Causal network analysis of head and neck keloid tissue identifies potential master regulators

Placental mesenchymal stem cells-secreted proenkephalin suppresses the p38 MAPK signaling to block hyperproliferation of keloid fibroblasts

BACKGROUND

Thanks to their multi-potency and secretory functions, mesenchymal stem cells (MSCs) have long been established as an ideal cell type for skin wound healing and a candidate therapeutic strategy for excessive pathological scarring in the meantime. This study focuses on the effect of placental MSCs (PMSCs) on the activity of keloid fibroblasts (KFs) and the potential involvement of proenkephalin (PENK).

METHODS

Secretory protein of PMSC that are lowly expressed in KFs were predicted by bioinformatics analyses. The expression of PENK in KFs was detected by RT-qPCR and western blot analysis. PMSCs were co-cultured with KFs and dermal fibroblasts (DFs) to examine their effect on proliferation, migration, invasion, and apoptosis of the distinct cell types. PENK secretion by PMSCs and its uptake by KFs were examined by ELISA, WB, and immunofluorescence staining. Loss-of-functions of PENK and p38-MAPK were induced to examine the activity of KFs in vitro and in mice.

RESULTS

PENK, a secretory protein of PMSCs, was conspicuously downregulated in KFs compared to normal DFs. PMSC stimulation suppressed proliferation, migration, invasion, and resistance to apoptosis of the co-cultured KFs but not DFs, which was ascribed to the upregulation of PENK protein in KFs. PMSCs-secreted PENK suppressed p38 phosphorylation in KFs. The proliferative and aggressive properties of KFs in vitro and the nodule-forming capacity of KFs in vivo were promoted upon PENK downregulation but suppressed by the p38 MAPK inhibitor SB202190.

CONCLUSION

This work unravels that PMSCs-secreted PENK suppresses the p38 MAPK signaling to block hyperproliferation of KFs.

Methylation-based reclassification and risk stratification of skull-base chordomas

BACKGROUND

Skull-base chordomas are rare malignant bone cancers originating from the remnant of the notochord. Survival is variable, and clinical or molecular factors cannot reliably predict their outcomes. This study therefore identified epigenetic subtypes that defined new chordoma epigenetic profiles and their corresponding characteristics.

METHODS

Methylation profiles of 46 chordoma-resected neoplasms between 2008 and 2014, along with clinical information, were collected. K-means consensus clustering and principal component analysis were used to identify and validate the clusters. Single-sample gene set enrichment analysis, methylCIBERSORT algorithm, and copy number analysis were used to identify the characteristics of the clusters.

RESULTS

Unsupervised clustering analysis confirmed two clusters with a progression-free survival difference. Gene set enrichment analysis indicated that the early and late estrogen response pathways and the hypoxia pathway were activated whereas the inflammatory and interferon gamma responses were suppressed. Forty-six potential therapeutic targets corresponding to differentially methylated sites were identified from chordoma patients. Subgroups with a worse outcome were characterized by low immune cell infiltration, higher tumor purity, and higher stemness indices. Moreover, copy number amplifications mostly occurred in cluster 1 tumors and the high-risk group. Additionally, the presence of a CCNE1 deletion was exclusively found in the group of chordoma patients with better outcome, whereas RB1 and CDKN2A/2B deletions were mainly found in the group of chordoma patients with worse outcome.

CONCLUSIONS

Chordoma prognostic epigenetic subtypes were identified, and their corresponding characteristics were found to be variable.

Hepatic transcript signatures predict atherosclerotic lesion burden prior to a 2-year high cholesterol, high fat diet challenge

The purpose of this study was to identify molecular mechanisms by which the liver influences total lesion burden in a nonhuman primate model (NHP) of cardiovascular disease with acute and chronic feeding of a high cholesterol, high fat (HCHF) diet. Baboons (47 females, 64 males) were fed a HCHF diet for 2 years (y); liver biopsies were collected at baseline, 7 weeks (w) and 2y, and lesions were quantified in aortic arch, descending aorta, and common iliac at 2y. Unbiased weighted gene co-expression network analysis (WGCNA) revealed several modules of hepatic genes correlated with lesions at different time points of dietary challenge. Pathway and network analyses were performed to study the roles of hepatic module genes. More significant pathways were observed in males than females. In males, we found modules enriched for genes in oxidative phosphorylation at baseline, opioid signaling at 7w, and EIF2 signaling and HNF1A and HNF4A networks at baseline and 2y. One module enriched for fatty acid β oxidation pathway genes was found in males and females at 2y. To our knowledge, this is the first study of a large NHP cohort to identify hepatic genes that correlate with lesion burden. Correlations of baseline and 7w module genes with lesions at 2y were observed in males but not in females. Pathway analyses of baseline and 7w module genes indicate EIF2 signaling, oxidative phosphorylation, and μ-opioid signaling are possible mechanisms that predict lesion formation induced by HCHF diet consumption in males. Our findings of coordinated hepatic transcriptional response in male baboons but not female baboons indicate underlying molecular mechanisms differ between female and male primate atherosclerosis.

