Biology subjects

Zhuang, L.

Publications and source records attributed to Zhuang, L..

18 recordsLinked to original sources

bioRxiv2026

Spatially resolved transcriptomic and proteomic profiling reveals cell interaction programs that predict Barrett's esophagus progression

Barretts esophagus (BE) is the precursor lesion of esophageal adenocarcinoma (EAC). It affects approximately 5% of adults in the United States and significantly increases the risk of developing EAC. However, current surveillance strategies cannot reliably distinguish patients who will progress from those who will remain stable. Direct studies of progressor BE are extremely limited due to availability of tissue with known progression outcomes, and have largely been restricted to genomic profiling approaches. The premalignant cellular landscape of progressor BE remains poorly understood. Here, we used complementary spatial transcriptomic and proteomic imaging to profile 34 non-dysplastic BE patients under endoscopic surveillance, including those who subsequently progressed to dysplasia or EAC, termed "Progressors" and those who remained stable, termed "Non-progressors". Transcriptomics based Xenium analysis captured 974,604 cells across 70 whole-biopsy regions, while protein based imaging mass cytometry profiled 372,242 cells across 119 selected regions. FUME-TCRseq further quantified T cell clonotypes from matched tissues scrolls. Cellular composition was generally similar between Progressors and Non-progressors. However, Progressors showed increased intestinal Barretts columnar cells, B cells and gastric progenitor-like cells, together with enhanced immune-epithelial interactions, whereas Non-progressors retained coordinated stromal organization. Spatial interaction features strongly outperformed cell composition and density for progression prediction. Combined spatial interaction model achieved an area under the curve (AUC) of 0.97, compared with 0.62 and 0.68 for comparison and density alone. Complementary imaging mass cytometry further resolved the underlying immune programs, identifying cytotoxic and antigen presenting myeloid features enriched in progressors, and CD56 associated memory T cell interactions enriched in non progressors. Together, these findings support a model that BE progression is driven by progressive remodeling of epithelial-immune-stromal architecture rather than emergence of distinct dysplasia-like cell subsets. Increased T cell clonal diversity and recruitment of cytotoxic and antigen-presenting immune niches may also reflect an evolving response to genomic alteration prior to dysplasia. These results establish spatial tissue architecture, rather than specific cell types, captures progression associated microenvironmental states in BE and provides a framework for spatially informed patient stratification and early cancer risk assessment.

