Biology subjects

Wu, H.

Publications and source records attributed to Wu, H..

At least 109 records · Page 6Linked to original sources

bioRxiv2025

STEAP4+ neutrophils: a promising circulating biomarker for lung metastasis

As the leading contributor to cancer-related mortality, metastasis often evades detection until advanced stages, underscoring the critical need for early predictive biomarkers. Neutrophils are naturally circulating sentinels that have been implicated in pioneering pre-metastatic niche formation in distant organs. Nevertheless, their heterogeneity within evolving metastatic microenvironments remains poorly characterized. Here, through dynamically delineating neutrophil subsets via single-cell transcriptomics, we identified a conserved feature of lung metastasis in breast cancer and other cancer models. Among the core genes, a cell surface marker, STEAP4, was selected and validated to indicate lung metastases at both RNA and protein levels. In both humans and mice, these STEAP4+ neutrophils were detectable not only in lung metastatases but also in the circulation. Clinically, the abundance of circulating STEAP4+ neutrophils robustly discriminates patients with lung metastasis from those with localized primary tumor. Our findings uncover STEAP4+ neutrophils as a promising biomarker and lay the groundwork for a non-invasive, blood-based diagnostic strategy for metastatic disease.

cancer biology↗

bioRxiv2025

A near-complete lamprey genome illuminates ancestral vertebrate innovations

The origin of vertebrates is characterized by a suite of phenotypic innovations, yet the underlying genetic mechanisms remain poorly understood. As a living representative of jawless vertebrates, the lamprey serves as a pivotal model for investigating the genomic basis of early vertebrate evolutioin. Here, we report a near telomere-to-telomere (T2T) genome assembly of the reissner lamprey (Lethenteron reissneri), generated from sperm DNA that is not subject to programmed genome rearrangement. The 1.25 Gb assembly resolves over 97% of chromosome sequences into single contigs, enabling reconstruction of previously inaccessible genomic regions. Centromeres display highly diversified, lamprey-specific repeat units and structural architectures, whereas telomeres contain both conserved and lineage-specific satellite repeats. Deep transcriptomic profiling across representative organs and developmental stages substantially improved genome annotation. Comparative genomic analyses revealed a major expansion of 1,562 gene families at the base of the vertebrate lineage, and they are significantly enriched for functions related to neural development, skeletal formation, and cardiac function, echoing the known phenotypic innovations in vertebrates. Notably, the CDH2 gene family underwent vertebrate-specific copy number expansion and acquired conserved cis-regulatory elements (CREs), highlighting its potential role in shaping the early vertebrate circulatory system. Histological analyses and functional knockout experiments demonstrated that one CDH2 paralog (CDH2_H) is essential for lamprey heart development and chamber formation, playing a critical role in the emergence of the closed circulatory system in early vertebrates. This high-quality lamprey genome provides a foundational resource for dissecting the genetic basis of key innovations that shaped vertebrate evolution.

genomics↗

bioRxiv2025

Decoding the interactome for Cyclic-di-AMP-producing enzyme diadenylate cyclase (DacA)

