Biology subjects

Hu, Y.

Publications and source records attributed to Hu, Y..

At least 181 records · Page 10Linked to original sources

bioRxiv2025

Multimodal brain cell atlas across the adult macaque lifespan

High-throughput single-cell omics of non-human primate tissues present a remarkable opportunity to study primate brain aging. Here, we introduce a transcriptomic and chromatin accessibility landscape of 1,985,317 cells from eight brain regions of 13 cynomolgus female monkeys spanning adult lifespan including exceptionally old individuals up to 29-years old. This dataset uncovers dynamic molecular changes in critical brain functions such as synaptic communication and axon myelination, exhibiting a high degree of cell type and brain region specificity. We identify the multicellular networks of the pons and medulla as a previously unrecognized hotspot for aging. Furthermore, comparative analyses with human neurodegeneration datasets highlight both shared and distinct mechanisms contributing to aging and disease. In addition, we uncover transcription factors implicated in monkey brain aging and pinpoint aging-regulated loci linked to longevity and neurodegeneration. This spatiotemporal atlas will advance our understanding of primate brain aging and its broader implications for health and disease.

neuroscience↗

bioRxiv2025

Two-Stage CD8+ CAR T-Cell Differentiation in Patients with Large B-Cell Lymphoma

Chimeric antigen receptor (CAR) T-cell therapy has expanded therapeutic options for patients with diffuse large B-cell lymphoma (DLBCL). However, progress in improving clinical outcomes has been limited by an incomplete understanding of CAR T-cell differentiation in patients. To comprehensively investigate CAR T-cell differentiation in vivo, we performed single-cell, multi-modal, and longitudinal analyses of CD28-costimulated CAR T cells from infusion product and peripheral blood (day 8-28) of patients with DLBCL who were successfully treated with axicabtagene ciloleucel. Here, we show that CD8+ CAR T cells undergo two distinct waves of clonal expansion. The first wave is dominated by CAR T cells with an exhausted-like effector memory phenotype during the peak expansion period (day 8-14). The second wave is dominated by CAR T cells with a terminal effector phenotype during the post-peak persistence period (day 21-28). Importantly, the two waves have distinct ontogeny and are biologically uncoupled. Furthermore, lineage tracing analysis via each CAR T cells endogenous TCR clonotype demonstrates that the two waves originate from different effector precursors in the infusion product. Precursors of the first wave exhibit more effector-like signatures, whereas precursors of the second wave exhibit more stem-like signatures. These findings suggest that pre-infusion heterogeneity mediates the two waves of in vivo clonal expansion. Our findings provide evidence against the intuitive idea that the post-peak contraction in CAR abundance is solely apoptosis or extravasation of short-lived CAR T cells from peak expansion. Rather, our findings demonstrate that CAR T-cell expansion and persistence are mediated by clonally, phenotypically, and ontogenically distinct CAR T-cell populations that serve complementary clinical purposes.

immunology↗

bioRxiv2025

Repulsive interactions instruct synaptic partner matching in an olfactory circuit

Neurons exhibit extraordinary precision in selecting synaptic partners. Although cell-surface proteins (CSPs) mediating attractive interactions between developing axons and dendrites have been shown to instruct synaptic partner matching1,2, the degree to which repulsive interactions play a role is less clear. Here, using a genetic screen guided by single-cell transcriptomes3,4, we identified three CSP pairs--Toll2-Ptp10D, Fili-Kek1, and Hbs/Sns- Kirre--in mediating repulsive interactions between non-partner olfactory receptor neuron (ORN) axons and projection neuron (PN) dendrites in the developing Drosophila olfactory circuit. Each CSP pair exhibits inverse expression patterns in the select ORN-PN partners. Loss of each CSP in ORNs led to similar synaptic partner matching deficits as the loss of its partner CSP in PNs, and mistargeting phenotypes caused by overexpressing one CSP could be suppressed by loss of its partner CSP. All CSP pairs are also differentially expressed in other brain regions. Together, our data reveal that multiple repulsive CSP pairs work together to ensure precise synaptic partner matching during development by preventing neurons from forming connections with non-cognate partners.

