Biology subjects

Hu, P.

Publications and source records attributed to Hu, P..

At least 19 recordsLinked to original sources

bioRxiv2026

Single-cell variant landscape of the human mitochondrial genome reveals cell type-specific functions and disease mechanisms

Mitochondrial DNA (mtDNA) heteroplasmy is a significant source of cellular genetic diversity and can cause disease yet its distribution and functional importance across different human cell types are poorly understood. Here we present scMOCHA (Single-Cell Mitochondrial Omics for Cellular Heteroplasmy Analysis), a scalable computational framework that resolves highconfidence, single-cell resolution mtDNA heteroplasmy directly from standard single-cell RNA sequencing (scRNA-seq) data. Using this tool to interrogate publicly available scRNA-seq datasets from human peripheral blood mononuclear cells (PBMC) and bone marrow (BM) uncovered the single-cell landscape of mtDNA single-nucleotide variants (SNVs) and heteroplasmy across ages in human hematopoietic cell types. PBMCs and BM share many inherited homoplasmic and highly heteroplasmic SNVs, whereas somatic SNVs are tissue- and cell type-specific and distributed across the mtDNA genome, suggesting that they arise largely stochastically. mtDNA replication error is a dominant force shaping homoplasmic variants, while oxidative stress potentially drives a significant portion of heteroplasmic and somatic mutations. Importantly, we discover previously unknown cell type-specific and human disease-associated mtDNA SNVs. By coupling mtDNA genotypes with matched single-cell nuclear transcriptomes and structural modeling, we uncover potential molecular mechanisms by which disease-associated mtDNA SNVs impact cellular processes such as inflammation and contribute to disease. Together, these findings define the single-cell variant landscape of the human mitochondrial genome and reveal previously unrecognized lineage- and disease-associated patterns of mtDNA variation in the human hematopoietic system.

genetics↗

bioRxiv2026

Immunomodulatory RIG-I Agonist SLR14 Confers Protection Against a Range of Highly Pathogenic Negative Sense RNA viruses

Emerging and re-emerging zoonotic RNA viruses, including filoviruses, henipaviruses and Rift Valley Fever virus (RVFV), pose a significant threat to human health. Due to their epidemic potential and high pathogenicity, these viruses are categorized as WHO priority pathogens, yet we still lack effective medical countermeasures (MCMs) against most of these dangerous pathogens, supporting that host-directed antivirals will be advantageous for broadly acting MCMs. Here we assessed the antiviral efficacy of SLR14, an immunomodulatory stem-loop RNA that activates RIG-I, for its activity against a panel of highly pathogenic viruses. SLR14 treatment provided broad-spectrum protection, markedly reducing infection with Ebola virus (EBOV), Marburg virus, and Sudan virus in human primary monocyte-derived macrophages, and Nipah virus replication in iPSC-derived endothelial cells, whether administered prophylactically or therapeutically. In vivo, a single dose of SLR14 protected mice against lethal RVFV infection when administered prophylactically, and, notably, retained significant efficacy when administered up to two days post-infection. Therapeutic SLR14 administration also improved survival rates of EBOV-infected mice. Although EBOV infection and SLR14 treatment activated overlapping innate immune pathways in human macrophages, viral infection induced a nonprotective response, whereas SLR14 elicited a well-regulated, markedly stronger and protective interferon-stimulated and inflammatory gene signature while avoiding prolonged IFN gene upregulation. Our data identify SLR14 as a potent host-directed therapeutic with broad antiviral efficacy against some of the most lethal viral pathogens.

microbiology↗

bioRxiv2026

Unifying physical and molecular coordinate systems across modalities in spatial biology

Establishing a unified physical and molecular coordinate system from fragmented multi-modal data is a longstanding challenge in biology. Here, we present MAPS, a modality-agnostic platform for spatial biology comprising (1) MAPS-alignment for ultrafast alignment of any modality, (2) MAPS-integration for both anchored and unanchored integration across orthogonal modalities for 3D multi-modal reconstruction, and (3) MAPS-Explorer for large-scale interactive 3D analysis. MAPS outperformed existing methods across extensive benchmarks on 34 datasets spanning 16 technology platforms and 6 modalities, while delineating fine-grained multi-modal tissue architectures across diverse biological systems in mouse and human. At cross-consortium scale, MAPS integrated 434 slices comprising 21 million cells from 18 atlases and 5 modalities to construct the most comprehensive 3D multi-modal mouse brain atlas. At individual laboratory scale, MAPS empowered routine 2D spatial assays to reconstruct continuous 3D multi-modal landscapes of human hepatocellular carcinoma, revealing the limitations of 2D spatial relationships and uncovering depth-dependent immune-state transitions.

