Biology subjects

Hu, R.

Publications and source records attributed to Hu, R..

At least 19 recordsLinked to original sources

bioRxiv2026

ScProteoAgent enables natural-language-driven single-cell proteomics analysis and interpretation

Single-cell proteomics requires computational choices to remain aligned with experimental design as research questions evolve. Here we present ScProteoAgent, which translates natural-language requests into domain-specific calculations and preserves research intent, analysis design, matrix-processing history and statistical outputs as reusable analytical state. Follow-up requests reuse applicable inputs and initiate new calculations when contrasts or experimental units change. We assembled a benchmark comprising 55 tasks and 33 reference conclusions from 11 published studies, combining progressive questions within studies with complementary biological and analytical settings. In a retrospective comparison of 88 archived outputs from eight systems, ScProteoAgent achieved the highest mean score of 93.67 under a common six-dimensional rule-based evaluation. A HeLa migration case connected phenotype composition with proteomic clusters, candidate differences and original-observation support. In liver zonation, a researcher-guided follow-up reused a saved matrix to test mouse-level spatial contrasts and compare full-matrix and observed-only results. Applications in brain development, sample preservation and hematopoiesis illustrated how interpretation depends on processing choices and experimental units. ScProteoAgent connects research questions with statistical results and their analytical context, enabling existing analyses to support more specific biological investigations.

bioinformatics↗

bioRxiv2026

SMCHD1's DNA binding activity enables its stable retention on chromatin

Chromatin proteins play critical roles in gene regulation, yet frequently we do not fully understand how weak DNA binding affinity of such proteins contributes to their locus-specific actions. Here, we studied SMCHD1, a non-canonical SMC-family protein involved in three-dimensional genome organization and gene repression of the inactive X chromosome and its autosomal targets. We replaced endogenous SMCHD1 with GFP-tagged wild-type or hinge-domain DNA-binding mutant SMCHD1 to define the cellular role of DNA binding. The mutant showed reduced enrichment at the inactive X chromosome in female cells, while retaining stable binding at most autosomal binding sites. Impaired DNA binding weakens SMCHD1-mediated gene repression and chromatin-state regulation, producing hypomorphic effect. Multiple live-cell imaging methods reveal that DNA binding constrains SMCHD1 mobility and supports maintenance, rather than initial recruitment, of chromatin-bound SMCHD1 both during interphase and mitosis. Thus, SMCHD1's weak and sequence-independent DNA binding is a key determinant of its chromatin residence, localization and function. Our findings provide a framework for understanding SMCHD1 and other chromatin proteins with sequence-independent DNA binding activity.

genomics↗

bioRxiv2026

Redirecting carbon and electron flow in methanogenic laboratory scale anaerobic digestors with hypophosphite

In anaerobic digestion, formate is a central electron carrier linking primary and secondary fermentation to methanogenesis. Efforts to alter methane production have largely focused on directly targeting methanogens, while disruption of other trophic levels is underexplored. We recently demonstrated that hypophosphite is a naturally occurring inhibitor of formate exchange in syntrophic methanogenic systems. Here, we investigated whether intercepting formate exchange using hypophosphite can modulate methane production in a complex fermentative methanogenic system and what the longer-term consequences are for the structure and function of the microbiome. Using continuous up-flow anaerobic sludge blanket (UASB) columns fed with whey, we found that 100 M hypophosphite resulted in a transient (17 days) reduction in methane production by 20% to 50%, while carbon and electron flow was redirected towards hydrogen and volatile fatty acids. Accumulation of propionate, butyrate, branched-chain fatty acids, and not acetate indicated disruption of syntrophic formate metabolism. Following recovery of methane production in hypophosphite treated columns, we increased hypophosphite concentrations to millimolar levels and saw no repeated suppression of methane production. 16S rDNA amplicon sequencing revealed that hypophosphite treatment did not cause significant changes to microbiome composition. Methanogenic activity assays revealed a loss of formatotrophic methanogenic capacity in hypophosphite treated columns. Together, these results show that specific inhibition of formate exchange between syntrophs and methanogens decouples fermentative and methanogenic processes without altering microbiome composition with carbon and electron flow to methane ultimately redirected through hydrogen or acetate. This work demonstrates that hypophosphite can intercept syntrophic formate exchange in an engineered system and that long- term treatment with hypophosphite redirects electron flow towards electron carriers other than formate.

