Biology subjects

Wang, C.

Publications and source records attributed to Wang, C..

At least 361 records · Page 20Linked to original sources

bioRxiv2025

Bacteriophage protein Dap2 inhibits bacterial type III secretion system and synergizes with Dap1 to evade anti-phage immunity

The evolutionary arms race between bacterial immunity and phages has driven the emergence of sophisticated anti-defense systems (ADSs). However, certain ADSs exhibit incomplete suppression of their cognate defense systems, suggesting functional cooperation between multiple ADSs targeting the same bacterial safeguard. In this study, we characterize Dap2, a protein encoded by a Pseudomonas aeruginosa phage PaoP5, which directly binds to the Lon protease to prevent the degradation of the phage-encoded HNH endonuclease. Deletion of dap2 in PaoP5 exhibits significantly impaired genome packaging due to insufficient levels of HNH. Strikingly, Dap2 synergizes with its genomically adjacent partner Dap1, a previously identified HNH-binding protein providing partial Lon resistance, to achieve complete protection of HNH. Beyond anti-defense activity, Dap2 disrupts host virulence by sequestering the type III secretion system (T3SS) transcriptional activator ExsA, suppressing bacterial pathogenicity while redirecting metabolic resources toward phage progeny production. This study unveils a dual functional ADS that simultaneously modulates bacterial virulence and anti-phage immunity, both aimed at ensuring phage survival and maximizing progeny production. Furthermore, it elucidates a novel mechanism whereby phages employ synergistic ADS pairs (Dap1/Dap2) to achieve complete neutralization of a bacterial defense system, when individual components provide only partial protection. These findings significantly enhance our understanding of the intricate evolutionary arms race between phages and their bacterial hosts.

microbiology↗

bioRxiv2025

Design of solubly expressed miniaturized SMART MHCs

The precise recognition of specific peptide-MHC (pMHC) complexes by T-cell receptors (TCRs) plays a key role in infectious disease, cancer and autoimmunity. A critical step in many immunobiological studies is the identification of T-cells expressing TCRs specific to a given pMHC antigen. However, the intrinsic instability of empty class-I MHCs limits their soluble expression in Escherichia coli (E. coli) and makes it very difficult to characterize even a small fraction of possible pMHC/TCR interactions. To overcome this limitation, we designed small proteins which buttress the peptide binding groove of class I MHCs, replacing {beta}2-microglobulin ({beta}2m) and the heavy chain 3 domain, and enable soluble expression of both H-2Db and A*02:01 in E. coli. We demonstrate that these soluble, monomeric, antigen-receptive, truncated (SMART) MHCs retain both peptide- and TCR-binding specificity, and that peptide-bound structures of both allomorphs are similar to their full-length, native counterparts. With extension to the majority of HLA alleles, SMART MHCs should be broadly useful for probing the T-cell repertoire in approaches ranging from yeast display to T-cell staining. SignificanceDespite the critical role that TCR/pMHC interactions play in human health, it has remained difficult to produce reagents necessary to study them. Requirements for refolding or sequence optimization limit immunologists and biochemists ability to characterize diverse pMHC/TCR interactions. Here, we develop a de-novo designed protein domain that stabilizes the H-2Db and A*02:01 class I MHC allomorphs, allowing soluble expression in E. coli without the need for a stabilizing peptide, and improving display on the yeast surface, while maintaining peptide and TCR binding interactions. These features facilitate a wide range of experiments to more fully understand the nature of pMHC/TCR interactions, and pave the way for the development of stabilizing domains for all MHC allomorphs.

biochemistry↗

bioRxiv2025

Obesity Increases Atherosclerosis Susceptibility via Inter-tissue miR-30e-SLC7A11 Axis

