Biology subjects

Jiang, J.

Publications and source records attributed to Jiang, J..

At least 109 records · Page 6Linked to original sources

bioRxiv2025

An atlas of cell type specific regulatory effects in cattle

Understanding the genetic and molecular architecture of complex traits and artificial selection is crucial for advancing sustainable precision breeding in cattle and other livestock. Yet, how genetic variation affects cellular gene expression remains elusive in cattle. Here, by integrating 8,866 bulk RNA-seq samples and 999,192 single cells of 81 cell types in 22 bovine tissues, we presented a comprehensive atlas of regulatory variants at the cell type resolution in cattle. By colocalizing with bulk-tissue expression quantitative trait loci (beQTL), we detected 57,043 novel cell-type stratified eQTL and cell-type/state interaction eQTL in 18,153 genes, which also exhibited a stronger tissue/cell-type specificity than beQTL. By examining genome-wide associations (GWAS) of 44 complex traits, these cell-resolved eQTL were colocalized with 505 (24%) additional GWAS loci compared to beQTL. Through integrating this resource with selection signatures between dairy and beef cattle, we provided tissue/cell-specific regulatory insights into cattle breeding. Overall, the current atlas of cell-type-specific regulatory variants will serve as an invaluable resource for cattle genomics and selective breeding.

genetics↗

bioRxiv2025

Multimodal Evidence for Hippocampal Engagement and Modulation by Functional Connectivity-Guided Parietal TMS

Hippocampal activity supports memory and many other brain functions. Transcranial magnetic stimulation (TMS) guided by hippocampal functional connectivity (FC) shows promise in improving memory, but direct neural evidence of its capacity to engage and modulate hippocampal activity is lacking. Here we combined TMS with intracranial electroencephalography (iEEG) in 8 neurosurgical patients and with functional magnetic resonance imaging (fMRI) in 79 neurologically healthy participants. We identified that (1) single-pulse TMS to individualized parietal cortex guided by hippocampal-FC preferentially evoked distinct temporal and spectral activity patterns in the hippocampus, (2) variability in TMS-evoked hippocampal responses related to individual differences in parietal-hippocampus FC strength, and (3) repetitive TMS to hippocampal-FC-guided parietal cortex selectively suppressed hippocampal theta oscillations. These findings provide multimodal causal neural evidence and important mechanistic insights supporting the development of personalized neuromodulation strategies aimed at improving hippocampus-dependent functions.

neuroscience↗

bioRxiv2025

Antigen-specific Th17 T cells offset the age-related decline in durable T cell immunity

Older adults are susceptible to infections, in part due to waning of immune memory. To determine mechanisms that determine long-lasting versus short-term immunity, we examined varicella zoster virus (VZV) vaccination as a model system. We contrasted VZV antigen-specific T cells several years after vaccination in adults who had been vaccinated at young (<20 years) or older age (>50 years) with a live-attenuated vaccine that confers durable protection only when given at young age, or with an adjuvanted VZV component vaccine that elicits effective, long-lasting immunity in older adults. CD8+ T cells were highly sensitive to age-related changes showing T cell subset shifts, loss in TCR diversity and reduced stem-like features while gaining NK-like signatures without evidence for cellular senescence or exhaustion. VZV-specific CD4+ T cells were largely resilient to age and maintained phenotypic and TCR diversity. Immunization of older adults with the adjuvanted VZV vaccine did not reverse age-associated defects in CD8+ T cells. Instead, it selectively improved the functionality of VZV-specific Th17 CD4+ T cells and prevented their acquisition of Treg features, likely as consequence of lipid metabolic pathways. Collectively, our data indicate that effective vaccination in older adults is supported by the generation of a durable, antigen-specific CD4+ Th17 population that resists mis-differentiation into Tregs and that compensates for age-related defects in CD8+ T cells. One sentence summaryAging primarily impairs the CD8+ T cell VZV vaccine response, while effective VZV vaccination in older adults induces antigen-specific Th17 CD4+ T cells to compensate for aging defects.

immunology↗

bioRxiv2025

RPcontact: Improved prediction of RNA-protein contacts using RNA and protein language models

