scholarly journals Preanalytical mRNA Stabilization of Whole Bone Marrow Samples

2007 ◽  
Vol 53 (4) ◽  
pp. 587-593 ◽  
Author(s):  
Claudia Langebrake ◽  
Kalle Günther ◽  
Jürgen Lauber ◽  
Dirk Reinhardt

Abstract Background: Gene expression profiling is a useful tool for cancer diagnosis and basic research. A major limitation is that, even during short-term storage of native specimens of peripheral blood or bone marrow (BM) and/or RNA isolation, significant changes of gene expression pattern can occur because of gene induction, repression, and RNA degradation. Methods: We investigated the effectiveness of a newly developed RNA stabilization and preparation system for BM specimens (PAXgene™ Bone Marrow RNA System) over time. We analyzed 256 RNA samples, processed from 64 BM specimens. Results: Although the overall RNA yield (normalized to 1 × 107 leukocytes) was not different, the RNA preparation using unstabilized reference samples had an ∼3 times higher failure rate. With the PAXgene system, we observed significantly higher RNA integrity compared with the reference RNA preparation system (P <0.01). In the stabilized samples, we found very high pairwise correlation in gene expression (ΔΔCT 0.16–0.53) for the analyzed genes (GATA1, RUNX1, NCAM1, and SPI1) after 48-h storage compared with immediate preparation of RNA (2 h after BM collection). However, we found major differences in half of the analyzed genes using the reference RNA isolation procedure (ΔΔCT 1.07 and 1.32). Conclusions: The PAXgene system is able to stabilize RNA from clinical BM samples and is suitable to isolate high-quality and -quantity RNA.

Blood ◽  
2006 ◽  
Vol 108 (11) ◽  
pp. 4407-4407
Author(s):  
Claudia Langebrake ◽  
Kalle Guenther ◽  
Juergen Lauber ◽  
Dirk Reinhardt

Abstract Background: Gene expression profiling is a useful tool for the diagnosis and basic research of cancer. One of the major limitations of this approach is that already a short-term storage of native specimens of peripheral blood (PB) or bone marrow (BM) and/or the method of RNA isolation has significant influence on gene expression due to gene induction, repression and RNA degradation. The objective of the current study was to investigate the influence of a newly developed RNA stabilization and preparation system for BM specimens (PAXgeneTM Bone Marrow RNA System), focusing on RNA-yield, RNA-integrity and stability of gene expression profiles over time of BM sample storage. Patients and methods: 180 RNA samples that have been processed from 45 heparinized BM specimens of unselected children with acute leukemia at initial diagnosis, during treatment or without pathological findings in hematopoiesis were analyzed. Immediately after collection, heparinized BM specimens were divided into two PAXgeneTM RNA tubes and two standard tubes, each. RNA isolation using either the PAXgeneTM protocol (P) or a reference protocol (R) was performed after 2 hours (P0 and R0) or after 48 hours (P2 and R2). Results: The overall RNA yield (normalized to 1×107 leukocytes) was not different in all four isolation procedures, however the integrity of the RNA using the PAXgeneTM system was significantly higher at both time-points than that of the reference system: 8.6±0.2 (P0) vs. 6.8±0.4 (R0), p=0.0003 and 8.1±0.2 (P2) vs. 6.7±0.5 (R2), p=0.008. For the stabilized samples, we found very good pairwise correlation in gene expression for either gene at P2 compared to P0: GATA1 89±6%, RUNX1 83±10%, NCAM 69±12% and SPI1 89±6%. However, there were significant differences in two of the analyzed genes using the reference RNA isolation procedure: 40±6%, p<0.001 (GATA1) and 47±8%, p=0.005 (NCAM), respectively. Comparing the two RNA isolation procedures, there are significant differences in the expression levels of the analyzed genes. Discussion: The PAXgeneTM system is appropriate for the stabilization of gene expression levels in BM samples after short-term storage. However, as in some genes the reference RNA isolation procedure resulted in similar gene expression levels, the use of a stabilization reagent has to be carefully evaluated within the preanalytical handling of the samples. Our analysis has shown that it is not suitable to compare RNA expression levels derived from different isolation procedures. In conclusion, the PAXgeneTM system is able to stabilize RNA from clinical BM samples while being suitable to isolate high quality and quantity RNA.


2008 ◽  
Vol 83 (7) ◽  
pp. 531-539 ◽  
Author(s):  
Agostino Cortelezzi ◽  
Gualtiero Colombo ◽  
Caterina Pellegrini ◽  
Ilaria Silvestris ◽  
Lorenza Moronetti Mazzeo ◽  
...  

