Biology subjects

Gong, D.

Publications and source records attributed to Gong, D..

At least 19 recordsLinked to original sources

bioRxiv2026

Pharmacologic eIF2B Activation Rescues Neuropathy in CMT2 Subtypes by Normalizing the Integrated Stress Response

Among the many subtypes of Charcot-Marie-Tooth (CMT) disease, several result from mutations in genes encoding aminoacyl-tRNA synthetases, enzymes required for tRNA charging during cytoplasmic and mitochondrial translation. We report that activation of the integrated stress response (ISR) pathway is a shared molecular feature of tRNA synthetase-associated and other axonal CMT subtypes. RTX-117, a CNS-penetrant small molecule currently in Phase 1 clinical trials, targets eukaryotic initiation factor 2B (eIF2B), a key modulator of protein synthesis and the ISR pathway. Using cryo-EM studies, we have characterized the binding mode of RTX-117 to the eIF2B decamer. In GarsP278KY/+ mice, which develop early onset motor defects and axonal pathology that recapitulate CMT2D symptoms from tRNA synthetase mutations, RTX-117 treatment started after disease onset reduced chronic ISR activation and produced significant functional and electrophysiological improvement. We further identify ISR targets, including secreted proteins such as GDF15 and FGF21 that may serve as translational biomarkers for treatment response to RTX-117 in CMT disease. Broader surveillance of the ISR pathway across models of neurodegeneration reveals strong activation in several diseases and a correlation with disease progression, particularly in models of Alzheimers disease. These findings identify chronic ISR activation as a recurrent, though not universal, pathological mechanism of neurodegenerative disease models. Overall, our study identifies candidate biomarkers for CMT disease subtypes associated with defects in translational homeostasis and supports eIF2[a]-ATF4 axis modulation as a promising therapeutic strategy for this disease class. One Sentence SummaryRTX-117, a clinical stage eIF2B activator, blunts chronic ISR activation and improves nerve and motor function in a mouse model of Charcot-Marie-Tooth Disease Type 2D.

cell biology↗

bioRxiv2026

Mapping absolute membrane voltage using dynamic photocycle control

Fluorescent voltage indicators are widely used to report relative changes in membrane potential, but mapping absolute voltages remains difficult. Here we present Voltage Measurement by Activated Photocycles (VMAP), a simple method for absolute voltage imaging based on a photophysical switch between voltage-insensitive and sensitive indicator states. VMAP requires no specialized hardware or additional labeling, and is applicable across species, sample preparations, and microscope configurations. Using VMAP, we quantified drug-induced shifts in neuronal resting potential, revealed the emergence of bioelectric patterns during multi-day recordings of human iPSC populations, and created 3D membrane-potential maps across whole live zebrafish embryos. By making absolute voltage imaging accessible from cellular to organismal scales and from milliseconds to days, VMAP opens a route to mapping bioelectrical organization in complex living systems.

biophysics↗

bioRxiv2026

Distinct neural correlates for focusing on similar memory contents originating from current or previous experience

Flexible, goal-directed behavior depends on the ability to select and prioritize information from memory representations freshly encoded from the sensory stream as well as retrieved from previous experience. The spatial gating signatures of internal attention in working memory (WM) are increasingly well characterized, but it remains unclear whether the same neurophysiological mechanisms are recruited for orienting attention to items from long-term memory (LTM). We recorded EEG and eye movements while participants focused on WM versus LTM representations in a unified precision-report task. Retrocues improved performance for both WM and LTM items, but with larger behavioral gains for WM items. Neural and oculomotor markers of spatial orienting, including contralateral posterior alpha suppression and gaze biases toward remembered locations, were robust when focusing on WM items; but were reliably weakened or absent when focusing on LTM items. Multivariate pattern analyses provided complementary evidence for the recruitment of dissociable neural mechanisms when focusing on WM vs. LTM items, which unfolded with similar time courses. Together, the results establish the existence of dissociable neural mechanisms for internal attention, which can be deployed flexibly depending on the relevant memory trace to guide performance. The findings raise interesting and tractable questions about whether differences in representational formats or representational domains drive the distinct internal attention mechanisms.

