Biology subjects

Huang, Z.

Publications and source records attributed to Huang, Z..

At least 91 records · Page 5Linked to original sources

bioRxiv2026

Impacts of mutation accumulation and order on tumor initiation revealed by engineered murine colorectal cancer organoids

Tumorigenesis typically follows a multi-hit trajectory, driven by accumulating oncogenic mutations. Colorectal cancer (CRC) has long served as a paradigmatic model of multi-hit tumorigenesis, characterized by adenoma-carcinoma transition accompanied by acquisition of specific oncogene and tumor suppressor mutations. However, how the temporal order of early mutations influences CRC initiation remains poorly understood. To address this, we established a CRC tumorigenesis model using murine intestinal organoids. By introducing defined combinations of key CRC driver mutations (Kras, Apc, and Trp53) in distinct orders, we systematically investigated how the order of mutation accumulation affects tumor initiation. Our results reveal that the mutation accumulation confers growth advantages in both in vitro and in vivo models. Strikingly, mutation order also influenced the tumorigenic properties of the organoids. Whereas organoids with Trp53 loss before or after Apc loss similarly affected organoid phenotypes in vitro or tumorigenicity in immunodeficient mice, organoids with Trp53 loss preceding Apc inactivation exhibited reduced tumor-forming potential in immunocompetent mice, likely due to their distinct immunological features. Collectively, our study reveals a critical role of ordered mutation accumulation in CRC initiation, an insight that may hold clinical relevance.

cancer biology↗

bioRxiv2025

Comparative Genomics Reveals Deep Conservation and Lineage-specific Evolution of Mammalian microRNAs

microRNAs (miRNAs) are central post-transcriptional regulators that shape cellular functions, development, and phenotypic diversity. Yet their evolutionary history in mammals remains poorly resolved, largely due to incomplete genome-wide annotation and the difficulties in establishing miRNA orthology. Using a homology-based framework paired with genome synteny for orthology assignment, we characterised miRNA families and investigated their evolutionary dynamics across mammals. Compared to Infernal and MirMachine using a consensus pseudo-ground-truth framework, our method demonstrated better sensitivity-specificity balance, allowing divergent miRNA detection while reducing false positives. Analysis of 73 mammalian genomes revealed major miRNA family gains at the ancestral nodes of Eutheria, Marsupialia, and Haplorrhini, contrasted with substantial losses in Eulipotyphla and Scandentia. Copy number evolution was largely conserved across families, with only a few families (e.g., MIR-145, MIR-2285) showing lineage-specific duplication acceleration. Comparative genome microsynteny further resolved orthology for the multi-copy family LET-7, spanning eight deeply conserved syntenic blocks, as well as for 143 individual miRNAs. We showed that most miRNAs are deeply conserved, with the seed region being most constrained, followed by the mature, star, and loop regions. Within the seed region, positions 4-6 displayed higher conservation than other seed positions, consistent with their roles in core target recognition. Ancestral seed-state reconstruction further revealed diverse evolutionary signatures, including ancestral shifts, recurrent substitutions, and homoplasious changes. Collectively, these findings provide an unprecedented comparative overview of mammalian miRNA evolution and create new opportunities to investigate how shifts in miRNA repertoires and sequence features may underlie lineage-specific regulatory and phenotypic diversification.

genomics↗

bioRxiv2025

DeepDOX1: A Dual-Drive Framework Integrating Deep Learning and First-Principles Physics for Drug-Protein Affinity Prediction

In this work, we present DeepDOX1, a dual-drive drug-protein affinity (DPA) prediction tool features the tight integration of a concise AI architecture and a quantum mechanics based representation. The first-principle physics generated features incorporating the interactions between the drug and the protein pocket allows a relatively simple CNN model trained on a relatively small training set to exhibit exceptional generalization capabilities across extensive testing. Notably, DeepDOX1 outperforms popular AI models in the tests simulating real-world drug design scenario and a highly challenging test set featuring covalent ligands, halogenated ligands and metalloproteins. In addition, we designed a series of novel covalent inhibitors targeting the diabetes target hu-FBPase using DeepDOX1. Subsequent experimental validation including enzyme-level bioactivity assays and crystal structure determination confirmed the DeepDOX1s effectiveness in real-world drug design applications. It is conceivable that the combination of AI and first-principle QM might be one of the next breakthrough points of DPA prediction.