microbiology↗

bioRxiv2026

A Biophysical Platform for Electromechanical Stimulation of Engineered Cardiac Tissues

Human engineered cardiac tissues (ECTs) provide an in vitro model for studying human cardiac physiology and drug responses, but their performance remains limited by culture systems that do not fully reproduce the heart's electrical and mechanical environment. Electrical stimulation (ES) and mechanical stimulation (MS) have each been used to improve ECT function. Their combination, referred to as electromechanical stimulation (ES+MS), can provide further benefits. However, ES+MS depends not only on the presence of both cues but also on how they are coordinated in time. Here, we developed an incubator-compatible biophysical platform that delivers ES and MS independently or in combination, with programmable control over timing, amplitude, frequency, duration, and waveform. Calibration and dynamic characterization demonstrated tissue-relevant strain delivery, rapid and repeatable motion, and minimal attenuation and timing lag at the designated frequency of 1.5 Hz. We then compared four 6 h conditioning regimens: unstimulated control, ES alone, unsynchronized ES+MS, and synchronized ES+MS. We hypothesized that the synchronized ES+MS group, in which electrical excitation was aligned with peak externally applied strain, would produce the greatest increase in contractile force. Consistent with this hypothesis, synchronized ES+MS increased normalized twitch force by approximately 44% on average, whereas the other groups showed no comparable improvement. Twitch-timing metrics did not exhibit coordinated enhancement after 6 h, suggesting that the force increase reflects an adaptive biomechanical response rather than broad tissue maturation. These findings identify ES-MS timing as an important design parameter for ECT conditioning.

bioengineering↗

bioRxiv2026

The MOS4-associated complex subunit MAC5A maintains meristem development by regulating transcription elongation in Arabidopsis

The precise coordination of co-transcriptional RNA processing with transcriptional elongation is essential for eukaryotic gene regulation, yet the machineries coupling these processes remain largely elusive. Here, we reveal a role for the spliceosome-associated MOS4-associated complex (MAC) in regulating plant development through the direct regulation of transcriptional elongation. We demonstrate that the MAC subunit MAC5A physically interacts with Elongator Protein 6 (ELP6), a core component of the transcriptional Elongator complex. Genetic analyses reveal that MAC5A and ELP6 function synergistically to regulate apical meristem activity. Importantly, the MAC5A-Elongator module is required for the efficient expression of the critical auxin efflux carrier PIN-FORMED1 (PIN1) by enhancing RNA Polymerase II (RNAPII) occupancy across the PIN1 locus. Furthermore, we show that this elongation-promoting function is not unique to MAC5A, as other core MAC components are similarly required for efficient transcription progression. Together, our findings uncover a splicing-elongation nexus where MAC5A likely acts as a molecular bridge between the spliceosome and the elongation polymerase. This functional coupling ensures the efficient transcription of key developmental regulators, providing a mechanistic framework for the coupling of RNA processing to transcription and suggesting a conserved principle of gene expression control across eukaryotes.

plant biology↗

bioRxiv2026

A Novel Syngeneic Mouse Model to Study Immune Evasion in Head and Neck Squamous Cell Carcinoma

Head and neck squamous cell carcinoma (HNSCC) is the sixth most common cancer worldwide, and patient outcomes have remained largely unchanged despite advances in multimodal therapy. Immune checkpoint inhibitors (ICIs), which block the PD-1/PD-L1 axis to restore T cell-mediated anti-tumor immunity, have emerged as a promising treatment strategy. However, response rates remain below 20% in HNSCC, underscoring the need to better understand mechanisms of immune evasion within the tumor microenvironment. Syngeneic mouse models are essential for studying tumor-immune interactions, yet currently available HNSCC models are limited. Here, we report the development of a novel FVB/NJ-derived syngeneic HNSCC model generated from 7,12-dimethylbenz(a)anthracene (DMBA)-induced primary on floor of mouth/buccal tumors, designated FMOC1, FMOC2, and FMOC3 (FVB/NJ Mouse Oral Cancer). In vitro, all FMOC cell lines exhibited robust proliferative capacity with distinct proliferation kinetics. In vivo, all FMOC cell lines exhibited characteristic HNSCC histopathology, including cytokeratin 5 positivity, and were tumorigenic in immunodeficient NCG mice; however, in syngeneic immunocompetent mice, only FMOC1 demonstrated sustained tumor growth at orthotopic and flank sites, whereas FMOC2 and FMOC3 tumors underwent spontaneous regression within 2 weeks, indicating differential immune-dependent tumorigenicity among the lines. Consistent with this, depletion of CD4+ and/or CD8+ T cells restored tumor growth in FMOC2 and FMOC3 models, indicating a critical role for T cell-mediated immunity in tumor suppression. Notably, FMOC1 tumors were responsive to anti-PD-L1 and anti-CTLA-4 therapy, supporting their utility for evaluating immunotherapeutic strategies. Collectively, these findings establish the FMOC model as a novel and versatile platform to study tumor-immune interactions and immune evasion mechanisms in HNSCC, with potential applications in preclinical immunotherapy development.

