Biology subjects

Xin, T.

Publications and source records attributed to Xin, T..

12 recordsLinked to original sources

bioRxiv2026

Decoding natural scenes from patterned optogenetic responses in mouse visual cortex

A central challenge in developing visual cortical prostheses is to determine how visual stimuli should be transformed into effective patterns of cortical stimulation. Although advances in stimulation technologies, including optogenetics, provide increasingly precise control over cortical activity, it remains unclear whether artificially evoked activity can reproduce the information content of naturally evoked visual representations. Here we establish a quantitative framework for evaluating visual encoding strategies by decoding cortical responses evoked by natural vision and patterned optogenetic stimulation. We developed a novel dual-modal paradigm in awake mice to bridge the gap between endogenous photostimulation and artificial network driving. By co-expressing the high-performance calcium indicator GCaMP6s and the red-shifted, ultra-sensitive opsin rsChRmine-oScarlet in the primary visual cortex (V1), we successfully translated dynamic natural movie frames into patterned, spatiotemporal optogenetic stimulation. Quantitative comparisons of macro-scale dynamics demonstrated that this patterned optogenetic injection evokes cortical states highly comparable and representationally aligned with those driven by actual visual photostimulation. To systematically evaluate the fidelity of these responses, we developed STAR, a deep learning model featuring spatial and temporal attention mechanisms, and successfully reconstructed the frames of natural movies from V1 signals under both experimental modalities. Collectively, our results demonstrate that complex sensory information can be both naturally encoded and synthetically injected into V1 circuits with high decoding fidelity. This work provides an empirical and computational proof-of-concept for intelligent, closed-loop biomimetic encoders, establishing a robust framework for next-generation cortical visual neuroprostheses and bidirectional brain-machine interfaces.

neuroscience↗

bioRxiv2026

Sharp cell type boundaries emerge from coordinated morphogen signaling

Classic models of the French flag problem depict sharp cell-type boundaries emerging from threshold responses to morphogen gradients. How discrete cell-type boundaries arise from morphogen signals that vary continuously across developing tissues is not completely understood. We use hair follicle dermal condensate formation to study a sharp developmental transition in which proliferative progenitors undergo cell-cycle exit concurrent with molecular differentiation. Using genetic and genomic approaches, we show that Wnt and Hedgehog signaling interact to coordinate the timing of these two processes. We identify a division of labor between the pathways: Wnt signaling promotes cell-cycle exit by regulating chromatin binding of the Hedgehog mediator GLI3, while Hedgehog signaling induces differentiation genes in a Wnt-dependent manner and simultaneously elevates Wnt activity. When Wnt and Hedgehog activities are temporally aligned, differentiation and cell-cycle exit occur within the same developmental window, restricting both the duration and abundance of intermediate states and producing a sharp cell-type boundary. When these signals are misaligned, intermediate states persist and expand, producing fuzzy boundaries. These findings reveal a mechanism in which interacting morphogen signals regulate the duration and abundance of intermediate states during a developmental transition, thereby controlling how continuous cell-state progression is translated into discrete tissue patterning.

developmental biology↗

bioRxiv2026

SnapG: An Automated Tool for Myelin g-ratio Measurement with Batch Processing Capability

The g-ratio, calculated as the axon diameter divided by the total myelinated fiber diameter, is widely used to assess the degree of myelination in the central and peripheral nervous systems. Changes in g-ratios accompany demyelinating, hypomyelinating, and remyelinating conditions, and can also result from activity-dependent, adaptive myelination. Although manual tracing from electron micrographs has been the gold-standard to measure g-ratios, this process is laborious and limits throughput. To address this challenge, we developed SnapG, an automated and user-friendly software tool to streamline g-ratio analysis from electron micrographs. SnapG implements an end-to-end pipeline for axon and myelin segmentation on EM images. The tool integrates robust segmentation and post-processing steps to extract axon and fiber diameters and generates both per-image and cohort-level summary statistics. SnapG produces g-ratio distributions that agree well with expert manual annotations and established tools across imaging modalities. It reduces user intervention, supports large image and batch processing, and achieves faster processing times while delivering accurate, reproducible measurements. SnapGs automated reporting thereby facilitates high-throughput analyses and improves consistency across experiments. SnapG can accelerate studies of myelin biology and provides a practical alternative to existing tools.

