Chapter 4 Specific Projects

Alissa
My two main projects are 1) Modeling ITH in cancer cell lines with a focus on dynamics, differential drug sensitivity, and cancer cell-cancer cell interactions in HNSCC (with Rotem). 2) Spatial transcriptomics of GBM (in collaboration with the Suva Lab).

Rony
My thesis focuses on GBM intra-tumor heterogeneity, for which I have 3 projects in collaboration with Mario Suva’s lab at MGH: 1) modeling the GBM states in cancer cell lines and a mouse model of GBM, 2) exploring the GBM microenvironment cell-cell interactions in regards to the cellular states, and 3) targeting the GBM states as a therapeutic approach for GBM.

Mike
My work concerns deconvolution of bulk RNA-seq data to identify signatures of tumour subpopulations or cell states. My current project focuses on distinguishing EMT (or partial EMT) from stromal cells in bulk transcriptomes.

Michael
My work broadly focuses on ITH in head and neck cancer. In collaboration with Sid Puram’s lab I analyse scRNASeq data from patients with oropharyngeal, laryngeal and oral cavity cancer in order to find tumour genetic subclones and functional metaprograms in the cancer cells and microenvironment.

Noam H
My work is to do a regulatory follow up to lab discoveries on chromatin organization level using single cell ATAC-seq on two main ITH projects: 1) head and neck cancer 2) GBM.

Julie
My work focuses on understanding expression heterogeneity in gliomas. I analyse primarily scRNA-seq data from the Suva lab to 1) define the subpopulations of cancer cells that exist in different glioma types, 2) understand the emergence of these subpopulations as a function of cell lineage, genetics and the TME and 3) revisit the distinctions between glioma types.

Noam G
My project focuses on deconvolution of bulk RNA-seq data to identify and distinguish IFN response and MHC class ii genes in cancer cells from immune cells.