BackgroundWith obesity as a risk factor for atherosclerotic disease, recent research suggests that adipose tissue in obese animal models and humans can generate endocrine-like molecules that affect arterial health later on. Previous studies showed that microRNA-30e (miR-30e) level is elevated in atherosclerosis and solute carrier family 7 member 11 (SLC7A11), a cystine/glutamate transporter, is involved in atherogenesis. However, whether an endocrine-like link between the adipose-derived miR-30e-5p and SLC7A11 in the vascular endothelium can lead to obesity-caused atherosclerosis is unknown. MethodsMiRNA data mining and RT-PCR validations were used to demonstrate the positive association among serum level of miR-30e-5p, obesity, and coronary arterial disease in human patients. Transcriptomics (RNA-seq and single-nucleus RNA-seq), metabolomics, and in silico analysis were used to establish a miR-30e-5p-SLC7A11 regulation of central carbon metabolism, mitochondrial and endothelial cell (EC) function. Mouse models with EC-specific Slc7a11 knockout (EC-Slc7a11-/-) and gain or loss of function of miR-30e-5p were used to elucidate the detrimental role of this endocrine-like axis in obesity-related atherosclerosis. ResultsThe level of adipocyte-derived miR-30e-5p was significantly upregulated in obese humans with coronary artery disease and obese and atherosclerotic mice. Via serum exosomes, the adipocyte-generated miR-30e-5p targeted SLC7A11 mRNA in vascular ECs. SLC7A11 deficiency due to miR-30e-5p targeting dysregulated glutamate/cystine metabolism increased glycolysis, reduced oxidative phosphorylation, and impaired mitochondrial function. The EC dysfunction could be rectified by SLC7A11 overexpression or miR-30e-5p antagonism. Exogenously delivered miR-30e-5p phenocopied the increased atherosclerosis in EC-Slc7a11-/- mice. In contrast, miR-30e-5p antagomir treatment reduced atherosclerosis in Apoe-/- and ob/ob mice. ConclusionOur multi-omics approaches demonstrates that the adipose-derived miR-30e-5p downregulated SLC7A11 mRNA in ECs via tissue crosstalk. The resulting EC dysfunction led to obesity-related atherosclerosis in mice. These findings underscore a causality between obesity and atherosclerosis in the context of cardiovascular-kidney-metabolic syndrome.

molecular biology↗

bioRxiv2025

Anticlustering for Sample Allocation To Minimize Batch Effects

High throughput sequencing is a powerful tool for processing large amounts of DNA and RNA samples in batches. Proper experimental design and statistical methods are required to mitigate systematic technical factors due to differences in batches ("batch effects"), as data variation due to these non-biological factors can mask actual biological differences. We propose using anticlustering as an automated method to assign samples to balanced batches. Anticlustering effectively negates differences in (numeric and/or categorical) covariates among batches, and implements user-defined restrictions on the number of batches, the number of samples per batch, and whether to assign certain samples to the same batch ("must-link constraints"). A simulation study shows that anticlustering is better at achieving balance among batches than previous approaches. An application from the UCSF-Stanford Endometriosis Center for Discovery, Innovation, Training and Community Engagement ("ENACT", https://enactcenter.org/) is presented as a real-life example. In the application, multiple samples provided by an individual had to be processed on the same batch, so that comparisons among different samples of the same patient were not diluted by batch effects. The novel Two Phase Must Link (2PML) anticlustering algorithm realized the must-link restrictions while simultaneously obtaining balance among batches regarding disease stage, menstrual cycle phase, case versus control sample, and clinical site. All methods presented here are accessible via the free and open source R package anticlust (https://cran.r-project.org/package=anticlust). An interactive visualization and web-based batch assignment tool are made available in the Rshiny app "anticlust" (https://anticlust.org/).

