Biology subjects

Zhang, C.

Publications and source records attributed to Zhang, C..

At least 145 records · Page 8Linked to original sources

bioRxiv2026

Reciprocal adipose-heart regulation of NRAC

Fatty acids (FAs) are a major energy substrate, and their storage and utilization must be balanced across tissues to maintain metabolic homeostasis. White adipose tissue (WAT) and the heart play opposing roles in FA metabolism, with WAT serving as the primary site of FA storage and the heart relying heavily on FAs as an energy source. However, the molecular factors regulating FA handling between the two tissues remain incompletely understood. We previously identified NRAC as a nutritionally regulated adipose- and cardiac-enriched protein; however, how its expression is regulated between these tissues across nutritional states, and how this relates to systemic FA homeostasis, remains unclear. Here, we integrate analyses of human transcriptomic datasets with nutritional and genetic perturbations in mice to examine the association between NRAC and FA metabolism. Human single-cell transcriptomic data from GTEx show enrichment of NRAC expression in adipocytes and cardiomyocytes, and analysis of subcutaneous adipose tissue from the UK Twins cohort reveals strong associations between NRAC expression and the abundance of multiple adipose lipid species. In mice, NRAC expression in WAT and heart was reciprocally regulated by fasting and refeeding and showed opposing associations with circulating free fatty acid (FFA) levels; moreover, whole-body deletion of NRAC elevated circulating FFA. Together, these findings support a role for NRAC in nutritionally responsive inter-organ regulation of FA between WAT and the heart, with implications for systemic lipid homeostasis.

physiology↗

bioRxiv2026

Epigenetic Programming of Macrophage Phenotypes by STING-IRF3 Drives Inflammation in Ascending Thoracic Aortic Dissection

BackgroundAscending thoracic aortic dissection (ATAD) is characterized by extensive macrophage (M{Phi}) accumulation and profound inflammation; however, the mechanisms sustaining pro-inflammatory M{Phi} activation remain incompletely defined. Emerging evidence indicates that epigenetically generated immune memory drives innate immune cells toward persistent inflammatory states. In this study, we investigated whether epigenetic reprogramming governs M{Phi} phenotypic fate and contributes to ATAD pathogenesis. MethodsWe performed single-cell RNA sequencing of human ascending aortic tissues from controls, patients with ascending thoracic aortic aneurysm (ATAA), and patients with acute ascending thoracic aortic dissection (ATAD). We also performed integrated single-cell RNA sequencing, single-cell ATAC sequencing, and spatial transcriptomics in an angiotensin II (Ang II)-infused mouse model. The role of the STING-IRF3 signaling axis in M{Phi} epigenetic programming was examined using M{Phi}-Sting -/- and M{Phi}-Irf3-/- mice. ResultsIn human and mouse aortic tissues, we identified multiple functional M{Phi} populations including pro-inflammatory, phagocytic/anti-inflammatory, proliferative, and reparative/healing M{Phi}s. Aortic M{Phi}s in both sporadic ATAD patients and Ang II-induced ATAD mice exhibited a pronounced pro-inflammatory bias with enhanced differentiation toward pro-inflammatory M{Phi}s and impaired differentiation toward phagocytic/anti-inflammatory states. Pro-inflammatory M{Phi}s were particularly abundant in dissection sites, whereas phagocytic M{Phi}s were enriched in discrete adventitial niches. Origin analyses revealed a substantial increase in CCR2 recruited M{Phi}s within the aortic wall, which preferentially differentiated into pro-inflammatory M{Phi}s. In contrast, LYVE1 resident M{Phi}s-- predominantly biased toward phagocytic phenotypes--were markedly depleted in ATAD. Single-cell ATAC sequencing identified coordinated chromatin remodeling with increased accessibility at pro-inflammatory gene loci and decreased accessibility at phagocytic gene loci. Among candidate transcriptional regulators identified, IRF family TFs, including IRF3 emerged as unique factors capable of simultaneously promoting pro-inflammatory gene programs while suppressing phagocytic gene expression. Mechanistically, STING-IRF3 signaling orchestrates this biased transcriptional state, likely through coordinated BRG1-dependent chromatin opening at pro-inflammatory gene loci and chromatin closing at phagocytic/anti-inflammatory gene loci. M{Phi} specific Sting -/- and Irf3-/- mice exhibited attenuated inflammatory reprogramming and reduced aortic destruction and dissection. ConclusionsThese findings identify STING-IRF3-mediated epigenetic programming of M{Phi}s as a fundamental mechanism driving aortic inflammation and ATAD development. Targeting M{Phi} epigenetic programming may represent a promising therapeutic strategy to prevent aortic dissection. Graphic Abstract O_FIG O_LINKSMALLFIG WIDTH=189 HEIGHT=200 SRC="FIGDIR/small/701198v1_ufig1.gif" ALT="Figure 1"> View larger version (29K): org.highwire.dtl.DTLVardef@c97bcdorg.highwire.dtl.DTLVardef@1df0ca8org.highwire.dtl.DTLVardef@b7fd04org.highwire.dtl.DTLVardef@1443e16_HPS_FORMAT_FIGEXP M_FIG C_FIG

