Extracellular Matrix Regulation Research Articles

Ecliptasaponin A attenuates renal fibrosis by regulating the extracellular matrix of renal tubular cells

Renal fibrosis is the most common manifestation of end-stage renal disease (ESRD), including diabetic kidney disease (DKD), but there is no effective treatment in renal fibrosis. Natural products are a rich source of clinical drug research and have been used in the clinical research of various diseases. In this study, we searched for traditional Chinese medicine monomers that attenuate fibrosis and assessed their effect on the fibrosis marker connective tissue growth factor (CTGF) in cells which we found ecliptasaponin A. Subsequently, we evaluated the effect of ecliptasaponin A on renal fibrosis in the classic renal fibrosis unilateral ureteral obstruction (UUO) mouse model and found that ecliptasaponin A could reduce the renal collagen fiber deposition and renal extracellular matrix (ECM) protein expression in UUO mice. In vitro, ecliptasaponin A can inhibit ECM protein expression in human kidney-2 (HK-2) cells induced by transforming growth factor-beta1 (TGFβ1). To further clarify the mechanism of ecliptasaponin A in attenuating renal fibrosis, we performed transcriptome sequencing of HK-2 cells treated with TGFβ1 and ecliptasaponin A. The functions and pathways were mainly enriched in the extracellular matrix and TGFβ signalling pathway. Matrix metalloproteinase 10 (MMP10) and matrix metalloproteinase 13 (MMP13) are the main differentially expressed genes in extracellular matrix regulation. Then, we measured MMP10 and MMP13 in the cells and found that ecliptasaponin A had a significant inhibitory effect on MMP13 expression but not on MMP10 expression. Furthermore, we overexpressed MMP13 in HK-2 cells treated with TGFβ1 and found that MMP13 promoted HK-2 cell injury. Our findings suggest that ecliptasaponin A can attenuate renal fibrosis, which may provide a new method for treating renal fibrosis clinically.

Genomic Characterization of Cervical Tumors Driven by Rare High-Risk HPV Subtypes Utilizing a Deep Learning Framework

As many as 30-50% of patients with locally advanced cervical cancer (LACC) experience recurrence after chemoradiation therapy (CRT). More sophisticated prognostic schemes and targeted therapeutic options are urgently needed. Human papillomavirus (HPV) is responsible for the majority of invasive cervical carcinomas, most commonly HPV 16 and 18 subtypes. In large part due to their rarity, little is known about the biologic behavior of LACC driven by non-16/18 HPV genotypes. We hypothesized that rare HPV subtypes drive distinct gene expression patterns. To aid in the common dilemma of limited sample procurement, we developed a tool which leverages population data and generative adversarial neural network (GAN) modelling to exploit patterns of gene expression of small phenotypic groups for downstream analysis. Here, we employed a deep learning approach to identify gene expression patterns unique to tumors caused by rare HPV subtypes. Whole transcriptome analysis of tumor biopsies from an institutional LACC tumor bank were employed including 130 HPV16/18 positive, and at least 3 each of rare HPV subtypes 31, 33, 39, 45, 52, 58, and 59. A Wasserstein GAN model (WGAN) was trained for each rare HPV subtype, and used to generate augmented rare HPV population data for downstream differential expression testing between rare HPV subtypes and HPV16/18. K-means clustering analysis was performed using R stats package. Differential gene expression testing between rare HPV subtype populations was performed using the EdgeR R-package. Pathway Enrichment analysis was conducted using EnrichR software. By minimizing intergroup clustering distance, 3 clusters of HPV driven disease were demonstrated. The first cluster demonstrated biology similar to HPV16 and HPV18. Namely, pathway enrichment analysis performed on lists of differentially expressed genes between GAN augmented rare HPV subtypes (HPV45, HPV52, and HPV58) and classical HPV subtypes 16 and 18, yielded no significant statistical differences. The second cluster demonstrated enriched gene expression in proinflammatory IL-1 and IL-6 family cytokines and focal adhesion signaling (HPV31, HPV33, HPV39) (IL-1 regulation of extracellular matrix, p = 5.0e-6; Oncostatin M signaling, p = 2.0e-7; Integrin Signaling, 2.5e-7). The last cluster demonstrated an increased Th2/myeloid signature (HPV59) (T helper cell surface molecules 1.2e-7, myeloid cell signature 8.5e-9). Utilizing a deep learning architecture to model gene expression of rare HPV subtypes we demonstrate 3 groups of HPV driven cervical cancer biology. These groups include a classical subtype, a high IL-1/IL-6 high subtype, and a myeloid associated subtype. Knowledge of such tumor heterogeneity can aid in the future development of targeted treatment plans and patient prognosis.

