Extracellular Matrix Remodeling Pathways Research Articles

Topical Platelet Exosomes Reduce Senescence Signaling in Human Skin: An Exploratory Prospective Trial.

Cellular senescence, an irreversible cell cycle arrest with secretory phenotype, is a hallmark of skin aging. Regenerative exosome-based approaches, such as topical human platelet extract (HPE), are emerging to target age-related skin dysfunction. To evaluate the cellular and molecular effects of topical HPE for skin rejuvenation after 12 weeks of twice daily use. Skin biopsies were obtained for histological evaluation of senescence markers, p16INK4a and p21CIP1/WAF1. Telomere-associated foci, coassociation of telomeres, and DNA damage marker, γH2AX, were assessed. RNA sequencing evaluated senescence associated secretory phenotype (SASP) and extracellular matrix pathways. p16INK4a and p21CIP1/WAF1 staining in senescent skin cells revealed low and high expression subgroups that did not correspond to chronological age. Topical HPE significantly reduced high p16INK4a cells in the dermis (p = .02). There was also a decrease in telomere damage after topical HPE (p = .03). In patients with high senescent cells at baseline, there was a 40% reduction in proinflammatory SASP. Extracellular matrix remodeling pathways, including collagen and elastic fibers, were up-regulated. Topical HPE, applied on intact skin, reduced senescence signaling and senescence-associated telomere damage after 12 weeks of twice daily use, targeting a path for skin longevity or healthy skin aging.

Extracellular matrix remodelling pathway in peripheral blood mononuclear cells from severe COVID-19 patients: an explorative study.

There is a reciprocal relationship between extracellular matrix (ECM) remodelling and inflammation that could be operating in the progression of severe COVID-19. To explore the immune-driven ECM remodelling in COVID-19, we in this explorative study analysed these interactions in hospitalised COVID-19 patients. RNA sequencing and flow analysis were performed on peripheral blood mononuclear cells. Inflammatory mediators in plasma were measured by ELISA and MSD, and clinical information from hospitalised COVID-19 patients (N=15) at admission was included in the analysis. Further, we reanalysed two publicly available datasets: (1) lung tissue RNA-sequencing dataset (N=5) and (2) proteomics dataset from PBCM. ECM remodelling pathways were enriched in PBMC from COVID-19 patients compared to healthy controls. Patients treated at the intensive care unit (ICU) expressed distinct ECM remodelling gene profiles compared to patients in the hospital ward. Several markers were strongly correlated to immune cell subsets, and the dysregulation in the ICU patients was positively associated with plasma levels of inflammatory cytokines and negatively associated with B-cell activating factors. Finally, our analysis of publicly accessible datasets revealed (i) an augmented ECM remodelling signature in inflamed lung tissue compared to non-inflamed tissue and (ii) proteomics analysis of PBMC from severe COVID-19 patients demonstrated an up-regulation in an ECM remodelling pathway. Our results may suggest the presence of an interaction between ECM remodelling, inflammation, and immune cells, potentially initiating or perpetuating pulmonary pathology in severe COVID-19.

Abstract 4277: CREB-ROCK driven extracellular matrix remodeling exasperates pancreatic cancer progression

Abstract Background: Pancreatic Ductal Adenocarcinoma (PDAC) is characterized by a heightened oncogenic mutational burden, an immunosuppressive tumor microenvironment, and a dense desmoplastic stroma. During the tumor progression from in situ carcinoma to intraductal neoplasia, cancer cells manage to evade the stromal compartment and infiltrate into the ducts. This invasive tumor progression is often associated with the overexpression of extracellular matrix (ECM) modulating genes. Despite this correlation, there are currently no effective and specific inhibitors of ECM-altering pathways. By understanding the signaling mechanism, the ECM remodeling pathways may be intercepted to prevent invasive tumor progression. This study aims to elucidate the role of cAMP-response element binding protein 1 (CREB1) and its downstream effectors in regulating PDAC ECM remodeling. Methods: The Cancer Genome Atlas (TCGA) was quired for CREB1 expression and other ECM modulators in PDAC patients. In vitro, CRISPR/CAS9-based genomic editing was utilized to knockout CREB1 in the murine KPC cell line, on which RNA-seq analysis was performed. To investigate the effects of CREB in PDAC progression, a novel conditional CREB1 knockout (CREBfl/fl) was created in LSL-KrasG12D/+; Trp53 R172H/+; Pdx1Cre/+ (KPC) mice (KPCC-/-). Tumors were extracted and histologically evaluated. Immunoblotting and staining were conducted on both in vitro and in vivo samples. Chromatin immunoprecipitation sequencing (ChIP-seq) and qPCR were performed on the KPC CREBKO. Eukaryotic Promoter Database (EPD) and ENCODE databases were explored to evaluate the transcriptional role of CREB in regulating ECM genes. Results: Patient PDAC samples data from TCGA revealed elevated levels of CREB1, ROCK1, and ROCK2 compared to normal pancreatic tissues. When comparing high CREB expression to low CREB expression, upregulation of several ECM genes was noted, including ROCK1 and ROCK2 in patients with high CREB expression. In CREBKO, RNA-seq analysis revealed the downregulation of key ECM genes, including Mmp3, Mmp10, Lama3, and Fn1 compared to CREB wildtype. In our novel murine conditional knockout model, a substantial reduction in fibrosis was observed. In both in vitro and in vivo, immunoblot and staining demonstrated a marked reduction in the expression of ECM remodeling proteins upon CREB deletion. Through ChIP-seq, the direct involvement of CREB1 in the transcriptional regulation of Rock1 and Rock2 was established. EPD and ENCODE were utilized to confirm and validate our CREB regulation experimental findings. Conclusion: These findings demonstrate the role of CREB in PDAC progression, which may provide a potential target to intercept ECM remodeling via inhibition of the CREB-ROCK axis to suppress PDAC tumor progression and invasion. Citation Format: Sudhakar Jinka, Siddharth Mehra, Varunkumar Krishnamoorthy, Anna Bianchi, Karthik Rajkumar, Andrew Adams, Haleh Amirian, Samara Singh, Edmond W. Box, Erin Dickey, Nivelo L. Alberto, Ban Yuguang, Jashodeep Datta, Nipun Merchant, Nagaraj Nagathihalli. CREB-ROCK driven extracellular matrix remodeling exasperates pancreatic cancer progression [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 4277.

