Biology subjects

Lin, H.

Publications and source records attributed to Lin, H..

At least 109 records · Page 6Linked to original sources

bioRxiv2025

A Hyperbolic Discrete Diffusion 3D RNA Inverse Folding Model for functional RNA design

Generative design of functional RNAs presents revolutionary opportunities for diverse RNA-based biotechnologies and biomedical applications. To this end, RNA inverse folding is a promising strategy for generatively designing new RNA sequences that can fold into desired topological structures. However, three-dimensional (3D) RNA inverse folding remains highly challenging due to limited availability of experimentally derived 3D structural data and unique characteristics of RNA 3D structures. In this study, we propose RIdiffusion, a hyperbolic denoising diffusion generative RNA inverse folding model, for 3D RNA design tasks. By embedding geometric features of RNA 3D structures and topological properties into hyperbolic space, RIdiffusion efficiently recovers the distribution of nucleotides for targeted RNA 3D structures based on limited training samples using a discrete diffusion model. We perform extensive evaluations on RIdiffusion using different datasets and strict data-splitting strategies and the results demonstrate that RIdiffusion consistently outperforms baseline generative models for RNA inverse folding. This study introduces RIdiffusion as a powerful tool for the generative design of functional RNAs, even in structure-data-scarce scenarios. By leveraging geometric deep learning, RIdiffusion enhances performance and holds promise for diverse downstream applications.

bioinformatics↗

bioRxiv2025

Benchmarking Pre-trained Genomic Language Models for RNA Sequence-Related Predictive Applications

RNA plays a pivotal role in diverse cellular functions across organisms. Developing computational algorithms for RNA sequence related questions is highly valuable. Recently, genomic language models (gLMs) with pre-training have emerged, offering flexibility for various downstream prediction tasks. However, comprehensive and fair evaluations of gLMs are lacking. In this study, we benchmark eight gLMs on prediction tasks covering four RNA processes, highlighting their strengths and limitations. While gLMs excel in performance overall, the larger model is not always better. Interestingly, models that integrate biological information consistently perform well in related tasks. Notably, gLMs demonstrate superior performance with limited training data, whereas task-specific methods achieve comparable performance with better computational efficiency when sufficient training data is available. Finally, we provide recommendations for model selection in different scenarios. These evaluation results underscore the potential of gLMs and suggest areas for future improvement.

genomics↗

bioRxiv2025

Spatial and single-cell expression analyses reveal complex expression domains in early wheat spike development

Wheat is important for global food security and understanding the molecular mechanisms driving spike and spikelet development can inform the development of more productive varieties. In this study, we integrated single-molecule fluorescence in situ hybridization (smFISH) and single-cell RNA sequencing (scRNA-seq) to generate an atlas of cell clusters and expression domains during the early stages of wheat spike development. We characterized spatiotemporal expression of 99 genes by smFISH in 48,225 cells at the early transition, late double ridge, and floret primordia stages. These cells were grouped into 21 different expression domains, including four in the basal region of the developing spikelets and three different meristematic regions, which were consistent across spikelets and sections. Using induced mutants, we revealed functional roles associated with the specific expression patterns of LFY in intercalary meristems, SPL14 in inflorescence meristems, and FZP in glume axillae. Complementary scRNA-seq profiling of 26,009 cells from W2.5 and W3.5 stages identified 23 distinct cell clusters. We used the scRNA-seq information to impute the expression of 74,464 genes into the spatially anchored smFISH-labelled cells and generated a public website to visualize them. We used experimental and imputed expression profiles, together with co-expression studies and correlation matrices, to annotate the scRNA-seq clusters. From co-expression analyses, we uncovered genes associated with boundary genes TCP24 and FZP, as well as the meristematic genes AGL6 and ULT1. The smFISH and scRNA-seq studies provided complementary tools for dissecting gene networks that regulate spike development and identifying new co-expressed genes for functional characterization.

plant biology↗

bioRxiv2025

A pathological phosphorylation pattern enhances taucooperativity on microtubules and facilitates tau filamentassembly

