Bioinformatics analysis of fibroblasts exposed to TGF‑β at the early proliferation phase of wound repair

Pulsed electromagnetic fields used in regenerative medicine: An in vitro study of the skin wound healing proliferative phase

Numerous studies have demonstrated the efficacy of extremely low frequency-pulsed electromagnetic fields (ELF-PEMF) in accelerating the wound healing process in vitro and in vivo. Our study focuses specifically on ELF-PEMF applied with the Magnomega® device and aims to assess their effect during the main stages of the proliferative phase of dermal wound closure, in vitro. Thus, after the characterization of the EMFs delivered by the Magnomega® unit, primary culture of human dermal fibroblasts (HDFs) were exposed, or not for the control culture, to 10-12 and 100 Hz ELF-PEMF. These parameters are used in clinical practice by physiotherapists in order to enhance healing of dermal lesions in patients. HDFs proliferation was first assessed and revealed an increase in the expression of one of the two genetic markers of cell proliferation tested (PCNA and MKI67), after initial exposure of the cells to 10-12 Hz PEMF. Next, migration of HDFs was investigated by performing scratch assays on HDF layers. The observed wound closure kinetics corroborate the early organization of actin stress fibers that was revealed in the cytoplasm of HDFs exposed to 100 Hz ELF-PEMF. Also, maturation of HDFs into myofibroblasts was significantly increased in cells exposed to 10-12 or to 100 Hz PEMF. The present study is the first to demonstrate, in vitro, an early stimulation of HDFs, after their exposure to ELF-PEMF delivered by the Magnomega® device, which could contribute to an acceleration of the wound healing process.

Evaluation of intervention effects of dietary coenzyme Q10 supplementation on oxidized fish oil-induced stress response in largemouth bass Micropterus salmoides

The aim of this experiment was to investigate whether dietary coenzyme Q10 could alleviate stress response of Micropterus salmoides caused by oxidized fish oil. Four isonitrogenous and isoenergetic diets were formulated to contain 100% fresh fish oil (FFO), 50% fresh fish oil + 50% oxidized fish oil (BFO), 100% oxidized fish oil (OFO) and 100% oxidized fish oil + 0.1% coenzyme Q10 (QFO) and were fed to Micropterus salmoides (95 ± 0.60 g) for 70 days. Higher weight gain rate was recorded in fish fed diet supplemented with coenzyme Q10 (CoQ10). FFO and BFO significantly increased contents of fat and energy in whole-body, while protein and energy retention significantly decreased in fish fed OFO. Apparent digestibility of energy and fat showed a significant decrease trend with increased the proportion of dietary oxidized fish oil. Fish fed OFO significantly increased activities of superoxide dismutase and catalase, while CoQ10 supplementation significantly reduced activities of alanine aminotransferase and aspartate aminotransferase in plasma. Contents of n-3 polyunsaturated fatty acids and highly unsaturated fatty acids, especially EPA and DHA in liver and muscle significantly decreased in fish fed OFO. Transcriptome analysis indicated that a total of 1238, 1189 and 1773 differentially expressed genes (DEGs, |log₂(fold change) | >= 1 and q-value<=0.001) were found in the three comparison groups (FFO vs. OFO, FFO vs. QFO, OFO vs. QFO), respectively. After KEGG enrichment, the main changed pathways in the two comparison groups (FFO vs. OFO, OFO vs. QFO) related to the immune system. Dietary OFO up-regulated the expression of immune-related genes and inflammatory factors, while dietary CoQ10 supplementation reduced these effects.

Integrative analyses of mRNA and microRNA expression profiles reveal the innate immune mechanism for the resistance to Vibrio parahaemolyticus infection in Epinephelus coioides

Vibrio parahaemolyticus, as one of the main pathogens of marine vibriosis, has brought huge losses to aquaculture. However, the interaction mechanism between V. parahaemolyticus and Epinephelus coioides remains unclear. Moreover, there is a lack of comprehensive multi-omics analysis of the immune response of grouper spleen to V. parahaemolyticus. Herein, E. coioides was artificially injected with V. parahaemolyticus, and it was found that the mortality was 16.7% in the early stage of infection, and accompanied by obvious histopathological lesions in the spleen. Furthermore, 1586 differentially expressed genes were screened by mRNA-seq. KEGG analysis showed that genes were significantly enriched in immune-related pathways, Acute-phase immune response, Apoptosis, Complement system and Cytokine-cytokine receptor interaction. As for miRNA-seq analysis, a total of 55 significantly different miRNAs were identified. Further functional annotation analysis indicated that the target genes of differentially expressed miRNAs were enriched in three important pathways (Phosphatidylinositol signaling system, Lysosome and Focal adhesions). Through mRNA-miRNA integrated analysis, 1427 significant miRNA–mRNA pairs were obtained and “p53 signaling pathway”, “Intestinal immune network for IgA production” were considered as two crucial pathways. Finally, miR-144-y, miR-497-x, novel-m0459-5p, miR-7133-y, miR-378-y, novel-m0440-5p and novel-m0084-3p may be as key miRNAs to regulate immune signaling pathways via the miRNA-mRNA interaction network. The above results suggest that the mRNA-miRNA integrated analysis not only sheds new light on the molecular mechanisms underlying the interaction between host and V. parahaemolyticus but also provides valuable and new insights into resistance to vibrio infection.