bioinformatics↗

bioRxiv2025

hypeR-GEM: connecting metabolite signatures to enzyme-coding genes via genome-scale metabolic models

Enrichment analysis is a cornerstone of "omics" data interpretation, enabling researchers to connect analysis results to biological processes and generate testable hypotheses. While well-established tools exist for transcriptomics and other omics layers, the development of robust enrichment resources for metabolomics remains comparatively limited. To address this gap, we developed hypeR-GEM, a methodology and associated R package that adapts gene set enrichment analysis to metabolomics. hypeR-GEM leverages genome-scale metabolic models (GEMs) to infer reaction-based links between metabolites and enzyme-coding genes, enabling the mapping of metabolite signatures to gene signatures and their subsequent annotation via gene set enrichment analysis. We validated hypeR-GEM using paired metabolomics-proteomics and metabolomics-transcriptomics datasets by assessing whether genes mapped from metabolites significantly overlapped with differentially expressed proteins or transcripts. We further evaluated whether pathways enriched via hypeR-GEM-mapped genes corresponded to those derived from paired proteomic or transcriptomic data. In most datasets analyzed, both the predicted enzyme-coding genes and the associated enriched pathways showed significant concordance with independently derived omics signatures, supporting the utility and robustness of hypeR-GEM. Finally, we applied hypeR-GEM to the analysis of age-associated metabolic signatures from the New England Centenarian Study. The results revealed consistent enrichment of lipid-related pathways, aligning with the well-established role of lipid metabolism in aging, and highlighted additional pathways not captured in the metabolites annotation, demonstrating hypeR-GEMs practical utility in a real-world use case.

bioinformatics↗

bioRxiv2025

Harnessing anti-CRISPR to suppress, subtract, and segregate Cas9 activity for precision CRISPR in Drosophila

Tissue-specific CRISPR (ts-CRISPR) is a powerful approach for studying cell and developmental biology by restricting mutagenesis to specific tissues. However, the precision of this approach is often compromised by non-specific, "leaky" Cas9 activity that confounds phenotypic analysis and destabilizes Cas9/gRNA stocks. To address these limitations in Drosophila, we developed a toolkit based on the Anti-CRISPR (Acr) protein AcrIIA4. We first identified AcrIIA4 as a potent in vivo Cas9 inhibitor with high stability and established the temporal requirements for its function. Based on these findings, we generated three classes of Acr tools. First, a collection of AcrIIA4-bearing balancers robustly suppresses Cas9 and enables the stable maintenance of complex Cas9/gRNA stocks. Importantly, maternal deposition of AcrIIA4 from these balancers provides a means of temporal control, delaying Cas9 activity until metamorphosis. Second, tissue-specific AcrIIA4 transgenes refine leaky Cas9 drivers in a "tissue-subtraction" strategy. Finally, germline-specific and soma-specific Acr tools efficiently segregate Cas9 activity, solving bidirectional leakiness between these two compartments. This comprehensive AcrIIA4 toolkit provides new levels of precision, versatility, and temporal control for Drosophila CRISPR applications.

genetics↗

bioRxiv2025

Androgen receptor contributes to radioresistance through DNA repair and autophagy in AR-positive prostate cancer cells