Diadenylate cyclase (DacA) synthesizes the second messenger cyclic di-AMP (c-di-AMP), which regulates essential cellular processes across many Gram-positive and select Gram-negative bacteria/archaeal lineages. Although DacA is known to interact with regulators such as GlmM and CdaR, the breadth and functional relevance of its interactome remains poorly defined. Our study seeks to identify novel protein-protein interactions to further elucidate their unknown regulatory mechanisms and cellular roles. Using Streptococcus mutans as a model, we engineered a Flag-tagged strain (DacA-FLAG) and then performed co-immunoprecipitation under non-crosslinked and crosslinked conditions followed by mass spectrometry. We identified 22 candidates interacting proteins in non-crosslinked samples, 18 in crosslinked samples, and 6 shared between conditions. Selected partners were validated in vivo using split luciferase complementation. Notably, SMU_723 emerged as a key binding partner. AlphaFold-guided modeling predicated a direct DacA and SMU_723 interaction interface involving threonine 147, glutamine 148, and threonine 149 in DacA . Site-directed mutagenesis of these residues impaired binding, confirming their critical role. An SMU_723 deletion phenocopied a dacA deletion strain, sharing prolonged lag phase, aberrant cell morphology, reduced acid production and acid tolerance, impaired sorbitol metabolism, decreased colonization in a Drosophila model, and delayed growth upon calcium stimulation. These shared phenotypes suggest a functional and possibly regulatory link between DacA and SMU_723. Given SMU_723 sequence homology consistent with a calcium transporter, these data suggest that the DacA-723 interaction contributes to calcium homeostasis and/or calcium-responsive signaling. Collectively, our findings expand the DacA interaction network and implicate calcium transport in c-di-AMP-mediated regulation in S. mutans. ImportanceMapping the DacA interactome reveals how environmental and intracellular cues tune c-di-AMP signaling to control stress adaptation, ion balance, and virulence traits in S. mutans. By identifying new DacA-associated proteins and validating SMU_723 as a previously unrecognized interactor with genetic and phenotypic linkage to DacA, this study provides new insights into the mechanistic framework for c-di-AMP regulation in S. mutans. The connection between DacA and a putative calcium transporter highlights a plausible axis that couples second-messenger signaling to calcium homeostasis, with implications for biofilm physiology and pathogenesis. These insights open new avenues to therapeutically modulate c-di-AMP pathways.

microbiology↗

bioRxiv2025

Matrix Metalloproteinase (MMP) inhibition rescues endothelial glycocalyx damage and reduces neutrophil infiltration in sepsis-associated acute kidney injury

Endothelial glycocalyx (eGlx), a carbohydrate-rich endothelial coat, maintains vascular homeostasis, and its disruption contributes to several vascular diseases. We previously identified matrix metalloproteinase (MMP) 2 and 9-mediated eGlx shedding as a key mechanism in human glomerular endothelial cell (GEnC) damage and kidney dysfunction in diabetes. Here, we sought to determine whether this mechanism contributes to renal and systemic microvascular endothelial cell injury in sepsis-AKI. Sepsis-AKI was induced in mice by lipopolysaccharide (LPS) injection. Confocal microscopy demonstrated glomerular and peritubular eGlx damage, and increased circulating SDC4 demonstrated systemic eGlx shedding. These were associated with enhanced mRNA expression of eGlx components (syndecans 1 and 4) and endothelial inflammatory markers, Intercellular and Vascular Cell Adhesion Molecules (ICAM and VCAM) in the kidney. Additionally, sepsis-AKI markers, serum creatinine and urea, were increased. We found that renal and circulating MMP9, but not MMP2, levels were raised in sepsis-AKI. Moreover, MMP9 staining colocalises with neutrophil, endothelial and mesangial staining in glomeruli in sepsis-AKI. Treatment with MMP2 and 9 inhibitor 1, 1h before LPS injection, prevented glomerular, peritubular and systemic eGlx damage in sepsis-AKI. MMP inhibition also attenuated glomerular leucocyte numbers in sepsis-AKI. We confirmed increased MMP9 activity, shedding of eGlx syndecan 1 and elevated angiopoietin 2 levels, an endothelial damage marker, in sepsis-AKI in humans. Moreover, we used human glomerular endothelial cells (GEnC) in vitro to demonstrate that human sepsis-AKI serum directly damages GEnC eGlx. Our studies confirm that MMP-mediated eGlx damage is a key contributor to renal and systemic microvascular dysfunction in sepsis-AKI and represents a potential therapeutic target for protecting the microvasculature.

cell biology↗

bioRxiv2025

Molecular Surveillance Identifies Evidence of Getah Virus (GETV) in Mosquito Vectors in Alabama, USA

