Comparison of ethanol versus formalin fixation on preservation of histology and RNA in laser capture microdissected brain tissues

Although RNA can be retrieved from formalin-fixed, paraffin-embedded (FFPE) tissues, the yield is low, and the RNA is fragmented. Recent advances in gene expression profiling underscore the importance of identifying a fixative that preserves histology and mRNA. We demonstrated that, for immersion fixation of brains, 70% ethanol is superior to formalin for mRNA preservation. RNA yield from ethanol-fixed tissues was 70% of the yield from fresh frozen specimens, but only a negligible quantity was recovered from formalin-fixed tissues. RNA from ethanol-fixed brains showed integrity comparable to RNA from fresh frozen tissues, and RT-PCR using RNA from ethanol-fixed tissues was consistently successful. RNA from FFPE tissues composed of low-molecular weight fragments, and their use in RT-PCR failed repeatedly. The yield and quality of RNA from ethanol-fixed brains were unaffected after immersion at 4 degrees C for 2 weeks. In a blinded comparison to FFPE tissues, ethanol-fixed specimens were judged to show comparable histology and superior immunostaining. After laser capture microdissection (LCM), we failed to recover mRNA from FFPE tissues but retrieved mRNA from ethanol-fixed tissues for RT-PCR and cDNA microarray analysis. We conclude that 70% ethanol preserves RNA integrity and is suitable for expression profiling of brain tissues by LCM and cDNA microarray.     

Quantitative PCR based expression analysis on a nanoliter scale using polymer nano-well chips

The analysis of gene expression is an essential element of functional genomics. Expression analysis is mainly based on DNA microarrays due to highly parallel readout and high throughput. Quantitative PCR (qPCR) based expression profiling is the gold standard for the precise monitoring of selected genes, and therefore used for validation of microarray data. Doing qPCR-based expression analysis in an array-like format can combine the higher sensitivity and accuracy of the qPCR methodology with a high data density at relatively low costs. This paper describes the development of an open-well based miniaturized platform for liquid PCR-based assays on the nanoliter scale using cost-effective polypropylene micro reactors (microPCR Chip). We show the quantification ability and reliability of qPCR in 200 nl with the microPCR chip down to 5 starting target molecules using TaqMan chemistry. An RNA expression analysis of four genes in mouse brain, liver and kidney tissues showed similar results in 200 nl as compared to standard 10 microl assays. The high sensitivity and quantification capability of the microPCR chip platform developed herein makes it a promising technology for performing high-throughput qPCR-based analysis in the nanoliter volume range.     

Quantitative nuclease protection assay in paraffin-embedded tissue replicates prognostic microarray gene expression in diffuse large-B-cell lymphoma

Gene expression profiling (GEP) has identified genes whose expression levels predict patient survival in diffuse large-B-cell lymphoma (DLBCL). Such discovery techniques generally require frozen samples unavailable for most patients. We developed a quantitative nuclease protection assay to measure expression levels of prognostic DLBCL genes using formalin-fixed, paraffin-embedded (FFPE) tissue. FFPE tissue was sectioned, permeabilized, denatured in the presence of specific probes, and hybridized to mRNA in situ. Nuclease subsequently destroyed non-hybridized probe. Alkaline hydrolysis freed mRNA-bound probes from tissue, which were transferred to ArrayPlates for probe capture and chemiluminescent quantification. We validated assay performance using frozen, fresh, and FFPE DLBCL samples, then used 39 archived DLBCL, previously microarray analyzed, to correlate GEP and ArrayPlate results. We compared old (>18 years) with new (<2 months) paraffin blocks made from previously frozen tissue from the original biopsy. ArrayPlate gene expression results were confirmed with immunohistochemistry for BCL2, BCL6, and HLA-DR, showing agreement between mRNA species and the proteins they encode. Assay performance was linear to approximately 1 mg sample/well. RNase and DNase treatments demonstrated assay specificity for RNA detection, both fixed and soluble RNA detection. Comparisons were excellent for lysate vs snap-frozen vs FFPE (R(2)>0.98 for all comparisons). Coefficients of variation for quadruplicates on FFPE were generally <20%. Correlation between new and old paraffin blocks from the same biopsy was good (R(2)=0.71). Comparison of ArrayPlate to Affymetrix and cDNA microarrays showed reasonable correlations. Insufficient power from small sample size prevented successfully correlating results with patient survival, although hazard ratios trended the expected directions. We developed an assay to quantify expression levels of survival prediction genes in DLBCL using FFPE, fresh, or frozen tissue. While this technique cannot replace GEP for discovery, it indicates that expression differences identified by GEP can be replicated on a platform applicable to archived FFPE samples.     