bioinformatics↗

bioRxiv2025

Nitrate-driven dark oxygen production by diverse deep-sea microorganisms

To date, only three biotic pathways for light-independent oxygen production (i.e., dark oxygen) have been reported: chlorate dismutation, nitric oxide dismutation, and methanobactin-dependent water lysis. Oxygen has been shown to be produced and consumed in dark and anoxic environments, as evidenced by its prevalence in deep-sea surface sediments. However, the microbial communities and pathways driving deep-sea dark oxygen production (DOP) remain poorly understood. Here we identify a novel DOP pathway driven by dissimilatory nitrate reduction to ammonium (DNRA) in two deep-sea Deferribacterota strains. The DOP activity of these Deferribacterota strains potentially promotes the formation of manganese nodules and influences the growth and metabolism of both aerobic and anaerobic microbes, underscoring the significant role of microbial DOP in shaping deep-sea geological and ecological systems. We also cultured several deep-sea DOP-capable microorganisms from the Campylobacterota, Deinococcota, and Pseudomonadota phyla, which generate dark oxygen through unidentified nitrate-driven pathways. Combined with previous geological evidence, our results suggest that nitrate-driven dark oxygen, alongside photosynthetic oxygen, jointly contributed to early Earths oxygenation, driving the Great Oxidation Event. Overall, our findings provide novel insights into deep-sea oxygen sources, shed light on the origins of early Earths oxygen, and expand perspectives on the potential for terraforming other planets.

microbiology↗

bioRxiv2025

Developmental regulators enable rapid and efficient soybean transformation and CRISPR-mediated genome editing

Soybean transformation remains challenging and has not kept pace with the rapid advancement of genetic engineering technologies due to low efficiency, lengthy timelines, and genotype dependency. Here, we developed a streamlined transformation method by leveraging developmental regulators (DRs) to promote de novo shoot regeneration directly from growing soybean plants. By evaluating multiple DR combinations, our results showed that co-expression of WUSCHEL2 (WUS2) and isopentenyltransferase (IPT) achieved higher transformation efficiencies (15.2% to 22.3%) in Williams 82 and Bert varieties than individual DRs without requiring exogenous hormones or selection agents. Moreover, this method produces heritable transgenic events within 9-11 weeks and successfully delivers CRISPR-Cas9 components, generating heritable mutations with 20% efficiency. The temporal transcriptomic and gene regulatory network analyses revealed that WUS2/IPT synergistically modulates stress responses and activates developmental pathways, orchestrating a transition from initial stress adaptation to regenerative programming. Together, our findings demonstrate that this DR-enabled approach significantly enhances soybean transformation efficiency, reduces tissue culture requirements, and offers a promising genome editing platform for soybean improvement.

plant biology↗

bioRxiv2025

High-Parameter Spatial Multi-Omics through Histology-Anchored Integration

Spatial omics face challenges in achieving high-parameter, multi-omics co-profiling. Serial-section profiling of complementary panels mitigates technical trade-offs but introduces the spatial diagonal integration problem. To address this, we present SpatialEx and its extension SpatialEx+, computational frameworks leveraging histology as a universal anchor to integrate spatial molecular data across tissue sections. SpatialEx combines a pre-trained H&E foundation model with hypergraph and contrastive learning to predict single-cell omics from histology, encoding multi-neighborhood spatial dependencies and global tissue context. SpatialEx+ further introduces an omics cycle module that encourages cross-omics consistency via slice-invariant mappings, enabling seamless integration without co-measured training data. Extensive validations show superior H&E-to-omics prediction, panel diagonal integration, and omics diagonal integration across various biological scenarios. The frameworks scale to datasets exceeding one million cells, maintain robustness with non-overlapping or heterogeneous sections, and support unlimited omics layers in principle. Our work makes multi-modal spatial profiling broadly accessible.

bioinformatics↗

bioRxiv2025

Color-neutral and reversible tissue transparency enables longitudinal deep-tissue imaging in live mice

