Gene expression changes in blood after phlebotomy: implications for gene expression profiling

The pre-analytical phase of the liquid biopsy

The term 'liquid biopsy', introduced in 2013 in reference to the analysis of circulating tumour cells (CTCs) in cancer patients, was extended to cell-free nucleic acids (cfNAs) circulating in blood and other body fluids. CTCs and cfNAs are now considered diagnostic and prognostic markers, used as surrogate materials for the molecular characterisation of solid tumours, in particular for research on tumour-specific or actionable somatic mutations. Molecular characterisation of cfNAs and CTCs (especially at the single cell level) is technically challenging, requiring highly sensitive and specific methods and/or multi-step processes. The analysis of the liquid biopsy relies on a plethora of methods whose standardisation cannot be accomplished without disclosing criticisms related to the pre-analytical phase. Thus, pre-analytical factors potentially influencing downstream cellular and molecular analyses must be considered in order to translate the liquid biopsy approach into clinical practice. The present review summarises the most recent reports in this field, discussing the main pre-analytical aspects related to CTCs, cfNAs and exosomes in blood samples for liquid biopsy analysis. A short discussion on non-blood liquid biopsy samples is also included.

Stabilization of circulating thyroglobulin mRNA transcripts in patients treated for differentiated thyroid carcinoma

Background The clinical utility of serum thyroglobulin in the follow-up of patients with differentiated thyroid carcinoma may be compromised by the presence of endogenous antithyroglobulin antibodies. To prevent interference by antithyroglobulin antibodies several groups have developed real-time PCR-based assays for quantification of blood thyroglobulin mRNA levels. For accurate quantification of thyroglobulin mRNA in blood preanalytical factors must be recognized and controlled. In this study, we evaluate the effect of different blood RNA stabilizing systems - the Tempus Blood RNA system and the PAXgene Blood RNA system - and storage time on RNA yield and quality, and thyroglobulin mRNA stability. Methods Blood samples from 11 patients previously treated for differentiated thyroid carcinoma were collected in K₂-EDTA, Tempus and PAXgene tubes and maintained at room temperature. RNA was isolated following storage for 0 and 72 h, and RNA yield, integrity and purity was determined. Thyroglobulin, GAPDH and ACTB mRNA levels were quantified by semi-quantitative real-time PCR. Results The RNA yield was significantly higher for blood collected in Tempus tubes compared with PAXgene tubes following storage for 72 h at room temperature ( P = 0.0011). High-quality RNA could be extracted from blood collected in PAXgene and Tempus tubes. Blood collected in K₂-EDTA tubes, but not in PAXgene and Tempus tubes, showed significant changes in thyroglobulin mRNA levels following storage for 72 h at room temperature ( P = 0.0263). Conclusions Stabilization of blood in PAXgene and Tempus tubes enables storage at room temperature for up to 72 h, without compromising thyroglobulin mRNA levels.

Biobanking in genomic medicine

CONTEXT

Genomic medicine requires the identification of biomarkers and therapeutic targets, which in turn, requires high-quality biospecimens. Achieving high-quality biospecimens requires implementing standard operating procedures to control the variations of preanalytic variables in biobanking. Currently, most biobanks do not control the variations of preanalytic variables when collecting, processing, and storing their biospecimens. However, those variations have been shown to affect the quality of biospecimens and gene expression profiling.

OBJECTIVE

To identify evidence-based preanalytic parameters that can be applied and those parameters that need further study.

DATA SOURCES

We searched the Biospecimen Research and PubMed databases using defined key words. We retrieved and reviewed 212 articles obtained through those searches. We included 58 articles (27%) according to our inclusion and exclusion criteria for this review.

CONCLUSION

-Preanalytic variables in biobanking can degrade the quality of biospecimens and alter gene expression profiling. Variables that require further study include the effect of surgical manipulation; the effect of warm ischemia; the allowable duration of delayed specimen processing; the optimal type, duration, and temperature of preservation and fixation; and the optimal storage duration of formalin-fixed, paraffin embedded specimens in a fit-for-purpose approach.