MMP-2 Associates With Incident Heart Failure and Atrial Fibrillation: The ARIC Study.

MMP (matrix metalloproteinase)-2 participates in extracellular matrix regulation and may be involved in heart failure (HF), atrial fibrillation (AF), and coronary heart disease. Among the 4693 ARIC study (Atherosclerosis Risk in Communities) participants (mean age, 75±5 years; 42% women) without prevalent HF, multivariable Cox proportional hazard models were used to estimate associations of plasma MMP-2 levels with incident HF, HF with preserved ejection fraction (≥50%), HF with reduced ejection fraction (<50%), AF, and coronary heart disease. Mediation of the association between MMP-2 and HF was assessed by censoring participants who developed AF or coronary heart disease before HF. Multivariable linear regression models were used to assess associations of MMP-2 with measures of left ventricular and left atrial structure and function. Compared with the 3 lower quartiles, the highest MMP-2 quartile associated with greater risk of incident HF overall (adjusted hazard ratio, 1.48 [95% CI, 1.21-1.81]), incident HF with preserved ejection fraction (1.44 [95% CI, 1.07-1.94]), incident heart failure with reduced ejection fraction (1.48 [95% CI, 1.08-2.02]), and incident AF (1.44 [95% CI, 1.18-1.77]) but not incident coronary heart disease (0.97 [95% CI, 0.71-1.34]). Censoring AF attenuated the MMP-2 association with HF with preserved ejection fraction. Higher plasma MMP-2 levels were associated with larger left ventricular end-diastolic volume index, greater left ventricular mass index, higher E/e' ratio, larger left atrial volume index, and worse left atrial reservoir and contractile strains (all P<0.001). Higher plasma MMP-2 levels associate with diastolic dysfunction, left atrial dysfunction, and a higher risk of incident HF and AF. AF is a mediator of MMP-2-associated HF with preserved ejection fraction risk.

A bronchial gene signature specific for severe COPD that is retained in the nose.

A subset of COPD patients develops advanced disease with severe airflow obstruction, hyperinflation and extensive emphysema. We propose that the pathogenesis in these patients differs from mild-moderate COPD and is reflected by bronchial gene expression. The aim of the present study was to identify a unique bronchial epithelial gene signature for severe COPD patients. We obtained RNA sequencing data from bronchial brushes from 123 ex-smokers with severe COPD, 23 with mild-moderate COPD and 23 non-COPD controls. We identified genes specific to severe COPD by comparing severe COPD to non-COPD controls, followed by removing genes that were also differentially expressed between mild-moderate COPD and non-COPD controls. Next, we performed a pathway analysis on these genes and evaluated whether this signature is retained in matched nasal brushings. We identified 219 genes uniquely differentially expressed in severe COPD. Interaction network analysis identified VEGFA and FN1 as the key genes with the most interactions. Genes were involved in extracellular matrix regulation, collagen binding and the immune response. Of interest were 10 genes (VEGFA, DCN, SPARC, COL6A2, MGP, CYR61, ANXA6, LGALS1, C1QA and C1QB) directly connected to fibronectin 1 (FN1). Most of these genes were lower expressed in severe COPD and showed the same effect in nasal brushings. We found a unique severe COPD bronchial gene signature with key roles for VEGFA and FN1, which was retained in the upper airways. This supports the hypothesis that severe COPD, at least partly, comprises a different pathology and supports the potential for biomarker development based on nasal brushes in COPD.