immunology↗

bioRxiv2026

Geometric structure of features underlies human VTC object recognition.

The ventral temporal cortex (VTC) plays a crucial role in human object recognition. Within VTC neural space, object-specific domains align with domain-general features, e.g. face- and scene-domain align with the feature distribution of animacy, generating a hierarchical knowledge structure for categorization. However, the neural process of integrating information from VTC to distinguish different objects remains unclear. Here, we employed a combination of ANN modeling, functional MRI, and MEG to investigate how VTC features affect object manifold separability. The representational geometry analysis shows that domain-general features in VTC form a unique structure, different from ANN, to assist object classification. Moreover, VTC dynamically adjusts the geometrical relationship of these features during object recognition, influencing the geometrical properties of object manifolds and, consequently, their separability. These findings advance our understanding of the neural computation involved in VTC object recognition, revealing how downstream neurons can flexibly access category information in diverse recognition tasks.

neuroscience↗

bioRxiv2026

High-PepBinder: A pLM-Guided Latent Diffusion Framework for Affinity-Aware Target-Specific Peptide Design

Peptides, as therapeutic molecules, offer unique advantages in targeting complex protein surfaces, yet their rational design remains limited by the vastness of the sequence space and the constraints of traditional approaches. Here, we propose High-PepBinder, a sequence-only conditional diffusion framework for target-specific peptide generation. Guided by the target protein sequence, High-PepBinder adopts a dual encoder architecture that integrates protein language models (pLMs) with the diffusion model. This approach cascades the peptide generation model with an affinity classifier and enables the generation process to capture affinity-related features of the peptides through lightweight joint optimization. Due to the scarcity of protein-peptide affinity data, we constructed PepPBA, to our knowledge the most comprehensive dataset to date, and established a structure- and physics-based screening pipeline to prioritize top candidates. Results show that High-PepBinder demonstrates competitive performance across multiple peptide generation and affinity-related tasks. For representative targets, including KEAP1, XIAP, and EGFR, the generated peptides preserve key binding geometries and interface patterns of reference peptides in predicted complexes, while maintaining sequence diversity and favorable predicted properties. Overall, High-PepBinder contributes toward a general and sequence-only strategy for peptide design, offering a computational framework for expanding peptide discovery against challenging targets.

bioinformatics↗

bioRxiv2026

Lysosomal Aspartylglucosaminidase Couples Glycoprotein Catabolism to Cell-Surface GlycoRNA Production

GlycoRNAs, small non-coding RNAs covalently linked to N-glycans, reveal an unexpected intersection between RNA biology and glycosylation, with potential roles in immunity and cell-cell communication. The origins and biogenesis of their glycans remain unclear. Using CRISPR-Cas9 screening, metabolic glycan labeling and lysosome-targeted proteomics, we reconfirm canonical N-glycosylation enzymes (STT3A/B) and identify components of the mannose-6-phosphate (M6P) lysosomal sorting pathway (GNPTAB, M6PR) as essential contributors. Strikingly, lysosomal aspartylglucosaminidase (AGA) acts as a rate-limiting regulator, linking glycoprotein catabolism to glycoRNA formation. Loss of AGA collapses both abundance and diversity of RNA-linked N-glycans, while pulse-chase tracing shows glycoprotein-derived glycans are repurposed for RNA glycosylation. These findings position lysosomes as active participants in RNA modification and redefine glycoRNA biogenesis as a metabolically integrated process.

