Developing a risk scoring system based on immune-related lncRNAs for patients with gastric cancer

The immune system and the tumor interact closely during tumor development. Aberrantly expressed long non-coding RNAs (lncRNAs) may be potentially applied as diagnostic and prognostic markers for gastric cancer (GC). At present, the diagnosis and treatment of GC patients remain a formidable clinical challenge. The present study aimed to build a risk scoring system to improve the prognosis of GC patients. In the present study, ssGSEA was used to evaluate the infiltration of immune cells in GC tumor tissue samples, and the samples were split into a high immune cell infiltration group and a low immune cell infiltration group. About 1262 differentially expressed lncRNAs between the high immune cell infiltration group and the low immune cell infiltration group. About 3204 differentially expressed lncRNAs between GC tumor tissues and paracancerous tissues were identified. Then, 621 immune-related lncRNAs were screened using a Venn analysis based on the above results, and 85 prognostic lncRNAs were identified using a univariate Cox analysis. We constructed a prognostic signature using LASSO analysis and evaluated the predictive performance of the signature using ROC analysis. GO and KEGG enrichment analyses were performed on the lncRNAs using the R package, ‘clusterProfiler’. The TIMER online database was used to analyze correlations between the risk score and the abundances of the six types of immune cells. In conclusion, our study found that specific immune-related lncRNAs were clinically significant. These lncRNAs were used to construct a reliable prognostic signature and analyzed immune infiltrates, which may assist clinicians in developing individualized treatment strategies for GC patients.     

Real-life use of vitamin D3-fortified bread and milk during a winter season: the effects of CYP2R1 and GC genes on 25-hydroxyvitamin D concentrations in Danish families,the VitmaD study

Common genetic variants rs10741657 and rs10766197 in CYP2R1 and rs4588 and rs842999 in GC and a combined genetic risk score (GRS) of these four variants influence late summer 25-hydroxyvitamin D (25(OH)D) concentrations. The objectives were to identify those who are most at risk of developing low vitamin D status during winter and to assess whether vitamin D₃-fortified bread and milk will increase 25(OH)D concentrations in those with genetically determined low 25(OH)D concentrations at late summer. We used data from the VitmaD study. Participants were allocated to either vitamin D₃-fortified bread and milk or non-fortified bread and milk during winter. In the fortification group, CYP2R1 (rs10741657) and GC (rs4588 and rs842999) were statistically significantly associated with winter 25(OH)D concentrations and CYP2R1 (rs10766197) was borderline significant. There was a negative linear trend between 25(OH)D concentrations and carriage of 0–8 risk alleles (p < 0.0001). No association was found for the control group (p = 0.1428). There was a significant positive linear relationship between different quintiles of total vitamin D intake and the increase in 25(OH)D concentrations among carriers of 0–2 (p = 0.0012), 3 (p = 0.0001), 4 (p = 0.0118) or 5 (p = 0.0029) risk alleles, but not among carriers of 6–8 risk alleles (p = 0.1051). Carriers of a high GRS were more prone to be vitamin D deficient compared to carriers of a low GRS. Furthermore, rs4588-AA carriers have a low but very stable 25(OH)D concentration, and interestingly, also low PTH level.

Electronic supplementary material

The online version of this article (doi:10.1007/s12263-014-0413-7) contains supplementary material, which is available to authorized users.     

Genetic predisposition scores for dyslipidaemia influence plasma lipid concentrations at baseline,but not the changes after controlled intake of n-3 polyunsaturated fatty acids

