Biology subjects

Liao, D.

Publications and source records attributed to Liao, D..

13 recordsLinked to original sources

bioRxiv2026

Apoptotic Quality Control of Cellular Competence Limits Cryptic Germinal Center B Cell States

Germinal center (GC) B cells undergo extensive apoptosis, but how this process shapes evolving GC populations remains unclear. Using mice lacking intrinsic apoptotic effectors BAK and BAX in B cells, we found that mitochondrial apoptosis was dispensable for affinity maturation but critical for controlling GC size and cellular composition, showing that GC population dynamics and affinity maturation can be uncoupled. BAK/BAX-deficient mice mounted enlarged and prolonged GC responses, largely due to the accumulation of non-proliferating Ki-67loCD71lo dark zone (DZ) B cells. CD71hi and CD71lo DZ cells exhibited similar B-cell receptor (BCR) avidity, retained potential for proliferation and plasmacytic differentiation, and shared clonal lineages, indicating recurrent emergence of non-proliferating DZ populations. A subset also carried Somatic-hypermutation-derived defects that abolished antibody expression despite apparently productive V(D)J sequences; reversion of a single amino acid substitution often restored expression. Mitochondrial apoptosis thus enforces cellular quality control in the GC by limiting the persistence of non-proliferating and expression-defective states while remaining dispensable for affinity maturation.

immunology↗

bioRxiv2026

Antibody feedback limits specific B-cell entry and alters germinal center repertoires by antibody-antigen complexes

Antibody (Ab) feedback impacts germinal center (GC) responses. Mice given IgG1 or IgG2c recombinant Ab (rAb) specific for the receptor binding site (RBS) of H3 hemagglutinin (HA) and later immunized with the H3 HA trimer exhibited altered GC repertoires. Passive RBS rAb had no effect on the magnitude of ensuing primary GC responses but reduced the numbers of RBS-specific GC B cells. These losses were matched by increases in "unspecific" B cells which did not bind the HA immunogen, with no changes in B cells specific for distal epitopes. These effects were independent of IgG subclass. Higher doses of passive rAb resulted in reduced epitope-specific affinity maturation and clonal proliferation in GCs. Passive rAb generated Ab:HA complexes and favored recruitment of rare HA-specific GC B cells with enhanced avidity for the rAb:HA immune complex (IC). We show that some no- and low-affinity GC B cells represent responses to local ICs.

immunology↗

bioRxiv2026

Functional Data Analysis of Spatial Clustering Identifies Prognostic T Cell Patterns in Ovarian Cancer

Spatial proteomic imaging technologies enable the simultaneous assessment of immune cell abundance and spatial organization within the tumor microenvironment. Spatial clustering is commonly summarized using measures such as Ripleys K or nearestOneighbor G-functions at a fixed radius. However, these approaches depend on scale selection and may obscure biologically relevant patterns occurring across spatial ranges. We propose a functional data analysis (FDA) framework to model spatial clustering trajectories derived across a continuum of radii. Functional principal component analysis (FPCA) was used to summarize dominant modes of spatial variation, and resulting scores were incorporated into Cox proportional hazards models as both main effects and interaction with immune cell abundance. The approach was applied to multiplex immunofluorescence data from five ovarian cancer studies, comprising 773 highOgrade ovarian serous tumors. Analyses focused on CD3+ and CD8+ T cell populations within the tumor compartment of the tissue, adjusting for age at diagnosis and cancer stage, with study-specific estimates combined using random-effects meta-analysis. Higher abundance of both T cells and CD8+ T cells was consistently associated with improved overall survival. Beyond abundance, spatial features captured by the leading functional principal component were independently associated with survival, particularly for CD8+ T cells. Interaction models further showed that the prognostic effect of immune infiltration depended on spatial clustering, with tumors characterized by high abundance and low spatial clustering exhibiting the most favorable outcomes. These findings indicate that spatial organization provides complementary prognostic information beyond abundance alone and suggests that more diffuse immune infiltration may reflect more effective anti-tumor activity in ovarian cancer. Overall, FDA offers a flexible and interpretable framework for modeling spatial clustering across scales and identifying prognostic spatial features not captured by fixed-radius or distance analyses.

cancer biology↗

bioRxiv2026

Sex-specific hormone-sensitive regulatory architecture in adolescence as a scaffold for depression vulnerability

