Powerful Identification of Cis-regulatory SNPs in Human Primary Monocytes Using Allele-Specific Gene Expression

A large number of genome-wide association studies have been performed during the past five years to identify associations between SNPs and human complex diseases and traits. The assignment of a functional role for the identified disease-associated SNP is not straight-forward. Genome-wide expression quantitative trait locus (eQTL) analysis is frequently used as the initial step to define a function while allele-specific gene expression (ASE) analysis has not yet gained a wide-spread use in disease mapping studies. We compared the power to identify cis-acting regulatory SNPs (cis-rSNPs) by genome-wide allele-specific gene expression (ASE) analysis with that of traditional expression quantitative trait locus (eQTL) mapping. Our study included 395 healthy blood donors for whom global gene expression profiles in circulating monocytes were determined by Illumina BeadArrays. ASE was assessed in a subset of these monocytes from 188 donors by quantitative genotyping of mRNA using a genome-wide panel of SNP markers. The performance of the two methods for detecting cis-rSNPs was evaluated by comparing associations between SNP genotypes and gene expression levels in sample sets of varying size. We found that up to 8-fold more samples are required for eQTL mapping to reach the same statistical power as that obtained by ASE analysis for the same rSNPs. The performance of ASE is insensitive to SNPs with low minor allele frequencies and detects a larger number of significantly associated rSNPs using the same sample size as eQTL mapping. An unequivocal conclusion from our comparison is that ASE analysis is more sensitive for detecting cis-rSNPs than standard eQTL mapping. Our study shows the potential of ASE mapping in tissue samples and primary cells which are difficult to obtain in large numbers.     

Random X Inactivation and Extensive Mosaicism in Human Placenta Revealed by Analysis of Allele-Specific Gene Expression along the X Chromosome

Imprinted inactivation of the paternal X chromosome in marsupials is the primordial mechanism of dosage compensation for X-linked genes between females and males in Therians. In Eutherian mammals, X chromosome inactivation (XCI) evolved into a random process in cells from the embryo proper, where either the maternal or paternal X can be inactivated. However, species like mouse and bovine maintained imprinted XCI exclusively in extraembryonic tissues. The existence of imprinted XCI in humans remains controversial, with studies based on the analyses of only one or two X-linked genes in different extraembryonic tissues. Here we readdress this issue in human term placenta by performing a robust analysis of allele-specific expression of 22 X-linked genes, including XIST, using 27 SNPs in transcribed regions. We show that XCI is random in human placenta, and that this organ is arranged in relatively large patches of cells with either maternal or paternal inactive X. In addition, this analysis indicated heterogeneous maintenance of gene silencing along the inactive X, which combined with the extensive mosaicism found in placenta, can explain the lack of agreement among previous studies. Our results illustrate the differences of XCI mechanism between humans and mice, and highlight the importance of addressing the issue of imprinted XCI in other species in order to understand the evolution of dosage compensation in placental mammals.     

Analysis of Allele-Specific Expression in Mouse Liver by RNA-Seq: A Comparison With Cis-eQTL Identified Using Genetic Linkage

We report an analysis of allele-specific expression (ASE) and parent-of-origin expression in adult mouse liver using next generation sequencing (RNA-Seq) of reciprocal crosses of heterozygous F₁ mice from the parental strains C57BL/6J and DBA/2J. We found a 60% overlap between genes exhibiting ASE and putative cis-acting expression quantitative trait loci (cis-eQTL) identified in an intercross between the same strains. We discuss the various biological and technical factors that contribute to the differences. We also identify genes exhibiting parental imprinting and complex expression patterns. Our study demonstrates the importance of biological replicates to limit the number of false positives with RNA-Seq data.     