Phosphorylation plays a crucial role in both normal and disease processes involving the microtubule-associated protein tau. Physiologically, phosphorylation regulates taus subcellular localization within neurons and is involved in fetal development and animal hibernation. However, abnormal phosphorylation of tau is linked to the formation of neurofibrillary tangles (NFTs) in various human tauopathies. Interestingly, the patterns of tau phosphorylation are similar in both normal and abnormal processes, leaving unclear whether phosphorylated tau retains its functional role in normal processes. The relationship between tau phosphorylation and NFT assembly in tauopathies is also still debated. To address these questions, we investigated the effects of tau phosphorylation on microtubule binding, cooperative protein envelope formation, and NFT filament assembly relevant to tauopathies. Consistent with previous results, our findings show that tau phosphorylation decreases taus overall affinity for microtubules, but we reveal that phosphorylation more dramatically impacts the cooperativity between tau molecules during tau envelope formation along microtubules. Additionally, we observed that the specific pattern of phosphorylation, rather than overall phosphorylation level, strongly impacts the assembly of tau filaments in vitro. Our results reveal new insights into how tau phosphorylation impacts taus physiological roles on microtubules and its pathoconversion into NFTs.

biochemistry↗

bioRxiv2025

Targeting Runx1 protects against heart failure with preserved ejection fraction

Heart failure with preserved ejection fraction (HFpEF) is a public health problem and an elusive illness for which there are few treatment options. HFpEF is a systemic condition with a broad phenotype including diastolic dysfunction, pulmonary oedema, exercise intolerance, and left ventricular (LV) hypertrophy, collectively resulting in enhanced morbidity and mortality. Master-regulator transcription factor RUNX1 has recently been identified as a mediator of pathological changes in many cardiac diseases, however its role in HFpEF was unknown. Here we show that inhibition of Runx1 limits adverse cardiac remodelling in a clinically relevant mouse model of HFpEF. Cardiomyocyte-specific tamoxifen-inducible Runx1-deficient mice with HFpEF are protected, with preservation of diastolic function, and attenuation of pulmonary oedema, exercise intolerance, and hypertrophy. Furthermore, targeting Runx1 in HFpEF by using gene transfer or small molecule inhibitors improves diastolic function, both in female and male mice. Overall, our research enhances our understanding of RUNX1 in cardiac disease and demonstrates a novel translational target for the treatment of HFpEF. Keywords: Heart failure with preserved ejection fraction, metabolic heart failure, diastolic dysfunction, hypertrophy, pulmonary oedema, exercise intolerance CLINICAL PERSPECTIVEHeart failure (HF) is a leading cause of death world-wide and traditionally divided into different subtypes according to cardiac ejection fraction (EF). In contrast to HF with reduced EF (HFrEF), there are limited treatment options for HF with preserved EF which is of considerable concern given that HFpEF is projected to become the dominant HF subtype in the future 1. RUNX1 has been demonstrated to play an important role in the development of many cardiac and non-cardiac diseases. As a result, the potential for RUNX1 inhibitors as therapeutic agents across various conditions has become increasingly evident. In this study we established the therapeutic potential of targeting RUNX1 in the context of HFpEF. Targeting RUNX1 in cardiomyocytes markedly attenuates the development of the HFpEF phenotype and therefore this novel translational therapeutic target has great potential to address one of the biggest challenges in cardiac research.

physiology↗

bioRxiv2025

Battery-powered Wearable Utilizing Flexible Printed Circuit-based Organic Electrochemical Transistor Embedded with Simple Circuits of Voltage Divider and Regulator for Biosignal Measurement