neuroscience↗

bioRxiv2025

Themis dominates T cell exhaustion by regulation of TCR and PD-1 signaling

T cell exhaustion is important to protect the host from immunopathology during chronic viral infection, but it also impairs T cell anti-tumor immunity1-5. A fundamental unresolved question is whether and how T cell exhaustion is determined at the onset of TCR signaling6-8. Here we report an unexpected role of Themis, a TCR-proximal signaling molecule9, in T cell exhaustion. Chronic viral infection in mice usually leads to T cell exhaustion and survival of the host. Surprisingly, Themis T-cell conditional knockout mice died from severe CD8+-dependent lung immunopathology in chronic viral infection, showing Themis importance in establishing T cell exhaustion. We found that Themis-deficient CD8+ T cells were hyperactivated at the single-cell level - producing more TNF and IFN{gamma} compared to wild-type counterparts - but defective in population-level expansion. Moreover, TCF-1 and TOX expression were inhibited in Themis-deficient CD8+ T cells, thereby impairing differentiation of exhausted T cell precursors (T-pex) and maintenance of terminally exhausted T cells (T-ex), respectively. Mechanistically, Themis initially promotes TCR signaling to induce PD-1 expression and subsequently mediates PD-1 signaling. In the latter, Themis binds to PD-1 and promotes PD-1 phosphorylation and its recruitment of SHP2, thereby acting as a negative regulator to inhibit T cell effector functions. Without Themis, the orderly regulation of TCR and PD-1 signaling, and therefore exhaustion, is disrupted. Thus, our results unequivocally demonstrate that Themis-mediated early TCR signaling plays a decisive role in T cell exhaustion and provide a novel mechanism of PD-1 signaling through Themis.

immunology↗

bioRxiv2025

Clonal memory of colitis accumulates and promotes tumor growth

Chronic inflammation is a well-established risk factor for cancer, but the underlying molecular mechanisms remain unclear. Using a mouse model of colitis, we demonstrate that colonic stem cells retain an epigenetic memory of inflammation following disease resolution, characterized by a cumulative gain of activator protein 1 (AP-1) transcription factor activity. Further, we develop SHARE-TRACE, a method that enables simultaneous profiling of gene expression, chromatin accessibility and clonal history in single cells, enabling high resolution tracking of epigenomic memory. This reveals that inflammatory memory is propagated cell-intrinsically and inherited through stem cell lineages, with certain clones demonstrating dramatically stronger memory than others. Finally, we show that colitis primes stem cells for amplified expression of regenerative gene programs following oncogenic mutation that accelerate tumor growth. This includes a subpopulation of tumors that have exceptionally high AP-1 activity and the additional upregulation of pro-oncogenic programs. Together, our findings provide a mechanistic link between chronic inflammation and malignancy, revealing how long-lived epigenetic alterations in regenerative tissues may contribute to disease susceptibility and suggesting potential therapeutic strategies to mitigate cancer risk in patients with chronic inflammatory conditions.

cancer biology↗

bioRxiv2025

Machine Learning-Enhanced Extraction of Protein Signatures of Renal Cell Carcinoma from Proteomics Data

