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Cellular senescence is a stable cell cycle arrest that occurs in response to various stress stimuli and affects multiple cell types, including endothelial cells (ECs). Senescent cells accumulate with age, and their removal has been linked to reduced age-related diseases. However, some senescent cells are important for tissue homeostasis. Therefore, understanding the diversity of senescent cells in a cell-type-specific manner and their underlying molecular mechanisms is essential. Senescence impairs key ECs functions which are necessary for vascular homeostasis, leading to endothelial dysfunction and age-related vascular diseases. In order to gain insights into these mechanisms, we analyzed publicly available RNA-seq datasets to identify gene expression changes in senescent ECs induced by doxorubicin, irradiation, and replication exhaustion. While only a few genes were consistently differentially expressed across all conditions, some gene ontologies (GO) were shared. Among these, our analysis focused on validating the expression of genes associated with the matrisome, which includes genes encoding for extracellular matrix (ECM) structural components and ECM-associated proteins, in a doxorubicin-induced senescence model. Our results show that the matrisome transcriptome undergoes significant remodeling in senescent endothelial cells, regardless of the specific inducers of senescence, highlighting the importance of understanding how ECM alterations affect senescence. [ABSTRACT FROM AUTHOR]

Introduction: Scarring from traumatic injury, burns, and other complications remains a significant problem that diminishes quality of life for millions of people worldwide. A common target for the development of new therapies to promote healing and reduce scarring are myofibroblasts because of their central role in pathological scarring. Recent work indicates that adipocyte lineage cells also contribute to the wound healing process, including clinical reports that indicate that the placement of autologous adipose micrografts at the surgical site improves the appearance and pliability of existing scars. Methods: To better understand how adipocyte lineage cells interact with fibroblasts to promote healing, we first utilized an in vitro model of wound healing to visualize fibroblast spheroid collagen deposition via time-lapse imaging. We then introduced pre-adipocyte and adipocyte spheroids to visualize pair-wise spheroid interactions and collagen deposition among all three cell types. Finally, we quantified differences in the extracellular matrix (ECM) proteins produced using liquid chromatography with tandem mass spectrometry (LC-MS/MS). Results: We found that all three cell-types contribute to ECM deposition and that the composition of the ECM proteins, or matrisome, was significantly different depending on which cells were co-cultured together. Conclusions: By better understanding the interactions among these cell types, novel adipose-tissue-based therapeutic approaches can be developed to improve wound healing and reduce scar tissue. [ABSTRACT FROM AUTHOR]

The Parkinson's disease protein, alpha-synuclein (α-syn/SNCA), is highly expressed in neurons and melanomas. The goal of this study was to reveal the mechanism(s) of α-syn's involvement in melanoma pathogenesis. To decipher the genes and pathways affected by α-syn, we conducted an RNA sequencing analysis of human SK-MEL-28 cells and several SK-MEL-28 SNCA-KO clones. We identified 1098 significantly up-regulated genes and 660 significantly down-regulated genes. Several of the upregulated genes are related to the immune system, i.e., the inflammatory response and the matrisome. We validated five upregulated genes (IL-1β, SAA1, IGFBP5, CXCL8, and CXCL10) by RT-qPCR and detected IGFBP5 and IL-1β in spent media of control and SNCA-KO cells. The levels of each of these secreted proteins were significantly higher in the spent media of the SNCA-KO clones than control cells. These secreted proteins quite likely activate the immune response against SNCA-KO cells. We suggest that, conversely, high levels of α-syn expression in melanoma cells helps the cells evade the immune system by inhibiting the secretion of these immune activating factors. [ABSTRACT FROM AUTHOR]