Reduced Kv1.3 Potassium Channel Expression in Human Prostate Cancer

The presence of Kv1.3 voltage-gated potassium channels in rat and human prostate epithelial cells has been previously reported. We examined, by immunohistochemistry, Kv1.3 levels in 10 normal human prostate, 18 benign prostatic hyperplasia (BPH) and 147 primary human prostate cancer (Pca) specimens. We found high epithelial expression of Kv1.3 in all normal prostate, 16 BPH and 77 (52%) Pca specimens. Compared to normal, Kv1.3 levels were reduced in 1 (6%) BPH specimen and in 70 (48%) Pca specimens. We found a significant inverse correlation between Kv1.3 levels and tumor grade (r = −0.25, P = 0.003) as well as tumor stage (r = −0.27, P = 0.001). Study of an additional 30 primary Pca specimens showed that 15 (50%) had reduced Kv1.3 immunostaining compared to matched normal prostate tissue. Our data suggest that in Pca reduced Kv1.3 expression occurs frequently and may be associated with a poor outcome.     

Evaluating the Clinical Impact of a Genomic Classifier in Prostate Cancer Using Individualized Decision Analysis

Background

Currently there is controversy surrounding the optimal way to treat patients with prostate cancer in the post-prostatectomy setting. Adjuvant therapies carry possible benefits of improved curative results, but there is uncertainty in which patients should receive adjuvant therapy. There are concerns about giving toxicity to a whole population for the benefit of only a subset. We hypothesized that making post-prostatectomy treatment decisions using genomics-based risk prediction estimates would improve cancer and quality of life outcomes.

Methods

We developed a state-transition model to simulate outcomes over a 10 year horizon for a cohort of post-prostatectomy patients. Outcomes included cancer progression rates at 5 and 10 years, overall survival, and quality-adjusted survival with reductions for treatment, side effects, and cancer stage. We compared outcomes using population-level versus individual-level risk of cancer progression, and for genomics-based care versus usual care treatment recommendations.

Results

Cancer progression outcomes, expected life-years (LYs), and expected quality-adjusted life-years (QALYs) were significantly different when individual genomics-based cancer progression risk estimates were used in place of population-level risk estimates. Use of the genomic classifier to guide treatment decisions provided small, but statistically significant, improvements in model outcomes. We observed an additional 0.03 LYs and 0.07 QALYs, a 12% relative increase in the 5-year recurrence-free survival probability, and a 4% relative reduction in the 5-year probability of metastatic disease or death.

Conclusions

The use of genomics-based risk prediction to guide treatment decisions may improve outcomes for prostate cancer patients. This study offers a framework for individualized decision analysis, and can be extended to incorporate a wide range of personal attributes to enable delivery of patient-centered tools for informed decision-making.     

Annexin Ⅰ蛋白在人前列腺癌中的表达及临床意义

目的:探讨Annexin Ⅰ蛋白在前列腺癌组织中的表达及其与前列腺癌发生、发展、转移及预后的关系.方法:回顾性分析110例前列腺癌及40例前列腺增生组织中Annexin Ⅰ蛋白的表达与前列腺癌Gleason分级、年龄、临床分期、转移及预后的相关性.结果:前列腺癌患者的Armexin Ⅰ表达水平显著地低于良性前列腺增生症患者(P＜0.05);Annexin Ⅰ在低分化癌中表达较高,与高、中分化癌相比有显著性差异(P＜0.05);而高、中分化癌之间Annexin Ⅰ表达均较低,两者之间无显著性差异(P＞0.05).前列腺癌Annexin Ⅰ蛋白表达与年龄无关,而与临床分期、淋巴结转移及预后有关(P＜0.05).结论:Annexin Ⅰ蛋白表达下调与前列腺癌发生发展和预后密切相关,可作为反映前列腺癌生物学行为和判断预后的生物标记物.     

骨形态发生蛋白7 在前列腺癌中的表达

目的:探讨骨形态发生蛋白( BMP-7)在前列腺癌组织中的表达及其与临床分期之间的关系.方法:应用免疫印迹法检测30例前列腺癌患者及30例前列腺良性增生患者前列腺组织中BMP-7的表达情况.结果:前列腺癌组织中BMP-7的表达显著高于前列腺良性增生组织,且BMP-7的表达随前列腺癌的临床分期、Gleason分级增高而增加.结论:BMP-7在前列腺癌中的表达明显增高,其表达量与临床分期相关,前列腺癌组织中BMP-7的表达增高提示预后不佳.     

