Tumor diversity and evolution revealed through RADseq

Abstract

SummaryCancer is an evolutionary disease, and there is increasing interest in applying tools from evolutionary biology to understand cancer progression. Restriction-site associated DNA sequencing (RADseq) was developed for the field of evolutionary genetics to study adaptation and identify evolutionary relationships among populations. Here we apply RADseq to study tumor evolution, which allows for unbiased sampling of any desired frequency of the genome, overcoming the selection bias and cost limitations inherent to exome or whole-genome sequencing. We apply RADseq to both human pancreatic cancer and zebrafish melanoma samples. Using either a low-frequency (SbfI, 0.4% of the genome) or high-frequency (NsiI, 6-9% of the genome) cutter, we successfully identify single nucleotide substitutions and copy number alterations in tumors, which can be augmented by performing RADseq on sublineages within the tumor. We are able to infer phylogenetic relationships between primary tumors and metastases. These same methods can be used to identify somatic mosaicism in seemingly normal, non-cancerous tissues. Evolutionary studies of cancer that focus on rates of tumor evolution and evolutionary relationships among tumor lineages will benefit from the flexibility and efficiency of restriction-site associated DNA sequencing.

The mutREAD method detects mutational signatures from low quantities of cancer DNA

“…mutREAD could further improve the mutational signature-based prediction of homologous recombination deficiency in clinical samples 14,26 . Together with computational tools for coarse-grained copy alteration detection 22,27 , mutREAD could provide a detailed view of the role of mutational processes in cancer progression and evolution from archived material. Finally, correlative analyses of mutational signatures with endogenous and environmental parameters to understand the source of so far unknown mutational signatures will shed light on the etiology of cancers.…”

“…Here, we propose an easy-to-use method for mutational signature detection building on reduced representation sequencing (RR-seq) approaches that have been successfully applied in population genetics analyses 21,22 . Our protocol is based on sequencing a reproducible, random subset of genomic regions generated by double-enzymatic digestion and subsequent fragment size-selection of the DNA sample.…”

Effects of the MDM-2 inhibitor Nutlin-3a on PDAC cells containing and lacking WT-TP53 on sensitivity to chemotherapy, signal transduction inhibitors and nutraceuticals

“…Network analysis (Zhang et al, 2017) is also being used to identify genes which may be involved in PDAC. Novel genes implicated in tumor diversity and evolution are being identified by restriction-site associated DNA sequencing (RADseq) (Perry et al, 2017). Patient-derived xenografts made from human PDAC tumor specimens are also being created to identify additional genes that are aberrantly expressed in PDAC.…”

Down‐regulation of metabolic pathways could offset the poor prognosis conferred by co‐existent diabetes mellitus in pancreatic (head) adenocarcinoma

“…These subtypes have laid the foundation for an understanding of the genomic landscape of PDAC. However, given the dismal prognosis of patients suffering from PDAC, an appreciation of the tumour biology that ultimately determines survival in PDAC 43,44 tempered by knowledge of tumour diversity, 45 should guide improvement of outcomes in PDAC. The Class 1 subtype in the present study appears to be more closely related to the ADEX subtype of Bailey, 17 somewhat similar to the exocrine‐like subtype of Collisson, 12 that was also noted by Moffitt et al 16 The Class 2 in our study, on the other hand, neither resembles the ‘basal‐like’ subtype of Moffitt, 16 nor the ‘classical’ subtype of Collisson 12 and Moffitt 16 as there was no difference in GATA6 expression between the two subtypes (Fig.…”