Extracellular Matrix Organization Research Articles

Abstract TP346: Investigating Transcriptomic Profiles of Peripheral Blood Mononuclear Cells in Moyamoya Disease Using Single-Cell RNAseq

Objectives: Moyamoya Disease (MMD) is a complex cerebrovascular disease marked by progressive narrowing in the cerebral arteries. Previous studies have suggested that dysregulated genes in the peripheral blood of MMD patients are involved in extracellular matrix organization and immune responses. However, the mechanism by which the immune response contributes to MMD progression is unclear. In this study we investigated the immune landscape in the peripheral blood mononuclear cells (PBMCs) of MMD patients using single-cell RNA sequencing (scRNA-seq). Methods: Blood samples were collected from 3 bilateral MMD patients and 2 healthy controls. PBMCs were isolated and processed for 10x single-cell RNA sequencing. Immune cell heterogeneity and differentially expressed genes (DEGs) in each cell type were identified. Top biological pathways were determined using Ingenuity Pathway Analysis (IPA). Flow cytometry with an 11-fluorochrome panel was use to validate key immune populations and fluorescence-activated cell sorting (FACS) was used to isolate specific immune populations for transcriptome analysis. Results: Preliminary analysis revealed notable increase of cell percentages in certain cell types in MMD, such as CD8+T (9.21% vs 7.11%), B cells (6.94% vs 3.45%) and CD4+NKT (5.78% vs 3.22%), and decrease in CD8+NKT (9.59% vs 15.74%), compared to controls. Higher transcriptome dynamics were observed in certain cell type in MMD, with 2402 DEGs in classical monocytes, 1379 DEGs in CD4+T, 1312 DEGs in CD8+NKT and 997 DEGs in B cells. Interestingly, many cell types, except for classical and non-classical monocytes, displayed a higher number of downregulated DEGs in MMD, particularly in T cells, B cells, and NKT cells. Pathway analysis indicated that CD4+T, CD8+NKT, and B cells show predicted inhibition in several pathways, including T cell receptor and mTOR signaling, interleukins and CXCR4 signaling, as well as cell surface interactions at the vascular wall. Conclusion: These preliminary findings point to a distinct immunological profile in MMD, suggesting significant alterations in both immune cell activity and interaction within the vascular environment. Ongoing studies utilize FACS to validate specific immune populations and their transcriptomes in a larger cohort. These findings reveal unique transcriptomic signatures of peripheral blood immune cells in MMD and highlight key immune cell types that may contribute to its pathogenesis.

Role of intraperitoneal paclitaxel in eosinophil activation and recruitment in the peritoneal cavity and anti-tumor effects against peritoneal metastasis from gastric cancer.

471 Background: Recent studies indicate that the efficacy of chemotherapy is significantly influenced by the tumor immune microenvironment. Peritoneal cavity contains many immune cells, however, the relationship between immune response within the peritoneal cavity and tumor response remains poorly understood. Methods: Single cell suspensions were obtained from ascites or peritoneal lavages from 41 patients with PM from GC. In 28 patients, cells were collected both before and after 1-3 courses of IP chemotherapy. These samples were immunestained with mAbs targeting to specific lymphoid or myeloid subsets, and their proportions in CD45(+) leukocytes were analyzed using flowcytometry. Eosinophils were purified by magnetic cell sorting for subsequent RNA-Seq analysis. Results: Among 41 patients with PM, tumor leukocyte ratio (TLR) calculated as CD326(+) tumor cells divided by CD45(+) leukocytes varied from 0.002% to 58.1%. TLR was not correlated with any ratios of immune cells, however, the ratios of CD8(+) T cells, NK cells and CD16(-) CD193(+) eosinophils tended to decrease with the increase in TLR. Conversely, the ratios of CD19(+) B cell, CD14(+) macrophages and CD16(+) neutrophils increased with elevated TLR. Mean survival time of these patients was 17.7 months. None of the leukocyte subsets showed significant association with patient outcome. In 28 patients, the ratios of lymphocytes mostly decreased with significant difference in CD4(+) T cells and CD19(+) B cells after IP treatment. In contrast, the ratio of CD11b(+) myeloid cells increased in peritoneal cavity after IP treatment. Among the myeloid cells, the ratio of CD16(-) CD193(+) eosinophils significantly increased. The change was particularly prominent in in post-treatment negative peritoneal lavage cytology (CY0) patients (M=0.47% vs M=10.0%, p<0.0001), while the difference was not significant in post-treatment positive peritoneal lavage cytology (CY1) patients (M=0.93% vs M=0.97%, p=0.84). Patients with eosinophil ratio of ≥2% after IP chemotherapy in peritoneal cavity had significantly longer overall survival compared to those with lower eosinophil ratios (17.3 mo vs 26.7 mo, p=0.034; HR =0.23[0.06-0.89]). The peritoneal eosinophils after IP treatment exhibited elevated levels of CD11b and CD63 expression compared to circulating eosinophils (p<0.01), while SSC-A levels tended to be lower. Gene ontology pathways revealed enrichment of cytokine-mediated signaling pathway, extracellular matrix organization and response to interferon-gamma in peritoneal eosinophils (p<0.0001). Conclusions: IP-PTX induces eosinophil activation and recruitment in the peritoneal cavity, while also affecting other types of immune cells. These effects may potentially contribute to the anti-tumor response against peritoneal metastases.

