Identification of potential crucial genes associated with steroid-induced necrosis of femoral head based on gene expression profile

Upregulation of microRNA-576-5p protects from steroid-induced avascular necrosis of the femoral head by suppressing ANXA2

Steroid-induced avascular necrosis of the femoral head (SANFH) is a common orthopedic disease. Evidence has shown that microRNAs (miRNAs) played essential roles in the development of SANFH. Nevertheless, the role of miR-576-5p in SANFH remains unknown. The rabbit SANFH models were constructed by injection of horse serum and methylprednisolone. Bone mineral density (BMD) of the proximal femur (including the femoral head), pathological changes, bone cell apoptosis and expressions of OPG/RANK in femoral head bone tissue were assessed upon treatment of up-regulation of miR-576-5p or knockdown of ANXA2. Osteoblasts were extracted from SANFH rabbit femoral head and cultured. Proliferation, apoptosis and mineralization were tested upon treatment of up-regulation of miR-576-5p or knockdown of ANXA2. The targeting relationship between miR-576-5p and ANXA2 was verified. Up-regulated miR-576-5p or down-regulated ANXA2 inhibited the decrease of BMD, improved pathological changes, limited cell apoptosis and increased OPG/RANKL ratio in bone tissues of SANFH rabbits. Up-regulating miR-576-5p or down-regulating ANXA2 promoted proliferation and mineralization and inhibited apoptosis of osteoblasts from SANFH rabbits. In addition, ANXA2 was found to be a target gene of miR-576-5p. Furthermore, overexpression of ANXA2 abolished the protective role of elevated miR-576-5p against femoral head necrosis. Elevated miR-576-5p or reduced ANXA2 repressed the progression of SANFH. This study may provide novel biomarkers for SANFH diagnosis and treatment.

Identification of potential crucial genes in monocytes for atherosclerosis using bioinformatics analysis

Objective

To use bioinformatics tools to screen for gene biomarkers from monocytes, which play an important role in the pathogenesis of atherosclerosis.

Methods

Two expression profiling datasets (GSE27034 and GSE10195) were obtained from the Gene Expression Omnibus dataset and the differentially expressed genes (DEGs) between atherosclerotic human peripheral blood mononuclear cells (PBMC) samples and control subjects were screened using GEO2R. Gene Ontology and Kyoto Encyclopedia of Genes and Genomes pathway enrichment analyses were conducted for the DEGs. STRING and MCODE plug-in of Cytoscape were used for constructing a protein–protein interaction network and analysing hub genes.

Results

The two datasets had 237 DEGs in common between non-atherosclerotic- and atherosclerotic PBMC samples. Functional annotation demonstrated that these DEGs were mainly enriched in protein binding, positive regulation of transcription from RNA polymerase II promoter, nucleus and viral carcinogenesis. Five hub genes, FBXL4, UBOX5, KBTBD6, FZR1 and FBXO2, were identified.

Conclusion

This present bioinformatics analysis identified that the FBXL4, UBOX5, KBTBD6 and FBXO21 genes might play vital roles in the pathogenesis of atherosclerosis. These four genes might represent new biomarkers for the diagnosis and treatment of atherosclerosis.

Identifying the Potential Differentially Expressed miRNAs and mRNAs in Osteonecrosis of the Femoral Head Based on Integrated Analysis

Purpose

Osteonecrosis of the femoral head is a common disease of the hip that leads to severe pain or joint disability. We aimed to identify potential differentially expressed miRNAs and mRNAs in osteonecrosis of the femoral head.

Methods

The data of miRNA and mRNA were firstly downloaded from the database. Secondly, the regulatory network of miRNAs-mRNAs was constructed, followed by function annotation of mRNAs. Thirdly, an in vitro experiment was applied to validate the expression of miRNAs and targeted mRNAs. Finally, GSE123568 dataset was used for electronic validation and diagnostic analysis of targeted mRNAs.

