Real-time RT-PCR normalisation; strategies and considerations

Expression profiling of intermingled long-range projection neurons harvested by laser capture microdissection

Gene expression data are most useful if they can be associated with specific cell types. This is particularly so in an organ such as the brain, where many different cell types lie in close proximity to each other. We used zebra finches (Taeniopygia guttata), fluorescent tracers and laser capture microdissection (LCM) to collect projection neurons and their RNAs from two interspersed populations from the same animal. RNA amplified from each cell class was reverse transcribed, fluorescently labeled, and hybridized to cDNA microarrays of genes expressed in the zebra finch brain. We applied strict fold-expression criteria, supplemented by statistical analysis, to single out genes that showed the most extreme and consistent differential expression between the two cell classes. Confirmation of the true expression pattern of these genes was made by in situ hybridization and Taqman quantitative PCR (qPCR). High quality RNA was obtained, too, from backfilled neurons birth-dated with bromodeoxyuridine (BrdU). We also quantified changes in the levels of three genes after singing behavior using qPCR. Thus, we have brought together a combination of techniques allowing for the molecular profiling of intermingled populations of projection neurons of known connectivity, age and experience, which should constitute a powerful tool for CNS research.

Myobacterium tuberculosis induces selective up-regulation of TLRs in the mononuclear leukocytes of patients with active pulmonary tuberculosis

Human and mouse studies indicate that TLRs are important in mycobacterial infections. We investigated TLR gene expression in fresh unstimulated blood and bronchoalveolar lavage from patients with pulmonary tuberculosis using a well-validated, real-time PCR. A human splice variant of TLR1, designated hsTLR1, was found in all donors tested. hsTLR1 mRNA lacks exon 2, which is a 77-bp region of the 5'-untranslated region, but contains the same coding sequence as TLR1. Compared with the matched controls, whole blood from patients had increased levels of mRNA encoding TLR2 (p = 0.0006), TLR1 (p = 0.004), hsTLR1 (p = 0.0003), TLR6 (p < 0.0001), and TLR4 (p = 0.0002). By contrast, expression of these TLRs was not increased in bronchoalveolar lavage. An increased level of hsTLR1 mRNA was found in both CD3- (p = 0.0078) and CD4+ cells (p = 0.028), resulting in an increased ratio of hsTLR1 mRNA to TLR1 and to TLR6 mRNA. An in vitro study in THP1 cells suggested that this relative increase in hsTLR1 might be attributable to a direct effect of mycobacterial components because it could be mimicked by mycobacterial preparations in the absence of IFN-gamma or T cells and by the TLR1/2 agonist Pam3CysK4. Half-life studies using blood from patients with pulmonary tuberculosis and THP1 cells exposed to Myobacterium tuberculosis in vitro showed p38 MAPK-independent stabilization of mRNAs encoding hsTLR1 and TLR1. We conclude that M. tuberculosis exerts direct effects on patterns of TLR expression, partly via changes in mRNA half-life. The significance of these changes in the pathogenesis of disease deserves further investigation.

Two hexamerin genes from the termite Reticulitermes flavipes: Sequence, expression, and proposed functions in caste regulation

Previous molecular studies on the termite Reticulitermes flavipes have revealed that two hexamerin proteins serve an important status quo role in the regulation of juvenile hormone (JH)-dependent caste differentiation. Here, we report sequence data and other experimental evidence suggesting how these two hexamerins function in achieving caste regulation. The two hexamerin genes, named Hex-1 and Hex-2, encode highly unique sequence features relative to the 100+ other known insect hexamerins. These features include a long hydrophobic tail and prenylation motif in Hex-1, and a long hydrophilic insertion plus several putative protease cleavage sites in Hex-2. Both hexamerin genes are primarily expressed in fat body tissue, but only Hex-2 expression is substantially induced by JH. SDS-PAGE showed that the hexamerin proteins constitute a major proportion of total soluble termite protein. Also, although each protein occurs in both the membrane and soluble protein fractions, Hex-2 has stronger membrane affinity. Anti-JH antiserum specifically recognizes hemolymph-soluble Hex-1 protein, supporting that the unique prenylation site in Hex-1 facilitates covalent JH binding to the primary amino acid chain. Finally, increased ratios of Hex-2 to Hex-1 transcription occur in caste phenotypes and developmental stages that differentiate in response to rising JH titers. Two main conclusions can be taken from these studies. First, elevated ratios of Hex-2 to Hex-1 expression are associated with caste phenotypes that differentiate in response to rising JH titers (i.e., workers, presoldiers and soldiers). Second, due to their unique structural features and other observed characteristics, our findings support the hypothesis that the two hexamerins participate in the regulation of caste-differentiation by modulating JH availability.