bioinformatics↗

bioRxiv2026

DPF3a couples H3K36me2-dependent chromatin remodeling to genome architecture during myogenesis

Chromatin remodelers are generally thought to regulate gene expression through nucleosome mobilization and modulation of local chromatin accessibility. Whether these complexes can instead control transcription through higher-order chromatin organization remains poorly understood. Here we identify the BAF subunit DPF3a as an essential regulator of skeletal muscle regeneration and myogenic differentiation. DPF3a functions through association with the H3K36me2/3 reader HRP2 and preferentially localizes to a distinctive chromatin state characterized by focal depressions within broad H3K36me2 domains. Biochemical reconstitution demonstrates that H3K36 methylation directly enhances remodeling activity of the DPF3a-containing cBAF complex. Unexpectedly, despite profound transcriptional defects, loss of DPF3a produces minimal changes in local chromatin accessibility. Instead, DPF3a is required for long-range chromatin looping associated with activation of myogenic genes. Together, our findings uncover a non-canonical mechanism whereby a chromatin remodeler regulates transcription primarily through three-dimensional genome organization rather than local accessibility control, and establish histone modification-guided chromatin remodeling as a key principle in gene regulation.

molecular biology↗

bioRxiv2026

An integrative single-cell and spatial transcriptomics atlas highlights candidate regulatory factors in the development of gerbera capitulum

In Asteraceae species, the capitulum is a compact inflorescence, featuring a characteristic reproductive structure. Despite the identification of a few key regulatory factors, the transcriptome-level information on the developing capitulum remains limited. Here, we applied single-cell and spatial transcriptome sequencing to investigate the developing Gerbera hybridas capitulum during floret differentiation. We obtained a transcriptomics atlas encompassing different stages of the Gerbera capitulum and analyzed the cellular and spatial dynamics of gene expression. Using marker gene expression and GO enrichment of cluster-specific DEGs, we annotated putative cell types and described changes in gene expression across sampled stages, potentially associated with ongoing developmental processes. We detected activity of previously undescribed MADS-box genes and defined their spatial expression patterns. Notably, the MADS-box gene GAGL12 was found to be enriched in the putative capitulum phloem cells. The GAGL12 protein was shown in yeast two-hybrid assays to interact with several other MADS-domain proteins with hypothesized functions in vasculature development, and further detailed in silico analyses supported a candidate role in the development of capitulum vasculature. Altogether, we provide integrative and dynamic transcriptomic insight into capitulum and floret development and lay a basis for future functional studies of the control and development of this intriguing reproductive structure.

plant biology↗

bioRxiv2026

iCNG99: a validated genome-scale metabolic model of Cryptococcus neoformans strain H99

Cryptococcus neoformans is a ubiquitous environmental fungus that can also cause life-threatening infections in immunocompromised individuals. As a competent pathogen, Cryptococcus needs to reprogram its metabolism to adapt to the drastic differences between environmental niches and host niches. A well-curated genome-scale metabolic model (GEM) is a powerful tool to facilitate the investigation of the metabolic resilience of an organism. Here we reconstructed and validated iCNG99, a GEM for C. neoformans reference strain H99, and evaluated its predictive performance across 43 growth conditions and gene essentiality benchmarks. The model achieved high confidence essential gene prediction (precision = 0.77) and recapitulated pathways targeted by clinically available antifungals. Integration with transcriptomic and metabolomic data enabled iCNG99 to capture condition-specific metabolic adaptations and to identify candidate vulnerabilities in drug tolerance, revealing metabolic adaptations associated with survival within host conditions and drug susceptibility. Together, iCNG99 provides a systems-level computational platform for investigating C. neoformans metabolism and for prioritizing antifungal vulnerabilities.