Inconsistent effects of fish oil supplementation on plasma lipids may be influenced by genetic variation. We investigated 12 single nucleotide polymorphisms (SNPs) associated with dyslipidaemia in genome-wide association studies, in 310 participants randomised to treatment with placebo or 0.45, 0.9 and 1.8 g/day eicosapentaenoic acid (20:5n-3, EPA) and docosahexaenoic acid (22:6n-3, DHA) (1.51:1) in a 12-month parallel controlled trial. Effects of risk alleles were assessed as trait-specific genetic predisposition scores (GPS) and singly. GPS were positively associated with baseline concentrations of plasma total cholesterol, low-density-lipoprotein cholesterol and triglyceride (TG) and negatively with high-density-lipoprotein cholesterol. The TG-GPS was associated with 0.210 mmol/L higher TG per risk allele (P < 0.0001), but no effects of single TG SNPs were significant at baseline. After treatment with EPA and DHA, TG-GPS was associated with 0.023 mmol/L lower TG per risk allele (P = 0.72). No interactions between GPS and treatment were significant; however, FADS1 SNP rs174546 C/T interaction with treatment was a significant determinant of plasma TG concentration (P = 0.047, n = 267). Concentration differed between genotype groups after the 1.8 g/day dose (P = 0.026), decreasing by 3.5 (95 % CI −15.1 to 8.2) % in non-carriers of the risk T-allele (n = 30) and by 21.6 (95 % CI −32.1 to −11.2) % in carriers (n = 37), who showed a highly significant difference between treatments (P = 0.007). Carriers of the FADS1 rs174546 risk allele could benefit from a high intake of EPA and DHA in normalising plasma TG.

Electronic supplementary material

The online version of this article (doi:10.1007/s12263-014-0412-8) contains supplementary material, which is available to authorized users.     

Genetic predisposition to obesity and risk of subclinical atherosclerosis

Obesity has been associated with increased common carotid artery (CCA) intima–media thickness (IMT), a measure of subclinical atherosclerosis. We assessed the association between genetic predisposition to obesity and CCA IMT. The study included 428 young Chinese adults with CCA IMT measured using a high-resolution B-mode tomographic ultrasound system. We created a genetic risk score (GRS) by summing the risk alleles of 6 obesity-associated genetic variants confirmed in our previous analyses. The GRS was significantly associated with greater CCA IMT (p < 0.001) after adjustment for age and gender. Per 2 alleles of the GRS was related to 0.023 mm increment in IMT. The association was attenuated by one half with additional adjustment for obesity status, but remained significant (p = 0.009). In addition, we found that blood pressure significantly modified the association between the GRS and CCA IMT (p for interaction = 0.001). The associations between the GRS and CCA IMT were stronger in participants with systolic blood pressure (SBP) ≥ 120 mm Hg and/or diastolic blood pressure (DBP) ≥ 80 mm Hg (per 2 allele increment of the GRS relating to 0.028 mm greater CCA IMT, p for trend < 0.001) than those with SBP < 120 mm Hg and DBP < 80 mm Hg (per 2 allele increment of the GRS relating to 0.001 smaller CCA IMT, p for trend = 0.930). Our data provides suggestive evidence supporting the potential causal relation between obesity and development of subclinical atherosclerosis. Elevated blood pressure might amplify the adverse effect of obesity on cardiovascular risk.     

Pathway analysis of genome-wide association study on serum prostate-specific antigen levels

The wide application of prostate-specific antigen (PSA) has contributed to the early diagnosis and improved management of prostate cancer (PCa). Accumulating evidence has suggested the involvement of genetic components in regulating serum PSA levels, and several single nucleotide polymorphisms (SNPs) have been identified by genome-wide association studies (GWASs). However, the GWASs' results have the limited power to identify the causal variants and pathways. After the quality control filters, a total of 330,540 genotyped SNPs from one GWAS with 657 PCa-free Caucasian males were included for the identify candidate causal SNPs and pathways (ICSNPathway) analysis. In addition, the genotype–phenotype association analysis has been conducted with the data from HapMap database. Overall, a total of four SNPs in three genes and six pathways were identified by ICSNPathway analysis, which in total provided three hypothetical mechanisms. First, CYP26B1 rs2241057 polymorphism (nonsynonymous coding) which leads to a Leu-to-Ser amino acid shift at position 264, was implicated in the pathways including meiosis, proximal/distal pattern formation, and M phase of meiotic cell cycle. Second, CLIC5 rs3734207 and rs11752816 polymorphisms (regulatory region) to the 2 iron, 2 sulfur cluster binding pathway through regulating expression levels of CLIC5 mRNA. Third, rs4819522 polymorphism (nonsynonymous coding) leads to a Thr-to-Met transition at position 350 of TBX1 and involves in the pathways about gland and endocrine system development. In summary, our results demonstrated four candidate SNPs in three genes (CYP26B1 rs2241057, CISD1 rs2251039, rs2590370, and TBX1 rs4819522 polymorphisms), which were involved in six potential pathways to influence serum PSA levels.     

