基因差异表达分析技术进展

比较了目前几种主要的基因差异表达分析技术并简要地归纳了各种基因差异表达分析方法的特点,重点介绍了经典的基因差异表达分析技术———差异显示技术及其改进与完善,最后根据差异显示技术在高等植物方面已取得的成就乐观地展现了该技术在园艺植物研究上的应用前景.     

Clinically Evident,Non-terminal Infections with Herpesviruses and the Wart Virus in Immunosuppressed Renal Allograft Recipients

The clinical incidence of herpes simplex lesions, herpes zoster, cytomegalovirus infection, and warts has been determined in a group of renal allograft recipients. Herpes simplex lesions appeared to be no more common after transplantation than before in those patients subject to recurrent attacks. Among 74 patients there were seven cases of herpes zoster and seven serologically proved cases of cytomegalovirus infection with clinical manifestations. The incidence of warts increased with length of time after transplantation, 42% of patients being affected more than one year after transplantation. All of the viral infections studied behaved as in healthy adults, and serious illness, dissemination, wide-spread lesions, and complications were not seen. No factors other than immunosuppression and steroid therapy could be identified with certainty as predisposing to these infections.     

Identification of Differentially Expressed Transcripts and Pathways in Blood One Week and Six Months Following Implant of Left Ventricular Assist Devices

Introduction

Continuous-flow left ventricular assist devices (LVADs) are an established therapy for patients with end-stage heart failure. The short- and long-term impact of these devices on peripheral blood gene expression has not been characterized, and may provide insight into the molecular pathways mediated in response to left ventricular remodeling and an improvement in overall systemic circulation. We performed RNA sequencing to identify genes and pathways influenced by these devices.

Methods

RNA was extracted from blood of 9 heart failure patients (8 male) prior to LVAD implantation, and at 7 and 180 days postoperatively. Libraries were sequenced on an Illumina HiSeq2000 and sequences mapped to the human Ensembl GRCh37.67 genome assembly.

Results

A specific set of genes involved in regulating cellular immune response, antigen presentation, and T cell activation and survival were down-regulated 7 days after LVAD placement. 6 months following LVAD placement, the expression levels of these genes were significantly increased; yet importantly, remained significantly lower than age and sex-matched samples from healthy controls.

Conclusions

In summary, this genomic analysis identified a significant decrease in the expression of genes that promote a healthy immune response in patients with heart failure that was partially restored 6 months following LVAD implant.     

Identification of Differentially Expressed Genes Associated with Osteochondrosis in Standardbred Horses Using RNA Arbitrarily Primed PCR

The aim of this study was to investigate genes for differential expression in cartilage of foals predisposed to osteochondrosis (OC). Tissue was sampled from the cranial part of the distal intermediate ridge of the tibia in the tarso-crural joint. Foals were considered predisposed to OC when parents had OC at the distal intermediate ridge of the tibia. RNA was isolated and subjected to arbitrarily primed PCR (RAP-PCR) followed by fingerprinting to screen for differentially expressed genes. By verification of results from the RAP-PCR fingerprint screening using real-time RT-PCR, we identified two genes not previously correlated with OC as differentially expressed. The two genes, which were identical to TLK2 and an equine EST, are good targets for future research on OC.     

鼻咽癌差异表达基因PROL4特性分析

在正常成人鼻咽与鼻咽癌活检组织之间进行抑制性消减杂交和微阵列(microarray)杂交,获得了鼻咽癌差异表达基因PROL4的全长cDNA序列,其GenBank登录号为：AF530472.该基因包含567个核苷酸,其编码产物是由134个氨基酸组成的富含脯氨酸蛋白.采用RT-PCR证实了PROL4基因在鼻咽癌细胞株HNE1和鼻咽癌活检组织中表达下调或缺失（42/48）.12种组织RNA印迹显示：PROL4基因在人骨骼肌、胸腺和肺组织中表达,其转录本大小约为0.6 kb,与所克隆的PROL4基因的cDNA大小一致.进而通过肿瘤表达谱阵列（cancer profiling array）杂交检测了其在乳腺癌、子宫癌、结肠癌、胃癌、卵巢癌、肺癌、肾癌、直肠癌、甲状腺癌、子宫颈癌、前列腺癌、胰腺癌、小肠癌组织及其配对的正常组织的表达状况.     