In this study, we generated label-free data-independent acquisition (DIA)-based liquid chromatography (LC)-mass spectrometry (MS) proteomics data from 261 renal cell carcinomas (RCC) and 195 normal adjacent tissues (NAT). The RCC tumors included 48 non-clear cell renal cell carcinomas (non-ccRCC) and 213 ccRCC. A total of 219,740 peptides and 11,943 protein groups were identified with 9,787 protein groups per sample on average. We adopted a comprehensive approach to select representative samples with different mutation sites, considering histopathological, immune, methylation, and non-negative matrix factorization (NMF)-based subtypes, along with clinical characteristics (gender, grade, and stage) to capture the complexity and diversity of ccRCC tumors. We used machine learning identified 55 protein signatures that distinguish RCC tumors from NATs. Furthermore, 39 protein signatures that differentiate different RCC tumor subtypes were also identified. Our findings offer an extensive perspective of the proteomic landscape in RCC, illuminating specific proteins that serve to distinguish RCC tumors from NATs and among various RCC tumor subtypes.

cancer biology↗

bioRxiv2025

A versatile miniature two-photon microscope enabling multicolor deep-brain imaging

Here we present the FHIRM-TPM 3.0, a 2.6 g miniature two-photon microscope capable of multicolor deep-brain imaging in freely behaving mice. The system was integrated with a broadband anti-resonant hollow-core fiber featuring low transmission loss, minimal dispersion from 700-1060 nm, and high tolerance of laser power. By correcting chromatic and spherical aberrations and optimizing the fluorescence collection aperture, we achieved cortical neuronal imaging at depths exceeding 820 m and, using a GRIN lens, hippocampal Ca2+ imaging at single dendritic spine resolution. Moreover, we engineered three interchangeable parfocal objectives, allowing for a tenfold scalable field-of-view up to 1x0.8 mm{superscript 2}, with lateral resolutions ranging from 0.68 to 1.46 m. By multicolor imaging at excitation wavelengths of 780 nm, 920 nm and 1030 nm, we investigated mitochondrial and cytosolic Ca2+ activities relative to the deposition of amyloid plaques in the cortex of awake APP/PS1 transgenic mice. Thus, the FHIRM-TPM 3.0 provides a versatile imaging system suitable for diverse brain imaging scenarios.

neuroscience↗

bioRxiv2025

TF2TG: an online resource mining the potential gene targets of transcription factors in Drosophila

Sequence-specific transcription factors (TFs) are key regulators of many biological processes, controlling the expression of their target genes through binding to the cis-regulatory regions such as promoters and enhancers. Each TF has unique DNA binding site motifs, and large-scale experiments have been conducted to characterize TF-DNA binding preferences. However, no comprehensive resource currently integrates these datasets for Drosophila. To address this need, we developed TF2TG ("transcription factor to target gene"), a comprehensive resource that combines both in vitro and in vivo datasets to link transcription factors (TFs) to their target genes based on TF-DNA binding preferences along with the protein-protein interaction data, tissue-specific transcriptomic data, and chromatin accessibility data. Although the genome offers numerous potential binding sites for each TF, only a subset is actually bound in vivo, and of these, only a fraction is functionally relevant. For instance, some TFs bind to their specific sites due to synergistic interactions with other factors nearby. This integration provides users with a comprehensive list of potential candidates as well as aids users in ranking candidate genes and determining condition-specific TF binding for studying transcriptional regulation in Drosophila.

bioinformatics↗

bioRxiv2025

Generalization but not strengthening of negative memories drives the development of depression-like behaviors

Individuals with depression exhibit intensified and generalized negative memories. However, how prior memories actually influence onset and/or progression of depression, particularly whether the strengthening or the generalization of prior memories play a key role, is poorly understood. Here, we introduced behavioral paradigms to differentiate between memory strengthening and generalization, and found that negative experiences that produced memory overgeneralization, but not strengthening, induced depression-like behaviors. Furthermore, we identified that the medial prefrontal cortex (mPFC) to the bed nucleus of the stria terminals (BNST) projection functionally linked memory generalization to depression, together with single-cell calcium imaging which revealed a significant overlap in the mPFCBNST neuronal ensemble encoding depression-like behaviors with that encoding generalized memory, but not memory strength. Circuit-based transcriptomic analysis and chromophore-assisted light inactivation demonstrated that triggering actin remodeling in the mPFCBNST neurons, a memory consolidation mechanism enhanced generalization while reducing memory strength, also induced depression-like behaviors. Collectively, these findings suggest generalization of negative memories as a primary factor that drives depression-like behaviors, highlighting the importance of early identification of individuals at risk for depression who exhibit overgeneralized negative memories, and targeting overgeneralized negative memories in the treatment of depression.

