Trans-omic approach to colorectal cancer: an integrative computational and clinical perspective
At a glance
- Project leader : Dr. Maria Anisimova
- Project team : Inbar Leaf, Oxana Lundström , Max Verbiest, Huifang You
- Project budget : CHF 2'900'000
- Project status : ongoing
- Funding partner : SNSF (Sinergia / Projekt Nr. 193832)
- Project partner : IBM Research GmbH, Universität Bern, Eidgenössische Technische Hochschule Zürich ETH
- Contact person : Maria Anisimova
Colorectal Cancer (CRC) is an important cause of cancer-related mortality world-wide. The Consensus Molecular Subtypes represent the first comprehensive molecular classification with clinical implications, but many aspects are still missing. We use a transomic approach to improve the stratification, prognosis, and treatment prediction of CRC patients. What is the novelty of the proposed approach? Precision medicine is a reality in some tumor types, yet this cannot be said for CRC, where predictive biomarkers are scarce and are more effective at identifying non-responders than patients who may benefit from treatment. Here, we aim to provide insights into CRC and therapy responsiveness by combining different omics approaches, such as genomics, histomics, and pharmacogenomics, and integrating these by means of an AI-driven multimodal classifier. To improve the current understanding of the molecular basis of CRC we work on characterizing the relationship between morphology and molecular cancer variants in genotype, transcriptome, proteome and single-cell image data. In particular, variations in short tandem repeats of human genomes are associated with gene expression changes in samples from CRC patients. Here, we will systematically search for tandem repeat variations in tumors, annotating and cataloguing those variants that lead to tumorigenesis of colorectal cancer.
Verbiest, Max; Maksimov, Mikhail; Jin, Ye; Anisimova, Maria; Gymrek, Melissa; Bilgin Sonay, Tugce,
Mutation and selection processes regulating short tandem repeats give rise to genetic and phenotypic diversity across species.
Journal of Evolutionary Biology.
Available from: https://doi.org/10.1111/jeb.14106
Nguyen, Huu-Giao; Lundström, Oxana; Blank, Annika; Dawson, Heather; Lugli, Alessandro; Anisimova, Maria; Zlobec, Inti,
Image-based assessment of extracellular mucin-to-tumor area predicts consensus molecular subtypes (CMS) in colorectal cancer.
35, pp. 240-248.
Available from: https://doi.org/10.1038/s41379-021-00894-8
Delucchi, Matteo; Näf, Paulina; Bliven, Spencer; Anisimova, Maria,
TRAL 2.0 : tandem repeat detection with circular profile hidden Markov models and evolutionary aligner.
Frontiers in Bioinformatics.
Available from: https://doi.org/10.3389/fbinf.2021.691865
Verbiest, Max; Delucchi, Matteo; Bilgin Sonay, Tugce; Anisimova, Maria,
Beyond microsatellite instability : intrinsic disorder as a potential link between protein short tandem repeats and cancer.
Frontiers in Bioinformatics.
Available from: https://doi.org/10.3389/fbinf.2021.685844