Identifying health risk determinants and molecular targets in patients with idiopathic pulmonary fibrosis via combined differential and weighted gene co-expression analysis

IntroductionIdiopathic pulmonary fibrosis (IPF) is a rare but debilitating lung disease characterized by excessive fibrotic tissue accumulation, primarily affecting individuals over 50 years of age. Early diagnosis is challenging, and without intervention, the prognosis remains poor. Understanding the molecular mechanisms underlying IPF pathogenesis is crucial for identifying diagnostic markers and therapeutic targets.MethodsWe analyzed transcriptomic data from lung tissues of IPF patients using two independent datasets. Differentially expressed genes (DEGs) were identified, and their functional roles were assessed through pathway enrichment and tissue-specific expression analysis. Protein-protein interaction (PPI) networks and co-expression modules were constructed to identify hub genes and their associations with disease severity. Machine learning approaches were applied to identify genes capable of differentiating IPF patients from healthy individuals. Regulatory signatures, including transcription factor and microRNA interactions, were also explored, alongside the identification of potential drug targets.ResultsA total of 275 and 167 DEGs were identified across two datasets, with 67 DEGs common to both. These genes exhibited distinct expression patterns across tissues and were associated with pathways such as extracellular matrix organization, collagen fibril formation, and cell adhesion. Co-expression analysis revealed DEG modules correlated with varying IPF severity phenotypes. Machine learning analysis pinpointed a subset of genes with high discriminatory power between IPF and healthy individuals. PPI network analysis identified hub proteins involved in key biological processes, while functional enrichment reinforced their roles in extracellular matrix regulation. Regulatory analysis highlighted interactions with transcription factors and microRNAs, suggesting potential mechanisms driving IPF pathogenesis. Potential drug targets among the DEGs were also identified.DiscussionThis study provides a comprehensive transcriptomic overview of IPF, uncovering DEGs, hub proteins, and regulatory signatures implicated in disease progression. Validation in independent datasets confirmed the relevance of these findings. The insights gained here lay the groundwork for developing diagnostic tools and novel therapeutic strategies for IPF.

P0121 Molecular features of extracellular matrix activity persist in patients who achieve mucosal healing with ustekinumab induction