Screening of potential hub genes in pulmonary thromboembolism

Pulmonary thromboembolism (PTE) is a fatal clinical syndrome that usually occurs in elderly individuals. The present study aimed to identify functional and key genes involved in the early diagnosis of PTE using bioinformatics analysis. The GSE84738 dataset was retrieved from the Gene Expression Omnibus database. Gene Ontology and Kyoto Encyclopedia of Genes and Genomes pathway enrichment analyses were subsequently performed. In addition, Cytoscape software v.3.7.2 was used to construct a protein-protein interaction (PPI) network. Serum samples from patients with PTE and healthy individuals were collected and the expression levels of Toll-like receptor (TLR)4, TLR2, IL-1β, JUN, prostaglandin-endoperoxide synthase 2 (PTGS2), osteopontin (SPP1) and endothelin-1 (ET-1) were analyzed by reverse transcription-quantitative PCR. A total of 160 upregulated and 159 downregulated differentially expressed genes were identified between patients with PTE and healthy individuals. TNF, IL-1β, JUN, TLR4, PTGS2, vascular cell adhesion molecule 1, SPP1, ryanodine receptor 2, TLR2 and ET-1 were considered as hub genes, which are defined as the genes with the highest degree of interaction in the enrichment and PPI network analyses. The top 10 common genes with the highest degree in the PPI network and the top 10 genes in modules 1 and 2 were TLR4, TLR2, IL-1β, JUN, PTGS2, SPP1 and ET-1. Taken together, the present study suggested that TLR4, TLR2, IL-1β and SPP1 were enriched in patients with PTE, thus providing novel potential biomarkers for the diagnosis of PTE.

Ultrasound enhanced synthetic platelet therapy for augmented wound repair

Native platelets perform a number of functions within the wound healing process, including interacting with fibrin fibers at the wound site to bring about retraction after clot formation. Clot retraction improves clot stability and enhances the function of the fibrin network as a provisional matrix to support cellular infiltration of the wound site, thus facilitating tissue repair and remodeling after hemostasis. In cases of traumatic injury or disease, platelets can become depleted and this process disrupted. To that end, our lab has developed synthetic platelet-like particles (PLPs) that recapitulate the clot retraction abilities of native platelets through a Brownian-wrench driven mechanism that drives fibrin network densification and clot retraction over time, however, this Brownian-motion driven process occurs on a longer time scale than native active actin/myosin-driven platelet-mediated clot retraction. We hypothesized that a combinatorial therapy comprised of ultrasound stimulation of PLP motion within fibrin clots would facilitate a faster induction of clot retraction on a more platelet-mimetic time scale and at a lower dosage than required for PLPs acting alone. We found that application of ultrasound in combination with a subtherapeutic dosage of PLPs resulted in increased clot density and stiffness, improved fibroblast migration in vitro and increased epidermal thickness and angiogenesis in vivo, indicating that this combination therapy has potential to facilitate multiphase pro-healing outcomes. Additionally, while these particular studies focus on the role of ultrasound in enhancing specific interactions between fibrin-binding synthetic PLPs embedded within fibrin networks, these studies have wide applicability in understanding the role of ultrasound stimulation in enhancing multi-scale colloidal interactions within fibrillar matrices.