Results

Several regulatory interaction pairs between miRNA and mRNAs were identified, such as hsa-miR-378c-WNT3A/DACT1/CSF1, hsa-let-7a-5p-RCAN2/IL9R, hsa-miR-28-5p-RELA, hsa-miR-3200-5p-RELN, and hsa-miR-532-5p-CLDN18/CLDN10. Interestingly, CLDN10, CLDN18, CSF1, DACT1, IL9R, RCAN2, RELN, and WNT3A had the diagnostic value for osteonecrosis of the femoral head. Wnt signaling pathway (involved WNT3A), chemokine signaling pathway (involved RELA), focal adhesion and ECM-receptor interaction (involved RELN), cell adhesion molecules (CAMs) (involved CLDN18 and CLDN10), cytokine-cytokine receptor interaction, and hematopoietic cell lineage (involved CSF1 and IL9R) were identified.

Conclusion

The identified differentially expressed miRNAs and mRNAs may be involved in the pathology of osteonecrosis of the femoral head.

MYBPC2 and MYL1 as Significant Gene Markers for Rhabdomyosarcoma

BACKGROUND

Rhabdomyosarcoma is the most common soft tissue tumor in children. Rhabdomyosarcoma commonly results in pain and bleeding caused by tumor compression and is prone to early metastasis and recurrence, which can seriously affect the therapeutic outcomes and long-term prognosis. Up to 37.7% of rhabdomyosarcomas may metastasize. Therefore, the molecular mechanisms underlying rhabdomyosarcoma must be explored to identify an effective target for its early diagnosis and specific treatment.

METHODS

A dataset of 18 rhabdomyosarcoma tissue samples and 6 healthy skeletal muscle samples was downloaded. Differentially expressed genes between rhabdomyosarcoma and healthy tissue samples were identified by GEO2R. Kyoto Encyclopedia of Genes and Genomes and gene ontology pathway enrichment analyses were performed. A protein-protein interaction network was constructed, and hub genes were identified. Expression and survival analyses of hub genes were performed. Additionally, 30 patients with rhabdomyosarcoma were recruited, and overall survival information and samples were collected. Reverse transcription quantitative real-time polymerase chain reaction assays were performed to verify the expression of MYBPC2 and MYL1 in rhabdomyosarcoma tumor tissues. The Kaplan-Meier method was used to explore overall survival based on our clinical data.

RESULTS

In total, 164 genes were up-regulated and 394 were down-regulated in rhabdomyosarcoma tumor tissues. Gene ontology analysis revealed that variations were predominantly enriched in the cell cycle, muscle contraction, muscle system processes, cytoskeleton, nucleotide binding, and cytoskeletal protein binding. The protein-protein interaction network revealed 3274 edges, and 441 nodes were constructed. Ten hub genes were identified; of these, MYBPC2 and MYL1 were significantly up-regulated in rhabdomyosarcoma. Compared with the healthy group, patients with rhabdomyosarcoma exhibiting high expression of MYBPC2 and MYL1 exhibited significantly worse overall survival.

CONCLUSIONS

We found differentially expressed genes between rhabdomyosarcoma and healthy tissue samples. MYBPC2 and MYL1 may be involved in the pathogenesis of rhabdomyosarcoma and therefore deserve further exploration.

Identification of key non-coding RNAs and transcription factors regulators and their potential drugs for steroid-induced femoral head necrosis

Steroid-induced necrosis of femoral head (SINFH) is a femoral head necrotic disease caused by prolonged use of hormones. The detailed pathogenesis has not been fully demonstrated. In this study, we employed the bioinformatics approach to probe the roles of SINFH inhibitors. Core dysfunction modules related to SINFH was obtained. Meanwhile, GO and KEGG analysis of genes in dysfunction modules are carried out. Furthermore, the pivot prediction analysis of dysfunction modules related to ncRNA and transcription factor (TF) has been performed. The functions of the enriched modules were focused on multiple perspectives, including circulation, gland development, bone development and reconstruction, calcium production, and fatty acid metabolism regulation. The ncRNAs and TFs analysis showed that miR-322-5p, miR-124-3p, miR-125a-3p, and Ctnnb1 were important members of SINFH dysfunction. Drug targets suggested that Zinc and adenosine monophosphate may have an impact on SINFH dysfunction. SINFH was closely related to bone development and reconstruction.