animal behavior and cognition↗

bioRxiv2025

Divergent stem cell mechanisms governing the primary body axis and appendage regeneration in the axolotl

Exploring the fundamental mechanisms of organ regeneration is crucial for advancing regenerative medicine. The axolotl tail represents a unique opportunity to study regeneration of the primary axis including segmented muscle, vertebrae and skin. During tail development, muscle stem cells (MuSCs) displayed expected specificity to the muscle lineage. Tail amputation, however, induced expansion of MuSC potential yielding clonal contribution to muscle, connective tissue including cartilage, pericytes, and fibroblasts. This expanded potential was not observed during limb regeneration, and cross-transplantation showed these differences in potential are intrinsic. ScRNA-Seq profiling revealed that tail MuSCs revert to an embryonic mesoderm-like state. Through genetic manipulation involving the over-expression of constitutively active TGF-{beta} receptors or Smad7 (antagonist of TGF-{beta} signaling) in MuSCs, we demonstrated that the levels of TGF-{beta} signal determine the fate outcome of MuSCs to connective tissue lineage or muscle respectively. Our findings illustrate a fundamental difference between regeneration of primary axis versus limb and offers a novel stem cell source for regeneration of axial skeletal tissues.

developmental biology↗

bioRxiv2025

scKAN: Interpretable Single-cell Analysis for Cell-type-specific Gene Discovery and Drug Repurposing via Kolmogorov-Arnold Networks

Single-cell analysis has revolutionized our understanding of cellular heterogeneity, yet current approaches face challenges in efficiency and interpretability. In this study, we present scKAN, a framework that leverages Kolmogorov-Arnold Networks for interpretable single-cell analysis through three key innovations: efficient knowledge transfer from large language models through a lightweight distillation strategy; systematic identification of cell-type-specific functional gene sets through KANs learned activation curves; and precise marker gene discovery enabled by KANs importance scores with potential for drug repurposing applications. The model achieves superior performance on cell-type annotation with a 6.63% improvement in macro F1 score compared to state-of-the-art methods. Furthermore, scKANs learned activation curves and importance scores provide interpretable insights into cell-type-specific gene patterns, facilitating both gene set identification and marker gene discovery. We demonstrate the practical utility of scKAN through a case study on pancreatic ductal adenocarcinoma, where it successfully identified novel therapeutic targets and potential drug candidates, including Doconexent as a promising repurposing candidate. Molecular dynamics simulations further validated the stability of the predicted drug-target complexes. Our approach offers a comprehensive framework for bridging single-cell analysis with drug discovery, accelerating the translation of single-cell insights into therapeutic applications.

bioinformatics↗

bioRxiv2025

Peritoneal cavity-derived GATA6+ macrophages inhibit fibrosis through IL33 in endometrium