An obesity genetic risk score is associated with metabolic syndrome in Chinese children

Recent genome-wide association studies have identified several single nucleotide polymorphisms (SNPs) associated with body mass index (BMI)/obesity. In this study, we aim to examine the associations of obesity related loci with risk of metabolic syndrome (MetS) in a children population from China. A total of 431 children with MetS and 3046 controls were identified based on the modified ATPIII definition. 11 SNPs (FTO rs9939609, MC4R rs17782313, GNPDA2 rs10938397, BDNF rs6265, FAIM2 rs7138803, NPC1 rs1805081, SEC16B rs10913469, SH2B1 rs4788102, PCSK1rs6235, KCTD15 rs29941, BAT2 rs2844479) were genotyped by TaqMan 7900. Of 11 SNPs, GNPDA2 rs10938397, BDNF rs6265, and FAIM2 rs7138803 were nominally associated with risk of MetS (GNPDA2 rs10938397: odds ratio (OR) = 1.21, 95% confidence interval (CI) = 1.04–1.40, P = 0.016; BDNF rs6265: OR = 1.19, 95% CI = 1.03–1.39, P = 0.021; FAIM2 rs7138803: OR = 1.20, 95% CI = 1.02–1.40, P = 0.025); genetic risk score (GRS) was significantly associated with risk of MetS (OR = 1.09, 95% CI = 1.04–1.15, P = 5.26 × 10^− 4). After further adjustment for BMI, none of SNPs were associated with risk of MetS (all P > 0.05); the association between GRS and risk of MetS remained nominally (OR = 1.02, 95%CI = 0.96–1.08, P = 0.557). However, after correction for multiple testing, only GRS was statistically associated with risk of MetS in the model without adjustment for BMI. The present study demonstrated that there were nominal associations of GNPDA2 rs10938397, BDNF rs6265, and FAIM2 rs7138803 with risk of MetS. The SNPs in combination have a significant effect on risk of MetS among Chinese children. These associations above were mediated by adiposity.     

Hereditary hearing loss: a 96 gene targeted sequencing protocol reveals novel alleles in a series of Italian and Qatari patients

Deafness is a really common disorder in humans. It can begin at any age with any degree of severity. Hereditary hearing loss is characterized by a vast genetic heterogeneity with more than 140 loci described in humans but only 65 genes so far identified. Families affected by hearing impairment would have real advantages from an early molecular diagnosis that is of primary relevance in genetic counseling. In this perspective, here we report a family-based approach employing Ion Torrent DNA sequencing technology to analyze coding and UTR regions of 96 genes related to hearing function and loss in a first series of 12 families coming from Italy and Qatar. Using this approach we were able to find the causative gene in 4 out of these 12 families (33%). In particular 5 novel alleles were identified in the following genes LOXHD1, TMPRSS3, TECTA and MYO15A already associated with hearing impairment. Our study confirms the usefulness of a targeted sequencing approach despite larger numbers are required for further validation and for defining a molecular epidemiology picture of hearing loss in these two countries.     

