Biology subjects

Ma, R.

Publications and source records attributed to Ma, R..

At least 19 recordsLinked to original sources

bioRxiv2026

Imbalance between RNA-binding proteins and the WAVE regulatory complex underlies the toxic gain-of-function effects of the CYFIP2 Arg87Cys variant in neurodevelopmental disorders

Pathogenic variants in cytoplasmic FMR1-interacting protein 2 (CYFIP2) cause neurodevelopmental disorders, with hotspot substitutions at arginine 87 (Arg87) associated with particularly severe symptoms. CYFIP2 functions both as a component of the WAVE (Wiskott-Aldrich syndrome protein family verprolin-homologous protein) regulatory complex (WRC), regulating the actin cytoskeleton, and as an interactor of RNA-binding proteins (RBPs) involved in mRNA processing/translation. Although Arg87 variants reduce CYFIP2 protein stability, heterozygous knock-in mice carrying Arg87Cys (Cyfip2+/R87C) show markedly more severe phenotypes than heterozygous knockout (Cyfip2+/-) mice, supporting a toxic gain-of-function mechanism. However, how the dual roles of CYFIP2 contribute to this mechanism remains unclear. To address this, we examined Cyfip2+/R87C mice at postnatal week 7, before overt neuronal loss and gliosis, focusing on the progressive dispersion of hippocampal cornu ammonis 1 (CA1) pyramidal neurons, a phenotype absent in Cyfip2+/- mice. Single-nucleus RNA sequencing suggested candidate alterations related to translation and cell adhesion/migration in CA1 pyramidal neurons. Complementarily, human embryonic kidney 293T cells expressing CYFIP2 Arg87Cys showed defects in proliferation and morphology, accompanied by altered expression of cell adhesion-related genes. Quantitative proteomic analysis of the CA1 region uncovered an imbalance between CYFIP2-associated protein networks, characterized by increased RBPs and reduced WRC components. Phosphoproteomic analysis further revealed altered phosphorylation of synaptic and translational regulators. Consistently, whole-cell recordings and biocytin-based morphological analyses showed increased frequency of miniature excitatory postsynaptic currents and altered dendritic morphology in Cyfip2+/R87C CA1 pyramidal neurons, most prominently in the more severely dispersed deep-layer neurons. Moreover, the cell adhesion molecule Eph receptor A3 was reduced, possibly as a result of RBP dysregulation. Together, these findings suggest that an imbalance between RBP- and WRC-associated pathways underlies the gain-of-function effects of CYFIP2 Arg87Cys and contributes to early neuronal phenotypes, most notably CA1 layer dispersion. This mechanism, distinct from CYFIP2 haploinsufficiency, supports allele-specific therapeutic strategies for Arg87 variants.

neuroscience↗

bioRxiv2026

MHC restriction is structurally encoded by the T cell receptor germline

MHC restriction -- the requirement for {beta} T cell receptors (TCRs) to recognize Major Histocompatibility Complex (MHC) molecules when presenting peptide antigens -- is a pillar of adaptive immunity. Here, we provide direct structural evidence for TCR germline-encoded recognition of MHC molecules irrespective of antigenic peptide. We engineered "germline-like" TCRs to eliminate CDR3 specificity for peptide, and a molecular clamping strategy to trap ultra-low-affinity complexes with peptide-MHC for cryo-EM. We find that germline-like TCR/pMHC docking modes are identical to wild-type T cell receptors with intact CDR3 loops, across distinct peptide antigens and MHC alleles. Analysis of human TCR repertoires reveals enrichment of specific V genes and V-V{beta} pairing patterns associated with HLA-A*02 contexts. Thus, the TCR germline encodes the blueprint for MHC restriction, providing a sequence-based framework that could inform computational and AI-driven prediction of TCR specificity.

immunology↗

bioRxiv2026

FlowMap: Geometry Dynamics Consistent Embedding of RNA Velocity for Interpretable Cellular Trajectories

Single-cell RNA sequencing reveals how cells vary across states, but these measurements capture only static snapshots of dynamic biological processes. RNA velocity addresses this limitation by estimating how gene expression is changing over time, providing directional information about cell state transitions. However, current approaches treat cellular state and dynamics separately, leading to representations that violate fundamental geometric consistency and obscure biological interpretation. Here, we present FlowMap, a framework that jointly models cellular states and their dynamics within a unified geometric representation. FlowMap simultaneously reconstructs a smooth low-dimensional manifold of gene expression and constrains RNA velocity to follow its local geometry, producing coherent and denoised representations of cellular trajectories. Across simulated and real datasets, FlowMap recovers interpretable dynamical patterns, including continuous progressions, branching events, cyclic behaviors, and stable-like states. It highlights key genes and gene programs involved in development that play distinct roles in these dynamics, and extends naturally to spatial transcriptomics, where it captures spatially organized developmental processes. Together, FlowMap establishes a principled geometric framework for modeling cellular dynamics, bridging representation learning and dynamical inference in single-cell analysis.