Abstract Background Phase 3 trials demonstrate rates of secondary loss of response of up to 40% for many advanced therapies in ulcerative colitis (UC). At a molecular level, this may be explained by persistence of inflammatory mediators in the mucosa despite successful treatment induction, and transcripts involved in leukocyte infiltration persist in patients responding to infliximab and vedolizumab compared to non-IBD controls [1]. We considered if any disease-relevant transcripts persisted in ustekinumab induction responders and if these differed depending on symptom resolution. Methods We interrogated data from the UNIFI trial, where baseline mucosal biopsies from patients treated with ustekinumab for moderate-to-severe UC underwent RNA profiling (Gene Expression Omnibus, GSE206285). Patients who achieved combined histo-endoscopic (mucosal) healing either with (disease clearance, “DC”) or without (mucosal healing, “MH only”) clinical remission at week 8 were included in subsequent analyses, along with non-IBD controls from this cohort (n=18). We compared gene expression and the enrichment of functional pathways using limma and GSEA (gene set enrichment analysis), respectively, between the two groups of responders and controls in R (v 4.2.3, Vienna). The Reactome database of pathway annotations was used. Gene signature enrichment was calculated by gene set variation analysis. Results Of the 54 patients who responded to ustekinumab, 15 experienced MH only and 39 had DC. Principal component analysis showed that these responders were distinct from controls but overlapped with each other (figure 1). For MH only compared to controls, there were 8375 differentially expressed genes (DEGs), of which 4936 were upregulated. There were 8778 DEGs between DC and controls, with 5331 upregulated. GSEA revealed that the DEGs in each comparison mainly represented pathways relating to the extracellular matrix (ECM), such as ECM degradation and collagen formation. There were no DEGs between MH only and DC but GSEA suggested that interleukin signalling and ECM organisation were upregulated in MH only. Interestingly, there was large heterogeneity in enrichment of the DEGs amongst all the responders. Similarly, there was wide variation in the enrichment of genes relating to the ECM. Conclusion Despite resolution of histo-endoscopic disease activity at week 8 in ustekinumab-treated UC patients, there was persistence of molecular inflammation, particularly ECM-related genes. However, the extent of this varied between patients; future work will examine if this explains why some eventually lose response whilst others maintain long-term remission. Ongoing inflammatory mechanisms may explain symptom persistence despite mucosal healing.

Identification of CDKN3 overexpression as a marker of poor prognosis and potential therapeutic target in low-grade glioma

Low-grade glioma (LGG) is a primary, slow-growing brain tumor; however, its treatment and prognosis remain challenging. In this study, we analyzed cancer data from the TCGA database, focusing particularly on the expression of the CDKN3 gene in LGG. The results showed that high CDKN3 expression in LGG patients was significantly associated with poor survival outcomes. Further gene expression analysis revealed that 379 genes were significantly upregulated in LGG samples with high CDKN3 expression, and these genes were primarily involved in the mitotic cell cycle and extracellular matrix organization. Additionally, high CDKN3 expression was closely linked to key signaling pathways such as tumor inflammation, hypoxic response, and tumor proliferation. Immune microenvironment analysis showed that high CDKN3 expression significantly increased the expression of CD4 + T cells and specific immune checkpoint genes, suggesting a potentially poor response to immune checkpoint blockade therapy. Through in vitro and in vivo experiments, we confirmed that CDKN3 silencing significantly inhibited the proliferative capacity of LGG cells. Proteomics revealed that CDKN3 can bind ARG1 and inhibite the intracellular arginase activity. These findings not only improve our understanding of LGG biology but also provide scientific evidence for developing potential therapeutic strategies targeting CDKN3.

CRYβB2 alters cell adhesion to promote invasion in a triple-negative breast cancer cell line

ObjectiveAfrican American women with breast cancer experience disproportionately poor survival outcomes, primarily due to the high prevalence of the deadliest subtype; triple-negative breast cancer (TNBC). The CRYβB2 gene is upregulated in tumors from African American patients across all breast cancer subtypes, including TNBC, and is associated with worse survival rates. This study investigated the effect of CRYβB2 on the invasion of TNBC cells and the underlying mechanisms contributing to this phenotype.ResultsWe utilized the SUM159 cells with stable CRYβB2 overexpression in a 3D-culture tumor spheroids model in our investigation. A quantitative 3D invasion assay demonstrated that CRYβB2 overexpression significantly enhanced invasion (median invasion %; SUM159 = 0.14 and SUM159 + CRYβB2 = 0.33). RNA sequencing analysis indicated that CRYβB2 overexpression modulated cell-cell adhesion and extracellular matrix organization pathways, which are critical to invasion of cancer cells. Specifically, CRYβB2 suppressed the expression of key cell-cell adhesion genes known as clustered protocadherins and promoted the expression of PCDH7, a nonclustered protocadherin with known oncogenic roles in various cancers. Notably, the knockout of PCDH7 diminished the invasive capacity induced by CRYβB2 (median invasion %; SUM159 = 0.093, SUM159 + CRYβB2 = 0.184 and SUM159 + CRYβB2/PCDH7−/−=0.082). These findings provide a novel link between a previously identified differentially expressed gene, CRYβB2, in driving breast cancer phenotypes by modulating a class of adhesion proteins.