systems biology↗

bioRxiv2026

HuR inhibition attenuates hypertension and fibrosis in chronic kidney disease

BackgroundElevated RNA-binding protein HuR has been reported in patients with chronic kidney disease (CKD), but its specific pathogenic role remains unclear. Here, we investigated HuR involvement in progressive CKD induced by deoxycorticosterone acetate (DOCA) plus angiotensin II (Ang II) in mice and evaluated the therapeutic efficacy and mechanisms of the HuR inhibitor KH3. MethodsAdult male mice underwent uninephrectomy and were subjected to DOCA + Ang II infusion with 1% NaCl in drinking water. Mice were then treated with KH3 or vehicle for 3 weeks. Control mice received saline injections without DOCA and Ang II infusion. ResultsDOCA + Ang II infusion markedly increased HuR expression in circulating exosomes and kidney tissues, which was attenuated by KH3. KH3 halted the progression of albuminuria and improved renal function, and reduced kidney hypertrophy and glomerular and tubulointerstitial fibrosis compared with untreated DOCA + Ang II mice. These improvements were associated with reduced podocyte and tubular injury. KH3 also decreased renal macrophage infiltration and suppressed NF-{kappa}Bp65, Nox2, AKT phosphorylation, TGF-{beta}1, and Wisp1, consistent with reduced inflammation, oxidative stress, and fibrosis. In addition, KH3 partially lowered arterial blood pressure in DOCA + Ang II-infused mice, an effect that may involve suppression of SGLT2-associated profibrotic vascular responses, as supported by studies in cultured VSMCs and mesenteric resistance arteries. ConclusionsHuR is upregulated in DOCA + Ang II-induced renal and vascular injury and contributes to hypertensive, inflammatory, oxidative, and fibrotic responses in CKD. Pharmacologic inhibition of HuR-RNA interactions represents a promising therapeutic strategy for CKD. NOVELTY AND RELEVANCEO_ST_ABSWhat Is New?C_ST_ABSThis study identifies the RNA-binding protein HuR (ELAVL1) as a previously unrecognized upstream post-transcriptional regulator of blood pressure in hypertensive chronic kidney disease. We demonstrate for the first time that pharmacologic disruption of HuR-RNA interactions lowers arterial blood pressure in vivo. In addition, we uncover a novel HuR-SGLT2-vascular smooth muscle cell (VSMC) signaling axis, revealing that HuR regulates inducible vascular SGLT2 expression and Ang II-mediated vasoconstrictive responses. What Is Relevant?Hypertension in CKD arises from integrated renal and vascular dysfunction that is incompletely controlled by current therapies. Our findings are highly relevant because we identify HuR as a nodal post-transcriptional regulator that coordinates renal injury, vascular inflammation, and smooth muscle contractility, rather than acting within a single cell type or signaling pathway. Clinical and Pathophysiological ImplicationThese data support a model in which HuR-driven RNA regulatory programs amplify Ang II-dependent vascular hypercontractility and hypertension in CKD. Therapeutic targeting of HuR-RNA interactions represents a novel antihypertensive strategy that may complement renin-angiotensin-aldosterone system (RAAS) blockade and provides mechanistic insight into the blood pressure-lowering and vascular protective effects of SGLT2 inhibitors, including in non-diabetic CKD.

pathology↗

bioRxiv2026

Polyclonal and single clonal patient-derived organoid models of Barrett oesophagus and oesophageal adenocarcinoma establish a platform for the analysis of heterogeneity in disease progression and therapy response

SUMMARY/ABSTRACTOesophageal adenocarcinoma (OAC) is a major cause of morbidity and mortality. OAC and its precursor, Barrett oesophagus (BO), are defined by substantial early heterogeneity, complicating prevention and treatment of OAC and remaining poorly recapitulated by current in vitro and animal model systems. We have generated 116 patient- and healthy donor-derived organoids (PDOs) spanning normal oesophagogastric tissue, BO and OAC. These PDOs capture population diversity and recapitulate phenotypic, genomic and transcriptomic features of their respective disease stages. We develop a single cell-derived clonal organoid approach and show that this enables us to capture the heterogeneity and isolate high-risk, subclonal populations that are difficult to discern and maintain in bulk PDO cultures. Using this platform, we demonstrate functional importance of this biobank across the pre-malignant to invasive disease spectrum, including a role for BO in shaping fibroblast phenotype within assembloids, and diverse responses of OAC to chemotherapy, radiotherapy and targeted CDK4/6 inhibition. HIGHLIGHTSO_LIPatient- and healthy donor-derived organoids (PDOs) provide a functional platform of disease progression and heterogeneity across normal gastric, non-dysplastic and dysplastic Barrett oesophagus (BO) and oesophageal adenocarcinoma (OAC). C_LIO_LIWe provide a quantitative phenotypic and molecular framework to assess the provenance and fidelity of each PDO model given the heterogeneity of this disease. C_LIO_LIPDOs recapitulate key features of non-dysplastic and dysplastic BO, as well as invasive OAC. C_LIO_LISingle cell-derived clonal organoids (sc-organoids) isolate and maintain high-risk subclonal populations. C_LIO_LIOAC PDOs mirror known population level variation in response to systemic anti-cancer therapies. C_LI