长期冻存和新鲜胃癌组织总RNA提取方法的比较

背景：目前两种最可靠、应用最广的高通量RNA分离技术是基于异硫氰酸胍-酚︰氯仿的RNA分离技术和基于硅胶柱的RNA分离技术。在临床应用非常有限的组织材料时,有必要对RNA分离技术的可重复性和可靠性分别进行先期评价。 目的：系统比较采用硅胶柱法和Trizol法从冻存、新鲜胃癌组织中分离总RNA的效果。 方法：硅胶柱法和Trizol法分别提取长期-80 ℃冻存的(2年以上)和新鲜胃癌组织总RNA,紫外分光光度法比较RNA纯度,琼脂糖凝胶电泳分析28 S和18 S吸光度比值,进一步通过实时反转录-聚合酶链反应对扩增距mRNA polyA尾端不同大小片段的Ct值进行比较,间接判断不同大小mRNA的拷贝数及完整性。 结果与结论：硅胶柱技术和Trizol方法在总RNA提取的纯度方面都表现很好。然而在RNA完整性方面,基于硅胶柱技术的提取方法要好于Trizol法,因为其核糖体RNA形式完好而且更好地保持了不仅短的及中等大小片段,对于较大的mRNA片段也保持更好。另外,与新鲜组织相比,长时间冻存对胃癌组织总RNA提取的影响很小。     

MicroRNA Expression Profiling Outperforms mRNA Expression Profiling in Formalin-fixed Paraffin-embedded Tissues

microRNAs (miRNAs) are ∼22nt RNAs that regulate target gene expression. Altered expression of miRNAs has been demonstrated in many different human cancers. Many studies using microarray technologies to characterize miRNA expression profiles have relied on fresh tissue to determine the miRNA signatures. In this study, we prepared total RNA from paired samples of formalin-fixed paraffin-embedded (FFPE) and fresh frozen malignant melanoma, and used that in microarray experiments to compare miRNA expression profiles between FFPE and fresh tissue with corresponding mRNA expression profiles from the same tissue sources. We demonstrate that miRNA expression profile from FFPE tissues closely resembles that from fresh tissues, and the correlation is significantly better than that for mRNA profiles from FFPE and fresh tissues. These results underscore the suitability of FFPE tissues as appropriate resources for molecular expression analyses and support the notion that miRNAs are more vigorous analytes for this purpose than mRNAs.     

29A microRNA expression profiling study of matching fresh frozen and formalin-fixed paraffin-embedded samples

The purpose of this study was to investigate the correlation between microRNA expression profiles from matching fresh frozen (FrFr) and formalin-fixed paraffin-embedded (FFPE) samples. We isolated RNA from eight different murine organs, each divided in half and prepared as either FrFr or FFPE samples. To evaluate the quality and reliability of the RNA isolations performed on the FFPE samples, we compared three different commercially available FFPE RNA preparation kits. The quality of the extracted RNA was analyzed on the Bioanalyzer from Agilent, and the microRNA expression profiling was carried out using the LNA-based miRCURY microarray platform.
Our studies show that despite a high degree of RNA degradation predominantly in the FFPE samples, we get an excellent correlation between the matching FrFr and FFPE samples. Thus, for two out of three extraction methods the correlation coefficient (R²) was above 0.95 in all eight murine organs.     

Efficacy of quantitative RT-PCR for detection of the nucleoprotein gene from different porcine rubulavirus strains

Blue-eye disease is an emergent viral swine infection caused by porcine rubulavirus (PoRV). We have developed a qRT-PCR method to detect and quantify expression of the nucleoprotein gene for different PoRV strains. The limit of detection for this assay was 10² copies of synthetic RNA. Viral RNA from PoRV was detectable at a TCID₅₀ of 0.01. Significant differences were observed between viral RNA quantification and virus titration results for nine PoRV strains. For nasal and oral swab samples that were collected from experimentally infected pigs, the qRT-PCR assay was more sensitive (87.1–83.9 %) for the detection of positive samples than methods involving isolation of virus. The implementation of highly sensitive assays that yield results quickly will be of great assistance in the eradication of PoRV from Mexico. We also believe that the newly developed qRT-PCR assay will help reduce the spread of this viral infection to other countries.     

人TRAF2新剪切体的鉴定与表达分析

目的:对TRAF2的新剪切体进行鉴定与表达分析.方法:以人脑库为模板,利用PCR扩增,电泳确定新剪切体的存在.再提取不同细胞与组织的总RNA,逆转录得到cD-NA后作为模板对两种不同剪切体的表达进行比较分析.结果:利用P1与P2引物对从人脑库扩增出1条约1 500 bp的条带,而利用P3与P4引物对则得到2条明显电泳带,通过测序表明其中1条包含TRAF2的第6外显子,另1条缺失了TRAF2的第6外显子.通过对新剪切体TRAF2Δ6与全长剪切体TRAF2的表达量比较表明在T47D中全长剪切体表达占优势;而在Hep3B、GC-1与MCF7中TRAT△6剪切体表达占优势;在HepG2、HBL100、A549与HeLa细胞中未发现两种剪切体的明显表达;在PANCI与SW480中两种剪切体表达量相近.在胎大脑与一级神经胶质瘤中TRAF2Δ6表达占优,而二级与三级神经胶质瘤中则全长剪切体TRAF2表达占优势.结论:人体TRAF2基因除可表达全长TRAF2 mRNA外,还可通过可变剪切表达缺失第6外显子的TRAF2Δ6 mRNA.而且这两种剪切体的表达存在细胞与组织特异性.     