Androgen receptor (AR) is a critical therapeutic target in prostate cancer (PCa), and androgen blockade is known to act synergistically with radiation therapy. However, the mechanisms through which AR modulates radiation response are not yet fully understood. In this study, we aimed to investigate the role of AR in mediating radioresistance in PCa. AR-positive LNCaP and castration-resistant C4-2 cells exhibited significantly higher radioresistance than AR-negative cells, as determined by apoptosis and cell viability assays. Following irradiation, most LNCaP cells were arrested in the G1 phase, accompanied by rapid p53 activation and p21 induction. Consistently, AR silencing significantly increased radiosensitivity and reduced DNA-PKcs expression and phosphorylation, suggesting that AR enhances DNA repair, likely through non-homologous end joining (NHEJ). At the cellular level, irradiation markedly induced macroautophagy in LNCaP and C4-2 cells, as evidenced by increased LC3B-II accumulation and autophagic vacuole formation, and the upregulation of 11 autophagy-related genes was identified by whole-transcriptomic analysis. To assess their functional relevance, we performed siRNA-mediated knockdown of selected autophagy-related genes and assessed cell viability and Annexin V/PI staining. Notably, BECN1 and LC3 knockdown significantly enhanced radiosensitivity, with BECN1 knockdown showing an effect comparable to that observed with AR silencing. These results suggest that radiation-induced autophagy promotes the survival of AR-positive prostate cancer cells. Moreover, immunohistochemical analysis of ex vivo-irradiated, patient-derived PCa tissues from patients with newly diagnosed high-Gleason score prostate cancer undergoing prostatectomy further demonstrated that radiation-induced autophagy supports the survival of high-grade AR-positive tumor cells. Collectively, our findings reveal that AR promotes radioresistance in PCa by enhancing both DNA repair and autophagy. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=138 SRC="FIGDIR/small/690226v1_ufig1.gif" ALT="Figure 1"> View larger version (45K): org.highwire.dtl.DTLVardef@3f713corg.highwire.dtl.DTLVardef@1233a11org.highwire.dtl.DTLVardef@1b94e5eorg.highwire.dtl.DTLVardef@c8338c_HPS_FORMAT_FIGEXP M_FIG C_FIG

cancer biology↗

bioRxiv2025

Dorsomedial hypothalamus cold-sensitive neurons drive shivering thermogenesis

Hypothermia, a decline in core body temperature below 35{degrees}C in homeotherms, elicits rapid, asynchronous involuntary shivering thermogenesis; however, the hypothalamic neurons responsible for initiating this response remain uncharacterized. Here, retrograde transsynaptic tracing combined with RNA-seq identified a distinct population of VGLUT2-positive neurons enriched with Calbindin D28k (CALB1) within the dorsomedial hypothalamic nucleus (DMHCalb1/Vglut2). Convergent evidence from chemogenetic, optogenetic, fiber photometry calcium imaging, and electromyography (EMG) experiments demonstrated that these neurons selectively mediate hypothermia-triggered shivering thermogenesis. Bidirectional perturbation of DMHCalb1/Vglut2 activity modulated shivering intensity, while CALB1-negative VGLUT2-expressing DMH neurons were responsible for non-shivering thermogenesis (NST). Genetic ablation of afferent inputs from LSI/POA/VLPAG projecting to DMHCalb1/Vglut2, as well as ex vivo pharmacological synaptic blockade, failed to eliminate shivering responses during hypothermia, indicating that their activation is independent of canonical cold-responsive circuits. Hypothermia significantly suppressed transient A-type K (IA) currents, without affecting delayed rectifier K (IK) currents, accompanied by a pronounced reduction in the IA inactivation time constant relative to normothermic 36 {degrees}C. Collectively, hypothermia elevates DMHCalb1/Vglut2 excitability through IA-dependent reshaping of action potential dynamics. Shortened action potential repolarization and afterhyperpolarization duration cooperatively boost neuronal firing, constituting an intrinsic mechanism for DMHCalb1/Vglut2 neuron-driven shivering initiation.