Abstract 6033: Understanding the role of Cep55 in initiation and progression of cancers

Abstract CEP55 is a cancer-testis antigen, highly expressed in a wide range of solid tumors as well as chromosomally unstable cancers. CEP55 is normally silent in most adult somatic tissues except germ cells; however, its expression is induced early during cell transformation. Numerous studies using cell line xenografts have shown that CEP55 is required for the viability and survival of a diverse range of cancers in vitro and in vivo. To decipher the mechanisms by which Cep55 promotes chromosomal instability and tumorigenesis in vivo, we developed a novel knock-in transgenic mouse model that ubiquitously overexpresses Cep55 (Cep55Tg/Tg) and a conditional knockout (cKO) mouse model of Cep55 (Cep55-/-). While overexpression of Cep55 was sufficient to cause spontaneous tumorigenesis in vivo, Cep55 loss hindered tumorigenesis. When we bred adult Cep55 cKO mice with other tumor-prone models: oncogenic Kras expression (Kras G12D) and Pten tumor-suppressor loss, Cep55 loss significantly delayed tumorigenesis and prolonged survival validating it as a promising therapeutic target for diverse cancers. This reduction of tumorigenesis is concomitant with the downregulation of AKT and ERK signaling pathways, attenuation of epithelial to mesenchymal transition, and increased cytotoxic CD4/CD8 T-cell tumor infiltration. This indicates that Cep55 can impair the establishment of the adaptive immune response through modification in the tumor microenvironment and regulation of cell signaling. Mass spectrophotometry of mouse embryo fibroblasts and derived exosomes from wild-type and KO mice revealed the pathways altered by Cep55 such as extracellular matrix remodeling pathways, integrin-related signaling and cellular trafficking mediators indicating the contributions of Cep55 to cancer are beyond what have been reported so far. Overall, CEP55 is a promising target to prevent tumorigenesis and the progression of cancer through various mechanisms. Citation Format: Behnam Rashidieh, Simon M. Tria, Kum Kum Khanna. Understanding the role of Cep55 in initiation and progression of cancers [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 6033.

Fecal carriage of vanB antibiotic resistance gene affects adipose tissue function under vancomycin use

ABSTRACT Detrimental consequences of antibiotic treatment may include long-lasting disruption of the gut microbiota. Previous studies found no negative effects of antibiotics on metabolic health, although individualized responses were observed. Here, we aimed to investigate the subject-specific response to vancomycin use in tissue-specific insulin sensitivity by stratifying individuals based on the presence of antibiotic resistance genes (ARGs) or opportunistic pathogens (OPs) in the baseline fecal microbiota. Quantitative Polymerase Chain Reaction (qPCR) was used to detect ARGs and OPs in DNA isolated from fecal samples of 56 males with overweight/obesity (Body Mass Index: 25–35 kg/m2) and impaired glucose metabolism (fasting plasma glucose ≥5.6 mmol/L and/or 2-hour glucose 7.8–11.1 mmol/L). A two-step hyperinsulinemic-euglycemic clamp was performed to determine tissue-specific insulin sensitivity. Abdominal subcutaneous adipose tissue (AT) gene expression was assessed using Affymetrix microarray. Gut microbial composition was determined using the Human Intestinal Tract Chip (HITChip) microarray. At baseline, the vancomycin resistance gene vanB was present in 60% of our population. In individuals that were vanB-negative at baseline, AT insulin sensitivity (insulin-mediated suppression of plasma free fatty acids) improved during vancomycin use, while it decreased among vanB-positive individuals (% change post versus baseline: 14.1 ± 5.6 vs. −6.7 ± 7.5% (p = .042)). The vancomycin-induced increase in AT insulin sensitivity was accompanied by downregulation of inflammatory pathways and enrichment of extracellular matrix remodeling pathways in AT. In the vanB-positive group, well-known vanB-carrying bacteria, Enterococcus and Streptococcus, expanded in the gut microbiome. In conclusion, microbiome composition and adipose tissue biology were differentially affected by vancomycin treatment based on fecal vanB carriage.

