Whole genome microarray data of chronic wound debridement prior to application of dermal skin substitutes

The role of the skin microbiome in wound healing

The efficient management of skin wounds for rapid and scarless healing represents a major clinical unmet need. Nonhealing skin wounds and undesired scar formation impair quality of life and result in high healthcare expenditure worldwide. The skin-colonizing microbiota contributes to maintaining an intact skin barrier in homeostasis, but it also participates in the pathogenesis of many skin disorders, including aberrant wound healing, in many respects. This review focuses on the composition of the skin microbiome in cutaneous wounds of different types (i.e. acute and chronic) and with different outcomes (i.e. nonhealing and hypertrophic scarring), mainly based on next-generation sequencing analyses; furthermore, we discuss the mechanistic insights into host-microbe and microbe-microbe interactions during wound healing. Finally, we highlight potential therapeutic strategies that target the skin microbiome to improve healing outcomes.

Epigenetic regulation of macrophage polarization in wound healing

The immune microenvironment plays a critical role in regulating skin wound healing. Macrophages, the main component of infiltrating inflammatory cells, play a pivotal role in shaping the immune microenvironment in the process of skin wound healing. Macrophages comprise the classic proinflammatory M1 subtype and anti-inflammatory M2 population. In the early inflammatory phase of skin wound closure, M1-like macrophages initiate and amplify the local inflammatory response to disinfect the injured tissue. In the late tissue-repairing phase, M2 macrophages are predominant in wound tissue and limit local inflammation to promote tissue repair. The biological function of macrophages is tightly linked with epigenomic organization. Transcription factors are essential for macrophage polarization. Epigenetic modification of transcription factors determines the heterogeneity of macrophages. In contrast, transcription factors also regulate the expression of epigenetic enzymes. Both transcription factors and epigenetic enzymes form a complex network that regulates the plasticity of macrophages. Here, we describe the latest knowledge concerning the potential epigenetic mechanisms that precisely regulate the biological function of macrophages and their effects on skin wound healing.

Characterisation of key biomarkers in diabetic ulcers via systems bioinformatics

Diabetic ulcers (DUs) are characterised by a high incidence and disability rate. However, its pathogenesis remains elusive. Thus, a deep understanding of the underlying mechanisms for the pathogenesis of DUs has vital implications. The weighted gene co-expression network analysis was performed on the main data from the Gene Expression Omnibus database. Gene Ontology (GO) terms, Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis were adopted to analyse the potential biological function of the most relevant module. Furthermore, we utilised CytoHubba and protein-protein interaction network to identify the hub genes. Finally, the hub genes were validated by animal experiments in diabetic ulcer mice models. The expression of genes from the turquoise module was found to be strongly related to DUs. GO terms, KEGG analysis showed that biological functions are closely related to immune response. The hub genes included IFI35, IFIT2, MX2, OASL, RSAD2, and XAF1, which were higher in wounds of DUs mice than that in normal lesions. Additionally, we also demonstrated that the expression of hub genes was correlated with the immune response using immune checkpoint, immune cell infiltration, and immune scores. These data suggests that IFI35, IFIT2, MX2, OASL, RSAD2, and XAF1 are crucial for DUs.

Methylome and Transcriptome-Based Integration Analysis Identified Molecular Signatures Associated With Meningitis Induced by Glaesserella parasuis