systems biology↗

bioRxiv2026

HMA proteins produce 2',3'-cNMP signaling molecules and activate CNL-mediated immunity in rice

Plants deploy a sensor repertoire, usually NLRs, to perceive pathogen effectors and activate executor NLR-triggered immunity. Here we reveal that rice HMA proteins function as sensors detecting the Magnaporthe oryzae MAX effector AvrPigm to trigger broad-spectrum blast resistance mediated by the CNL PigmR. AvrPigm is conserved with multiple copies in blast genomes and targets HMA proteins, facilitating HMA translocation into the cytoplasm. Cryo-EM structure of the HPP04HMA reveals a filament-like oligomer with ssDNA/RNA bound inside the filament, which display cyclic nucleotide synthase activity to generate 2',3'-cNMP in a CNL-dependent manner. We further discovered that the LRR domains of the executor CNLs perceive 2',3'-cNMP to mount immunity. Our study thus establishes an unrecognized immunity mode with a distinct repertoire of sensor receptors that produce signaling molecules that are perceived by the LRR domains of executor NLRs to mediate immunity, shedding new light on the sensor-executor conception and immune activation in plants. HighlightsO_LIHMA proteins and CNL receptors form a new sensor-executor mode in plant immunity C_LIO_LICryo-EM reveals the filament-like structure of HMA-ssRNA/ssDNA C_LIO_LIHMA proteins are cyclic nucleotide synthetases to generate 2',3'-cNMP C_LIO_LILRR domains of CNLs perceive 2',3'-cNMP to mediate immunity C_LI

plant biology↗

bioRxiv2026

The diversity of lesion network mapping findings

Lesion network mapping (LNM) has emerged as a popular framework to map the network mechanism of brain disorders using lesions and normative brain connectome (NBC)1. It was first demonstrated in neurological symptoms and was rapidly extended to a broad range of brain disorders in the past decade. A recent study by Van den Heuvel et al. questioned the methodological foundations of LNM2. We here raise concerns regarding their errors and biases in the methodology and visualization. The conclusion of that study--LNM maps circumscribed brain changes mostly to one and the same outcome--is not supported by the data presented.

neuroscience↗

bioRxiv2026

A lightweight, ultrafast and general embedding framework for large-scale spatial omics data

Deciphering ultra-large-scale omics data with minimal resources while maintaining high computational efficiency is a longstanding challenge in biology. Here, we present Local Pooling (LP), a lightweight, ultrafast and general framework that leverage neighbor-indexing strategy and local pooling module to generate omics embedding and compatible with variety of downstream analyses. We developed its adaptation for spatial omics, SpaLP, and evaluated it on over 20 large-scale datasets spanning 9 technology platforms. SpaLP consistently outperformed baseline methods across multiple benchmarks, including niche identification, expression reconstruction, multiple slices integration, 3D organ construction, multi-omics integration and cross-platform generalization. Notably, SpaLP processed a 1.35-million-cell mouse embryo slice in just 47 seconds, achieving up to 300-fold increase in computational efficiency compared to Graph Neural Network (GNN)-based methods. Meanwhile, SpaLP increased the average adjusted rand index (ARI) by over 30% for niche identification in simulated and realistic settings. Furthermore, we applied SpaLP to integrate 8.4 million mouse brain cells within 4 minutes on a single GPU and constructed a 3D spatial atlas. Finally, we explored SpaLPs ability of cross-platform generalization and potential for developing an omics foundation model. As a novel and general framework, we believe that LP could help more researchers develop new model on large-scale data and overcome the research barriers caused by computing resources in more fields.

bioinformatics↗

bioRxiv2026

The non-coding facet of Pink1 mRNA regulates mitochondria homeostasis

Coding and non-coding RNAs have traditionally been viewed as functionally distinct entities. Here, we found that the down-regulation of Pink1 due to Tet2 knockout (KO) in muscle cells resulted in mitochondria dysfunction and muscle fatigue. Surprisingly, both Pink1 mRNA alone and untranslatable ATG-deficient Pink1 RNA were sufficient to rescue the mitochondria defects in Tet2 KO cells. PINK1 protein was fast degraded shortly after translation and dispensable for functions of Pink1 mRNA in muscle cells. Moreover, a portion of Pink1 mRNA was located in mitochondria and interacted directly with mitochondria inner membrane located protein YME1L1, promoting its proteolytic cleavage of Opa1, a master regulator of mitochondria fusion, to generate the mature protein form. These findings uncovered a bona fide non-coding role for a canonical mRNA, suggesting that translation independent functions could be present in mRNAs with coding potentials, blurring the conventional dichotomy between coding and non-coding RNAs.