Abstract P5-16-09: Transcriptome modulation by mifepristone treatment in breast cancer patients with higher levels of progesterone receptor A than B

Abstract Background: Preclinical data suggests that antiprogestins inhibit the growth of luminal breast carcinomas expressing higher levels of progesterone receptor isoform A (PRA) than isoform B (PRB). Thus, we designed a pre-surgical window of opportunity trial to determine the therapeutic effects of oral mifepristone (MFP) in 20 breast cancer patients selected by their high PRA/PRB isoform ratio (MIPRA; NCT02651844).Methods. MIPRA is an open-label, one-arm, prospective interventional study. After the selection process, 20 patients that met the inclusion criteria, with ER+, PRA/PRB>1.5 determined by Western blots, and total PR ≥50% determined by immunohistochemistry (IHC), were included for daily MFP treatment (200 mg/day p.o., 14 days). Core needle biopsies and surgical samples were formalin-fixed for IHC studies, and others were snap-frozen for further molecular studies. Besides, plasma samples were obtained for MFP dosing by LC-MS/MS. RNA was extracted from frozen tissue with a column-based method. The library for sequencing was constructed using SMART-Seq v4 Ultra Low Input RN from 8 paired samples in which tissue was available and passed the RNA quality control. Sequencing data was aligned with STAR and processed in R/Bioconductor. The counts matrix was obtained with featureCounts and differential expression paired analysis was performed with DESeq2. Gene set enrichment analysis (GSEA) was executed with the MSigDB collection.Results: A 49.62% decrease in Ki-67 staining was registered in all surgical specimens compared to baseline (p = 0.0003). Using the pre-specified response parameter (30% relative reduction) we identified 14/20 responders. Mifepristone was detected in all available plasma samples and the mean concentration was 308.33 ±57.91 ng/ml (716.71 ±134.62 nM). We conducted an RNA-seq analysis to explore changes at the transcript level. First, we conducted the study with all pairs of samples, without considering the response to MFP in Ki-67 studies. Unsupervised analysis showed the paired samples clustered together but neither the principal component analysis, nor the hierarchical clustering, showed any relevant cluster. The differential expression analysis identified 11 and 76 genes down- and up-regulated, respectively. We performed a GSEA based on KEGG databases and determined enriched pathways related to modulation of cell cycle and apoptosis. When the analysis was conducted with the REACTOME up-modulation of immune bioprocess and extracellular matrix re-modeling pathways such as degradation of extracellular matrix, activation of matrix metalloproteinases and collagen formation, were observed in the latter. Additionally, we observed down-modulation of pathways related to cell cycle such as DNA replication and synthesis, APC/C, and phase transition pathways. Interestingly, when we considered the tumors that responded to MFP according to Ki-67 data (n=4) and those that did not respond (n=4), we found that the non-responsive group shared some of the up and down modulated pathways as the responsive group.Conclusion: The results obtained in RNA-Seq data support the findings obtained by IHC indicating that MFP inhibits cell proliferation in luminal breast carcinomas with higher levels of PRA than PRB. The fact that MFP increased immune-related pathways is in line with previous preclinical data from our laboratory suggesting that MFP may prime this group of tumors for. further immune therapy. Interestingly, we found that some relevant pathways regarding inhibition of cell proliferation were also modulated in the non-responsive group suggesting that tumors in which a decrease in Ki-67 was not evident, may be still responding to MFP treatment. Ongoing analysis will determine changes in other markers that may help to further define MFP-responsive patients. Citation Format: Andres Elia, Martin Abba, Hugo Gass, Caroline A Lamb, Victoria T Fabris, Paula Martinez Vazquez, Javier Burruchaga, Eunice Spengler, Ines Caillet Bois, Alejandra Castets, Silvia Lovisi, Marcos Liguori, Gabriela Pataccini, Maria Florencia Abascal, Virginia Novaro, Alfredo Molinolo, Silvia I Vanzulli, Paola Rojas, Claudia Lanari. Transcriptome modulation by mifepristone treatment in breast cancer patients with higher levels of progesterone receptor A than B [abstract]. In: Proceedings of the 2021 San Antonio Breast Cancer Symposium; 2021 Dec 7-10; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2022;82(4 Suppl):Abstract nr P5-16-09.

CX3CR1-Expressing Myeloid Cells Regulate Host-Helminth Interaction and Lung Inflammation.