Light scattering in biological tissue presents a significant challenge for deep in vivo imaging. Our previous work demonstrated the ability to achieve optical transparency in live mice using intensely absorbing dye molecules, which created transparency in the red spectrum while blocking shorter-wavelength photons. In this paper, we extend this capability to achieve optical transparency across the entire visible spectrum by employing molecules with strong absorption in the ultraviolet spectrum and sharp absorption edges that rapidly decline upon entering the visible spectrum. This new color-neutral and reversible tissue transparency method enables optical transparency for imaging commonly used fluorophores in the green and yellow spectra. Notably, this approach facilitates tissue transparency for structural and functional imaging of the live mouse brain labeled with yellow fluorescent protein and GCaMP through the scalp and skull. We show that this method enables longitudinal imaging of the same brain regions in awake mice over multiple days during development. Histological analyses of the skin and systemic toxicology studies indicate minimal acute or chronic damage to the skin or body using this approach. This color-neutral and reversible tissue transparency technique opens new opportunities for noninvasive deep-tissue optical imaging, enabling long-term visualization of cellular structures and dynamic activity with high spatiotemporal resolution and chronic tracking capabilities. Significance StatementTissue scattering represents a major barrier to deep tissue imaging in vivo. We recently showed that tissue can be rendered transparent in the red spectrum using intensely absorbing dye molecules. Here, we introduce a new, color-neutral and reversible tissue transparency approach. We demonstrate longitudinal structural and functional imaging in the deep tissue of awake mice.

bioengineering↗

bioRxiv2025

Conditional Diffusion with Locality-Aware Modal Alignment for Generating Diverse Protein Conformational Ensembles

Recent advances in AI have enabled the accurate prediction of a single stable protein structure solely based on its amino acid sequence. However, capturing the complete conformational landscape of a protein and its dynamic flexibility remains challenging. In this work, we developed Modal-aligned conditional Diffusion (Mac-Diff), a score based diffusion model for generating the conformational ensembles for unseen proteins. Central to Mac-Diff is an innovative attention module that enforces a delicate, locality-aware alignment between the conditional view (protein sequence) and the target view (residue pair geometry) to compute highly contextualized features for effective structural denoising. Furthermore, Mac-Diff leverages semantically rich sequence embedding from Protein Language Models like ESM-2 in enforcing the protein sequence condition that captures evolutionary, structural and functional information. This compensates for protein structural heterogeneity more effectively than embeddings from structure prediction models that are possibly biased to the dominant conformation. Mac-Diff showed promising results in generating realistic and diverse protein structures. It successfully recovered conformational distributions of fast folding proteins, captured multiple meta-stable conformations that were only observed in long MD simulation trajectories and efficiently predicted alternative conformations for allosteric proteins. We believe that Mac-Diff offers a useful tool to improve understanding of protein dynamics and structural variability, with broad implications for structural biology, drug discovery, and protein engineering.

bioinformatics↗

bioRxiv2025

Structure of the human TWIK-2 potassium channel and its inhibition by pimozide

The potassium channel TWIK-2 is crucial for ATP-induced activation of the NLRP3 inflammasome in macrophages. The channel is a member of the two-pore domain potassium (K2P) channel superfamily and an emerging therapeutic target to mitigate severe inflammatory injury involving NLRP3 activation. We report the cryo-EM structure of human TWIK-2. In comparison to other K2P channels, the structure reveals a unique up conformation of Tyr111 in the selectivity filter and a SF1-P1 pocket behind the filter that could serve as a binding site for channel modulators. Density for acyl chains is present in fenestrations within the transmembrane region that connect the central cavity of the pore to the lipid membrane. Limited pharmacological tools are available for TWIK-2 despite its importance as a drug target. We show that the small molecule pimozide inhibits TWIK-2 and determine a structure of the channel with pimozide. Pimozide displaces the acyl chains and binds below the selectivity filter to block ion conduction. The drug may access its binding site via the membrane, suggesting that other hydrophobic small molecules could have utility for inhibiting TWIK-2. The work defines the structure of TWIK-2 and provides a structural foundation for development of specific inhibitors with potential utility as anti-inflammatory drugs. Significance StatementThe TWIK-2 potassium channel is a member of the two-pore domain potassium (K2P) channel superfamily and a potential therapeutic target to control severe inflammatory injury involving the NLRP3 inflammasome. We report the cryo-EM structure of the human TWIK-2 channel at 2.85 [A] resolution, revealing differences in comparison to other K2P channels. We identify that pimozide, an FDA-approved drug for Tourette syndrome, inhibits TWIK-2. A cryo-EM structure of TWIK-2 in complex with pimozide identifies its binding location and mechanism of inhibition. The work provides a structural foundation for development of specific TWIK-2 inhibitors that have potential therapeutic utility for inflammatory diseases involving NLRP3 activation.