Adolescence is a critical developmental period during which sex differences in depression risk emerge, yet the underlying molecular mechanisms remain unclear. Here, we integrated longitudinal transcriptomic, epigenomic, and gene regulatory network analyses to characterize sex-specific regulatory dynamics of the brain across adolescence under normative conditions and elucidate how baseline molecular differences may shape later vulnerability. We observed that immediate early genes exhibited the strongest sex-biased signals, with males and females showing opposing developmental trajectories, suggesting a role in sex-specific stress-responsive programs. Across analyses, a consistent pattern emerged: males showed stronger activity-dependent neuronal signatures, whereas females showed stronger stress- and immune-related signatures. Extending these findings to a disease context using single-nucleus chromatin accessibility data, we identified hormone-responsive regulatory elements enriched in depression-associated regions, with sex- and cell type-specific links to genetic risk. Grounded in established models of sex-specific stress responses, these findings offer a developmental regulatory framework for understanding the differential presentation of, and vulnerability to, depression.

genomics↗

bioRxiv2025

Yorzoi: Predicting RNA-seq coverage from DNA sequence in yeast

Yeast is one of the principal model organisms in synthetic biology and a widely used chassis for testing heterologous DNA sequences. However, designing DNA constructs correctly is currently limited by our incomplete quantitative understanding of how sequences are transcribed and translated, especially non-native sequences. Here, we present Yorzoi, a sequence-to-expression model for bakers yeast that predicts RNA-seq coverage for a 5 kilobase, multi-gene window of DNA at 10 base pair (bp) resolution. To extend its predictive ability beyond native DNA, Yorzoi has been pretrained on a comprehensive dataset not only including native yeast sequences but also human sequences expressed in yeast and structurally rearranged synthetic yeast chromosomes. We demonstrate that our model has learned general rules of yeast transcription by achieving high predictive performance on various downstream tasks. Yorzoi is a powerful tool for in-silico testing of DNA sequences and directly applicable for sequence design. A web application to use our model is available at yorzoi.eu and the code open source on GitHub.

synthetic biology↗

bioRxiv2025

Fluorescence-barcoded cell lines stably expressing membrane-anchored influenza neuraminidases

The discovery of broadly protective antibodies to the influenza virus neuraminidase (NA) has raised interest in NA as a vaccine target. However, recombinant, solubilized tetrameric NA ectodomains are often challenging to express and isolate, hindering the study of anti-NA humoral responses. To address this obstacle, we established a panel of 22 non-adherent cell lines stably expressing native, historical N1, N2, N3, N9, and NB NAs anchored on the cell surface. The cell lines are barcoded with fluorescent proteins, enabling high-throughput, 16-plex analyses of antibody binding with commonly available flow cytometers. The cell lines were at least as efficient as a Luminex multiplex binding assay at identifying NA antibodies from a library of unselected clonal IgGs derived from human memory B cells. The cell lines were also useful for measuring the magnitude and breadth of the serum antibody response elicited by experimental infection of rhesus macaques with influenza virus. The membrane-anchored NAs are catalytically active and are compatible with established sialidase activity assays. NA-expressing K530 cell lines therefore represent a useful tool for studying NA immunity and evaluating influenza vaccine efficacy.

immunology↗

bioRxiv2024

OsWHY1/OsTRXz/OsMORFs complex is essential for RNA modification and early chloroplast development in rice

WHIRLY (WHY) proteins are single-stranded DNA/RNA-binding proteins that play multifaceted roles in various plant species. The regulatory mechanisms of WHY proteins in rice remains blank. Here we demonstrate that OsWHY1 in rice is required for early chloroplast development. CRISPR/Cas9-generated oswhy1 knockout lines displayed albino seedling phenotypes, abnormal chloroplast structure and comprised redox balance in leaves. OsWHY1 interacts with multiple plastid proteins, including the thioredoxin OsTRXz and two multiple organellar RNA editing factors (OsMORF8 and OsMORF9) in chloroplasts. Accordingly, several plastid genes dependent on plastid-encoded RNA polymerase (PEP) in the oswhy1 mutants were significantly depressed at both transcript and protein levels. The editing of rps14 transcripts and splicing of rpl2, along with their protein expression, were defective in the oswhy1 mutants. OsWHY1 exhibited RNA-binding activity, specifically binding to rps14 and rpl2 precursor RNAs, which underscores its role as a post-transcriptional regulator essential for normal protein synthesis in chloroplasts. Loss-of- function mutants of either OsWHY1 or OsMORF9 and OsTRXz displayed albino phenotypes, disrupted H2O2 homeostasis, and defective RNA processing in rps14 and rpl2, suggesting the OsWHY1-OsTRXz-OsMORFs regulatory module is vital for maintaining chloroplast stability and integrity through its RNA-binding activity and its role in recruiting OsTRXz and OsMORFs to ensure proper RNA modification. One sentence summaryOsWHY1 is integral to chloroplast development in rice through its RNA-binding activity and its role in recruiting OsTRXz and OsMORFs to ensure proper RNA modification.

