Our lab studies how gene expression is post-transcriptionally dysregulated in various cancers, leading to generation and progression of malignancy. In particular, we are interested in RNA Binding Proteins (RBPs) that play a role in cancer development and progression by controlling localisation, stability, and translation of different functional categories of transcripts:
We use various omics technologies to study the role of RBPs in different aspects of post-transcriptional gene expression regulation. In particular, we are experts in Mass Spectrometry (MS) based proteomics, using various MS techniques to quantitatively study processes such as protein translation and RNA-Protein interactions, as well as combining proteomics data with RNA-sequencing to reveal the intricacies of post-transcriptional regulation by RBPs.
• Dodel M, Guiducci G, Dermit M, Krishnamurthy S, Stojic L*, Mardakheh FK* (2023) TREX reveals proteins that bind to specific RNA regions in living cells. BioRxiv (https://doi.org/10.1101/2023.06.30.547259).
• Khoroshkin MS, Buyan A, Dodel M, Navickas A, Yu J, Trejo F, Doty A, Baratam R, Zhou S, Joshi T, Miglani S, Choi B, Subramanyam V, Modi H, Corces R, Markett D, Kulakovskiy IV, Mardakheh FK*, Goodarzi H* (2023)
Systematic identification of post-transcriptional regulatory modules. BioRxiv (https://doi.org/10.1101/2023.02.27.530345).
• Azman MS, Alard EL, Dodel M, Capraro F, Faraway R, Dermit M, Fan W, Chakraborty A, Ule J, Mardakheh FK*. (2023) An ERK1/2-driven RNA-binding switch in nucleolin drives ribosome biogenesis and pancreatic tumorigenesis downstream of RAS oncogene. EMBO J. e110902.
• Dermit M
, Dodel M , Lee FCY, Azman MS
, Schwenzer H, Jones JL, Blagden
SP, Ule J, Mardakheh FK*. (2020) Subcellular mRNA localization regulates
ribosome biogenesis in migrating cells. Developmental Cell. 55(3):298-313.
• Dermit M, Dodel M, Mardakheh FK*. (2017) Methods
for monitoring and measurement of protein translation in time and space. Mol Biosyst. 13:2477-2488.
• Mardakheh FK*, Paul A, Kümper S, Sadok A, Paterson
H, Mccarthy A, Yuan Y, and Marshall
CJ. (2015) Global
analysis of mRNA, translation, and protein localizations: local translation is a key regulator of cell-protrusions. Developmental Cell. 35:344-57.