Bioinformatics analysis of gene expression profiles in the rat cerebral cortex following traumatic brain injury

BACKGROUND

Traumatic brain injury (TBI) is a serious neurodisorder commonly caused by sports related events or violence. It is the leading cause of disability in people under 40.

AIM

In order to elucidate the molecular mechanism of the secondary injury after TBI.

MATERIALS AND METHODS

In this study, we downloaded gene expression profile on TBI model with sham controls for gene set enrichment analysis and pathway analysis.

RESULTS

At a q-value of 5%, 361 genes were up-regulated and 373 were down-regulated in samples obtained at 48 hours after TBI. Functional analyses revealed that steroid biosynthesis, cell cycle, metal ion transport, inflammation and apoptosis were significantly dysregulated during the late period after trauma. In addition, MAPK3 (mitogen-activated protein kinase 3), was identified as the hub node in the protein-protein interaction (PPI) network constructed by the differentially expressed genes (DEGs).

CONCLUSIONS

Further elucidation of genes and proteins in our study may reveal their potential as novel therapeutic targets.

Clinical-dosimetric relationship between lacrimal gland dose and ocular toxicity after intensity-modulated radiotherapy for sinonasal tumours

OBJECTIVE

To characterise the relationship between lacrimal gland dose and ocular toxicity among patients treated by intensity-modulated radiotherapy (IMRT) for sinonasal tumours.

METHODS

40 patients with cancers involving the nasal cavity and paranasal sinuses were treated with IMRT to a median dose of 66.0 Gy. Toxicity was scored using the Radiation Therapy Oncology Group morbidity criteria based on conjunctivitis, corneal ulceration and keratitis. The paired lacrimal glands were contoured as organs at risk, and the mean dose, maximum dose, V10, V20 and V30 were determined. Statistical analysis was performed using logistic regression and the Akaike information criterion (AIC).

RESULTS

The maximum and mean dose to the ipsilateral lacrimal gland were 19.2 Gy (range, 1.4-75.4 Gy) and 14.5 Gy (range, 11.1-67.8 Gy), respectively. The mean V10, V20 and V30 values were 50%, 25% and 17%, respectively. The incidence of acute and late Grade 3+ toxicities was 23% and 19%, respectively. Based on logistic regression and AIC, the maximum dose to the ipsilateral lacrimal gland was identified as a more significant predictor of acute toxicity (AIC, 53.89) and late toxicity (AIC, 32.94) than the mean dose (AIC, 56.13 and 33.83, respectively). The V20 was identified as the most significant predictor of late toxicity (AIC, 26.81).

CONCLUSION

A dose-response relationship between maximum dose to the lacrimal gland and ocular toxicity was established. Our data suggesting a threshold relationship may be useful in establishing dosimetric guidelines for IMRT planning that may decrease the risk of acute and late lacrimal toxicities in the future.

ADVANCES IN KNOWLEDGE

A threshold relationship between radiation dose to the lacrimal gland and ocular toxicity was demonstrated, which may aid in treatment planning and reducing the morbidity of radiotherapy for sinonasal tumours.

Autoantibody detection to tumor-associated antigens of P53, IMP1, P16, cyclin B1, P62, C-myc, Survivn, and Koc for the screening of high-risk subjects and early detection of esophageal squamous cell carcinoma

The aim of this study was to evaluate the diagnostic values by detecting sera autoantibodies to eight tumor-associated antigens (TAAs) of P53, IMP1, P16, cyclin B1, P62, C-myc, Survivn and Koc full-length recombinant proteins for the screening of high-risk subjects and early detection of esophageal squamous cell carcinoma (ESCC). Enzyme-linked immunosorbent assay was used to detect autoantibodies against the eight selected TAAs in 567 sera samples from four groups, including 200 individuals with normal esophageal epithelia (NOR), 214 patients with esophageal basal cell hyperplasia (BCH), 65 patients with esophageal dysplasia (DYS), and 88 patients with ESCC. In addition, the expression of the eight antigens in esophageal tissues was analyzed by immunohistochemistry. Statistically significant distribution differences were identified among the four groups for each of the individual autoantibodies to six TAAs (P53, IMP1, P16, cyclin B1, P62, and C-myc); the detection rates of antoantibodies were positively correlated with the progression of ESCC. When autoantibody assay successively accumulated to six TAAs (P53, IMP1, P16, cyclin B1, P62, and C-myc), a stepwise increased detection frequency of autoantibodies was found in the four sera groups (6% in NOR, 18% in BCH, 38% in DYS, and 64% in ESCC, respectively), the risks to BHC, DYS, and ESCC steadily increased about 3-, 9-, and 27-folds. The sensitivity and the specificity for autoantibodies against the six TAAs in diagnosing ESCC reached up to 64% and 94%, respectively. The area under the receiver operating characteristic curve for the six anti-TAA autoantibodies was 0.78 (95% confidence interval 0.74-0.83). No more increasing in sensitivity was found with the addition of new anti-TAA autoantibodies. A combination detection of autoantibodies to TAAs might distinguish ESCC patients from normal individuals and the patients with esophageal precancerous lesions.