Molecular Mechanisms Underlying Intestinal Ischemia/Reperfusion Injury: Bioinformatics Analysis and In Vivo Validation

Background

Intestinal ischemia/reperfusion (I/R) injury is a serious clinical complication. This study aimed to explore the hub genes and pathways of intestinal I/R injury.

Material/Methods

GSE96733 from the GEO website was extracted to analyze the differentially expressed genes (DEGs) of intestinal I/R injured and sham-operated mice at 3 h and 6 h after surgery. The DAVID and STRING databases were used to construct functional enrichment analyses of DEGs and the protein–protein interaction (PPI) network. In Cytoscape software, cytoHubba was used to identify hub genes, and MCODE was used for module analysis. Testing by qRT-PCR detected the expression of hub genes in intestinal I/R injury. Western blot analysis detected the key proteins involved with the important pathways of intestinal I/R injury.

Results

IL-6, IL-10, CXCL1, CXCL2, and IL-1β were identified as critical upregulated genes, while IRF7, IFIT3, IFIT1, Herc6, and Oasl2 were identified as hub genes among the downregulated genes. The qRT-PCR testing showed the expression of critical upregulated genes was significantly increased in intestinal I/R injury (P<0.05), while the expression of hub downregulated genes was notably reduced (P<0.05). The proteins of CXCL1 and CXCR2 were upregulated following intestinal I/R injury (P<0.05) and the CXCL1/CXCR2 axis was involved with intestinal I/R injury.

Conclusions

The results of the present study identified IL-6, IL-10, CXCL1, CXCL2, IL-1β, IRF7, IFIT3, IFIT1, Herc6, and Oasl2 as hub genes in intestinal I/R injury and identified the involvement of the CXCL1/CXCR2 axis in intestinal I/R injury.

Engineering EHD1-Targeted Natural Borneol Nanoemulsion Potentiates Therapeutic Efficacy of Gefitinib against Nonsmall Lung Cancer

Despite the effective targeting of the epidermal growth factor receptor (EGFR), the use of gefitinib (GFT) for nonsmall cell lung cancer (NSCLC) treatment meets a failure because of the insufficient drug accumulation in the tumor region. Therefore, developing chemosensitizers of GFT with synergistic therapeutic effects is urgently needed for advanced cancer therapy. Herein, a natural chemosensitizer, natural borneol (NB), is reformulated as an oil-in-water nanoemulsion to enhance its solubility, distribution, and to ultimately increase the therapeutic index with GFT. The nanolization of NB (NBNPs) displays stronger targeted delivery and cytotoxicity than NB by selectively identifying eight specific protein targets in A549 NSCLC cells as revealed by the proteomic studies. Consistently, NBNPs realize stronger chemosensitization effects than NB with GFT by effectively regulating EGFR/EHD1-mediated apoptosis in A549 NSCLC cells. Owing to the satisfying synergistic effect between NBNPs and GFT, the combined therapy not only enhances the anticancer ability of GFT against NSCLC proliferation but also avoids heavy double toxicity in vivo. This finding demonstrates the effective synergism between NBNPs and GFT with clear mechanistic investigation and is expected to extend the application of NBNPs as a novel chemosensitizer for advanced cancer chemotherapy.

microRNA-148a-3p in extracellular vesicles derived from bone marrow mesenchymal stem cells suppresses SMURF1 to prevent osteonecrosis of femoral head