The shared KEGG pathways between icariin-targeted genes and osteoporosis

Osteoporosis is a common metabolic bone disease that affects about 40% of postmenopausal women. Treatment options for osteoporosis are limited, however. Icariin is an herbal substance that has been shown to improve bone mass, but the mechanisms are largely unknown. Using bioinformatics analysis, we have identified the hub genes and KEGG pathways shared between icariin-targeted genes and osteoporosis. The top five shared KEGG pathways were the Toll-like receptor signaling pathway, adipocytokine pathway, neurotrophin signaling pathway, NOD-like receptor signaling, and B cell receptor signaling pathway; the hub genes were RELA, NFKBIA, and IKBKB, belonging to the NF-κB family. The identified icariin-targeted genes are involved in inflammation, insulin resistance, apoptosis, and immune responses, and regulate the PI3K-Akt, NF-κB, MAPK, and JNK signaling pathways. Our in vitro data show that icariin inhibits apoptosis in human mesenchymal stem cells by suppressing JNK/c-Jun signaling pathway. Together, these findings indicate that icariin exerts its anti-osteoporotic function by inhibiting JNK/c-Jun signaling pathway, and suggest that icariin may be a promising treatment option for osteoporosis.

Longitudinal linear combination test for gene set analysis

Background

Although microarray studies have greatly contributed to recent genetic advances, lack of replication has been a continuing concern in this area. Complex study designs have the potential to address this concern, though they remain undervalued by investigators due to the lack of proper analysis methods. The primary challenge in the analysis of complex microarray study data is handling the correlation structure within data while also dealing with the combination of large number of genetic measurements and small number of subjects that are ubiquitous even in standard microarray studies. Motivated by the lack of available methods for analysis of repeatedly measured phenotypic or transcriptomic data, herein we develop a longitudinal linear combination test (LLCT).

Results

LLCT is a two-step method to analyze multiple longitudinal phenotypes when there is high dimensionality in response and/or explanatory variables. Alternating between calculating within-subjects and between-subjects variations in two steps, LLCT examines if the maximum possible correlation between a linear combination of the time trends and a linear combination of the predictors given by the gene expressions is statistically significant. A generalization of this method can handle family-based study designs when the subjects are not independent. This method is also applicable to time-course microarray, with the ability to identify gene sets that exhibit significantly different expression patterns over time. Based on the results from a simulation study, LLCT outperformed its alternative: pathway analysis via regression. LLCT was shown to be very powerful in the analysis of large gene sets even when the sample size is small.

Conclusions

This self-contained pathway analysis method is applicable to a wide range of longitudinal genomics, proteomics, metabolomics (OMICS) data, allows adjusting for potentially time-dependent covariates and works well with unbalanced and incomplete data. An important potential application of this method could be time-course linkage of OMICS, an attractive possibility for future genetic researchers.

Availability: R package of LLCT is available at: https://github.com/its-likeli-jeff/LLCT

Cutaneous Bone Formation Associated With Melanocytic Nevus

AIM

Cutaneous bone formation is an uncommon lesion of the skin. It may be primary or secondary. Secondary lesions are mostly associated with melanocytic nevi. Although many different theories have been proposed to explain the etiology, extraskeletal bone formation is complex and poorly understood phenomenon.Here the authors report a series of melanocytic nevi with cutaneous bone formation and the authors described morphologic and clinicopathologic features such as age, sex, location, focus number and size of the lesion.

MATERIAL AND METHOD

Through a single center, this retrospective study presents total number of 20 patients with melanocytic nevus with or without osseous metaplasia. Histologic and clinicopathologic features such as age, sex, location, focus, and size of lesion were compared.

RESULTS

Lesions were identified in 10 female patients. All of the cases were seen in the head and neck region such as face, forehead, eyebrow, lip, and neck and most of them were solitary. The nevi were usually associated with the single focus of ossification. Most of patients (50%) had acne symptoms and treatment anamnesis. Granulomatous dermal inflammation was seen in 2 patients. There was no difference in nevus morphology and the size of the nevi between the osteonevi and the other types of nevi.

CONCLUSION

In conclusion, this study revealed that although it is rare it has distinctive features such as female patients, face location, and acne anamnesis. Therefore it may be speculated that the osteogenic factors may be involved with inflammatory-induced metaplastic ossification and tend to be related female sex.

Shared KEGG pathways of icariin-targeted genes and osteoarthritis

The beneficial effects of icariin in the management of many diseases, such as chronic renal failure and heart failure, are well known. Icariin has also been shown to ameliorate osteoarthritis (OA) symptoms; however, the underlying mechanisms remain unclear. In this study, a bioinformatics analysis was performed to investigate the KEGG pathways of icariin-targeted genes involved in OA. Our study suggests that icariin plays a role in OA by regulating inflammatory cytokine production, insulin resistance, and cell survival through modulation of the NF-κB, MAPK, and Akt signaling pathways. Importantly, IKBKB, NFKBIA, MAPK8, MAPK9, and MAPK10 may be the hub genes affected by icariin when providing its beneficial effects on OA. In addition, we found that icariin decreases proinflammatory factors and inhibits chondrocyte apoptosis through suppression of the NF-κB pathway. Our study highlights a set of KEGG pathways that could explain the molecular mechanism of icariin's action on OA, suggesting that icariin could be considered as a promising therapeutic option for OA.