Determining key contacts between RNA-protein interactions is essential for understanding the molecular mechanisms of numerous biological processes, including transcription, splicing, and translation. However, progress in this area has been impeded by the scarcity of RNA-protein complex structures in the Protein Data Bank (PDB) and the challenges posed by traditional structural determination techniques. Recent computational advancements, including deep learning methods like AlphaFold 3 and RoseTTAFoldNA, have improved contact prediction but are still limited by the availability of homologous sequences and templates. Here, we introduce RPcontact, a novel computational method designed to predict RNA-protein contacts using large language models tailored for RNA (ERNIE-RNA) and proteins (ESM-2). Despite being trained entirely on ribosomal RNA-protein (rRNA-protein) complexes, RPcontact demonstrates robust and generalized performance in predicting contacts for both dimeric and multimeric non-rRNA-protein complexes. The performance of RPcontact on contact predictions significantly improves over the binary contacts inferred from RNA-protein complex structures predicted by AlphaFold 3 and RoseTTAFoldNA, highlighting its potential in RNA-protein complex structure and function prediction.

bioinformatics↗

bioRxiv2025

Intratumoral cDC1-T Cell Clusters Serve as Sites of Local Costimulation to Enhance CTL-Mediated Tumor Rejection

T cells are essential for anti-tumor immunity, but their ability to eliminate tumors depends on coordinated interactions with type 1 conventional dendritic cells (cDC1s). While cDC1s are known for cross-presenting tumor-derived antigens in lymph nodes to prime CD8+ T cells, their role within the tumor itself remains less well understood. Here, we use the Skin Tumor Array by Micro-Poration (STAMP) model to investigate how cDC1-T cell interactions shape immune responses and influence tumor fate. Our data reveal that it is the spatial distribution of both cDC1s and T cells that determines whether a tumor can be rejected. We defined three primary immunotypes based on the spatial distribution of T cells and cDC1s: T cell-inflamed/dendritic cell-inflamed (TC-In/DC-In) tumors, where T cells and cDC1s co-infiltrate the tumor; T cell-inflamed/dendritic cell-excluded (TC-In/DC-Ex) tumors, where T cells infiltrate but cDC1s remain at the periphery; and T cell-excluded/dendritic cell-excluded (TC-Ex/DC-Ex) tumors, which lack both cDC1 and T cell infiltration. Notably, TC-In/DC-In tumors are more likely to undergo rejection, whereas TC-In/DC-Ex tumors persist despite T cell infiltration. Within TC-In/DC-In tumors, cDC1s engage in direct interactions with T cells, upregulate co-stimulatory molecules, and sustain effector T cell responses, while cDC1s in TC-In/DC-Ex tumors express higher migration-associated genes, suggesting a propensity to exit the tumor. We further show that chemokine modulation, particularly through CXCL9, CCL5, and XCL1, can reshape immune infiltration patterns to promote intra-tumoral cDC1-T cell clustering and improve tumor rejection. These findings underscore the unexpectedly important role of cDC1 positioning and function in sustaining effective anti-tumor immunity and highlight spatially organized cDC1-T cell clusters as critical hubs for local T cell activation.

immunology↗

bioRxiv2025

Tenotomized Achilles tendons of MRL/MpJ mice show scar-mediated healing, but have superior recovery of biomechanical properties

Tendon healing in Murphy Ross Large (MRL/MpJ) mice was examined using an Achilles tendon tenotomy model, a full transection model, compared to a patella focal injury model in which tendons in MRL/MpJ mice showed regenerative healing. After complete transection, the Achilles tendons of MRL/MpJ mice healed via scar formation, regardless of sex, as did C57BL/6J mice. Tensile testing found that mechanical properties of injured tendons of both MRL/MpJ female and male mice exhibited comparable levels to those of C57BL/6J female and male mice, respectively after 4 weeks of healing, which is during the remodeling phase. After 10 weeks of healing, injured tendons of MRL/MpJ mice possessed smaller heterotopic ossification volumes than those of C57BL/6J mice. Proteomics analysis revealed similar alterations to signaling pathways in injured tendons of MRL/MpJ and C57BL/6J male mice after 4 weeks of healing. However, among the altered pathways, actin cytoskeleton and integrin signaling pathways were two of the top pathways that were more prominently activated in C57BL/6J males than in MRL/MpJ males. These findings indicate that MRL/MpJ mice possess limited capacity to regenerate injured tendons after complete rupture, and that tenotomized Achilles tendons of MRL/MpJ male mice have lesser induction of heterotopic ossification and lower activation of the signaling pathways also induced with injury in C57BL/6J male mice.