Extracellular vesicle (EV)-associated microRNAs (miRNAs) have been found as the important biomarkers participating in the development of osteonecrosis of the femoral head (ONFH). Consequently, this study sought to examine the underlying mechanism of bone marrow mesenchymal stem cell (BMSC)-derived EVs containing miR-148a-3p in ONFH. The ONFH rat models were established. Reverse transcription quantitative polymerase chain reaction (RT-qPCR) and Western blot analysis were applied to detect miR-148a-3p, Smad ubiquitination regulatory factor 1 (SMURF1), SMAD7 and B-cell CLL/lymphoma 2 (BCL2) expression, followed by determination of relationship between miR-148a-3p and SMURF1. BMSCs were isolated from normal rats and ONFH rats, and EVs were extracted from BMSCs of normal rats. BMSCs from ONFH rats were treated with mimic, inhibitor, small interfering RNA or EVs from miR-148a-3p mimic-treated BMSCs from normal rats (BMSC-EV-miR-148a-3p mimic). Cell Counting Kit-8 and alizarin red staining were utilized to detect cell viability and osteogenic differentiation of BMSCs. ONFH rats were injected with BMSC-EV-miR-148a-3p mimic to explore the function of BMSC-EV-delivered miR-148a-3p in vivo. miR-148a-3p was down-regulated in BMSCs and EVs from ONFH rats following decreased BMSCs viability and osteogenic differentiation. SMURF1 was a target gene of miR-148a-3p, and resulted in ubiquitination and degradation of SMAD7 to decreased BCL2 expression. The proliferation and differentiation of BMSCs were promoted by BMSC-EV-miR-148a-3p mimic or SMURF1 silencing. Additionally, BMSC-EV-miR-148a-3p mimic increased cell proliferation and osteogenic response, diminished SMURF1 expression, and elevated SMAD7 and BCL2 expression in ONFH rats. Collectively, miR-148a-3p overexpressed in BMSC-EVs promoted SMAD7 and BCL2 expression by inhibiting SMURF1, thus alleviating ONFH.

Identification and Validation of Potential Biomarkers and Their Functions in Acute Kidney Injury

Acute kidney injury (AKI) is a global public health concern associated with high morbidity, mortality, and health-care costs, and the therapeutic measures are still limited. This study aims to investigate crucial genes correlated with AKI, and their potential functions, which might contribute to a better understanding of AKI pathogenesis. The high-throughput data GSE52004 and GSE98622 were downloaded from Gene Expression Omnibus; four group sets were extracted and integrated. Differentially expressed genes (DEGs) in the four group sets were identified by limma package in R software. The overlapping DEGs among four group sets were further analyzed by the VennDiagram package, and their potential functions were analyzed by the GO and KEGG pathway enrichment analyses using the DAVID database. Furthermore, the protein-protein interaction (PPI) network was constructed by STRING, and the functional modules of the PPI network were filtered by MCODE and ClusterOne in Cytoscape. Hub genes of overlapping DEGs were identified by Cyto-Hubba and cytoNCA. The expression of 35 key genes was validated by quantitative real-time PCR (qRT-PCR). Western blot and immunofluorescence were performed to validate an important gene Egr1. A total of 722 overlapping DEGs were differentially expressed in at least three group sets. These genes mainly enriched in cell proliferation and fibroblast proliferation. Additionally, 5 significant modules and 21 hub genes, such as Havcr1, Krt20, Sox9, Egr1, Timp1, Serpine1, Edn1, and Apln were screened by analyzing the PPI networks. The 5 significant modules were mainly enriched in complement and coagulation cascades and Metabolic pathways, and the top 21 hub genes were mainly enriched in positive regulation of cell proliferation. Through validation, Krt20 were identified as the top 1 upregulated genes with a log2 (fold change) larger than 10 in all these 35 genes, and 21 genes were validated as significantly upregulated; Egr1 was validated as an upregulated gene in AKI in both RNA and protein level. In conclusion, by integrated analysis of different high-throughput data and validation by experiment, several crucial genes were identified in AKI, such as Havcr1, Krt20, Sox9, Egr1, Timp1, Serpine1, Edn1, and Apln. These genes were very important in the process of AKI, which could be further utilized to explore novel diagnostic and therapeutic strategies.