neuroscience↗

bioRxiv2026

Cross-species single-cell atlases chart progression, therapy-driven remodelling and immune evasion in pancreatic cancer

Pancreatic ductal adenocarcinoma (PDAC) is typically diagnosed at advanced stages, yet single-cell datasets that capture late-stage and treated disease remain sparse, hindering progress in understanding tumour heterogeneity and therapy resistance. Here, we have generated integrated single-cell transcriptomic atlases of human and mouse PDAC to define the cellular and molecular landscape of the disease, from early to advanced and metastatic stages, including post-treatment disease, and to enable direct cross-species comparison. Using scANVI to harmonize 16 human studies comprising 257 donors and representative mouse models (101 tumours), we compiled over 1.6 million cells and established a four-level hierarchical taxonomy of more than 60 distinct cell states spanning malignant, stromal, immune, endothelial, adipose, exocrine and endocrine compartments. We resolve ten malignant programmes linked to progression and uncover rare immune phenotypes, including CD4CD8 double-positive T cells that remain poorly characterized in PDAC. Notably, we show that radiotherapy (RT) exposure is associated with enrichment of an EMT-persistent malignant state and an immunosuppressive microenvironment characterized by expansion of tumour-associated endothelium, depletion of intratumoral T cells and heightened laminin-CD44 signalling, with RT-associated genes linked to adverse prognosis in independent cohorts. Cross-species mapping reveals that orthotopic syngeneic allografts more faithfully recapitulate the cellular diversity and EMT-enriched states of advanced human PDAC, underrepresented in autochthonous genetically engineered models, with differences driven primarily by cell-type composition rather than pathway divergence. Together, these atlases and pretrained models provide a broadly accessible reference for benchmarking PDAC model fidelity and for interrogating mechanisms of tumour progression, microenvironmental remodelling and therapy response and resistance.

cancer biology↗

bioRxiv2025

The Pdgfd-Pdgfrb axis orchestrates tumor-nerve crosstalk in pancreatic cancer

Nerves are an integral component of the tumor microenvironment, contributing to cancer progression, metastasis, morbidity, and mortality. In pancreatic ductal adenocarcinoma (PDAC), worse clinical outcomes are associated with perineural invasion (PNI), a process by which cancer cells surround and invade nerves. Here, we employed whole-transcriptome and single-cell spatial transcriptomics to identify candidate tumor-nerve interactions that promote PNI. We discovered that Pdgfd signaling promotes key features of nerve invasion. Mechanistically, Pdgfd stimulated cancer cell invasiveness, neurite outgrowth, and direct physical engagement with glia. Pharmacological blockade of this axis reduced each of these processes in vitro as well as PNI in vivo. Thus, Pdgfd-Pdgfrb signaling mediates PNI by coordinating multifaceted cancer-neuron-glia interactions and represents a promising therapeutic strategy aimed at disrupting harmful cancer-nerve crosstalk.

cancer biology↗

bioRxiv2025

Tissue architecture dynamics underlying immune development and decline in the thymus

The age-associated decline in adaptive immune function, widely observed in vertebrates, has been attributed to thymic involution. To gain insights into the structural and transcriptional changes underlying this phenomenon, we employed high-resolution spatial transcriptomics and T-cell receptor (TCR) sequencing in mice. By analyzing 21 thymus samples spanning mouse lifespan, we uncovered significant alterations in thymic organization, including disrupted T cell development and the emergence of B cell aggregates. We also observed age- related changes in cell-cell interactions, marked by increased antigen-presenting cell presence in thymic medullary regions and a shift from inflammatory to suppressive macrophages, fostering an immunosuppressive niche. Furthermore, aged thymus tissues exhibited an abundance of regions with reduced TCR diversity, accompanied by distinct changes to gene expression profiles. Our study establishes a valuable reference for understanding aging-related alterations in adaptive immunity, revealing mechanisms underlying age-induced immunological decline.