cancer biology↗

bioRxiv2025

Wavelet Based Whole Genome Doubling Aware Single Cell Copy Number Calling

Advances in single cell whole genome sequencing enable profiling of the copy number state of thousands of cells with minimal sequencing bias across the genome. The Direct Library Preparation + technique is an whole genome amplification-free single cell whole genome sequencing method that achieves high throughput by fragmenting each cells genome and ligating sequencing adapters using a modified Tn5 transposase, and sequencing to less than 0.1x coverage. Despite recent advances in experimental approaches, data analysis of single cell whole genome sequencing lags behind and the existing methods are not optimized for the analysis of frozen samples with variable DNA preservation. Furthermore, existing tools predominantly rely on read depth ratio in predefined genomic bins to call copy number, making whole genome duplication unidentifiable. To address this, we introduce Songbird, a single cell whole genome sequencing copy number caller that is whole genome duplication sensitive, and outperforms existing tools both in breakpoints identification and true copy number detection. We demonstrate that Songbird is robust down to extremely low coverage, adaptable to a variety of genome versions (hg19, hg38, hs.1), and is extensible to other single cell whole genome sequencing methods that rely on Tn5 tagmentation to fragment the genome.

bioinformatics↗

bioRxiv2025

A Population-scale Single-cell Spatial Transcriptomic Atlas of the Human Cortex

The genetic and spatial determinants of cell type diversity in human cerebral cortices remain poorly defined. Here, we present a population-level single-cell spatial transcriptomic atlas of human cortices from 71 donors across the lifespan. We identified 906 layer-specific genes showing conserved and divergent laminar expression patterns between humans and other species. Spatial analysis revealed neuronal vulnerability and glial activation during aging, together with a decline in the proportion of superficial SST neurons and their interactions with other cells. Disease-associated genes exhibited high cell-type and layer-specific expression, implicating the pathogenic role of spatially specific gene expression. Spatial cis-eQTL analysis identified regulatory variants linked to genes related to diseases like Tourette syndrome. Cross-species comparison demonstrated glial expansion in the human cortex, accompanied by enhanced neuron-glia communication via the neuregulin signaling. Together, we provide a comprehensive single-cell atlas of the human cortex that is essential for understanding aging, evolution, and disease pathogenesis.

neuroscience↗

bioRxiv2025

PRRT2 as an auxiliary regulator of Nav channel slow inactivation

During sustained activity, voltage-gated sodium (Nav) channels enter a slow-inactivated state to limit cellular hyperexcitability. Disruption of this regulatory process has been implicated in skeletal, cardiac and neurological disorders. While the kinetics of this process are well characterized, its endogenous modulators remain unclear. Here, we identify Proline-Rich Transmembrane Protein 2 (PRRT2) as a native regulator of Nav channel slow inactivation. We show that PRRT2 facilitates the entry of Nav channels into the slow-inactivated state and delays their recovery, a regulatory effect conserved from zebrafish to humans. PRRT2 forms molecular complexes with Nav channels both in vitro and in vivo. In the mouse cortex, PRRT2 deficiency impairs the slow inactivation of Nav channels in neuronal axons, leading to reduced cortical resilience in response to hyperexcitable challenges. Together, these findings establish PRRT2 as a physiological modulator of Nav channel slow inactivation and reveal a mechanism that supports cortical resilience to pathological perturbations.

neuroscience↗

bioRxiv2025

Computational Fluid Dynamics (CFD) Modeling of Ilamycin E Production in Streptomyces atratus SCSIO ZH16 Submerged Fermentation