The Getah virus (GETV) is a mosquito-borne RNA virus in the Togaviridae family and the Alphavirus genus, associated with severe disease outbreaks in livestock across Asia-Pacific regions. Since its first isolation in Malaysia in 1955, GETV has been reported in Eurasia and the South Pacific, yet documented cases in the United States remain exceptionally rare, leaving major gaps in regional vector competence and surveillance data. To evaluate the potential of local mosquito populations as GETV carriers, field collections were conducted in Montgomery and Pike Road neighborhoods of Alabama from 2023 to 2024, capturing multiple mosquito species for molecular screening. Initial real-time qPCR assays on 200 pooled and individual samples suggested that approximate 30% of specimens demonstrated possible GETV carriage potential. To validate viral presence, two distinct primer sets were designed to amplify viral genome fragments. Mosquito RNA was reverse-transcribed into cDNA, followed by conventional PCR. The first PCR, targeting [~]280 bp, produced single or multiple amplicon bands in 32% of samples via gel electrophoresis. These positive cDNAs were re-amplified with a second primer pair targeting a [~]430 bp fragment from a separate genomic region, yielding confirmatory bands in 30% of specimens. Amplified products were purified and Sanger sequenced, revealing approximate 95% nucleotide similarity to the wild-type GETV reference genome. This study delivers the first field-based molecular evidence supporting GETV detection in Alabama mosquitoes, signaling either localized emergence or potential introduction of the virus. These findings underscore the need for expanded vector competence profiling, arboviral surveillance, and livestock disease preparedness in the southeastern United States, strengthening both public health readiness and state-level vector monitoring strategies.

microbiology↗

bioRxiv2025

Single-cell transcriptomic dynamics exposes hidden survival trajectory under antibiotic treatment

Heterogeneity plays a major role in bacterial resistance to antibiotic treatment while the mechanism at single-cell level is largely unknown. Here, we employed a robust integration of bulk and bacterial single-cell RNA-seq (scRNA-seq) to uncover how individual cells of Acinetobacter baumannii reorganise the heterogenous transcriptome in response to antibiotic. Using polymyxin as a representative, bulk RNA-seq showed canonical envelope- and efflux-centred responses but obscured underlying heterogeneity. Single-cell profiling resolved these averages into discrete subpopulations whose abundances shifted with concentration and time. Specifically, in early time an envelope-stress programme predominated survival at the low concentration, whereas an outer-membrane repair/efflux programme dominated survival at the high concentration. These patterns revealed structured and time-resolved heterogeneity, highlighting an ingenious bacterial stress responsive strategy. Through trajectory inference, we further revealed a concentration-dependent bifurcation of cell fates: low-concentration treated cells detoured through a transient stress state and rejoined growth, whereas high-concentration treated survivors diverted into a slow-growing, tolerant branch. Perturbing marker genes from these programmes altered fitness eventually and rapidly increased permeability, depolarisation and reactive-oxygen burden, linking state to survival capability. Collectively, we map a dynamic, concentration-structured landscape of antibiotic responses at the single-cell level, revealing diverse survival trajectories that are obscured in conventional population-averaged analyses. Our developed single-cell based framework revealed tolerant bacterial cells with rewiring of the transcriptional landscape, causing emergence of antibiotic resistance. Importantly, these findings urge precision antimicrobial therapy in patients to minimise emergence of antibiotic resistance.

microbiology↗

bioRxiv2025

Optimizing marker density for maximizing the accuracy of genomic prediction and heritability estimates in three major North American and European spruce species

Genomic prediction, also called genomic selection (GS), is being increasingly used in tree breeding with aim to accelerate genetic gains by shortening the long breeding cycles. However, high genotyping costs remain a challenge. This study aimed to determine the optimal marker density in genome coverage, to maximize GS accuracy and precision of heritability estimates for growth and wood quality traits. Thousands of SNPs representative of the exome of three major spruce species were used: 18,275 SNPs for black spruce (representing 10,894 distinct gene loci), 11,328 SNPs for white spruce (8647 gene loci), and 116,765 SNPs for Norway spruce (20,695 gene loci). For each species, a similar experimental design was used with related full-sib families replicated on two sites, and GBLUP prediction models were developed. The effect of varying the number of SNPs was examined by re-sampling subsets from 500 to 100,000 SNPs. Results indicated that plateaus in heritability estimates were reached as the marker density increased, stabilizing between 4000 to 8000 SNPs for a spruce genome size of around 2000 centimogans, a trend consistent across all traits and species. Predictive ability and prediction accuracy both increased with the number of SNPs up to a similar level, beyond which further improvements were marginal. Such optimal marker density should be financially attainable for most spruce breeding programs, striking a balance between the need for maximizing accuracy and that for minimizing genotyping costs. These findings should support the further deployment of GS in conifer breeding programs, with high selection precision and by reducing the financial burden of very high-density SNP coverage, even for conifers characterized by large giga-genomes.