cancer biology↗

bioRxiv2026

Morphology-robust quantification of subcellular organization in complex cells

Quantitative analysis of subcellular protein organization is often confounded by variation in cell morphology, limiting the identification and interpretation of localization patterns in fluorescence microscopy data from morphologically complex cells, such as neurons and glia. We introduce CellAligner, an unsupervised framework that uses fused unbalanced Gromov-Wasserstein couplings to map protein distributions from morphologically distinct cells into shared anchor-cell geometries, enabling morphology-robust comparison of subcellular localization. In neuronal imaging benchmarks, applying current image-analysis methods (CellProfiler, Cytoself, Paired Cell Inpainting) to CellAligners anchor-cell representations substantially reduced morphology-associated confounding while approximately doubling their multiclass MCC for localization classification. We demonstrate its biological utility by identifying U18666A-induced lysosomal trafficking defects in human iPSC-derived neurons. To scale the approach, we developed dCellAligner-OT, a fast deep metric learning model that approximates CellAligners optimal transport distances and anchor-cell representations, enabling atlas-scale analyses. CellAligner provides a general framework for morphology-robust analysis of subcellular organization in complex cellular systems.

bioinformatics↗

bioRxiv2026

BARseq3: a modular system for integrating spatial multi-omics and cellular barcoding in single cells

Understanding cellular identity requires multimodal measurements in single cells. Cellular barcoding provides powerful tools for recording the properties or history of individual cells in nucleic acids, while spatial omics techniques enable the measurement of a growing list of molecular features at micron resolution in tissue. However, existing methods that integrate these approaches in single samples are limited in the modalities they support, their flexibility, and efficiency. Here, we present BARseq3, a modular system that combines cellular barcoding with high-efficiency spatial transcriptomics and translatomics at subcellular resolution in tissue. BARseq3 is compatible with fixed samples, immunostaining, diverse species, and can be easily extended to include other spatial assays, enabling a multimodal understanding of cellular identity.

genomics↗

bioRxiv2026

CXCL13-CXCR5 Signaling in CD8⁺ T Cell Recruitment and Lymphoid Immune Organization in Clear Cell Renal Cell Carcinoma

Clear cell renal cell carcinoma (ccRCC) exhibits heterogeneity in immune infiltration and clinical outcomes, but the mechanisms governing recruitment and organization of tumor-reactive CD8 T cells remain incompletely defined. We investigated the role of the CXCL13-CXCR5 axis in shaping CD8 T cell recruitment, differentiation, and immune organization in high-risk, non-metastatic ccRCC. Human tumor, plasma, and matched adjacent kidney specimens were analyzed using ELISA, quantitative PCR, migration assays, multiplex immunofluorescence, single-cell RNA sequencing, spatial transcriptomics, and a syngeneic mouse model. CXCL13 was among the most upregulated chemokines in ccRCC relative to matched normal kidney and was embedded within a CD8 T cell-associated inflammatory transcriptional program. In transwell and microphysiological system (MPS) assays, CXCL13 promoted CD8 T cell migration, enriched CXCR5 cells among migrating CD8 T cells and showed reduced migration after CXCL13 or CXCR5 blockade. Single-cell analyses identified CXCR5 expression within stem-like CD8 T cell states associated with TCF7 and IL7R, whereas CXCL13 associated with later cytotoxic/exhausted states along a continuous differentiation landscape. Spatial transcriptomics demonstrated that stem-like CD8 T cells localized within structured lymphoid aggregates enriched for B cells, coordinated CXCL13/CXCR5 expression, and signaling programs. In vivo, tumor-derived CXCL13 suppressed tumor growth, increased intratumoral CD8 T cell infiltration, and enriched CXCR5TCF1CD8 stem-like T cells. In human tumors, higher CXCL13 expression correlated with increased CXCR5CD8 T cell infiltration and improved recurrence-free survival. These findings identify CXCL13 as a regulator of immune recruitment and niche organization and support the CXCL13-CXCR5 axis as a biomarker and possible therapeutic target in ccRCC.