pathology↗

bioRxiv2025

Human Messenger RNA Harbors Widespread Noncoding Splice Isoforms

Pre-messenger RNA transcribed from canonical protein-coding genes is frequently alternatively spliced into diverse mature mRNA isoforms, thus translating into various protein products. However, it remains unknown whether human mRNA from a protein-coding gene harbors noncoding splice isoforms in the genome. Herein, we discovered 15,836 mRNA noncoding splice isoforms across 7,298 protein-coding genes in human. mRNA noncoding isoforms are mainly produced by alternative splicing and polyadenylation, which display tissue-specific distributions and involve in RNA processing pathways. Notably, mRNA noncoding isoforms are frequently upregulated in cancer. Differentially expressed mRNA noncoding isoforms are associated with the cancer hallmarks and can independently predict patient survival. These findings unraveled human mRNA harbors widespread noncoding splice isoforms, and highlight the dual characters of mRNA including protein-translation isoforms and noncoding splice isoforms, providing a new dimension to our understanding of mRNA functional property.

genomics↗

bioRxiv2025

A computational framework for mapping isoform landscape and regulatory mechanisms from spatial transcriptomics data

Transcript diversity including splicing and alternative 3 end usage is crucial for cellular identity and adaptation, yet its spatial coordination remains poorly understood. Here, we present SPLISOSM (SpatiaL ISOform Statistical Modeling), a computational framework for detecting isoform-resolution patterns from spatial transcriptomics data. SPLISOSM leverages multivariate testing to account for spot- and isoform-level dependencies, demonstrating robust and theoretically grounded performance on sparse data. In the mouse brain, we identify over 1,000 spatially variable transcript diversity events, primarily in synaptic signaling pathways linked to neuropsychiatric disorders, and uncover both known and novel regulatory relationships with region-specific RNA binding proteins. We further show that these patterns are evolutionarily conserved between mouse and human prefrontal cortex. Analysis of human glioblastoma highlights pervasive transcript diversity in antigen presentation and adhesion genes associated with specific microenvironmental conditions. Together, we present a comprehensive spatial splicing analysis in the brain under normal and neoplastic conditions.

bioinformatics↗

bioRxiv2025

Calpain cleaves the carboxyl terminus of TRPV1 and modulates receptor tachyphylaxis

Transient receptor potential vanilloid-1 (TRPV1) plays a critical role in noxious heat sensation and pain hypersensitivity development in chronic pain. Sustained or repeated exposure to capsaicin, a classic TRPV1 agonist, induces TRPV1 desensitization. This partially accounts for the analgesic effect of capsaicin. However, the regulatory mechanisms of TRPV1 desensitization remain poorly understood. In this study, we found that capsaicin acts on TRPV1 to induce the activation of calpain, a Ca2+-sensitive cysteine protease, in a manner unrelated to cellular injury. Calpain cleaves rTRPV1 at the carboxyl terminus of G819/S820. Lack of the distal carboxyl terminus leads to reduced TRPV1 localization on the plasma membrane, potentially due to increased receptor internalization and impaired subunit assembly. This finding was corroborated by whole-cell patch clamp recordings. Additionally, the {Delta}820-838 mutant of rTRPV1 shows resistance to tachyphylaxis as induced by repetitive capsaicin stimulation. This study reveals a pivotal role for calpain in TRPV1 desensitization where its activation constrains TRPV1 channel function while simultaneously increasing its resistance to tachyphylaxis, thereby acting to maintain TRPV1 activity within an appropriate range.

neuroscience↗

bioRxiv2025

Evolution of T cell responses in the tuberculin skin test reveals generalisable Mtb-reactive T cell metaclones.