With the distinctive advantages of high transconductance, low operating voltage, mixed ionic-electronic conductivities, and dynamic versatility, organic electrochemical transistor (OECT) has emerged as a promising wearable technology capable of measuring various biophysical and biochemical signals. Despite the intensive research efforts towards enhancing its wearability, challenges related to signal conversion, voltage sourcing, and manufacturing scalability are seldom addressed. Herein, we report a compact and easy-to-build integrated module that provides stable biasing from batteries while enabling current-to-voltage conversion and additional amplification of OECTs responses. Given the known amplitude of target signals, transistor bias and amplification gain can be adjusted easily on site by tuning two key resistance values and ensuring sufficient battery voltage. Furthermore, the flexible OECTs in this work were fabricated through an industrial manufacturing process for flexible printed circuits (FPC), in which the polymeric channel material and device architecture were both customized to accommodate the fabrication constraints. Notably, preliminary measurements based on the battery-powered unit comprising our OECT and module demonstrate significantly amplified bio-signals compared to electrodes. The successful acquisition of on-body electrocardiogram voltages further underscores the potential of this platform to support current and future OECT interfaces.

bioengineering↗

bioRxiv2025

Peptide Design through Binding Interface Mimicry

Peptides offer distinct advantages for targeted therapy, including oral bioavailability, cellular permeability, and high specificity, which set them apart from conventional small molecules and biologics. In this work, we developed an AI algorithm, named PepMimic, to transform a known protein receptor or an existing antibody of a target into a short peptide drug by mimicking the binding interfaces between targets and known binders. The structural root mean square deviation and interface DockQ with reference binders were 61% and 75% better than the best existing methods on the PepBench datasets. We then applied this novel peptide-design methodology to five drug targets: PD-L1, CD38, BCMA, HER2, and CD4. SPRi results show that 8% of the peptides exhibited dissociation constant (KD) values at the 10-8M level, and 26 peptides achieving KD values as low as 10-9M. This success rate was 20,000 times higher than that observed in a random library screening conducted under identical conditions. PepMimic was applied to target proteins lacking available binders by first utilizing AI algorithms to design protein binders, followed by the generation of peptides through simulation of these artificial interfaces. The top-ranked peptides underwent extensive cellular validation and in vivo testing through tail vein injections in breast, myeloma, and lung tumor mouse models. Experimental results demonstrated effective membrane binding and highlighted the strong potential of these peptides for clinical diagnostic imaging and targeted therapeutic applications.

biochemistry↗

bioRxiv2025

OcuPair, a novel photo-crosslinkable dendrimer-hyaluronic acid hydrogel bandage/bioadhesive for corneal injuries and temporary corneal repair

Traumatic corneal injuries are a leading cause of blindness among military personnel. These injuries need immediate attention at the combat zone, but treatment options are limited as life-saving measures are often prioritized. To address this critical gap, we have developed OcupairTM, a two-component hydrogel system that consists of (i) an injectable viscoelastic filler that stabilizes the ocular cavity and prevents hypotony. (ii) An in-situ photo-curable adhesive hydrogel comprising of methacrylated PAMAM dendrimer and hyaluronic acid engineered to form a transparent, flexible and robust bandage within 90 seconds, adhering to corneal surface and ensuring a water-tight seal securing full-thickness corneal wounds. Ex vivo studies demonstrated that the adhesive hydrogel is mechanically robust and withstands intraocular pressures beyond physiological range. In a rabbit corneal injury model, OcuPair effectively seals complex full thickness wounds and preserves the eye with favorable clinical outcomes for 5 days with no toxicity over 30 days. In this study, we have validated the pilot scale synthesis, formulation optimization, GMP scale-up and IDE-enabling GLP toxicity, essential for clinical translation as a battlefield-ready solution.

bioengineering↗

bioRxiv2024

Assessment of DNA methylation from a single genomic region of ELOV2 is sufficient to predict chronological age

Estimation of chronological age is particularly informative in forensic contexts. Assessment of DNA methylation status allows for the prediction of age, though the accuracy and ease of manipulation may vary across different models. In this study, we started with a carefully designed discovery cohort recruiting more elderly subjects than other age categories, to diminish the effect of epigenetic drifting. We analyzed DNA methylation from a single genomic region of ELOV2, which was sufficient to construct an age-prediction model comprising 15 CpG sites. This model is further validated by an independent cohort as well as a multi-center test using trace dried bloodstains. The nature of our analytical pipeline, when combined the assessment of a single genomic locus with high-throughput sequencing, can easily be scaled up with low cost. Taken together, we propose a new age-prediction model featuring accuracy, ease of manipulation, high-throughput, and low cost. This model can be readily applied in both classic and newly emergent forensic contexts that require age estimation.