The protective effects of microRNA-26a in steroid-induced osteonecrosis of the femoral head by repressing EZH2

Recently, the role of microRNAs (miRs) in human diseases has been verified. This study was determined to explore the protective effects of microRNA-26a (miR-26a) in steroid-induced osteonecrosis of the femoral head (SONFH) with the involvement of enhancer of zeste homologue 2 (EZH2).Femoral head (FH) samples from SONFH patients and patients with femoral neck fracture were collected, and rat SONFH models were established by Escherichia coli endotoxin combining with large dose steroid pulse assay. The hemorheology, blood lipid, inflammatory factors, and pathologic changes were measured by a series of experiments. Moreover, the detection of osteoblasts, osteoclasts, miR-26a expression, EZH2 expression, osteoprotegerin (OPG) and osteoprotegerin ligand (OPGL), and the apoptosis of osteocytes were conducted. The target relation between miR-26a and EZH2 was clarified by bioinformatics and dual-luciferase reporter gene assay.MiR-26a was poorly expressed, while EZH2 was highly expressed in SONFH, and the elevation of miR-26a could repress EZH2 expression. Elevated miR-26a and reduced EZH2 were able to decelerate the apoptosis of osteocytes, increase osteoblasts, and decrease osteoclasts, resulting in a repression of SONFH progression. Additionally, EZH2 was a target gene of miR-26a. Furthermore, the elevation of EZH2 could reverse the repression of SONFH progression that is induced by elevated miR-26a.We found that up-regulation of miR-26a and knockdown of EZH2 could suppress the development of SONFH, which would contribute to the therapy of SONFH.

Bioinformatics analyses on the immune status of renal transplant patients, a systemic research of renal transplantation

BACKGROUND

Kidney transplantation is the most effective treatment for end-stage renal disease. Allograft rejections severely affect survivals of allograft kidneys and recipients.

METHODS

Using bioinformatics approaches, the present study was designed to investigate immune status in renal transplant recipients. Fifteen datasets from Gene Expression Omnibus (GEO) were collected and analysed. Analysis of gene enrichment and protein-protein interactions were also used.

RESULTS

There were 40 differentially expressed genes (DEGs) identified in chronic rejection group when compared with stable recipients, which were enriched in allograft rejection module. There were 135 DEGs identified in acute rejection patients, compared with stable recipients, in which most genes were enriched in allograft rejection and immune deficiency. There were 288 DEGs identified in stable recipients when compared to healthy subjects. Most genes were related to chemokine signalling pathway. In integrated comparisons, expressions of MHC molecules and immunoglobulins were increased in both acute and chronic rejection; expressions of LILRB and MAP 4 K1 were increased in acute rejection patients, but not in stable recipients. There were no overlapping DEGs in blood samples of transplant recipients.

CONCLUSION

By performing bioinformatics analysis on the immune status of kidney transplant patients, the present study reports several DEGs in the renal biopsy of transplant recipients, which are requested to be validated in clinical practice.

Identification of differentially expressed genes in hip cartilage with femoral head necrosis, based on genome‑wide expression profiles

Necrosis of the femoral head (NFH), a severe orthopedic disease in adults, involves the collapse of the femoral head. The pathophysiological mechanisms underlying NFH are yet to be fully investigated. The aim of the present study was to identify potentially important genes and signaling pathways involved in NFH and investigate their molecular mechanisms. Gene expression profiles of patients with NFH and healthy controls were compared using the Gene Expression Omnibus (GEO) database repository of the National Center of Biotechnology Information. GSE74089 from the GEO database included 4 patients with NFH and 4 healthy individuals. A total of 1,191 differentially expressed genes (DEGs) were identified between the patients with NFH and controls, including 743 upregulated and 448 downregulated DEGs. Then, Gene Ontology and Kyoto Encyclopedia of Genes and Genomes pathway enrichment analysis revealed that upregulated DEGs were mainly involved in the phosphoinositide 3-kinase/protein kinase B signaling pathway, focal adhesion and extracellular matrix-receptor interactions. Additionally, protein-protein interaction (PPI) analysis identified the most central DEGs as vascular endothelial growth factor A, Jun proto-oncogene, cyclin D1, fibroblast growth factor 2, HECT domain and ankyrin repeat-containing E3 ubiquitin protein ligase 1, protein kinase Cα, bone morphogenetic protein 2 and prostaglandin-endoperoxide synthase 2. PPI analysis also identified guanine nucleotide-binding protein, γ13 as the most commonly downregulated gene based on different centrality. The results of the present study may provide novel insight into the genes and associated pathways involved in NFH, and aid the identification of novel therapeutic targets and biomarkers in the treatment of NFH.

