Yang, Tsun-Po
(2022).
Cell type-specific dynamics of DNA replication timing in primary cancer whole-genome sequences.
PhD thesis, Universität zu Köln.
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Abstract
Although the whole-genome tumour DNA from human primary cancers have been routinely sequenced in recent large-scale cancer sequencing studies to identify somatic mutations, little is known about their roles in DNA replication timing. However, mechanisms underlying this timing programme are also implicated in transcriptional activities and the mutational landscape of the cancer genome in a cell type-specific manner. Understanding where exactly, and how differently, DNA replication is initiated and terminated across different cancer genomes is of fundamental importance and will help to understand the cellular plasticity that give rise to cancer and help cancer cells survive during cancer cell proliferation. In this thesis, I propose to fully explore the entire primary cancer whole-genome sequences, and hypothesise that they may provide a snapshot in time, in space, and in specific cell type of the tumour replication timing programme. In Chapter 2, I measure the proportion of S phase cells present in a primary tumour using whole-genome sequencing (WGS) data, and use it to separate tumour samples based on their cell cycle status, referred to as in silico sample sorting method. Upon in silico sorting of primary tumour samples, in Chapter 3, I adapt the S to G1 read depth ratio approach, and apply it to directly profile the tumour replication timing (RT) from 256 cancer whole genomes of three tumour types. Finally, I demonstrate that the temporal dynamics of tumour replication timing is preserved in closely related normal tissues, as well as in lineage-specific cancer cell lines, suggesting the cellular plasticity of the timing programme captured by my direct profiling approach. Furthermore, in Chapter 4, I introduce a novel resampling-based replication fork directionality (RFD) methodology to model the stochastic but symmetrical nature of bi-directional replication, and use it to simultaneously fine map the replication origins and termini at 1 kb (kilobase) resolution using the same primary cancer WGS data. Unexpectedly, I find that the genome-wide distribution of termination events is tightly coordinated with the initiation activities in both the normal and cancer genomes, which has not been previously reported in humans using directional sequencing of Okazaki fragments (OK-seq) in vitro. However, the distribution of my reconstructed RFD domains suggests that replication termini are determined by, and located between two activating origin firings in the human genome, which is consistent with the consensus notion widely reported in yeast. Nevertheless, I find that the spatial landscapes of my reconstructed RFD domains are also preserved in closely related normal tissues and lineage-specific cancer cell lines, in line with the cellular plasticity of tumour RT shown in Chapter 3. Furthermore, in Chapter 5, I demonstrate that my reconstructed RFD domains are significantly coupled with the transcriptional activities across three tumour types, thus providing strong support for a bona fide mapping on fork initiation, progression, and termination by my novel resampling-based RFD methodology. Altogether, my novel in silico framework allows one to assess the tumour RT and RFD domains directly using primary cancer whole-genome sequences without the need for in vitro sorting procedures, and therefore opens up opportunities for the routinely performed WGS data from the broader cancer genomics community. The cell type specificity of the tumour timing programme recapitulated by my novel in silico framework also adds a new spatiotemporal perspective to the three-dimensional cancer genome, thus could provide new insights into the identification of potential cancer targets that is topologically preserved in specific cancer types.
| Item Type: | Thesis (PhD thesis) | ||||||||
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| URN: | urn:nbn:de:hbz:38-551524 | ||||||||
| Date: | 2022 | ||||||||
| Language: | English | ||||||||
| Faculty: | Faculty of Mathematics and Natural Sciences | ||||||||
| Divisions: | Faculty of Medicine > Sonstiges > Translationale Genomik | ||||||||
| Subjects: | Natural sciences and mathematics Life sciences Medical sciences Medicine |
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| Date of oral exam: | 9 February 2022 | ||||||||
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| Refereed: | Yes | ||||||||
| URI: | http://kups.ub.uni-koeln.de/id/eprint/55152 |
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