Single cell sequencing

Biologically important differences between individual cells are averaged out in sequencing approaches from bulk tumor cell populations. This is a fundamental problem in oncology since the clinically highly relevant information on tumor heterogeneity is lost with respect to the initial tumor composition, the cellular response to drug treatment and the relapse of the tumor. To address these current limitations single cell sequencing (sc-seq) based 'omics' methods (genomics, transcriptomics and epigenomics) are emerging. They synergize with imaging and cell sorting technologies as an important new opportunity to dissect cancer cell populations in personalized medicine approaches. Furthermore, they are compementary to the chromatin perturbances methods used in our lab with fluorescence microscopy readouts.

Immune cell types in the bone marrow based identified byCITE-seq (scRNA-seq plus 192 surface markers).

Key references

Sant P, Rippe K, Mallm JP (2023) Approaches for single-cell RNA sequencing across tissues and cell types. Transcription, published online 16 April 2023. doi: 10.1080/21541264.2023.2200721 | Abstract | Reprint | Article metrics

Friedrich MJ, Neri P, Kehl N, Michel J, Steiger S, Kilian M, Leblay N, Maity R, Sankowski R, Lee H, Barakat E, Ahn S, Weinhold N, Rippe K, Bunse L, Platten M, Müller-Tidow C, Goldschmidt H, Raab MS, Bahlis NJ (2023) The preexisting T Cell landscape determines response to T cell-engagers therapy. Cancer Cell 41, 711-725 e6. doi: 10.1016/j.ccell.2023.02.008 | Abstract | Reprint | Article metrics

Tirier SM, Mallm J-P, Steiger S, Poos AM, Awwad M, Giesen N, Casiraghi N, Susak H, Bauer K, Baumann A, John L, Seckinger A, Hose D, Müller-Tidow C, Goldschmidt H, Stegle O, Hundemer M, Weinhold N, Raab MS, Rippe K (2021) Subclone specific microenvironmental impact and drug response in refractory multiple myeloma revealed by single cell transcriptomics. Nat Commun 12, 6960. doi: 10.1038/s41467-021-26951-z | Abstract | Reprint | Article metrics