Decoding the transcriptome of Duchenne muscular dystrophy to the single nuclei level reveals clinical-genetic correlations

Duchenne muscular dystrophy is a genetic disease produced by mutations in the dystrophin gene characterized by early onset muscle weakness leading to severe and irreversible disability. The cellular and molecular consequences of the lack of dystrophin in humans are only partially known, which is crucial for the development of new therapies aiming to slow or stop the progression of the disease. Here we have analyzed quadriceps muscle biopsies of seven DMD patients aged 2 to 4 years old and five age and gender matched controls using single nuclei RNA sequencing (snRNAseq) and correlated the results obtained with clinical data. SnRNAseq identified significant differences in the proportion of cell population present in the muscle samples, including an increase in the number of regenerative fibers, satellite cells, and fibro-adipogenic progenitor cells (FAPs) and a decrease in the number of slow fibers and smooth muscle cells. Muscle samples from the younger patients with stable mild weakness were characterized by an increase in regenerative fibers, while older patients with moderate and progressive weakness were characterized by loss of muscle fibers and an increase in FAPs. An analysis of the gene expression profile in muscle fibers identified a strong regenerative signature in DMD samples characterized by the upregulation of genes involved in myogenesis and muscle hypertrophy. In the case of FAPs, we observed upregulation of genes involved in the extracellular matrix regeneration but also several signaling pathways. Indeed, further analysis of the potential intercellular communication profile showed a dysregulation of the communication profile in DMD samples identifying FAPs as a key regulator of cell signaling in DMD muscle samples. In conclusion, our study has identified significant differences at the cellular and molecular levels in the different cell populations present in skeletal muscle samples of patients with DMD compared to controls.

Effect of Aloe Vera On Mmp-1 And Timp-1 Expression on Diabetic Wound Healing

Aim: The aim of this study is to investigate the healing aspect of aloe vera in diabetes mellitus, which inhibits wound healing.&#x0D; Methods: Diabetes model was created with streptozotocin. At the end of the 14-day experiment, blood glucose was measured from the tail vein of animals in all groups and blood was taken from the heart and sacrificed. Histopathology and immunohistochemical statistics and evaluation were performed.&#x0D; Results: Pycnosis and degeneration of epithelial cells were observed in diabetes groups. Leukocyte infiltration in the dermal papilla, degeneration of collagen fibers and an increase in the extracellular matrix were observed. It was observed that the epithelial layer in the aloe vera group was histologically close to the control group. It was observed that decreased inflammation in the dermal papilla and decreased in organized collagen fibers and vessel dilatation were observed. In the control group, MMP-1 and TIMP-1 expression were positive in the epidermis and dermis layers. In the diabetes group, weak expression of MMP-1 and TIMP-1 was observed in cells in the epidermis and dermis. The expression of MMP-1 and TIMP-1 in the surface epithelium in the aloe vera group was increased compared to the diabetes group.&#x0D; Conclusions: Aloe vera accelerated cell and extracellular matrix regeneration with its anti-oxidative activity

Predictors of aneurysmal occlusion following intracranial aneurysms treatment with pipeline embolization device.

Pipeline embolization device (PED) is thought to induce aneurysmal occlusion through diversion of flow away from the aneurysmal sac with subsequent thrombosis and endothelialization. The impact of different factors especially hypertension (HTN)-a known predisposing factor to hypercoagulability and altered endothelial function-on aneurysmal occlusion after flow diversion has not been studied. We sought to determine predictors of aneurysmal occlusion following PED treatment focusing on impact of blood pressure. Database of patients with cerebral aneurysms treated with PED from 2013 to 2019 at our institution was retrospectively reviewed. Patients were defined as hypertensive if (1) they had a documented history of HTN requiring anti-HTN medications or (2) average systolic blood pressure on three measurements was > 130mmHg. The primary outcome was aneurysm occlusion status at the last imaging follow-up. Multivariable logistic regression model was constructed to assess the effect of HTN on occlusion, controlling for age, smoking, aneurysmal size, fusiform morphology, posterior circulation location, and incorporated branches. A total of 331 aneurysms in 294 patients were identified for this analysis. The mean age was 59years (79.9% female). Fifty-five percent of the cohort were classified as hypertensive. When controlling for other potential confounders, hypertensive patients trended toward higher odds of achieving complete occlusion compared to non-hypertensive patients (OR = 2.05; 95% CI = 0.99-4.25; p = 0.052). Meanwhile, age (OR = 0.91; 95% CI = 0.88-0.95; p < 0.001) and an incorporated branch into an aneurysm (OR = 0.22; 95% CI = 0.08-0.58; p < 0.002) were associated with decreased odds for complete aneurysmal occlusion. Hypertensive patients show a trend toward higher odds of achieving complete occlusion when controlling for potential confounders. The HTN-induced hypercoagulable state, enhanced endothelial activation, and altered extracellular matrix regulation might be the contributing factors. Further research is warranted to explore clinical implications of these findings.