Bioinformatics Analysis of Differentially Expressed Genes, Methylated Genes, and miRNAs in Unexplained Recurrent Spontaneous Abortion

Approximately half of the unexplained recurrent spontaneous abortions remain unexplained (URSAs). We aimed to provide novel insights into the biological characteristics and related pathways of differentially expressed genes (DE-genes), DE-methylated genes, and DE-miRNAs in URSA, and construct a molecular miRNAs-mRNAs network. Four data sets (GSE22490, GSE121950, GSE73025, and GSE43256) were gained from GEO data sets. We identified the DE-genes, DE-methylated genes, and DE-miRNAs using the LIMMA package in R software. Function and enrichment analyses were conducted using DAVID. A protein-protein network was performed by STRING. We predicted the target genes of DE-miRNA using DIANA-microT-CDS. Then, we constructed miRNAs-mRNAs network. There were 137 genes that overlapped in two expression profile data sets (GSE121950 and GSE22490). We found 10 overlapping DE-methylated genes and DE-genes with opposite expression alteration trends. All those 10 genes were hypermethylated lowly expressed genes. Pathway analysis illustrated that DE-genes were enriched in osteoclast differentiation, leishmaniasis, NF-kappa B signaling pathway, Toll-like receptor signaling pathway, and tuberculosis. Based on protein-protein interaction analysis, TLR8, TLR2, CD86, TLR4, IL10, CD163, FCGR1A, CXCL8, FCGR3A, HCK, PLEK, and MNDA were identified as hub genes for DE-genes. We screened out 47 DE-miRNAs and 42 overlapping DE-genes between predicted target genes of DE-miRNAs and the 137 DE-genes. We then constructed miRNAs-mRNAs network. This study identified several genes and miRNAs involved in the development and progression of URSA, including FCGR1A, FCGR3A, CXCL8, HCK, PLEK, IL10, hsa-miR-498, and hsa-miR-4530. Although further in vivo and in vitro validations are required, our results may provide a theoretical basis for future studies.

The expression of chondrogenesis-related and arthritis-related genes in human ONFH cartilage with different Ficat stages

Background

It has been well known that the degeneration of hip articular cartilage with osteonecrosis of the femoral head (ONFH) increases the instability of hip and accelerates the development process of ONFH. A better understanding of the expression of chondrogenesis-related and arthritis-related genes of cartilage along with the progression of ONFH seems to be essential for further insight into the molecular mechanisms of ONFH pathogenesis.

Methods

We analyzed the differentially expressed gene profile (GSE74089) of human hip articular cartilage with ONFH. The functions and pathway enrichments of differentially expressed genes (DEGs) were analyzed via GO and KEGG analysis. The expression of six selected critical chondrogenesis-related and four arthritis-related genes in eight human hip articular cartilage with femoral neck fracture (FNF) and 26 human hip articular cartilage with different stages ONFH (6 cases of Ficat stage II, 10 cases of Ficat stage III and 10 cases of Ficat stage IV) were detected.

Results

A total of 2,174 DEGs, including 1,482 up-regulated and 692 down-regulated ones, were obtained in the ONFH cartilage specimens compared to the control group. The GO and KEGG enrichment analysis indicated that the function of these DEGs mainly enriched in extracellular matrix, angiogenesis, antigen processing and presentation. The results showed a significant stepwise up-expression of chondrogenesis-related genes, including MMP13, ASPN, COL1A1, OGN, COL2A1 and BMP2, along with the progression of ONFH. The arthritis-related genes IL1β, IL6 and TNFα were only found up-expressed in Ficat IV stage which indicated that the arthritis-related molecular changes were not significant in the progression of ONFH before Ficat III stage. However, the arthritis-related gene PTGS2 was significant stepwise up-expression along with the progression of ONFH which makes it to be a sensitive arthritis-related biomarker of ONFH.