immunology↗

bioRxiv2025

Integrated spatial morpho-transcriptomics predicts functional traits in pancreatic cancer

Analyses of patient-derived cell lines have greatly enhanced discovery of molecular biomarkers and therapeutic targets. However, characterization of cellular morphological properties is limited. We studied cell morphologies of human pancreatic adenocarcinoma (PDAC) cell lines and their associations with drug sensitivity, gene expression, and functional properties. By integrating live cell and spatial mRNA imaging, we identified KRAS inhibitor-induced morphological changes specific for drug-resistant cells that correlated with gene expression changes. We then categorized a large panel of patient-derived PDAC cell lines into morphological (e.g., polygonal, irregular, spheroid) and organizational (e.g., tightly aggregated, multilayered, dispersed) subtypes and found differences in gene expression, therapeutic targeting potential, and metastatic proclivity. In human PDAC tissues, we identified prognostic expression signatures associated with distinct cancer cell organization patterns. In summary, we highlight the potential of cell morphological information in rapid, cost-effective assays to aid precision oncology efforts leveraging patient-derived in vitro models and tissues.

cancer biology↗

bioRxiv2025

MicroSplit: Semantic Unmixing of Fluorescent Microscopy Data

Fluorescence microscopy, a key driver for progress in the life sciences, faces limitations due to the microscopes optics, fluorophore chemistry, and photon exposure limits, necessitating trade-offs in imaging speed, resolution, and depth. Here, we introduce Micro[S]plit, a computational multiplexing technique based on deep learning that allows multiple cellular structures to be imaged in a single fluorescent channel and then unmix them by computational means, allowing faster imaging and reduced photon exposure. We show that Micro[S]plit efficiently separates up to four superimposed noisy structures into distinct denoised fluorescent image channels. Furthermore, using Variational Splitting Encoder-Decoder (VSE) networks, our approach can sample diverse predictions from a trained posterior of solutions. The diversity of these samples scales with the uncertainty in a given input, allowing us to estimate the true prediction errors by computing the variability between posterior samples. We demonstrate the robustness of Micro[S]plit networks, which are trained for each splitting task at hand, across various datasets and noise levels and show its utility to image more, to image faster, and to improve downstream analysis. We provide Micro[S]plit along with all associated training and evaluation datasets as open resources, enabling life scientists to immediately benefit from the potential of computational multiplexing and thus help accelerate the rate of their scientific discovery process.

bioinformatics↗

bioRxiv2025

Pan-Cancer Biomarker Analysis from the Cancer Dependency Map: A Blueprint for Precision Oncology

The diversity of therapeutic modalities and targets continue to grow, and the number of cancer patients eligible for targeted therapy has expanded accordingly. Despite advances, response rates to individual targeted therapy drugs remain variable, rarely achieving uniform tumor shrinkage across patients. Biomarkers are crucial for identifying patients likely to respond to therapy while sparing non-responders from toxicity and guiding them toward alternative treatments. We conducted a multi-omic analysis of biomarker-dependency relationships across 1,150 cancer molecular profiles to identify novel biomarkers for patient stratification. We first validated the Cancer Dependency Maps sensitivity and specificity in predicting therapeutic windows for targeted therapies. Next, we identified predictive biomarkers for single- and multi-gene dependencies, assessing their selectivity within biomarker-defined populations. Protein abundance analysis revealed potential immunohistochemistry (IHC) biomarkers for clinically deployed therapeutic compounds. We performed an analysis of lineage-enriched dependencies, highlighting new opportunities for target validation and drug development. Finally, we screen for associations between hotspot mutations, damaging mutations, and protein abundance, providing insights for developing heterobifunctional small molecules for induced proximity and protein degradation. These findings advance our understanding of cancer dependencies and inform biomarker-driven strategies to optimize therapeutic outcomes.