cell biology↗

bioRxiv2026

A hypothalamo-septo-hippocampal circuit for REM sleep-dependent consolidation of social memory

REM sleep constitutes a critical window for memory consolidation, yet the brain circuits orchestrating this process remain incompletely defined. Here, we identify a lateral supramammillary nucleus (SuM)-medial septum (MS) projection as a REM sleep-specialized pathway essential for hippocampal memory consolidation. Fiber photometry and optrode recordings revealed that lateral SuM-MS projecting neurons were selectively active during REM sleep. REM-specific optogenetic silencing of this projection impaired consolidation of both social and contextual fear memories. Crucially, silencing of its downstream target, the MS-CA2 pathway, during REM sleep selectively disrupted social memory while sparing contextual fear memory. This functional dissection establishes a hypothalamo-septo-hippocampal circuit (lateral SuM-MS-CA2) dedicated to social memory processing, in parallel to the recently-described direct SuM-CA2 pathway. These results also position the SuM as a REM sleep-hub that routes information via parallel septal pathways to consolidate distinct memory modalities.

neuroscience↗

bioRxiv2026

MTFP1 preserves β-cell cristae structure and bioenergetics to ensure insulin release and glucose homeostasis

Pancreatic {beta}-cells are uniquely dependent on mitochondrial metabolism to couple glucose sensing to insulin secretion, a process impaired in diabetes. Mitochondrial fission process 1 (MTFP1) is an inner mitochondrial membrane protein that plays pleiotropic, tissue-specific roles in mitochondrial function and dynamics. Our previous work has identified Mtfp1 mRNA as a target for miR-125b, a microRNA that negatively regulates insulin secretion from {beta}-cells. Nevertheless, the function of MTFP1 in these cells remained unexplored. Here, we show that MTFP1 is essential for normal glucose-stimulated insulin secretion (GSIS) in mouse and human cell lines and islets, and that mice with {beta}-cell-specific elimination of MTFP1 develop glucose intolerance. Whereas {beta}-cell survival and mitochondrial content were unaffected, oxidative phosphorylation and ATP production were sharply lowered. These changes were accompanied by disruption of mitochondrial cristae structure and a reduced contact surface with the endoplasmic reticulum, providing a mechanistic basis for defective stimulus-secretion coupling. Conversely, MTFP1 overexpression in mouse and human islets sufficed to improve mitochondrial respiration and GSIS. Finally, MTFP1 downregulation blocked the positive effects of miR-125b elimination in GSIS and mitochondrial respiration, unveiling MTFP1 as a downstream effector of miR-125b. Together, our findings identify MTFP1 as a critical regulator of {beta}-cell mitochondrial architecture and function, necessary for efficient insulin secretion and glucose homeostasis, and a potential therapeutic target to enhance {beta}-cell bioenergetic resilience in diabetes.

cell biology↗

bioRxiv2026

Interorganelle competition for linoleic acid underlies steatotic liver pathology

Lipid droplets (LDs) are traditionally viewed as protective organelles that sequester potentially cytotoxic lipids. However, whether and how LD biogenesis in pathological contexts actively rewires interorganelle lipid homeostasis to drive organelle dysfunction and disease progression remains unexplored. Here, we identify the adipocyte-enriched protein calsyntenin 3{beta} (CLSTN3B) as a critical promoter of metabolic dysfunction-associated steatotic liver disease (MASLD). CLSTN3B, an ER-LD contact protein previously shown to support LD maturation in adipocytes, is robustly induced in mouse hepatocytes by peroxisome proliferator-activated receptor {gamma} (PPAR{gamma}) in response to dietary caloric overload. CLSTN3B drives LD biogenesis and neutral lipid storage by stabilizing hemifusion-like ER-LD membrane bridges via its arginine-rich segment. These bridges preferentially recruit cone-shaped linoleoylated phosphatidic acid (PA), diverting linoleic acid (LA) into triacylglycerides (TAGs) rather than mitochondrial cardiolipin (CL), leading to disrupted cristae architecture, deficient ETC supercomplex assembly, elevated electron leak, and oxidative stress. Hepatocyte-specific CLSTN3B deletion impairs LD formation, reduces TAG accumulation, enhances fatty acid oxidation, restores CL maturation, and mitigates oxidative stress, collectively attenuating MASLD progression. Consistently, hepatic CLSTN3B expression correlates with fibrosis severity and progression in human MASLD. These findings position LDs as active regulators of interorganelle lipid partitioning and establish CLSTN3B as a key determinant of mitochondrial vulnerability, providing a general framework for how dysregulated organelle interfaces shape disease.