Conclusion

Expression changes of six chondrogenesis-related and four arthritis-related genes were found in hip articular cartilage specimens with different ONFH Ficat stages. These findings are expected to a get a further insight into the molecular mechanisms of ONFH progression.

[Microarchitecture features and pathology of necrotic region in patients with steroid-induced and alcohol-induced osteonecrosis of femoral head]

Objective

To investigate the pathological and microstructural features of the osteonecrosis samples from subjects with steroid-induced or alcohol-induced osteonecrosis of the femoral head (ONFH).

Methods

Thirty femoral head bone samples were collected from ONFH patients who underwent total hip arthroplasty between August 2015 and April 2016. There were 22 males and 8 females. The etiology of ONFH was alcohol-induced in 15 patients and steroid-induced in 15 patients. No significant difference of Association Research Circulation Osseous (ARCO) stage was found between alcohol-induced and steroid-induced ONFH ( Z=2.143, P=0.143). The femoral head bone samples in different areas (necrosis, sclerosis, and normal) from involved subjects was taken, and gross observation, HE staining were carried out (the rate of empty lacunaes was calculated). The intact femoral head was scanned by Micro-CT and the parameters of bone microstructure were analyzed quantitatively. The parameters included bone volume to total volume (BV/TV), bone surface area to bone volume ratio (BS/BV), bone mineral density (BMD), bone mineral content (BMC), structural model index (SMI), trabecular plate number (Tb. N), trabecular plate thickness (Tb. Th), and trabecular spacing (Tb. Sp).

Results

As observed in hard tissue slicing of both groups, the integrity of trabecular bone was destructed and cystic lesions left by the bone resorption was replaced by granulation tissues. Significant revascularization was found in granulation tissues of steroid-induced ONFH, but not in the alcohol-induced one. HE staining showed that the bone marrow structure was disordered in both group, as well as bone marrow necrosis and empty bone lacunaes noticed. The structure and integrity of trabecular bone of steroid-induced ONFH was far more severe whereas that of alcohol-induced one were thicker and better. The rate of empty bone lacunae in necrosis area of steroid-induced group was significantly higher than that of alcohol-induced one ( P<0.05), but no significant difference was found in sclerotic and normal areas between 2 groups ( P>0.05). Micro-CT showed that necrotic and sclerotic areas of both groups were low bone density. Bone structure in the former area was mostly heterogeneous. Further blood-rich granulation tissues formation was observed in the same places of hard tissue slicing, while the sclerotic one wasn't. The results of quantitative bone structure analysis showed that BV/TV, BMD, BMC, Tb.N, and Tb.Th of the necrotic and sclerotic areas of steroid-induced ONFH were significantly lower than those of alcohol-induced one ( P<0.01), BS/BV, SMI, and Tb.Sp of steroid-induced ONFH were significantly higher than those of alcohol-induced one ( P<0.01). No significant difference among the indexes above was found in the normal areas of both groups ( P>0.05).

Conclusion

The integrity of trabecular bone was destroyed in necrotic area of steroid-induced or alcohol-induced ONFH. However, they performed different features of osteonecrosis and contrasted with each other. The steroid-induced ONFH was characterized by multiple "osteolytic bone destruction", while the alcohol-induced one was manifested by some kinds of "coagulative destruction".

Bioinformatics analysis of aberrantly methylated-differentially expressed genes and pathways in hepatocellular carcinoma

AIM

To discover methylated-differentially expressed genes (MDEGs) in hepatocellular carcinoma (HCC) and to explore relevant hub genes and potential pathways.