T cells contribute to immune protection and pathogenesis in tuberculosis, but measurements of polyclonal responses have failed to resolve correlates of outcome. We report the first temporal evaluation of the human in vivo clonal repertoire of Mtb-reactive T cell responses, by T cell receptor (TCR) sequencing at the site of a standardised antigenic challenge. Initial recruitment of non-Mtb reactive T cells is followed by enrichment of Mtb-reactive clones arising from oligoclonal T cell proliferation. We introduce a modular computational pipeline, Metaclonotypist, to sensitively cluster distinct TCRs with shared epitope specificity, which we apply here to establish a catalogue of public Mtb-reactive HLA-restricted T cell metaclones. Although most in vivo Mtb-reactive T cells are private, 10 metaclones were sufficient to identify Mtb-T cell reactivity across our study population (N[≥]128), indicating striking population level immunodominance of specific TCR-peptide interactions that may offer novel approaches to patient stratification and vaccine development.

immunology↗

bioRxiv2025

How Task Representations Integrate Information from Multiple Sources

Adaptive behavior requires integrating information from multiple sources. These sources can originate from distinct channels, such as internally maintained latent cognitive representations or externally presented sensory cues. Because these signals are often stochastic and carry inherent uncertainty, integration is challenging. However, the neural and computational mechanisms that support the integration of such stochastic information remain unknown. We introduce a computational neuroimaging framework to elucidate how brain systems integrate internally maintained and externally cued stochastic information to guide behavior. Neuroimaging data were collected from healthy adult human participants (both male and female). Our computational model estimates trial-by-trial beliefs about internally maintained latent states and externally presented perceptual cues, then integrates them into a unified joint probability distribution. The entropy of this joint distribution quantifies overall uncertainty, which enables continuous tracking of probabilistic task beliefs, prediction errors, and updating dynamics. Results showed that latent state beliefs are encoded in distinct regions from perceptual beliefs. Latent-state beliefs were encoded in the anterior middle frontal gyrus, mediodorsal thalamus, and inferior parietal lobule, whereas perceptual beliefs were encoded in spatially distinct regions including lateral temporo-occipital areas, intraparietal sulcus, and precentral sulcus. The integrated joint probability and its entropy converged in frontoparietal hub areas, notably middle frontal gyrus and intraparietal sulcus. These findings suggest that frontoparietal hubs read out and resolve distributed uncertainty to flexibly guide behavior, revealing how frontoparietal systems implement cognitive integration. SignificanceFlexible human behavior often depends on integrating information from multiple sources, such as memory and perception, each of which can be corrupted by noise. For example, a driver must integrate traffic signals (external cues) with their destination plan (internal goals) to decide when to turn. This study reveals how the human brain integrates multiple information sources to guide flexible behavior. More specifically, distinct brain regions encode internal beliefs and external sensory representations, while frontoparietal regions integrate this information in response to input noise. These findings provide a complete account of how the brain encodes and integrates multiple inputs to guide adaptive behavior.

neuroscience↗

bioRxiv2025

MAIS: an in-vitro sandbox enables adaptive neuromodulation via scalable neural interfaces

Brain-machine interfaces (BMIs) predominantly rely on static digital architectures to decode biological neuronal networks, a paradigm that is incompatible with natural neural coding in the human brain1-4. Bridging this gap is a critical step in combating neuronal dysfunction, enhancing brain functionality, and refining the precision of neuroprosthetics5. The integration of brain organoids with microelectrode array (MEA), as a class of BMIs, offers a humanized in vitro platform with unique biological compatibility advantages for dynamic neuronal decoding. This study resolves the biological-electronic encoding incompatibility of brain organoid-MEA Integration through three progressive breakthroughs. First, a human-machine hybrid agent is developed as a newly proposed bioengineered platform that couples brain organoids together with high-density MEAs and computational chips, enabling closed-loop perturbation of biological neuronal networks via exogenous signals. Second, through plasticity-driven real-time tracking of neuronal activity, we establish dynamically reconfigurable stimulation nodes that self-align with the electrophysiological states of the organoids. This resolves the exogenous-endogenous encoding mismatch by implementing plasticity-driven adaptation principles that ensure biological compatibility through spatially adaptive coordination. Finally, through shared plasticity rules rather than centralized control, we construct the first scalable multi-agent interactive system (MAIS) and demonstrate its real-world applications. Through designed scenarios of pathological/normal neuronal network interaction, we validate that MAIS achieves stable cross-network coordination. MAIS embodies a self-evolving neural coding sandbox in which plasticity-driven dynamic decoding bridges the compatibility gaps between biological and digital systems, providing a scalable and foundational infrastructure for human-centered neural interfaces.