Integration of plasma and CSF metabolomics with CSF proteomic reveals novel associations between lipid mediators and central nervous system vascular and energy metabolism

Integration of the omics data, including metabolomics and proteomics, provides a unique opportunity to search for new associations within metabolic disorders, including Alzheimer’s disease. Using metabolomics, we have previously profiled oxylipins, endocannabinoids, bile acids, and steroids in 293 CSF and 202 matched plasma samples from AD cases and healthy controls and identified both central and peripheral markers of AD pathology within inflammation-regulating cytochrome p450/soluble epoxide hydrolase pathway. Additionally, using proteomics, we have identified five cerebrospinal fluid protein panels, involved in the regulation of energy metabolism, vasculature, myelin/oligodendrocyte, glia/inflammation, and synapses/neurons, affected in AD, and reflective of AD-related changes in the brain. In the current manuscript, using metabolomics-proteomics data integration, we describe new associations between peripheral and central lipid mediators, with the above-described CSF protein panels. Particularly strong associations were observed between cytochrome p450/soluble epoxide hydrolase metabolites, bile acids, and proteins involved in glycolysis, blood coagulation, and vascular inflammation and the regulators of extracellular matrix. Those metabolic associations were not observed at the gene-co-expression level in the central nervous system. In summary, this manuscript provides new information regarding Alzheimer’s disease, linking both central and peripheral metabolism, and illustrates the necessity for the “omics” data integration to uncover associations beyond gene co-expression.

Substrate Stiffness Modulates TGF-β Activation and ECM-Associated Gene Expression in Fibroblasts.

Transforming growth factor-β (TGF-β) is a multifunctional cytokine that regulates the expression of ECM-associated genes during early injury. Tissue fibrosis development is driven by synergistic cues between the evolving biochemical and mechanical milieu. Few studies have addressed the role of substrate stiffness on TGF-β activity and extracellular matrix (ECM)-associated genes. We used a commercial formulation of polydimethylsiloxane (PDMS) to fabricate substrates of 40 kPa, 300 kPa, and 1.5 MPa stiffness, and cultured the HMF3S fibroblasts on substrates. We quantified TGF-β protein secreted by HMF3S cells on different substrates using a TGF-β responsive promoter reporter assay. We also tested for variations in gene expression levels on the substrates using RT-PCR and Western blotting and determined the MMP-2 and MMP-9 activities with gelatin zymography. The results showed that TGF-β protein activation was significantly compromised at lower stiffnesses. The expression of integrin α5 decreased on lower stiffness substrates and correlated with inefficient TGF-β protein activation. Collagen I, collagen III, and MMP-2 expression levels were lower on softer substrates; there was little MMP-9 activity on all substrates. Cell and nuclear morphologies were more rounded on compliant substrates, correlating with increased tubulin expression. Proliferations were higher on stiffer substrates, whereas cells on softer substrates showed cell cycle arrest. These results demonstrated critical feedback mechanisms between substrate stiffness and ECM regulation by fibroblasts, relevant in fibrosis.

Analysis of matrisome expression patterns in murine and human dorsal root ganglia.