biochemistry↗

bioRxiv2025

Effects of Inflammatory Factors on the Migration and Repair of Intestinal Mucosal Cells at Pancreaticojejunostomy Anastomosis: An Experimental Study in Beagle Dogs

ObjectiveTo investigate the effects of inflammatory factors on the migration and repair of intestinal mucosal cells at the site of pancreaticojejunostomy (PJ) anastomosis and to observe the safety and feasibility of PJ with mucosal-priority healing (PM-PJ). Materials and methodsThirty-six Beagle dogs were randomly divided into two groups: the PM-PJ group (n=18) and the control group (n=18), which included classic end-to-side invagination pancreaticojejunostomy (IPJ). Six Beagles were sacrificed on the 7th, 14th, and 21st days after surgery to obtain pancreaticojejunostomy anastomosis tissues. The primary outcomes were postoperative mortality, morbidity, and pathological changes in the anastomosis. The secondary outcomes were the expression levels of the cytokines TGF-{beta}1, IL-10, TNF-, IL-6, collagen, and -SMA. ResultsAll surgeries were successfully performed. In the study group, the incidences of anastomotic leakage and pancreatitis were 0% and 11.1% (2/18), respectively, whereas in the control group, the incidences were 5.6% (1/18) and 16.7% (3/18), respectively. The levels of serum TGF-{beta}1, IL-10, TNF-, and IL-6 were increased at all time points after surgery in both groups, and these increases were more significant at certain time points in the study group. Pathological observation revealed that the degree of anastomotic healing in the study group was greater than that in the control group at all time points. The protein expression levels of collagen I/III and -SMA in the anastomoses of both groups changed over time, and the changes were more significant at certain time points in the study group. ConclusionInflammatory factors play a positive role in the early stage of PJ anastomosis healing by stimulating collagen secretion and synthesis. PM-PJ is a safe and simple surgery with good anastomotic healing and a low incidence of complications.

animal behavior and cognition↗

bioRxiv2025

Open-source Photobleacher for Fluorescent Imaging of Large Pigment-Rich Tissues

Fluorescent imaging enables visualization of the specific molecules of interest with high contrast, and the use of multiple fluorophores in a single tissue sample allows visualization of complex relationships between biological molecules, cell types, and anatomy. The utility of fluorescent imaging in human tissue has been limited by endogenous pigments that can block the light path or emit an autofluorescence, thereby interfering with the specific imaging of target molecules. Although photobleachers have been developed to quench endogenous pigments, the lack of customizability limits their utility for a broad range of applications. Here, we present a high luminous-intensity photobleacher that is based on rigorous simulations of illumination patterns using the laws of radiation, along with the framework to maximize bleaching efficiency. This open-source project is designed to help researchers customize and scale according to the tissue types and the research goals. The photobleacher is applicable to both thin tissue slices and large-volume cleared tissue samples to enable serial three-dimensional imaging of postmortem human brain using multiplexed antibody or oligonucleotide probes. SIGNIFICANCE STATEMENTPhotobleaching is an effective technique for quenching endogenous pigments, enabling multiplexed fluorescent imaging of pigment-rich tissues, such as postmortem human samples. While many photobleaching strategies have been proposed, there is no standard guidance on how to design and use a photobleacher. This study introduces a general strategy for designing an effective, scalable, and customizable photobleacher, and proposes a workflow for properly treating tissues with the photobleacher. The technique enables high-contrast molecular visualization in tissues of various sizes, including large volumetric cleared tissues. Our framework will accelerate the quantitative understanding of human molecular anatomy and is applicable to diverse biological fields, including medical diagnostics.