Many helminth life cycles, including hookworm, involve a mandatory lung phase, where myeloid and granulocyte subsets interact with the helminth and respond to infection-induced lung injury. To evaluate these innate subsets in Nippostrongylus brasiliensis infection, reporter mice for myeloid cells (CX3CR1GFP ) and granulocytes (PGRPdsRED ) are employed. Nippostrongylus infection induces lung infiltration of reporter cells, including CX3CR1+ myeloid cells and PGRP+ eosinophils. Strikingly, CX3CR1GFP/GFP mice, which are deficient in CX3CR1, are protected from Nippostrongylus infection with reduced weight loss, lung leukocyte infiltration, and worm burden compared to CX3CR1+/+ mice. This protective effect is specific for CX3CR1 as CCR2-deficient mice do not exhibit reduced worm burdens. Nippostrongylus co-culture with lung Ly6C+ monocytes or CD11c+ cells demonstrates that CX3CR1GFP/GFP monocytes secrete more pro-inflammatory cytokines and actively bind the parasites causing reduced motility. RNA sequencing of Ly6C+ or CD11c+ cells shows Nippostrongylus-induced gene expression changes, particularly in monocytes, associated with inflammation, chemotaxis, and extracellular matrix remodeling pathways. Analysis reveals cytotoxic and adhesion molecules as potential effectors against the parasite, such as Gzma and Gzmb, which are elevated in CX3CR1GFP/GFP monocytes. These studies validate a dual innate cell reporter for lung helminth infection and demonstrate that CX3CR1 impairs monocyte-helminth interaction.

A Zebrafish Model of Metastatic Colonization Pinpoints Cellular Mechanisms of Circulating Tumor Cell Extravasation.

Metastasis is a multistep process in which cells must detach, migrate/invade local structures, intravasate, circulate, extravasate, and colonize. A full understanding of the complexity of this process has been limited by the lack of ability to study these steps in isolation with detailed molecular analyses. Leveraging a comparative oncology approach, we injected canine osteosarcoma cells into the circulation of transgenic zebrafish with fluorescent blood vessels in a biologically dynamic metastasis extravasation model. Circulating tumor cell clusters that successfully extravasated the vasculature as multicellular units were isolated under intravital imaging (n = 6). These extravasation-positive tumor cell clusters sublines were then molecularly profiled by RNA-Seq. Using a systems-level analysis, we pinpointed the downregulation of KRAS signaling, immune pathways, and extracellular matrix (ECM) organization as enriched in extravasated cells (p < 0.05). Within the extracellular matrix remodeling pathway, we identified versican (VCAN) as consistently upregulated and central to the ECM gene regulatory network (p < 0.05). Versican expression is prognostic for a poorer metastasis-free and overall survival in patients with osteosarcoma. Together, our results provide a novel experimental framework to study discrete steps in the metastatic process. Using this system, we identify the versican/ECM network dysregulation as a potential contributor to osteosarcoma circulating tumor cell metastasis.

Comprehensive proteomic analysis reveals distinct functional modules associated with skull base and supratentorial meningiomas and perturbations in collagen pathway components

Meningiomas are brain tumors that originate from the meninges and has been primarily classified into three grades by the current WHO guidelines. Although widely prevalent and can be managed by surgery there are instances when the tumors are located in difficult regions. This results in considerable challenges for complete surgical resection and further clinical management. While the genetic signature of the skull base tumors is now known to be different from the non-skull base tumors, there is a lack of information at the functional aspects of these tumors at the proteomic level. Thus, the current study thereby aims to obtain mechanistic insights between the two radiologically distinct groups of meningiomas, namely the skull base & supratentorial (non-skull base-NSB) regions. We have employed a comprehensive mass spectrometry-based label-free quantitative proteomic analysis in Skull base and supratentorial meningiomas. Further, we have used an Artificial Neural Networking employing a sparse Multilayer perceptron (MLP) architecture to predict protein concordance. A patient-derived spectral library has been employed for a novel peptide-level validation of proteins that are specific to the radiological regions using the SRM assay based targeted proteomics approach. The comprehensive proteomics enabled the identification of nearly 4000 proteins with high confidence (1%FDR ≥ 2 unique peptides) among which 170 proteins were differentially abundant in Skull base vs Supratentorial tumors (p-value ≤0.05). In silico analysis enabled mapping of the major alterations and hinted towards an overall perturbation of extracellular matrix and collagen biosynthesis components in the non-skull base meningiomas and a prominent perturbation of molecular trafficking in the skull base meningiomas. Therefore, this study has yielded novel insights into the functional association of the proteins that are differentially abundant in the two radiological subgroups. SignificanceIn the current study, we have performed label-free proteomic analysis on fresh frozen tissue of 14 Supratentorial (NSB) and 7 Skull base meningiomas to assess perturbations in the global proteome, we have further employed an in-depth in silico analysis to map the pathways that have enabled functional mapping of the differentially abundant proteins in the Skull base and Supratentorial tumors. The findings from the above were also subjected to a machine learning-based neural networking to find out the proteins that have the most concordance of occurrence to determine the most influential proteins of the network. We further validated the differential abundance of identified protein markers in a larger patient cohort of Skull base and Supratentorial employing targeted proteomics approach to validate key protein candidates emerging from ours and other recent studies.The previous studies that have explored the skull base and convexity meningiomas have been able to reveal alterations in the genetic mutations in these tumor types. However, there are not many studies that have explored the functional aspects of these tumors, especially at the proteome level. We have attempted for the first time to map the functional modules associated with altered proteins in these tumors and have been able to identify that there is a possibility that the Skull base meningiomas to be considerably different from the Non-skull base (NSB) tumors in terms of the perturbed pathways. Our study employed global as well as targeted proteomics to examine the proteomic alterations in these two tumor groups. The study indicates that proteins that were more abundant in Skull base tumors were part of molecular transport components, non-skull base proteins majorly mapped to the components of extracellular matrix remodeling pathways. In conclusion, this study substantiates the distinction in the proteomic signatures in the skull base and supratentorial meningiomas paving way for further investigation of the identified markers for determining if some of these proteins can be used for therapeutic interventions for cases that pose considerable challenges for complete resection.