A computational fluid dynamics (CFD) model was developed and validated against experiments for a laboratory-scale 5-L bioreactor. Numerical simulation was performed to describe the bioreaction of Streptomyces atratus SCSIO ZH16 fermentation for ilamycin E production with the dynamic changes in viscosity of the fermentation broth due to biomass growth and decay. This model can account for the two-way coupling between the fermentation environment and medium, which allowed for the elucidation of the impact of the flow field in the bioreactor on bacterial growth and production, as well as the influence of viscosity changes on the flow field. This work represents the first integration of Streptomyces fermentation with CFD, enabling the simulation of flow field and mass transfer under varying stirring speed, aeration rate, and viscosity during Streptomyces fermentation. An optimum range of fermentation broth viscosity (10-30 mPa s) was identified for ilamycin E production by S. atratus SCSIO ZH16 fermentation. Furthermore, the addition of sorbitol to optimize the viscosity of the fermentation broth in the later stages of fermentation. The enhanced mass transfer efficiency strengthens the respiration, energy supply, and carbon source consumption in Streptomyces, thereby increasing the ilamycin E production. This research offers a practical strategy for the process intensification and industrial scale-up for such bioreactors. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=78 SRC="FIGDIR/small/630827v1_ufig1.gif" ALT="Figure 1"> View larger version (27K): org.highwire.dtl.DTLVardef@3d463corg.highwire.dtl.DTLVardef@ce3859org.highwire.dtl.DTLVardef@d55c7forg.highwire.dtl.DTLVardef@1abaee5_HPS_FORMAT_FIGEXP M_FIG C_FIG

bioengineering↗

bioRxiv2024

Unraveling the Complexity of Abdominal Aortic Aneurysm: Multiplexed Imaging Insights into C-Reactive Protein-Related Variations

BackgroundAbdominal aortic aneurysm (AAA) is a potentially lethal condition that often remains asymptomatic until it ruptures. Recent research suggests that immune-inflammatory processes are associated with AAA development, yet the exact mechanisms remain unclear. Serum C-reactive protein (CRP) serves as a prognostic marker for AAA and various cardiovascular diseases. When CRP accumulates in damaged tissues, it transforms into a monomeric form, exacerbating tissue damage. Our previous study confirmed the presence of CRP deposition in eroded AAA and atherosclerosis regions, accompanied by an increased infiltration of inflammatory cells. However, a comprehensive understanding of the specific changes in the inflammatory cellular landscape attributable to CRP deposition is lacking. Here, we aimed to explore cellular-level alterations in AAAs associated with varying CRP levels. MethodsWe categorized AAA patients into High-CRP ([≥]0.1 mg/dL, and [≥]3+ CRP IHC score, n=6) and Low-CRP ([≤]0.1 mg/dL, and [≤]1+ CRP IHC score, n=3), and used normal aorta specimens as a baseline control. The cellular landscape of immune and stromal components was characterized using Co-Detection by Indexing (CODEX) tissue imaging with 31 DNA-barcoded antibodies, followed by single-cell-based analysis and GPU-accelerated unsupervised clustering. ResultsWe identified 51 distinct immune and stromal cell types in the cohort and revealed significant differences in protein expression patterns among the groups. In AAA, stromal cells decreased significantly, while immune cell proportions sharply increased. Lag3+ T cell regulators decreased, leading to an increase in CD3+ T cells. The composition of immune cells within atherosclerotic plaques was associated with the degree of CRP deposition in AAA. The High-CRP group showed increased M1 and Ki67+ proliferating macrophages, while the Low-CRP group exhibited intensified fibrosis with M2 macrophages. ConclusionsOur study found significant variations in immune cell distribution within AAA walls based on CRP levels. These findings suggest a potential link between CRP-related immune changes and AAA progression. HIGHLIGHTSO_LIBy performing CODEX (co-detection by indexing) multiplexed imaging on paraffin-embedded, formalin-fixed archived abdominal aortic aneurysm (AAA) tissue samples with varying CRP levels, we segmented 415,365 cells into 51 distinct clusters. C_LIO_LIIn AAA, the presence of CRP deposition led to variations in the spatial relationships, distances, and enrichment patterns among immune and stromal cells.. C_LIO_LIIn AAA-High CRP, there was an intensified infiltration of M1 macrophages and various immune cells observed in the atherosclerotic plaque. C_LIO_LIIn AAA-Low CRP, severe stromal fibrosis was associated with M2 macrophages. C_LIO_LIOur results suggest that the deposition of CRP into the atherosclerotic plaque alters the immune-stromal landscape in AAA. C_LI

pathology↗

bioRxiv2023

Multi-omics map revealed PPARalpha activation protecting against myocardial ischemia-reperfusion injury by maintaining cardiac metabolic homeostasis