bioinformatics↗

bioRxiv2026

Functional Pairing of TCR-peptide-MHC Interactomes by Single-cell Clonal Expansion

T cell antigen-specific immunity depends on pairwise interactions between T cell receptors and peptide-MHC, yet isolating the TCR-pMHC pairs that drive productive engagement remains a major obstacle for antigen-specific therapeutics and for decoding TCR specificity. We overcome this by co-encoding TCR and pMHC in a single founder cell, then clonally expanding it inside a semi-permeable capsule so that genetically identical daughter cells engage in trans. T cell activation, rather than binding affinity, is used to sort cells with functional pairs, and a single PCR on the clone's linked genomic library captures both partners. This platform, LINC-seq, recovered known cognate pairs from pooled libraries at up to 95% accuracy and performed simultaneous, library-on-library deep mutational scanning of both partners. Wild-type clonotypes ranked among the top-enriched sequences in complex mixtures, and the screens resolved co-evolutionary epistasis and cross-reactivity rules inaccessible to one-sided mutagenesis. The approach generalizes to any receptor-ligand pair whose trans-engagement drives a reporter.

immunology↗

bioRxiv2026

Sequence-Specific Targeting of GC-Rich Gene Loci by Parallel Triplex-Forming Oligonucleotides Containing a Modified Nucleobase

Targeting GC-rich gene loci is a major challenge owing to their high duplex stability, repetitive sequence composition, and propensity to adopt alternative DNA structures. Triplex-forming oligonucleotides (TFOs) provide a programmable strategy towards the recognition of GC-rich DNA, but their application is restricted by the limited recognition capabilities of natural nucleobases in a cellular setting. Here, we overcome this barrier using parallel-binding TFOs containing the synthetic nucleobase 6-amino-5-nitropyridin-2-one (Z), which enables pH-independent recognition of G-C base pairs. Using two structurally distinct regulatory elements within the MYC promoter, we show that Z-modified TFOs form stable, sequence-selective triplexes that repress promoter activity by 50-80% in both episomal reporter assays and at endogenous gene loci. Notably, the greatest repression was observed at a GC-rich quadruplex-forming element that functions as a structural hub for transcription factor recruitment. To our knowledge, this represents the first demonstration that a simple nucleobase modification alone is sufficient to enable parallel-binding TFOs to repress expression of an endogenous gene, establishing a general strategy for targeting GC-rich regulatory elements through programmable DNA recognition. TOC graphic O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=81 SRC="FIGDIR/small/741700v1_ufig1.gif" ALT="Figure 1"> View larger version (24K): org.highwire.dtl.DTLVardef@1ee4ad6org.highwire.dtl.DTLVardef@173299eorg.highwire.dtl.DTLVardef@1b14d05org.highwire.dtl.DTLVardef@1379384_HPS_FORMAT_FIGEXP M_FIG C_FIG

cell biology↗

bioRxiv2026

Molecular Basis of High-light Adaptation in Cyanobacteria and Cyanophages through the D1/D2 subunits of Photosystem II

High-light (HL) stress imposes substantial pressure on oxygenic photosynthesis by promoting the formation of reactive oxygen species (ROS) and photodamage in Photosystem II (PSII), particularly within its reaction-center core subunits D1 and D2. Prochlorococcus and Synechococcus, along with their cyanophages, dominate oligotrophic oceans and experience persistent HL exposure, yet the molecular basis of PSII adaptation in these systems remains poorly understood. In this manuscript, we integrate large-scale phylogenetic analysis with residue-level sequence comparison and AlphaFold3-based structural prediction to investigate D1/D2 across Prochlorococcus ecotypes, Synechococcus, and their associated cyanophages. Prochlorococcus species are known to form ecotypes based on light conditions, and the D1 and D2 phylogenies showed consistent organization across our phylogenetic trees. Synechococcus does not fall into the same light-based ecotypes, but we found that D1 and D2 isoforms still form meaningful clusters for these species. Cyanophage-encoded D1 and D2 sequences did not form separate viral clades, but instead were embedded within host-associated diversity and showed closer affinity to HL-adapted Prochlorococcus than to low-light-adapted (LL) lineages. Mapping ecotype- and phage-associated substitutions onto predicted D1/D2 structures, with reference to experimental PSII structures, suggested that some LL-to-HL variants in Prochlorococcus may enhance resistance to ROS-associated damage. Some LL-to-HL substitutions increase methionine and cysteine enrichment near redox-active cofactors, potentially improving redox buffering and ROS scavenging. In contrast, others may favor more efficient electron transfer, reduce charge recombination, and thereby limit ROS production. These results support a model in which PSII adaptation in cyanobacteria is shaped by fine-scale protein-level tuning linked to ecological diversification and cyanophage-host coevolution, with viral-host interactions contributing to the evolutionary optimization of oxygenic photosynthesis under HL stress.