Blood ◽  
2012 ◽  
Vol 120 (21) ◽  
pp. 908-908
Author(s):  
Djamel Aggoune ◽  
Nathalie Sorel ◽  
Sanaa El Marsafy ◽  
Marie Laure Bonnet ◽  
Denis Clay ◽  
...  

Abstract Abstract 908 There is growing evidence that the bone marrow microenvironment could participate to the progression of chronic myeloid leukemia (CML). Recent data show indeed that placental growth factor (PGF) expression is highly induced in stromal cells from CML patients although they are not part of the leukemic clone as they are Ph1-negative (Schmidt et al, Cancer Cell 2011). It is possible that leukemic cells instruct the niche components via extracellular or contact signals, transforming progressively the “normal niche” into a functionally “abnormal niche” by inducing aberrant gene expression in these cells, similar to the pattern that has been identified in cancer-associated fibroblasts (CAF). In an effort to identify the differential gene expression pattern in the CML niche, we have undertaken two strategies of gene expression profiling using a Taqman Low Density Arrays (TLDA) protocol designed for 93 genes involved in antioxidant pathways (GPX, PRDX, SOD families), stromal cell biology (Collagen, clusterin, FGF, DHH), stem cell self-renewal (Bmi1, MITF, Sox2) and hematopoietic malignancies (c-Kit, hTERT, Dicer, beta-catenin, FOXO3). The first strategy consisted in the analysis of mesenchymal stem cells (MSCs) isolated from the bone marrow of newly diagnosed CP-CML patients (n=11). As a control, we have used MSCs isolated from the bone marrow of age-matched donors (n=3). MSCs were isolated by culturing 6–8.106 bone marrow mononuclear cells in the presence of b-FGF (1 ng/ml). At 2–3 weeks, cells were characterized by the expression of cell surface markers (CD105+, CD90+) and by their potential of differentiation towards osteoblastic, chondrocytic and adipocytic lineages. The second strategy aimed to study the potential instructive influence of leukemic cells in the gene expression program of normal MSC after co-culture with either the UT7 cell line expressing BCR-ABL (3 days) or with CD34+ cells isolated from CP-CML at diagnosis (5 days) as compared to co-culture with cord blood CD34+ cells. After culture, CD45-negative MSC were cell-sorted and analyzed by TLDA. All results were analyzed using the StatMiner software. Results: TLDA analysis of gene expression pattern of MSC from CML patients (n=11) as compared to normal MSCs (n=3) identified 6 genes significantly over-expressed in CML-MSC: PDPN (10-Fold Increase), V-CAM and MITF (∼8 Fold increase), MET, FOXO3 and BMP-1 (∼ 5 Fold increase). To confirm these results we have performed Q-RT-PCR in a cohort of CML-MSC (n= 14, including the 11 patients as analyzed in TLDA) as compared to normal MSC. High levels of PDPN (Podoplanin, ∼8 fold increase), MITF (Microphtalmia Associated Transcription factor, 4-Fold) and VCAM (Vascular Cell Adhesion Protein, 2 fold increase) mRNA were again observed on CML MSCs. Our second strategy (co-culture of normal MSC with BCR-ABL-expressing UT7) revealed an increase of IL-8 and TNFR mRNA expression in co-cultured MSCs (∼5-fold ) whereas there was a major decrease in the expression of DHH (∼ 25-fold) upon contact with BCR-ABL-expressing cells. No modification of the expression of PDPN, MITF or VCAM was noted in normal MSC after this 3-day co-culture strategy using UT7-BCR-ABL cells. Current experiments are underway to determine if primary CD34+ cells from CML patients at diagnosis could induce a specific gene expression pattern in normal MSC after 5 days of co-culture. PDPN is a glycoprotein involved in cell migration and adhesion, acting downstream of SRC. It has been shown to promote tumor formation and progression in solid tumor models and is highly expressed in CAFs. MITF is a bHLH transcription factor involved in the survival of melanocyte stem cells and metastatic melanoma. Finally, high VCAM1 mRNA expression by MSCs from CML patients could be involved in increased angiogenesis known to be present on CML microenvironment. In conclusion, our results demonstrate an abnormal expression pattern of 3 important genes (PDPN, MITF and VCAM1) in MSC isolated in CP-CML patients at diagnosis. The mechanisms leading to an increased mRNA expression (instructive or not instructive by leukemic cells) and their relevance to CML biology are under evaluation. Our results, confirming previous data, suggest strongly the existence of a molecular cross-talk between leukemic cells and the leukemic niche. The elucidation of such aberrant pathways in the microenvironment could lead to the development of “niche-targeted” therapies in CML. Disclosures: Turhan: Novartis, Bristol Myers Squibb: Honoraria, Research Funding.