The extracellular matrix (ECM) is a dynamic structure of molecules that can be divided into six different categories and are collectively called the matrisome. The ECM plays pivotal roles in physiological processes in many tissues, including the nervous system. Intriguingly, alterations in ECM molecules/pathways are associated with painful human conditions and murine pain models. Nevertheless, mechanistic insight into the interplay of normal or defective ECM and pain is largely lacking. The goal of this study was to integrate bulk, single-cell, and spatial RNA sequencing (RNAseq) datasets to investigate the expression and cellular origin of matrisome genes in male and female murine and human dorsal root ganglia (DRG). Bulk RNAseq showed that about 65% of all matrisome genes were expressed in both murine and human DRG, with proportionally more core matrisome genes (glycoproteins, collagens, and proteoglycans) expressed compared to matrisome-associated genes (ECM-affiliated genes, ECM regulators, and secreted factors). Single cell RNAseq on male murine DRG revealed the cellular origin of matrisome expression. Core matrisome genes, especially collagens, were expressed by fibroblasts whereas matrisome-associated genes were primarily expressed by neurons. Cell-cell communication network analysis with CellChat software predicted an important role for collagen signaling pathways in connecting vascular cell types and nociceptors in murine tissue, which we confirmed by analysis of spatial transcriptomic data from human DRG. RNAscope in situ hybridization and immunohistochemistry demonstrated expression of collagens in fibroblasts surrounding nociceptors in male and female human DRG. Finally, comparing human neuropathic pain samples with non-pain samples also showed differential expression of matrisome genes produced by both fibroblasts and by nociceptors. This study supports the idea that the DRG matrisome may contribute to neuronal signaling in both mouse and human, and that dysregulation of matrisome genes is associated with neuropathic pain.

The specific DNA methylation landscape in focal cortical dysplasia ILAE type 3D

Focal Cortical Dysplasia (FCD) is a frequent cause of drug-resistant focal epilepsy in children and young adults. The international FCD classifications of 2011 and 2022 have identified several clinico-pathological subtypes, either occurring isolated, i.e., FCD ILAE Type 1 or 2, or in association with a principal cortical lesion, i.e., FCD Type 3. Here, we addressed the DNA methylation signature of a previously described new subtype of FCD 3D occurring in the occipital lobe of very young children and microscopically defined by neuronal cell loss in cortical layer 4. We studied the DNA methylation profile using 850 K BeadChip arrays in a retrospective cohort of 104 patients with FCD 1 A, 2 A, 2B, 3D, TLE without FCD, and 16 postmortem specimens without neurological disorders as controls, operated in China or Germany. DNA was extracted from formalin-fixed paraffin-embedded tissue blocks with microscopically confirmed lesions, and DNA methylation profiles were bioinformatically analyzed with a recently developed deep learning algorithm. Our results revealed a distinct position of FCD 3D in the DNA methylation map of common FCD subtypes, also different from non-FCD epilepsy surgery controls or non-epileptic postmortem controls. Within the FCD 3D cohort, the DNA methylation signature separated three histopathology subtypes, i.e., glial scarring around porencephalic cysts, loss of layer 4, and Rasmussen encephalitis. Differential methylation in FCD 3D with loss of layer 4 mapped explicitly to biological pathways related to neurodegeneration, biogenesis of the extracellular matrix (ECM) components, axon guidance, and regulation of the actin cytoskeleton. Our data suggest that DNA methylation signatures in cortical malformations are not only of diagnostic value but also phenotypically relevant, providing the molecular underpinnings of structural and histopathological features associated with epilepsy. Further studies will be necessary to confirm these results and clarify their functional relevance and epileptogenic potential in these difficult-to-treat children.