genomics↗

bioRxiv2025

Steady-state epithelial apical flatness is characterized by MLCK morphodynamics and asynchronous Ca2+ oscillations, but not underlying ECM geometry

The canonical simple epithelium is a flat sheet-like tissue of horizontally packed cells. While the basal surface is delineated by the basement membrane of extracellular matrix (ECM), little is known about how a flat apical surface is maintained, or if apical/basal dynamics are coordinated. The current study tests the role of the apical domain, to define mechanisms involved in maintaining a flat apical geometry in an epithelium. When the basal geometry is modulated, Madin-Darby Canine Kidney (MDCK) cells adjust their morphology to maintain an overall apical flatness of the confluent layer. Pharmacological and transgenic disruption of non-muscle myosin ATPase, and MLCK activity results in an uneven apical structure, and overall loss of the flat geometry typical of a confluent epithelium. Surprisingly, transgenic experimentation showed that forces maintaining individual MDCK cell flatness are cell-autonomous. Finally, Ca2+ imaging reveals an asynchronous calcium flux across a confluent epithelium, suggesting a myosin II-mediated mechanism for maintaining a flat apical architecture. Our results highlight that apical/basal cellular surfaces may not be tightly coordinated, but rather independently regulated. This study provides a new paradigm for how apical flatness is regulated at steady state. Impact StatementO_LIHow surface flatness of an epithelium is established and maintained is unknown; the data reveal that apical flatness is controlled independently from basement membrane geometry, and require balancing of myosin II morphodynamics. C_LI

cell biology↗

bioRxiv2025

SCAPE: An AI-Driven Platform for Comprehensive Single-Cell Data Analysis

Single-cell RNA sequencing (scRNA-seq) has transformed the study of cellular heterogeneity, but downstream analysis remains fragmented and technically demanding. Current pipelines often lack analytical diversity, require programming expertise, and offer limited integration of advanced methods. To address these challenges, we developed SCAPE, an AI-driven automated and interactive platform that unifies multi-omics, multi-resource, and multi-modal single-cell data analysis. SCAPE provides platform-independent installation, customizable workflows, and integration of R- and Python-based tools. Beyond Seurat and Scanpy, it incorporates modules for transcription factor and pathway inference, pseudotime trajectory reconstruction, spatial transcriptomics deconvolution, and cell-cell communication analysis. To demonstrate SCAPE, we curated a unified atlas of lung cancer progression in human patients and mouse models, spanning primary tumors and metastatic sites. The platform enabled harmonized integration, regulatory program inference, and spatial mapping, revealing conserved epithelial programs that promote metastatic seeding and organ-specific adaptations driven by microenvironments. Collectively, SCAPE offers an accessible and comprehensive framework for single-cell analysis, providing new insights into cancer progression and broad utility across biological systems.

cancer biology↗

bioRxiv2025

Differential Tissue Coupled Powering for Battery-Free Injectable Electroceuticals

Electroceutical implants that deliver targeted neural stimulation have shown therapeutic potential for a wide range of neurological and peripheral disorders, yet wirelessly powering ultra-miniaturized, fully injectable systems remains a critical challenge. Here we report a Thread-like Injectable Neural TechnologY (TINY), powered via a differential tissue-coupled powering (DTCP) scheme. DTCP employs mid-frequency differential potentials applied across external electrodes on a compact, wearable transmitter to deliver energy through tissue to an ultra-miniaturized, thread-like implant that integrates a custom ASIC and PEDOT-coated receiver and stimulation electrodes. Benchtop experiments in agar phantoms characterize the power-transfer efficiency (PTE) and reveal that PTE increases with implant length while maintaining strong tolerance to angular misalignment. In vivo tests in rat hindlimbs further demonstrate wireless activation of the sciatic nerve through tissue at centimeter-scale depths, confirming effective transcutaneous energy delivery for neurostimulation. A 20-day implantation study shows stable positioning of the device with minimal tissue response, indicating excellent chronic compatibility. These findings address long-standing challenges in wirelessly powering injectable electroceuticals and establish DTCP as a scalable and alignment-robust powering strategy for future minimally invasive neuromodulation therapies.

