromatin accessibility of disease-associated genes in human SG and DRG, we identify cell types that may underlie various peripheral neuropathies. This atlas serves as a valuable resource for understanding the intricate cell-type-specific molecules and interactions in the human PNS and their implications in human health and diseases.

neuroscience↗

bioRxiv2024

L-Type calcium channels and TRPC3 channels shape brain pericyte calcium signaling and hemodynamics throughout the arteriole to capillary network in vivo

Pericytes play a crucial role in regulating cerebral blood flow (CBF) through processes like vasomotion and neurovascular coupling (NVC). Recent work has identified different pericyte types at distinct points in the cerebrovascular network, such as the arteriole-capillary transition zone (ACT) and distal capillaries, sparking debate about their functional roles in blood flow control. Part of this discussion has comprised the possible mechanisms that may regulate pericyte Ca2+ signaling. Using in vivo two-photon Ca2+ imaging and a pharmacological approach with Ca2+ channel blockers (nimodipine and Pyr3), we assessed the contribution of L-type voltage-gated Ca2+ channels (VGCC) and transient receptor potential canonical 3 (TRPC3) channels to Ca2+ signaling in different pericyte types, ensheathing and capillary pericytes. We also measured local hemodynamics such as vessel diameter, blood cell velocity and flux during vasomotion, and following somatosensory stimulation to evoke NVC. We report that VGCC and TRPC3 channels underlie spontaneous fluctuations in ensheathing pericyte Ca2+ that trigger vasomotor contractions, but the contribution of each of these mechanisms to vascular tone depends on the specific branch of the ACT. Distal capillary pericytes also express L-type VGCCs and TRPC3 channels and they mediate spontaneous Ca2+ signaling in these cells. However, only TRPC3 channels maintain resting capillary tone, possibly by a receptor-operated Ca2+ entry mechanism. By applying the Ca2+ channel blockers during NVC, we found a significant involvement of L-type VGCCs in both pericyte types, influencing their ability to dilate during functional hyperemia. These findings provide new evidence of VGCC and TRPC3 activity in pericytes in vivo and establish a clear distinction between brain pericyte types and their functional roles, opening avenues for innovative strategies to selectively target their Ca2+ dynamics for CBF control. Significance StatementAlthough brain pericytes contribute to the regulation of CBF, there is uncertainty about how different types of pericytes are involved in this process. Ca2+ signaling is believed to be important for the contractility and tone of pericytes, but there is a limited understanding of the Ca2+ pathways in specific pericyte types. Here, we demonstrate that both VGCC and TRPC3 channels are active in distinct types of pericytes throughout the cerebrovascular network, but have different roles in pericyte tone depending on the pericyte location. This has important implications for how pericytes influence vasomotion and neurovascular coupling, which are central processes in CBF regulation. This work also provides the first evidence of TRPC3 channel activity in pericytes in vivo, furthering our understanding of the diverse signaling pathways within these brain mural cells.

neuroscience↗

bioRxiv2023

Lateral inhibition in V1 controls neural & perceptual contrast sensitivity

Lateral inhibition is a central principle for sensory system function. It is thought to operate by the activation of inhibitory neurons that restrict the spatial spread of sensory excitation. Much work on the role of inhibition in sensory systems has focused on visual cortex; however, the neurons, computations, and mechanisms underlying cortical lateral inhibition remain debated, and its importance for visual perception remains unknown. Here, we tested how lateral inhibition from PV or SST neurons in mouse primary visual cortex (V1) modulates neural and perceptual sensitivity to stimulus contrast. Lateral inhibition from PV neurons reduced neural and perceptual sensitivity to visual contrast in a uniform subtractive manner, whereas lateral inhibition from SST neurons more effectively changed the slope (or gain) of neural and perceptual contrast sensitivity. A neural circuit model identified spatially extensive lateral projections from SST neurons as the key factor, and we confirmed this with anatomy and direct subthreshold measurements of a larger spatial footprint for SST versus PV lateral inhibition. Together, these results define cell-type specific computational roles for lateral inhibition in V1, and establish their unique consequences on sensitivity to contrast, a fundamental aspect of the visual world.

neuroscience↗

bioRxiv2023

Serological evidence of high pathogenicity virus infection in Eidolon helvum fruit bats in Nigeria