Polycystin-1 regulates tendon-derived mesenchymal stem cells fate and matrix organization in heterotopic ossification

Mechanical stress modulates bone formation and organization of the extracellular matrix (ECM), the interaction of which affects heterotopic ossification (HO). However, the mechanically sensitive cell populations in HO and the underlying mechanism remain elusive. Here, we show that the mechanical protein Polysyctin-1 (PC1, Pkd1) regulates CTSK lineage tendon-derived mesenchymal stem cell (TDMSC) fate and ECM organization, thus affecting HO progression. First, we revealed that CTSK lineage TDMSCs are the major source of osteoblasts and fibroblasts in HO and are responsive to mechanical cues via single-cell RNA sequencing analysis and experiments with a lineage tracing mouse model. Moreover, we showed that PC1 mediates the mechanosignal transduction of CTSK lineage TDMSCs to regulate osteogenic and fibrogenic differentiation and alters the ECM architecture by facilitating TAZ nuclear translocation. Conditional gene depletion of Pkd1 or Taz in CTSK lineage cells and pharmaceutical intervention in the PC1-TAZ axis disrupt osteogenesis, fibrogenesis and ECM organization, and consequently attenuate HO progression. These findings suggest that mechanically sensitive CTSK-lineage TDMSCs contribute to heterotopic ossification through PC1-TAZ signaling axis mediated cell fate determination and ECM organization.

Parenchymal and Inflammatory Responses to Ozone Exposure in the Aging Healthy and Surfactant Protein C Mutant Lung.

Ozone (O3) is a ubiquitous pollutant known to produce acute, transient inflammation through oxidative injury and inflammation. These effects are exacerbated in susceptible populations, such as the elderly and those exhibiting genetic mutations in central nodes of pulmonary function. To comprehend the impact of these predisposing factors, the present study examines structural, mechanical, and immunological responses to single acute O3 exposure (0.8 ppm, 3h) in young (8-14 week old), middle-aged (44-52 week old), and old (>80 week old) mice. Furthermore, this work compares the impact of a clinically relevant mutation in the gene encoding for the alveolar epithelial type 2 specific surfactant protein C. Aging was associated with reduced lung resistance and increases in respiratory elastic properties, the latter of which was exacerbated in SP-C mutant mice. Ozone exposure produced focal injury localized at the terminal bronchiole-to-alveolar junctions and enlarged alveoli in aged SP-C mutant lungs. Flow cytometric analysis revealed increases in mononuclear myeloid abundance in aged SP-C mutant lungs, paired with a contraction in CD8+ expressing cells. Expansion of tertiary lymphoid tissues was also noted in aged groups, more evident in the mutant mice. Spatial transcriptomics of CD68+ macrophages and CD45- non-immune parenchymal cells highlighted age-dependent shifts in inflammatory and extracellular matrix organization signaling, and enrichment in senescence and chromatin remodeling pathways. These results illustrate the structural and immunological impact of O3 in the aging wild type and mutant lung and emphasize the significance of modeling environmental exposure in at-risk populations.

Genomic and transcriptomic signatures of sequential carcinogenesis from papillary neoplasm to biliary tract cancer.

