Metabolic Engineering - Bioinformatics Dr. Olga Papadodima | Research Scientist, Group Leader
Research Directions
Our group works on translational research in Life Sciences, by exploiting experimental and computational approaches, aiming at the deeper understanding of molecular mechanisms implicated in several pathologies. During the last years, our research focuses mainly on the field of cancer genomics, with the goal to identify alterations and regulatory networks governing the pathophysiology of cancer and identify candidate new biomarkers and therapeutic targets.
The main directions of our research are:
a) mapping the mutational and transcriptional profile of different tumors
b) profiling the transcriptome of cancer cells in response to treatment with selected bioactive molecules
c) developing bioinformatics tools for the analysis of in-house generated genomic data and for the exploration of molecular and clinical data from well-known cancer-associated repositories
Research Objectives
The main objective of our research is the identification of driver genes, mutations or cellular networks that could represent candidate biomarkers or therapeutic targets. To this end, we focus mainly on the analysis of genomic and transcriptomic data (Next Generation Sequencing methodologies, microarrays) and taking advantage of sophisticated bioinformatics tools, high-dimensional statistics, information theory and machine learning we attempt to holistically describe complex biological processes, like cancer manifestation and progression. In this context, we are interested in the derivation of informative gene signatures that could reflect the underlying disease–related mechanisms and could act as a pool of putative biomarkers for characterization of disease state, prediction of drug susceptibility and ultimately enable patient stratification. In the concept of precision oncology, we collaborate with clinical doctors in an effort to exploit genomics to group patients into molecular disease sub-types that could benefit from tailored therapeutic approaches. In parallel, in collaboration with other groups of ICB, we are studying the cellular response upon treatment with selected bioactive molecules, aiming to elucidate the triggered molecular mechanisms and reveal new therapeutic targets or possible combinatorial therapeutic interventions.
Group Structure and Personnel
Olga Papadodima, PhD, Research Scientist
Aristotelis Chatziioannou, PhD, Collaborating Researcher
Konstantinos Voutetakis, MSc, PhD, Technical Scientific Personnel
TRANSITION: “TRANSlating the complexIty of melanoma diagnosis into raTional therapeutic stratificatiON” (MIS 5031295) which is implemented under the Action “Research-Create-Innovate”, funded by the Operational Programme "Competitiveness, Entrepreneurship and Innovation" (NSRF 2014-2020) and co-financed by Greece and the European Union (European Regional Development Fund), 136398.36 €, 24/7/2018-24/4/2021
STHENOS β (KRIPIS ΙΙ): ‘Targeted therapeutic approaches against degenerative diseases with special focus on cancer and ageing-optimisation of the targeted bioactive molecules’, MIS: 5002398. Operational Programme "Competitiveness, Entrepreneurship and Innovation" (NSRF 2014-2020), 22000 €, 01/11/2017-30/06/2021
ELIXIR-GR: “The Hellenic infrastructure for biological data management and analysis” (MIS: 5002780) which is implemented under the Action “Reinforcement of the Research and Innovation Infrastructure”, funded by the Operational Programme "Competitiveness, Entrepreneurship and Innovation" (NSRF 2014-2020) and co-financed by Greece and the European Union (European Regional Development Fund), 6175 €, 18/12/2017-31/12/2021
HPMNC: Hellenic Precision Medicine Network on Cancer, Greek state-SIEMENS agreement, total NHRF budget 250000 €, 22/8/2018-31/12/2021
Recent publications
