Sequencing cancer

Abstract: Cancer forms highly heterogeneous tissues at several molecular levels, genomic, proteomic, transcriptomic and other epigenetic traits. The level of complexity is further augmented by the dynamic nature of tumor progression with cancer cell populations evolving in a clonal manner. The clonal evolution of tumors is shaped by selective pressure exerted by endogenous factors such as intra tumor dynamics between different clones and exogenous factors such as microenvironment and therapeutics. The technical advances in next generation sequencing has accelerated and facilitated a massive acquisition of genomic and transcriptional data from different cancers during the last decade. Despite the increased knowledge in the transcriptional and genomic landscape of tumors, many questions have still not been fully addressed and one of the explanations lies in the heterogenetic nature of cancer tissues that has to be desiccated into its fundamental parts - the single cancer cells. In this thesis the heterogenetic nature of normal- and cancer tissues and the implications to single-cell based methods are discussed. In order to study the transcriptome of single-cells delicate molecular tools needs to be developed. In the two first papers we describe a single-cell RNA sequencing method that is highly sensitive and can produce full gene expression profiles of hundreds of single-cells per sequencing experiment. Several models have been proposed for tumor evolution and one fundamental question is the hierarchical organization of tumor propagating cells. In paper III we studied the tumor progression in myelodysplastic syndromes (MDS), a clonal hematological disorder in which multiple haematological lineages are affected. We found that the putative MDS-stem cell (SC) population is functionally and molecularly distinct from its downstream progenitors and that in MDS, self-renewal and that acquisition of somatic mutations was restricted to the MDS-stem cell population. By targeted sequencing of purified populations and single-cell derived stem cell clones we could track all somatic mutations found in the bone marrow of MDS patients to the distinct MDS-stem cells providing definitive evidence for the existence of rare human MDSSCs in vivo. Another aspect of heterogeneity in solid tumors is the genetic heterogeneity between primary tumor and the metastatic lesions. In paper IV we addressed the heterogeneity in metastatic breast cancer by comparing the genetic profiles of ten pairs of primary tumor to their metastatic lesion obtained from exome sequencing. We found a marked heterogeneity in number of somatic mutations as well as the extent of chromosomal aberrations in the metastatic lesions. We also found a number of mutated genes to be significantly enriched in the metastases. The clinical implications to metastatic heterogeneity is supported by altered receptor status and drug resistance in metastatic lesions and suggest that extended characterization of the metastases is of great importance. In summary, heterogeneity is the main characteristic of both normal and cancer tissues. To resolve the mixed patterns of gene regulation and genomic aberrations, single-cell based approaches needs to be applied and will be a powerful tool to shed light on questions in tumor biology such as transcription dynamics and genetic selection.

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