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Carlsson, Jessica
Publications (4 of 4) Show all publications
Carlsson, J., Davidsson, S., Helenius, G., Karlsson, M., Lubovac, Z., Andren, O., . . . Klinga-Levan, K. (2011). A miRNA expression signature that separates between normal and malignant prostate tissues. Cancer Cell International, 11, 14
Open this publication in new window or tab >>A miRNA expression signature that separates between normal and malignant prostate tissues
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2011 (English)In: Cancer Cell International, ISSN 1475-2867, E-ISSN 1475-2867, Vol. 11, p. 14-Article in journal (Refereed) Published
Abstract [en]

Background: MicroRNAs (miRNAs) constitute a class of small non-coding RNAs that post-transcriptionally regulate genes involved in several key biological processes and thus are involved in various diseases, including cancer. In this study we aimed to identify a miRNA expression signature that could be used to separate between normal and malignant prostate tissues. Results: Nine miRNAs were found to be differentially expressed (p < 0.00001). With the exception of two samples, this expression signature could be used to separate between the normal and malignant tissues. A cross-validation procedure confirmed the generality of this expression signature. We also identified 16 miRNAs that possibly could be used as a complement to current methods for grading of prostate tumor tissues. Conclusions: We found an expression signature based on nine differentially expressed miRNAs that with high accuracy (85%) could classify the normal and malignant prostate tissues in patients from the Swedish Watchful Waiting cohort. The results show that there are significant differences in miRNA expression between normal and malignant prostate tissue, indicating that these small RNA molecules might be important in the biogenesis of prostate cancer and potentially useful for clinical diagnosis of the disease.

Place, publisher, year, edition, pages
BioMed Central, 2011
National Category
Cancer and Oncology
Research subject
Medical sciences
Identifiers
urn:nbn:se:his:diva-5544 (URN)10.1186/1475-2867-11-14 (DOI)000292110200001 ()2-s2.0-79957484812 (Scopus ID)
Available from: 2012-03-09 Created: 2012-03-01 Last updated: 2017-12-07Bibliographically approved
Deo, A., Carlsson, J. & Lindlof, A. (2011). HOW TO CHOOSE A NORMALIZATION STRATEGY FOR MIRNA QUANTITATIVE REAL-TIME (QPCR) ARRAYS. Journal of Bioinformatics and Computational Biology, 9(6), 795-812
Open this publication in new window or tab >>HOW TO CHOOSE A NORMALIZATION STRATEGY FOR MIRNA QUANTITATIVE REAL-TIME (QPCR) ARRAYS
2011 (English)In: Journal of Bioinformatics and Computational Biology, ISSN 0219-7200, E-ISSN 1757-6334, Vol. 9, no 6, p. 795-812Article in journal (Refereed) Published
Abstract [en]

Low-density arrays for quantitative real-time PCR (qPCR) are increasingly being used as an experimental technique for miRNA expression profiling. As with gene expression profiling using microarrays, data from such experiments needs effective analysis methods to produce reliable and high-quality results. In the pre-processing of the data, one crucial analysis step is normalization, which aims to reduce measurement errors and technical variability among arrays that might have arisen during the execution of the experiments. However, there are currently a number of different approaches to choose among and an unsuitable applied method may induce misleading effects, which could affect the subsequent analysis steps and thereby any conclusions drawn from the results. The choice of normalization method is hence an important issue to consider. In this study we present the comparison of a number of data-driven normalization methods for TaqMan low-density arrays for qPCR and different descriptive statistical techniques that can facilitate the choice of normalization method. The performance of the normalization methods was assessed and compared against each other as well as against standard normalization using endogenous controls. The results clearly show that the data-driven methods reduce variation and represent robust alternatives to using endogenous controls.