cancer biology↗

bioRxiv2026

Quinone reductase 2 reads H3 serotonylation to support neuronal maturation

Histone H3 Gln5 serotonylation (H3Q5ser) is a recently described posttranslational modification1 that plays important roles in guiding transcriptional permissiveness in brain and peripheral systems2-5. H3Q5ser has been implicated in diverse physiological and pathological processes ranging from neural differentiation1 to sensory processing6, circadian rhythmicity7, stress responsivity8, placental gene regulation9, and tumorigenesis10-19. Since H3Q5ser can occur in combination with H3 Lys4 trimethylation (H3K4me3), most mechanistic studies to date have focused on H3Q5sers roles in modulating H3K4me3 reader interactions, where it has been shown to potentiate TAF3/TFIID binding to H3K4me31,20,21 and inhibit the recruitment of K4me3 demethylases21; however, whether H3 serotonylation functions as an autonomous chromatin signaling mark through dedicated reader proteins has remained unknown. Here, using a combination of proteomic-, structural-, molecular-, epigenomic-, and cellular-based approaches, we demonstrate that the Quinone reductase 2 (QR2) enzyme reads H3Q5ser independently of H3K4me3. CRISPR-Cas9-mediated disruption of H3 serotonylation or QR2s binding to the mark in human induced pluripotent stem cell-derived neurons impairs the establishment of neuronal transcriptional programs, alters synaptic connectivity, and disrupts electrophysiological maturation. These findings thus uncover an H3 serotonylation-dependent chromatin signaling axis that is essential for human neurodevelopment.

molecular biology↗

bioRxiv2026

Hypophosphite is a naturally-occurring selective inhibitor of syntrophic methanogenesis

Microbial methanogenesis is a major contributor to global warming and methane fluxes represent a loss of energy and electrons from industrial ecosystems. The chemical space of methane control strategies is still under-explored. Most known methanogenesis inhibitors target methanogenic archaeal enzymes. However, interference with syntrophic electron exchange in methanogenic systems presents an additional target for methane control. Here we show that hypophosphite (H2PO2-), an inorganic formate analog, is a potent and selective inhibitor of syntrophic methanogenesis versus primary fermentation in rice field sediments and cattle rumens. Hypophosphite is also generally recognized as safe and relatively non-toxic to plants and animals. Genetic screens and physiological assays in the model methanogen Methanococcus maripaludis S2 implicate formate metabolism as the target of hypophosphite inhibition. Currently, there is no known biological pathway for anaerobic hypophosphite oxidation and hypophosphite is stable in anoxic sediments for weeks to months. Given its widespread natural occurrence, we propose that hypophosphite may modulate carbon cycling in natural environments. Taken together, our results suggest that hypophosphite could be used as a safe, inexpensive, strategy for methane control in syntrophic methanogenic ecosystems.

microbiology↗

bioRxiv2026

SR2P: an efficient stacking method to predict protein abundance from gene expression in spatial transcriptomics data

Spatial transcriptomics data are largely available with RNA expression alone, limiting the detection of cell states defined by surface protein abundance. The lack of multi-omics spatial data limits the ability to identify immune cells and their signaling in the tumor microenvironment, as most solid tumors are immunologically poor and exhibit protein-RNA abundance discordance in critical immune cell surface markers. Although emerging technologies enable spatial multi-omics profiling, technical and cost constraints remain a hurdle. We introduce SR2P, a stacking-based machine-learning framework for predicting spatial protein abundance from RNA expression. SR2P integrates 11 complementary predictive models and consistently outperforms existing methods across multiple spatial multi-omics benchmark. We showcased an application of SR2P recovered macrophage-enriched regions and identified potential immune markers associated with therapeutic response from head-and-neck squamous cell carcinoma patients. SR2P enables protein-abundance inference from RNA-only spatial data, extending the analytical capabilities of current spatial platforms for studies of tumor immunology.