neuroscience↗

bioRxiv2025

A Mesoscale Framework for Psychedelic Drug Action in the Human Brain

The mechanism of psychedelic drug action is a dynamic area of neuroscience, with two major lines of investigation: (1) laboratory studies at the molecular and cellular level, and (2) human neuroimaging studies of functional brain networks. Despite considerable progress, there remains insufficient understanding of the link between molecular/cellular substrates of psychedelics and the whole-brain network effects that result. Here we report a study of psychedelic action that focuses on the intermediate spatial scale of local brain regions (<1cm3). We analyzed the effects of classical psychedelics (dimethyltryptamine [DMT], lysergic acid diethylamide [LSD], psilocybin) and non-classical psychedelics (nitrous oxide, ketamine) in humans using functional magnetic resonance imaging. We found that all five drugs reduced regional homogeneity, that is, they disrupted local synchrony, in small-scale brain regions; this disruption occurred extensively in cortical regions and sparsely in subcortical regions. Dynamic analysis of both regional homogeneity and global functional connectivity showed an inverse pattern, with large-scale functional connectivity being enhanced as local synchrony declined. We then conducted dominance analysis to assess the contribution of various neurotransmitter receptors to changes in regional homogeneity. DMT, LSD, and psilocybin showed the 5-HT receptors as the most dominant association; by contrast, regional homogeneity changes attributable to both nitrous oxide and ketamine were most strongly associated with the NMDA receptor. Both neuronal (including interneurons) and non-neuronal cell types were linked to psychedelic-induced changes in synchrony at the level of local brain regions. These data, across five drugs from two drug classes, provide evidence that a diverse set of molecular and cellular events lead to a common outcome of disrupted synchrony in local brain regions, which in turn mediate drug-specific changes in global functional connectivity.

neuroscience↗

bioRxiv2025

Clathrin adaptors drive phase separation in endocytosis and trafficking

Liquid-liquid phase separation (LLPS) underlies the formation of biomolecular condensates that organize cellular processes, including endocytosis and membrane trafficking. Although LLPS has been implicated in clathrin-mediated pathways, the specific contribution of adaptor proteins to condensate formation and function remains unclear. Here we show that two yeast adaptors, Ent5 and Sla2, undergo LLPS in vitro and that this property correlates with their distinct roles in membrane trafficking and condensate recruitment in vivo. Ent5 condensation is driven by a dynamic helix within its disordered region that acts as a molecular "sticker." Deletion of this helix disrupts membrane-associated condensation and leads to altered cargo trafficking dynamics in vivo, with Ent5-dependent transport events becoming delayed. In contrast, Sla2 behaves both as a driver and as a client of LLPS, with its coiled-coil (CC) region mediating condensation. Together, these findings reveal that endocytic adaptors can promote condensate formation through distinct structural features, thereby coupling clathrin binding and membrane association through phase separation.

biophysics↗

bioRxiv2025

DNA methylation landscapes in human cells and their chromatin determinants

DNA methylation patterns are established during development and are propagated in a cell type specific manner, but these patterns may become aberrant during aging and cancer. Regions of alternating high and moderate to low levels of DNA methylation exist along all chromosomes in human cells. It is unclear how these distinct DNA methylation blocks are established. Here we have profiled DNA methylation at single base resolution and various histone modifications in human bronchial epithelial cells. We found that many regions of lower DNA methylation are characterized by presence of the Polycomb repressive complex 2 (PRC2) mark histone H3 K27 trimethylation but less so by the PRC1 mark histone H2A K119 monoubiquitylation. These same PRC2-marked regions also showed a depletion of histone H3K36 di- and tri-methylation. Since H3K36me2 and H3K36me3 are recognized by the reader domains of the DNA methyltransferases DNMT3A and DNMT3B and H3K36 methylation is a block to the PRC2 methyltransferases, these crosstalks explain the stable maintenance and antagonism of H3K27me3 and DNA methylation domains. The data give insight into how DNA methylation patterns are established in human cells. We discuss these findings and their potential relevance for altered DNA methylation patterns seen in aging tissues and in cancer cells.

genomics↗

bioRxiv2025

High-salt diet disturbs the physiological uterine endothelial junction remodeling during pregnancy