Real-time reverse transcription PCR and the detection of occult disease in colorectal cancer

Molecular diagnostics offers the promise of accurately matching patient with treatment, and a resultant significant effect on improved disease outcome. More specifically, the real-time reverse transcription polymerase chain reaction (qRT-PCR), with its combination of conceptual simplicity and technical utility, has the potential to become a valuable analytical tool for the detection of mRNA targets from tissue biopsies and body fluids. Its potential is particularly promising in cancer patients, both as a prognostic assay and for monitoring response to therapy. Colorectal cancer provides an instructive paradigm for this potential as well as the problems associated with its use as a clinical assay. Currently, histopathological staging, which provides a static description of the anatomical extent of tumour spread within a surgical specimen, defines patient prognosis. The detection of lymph node (LN) metastasis constitutes the most important prognostic factor in colorectal cancer and as the primary indicator of systemic disease spread, LN status determines the choice of postoperative adjuvant chemotherapy. However, its limitations are emphasised by the considerable prognostic heterogeneity of patients within a given tumour stage: not all patients with LN-negative cancers are cured and not all patients with LN-positive tumours die from their disease. This has resulted in a search for more accurate staging protocols and has seen the introduction of the concept of "molecular staging", the incorporation of molecular parameters into clinical tumour staging. Quantification of disease-associated mRNA is one such parameter that utilises the qRT-PCR assay's potential for generating quantitative results. These are not only more informative than qualitative data, but contribute to assay standardisation and quality management. This review provides an assessment of the practical value to the clinician of RT-PCR-based molecular diagnostics. It points out reasons for the many contradictory results encountered in the literature and concludes that there is an urgent need for standardisation at every level, starting with pre-assay sample acquisition and template preparation, assay protocols and post-assay analysis.

Comparison of P2X and TRPV1 receptors in ganglia or primary culture of trigeminal neurons and their modulation by NGF or serotonin

BACKGROUND

Cultured sensory neurons are a common experimental model to elucidate the molecular mechanisms of pain transduction typically involving activation of ATP-sensitive P2X or capsaicin-sensitive TRPV1 receptors. This applies also to trigeminal ganglion neurons that convey pain inputs from head tissues. Little is, however, known about the plasticity of these receptors on trigeminal neurons in culture, grown without adding the neurotrophin NGF which per se is a powerful algogen. The characteristics of such receptors after short-term culture were compared with those of ganglia. Furthermore, their modulation by chronically-applied serotonin or NGF was investigated.

RESULTS

Rat or mouse neurons in culture mainly belonged to small and medium diameter neurons as observed in sections of trigeminal ganglia. Real time RT-PCR, Western blot analysis and immunocytochemistry showed upregulation of P2X(3) and TRPV1 receptors after 1-4 days in culture (together with their more frequent co-localization), while P2X(2) ones were unchanged. TRPV1 immunoreactivity was, however, lower in mouse ganglia and cultures. Intracellular Ca(2+) imaging and whole-cell patch clamping showed functional P2X and TRPV1 receptors. Neurons exhibited a range of responses to the P2X agonist alpha, beta-methylene-adenosine-5'-triphosphate indicating the presence of homomeric P2X(3) receptors (selectively antagonized by A-317491) and heteromeric P2X(2/3) receptors. The latter were observed in 16 % mouse neurons only. Despite upregulation of receptors in culture, neurons retained the potential for further enhancement of P2X(3) receptors by 24 h NGF treatment. At this time point TRPV1 receptors had lost the facilitation observed after acute NGF application. Conversely, chronically-applied serotonin selectively upregulated TRPV1 receptors rather than P2X(3) receptors.

CONCLUSION

Comparing ganglia and cultures offered the advantage of understanding early adaptive changes of nociception-transducing receptors of trigeminal neurons. Culturing did not prevent differential receptor upregulation by algogenic substances like NGF or serotonin, indicating that chronic application led to distinct plastic changes in the molecular mechanisms mediating pain on trigeminal nociceptors.