Physical inactivity and aging cause significant impairment of skeletal muscle functionality and mechanical properties, as well as remodeling of the extracellular matrix (ECM). The purpose of this work was to study the effect of chronic decrease in physical activity and age on the biogenesis of ECM in skeletal muscle. Biopsy samples from m. vastus lateralis were taken for quantitative mass spectrometry-based proteomic analysis and RNA sequencing in 15 young healthy volunteers and 8 young and 37 elderly patients with long-term primary osteoarthritis of the knee/hip joint as a model to study the effects of chronic muscle motor decline. In total, 1022 mRNAs and 101 ECM proteins and ECM-associated proteins (matrisome) were detected. An increase in the expression of two dozen highly abundant matrisome proteins specific to elderly and young patients (relative to young healthy subjects) was identified; however, changes in the expression of mRNAs encoding matrisome regulators (enzymatic regulators and secreted proteins) were similar. Comparison with previous proteomic and transcriptomic data showed that the described matrisome changes were markedly different from those induced by aerobic physical training in young healthy individuals, in particular in the expression of dominant ECM proteins and, especially, in the expression of mRNAs of ECM enzymatic regulators and secreted proteins. Matching the expression profiles of these regulatory genes may be useful for finding pharmacological targets for preventing adverse changes/activation of ECM biogenesis in various pathological conditions/physical training. [ABSTRACT FROM AUTHOR]

MIS-C is a rare, highly inflammatory state resembling incomplete Kawasaki disease, temporarily associated with COVID-19. The pathogenesis is not completely known. RNAseq was carried out on whole blood of six treatment-naïve MIS-C patients. This was compared against RNAseq transcriptomics data of five healthy controls (HC), four Kawasaki Disease (KD) and seven systemic Juvenile Idiopathic Arthritis (sJIA). Using PCA, MIS-C clustered separately from HC, KD and sJIA. Amongst the top 50 significant genes in the three comparisons with HC, KD, and sJIA, common genes were: TMCC2, ITGA2B, DMTN, GFI1B, PF4, QSER1, GRAP2, TUBB1. DSEA revealed that maximum number of hits for overexpressed pathways was for NABA matrisome activation when MIS-C was compared against HC. Cytokine stimulated cellular activation pathways, specifically IL-10 were downregulated. MIS-C had more activated pathways of neutrophil degranulation and acquired immune activation but less of coagulation system or heat-shock system involvement as compared to KD. As compared to sJIA, humoral immune response and complements were activated. Matrisome activation was higher, with increased cell–cell interaction and ECM signalling. This analysis revealed novel insights into the pathogenesis of MIS-C, including the potential role of matrisomes, humoral immune system and down-regulated interleukin-10 pathways. [ABSTRACT FROM AUTHOR]

Purpose: Human extracellular matrix (ECM) exhibits complex protein composition and architecture depending on tissue and disease state, which remains challenging to reverse engineer. One promising approach is based on cell-secreted ECM from primary human fibroblasts that can be decellularized into acellular biomaterials. However, fibroblasts cultured on rigid culture plastic or biomaterial scaffolds can experience aberrant mechanical cues that perturb the biochemical, mechanical, and the efficiency of ECM production. Methods: Here, we demonstrate a method for preparing decellularized ECM using primary human fibroblasts with tissue and disease-specific features with two case studies: (1) cardiac fibroblasts; (2) lung fibroblasts from healthy or diseased donors. Cells aggregate into engineered microtissues in low adhesion microwells that deposited ECM and can be decellularized. We systematically investigate microtissue morphology, matrix architecture, and mechanical properties, along with transcriptomic and proteomic analysis. Results: Microtissues exhibited tissue-specific gene expression and proteomics profiling, with ECM complexity similar to native tissues. Healthy lung microtissues exhibited web-like fibrillar collagen compared to dense patches in healthy heart microtissues. Diseased lung exhibited more disrupted collagen architecture than healthy. Decellularized microtissues had tissue-specific mechanical stiffness that was physiologically relevant. Importantly, decellularized microtissues supported viability and proliferation of human cells. Conclusions: We show that engineered microtissues of primary human fibroblasts seeded in low-adhesion microwells can be decellularized to produce human, tissue and disease-specific ECM. This approach should be widely applicable for generating personalized matrix that recapitulate tissues and disease states, relevant for culturing patient cells ex vivo as well as implantation for therapeutic treatments. [ABSTRACT FROM AUTHOR]