Papillary neoplasms of the biliary tree, including intraductal papillary neoplasms (IPN) and intracholecystic papillary neoplasms (ICPN), are recognized as precancerous lesions. However, the genetic characteristics underlying sequential carcinogenesis remain unclear. Whole-exome sequencing was performed on 166 neoplasms (33 intrahepatic IPNs, 44 extrahepatic IPNs, and 89 ICPNs), and 41 associated carcinomas. Nine available cases were also subjected to spatial transcriptomic analysis. Mutations in the MAPK (48%), genomic integrity maintenance (42%), and Wnt/β-catenin (33%) pathways were prevalent in intrahepatic IPNs, extrahepatic IPNs, and ICPNs, respectively. KRAS mutations were enriched in intrahepatic IPN (42%, P<0.001), whereas SMAD4 mutations were enriched in extrahepatic IPN (21%, P=0.005). ICPNs frequently exhibit CTNNB1 mutations, particularly in low-grade lesions. Mutational signature analysis revealed that SBS1 and SBS5 signatures were homogeneously enriched in intrahepatic IPN, in contrast to the heterogeneous distribution of SBS1, SBS2, SBS5, SBS13, SBS7b, and SBS23 in extrahepatic IPN and ICPN. Copy number aberrations gradually increased from low- to high-grade intraepithelial neoplasia and eventually to carcinoma. Phylogenetic analysis revealed that 89% of carcinomas were derived from IPN/ICPN through sequential carcinogenesis, with the majority sharing driver mutations between IPN/ICPN and carcinoma. Furthermore, multifocal, independent carcinogenesis events were observed in IPNs/ICPNs, resulting in mutationally distinct carcinoma lesions. Carcinogenesis of IPN/ICPN occurs in multiple subclones through mutational accumulation and transcriptomic alterations that affect vascular development, cell morphogenesis, extracellular matrix organization, and growth factor response. With the largest IPN/ICPN cohort reported to date, our study provides a genome- and spatial transcriptome-level portrait of sequential carcinogenesis and differences in the anatomical location of biliary papillary neoplasms. Biliary tract cancer is a fatal malignancy. However, its genome-level sequential carcinogenesis from intraepithelial neoplasia to carcinoma has not yet been evaluated in a sufficiently large cohort. Papillary lesions of the bile duct and gallbladder are collectively termed intraductal papillary neoplasms (IPN) of the bile duct and intracholecystic papillary neoplasms (ICPN), respectively. They are primarily diagnosed based on histopathological studies. This study provides a comprehensive mutational and spatial transcriptomic landscape of papillary neoplasms of the bile duct and gallbladder. The results of this study offer insights into the mechanism of sequential carcinogenesis in papillary biliary tract tumors, pathology-genomics correlation, and potential therapeutic targets.

Effect of Notch1 signaling on muscle engraftment and maturation from pluripotent stem cells.

Pax3-induced pluripotent stem cell-derived myogenic progenitors display an embryonic molecular signature but become postnatal upon transplantation. Because this correlates with upregulation of Notch signaling, here we probed whether NOTCH1 is required for invivo maturation by performing gain- and loss-of-function studies in inducible Pax3 (iPax3) myogenic progenitors. Transplantation studies revealed that Notch1 signaling did not change the number of donor-derived fibers; however, the NOTCH1 overexpression cohorts showed enhanced satellite cell engraftment and more mature fibers, as indicated by fewer fibers expressing the embryonic myosin heavy-chain isoform and more type IIX fibers. While donor-derived Pax7+ cells were detected in all transplants, in the absence of Notch1, secondary grafts exhibited a high fraction of these cells in the interstitial space, indicating that NOTCH1 is required for proper satellite cell homing. Transcriptional profiling of NOTCH1-modified donor-derived satellite cells suggests that this may be due to changes in the extracellular matrix organization, cell cycle, and metabolism.

Evolution of the umbilical cord blood proteome across gestational development

Neonatal health is dependent on early risk stratification, diagnosis, and timely management of potentially devastating conditions, particularly in the setting of prematurity. Many of these conditions are poorly predicted in real-time by clinical data and current diagnostics. Umbilical cord blood may represent a novel source of molecular signatures that provides a window into the state of the fetus at birth. In this study, we comprehensively characterized the cord blood proteome of infants born between 25 to 42 weeks using untargeted mass spectrometry and functional enrichment analysis. We determined that the cord blood proteome at birth varies significantly across gestational development. Proteins that function in structural development and growth (e.g., extracellular matrix organization, lipid particle remodeling, and blood vessel development) are more abundant earlier in gestation. In later gestations, proteins with increased abundance are in immune response and inflammatory pathways, including complements and calcium-binding proteins. These data contribute to the knowledge of the physiologic state of neonates across gestational age, which is crucial to understand as we strive to best support postnatal development in preterm infants, determine mechanisms of pathology causing adverse health outcomes, and develop cord blood biomarkers to help tailor our diagnosis and therapeutics for critical neonatal conditions.