人PSP94的分泌表达及其表达产物抗前列腺癌作用

将编码人 94个氨基酸的前列腺分泌蛋白 ( PSP94) c DNA与酵母整合载体 p PICZαA重组 ,构建的重组质粒线性化后转染酵母细胞 GS1 1 5,获得了 PSP94在酵母细胞中遗传性稳定表达酵母工程细胞 .诱导后的培养物中 ,rh PSP94表达量约为 0 .9mg/L,分子量约 1 6.5k D.培养上清经离子交换层析纯化后 ,目的蛋白的纯度为 92 % .体外在人前列腺癌细胞上活性分析表明 ,rh PSP94以1 0 0μg/L ,对该细胞的抑制率 2 0 .4% ;单纯新型 TNF,以 1 0 3 U/ml,抑制率 2 9.8% ;rh PSP94和新型 TNF以上述同样剂量联合应用 ,抑制率为 86.3% .提示 PSP94在体外对抗前列腺癌细胞有杀伤作用 ,但不明显 ;PSP94与新型 TNF联合应用 ,可使抑制率明显提高 ,可能 PSP94与新型 TNF有协同抗前列腺癌的作用 .     

利用GAP启动子在毕赤酵母中组成型表达人鹅型溶菌酶2

利用甘油醛三磷酸脱氢酶(glyceraldehydes-3-phosphatedehydrogenase,GAP)启动子在毕赤酵母中表达人鹅型溶菌酶2(human goose-type lysozyme 2,h LysG2),并在小试规模建立一套有效的重组hLysG2(recombinant h LysG2,rh LysG2)生产工艺流程。根据毕赤酵母密码子偏爱性设计并人工合成hLysG2基因,将其连接至pGAPZαA质粒中,构建重组表达质粒pGAPZαA-h LysG2。将重组表达载体线性化后电转化毕赤酵母GS115感受态细胞,通过Zeocin抗性筛选获取高拷贝重组菌株,并在5L生物反应器中进行发酵培养。发酵60h后发酵液上清酶活性达到最高,发酵液上清经SDS-PAGE及Western blot检测证实rh LysG2得到表达。与诱导型表达相比,组成型表达发酵时间缩短了48h,上清中rhLysG2总活性提高了23.8%;使用甲壳素亲和层析和分子筛层析对rhLysG2进行纯化后,每升发酵液上清可纯化到187.4mg重组蛋白,纯化产物纯度达99.0%以上;浊度测定法分析显示,在p H 5.6、30℃和0.1mol/L Na+的条件下,rhLysG2可达到最大酶活性13 500U/mg。利用GAP启动子在毕赤酵母中成功表达了高纯度和高活性的rh LysG2,避免了甲醇的使用,缩短了发酵时间,提高了蛋白产量,为将rhLysG2开发为新型抗耐药菌药物奠定了基础。     

miR-221 通过作用DVL2 影响前列腺癌细胞系的侵袭功能*

目的:评价miR-221在前列腺癌细胞系中表达的变化对其神经内分泌样转化及其侵袭功能的影响。方法:以Northern blot检测LNCaP,LNCaP-AI两种前列腺癌细胞系中7种microRNA的表达变化;细胞转染法检测在雄激素剥夺环境中LNCaP和LNCaP-AI细胞系中miR-221的作用;CCK-8法检测细胞在不同阶段的生长增殖水平;Transwell法检测转染细胞的侵袭能力;qRT-PCR和Western blot检测转染的细胞中神经元特异性烯醇化酶(NSE)及dishevelled-2(DVL2)表达的变化。结果:与雄激素依赖性前列腺癌(ADPC)的细胞系LNCaP相比,miR-221在雄激素非依赖性前列腺癌(AIPC)的细胞系LNCaP-AI中明显高表达。通过转染使miR-221在LNCaP细胞系中高表达可促进细胞的NSE表达,加速其神经内分泌样分化。而在LNCaP-AI细胞系中下调miR-221水平则会升高靶基因DVL2的表达水平,并增强LNCaP-AI细胞的迁移和侵袭能力。结论:该实验证实在AIPC和ADPC细胞系中miR-221存在表达差异。miR-221可促进前列腺癌细胞的神经内分泌样转化,这可能是导致前列腺癌雄激素非依赖转化的重要原因。MiR-221可通过作用DVL2调节晚期前列腺癌细胞的转移和侵袭。