In recent years, the matrisome, a set of proteins that make up the extracellular matrix (ECM) or are closely involved in ECM behavior, has been shown to have great importance for characterizing and understanding disease pathogenesis and progression. The matrisome is especially critical for examining diseases characterized by extensive tissue remodeling. Endometriosis is characterized by the extrauterine growth of endometrial tissue, making it an ideal condition to study through the lens of matrisome gene expression. While large gene expression datasets have become more available and gene dysregulation in endometriosis has been the target of several studies, the gene expression profile of the matrisome specifically in endometriosis has not been well characterized. In our study, we explored four Gene Expression Omnibus (GEO) DNA microarray datasets containing eutopic endometrium of people with and without endometriosis. After batch correction, menstrual cycle phase accounted for 53% of variance and disease accounted for 23%; thus, the data were separated by menstrual cycle phase before performing differential expression analysis, statistical and machine learning modeling, and enrichment analysis. We established that matrisome gene expression alone can effectively differentiate endometriosis samples from healthy ones, demonstrating the potential of matrisome gene expression for diagnostic applications. Furthermore, we identified specific matrisome genes and gene networks whose expression can distinguish endometriosis stages I/II from III/IV. Taken together, these findings may aid in developing future in vitro models of disease, offer insights into novel treatment strategies, and advance diagnostic tools for this underserved patient population. [ABSTRACT FROM AUTHOR]

We aimed to investigate the effect of 8 weeks of moderate endurance training without considerable mechanical stress on the activation of extracellular matrix (ECM) gene expression in human skeletal muscles. Mechanical stress activates ECM biogenesis in the skeletal muscles, therefore aerobic exercise on a cycling ergometer with concentric muscle contractions only was used in the study. Skeletal muscle samples from m. vastus lateralis were taken from seven young untrained men before and after 8 weeks of aerobic training. Changes in the transcriptome (RNA sequencing) and proteome (shotgun quantitative proteomics analysis) were assessed in the samples; ECM-associated proteins (or matrisome) were determined using the Matrisome DB database. After the training period, a change (mainly an increase) in the content of 14 ECM proteins and 134 mRNAs of ECM proteins was found. The largest increase in protein content was found for collagens type 1 and 3 (1.7 and 2.2 times, respectively), the main proteins of the human skeletal muscle's ECM, which was consistent with an increase in the corresponding mRNA by 10–20 times. In addition, an increase in the expression of more than a hundred mRNAs of collagens, glycoproteins, proteoglycans, and enzymatic regulators of ECM was found, which occurs simultaneously with an increase in the expression of genes of growth factors (IGF1, PDGFs, TGFB1, MDK, etc.), which play a main role in ECM biogenesis regulation. In conclusion, 8-week aerobic exercise training without considerable mechanical stress is a powerful stimulus for the activation of ECM biogenesis in skeletal muscle. [ABSTRACT FROM AUTHOR]

Ovarian age is classically considered the main cause of female reproductive infertility. In women, the process proceeds as an ongoing decline in the primordial follicle stockpile and it is associated with reduced fertility in the mid-thirties, irregular menstruation from the mid-forties, cessation of fertility, and, eventually, menopause in the early fifties. Reproductive aging is historically associated with changes in oocyte quantity and quality. However, besides the oocyte, other cellular as well as environmental factors have been the focus of more recent investigations suggesting that ovarian decay is a complex and multifaceted process. Among these factors, we will consider mitochondria and oxidative stress as related to nutrition, changes in extracellular matrix molecules, and the associated ovarian stromal compartment where immune cells of both the native and adaptive systems seem to play an important role. Understanding such processes is crucial to design treatment strategies to slow down ovarian aging and consequently prolong reproductive lifespan and, more to this, alleviaingt side effects of menopause on the musculoskeletal, cardiovascular, and nervous systems. [ABSTRACT FROM AUTHOR]