Timely percutaneous coronary intervention is the most effective initial therapy for the acute myocardial infarction (MI). However, the mechanism in energy metabolism underlying time-dependent coronary reperfusion remains largely unknown. Here, we generated an integrative map of cardiac cells using bulk and single-nucleus RNA-seq combined with metabolomics profiling of hearts with reperfusion at distinct time points post MI in rat. We found early time reperfusion (ETR), but not late time reperfusion (LTR) reduced myocardial injury by maintaining cardiac energy homeostasis. PPAR was identified as a key regulator for maintaining fatty acid metabolism after MI/R injury. Importantly, pretreatment with FDA-approved PPAR agonist, fenofibrate, improved the transcriptional signatures, and ameliorated the function of the MI/R injured hearts, particularly in the ETR. Together, our data not only deciphered the protective effect of ETR by maintaining cardiac energy homeostasis, but also provided insights into the translational potential of PPAR activation in alleviating MI/R injury.

cell biology↗

bioRxiv2023

The lncRNA TRG-AS1 promotes the growth of colorectal cancer cells through the regulation of P2RY10/GNA13

PurposeThe lncRNA TRG-AS1 and its co-expressed gene P2RY10 are important for colorectal cancer (CRC) occurrence and development. The purpose of our research was to explore the roles of TRG-AS1 and P2RY10 in CRC progression. MethodsThe abundance of TRG-AS1 and P2RY10 was determined in CRC cell lines. LoVo cells were transfected with si-TRG-AS1 and si-P2RY10 constructs. Subsequently, the viability, colony formation, and migration of the transfected cells were analyzed using cell counting kit-8, clonogenicity, and scratch-wound/Transwell(R) assays, respectively. Cells overexpressing GNA13 were used to further explore the relationship between TRG-AS1 and P2RY10 along with their downstream functions. Finally, nude mice were injected with different transfected cell types to observe tumor formation in vivo. ResultsTRG-AS1 and P2RY10 were significantly upregulated in HT-29 and LoVo compared to FHC cells. TRG-AS1 knockdown and P2RY10 silencing suppressed the viability, colony formation, and migration of LoVo cells. TRG-AS1 knockdown downregulated the expression of P2RY10, GNA12, and GNA13, while P2RY10 silencing downregulated the expression of TRG-AS1, GNA12, and GNA13. Additionally, GNA13 overexpression reversed the cell growth and gene expression changes in LoVo cells induced by TRG-AS1 knockdown or P2RY10 silencing. In vivo experiments revealed that CRC tumor growth was suppressed by TRG-AS1 knockdown and P2RY10 silencing. ConclusionsTRG-AS1 knockdown repressed the growth of CRC cells by regulating P2RY10 and GNA13 expression, thereby controlling CRC occurrence and development.

molecular biology↗

bioRxiv2023

Dual-modality imaging of immunofluorescence and imaging mass cytometry for whole slide imaging with accurate single-cell segmentation