METHODS

The data of expression profiling GSE25097 and methylation profiling GSE57956 were gained from GEO Datasets. We analyzed the differentially methylated genes and differentially expressed genes online using GEO2R. Functional and enrichment analyses of MDEGs were conducted using the DAVID database. A protein-protein interaction (PPI) network was performed by STRING and then visualized in Cytoscape. Hub genes were ranked by cytoHubba, and a module analysis of the PPI network was conducted by MCODE in Cytoscape software.

RESULTS

In total, we categorized 266 genes as hypermethylated, lowly expressed genes (Hyper-LGs) referring to endogenous and hormone stimulus, cell surface receptor linked signal transduction and behavior. In addition, 161 genes were labelled as hypomethylated, highly expressed genes (Hypo-HGs) referring to DNA replication and metabolic process, cell cycle and division. Pathway analysis illustrated that Hyper-LGs were enriched in cancer, Wnt, and chemokine signalling pathways, while Hypo-HGs were related to cell cycle and steroid hormone biosynthesis pathways. Based on PPI networks, PTGS2, PIK3CD, CXCL1, ESR1, and MMP2 were identified as hub genes for Hyper-LGs, and CDC45, DTL, AURKB, CDKN3, MCM2, and MCM10 were hub genes for Hypo-HGs by combining six ranked methods of cytoHubba.

CONCLUSION

In the study, we disclose numerous novel genetic and epigenetic regulations and offer a vital molecular groundwork to understand the pathogenesis of HCC. Hub genes, including PTGS2, PIK3CD, CXCL1, ESR1, MMP2, CDC45, DTL, AURKB, CDKN3, MCM2, and MCM10, can be used as biomarkers based on aberrant methylation for the accurate diagnosis and treatment of HCC.

LCK as a Potential Therapeutic Target for Acute Rejection after Kidney Transplantation: A Bioinformatics Clue

Objectives

We aim to identify the key biomarker of acute rejection (AR) after kidney transplantation via bioinformatics methods.

Methods

The gene expression data GSE75693 of 30 samples with stable kidney transplantation recipients and 15 AR samples were downloaded and analyzed by the limma package to identify differentially expressed genes (DEGs). Then, Gene Ontology (GO) functional enrichment analysis and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis were done to explore the biological functions and potential important pathways of DEGs. Finally, protein-protein interactions (PPIs) and literature mining were applied to construct the cocitation network and to select the hub protein.

Results

A total of 437 upregulated genes and 353 downregulated genes were selected according to P < 0.01 and |log₂(fold change)| > 1.0. DEGs of AR are mainly located on membranes and impact the activation of receptors in immune responses. In the PPI network, Src kinase, lymphocyte kinase (LCK), CD3G, B2M, interferon-γ, CD3D, tumor necrosis factor, VAV1, and CD3E in the T cell receptor signaling pathway were selected as important factors, and LCK was identified as the hub protein.

Conclusion

LCK, via acting on T-cell receptor, might be a potential therapeutic target for AR after kidney transplantation.

Identification of potential key protein interaction networks of BK virus nephropathy in patients receiving kidney transplantation

We aim to identify the key protein interaction networks and implicated pathways of BK virus nephropathy (BKVN) via bioinformatic methods. The microarray data GSE75693 of 30 patients with stable kidney transplantation and 15 with BKVN were downloaded and analyzed by using the limma package to identify differentially expressed genes (DEGs). Then the gene ontology (GO) functional enrichment analysis and the Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis were done to investigate the molecular function (MF), biological process (BP), cellular components (CC) and pathways of DEGs. Finally, protein-protein interactions (PPIs) were constructed, and the hub proteins were  identified. As a result, 249 up-regulated genes and 253 down-regulated genes of BKVN patients were selected based on criteria of P > 0.01 and fold change >2.0. GO and KEGG showed that DEGs were mainly located in nucleus and cytosol, and were implicated in the immune responses. In the PPI analysis, 26 up-regulated and 8 down-regulated proteins composed the pivotal interaction network. CXCL10, EGF and STAT1 were identified as hub proteins in BKVN. In conclusion, CXCL10, EGF and STAT1 may induce kidney injuries by promoting inflammation and prohibiting reparation of tissue damage in BKVN.