plant biology↗

bioRxiv2024

Proteolysis targeting chimera extracellular vesicles for therapeutic development treating triple negative breast cancer

Proteolysis targeting chimeras (PROTACs) are an emerging targeted cancer therapy approach, but wide-spread clinical use of PROTAC is limited due to poor cell targeting and penetration, and instability in vivo. To overcome such issues and enhance the in vivo efficacy of PROTAC drugs, microfluidic droplet-based electroporation ({micro}DES) was developed as a novel extracellular vesicle (EVs) transfection system, which enables the high-efficient PROTAC loading and effective delivery in vivo. Our previously developed YX968 PROTAC drug had shown the selectively degradation of HDAC3 and 8, which effectively suppresses the growth of breast tumor cell lines, including MDA-MB-231 triple negative breast cancer (TNBC) line, via dual degradation without provoking a global histone hyperacetylation. In this study, we demonstrated that {micro}DES-based PROTAC loading in EVs significantly enhanced therapeutic function of PROTAC drug in vivo in the TNBC breast tumor mouse model. NSG mice with pre-established MDA-MB-231 tumors and treated with intraperitoneal injection of EVs for tumor inhibition study, which showed significantly higher HDAC 3 and 8 degradation efficiency and tumor inhibition than PROTAC only group. The liver, spleen, kidney, lung, heart, and brain were collected for safety testing, which exhibited improved toxicity. The EV delivery of PROTAC drug enhances drug stability and bioavailability in vivo, transportability, and drug targeting ability, which fills an important gap in current development of PROTAC therapeutic functionality in vivo and clinical translation. This novel EV-based drug transfection and delivery strategy could be applicable to various therapeutics for enhancing in vivo delivery, efficacy, and safety.

bioengineering↗

bioRxiv2024

PhyloMix: Enhancing microbiome-trait association prediction through phylogeny-mixing augmentation

MotivationUnderstanding the associations between traits and microbial composition is a fundamental objective in microbiome research. Recently, researchers have turned to machine learning (ML) models to achieve this goal with promising results. However, the effectiveness of advanced ML models is often limited by the unique characteristics of microbiome data, which are typically high-dimensional, compositional, and imbalanced. These characteristics can hinder the models ability to fully explore the relationships among taxa in predictive analyses. To address this challenge, data augmentation has become crucial. It involves generating synthetic samples with artificial labels based on existing data and incorporating these samples into the training set to improve ML model performance. ResultsHere we propose PhyloMix, a novel data augmentation method specifically designed for microbiome data to enhance predictive analyses. PhyloMix leverages the phylogenetic relationships among microbiome taxa as an informative prior to guide the generation of synthetic microbial samples. Leveraging phylogeny, PhyloMix creates new samples by removing a subtree from one sample and combining it with the corresponding subtree from another sample. Notably, PhyloMix is designed to address the compositional nature of microbiome data, effectively handling both raw counts and relative abundances. This approach introduces sufficient diversity into the augmented samples, leading to improved predictive performance. We empirically evaluated PhyloMix on six real microbiome datasets across five commonly used ML models. PhyloMix significantly outperforms distinct baseline methods including sample-mixing-based data augmentation techniques like vanilla mixup and compositional cutmix, as well as the phylogeny-based method TADA. We also demonstrated the wide applicability of PhyloMix in both supervised learning and contrastive representation learning. AvailabilityThe Apache licensed source code is available at (https://github.com/batmen-lab/phylomix).

bioinformatics↗

bioRxiv2021

The DAXX-SREBP axis promotes oncogenic lipogenesis and tumorigenesis

De novo lipogenesis produces lipids for membrane biosynthesis and cell signaling. Elevated lipogenesis is a major metabolic feature in cancer cells. In breast and other cancer types, genes involved in lipogenesis are highly upregulated, but the mechanisms that control their expression remain poorly understood. DAXX modulates gene expression through binding to diverse transcription factors although the functional impact of these diverse interactions remains to be defined. Our recent analysis indicates that DAXX is overexpressed in diverse cancer types. However, mechanisms underlying DAXXs oncogenic function remains elusive. Using global integrated transcriptomic and lipidomic analyses, we show that DAXX plays a key role in lipid metabolism. DAXX depletion attenuates, while its overexpression enhances, lipogenic gene expression, lipid synthesis and tumor growth. Mechanistically, DAXX interacts with SREBP1 and SREBP2 and activates SREBP-mediated transcription. DAXX associates with lipogenic gene promoters through SREBPs. Underscoring the critical roles for the DAXX-SREBP interaction for lipogenesis, SREBP2 knockdown attenuates tumor growth in cells with DAXX overexpression, and a DAXX mutant unable to bind SREBPs are incapable of promoting lipogenesis and tumor growth. Our results identify the DAXX-SREBP axis as an important pathway for tumorigenesis.

