A5018247006- Prostate Cancer Treatment and Research
- Genomics and Chromatin Dynamics
- Cancer, Lipids, and Metabolism
- Epigenetics and DNA Methylation
- Gene expression and cancer classification
- Advanced Proteomics Techniques and Applications
- Metabolomics and Mass Spectrometry Studies
- RNA and protein synthesis mechanisms
- RNA Research and Splicing
- Genomics and Phylogenetic Studies
- Genetics, Bioinformatics, and Biomedical Research
- Cancer-related molecular mechanisms research
- Genetic and phenotypic traits in livestock
- Aquaculture Nutrition and Growth
- Cholesterol and Lipid Metabolism
- RNA modifications and cancer
- Fish Ecology and Management Studies
- Molecular Biology Techniques and Applications
- Cancer-related gene regulation
- Protein Tyrosine Phosphatases
- Prostate Cancer Diagnosis and Treatment
- Mass Spectrometry Techniques and Applications
- Cell Image Analysis Techniques
- Cytokine Signaling Pathways and Interactions
- Radiation Therapy and Dosimetry
St Olav's University Hospital
2016-2024
Norwegian University of Science and Technology
2015-2024
Akvaforsk Genetics Center (Norway)
1991-2014
Oslo University Hospital
2013
University of Oslo
2013
Norwegian Computing Center
2013
University of Bergen
2013
National Institute Of Hygiene And Epidemiology
1971
Institute of Pharmacology
1971
Abstract Background Prostate cancer (PCa) has the highest incidence rates of cancers in men western countries. Unlike several other types cancer, PCa few genetic drivers, which led researchers to look for additional epigenetic and transcriptomic contributors development progression. Especially datasets on DNA methylation, most commonly studied marker, have recently been measured analysed patient cohorts. methylation is associated with downregulation gene expression. However, positive...
Abstract Background Prostate cancer tissues are inherently heterogeneous, which presents a challenge for metabolic profiling using traditional bulk analysis methods that produce an averaged profile. The aim of this study was therefore to spatially detect metabolites and lipids on prostate tissue sections by mass spectrometry imaging (MSI), method facilitates molecular heterogeneous sections, can subsequently be related the histology same section. Methods Here, we simultaneously obtained...
Abstract We investigated genomic and transcriptomic changes in paired tumor samples of 29 in-house multiple myeloma (MM) patients 28 from the MMRF CoMMpass study before after treatment. A change clonal composition was found 46/57 (82%) patients, single-nucleotide variants (SNVs) increased median 67 to 86. The highest increase prevalence genetic aberrations RAS genes (60% 72%), amp1q21 (18% 35%), TP53 (9% 18%). SBS-MM1 mutation signature detected both receiving high low dose melphalan. total...
microRNAs (miRNAs) exist in blood an apparently stable form. We have explored whether serum miRNAs can be used as non-invasive early biomarkers of colon cancer. Serum samples from 30 patients with cancer stage IV and 10 healthy controls were examined for the expression 375 cancer-relevant miRNAs. Based on miRNA profile this study, 34 selected measured 40 I–II additional controls. Twenty differentially expressed compared (P<0.01). Unsupervised clustering revealed four subgroups; one...
Abstract Reactive stroma is a tissue feature commonly observed in the tumor microenvironment of prostate cancer and has previously been associated with more aggressive tumors. The aim this study was to detect differentially expressed genes metabolites according reactive content measured on exact same sample. evaluated using histopathology from 108 fresh frozen samples gathered 43 patients after prostatectomy (Biobank1). A subset analyzed both for metabolic (n = 85) transcriptomic alterations...
// Elise Sandsmark 1 , Ailin Falkmo Hansen Kirsten M. Selnæs Helena Bertilsson 2, 3 Anna Bofin 4 Alan J. Wright 5 Trond Viset 6 Elin Richardsen 7, 8 Finn Drabløs Tone F. Bathen May-Britt Tessem 1, * Morten B. Rye 3, 9, Department of Circulation and Medical Imaging, Faculty Medicine, NTNU - Norwegian University Science Technology, Trondheim, Norway 2 Urology, St. Olavs Hospital, Trondheim Cancer Research Molecular Laboratory Children's Women's Health, UK Cambridge Institute, Cambridge, United...
Glutaminase inhibitors target cancer cells by blocking the conversion of glutamine to glutamate, thereby potentially interfering with anaplerosis and synthesis amino acids glutathione. The drug CB-839 has shown promising effects in preclinical experiments is currently undergoing clinical trials several human malignancies, including triple-negative breast (TNBC). However, response glutaminase variable there a need for identification predictive biomarkers. aim this study was determine how...
Chromatin immunoprecipitation (ChIP) followed by high throughput sequencing (ChIP-seq) is rapidly becoming the method of choice for discovering cell-specific transcription factor binding locations genome wide. By aligning sequenced tags to genome, appear as peaks in tag profile. Several programs have been designed identify such peaks, but program evaluation has difficult due lack benchmark data sets. We created sets three factors manually evaluating a selection potential regions that cover...
Abstract To truly understand the cancer biology of heterogenous tumors in context precision medicine, it is crucial to use analytical methodology capable capturing complexities multiple omics levels, as well spatial heterogeneity tissue. Different molecular imaging techniques, such mass spectrometry (MSI) and transcriptomics (ST) achieve this goal by spatially detecting metabolites mRNA, respectively. take full advantage multi-omics data, individual measurements need be integrated into one...