cell biology↗

bioRxiv2025

A minor muscle stem cell population functions as metabolic Trojan horse fueling systemic aging by succinate induced epigenetic reprogramming

Inflammaging, the sustained chronic inflammation, is a hallmark of aging, yet its sustained activation mechanism remains elusive. Here, we identified muscle stem cells (MuSCs) as a driver of systemic inflammaging, evidenced by the multi-organ inflammation and aging phenotypes in MuSC specific Tet2 knockout mice. Tet2-Hdac11-Acod1-SDH axis maintained normal succinate level in MuSCs. Tet2 knockout disrupted this enzymatic cascade and led to succinate accumulation, fueling H4K31succ elevation to directly activate inflammatory gene transcription in MuSCs. The excess succinate was delivered to muscle fibers by sporadic fusion of Tet2 knockout MuSCs during muscle homeostasis, activated pro-inflammatory program, and transformed muscle to a persistent pro-inflammatory factor secretory organ, sustaining systemic inflammaging. Moreover, Tet2 was downregulated in aged MuSCs suggesting that this coupled metabolic-epigenetic mechanism was active in physiological aging. These findings reveal that a small subset of dysregulated MuSCs activate sustained whole-body inflammaging and multi-organ aging, providing new targets for rejuvenation strategy development.

cell biology↗

bioRxiv2025

Single-cell transcriptomic dynamics exposes hidden survival trajectory under antibiotic treatment

Heterogeneity plays a major role in bacterial resistance to antibiotic treatment while the mechanism at single-cell level is largely unknown. Here, we employed a robust integration of bulk and bacterial single-cell RNA-seq (scRNA-seq) to uncover how individual cells of Acinetobacter baumannii reorganise the heterogenous transcriptome in response to antibiotic. Using polymyxin as a representative, bulk RNA-seq showed canonical envelope- and efflux-centred responses but obscured underlying heterogeneity. Single-cell profiling resolved these averages into discrete subpopulations whose abundances shifted with concentration and time. Specifically, in early time an envelope-stress programme predominated survival at the low concentration, whereas an outer-membrane repair/efflux programme dominated survival at the high concentration. These patterns revealed structured and time-resolved heterogeneity, highlighting an ingenious bacterial stress responsive strategy. Through trajectory inference, we further revealed a concentration-dependent bifurcation of cell fates: low-concentration treated cells detoured through a transient stress state and rejoined growth, whereas high-concentration treated survivors diverted into a slow-growing, tolerant branch. Perturbing marker genes from these programmes altered fitness eventually and rapidly increased permeability, depolarisation and reactive-oxygen burden, linking state to survival capability. Collectively, we map a dynamic, concentration-structured landscape of antibiotic responses at the single-cell level, revealing diverse survival trajectories that are obscured in conventional population-averaged analyses. Our developed single-cell based framework revealed tolerant bacterial cells with rewiring of the transcriptional landscape, causing emergence of antibiotic resistance. Importantly, these findings urge precision antimicrobial therapy in patients to minimise emergence of antibiotic resistance.

microbiology↗

bioRxiv2025

Histology-informed spatial domain identification through multi-view graph convolutional networks

Identifying spatial domains is crucial in spatial transcriptomics, yet effectively integrating gene expression, spatial location, and histology remains challenging. We present STESH, a Spatial Transcriptomics clustering method that combines Expression, Spatial information and Histology. STESH extracts histological features using a convolutional neural network and generates expression, histology, spatial, and collaborative convolution modules for a multi-view graph convolutional network with a decoder and attention mechanism. We evaluated STESH on multiple tissue types and technology platforms. STESH consistently outperformed ten state-of-the-art methods, achieving superior clustering accuracy with the highest scores in adjusted Rand index, normalized mutual information, and Fowlkes-Mallows index.

