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Biology subjects

El-Kamand, S.

Publications and source records attributed to El-Kamand, S..

3 recordsLinked to original sources

CBL mutations in pediatric solid and CNS tumors are a marker of receptor tyrosine kinase activation and a potential therapeutic target

Mutations in CBL, an E3 ubiquitin ligase that negatively regulates receptor tyrosine kinases (RTKs) and potentiates intracellular signaling, have been extensively characterized in hematological malignancies. However, the impacts are unknown in other cancer types. We have identified established and novel aberrations in CBL in molecularly diverse pediatric CNS and solid tumors. Additionally, we present novel CBL splice mutations, including in the germline of a high-grade glioma patient, and alternative CBL splicing without corresponding genomic alterations. Functionally, we demonstrate that CBL exon 8/9{Delta}, typically associated with acute myeloid leukemia, is RTK activating in neuroblastoma and that novel CBL variants, CBL E366_E373del and CBL C384G, can cooperate with overexpression of EGFR to transform Ba/F3 cells. Collectively, these data represent a novel form of RTK activation in pediatric patients with solid and CNS tumors who might benefit from RTK-targeted therapies. Statement of significanceMolecularly targeted therapies improve childhood cancer outcomes. Therapies targeting genes called receptor tyrosine kinases are particularly effective. We have identified new genetic alterations that may be a marker for receptor tyrosine kinase activation and drug sensitivity, enabling more patients to benefit from targeted treatments.

cancer biology↗

CRUX, a platform for visualising, exploring and analysing cancer genome cohort data

To better understand how tumours develop, identify prognostic biomarkers, and find new treatments, researchers have generated vast catalogues of cancer genome data. However, these datasets are complex so interpreting their important features requires specialized computational skills and analytical tools, which presents a significant technical challenge. To address this, we developed CRUX, a platform for exploring genomic data from cancer cohorts. CRUX enables researchers to perform common analyses including cohort comparisons, biomarker discovery, survival analysis, and create visualisations including oncoplots and lollipop charts. CRUX simplifies cancer genome analysis in several ways: (1) it has an easy-to-use graphical interface; (2) it enables users to create custom cohorts, as well as analyse precompiled public and private user-created datasets; (3) it allows analyses to be run locally to address data privacy concerns (though an online version is also available); and (4) it makes it easy to use additional specialized tools by exporting data in the correct formats. We showcase CRUXs capabilities with case studies employing different types of cancer genome analysis, demonstrating how it can be used flexibly to generate valuable insights into cancer biology. CRUX is freely available at https://github.com/CCICB/CRUX and https://ccicb.shinyapps.io/crux (DOI: 10.5281/zenodo.8015714).

bioinformatics↗

A biophysical and structural analysis of DNA binding by oligomeric hSSB1 (NABP2/OBFC2B)

The oxidative modification of DNA can result in the loss of genome integrity and must be repaired to maintain overall genomic stability. We have recently demonstrated that human single stranded DNA binding protein 1 (hSSB1/NABP2/OBFC2B) plays a crucial role in the removal of 8-oxo-7,8-dihydro- guanine (8-oxoG), the most common form of oxidative DNA damage. The ability of hSSB1 to form disulphide-bonded tetramers and higher oligomers in an oxidative environment is critical for this process. In this study, we have used nuclear magnetic resonance (NMR) spectroscopy and surface plasmon resonance (SPR) experiments to determine the molecular details of ssDNA binding by oligomeric hSSB1. We reveal that hSSB1 oligomers interact with single DNA strands containing damaged DNA bases; however, our data also show that oxidised bases are recognised in the same manner as undamaged DNA bases. We further demonstrate that oxidised hSSB1 interacts with ssDNA with a significantly higher affinity than its monomeric form confirming that oligomeric proteins such as tetramers can bind directly to ssDNA. NMR experiments provide evidence that oligomeric hSSB1 is able to bind longer ssDNA in both binding polarities using a distinct set of residues different to those of the related SSB from Escherichia coli.

biochemistry↗