Association between α-synuclein blood transcripts and early, neuroimaging-supported Parkinson's disease

There are no cures for neurodegenerative diseases and this is partially due to the difficulty of monitoring pathogenic molecules in patients during life. The Parkinson's disease gene α-synuclein (SNCA) is selectively expressed in blood cells and neurons. Here we show that SNCA transcripts in circulating blood cells are paradoxically reduced in early stage, untreated and dopamine transporter neuroimaging-supported Parkinson's disease in three independent regional, national, and international populations representing 500 cases and 363 controls and on three analogue and digital platforms with P < 0.0001 in meta-analysis. Individuals with SNCA transcripts in the lowest quartile of counts had an odds ratio for Parkinson's disease of 2.45 compared to individuals in the highest quartile. Disease-relevant transcript isoforms were low even near disease onset. Importantly, low SNCA transcript abundance predicted cognitive decline in patients with Parkinson's disease during up to 5 years of longitudinal follow-up. This study reveals a consistent association of reduced SNCA transcripts in accessible peripheral blood and early-stage Parkinson's disease in 863 participants and suggests a clinical role as potential predictor of cognitive decline. Moreover, the three independent biobank cohorts provide a generally useful platform for rapidly validating any biological marker of this common disease.

Research note: methodology for high-quality RNA extraction from poultry whole blood for further gene expression analysis

1. There are no published methods for RNA isolation from avian whole blood where nucleated red blood cells prevent the use of established mammalian protocols. The aim of this study was therefore to develop a protocol for total RNA extraction using avian whole blood by defining the effect of anticoagulants and sample purification protocols on RNA yield and quality. 2. Blood collections from the cutaneous ulnar or medial metatarsal veins of birds yielded adequate blood volume (2-3 ml) draws. The experiment was a 2 × 2 × 3 factorial arrangement of treatments, with two levels of DNase (0 and TURBO DNA-free Kit), two levels of Cleanup (0 and RNeasy MinElute Cleanup Kit), and three anticoagulants (no anticoagulant, EDTA, or sodium citrate). 3. RNA was isolated successfully by adding TRIzol LS to 0.25 ml of chicken whole blood at 3:1 ratio. From 0.125 ml of avian whole blood, 2-3 µg of RNA with RNA integrity number values of 7.75 was successfully isolated with the TRIzol LS extraction and an RNeasy MinElute Cleanup Kit. 4. This reliable protocol can be used to extract high yield and quality of total RNA from a small amount of whole blood.

Evaluation of a low-cost procedure for sampling, long-term storage, and extraction of RNA from blood for qPCR analyses

In large clinical trials, where RNA cannot be extracted immediately after sampling, preserving RNA in whole blood is a crucial initial step in obtaining robust qPCR data. The current golden standard for RNA preservation is costly and designed for time-consuming column-based RNA-extraction. We investigated the use of lysis buffer for long-term storage of blood samples for qPCR analysis.

Blood was collected from 13 healthy adults and diluted in MagMAX lysis/binding solution or PAXgene Blood RNA tubes and stored at –20 °C for 0, 1, or 4 months before RNA extraction by the matching method. RNA integrity, yield and purity were evaluated and the methods were compared by subsequent analyses of the gene expression levels of

The MagMAX system extracted 2.3–2.8 times more RNA per mL blood, with better performance in terms of purity, and with comparable levels of integrity relative to the PAXgene system. Gene expression analysis using qPCR of

: The MagMAX system can be used for storage of human blood for up to 4 months and is equivalent to the PAXgene system for RNA extraction. It furthermore, provides a means for significant cost reduction in large clinical trials.