evolutionary biology↗

bioRxiv2026

A missense mutation in FBXL3 links circadian regulation to out-of-season estrus in sheep

Seasonal breeding is a remarkable adaptive trait, but it constrains efficient production in the sheep industry. Recent studies have shown that seasonal breeding is associated with endogenous circannual rhythms, which are regulated in part by the circadian clock system. FBXL3, a pivotal component of the SCF (SKP1 - CUL1 - F-box) E3 ubiquitin ligase complex, is a known determinant of the mammalian circadian period. In this study, we identified a missense mutation, T183M, in FBXL3 through selective sweep analysis. The allele frequency of this mutation differed significantly between sheep breeds exhibiting year-round estrus and those showing seasonal breeding patterns. The association between the T183M mutation and seasonal breeding was further validated using an ovariectomized, estradiol-implanted sheep model. We then generated mice carrying the homologous T183M mutation and found that they exhibited significantly lengthened circadian periods, accompanied by reduced CRY1 expression and increased CLOCK expression. Co-immunoprecipitation assays confirmed that the mutation reduced the interaction between FBXL3 and CRY1. These findings demonstrate an evolutionarily conserved role of FBXL3 in the circadian clock system. We propose that the T183M mutation disrupts day-length recognition, thereby influencing seasonal estrus in sheep. Author summarySeasonal breeding limits sheep productivity and is regulated by circadian rhythms, yet the key genetic determinants remain poorly understood. Here, we identified an FBXL3 T183M missense mutation whose allele frequency differed markedly between year-round-estrous and seasonally breeding sheep, and validated its association with seasonal reproduction in a sheep population. Functional analyses in mutant mice showed that this variant lengthened the circadian period, disrupted the expression of core clock genes, and weakened the interaction between FBXL3 and CRY1. These findings suggest that the FBXL3 T183M variant impairs day-length perception, thereby modulating seasonal estrus in sheep. Our study reveals a conserved circadian mechanism underlying seasonal breeding and highlights FBXL3 T183M as a promising genetic target for improving reproductive performance in sheep.

genetics↗

bioRxiv2026

H3 dopaminylation and CaMKII modulate diffuse midline glioma response to CDK9 inhibition

Aberrant neurotransmitter signaling and transcriptional dysregulation are hallmarks of gliomagenesis and represent potential therapeutic targets. Monoamine neurotransmitters such as dopamine and serotonin primarily activate GPCRs but can also function epigenetically as histone H3 modifications. Here, we uncover mechanisms of crosstalk between monoamine neurotransmitter signaling, H3 dopaminylation, and RNA polymerase II (Pol2) transcription in diffuse midline glioma (DMG). We find that co-treatment with Pol2-targeting CDK9 inhibitors (CDK9i) and FDA-approved neuropsychiatric drugs, including selective serotonin reuptake inhibitors (SSRIs), synergistically reduces DMG growth. Mechanistically, CDK9i+SSRI treatment alters H3 dopaminylation patterns and represses synaptic and neurodevelopmental gene transcription associated with CDK9i resistance. Further phospho-proteomic analyses show that CDK9i monotherapy activates pro-survival CaMKII signaling, which can be suppressed by co-treatment with neuromodulatory drugs. These studies establish roles for H3 dopaminylation and neurotransmitter signaling in DMG gene regulation and response to CDK9i, suggesting that monoamine neurotransmitter pathways may be exploited as a therapeutic strategy for DMG.

cancer biology↗

bioRxiv2026

A genome-wide CRISPR Screening identifies targets that drive Tolerogenic Dendritic Cells