genetics↗

bioRxiv2024

A Label-free Nanowell-based Impedance Sensor for Ten-minute SARS-CoV-2 Detection

This work explores label-free biosensing as an effective method for biomolecular analysis, ensuring the preservation of native conformation and biological activity. The focus is on a novel electronic biosensing platform utilizing micro-fabricated nanowell-based impedance sensors, offering rapid, point-of-care diagnosis for SARS-CoV-2 (COVID-19) detection. The nanowell sensor, constructed on a silica substrate through a series of microfabrication processes including deposition, patterning, and etching, features a 5x5 well array functionalized with antibodies. Real-time impedance changes within the nanowell array enable diagnostic results within ten minutes using small sample volumes (<5 {micro}L). The research includes assays for SARS-CoV-2 spike proteins in Phosphate-buffered saline (PBS) and artificial saliva buffers to mimic real human SARS-CoV-2 samples, covering a wide range of concentrations. The sensor exhibits a detection limit of 0.2 ng/mL (1.5 pM) for spike proteins. Middle East Respiratory Syndrome (MERS-CoV) spike proteins are differentiated from SARS-CoV-2 spike proteins, demonstrating specificity. TOC Graphic O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=113 SRC="FIGDIR/small/627986v1_ufig1.gif" ALT="Figure 1"> View larger version (58K): org.highwire.dtl.DTLVardef@1a9f2a7org.highwire.dtl.DTLVardef@79d5acorg.highwire.dtl.DTLVardef@bb1bc1org.highwire.dtl.DTLVardef@1b5098_HPS_FORMAT_FIGEXP M_FIG C_FIG

bioengineering↗

bioRxiv2024

Restoration of PKM1 improves functional maturation of human stem-cell derived-β cell by regulating PEP metabolism

Human stem cell-derived {beta} (SC-{beta}) cells still exhibit limited glucose response required for insulin secretion due to glycolytic bottlenecks, yet how these metabolic abnormalities impact glucose response and functional maturation of SC-{beta} cells remains unclear. In this study, we identified a metabolic checkpoint located at PEP accumulation that impeded the functional maturation, which was rescued by restoration of pyruvate kinase 1 (PKM1). Glucose-tracing metabolomics in human stem cell-derived islets revealed abnormal glycolytic PEP accumulation at resting condition, resulting in impaired calcium response and insulin secretion upon high glucose or glycolytic metabolite stimulation. Mechanistically, elevated PEP significantly raised intracellular basal calcium levels, leading to downregulated expression of genes involved in TCA cycle elucidated by single cell transcriptomics. Furthermore, the activity of pyruvate kinase, which metabolizes PEP, was notably reduced due to low PKM1 expression. By overexpressing PKM1, the impairment of TCA-related genes caused by PEP accumulation was reversed via modulating PEP metabolism, resulting in enhanced calcium responses and insulin secretion upon high glucose stimulation. Together, we discovered a novel role of PKM1-regulated PEP metabolism in mediating the functional maturation of human SC-{beta} cells. This study highlights the importance of metabolic reprogramming in human SC-{beta} cell maturation, advancing cell therapy approaches for diabetes treatment.

cell biology↗

bioRxiv2024

OsMORF protein selectively promotes the dual-localized RNA editing factor OsPGL1 binding to its target RNA