Validation of two reference genes for mRNA level studies of murine disease models in neurobiology

Reverse transcription of extracted cellular RNA combined with real-time PCR is now an established method for sensitive detection and quantification of specific mRNA level changes in experimental models of neurological diseases. To neutralize the impact of experimental error and make quantification more precise, normalization of test gene data using data from a constantly expressed gene, a reference gene that is tested along with the test gene, is required. There is no single gene constantly expressed under all experimental conditions. For a given set of conditions or a given disease model, identification of an unaffected reference gene is necessary. In this report, we present our findings from evaluation and validation of the genes encoding hypoxanthine guanine phosphoribosyl transferase 1 (HPRT1) and glyceraldehyde phosphate dehydrogenase (GAPDH) as individual reference genes in mRNA level studies involving four murine neurological disease models. We find both genes are suitable as a reference gene with these four models, provided quantification of subtle changes are avoided. We furthermore demonstrate that above a certain threshold of test mRNA level changes and given high quality RNA processing, normalization to total RNA alone provides for equally reliable quantitative mRNA level results.

Social exploitation of hexamerin: RNAi reveals a major caste-regulatory factor in termites

Lower termites express a unique form of eusocial polyphenism in that totipotent workers can differentiate into either soldier or reproductive caste phenotypes. In this initial effort using RNA interference in termites, we found that two hexamerin genes, Hex-1 and Hex-2, participate in the regulation of caste polyphenism. Our methodology involved a dual gene-silencing approach that used a single short-interfering RNA fragment to silence the two homologous hexamerin genes. We performed validation studies that evaluated effects on nontarget housekeeping genes, silencing of a nonhousekeeping control gene, and effects at the protein level. We found that the two hexamerin proteins, which are inducible by the morphogenetic juvenile hormone and which constitute a significant proportion of total termite protein, suppress juvenile-hormone-dependent worker differentiation to the soldier caste phenotype. This mechanism allows termite colonies to retain high proportions of altruistic worker caste members, thus apparently enhancing colony-inclusive fitness. These findings demonstrate a unique status quo regulatory mechanism for termite worker caste retention and provide an example of previously undescribed preadult developmental/caste-regulatory genes from any social insect.

SMN mRNA and protein levels in peripheral blood: biomarkers for SMA clinical trials

BACKGROUND

Clinical trials of drugs that increase SMN protein levels in vitro are currently under way in patients with spinal muscular atrophy.

OBJECTIVE

To develop and validate measures of SMN mRNA and protein in peripheral blood and to establish baseline SMN levels in a cohort of controls, carriers, and patients of known genotype, which could be used to follow response to treatment.

METHODS

SMN1 and SMN2 gene copy numbers were determined in blood samples collected from 86 subjects. Quantitative reverse transcription PCR was used to measure blood levels of SMN mRNA with and without exon 7. A cell immunoassay was used to measure blood levels of SMN protein.

RESULTS

Blood levels of SMN mRNA and protein were measured with high reliability. There was little variation in SMN levels in individual subjects over a 5-week period. Levels of exon 7-containing SMN mRNA and SMN protein correlated with SMN1 and SMN2 gene copy number. With the exception of type I SMA, there was no correlation between SMN levels and disease severity.

CONCLUSION

SMN mRNA and protein levels can be reliably measured in the peripheral blood and used during clinical trials in spinal muscular atrophy, but these levels do not necessarily predict disease severity.

Comparison of in vitro and in vivo reference genes for internal standardization of real-time PCR data

Real-time PCR is a powerful technique for gene expression studies, which have become increasingly important in a large number of clinical and scientific fields. The significance of the obtained results strongly depends on the normalization of the data to compensate for differences between the samples. The most widely used approach is to use endogenous reference genes (housekeeping genes) as internal standards. This approach is controversially discussed in the literature because none of the reference genes is stably expressed throughout all biological samples. Therefore, candidate reference genes have to be validated for each experimental condition. In our studies, we introduced and evaluated an in vitro synthesized reference cRNA for internal standardization of relative messenger RNA (mRNA) expression patterns. This reference, consisting of the in vitro transcribed coding sequence of aequorin, a jellyfish protein, was incorporated in the extracted RNA. The experimental significance of this approach was representatively tested for the expression of the neurotrophin-3 mRNA in distinct regions of mouse brains. A comparison to three stably expressed reference genes [β-actin, glyceralde-hyde-3-phosphate dehydrogenase (GAPDH), and hypoxanthine phosphoribosyl-transferase 1 (HPRT1)] gave evidence that the spiking of template RNA with in vitro transcribed cRNA is a valuable tool for internal standardization of real-time PCR experiments.