cancer biology↗

bioRxiv2024

Imaging of developing human brains with ex vivo PSOCT and dMRI

The human brain undergoes substantial developmental changes in the first five years of life. Particularly in the white matter, myelination of axons occurs near birth and continues at a rapid pace during the first 2 to 3 years. Diffusion MRI (dMRI) has revolutionized our understanding of developmental trajectories in white matter. However, the mm-resolution of in vivo techniques bears significant limitation in revealing the microstructure of the developing brain. Polarization sensitive optical coherence tomography (PSOCT) is a three-dimensional (3D) optical imaging technique that uses polarized light interferometry to target myelinated fiber tracts with micrometer resolution. Previous studies have shown that PSOCT contributes significantly to the elucidation of myelin content and quantification of fiber orientation in adult human brains. In this study, we utilized the PSOCT technique to study developing brains during the first 5 years of life in combination with ex vivo dMRI. The results showed that the optical properties of PSOCT quantitatively reveal the myelination process in young children. The imaging contrast of the optic axis orientation is a sensitive measure of fiber orientations in largely unmyelinated brains as young as 3-months-old. The micrometer resolution of PSOCT provides substantially enriched information about complex fiber networks and complements submillimeter dMRI. This new optical tool offers great potential to reveal the white matter structures in normal neurodevelopment and developmental disorders in unprecedented detail.

neuroscience↗

bioRxiv2024

Earlier finish of motor planning in the premotor cortex predicts faster motor command in the primary motor cortex: human intracranial EEG evidence

The human motor system has a hierarchical control during finger movements. The non-primary motor cortex (premotor cortex, PM, and supplementary motor area, SMA) organizes motor planning, while the primary motor cortex (M1) is responsible for motor execution. We utilized the human intracranial EEGs high temporal and spatial resolution to investigate how the temporal dynamics of the high-gamma neural oscillations in the hierarchically organized motor sub-regions, during both pre-movement planning and motor execution, correlated with reaction times (RTs) in a cued finger movement task. Our results showed that the high-gamma power of PM, SMA, and M1 activated sequentially. More importantly, the sustained high-gamma power activation in the non-primary motor cortex and the peak latency of high-gamma power in M1 had a significant predictive relationship with the RTs. In particular, the faster the activation of the non-primary motor cortex returned to baseline, the faster the motor command in M1, and accordingly the shorter the RTs. Further, pairwise phase coherence between the motor areas showed that the more sustained the connection between the motor areas, the longer the RTs would be. The current findings illustrate the relationship between the temporal profiles of high-gamma power in human motor areas and response performance.

neuroscience↗

bioRxiv2023

Quantitative imaging of three-dimensional fiber orientation in the human brain via two illumination angles using polarization-sensitive optical coherence tomography

The accurate measurement of three-dimensional (3D) fiber orientation in the brain is crucial for reconstructing fiber pathways and studying their involvement in neurological diseases. Optical imaging methods such as polarization-sensitive optical coherence tomography (PS-OCT) provide important tools to directly quantify fiber orientation at micrometer resolution. However, brain imaging based on the optic axis by PS-OCT so far has been limited to two-dimensional in-plane orientation, preventing the comprehensive study of connectivity in 3D. In this work, we present a novel method to obtain the 3D fiber orientation in full angular space with only two illumination angles. We measure the optic axis orientation and the apparent birefringence by PS-OCT from a normal and a 15 deg tilted illumination, and then apply a computational method yielding the 3D optic axis orientation and true birefringence. We verify that our method accurately recovers a large range of through-plane orientations from -85 deg to 85 deg with a high angular precision. We further present 3D fiber orientation maps of entire coronal sections of human cerebrum and brainstem with 10 m in-plane resolution, revealing unprecedented details of fiber configurations. We envision that further development of our method will open a promising avenue towards large-scale 3D fiber axis mapping in the human brain and other complex fibrous tissues at microscopic level.

neuroscience↗

bioRxiv2023

Chromosome-scale genome assembly of Tinospora sagittata (Oliv.) Gagnep. enhances identifying genes involved in the biosynthesis of jatrorrhizine