KEAP1 mutations as key crucial prognostic biomarkers for resistance to KRAS-G12C inhibitors

BackgroundKRAS-G12C inhibitors mark a notable advancement in targeted cancer therapies, yet identifying predictive biomarkers for treatment efficacy and resistance remains essential for optimizing clinical outcomes.MethodsThis systematic meta-analysis synthesized studies available through September 2024 across PubMed, Cochrane Library, SpringerLink, and Embase. Using CRISPR/Cas9 technology, this study generated cells with KEAP1 and STK11 knockouts, and utilized lentiviral vectors to overexpress PD-L1. Cellular sensitivity to KRAS-G12C inhibitors—AMG510, MRTX849, and JAB-21822—was evaluated through CCK-8 assays. Comprehensive bioinformatics analyses on stably transfected cell lines were conducted to elucidate pathways mediating resistance.ResultsAnalysis of 13 studies involving 1132 patients highlighted the significant efficacy of KRAS-G12C inhibitor monotherapy, particularly among elderly and female patients. Treatment response was notably affected by liver and brain metastases, with KEAP1 mutations identified as a primary negative prognostic factor, closely associated with early resistance to treatment. Validation studies in NCI-H358 cells showed a marked increase in IC50 values for AMG510, MRTX849, and JAB-21822 after KEAP1 knockout (P < 0.0001), with IC50 values rising from 27.78 nm, 116.9 nm, and 118.7 nm in controls, respectively. Comparative analysis of differentially expressed genes in KEAP1 knockout cells versus controls, utilizing GO, KEGG, and Reactome pathway analyses, revealed substantial enrichment in pathways linked to extracellular matrix organization and cell adhesion processes. Although STK11 mutations and heightened PD-L1 expression indicated a trend toward poorer outcomes, these correlations lacked statistical significance.ConclusionThis research affirms KRAS-G12C inhibitors as promising treatments, especially for certain patient subgroups, and underscores KEAP1 mutations as key biomarkers for resistance. The findings highlight the urgent need for alternative therapeutic approaches in KEAP1-mutant patients and emphasize the role of molecular profiling in tailored treatment strategies.

Alterations in whole muscle quality and physiological cross-sectional area measured with quantitative MRI following ACL injury

BackgroundEmerging evidence suggests that there are morphological and physiological changes to the vastus lateralis after an anterior cruciate ligament (ACL) tear. However, it is unclear whether these alterations are limited to just the vastus lateralis or are more representative of widespread changes across the thigh musculature and/or if these changes precede reconstruction. The purpose of this study was to determine T1ρ relaxation time, a measure of extracellular matrix organization in muscle, and physiological cross-sectional area (PCSA) for muscles of the quadriceps and hamstrings of the ACL-deficient and contralateral limbs soon after ACL injury.MethodsT1ρ and diffusion tensor magnetic resonance imaging were performed on both limbs of 10 participants after primary ACL tear (< 10 weeks). T1ρ relaxation time and PCSA were calculated for all muscles of the quadriceps and hamstrings. Shapiro-Wilks tests were performed to assess normality. Outcomes were compared between limbs for each muscle of interest with paired t-tests or Wilcoxon signed-rank tests with the alpha level set to 0.05.ResultsT1ρ relaxation times were significantly longer for the vastus lateralis (7.0%), rectus femoris (15.4%), and vastus intermedius (9.4%) of ACL-deficient limb; whereas, relaxation times were similar between limbs for all hamstring muscles. PCSA was smaller for the vastus lateralis (-19.6%), vastus intermedius (-20.9%), vastus medialis (-26.0%), and semitendinosus (-15.0%) of the ACL-deficient limb compared to the contralateral limb.ConclusionsThese results provide evidence that morphological and physiological alterations occur within multiple muscles of quadriceps but not the hamstrings prior to ACL reconstruction. Establishing these differences between the quadriceps and hamstrings suggests there is a differential response within the thigh musculature to an ACL injury, providing a framework for more targeted interventions.

Differential Gene Expression Analysis in a Lumbar Spinal Stenosis Rat Model via RNA Sequencing: Identification of Key Molecular Pathways and Therapeutic Insights.