Dual RNA-seq reveals the effect of the flgM gene of Pseudomonas plecoglossicida on the immune response of Epinephelus coioides

Pseudomonas plecoglossicida is an important and highly pathogenic bacterium for aquaculture and causes serious losses. The expression level of flgM was found to be significantly upregulated post-infection compared with in vitro results, which was confirmed by quantitative real-time PCR. RNAi significantly reduced the expression level of flgM mRNA of P. plecoglossicida. Compared with infection with the wild-type strain, infection with the flgM-RNAi strain resulted in a delay in death and a 75% reduction in the mortality of Epinephelus coioides, followed by alleviation of the symptoms in E. coioides spleen. Moreover, compared with infection with the wild-type strain, infection with the flgM-RNAi strain of P. plecoglossicida resulted in a significant change in the transcriptome of the spleens of infected E. coioides and P. plecoglossicida. KEGG analysis for E. coioides showed that genes of 17 immune pathways were most affected by flgM-RNAi of P. plecoglossicida. Among them, the expression of mhc2, zap70, rhoh, tlr2, ca79a, hcst and cd32 in E. coioides spleen was predicted to be negatively related to flgM in P. plecoglossicida but positively related to genes involved in communication, metabolism and motility.

Dual RNA-Seq reveals the role of a transcriptional regulator gene in pathogen-host interactions between Pseudomonas plecoglossicida and Epinephelus coioides

Pseudomonas plecoglossicida is a highly pathogenic bacterium for maricultured fish and causes serious losses. A transcriptional regulator gene RK21_RS10315 was found up-regulated during the whole infection process, which was confirmed by qRT-PCR. Five shRNA were designed to silence RK21_RS10315 gene, and the gene expression was reduced up to 96.1%. Compared with the counterpart infected with wild type strain, the infection of RK21_RS10315-RNAi strain resulted in the death time delay, and 90% reduction in mortality of Epinephelus coioides, as well as the alleviation in the symptoms of E. coioides spleen. Moreover, compared with the fish infected with wild type strain, the infection of RK21_RS10315-RNAi strain of P. plecoglossicida resulted in a significant change both in transcriptome of spleen of infected E. coioides and P. plecoglossicida. The KEGG analysis showed that genes of 16 immune pathways in E. coioides were affected by the silence of RK21_RS10315 of P. plecoglossicida. Among them, intestinal immune network for IgA production pathway and leukocyte transendothelial migration pathway were more prominent than other pathways. 19 euk-DEMs in these immune pathways had varying degrees of correlation with 19 pro-DEMs, and the expression of ipxA, grpE, yhbJ, truD and suhB from 19 pro-DEMs were predicted more related to RK21_RS10315 in P. plecoglossicida.

Integration of RNAi and RNA-seq Reveals the Immune Responses of Epinephelus coioides to sigX Gene of Pseudomonas plecoglossicida

Pseudomonas plecoglossicida is an important pathogen for aquaculture and causes high mortality in various marine fishes. Expression of sigX was found significantly up-regulated at 18°C than at 28°C, which was verified by quantitative real-time PCR (qRT-PCR). RNAi significantly reduced the content of sigX mRNA of P. plecoglossicida, whether in in vitro or in the spleen at all sampling time points. Compared with the wild-type strain, the infection of sigX-RNAi strain resulted in the onset time delay, and 20% reduction in mortality of Epinephelus coioides, as well as alleviates in the symptoms of E. coioides spleen. Compared with wild-type strain, the gene silence of sigX in P. plecoglossicida resulted in a significant change in transcriptome of infected E. coioides. The result of gene ontology and KEGG analysis on E. coioides showed that genes of serine-type endopeptidase and chemokine signaling pathway, coagulation and complement system, and intestinal immune network for IgA production pathway were mostly affected by sigX of P. plecoglossicida. Meanwhile, the immune genes were associated with different number of miRNA and lncRNA, and some miRNAs were associated with more than one gene at the same time. The results indicated that sigX was a virulent gene of P. plecoglossicida. The up-regulation of the immune pathways made E. coioides more likely to kill sigX-RNAi strain than the wild-type strain of P. plecoglossicida, while the immune genes were regulated by miRNA and lncRNA by a complex mode.