Integrated analysis of gene expression and genomic aberration data in osteosarcoma (OS)

Cytogenetic analyses have revealed that complex karyotypes with numerous and highly variable genomic aberrations including single-nucleotide polymorphisms (SNPs) and copy number variants (CNVs), are observed in most of the conventional osteosarcomas (OSs). Several genome-wide studies have reported that the dysregulated expression of many genes is correlated with genomic aberrations in OS. We first compared OS gene expression in Gene Expression Omnibus (GEO) data sets and genomic aberrations in International Cancer Genome Consortium (ICGC) database to identify differentially expressed genes (DEGs) associated with SNPs or CNVs in OS. Then the function annotation of SNP- or CNV-associated DEGs was performed in terms of gene ontology analysis, pathway analysis and protein-protein interactions (PPIs). Finally, the expression of genes correlated with both SNPs and CNVs were confirmed by quantitative reverse-transcription PCR. Eight publicly available GEO data sets were obtained, and a set of 979 DEGs were identified (472 upregulated and 507 downregulated DEGs). Moreover, we obtained 1039 SNPs mapped in 938 genes, and 583 CNV sites mapped in 2915 genes. Comparing genomic aberrations and DGEs, we found 41 SNP-associated DEGs and 124 CNV-associated DEGs, in which 7 DGEs were associated with both SNPs and CNVs, including WWP1, EXT1, LDHB, C8orf59, PLEKHA5, CCT3 and VWF. The result of function annotation showed that ossification, bone development and skeletal system development were the significantly enriched terms of biological processes for DEGs. PPI network analysis showed that CCT3, COPS3 and WWP1 were the significant hub proteins. We conclude that these genes, including CCT3, COPS3 and WWP1 are candidate driver genes of importance in OS tumorigenesis.

Coronary Artery Disease Associated Transcription Factor TCF21 Regulates Smooth Muscle Precursor Cells that Contribute to the Fibrous Cap

TCF21 is a basic helix-loop-helix transcription factor that has recently been implicated as contributing to susceptibility to coronary heart disease based on genome wide association studies. In order to identify transcriptionally regulated target genes in a major disease relevant cell type, we performed siRNA knockdown of TCF21 in in vitro cultured human coronary artery smooth muscle cells and compared the transcriptome of siTCF21 versus siCONTROL treated cells. The raw (FASTQ) as well as processed (BED) data from 3 technical replicates per treatment has been deposited with Gene Expression Omnibus (GSE44461).

Autonomic dysreflexia during cystolitholapaxy in patients with spinal cord injury

AIM

This study aims to explore the risk factors associated with autonomic dysreflexia (AD) reflex during cystolitholapaxy and increase the awareness of urologists on the dangerous reaction of AD in patients with spinal cord injury (SCI).

METHODS

Data of 89 SCI patients with bladder stone who underwent cystolitholapaxy were retrospectively analyzed. Patients were divided into two groups according to the presence or absence of AD. Risk factors may associated with AD during the endoscopic procedure were analyzed by comparing clinical and operative features between the two groups.

RESULTS

Of the 89 patients, 31 (34.83%) developed AD during the procedure. The patients who developed AD had larger stones (4.58±1.26 cm vs. 3.75±1.15 cm, P<0.01), more stones (2.29±0.86 vs. 1.74±0.81, P<0.01), and greater injury (83.87% vs. 41.38%, above T6, P<0.01) than those who did not develop AD. The patients who developed AD suffered higher irrigation (83.55± 13.05 cm vs. 77.47±10.91 cm, P<0.05) and longer operation time (60.65±17.78 min vs. 49.31±14.31 min, P<0.01) than those who did not develop AD. The AD group also received local anesthetics to a larger extent compared with non-AD group, which more often had spinal anesthesia.

CONCLUSION

The patients who developed AD during the procedure had larger stones, more stone number, injury level more often above T6, higher hydraulic irrigation height, and longer operation time compared with the patients who did not develop AD. Urologists should pay extra care when performing cystolitholapaxy on individuals with these features.

An association analysis between psychophysical characteristics and genome-wide gene expression changes in human adaptation to the extreme climate at the Antarctic Dome Argus