cell biology↗

bioRxiv2026

Regulation of spikelet number during wheat spike development

Wheat produces unbranched inflorescences (spikes) composed of smaller inflorescences (spikelets) as their fundamental building units. The spikelet number per spike (SNS) is a major determinant of grain yield and the gene networks that regulate this trait are the focus of this review. Spikelet development starts with the transition of the shoot apical meristem into an inflorescence meristem (IM) that produces lateral spikelet meristems (SMs). The rate at which SMs are produced and the timing of the IM transition into a terminal spikelet (IM[->]TS) determine the final SNS. These two traits are regulated by genes expressed in the IM (e.g. meristem identity genes), as well as by the amount of FLOWERING LOCUS T1 (florigen) transported from leaves to developing spikes. Spikelet number can also be increased by the production of spikes with supernumerary spikelets (SS) or branch-like structures that resemble small spikes. Mutations that promote a reversion from SM to IM identity can induce the formation of SS or branches. Initial efforts to incorporate these mutations into commercial wheat varieties have faced trade-offs in fertility and grain weight, which will require additional research and breeding efforts. Meanwhile, genes and allele combinations that increase SNS without affecting the number of spikelets per node have been identified and are being deployed in wheat breeding programs. Recent spatial transcriptomics, single-cell analyses, and multi-omics studies of wheat spike development are accelerating the discovery of new genes affecting SNS and enhancing our ability to engineer more productive wheat spikes.

plant biology↗

bioRxiv2026

A three-compartment microfluidic platform for investigating signal transmission in the human sensory pathway

Neuropathic pain remains a significant challenge due to limited understanding of sensory signal transmission mechanisms along the sensory pathway. The sensory pathway involves peripheral nociceptors in the dorsal root ganglia (DRG) that transmit signals from skin to the central nervous system via dorsal horn neurons. Current in vitro models lack the compartmentalization and resolution needed to investigate signal modulation at distinct anatomical sites along this pathway. Here, we developed a three-compartment microfluidic platform combining human induced pluripotent stem cell (iPSC)-derived sensory neurons (hiSNs) with human primary epidermal keratinocytes (HPEKs) and iPSC-derived dorsal horn neurons (hiDHNs) in a spatially organized arrangement. The platform integrates polydimethylsiloxane (PDMS) axon-guiding microstructures with high-density microelectrode arrays (HD-MEAs), enabling single-axon electrophysiological recordings and sub-cellular level stimulation. We established viable co-cultures maintained for up to six weeks and characterized spontaneous activity across all conditions. Keratinocytes increased the number of active sensory neuron axons and their firing rates, demonstrating peripheral modulation of neuronal activity. Systematic frequency-dependent electrical stimulation revealed low-pass filtering properties at sensory neuron somata, with filtering characteristics modulated by co-culture with keratinocytes. This platform enables compartment-specific investigation of signal processing in the human sensory pathway and provides a tool for studying neuropathic pain mechanisms and testing potential therapeutics.