bioinformatics↗

bioRxiv2026

MATR3 is essential for oocyte growth and maturation quality through a dual molecular mechanism

The molecular mechanisms governing mRNA accumulation during oocyte growth, essential for developmental competence, remain poorly understood. This study investigates the role of Matrin-3 (MATR3), a highly expressed RNA-binding protein in growing oocytes (GOs), using oocyte-specific knockout mouse models and human oocyte maturation arrest (OMA) samples. The results showed that MATR3 was more abundant in GOs than fully-grown oocytes (FGOs), highly expressed in the nucleus of non-surrounded nucleolus (NSN) oocytes, and exited the nucleus during the NSN-to-surrounded nucleolus (SN) transition. In OMA patients, MATR3 nuclear localization was missed, with smaller oocytes than FGOs. Further, Matr3 deletion in mouse GOs caused restricted oocyte growth, global transcription disorders, follicle development failure, blocked GO-granulosa cell communication (via reduced Gdf9 and Radixin expression), and infertility. Mechanistically, MATR3 regulated transcription by recruiting H3K9me2-demethylating lysine-specific demethylase 3B or binding target gene promoters, like Radixin. These findings reveal a critical role of MATR3 in orchestrating transcription and paracrine signaling during oogenesis and suggest its potential as a diagnostic and therapeutic target for OMA.

physiology↗

bioRxiv2026

H4K20me3 and CTCF act reciprocally at TAD boundaries to regulate cell state transitions

Reversible transitions between proliferative and quiescent cell states involve widespread gene expression changes despite stable topologically associating domain (TAD) boundaries. We report a reciprocal antagonism between TAD boundary element CTCF and histone modification H4K20me3 as a central mechanism governing the proliferation-quiescence transition. Genome-wide studies and functional perturbations reveal that elevated H4K20me3 in quiescent fibroblasts displaces CTCF at specific TAD boundaries while CTCF binding predominates in proliferating cells. Increased H4K20me3 reversibly induces a compact chromatin state, elliptical nuclear morphology, and transcriptional programs associated with quiescence. Conversely, elevated CTCF binding drives open chromatin, proliferative gene expression, and cell division despite quiescence signals. Fibroblasts lacking H4K20me3 methyltransferase KMT5C/Suv4-20h2 are hyper-proliferative and KMT5C-deficient mice are larger. Our findings provide a mechanistic framework for how architectural and epigenetic regulators exchange at TAD boundaries to coordinate reversible cell state transitions, a finding with implications for organismal development and diseases of dysregulated proliferation.

cell biology↗

bioRxiv2026

Identification of Novel Extracellular Vesicles Scaffold Proteins for Versatile Cargo Engineering

Extracellular vesicles (EVs) are promising drug delivery platforms that have been engineered to carry various drug modalities. Key strategies for generating those therapeutic EVs involve the direct fusion of protein of interest (POI) to EVs scaffold proteins with inherently high EVs-sorting ability. In this work, we identified raftlin (RFTN1) and poliovirus receptor (PVR) as novel EVs scaffold proteins for loading EVs lumen and surface cargos respectively. Truncation studies revealed that the N-terminus 15 residues from RFTN1 (RFTN1-N15) were sufficient for EVs engineering, as demonstrated by distinct cargos including gene editing tools, cytosolic enzymes as well as type II transmembrane proteins. On the other hand, PVR efficiently displayed secreted proteins including antibodies and serum albumins on EVs surface. Critically, RFTN1 and PVR-engineered EVs demonstrated consistent and efficient cargo delivery in vivo. In summary, the discovery of RFTN1 and PVR can potentially benefit EVs engineering for both fundamental research and clinical translation in the future.

bioengineering↗

bioRxiv2025

RNA editing fine-tunes transcriptional plasticity and enhances the adaptability of Myzus persicae to diverse host plants