bioinformatics↗

bioRxiv2025

FlexRibbon: Joint Sequence and Structure Pretraining for Protein Modeling

AO_SCPLOWBSTRACTC_SCPLOWProtein foundation models have advanced rapidly, with most approaches falling into two dominant paradigms. Sequence-based language models (e.g., ESM-2) capture sequence semantics at scale, and a number of recent works incorporate structural signals into sequence encoders. MSA-based predictors (e.g., AlphaFold 2/3) achieve accurate folding by exploiting evolutionary couplings, but their reliance on homologous sequences makes them less reliable in highly mutated or alignment-sparse regimes. We present FlexRibbon{ddagger}, a pretrained protein model that jointly learns from amino acid sequences and three-dimensional structures. Our pretraining strategy combines masked language modeling with diffusion-based denoising, enabling bidirectional sequence-structure learning without requiring MSAs. Trained on both experimentally resolved structures and AlphaFold 2 predictions, FlexRibbon captures global folds as well as flexible conformations critical for biological function. Evaluated across diverse tasks spanning interface design, intermolecular interaction prediction, and protein function prediction, FlexRibbon establishes new state-of-the-art performance on 12 different tasks, with particularly strong gains in mutation-rich settings where MSA-based methods often struggle.

molecular biology↗

bioRxiv2025

Haploinsufficiency of KPNA7 causes otosclerosis, likely due to the release of import inhibition of PTHrP and the reactivation of chondrogenesis in the globuli interossei

Otosclerosis is a genetic bone disorder restricted to the otic capsule and a common cause of conductive hearing loss with both familial and sporadic cases. To date, 14 genomic loci (OTSC) and four underlying OTSC genes (MEPE, SERPINF1, FOXL1, SMARCA4) have been identified in autosomal dominant families. A combined genetic/genomics approach on five affected siblings of Northern European ancestry from the island of Newfoundland, Canada identified a premature stop mutation in Karyopherin subunit 7 (KPNA7, c.49C>T, p.R17X). KPNA7 maps to OTSC2 (7q22.1) and encodes the newest of the seven-member importin- family of nuclear transporters and plays a critical role in early embryonic cleavage events and zygotic genome activation. Previous studies reveal that recessive KPNA7 variants cause skeletal abnormalities, including scoliosis and ocular hypertelorism in two sisters with Partial Corpus Callosum Agenesis-Cerebellar Vermis Hypoplasia With Posterior Fosa Cysts Syndrome and more recently, have been implicated in preimplantation embryo arrest (PREMBA) (OMIM 614107). Interestingly, KPNA7 is also a maternal factor with an exclusively embryonic role and likely inhibits non-classical NLS transport of PTHrP, a known activator of chondrogenesis. We propose that KPNA7 haploinsufficiency causes a failure in nuclear transport inhibition of PTHrP in the quiescent embryonic cells of the globuli interossei in the otic capsule and re-activates chondrogenesis. The KPNA7 discovery provides new insights into the pathogenesis of otosclerosis and potential for targeted therapies. Author SummaryOtosclerosis is a distinctly human genetic bone disorder of the otic capsule and a major cause of progressive hearing loss in young adults, particularly in females. Even though otosclerosis has been recognized as a distinct entity for a long time, both its pathogenesis and restriction to the otic capsule remains a mystery. Here, we use a combined genetic/genomics approach to identify a premature stop mutation in five affected siblings of Northern European ancestry from the island of Newfoundland, Canada. KPNA7 encodes the newest of the seven-member importin- family of nuclear transporters and plays a critical role in early embryonic cleavage events and zygotic genome activation. Based on the unique features of the otic capsule, we hypothesize that the premature stop mutation in KPNA7 leads to haploinsufficiency causing a failure in nuclear transport inhibition of PTHrP and reactivates chondrogenesis in the otherwise quiescent embryonic cells within the otic capsule. The KPNA7 discovery provides new insights into the pathogenesis of otosclerosis and potential for targeted therapies.