Moderate aerobic exercise prevents matrix degradation and death in a mouse model of aortic dissection and aneurysm.

Thoracic aortic aneurysm and dissection (TAAD) is a deadly disease characterized by intimal disruption induced by hemodynamic forces of the circulation. The effect of exercise in patients with TAAD is largely unknown. β-Aminopropionitrile (BAPN) is an irreversible inhibitor of lysyl oxidase that induces TAAD in mice. The objective of this study was to investigate the effect of aerobic exercise on BAPN-induced TAAD. Upon weaning, mice were given either BAPN-containing water or standard drinking water and subjected to either conventional cage activity (BAPN-CONV) or forced treadmill exercise (BAPN-EX) for up to 26 wk. Mortality was 23.5% (20/85) for BAPN-CONV mice versus 0% (0/22) for BAPN-EX mice (hazard ratio 3.8; P = 0.01). BAPN induced significant elastic lamina fragmentation and intimal-medial thickening compared with BAPN-untreated controls, and aneurysms were identified in 50% (5/10) of mice that underwent contrast-enhanced CT scanning. Exercise significantly decreased BAPN-induced wall thickening, calculated circumferential wall tension, and lumen diameter, with 0% (0/5) of BAPN-EX demonstrating chronic aortic aneurysm formation on CT scan. Expression of selected genes relevant to vascular diseases was analyzed by qRT-PCR. Notably, exercise normalized BAPN-induced increases in TGF-β pathway-related genes Cd109, Smad4, and Tgfβr1; inflammation-related genes Vcam1, Bcl2a1, Ccr2, Pparg, Il1r1, Il1r1, Itgb2, and Itgax; and vascular injury- and response-related genes Mmp3, Fn1, and Vwf. Additionally, exercise significantly increased elastin expression in BAPN-treated animals compared with controls. This study suggests that moderate aerobic exercise may be safe and effective in preventing the most devastating outcomes in TAAD.NEW & NOTEWORTHY Moderate aerobic exercise was shown to significantly reduce mortality, extracellular matrix degradation, and thoracic aortic aneurysm and dissection formation associated with lysyl oxidase inhibition in a mouse model. Gene expression suggested a reversal of TGF-β, inflammation, and extracellular matrix remodeling pathway dysregulation, along with augmented elastogenesis with exercise.

Hemozoin Promotes Lung Inflammation via Host Epithelial Activation.

Respiratory distress in severe malaria is associated with high mortality, but its pathogenesis remains unclear. The malaria pigment hemozoin (HZ) is abundant in target organs of severe malaria, including the lungs, and is known to be a potent innate immune activator of phagocytes. We hypothesized that HZ might also stimulate lung epithelial activation and thereby potentiate lung inflammation. We show here that airway epithelium stimulated with HZ undergoes global transcriptional reprogramming and changes in cell surface protein expression that comprise an epithelial activation phenotype. Proinflammatory signaling is induced, and key cytoadherence molecules are upregulated, including several associated with severe malaria, such as CD36 and ICAM1. Epithelial and extracellular matrix remodeling pathways are transformed, including induction of key metalloproteases and modulation of epithelial junctions. The overall program induced by HZ serves to promote inflammation and neutrophil transmigration, and is recapitulated in a murine model of HZ-induced acute pneumonitis. Together, our data demonstrate a direct role for hemozoin in stimulating epithelial activation that could potentiate lung inflammation in malaria.IMPORTANCE Respiratory distress (RD) is a complication of severe malaria associated with a particularly high risk for death in African children infected with the parasite Plasmodium falciparum The pathophysiology underlying RD remains poorly understood, and the condition is managed supportively. The parasite-derived factor HZ accumulates in target organs of severe malaria, including the lungs, and is a potent stimulator of immune cells. Our findings demonstrate that HZ causes global activation of lung epithelial cells, a response that directly promotes lung inflammation. HZ stimulates expression of key proinflammatory and cell surface molecules, alters signaling pathways involved in epithelial-matrix remodeling, and promotes neutrophil transmigration and airway inflammation. The lung epithelial activation induced by HZ mimics patterns seen in malarial lung injury and provides new insights into the molecular pathogenesis of RD.

Metformin alters skeletal muscle transcriptome adaptations to resistance training in older adults.