Tolerogenic dendritic cells (TolDCs) are essential for immune tolerance and offer promise for treating autoimmune diseases. Despite the clinical evidence of their therapeutic potential, the key molecular pathways guiding their differentiation and tolerogenic phenotype remain elusive due to complex interactions identified in functional assays. Here we investigated the molecular profiles and regulatory programs underlying the functional status of tolerogenic dendritic cell populations in response to known tolerizing agents. We identified CD86 as a consistent and robust marker downregulated in tolerogenic state. Using CD86 blocking antibodies or CRISPR-mediated gene inactivation we demonstrated that CD86 is functionally required for TolDC-mediated suppression of T cell proliferation and cytokine secretion, establishing CD86 as both a consensus phenotypic and functional screening marker and a mechanistic regulator of tolerance. Leveraging CD86 as a scalable readout, we performed a pooled genome-wide CRISPR-Cas9 knockout screen to identify regulators of TolDC function. This approach uncovered UBE2L6 as a novel modulator that promotes the tolerogenic phenotype and restricts TolDC-mediated T cell activation. Mechanistically, UBE2L6 deficiency leads to coordinated upregulation of ISG15 and USP18, indicating a possible ISGylation-dependent pathway regulating CD86 expression and tolerogenic function. Together, this study identifies pathways that can be targeted to promote immune tolerance in immune-mediated inflammatory diseases. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=105 SRC="FIGDIR/small/713621v1_ufig1.gif" ALT="Figure 1"> View larger version (33K): org.highwire.dtl.DTLVardef@4c3636org.highwire.dtl.DTLVardef@17b27e5org.highwire.dtl.DTLVardef@783d95org.highwire.dtl.DTLVardef@1337ce_HPS_FORMAT_FIGEXP M_FIG C_FIG

immunology↗

bioRxiv2026

A feed-forward loop between niche adenosine and Gzmk⁺ CD8 T cells propagates systemic inflammaging

The causal link between the aging microenvironment and T cell aging remains elusive. Here, we demonstrate that adenosine within aging tissues actively reprograms CD8+ T cells into a pro-aging Granzyme K+ (Gzmk+) population. Mechanistically, senescent cells create an adenosine-rich niche via p16-dependent CD39 upregulation, triggering A2aR signaling to induce Gzmk+ T cell differentiation. Once released, Gzmk promotes systemic inflammaging through PAR1 and complement activation. Crucially, targeting this axis--either via genetic Gzmk ablation or pharmacological A2aR blockade--reverses multi-organ aging phenotypes and significantly extends healthy lifespan in mice. Human analysis reveals age-dependent Gzmk+ T cell accumulation in multi organs, while coffee intake (an A2aR antagonist) inversely correlates with plasma Gzmk levels. Our findings uncover how metabolic niche changes drive T cell aging and establish the adenosine-Gzmk axis as a pivotal therapeutic target for combating age-related diseases.

immunology↗

bioRxiv2026

Non-canonical peptidoglycan cross-linking is essential for Mycobacterium tuberculosis acid resistance

Mycobacterium tuberculosis withstands acidic conditions to survive and replicate within macrophages. To define the genetic determinants of this adaptation, we performed a transposon screen in a lipid-rich, acidic medium that mimics the host environment and supports robust M. tuberculosis growth. This screen identified ldtB, encoding an L,D-transpeptidase, as essential for growth and survival under acid stress. Loss of LdtB decreased 3-3 peptidoglycan cross-linking, disrupted cell wall architecture, and impaired intrabacterial pH homeostasis, resulting in increased susceptibility to cell wall-active antibiotics. Notably, M. tuberculosis lacking LdtB displayed heightened sensitivity to meropenem within macrophages, suggesting that targeting this enzyme could potentiate {beta}-lactam efficacy during infection. These findings establish LdtB as a key mediator linking peptidoglycan homeostasis to acid stress resistance and underscores the importance of in vitro culture models that recapitulate the host microenvironment for uncovering new in vivo active therapeutic targets. TeaserDisabling a key peptidoglycan cross-linking enzyme compromises M. tuberculosis survival under acidic stress and antibiotic exposure.

microbiology↗

bioRxiv2026

MOSAIC: A Spectral Framework for Integrative Phenotypic Characterization Using Population-Level Single-Cell Multi-Omics

Population-scale single-cell multi-omics offers unprecedented opportunities to link molecular variation to human health and disease. However, existing methods for single-cell multi-omics analysis are either cell-centric, prioritizing batch-corrected cell embeddings that neglect feature relationships, or feature-centric, imposing global feature representations that overlook inter-sample heterogeneity. To address these limitations, we present MOSAIC, a spectral framework that learns a high-resolution feature x sample joint embedding from population-scale single-cell multi-omics data. For each individual, MOSAIC constructs a sample-specific coupling matrix capturing complete intra- and cross-modality feature interactions, then projects these into a shared latent space via spectral decomposition. The joint feature x sample embedding defines each features connectivity profile per sample, enabling three downstream applications. Differential Connectivity analysis identifies features with regulatory network rewiring across conditions even when their abundance remains unchanged, revealing rewiring of proliferation programs in activated T cells from a vaccination cohort. Unsupervised subgroup detection isolates coherent feature modules to discover hidden patient subtypes, uncovering a stress-driven neuronal subtype within an HIV+ cohort. Clinical outcome prediction using connectivity-derived features complements abundance-based analysis, improving COVID-19 severity classification when integrated. MOSAIC provides a general-purpose framework for systems-level phenotypic characterization, bridging network-level discovery with clinical outcome prediction in population-scale single-cell studies.

