Biology subjects

Manjila, S. B.

Publications and source records attributed to Manjila, S. B..

5 recordsLinked to original sources

bioRxiv2026

Neuronal and vascular genome-maintenance states organize opposing multicellular architectures in the aging brain

Genome maintenance is usually treated as cell-intrinsic, yet brain cells age within multicellular neighborhoods. Whether a cell's DNA damage response (DDR) state is systematically embedded in native tissue architecture is unknown. We used MERFISH to map curated repair programs across 604,252 cells in matched sections from 2-3 and 22-month-old mice. Regional DDR expression and coordination formed an age-dependent mosaic, accompanied by immune and oligodendroglial shifts. Independent metacell and distance-resolved analyses identified a consistent anchor-dependent organization. Low-DDR neurons occupied immune- and OPC-oligodendroglial-rich niches. In contrast, DDR-high vascular anchors were associated with vascular-cell enrichment and, in cortex and cerebral nuclei, OPC-oligodendroglial enrichment, whereas immune cells were enriched around DDR-low vascular anchors. Thus, genome-maintenance state was associated with distinct anchor-cell-specific spatial context depending on anchor-cell identity and its DDR transcriptional state. These opposing neuronal and vascular patterns define anchor-dependent genome-maintenance niches as a spatial feature of brain aging, with implications for regional vulnerability.

neuroscience↗

bioRxiv2026

Scale-Aware Compositional Inference Improves Reproducibility and Uncovers Convergent Aging Programs in Spatial Transcriptomics

Spatial transcriptomics enables analysis of molecular organization with anatomical context. Existing spatial differential expression methods are restricted to within-sample inference, forcing between-sample comparisons to rely on approaches adapted from single-cell RNA-seq. Here, we establish a scale-aware inference framework for spatial differential expression by modeling compositional constraints and variation in total RNA abundance rather than removing them through normalization, enabling calibrated between-sample inference at cell-level resolution. Our method produces more reliable results in simulated data and different spatial platforms. When applied to aged mouse brains, the analysis reveals converging aging-associated programs involving cellular signaling, membrane homeostasis, and neurovasculature across independent datasets.

genomics↗

bioRxiv2024

Brain-wide connectivity and novelty response of the dorsal endopiriform nucleus in mice

The dorsal endopiriform nucleus (EPd) is an enigmatic cortical subplate structure located inside the piriform cortex that shares a similar developmental origin with the claustrum. Although the EPd has been previously implicated in epilepsy and olfactory processing, its anatomical organization, connectivity patterns, and function remain largely unclear due to a lack of specific molecular markers. Our previous mapping study serendipitously identified that the Oxt receptor (Oxtr) is densely expressed in the EPd. Subsequent immunohistochemical and spatial transcriptomic analyses confirmed that Oxtr expression is enriched in the EPd, revealing distinct molecular organization compared to the neighboring claustrum. Whole brain input-output mapping of EPd Oxtr-positive neurons unveils extensive bidirectional connections to the ventral half of the brain, orchestrating functional circuits regulating olfaction, internal state, and emotion. Furthermore, our in-vivo miniscope recordings show that EPd Oxtr neurons exhibit high baseline activity during exploratory behavior, with a sharp decrease in activity in response to novel stimuli. This suggests that the EPd regulates interoceptive states and likely plays a role in adapting to novel exteroceptive cues.

neuroscience↗

bioRxiv2023

Developmental Mouse Brain Common Coordinate Framework

3D standard reference brains serve as key resources to understand the spatial organization of the brain and promote interoperability across different studies. However, unlike the adult mouse brain, the lack of standard 3D reference atlases for developing mouse brains has hindered advancement of our understanding of brain development. Here, we present a multimodal 3D developmental common coordinate framework (DevCCF) spanning mouse embryonic day (E) 11.5, E13.5, E15.5, E18.5, and postnatal day (P) 4, P14, and P56 with anatomical segmentations defined by a developmental ontology. At each age, the DevCCF features undistorted morphologically averaged atlas templates created from Magnetic Resonance Imaging and co-registered high-resolution templates from light sheet fluorescence microscopy. Expert-curated 3D anatomical segmentations at each age adhere to an updated prosomeric model and can be explored via an interactive 3D web-visualizer. As a use case, we employed the DevCCF to unveil the emergence of GABAergic neurons in embryonic brains. Moreover, we integrated the Allen CCFv3 into the P56 template with stereotaxic coordinates and mapped spatial transcriptome cell-type data with the developmental ontology. In summary, the DevCCF is an openly accessible resource that can be used for large-scale data integration to gain a comprehensive understanding of brain development.

neuroscience↗

bioRxiv2020

Wiring diagram of the oxytocin system in the mouse brain

Oxytocin (OT) neurons regulate diverse physiological responses via direct connections with different neural circuits. However, the lack of comprehensive input-output wiring diagrams of OT neurons and their quantitative relationship with OT receptor (OTR) expression presents challenges to understanding circuit specific OT functions. Here, we establish a whole-brain distribution and anatomical connectivity map of OT neurons, and their relationship with OTR expression using cell type specific viral tools and high-resolution 3D mapping methods. We utilize a flatmap to describe OT neuronal expression in four hypothalamic domains including under-characterized OT neurons in the tuberal nucleus. OT neurons in the paraventricular hypothalamus (PVH) broadly project to nine functional circuits that control cognition, brain state, and somatic visceral response. In contrast, OT neurons in the supraoptic (SO) and accessory nuclei have limited central projection to a small subset of the nine circuits. Surprisingly, quantitative comparison between OT output and OTR expression showed no significant correlation across the whole brain, suggesting abundant indirect OT signaling in OTR expressing areas. Unlike output, OT neurons in both the PVH and SO receive similar mono-synaptic inputs from a subset of the nine circuits mainly in the thalamic, hypothalamic, and cerebral nuclei areas. Our results suggest that PVH-OT neurons serve as a central modulator to integrate external and internal information via largely reciprocal connection with the nine circuits while the SO-OT neurons act mainly as unidirectional OT hormonal output. In summary, our OT wiring diagram provides anatomical insights about distinct behavioral functions of OT signaling in the brain. Significance StatementOxytocin (OT) neurons regulate diverse physiological functions from pro-social behavior to pain sensation via central projection in the brain. Thus, understanding detailed anatomical connectivity of OT neurons can provide insight on circuit specific roles of OT signaling in regulating different physiological functions. Here, we utilize high resolution mapping methods to describe the 3D distribution, mono-synaptic input and long-range output of OT neurons, and their relationship with OT receptor (OTR) expression across the entire mouse brain. We found OT connections with nine functional circuits controlling cognition, brain state, and somatic visceral response. Furthermore, we identified a quantitatively unmatched OT-OTR relationship, suggesting broad indirect OT signaling. Together, our comprehensive OT wiring diagram advances our understanding of circuit specific roles of OT neurons.

neuroscience↗