Can computers help estimate the quality of cancer cell lines?
13 July 2022
Can computers help estimate the quality of cancer cell lines?
In a study funded by Open Targets, Lucia Trastulla and Francesco Iorio discuss the limitations of immortal cancer cell lines (CCLs) to investigate cancer biology in vitro and review the latest computational methods to evaluate the suitability of each CCL as experimental model on a case-by-case basis.
Immortal CCLs are widely adopted models to study cancer biology in vitro and are often used in high-throughput screening for drug discovery. However, misidentification, misclassification, and heterogeneity, as well as usage out of the original in vivo tumour context, not always make CCLs appropriate to translate findings from the bench to the bedside.
Lucia Trastulla and Francesco Iorio at the HT Computational Biology Research Centre, in collaboration with colleagues from the Cancer Dependency Map Project at the Broad Institute, USA, provide an overview of the main limitations of using CCLs as in vitro surrogates for in vivo cancer features and describe how computational methods can be leveraged to identify the best and most representative CCLs depending on the type of primary tumor under investigation. Furthermore, the researchers discuss how machine-learning-based approaches may help reduce discrepancies arising from multi-omics analyses, transfer CCL-based findings to more complex model systems and develop approaches for the realization of personalised medicine.
The review is now published in Molecular Systems Biology.
Human Technopole is honoured to have participated in today’s meeting at the Quirinale, where President of the Republic Sergio Mattarella welcomed a delegation from MIND on the occasion of the tenth anniversary of the universal exposition Milano EXPO 2015.
Meet Carlos Jimenez, Postdoc in the Bienko Group (Genomics), who has been awarded a prestigious Marie Skłodowska-Curie Actions Postdoctoral Fellowship from the European Union. The grant, totalling €172,750.08 and covering a two-year period, will support his groundbreaking project PRUNE – Uncovering the Proteomic Radial Organisation within the Eukaryotic Nucleus – to study how the spatial arrangement of nuclear proteins contributes to optimal cell functioning.
By developing a sophisticated in vitro system coupled with advanced imaging techniques and CRISPR genome editing, an international team of researchers from Human Technopole (Italy) and the TUD Dresden University of Technology (Germany) shows that tubulin tyrosination/detyrosination regulates the bidirectional IFT train movement and avoids collision between trains moving in opposite directions along the cilium. The research was funded by the ERC and the DFG “Physics of Life” Excellence Cluster. The results are published in Nature Communications.
The public notice for the creation of a list of lawyers, from which legal representation assignments may be drawn in the interest of the Human Technopole Foundation, is now online.
Using advanced cryo-electron microscopy and cross-linking mass spectrometry, HT researchers provide unprecedented insight into how SNAPc works as a “dual recruiter” for RNA Polymerase II and III. The findings are published in Nature Communications.
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