2021 ◽  
Author(s):  
Eleanor S. Johnson ◽  
Kendra E. Stenzel ◽  
Sangderk Lee ◽  
Eric M. Blalock

AbstractRNA integrity numbers (RINs) are a standardized method for semi-quantification of RNA degradation, and are used in quality control prior to transcriptional profiling analysis. Recent work has demonstrated that RINs are associated with downstream transcriptional profiling, and correction procedures are typically employed in bioinformatic analysis pipelines to attempt to control for RIN’s influence on gene expression. However, relatively little work has been done to determine whether RIN’s influence is random, or is specifically targeted to a subset of mRNAs. We tested the hypothesis that RIN would be associated with a robust transcriptional profile seen across multiple studies.To test this, we downloaded subsets of raw transcriptional data from six published studies. We only included control, non-pathological post-mortem human brain tissue (n = 383 samples) in which independent subjects’ RIN values were also reported. A robust set of mRNAs consistently and significantly correlated with RIN across multiple studies, appearing to be selectively degraded as RIN declines. Many of the affected gene expression pathways are related to neurons (e.g., vesicle, mRNA transport, synapse, and mitochondria), suggesting that neuronal synaptic mRNA may be particularly vulnerable to degradation. Subsequent analysis of the relationship between RIN and vulnerable mRNA expression revealed most of the decay occurred over a relatively narrow RIN range of 7.2-8.6, with RIN values > 8.6 showing a ceiling effect, and those < 7.2 showing a floor effect on gene expression. Our data suggests that the RIN effect is pathway selective and non-linear, which may be an important consideration for current bioinformatic RIN correcting procedures, particularly in datasets in which declining RIN is confounded with a pathology under study (e.g., in Alzheimer’s disease).


Circulation ◽  
2008 ◽  
Vol 118 (suppl_18) ◽  
Author(s):  
Suna Wang ◽  
Yifu Zhou ◽  
Xiuli Xu ◽  
Timothy Hunt ◽  
Robert F Hoyt ◽  
...  

Background: Cell-based transplantation therapy in a large animal model has been shown to improve angiogenesis and function of ischemic myocardium. These improvements may be due to the endothelial progenitor cells from bone marrow derived stem cells (BMC) generated under ischemic or hypoxic conditions. However the molecular activities of porcine BMC (PBMC) are largely unknown. Thus, a comprehensive gene expression pattern for PBMC is needed to advance the preclinical work necessary for future human treatment. Methods: Fifteen PBMC were cultured in the medium of EGM 2 for 4 weeks, and then incubated either in a monitored hypoxic chamber (1% O2, 5% CO2) (H) or in normal culture conditions (normoxia, N) for 6, 12, 24 and 48 hrs. Twenty RNAs comprising 5 Ns and 15 Hs (6, 12 and 24hr) were hybridized to Affymetrix Porcine arrays. An additional 40 samples were prepared for data confirmation by qRTPCR and Western blot. Data normalization and pattern recognition in each of these subgroups were achieved using R package 2.4 and GeneSpringGX. Homologous gene search and functional classification based on NCBI Pig Genomic Resources and DAVID Bioinformatics Resources 2007. Results: Significant gene expression levels among the four groups were identified. The patterns of three hypoxia (H) groups were clearly distinct from that of normoxia (N) group. However, the expression pattern of 12hr H was more similar to 24hr H than that of 6hr H. Of 23,928 probes, 394 genes were statistically regulated rapidly in 6hr Hs vs. Ns, including HIF2alpha, VEGFA, PDGFA, ANGPT2, CXCL14 and PGD. Only 182 genes were modulated in 12hr Hs, but 84% (152/182) of the genes appeared either with 6hr or 24hr H groups. 227 genes were significantly over- or down- regulated in 24hr Hs, among the 94 genes were overlapped with 6hr and 12hr Hs. Notably, the 94 genes were the most differentially modulated in all three H groups, some of the genes were known involving in the processes of hypoxic stress, response to inflammatory, wounding, apoptosis and angiogenesis. The 94 genes are considered as hypoxic targets for further study. Conclusions: Our results confirmed the role of several genes involved in hypoxic or ischemic states, and captured a set of genes that associated the PBMC response to hypoxic or ischemic surroundings.


Blood ◽  
2013 ◽  
Vol 122 (21) ◽  
pp. 1892-1892
Author(s):  
Alicia Baez ◽  
Jose Ignacio Piruat ◽  
Teresa Caballero-Velazquez ◽  
María Victoria Barbado ◽  
Isabel Alvarez-Laderas ◽  
...  