bioinformatics↗

bioRxiv2026

Antibody Fc receptor CD16a mediates natural killer cell activation via mechanotransduction of piconewton forces

Natural Killer(NK) cells eliminate target cells through antibody-dependent cell-mediated cytotoxicity(ADCC), initiated by CD16a(Fc{gamma}RIIIa) recognizing the Fc region of antibodies bound to the target cell surface. While the recognition is considered to be driven by CD16a-Fc binding avidity, it fails to explain why Fc multimers inhibit ADCC rather than trigger it. Here, we reveal that CD16a transduces piconewton forces, and acts as a mechanosensor to facilitate NK activation. We demonstrate that CD16a force and the actin foci formation associated with it are essential for the phosphorylation of mechanosensitive adaptor Cas-L and signaling adaptor LAT, reshaping NK cell cytoskeletal dynamics and signaling. Our findings show that NK activation is an intricate process that integrates both biochemical and biophysical information, and provides new mechanistic insight for immunoengineering.

biophysics↗

bioRxiv2026

Data-Driven Retrieval of Effective Point Spread Functions for Super-Resolution Optoacoustic Imaging

Localization-based super-resolution techniques have revolutionized biomedical imaging by surpassing classical diffraction limits. However, their performance is fundamentally constrained by distortions of the point spread function (PSF) induced by the system and the sample, which are particularly prominent in the case of spatially under-sampling. Here we introduce a data-driven effective point spread function retrieval (DEPR) method that directly learns continuous, field-dependent system responses from experimental point source datasets. Through statistical aggregation of thousands of targets and iterative self-supervised refinement, DEPR captures spatially variant imaging characteristics in situ without prior assumptions or external calibrations. When integrated into the localization optoacoustic tomography (LOT) pipeline, DEPR achieves accurate sub-pixel localization despite under-sampled conditions, thus enhancing resolution while reducing computational burden. We demonstrate its efficacy by in vivo imaging of the murine brain microvasculature using microparticle contrast agents in the first (NIR-I) and second (NIR-II) near-infrared windows, achieving significant improvement in data utilization efficiency and substantial reduction of gridded artifacts compared to conventional approaches. The method resolves vascular structures with [~]41 m separation across a [~]3 mm imaging depth range. This framework addresses fundamental challenges shared across diverse localization-based imaging modalities, offering a robust and generalizable strategy for high-precision imaging in complex biological systems.

neuroscience↗

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

Trajectory-informed gene feature selection in single-cell analysis with SEEK-VFI

The prioritization of highly-variable genes is an important step in single-cell trajectory inference. However, when variability arises from a continuous latent cell development trajectory, standard methods may fail to differentiate trajectory-relevant from uninformative genes. SEEK-VFI is an ensemble topic-modeling machine learning algorithm for trajectory inference preprocessing that prioritizes trajectory-relevant genes. It outperforms existing methods, and identifies key genes that improve trajectory topology reconstruction, enhance visualization, and augment downstream trajectory analyses.

bioinformatics↗

bioRxiv2025

SEEK-VEC: Robust Latent Structure Discovery via Ensemble Topic Modeling

Count data are ubiquitous across many applications in which understanding latent patterns is of interest. Topic modeling is a powerful tool for detecting latent structure in count data. However, standard topic modeling methods are often constrained by their restrictive assumptions, susceptible to noise, and sensitive to misspecification of the number of topics. Here, we introduce SEEK-VEC (Spectral Ensembling of topic models with Eigenscore for K-agnostic Vocabulary Embedding and Classification), an ensemble topic modeling framework that integrates insights from multiple candidate topic models through a spectral ensembling procedure. SEEK-VEC produces a meta-structure matrix containing prioritization scores and grouping scores that enable variable classification, interactive pattern discovery, and model diagnostics. Through simulations, we demonstrate that SEEK-VEC augments the performance of standard topic models for identifying important vocabulary words and understanding the relationships among them, particularly when signal strength is weak. We apply SEEK-VEC to the MADStat dataset of statistical abstracts and demonstrate its utility for evaluating the proposed interpretation of a topic model.

bioinformatics↗