Mutational Evolution in a Lobular Breast Cancer Demonstrates Value of DNA sequencing

[Hopeful]

Nature. 2009 Oct 1;461(7265):809-813, SP Shah, RD Morin, J Khattra, L Prentice, T Pugh, A Burleigh, A Delaney, K Gelmon, R Guliany, J Senz, C Steidl, RA Holt, S Jones, M Sun, G Leung, R Moore, T Severson, GA Taylor, AE Teschendorff, K Tse, G Turashvili, R Varhol, RL Warren, P Watson, Y Zhao, C Caldas, D Huntsman, M Hirst, MA Marra, S Aparicio

ABSTRACT
Recent advances in next generation sequencing have made it possible to precisely characterize all somatic coding mutations that occur during the development and progression of individual cancers. Here we used these approaches to sequence the genomes (>43-fold coverage) and transcriptomes of an oestrogen-receptor- -positive metastatic lobular breast cancer at depth. We found 32 somatic non-synonymous coding mutations present in the metastasis, and measured the frequency of these somatic mutations in DNA from the primary tumour of the same patient, which arose 9 years earlier. Five of the 32 mutations (in ABCB11, HAUS3, SLC24A4, SNX4 and PALB2) were prevalent in the DNA of the primary tumour removed at diagnosis 9 years earlier, six (in KIF1C, USP28, MYH8, MORC1, KIAA1468 and RNASEH2A) were present at lower frequencies (1–13%), 19 were not detected in the primary tumour, and two were undetermined. The combined analysis of genome and transcriptome data revealed two new RNA-editing events that recode the amino acid sequence of SRP9 and COG3. Taken together, our data show that single nucleotide mutational heterogeneity can be a property of low or intermediate grade primary breast cancers and that significant evolution can occur with disease progression.

Supplementary editorial provided by OncologySTAT

In this study, Shah et al revealed the evolutionary nature of the tumor genome during progression of a low-intermediate grade, estrogen-receptor–positive lobular breast cancer. Sequencing of tumor genomes and transcriptomes from the same patient was used to compare genomic changes that occurred over a 9-year period during which the tumor had metastasized. Of the 32 nonsynonymous coding mutations found in metastatic cells, 19 were not present in the primary tumor DNA at diagnosis. In contrast, 11 of the 32 mutations were present in the primary tumor, signifying that the primary tumor itself exhibited genetic heterogeneity. Validation of 75 RNA editing events yielded 2 high-frequency nonsynonymous mutations located within the COG3 and SRP9 genes.

The results revealed that, not only was the primary tumor genetically heterogeneous, but also that a significant amount of genetic evolution had occurred during progression. Tumor protein translation was altered, as evidenced by changes in the DNA sequence and by modifications of RNA transcripts. It is unclear whether these changes were a consequence of radiotherapy or of tumor progression.

EXPERT COMMENTARY

Axel Grothey, MD, Associate Editor
Genetic instability, one of the hallmarks of cancer, not only leads to tumor cell heterogeneity, but it also contributes to various aspects of the malignant phenotype of cancer cells, as well as to the resistance of cancer cells to tumor-directed therapy. Differences in genetic markers and gene expression between primary tumors and metastases have previously been confirmed for specific genes and proteins, but genetic differences have not been determined on a genome-wide level due to technical limitations. As exemplified by the study conducted by Shah et al, the ability to sequence whole genomes of tumors within a short time frame allows us to obtain a better understanding of genetic factors that drive tumor biology in individual patients. Success in this area of research ultimately promises to open the door for the utmost individualization of therapeutic approaches in cancer.

Principal Investigator's Perspective
2009 Nov 4, Karen A. Gelmon, MD, FRCP(C)
Karen A. Gelmon, MD, FRCP(C) is Clinical Professor of Medicine, University of British Columbia, and Medical Oncologist, British Columbia Cancer Agency, Vancouver Cancer Centre, Vancouver, British Columbia, Canada.

Our research confirms that it is possible to sequence the entire genome of both a primary breast cancer tumor and a metastatic tumor. Our results, obtained from a single patient with lobular breast cancer, revealed that the primary tumor was genetically heterogeneous and that the tumor heterogeneity evolved significantly over time, such that certain mutations in the metastatic cancer cells were not present in the primary tumor.

Specifically, we found 32 mutations in the metastatic tumor, which was analyzed 9 years after the primary tumor was diagnosed. Of these 32 mutations, only 11 were also present in the primary tumor, and of these, only 5 could have been present in all of the tumor cells. The other 6 mutations were minimally represented in only a fraction of the primary tumor cells.

We believe that these results provide researchers and clinicians alike with considerable insights into how breast cancer develops and progresses, and it changes our views on how to approach treatment. Traditionally, we have assumed that tumor cells are genetically uniform, all containing the same mutations. Treatments are chosen based on the mutations or biomarkers present in those cells. Now that we know that subsets of cells with different mutations appear to exist from the outset, and that these cells have the capacity to evolve genetically, it becomes clear that genomic analysis will be important at every stage of the disease. Thus, tracking the genetic evolution of a tumor will be essential to tailoring therapy for an individual patient at a specific point in time. This will be an important step in personalizing medical treatment for patients with breast cancer and, we presume, other tumor types.

The state-of-the-art DNA sequencing used in this investigation represents a vast improvement in capacity and scale over previous technology, allowing us to obtain more detailed information much more rapidly than before. And DNA sequencing technology continues to evolve.

Our focus going forward will be to genetically characterize distinct subtypes of breast cancer, beginning with those that are particularly aggressive and therefore less responsive to available treatment options. This work will culminate in a comprehensive map of breast cancer mutations, based on genetic analysis of approximately 2000 cancers. We also plan to sequence the DNA from tumors of patients enrolled in clinical trials, for the purpose of evaluating any mutations that may be predictive of sensitivity or resistance to specific drugs.


Hopeful