Genome-wide gene expression measurements have enabled comprehensive studies that integrate the changes of gene expression and phenotypic information to uncover their novel associations. Here we reported the association analysis between psychophysical phenotypes and genome-wide gene expression changes in human adaptation to one of the most extreme climates on Earth, the Antarctic Dome Argus. Dome A is the highest ice feature in Antarctica, and may be the coldest, driest and windiest location on earth. It is considered unapproachable due to its hostile environment. In 2007, a Chinese team of 17 male explorers made the expedition to Dome A for scientific investigation. Overall, 133 psychophysical phenotypes were recorded, and genome-wide gene expression profiles from the blood samples of the explorers were measured before their departure and upon their arrival at Dome A. We found that mood disturbances, including tension (anxiety), depression, anger and fatigue, had a strong, positive, linear relationship with the level of a male sex hormone, testosterone, using the Pearson correlation coefficient (PCC) analysis. We also demonstrated that significantly lowest-level Gene Ontology groups in changes of gene expression in blood cells with erythrocyte removal were consistent with the adaptation of the psychophysical characteristics. Interestingly, we discovered a list of genes that were strongly related to significant phenotypes using phenotype and gene expression PCC analysis. Importantly, among the 70 genes that were identified, most were significantly related to mood disturbances, where 42 genes have been reported in the literature mining, suggesting that the other 28 genes were likely novel genes involved in the mood disturbance mechanism. Taken together, our association analysis provides a reliable method to uncover novel genes and mechanisms related to phenotypes, although further studies are needed.

MLK3 promotes melanoma proliferation and invasion and is a target of microRNA-125b

BACKGROUND

Metastatic melanoma is a disease with high mortality and limited therapeutic options. MicroRNAs (miRNAs) can be used to classify melanoma stage.

METHODS

Expression of the miRNA miR-125b and serine/threonine kinase mixed lineage kinase (MLK)3 was assessed in primary malignant melanoma tissues and several melanoma cell lines by quantitative reverse transcription PCR. The effect of MLK3 and miR-125b on cell proliferation was evaluated by MTS assay, and cell invasion was evaluated by Transwell invasion assays. Targeting of MLK3 by miR-125b was evaluated using luciferase reporter assay and western blotting.

RESULTS

We found significantly increased levels of MLK3 in metastatic primary malignant melanomas and melanoma cell lines, with levels being especially high in metastatic lines. To investigate the functional significance of MLK3, we used knockdown MLK3, which was found to suppress cell growth and invasion. Using bioinformatics, we identified MLK3 as one potential target of miR-125b. miRNA transfection and luciferase assay confirmed that MLK3 was regulated by miR-125b at both the transcriptional and translational levels. Cell proliferation and cell invasion was inhibited by overexpression of miR-125b.

CONCLUSIONS

MLK3 is upregulated in metastatic melanoma, and regulates cell proliferation and invasion in melanoma cells. MLK3 is a direct target of miR-125b.

Glial cell line-derived neurotrophic factor promotes proliferation of neuroglioma cells by up-regulation of cyclins PCNA and Ki-67

OBJECTIVE

We wished to test whether glial cell line-derived neurotrophic factor (GDNF) stimulates proliferation of gliomas by up-regulating expression of nuclear cyclins PCNA and Ki37.

MATERIALS AND METHODS

As a model, we tested rat C6 glioma cell line exposed to basal conditions, vehicle control, or exogenous GDNF at different concentrations (0-90 µg/L) or different times (0-72 hours). Cell proliferation was quantified by MTT test, cell cycle by flow cytometry and propidium iodide staining, expression of PCNA and Ki67 by intracellular antibody staining and flow cytometry.

RESULTS

We first observed that cell proliferation was most stimulated by GDNF at concentration of 70 µg/L and incubation time of 48 hours. Using this concentration and incubation time, we next documented that GDNF increased the percentage of cells in the S phase (47.98% vs. 32.57% in basal cells; p < 0.05), while not affecting the percentage of cells in G0/G1 or G2/M phases. Finally, we demonstrated that expression of both PCNA and Ki67 was significantly increased in cells exposed to GDNF.

CONCLUSIONS

We demonstrate that GDNF stimulates proliferation of glioma cells by up-regulating expression of cyclins PCNA and Ki-67.

Shape memory embracing fixator for Vancouver type B and type C periprosthetic femoral fractures

The purpose of this study was to analyze clinical and radiographical results of a group of patients with periprosthetic femoral fractures treated with the shape memory embracing fixator. We retrospectively reviewed twelve patients in whom a total of twelve periprosthetic femoral fractures were treated with the shape memory embracing fixator between August 2004 and February 2013. The patients were 3 men and 9 women (mean age, 69.9 years; range 42-92 years). The average duration of follow-up was 39.3 months (range 4-103 months). In one case, bone grafting was used. Postoperative evaluation was based on radiographs and Harris hip scores. All fractures healed at on average 4.4 months (range: 3 to 6 months) after surgery. None of the patients developed nonunion or malunion during the follow up. And there was no implant failure and no infection during follow up. The average Harris hip score at the final follow-up examination was 84.8 points. Results show that the shape memory embracing fixator is a safe and effective means for Vancouver type B and type C periprosthetic femoral fractures following hip arthroplasty.