E-PASS评分系统用于评估老龄患者消化道手术后并发症和转归的临床价值研究

目的:评价日常活动和手术应激评估(Estimation of physiologic ability and surgical stress,E-PASS)系统用于评估老龄患者消化道手术后并发症和转归的临床价值。方法:回顾性分析2011年7月至2013年7月西京医院消化外科所有65岁以上的患者的临床资料,计算其中行消化道手术者的E-PASS评分,并记录这些患者术后并发症的发生情况和患者术后的住院时间。分析E-PASS评分和几项该评分未涉及的因素与老龄患者消化道手术后并发症的发病率、死亡率、住院时间的相关性。结果:研究共纳入1236例老龄行消化道手术的患者,其中521例发生术后并发症(42.15%),8例死亡(0.65%)。患者术前E-PASS评分系统中,三项评分均与术后住院时间相关,术前风险评分(Preoperative risk score,PRS)和综合风险评分(Comprehensive risk score,CRS)与术后并发症的发病率和死亡率显著相关(P均0.05)。E-PASS评分系统未包含的指标中,麻醉方法与术后并发症发生和住院时间无关,术后入ICU、术中使用血管活性药物和急诊手术与术后发病率、死亡率和住院时间相关(P均0.05)。结论:E-PASS评分系统可用于预测老龄患者行消化道手术后并发症的发生情况和转归,纳入术后入ICU、术中使用血管活性药物和急诊手术三项指标可能进一步提高E-PASS评分系统的预测准确性。     

载脂蛋白亚型与糖尿病合并冠心病的相关性研究

目的:探讨载脂蛋白亚型与糖尿病合并冠脉病变严重程度相关性,为预防及治疗糖尿病伴发的动脉粥样硬化性疾病提供新的依据。方法:选取440名心内科患者,根据冠脉造影有无冠脉狭窄及是否合并糖尿病分为四组:冠脉内膜光滑组94人(A组);单纯冠脉狭窄组108人(B组);糖尿病合并冠脉狭窄组共184人(C组);糖尿病冠脉无狭窄组44人(D组),记录患者空腹血糖、餐后血糖、传统血脂脂谱、载脂蛋白A(apoA)、载脂蛋白B(apoB)及两者的比值(apoB/apoA);采用Gensini评分比较传统血脂、apoA、apoB及与Gensini积分值的相关性。结果:与正常对照组比较,糖尿病冠脉无狭窄组apoB、apoB/apoA、LDL和TG升高,apoA和HDL降低,B组和C组apoA与Gensini积分值存在负相关(P=0.01570.05);apoB;apoB/apoA与Gensini积分值存在正相关(P0.0001);两组中,apoB与Gensini积分值相关系数最大(r=0.85795,0.85941),且apoB与Gensini积分值的相关性都强于LDL与积分值的相关性。结论:在糖尿病患者预测心血管风险上,apoB,apoA,apoB/apoA的测定可能优于传统的血脂指标。     

Spatial heterogeneity in the Mediterranean Biodiversity Hotspot affects barcoding accuracy of its freshwater fishes

Incomplete knowledge of biodiversity remains a stumbling block for conservation planning and even occurs within globally important Biodiversity Hotspots (BH). Although technical advances have boosted the power of molecular biodiversity assessments, the link between DNA sequences and species and the analytics to discriminate entities remain crucial. Here, we present an analysis of the first DNA barcode library for the freshwater fish fauna of the Mediterranean BH (526 spp.), with virtually complete species coverage (498 spp., 98% extant species). In order to build an identification system supporting conservation, we compared species determination by taxonomists to multiple clustering analyses of DNA barcodes for 3165 specimens. The congruence of barcode clusters with morphological determination was strongly dependent on the method of cluster delineation, but was highest with the general mixed Yule‐coalescent (GMYC) model‐based approach (83% of all species recovered as GMYC entity). Overall, genetic morphological discontinuities suggest the existence of up to 64 previously unrecognized candidate species. We found reduced identification accuracy when using the entire DNA‐barcode database, compared with analyses on databases for individual river catchments. This scale effect has important implications for barcoding assessments and suggests that fairly simple identification pipelines provide sufficient resolution in local applications. We calculated Evolutionarily Distinct and Globally Endangered scores in order to identify candidate species for conservation priority and argue that the evolutionary content of barcode data can be used to detect priority species for future IUCN assessments. We show that large‐scale barcoding inventories of complex biotas are feasible and contribute directly to the evaluation of conservation priorities.