Evidence from clinical trials and observational studies suggests that both progressive resistance exercise training (PRT) and metformin delay a variety of age-related morbidities. Previously, we completed a clinical trial testing the effects of 14 weeks of PRT + metformin (metPRT) compared to PRT with placebo (plaPRT) on muscle hypertrophy in older adults. We found that metformin blunted PRT-induced muscle hypertrophic response. To understand potential mechanisms underlying the inhibitory effect of metformin on PRT, we analyzed the muscle transcriptome in 23 metPRT and 24 plaPRT participants. PRT significantly increased expression of genes involved in extracellular matrix remodeling pathways, and downregulated RNA processing pathways in both groups, however, metformin attenuated the number of differentially expressed genes within these pathways compared to plaPRT. Pathway analysis showed that genes unique to metPRT modulated aging-relevant pathways, such as cellular senescence and autophagy. Differentially expressed genes from baseline biopsies in older adults compared to resting muscle from young volunteers were reduced following PRT in plaPRT and were further reduced in metPRT. We suggest that although metformin may blunt pathways induced by PRT to promote muscle hypertrophy, adjunctive metformin during PRT may have beneficial effects on aging-associated pathways in muscle from older adults.

Respiratory Syncytial Virus Infection Induces Chromatin Remodeling to Activate Growth Factor and Extracellular Matrix Secretion Pathways

Lower respiratory tract infection (LRTI) with respiratory syncytial virus (RSV) is associated with reduced lung function through unclear mechanisms. In this study, we test the hypothesis that RSV infection induces genomic reprogramming of extracellular matrix remodeling pathways. For this purpose, we sought to identify transcriptionally active open chromatin domains using assay for transposase-accessible-next generation sequencing (ATAC-Seq) in highly differentiated lower airway epithelial cells. High confidence nucleosome-free regions were those predicted independently using two peak-calling algorithms. In uninfected cells, ~12,650 high-confidence open chromatin regions were identified. These mapped to ~8700 gene bodies, whose genes functionally controlled organelle synthesis and Th2 pathways (IL6, TSLP). These latter cytokines are preferentially secreted by RSV-infected bronchiolar cells and linked to mucous production, obstruction, and atopy. By contrast, in RSV infection, we identify ~1700 high confidence open chromatin domains formed in 1120 genes, primarily in introns. These induced chromatin modifications are associated with complex gene expression profiles controlling tyrosine kinase growth factor signaling and extracellular matrix (ECM) secretory pathways. Of these, RSV induces formation of nucleosome-free regions on TGFB1/JUNB//FN1/MMP9 genes and the rate limiting enzyme in the hexosamine biosynthetic pathway (HBP), Glutamine-Fructose-6-Phosphate Transaminase 2 (GFPT2). RSV-induced open chromatin domains are highly enriched in AP1 binding motifs and overlap experimentally determined JUN peaks in GEO ChIP-Seq data sets. Our results provide a topographical map of chromatin accessibility and suggest a growth factor and AP1-dependent mechanism for upregulation of the HBP and ECM remodeling in lower epithelial cells that may be linked to long-term airway remodeling.

Magnesium prevents vascular calcification in Klotho deficiency

Klotho knock-out mice are an important model for vascular calcification, which is associated with chronic kidney disease. In chronic kidney disease, serum magnesium inversely correlates with vascular calcification. Here we determine the effects of serum magnesium on aortic calcification in Klotho knock-out mice treated with a minimal or a high magnesium diet from birth. After eight weeks, serum biochemistry and aorta and bone tissues were studied. Protective effects of magnesium were characterized by RNA-sequencing of the aorta and micro-CT analysis was performed to study bone integrity. A high magnesium diet prevented vascular calcification and aortic gene expression of Runx2 and matrix Gla protein found in such mice on the minimal magnesium diet. Differential expression of inflammation and extracellular matrix remodeling genes accompanied the beneficial effects of magnesium on calcification. High dietary magnesium did not affect serum parathyroid hormone, 1,25-dihydroxyvitamin D3 or calcium. High magnesium intake prevented vascular calcification despite increased fibroblast growth factor-23 and phosphate concentration in the knock-out mice. Compared to mice on the minimal magnesium diet, the high magnesium diet reduced femoral bone mineral density by 20% and caused excessive osteoid formation indicating osteomalacia. Osteoclast activity was unaffected by the high magnesium diet. In Saos-2 osteoblasts, magnesium supplementation reduced mineralization independent of osteoblast function. Thus, high dietary magnesium prevents calcification in Klotho knock-out mice. These effects are potentially mediated by reduction of inflammatory and extracellular matrix remodeling pathways within the aorta. Hence magnesium treatment may be promising to prevent vascular calcification, but the risk for osteomalacia should be considered.