Macrophages exhibit a high degree of plasticity and play pivotal roles both in the normal physiological cycle of the endometrium and in its regeneration following injury. Although some new subsets of endometrial macrophages have been identified, their origins and functions remain to be further explored. In this study, we employed single-cell sequencing to analyze the endometrium of patients with normal endometrium and intrauterine adhesion (IUA) caused by injury. We identified a unique subset of macrophages distinguished by the expression of GATA6, a marker indicative of cavity macrophages. We verified that these GATA6+ macrophages were large peritoneal macrophages (LPMs) that migrated from the peritoneal cavity to the injured endometrium. Upon activation by injured endometrium, these LPMs demonstrated increased expression of Interleukin-33 (IL33), mediated by the Lars-Fos signaling axis, which interacts with the IL33 enhancer. Moreover, our studies revealed that IL33 derived from LPMs inhibited the differentiation of endometrial stromal cells (ESCs) into myofibroblasts, a critical step in the development of endometrial fibrosis. Furthermore, we confirmed the inhibitory effect occurred through the binding of IL33 to the ST2 receptor on ESCs, leading to the upregulation of JMJD3 and subsequent suppression of myofibroblast differentiation. Our findings highlight the essential role of LPMs in promoting endometrial repair and inhibiting fibrosis in IUA. Significance StatementThis study reveals the presence of a unique population of macrophages within the endometrium, originating from large peritoneal macrophages (LPMs), that are pivotal in endometrial repair. This finding offers new insights into the plasticity of macrophages and their potential therapeutic applications in treating endometrial fibrotic disorders.

immunology↗

bioRxiv2025

DARG: a Database of Alzheimer Related Genes in Model Organisms

Alzheimer disease is affecting a significant portion of the aging population worldwide. Despite extensive research over the years, a comprehensive understanding of its underlying mechanisms and effective treatments remains elusive. Meanwhile, animal models, such as mouse, zebrafish, Drosophila, and C. elegans, have proven invaluable in studying human diseases. In response, we have developed DARG, a Database of Alzheimer disease-related genes in model organisms, designed to bridge the gap between human geneticists investigating the molecular mechanisms of the disease and the model organisms that can be used to explore the functions of disease-associated genes. DARG allows users to search and browse Alzheimer-related human genes from various resources and datasets, identify orthologs in model organisms, and access data on their gene expression and related phenotypes in Drosophila.

bioinformatics↗

bioRxiv2025

SCGclust: Single Cell Graph clustering using graphautoencoders integrating SNVs and CNAs

Intra-tumor heterogeneity (ITH) is a compounding factor for cancer prognosis and treatment. Single-cell DNA sequencing (scDNA-seq) provides cellular resolution of the variations in a cell and has been widely used to study cancer progression and responses to drug and treatment. While the low coverage scDNA-seq technologies typically provides a large number of cells, accurate cell clustering is essential for effectively characterizing ITH. Existing cell clustering methods typically are based on either single nucleotide variations (SNV) or copy number alterations (CNA), without leveraging both signals together. Since both SNVs and CNAs are indicative of the cell subclonality, in this paper, we designed a robust cell clustering tool that integrates both signals using a graph autoencoder. Our model co-trains the graph autoencoder and a graph convolutional network (GCN) to guanrantee meaningful clustering results and to prevent all cells from collapsing into a single cluster. Given the low dimensional embedding generated by the autoencoder, we adopted a Gaussian Mixture Model to further cluster cells. We evaluated our method on eight simulated datasets and a real cancer sample. Our results demonstrate that our method consistently achieves higher V-measure scores compared to SBMClone, a SNV-based method, and a K-means method, which relies solely on CNA signals. These findings highlight the advantage of integrating both SNV and CNA signals within a graph autoencoder framework for accurate cell clustering. SCGclust is publicly available at https://github.com/compbio-mallory/cellClustering_GNN.

bioinformatics↗

bioRxiv2025

Refining the cis-regulatory grammar learned by sequence-to-activity models by increasing model resolution