Tinospora sagittata (Oliv.) Gagnep. is an important medicinal tetraploid plant in the Menispermaceae family. Its tuber, namely "Radix Tinosporae" used in Traditional Chinese Medicine, is rich in medicinal terpenoids and benzylisoquinoline alkaloids (BIAs), To enhance understanding the biosynthesis of medicinal compounds, we, herein, report the assembly of a high quality chromosome-scale genome with both PacBio HiFi and Illumina sequencing technologies. The size of assembled genome was 2.33 Gb consisting of 4070 scaffolds (N50=42.06Mb), of which 92.05% were assigned to 26 pseudochromosomes in A and B sub-genomes. A phylogenetic analysis with the T. sagittata and other 16 plant genomes estimated the evolutionary placement of T. sagittata and its divergence time in Ranunculales. Further genome evolution analysis characterized one round tandem duplication about 1.5 million years ago (MYA) and one whole-genome duplication (WGD) about 86.9 MYA. WGD contributed to the duplication of clade-specific cytochrome P450 gene family in Ranunculales. Moreover, sequencing mining obtained genome-wide genes involved in the biosynthesis of alkaloids and terpenoids. TsA02G014550, one candidate, was functionally characterized to catalyze the formation of (S)-canadine in the jatrorrhizine biosynthetic pathway. Taken together, the assembled genome of T. sagittata provides useful sequences to understand the biosynthesis of jatrorrhizine and other BIAs in plants.

genomics↗

bioRxiv2023

Therapy-associated remodeling of pancreatic cancer revealed by single-cell spatial transcriptomics and optimal transport analysis

In combination with cell intrinsic properties, interactions in the tumor microenvironment modulate therapeutic response. We leveraged high-plex single-cell spatial transcriptomics to dissect the remodeling of multicellular neighborhoods and cell-cell interactions in human pancreatic cancer associated with specific malignant subtypes and neoadjuvant chemotherapy/radiotherapy. We developed Spatially Constrained Optimal Transport Interaction Analysis (SCOTIA), an optimal transport model with a cost function that includes both spatial distance and ligand-receptor gene expression. Our results uncovered a marked change in ligand-receptor interactions between cancer-associated fibroblasts and malignant cells in response to treatment, which was supported by orthogonal datasets, including an ex vivo tumoroid co-culture system. Overall, this study demonstrates that characterization of the tumor microenvironment using high-plex single-cell spatial transcriptomics allows for identification of molecular interactions that may play a role in the emergence of chemoresistance and establishes a translational spatial biology paradigm that can be broadly applied to other malignancies, diseases, and treatments.

cancer biology↗

bioRxiv2023

Focusing attention in human working memory and long-term memory: benefits through dissociable processes

We developed a new experimental approach to compare how attentional orienting facilitates retrieval from working memory (WM) and long-term memory (LTM), and how selective attention within these two memory types impacts incoming sensory information processing. In three experiments with healthy young adults, retrospective attention cues prioritized an item represented in WM or LTM. Participants then retrieved a memory item or performed a perceptual task. The retrocue was informative for the retrieval task but not for the perceptual task. Attentional orienting benefited performance for both WM and LTM, with stronger effects for WM. Eye-tracking revealed significant gaze shifts and microsaccades correlated with attention in WM but not LTM. Visual discrimination of unrelated visual stimuli was consistently improved for items matching attended WM locations. Similar effects occurred at LTM locations but less consistently. The findings suggest potent and at least partly dissociable attention-orienting processes for different memory types.

neuroscience↗

bioRxiv2022

Host genetic background is a barrier to vaccine-induced protection against infection