Koumaki, K., Kontogianni, G., Kosmidou, V., Pahitsa, F., Kritsi, E., Zervou, M., Chatziioannou, A., Souliotis, V.L., Papadodima, O., Pintzas, A. (2021). BRAF paradox breakers PLX8394, PLX7904 are more effective against BRAFV600Ε CRC cells compared with the BRAF inhibitor PLX4720 and shown by detailed pathway analysis. Biochimica et Biophysica Acta - Molecular Basis of Disease, 1867 (4), art. no. 166061 https://doi.org/10.1016/j.bbadis.2020.166061
Maglogiannis, I., Kontogianni, G., Papadodima, O., Karanikas, H., Billiris, A., Chatziioannou, A. (2021). An Integrated Platform for Skin Cancer Heterogenous and Multilayered Data Management. Journal of Medical Systems, 45 (1), art. no. 10 https://doi.org/10.1007/s10916-020-01679-3
Maurel, M., Obacz, J., Avril, T., Ding, Y.-P., Papadodima, O., Treton, X., Daniel, F., Pilalis, E., Hörberg, J., Hou, W., Beauchamp, M.-C., Tourneur-Marsille, J., Cazals-Hatem, D., Sommerova, L., Samali, A., Tavernier, J., Hrstka, R., Dupont, A., Fessart, D., Delom, F., Fernandez-Zapico, M.E., Jansen, G., Eriksson, L.A., Thomas, D.Y., Jerome-Majewska, L., Hupp, T., Chatziioannou, A., Chevet, E., Ogier-Denis, E., (2019). Control of anterior GRadient 2 (AGR2) dimerization links endoplasmic reticulum proteostasis to inflammation EMBO Molecular Medicine (2019) 11:e10120 https://doi.org/10.15252/emmm.201810120
Vlachavas, E.I., Pilalis, E., Papadodima, O., Koczan, D., Willis, S., Klippel, S., Cheng, C., Pan, L., Sachpekidis, C., Pintzas, A., Gregoriou, V., Dimitrakopoulou-Strauss, A., Chatziioannou, A., (2019). Radiogenomic Analysis of F-18-Fluorodeoxyglucose Positron Emission Tomography and Gene Expression Data Elucidates the Epidemiological Complexity of Colorectal Cancer Landscape. Computational and Structural Biotechnology Journal, 17, pp. 177-185. https://doi.org/10.1016/j.csbj.2019.01.007
Papadodima, O., Kontogianni, G., Piroti, G., Maglogiannis, I., Chatziioannou, A., (2019). Genomics of cutaneous melanoma: focus on next-generation sequencing approaches and bioinformatics. J Transl Genet Genom 2019; 3:7. https://doi.org/10.20517/jtgg.2018.33
Kontogianni, G., Piroti, G., Maglogiannis, I., Chatziioannou, A., Papadodima, O., (2018) Dissecting the mutational landscape of cutaneous melanoma: An omic analysis based on patients from Greece. Cancers, 10 (4), art. no. 96. https://doi.org/10.3390/cancers10040096
Lhomond, S., Avril, T., Dejeans, N., Voutetakis, K., Doultsinos, D., McMahon, M., Pineau, R., Obacz, J., Papadodima, O., Jouan, F., Bourien, H., Logotheti, M., Jégou, G., Pallares-Lupon, N., Schmit, K., Le Reste, P.-J., Etcheverry, A., Mosser, J., Barroso, K., Vauléon, E., Maurel, M., Samali, A., Patterson, J.B., Pluquet, O., Hetz, C., Quillien, V., Chatziioannou, A., Chevet, E., (2018). Dual IRE1 RNase functions dictate glioblastoma development. EMBO Molecular Medicine, 10 (3), art. no. e7929, 95 https://doi.org/10.15252/emmm.201707929
Rubio-Patino, C., J. P. Bossowski, G. M. De Donatis, L. Mondragon, E. Villa, L. E. Aira, J. Chiche, R. Mhaidly, C. Lebeaupin, S. Marchetti, K. Voutetakis, A. Chatziioannou, F. A. Castelli, P. Lamourette, E. Chu-Van, F. Fenaille, T. Avril, T. Passeron, J. B. Patterson, E. Verhoeyen, B. Bailly-Maitre, E. Chevet and J. E. Ricci (2018). Low-Protein Diet Induces IRE1alpha-Dependent Anticancer Immunosurveillance. Cell Metab 27(4): 828-842 e827. https://doi.org/10.1016/j.cmet.2018.02.009
Le Reste PJ, Pineau R, Voutetakis K, Samal J, Jégou G, Lhomond S, Gorman AM, Samali A, Patterson JB, Zeng Q, Pandit A, Aubry M, Soriano N, Etcheverry A, Chatziioannou A, Mosser J, Avril T, Chevet E. Local intracerebral inhibition of IRE1 by MKC8866 sensitizes glioblastoma to irradiation/chemotherapy in vivo. Cancer Lett. 2020 Dec 1;494:73-83. Epub 2020 Sep 1. PMID: 32882336. https://doi.org/10.1016/j.canlet.2020.08.028
Yeles C., Vlachavas E.-I., Papadodima O., Pilalis E., Vorgias C.E., Georgakilas A.G., Chatziioannou A. Integrative bioinformatic analysis of transcriptomic data identifies conserved molecular pathways underlying ionizing radiation-induced bystander effects (RIBE). Cancers, 2017, 9 (12), art. no. 160 https://doi.org/10.3390/cancers9120160