SPIDIA-RNA: second external quality assessment for the pre-analytical phase of blood samples used for RNA based analyses

One purpose of the EC funded project, SPIDIA, is to develop evidence-based quality guidelines for the pre-analytical handling of blood samples for RNA molecular testing. To this end, two pan-European External Quality Assessments (EQAs) were implemented. Here we report the results of the second SPIDIA-RNA EQA. This second study included modifications in the protocol related to the blood collection process, the shipping conditions and pre-analytical specimen handling for participants. Participating laboratories received two identical proficiency blood specimens collected in tubes with or without an RNA stabilizer. For pre-defined specimen storage times and temperatures, laboratories were asked to perform RNA extraction from whole blood according to their usual procedure and to return extracted RNA to the SPIDIA facility for further analysis. These RNA samples were evaluated for purity, yield, integrity, stability, presence of interfering substances, and gene expression levels for the validated markers of RNA stability: FOS, IL1B, IL8, GAPDH, FOSB and TNFRSF10c. Analysis of the gene expression results of FOS, IL8, FOSB, and TNFRSF10c, however, indicated that the levels of these transcripts were significantly affected by blood collection tube type and storage temperature. These results demonstrated that only blood collection tubes containing a cellular RNA stabilizer allowed reliable gene expression analysis within 48 h from blood collection for all the genes investigated. The results of these two EQAs have been proposed for use in the development of a Technical Specification by the European Committee for Standardization.

Effects of preanalytical variables on peptide and protein measurements in human serum and plasma: implications for clinical proteomics

There is a wealth of knowledge in the field of in vitro diagnostics with regard to preanalytical variables and their impact on the determination of peptide and protein analytes in human serum and plasma. This information is applicable to clinical proteomics investigations, which utilize the same sample types. Studies have demonstrated that the majority of variations and errors in in vitro diagnostics seem to occur in the preanalytical phase prior to specimen analysis. Preanalytical processes include study design, compliance of the subjects investigated, compliance of the technical staff in adherence to protocols, choice of specimens utilized and sample collection and processing. These variables can have a dramatic impact on the determination of analytes and can affect result outcomes, reproducibility and the validity of investigations. By drawing analogies to in vitro diagnostics practices, specific variables that are likely to impact the results of proteomics studies can be identified. Recognition of such variables is the first step towards their understanding and, eventually, controlling their impact. In this article, we will review preanalytical variables, provide examples for their effects on the determination of distinct peptides and proteins and discuss potential implications for clinical proteomics investigations.

Transcriptomic analysis of circulating leukocytes reveals novel aspects of the host systemic inflammatory response to sheep scab mites

Infestation of ovine skin with the ectoparasitic mite Psoroptes ovis results in the development of a rapid cutaneous inflammatory response, leading to the crusted skin lesions characteristic of sheep scab. To facilitate the identification of novel diagnostic and therapeutic targets, a better understanding of the host-parasite relationship in sheep scab is essential. Although our knowledge of the host's local cutaneous inflammatory response to sheep scab has increased in recent years, we still know relatively little about the mechanisms of this response at the systemic level. This study used a combined network and pathway analysis of the in vivo transcriptomic response of circulating leukocytes to infestation with P. ovis, during a 6 week period. Network graph analysis identified six temporally-associated gene clusters, which separated into two distinct sub-networks within the graph, representing those genes either up or down-regulated during the time course. Functional and pathway analysis of these clusters identified novel insights into the host systemic response to P. ovis infestation, including roles for the complement system, clotting cascade and fibrinolysis. These analyses also highlighted potential mechanisms by which the systemic immune response to sheep scab can influence local tissue responses via enhanced leukocyte activation and extravasation. By analysing the transcriptomic responses of circulating leukocytes in sheep following infestation with P. ovis, this study has provided key insights into the inflammatory response to infestation and has also demonstrated the utility of these cells as a proxy of events occurring at local tissue sites, providing insight into the mechanisms by which a local allergen-induced inflammatory response may be controlled.