neuroscience↗

bioRxiv2025

Multiplexed Neuromodulatory-Type-Annotated EM-Reconstruction of Larval Zebrafish

Diverse neuromodulatory systems confer functional flexibility upon the hardwired sensorimotor pathways of the brain1-6. Among these, the evolutionarily conserved locus coeruleus (LC)-norepinephrinergic (NE) system integrates and broadcasts information globally7-9. While previous studies have primarily focused on its axonal outputs and effects on neural processing, the organizational logic of its synaptic inputs, enabling it to sense global brain states and in turn shape its activity dynamics for appropriate neuromodulation10,11, remains poorly explored. To address this, we mapped the synaptic input architecture of individual LC-NE neurons by establishing Fish-X, a whole-brain microscale reconstruction of larval zebrafish with neuron-type annotations. This dataset encompasses the retina, brain and anterior spinal cord, capturing >240,000 cells and >25 million synapses. Monoaminergic (including NE, dopaminergic, and serotonergic), hypocretinergic, and glycinergic neurons were resolved by multiplexed subcellular APEX2 labeling, while glutamatergic and GABAergic identities were inferred via morphology comparison with a zebrafish mesoscopic atlas12,13. Compared with other neuronal populations, LC-NE neurons display distinct perisomatic features and high dendritic indegrees. Reconstruction of near-complete dendritic inputs to individual LC-NE neurons reveals their broad yet sparse synaptic convergence across the brain. These synaptic inputs are not randomly distributed but instead organized according to sensory/motor modality, excitatory/inhibitory identity, and synaptic strength. Individual LC-NE neurons share common inputs, a feature conserved within and across monoaminergic systems, suggesting a co-innervation mechanism for coordinated neuromodulation. Thus, our study uncovers multi-level principles governing the spatial organization of LC-NE neurons broad-yet-sparse inputs and provides a pivotal resource for deciphering the microscale architecture of neuromodulatory systems.

neuroscience↗

bioRxiv2024

Connectomic Organization of the Suprachiasmatic Nucleus

The suprachiasmatic nucleus (SCN), the mammalian master clock, is a special structure dedicated to the time computation. However, a connectomic understanding of the nucleus as a whole is lacking. Using serial section electron microscopy, we reconstructed multiscale and multimodal SCN communication networks. Intra-SCN synaptic network consists of 9,566 morphologically similar neurons and 4.3 million synapses, organized into multiscale circuitries that interact with SCN-traversing axon fascicles. Strikingly, SCN neurons engage in unique soma-soma ephaptic interaction, forming 2,038 electrotonic integrative units with the largest overlapping the light-responsive area (LRA). SCNs paracrine modality contains 47,396 m3 dense core vesicles, with notable scarcity in the LRA, suggesting cross-modal coordination and functional integration. These distinct network features provide comprehensive insights into the system architecture of the mammalian circadian clock.

neuroscience↗

bioRxiv2022

Multiplex Epigenome Editing of MECP2 to Rescue Rett Syndrome Neurons

Rett syndrome (RTT) is an X-linked neurodevelopmental disorder caused by loss-of-function heterozygous mutations of Methyl CpG-binding Protein 2 (MECP2) on the X chromosome in girls. Reactivation of the silent wild-type MECP2 allele from the inactive X chromosome (Xi) represents a promising therapeutic opportunity for female patients with RTT. Here, we applied a multiplex epigenome editing approach to reactivate MECP2 from Xi in RTT human embryonic stem cells (hESCs) and derived neurons. Demethylation of the MECP2 promoter by dCas9-Tet1 with target sgRNA reactivated MECP2 from Xi in RTT hESCs without detectable off-target effects at the transcriptional level. Neurons derived from methylation-edited RTT hESCs maintained MECP2 reactivation and reversed the smaller soma size and electrophysiological abnormalities, two hallmarks of RTT. In RTT neurons, insulation of the methylation edited MECP2 locus by dCpf1-CTCF with target CRISPR RNA enhanced MECP2 reactivation and rescued RTT-related neuronal defects, providing a proof-of-concept study for epigenome editing to treat RTT and potentially other dominant X-linked diseases. One-Sentence SummaryReactivation of MECP2 from the inactive X chromosome by multiplex epigenome editing rescues Rett syndrome neurons in vitro.

