Molecular phenotyping describes the technique of quantifying pathway reporter genes, ''i.e.'' pre-selected genes that are modulated specifically by metabolic and signaling pathways, in order to infer activity of these pathways. In most cases, molecular phenotyping quantifies changes of pathway reporter

gene expression Gene expression is the process (including its Regulation of gene expression, regulation) by which information from a gene is used in the synthesis of a functional gene product that enables it to produce end products, proteins or non-coding RNA, ...

to characterize modulation of pathway activities induced by perturbations such as therapeutic agents or stress in a cellular system ''in vitro''. In such contexts, measurements at early time points are often more informative than later observations because they capture the primary response to the perturbation by the cellular system. Integrated with quantified changes of

phenotype In genetics, the phenotype () is the set of observable characteristics or traits of an organism. The term covers the organism's morphology (physical form and structure), its developmental processes, its biochemical and physiological propert ...

induced by the perturbation, molecular phenotyping can identify pathways that contribute to the phenotypic changes. Currently molecular phenotyping uses

RNA sequencing RNA-Seq (named as an abbreviation of RNA sequencing) is a technique that uses next-generation sequencing to reveal the presence and quantity of RNA molecules in a biological sample, providing a snapshot of gene expression in the sample, also kn ...

and

mRNA In molecular biology, messenger ribonucleic acid (mRNA) is a single-stranded molecule of RNA that corresponds to the genetic sequence of a gene, and is read by a ribosome in the process of Protein biosynthesis, synthesizing a protein. mRNA is ...

expression to infer pathway activities. Other technologies and readouts such as

mass spectrometry Mass spectrometry (MS) is an analytical technique that is used to measure the mass-to-charge ratio of ions. The results are presented as a ''mass spectrum'', a plot of intensity as a function of the mass-to-charge ratio. Mass spectrometry is used ...

and protein abundance or phosphorylation levels can be potentially used as well.

Application in early drug discovery

Current data suggest that by quantifying pathway reporter

, molecular phenotyping is able to cluster compounds based on pathway profiles and dissect associations between pathway activities and disease

s simultaneously. Furthermore, molecular phenotyping can be applicable to compounds with a range of binding specificities and is able to triage false positives derived from high-content screening assays. Furthermore, molecular phenotyping allows integration of data derived from ''in vitro'' and ''in vivo'' models as well as patient data into the drug discovery process.

References

{{reflist Molecular biology RNA Gene expression Drug discovery Pharmaceutical industry