Identification of reference microRNAs and suitability of archived hemopoietic samples for robust microRNA expression profiling

In many cancers, including neuroblastoma, microRNA (miRNA) expression profiling of peripheral blood (PB) and bone marrow (BM) may increase understanding of the metastatic process and lead to the identification of clinically informative biomarkers. The quality of miRNAs in PB and BM samples archived in PAXgene™ blood RNA tubes from large-scale clinical studies and the identity of reference miRNAs for standard reporting of data are to date unknown. In this study, we evaluated the reliability of expression profiling of 377 miRNAs using quantitative polymerase chain reaction (qPCR) in PB and BM samples (n=90) stored at -80 °C for up to 5 years in PAXgene™ blood RNA tubes. There was no correlation with storage time and variation of expression for any single miRNA (r < 0.50). The profile of miRNAs isolated as small RNAs or co-isolated with small/large RNAs was highly correlated (r=0.96). The mean expression of all miRNAs and the geNorm program identified miR-26a, miR-28-5p, and miR-24 as the most stable reference miRNAs. This study describes detailed methodologies for reliable miRNA isolation and profiling of PB and BM, including reference miRNAs for qPCR normalization, and demonstrates the suitability of clinical samples archived at -80 °C into PAXgene™ blood RNA tubes for miRNA expression studies.

Gene expression profiling in whole blood identifies distinct biological pathways associated with obesity

Background

Obesity is reaching epidemic proportions and represents a significant risk factor for cardiovascular disease, diabetes, and cancer.

Methods

To explore the relationship between increased body mass and gene expression in blood, we conducted whole-genome expression profiling of whole blood from seventeen obese and seventeen well matched lean subjects. Gene expression data was analyzed at the individual gene and pathway level and a preliminary assessment of the predictive value of blood gene expression profiles in obesity was carried out.

Results

Principal components analysis of whole-blood gene expression data from obese and lean subjects led to efficient separation of the two cohorts. Pathway analysis by gene-set enrichment demonstrated increased transcript levels for genes belonging to the "ribosome", "apoptosis" and "oxidative phosphorylation" pathways in the obese cohort, consistent with an altered metabolic state including increased protein synthesis, enhanced cell death from proinflammatory or lipotoxic stimuli, and increased energy demands. A subset of pathway-specific genes acted as efficient predictors of obese or lean class membership when used in Naive Bayes or logistic regression based classifiers.

Conclusion

This study provides a comprehensive characterization of the whole blood transcriptome in obesity and demonstrates that the investigation of gene expression profiles from whole blood can inform and illustrate the biological processes related to regulation of body mass. Additionally, the ability of pathway-related gene expression to predict class membership suggests the feasibility of a similar approach for identifying clinically useful blood-based predictors of weight loss success following dietary or surgical interventions.

Assessment of mRNA and microRNA Stabilization in Peripheral Human Blood for Multicenter Studies and Biobanks

In this study we evaluate the suitability of two methods of RNA conservation in blood samples, PAXgene and RNAlater, in combination with variable shipping conditions for their application in multicenter studies and biobanking. RNA yield, integrity, and purity as well as levels of selected mRNA and microRNA species were analyzed in peripheral human blood samples stabilized by PAXgene or RNAlater and shipped on dry ice or at ambient temperatures from the study centers to the central analysis laboratory. Both examined systems were clearly appropriate for RNA stabilization in human blood independently of the shipping conditions. The isolated RNA is characterized by good quantity and quality and well suited for downstream applications like quantitative RT-PCR analysis of mRNA and microRNA. Superior yield and integrity values were received using RNAlater. It would be reasonable to consider the production and approval of blood collection tubes prefilled with RNAlater to facilitate the use of this excellent RNA stabilization system in large studies.

Characterization of whole blood gene expression profiles as a sequel to globin mRNA reduction in patients with sickle cell disease

Global transcriptome analysis of whole blood RNA using microarrays has been proven to be challenging due to the high abundance of globin transcripts that constitute 70% of whole blood mRNA. This is a particular problem in patients with sickle cell disease, secondary to the high abundance of globin-expressing nucleated red blood cells and reticulocytes in the circulation. In order to accurately measure the steady state blood transcriptome in sickle cell patients we evaluated the efficacy of reducing globin transcripts in PAXgene stabilized RNA for genome-wide transcriptome analyses using microarrays. We demonstrate here by both microarrays and Q-PCR that the globin mRNA depletion method resulted in 55–65 fold reduction in globin transcripts in whole blood collected from healthy volunteers and sickle cell disease patients. This led to an improvement in microarray data quality by reducing data variability, with increased detection rate of expressed genes and improved overlap with the expression signatures of isolated peripheral blood mononuclear (PBMC) preparations. Analysis of differences between the whole blood transcriptome and PBMC transcriptome revealed important erythrocyte genes that participate in sickle cell pathogenesis and compensation. The combination of globin mRNA reduction after whole-blood RNA stabilization represents a robust clinical research methodology for the discovery of biomarkers for hematologic diseases.

