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Evaluation of Reference Gene Stability for Investigations of Intracellular Signalling in Human Cancer and Non-Malignant Mesenchymal Stromal Cells.
Front Biosci (Schol Ed)
December 2024
Laboratory of Intracellular Membranes Dynamics, Institute of Cytology of the Russian Academy of Sciences, 194064 Saint Petersburg, Russia.
Background: Real-time reverse transcription quantitative polymerase chain reaction (RT-qPCR) is a powerful tool for analysing target gene expression in biological samples. To achieve reliable results by RT-qPCR, the most stable reference genes must be selected for proper data normalisation, particularly when comparing cells of different types. We aimed to choose the least variable candidate reference genes among eight housekeeping genes tested within a set of human cancer cell lines (HeLa, MCF-7, SK-UT-1B, A549, A431, SK-BR-3), as well as four lines of normal, non-malignant mesenchymal stromal cells (MSCs) of different origins.
View Article and Find Full Text PDFInPAS: An R/Bioconductor Package for Identifying Novel Polyadenylation Sites and Alternative Polyadenylation from Bulk RNA-seq Data.
Front Biosci (Schol Ed)
December 2024
Department of Molecular, Cell and Cancer Biology, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA.
Background: Alternative cleavage and polyadenylation (APA) is a crucial post-transcriptional gene regulation mechanism that regulates gene expression in eukaryotes by increasing the diversity and complexity of both the transcriptome and proteome. Despite the development of more than a dozen experimental methods over the last decade to identify and quantify APA events, widespread adoption of these methods has been limited by technical, financial, and time constraints. Consequently, APA remains poorly understood in most eukaryotes.
View Article and Find Full Text PDFShared Gene Expression Dysregulation Across Subtypes of Sanfilippo and Morquio Diseases: The Role of PFN1 in Regulating Glycosaminoglycan Levels.
Front Biosci (Landmark Ed)
December 2024
Department of Molecular Biology, Faculty of Biology, University of Gdansk, 80-308 Gdansk, Poland.
Background: Mucopolysaccharidosis (MPS) is a class of hereditary metabolic diseases that demonstrate itself by accumulating incompletely degraded glycosaminoglycans (GAGs). MPS are classified according to the kind(s) of stored GAG(s) and specific genetic/enzymatic defects. Despite the accumulation of the same type of GAG, two MPS diseases, Sanfilippo (MPS III) and Morquio (MPS IV), are further distinguished into subclasses based on different enzymes that are deficient.
View Article and Find Full Text PDFGene Fusion Detection in Long-Read Transcriptome Datasets from Multiple Cancer Cell Lines.
Front Biosci (Landmark Ed)
December 2024
Graduate School of Information Science and Technology, Osaka University, 565-0871 Suita, Osaka, Japan.
Background: Fusion genes are important biomarkers in cancer research because their expression can produce abnormal proteins with oncogenic properties. Long-read RNA sequencing (long-read RNA-seq), which can sequence full-length mRNA transcripts, facilitates the detection of such fusion genes. Several tools have been proposed for detecting fusion genes in long-read RNA-seq datasets derived from cancer cells.
View Article and Find Full Text PDFElectrochemical Biosensors for Cancer Diagnosis: Multitarget Analysis to Present Molecular Characteristics of Tumor Heterogeneity.
JACS Au
December 2024
Center for Molecular Recognition and Biosensing, Shanghai Engineering Research Center of Organ Repair, Joint International Research Laboratory of Biomaterials and Biotechnology in Organ Repair (Ministry of Education), School of Life Sciences, Shanghai University, Shanghai 200444, China.
Electrochemical biosensors are gaining attention as powerful tools in cancer diagnosis, particularly in liquid biopsy, due to their high efficiency, rapid response, exceptional sensitivity, and specificity. However, the complexity of intra- and intertumor heterogeneity, with variations in genetic and protein expression profiles and epigenetic modifications, makes electrochemical biosensors susceptible to false-positive or false-negative diagnostic outcomes. To address this challenge, there is growing interest in simultaneously analyzing multiple biomarkers to reveal molecular characteristics of tumor heterogeneity for precise cancer diagnosis.
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