Project 1: Genetic and adaptive dynamics of microbiome in colorectal cancer: How do microbes adapt to the hostile tumour microenvironment? (ADAPT-MIC)
Nordic EMBL PIs: Rafa Najumudeen (FIMM) and Chinmay Dwibedi (MIMS)
Current research in the cancer microbiome highlights the interaction between gut microbes and the host in tumor progression, but the adaptation of these microbes to the tumor's hostile microenvironment remains poorly understood. This project aims to identify the spatial genetic and adaptive dynamics of tumour microbiome in colorectal cancer. To do so, we will integrate single-cell genomics, transcriptomics and clinical data using unique novel mouse models, spatial technologies and analytical methods.
Host institution and employment: FIMM, University of Helsinki, Finland
Collaborating site: MIMS, Umeå University, Sweden
Find all information and apply here.
Project 2: Novel insights into the cancer genome and epigenome using long-read sequencing and machine learning
Nordic EMBL PIs: Esa Pitkänen (FIMM) and Biswajyoti Sahu (NCMM)
Human tumors are characterized by recurrent mutations in the well-defined cancer driver genes, but also non- mutational epigenetic reprogramming and phenotypic plasticity controlled by transcription factors are important contributors to tumorigenesis. We will utilize cutting-edge long-read nanopore sequencing combined with deep machine learning approaches to model the epigenetic changes and mutational mechanisms in cancers originating from endodermal tissues. The project aims to reveal novel mechanistic details about the development of human cancer.
Host institution and employment: FIMM, University of Helsinki, Finland
Collaborating site: NCMM, University of Oslo, Norway
Find all information and apply here.
Project 3: Revealing the epigenetic history of colon cancer progression (REVEAL)
Nordic EMBL PIs: Biswajyoti Sahu (NCMM) and Rafa Najumudeen (FIMM)
Colorectal cancers (CRC) are driven by complex genetic and epigenetic changes that enable cancer cells to adapt to their dynamic environment. We aim to uncover the epigenetic mechanisms underlying colon cancer initiation, progression, and therapy resistance by using genome scale Massively Parallel Reporter Assays in organoid models to identify key transcription factors and cis-regulatory elements driving oncogenic processes. After validation of these findings, we will record the epigenetic reprogramming in vivo. Our approach integrates genomic and epigenomic technologies to map the temporal epigenetic history of colon cancer.
Host institution and employment: NCMM, University of Oslo, Norway
Collaborating site: FIMM, University of Helsinki, Finland
Find all information and apply here.