bioengineering↗

bioRxiv2025

The Structural Basis of Pacs1-Wdr37 Complex Assembly and Stability

Phosphofurin acidic cluster sorting protein 1 (Pacs1) is a multidomain adaptor proposed to bind transmembrane cargo proteins to facilitate their intracellular trafficking. Pacs1 also forms a complex with WD-repeat protein 37 (Wdr37), which is essential for lymphocyte homeostasis. Despite numerous proposed binding partners, a validated structure for Pacs1-containing protein complexes is lacking. Here, we present the cryo-electron microscopy structure of the Pacs1-Wdr37 complex. Pacs1 binds Wdr37 through a conserved interface within its furin-binding region (FBR), the domain previously linked to cargo recognition. This interaction stabilizes Wdr37 and is critical for the expression of both proteins. A gain-of-function mutation in PACS1 (R203W) causes a highly penetrant neurodevelopmental syndrome. This pathogenic mutation lies on a solvent-exposed surface of the FBR and does not disrupt complex formation. Instead, Pacs1-R203W remains dependent on Wdr37 for stability and its levels can be reduced through targeted Wdr37 proteolytic degradation. Structural homology of the FBR to synaptotagmin C2 domains reveals a previously unrecognized ability of Pacs1 to bind negatively charged phospholipids through a unique positively charged cleft. Together these findings define the structural basis for Pacs1-Wdr37 complex assembly and stability, present potential strategies for Pacs1-mediated neurodevelopmental disease, and suggest novel Pacs1 functions in membrane association.

biochemistry↗

bioRxiv2025

When splicing is not all or none: Implications for variant classification

Variants with intermediate functional effects--those that neither eliminate nor fully maintain normal gene function--represent an underrecognized source of genetic complexity and constitute a grey zone that challenges variant classification. Here, we address this issue using GT>GC (+2T>C) 5' splice-site variants as a tractable model, as approximately 15% of such substitutions retain variable amounts of wild-type (WT) transcript. Using residual WT transcript as a quantitative readout, we first show that disease-associated GT>GC variants known to generate substantial WT transcript (for example, SPINK1 c.194+2T>C, HBB c.315+2T>C, and BRCA2 c.8331+2T>C) consistently complicate classification efforts. We then carried out a locus-wide assessment of all 26 GT>GC substitutions in CFTR, applying SpliceAI delta donor-loss scores as an initial screen and cross-checking classifications in expert-curated database. This evaluation indicated that three variants with low or intermediate SpliceAI scores are likely to retain WT transcript. Minigene analyses of four selected CFTR variants, together with additional examination of a BAP1 GT>GC variant with conflicting clinical interpretations, illustrate the methodological challenges in predicting and experimentally quantifying residual WT transcript. These results emphasize that (i) in silico predictors cannot reliably discriminate between complete and partial splice disruption and (ii) experimental systems differ in their ability to detect subtle splicing outcomes. Overall, our integrative analysis shows that GT>GC variants generating appreciable WT transcript exemplify a broader class of intermediate-effect alleles that complicate both computational prediction and experimental assessment, underscoring the need for classification frameworks that incorporate quantitative functional data and better capture the continuum of variant effects.

genetics↗

bioRxiv2025

Structural basis of HSV-1 DNA replication origin-binding protein UL9

The herpesvirus DNA replication machinery comprises a battery of viral enzymes that orchestrate viral genome synthesis. In herpes simplex virus type 1 (HSV-1), the machinery consists of seven essential components, including the origin-binding protein UL9, the single-stranded DNA (ssDNA)-binding protein ICP8, the heterodimeric DNA polymerase complex UL30-UL42, and the heterotrimeric helicase-primase complex UL5-UL8-UL52. UL9, a superfamily 2 (SF2) helicase, functions as a dimer that specifically recognizes replication origins and unwinds duplex DNA to initiate replication. Furthermore, UL9 recruits the replication machinery through interactions with viral components and engages cellular proteins that regulate its function. However, the molecular mechanisms underlying UL9s multifunctionality remain incompletely understood due to the lack of structural information. Here, we present cryo-electron microscopy structures of UL9 in both apo and DNA-bound states. Together with biochemical and enzymatic assays, we elucidate the molecular basis of UL9 dimerization, origin recognition and allosteric regulation by ICP8.

microbiology↗

bioRxiv2025

Chronic sensing of host-derived lipids is an all-in-one signal that primes and activates NLRP3.