The Eidolon helvum fruit bat is the most widely distributed fruit bat in Africa and is known to be a reservoir for several pathogenic viruses that can cause disease in humans. To assess the risk of zoonotic spillover, we conducted a serological survey of 304 serum samples from E. helvum bats that were captured for human consumption in Makurdi, Nigeria. Using pseudotyped viruses, we screened the samples for neutralising antibodies against viruses from the Coronaviridae, Filoviridae, Orthomyxoviridae and Paramyxoviridae families. We report the presence of neutralising antibodies against henipavirus lineage GH-M74a virus (odds ratio 6.23; p<0.001), Nipah virus (odds ratio 4.04; p=0.00031), bat influenza H17N10 virus (odds ratio 7.25; p<0.001) and no significant association with Ebola virus (odds ratio 0.56; p=0.375) in the bat cohort. The data suggest a potential risk of zoonotic spillover including the possible circulation of highly pathogenic viruses in E. helvum populations. These findings highlight the importance of maintaining sero-surveillance of E. helvum to monitor changes in virus prevalence and distribution over time and across different geographic locations. Article summary lineThe detection of neutralizing antibodies against henipavirus GH-M74a virus, Nipah virus, and H17N10 virus in Eidolon helvum bat sera from Nigeria using pseudotyped viruses suggests a potential risk of zoonotic spillover.

microbiology↗

bioRxiv2022

Narrowband gamma oscillations propagate and synchronize throughout the mouse thalamocortical visual system

Rhythmic oscillations of neural activity permeate sensory systems. Studies in the visual system propose that broadband gamma oscillations (30 - 80 Hz) facilitate neuronal communication underlying visual perception. However, broadband gamma oscillations within and across visual areas show widely varying frequency and phase, providing constraints for synchronizing spike timing. Here, we analyzed data from the Allen Brain Observatory and performed new experiments that show narrowband gamma (NBG) oscillations (50 - 70 Hz) propagate and synchronize throughout the awake mouse thalamocortical visual system. Lateral geniculate (LGN) neurons fired with millisecond precision relative to NBG phase in primary visual cortex (V1) and multiple higher visual areas (HVAs). NBG in HVAs depended upon retinotopically aligned V1 activity, and neurons that fired at NBG frequencies showed enhanced functional connectivity within and across visual areas. Remarkably, LGN ON versus OFF neurons showed distinct and reliable spike timing relative to NBG oscillation phase across LGN, V1, and HVAs. Taken together, NBG oscillations may serve as a novel substrate for precise coordination of spike timing in functionally distinct subnetworks of neurons spanning multiple brain areas during awake vision.

neuroscience↗

bioRxiv2020

Spatial modulation of dark versus bright stimulus responses in mouse visual cortex

A fundamental task of the visual system is to respond to luminance increments and decrements. In primary visual cortex (V1) of cats and primates, luminance decrements elicit stronger, faster, and more salient neural activity (OFF responses) than luminance increments (ON responses). However, studies of V1 in ferrets and mice show that ON responses may be stronger. These discrepancies may arise from differences in species, experimental conditions, or from measuring responses in single neurons versus populations. Here, we examined OFF versus ON responses across different regions of visual space in both single neurons and populations of mouse V1. We used high-density silicon probes and whole-cell patch-clamp recordings to assess OFF versus ON dominance in local field potential (LFP), single neuron, and membrane potential responses. Across these levels, we found that OFF responses clearly dominated in the central visual field, whereas ON responses were more evident in the periphery. These observations were clearest in LFP and subthreshold membrane potential. Our findings consolidate and resolve prior conflicting results and reveal that retinotopy may provide a common organizing principle for spatially biasing OFF versus ON processing in mammalian visual systems.

neuroscience↗

bioRxiv2019

Diminished cortical excitation during perceptual impairments in a mouse model of autism

Sensory impairments are a core feature of autism spectrum disorder (ASD). These impairments affect visual perception (Robertson and Baron-Cohen, 2017), and have been hypothesized to arise from imbalances in cortical excitatory and inhibitory activity (Rubenstein and Merzenich, 2003; Nelson and Valakh, 2015; Sohal and Rubenstein, 2019); however, there is little direct evidence testing this hypothesis in identified excitatory and inhibitory neurons during impairments of sensory perception. Several recent studies have examined cortical activity in transgenic mouse models of ASD (Goel et al., 2018; Antoine et al., 2019; Lazaro et al., 2019), but have provided conflicting evidence for excitatory versus inhibitory activity deficits. Here, we utilized a genetically relevant mouse model of ASD (CNTNAP2-/- knockout, KO; Arking et al., 2008; Penagarikano et al., 2011) and directly recorded putative excitatory and inhibitory population spiking in primary visual cortex (V1) while measuring visual perceptual behavior (Speed et al., 2019). We found quantitative impairments in the speed, accuracy, and contrast sensitivity of visual perception in KO mice. These impairments were simultaneously associated with elevated inhibitory and diminished excitatory neuron activity evoked by visual stimuli during behavior, along with aberrant 3 - 10 Hz oscillations in superficial cortical layers 2/3 (L2/3). These results establish that perceptual deficits relevant for ASD can arise from diminished sensory activity of excitatory neurons in feedforward layers of cortical circuits.

neuroscience↗