Recovery of microarray-quality RNA from frozen EDTA blood samples

INTRODUCTION

The availability of blood collection systems with RNA stabilizing additives (e.g. PAXgene) has opened the field for gene expression profiling in large multi-center clinical trials. Here, we investigated whether the PAXgene system also offers a method for extraction of RNA from frozen EDTA blood samples, which do not yield RNA of high enough quality for RNA expression profiling, when extracted with standard protocols.

METHODS

Whole blood was obtained from six healthy volunteers in conventional EDTA tubes and frozen. The thawed EDTA blood was transferred into PAXgene tubes, and the RNA was extracted using the PAXgene RNA extraction kit. Microarray analysis was performed to asses the effect of RNA quality on gene expression profiles.

RESULTS

The RNA yield of the transferred samples was 1.76+/-0.88 microg/ml. This yield was clearly lower than the yield from a PAXgene reference group (2.84+/-0.62 microg/ml), but considerably higher than the yield resulting from a standard protocol usually applied to fresh EDTA blood samples (0.07+/-0.06 microg/ml). The RNA integrity number (RIN) of the transferred samples was 6.1+/-0.8 as compared to 9.8+/-0.1 for the PAXgene reference. Microarray analysis of the extracted RNA suggested that samples with RIN values above 5 produce data that fulfill the quality criteria defined by the manufacturer.

DISCUSSION

The transfer of thawed EDTA blood into PAXgene blood collection tubes offers a method to recover sufficient RNA of acceptable quality for microarray experiments.

Serum biobank certification and the establishment of quality controls for biological fluids: examples of serum biomarker stability after temperature variation

BACKGROUND

One of the main issues in biobanking is the establishment of standard operating procedures for specimen collection, preparation and storage to control for pre-analytical variation. For biological fluids such as serum, there is currently a lack of sensitive biomarkers for the quality control of cryopreservation conditions.

METHODS

The process approach was used to establish an ISO 9001:2000 quality management system. Immunoenzymatic and functional assays were used to assess the stability of the following candidate quality control biomarkers: secretory phospholipase A2, matrix metalloprotease 7, transforming growth factor beta1 and anti-HBs immunoglobulin.

RESULTS

Five product processes and their corresponding indicators were identified. In the preparation-aliquoting-storage process, no quality control indicator for serum was identified. Only matrix metalloprotease 7 showed moderate susceptibility to freeze-thaw cycles.

CONCLUSIONS

Biomarkers that have an on-off response to temperature variation could serve as quality indicators for the core processes of biobanking, which are the preparation and storage of biological fluids. The identification of such biomarkers is needed.

Effects of storage, RNA extraction, genechip type, and donor sex on gene expression profiling of human whole blood

BACKGROUND

Gene expression profiling of whole blood may be useful for monitoring toxicological exposure and for diagnosis and monitoring of various diseases. Several methods are available that can be used to transport, store, and extract RNA from whole blood, but it is not clear which procedures alter results. In addition, characterization of interindividual and sex-based variation in gene expression is needed to understand sources and extent of variability.

METHODS

Whole blood was obtained from adult male and female volunteers (n = 42) and stored at various temperatures for various lengths of time. RNA was isolated and RNA quality analyzed. Affymetrix GeneChips (n = 23) were used to characterize gene expression profiles (GEPs) and to determine the effects on GEP of storage conditions, extraction techniques, types of GeneChip, or donor sex. Hierarchical clustering and principal component analysis were used to assess interindividual differences. Regression analysis was used to assess the relative impact of the studied variables.