Abstract Background Locally advanced breast cancer is a heterogeneous disease with respect to response neoadjuvant chemotherapy (NACT) and survival. It currently not possible accurately predict who will benefit from the specific types of NACT. DNA methylation an epigenetic mechanism known play important role in regulating gene expression may serve as biomarker for treatment We investigated potential prognostic marker long-term survival (> 5 years) after NACT cancer. Methods profiles...
The immense increase in availability of genomic scale datasets, such as those provided by the ENCODE and Roadmap Epigenomics projects, presents unprecedented opportunities for individual researchers to pose novel falsifiable biological questions. With this opportunity, however, are faced with challenge how best analyze interpret their genome-scale datasets. A powerful way representing data is feature-specific coordinates relative reference genome assemblies, i.e. tracks. Genomic HyperBrowser...
// Caroline K. Søgaard 1, 7 , Siver A. Moestue 2, 3, 4 Morten B. Rye Jana Kim 5 Anala Nepal 1 Nina-Beate Liabakk Siri Bachke Tone F. Bathen Marit Otterlei 6, and Deborah Hill Department of Cancer Research Molecular Medicine, Norwegian University Science Technology (NTNU), Trondheim, Norway 2 Circulation Medical Imaging, 3 Laboratory Women's Children's Health, Pharmacy, Faculty Health Sciences, Nord University, Namsos, Radiology, St. Olavs Hospital, Trondheim 6 APIM Therapeutics A/S, Clinic...
TMPRSS2-ERG has been proposed to be a prognostic marker for prostate cancer. The aim of this study was identify changes in metabolism, genes and biochemical recurrence related by using an integrated approach, combining metabolomics, transcriptomics, histopathology clinical data cohort 129 human samples (41 patients). Metabolic analyses revealed lower concentrations citrate spermine comparing ERGhigh ERGlow samples, suggesting increased cancer aggressiveness compared ERGlow. These results...
Deciphering the most common modes by which chromatin regulates transcription, and how this is related to cellular status processes an important task for improving our understanding of human biology. The FANTOM5 ENCODE projects represent two independent large scale efforts map regulatory transcriptional features genome. Here we investigate around a comprehensive set transcription start sites in four cell lines integrating data from these projects. Transcription can be distinguished states...
PRL-3 is a phosphatase implicated in oncogenesis multiple cancers. In some cancers, notably carcinomas, also associated with inferior prognosis and increased metastatic potential. this study we investigated the expression of mRNA fresh-frozen samples from patients undergoing radical prostatectomy because prostate cancer (PC) biological function cells. Samples 41 specimens (168 total) divided into low (Gleason score ≤ 6), intermediate = 7) high ≥ 8) risk were analyzed gene profiling compared...
Molecular analysis of patient tissue samples is essential to characterize the in vivo variability human cancers which are not accessible cell-lines or animal models. This applies particularly studies tumor metabolism. The challenge is, however, complex mixture various types within each sample, such as benign epithelium, stroma and cancer tissue, can introduce systematic biases when compared normal samples. In this study we apply a simple strategy remove using sample selections where average...
Intestinal epithelial homeostasis is maintained by adult intestinal stem cells, which, alongside Paneth appear after birth in the neonatal period. We aimed to identify regulators of development testing a small library epigenetic modifier inhibitors cell-skewed organoid cultures. found that lysine-specific demethylase 1A (Kdm1a/Lsd1) absolutely required for cell differentiation. Lsd1-deficient crypts, devoid are still able form organoids without requirement exogenous or endogenous Wnt....
A novel approach for revealing patterns of proteome variation among series 2-DE gel images is presented. The utilises image alignment to ensure that each pixel represents the same information across all gels. Gel are normalised, and background corrected, followed by unfolding 1-D vectors analysing multivariate data modelling. Information resulting from analysis refolded back domain visualisation interpretation. method rapid suitable automatic routines applied after alignment. compared with...
Transcription factor binding to DNA requires both an appropriate element and suitably open chromatin, which together help define regulatory elements within the genome. Current methods of identifying elements, such as promoters or enhancers, typically rely on sequence conservation, existing gene annotations specific marks, histone modifications p300 methods, each has its own biases.Herein we show that approach based clustering transcription peaks from high-throughput sequencing coupled with...
Increased knowledge of the molecular differences between indolent and aggressive prostate cancer is needed for improved risk stratification treatment selection. Secreted frizzled-related protein 4 (SFRP4) a modulator cancer-associated Wnt pathway, previously suggested as potential marker aggressiveness. In this study, we investigated validated association SFRP4 gene expression aggressiveness in nine independent cohorts (n = 2157). By differential combined meta-analysis all cohorts, detected...
The DNA damage inducible SOS response in bacteria serves to increase survival of the species at cost mutagenesis. first initiates error-free repair followed by error-prone repair. Here, we have employed a multi-omics approach elucidate temporal coordination response. Escherichia coli was grown batch cultivation bioreactors ensure highly controlled conditions, and low dose antibiotic ciprofloxacin used activate while avoiding extensive cell death. Our results show that expression genes...