Imaging mass cytometry (IMC) is a powerful multiplexed tissue imaging technology that allows simultaneous detection of more than 30 makers on a single slide. It has been increasingly used for singlecell-based spatial phenotyping in a wide range of samples. However, it only acquires a small, rectangle field of view (FOV) with a low image resolution that hinders downstream analysis. Here, we reported a highly practical dual-modality imaging method that combines high-resolution immunofluorescence (IF) and high-dimensional IMC on the same tissue slide. Our computational pipeline uses the whole slide image (WSI) of IF as a spatial reference and integrates small FOVs IMC into a WSI of IMC. The high-resolution IF images enable accurate single-cell segmentation to extract robust high-dimensional IMC features for downstream analysis. We applied this method in esophageal adenocarcinoma of different stages, identified the single-cell pathology landscape via reconstruction of WSI IMC images, and demonstrated the advantage of the dual-modality imaging strategy. MotivationHighly multiplexed tissue imaging allows visualization of the spatially resolved expression of multiple proteins at the single-cell level. Although imaging mass cytometry (IMC) using metal isotope-conjugated antibodies has a significant advantage of low background signal and absence of autofluorescence or batch effect, it has a low resolution that hampers accurate cell segmentation and results in inaccurate feature extraction. In addition, IMC only acquires mm2-sized rectangle regions, which limits its application and efficiency when studying larger clinical samples with non-rectangle shapes. To maximize the research output of IMC, we developed the dual-modality imaging method based on a highly practical and technical improvement requiring no extra specialized equipment or agents and proposed a comprehensive computational pipeline that combines IF and IMC. The proposed method greatly improves the accuracy of cell segmentation and downstream analysis and is able to obtain whole slide image IMC to capture the comprehensive cellular landscape of large tissue sections.

bioinformatics↗

bioRxiv2022

Cardiac patch treatment alleviates ischemic cardiomyopathy correlated with reverting Piezo1/2 expression by unloading left ventricular myocardium

Pathologically elevated mechanical load promotes the adverse remodeling of left ventricle (LV) post myocardial infarction, which results in the progression from ischemic cardiomyopathy to heart failure. Cardiac patches could attenuate adverse LV remodeling by providing mechanical support to infarcted myocardium and border zone tissue. However, the mechanism of the translation from mechanical effects to favorable therapeutic outcome is still not clear. By transcriptome analysis, we found that the myocardial transcription levels of mechanosensitive ion channel proteins Piezo1 and Piezo2 significantly increased in patients with ischemic cardiomyopathy. In vitro tensile tests with local tissue information revealed a significant decrease in local strain and mechanical load in rat infarct. Cardiac function and geometry were preserved compared to non-treated control. Further, in LV myocardium of the patch-treated group, MI induced expression levels of Piezo1/2 were significantly reverted to the similar levels of the Sham group, indicating that cardiac patch beneficial effects were correlated with suppressing mechanosensitive genes, particularly Piezo1/2. These findings demonstrated the potential of cardiac patches in treating ICM patients with remodeling risks, and could provide guidance for improvement in next generation of patch devices.

pathology↗

bioRxiv2022

Single-cell analysis reveals a pathogenic cellular module associated with early allograft dysfunction after liver transplantation

Liver transplantation (LT) is the standard therapy for patients with end-stage liver disease. Although LT technology has markedly progressed in recent decades, early allograft dysfunction (EAD) exacerbates the current organ shortage and impacts the prognosis of recipients. However, understanding of cellular characteristics and molecular events contributing to EAD is limited. Here, a large single-cell transcriptomic atlas of transplanted livers collected from four patients is constructed, including 58,243 cells, which are classified into 14 cell types and 29 corresponding subtypes with known markers, including liver parenchymal cells and non-parenchymal cells with different cell states. Compared to the pre-LT livers, graft remodeling is noted in the post-LT livers, with marked changes in several immune cells in either cell ratios or cell states. More importantly, an EAD-associated pathogenic cellular module is identified, consisting of mucosal-associated invariant T (MAIT) cells, granzyme B (GZMB)+ granzyme K (GZMK)+ natural killer (NK) cells, and S100A12+ neutrophils, all of which are elevated in EAD patient after LT. This cellular module is also verified in two independent datasets. Collectively, these results reveal the cellular characteristics of transplanted livers and the EAD-associated pathogenic cellular module at the single-cell level, offering new insights into the EAD occurrence after LT.

genomics↗

bioRxiv2021

The nonstructural protein 5 of coronaviruses antagonizes GSDMD-mediated pyroptosis by cleaving and inactivating its pore-forming p30 fragment

