A polymorphic MYC response element in KBTBD11 influences colorectal cancer risk, especially in interaction with an MYC-regulated SNP rs6983267

Background

MYC is a well-established cancer driver gene regulating the expression of numerous genes, indicating that polymorphisms in MYC response elements could affect tumorigenesis through altering MYC regulation. We performed integrative multistage study to evaluate the effects of variants in MYC response elements and colorectal cancer (CRC) risk.

Patients and methods

We systematically integrated ChIP-Seq, DNase-Seq and transcription factor motif data to screen variants with potential ability to affect the MYC binding affinity. Then, we conducted a two-stage case-control study, totally consisting of 4830 CRC cases and 4759 controls in Chinese population to identify risk polymorphisms and interactions. The effects of risk variants were confirmed by functional assays in CRC LoVo, SW480 and HCT15 cells.

Results

We identified a novel polymorphism rs11777210 in KBTBD11 significantly associated with CRC susceptibility (P = 2.43 × 10-12). Notably, we observed a significant interaction between rs11777210 and MYC nearby rs6983267 (P-multi = 0.003, P-add = 0.005), subjects carrying rs6983267 GG and rs11777210 CC genotypes showing higher susceptibility to CRC (2.83-fold) than those carrying rs6983267 TT and rs11777210 TT genotypes. We further demonstrated that rs6983267 T > G increased MYC expression, and MYC bound to and negatively regulated KBTBD11 expression when the rs11777210 C risk allele was present. KBTBD11 was downregulated in tumor tissues, and KBTBD11 knockdown promoted cell proliferation and inhibited cell apoptosis.

Conclusion

The rs11777210 is a potential predictive biomarker of CRC susceptibility, and KBTBD11 functions as a putative tumor suppressor in tumorigenesis. Our study highlighted the high CRC risk of people carrying rs6983267 G and rs11777210 C alleles, and provided possible biological mechanism of the interaction.

Effects of online cone-beam computed tomography with active breath control in determining planning target volume during accelerated partial breast irradiation

PURPOSE

To test if active breath control during cone-beam computed tomography (CBCT) could improve planning target volume during accelerated partial breast radiotherapy for breast cancer.

METHODS

Patients who were more than 40 years old, underwent breast-conserving dissection and planned for accelerated partial breast irradiation, and with postoperative staging limited to T1-2 N0 M0, or postoperative staging T2 lesion no larger than 3cm with a negative surgical margin greater than 2mm were enrolled. Patients with lobular carcinoma or extensive ductal carcinoma in situ were excluded. CBCT images were obtained pre-correction, post-correction and post-treatment. Set-up errors were recorded at left-right, anterior-posterior and superior-inferior directions. The differences between these CBCT images, as well as calculated radiation doses, were compared between patients with active breath control or free breathing.

RESULTS

Forty patients were enrolled, among them 25 had active breath control. A total of 836 CBCT images were obtained for analysis. CBCT significantly reduced planning target volume. However, active breath control did not show significant benefit in decreasing planning target volume margin and the doses of organ-at-risk when compared to free breathing.

CONCLUSION

CBCT, but not active breath control, could reduce planning target volume during accelerated partial breast irradiation.

Surface Collective Modes in the Topological Insulators Bi_{2}Se_{3} and Bi_{0.5}Sb_{1.5}Te_{3-x}Se_{x}

We used low-energy, momentum-resolved inelastic electron scattering to study surface collective modes of the three-dimensional topological insulators Bi_{2}Se_{3} and Bi_{0.5}Sb_{1.5}Te_{3-x}Se_{x}. Our goal was to identify the "spin plasmon" predicted by Raghu and co-workers [Phys. Rev. Lett. 104, 116401 (2010)]. Instead, we found that the primary collective mode is a surface plasmon arising from the bulk, free carriers in these materials. This excitation dominates the spectral weight in the bosonic function of the surface χ^{"}(q,ω) at THz energy scales, and is the most likely origin of a quasiparticle dispersion kink observed in previous photoemission experiments. Our study suggests that the spin plasmon may mix with this other surface mode, calling for a more nuanced understanding of optical experiments in which the spin plasmon is reported to play a role.

Investigation of polymorphisms in exon7 of the NSUN7 gene among Chinese Han men with asthenospermia

Previous studies have shown that genetic polymorphisms in exon7 of the NSUN7 gene can be used as an infertility marker in Iranian men with asthenospermia. However, there have been no equivalent studies in China. In the present study, we investigated the possible association between the genetic polymorphisms in exon7 of NSUN7 and asthenospermia in a Chinese Han population. We recruited 240 asthenospermic men as a patient group and 256 normospermic men as a control group, and analyzed the semen parameters on the basis of World Health Organization (WHO) guidelines. The genetic polymorphisms in exon7 of NSUN7 were detected by DNA sequence analysis. The results were analyzed statistically and a P value < 0.05 was considered significant. There were two genetic polymorphisms, c.906C>T and c.922T>G, in exon7 of NSUN7. We found relatively similar genotypes and allele frequencies between the two groups (P = 0.928, P = 0.928, respectively). The combined genotypes of the two polymorphisms did not identify a haplotype associated with asthenospermia (P = 0.824, P = 0.824, respectively). Our findings revealed that genetic polymorphisms in exon7 of the NSUN7 gene are not associated with asthenospermia in Chinese Han men.

DIGRE: Drug-Induced Genomic Residual Effect Model for Successful Prediction of Multidrug Effects

Multidrug regimens are a promising strategy for improving therapeutic efficacy and reducing side effects, especially for complex disorders such as cancer. However, the use of multidrug therapies is very challenging, due to a lack of understanding of the mechanisms of drug interactions. We herein present a novel computational approach-Drug-Induced Genomic Residual Effect (DIGRE) Computational Model-to predict drug combination effects by explicitly modeling drug response curves and gene expression changes after drug treatments. The prediction performance of DIGRE was evaluated using two datasets: (i) OCI-LY3 B-lymphoma cells treated with 14 different drugs and (ii) MCF breast cancer cells treated with combinations of gefitinib and docetaxel at different doses. In both datasets, the predicted drug combination effects significantly correlated with the experimental results. The results indicated the model was useful in predicting drug combination effects, which may greatly facilitate the discovery of new, effective multidrug therapies.

An analysis of the small RNA transcriptome of four developmental stages of the citrus red mite (Panonychus citri)

The citrus red mite (Panonychus citri) can feed on more than 112 plant species around the world. Endogenous small RNAs (sRNAs) have proved to be important components of gene regulation in many eukaryotes. Recently, many sRNAs have been shown to be involved in various biological processes, such as development in many animals, including insects; however, to date, no sRNAs have been reported in the citrus red mite. Using Illumina sequencing, several categories of sRNAs were identified, including 594 known microRNAs (miRNAs) grouped into 206 families and 31 novel miRNAs in the four developmental stages of citrus red mite. In addition, according to bioinformatics analysis and S-Poly(T) miRNA assays, the expression level of many miRNAs varied among the developmental stages. Furthermore, the prediction of miRNAs target genes and their functional annotation indicated that miRNAs are involved in the regulation of multiple pathways in the citrus red mite. As the first report of the sRNA world in citrus red mite, the present study furthers our understanding of the roles played by sRNAs in the development of citrus red mite and the data may help to develop methods of controlling the pests in the field.

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.