Glaesserella parasuis (G. parasuis) can elicit serious inflammatory responses and cause meningitis in piglets. Previous epigenetic studies have indicated that alterations in host DNA methylation may modify the inflammatory response to bacterial infection. However, to date, genome-wide analysis of the DNA methylome during meningitis caused by G. parasuis infection is still lacking. In this study, we employed an unbiased approach using deep sequencing to profile the DNA methylome and transcriptome from G. parasuis infected porcine brain (cerebrum) and integrated the data to identify key differential methylation regions/sites involved in the regulation of the inflammatory response. Results showed that DNA methylation patterns and gene expression profiles from porcine brain were changed after G. parasuis infection. The majority of the altered DNA methylation regions were found in the intergenic regions and introns and not associated with CpG islands, with only a low percentage occurring at promoter or exon regions. Integrated analysis of the DNA methylome and transcriptome identified a number of inversely and positively correlated genes between DNA methylation and gene expression, following the criteria of |log₂FC| > 0.5, |diffMethy| > 0.1, and P < 0.05. Differential expression and methylation of two significant genes, semaphoring 4D (SEMA4D) and von Willebrand factor A domain containing 1 (VWA1), were validated by qRT-PCR and bisulfite sequencing. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses demonstrated that DNA methylation inversely correlated genes in G. parasuis infected porcine brains were mainly involved with cell adhesion molecules (CAMs), bacterial invasion of epithelial cells, RIG-1-like receptor signaling pathways, and hematopoietic cell lineage signaling pathways. In addition, a protein-protein interaction network of differentially methylated genes found potential candidate molecular interactions relevant to the pathology of G. parasuis infection. To the best of our knowledge, this is the first attempt to integrate the DNA methylome and transcriptome data from G. parasuis infected porcine brains. Our findings will help understanding the contribution of genome-wide DNA methylation to the pathogenesis of meningitis in pigs and developing epigenetic biomarkers and therapeutic targets for the treatment of G. parasuis induced meningitis.

Varying Negative Pressure Wound Therapy Acute Effects on Human Split-Thickness Autografts

Over 6.5 million people in the United States suffer from traumatic, burn, acute, and chronic wounds yearly. When reconstruction is required, split and full-thickness autografts are a first line of treatment intervention. Negative pressure wound therapy (NPWT) is gaining traction as an adjunct modality to improve graft survival, yet the specifics on what settings to apply topically over the graft is unsubstantiated and associated with morbidities. This study was performed in an effort to understand initial changes in wound and graft healing with a long-term goal of surface pressure optimization. Excess skin from elective procedures from six human subjects was trimmed to 0.012 inch in order represent a split-thickness autografts. These grafts were treated continuously with either -75 mm Hg (n = 4), -125 mm Hg (n = 4), or no pressure (n = 4) for 3 hours. Six skin grafts were treated with no sponge or pressure control (n = 6). RNAseq was performed on all treatment groups and compared with no pressure control. Significant gene expression changes with a subset focusing on inflammatory, cellular/extracellular matrix proliferation and angiogenic mediators and having greater than 2-fold were confirmed with immunohistochemistry staining. There are 95 significant gene transcription differences among all treatment groups. NPWT leads to significantly increased gene expression of FGFR1, ET-1, and 22 Keratin proteins. Between -75 and -125 mm Hg groups, there are 19 significant gene changes. Proinflammatory genes S100A8 and Tenacin C (TNC) demonstrate an 8.8- and 9.1-fold change, respectively, and is upregulated in -125 mm Hg group and downregulated in -75 mm Hg group. Fibrinogen genes fibrinogen gamma chain and fibrinogen alpha chain had respective log2-fold changes of -7.9 and -7.4 change between treatment groups and were downregulated in -125 mm Hg group and upregulated in -75 mm Hg group. There are varying effects of surface pressures on human split-thickness autografts during the imbibition time period. NPWT may improve cellular migration, proliferation, and angiogenesis over controls. Human skin grafts respond differently to -125 and -75 mm Hg within 3 hours of NPWT treatment. The results suggest -75 mm Hg leads to less inflammation and increased fibrinogen production compared with the -125 mm Hg group, at least initially. Reducing "time to heal" with NPWT is critical to successful outcomes and quality of life within young patients who often experience pain/discomfort when treated at the current standard pump settings. The results from this study and continued investigation may quickly translate to the clinical setting by finding the ideal pressure setting utilized in an effort to reduce NPWT length of treatment, improve patient comfort, satisfaction, and psychosocial well-being.