neuroscience↗

bioRxiv2025

Emergent modularity in large language models: Insights from aphasia simulations

Recent large language models (LLMs) have demonstrated remarkable proficiency in complex linguistic tasks and have been shown to share certain computational principles with human language processing. However, whether LLMs internal components perform distinct functions, like semantic and syntactic processing in human language systems, remains unclear. Here, we systematically disrupted components of LLMs to simulate the behavioral profiles of aphasia--a disorder characterized by specific language deficits resulting from brain injury. Our findings showed that lesioning specific components of LLMs could replicate behaviors characteristic of different aphasia subtypes. Notably, while semantic deficits as those observed in Wernickes and Conduction aphasia, were relatively straightforward to simulate, reproducing syntactic and lexical impairments, as seen in Brocas and Anomic aphasia, proved more challenging. Together, these results highlight both parallels and discrepancies between emergent modularity in LLMs and the human language system, providing new insights into how information is represented and processed in artificial and biological intelligence.

neuroscience↗

bioRxiv2025

Coro1a promotes the multivesicular body and plasma membrane fusion by facilitating PKM2-mediated SNAP-23 phosphorylation

During the formation of endosomal pathway-dependent extracellular vesicles (EVs), intraluminal vesicles in multivesicular bodies (MVBs) fuse with the plasma membrane (PM), releasing intraluminal vesicles to produce exosomes. Soluble N-ethylmaleimide-sensitive factor attachment protein receptor (SNARE) complex, membrane fusion effector, is essential in this process. However, which SNARE complex is involved in MVB and PM fusion and how its assembly is regulated remain elusive. We have demonstrated that neddylation of Coro1a inhibits EV secretion by inducing Rab7-mediated degradation of MVBs. Here, we find that Coro1a increases EV biogenesis by promoting the assembly of SNARE complex STX-12-SNAP-23-VAMP-7 in a neddylation-independent manner. Coro1a activates PKM2 to enhance SNAP-23 phosphorylation in the presence of neddylation inhibitor MLN4924, which drives SNAP-23 to recruit more STX-12 and VAMP7, leading to increased formation of the STX-12-SNAP-23-VAMP-7 complex. Correspondingly, Coro1a-induced EV biogenesis is eliminated by PKM2 inhibitor or SNAP-23 silencing independent of neddylation. Reduced EVs from tumors due to Coro1a knockout cannot be observed in MLN4924-treated tumor mice with PKM2 inhibitor treatment either. Furthermore, Coro1a increases in tumor tissues from lung tumor patients with tumor progression, and high Coro1a indicates unfavorable survival of tumor patients, suggesting that increased Coro1a-mediated enhanced EV production from tumors accelerates tumor progression. Altogether, our data demonstrate that Coro1a facilitates EV biogenesis by promoting the assembly of STX-12-SNAP-23-VAMP-7 complex during MVB and PM fusion independent of neddylation, thereby being involved in the progression of EV-related diseases.

cell biology↗

bioRxiv2025

Plat safeguards maternally aged oocytes against programmed cell death through activating the Erk1/2 pathway

The decline in oocytes quality and developmental potential with female reproductive aging is well recognized, yet the underlying mechanisms remain insufficiently investigated. In this study, through an integrative analysis of transcriptomes and morphologies of individual oocytes from young and aged mice, morphologically defective aged oocytes are identified with distinct transcriptomic features. Further analysis demonstrates that both apoptotic and ferroptotic pathways are activated in the defective aged oocytes, and simultaneously blocking both pathways reverses the defective morphology to the largest extent. The Plat gene, which encodes tissue-type plasminogen activator (tPA), is downregulated with oocyte aging, and Plat knockdown increases oocytes susceptibility to both apoptosis and ferroptosis. Mechanistically, tPA functions as an upstream signaling molecule for Erk1/2 activation by interacting with particular phosphorylation kinases such as Alk. Consequently, Plat loss downregulates Erk1/2 pathway activity in oocytes, leading to degeneration through programmed cell death. Supplementing exogenous tPA in in vitro oocyte maturation cultures reduces defect rate of aged oocytes, thereby improving oocyte quality and developmental potential. Collectively, Plat plays a pivotal role in protecting aged mouse oocytes from programmed cell death, and tPA supplementation may serve as a potential clinical strategy to enhance oocyte quality in females of advanced maternal age.

