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Genomics

A selection of articles from European Pharmaceutical Review covering Genomics, NGS, RNA, microRNA, siRNA, Stem Cells, qPCR and Micro Arrays:

 

Inhibition of mutant P53 tumour cells by medicinal plants

Inhibition of mutant P53 tumour cells by medicinal plants

4 May 2016  •  Osuntokun Oludare Temitope and Ogunleye Adewale Joseph, Adekunle Ajasin University

The aetiology of tumours is attributed to changes in many internal (molecular) factors, most of which include mutations in several regulatory mechanisms and the loss of cell differentiation. Human isoforms of the p53 protein play a key role in maintaining genetic stability, functioning as active tumour suppressors. However, a mutation of the p53 gene leads to the production of mutant p53 protein, which contributes to the progression of malignancy. A large amount of work has been undertaken to understand the complex role of mutant p53 in malignancies, yet fairly little has been achieved using synthetic formulations to counter tumour metastasis. This article aims at reviewing the current advances in p53 research, as well as discussing the possibilities of inhibiting the expression and activity of mutant p53 genes in human malignancies through the use of medicinal plants...

Next-generation transcriptomic analysis in cancer vascular research

Next-generation transcriptomic analysis in cancer vascular research

3 September 2015  •  Joseph W. Wragg and Roy Bicknell, University of Birmingham

Over the past decade significant advances have been made in the fields of genomic and transcriptomic profiling, inspired by the advent of next-generation sequencing (NGS). Yet despite the considerable promise of these new technologies, uptake has been slow. The focus of this review is the use of next-generation transcriptomic analysis in the field of cancer endothelial biology, highlighting its advantages and a few of the disadvantages compared with current-generation technologies...

PCR in-depth focus 2015

PCR in-depth focus 2015

3 July 2015  •  European Pharmaceutical Review

In this PCR in-depth focus: Mikael Kubista from TATAA Biocenter addresses biological heterogeneity with single cell profiling, a look at quantitative PCR in the assessment of novel hepatic cell models, plus Q&A with Bio-Rad’s Javier Alba...

Stem Cells Supplement

Stem Cells: In-depth focus 2015

20 April 2015  •  Yu Wang, David Hay, Andreas Bender, Yasaman Kalantar Motamedi, Maryam Peymani, Mohammad Hossein

In this free-to-view stem cells in-depth focus, you can find out how computational ('in silico') methods can help to rationally choose bioactive small molecules to improve stem cell differentiation. The differentiation of pluripotent stem cells to hepatocyte-like cells is the focus of a second interesting article...

qPCR Supplement

qPCR: In-depth focus 2014

3 July 2014  •  Mikael Kubista, Theo P. Sloots, Michael D. Nissen

In this free-to-view in-depth focus: Prime time for qPCR – raising the quality bar, PCR to diagnose infectious disease, plus qPCR Roundtable...

René Dirks, Department of Molecular Biology, Radboud Institute for Molecular Life Sciences (RIMLS)

Understanding early mouse embryonic development using single-cell mRNA Sequencing

3 July 2014  •  René Dirks and Hendrik Marks, Department of Molecular Biology, Radboud Institute for Molecular Life Sciences (RIMLS)

Biomedical research often involves the use of cell lines that can be cultured in a laboratory. Individual cells within such cell lines often share a similar morphology. A remarkable exception are in vitro cultured mouse Embryonic Stem Cells (mESCs) – pluripotent cells derived from the blastocyst stage of the mouse developing embryo. Different from many other cell lines, mESCs show heterogeneity in morphology and gene expression between the individual cells within a population. This heterogeneity makes it challenging to characterise mESCs at a molecular level, since global profiling methods generally require large numbers of cells. However, new methods and technologies allow global transcriptome profiling of individual cells. By capturing the global transcriptome of many individual cells using single-cell next-generation mRNA-sequencing, our research focuses on the identification of novel transcription factor modules that contribute to the unique pluripotent state of mESCs, as well as to the differentiation of mESCs, as a model for early mouse embryonic development...