bioengineering↗

bioRxiv2026

Glucose is a ligand-like trigger for secretion of postprandial GLP-1

Glucagon-like peptide 1 (GLP-1) is secreted from the intestinal L cells in a glucose-dependent manner. However, the mechanism underlying how glucose stimulates the secretion remains unclear. Here, we found that glucose at postprandial concentrations near the Km of GK for glucose ([~]10 mM), as well as nonmetabolizable glucose analogs, triggers GLP-1 secretion by intestinal L cells through directly binding to glucokinase (GK), without increasing intracellular ATP levels. We also show that in postprandially high glucose, glucose-bound GK interacts and inhibits KATP, as assessed by immunoprecipitation and FRET-FLIM analyses, as well as patch clamping. In addition, we have utilized GK mutants identified in diabetics, demonstrating that those mutants defective in binding to glucose impair GLP-1 secretion in however high glucose, whereas mutants constitutively bound to glucose with defects in catalysis, promote GLP-1 secretion even in low glucose. Furthermore, the KATP mutant unable to bind to GK blocks GLP-1 secretion in high glucose. We have also provided evidence showing that sodium-glucose cotransporter 1 (SGLT1) plays an important role in the basal secretion of GLP-1, but not in high glucose. We have thus revealed that glucose the molecule itself and GK act as a ligand and the receptor, respectively, to induce GLP-1 secretion in response to high glucose, providing new therapeutic avenues targeting metabolic diseases.

biochemistry↗

bioRxiv2026

APIPred Web 1.0: A Web Platform to Predict Potential Aptamer Sequences for Protein targets

Aptamers are short single-stranded nucleic acids that bind protein targets with high specificity and are increasingly used in diagnostics and therapeutics, yet experimental discovery remains slow and variable in success. This creates a demand for computational systems that not only score candidate binders but also generate experimentally usable libraries under biologically meaningful constraints. Here, we present APIPred Web 1.0, a unified web platform that integrates constraint-aware aptamer library generation, machine learning- based aptamer- protein interaction prediction, and DNA secondary-structure analysis within a user-facing workflow. Users submit a target protein aminoacid sequence and define an aptamer template in a PREFIX - [VARIABLE] - SUFFIX format with real-time validation of key biological constraints (GC content and homopolymer limits). On the backend, sequences are converted into model- compatible features via optimized k-mer encodings (aptamer) and pseudo amino acid composition (PAAC) descriptors (protein), followed by inference with a trained XGBoost predictor. APIPred Web 1.0 improves the computational efficiency by applying precomputed protein features, vectorized batch processing (hundreds of sequences per batch), optimized XGBoost DMatrix inference, and a bounded heap that retains only the top 25 candidates during generation. The platform then computes minimum free energy (MFE) structures using ViennaRNA with parallel folding and returns ranked list of the top candidates with log-transformed interaction scores, complete sequences (variable region highlighted), dot-bracket structures, MFE values, and interactive 2D visualizations via persistent result links. In a demonstration study targeting CD64 protein, the platform produced 25 putative binders from a custom 40- nucleotide library and enabled selection of structurally diverse candidates for experimental testing. Flow cytometry showed specific binding to CD64-expressing THP-1 cells with minimal signal in Ramos control cells. Collectively, APIPred Web 1.0 offers a reproducible, structure-informed, and computationally efficient pipeline for rapid generation of aptamer candidates against target proteins for downstream experimental validation. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=50 SRC="FIGDIR/small/697194v1_ufig1.gif" ALT="Figure 1"> View larger version (14K): org.highwire.dtl.DTLVardef@1c1ca4dorg.highwire.dtl.DTLVardef@1c8b23dorg.highwire.dtl.DTLVardef@12dfe2dorg.highwire.dtl.DTLVardef@8a7c8f_HPS_FORMAT_FIGEXP M_FIG C_FIG

bioinformatics↗

bioRxiv2025

Discovery of Abundant Nano-scale Lymphatic-like Vessels in Brains

As one of the most metabolically active organs, the brain requires an exceptionally efficient system for waste clearance to sustain its high metabolic demands. However, whether such a system exists--and, if so, what structural features enable its efficiency--remains incompletely understood. More than a decade ago, the "glymphatic system" was proposed to describe neurofluid transport through cerebrospinal fluid (CSF) and perivascular spaces (PVS), in conjunction with dural and meningeal lymphatic pathways. Nevertheless, it remains unresolved whether neurofluid transport is organized as a structured, vessel-like flow network. Moreover, in stark contrast to the dense network of blood capillaries in the brain, only a sparse population of lymphatic vessels has been identified, raising doubts as to whether the currently recognized lymphatic architecture alone can support efficient metabolic waste clearance. By combining expansion microscopy with CRANAD-3, a pan-{beta}-amyloid fluorescent probe, we discovered abundant nanoscale lymphatic-like vessels (NLVs) within the brain parenchyma of both mice and humans. The majority of these structures have diameters below 1,000 nm and exhibit moderate positivity for multiple lymphatic markers, including LYVE-1, Prox-1, PDPN, and VEGFR3. NLVs frequently coil around blood vessels, and putative connections between vascular structures were observed. Notably, some NLVs traverse multiple cortical layers and display distinct orientation patterns that vary across cortical laminae. This discovery reveals a previously "hidden" vascular network in the brain parenchyma and raises the possibility that an abundant, highly organized system of nanoscale tubular structures may provide an efficient conduit for metabolic waste clearance. Such a system could represent a critical, previously unrecognized component supporting the brains extraordinary metabolic demands.