physiology↗

bioRxiv2022

Live imaging reveals chromatin compaction transitions and dynamic transcriptional bursting during stem cell differentiation in vivo

Stem cell differentiation requires dramatic changes in gene expression and global remodeling of chromatin architecture. How and when chromatin remodels relative to the transcriptional, behavioral, and morphological changes during differentiation remain unclear, particularly in an intact tissue context. Here, we develop a quantitative pipeline which leverages fluorescently-tagged histones and longitudinal imaging to track large-scale chromatin compaction changes within individual cells in a live mouse. Applying this pipeline to epidermal stem cells, we reveal that cell-to-cell chromatin compaction heterogeneity within the stem cell compartment emerges independent of cell cycle status, and instead is reflective of differentiation status. Chromatin compaction state gradually transitions over days as differentiating cells exit the stem cell compartment. Moreover, establishing live imaging of keratin-10 nascent RNA, which marks the onset of stem cell differentiation, we find that keratin-10 transcription is highly dynamic and largely precedes the global chromatin compaction changes associated with differentiation. Together, these analyses reveal that stem cell differentiation involves dynamic transcriptional states and gradual chromatin rearrangement.

genetics↗

bioRxiv2022

Oncogenic Kras induces spatiotemporally specific tissue deformation through converting pulsatile into sustained ERK activation

Tissue regeneration and maintenance rely on coordinated stem cell behaviors. This orchestration can be impaired by oncogenic mutations leading to tissue architecture disruption and ultimately cancer formation. However, it is still largely unclear how oncogenes perturb stem cells functions to break tissue architecture. Here, we used intravital imaging and a novel signaling reporter to investigate the mechanisms by which oncogenic Kras mutation causes tissue disruption in the hair follicle. Through longitudinally tracking the same hair follicles in live mice, we found that KrasG12D, a mutation that can lead to squamous cell carcinoma, induces epithelial tissue deformation in a spatiotemporally specific manner. This tissue architecture abnormality is linked with a spatial dysregulation of stem cell proliferation as well as abnormal migration during hair follicle growth. By using a reporter mouse that allows us to capture real-time ERK signal dynamics at the single cell level, we discovered that KrasG12D, but not a closely related mutation HrasG12V, converts the pulsatile ERK signal fluctuation in the stem cells into sustained activation. Furthermore, by combining drug treatment with longitudinal imaging, we demonstrated that temporary inhibiting ERK signal reverts the KrasG12D-induced tissue deformation, suggesting that sustained ERK activation leads to tissue architecture disruption in Kras mutant hair follicles. Altogether, our work suggests that oncogenic mutations induce tissue abnormalities when spatiotemporally specific conditions are met, which allows mutant stem cells to disturb local cell coordination through altering dynamic signal communications.

cancer biology↗

bioRxiv2022

Reorganizing Niche Architecture Still Preserves Organ Function in the Hair Follicle

Stem cells ability to build and replenish tissues depends on support from their niche. While niche architecture varies across different organs, the functional importance of niche architecture is unclear. During hair follicle growth, multipotent epithelial progenitors build hair via crosstalk with their remodeling fibroblast niche, the dermal papilla, providing a powerful model to functionally interrogate different niche architectures. Through intravital imaging, we show that dermal papilla fibroblasts remodel both individually and collectively to form a polarized, structurally robust niche. Polarized TGF{beta} signaling precedes structural niche polarity, and loss of TGF{beta} signaling in dermal papilla fibroblasts leads them to progressively lose their stereotypic architecture and instead surround the epithelium. The reorganized niche relocates multipotent progenitors, but nevertheless supports their proliferation and differentiation. However, progenitor differentiation is completed prematurely, resulting in compromised hair production. Overall, our results reveal that niche architecture optimizes organ efficiency, but is not absolutely essential for organ function.

developmental biology↗

bioRxiv2022

Anti-phasic oscillatory development for speech and noise processing in cochlear implanted toddlers