RESULTS

Storage of blood samples for >1 week at 4 degrees C diminished subsequent RNA quality. Interindividual GEP differences were seen, but larger effects were observed related to RNA extraction technique, GeneChip, and donor sex. The relative importance of the variables was as follows: storage < genechip < extraction technique < donor sex.

CONCLUSION

Sample storage and extraction methods and interindividual differences, particularly donor sex, affect GEP of human whole blood.

RNA extraction for arrays

DNA microarrays enable insights into global gene expression by capturing a snapshot of cellular expression levels at the time of sample collection. Careful RNA handling and extraction are required to preserve this information properly, ensure sample-to-sample reproducibility, and limit unwanted technical variation in experimental data. This chapter discusses important considerations for "array-friendly" sample handling and processing from biosamples such as blood, formalin-fixed, paraffin-embedded samples, and fresh or flash-frozen tissues and cells. It also provides guidelines on RNA quality assessments, which can be used to validate sample preparation and maximize recovery of relevant biological information.

Differential gene expression profiling in whole blood during acute systemic inflammation in lipopolysaccharide-treated rats

Microarrays have been used to evaluate the expression of thousands of genes in various tissues. However, few studies have investigated the change in gene expression profiles in one of the most easily accessible tissues, whole blood. We utilized an acute inflammation model to investigate the possibility of using a cDNA microarray to measure the gene expression profile in the cells of whole blood. Blood was collected from male Sprague-Dawley rats at 2 and 6 h after treatment with 5 mg/kg (ip) LPS. Hematology showed marked neutrophilia accompanied by lymphopenia at both time points. TNF-alpha and IL-6 levels were markedly elevated at 2 h, indicating acute inflammation, but by 6 h the levels had declined. Total RNA was isolated from whole blood and hybridized to the National Institute of Environmental Health Sciences Rat Chip v.3.0. LPS treatment caused 226 and 180 genes to be differentially expressed at 2 and 6 h, respectively. Many of the differentially expressed genes are involved in inflammation and the acute phase response, but differential expression was also noted in genes involved in the cytoskeleton, cell adhesion, oxidative respiration, and transcription. Real-time RT-PCR confirmed the differential regulation of a representative subset of genes. Principal component analysis of gene expression discriminated between the acute inflammatory response apparent at 2 h and the observed recovery underway at 6 h. These studies indicate that, in whole blood, changes in gene expression profiles can be detected that are reflective of inflammation, despite the adaptive shifts in leukocyte populations that accompany such inflammatory processes.

Gene expression profiling using RNA extracted from whole blood: technologies and clinical applications

Gene expression profiling promises to provide an insight into normal biologic and pathologic processes with the hope of predicting disease outcome or indicating individualized courses of therapy. The entire process for gene expression profiling from clinical samples consists of sample collection, transport and storage of clinical sample, isolation of nucleic acids, enzymatic modification of nucleic acids, detection and data analysis. All steps exert an influence on the quality, accuracy and reliability of the final result. A standardization of the entire process from sample collection to nucleic acid analysis is therefore required in order to achieve reliable gene expression results. After providing a general overview of technologies for gene expression profiling and respective caveats, this review will focus on clinical applications of blood sample profiling.

Global gene expression profiling in whole-blood samples from individuals exposed to metal fumes

Accumulating evidence demonstrates that particulate air pollutants can cause both pulmonary and airway inflammation. However, few data show that particulates can induce systemic inflammatory responses. We conducted an exploratory study using microarray techniques to analyze whole-blood total RNA in boilermakers before and after occupational exposure to metal fumes. A self-controlled study design was used to overcome the problems of larger between-individual variation interferences with observations of relatively smaller changes caused by environmental exposure. Moreover, we incorporated the dichotomous data of absolute gene expression status in the microarray analyses. Compared with nonexposed controls, we observed that genes with altered expression in response to particulate exposure were clustered in biologic processes related to inflammatory response, oxidative stress, intracellular signal transduction, cell cycle, and programmed cell death. In particular, the preinflammatory cytokine interleukin 8 and one of its receptors, chemokine receptor 4, seemed to play important roles in early-stage response to heavy metal exposure and were down-regulated. Furthermore, most observed expression variations were from nonsmoking exposed individuals, suggesting that smoking profoundly affects whole-blood expression profiles. Our study is the first to demonstrate that with a paired sampling study design of pre- and postexposed individuals, small changes in gene expression profiling can be measured in whole-blood total RNA from a population-based study. This technique can be applied to evaluate the host response to other forms of environmental exposures.