Activation of the NLRP3 inflammasome leads to the production of bioactive interleukin (IL)-1{beta} fostering atherosclerosis. The current dogma is that NLRP3 must be first primed by microbial stimuli, known as pathogen-associated molecular patterns (PAMPs), and then activated by either microbial or host-derived inflammatory cues. The mechanism that controls NLRP3 functioning in the context of non-communicable diseases lacking overt microbial infections remains debated. Here, we show that chronic exposure to atherosclerosis-associated oxidized phospholipids (oxPLs) simultaneously primes and activates NLRP3 independently of microbial cues. Mechanistically, chronic exposure to host-derived oxPLs activate the transcription factor NRF2, which is necessary and sufficient to prime and activate NLRP3 in a PAMP-independent manner. NRF2 chronic activation drives oxidized mitochondrial DNA to activate NLRP3. Ex vivo analyses of atherosclerotic plaques in mice and humans identify a population of monocytes-derived macrophages which activates NRF2 and expresses IL-1{beta}. Overall, our data point to oxPL-dependent NRF2 activation as an all-in-one signal necessary and sufficient to prime and activate NLRP3, sustaining atherogenesis.

immunology↗

bioRxiv2025

The alternated brain states in resting state after immoral decisions

Studies have shown that the pattern of the brain in tasks can be effectively predicted from resting brain features. However, few studies explore how task could, in turn, influence resting state connectivity. This work attempts to understand this through the lens of immoral decisions. Using resting-state and task-state fMRI data collected before, during, and after an information-passing task involving dishonest choices with rewards, we employed the Hidden Markov Model (HMM) to capture the changes in the brain dynamics state. First, the HMM results identified 4 intrinsic brain states across both resting scans and task scans, including one reward network (state 1) and one control network (state 3). The reward network are associated with high dishonesty, while the control network are associated with low dishonesty. Importantly, task engagement in immoral behavior altered the post-task brain state. As participants engaged in persistent dishonesty, the network reconfigures itself to priorities the reward network and suppress the control network. Such suppression persists beyond the immediate task timeframe and leaves lingering signatures in the post-task resting scan. Contrary to the view of resting-state as a static baseline, our analysis showed the "non-resting" nature of post-task resting scans, where dishonesty could have an "after-effect" on neural dynamics. Together, these findings suggest that the post-moral decision brain operates not as a static system but as a set of dynamically shifting states, whose adaptive trajectories may underlie the lasting effect of decision behavior in the prior task.

neuroscience↗

bioRxiv2025

Chronic kidney disease exacerbates hyperlipidemia and atherosclerosis via miR-148a-3p targeting SIK1/AMPKα1 in liver