Coronaviruses (CoV) are a family of RNA viruses that typically cause respiratory, enteric and hepatic diseases in animals and humans. Here, we used porcine epidemic diarrhea virus (PEDV) as a model of coronaviruses (CoVs) to illustrate the reciprocal regulation between CoVs infection and pyroptosis. For the first time, we clarified the molecular mechanism of porcine Gasdermin D (pGSDMD)-mediated pyroptosis and demonstrated that amino acids T239 and F240 within pGSDMD-p30 are critical for pyroptosis. Furthermore, 3C-like protease Nsp5 from SARS-CoV-2, MERS-CoV, PDCoV and PEDV can cleave human/porcine GSDMD at the Q193-G194 junction upstream of the caspase-1 cleavage site to produce two fragments which fail to trigger pyroptosis or inhibit viral replication. Thus, we provide clear evidence that coronoviruses may utilize viral Nsp5-GSDMD pathway to help their host cells escaping from pyroptosis, protecting the replication of the virus during the initial period, which suggest an important strategy for coronoviruses infection and sustain.

microbiology↗

bioRxiv2020

Rapid Neural Reorganization during Retrieval Practice Predicts Subsequent Long-term Retention and False Memory

Active retrieval can induce changes to the strength and content of a memory, yielding enhanced or distorted subsequent recall. But how consolidation influences these retrieval-induced seemingly contradictory outcomes remains unknown. Here we show rapid neural reorganization over eight runs of retrieval practice predicted subsequent recall. Behaviorally, retrieval practice boosted memory following a 24-hour (long-term) but not a 30-minute delay, and increased false memory at both delays. Long-term retention gains were predicted by multi-voxel representation distinctiveness in the posterior parietal cortex that increased progressively over retrieval practice. False memory was predicted by unstable representation distinctiveness in the medial temporal lobe during retrieval practice. Memory-related neural networks gradually reconfigured over retrieval practice, with the ventrolateral and medial prefrontal cortex acting as hubs for functional connections that predicted long-term retention gains and false memory outcomes respectively. Our findings demonstrate dynamic neural reorganization during retrieval practice, through which memories are arranged into discrete yet malleable representations for subsequent consolidation.

neuroscience↗

bioRxiv2020

The electrically conductive pili of Geobacter soli

Electrically conductive pili (e-pili) enable electron transport over multiple cell lengths to extracellular environments and play an important role in extracellular electron transfer (EET) of Geobacter species. To date, the studies of e-pili have mainly focused on Geobacter sulfurreducens and the closely related Geobacter metallireducens because of their developed genetic manipulation systems. We investigated the role of G. soli pili in EET by directly deleting the pilin gene, pilA, which is predicted to encode e-pili. Deletion of pilA, prevented the production of pili, resulting in poor Fe(III) oxide reduction and low current production, implying that G. soli pili is required for EET. To further evaluate the conductivity of G. soli pili compared with G. sulfurreducens pili, the pilA of G. soli was heterologously expressed in G. sulfurreducens, yielding the G. sulfurreducens strain GSP. This strain produced abundant pili with similar conductivity to the control strain that expressed native G. sulfurreducens pili, consistent with G. soli as determined by direct measurement, which suggested that G. soli pili is electrically conductive. Surprisingly, strain GSP was deficient in Fe(III) oxide reduction and current production due to the impaired content of outer-surface c-type cytochromes. These results demonstrated that heterologous pili of G. sulfurreducens severely reduces the content of outer-surface c-type cytochromes and consequently eliminates the capacity for EET, which strongly suggests an attention should be paid to the content of c-type cytochromes when employing G. sulfurreducens to heterologously express pili from other microorganisms. IMPORTANCEThe studies of electrically conductive pili (e-pili) of Geobacter species are of interest because of its application prospects in electronic materials. e-Pili are considered a substitution for electronic materials due to its renewability, biodegradability and robustness. Continued exploration of additional e-pili of Geobacter soli will improve the understanding of their biological role in extracellular electron transfer and expand the range of available electronic materials. Heterologously expressing the pilin genes from phylogenetically diverse microorganisms has been proposed as an emerging approach to screen potential e-pili according to high current densities. However, our results indicated that a Geobacter sulfurreducens strain heterologously expressing a pilin gene produced low current densities that resulted from a lack of content of c-type cytochromes, which were likely to possess e-pili. These results provide referential significance to yield e-pili from diverse microorganisms.

