| 1. |
- Andersson, Daniel, 1979, et al.
(författare)
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Preamplification with dUTP and cod UNG enables elimination of contaminating amplicons
- 2018
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Ingår i: International Journal of Molecular Sciences. - : MDPI AG. - 1422-0067. ; 19:10
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Tidskriftsartikel (refereegranskat)abstract
- Analyzing rare DNA and RNA molecules in limited sample sizes, such as liquid biopsies and single cells, often requires preamplification, which makes downstream analyses particularly sensitive to polymerase chain reaction (PCR) generated contamination. Herein, we assessed the feasibility of performing Cod uracil-DNA N-glycosylase (Cod UNG) treatment in combination with targeted preamplification, using deoxyuridine triphosphate (dUTP) to eliminate carry-over DNA. Cod UNG can be completely and irreversibly heat inactivated, a prerequisite in preamplification methods, where any loss of amplicons is detrimental to subsequent quantification. Using 96 target assays and quantitative real-time PCR, we show that replacement of deoxythymidine triphosphate (dTTP) with dUTP in the preamplification reaction mix results in comparable dynamic range, reproducibility, and sensitivity. Moreover, Cod UNG essentially removes all uracil-containing template of most assays, regardless of initial concentration, without affecting downstream analyses. Finally, we demonstrate that the use of Cod UNG and dUTP in targeted preamplification can easily be included in the workflow for single-cell gene expression profiling. In summary, Cod UNG treatment in combination with targeted preamplification using dUTP provides a simple and efficient solution to eliminate carry-over contamination and the generation of false positives and inaccurate quantification.
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| 2. |
- Andersson, Daniel, 1979, et al.
(författare)
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Properties of targeted preamplification in DNA and cDNA quantification
- 2015
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Ingår i: Expert Review of Molecular Diagnostics. - : Informa UK Limited. - 1473-7159 .- 1744-8352. ; 15:8, s. 1085-1100
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Forskningsöversikt (refereegranskat)abstract
- Objective: Quantification of small molecule numbers often requires preamplification to generate enough copies for accurate downstream enumerations. Here, we studied experimental parameters in targeted preamplification and their effects on downstream quantitative real-time PCR (qPCR). Methods: To evaluate different strategies, we monitored the preamplification reaction in real-time using SYBR Green detection chemistry followed by melting curve analysis. Furthermore, individual targets were evaluated by qPCR. Result: The preamplification reaction performed best when a large number of primer pairs was included in the primer pool. In addition, preamplification efficiency, reproducibility and specificity were found to depend on the number of template molecules present, primer concentration, annealing time and annealing temperature. The amount of nonspecific PCR products could also be reduced about 1000-fold using bovine serum albumin, glycerol and formamide in the preamplification. Conclusion: On the basis of our findings, we provide recommendations how to perform robust and highly accurate targeted preamplification in combination with qPCR or next-generation sequencing.
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| 3. |
- Forootan, Amin, et al.
(författare)
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Identification of Distinct and Common Subpopulations of Myxoid Liposarcoma and Ewing Sarcoma Cells Using Self-Organizing Maps
- 2023
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Ingår i: Chemosensors. - : MDPI AG. - 2227-9040. ; 11:1
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Tidskriftsartikel (refereegranskat)abstract
- Myxoid liposarcoma and Ewing sarcoma are the two most common tumor types that are characterized by the FET (FUS, EWSR1 and TAF15) fusion oncogenes. These FET fusion oncogenes are considered to have the same pathological mechanism. However, the cellular similarities between cells from the different tumor entities remain unknown. Here, we profiled individual myxoid liposarcoma and Ewing sarcoma cells to determine common gene expression signatures. Five cell lines were analyzed, targeting 76 different genes. We employed unsupervised clustering, focusing on self-organizing maps, to identify biologically relevant subpopulations of tumor cells. In addition, we outlined the basic concepts of self-organizing maps. Principal component analysis and a t-distributed stochastic neighbor embedding plot showed gradual differences among all cells. However, we identified five distinct and robust subpopulations using self-organizing maps. Most cells were similar to other cells within the same tumor entity, but four out of five groups contained both myxoid liposarcoma and Ewing sarcoma cells. The major difference between the groups was the overall transcriptional activity, which could be linked to cell cycle regulation. We conclude that self-organizing maps are useful tools to define biologically relevant subpopulations and that myxoid liposarcoma and Ewing sarcoma exhibit cells with similar gene expression signatures.
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| 4. |
- Kubista, Mikael, 1961, et al.
(författare)
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High Troughput single cell expression profiling: taking a closer look on biological
- 2011
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Ingår i: European Pharmaceutical Review. ; 16:2, s. 20-24
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Tidskriftsartikel (övrigt vetenskapligt/konstnärligt)abstract
- Molecular analysis of tissue and in most cases also of bodily fluids is complicated because of tissue heterogeneity and the presence of many different cell types. Even cells of apparently the same type show substantial variation in gene expression under virtually identical conditions. When analysing classical samples based on tens of thousands of cells, this natural variability among cells is lost. With the advent of real-time quantitative polymerase chain reaction (qPCR), we have a most powerful tool to study diversity on the single cell level and can detect rare cells that are critical to treatment or survival.