Human brain demonstrates amazing readiness for speech and language learning at birth, but the auditory development preceding such readiness remains unknown. Cochlear implanted (CI) children with prelingual deafness provide a unique opportunity to study this developmental stage. Using functional near-infrared spectroscopy, we revealed that the brain of CI children was nearly irresponsive to sounds at CI hearing onset. With increasing CI experiences up to 32 months, the brain demonstrated function, region and hemisphere specific development. Most strikingly, the left anterior temporal lobe showed an oscillatory trajectory, changing in opposite phases for speech and noise. In addition, speech responses increased linearly in left sylvian parieto-temporal area and right inferior frontal gyrus, and noise responses changed in U shape in right supramarginal gyrus. Such cortical development predicted behavioral improvement. The study provides the first longitudinal brain imaging evidence for early auditory development preceding speech acquisition in the human brain. Graphic abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=120 SRC="FIGDIR/small/483211v1_ufig1.gif" ALT="Figure 1"> View larger version (39K): org.highwire.dtl.DTLVardef@d84974org.highwire.dtl.DTLVardef@1be9ba0org.highwire.dtl.DTLVardef@db5fb7org.highwire.dtl.DTLVardef@68f420_HPS_FORMAT_FIGEXP M_FIG C_FIG HighlightsO_LIThe brain of cochlear implanted toddlers is functionally inferior to neonates C_LIO_LIHearing experiences drive functional development in auditory related cortical areas C_LIO_LISpeech and noise processing develop in anti-phasic oscillatory trajectories C_LIO_LIAuditory cortical development predicts post-implantation behavioral improvement C_LI

neuroscience↗

bioRxiv2022

Injury suppresses Ras cell competitive advantage through enhanced wild-type cell proliferation

Healthy skin is a tapestry of wild-type and mutant clones. Although injury can cooperate with Ras mutations to promote tumorigenesis, the consequences in genetically mosaic skin are unknown. Here, we show that wild-type cells prevent oncogenic Ras-induced aberrant growth after injury. Although HrasG12V/+ and KrasG12D/+ cells outcompete wild-type cells in uninjured, mosaic tissue, their competitive advantage is suppressed after injury due to a selective increase in wild-type cell proliferation. EGFR inhibition abolishes the competitive advantage of wild-type cells after injury of HrasG12V/+-mosaic skin. Global loss of the cell cycle inhibitor p21 increases wild-type cell proliferation even without injury, suppressing the competitive advantage of HrasG12V/+ cells. Thus, injury plays an unanticipated role in switching the competitive balance between oncogenic and wild-type cells in genetically mosaic skin. One sentence SummaryInjury-repair selectively induces wild-type cell proliferation to suppress oncogenic growth in Ras-mosaic skin epithelium.

cell biology↗

bioRxiv2017

Epidermal stem cells self-renew upon neighboring differentiation

Many adult tissues are dynamically sustained by the rapid turnover of stem cells. Yet, how cell fates such as self-renewal and differentiation are orchestrated to achieve long-term homeostasis remains elusive. Studies utilizing clonal tracing experiments in multiple tissues have argued that while stem cell fate is balanced at the population level, individual cell fate - to divide or differentiate - is determined intrinsically by each cell seemingly at random ( 1 2 3 4 5). These studies leave open the question of how cell fates are regulated to achieve fate balance across the tissue. Stem cell fate choices could be made autonomously by each cell throughout the tissue or be the result of cell coordination ( 6 7). Here we developed a novel live tracking strategy that allowed recording of every division and differentiation event within a region of epidermis for a week. These measurements reveal that stem cell fates are not autonomous. Rather, direct neighbors undergo coupled opposite fate decisions. We further found a clear ordering of events, with self-renewal triggered by neighbor differentiation, but not vice-versa. Typically, around 1-2 days after cell delamination, a neighboring cell entered S/G2 phase and divided. Functional blocking of this local feedback showed that differentiation continues to occur in the absence of cell division, resulting in a rapid depletion of the epidermal stem cell pool. We thus demonstrate that the epidermis is maintained by nearest neighbor coordination of cell fates, rather than by asymmetric divisions or fine-tuned cell-autonomous stochastic fate choices. These findings establish differentiation-dependent division as a core feature of homeostatic control, and define the relevant time and length scales over which homeostasis is enforced in epithelial tissues.

cell biology↗