Final Report Summary - CHROMOTHRIPSIS (Dissecting the Molecular Mechanism of Catastrophic DNA Rearrangement in Cancer)
We developed conceptual criteria (WP1), and standards, for the accurate inference of chromothripsis events, which have formed the basis for numerous follow-up research studies on chromothripsis (Korbel & Campbell, Cell 2013). We note that although written and submitted after the ERC application was made, publication of this conceptual paper occurred in 2013, i.e. prior to the start date of this ERC grant.
To efficiently detect and study the consequences of complex DNA rearrangements including chromothripsis events (WP3/WP4), we developed an integrative cell-based method (Mardin et al. Mol Sys Biol 2015) termed Complex Alterations after Selection and Transformation (CAST). The principle of this system is the use of cellular perturbations coupled with soft agar selection followed by massively-parallel sequencing (WP3). We employed the CAST methodology to characterize catastrophic structural rearrangement formation processes including breakage-fusion-bridge-cycles and chromothripsis events, to characterize their temporal sequence, as well as to investigate their impact on the transcriptome and on cell division. Additionally, we also studied the influence of chromothripsis on transcriptional states, and showed that hyperploid cells are particularly prone to undergo chromothripsis events. In addition, we also identified a link between telomere shortening and chromothripsis events.
Enabled by our ERC funding, we further analysed a large number of cancer genomic datasets from the Pan Cancer Analyses of Whole Genomes (PCAWG) Project, and from specific cancer types – in particular cancer genomes from children suffering from the brain tumor medulloblastoma. Our analyses enabled us to link germline genetic variants with a number of somatic mutational processes, including such leading to complex DNA rearrangements. We published our results in two manuscripts, one published in Lancet Oncology (Waszak et al. 2018) and on published as a preprint on the BioRxiv (Waszak et al. 2017, http://sci-hub.tw/10.1101/208330). Our analyses implicate damaging germline variants in several genes including TP53, BRCA1, BRCA2 and MBD4 with specific somatic mutation patterns. And although we found massively complex rearrangements especially in samples with genetic or epigenetic BRCA1 inactivation, it is likely that the process uncovered bears some difference to classical chromothripsis events suggesting involvement of DNA replication-associated genomic catastrophes (Waszak et al. BioRxiv 2017). Another pan-cancer study we pursued assessed somatic copy-number alterations, point mutations and transcriptomic changes, and indicated that overexpression of cell-cycle-related genes is primarily a characteristic of proliferation, and likely tumor evolution, rather than ongoing genomic instability (Buccitelli et al. Genome Res 2017).
More recently, we developed a single cell methodology suited to identify and fine-map structural rearrangement events (including catastrophic DNA rearrangement events) in cell lines and patient samples (work in progress). We discovered a subclonal chromothripsis/ chromoanasynthesis (for complex genomic rearrangement resulting from aberrant DNA replication) event in these samples, and uncovered a surprisingly high rate of complex rearrangements formed through breakage-fusion-bridge cycles in epithelial cells using this methodology (Sanders et all. submitted).
To efficiently detect and study the consequences of complex DNA rearrangements including chromothripsis events (WP3/WP4), we developed an integrative cell-based method (Mardin et al. Mol Sys Biol 2015) termed Complex Alterations after Selection and Transformation (CAST). The principle of this system is the use of cellular perturbations coupled with soft agar selection followed by massively-parallel sequencing (WP3). We employed the CAST methodology to characterize catastrophic structural rearrangement formation processes including breakage-fusion-bridge-cycles and chromothripsis events, to characterize their temporal sequence, as well as to investigate their impact on the transcriptome and on cell division. Additionally, we also studied the influence of chromothripsis on transcriptional states, and showed that hyperploid cells are particularly prone to undergo chromothripsis events. In addition, we also identified a link between telomere shortening and chromothripsis events.
Enabled by our ERC funding, we further analysed a large number of cancer genomic datasets from the Pan Cancer Analyses of Whole Genomes (PCAWG) Project, and from specific cancer types – in particular cancer genomes from children suffering from the brain tumor medulloblastoma. Our analyses enabled us to link germline genetic variants with a number of somatic mutational processes, including such leading to complex DNA rearrangements. We published our results in two manuscripts, one published in Lancet Oncology (Waszak et al. 2018) and on published as a preprint on the BioRxiv (Waszak et al. 2017, http://sci-hub.tw/10.1101/208330). Our analyses implicate damaging germline variants in several genes including TP53, BRCA1, BRCA2 and MBD4 with specific somatic mutation patterns. And although we found massively complex rearrangements especially in samples with genetic or epigenetic BRCA1 inactivation, it is likely that the process uncovered bears some difference to classical chromothripsis events suggesting involvement of DNA replication-associated genomic catastrophes (Waszak et al. BioRxiv 2017). Another pan-cancer study we pursued assessed somatic copy-number alterations, point mutations and transcriptomic changes, and indicated that overexpression of cell-cycle-related genes is primarily a characteristic of proliferation, and likely tumor evolution, rather than ongoing genomic instability (Buccitelli et al. Genome Res 2017).
More recently, we developed a single cell methodology suited to identify and fine-map structural rearrangement events (including catastrophic DNA rearrangement events) in cell lines and patient samples (work in progress). We discovered a subclonal chromothripsis/ chromoanasynthesis (for complex genomic rearrangement resulting from aberrant DNA replication) event in these samples, and uncovered a surprisingly high rate of complex rearrangements formed through breakage-fusion-bridge cycles in epithelial cells using this methodology (Sanders et all. submitted).