Stem Cells In-depth Focus

Stem Cells: In-depth focus 2014

15 April 2014  •  Sarah Baird, Graham Kelly, Gil Mor

In this free-to-view in-depth focus: Mesenchymal stem cells in cancer therapy - our chance to take charge, and Ovarian cancer stem cells - an essential target for durable remission...

Double Helix

RNA: Converting imaging-based cell biology to high-throughput biology

19 February 2014  •  Juha K. Rantala, Department of Biomedical Engineering and Knight Cancer Institute, Oregon Health and Science University

The last 10 years in biomedical research marks the period of deepening our understanding of the human genome. In the context of cancer research, The Cancer Genome Atlas (TCGA) and related international genomics efforts have now revealed the full complexity of genomic aberrations in human cancers that are postulated to contribute to the aspects of cancer pathophysiology. It is plausible that an ensemble of the numerous aberrations in each individual tumour collaborate at various strengths to deregulate master signalling pathways of cells, thereby enabling the established cancer ‘hallmarks’.

Roche acquires in vitro diagnostics company GeneWEAVE

Next generation sequencing: Application of next generation sequencing to preclinical cancer model profiling

15 December 2013  •  James R. Bradford, Oncology iMED, AstraZeneca Pharmaceuticals

Preclinical cancer models allow us to gain insight into therapeutic potential and mechanism of anti-cancer agents early in the drug discovery process. Whilst traditional array-based approaches have made a significant contribution to the characterisation of these models, the advent of next generation sequencing has revolutionised genomic research and is anticipated to make a huge impact on our understanding of preclinical models, leading to more targeted therapies for cancer patients. This article provides an overview of next generation sequencing in the context of cancer model profiling and evaluates the choice of technologies available and their application to both in vitro and in vivo model characterisation...

Next Generation Sequencing

Next generation sequencing: Using RNAseq to identify anti-cancer targets in the tumour vasculature

15 December 2013  •  Klarke M. Sample and Roy Bicknell, University of Birmingham

It is possible to attack the vasculature within solid tumours and achieve an anti-cancer effect. In the last decade, a number of studies have utilised cDNA libraries, SAGE analysis and microarrays to identify potential drug targets in the tumour endothelium. Modern sequencing technologies are likely to be a far more powerful and comprehensive tool for characterising the endothelial transcriptome...

PCR Supplement 2013

PCR: In-depth focus 2013

25 October 2013  •  Martina Weber (Emory University) / Billy Lau & Hanlee Ji (Stanford University School of Medicine)

Challenges for qRT-PCR in detecting / quantifying microRNA in vitro and in vivo.
Emerging clinical applications of digital PCR.
Workshop Preview: Advanced 3d cell based assays, preparation, analysis and troubleshooting.

microRNA: Small RNA molecules of great utility as diagnostic biomarkers in lung cancer

18 April 2013  •  Michela A. Denti and Margherita Grasso, Laboratory of RNA Biology and Biotechnology, Centre for Integrative Biology, University of Trento, Mattia Barbareschi and Chiara Cantaloni, Unit of Surgical Pathology, Santa Chiara Hospital

In 1993, the laboratories of Victor Ambros and Gary Ruvkun, studying the larval development of the nematode Caenorhabditis elegans, found a small RNA molecule (22 nucleotides) which regulated the translation of the lin-14 gene in an unusual way1,2. They observed that the sequence of the tiny lin-4 RNA was complementary to multiple conserved sites within the lin-14 mRNA 3’-UTR3 and that this base comple - mentarity was required for the repression of lin-14 protein expression by lin-4 RNA2. Immediately after their extraordinary discovery, and for almost 10 years, these small RNAs received relatively little attention from the scientific community. The tiny size of these RNA molecules probably contributed to their obscurity.

 

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