neuroscience↗

bioRxiv2025

The biochemical nature of senile plaques: intracellular destabilized-lysosome-enriched neural processes catabolizing extracellular hemorrhagic amyloid materials

The pathological mechanism of senile plaque formation in Alzheimers disease remains a challenging unresolved problem for over one hundred years. In this study, we investigated senile plaque pathogenesis based on immunohistochemistry, fluorescence imaging and quantitative analysis of AD front brain sections with multiple senile plaque related markers such as A{beta}, MAP2, phos-Tau, Cathepsin D, Sortilin 1, Ceruloplasmin and Hemin. Firstly, we confirmed that senile plaque A{beta} deposition mostly happened in MAP2-positive but degenerative neuritic processes. Secondly, we found an interesting dual-component granular or diffusive staining pattern of all of these senile plaque related markers, matching to two states of lysosomes, relatively-stable granule lysosomes and destabilized diffusive lysosomes as shown by lysosome-related marker Cathepsin D or Sortilin 1 staining. Thirdly, dystrophic senile plaque neural processes contain hemorrhage-related markers such as Ceruloplasmin and Hemin. In addition, A{beta} deposition, Tau phosphorylation, lysosome destabilization are all enriched at the sites of microaneurysm formation. Moreover, senile plaques are also characterized by a widespread binary phos-Tau staining pattern with difference in term of staining intensity. We concluded that senile plaques are formed by destabilized-lysosome-enriched neural processes catabolizing extracellular hemorrhagic amyloid materials, with microaneurysm as an important intermediate stage.

cell biology↗

bioRxiv2025

Semi-rational Engineering of Terminal Deoxynucleotidyl Transferase for High-efficiency Enzymatic de Novo DNA Synthesis

The 21st century has witnessed rapid advancements in synthetic biology, with DNA synthesis emerging as a foundational technology. Conventional phosphoramidite-based methods face significant limitations, including short DNA elongation lengths (<300 nt), hazardous chemical waste, and low stepwise incorporation efficiency. Enzymatic DNA synthesis using terminal deoxynucleotidyl transferase (TdT) offers a promising alternative, enabling kilobase-scale assembly with greater efficiency and minimal environmental impact. Here, we identified Bos taurus TdT (BtTdT) through UniProt database mining as a catalytically active scaffold for natural and 3'-modified dNTPs. Comprehensive characterization of BtTdTs enzymatic properties--including pH, temperature, metal ion dependence, and substrate specificity--revealed its optimal conditions. Truncation of the BRCT domain generated variants with enhanced activity compared to wild-type BtTdT. Guided by AlphaFold3-predicted structural models, we engineered a quintuple mutant (M5: Bt15AAR336L/K338G/L397M/E456S/D395G) optimized for 3'-ONH2-dNTP incorporation. M5 exhibited 30-fold activity enhancement relative to the triple mutant M3 (Bt15AAR336L/K338G/L397M) and achieved stepwise incorporation efficiency exceeding 98% in de novo synthesis of 10-nt ssDNA, demonstrating its potential for scalable enzymatic DNA synthesis. This work establishes a rational framework for TdT engineering through rational domain truncation and computational design, showing potential toward industrial-scale enzymatic DNA manufacturing.