bioengineering↗

bioRxiv2025

Mutations of short tandem repeats explain abundant trait heritability in Arabidopsis

Short tandem repeats (STRs) mutations are one of the most important fuels of evolution, but are often largely ignored despite their huge effects on phenotypic variations. Here, we leveraged seven Arabidopsis mutation accumulation lines to assess the STR mutation rate, which ranged from 1.93x10-2 to 4.40x10-3 per STR locus per generation and was much higher than the common SNP mutation rate at the level of 10-9-10-8. Interspecific comparison revealed rapid STR turnover, with a large proportion (71.8%) only present in Arabidopsis. In addition, intraspecific comparison of the ten assembled Arabidopsis genomes revealed that 29.3% of STRs were presence/absence variation (PAV), 36.5% of STRs were length variation (LV), 13.0% of STRs were no variation (NV) and the 21.1% STR loci with both LV and PAV. Based on 413 RNA-seq datasets, we identified that length variation of 3,871 STR loci (eSTRs) was associated with gene expression and 651 STR loci (sSTRs) were associated with splicing variation, and over one thousand eSTRs or sSTRs were linked with published genome-wide association study signals. In addition, a direct association between STR length variation and phenotypic variation uncovered a series of STR-trait associations. More notably, using the expression levels of 24,175 genes, the splice strength values of 12,784 splice sites, and 16 phenotypes of natural Arabidopsis populations, we revealed that the STR heritability is 0.111, 0.143 and 0.101, respectively. Overall, our results not only revealed the evolutionary dynamics of STRs, but highlighted the importance of STR variations as an important contributor to missing heritability in the regulation of complex traits.

evolutionary biology↗

bioRxiv2025

Enzyme Co-Scientist: Harnessing Large Language Models for Enzyme Kinetic Data Extraction from Literature

The extraction of molecular annotations from scientific literature is critical for advancing data-driven research. However, traditional methods, which primarily rely on human curation, are labor-intensive and error-prone. Here, we present an LLM-based agentic workflow that enables automatic and efficient data extraction from literature with high accuracy. As a demonstration, our workflow successfully delivers a dataset containing over 91,000 enzyme kinetics entries from around 3,500 papers. It achieves an average F1 score above 0.9 on expert-annotated subsets of protein enzymes and can be extended to the ribozyme domain in fewer than 3 days at less than $90. This method opens up new avenues for accelerating the pace of scientific research.

biochemistry↗

bioRxiv2025

Mechanistic Insights into the Substrate Egress Pathways of Human Glucose Transporters GLUT1 and GLUT9

Glucose transporters (GLUTs) play critical roles in cellular energy homeostasis and substrate-specific transport. Dysfunctional mutations can cause GLUT1 deficiency syndrome and excessive expression of GLUT1 is linked to cancer progression; while abnormal regulation of urate transport by GLUT9 is associated with hyperuricemia and gout. In this study, machine-learning driven molecular dynamics simulations have been employed to investigate the mechanistic insights into the substrate egress pathways of GLUT1 and GLUT9, including the inhibition mechanism of GLUT9 by apigenin. Our findings reveal that intracellular helices play a crucial role in facilitating the transition from inward-closed to inward-open conformations in both transporters. Additionally, aromatic residues, F291 and W388 in GLUT1, and W336 and F435 in GLUT9, are identified as key mediators of conformational changes. Analysis of substrate exit pathways provides mechanistic insights into transport profiles and aligns with clinically observed mutations. Furthermore, the inhibitory effect of apigenin on GLUT9 is shown to arise from steric hindrance due to increased substrate size, rather than stable interactions. These findings enhance our understanding of GLUT transporter dynamics and highlight the potential of targeting substrate pathways for therapeutic intervention.

biophysics↗

bioRxiv2025

Integrated Ultrasound Neuromodulation and Optical Neuroimaging in Awake Mice using a Transparent Ultrasound Transducer Cranial Window