Limitations of Commonly Used Internal Controls for Real-Time RT-PCR Analysis of Renal Epithelial-Mesenchymal Cell Transition

BACKGROUND/AIMS

Progressive renal fibrotic disease is accompanied by the massive accumulation of myofibroblasts as defined by alpha smooth muscle actin (alphaSMA) expression. We quantitated gene expression using real-time RT-PCR analysis during conversion of primary cultured human renal tubular cells (RTC) to myofibroblasts after treatment with transforming growth factor-beta1 (TGF-beta1). We report herein the limitations of commonly used reference genes for mRNA quantitation.

METHODS

We determined the expression of alphaSMA and megakaryoblastic leukemia-1 (MKL1), a transcriptional regulator of alphaSMA, by quantitative real-time PCR using three common internal controls, glyceraldehyde-3-phosphate dehydrogenase (GAPDH), cyclophilin A and 18S rRNA.

RESULTS

Expression of GAPDH mRNA and cyclophilin A mRNA, and to a lesser extent, 18S rRNA levels varied over time in culture and with exposure to TGF-beta1. Thus, depending on which reference gene was used, TGF-beta1 appeared to have different effects on expression of MKL1 and alphaSMA.

CONCLUSIONS

RTC converting to myofibroblasts in primary culture is a valuable system to study renal fibrosis in humans. However, variability in expression of reference genes with TGF-beta1 treatment illustrates the need to validate mRNA quantitation with multiple reference genes to provide accurate interpretation of fibrosis studies in the absence of a universal internal standard for mRNA expression.

Evaluation of potential reference genes in real-time RT-PCR studies of Atlantic salmon

Background

Salmonid fishes are among the most widely studied model fish species but reports on systematic evaluation of reference genes in qRT-PCR studies is lacking.

Results

The stability of six potential reference genes was examined in eight tissues of Atlantic salmon (Salmo salar), to determine the most suitable genes to be used in quantitative real-time RT-PCR analyses. The relative transcription levels of genes encoding 18S rRNA, S20 ribosomal protein, β-actin, glyceraldehyde-3P-dehydrogenase (GAPDH), and two paralog genes encoding elongation factor 1A (EF1A_A and EF1A_B) were quantified in gills, liver, head kidney, spleen, thymus, brain, muscle, and posterior intestine in six untreated adult fish, in addition to a group of individuals that went through smoltification. Based on calculations performed with the geNorm VBA applet, which determines the most stable genes from a set of tested genes in a given cDNA sample, the ranking of the examined genes in adult Atlantic salmon was EF1A_B>EF1A_A>β-actin>18S rRNA>S20>GAPDH. When the same calculations were done on a total of 24 individuals from four stages in the smoltification process (presmolt, smolt, smoltified seawater and desmoltified freshwater), the gene ranking was EF1A_B>EF1A_A>S20>β-actin>18S rRNA>GAPDH.

Conclusion

Overall, this work suggests that the EF1A_A and EF1A_B genes can be useful as reference genes in qRT-PCR examination of gene expression in the Atlantic salmon.

Present and future of rapid and/or high-throughput methods for nucleic acid testing

BACKGROUND

Behind the success of 'completing' the human genome project was a more than 30-year history of technical innovations for nucleic acid testing.

METHODS

Discovery of specific restriction endonucleases and reverse transcriptase was followed shortly by the development of the first diagnostic nucleic acid tests in the early 1970s. Introduction of Southern, Northern and dot blotting and DNA sequencing later in the 1970s considerably advanced the diagnostic capabilities. Nevertheless, it was the discovery of the polymerase chain reaction (PCR) in 1985 that led to an exponential growth in molecular biology and the introduction of practicable nucleic acid tests in the routine laboratory. The past two decades witnessed a continuing explosion of technological innovations in molecular diagnostics. In addition to classic PCR and reverse transcriptase PCR, numerous variations of PCR and alternative amplification techniques along with an ever-increasing variety of detection chemistries, closed tube (homogeneous) assays, and automated systems were developed. Discovery of real-time quantitative PCR and the development of oligonucleotide microarrays, the 'DNA chip', in the 1990s heralded the beginning of another revolution in molecular biology and diagnostics that is still in progress.