Parthenogenetic organisms can adapt to diverse and rapidly changing environments despite limited standing genetic variation, but the molecular mechanisms enabling such adaptability remain unclear. Here, we investigate this question in the green peach aphid (Myzus persicae, GPA), an asexual generalist herbivore capable of colonizing a wide range of host plants without underlying genetic change. By integrating RNA-seq and DNA-seq from genetically identical clones reared on different hosts, we identified 1,368 high-confidence RNA editing sites (RES), many of which exhibited strong host-dependent differences in editing levels. These RES encompassed all 12 possible nucleotide substitutions, with A-to-I, C-to-U, and U-to-C conversions being particularly prevalent. Editing at several sites shifted dynamically within 48 hours of host transfer and often coincided with changes in transcript abundance. Functional knockdown of the editing genes ADAR1 and ADAR2 reduced editing at specific sites, diminished fecundity, and abolished aphid survival on new hosts. Comparative analyses across aphid species reveal that although the biochemical signatures of A-to-I editing are deeply conserved, the genomic locations and functional roles of edited transcripts are species specific, reflecting lineage-specific adaptive strategies. Together, our findings demonstrate that RNA editing provides a rapid, reversible mechanism for environmental acclimation in GPA, enabling adaptive phenotypic plasticity even in the absence of genetic variation. This work establishes RNA editing as a key molecular basis for the remarkable ecological generalism of clonal organisms. Significance statementA major question in evolutionary biology is how clonal organisms with little genetic variation rapidly adapt to diverse, changing environments. Here we show that RNA editing provides a mechanism enabling the parthenogenetic green peach aphid (Myzus persicae) to colonize a wide range of host plants. RNA editing generates transcriptomic diversity, responds quickly to host shifts, and is essential for adaptation, as silencing ADAR genes disrupts A-to-I editing, reduces fitness, and prevents survival on new hosts. Comparative analyses across aphid species reveal that although the biochemical features of A-to-I editing are conserved, its genomic deployment and functional outcomes differ among species, reflecting lineage-specific strategies. These findings demonstrate that RNA editing creates a dynamic regulatory layer that offsets constraints of asexual reproduction.

molecular biology↗

bioRxiv2025

High-resolution MRI Guided Whole Mouse Brain Cell Type Atlas using Deep Learning

Cell types represent groupings of cells defined by shared anatomical and functional properties. Traditional mouse brain cell atlases rely heavily on single-cell sequencing, which provides valuable molecular detail but lacks whole-brain, isotropic resolution. Diffusion MRI (dMRI) offers a complementary approach for probing cytoarchitecture and myeloarchitecture, with quantitative metrics increasingly used as biomarkers of brain development and neurodegenerative disorders. Although prior work has linked dMRI metrics with gene expression, the capacity of dMRI to directly predict cell types remains unclear. Here, we present a deep learning framework that integrates high-resolution dMRI with three-dimensional light-sheet microscopy (LSM) registered to the Allen Mouse Brain Common Coordinate Framework (CCFv3). We investigated correlations between dMRI and spatial transcriptomics-derived cell types and generated a whole-brain cell type atlas at 10 {micro}m isotropic resolution. Together, these results establish an efficient, high-resolution strategy for brain cell atlas generation and underscore the potential of advanced imaging to illuminate cellular mechanisms of the brain.

neuroscience↗

bioRxiv2025

Orthogonal representational geometry in dACC underpins human hierarchical reasoning

Flexible adaptation requires inferring the causes of feedback and adjusting accordingly. When tasks are hierarchically structured with high-level rules governing low-level perceptual judgements, good performance requires hierarchical reasoning. Yet the computational and neural mechanisms underlying this process remain unclear. Here, building on Bayesian modelling and recurrent neural network simulation of hierarchical reasoning, we verified that such algorithm and representations are implemented in human dorsal anterior cingulate cortex (dACC). dACC encodes accumulated errors and perceptual difficulty to estimate high-level rule switch confidence. These two variables were represented along two separable dimensions, and could be approximated by Gaussian basis functions. Orthogonality between these two dimensions yielded an optimal two-dimensional representation for hierarchical reasoning. A closer-to-orthogonal representational geometry also predicted better performance. Together, these findings provide an integrated computational and neural representational basis for hierarchical reasoning.

neuroscience↗