Place, publisher, year, edition, pages
Imperial College Press, 2011
Keywords
miRNA, qPCR array normalization, quantitative real-time PCR
National Category
Biochemistry and Molecular Biology
Research subject
Natural sciences
Identifiers
urn:nbn:se:his:diva-5509 (URN)10.1142/S0219720011005793 (DOI)000297096300009 ()2-s2.0-80855161003 (Scopus ID)
Available from: 2012-03-29 Created: 2012-03-01 Last updated: 2017-12-07Bibliographically approved
Falck, E., Karlsson, S., Carlsson, J., Helenius, G., Karlsson, M. & Klinga-Levan, K. (2010). Loss of Glutathione peroxidase 3 expression is correlated with epigenetic mechanisms in endometrial adenocarcinoma. Cancer Cell International, 10, 46
Open this publication in new window or tab >>Loss of Glutathione peroxidase 3 expression is correlated with epigenetic mechanisms in endometrial adenocarcinoma
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2010 (English)In: Cancer Cell International, ISSN 1475-2867, E-ISSN 1475-2867, Vol. 10, p. 46-Article in journal (Refereed) Published
Abstract [en]

Glutathione peroxidase 3 (GPX3) is one of the key enzymes in the cellular defense against oxidative stress and the hepatocyte growth factor receptor, (MET) has been suggested to be influenced by the GPX3 gene expression. In a previous microarray study performed by our group, Gpx3 was identified as a potential biomarker for rat endometrial adenocarcinoma (EAC), since the expression was highly downregulated in rat EAC tumors. Herein, we have investigated the mRNA expression and Gpx3 and Met in rat EAC by real time quantitative PCR (qPCR), and the methylation status of Gpx3. In addition we have examined the expression of GPX3 and MET in 30 human EACs of different FIGO grades and 20 benign endometrial tissues. We found that the expression of GPX3 was uniformly down regulated in both rat and human EAC, regardless of tumor grade or histopathological subtype, implying that the down-regulation is an early event in EAC. The rate of Gpx3 promoter methylation reaches 91%, where biallelic methylation was present in 90% of the methylated tumors. The expression of the Met oncogene was slightly upregulated in EACs that showed loss of expression of Gpx3, but no tumor suppressor activity of Gpx3/GPX3 was detected. Preliminary results also suggest that the production of H2O2 is higher in rat endometrial tumors with down-regulated Gpx3 expression. A likely consequence of loss of GPX3 protein function would be a higher amount of ROS in the cancer cell environment. Thus, the results suggest important clinical implications of the GPX3 expression in EAC, both as a molecular biomarker for EAC and as a potential target for therapeutic interventions.

Place, publisher, year, edition, pages
BioMed Central, 2010
Keywords
Gpx3, endometrial cancer, methylation, real time PCR, FIGO grades
National Category
Natural Sciences
Research subject
Natural sciences
Identifiers
urn:nbn:se:his:diva-4708 (URN)10.1186/1475-2867-10-46 (DOI)000285883400001 ()2-s2.0-78549258157 (Scopus ID)
Available from: 2011-02-02 Created: 2011-02-02 Last updated: 2017-12-11Bibliographically approved
Carlsson, J., Helenius, G., Karlsson, M., Lubovac, Z., Andrén, O., Olsson, B. & Klinga-Levan, K. (2010). Validation of suitable endogenous control genes for expression studies of miRNA in prostate cancer tissues. Cancer Genetics and Cytogenetics, 202(2), 71-75
Open this publication in new window or tab >>Validation of suitable endogenous control genes for expression studies of miRNA in prostate cancer tissues
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2010 (English)In: Cancer Genetics and Cytogenetics, ISSN 2210-7762, E-ISSN 2210-7770, Vol. 202, no 2, p. 71-75Article in journal (Refereed) Published
Abstract [en]

When performing quantitative polymerase chain reaction analysis, there is a need for correction of technical variation between experiments. This correction is most commonly performed by using endogenous control genes, which are stably expressed across samples, as reference genes for normal expression in a specific tissue. In microRNA (miRNA) studies, two types of control genes are commonly used: small nuclear RNAs and small nucleolar RNAs. In this study, six different endogenous control genes for miRNA studies were investigated in prostate tissue material from the Swedish Watchful Waiting cohort. The stability of the controls was investigated using two different software applications, NormFinder and BestKeeper. RNU24 was the most suitable endogenous control gene for miRNA studies in prostate tissue materials.

Place, publisher, year, edition, pages
Elsevier Inc., 2010
National Category
Natural Sciences
Research subject
Natural sciences
Identifiers
urn:nbn:se:his:diva-4712 (URN)10.1016/j.cancergencyto.2010.02.009 (DOI)000282862400001 ()20875868 (PubMedID)2-s2.0-77957037880 (Scopus ID)
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Available from: 2011-02-02 Created: 2011-02-02 Last updated: 2017-12-11Bibliographically approved
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