Post-transcriptional RNA editing plays a key regulatory role and serves as a genetic information proofreading mechanism. In flowering plants, RNA editing typically involves the removal of amino groups from cytidine to produce uridine in both plastids and mitochondria. In our previous work, we identified OsPGL1 as a rare organelle editing factor that regulates both mitochondrial and chloroplast RNA in rice. This protein mediates RNA editing and is associated with several OsMORFs. We speculated that they may form editing complex to regulate editing events, but we are still unclear about the detailed mechanism between OsMORF proteins and OsPGL1, as well as their roles in target RNA recognition and binding. In this study, we found that three OsMORFs can significantly promote the binding of OsPGL1 to target RNA in vitro. Notably, OsMORF8 can promote OsPGL1 to form a homologous dimer, thereby enhancing RNA binding to a greater extent. The E and DYW motifs do not affect the role of MORF proteins in RNA editing events, ruling out the potential influence of these two special motifs. In addition, we predicted a series of supercomplex structures of OsPGL1, the OsPGL1-RNA ligand complex, the OsPGL1-OsMORF2-OsMORF8-OsMORF9 complex, and the OsPGL1-OsMORF2-OsMORF8-OsMORF9-RNA complex. We determined that the conformational changes and newly added positively charged surface caused by OsMORF on OsPGL1 are the main reasons for MORF to promote the binding of OsPGL1 to RNA. Based on some new discoveries, we have expanded the RNA editing complex model, which greatly enhances our understanding of plant RNA editing complexes. Short summaryPPRs and MORFs are two kinds of RNA editing factors, both can mediate organelle RNA editing, the difference between them is that PPR can directly bind target RNA, MORF does not directly bind RNA, but can independently or assist PPR in performing RNA editing. Function of MORF protein in post-transcriptional processing is not clear, our study verifies the function of MORFs in the process of PPR binding RNA through molecular biology. We also analyzed the interaction network between PPR-MORF-RNA from the perspective of structural biology.

plant biology↗

bioRxiv2024

Gut Bacteria Metabolize Natural and Synthetic Steroid Hormones via the Reductive OsrABC Pathway

Steroid hormone metabolism by the gut microbiome affects host physiology, but the underlying microbial pathways remain incompletely understood. Here, we isolate a novel human gut bacterium, Clostridium steroidoreducensT strain HCS.1 that reduces cortisol and related steroid hormones to 3{beta},5{beta}-tetrahydrosteroid products. Through transcriptomics and enzymatic discovery, we establish the C. steroidoreducens OsrABC steroid hormone pathway. OsrA is a 3-oxo-{Delta}1-steroid hormone reductase that targets synthetic glucocorticoids, including prednisolone-- a frontline Crohns disease therapy. OsrB is a 3-oxo-{Delta}4-steroid reductase that converts steroid hormones to 5{beta}-dihydrosteroid intermediates, which OsrC subsequently reduces to 3{beta},5{beta}-tetrahydro products. Homologs of osrA and osrB predict steroid-reducing activity across gut bacteria and are enriched in Crohns disease patient metagenomes. Consistent with a role in modulating drug efficacy, C. steroidoreducens colonization decreases prednisolone bioavailability in gnotobiotic mice. These findings thus define a previously unrecognized pathway for microbial steroid hormone inactivation and establish a mechanistic basis for bacterial interference with anti-inflammatory therapies.

microbiology↗

bioRxiv2024

Inter-Kingdom Interactions and Environmental Influences on the Oral Microbiome in Severe Early Childhood Caries

Dental caries arise from intricate interactions among oral microorganisms, impacting ecological stability and disease progression. This study delves into the bacterial-fungal dynamics in severe early childhood caries (S-ECC) among 61 children aged 3-4 years with complete deciduous dentition. We evaluated environmental factors such as saliva pH, buffering capacity, and trace elements (iron, fluoride). We examined the performance of 16S rRNA V1-V9 regions gene and internal transcribed spacer (ITS) primers for bacteria and fungi from plaque and saliva to characterize community compositions and diversity. Saliva pH and buffering capacity were also measured. Findings revealed significant shifts in bacterial diversity in S-ECC saliva samples, marked by decreased diversity and elevated abundance of cariogenic species, particularly Streptococcus mutans. Candida albicans was notably more prevalent in the S-ECC group, implicating its potential role in pathogenesis. Iron and fluoride concentrations showed no significant correlation with microbial community structure. Network analyses uncovered complex intra- and inter-kingdom interactions, underscoring cooperative and competitive dynamics. S-ECC children exhibited higher abundances of bacteria (Streptococcus mutans, Granulicatella, Actinomyces) and fungi (Candida albicans), with specific microbial taxa associated with reduced saliva pH. ImportanceThis study illuminates the intricate relationship between bacteria and fungi within the oral microbial community of children, specifically highlighting differences between those with severe early childhood caries (S-ECC) and those without caries. Through an extensive analysis of the microbial composition in both saliva and dental plaque, we identified a significant increase in the abundance of specific bacterial taxa (e.g., S. mutans, Granulicatella, Actinomyces) and fungal species (e.g., C. albicans) in the oral cavities of children with S-ECC. This finding underscores the potential role of these microorganisms in the development of caries. Contrary to previous studies that emphasize the importance of iron and fluoride in oral health, our research found no significant correlation between the concentrations of these elements and the composition of oral microbial communities. This result challenges conventional understanding and opens new avenues for future research. Additionally, we discovered an association between certain microbial species and reduced salivary pH, offering fresh insights into the relationship between the oral microenvironment and caries development. The implications of our findings are substantial for the development of prevention and intervention strategies targeting childhood caries. They also underscore the critical need for a deeper exploration of oral microbial interactions and their environmental influences.