A high-salt diet (HSD) induced excessive sodium intake is a major risk factor for various diseases. However, its specific effects on uterine endothelial cell and pregnancy outcomes remain poorly understood. In this study, we demonstrated that HSD induces gestation specific hypertension and adverse pregnancy outcomes in murine models. The proper spiral artery remodeling, which involved the decidual vascular endothelia, is thought to be essential for normal regulation of gestational blood pressure. We explored the molecular basis for the adaptation of vascular endothelial cell based on the transcriptome data, and uncovered the significant changes for the cell junction in the endothelia during this process. Furthermore, it was revealed that HSD induced more salt accumulation in the uteri and triggered the disturbed vascular endothelium cytoskeletal remodeling, which was associated impaired trophoblast cell invasion and incorporation into the vascular wall. Overall, our study identifies unique roles of decidual endothelium for pregnancy vascular remodeling, and demonstrates that HSD disrupts physiological spiral artery remodeling through endothelial maladaptation, which may concurrently induce systemic endothelial damage in maternal systemic vascular.

physiology↗

bioRxiv2025

A data and task-constrained mechanistic model of the mouse outer retina shows robustness to contrast variations

Visual processing starts in the outer retina where photoreceptors transform light into electrochemical signals. These signals are modulated by inhibition from horizontal cells and sent to the inner retina via excitatory bipolar cells. The outer retina is thought to play an important role in contrast invariant coding of visual information, but how the different cell types implement this computation together remains incompletely understood. To understand the role of each cell type, we developed a fully-differentiable biophysical model of a circular patch of mouse outer retina. The model includes 200 cone photoreceptors with a realistic phototransduction cascade and ribbon synapses as well as horizontal and bipolar cells, all with cell-type specific ion channels. Going beyond decades of work constraining biophysical models of neurons only by experimental data, we used a dual approach, constraining some parameters of the model with available measurements and others by a visual task: (1) We fit the parameters of the cone models to whole cell patch-clamp measurements of photocurrents and two-photon glutamate imaging measurements of synaptic release. (2) We then trained the spatiotemporal outer retina model with photoreceptors and the other cell types to perform a visual classification task with varying contrast and luminance levels. We found that our outer retina model could learn to solve the classification task despite contrast and luminance variance in the stimuli. Testing different cell type compositions and connectivity patterns, we found that feedback from horizontal cells did not further improve task performance beyond that of excitatory photoreceptors and bipolar cells. This is surprising given that horizontal cells are positioned to mediate communication across cones and that they add to the models number of trainable parameters. Finally, we found that our model generalized better to out of distribution contrast levels than a linear classifier. Our work shows how the nonlinearities found in the outer retina can accomplish contrast invariant classification and teases apart the contributions of different cell types.

neuroscience↗

bioRxiv2025

Atlas of Breast Cancer in Chinese Young Women Revealed by Single-cell RNA and ATAC Sequencing

Young women with breast cancer (YBC, age[<=]40) are particularly prevalent in Asian. YBCs usually show more aggressive pathology and poorer outcomes than non-young patients. However, YBCs are underrepresented in current BC risk models, with their tumor intrinsic subtypes and microenvironments lacking a systematic elucidation at the single-cell level, thereby limiting the young-specific therapies. We established a single-cell Chinese YBC landscape baseline, including 246,659 cells, by applying scRNA-seq and scATAC-seq on untreated patients. We developed a cross-modal feature selection algorithm to construct a young-intrinsic subtype classifier BCYtype, outperforming existing classifiers in pseudobulk, cellular, and external cohorts. Comparative analyses with non-young samples revealed a direct differentiation trajectory from mammary stem cells to mature luminal cells. Pseudotemporal analysis also demonstrated that tumor cells in younger patients undergo earlier carcinogenesis. Mechanistically, we found that CDH1 interacts with pTex and NKT cells, serving as a young-specific marker and a potential therapeutic target for HR+ young patients. The interaction between exhausted T cells and antigen-presenting cells revealed NKG2A as a candidate therapeutic target for triple-negative breast cancer in young patients.