沙眼衣原体3种二硫键异构酶基因表达研究

目的研究3种二硫键(dsb)异构酶基因dsbB、dsbD、dsbG在沙眼衣原体(Chlamydia trachornatis,Ct)发育周期内的表达水平,探讨它们同Ct不同发育形式包括原体(EB)及始体(RB)的关系。方法以25 cm~2细胞培养瓶培养小鼠成纤维细胞L_2,待L_2细胞长成致密单层后,用Ct血清型F/IC-Cal-13感染,感染后每4 h收获一次细胞,提取总RNA,用基因特异性引物反转录后,RT-PCR分别扩增dsb基因转录的cDNA,将产物在DNA凝胶成像系统内检测,半定量分析cDNA产量,从而分析Ct发育周期内3种dzb基因的表达水平。结果在感染后12 h开始检测到dsbG表达,16 h开始检测到dsbB、dsbD表达。所不同的是dsbG在感染后12 h开始,表达一直上升,持续维持在较高水平直到整个发育周期完成,EB释放。dsbB表达水平较低,于28 h达到高峰,随后下降;dsbD表达水平介于dsbB和dsbG之间,与dsbB相似,dsbD的表达于2,4～28 h达峰值,随后下降。结论在Ct的发育周期中,同一时间点dsbB、dsbD、dsbG的表达水平存在差异;就每一种dsb而言,不同时间点的表达水平也不同。总体上,Ct发育的早期阶段(由EB到RB),Dsb蛋白参与的程度不高,dsbG的转录在感染后12 h开始,并稳定上升,直到完成整个发育周期;而dsbB、dsbD则在感染后16 h开始表达并于20～28 h出现峰值,然后下降直到感染后40 h。以上3种Dsb蛋白,有可能在Ct的感染及发育过程中起作用。     

A TaqMan real-time RT-PCR for quantifying Mourilyan virus infection levels in penaeid shrimp tissues

A highly sensitive and specific TaqMan real-time quantitative RT-PCR (qRT-PCR) was developed to detect and quantify Mourilyan virus (MoV), a newly described bunya-like virus of penaeid shrimp. The PCR primers and TaqMan probe targeted a 67-nucleotide (nt) sequence in the MoV M RNA segment. Using dilution series of a 849 nt RNA transcribed in vitro from cDNA clone pMoV4.1, the assay could detect down to a single MoV RNA equivalent, reliably detected 10 RNA copies and had a log linear range up to 1 x 10(9) RNA copies. In experimentally infected Penaeus japonicus shrimp, the test was used to quantify increases in MoV loads over time in hemocytes, lymphoid organ and gills. Sequential increases in MoV RNA copy numbers occurred in lymphoid organ and gill tissues collected at 6, 24 and 48 h post-infection. However, RNA copy numbers decreased slightly in hemocytes sampled at 48 h compared to 24 h. The qRT-PCR data correlated well with amplicon yields generated using a conventional RT-nested PCR targeting the same MoV RNA segment. Moreover, histology and in situ hybridisation using shrimp cephalothorax sections identified increases in lymphoid organ spheroid numbers and confirmed that increases in MoV RNA detected in lymphoid organ tissue were due to expansion in the numbers of infected cells. The qRT-PCR assay should find use in high-throughput screening applications to detect MoV in broodstock and postlarvae used for culture or breeding purposes and for tracking changes in infection levels during shrimp grow-out.     

Analysis of biological and technical variability in gene expression assays from formalin-fixed paraffin-embedded classical Hodgkin lymphomas

Formalin-fixed paraffin-embedded (FFPE) tissues are invaluable sources of biological material for research and diagnostic purposes. In this study, we aimed to identify biological and technical variability in RT-qPCR TaqMan® assays performed with FFPE-RNA from lymph nodes of classical Hodgkin lymphoma samples. An ANOVA-nested 6-level design was employed to evaluate BCL2, CASP3, IRF4, LYZ and STAT1 gene expression. The most variable genes were CASP3 (low expression) and LYZ (high expression). Total variability decreased after normalization for all genes, except by LYZ. Genes with moderate and low expression were identified and suffered more the effects of the technical manipulation than high-expression genes. Pre-amplification was shown to introduce significant technical variability, which was partially alleviated by lowering to a half the amount of input RNA. Ct and Cy₀ quantification methods, based on cycle-threshold and the kinetic of amplification curves, respectively, were compared. Cy₀ method resulted in higher quantification values, leading to the decrease of total variability in CASP3 and LYZ genes. The mean individual noise was 0.45 (0.31 to 0.61 SD), indicating a variation of gene expression over ~ 1.5 folds from one case to another. We showed that total variability in RT-qPCR from FFPE-RNA is not higher than that reported for fresh complex tissues, and identified gene-, and expression level-sources of biological and technical variability, which can allow better strategies for designing RT-qPCR assays from highly degraded and inhibited samples.