RNA sequencing of transplant-stage idiopathic pulmonary fibrosis lung reveals unique pathway regulation

Idiopathic pulmonary fibrosis (IPF), the scarring of lung parenchyma resulting in the loss of lung function, remains a fatal disease with a significant unmet medical need. Patients with severe IPF often develop acute exacerbations resulting in the rapid deterioration of lung function, requiring transplantation. Understanding the pathophysiological mechanisms contributing to IPF is key to develop novel therapeutic approaches for end-stage disease.We report here RNA-sequencing analyses of lung tissues from a cohort of patients with transplant-stage IPF (n=36), compared with acute lung injury (ALI) (n=11) and nondisease controls (n=19), that reveal a robust gene expression signature unique to end-stage IPF. In addition to extracellular matrix remodelling pathways, we identified pathways associated with T-cell infiltration/activation, tumour development, and cholesterol homeostasis, as well as novel alternatively spliced transcripts that are differentially regulated in the advanced IPF lung versus ALI or nondisease controls. Additionally, we show a subset of genes that are correlated with percent predicted forced vital capacity and could reflect disease severity.Our results establish a robust transcriptomic fingerprint of an advanced IPF lung that is distinct from previously reported microarray signatures of moderate, stable or progressive IPF and identifies hitherto unknown candidate targets and pathways for therapeutic intervention in late-stage IPF as well as biomarkers to characterise disease progression and enable patient stratification.

MiR‐192/215‐5p act as tumor suppressors and link Crohn's disease and colorectal cancer by targeting common metabolic pathways: An integrated informatics analysis and experimental study

MicroRNAs have emerged as key regulators involved in a variety of biological processes. Previous studies have demonstrated that miR-192/215 participated in progression of Crohn's disease and colorectal cancer. However, their concrete relationships and regulation networks in diseases remain unclear. Here, we used bioinformatics methods to expound miR-192/215-5p macrocontrol regulatory networks shared by two diseases. For data mining and figure generation, several miRNA prediction tools, Human miRNA tissue atlas, FunRich, miRcancer, MalaCards, STRING, GEPIA, cBioPortal, GEO databases, Pathvisio, Graphpad Prism 6 software, etc . are extensively applied. miR-192/215-5p were specially distributed in colon tissues and enriched biological pathways were closely associated with human cancers. Emerging role of miR-192/215-5p and their common pathways in Crohn's disease and colorectal cancer was also analyzed. Based on results derived from multiple approaches, we identified the biological functions of miR-192/215-5p as a tumor suppressor and link Crohn's disease and colorectal cancer by targeting triglyceride synthesis and extracellular matrix remodeling pathways.

426 Transcriptome analysis determines a cosmetic formulation containing botanical extracts activates extracellular matrix remodeling in vitro

Vitamin C (ascorbic acid) is well known for its benefits to skincare. Previously, we demonstrated a cosmetic formulation containing extracts from 5 botanical fruits rich in vitamin C improved the appearance of multiple skin attributes over time, including skin tone, laxity, and texture. Here, we utilized transcriptome analysis to help understand the global effects of this cosmetic formulation on skin in vitro. Artificial skin explants were treated with the cosmetic formulation for 3 days, then RNA was harvested, amplified, and analyzed using the topic-defined PIQOR skin microarray. The genes modulated were further analyzed by PredictSearch software to determine the functional correlation between genetic networks. PredictSearch™ is a powerful data and text mining software that searches through millions of scientific publications and retrieves correlations between genes and biological processes or diseases. The analysis determined extracellular matrix remodeling was the main consequences of treatment. Next, we sought to validate the pathway by protein analysis. Artificial skin explants were treated with the cosmetic formulation for 6 days then tissue conditioned media was collected. Collagen and laminin were detected by ELISA, confirming the microarray findings. Interestingly, the extracellular matrix protein fibronectin was also upregulated even though did not appear on the microarray screen. These data suggest this cosmetic formulation impacts extracellular matrix remodeling pathways to clinically improve the appearance of skin laxity and texture.

MiR-192/215-5p Act as Tumor Suppressors and Link Crohn's Disease and Colorectal Cancer by Targeting Metabolic Pathways: A Comprehensive Database Mining and Experimental Study

Background: MicroRNAs (miRNAs) have emerged as key regulators involved in a variety of biological processes such as inflammatory bowel diseases and tumor progression. Previous studies have demonstrated that miR-192/215 participated in progression of Crohn's disease (CD) and colorectal cancer (CRC), respectively; however, their detailed functional relationships and molecular regulations between two diseases remain unclear. Methods: Here we used bioinformatics methods to systematically expound miR-192/215-5p macrocontrol regulatory networks shared by two diseases. For data mining and validation, several miRNA prediction tools including Tarbase, miRTARBASE, miRecored, miRpathDB, et al; Human miRNA tissue atlas, FunRich, miRcancer, MalaCards, GEPIA, cBioPortal, luciferase assay, et al. are extensively applied. Findings: miR-192/215-5p with identical seed sequence were specially distributed in colon tissues and enriched biological pathways were closely associated with human cancers. Emerging role of miR-192/215-5p in CD and CRC was also analyzed. In addition, we analyzed common pathways targeted by miR-192/215-5p in both diseases. Interpretation: Based on results derived from multiple approaches, we identified the biological functions of miR-192/215-5p as a tumor suppressor and link CD and CRC by targeting triglyceride synthesis and extracellular matrix remodeling pathways. Funding Statement: The research was supported by the Natural Science Foundation of Fujian Province [grant numbers 2012YZ0001-1 and 2016J01582], National Nature Science Foundation of China [grant numbers No.81402107 and No.81601618], Military Medical Science project [grant number No.15QNP025]. Declaration of Interests: No potential conflicts of interest were disclosed. Ethics Approval Statement: The study protocol was approved by the Ethics Committee of Fuzhou General Hospital, Xiamen University. Data collections and processions were performed according to policies of GEO and TCGA project.