Transmembrane collagens-Unexplored mediators of epidermal-dermal communication and tissue homeostasis

Tissue homeostasis is maintained through constant, dynamic and heterogeneous communication between cells and their microenvironment. Proteins that are at the same time active at the intracellular, cell periphery and deeper extracellular levels possess the ability to, on the individual molecular level, influence the cells and their microenvironment in a bidirectional manner. The transmembrane collagens are a family of such proteins, which are of notable interest for tissue development and homeostasis. In skin, expression of all transmembrane collagens has been reported and deficiency of transmembrane collagen XVII manifests with distinct skin phenotypes. Nevertheless, transmembrane collagens in skin remain understudied despite the association of them with epidermal wound healing and dermal fibrotic processes. Here, we present an overview of transmembrane collagens and put a spotlight on them as regulators of epidermal-dermal communication and as potential players in fibrinogenesis.

Unleashing the Diagnostic, Prognostic and Therapeutic Potential of the Neuronostatin/GPR107 System in Prostate Cancer

Certain components of the somatostatin-system play relevant roles in Prostate Cancer (PCa), whose most aggressive phenotype (Castration-Resistant-PCa (CRPC)) remains lethal nowadays. However, neuronostatin and the G protein-coupled receptor 107 (GPR107), two novel members of the somatostatin-system, have not been explored yet in PCa. Consequently, we investigated the pathophysiological role of NST/GPR107-system in PCa. GPR107 expression was analyzed in well-characterized PCa patient's cohorts, and functional/mechanistic assays were performed in response to GPR107-silencing and NST-treatment in PCa cells (androgen-dependent (AD: LNCaP) and androgen-independent (AI: 22Rv1/PC-3), which are cell models of hormone-sensitive and CRPC, respectively), and normal prostate cells (RWPE-1 cell-line). GPR107 was overexpressed in PCa and associated with key clinical parameters (e.g., advance stage of PCa, presence of vascular invasion and metastasis). Furthermore, GPR107-silencing inhibited proliferation/migration rates in AI-PCa-cells and altered key genes and oncogenic signaling-pathways involved in PCa aggressiveness (i.e., KI67/CDKN2D/MMP9/PRPF40A, SST5TMD4/AR-v7/In1-ghrelin/EZH2 splicing-variants and AKT-signaling). Interestingly, NST treatment inhibited proliferation/migration only in AI-PCa cells and evoked an identical molecular response than GPR107-silencing. Finally, NST decreased GPR107 expression exclusively in AI-PCa-cells, suggesting that part of the specific antitumor effects of NST could be mediated through a GPR107-downregulation. Altogether, NST/GPR107-system could represent a valuable diagnostic and prognostic tool and a promising novel therapeutic target for PCa and CRPC.

PRPF40A as a potential diagnostic and prognostic marker is upregulated in pancreatic cancer tissues and cell lines: an integrated bioinformatics data analysis

Background

Pre-mRNA processing factor 40 homolog A (PRPF40A) is an important protein involved in pre-mRNA splicing and is expressed in a variety of cell types. However, the function of PRPF40A in pancreatic cancer remains unclear. Therefore, our study is to investigate the role of PRPF40A in the pathogenesis of pancreatic cancer.

Materials and methods

We extracted expression data and clinical information of PRPF40A from different online databases, including the Cancer Genome Atlas (TCGA), Oncomine and the Gene Expression Omnibus (GEO). Subsequently, samples were collected from patients to validate gene expression using qPCR, Western blotting and immunohistochemical (IHC) analyses. Receiver operating characteristic (ROC) and Kaplan-Meier curve were used to evaluate the diagnostic and prognostic potential. Colony formation assays and CCK-8 assays were performed to measure the proliferative capacity of pancreatic cancer. Finally, gene ontology (GO) and pathway enrichment analyses of co-expressed genes of PRPF40A were conducted using the Database for Annotation, Visualization and Integrated Discovery (DAVID).