genetics↗

bioRxiv2025

Context-dependent regulatory variants in Alzheimer's disease

Noncoding genetic variants underlie many complex diseases, yet identifying and interpreting their functional impacts remains challenging. Late-onset Alzheimers disease (LOAD), a polygenic neurodegenerative disorder, exemplifies this challenge. The disease is strongly associated with noncoding variation, including common variants enriched in microglial enhancers and rare variants nominated at loci implicated in neurodevelopment and synaptic function. These variants may perturb regulatory sequences by disrupting transcription factor (TF) motifs or altering local regulatory sequence context, with potential consequences for gene expression and chromatin accessibility. However, assessing their impact is complicated by the context-dependent functions of regulatory sequences, underscoring the need to systematically examine variant effects across diverse tissues, cell types, and cellular states. Here, we combined in vitro and in vivo massively parallel reporter assays (MPRAs) with interpretable machine-learning models to systematically characterize common and rare variants across myeloid and neuron-enriched neural contexts. Parallel profiling of variants in four immune states in vitro and three mouse brain regions in vivo revealed that individual variants can differentially and even oppositely modulate reporter activity across cellular contexts, while a subset showed immune-state-dependent effects. Within the assayed candidate set, the relative effect sizes of common and rare variants reversed between contexts, with common variants showing larger effects in THP-1 macrophages and rare variants in brain tissue. Interpretable sequence-to-function models prioritized context-biased variants and generated motif-level hypotheses, including predicted transcription-factor motif disruption and subtler changes in local motif context. To probe endogenous consequences at a prioritized locus, we used CRISPR interference to perturb a rare-variant-containing enhancer at the SEC63-OSTM1 locus, revealing metabolic and biosynthetic transcriptional programs resembling those induced by SEC63 promoter perturbation, together with a stimulation-specific interferon response. These findings show that LOAD-associated noncoding variants exhibit context-dependent effects on reporter activity and predicted chromatin accessibility, and provide a framework for linking genetic association to regulatory activity, sequence grammar and endogenous transcriptional state.

genomics↗

bioRxiv2025

Genetically Programmable Adhesive Protein Hydrogels for Sealing Perforating Corneal Trauma

The cornea, situated at the forefront of the eyeball, is often subjected to varying degrees of mechanical laceration injuries due to various traumatic incidents. Timely and precise suturing of corneal wounds to prevent the leakage of intraocular contents is a significant clinical challenge. Although some studies have attempted to use hydrogels to accurately cover corneal injuries, most of these hydrogels are only suitable for adhering to focal stromal defects that do not involve the corneal stroma. Here, a fully protein-based hydrogel, based on SpyTag-SpyCatcher chemistry, was investigated for repairing corneal perforating injury models in rats and rabbits. The hydrogel formation relies on covalent bonding between SpyTag (A) and SpyCatcher (B) under physiologically mild conditions, eliminating requirements for organic solvents, elevated temperatures, or photoactivation Notably, integration of recombinant mussel foot protein 3 (Mfp3) endowed the hydrogels with exceptional water-resistant adhesiveness, while maintaining their original mechanical properties and biocompatibility. This study demonstrates the great potential of Mfp hydrogels in the timely and precise repair of corneal perforating injuries in complex physicochemical environments. TeaserBioinspired protein hydrogel rapidly seals corneal perforations, minimizing scarring and inflammation without sutures in animal models.

bioengineering↗

bioRxiv2025

Integrated single-cell and spatial multiomic analysis reveals widespread reactivation of developmental programs in diseased human hearts

The first organ to develop in utero, the human heart undergoes significant changes during development and must sustain its function over a lifetime. To better characterize molecular changes in human cardiac cell-types across sex, aging, developmental and disease, we analyzed single nucleus RNA sequencing (snRNA-seq) datasets from 299 donors, identifying many more differentially expressed genes (DEGs) across developmental and disease states than by sex and age. In cardiomyocytes and most non-cardiomyocyte cell types, developmental and disease DEGs showed significant overlap. Cardiac development and disease were associated with convergent changes in non-cardiomyocyte intercellular communication, including TGF{beta} signaling, but differences in cell-type proportions. By integrating snRNA-seq with 106 snATAC-seq datasets, we reveal potential transcriptional factors driving fetal reactivation in disease. Finally, using spatial transcriptomics data, we identify that fetal reactivation is highly localized in niches. This work offers the largest multimodal, cell-type resolved interrogation of the human heart, providing insights into convergence in development and disease.

genomics↗