MYC Promotes Aggressive Growth and Metastasis of a WNT-Medulloblastoma Mouse Model

Medulloblastoma (MB), the most common malignant pediatric brain tumor, comprises four molecularly and clinically distinct subgroups (termed WNT, SHH, group 3, and group 4). Prognosis varies based on genetic and pathological features associated with each molecular subgroup. WNT-MB, considered low-risk, is rarely metastatic and contains activating mutations in CTNNB1; group 3-MB (GRP3-MB), commonly classified as high-risk, is frequently metastatic and can contain genomic alterations, resulting in elevated MYC expression. Here, we compare model systems of low-risk WNT-MB and high-risk GRP3-MB to identify tumor and microenvironment interactions that could contribute to features associated with prognosis. Compared to GRP3-MB, we find that WNT-MB is enriched in gene sets related to extracellular matrix (ECM) regulation and cellular adhesion. Exogenous expression of MycT58A in a murine WNT-MB model significantly accelerates growth and results in metastatic disease. In addition to decreased ECM regulation and cell adhesion pathways, we also identified immune system interactions among the top downregulated signaling pathways following MycT58A expression. Taken together, our data provide evidence that increased Myc signaling can promote the growth and metastasis in a murine model of WNT-MB.

Effects of Pera Orange Juice and Moro Orange Juice in Healthy Rats: A Metabolomic Approach.

Sixty male Wistar rats were allocated into 3 groups: control (C), Pera orange juice (PO), and Moro orange juice (MO). PO and MO groups received Pera orange juice or Moro orange juice, respectively, and C received water with maltodextrin (100 g/L). Echocardiogram and euthanasia were performed after 4 weeks. Plasma metabolomic analysis was performed by high-resolution mass spectrometry. Type I collagen was evaluated in picrosirius red-stained slides and matrix metalloproteinase (MMP)-2 activity by zymography. MMP-9, tissue inhibitor of metalloproteinase (TIMP)-2, TIMP-4, type I collagen, and TNF-α protein expression were evaluated by Western blotting. We differentially identified three metabolites in PO (N-docosahexaenoyl-phenylalanine, diglyceride, and phosphatidylethanolamine) and six in MO (N-formylmaleamic acid, N2-acetyl-L-ornithine, casegravol isovalerate, abscisic alcohol 11-glucoside, cyclic phosphatidic acid, and torvoside C), compared to controls, which are recognized for their possible roles in cardiac remodeling, such as extracellular matrix regulation, inflammation, oxidative stress, and membrane integrity. Cardiac function, collagen level, MMP-2 activity, and MMP-9, TIMP-2, TIMP-4, type I collagen, and TNF-α protein expression did not differ between groups. Ingestion of Pera and Moro orange juice induces changes in plasma metabolites related to the regulation of extracellular matrix, inflammation, oxidative stress, and membrane integrity in healthy rats. Moro orange juice induces a larger number of differentially expressed metabolites than Pera orange juice. Alterations in plasma metabolomics induced by both orange juice are not associated with modifications in cardiac extracellular matrix components. Our results allow us to postulate that orange juice may have beneficial effects on pathological cardiac remodeling.

SPARC Is Highly Expressed in Young Skin and Promotes Extracellular Matrix Integrity in Fibroblasts via the TGF-β Signaling Pathway.

The matricellular secreted protein acidic and rich in cysteine (SPARC; also known as osteonectin), is involved in the regulation of extracellular matrix (ECM) synthesis, cell-ECM interactions, and bone mineralization. We found decreased SPARC expression in aged skin. Incubating foreskin fibroblasts with recombinant human SPARC led to increased type I collagen production and decreased matrix metalloproteinase-1 (MMP-1) secretion at the protein and mRNA levels. In a three-dimensional culture of foreskin fibroblasts mimicking the dermis, SPARC significantly increased the synthesis of type I collagen and decreased its degradation. In addition, SPARC also induced receptor-regulated SMAD (R-SMAD) phosphorylation. An inhibitor of transforming growth factor-beta (TGF-β) receptor type 1 reversed the SPARC-induced increase in type I collagen and decrease in MMP-1, and decreased SPARC-induced R-SMAD phosphorylation. Transcriptome analysis revealed that SPARC modulated expression of genes involved in ECM synthesis and regulation in fibroblasts. RT-qPCR confirmed that a subset of differentially expressed genes is induced by SPARC. These results indicated that SPARC enhanced ECM integrity by activating the TGF-β signaling pathway in fibroblasts. We inferred that the decline in SPARC expression in aged skin contributes to process of skin aging by negatively affecting ECM integrity in fibroblasts.