Measuring circulating neuroblastoma cells by quantitative reverse transcriptase-polymerase chain reaction analysis

BACKGROUND

Histologic examination of bone marrow (BM) is an accepted clinical standard for the detection of metastatic neuroblastoma (NB). Circulating tumor cells in peripheral blood (PB) derive from depots other than BM, and its measurement may provide additional information in the management of patients with NB.

METHODS

One hundred twenty patients with Stage 4 NB were evaluated for tumor cell content in PB by quantitative reverse transcriptase-polymerase chain reaction (qRT-PCR) analysis of GD2 synthase mRNA with a sensitivity of 1 NB cell in 10(6) normal cells. These findings were correlated with qRT-PCR analysis of their simultaneously sampled BM aspirates and 5 standard modalities of disease detection (histology, computed tomography/magnetic resonance imaging, bone scan, metaiodobenzylguanidine scan, and urinary homovanillic acid/vanillylmandelic acid levels).

RESULTS

Detection of GD2 synthase transcript was found in 62 patients: Eleven patients had positive (+) samples in their BM and PB (BM+PB+), 38 patients had BM+PB-negative (BM+PB-) specimens, and 13 patients had BM-PB+ samples. BM+PB+ paired samples had the highest transcript levels. When the extent of disease was scored (from 0 to 5) according to the number of positive disease detection modalities, the magnitude of the transcript level correlated with disease score. Ninety-one percent of patients with BM+PB+ samples had evidence of disease in >/= 3 modalities, whereas 97% of patients with BM-PB- samples and 100% of patients with BM-PB+ samples had low disease scores </= 2. Marker positivity in BM correlated with disease score. Patients who had positive marker in BM or PB had higher rates of relapse and death compared with patients who had negative marker. Kaplan-Meier analysis demonstrated a significantly greater risk of death for patients who had BM+PB+ specimens compared with patients who had BM-PB- samples (P = 0.03).

CONCLUSIONS

BM monitoring should continue to be an integral part of disease follow-up for patients with Stage 4 NB. PB monitoring to complement tumor surveillance in the BM can be informative.

The detection of circulating breast cancer cells in blood

At present, sampling of the lymph nodes or bone marrow for the detection of regions of metastatic disease in patients with breast cancer can only be undertaken at the time of initial diagnosis and surgery. However, the sampling of these tissues and the methods used are inaccurate, time consuming, and cannot be used for easy routine screening to determine disease recurrence and response to treatment. Because of the problems encountered with current methods and tissues sampled at the time of breast cancer diagnosis, this review discusses the urgent requirement for and potential development of a quick, simple, and accurate diagnostic test utilising the haematogenous system, a source of circulating tumour cells in patients with breast cancer, and highly sensitive molecular biological techniques, such as reverse transcription polymerase chain reaction. In addition, this review also highlights potential problems that may be encountered and should be avoided when devising such a test.

Genomics, transcriptomics, proteomics, and numbers

OBJECTIVE

To review the advances in clinically useful molecular biologic techniques and to identify their applications in clinical practice, as presented at the 11th Annual William Beaumont Hospital DNA Symposium.

DATA SOURCES

The 8 manuscripts submitted were reviewed, and their major findings were compared with literature on the same or related topics.