Abstract Introduction Memory B cells (MBCs) remain viable in a non-proliferative state for years. These cells express genes involved in cell survival and anti-apoptotic factors, while repress the expression of cell cycle regulatory genes. During their differentiation into plasma cells (PCs), these cells develop an opposite gene expression pattern, with a higher expression of genes implicated in cell proliferation and activation, and a lower expression of survival genes. In multiple myeloma (MM) the PCs accumulate into the bone marrow due, at least in part, to failure of pro-apoptotic mechanisms normally expressed in PCs. In the present study we analyzed the gene expression patterns of MBCs and PCs from healthy donors and patients with MM, in order to determine whether or not myelomatous PCs share characteristics of MBCs and/or normal PCs, and to identify possible genes related to the pathophysiology of the disease. Methods MBCs were obtained by immunomagnetic separation from buffy coats of 5 aged healthy donors. Likewise, PCs were isolated from bone marrow of 6 healthy donors and of 5 patients with MM. Using microarray techniques we analyzed the expression of 45000 genes in all samples. We performed unsupervised hierarchical cluster of gene expression data using the average linkage and the Euclidean distance. To identify differentially expressed genes among experimental groups we applied non-parametric Kruskal Wallis test. The differences in expression with a p value < 0.05 were considered significant. All analyses were performed using the Multi-experiment Viewer 4.7.1 software. Results From the hierarchical cluster obtained we clearly identified two groups, one which included normal PCs samples and the other one containing myelomatous PCs and MBCs. Interestingly, myelomatous PCs displayed intermediate features between MBCs and normal PCs (Figure 1). We found 5159 genes differentially expressed between normal and myelomatous PCs. Among these, we identified 3455 genes which displayed a similar expression pattern between MBCs and myelomatous PCs, including caspases inhibitors, MAP kinases, ubiquitins, transcription and translation factors. Conclusion Myelomatous PCs display an intermediate gene expression pattern between normal PCs and MBCs. These cells display high expression of genes involved in cell survival that should be normally inactivated in the transit of MBC to a normal PC, so that its expression pattern is closer to a MBC than a normal PC. Disclosures: No relevant conflicts of interest to declare.


BMC Genomics ◽  
2008 ◽  
Vol 9 (1) ◽  
pp. 166 ◽  
Author(s):  
Tatiana Tondreau ◽  
Marielle Dejeneffe ◽  
Nathalie Meuleman ◽  
Basile Stamatopoulos ◽  
Alain Delforge ◽  
...  

2021 ◽  
Author(s):  
Amanda J. Haack ◽  
Fang Yun Lim ◽  
Dakota S. Kennedy ◽  
John H. Day ◽  
Karen N. Adams ◽  
...  

ABSTRACTGene expression analysis (e.g., targeted small gene panels, transcriptomics) from whole blood can elucidate mechanisms of immune function and aid in the discovery of biomarkers. Conventional in-clinic venipuncture offers only a small snapshot of our broad immune landscape as immune responses may occur outside of the time and location parameters available for conventional venipuncture. A self-operated method that enables flexible sampling of liquid whole blood coupled with an immediate stabilization of cellular RNA is instrumental in facilitating capture and preservation of acute or transient immune fluxes. To this end, we developed homeRNA: a kit that allows for self-collection of peripheral blood (∼0.5 mL) and immediate stabilization of cellular RNA, using the Tasso-SST™ blood collection device paired with a specially designed stabilizer tube containing RNAlater™. To assess the usability and feasibility of homeRNA for self-collection and stabilization of whole blood RNA, we conducted a pilot study (n = 41 participants) where we sent homeRNA to participants aged 21-69, located across 10 US states (94% successful blood collections, n = 51). Among participants who successfully collected blood, 91% reported no or minimal pain/discomfort using the kit (n = 35), and 77% reported easy or somewhat easy stabilization protocol. Total RNA yield from the stabilized samples ranged between 0.24 µg and 5.99 µg (mean = 1.65 µg), while RNA Integrity Number (RIN) values were above 7.0 (mean = 7.9), indicating limited RNA degradation. Results from this study demonstrate the self-collection and RNA stabilization of whole blood with homeRNA by participants themselves, in their own home.


2011 ◽  
Vol 58 (4) ◽  
Author(s):  
Agnieszka Podolska ◽  
Bogumil Kaczkowski ◽  
Thomas Litman ◽  
Merete Fredholm ◽  
Susanna Cirera

The quality of RNA is crucial in gene expression experiments. RNA degradation interferes in the measurement of gene expression, and in this context, microRNA quantification can lead to an incorrect estimation. In the present study, two different RNA isolation methods were used to perform microRNA microarray analysis on porcine brain tissue. One method is a phenol-guanidine isothiocyanate-based procedure that permits isolation of total RNA. The second method, miRVana™ microRNA isolation, is column based and recovers the small RNA fraction alone. We found that microarray analyses give different results that depend on the RNA fraction used, in particular because some microRNAs appear very sensitive to the RNA isolation method. We conclude that precautions need to be taken when comparing microarray studies based on RNA isolated with different methods.


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