Results

We found that PRPF40A was upregulated based on data from both the online databases and our samples. PRPF40A possessed a significant diagnostic value, and its overexpression was associated with poor prognosis. PRPF40A knockdown inhibited cell proliferation in pancreatic cancer. GO and pathway analysis showed that the co-expressed genes were mainly involved in viral processing, mRNA splicing and the AMPK signaling pathway.

Conclusion

The results suggest that PRPF40A is an oncogene and can serve as a diagnostic and prognostic biomarker for pancreatic cancer. However, the underlying mechanisms remain to be elucidated.

Strain- and Species-Level Variation in the Microbiome of Diabetic Wounds Is Associated with Clinical Outcomes and Therapeutic Efficacy

Chronic wounds are a major complication of diabetes associated with high morbidity and health care expenditures. To investigate the role of colonizing microbiota in diabetic wound healing, clinical outcomes, and response to interventions, we conducted a longitudinal, prospective study of patients with neuropathic diabetic foot ulcers (DFU). Metagenomic shotgun sequencing revealed that strain-level variation of Staphylococcus aureus and genetic signatures of biofilm formation were associated with poor outcomes. Cultured wound isolates of S. aureus elicited differential phenotypes in mouse models that corresponded with patient outcomes, while wound "bystanders" such as Corynebacterium striatum and Alcaligenes faecalis, typically considered commensals or contaminants, also significantly impacted wound severity and healing. Antibiotic resistance genes were widespread, and debridement, rather than antibiotic treatment, significantly shifted the DFU microbiota in patients with more favorable outcomes. These findings suggest that the DFU microbiota may be a marker for clinical outcomes and response to therapeutic interventions.

Longitudinal expression profiling of CD4+ and CD8+ cells in patients with active to quiescent giant cell arteritis

Background

Giant cell arteritis (GCA) is the most common form of vasculitis affecting elderly people. It is one of the few true ophthalmic emergencies but symptoms and signs are variable thereby making it a challenging disease to diagnose. A temporal artery biopsy is the gold standard to confirm GCA, but there are currently no specific biochemical markers to aid diagnosis. We aimed to identify a less invasive method to confirm the diagnosis of GCA, as well as to ascertain clinically relevant predictive biomarkers by studying the transcriptome of purified peripheral CD4+ and CD8+ T lymphocytes in patients with GCA.

Methods

We recruited 16 patients with histological evidence of GCA at the Royal Victorian Eye and Ear Hospital, Melbourne, Australia, and aimed to collect blood samples at six time points: acute phase, 2–3 weeks, 6–8 weeks, 3 months, 6 months and 12 months after clinical diagnosis. CD4+ and CD8+ T-cells were positively selected at each time point through magnetic-assisted cell sorting. RNA was extracted from all 195 collected samples for subsequent RNA sequencing. The expression profiles of patients were compared to those of 16 age-matched controls.

Results

Over the 12-month study period, polynomial modelling analyses identified 179 and 4 statistically significant transcripts with altered expression profiles (FDR < 0.05) between cases and controls in CD4+ and CD8+ populations, respectively. In CD8+ cells, two transcripts remained differentially expressed after 12 months; SGTB, associated with neuronal apoptosis, and FCGR3A, associatied with Takayasu arteritis. We detected genes that correlate with both symptoms and biochemical markers used for predicting long-term prognosis. 15 genes were shared across 3 phenotypes in CD4 and 16 across CD8 cells. In CD8, IL32 was common to 5 phenotypes including Polymyalgia Rheumatica, bilateral blindness and death within 12 months.

Conclusions

This is the first longitudinal gene expression study undertaken to identify robust transcriptomic biomarkers of GCA. Our results show cell type-specific transcript expression profiles, novel gene-phenotype associations, and uncover important biological pathways for this disease. In the acute phase, the gene-phenotype relationships we have identified could provide insight to potential disease severity and as such guide in initiating appropriate patient management.

Electronic supplementary material

The online version of this article (10.1186/s12920-018-0376-4) contains supplementary material, which is available to authorized users.