Lumbar spinal stenosis (LSS) is a degenerative condition characterized by the narrowing of the spinal canal, resulting in chronic pain and impaired mobility. However, the molecular mechanisms underlying LSS remain unclear. In this study, we performed RNA sequencing (RNA-seq) to investigate differential gene expression in a rat LSS model and identify the key genes and pathways involved in its pathogenesis. We used bioinformatics analysis to identify significant alterations in gene expression between the LSS-induced and sham groups. Pearson's correlation analysis demonstrated strongly consistent intragroup expression (r > 0.9), with distinct gene expression between the LSS and sham groups. A total of 113 differentially expressed genes (DEGs) were identified, including upregulated genes such as Slc47a1 and Prg4 and downregulated genes such as Higd1c and Mln. Functional enrichment analysis revealed that these DEGs included those involved in key biological processes, including synaptic plasticity, extracellular matrix organization, and hormonal regulation. Gene ontology analysis highlighted critical molecular functions such as mRNA binding and integrin binding, as well as cellular components such as contractile fibers and the extracellular matrix, which were significantly affected by LSS. Our findings provide novel insights into the molecular mechanisms underlying LSS and offer potential avenues for the development of targeted therapies aimed at mitigating disease progression and improving patient outcomes.

Proteomic signature of HIV-associated subclinical left atrial remodeling and incident heart failure

People living with HIV are at higher risk of heart failure and associated left atrial remodeling compared to people without HIV. Mechanisms are unclear but have been linked to inflammation and premature aging. Here we obtain plasma proteomics concurrently with cardiac magnetic resonance imaging in two independent study populations to identify parallels between HIV-related and aging-related immune dysfunction that could contribute to atrial remodeling and clinical heart failure. We discover a plasma proteomic signature that may in part reflect or contribute to HIV-associated atrial remodeling, many features of which are associated with older age and time to incident heart failure among an independent community-based cohort without HIV. This proteomic profile was statistically enriched for immune checkpoint proteins, tumor necrosis factor signaling, ephrin signaling, and extracellular matrix organization, identifying possible shared pathways in HIV and aging that may contribute to risk of heart failure.

An FGF2-Derived Short Peptide Attenuates Bleomycin-Induced Pulmonary Fibrosis by Inhibiting Collagen Deposition and Epithelial-Mesenchymal Transition via the FGFR/MAPK Signaling Pathway.

Following the COVID-19 pandemic, the prevalence of pulmonary fibrosis has increased significantly, placing patients at higher risk and presenting new therapeutic challenges. Current anti-fibrotic drugs, such as Nintedanib, can slow the decline in lung function, but their severe side effects highlight the urgent need for safer and more targeted alternatives. This study explores the anti-fibrotic potential and underlying mechanisms of an endogenous peptide (P5) derived from fibroblast growth factor 2 (FGF2), developed by our research team. Using a bleomycin-induced pulmonary fibrosis mouse model, we observed that P5 alleviated fibrosis by inhibiting collagen deposition, as confirmed by CT scans and histological staining. In TGF-β-induced cell models, P5 effectively suppressed collagen deposition and epithelial-mesenchymal transition (EMT). Transcriptome analysis highlighted pathways related to receptor binding, extracellular matrix organization, and cell adhesion, with KEGG analysis confirming FGFR/MAPK signaling inhibition as the primary mechanism underlying its anti-fibrotic effects. In summary, our study demonstrates that P5 significantly attenuates pulmonary fibrosis through the inhibition of EMT, collagen deposition, and FGFR/MAPK signaling, providing a promising therapeutic approach for fibrosis.

From Cartilage to Matrix: Protocols for the Decellularization of Porcine Auricular Cartilage.

The shortage of tissues and damaged organs led to the development of tissue engineering. Biological scaffolds, created from the extracellular matrix (ECM) of organs and tissues, have emerged as a promising solution for transplants. The ECM of decellularized auricular cartilage is a potential tool for producing ideal scaffolds for the recellularization and implantation of new tissue in damaged areas. In order to be classified as an ideal scaffold, it must be acellular, preserving its proteins and physical characteristics necessary for cell adhesion. This study aimed to develop a decellularization protocol for pig ear cartilage and evaluate the integrity of the ECM. Four tests were performed using different methods and protocols, with four pig ears from which the skin and subcutaneous tissue were removed, leaving only the cartilage. The most efficient protocol was the combination of trypsin with a sodium hydroxide solution (0.2 N) and SDS (1%) without altering the ECM conformation or the collagen architecture. In conclusion, it was observed that auricular cartilage is difficult to decellularize, influenced by material size, exposure time, and the composition of the solution. Freezing and thawing did not affect the procedure. The sample thickness significantly impacted the decellularization time.

Peroxidasin is associated with a mesenchymal-like transcriptional phenotype and promotes invasion in metastatic melanoma.