Decoding the cis-regulatory syntax that controls gene expression is essential for improving our understanding of cell differentiation and disease. To identify regulatory motifs and their regulatory syntax, deep learning based sequence-to-activity (S2A) models learn transcription factor binding motifs and their combinations from DNA sequence by modeling measured chromatin accessibility. Previously, we developed AI-TAC, a S2A model that predicts chromatin accessibility across various immune cell types in multi-task fashion, effectively decoding the regulatory syntax underlying immune cell differentiation. While ATAC-seq is commonly used to measure regional accessibility, it also provides high-resolution profiles, the distribution of Tn5 insertion sites, that offer additional insights into the precise location and strength of TF binding sites. Here we demonstrate that modeling ATAC-seq profiles alongside accessibility consistently improves predictions of differential chromatin accessibility across cell types. Moreover, we also find that multi-task learning across related immune cell types consistently outperforms single-task models. To understand what additional information bpAI-TAC learns from ATAC-seq profiles, we systematically compare sequence attributions from models trained with and without ATAC-seq profiles. We identify novel motifs with strong effect sizes that emerge only when profile data is included. Our findings suggest that modeling ATAC-seq at base-pair resolution enables the model to learn a more nuanced and sensitive representation of the cis-regulatory syntax driving immune cell-specific chromatin landscapes.

genomics↗

bioRxiv2025

The epigenetic factor Zrf1 regulates intestinal stem cell proliferation during midgut regeneration

Stem cells are essential for tissue maintenance and regeneration, balancing self-renewal and differentiation to support homeostasis and repair. Through an RNAi screen in the Drosophila midgut, we identified the epigenetic factor Zrf1 as a critical regulator of intestinal stem cell (ISC) proliferation. Functional analyses reveal that Zrf1 integrates inputs from multiple signaling pathways and interacts with components of the RNA-induced silencing complex (RISC). Zrf1 mutants exhibit elevated expression of transposable elements (TEs) and chromatin disruption, highlighting a broader role in genome stability. Single-nuclei RNA sequencing (snRNA-seq) further demonstrated the influence of Zrf1 on chromatin organization and TE repression, particularly within stem cell progenitors. Our findings suggest that Zrf1 is potentially a key chromatin regulator necessary for maintaining stem cell proliferation and genome integrity, enhancing our understanding of the molecular controls underlying stem cell function and chromatin dynamics.

genetics↗

bioRxiv2025

Persistent interferon signaling that causes sensory neuron plasticity and pain in arthritis

While the inflammatory processes in rheumatoid arthritis have been described, mechanisms driving pain are poorly defined. Here, we used a multitude of approaches to uncover the neural basis, mediators, intracellular signaling pathway and the mechanism of inflammatory pain. In cartilage autoantibody-induced arthritis mice, an early immune-activation and a cytokine storm were mainly driven by vascular cells and monocyte/macrophages in the dorsal root ganglion. However, persistently elevated interferons and receptor-activation of the MNK1/2-eIF4E signaling pathway at all disease phases caused sensory-motor dysfunction and pain by inducing hyperexcitability and sensitization of Gfra3+ sensory neurons. Like mice, human sensory neurons expressed interferon receptors and interferons were elevated only in individuals with painful rheumatoid arthritis. Signaling pathway inhibition in vivo reversed pain and restored limb function. The finding that joint pain before and during arthritis is caused by a defined cytokine and signaling pathway holds promise for targeted therapies for pain relief in arthritis.

neuroscience↗

bioRxiv2025

An improved FLARE system for recording and manipulating neuronal activity

Recording and manipulating neuronal ensembles that underlie cognition and behavior in vivo is challenging. FLARE is a light- and calcium-gated transcriptional reporting system for labeling activated neurons on the order of minutes. However, FLARE is limited by its sensitivity to prolonged neuronal activities. Here, we present an improved version of FLARE, termed cytoFLARE. cytoFLARE incorporates cytosolic expression of the transcription factor and a more sensitive pair of calcium sensing domains. We showed that cytoFLARE provides more calcium- and light-dependent signals in HEK293T cells and higher signal-to-background ratios in neuronal cultures. We further established cytoFLARE transgenic Drosophila models and applied cytoFLARE to label activated neurons upon sensory or optogenetic stimulation within a defined time window. Notably, through cytoFLARE-driven expression of an optogenetic actuator, we successfully reactivated neurons involved in the larval nociceptive system. Our findings demonstrate the first characterization and application of time-gated calcium integrators in Drosophila.

bioengineering↗