Asymmetrical cortical vessel sign on susceptibility-weighted imaging: a novel imaging marker for early neurological deterioration and unfavorable prognosis

BACKGROUND AND PURPOSE

Susceptibility-weighted imaging (SWI) is a high spatial resolution technique that can indirectly demonstrate increased cerebral oxygen extraction. Our aim was to assess whether asymmetric cortical vessel sign (ACVS) on SWI could be associated with early neurological deterioration (END) as well as 90-day unfavorable outcome in patients with acute ischaemic stroke.

MATERIALS AND METHODS

Consecutive patients with acute middle cerebral artery (MCA) territory infarction were prospectively enrolled. ACVS was defined as more and/or larger vessels with greater signal loss than those in the opposite hemisphere on minimum intensity projection of SWI. The neurofunctional fluctuation during acute phase as well as 90-day outcomes were assessed. A National Institutes of Health Stroke Scale increment ≥2 points and ≥4 points despite standard treatment in the first 72 h after admission was defined as END2 and END4, respectively.

RESULTS

In all, 572 patients were finally enrolled. ACVS on SWI was present in 39 (6.8%) subjects. Multivariate analysis indicated that ACVS is an independent predictor for END2 [odds ratio (OR) 4.47, 95% confidence interval (CI) 1.99-10.05) and END4 (OR 4.24, 95% CI 1.94-9.23). Furthermore, ACVS also correlates with 90-day unfavorable outcome defined as a modified Rankin Scale score >1 point (OR 2.93, 95% CI 1.15-7.48). Both positive and negative predictive values of ACVS for END2, END4 and 90-day prognosis were reasonable and both could be slightly enhanced as long as patients with contralateral artery stenosis or occlusion were excluded.

CONCLUSION

In patients with MCA territory acute ischaemic stroke, especially in those without contralateral internal carotid artery/MCA stenosis or occlusion, ACVS might be considered as a neuroimaging predictor for END and unfavorable prognosis.

Chromosome 12p13 variants predict recurrence of ischaemic stroke in a Chinese population

BACKGROUND AND PURPOSE

A recent genome-wide association study identified two genetic variants (rs12425791 and rs11833579) on chromosome 12p13 that confer risk of ischaemic stroke. The purpose of this study was to examine whether these two polymorphisms are associated with stroke onset and prognosis in a Chinese population.

METHODS

rs12425791 and rs11833579 were genotyped using the improved multiple ligase detection reaction in 913 patients with ischaemic stroke. Analyses of genotype association with onset and prognosis outcomes were evaluated by the Kaplan-Meier method, the log-rank test and Cox proportional hazards models.

RESULTS

rs12425791 and rs11833579 were not associated with age of stroke onset (P = 0.786 and 0.340, respectively). However, these two polymorphisms were significantly associated with risk of stroke recurrence, especially for the large-artery atherosclerosis (LAA) subtype, in recessive models [hazard ratio (HR) 2.52; 95% confidence interval (CI) 1.04-6.12 for rs12425791; HR 2.13; 95% CI 1.03-4.40 for rs11833579]. The combined genotype of these two single-nucleotide polymorphisms showed a locus-dosage effect on recurrence of LAA subtype and was an independent prognostic factor for LAA subtype in the final multivariate Cox regression model.

CONCLUSIONS

These findings indicated that rs12425791 and rs11833579 on chromosome 12p13 may be useful biomarkers for predicting the prognosis of patients with the LAA subtype of ischaemic stroke.

Genetic tuning of the novel avian influenza A(H7N9) virus during interspecies transmission, China, 2013

A novel avian influenza A(H7N9) virus causing human infection emerged in February 2013 in China. To elucidate the mechanism of interspecies transmission, we compared the signature amino acids of avian influenza A(H7N9) viruses from human and non-human hosts and analysed the reassortants of 146 influenza A(H7N9) viruses with full genome sequences. We propose a genetic tuning procedure with continuous amino acid substitutions and reassorting that mediates host adaptation and interspecies transmission. When the early influenza A(H7N9) virus, containing ancestor haemagglutinin (HA) and neuraminidase (NA) genes similar to A/Shanghai/05 virus, circulated in waterfowl and transmitted to terrestrial poultry, it acquired an NA stalk deletion at amino acid positions 69 to 73. Then, receptor binding preference was tuned to increase the affinity to human-like receptors through HA G186V and Q226L mutations in terrestrial poultry. Additional mammalian adaptations such as PB2 E627K were selected in humans. The continual reassortation between H7N9 and H9N2 viruses resulted in multiple genotypes for further host adaptation. When we analysed a potential association of mutations and reassortants with clinical outcome, only the PB2 E627K mutation slightly increased the case fatality rate. Genetic tuning may create opportunities for further adaptation of influenza A(H7N9) and its potential to cause a pandemic.