Cutaneous melanoma is a highly invasive, heterogeneous and treatment resistant cancer. It's ability to dynamically shift between transcriptional states or phenotypes results in an adaptive cell plasticity that may drive cancer cell invasion or the development of therapy resistance. The expression of peroxidasin (PXDN), an extracellular matrix peroxidase, has been proposed to be associated with the invasive metastatic melanoma phenotype. We have confirmed this association by analysing the transcriptomes of 70 metastatic melanoma cell lines with variable levels of PXDN expression. This analysis highlighted a strong association between high PXDN expression and the undifferentiated invasive melanoma phenotype. To assess the functional role of PXDN in melanoma invasion, we performed a knockout of PXDN in a highly invasive cell line (NZM40). PXDN knockout decreased the invasive potential by ∼50% and decreased the expression of epithelial-mesenchymal transition and invasive marker genes as determined by RNAseq and substantiated by proteomics analysis. Bioinformatics analysis of differentially expressed genes following PXDN knockout highlighted decreases in genes linked to extracellular matrix formation, organisation and degradation as well as signalling pathways such as the WNT pathway. This study provides compelling evidence that PXDN plays a functional role in melanoma invasion by promoting an invasive, mesenchymal-like transcriptional phenotype.

Micropillar-induced changes in cell nucleus morphology enhance bone regeneration by modulating the secretome.

Nuclear morphology, which modulates chromatin architecture, plays a critical role in regulating gene expression and cell functions. While most research has focused on the direct effects of nuclear morphology on cell fate, its impact on the cell secretome and surrounding cells remains largely unexplored, yet is especially crucial for cell-based therapies. In this study, we fabricated implants with a micropillar topography using methacrylated poly(octamethylene citrate)/hydroxyapatite (mPOC/HA) composites to investigate how micropillar-induced nuclear deformation influences cell paracrine signaling for osteogenesis and cranial bone regeneration. In vitro, cells with deformed nuclei showed enhanced secretion of proteins that support extracellular matrix (ECM) organization, which promoted osteogenic differentiation in neighboring human mesenchymal stromal cells (hMSCs). In a mouse model with critical-size cranial defects, nuclear-deformed hMSCs on micropillar mPOC/HA implants elevated Col1a2 expression, contributing to bone matrix formation, and drove cell differentiation toward osteogenic progenitor cells. These findings indicate that micropillars not only enhance the osteogenic differentiation of human mesenchymal stromal cells (hMSCs) but also modulate the secretome, thereby influencing the fate of surrounding cells through paracrine effects.

IL-8 Downregulation Mediates the Beneficial Effects of Infection-Induced Fever on Breast Cancer Prognosis.

Previous studies have reported that infection-induced fever is associated with improved breast cancer prognosis, potentially through the modulation of cytokines. However, the key cytokines and the underlying mechanisms through which fever exerts its anti-tumor effects remain unclear. A total of 794 breast cancer patients were recruited between 2008 and 2017, with follow-up extending until October 31st, 2023. Infection-induced fever was assessed using questionnaires, while a multiplex assay evaluated a panel of 27 cytokines. The mediation effects of various cytokines were analyzed through model-based causal mediation analysis. Additionally, we explored modifications to these mediation effect by examining interactions among the cytokines themselves as well as their interactions with infection-induced fever. Bioinformatic analyses were conducted to elucidate the biological pathways mediating infection-induced fever. The relationship between infection-induced fever and improved breast cancer prognosis was mediated by a decrease in interleukin-8 (IL-8) levels. Furthermore, our findings revealed that the downregulation of IL-8, which mediates the beneficial effects of fever, was antagonized by IL-2, IL12p70 and IL-7. By intersecting the biological pathways influenced by IL-8, alongside those affected by IL-2, IL12p70, or IL-7, we found that these latter cytokines antagonized the mediation effects of IL-8 via regulating critical pathways such as neutrophil degranulation, extracellular matrix organization and asparagine N-linked glycosylation. Infection-induced fever may improve breast cancer prognosis through IL-8 downregulation and the mediation mechanisms may be involved in neutrophil degranulation, extracellular matrix organization and asparagine N-linked glycosylation. Such findings not only provide valuable insights into effectively managing febrile responses for breast cancer patients, but also underscore the therapeutic potential of cytokines in breast cancer patients.