BackgroundCardiovascular complications are the leading cause of death in patients with chronic kidney disease (CKD). As a major risk factor for atherosclerotic cardiovascular disease (ASCVD), hyperlipidemia is a common sequela of CKD, which is linked to increased lipid synthesis, impaired lipoprotein clearance, and maladapted reverse cholesterol transport. Because exosomes can transport miRNAs to modulate intercellular and tissue communication, we hypothesized that exosomal miRNAs can act as endocrine-like molecules to modulate the CKD-associated hyperlipidemia and ASCVD. MethodsSmall RNA-seq and qPCR were used to determine the differential plasma level of exosomal miR-148a-3p in ASCVD patients with and without CKD. RNA-seq and in silico analysis were used to establish the regulation of lipid metabolism via miR-148a-3p/salt-inducible kinase 1 (SIK1)/AMP-activated protein kinase alpha 1 subunit (AMPK1) in the liver. Inhibition of miR-148a-3p or overexpression of SIK1/AMPK1 in ApoE-/- mice with 5/6 nephrectomy was used to elucidate the role of the miR-148a-3p/SIK1/AMPK1 axis in CKD-related hyperlipidemia and atherosclerosis. ResultsThe plasma level of exosomal miR-148a-3p was significantly elevated in patients with ASCVD and CKD (ASCVD/CKD) and ApoE-/- mice with 5/6 nephrectomy. Via circulating exosomes, kidney-generated miR-148a-3p was delivered to the liver, where it targeted SIK1/AMPK1 transcripts, thereby upregulating SREBP2/PCSK9 and reciprocally downregulating LDLR. Levels of SIK1 and AMPK1 were decreased in hepatocytes transfected with miR-148a-3p or treated with plasma exosomes from ASCVD/CKD patients, with attendant SREBP2 activation and attenuated LDL-C binding. The decreased LDL-C binding was rectified by SIK1/AMPK1 or LNA-miR-148a-3p overexpression. LNA-miR-148a-3p or AAV8-SIK1/AMPK administration in 5/6 nephrectomy/ApoE-/- mice significantly ameliorated hyperlipidemia and atherosclerosis. ConclusionIn ASCVD/CKD patients and nephrectomy/ApoE-/- mice, kidney-originating miR-148a-3p targeted hepatic SIK1/AMPK1 mRNA. This exosome-mediated endocrine effect upregulated SREBP2/PCSK9 and reciprocally reduced LDLR level, which elevated plasma LDL-C level and exacerbated ASCVD. These findings underscore a kidney-liver-artery axis involved in cardiovascular-kidney-metabolic syndrome.

pathology↗

bioRxiv2025

A knowledge-guided approach to recovering important rare signals from high-dimensional single-cell data

Single-cell transcriptomic data are high-dimensional, with many genes profiled in each cell. Dimensionality reduction is routinely applied to improve interpretability, remove noise and redundancy, and enable visualization. Most existing methods aim at preserving the most prominent data properties, which can lead to omission of rare but important signals. Here we propose a novel framework that uses knowledge-derived genes of interest to guide dimensionality reduction, which can help cluster rare cells and separate highly similar cell sub-populations. We demonstrate the utility of our framework in identifying endocrine cell subtypes in the pancreatic islet, highly similar hematopoietic sub-populations, and rare senescent cells.

bioinformatics↗

bioRxiv2025

Integrated analysis reveals neuro-immune pathway in the central nervous system that supports SGLT2i`s protective effects in treatment of cardiac remodeling

BackgroundDespite growing evidence of sodium-dependent glucose transporters 2 inhibitors (SGLT2i) improving heart failure, their mechanisms remain unclear. This study explored the effects of empagliflozin (EM) on sympathetic nerve activity and potential neuroimmune pathways. MethodsSingle-nucleus RNA sequencing (snRNA-seq) was performed in hypothalamic tissue of a DOCA-salt mouse model to screen for cellular changes. Validation of relevant mechanisms in DOCA-salt and high-salt diet (HSD) mouse models. Additionally, clinical data from 1,189 hospitalized heart failure patients were analyzed to evaluate the translational relevance of the experimental findings. ResultsEM treatment was associated with protective effects against cardiac remodeling in both DOCA-salt and HSD mice. Both models exhibited sympatho-excitation and neuronal hyperactivity in pre-autonomic brain regions, which appeared to be blunted by EM co-treatment. snRNA-seq analysis suggested that cellular interplay among vascular cells, microglia, and inhibitory neurons might be involved in these processes. Specifically, high-salt intake was linked to peripheral immune activation, including lymphocytosis and elevated plasma interferon-{gamma}, which potentially mediated microglial state transitions. EM might counteract the disease-associated upregulation of protein ubiquitination. Clinically, SGLT2i use was significantly associated with reduced lymphocyte counts in specific patient subgroups. ConclusionsEmpagliflozin may attenuate cardiac remodeling caused by high sodium intake through neuroimmune effects by restoring microglial homeostasis and inhibiting sympathetic nerve activity.

molecular biology↗