microbiology↗

bioRxiv2019

Recombinant HcGAPDH Protein Expressed on Probiotic Bacillus subtilis Spores Protects Sheep from Haemonchus contortus Infection by Inducing both Humoral and Cell-mediated Responses

Probiotic Bacillales have been shown effective in controlling pathogens. In particular, live probiotic bacteria are thought to improve the composition of gastrointestinal microbiota, and to reduce pathogen colonization. However, how probiotics regulate immune responses and protect the host from parasitic infection remains largely unknown. In this study, we investigated whether Bacillales can be used against Haemonchus contortus, a parasitic nematode that infects small ruminants in sheep and goats worldwide. Using 16S ribosomal RNA sequencing, we found that Bacillales was highly depleted in the abomasal microbiota of sheep infected with H. contortus. We constructed a recombinant Bacillus subtilis strain (rBSCotB-HcG) that express glyceraldehyde-3-phosphate dehydrogenase of H. contortus (HcGAPDH) on its spore surface. However, mice orally administrated with the rBSCotB-HcG strain showed strong Th1-dominated immune responses; and sheep administrated per os with rBSCotB-HcG showed increased proliferation of peripheral blood mononuclear cells, elevated anti-HcGAPDH IgG levels in sera, and higher anti-HcGAPDH sIgA levels in intestinal mucus. In addition, treatment of H. contortus infected sheep with rBSCotB-HcG (Hc+rBSCotB-HcG) promoted the abundance of probiotic species in the abomasal microbiota; it also improved the average weight gain of the sheep by 27.7%. These Hc+rBSCotB-HcG sheep have reduced number of eggs per gram of feces (by 84.1%) and worm burdens (by 71.5%), with alleviated abomasal damage by H. contortus. Collectively, our data demonstrate the protective roles of CotB-HcGAPDH-expressing B. subtilis spores against H. contortus infection, suggesting a potential value of using this probiotic-based strategy in controlling parasitic nematodes of socioeconomic importance. ImportanceSequencing of the infected sheep s stomach flora revealed potential probiotics that could control H. contortus infection, and further genetically engineered recombinant probiotic spores expressing parasite protein, and validated their good immunogenicity in a mouse model. In the sheep infection model, the recombinant probiotics have proven to be effective against parasite infections.

microbiology↗

bioRxiv2018

H3.3K4M destabilizes enhancer epigenomic writers MLL3/4 and impairs adipose tissue development

Histone H3K4 mono-methyltransferases MLL3 and MLL4 (MLL3/4) are required for enhancer activation during cell differentiation, though the mechanism is incompletely understood. To address MLL3/4 enzymatic activity in enhancer regulation, we have generated two mouse lines: one expressing H3.3K4M, a lysine-4-to-methionine (K4M) mutation of histone H3.3 that inhibits H3K4 methylation, and the other carrying conditional double knockout of MLL3/4 enzymatic SET domains. Expression of H3.3K4M in lineage-specific precursor cells depletes H3K4 methylation and prevents adipogenesis and adipose tissue development. Mechanistically, H3.3K4M prevents enhancer activation in adipogenesis by destabilizing MLL3/4 proteins but not other Set1-like H3K4 methyltransferases. Notably, deletion of the enzymatic SET domain of MLL3/4 in lineage-specific precursor cells mimics H3.3K4M expression and prevents adipose tissue development. Interestingly, destabilization of MLL3/4 by H3.3K4M in adipocytes does not affect adipose tissue maintenance and function. Together, our findings indicate that H3.3K4M destabilizes enhancer epigenomic writers MLL3/4 and impairs adipose tissue development.

molecular biology↗