Bioinformatics study on different gene expression profiles of fibroblasts and vascular endothelial cells in keloids

Keloid is a benign fibroproliferative skin tumor. The respective functions of fibroblasts and vascular endothelial cells in keloid have not been fully studied. The purpose of this study is to identify the respective roles and key genes of fibroblasts and vascular endothelial cells in keloids, which can be used as new targets for diagnosis or treatment.The microarray datasets of keloid fibroblasts and vascular endothelial cells were obtained from the Gene Expression Omnibus (GEO) database. Differentially expressed genes (DEGs) were screened out. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) were used for functional enrichment analysis. The search tool for retrieval of interacting genes and Cytoscape were used to construct protein-protein interaction (PPI) networks and analyze gene modules. The hub genes were screened out, and the relevant interaction networks and biological process analysis were carried out.In fibroblasts, the DEGs were significantly enriched in collagen fibril organization, extracellular matrix organization and ECM-receptor interaction. The PPI network was constructed, and the most significant module was selected, which is mainly enriched in ECM-receptor interaction. In vascular endothelial cells, the DEGs were significantly enriched in cytokine activity, growth factor activity and transforming growth factor-β (TGF-β) signaling pathway. Module analysis was mainly enriched in TGF-β signaling pathway. Hub genes were screened out separately.In summary, the DEGs and hub genes discovered in this study may help us understand the molecular mechanisms of keloid, and provide potential targets for diagnosis and treatment.

Transcriptome Analysis of Hypoxic Lymphatic Endothelial Cells Indicates Their Potential to Contribute to Extracellular Matrix Rearrangement

Lymphedema (LE) affects millions of people worldwide. It is a chronic progressive disease with massive development of fibrosclerosis when untreated. There is no pharmacological treatment of lymphedema. The disease is associated with swelling of the interstitium of the affected organ, mostly arm or leg, impressive development of adipose tissue, fibrosis and sclerosis with accumulation of huge amounts of collagen, and Papillomatosis cutis. Malnutrition and reduced oxygenation of the affected tissues is a hallmark of lymphedema. Here, we investigated if the hypoxia of lymphatic endothelial cells (LECs) might contribute to fibrosis. We applied RNASeq and qPCR to study the concordant changes of the exome of three human foreskin-derived LEC isolates after 4 days of hypoxia (1% O₂) vs. normoxia (21% O₂). Of the approximately 16,000 genes expressed in LECs, 162 (1%) were up- or down-regulated by hypoxia. Of these, 21 genes have important functions in the production or modification of the extracellular matrix (ECM). In addition to the down-regulation of elastin, we found up-regulation of druggable enzymes and regulators such as the long non-coding RNA H19, inter-alpha-trypsin inhibitor heavy chain family member 5 (ITIH5), lysyl-oxidase (LOX), prolyl 4-hydroxylase subunit alpha 1 (P4HA1), procollagen-lysine 2-oxoglutarate 5-dioxygenase 2 (PLOD2), and others that are discussed in the paper. Initial lymphatics do not produce a continuous basement membrane; however, our study shows that hypoxic LECs have an unexpectedly high ability to alter the ECM.

Identifying miRNA modules associated with progression of keloids through weighted gene co-expression network analysis and experimental validation in vitro

Keloid is a type of skin fibroproliferative disease, characterized by excessive deposition of collagen in the extracellular matrix, myofibroblast activation and invasive growth to the surrounding normal skin tissue. However, the specific pathogenesis of keloids is not yet fully understood and existing treatment strategies are unsatisfied. It is therefore urgent to explore new biomarkers associated with its progression for keloids. In this study, the microarray dataset GSE113620 was downloaded from the Gene Expression Omnibus (GEO) database to screen out the differential expression of miRNAs (DEMs). The DEMs with large variance were applied to construct a weighted gene co-expression network to identify miRNA modules that are closely relevant to keloid progression. It is worth noting that miR-424-3p in the blue module (r = 0.98, p = 1e-18) is considered to be the ultimate target most relevant to keloid progression through co-expressed network analysis. Subsequently, the results of molecular biology experiments determine that miR-424-3p targeting Smad7 significantly enhanced the ability of cell proliferation, migration and collagen secretion after transfection with miR-424-3p mimic, while the apoptosis rate was significantly reduced. On the contrary, the miR-424-3p inhibitor performs the exact opposite function.

Epigenetic modification mechanisms involved in keloid: current status and prospect

Keloid, a common dermal fibroproliferative disorder, is benign skin tumors characterized by the aggressive fibroblasts proliferation and excessive accumulation of extracellular matrix. However, common therapeutic approaches of keloid have limited effectiveness, emphasizing the momentousness of developing innovative mechanisms and therapeutic strategies. Epigenetics, representing the potential link of complex interactions between genetics and external risk factors, is currently under intense scrutiny. Accumulating evidence has demonstrated that multiple diverse and reversible epigenetic modifications, represented by DNA methylation, histone modification, and non-coding RNAs (ncRNAs), play a critical role in gene regulation and downstream fibroblastic function in keloid. Importantly, abnormal epigenetic modification manipulates multiple behaviors of keloid-derived fibroblasts, which served as the main cellular components in keloid skin tissue, including proliferation, migration, apoptosis, and differentiation. Here, we have reviewed and summarized the present available clinical and experimental studies to deeply investigate the expression profiles and clarify the mechanisms of epigenetic modification in the progression of keloid, mainly including DNA methylation, histone modification, and ncRNAs (miRNA, lncRNA, and circRNA). Besides, we also provide the challenges and future perspectives associated with epigenetics modification in keloid. Deciphering the complicated epigenetic modification in keloid is hopeful to bring novel insights into the pathogenesis etiology and diagnostic/therapeutic targets in keloid, laying a foundation for optimal keloid ending.