cancer biology↗

bioRxiv2020

Mechanically Induced Integrin Ligation Mediates Intracellular Calcium Signaling with Single Pulsating Cavitation Bubbles

Ultrasound or shockwave-induced cavitation is used therapeutically to stimulate neural and muscle tissue, but the mechanisms underlying this mechanotransduction are unclear. Intracellular Ca2+ signaling is one of the earliest events in mechanotransduction. In this study, we investigate the mechanism of Ca2+ signaling in individual HEK293T cells stimulated by single cavitation bubbles. Ca2+ responses are rare at cell-bubble distance that avoids membrane poration, even with overexpression of the mechanosensitive ion channel Piezo1, but could be increased in frequency to 42% of cells by attaching RGD beads to the apical surface of the cells. By using Piezo1 knockout and Piezo1-expressing cells, integrin-blocking antibodies, and inhibitors of P2X ion channels, key molecular players are identified in the RGD bead-enhanced Ca2+ response: increased integrin ligation by substrate ECM triggers ATP release and activation of P2X--but not Piezo1--ion channels. These molecular players have not been examined previously in cavitation-induced Ca2+ signaling. The resultant Ca2+ influx causes dynamic changes in cell spread area. This approach to eliciting a Ca2+ response with cavitation microbubbles without cell injury, and the uncovered mechanotransduction mechanism by which increased integrin-ligation mediates ATP release and Ca2+ signaling will inform new strategies to stimulate tissues with ultrasound and shockwaves.

biophysics↗

bioRxiv2020

Sodium leak channel as a therapeutic target for neuronal sensitization in neuropathic pain

Neuropathic pain affects up to 10% of the total population and no specific target is ideal for therapeutic need. The sodium leak channel (NALCN), a voltage-independent cation channel, mediates the background Na+ leak conductance and controls neuronal excitability and rhythmic behaviors. Here, we show that increases of NALCN expression and function in dorsal root ganglion (DRG) and dorsal spinal cord contribute to chronic constriction injury (CCI)-induced neuropathic pain in rodents. NALCN current and neuronal excitability in acutely isolated DRG neurons and spinal cord slices of rats were increased after CCI which were decreased to normal levels by NALCN-siRNA. Accordingly, pain-related symptoms were significantly alleviated by NALCN-siRNA-mediated NALCN knockdown and completely reversed by NALCN-shRNA-mediated NALCN knockdown in rats or by conditional NALCN knockout in mice. Our results indicate that increases in NALCN expression and function contribute to CCI-induced neuronal sensitization; therefore, NALCN may be a novel therapeutic target for neuropathic pain.

neuroscience↗

bioRxiv2018

MYBPC3 Mutations cause Hypertrophic Cardiomyopathy by Dysregulating Myosin: Implications for Therapy

The mechanisms by which truncating mutations in MYBPC3 (encoding cardiac myosin binding protein-C; cMyBPC) or myosin missense mutations cause hyper-contractility and poor relaxation in hypertrophic cardiomyopathy (HCM) are incompletely understood. Using genetic and biochemical approaches we explored how depletion of cMyBPC altered sarcomere function. We demonstrate that stepwise loss of cMyBPC resulted in reciprocal augmentation of myosin contractility. Direct attenuation of myosin function, via a damaging missense variant (F764L) that causes dilated cardiomyopathy (DCM) normalized the increased contractility from cMyBPC depletion. Depletion of cMyBPC also altered dynamic myosin conformations during relaxation - enhancing the myosin state that enables ATP hydrolysis and thin filament interactions while reducing the super relaxed conformation associated with energy conservation. MYK-461, a pharmacologic inhibitor of myosin ATPase, rescued relaxation deficits and restored normal contractility in mouse and human cardiomyocytes with MYBPC3 mutations. These data define dosage-dependent effects of cMyBPC on myosin that occur across all phases of the cardiac cycle as the pathophysiologic mechanisms by which MYBPC3 truncations cause HCM. Therapeutic strategies to attenuate cMyBPC activity may rescue depressed cardiac contractility in DCM patients, while inhibiting myosin by MYK-461 should benefit the substantial proportion of HCM patients with MYBPC3 mutations.\n\nOne Sentence SummaryAnalyses of cardiomyocytes with hypertrophic cardiomyopathy mutations in MYBPC3 reveal that these directly activate myosin contraction by disrupting myosin states of relaxation, and that genetic or pharmacological manipulation of myosin therapeutically abates the effects of MYBPC3 mutations.

genetics↗