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| 5. |
- Svec, David, et al.
(författare)
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Direct cell lysis for single-cell gene expression profiling.
- 2013
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Ingår i: Frontiers in oncology. - : Frontiers Media SA. - 2234-943X. ; 3
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Tidskriftsartikel (refereegranskat)abstract
- The interest to analyze single and few cell samples is rapidly increasing. Numerous extraction protocols to purify nucleic acids are available, but most of them compromise severely on yield to remove contaminants and are therefore not suitable for the analysis of samples containing small numbers of transcripts only. Here, we evaluate 17 direct cell lysis protocols for transcript yield and compatibility with downstream reverse transcription quantitative real-time PCR. Four endogenously expressed genes are assayed together with RNA and DNA spikes in the samples. We found bovine serum albumin (BSA) to be the best lysis agent, resulting in efficient cell lysis, high RNA stability, and enhanced reverse transcription efficiency. Furthermore, we found direct cell lysis with BSA superior to standard column based extraction methods, when analyzing from 1 up to 512 mammalian cells. In conclusion, direct cell lysis protocols based on BSA can be applied with most cell collection methods and are compatible with most analytical workflows to analyze single-cells as well as samples composed of small numbers of cells.
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| 6. |
- Svec, David, et al.
(författare)
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Identification of inhibitors regulating cell proliferation and FUS-DDIT3 expression in myxoid liposarcoma using combined DNA, mRNA, and protein analyses.
- 2018
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Ingår i: Laboratory investigation; a journal of technical methods and pathology. - : Elsevier BV. - 1530-0307. ; 98, s. 957-967
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Tidskriftsartikel (refereegranskat)abstract
- FUS-DDIT3 belongs to the FET (FUS, EWSR1, and TAF15) family of fusion oncogenes, which collectively are considered to be key players in tumor development. Even though over 90% of all myxoid liposarcomas (MLS) have a FUS-DDIT3 gene fusion, there is limited understanding of the signaling pathways that regulate its expression. In order to study cell proliferation and FUS-DDIT3 regulation at mRNA and protein levels, we first developed a direct cell lysis approach that allows DNA, mRNA, and protein to be analyzed in the same sample using quantitative PCR, reverse transcription quantitative qPCR and proximity ligation assay, respectively. We screened 70 well-characterized kinase inhibitors and determined their effects on cell proliferation and expression of FUS-DDIT3 and FUS at both mRNA and protein levels in the MLS 402-91 cell line, where twelve selected inhibitors were evaluated further in two additional MLS cell lines. Both FUS-DDIT3 and FUS mRNA expression correlated with cell proliferation and both transcripts were co-regulated in most conditions, indicating that the common 5' FUS promotor is important in transcriptional regulation. In contrast, FUS-DDIT3 and FUS protein levels displayed more cell line dependent expression. Furthermore, most JAK inhibitors caused FUS-DDIT3 downregulation at both mRNA and protein levels. In conclusion, defining factors that regulate FUS-DDIT3 expression opens new means to understand MLS development at the molecular level.
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| 7. |
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| 8. |
- Åman, Pierre, 1953, et al.
(författare)
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Regulatory mechanisms, expression levels and proliferation effects of the FUS-DDIT3 fusion oncogene in liposarcoma.
- 2016
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Ingår i: The Journal of pathology. - : Wiley. - 1096-9896 .- 0022-3417. ; 238:5, s. 689-99
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Tidskriftsartikel (refereegranskat)abstract
- Fusion oncogenes are among the most common types of oncogene in human cancers. The gene rearrangements result in new combinations of regulatory elements and functional protein domains. Here we studied a subgroup of sarcomas and leukaemias characterized by the FET (FUS, EWSR1, TAF15) family of fusion oncogenes, including FUS-DDIT3 in myxoid liposarcoma (MLS). We investigated the regulatory mechanisms, expression levels and effects of FUS-DDIT3 in detail. FUS-DDIT3 showed a lower expression than normal FUS at both the mRNA and protein levels, and single-cell analysis revealed a lack of correlation between FUS-DDIT3 and FUS expression. FUS-DDIT3 transcription was regulated by the FUS promotor, while its mRNA stability depended on the DDIT3 sequence. FUS-DDIT3 protein stability was regulated by protein interactions through the FUS part, rather than the leucine zipper containing DDIT3 part. In addition, in vitro as well as in vivo FUS-DDIT3 protein expression data displayed highly variable expression levels between individual MLS cells. Combined mRNA and protein analyses at the single-cell level showed that FUS-DDIT3 protein expression was inversely correlated to the expression of cell proliferation-associated genes. We concluded that FUS-DDIT3 is uniquely regulated at the transcriptional as well as the post-translational level and that its expression level is important for MLS tumour development. The FET fusion oncogenes are potentially powerful drug targets and detailed knowledge about their regulation and functions may help in the development of novel treatments. Copyright © 2016 Pathological Society of Great Britain and Ireland. Published by John Wiley & Sons, Ltd.
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