Are expression profiles meaningless for cancer studies?

Jordan, Bertrand

doi:10.1002/bies.201200074

Cited by 4 publications

(3 citation statements)

References 22 publications

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“…It is the manifestation of the cell's general physiology and cannot be simply reduced to a particular molecular regulatory pathway or the expression of a small set of stemness genes. As a corollary, it is becoming increasingly clear that characterization of stem cells on the basis of a small number of biomarkers is biased, and hence unreliable, and global systemic detection methods of multiple features followed by a multiparametric statistical ana lysis of the data are needed to provide reliable results [24]. Similar conclusions showing that the use of a small number of biomarkers can be misleading were reached in other domains of molecular diagnosis [25].…”

Section: In Vitro Culture and Metabolismmentioning

confidence: 86%

Effects of the in Vitro Manipulation of Stem Cells: Epigenetic Mechanisms as Mediators of Induced Metabolic Fluctuations

Páldi¹

2013

Epigenomics

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The increasing popularity of stem cells in life science research has at least two major causes. On one hand, the study of stem cells may provide insights into one of the major secrets of biology: the mechanisms of cell differentiation. On the other hand, stem cells are potentially promising tools for regenerative therapy. The understanding of how environmental stimuli are translated into phenotypic differentiation through gene expression changes and how the same stimuli at the same time may perturb the normal process of cellular differentiation, growth and maintenance is a central issue for fundamental research but is also essential for the development of efficient and safe procedures for therapeutic use. This article assembles the known facts, as pieces of a puzzle, into a coherent picture around the idea of why stem cells are so sensitive to their culture environment and what practical consequences this implies.

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Section: In Vitro Culture and Metabolismmentioning

confidence: 86%

Effects of the in Vitro Manipulation of Stem Cells: Epigenetic Mechanisms as Mediators of Induced Metabolic Fluctuations

Páldi¹

2013

Epigenomics

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“…These findings give an immediate explanation to the recent 'iconoclastic' results obtained by Venet et al (2011) thoroughly commented in (Jordan 2012) demonstrating the practical equivalence between random collection of genes and specific signatures for breast cancer prognosis. Along the same line is the finding of the complete equivalence of different random gene selections for tracking hematopoietic differentiation demonstrated by Felli et al (2010).…”

Section: Fig 24mentioning

confidence: 54%

Why Systems Biology Can Promote a New Way of Thinking

Giuliani

2014

Systems and Synthetic Biology

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This chapter deals with the effect Systems Biology had on the Nature of what we consider 'an explanation' in Biological Science. I try and demonstrate how the most relevant change carried out by Systems Biology approach was the shift from the molecular layer as the definitive place where causative process start to the elucidation of the among elements (at any level of biological organization they are located) interaction network as the main goal of scientific explanations. This change of perspective allows to dissipate a widespread idealistic nightmare looking at the single molecules as Maxwell-demon-like intelligent agents. The recognition that genes work in networks has as consequence the existence of discrete 'allowed global modes' of gene expression. This theoretical expectation was verified by the incredibly narrow space of different tissues (each corresponding to a largely invariant gene expression profile)-around 200 tissue types for all the metazoans emerging from the transfinite number of possible combinations of the expression values of around 30,000 genes. This is a crucial step for generating a scientifically sound framework to address global biological regulation.Systems Biology approach makes obsolete the debate between 'reductionist' and 'holistic' approach in favor of a 'middle-out' paradygm formally identical to the time honored chemical thought. This is probably the brightest promise of Systems Biology to scientific knowledge.

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“…However, no attempts were made to actually use such data for quality control or evaluation of the expression data, or if they were, it was for cancer analysis within one tissue [116][117][118] or to study the expression of synonymous codons in plants [119]. This is despite the fact that questions over the validity of gene expression profiling results in breast cancer, for example, have been discussed [120]. Even where an attempt has been made to summarise gene expression data, it was only applied to microarrays [121,122] and not transferred to other types of expression data.…”

Section: Existing Expression Data Quality Control Methods and Their Amentioning

confidence: 99%