The Importance of Effective Ligand Concentration to Direct Epithelial Cell Polarity in Dynamic Hydrogels.

Epithelial cysts and organoids are multicellular hollow structures formed by correctly polarized epithelial cells. Important in steering these cysts from single cells is the dynamic regulation of extracellular matrix presented ligands, and matrix dynamics. Here, control over the effective ligand concentration is introduced, decoupled from bulk and local mechanical properties, in synthetic dynamic supramolecular hydrogels formed through noncovalent crosslinking of supramolecular fibers. Control over the effective ligand concentration is realized by 1) keeping the ligand concentration constant, but changing the concentration of nonfunctionalized molecules or by 2) varying the ligand concentration, while keeping the concentration of non-functionalized molecules constant. Theresults show that in 2D, the effective ligand concentration within thesupramolecular fibers rather than gel stiffness (from 0.1 to 8kPa) regulates epithelial polarity. In 3D, increasing the effective ligand concentration from 0.5 × 10-3 to 2 × 10-3 m strengthens the effect of increased gel stiffness from 0.1 to 2kPa, to synergistically yield more correctly polarized cysts. Through integrin manipulation, it isshown that epithelial polarity is regulated by tension-based homeostasis between cells and matrix. Theresults reveal the effective ligand concentration as influential factor in regulating epithelial polarity and provide insights on engineering of synthetic biomaterials for cell and organoid culture.

Unravelling potential biomarkers for acute and chronic brucellosis through proteomic and bioinformatic approaches.

This study aimed to identify biomarkers for acute and chronic brucellosis using advanced proteomic and bioinformatic methods. Blood samples from individuals with acute brucellosis, chronic brucellosis, and healthy controls were analyzed. Proteomic techniques and differential expression analysis were used to identify differentially expressed proteins. Co-expression modules associated with brucellosis traits were identified using weighted gene co-expression network analysis (WGCNA). 763 differentially expressed proteins were identified, and two co-expression modules were found to be significantly associated with brucellosis traits. 25 proteins were differentially expressed in all three comparisons, and 20 hub proteins were identified. Nine proteins were found to be both differentially expressed and hub proteins, indicating their potential significance. A random forest model based on these nine proteins showed good classification performance. The identified proteins are involved in processes such as inflammation, coagulation, extracellular matrix regulation, and immune response. They provide insights into potential therapeutic targets and diagnostic biomarkers for brucellosis. This study improves our understanding of brucellosis at the molecular level and paves the way for further research in targeted therapies and diagnostics.

Histological assessment and gene expression analysis of intra-oral soft tissue graft donor sites.

To determine the structural and gene expression features of different intra-oral soft tissue donor sites (i.e., anterior palate, posterior palate, maxillary tuberosity and retromolar pad). Standardized mucosal tissue punch biopsies were collected from at least one donor site per subject. Histological processing was performed to determine tissue morphometry and quantify collagen composition. Site-specific gene distribution was mapped using targeted gene expression analysis and validated using real time polymerase chain reaction (qPCR). A total of 50 samples from 37 subjects were harvested. Epithelial thickness did not differ between sites. However, lamina propria was thicker in the maxillary tuberosity (2.55 ± 0.92 mm) and retromolar pad (1.98 ± 0.71 mm) than in the lateral palate. Type I collagen was the predominant structural protein in the lamina propria (75.06%-80.21%). Genes involving collagen maturation and extracellular matrix regulation were highly expressed in the maxillary tuberosity and retromolar pad, while lipogenesis-associated genes were markedly expressed in the lateral palate. The retromolar pad showed the most distinct gene expression profile, and the anterior and posterior palate displayed similar transcription profiles. Tissue samples harvested from the anterior and posterior palate differed morphologically from those from the maxillary tuberosity and retromolar pad. Each intra-oral site showed a unique gene expression profile, which might impact their biological behaviour and outcomes of soft tissue augmentation procedures.