cancer biology↗

bioRxiv2025

4E-BP2-dependent translational control in GABAergic interneurons is required for long-term memory

mRNA translational repression by eukaryotic initiation factor 4E-binding proteins (4E-BPs), plays a critical role in synaptic plasticity and the formation of long-term memory (LTM). Among the three 4E-BP paralogs, 4E-BP2 is the predominant form expressed in neurons, and its full-body deletion in mice causes memory deficits. Mice lacking 4E-BP2 in GABAergic inhibitory interneurons, but not excitatory neurons, display autistic-like behaviors and deficits in object location and recognition. The specific mRNAs translationally regulated by 4E-BP2 in GABAergic interneurons, and how they contribute to spatial and associative memory, are unknown. Here, we show that conditional knockout (cKO) mice lacking 4E-BP2 selectively in GABAergic interneurons exhibit impairments in long-term spatial and contextual fear memory formation. We further demonstrate that 4E-BP2 deletion controls the translation of selective mRNAs in interneurons without increasing general protein synthesis. One of the mRNAs is Gal, which encodes a neuropeptide that modulates memory. Our findings provide evidence that 4E-BP2 selectively controls the translation of a subset of mRNAs in inhibitory neurons that are required for LTM formation.

neuroscience↗

bioRxiv2025

Environmental DNA Reveals Reykjavik's Human and Ecological History

Iceland was among the last large islands settled by humans, with colonization (Landnam) in the late 9th century CE (Common Era) and is often portrayed as an ecological disaster driven by the Norse settlers. Here, we revisit this narrative through environmental DNA (eDNA) and multiproxy analyses of sediment cores from Lake Tjornin in central Reykjavik, one of Icelands earliest and longest-occupied settlements. Originally a marine embayment, Tjornin became a freshwater lake around 660 CE. Our record reveals a human presence decades before the long-accepted arrival date of 877 CE, marked by the Landnam volcanic tephra. Early settlement brought livestock, barley cultivation, and other introduced taxa that enhanced nutrient cycling and unexpectedly increased local biodiversity. Contrary to the conventional view of rapid deforestation, eDNA shows that birch and willow expanded during the settlement period, likely supported by deliberate management. Pronounced ecological and land use shifts occurred after 1200 CE, but these were coeval with the Little Ice Age cooling, compounded by volcanic eruptions, storm surges, and plague, rather than anthropogenic degradation. Crop cultivation ceased, arboreal taxa retracted, and grazing pressure maintained open landscapes. Even more profound ecological changes came after c. 1750 CE with urbanization and industrialization, as wastewater discharge, heavy-metal pollution, and fossil fuel use reshaped Tjornins ecosystem. These findings challenge the prevailing model of Norse-induced environmental collapse, revealing instead a dynamic human-environment relationship shaped by both cultural practices and external stressors. By applying eDNA to a long-occupied urban catchment, we demonstrate the power of genomic methods to refine settlement chronologies, reassess ecological baselines and changes, and integrate natural and cultural histories. This approach offers a model for revisiting human-environment interactions in urban centers worldwide.

genomics↗

bioRxiv2025

GatorAffinity: Boosting Protein-Ligand Binding Affinity Prediction with Large-Scale Synthetic Structural Data

Protein-ligand binding affinity prediction is a fundamental task in computational drug discovery. Although substantial efforts have been made to enhance prediction accuracy using data-driven approaches, progress remains limited by persistent data scarcity. The widely used PDBbind dataset, for example, contains fewer than 20, 000 experimental structures with annotated binding affinities, while a vast number of affinity measurements remain underutilized due to missing structural data. Here, we investigate this untapped potential by curating more than 450, 000 synthetic protein-ligand complexes annotated with Kd and Ki values using the Boltz-1 structure prediction model. Building on this unprecedented scale of synthetic data, further augmented with over 1 million synthetic complexes from the recently released SAIR database annotated with IC50 values, we develop GatorAffinity, a geometric deep learning-based scoring function pretrained on large-scale synthetic data and fine-tuned using high-quality experimental structures from PDBbind. Extensive evaluation on a leak-proof benchmark demonstrates that GatorAffinity significantly outperforms state-of-the-art affinity prediction methods, offering superior accuracy and generalizability. Our findings show that augmenting available experimental data with synthetic complexes can effectively address the data scarcity challenge while maintaining strong predictive reliability. By releasing the pretrained GatorAffinity model and the large-scale synthetic dataset GatorAffinity-DB, we provide a scalable and reproducible foundation for affinity prediction, virtual screening, and broader structure-based drug design applications (https://github.com/AIDD-LiLab/GatorAffinity).