STUDY SELECTION

Manuscripts address the use of molecular techniques in microbiology to evaluate infectious disease and epidemiology; molecular microbiology methods, including rapid-cycle real-time polymerase chain reaction; peroxisome proliferator-activated receptor gamma as a potential therapeutic target in inflammatory bowel disease or colon cancer; the effect of nonapoptotic doses of the bisbenizamide dye Hoechst 33342 on luciferase expression in plasmid-transfected BC3H-1 myocytes; the routine use of cystic fibrosis screening and its challenges; and the use of flow cytometry and/or chromosomal translocation in the diagnostic evaluation of hematopoietic malignancies.

DATA SYNTHESIS

Three current issues related to the use of molecular tests in clinical laboratories are (1) the restriction on introducing new tests secondary to existing patents or licenses; (2) the preanalytic variables for the different specimen types currently in use, including whole blood, plasma, serum, fresh or frozen tissues, and free-circulating DNA; and (3) the interpretation of studies evaluating the association of complex diseases with a single mutation or single-nucleotide polymorphism. Molecular methods have had a major impact on infectious disease through the rapid identification of organisms, the evaluation of outbreaks, and the characterization of drug resistance when compared with standard culture techniques. The activation of peroxisome proliferator-activated receptor gamma stimulated by thiazolidinedione is useful in the treatment of type II diabetes mellitus and may have value in preventing inflammatory bowel disease or colon cancer. Hoechst 33342 binding to adenine-thymine-rich regions in the minor groove of DNA is a fluorescent stain for DNA and initiates apoptosis at >10 microg/mL. Lower doses of Hoechst 33342 promote luciferase expression by a mechanism that may involve binding to cryptic promoters facilitated by dye-associated misalignment of the tertiary structure of DNA. The routine use of cystic fibrosis screening is complicated by the more than 1000 mutations associated with the disease. The use of 4-color flow cytometry and the detection of chromosomal translocation are both invaluable aids in establishing the diagnosis of lymphoid or myeloid hematopoietic malignancies.

CONCLUSIONS

The current postgenomic era will continue to emphasize the use of microarrays and database software for genomic, transcriptomic, and proteomic screening in the search for useful clinical assays. The number of molecular pathologic techniques will expand as additional disease-associated mutations are defined.

Improvement of molecular monitoring of residual disease in leukemias by bedside RNA stabilization

The sensitivity of assays designed to monitor minimal residual disease (MRD) by RT-PCR in leukemia depend on quality and quantity of RNA derived from peripheral blood (PB) and bone marrow (BM) leukocytes. Shipment of material may lead to RNA degradation resulting in a loss of sensitivity and, potentially, false negative results. Furthermore, degradation may lead to inaccurate estimates of MRD in positive specimens. We sought to determine feasibility and efficacy of a novel blood collection and processing system which is based on integrated RNA stabilization at the time of phlebotomy (PAXgene Blood RNA Kit) by comparison with standard methods of RNA extraction (cesium chloride gradient ultracentrifugation and RNeasy Mini Kit) using unstabilized EDTA anticoagulated PB. In 26 patients with chronic myelogenous leukemia (CML) on therapy, PB was processed after a storage time at room temperature of 2 and 72 h according to these protocols. BCR-ABL, total ABL and glucose-6-phosphate dehydrogenase (G6PD) mRNA transcripts of PB samples were quantified as a measure for response to therapy and RNA integrity. RNA yield expressed as the ratio of ABL transcripts after a storage time of 72 h/ABL transcripts after a storage time of 2 h at room temperature was significantly higher with the stabilizing method (median 0.40) compared to the RNeasy method using unstabilized PB (median 0.13, P = 0.01). Furthermore, ratios BCR-ABL/ABL after 72 vs 2 h still correlated well using the PAXgene method (r = 0.99, P < 0.0001) in contrast to the standard method which did not (r = 0.65, P = 0.03). Even investigation of complete cytogenetic responders with very low tumor burden showed a good correlation of ratios BCR-ABL/ABL compared to the reference method. Comparable results were achieved using G6PD transcripts as standard. We conclude that the new PAXgene stabilization method could improve RNA quality and the comparability of molecular monitoring within and between multicenter trials.