Glycoproteomic analysis of regulatory effects of bisecting N-glycans on N-glycan biosynthesis and protein expressions in human HK-2 cells

Bisecting N-glycan is known to be a metastasis suppressor and plays a regulatory role in the biosynthesis of N-glycans. Previous studies have shown that bisecting N-glycans are capable of modulating both the branching and terminal modifications of glycans. However, these effects have been investigated mainly by glycomic approaches and it remains unclear how they alter when glycans are attached to different glycosites of proteins. Here, we systematically investigated the regulatory roles of bisecting N-glycans in human HK-2 cells using StrucGP, a strategy we developed for structural interpretation of site-specific N-glycans on glycoproteins. The glycoproteomics analysis showed that most of bisecting N-glycans are complex type and often occur in company with core fucosylation. With the overexpression and knockdown of MGAT3, the only enzyme responsible for bisecting N-glycan synthesis, we found that bisecting N-glycans can impact the biosynthesis of N-glycans from multiple aspects, including glycan types, branching, sialylation, fucosylation (different effects for core and terminal fucosylation) as well as the presence of terminal N-acetylglucosamine. Furthermore, gene ontology analysis suggested that most proteins with bisecting N-glycans located in the extracellular region or membrane, where they function mostly in cell adhesion, extracellular matrix regulation and cell signaling. Finally, we showed that overexpression of bisecting N-glycans had a broad impact on the protein expressions of HK-2 cells, involving multiple biological processes. Taken together, our work systematically demonstrated the expression profiles of bisecting N-glycans, and their regulatory effects on the biosynthesis of N-glycans and protein expressions, which provide valuable information for the functional elucidation of bisecting N-glycans.

More than just a small left ventricle: the right ventricular fibroblast and ECM in health and disease.

Fibroblasts intricately organize and regulate the extracellular matrix (ECM) in cardiac health and disease. Excess deposition of ECM proteins causes fibrosis, resulting in disrupted signaling conduction and contributing to the development of arrhythmias and impaired cardiac function. Fibrosis is causally involved in cardiac failure in the left ventricle (LV). Fibrosis likely occurs in right ventricle (RV) failure, yet mechanisms remain unclear. Indeed, RV fibrosis is poorly understood with mechanisms often extrapolated from the LV to the RV. However, emerging data suggest that the LV and RV are distinct cardiac chambers and differ in regulation of the ECM and response to fibrotic stimuli. In the present review, we will discuss differences in ECM regulation in the healthy RV and LV. We will discuss the importance of fibrosis in the development of RV disease in pressure overload, inflammation, and aging. During this discussion, we will highlight mechanisms of fibrosis with respect to the synthesis of ECM proteins while acknowledging the importance of considering collagen breakdown. We will also discuss current knowledge of antifibrotic therapies in the RV and the need for additional research to help delineate the shared and distinct mechanisms of RV and LV fibrosis.

Long-Term Chondrocyte Retention in Partially Decellularized Tracheal Grafts.

Decellularized tracheal grafts possess the biological cues necessary for tissue regeneration. However, conventional decellularization approaches to target the removal of all cell populations including chondrocytes lead to a loss of mechanical support. We have created a partially decellularized tracheal graft (PDTG) that preserves donor chondrocytes and the mechanical properties of the trachea. In this study, we measured PDTG chondrocyte retention with a murine microsurgical model. Murine in vivo time-point study. Research Institute affiliated with Tertiary Pediatric Hospital. PDTG was created using a sodium dodecyl sulfate protocol. Partially decellularized and syngeneic grafts were orthotopically implanted into female C57BL/6J mice. Grafts were recovered at 1, 3, and 6 months postimplant. Pre- and postimplant grafts were processed and analyzed via quantitative immunofluorescence. Chondrocytes (SOX9+, DAPI+) present in the host and graft cartilage was evaluated using ImageJ. Partial decellularization resulted in the maintenance of gross tracheal architecture with the removal of epithelial and submucosal structures on histology. All grafts demonstrated SOX9+ chondrocytes throughout the study time points. Chondrocytes in PDTG were lower at 6 months compared to preimplant and syngeneic controls. PDTG retained donor graft chondrocytes at all time points. However, PDTG exhibits a reduction in chondrocytes at 6 months. The impact of these histologic changes on cartilage extracellular matrix regeneration and repair remains unclear.