bioinformatics↗

bioRxiv2025

Deletion of Cd248 in Postn positive myofibroblast Fails to Attenuate Cardiac Remodeling and Fibrosis in a Murine Model of Pressure-Overload Cardiomyopathy

BackgroundCardiac fibrosis, driven by activated Periostin (Postn)-expressing myofibroblasts, is a key pathophysiological feature of heart failure induced by pressure overload. The clinic trial tested tumor vascular regulator CD248 has been validated as a potential anti-fibrotic target in ischemic heart injury. We therefore tested the hypothesis that targeting Cd248 specifically in Postn+ myofibroblasts ameliorates pressure-overload cardiomyopathy. MethodsSingle-cell RNA-sequencing data from murine hearts subjected to transverse aortic constriction (TAC) were analyzed to quantify the Cd248+/Postn+ fibroblast population. Subsequently, Postn+ myofibroblast-specific inducible Cd248 knockout mice were subjected to TAC. Gene deletion was induced with tamoxifen from the day of surgery. Cardiac remodeling and function were analyzed 8 weeks after TAC. ResultsAnalysis of scRNAseq data confirmed that about 1/3 of the fibroblasts in the 14-day TAC heart are Cd248+Postn+ fibroblasts. However, comprehensive echocardiographic analysis revealed no significant differences in key parameters of cardiac function or dimensions, including left ventricular ejection fraction, ventricular volumes, wall thickness and global muscle strain between PostnMCM+/-;Cd248fl/fl and PostnMCM+/- controls. Histological analysis at 8 weeks also showed no significant alteration in the extent of interstitial or perivascular fibrosis, myocardial vessel density, or cardiomyocyte hypertrophy. ConclusionThe specific deletion of Cd248 in Postn-expressing myofibroblasts does not mitigate pathological remodeling or fibrosis in response to chronic pressure overload. These findings suggest the role of Cd248 in this cell lineage is not a primary driver of pressure-overload pathology. Therefore, a better understanding of the context-dependent functions of CD248 is critical to successfully guide the clinical translation of CD248-based anti-fibrotic therapies.

pathology↗

bioRxiv2025

METABOLOMIC SIGNATURES OF EXTREME OLD AGE: FINDINGS FROM THE NEW ENGLAND CENTENARIAN STUDY

The New England Centenarian Study (NECS) provides a unique resource for the study of extreme human longevity (EL). To gain insight into biological pathways related to EL, chronological age and survival, we used an untargeted serum metabolomic approach (> 1,400 metabolites) in 213 NECS participants, followed by integration of our findings with metabolomic data from four additional studies. Compared to their offspring and matched controls, EL individuals exhibited a distinct metabolic profile characterized by higher levels of primary and secondary bile acids - most notably chenodeoxycholic acid (CDCA) and lithocholic acid (LCA) - higher levels of biliverdin and bilirubin, and stable levels of selected steroids. Notably, elevated levels of both bile acids and steroids were associated with lower mortality. Several metabolites associated with age and survival were inversely associated with metabolite ratios related to NAD+ production and/or levels (tryptophan/kynurenine, cortisone/cortisol), gut bacterial metabolism (ergothioneine/ trimethylamine N-oxide, aspartate/quinolinate), and oxidative stress (methionine/methionine sulfoxide), implicating these pathways in aging and/or longevity. We further developed a metabolomic clock predictive of biological age, with age deviations significantly associated with mortality risk. Key metabolites predictive of biological aging, such as taurine and citrate, were not captured by traditional age analyses, pointing to their potential role as biomarkers for healthy aging. These results highlight metabolic pathways that may be targeted to promote metabolic resilience and healthy aging.

systems biology↗