Correlation between oxidative stress and L-type calcium channel expression in the ventricular myocardia of selenium-deficient mice

OBJECTIVE

Expression of the Cacna1c (calcium channel, voltage-dependent, L-type, α1C subunit) gene was studied to investigate the relationship between oxidative stress and L-type calcium channels in the myocardium of selenium-deficient mice.

METHODS

Selenium levels in liver and heart tissue samples from mice fed normal or selenium-deficient diets were evaluated by fluorometry. In the same mice, glutathione peroxidase (GPx) and Cacna1c gene expression were analysed, malondialdehyde (MDA) content and superoxide dismutase (SOD) activity were measured, oxidoreductase gene expression profiles were analysed (by DNA microarray), and myocardial structural changes were studied.

RESULTS

In selenium-deficient versus control mice, GPx expression and SOD activity were decreased, and Cacna1c expression and MDA concentration were increased. Selenoprotein oxidoreductase and nonselenoprotein oxidoreductase gene expression differed significantly between selenium-deficient and control mice. In selenium-deficient mice, myocardial fibres were separated by loose collagenous tissue; electron microscopy showed shortened sarcomeres, dilated sarcoplasmic reticulum, scattered myofibril lysis and increased mitochondria with amorphous matrix densities.

CONCLUSION

L-type calcium channels were involved in selenium deficiency-induced cardiomyocyte injury, which was positively related to oxidative stress.

Systematic evaluation of validated type 2 diabetes and glycaemic trait loci for association with insulin clearance

AIMS/HYPOTHESIS

Insulin clearance is a highly heritable trait, for which few quantitative trait loci have been discovered. We sought to determine whether validated type 2 diabetes and/or glycaemic trait loci are associated with insulin clearance.

METHODS

Hyperinsulinaemic-euglycaemic clamps were performed in two Hispanic-American family cohorts totalling 1329 participants in 329 families. The Metabochip was used to fine-map about 50 previously identified loci for type 2 diabetes, fasting glucose, fasting insulin, 2 h glucose or HbA1c. This resulted in 17,930 variants, which were tested for association with clamp-derived insulin clearance via meta-analysis of the two cohorts.

RESULTS

In the meta-analysis, 38 variants located within seven loci demonstrated association with insulin clearance (p < 0.001). The top signals for each locus were rs10241087 (DGKB/TMEM195 [TMEM195 also known as AGMO]) (p = 4.4 × 10(-5)); chr1:217605433 (LYPLAL1) (p = 3.25 × 10(-4)); rs2380949 (GLIS3) (p = 3.4 × 10(-4)); rs55903902 (FADS1) (p = 5.6 × 10(-4)); rs849334 (JAZF1) (p = 6.4 × 10(-4)); rs35749 (IGF1) (p = 6.7 × 10(-4)); and rs9460557 (CDKAL1) (p = 6.8 × 10(-4)).

CONCLUSIONS/INTERPRETATION

While the majority of validated loci for type 2 diabetes and related traits do not appear to influence insulin clearance in Hispanics, several of these loci do show evidence of association with this trait. It is therefore possible that these loci could have pleiotropic effects on insulin secretion, insulin sensitivity and insulin clearance.

Composition and conductance distributions of single GeSi quantum rings studied by conductive atomic force microscopy combined with selective chemical etching

Atomic force microscopy imaging combined with selective chemical etching is employed to quantitatively investigate three-dimensional (3D) composition distributions of single GeSi quantum rings (QRs). In addition, the 3D quantitative composition distributions and the corresponding conductance distributions are simultaneously obtained on the same single GeSi QRs by conductive atomic force microscopy combined with selective chemical etching, allowing us to investigate the correlations between the conductance and composition distributions of single QRs. The results show that the QRs' central holes have higher Ge content, but exhibit lower conductance, indicating that the QRs' conductance distribution is not consistent with their composition distribution. By comparing the topography, composition and conductance profiles of the same single QRs before and after different etching processes, it is found that the conductance distributions of GeSi QRs do not vary with the change of composition distribution. Instead, the QRs' conductance distributions are found to be consistent with their topographic shapes, which can be supposed to be due to the shape determined electronic structures.

Proteomic analysis of the changed proteins of Trichinella spiralis infective larvae after co-culture in vitro with intestinal epithelial cells

The purpose of this study was to determine the protein changes in Trichinella spiralis muscle larvae (ML) after in vitro co-culture with intestinal epithelial cells, and to analyze the changed proteins. Muscle larvae were incubated with HCT-8 cells for 18 h and the ML soluble proteins were analyzed by SDS-PAGE and Western blot. Results showed that seven additional protein bands (123, 77, 58, 36, 30, 28 and 21 kDa) were recognized by sera from infected mice after culture with HCT-8 cells. Three protein bands (97, 51 and 23 kDa) were not recognized by infection sera compared with proteins from ML incubated in RPMI-1640 medium only. Three bands (58, 36 and 21 kDa) were excised from gels, digested with trypsin, and identified by liquid chromatography and tandem mass spectrometry (LC-MS/MS) combined with bioinformatics. In total, 211 kinds of proteins were identified, and numerous enzymes (e.g. metallo- and serine proteases, cysteine proteinases) were found to be highly expressed.