Ultrasound neuromodulation is a rapidly advancing, non-invasive technique with significant therapeutic potential for treating various neurological disorders. Although extensive in vitro and in vivo studies have provided valuable insights into its modulatory effects, the underlying mechanisms remain poorly understood, limiting its clinical translation. Optical neuroimaging techniques can help investigate these mechanisms; however, the opacity and bulkiness of conventional ultrasound transducers pose significant challenges for their integration with in vivo ultrasound neuromodulation studies, particularly in awake rodents. To address these limitations, we propose a straightforward solution: a miniaturized lithium niobate-based transparent ultrasound transducer (TUT) integrated as a thinned-skull cranial window for ultrasound stimulation while facilitating multimodal optical neuroimaging in awake mice brain. Using laser speckle contrast imaging and intrinsic optical signal imaging, we studied changes in brain hemodynamics in response to various ultrasound stimulation sequences. Our experiments demonstrated that TUT cranial window can robustly induce neuromodulatory effects with observed increase in both cerebral blood flow and total hemoglobin, with peak and cumulative hemodynamic changes directionally correlated with ultrasound stimulation duration and intensity. Overall, these findings highlight that TUT cranial window can seamlessly integrate ultrasound stimulation and optical neuroimaging in awake mouse brain models, offering promising prospects for uncovering the underlying mechanisms of ultrasound neuromodulation.

neuroscience↗

bioRxiv2025

Lack of motor defects and ALS-like neuropathology in heterozygous Sptlc1 Exon 2 deletion mice

Mutations in the human SPTLC1 gene have recently been linked to early onset amyotrophic lateral sclerosis (ALS), characterized by global atrophy, motor impairments, and symptoms such as tongue fasciculations. All known ALS-linked SPTLC1 mutations cluster within exon 2 and a specific variant, c.58G>T, results in exon 2 skipping. However, it is unclear how the exon 2 deletion affects SPTLC1 function in vivo and contributes to ALS pathogenesis. Leveraging the high genomic sequence similarity between mouse and human SPTLC1, we created a novel mouse model with a CRISPR/Cas9-mediated deletion of exon 2 in the endogenous murine Sptlc1 locus. While heterozygous mice did not develop motor defects or ALS-like neuropathology, homozygous mutants died prematurely. These findings indicate that Sptlc1 {Delta}Exon2 heterozygous mice do not replicate the disease phenotype but provide valuable insights into SPTLC1 biology and serve as a useful resource for future mechanistic studies.

neuroscience↗

bioRxiv2025

The fetal hydrops-associated single-residue mutation L322P abolishes mechanical but not chemical activation of the PIEZO1 ion channel

The mechanically activated PIEZO1 ion channel is genetically linked to numerous physiological and pathophysiological processes. For example, deleting PIEZO1 in mice leads to defective lymphatic vessel development, while nonsense mutations in humans are associated with autosomal recessive generalized lymphatic dysplasia (GLD) and non-immune hydrops fetalis. However, it remains unclear whether PIEZO1-dependent biological processes are directly mediated by its intrinsic mechanosensitivity. Here we identified a human fetal hydrops-associated single-residue mutation, L322P (corresponding to L329P in mouse PIEZO1), which completely abolishes PIEZO1s response to mechanical stimuli while maintaining normal plasma membrane expression and responsiveness to its chemical activators, Yoda1 and Jedi1. Remarkably, the mechanical response of the mutant can be restored by Yoda1. These findings demonstrate a direct link between the loss of PIEZO1s mechanosensitivity and the pathophysiological phenotype of fetal hydrops, and raise the therapeutic potential of using PIEZO1 chemical activators to restore the mechanosensitivity of PIEZO1 missense mutants that are associated with genetic diseases such as GLD and hydrops fetalis. Significance StatementGenetic deletion studies have revealed the diverse cellular, physiological, and pathophysiological roles of the mechanically activated PIEZO1 ion channel. However, whether these functions are directly mediated by its mechanosensitivity has remained experimentally unaddressed. In this study, we identified a novel fetal hydrops-associated single-residue mutation, hPIEZO1-L322P, which specifically abolishes PIEZO1s mechanical response while retaining its chemical activation. Remarkably, the mechanical response of the mutant can be fully restored by the PIEZO1 chemical activator Yoda1. These findings address the long-standing question of whether PIEZO1 relies on its mechanosensitivity to mediate in vivo functions, provide critical insights into the mechanosensing mechanism of PIEZO1, and highlight the therapeutic potential of using PIEZO1 chemical activators to rescue the loss of mechanosensitivity caused by missense mutations.

physiology↗