Understanding Keloid Pathobiology From a Quasi-Neoplastic Perspective: Less of a Scar and More of a Chronic Inflammatory Disease With Cancer-Like Tendencies

Keloids are considered as benign fibroproliferative skin tumors growing beyond the site of the original dermal injury. Although traditionally viewed as a form of skin scarring, keloids display many cancer-like characteristics such as progressive uncontrolled growth, lack of spontaneous regression and extremely high rates of recurrence. Phenotypically, keloids are consistent with non-malignant dermal tumors that are due to the excessive overproduction of collagen which never metastasize. Within the remit of keloid pathobiology, there is increasing evidence for the various interplay of neoplastic-promoting and suppressing factors, which may explain its aggressive clinical behavior. Amongst the most compelling parallels between keloids and cancer are their shared cellular bioenergetics, epigenetic methylation profiles and epithelial-to-mesenchymal transition amongst other disease biological (genotypic and phenotypic) behaviors. This review explores the quasi-neoplastic or cancer-like properties of keloids and highlights areas for future study.

Keloid research: current status and future directions

INTRODUCTION

Keloids and hypertrophic scars are fibroproliferative disorders of the skin that result from abnormal healing of injured or irritated skin. Multiple studies suggest that genetic, systemic and local factors may contribute to the development and/or growth of keloids and hypertrophic scars. A key local factor may be mechanical stimuli. Here, we provide an up-to-date review of the studies on the roles that genetic variation, epigenetic modifications and mechanotransduction play in keloidogenesis.

METHODS

An English literature review was performed by searching the PubMed, Embase and Web of Science databases with the following keywords: genome-wide association study; epigenetics; non-coding RNA; microRNA; long non-coding RNA (lncRNA); DNA methylation; mechanobiology; and keloid. The searches targeted the time period between the date of database inception and July 2018.

RESULTS

Genetic studies identified several single-nucleotide polymorphisms and gene linkages that may contribute to keloid pathogenesis. Epigenetic modifications caused by non-coding RNAs (e.g. microRNAs and lncRNAs) and DNA methylation may also play important roles by inducing the persistent activation of keloidal fibroblasts. Mechanical forces and the ensuing cellular mechanotransduction may also influence the degree of scar formation, scar contracture and the formation/progression of keloids and hypertrophic scars.

CONCLUSIONS

Recent research indicates that the formation/growth of keloids and hypertrophic scars associate clearly with genetic, epigenetic, systemic and local risk factors, particularly skin tension around scars. Further research into scar-related genetics, epigenetics and mechanobiology may reveal molecular, cellular or tissue-level targets that could lead to the development of more effective prophylactic and therapeutic strategies for wounds/scars in the future.

Genome-wide DNA methylation profiling of the regenerative MRL/MpJ mouse and two normal strains

Aim: We aimed to identify the pivotal differences in the DNA methylation profiles between the regeneration capable MRL/MpJ mouse and reference mouse strains. Materials & methods: Global DNA methylation profiling was performed in ear pinnae, bone marrow, spleen, liver and heart from uninjured adult females of the MRL/MpJ and C57BL/6J and BALB/c. Results & conclusion: A number of differentially methylated regions (DMRs) distinguishing between the MRL/MpJ mouse and both references were identified. In the ear pinnae, the DMRs were enriched in genes associated with development, inflammation and apoptosis, and in binding sites of transcriptional modulator Smad1. Several DMRs overlapped previously mapped quantitative trait loci of regenerative capability. The results suggest potential epigenetic determinants of regenerative phenomenon.

From genetics to epigenetics: new insights into keloid scarring

Keloid scarring is a dermal fibroproliferative response characterized by excessive and progressive deposition of collagen; aetiology and molecular pathology underlying keloid formation and progression remain unclear. Genetic predisposition is important in the pathogenic processes of keloid formation, however, environmental factors and epigenetic mechanisms may also play pivotal roles. Epigenetic modification is a recent area of investigation in understanding the molecular pathogenesis of keloid scarring and there is increasing evidence that epigenetic changes may play a role in induction and persistent activation of fibroblasts in keloid scars. Here we have reviewed three epigenetic mechanisms: DNA methylation, histone modification and the role of non-coding RNAs. We also review the evidence that these mechanisms may play a role in keloid formation - in future, it may be possible that epigenetic markers may be used instead of prognostic or diagnostic markers here. However, there is a significant amount of work required to increase our current understanding of the role of epigenetic modification in keloid disease.