Estimation of the Proportion of Differentially Expressed Genes Using Hellinger Distance

We consider the problem of estimating the proportion of differentially expressed genes from the distribution of P-values arising from statistical tests in a microarray experiment. A two-component mixture model is studied in which one component is uniform on [0,1] and corresponds to equally expressed genes and the other component corresponds to differentially expressed genes. Two different parametric families are explicitly investigated for modeling the nonuniform component—the Beta family and a mixture of uniform densities whose supports form a partition of [0,1]. The Minimum Hellinger discrepancy is used to estimate the mixture proportions which are then used to estimate the proportion of differentially expressed genes in the microarray study. The performance of the proposed methods are investigated using simulation studies in which they are also compared with selected other published procedures. The methods are illustrated through a case study involving data from a published microarray experiment.     

Increase of Th17 Cell Phenotype in Kidney Transplant Recipients with Chronic Allograft Dysfunction

This study was performed to determine the association of Th17 cell phenotype with chronic allograft dysfunction in kidney transplant recipients (KTRs). We compared the expression of Th17 cell phenotype in KTRs with chronic allograft dysfunction group (CAD, n = 52) with four control groups (long-term stable KTRs (LTS, n = 67), early stable KTRs (ES, n = 28), end stage renal disease (ESRD, n = 45), and healthy control (HC, n = 26). We also performed in vitro study using human proximal renal tubular epithelial cell line (HPRTEpiC) to evaluate the effect of IL-17 on human renal tubular epithelial cells. The CAD group showed increased percentage of Th17 cells out of CD4⁺ T cells and also increased proportion of IL-17 producing cells out of effector memory T cells or out of CCR4⁺CCR6⁺/CD4⁺ T cells compared to the LTS group and other control groups. Also, the serum level of IL-17, IL-33, and RAGE, and the expression of IL-1beta, RAGE, and HMGB1 mRNA showed an increase in the CAD group compared to the LTS group. In vitro study revealed that IL-17 increased production of IL-6 and IL-8 and up-regulated profibrotic gene expression such as ACTA-2 and CTGF in HPRTEpiC in a dose-dependent manner, which suggests that IL-17 has a role in the development of renal tubular cell injury. The results of our study may suggest that increase of Th17 cell phenotype could be a marker for the chronic allograft injury; hence there is a need to develop diagnostic and therapeutic tools targeting the Th17 cells pathway.     

用基因表达谱芯片研究人正常肝和肝细胞癌中差异表达的基因

以基因表达谱芯片对人正常肝及肝癌组织基因表达的差异性进行了研究比较。奖４０９６条人ｃＤＮＡ用点样仪点在特制玻片上制备成表达谱芯片;利用肝和肝癌组织的ｍＲＮＡ通过逆转录方法,将Ｃｙ３和Ｃｙ５２种荧光分别标记到两种组织的ｃＤＮＡ上,制备成ｃＤＮＡ探针,并与表达谱芯片进行杂交及扫描,重复４次实验,通过计算机数据处理判定基因是否在上述２种组织中有表达差异,筛选出差异表达的基因共９０３条。基因芯片技术可同时     

利用单酶切cDNA—AFLP技术分离玉米对生性状相关基因差异表达片段

为了深入地研究对生玉米这一珍贵的高产育种种质资源和植物形态发育突变材料形成的分子机理和调控机制,通过构建合适的玉米对生、互生近等基因系总RNA池,首次采用改进的单酶切cDNA-AFLP技术,对扩增的玉米对生性状相关基因的差异表达片段进行筛选、分离和生物信息学分析.结果共获得29条差异表达片段:对生玉米增强表达23条、抑制表达6条.选取其中5条(STT-TT、STT-TC、STT-CC、STT-GC、SCT-TG)增强表达片段进行克隆和测序,序列同源性分析表明:STT-GC与烟草细胞色素b5基因有80%的同源性、SCT-TC与玉米、牛筋草、大麦、狗尾草、水稻等的α-微管蛋白基因有90%以上的同源性.实验证明:单酶切cDNA-AFLP技术是一种研究玉米基因差异表达的实用方法.