microbiology↗

bioRxiv2024

Skeletal Metastasis of Prostate Cancer Is Augmented by Activation of EphA2 Noncanonical Signaling and Ligand-Deficient Bone Microenvironment

EphA2, a member of Eph family receptor tyrosine kinases (RTKs), is overexpressed in multiple types of solid human tumors, particularly at the late stages. However, whether and how it drives specific malignant processes remain elusive. We report that EphA2 is elevated during prostate cancer (PCa) progression in multiple syngeneic murine models. Interestingly, human metastatic PCa specimens from two Rapid Autopsy Programs showed selective overexpression of EphA2 in metastasis to the bone, but not to the lymph nodes or viscera. Serine 897 phosphorylation that mediates the pro-oncogenic, noncanonical signaling by EphA2 was also upregulated in bone metastasis. Analysis of human datasets shows EphA2 overexpression is associated with skeletal but not visceral metastases. Ephrin-A1, a major cognate ligand for EphA2, is lost in PCa bone metastasis, which is correlated with poor prognosis. Further, the bone microenvironment is unique in expressing little of the five EFNA genes, providing permissive microenvironment for bone colonization. S897A mutation that ablates EphA2 noncanonical signaling, suppressed PCa development. Restoration of ephrin-A1 expression in PC-3, a model cell line for double negative prostate cancer derived from bone metastasis and devoid of ephrin-As, profoundly changed global tyrosine phosphorylation profiles, inhibited basal ERK and Src activities in vitro, and suppressed tumor development in the bone. Together these results demonstrate EphA2 overexpression and concomitant loss of ligands in PCa lead to activation of noncanonical signaling that is sustained in ephrin-A1-deficient skeletal milieu to promote bone metastasis.

cancer biology↗

bioRxiv2024

Genome-wide screen overexpressing mycobacteriophage Amelie genes identifies multiple inhibitors of mycobacterial growth

The genome sequences of thousands of bacteriophages have been determined and functions for many of the encoded genes have been assigned based on homology to characterized sequences. However, functions have not been assigned to more than two-thirds of the identified phage genes as they have no recognizable sequence features. Recent genome-wide overexpression screens have begun to identify bacteriophage genes that encode proteins that reduce or inhibit bacterial growth. This study describes the construction of a plasmid-based overexpression library of 76 genes encoded by Cluster K1 mycobacteriophage Amelie, which is genetically similar to Cluster K phages Waterfoul and Hammy recently described in similar screens and closely related to phages that infect clinically important mycobacteria. 26 out of the 76 genes evaluated in our screen, encompassing 34% of the genome, reduced growth of the host bacterium Mycobacterium smegmatis to various degrees. More than one-third of these 26 toxic genes have no known function, and 10 of the 26 genes almost completely abolished host growth upon overexpression. Notably, while several of the toxic genes identified in Amelie shared homologs with other Cluster K phages recently screened, this study uncovered eight previously unknown gene families that exhibit cytotoxic properties, thereby broadening the repertoire of known phage-encoded growth inhibitors. This work, carried out under the HHMI-supported SEA-GENES project (Science Education Alliance Gene-function Exploration by a Network of Emerging Scientists), underscores the importance of comprehensive overexpression screens in elucidating genome-wide patterns of phage gene function and novel interactions between phages and their hosts.