The heterogeneity of immune responses observed in humans is difficult to model in standard inbred laboratory mice. To capture the diversity inherent in mice and better understand how host variation affects BCG-induced immunity against Mycobacterium tuberculosis, 24 unique Collaborative Cross (CC) recombinant inbred mouse strains and the C57BL/6 reference strain were vaccinated with or without BCG, and then challenged with low-dose aerosolized virulent M. tuberculosis. In contrast to standard lab strains, BCG protected only half of the CC strains tested. Furthermore, BCG efficacy is dissociable from inherent susceptibility to TB. As these strains differed primarily in the genes and alleles they inherited from the CC founder strains, we conclude that the host genetic background has a major influence on whether BCG confers protection against M. tuberculosis infection and indicates that host genetics should be considered as an important barrier to vaccine-mediated protection. Importantly, we wished to identify the components of the immune response stimulated by BCG, which were subsequently recalled after Mtb infection and associated with protection. The T cell immune response following BCG vaccination and Mtb challenge was extensively characterized. Although considerable diversity was observed, BCG vaccination had little impact on the composition of T cells recruited and maintained in the lung after infection. Instead, the variability was largely shaped by the genetic background. We developed models to detect vaccine-induced differences, which identified immune signatures associated with BCG-elicited protection against TB. Importantly, even when categorized as susceptible vs. resistant, and protected vs. unprotected, many of the protected CC strains had unique flavors of immunity, indicating multiple paths to protection. Thus, CC mice can be used to define correlates of protection and to identify vaccine strategies that protect a larger fraction of genetically diverse individuals instead of optimizing protection for a single genotype.

immunology↗

bioRxiv2022

Type 17 Follicular Helper T (Tfh17) Cells are Superior for Memory Maintenance

A defining feature of successful vaccination is the ability to induce long-lived antigen- specific memory cells. Follicular helper T (Tfh) cells specialize in providing help to B cells in mounting protective humoral immunity in infection and after vaccination. Memory Tfh cells that retain the CXCR5 expression can confer protection through enhancing humoral response upon antigen re-exposure but how they are maintained is poorly understood. CXCR5+ memory Tfh cells in human blood are divided into Tfh1, Tfh2 and Tfh17 cells by the expression of chemokine receptors CXCR3 and CCR6 associated with Th1 and Th17 respectively. Here, we developed a new method to induce Tfh1, Tfh2 and Tfh17-like (iTfh1, iTfh2 and iTfh17) cells in vitro. Although all three iTfh subsets efficiently support antibody responses in recipient mice with immediate immunization, iTfh17 cells are superior to iTfh1 and iTfh2 cells in supporting antibody response to a later immunization after extended resting in vivo to mimic memory maintenance. Notably, the counterpart human Tfh17 cells are selectively enriched in CCR7+ central memory Tfh (TfhCM) with survival and proliferative advantages. Furthermore, the analysis of multiple human cohorts that received different vaccines for HBV, influenza virus, tetanus toxin or measles revealed that vaccine-specific Tfh17 cells outcompete Tfh1 or Tfh2 cells for the persistence in memory phase. Therefore, the complementary mouse and human results showing the advantage of Tfh17 cells in maintenance and memory function supports the notion that Tfh17-induced immunization might be preferable in vaccine development to confer long-term protection.

immunology↗

bioRxiv2022

Estrogen suppresses DMRT1 expression during ovarian development in the chicken

Primary sex determination is the choice between two different developmental fates, a testis or an ovary. This selection is thought to require the action of a master regulator gene that triggers expression of a gene cascade in the bipotential gonad precursor in one sex. The selection of a particular developmental pathway is also thought to suppress the alternative developmental pathway. In birds, where the male is the homogametic sex (ZZ) and females the heterogametic sex (ZW), the Z-linked transcription factor DMRT1 is considered the master regulator and has been shown to be essential for testis development, and to also inhibit the ovarian pathway. Here, we characterise in detail, DMRT1 transcription and protein levels during gonadal development in the chick. Our analysis suggests that DMRT1 protein levels are equivalent in male and female gonads during the bipotential phase of development, and that DMRT1 protein levels are reduced in the developing ovary during the differentiation phase. The reduction in DMRT1 protein levels in the somatic cells of the female medulla, coincides with the induction of aromatase expression and the initiation of estrogen synthesis. Analysis of sex-reversed gonads and mixed-sex chimeric gonads, suggests that the reduction in DMRT1 protein is due to inhibition of DMRT1 expression by estrogen. Our data suggests that estrogen signalling is involved in primary sex determination by regulation of DMRT1 protein expression.

developmental biology↗