Quantitative Proteomics Analysis of Sporadic Medullary Thyroid Cancer Reveals FN1 as a Potential Novel Candidate Prognostic Biomarker.

Sporadic medullary thyroid cancer (MTC) is a rare neuroendocrine tumor. Currently, although the diagnosis of sporadic MTC is relatively simple, the need to discover novel candidate prognostic biomarkers for sporadic MTC and investigate the underlying mechanism involved in this rare disease is urgent. We employed tandem mass tag-based liquid chromatography-mass spectrometry to identify and analyze differentially expressed proteins (DEPs) in sporadic MTC. Western blotting was used to validate the DEPs. Immunohistochemistry was performed to investigate FN1 and RPS6KA3 in an independent set of sporadic MTC tissues. Immunohistochemical data were analyzed by different statistical methods. Three hundred eighty-eight DEPs were identified in mass spectrometry, mainly involved in the extracellular matrix, cytoskeletal remodeling, or oxidoreductase activity. Among them, THBS1, MMP9, FN1, RPS6KA3, SYT1, and carcinoembryonic antigen were successfully validated by Western blot. In addition, FN1 and RPS6KA3, enriched in extracellular matrix (ECM) remodeling and the mitogen-activated protein kinase (MAPK) signaling pathway, respectively, were investigated in an independent set of sporadic MTC tissues. Receiver-operator characteristic curve analysis showed that FN1 and RPS6KA3 can be used for discriminating sporadic MTC tumorous tissues from paired normal thyroid tissues, and the clinical biomarker calcitonin was positively correlated with FN1 and RPS6KA3 in tumorous tissues. Furthermore, the immunohistochemical scores of FN1 in tumorous tissue showed an inverse relationship with tumor classification, lymph node classification, and American Joint Committee on Cancer stage. Through univariate and multivariate analysis for progression-free survival, we also found that low FN1 expression in tumorous tissues was an independent worse prognostic factor for progression-free survival. We identified that the pathophysiology of sporadic MTC involve numerous pathways, including the synaptic vesicle pathway, the MAPK signaling pathway, and the ECM remodeling pathway. Furthermore, our study also identified FN1 as novel prognostic biomarkers related to the pathophysiologic changes in sporadic MTC. Proteomic dissection and prognostic biomarkers are scarce in sporadic medullary thyroid cancer (MTC). This article reports the use of proteomics technology to comprehensively investigate the molecular mechanisms of sporadic MTC, which resulted in the identification of FN1 as a novel candidate prognostic biomarker.

Substrate fiber alignment mediates tendon cell response to inflammatory signaling

Healthy tendon tissue features a highly aligned extracellular matrix that becomes disorganized with disease. Recent evidence suggests that inflammation coexists with early degenerative changes in tendon, and that crosstalk between immune-cells and tendon fibroblasts (TFs) can contribute to poor tissue healing. We hypothesized that a disorganized tissue architecture may predispose tendon cells to degenerative extracellular matrix remodeling pathways, particularly within a pro-inflammatory niche. This hypothesis was tested by analyzing human TFs cultured on electrospun polycaprolactone (PCL) mats with either highly aligned or randomly oriented fiber structures. We confirmed that fibroblast morphology, phenotype, and markers of matrix turnover could be significantly affected by matrix topography. More strikingly, the TF response to paracrine signals from polarized macrophages or by stimulation with pro-inflammatory cytokines featured significant downregulation of signaling related to extracellular synthesis, with significant concomitant upregulation of gene and protein expression of matrix degrading enzymes. Critically, this tendency towards degenerative re-regulation was exacerbated on randomly oriented PCL substrates. These novel findings indicate that highly aligned tendon cell scaffolds not only promote tendon matrix synthesis, but also play a previously unappreciated role in mitigating adverse resident fibroblast response within an inflammatory milieu. Statement of SignificanceUse of biomaterial scaffolds for tendon repair often results in tissue formation characteristic of scar tissue, rather than the highly aligned type-1 collagen matrix of healthy tendons. We hypothesized that non-optimal biomaterial surfaces may play a role in these outcomes, specifically randomly oriented biomaterial surfaces that unintentionally mimic structure of pathological tendon. We observed that disorganized scaffold surfaces do adversely affect early cell attachment and gene expression. We further identified that disorganized fiber surfaces can prime tendon cells toward pro-inflammatory signaling. These findings represent provocative evidence unstructured fiber surfaces may underlie inflammatory responses that drive aberrant collagen matrix turnover. This work could be highly relevant for the design of cell instructive biomaterial therapies that yield positive clinical outcomes.