synthetic biology↗

bioRxiv2025

Shifts in the human gut microbiome during cancer chemotherapy are diet-dependent

Numerous studies have implicated both dietary intake and the human gut microbiome in colorectal cancer (CRC) treatment outcomes. However, little is known about how patients adjust their dietary intake during cancer chemotherapy or if these dietary changes contribute to treatment-associated alterations in the gut microbiome. We performed paired longitudinal diet and microbiome analysis during CRC treatment with oral fluoropyrimidines (NCT04054908) and validated key associations using cell culture assays. At each timepoint, diet was measured by averaging up to 3 consecutive days of 24-hour dietary records (NCI ASA24; 35 patients; 2.5{+/-}1.1 timepoints per patient), while microbiome composition was measured from stool (16S rRNA gene sequencing, metagenomics, qPCR; 40 patients; 5.6{+/-}1.4 timepoints per patient). Diet quality significantly decreased during chemotherapy. Carbohydrate and refined grain intake increased, accompanied by decreased consumption of fats, nuts and seeds, and fat-soluble micronutrients. Multiple individual dietary components were strongly linked to the gut microbiome. Decreases in theobromine intake correlated with decreases in overall microbial diversity and more gastrointestinal toxicities. Diet shifts partly explained changes in bacterial abundance during chemotherapy, including more severe depletion of Faecalibacterium prausnitzii in patients with decreased vitamin K1 intake. Changes in diet were correlated with multiple bacterial gene families involved in micronutrient metabolism and drug sensitivity. Increased copper intake was linked to decreased Fusobacterium nucleatum in patients and inhibited F. nucleatum in cell assays. Together, these data suggest that changes in diet during chemotherapy contribute to changes in gut bacterial diversity, taxonomic composition, and gene abundance. Our approach may generalize to other cancer therapies and emphasizes the need for collecting more robust dietary data in clinical microbiome studies.

microbiology↗

bioRxiv2025

Vitreous Inflammation as an Early Indicator of Retinal Ganglion Cell Loss Following Acute Optic Nerve Injury in Mice

Retinal ganglion cell (RGC) degeneration in optic neuropathies is often preceded by neuroinflammatory changes, yet the earliest in vivo indicators of this process remain poorly defined. Here, we identified vitreous hyperreflective foci (VHRFs) by visible-light optical coherence tomography (vis-OCT) as an early inflammatory signature of RGC injury. Longitudinal vis-OCT imaging after optic nerve crush (ONC) revealed that VHRFs emerged as early as 6 hours post-injury and peaked before the significant RGC loss. Confocal analysis showed that these VHRFs corresponded to activated amoeboid microglia undergoing vertical migration from the outer to inner retina and horizontal movement toward the optic nerve head area. Similar amoeboid microglia were also observed in the anterior segment, suggesting a global ocular inflammatory response to the ONC injury. RNAscope in situ hybridization further demonstrated elevated IL-1{beta} expression in vitreous amoeboid microglia. Moreover, pharmacological blockade of IL-1 signaling with an IL-1 receptor antagonist significantly reduced VHRFs, suppressed microglial migration, and delayed RGC loss. Taken together, our findings identify VHRFs as a previously unrecognized early danger signal for RGC degeneration and highlight IL-1-mediated inflammation as a tractable early therapeutic target for preventing RGC degeneration and vision loss. Graphical Overview O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=88 SRC="FIGDIR/small/694725v1_ufig1.gif" ALT="Figure 1"> View larger version (27K): org.highwire.dtl.DTLVardef@1598c4aorg.highwire.dtl.DTLVardef@9637borg.highwire.dtl.DTLVardef@623bf4org.highwire.dtl.DTLVardef@14e21ce_HPS_FORMAT_FIGEXP M_FIG C_FIG

neuroscience↗

bioRxiv2025

Batch Effects Remain a Fundamental Barrier to Universal Embeddings in Single-Cell Foundation Models

Constructing a cell universe requires integrating heterogeneous single-cell RNA-seq datasets, but is hindered by diverse batch effects. Single-cell foundation models (scFMs), inspired by large language models, aim to learn universal cellular embeddings from large-scale single-cell data. However, unlike language, single-cell data are sparse, noisy, and strongly affected by batch effects that limit cross-dataset transferability. Our systematic evaluation across diverse batch scenarios reveals that current scFMs fail to effectively remove batch effects, with batch signals persisting in pretrained embeddings. Post-hoc batch-centering partially improves alignment, highlighting the need for future scFMs to integrate explicit batch-effect correction mechanisms to achieve true universal cellular embeddings.

bioinformatics↗