microbiology↗

bioRxiv2024

Metagenome-based diversity and functional analysis of culturable microbes in sugarcane

Sugarcane, widely acknowledged as the foremost crop for sugar and energy production on a worldwide scale, is confronted with many diseases that pose serious threats to its production. Biological control has become more popular as an approach for preventing and controlling diseases because of its environment-friendly characteristics. However, there is a lack of thorough investigation and use of microbial resources in sugarcane. This study conducted a thorough analysis of culturable microbes and their functional features in different tissues and rhizosphere soil of four diverse sugarcane species using metagenomics techniques. The results revealed significant microbial diversity in sugarcanes tissues and rhizosphere soil, including several important biomarker bacterial taxa identified, which are reported to engage in several processes that support plant growth. The LEfSe studies identified unique microbial communities in different parts of the same sugarcane species, particularly Burkholderia, which exhibited significant variations across the sugarcane species. Microbial analysis of carbohydrate-active enzymes (CAZymes) indicated that genes related to sucrose metabolism were mostly present in specific bacterial taxa, including Burkholderia, Pseudomonas, Paraburkholderia, and Chryseobacterium. This study improves understanding of the diversities and functions of endophytes and rhizosphere soil microbes in sugarcane. Moreover, the approaches and findings of this study provide valuable insights for microbiome research and the use of comparable technologies in other agricultural fields.

microbiology↗

bioRxiv2024

Integrated single-cell RNA-seq analysis revealed PTN secreted by fibroblasts acting on itself and macrophages via SDC4 ligand in myocardial hypertrophy

BackgroundHypertrophic cardiomyopathy (HCM) is characterized by massive myocardial hypertrophy, which is the most frequent cause of sudden death and can lead to heart failure (HF) or stroke. The objective of this study was to explore the communication network among various cells in the heart of pathological HCM derived from transverse aortic constriction (TAC) mouse model, and investigate the potential mechanism through data mining, biological informatics analysis, and experimental validation. Methods and ResultsThe integrated analyses including CellChat, Seurat, gene ontology (GO), pseudo-time trajectory analysis, and weighted gene co-expression network analysis (WGCNA) were performed based on the single-cell RNA-seq data (scRNA-seq). In vitro tests were conducted to verify bioinformatic analysis findings through enzyme-linked immunosorbent assay (ELISA), real-time quantitative PCR (RT-qPCR), Edu staining, and transwell assay. In vivo tests were also performed to further verify bioinformatic analysis findings by western blot and immunofluorescence assays based on our established TAC mouse model with myocardial hypertrophy. Our results showed that in the heart of TAC mouse, the interaction between cardiac fibroblasts and macrophages was most common, and the increasing pleiotrophin (PTN) secreted by cardiac fibroblasts could promote themselves proliferation or invasion as well as stimulate macrophage activation to release inflammatory cytokines, such as TNF-, IL-6, Cox-2, Cd83, Egr2, and IL-10 through acting on its ligand recombinant Syndecan 4 (SDC4), which may affect cardiomyocyte normal function and eventually cause HCM. This study first demonstrated that PTN derived from cardiac fibroblasts may act on SDC4 to play crucial role in myocardial hypertrophy, which may be a potential therapeutic targets for patients with pathological HCM. ConclusionsIn this study, the complex interaction network between cardiac fibroblasts and macrophages of TAC mice based on the scRNA-seq data was investigated, and we found that the increasing PTN secreted by cardiac fibroblasts under cardiac pressure overload could promote themselves proliferation or invasion as well as stimulate macrophage activation to release inflammatory cytokines through acting on SDC4 ligand, which may affect cardiomyocyte normal function and eventually cause HCM. In addition, our study suggested that PTN derived from cardiac fibroblasts may act on SDC4 ligand to play crucial role in myocardial hypertrophy, which may be a potential therapeutic targets for patients with pathological HCM.

cell biology↗