developmental biology↗

bioRxiv2025

Intense oocyte competition builds the female reproductive reserve in mice

During the process of ovariogenesis, more than two-thirds of germ cells are sacrificed to enhance the quality of the remaining oocytes. But the detail process of selection is not completely understood in mammals. Here, by creating a high resolution 4- dimensional ovariogenesis imaging system, we recorded the progress of oocyte fate determination in live mouse ovaries, and discovered an oocyte competition mechanism that determines the survival of oocytes. We found that dominant oocytes catch and absorb the cell debris from sacrificed oocytes to enrich their cytoplasm for survival. Single-cell sequencing demonstrated that this competition follows a classic autophagy- driven model. Blocking competition by suppressing autophagy resulted in an enlarged pool of survived oocytes. However, these oocytes lacking competition were unable to fully develop and contribute to fertility. Our study suggests that mammals have evolved a unique intensive competition system to enhance oocyte quality, necessary to support their long reproductive lifespan.

developmental biology↗

bioRxiv2025

Integrating bulk and single cell RNA-seq refines transcriptomic profiles of individual C. elegans neurons

Neuron-specific morphology and function are fundamentally tied to differences in gene expression across the nervous system. We previously generated a single cell RNA-seq (scRNA-Seq) dataset for every anatomical neuron class in the C. elegans hermaphrodite. Here we present a complementary set of bulk RNA-seq samples for 52 of the 118 canonical neuron classes in C. elegans. We show that the bulk RNA-seq dataset captures both lowly expressed and noncoding RNAs that are not detected in the scRNA-Seq profile, but also includes false positives due to contamination by other cell types. We present an analytical strategy that integrates the two datasets, preserving both the specificity of scRNA-Seq data and the sensitivity of bulk RNA-Seq. We show that this integrated dataset enhances the sensitivity and accuracy of transcript detection and differential gene analysis. In addition, we show that the bulk RNA-Seq data set detects differentially expressed non-coding RNAs across neuron types, including multiple families of non-polyadenylated transcripts. We propose that our approach provides a new strategy for interrogating gene expression by bridging the gap between bulk and single cell methodologies for transcriptomic studies. We suggest that these datasets advance the goal of delineating the mechanisms that define morphology and connectivity in the nervous system.

genomics↗

bioRxiv2025

Follicular mural granulosa cells stockpile glycogen to fuel corpus luteum pre-vascularization

The corpus luteum (CL) arises from the luteinization of follicular granulosa cells (GCs) and theca cells, marked by rapid progesterone elevation and angiogenesis. Intriguingly, angiogenesis lags behind progesterone elevation, creating an avascular phase during which luteal cells must fuel intensive steroidogenesis without perfusion. How the avascular CL meets this energetic demand remains a mystery. Here, we reveal a novel cellular adaptive mechanism-GC energy storage (GCES)-that resolves this enigma. We demonstrate that upon luteinization initiation, GCs enter a metabolically quiescent state yet enhance glucose uptake via SLC2A1, converting the glucose into glycogen through the hCG (LH)-MAPK-RUNX1-Insulin signaling axis. Catabolism of this glycogen reserve supplies the energy required for the avascular CL, ensuring normal luteogenesis. GCES is evolutionarily conserved across species. Genetic or pharmacological disruption of GCES or glycogenolysis induces luteal insufficiency, whereas timely glucose administration enhances GCES, improving luteal function and optimize reproductive outcome in both mouse and ovine models. In human study, orally intake of glucose post-hCG significantly augments GCES and enhances progesterone production in women. These results advance luteal physiology by uncovering a universal reproductive principle with direct clinical implications.

developmental biology↗