Abstract PR03: Pan-cancer analysis of the etiology and consequences of intra-tumor heterogeneity
Authors: Andor Noemi , Graham Trevor A. , Petritsch Claudia , Ji* Hanlee P. , Maley* Carlo C. 
Published: November 2015

Tumors are typically mosaics of mutant clones that have evolved from a common ancestral cell1–3. This intra-tumor heterogeneity (ITH) is thought to drive both neoplastic progression and acquired therapeutic resistance4–6. Availability of just one sample per tumor and moderate sequencing depth have limited systematic analysis of ITH during previous TCGA pan-cancer analyses7–9, confining the study of ITH to a small numbers of tumor samples and cancer types10–13. The molecular and histopathological causes of ITH and its prognostic significance have thus far remained uncertain14–17.

To overcome these limitations, we used an analysis method called EXPANDS18 that estimates the proportion of cells harboring specific mutations from exome sequencing data, as well as other methods that quantify ITH15,19. We extrapolate the number of genetically diverse clonal subpopulations in 1,165 primary tumors among 12 different cancer types from TCGA and investigate mechanisms underpinning ITH as well as the correlation of ITH and genomic instability with prognosis. Lastly we validate the prognostic significance of genomic instability in an independent, high-density SNP-array dataset consisting of 2010 tumor samples, across seven additional cancer types.

We found evidence of ITH in the vast majority of tumors. Driver gene mutations, prevalence of copy number gains and tumor microenvironment composition were significantly associated with increased ITH. Mutations in driver genes tended to have a characteristic clone size, suggesting differential fitness effects of those mutations. The detection of a mutation in a driver gene that typically appears in a small clone was a predictor of poor survival. In general, ITH was a universal biomarker of prognosis: across cancer types poor prognosis was associated with intermediate, rather than very low or high, levels of ITH. This was also true for the fraction of tumor genome affected by copy number alterations16,20: tumors with intermediate copy number burden (50 to 75% of the genome affected by copy number alterations) progressed faster than tumors with higher copy number burden, independent of cancer type. Chemo-radiation therapy administration was more efficient in decelerating tumor progression among patients with intermediate copy number burden than among patients with low or high copy number burden. These results were validated and confirmed in the independent SNP-array dataset.

This study suggests a tradeoff exists between the costs and benefits of genomic instability21,22 that impacts both the evolvability and fitness of the tumor cell population. In the future, this tradeoff might be exploited to improve survival. In summary, we have shown that ITH is a universal feature of human cancers that predicts survival.

References:

1. Marusyk, A. & Polyak, K. Tumor heterogeneity: causes and consequences. Biochim. Biophys. Acta 1805, 105–117 (2010).

2. Greaves, M. & Maley, C. C. Clonal evolution in cancer. Nature 481, 306–313 (2012).

3. Nowell, P. C. The clonal evolution of tumor cell populations. Science 194, 23–28 (1976).

4. Bonavia, R., Inda, M.-M., Cavenee, W. K. & Furnari, F. B. Heterogeneity maintenance in glioblastoma: a social network. Cancer Res. 71, 4055–4060 (2011).

5. Taylor, T. E., Furnari, F. B. & Cavenee, W. K. Targeting EGFR for treatment of glioblastoma: molecular basis to overcome resistance. Curr. Cancer Drug Targets 12, 197–209 (2012).

6. Forshew, T. et al. Noninvasive identification and monitoring of cancer mutations by targeted deep sequencing of plasma DNA. Sci. Transl. Med. 4, 136ra68 (2012).

7. Hoadley, K. A. et al. Multiplatform Analysis of 12 Cancer Types Reveals Molecular Classification within and across Tissues of Origin. Cell 158, 929–944 (2014).

8. Kandoth, C. et al. Mutational landscape and significance across 12 major cancer types. Nature 502, 333–339 (2013).

9. Zack, T. I. et al. Pan-cancer patterns of somatic copy number alteration. Nat. Genet. 45, 1134–1140 (2013).

10. Nik-Zainal, S. et al. The life history of 21 breast cancers. Cell 149, 994–1007 (2012).

11. Almendro, V. et al. Genetic and phenotypic diversity in breast tumor metastases. Cancer Res. 74, 1338–1348 (2014).

12. Wang, Y. et al. Clonal evolution in breast cancer revealed by single nucleus genome sequencing. Nature 512, 155–160 (2014).

13. Gerlinger, M. et al. Intratumor Heterogeneity and Branched Evolution Revealed by Multiregion Sequencing. N. Engl. J. Med. 366, 883–892 (2012).

14. Maley, C. C. et al. Genetic clonal diversity predicts progression to esophageal adenocarcinoma. Nat. Genet. 38, 468–473 (2006).

15. Mroz, E. A. et al. High intratumor genetic heterogeneity is related to worse outcome in patients with head and neck squamous cell carcinoma. Cancer 119, 3034–3042 (2013).

16. Birkbak, N. J. et al. Paradoxical relationship between chromosomal instability and survival outcome in cancer. Cancer Res. 71, 3447–3452 (2011).

17. Almendro, V. et al. Inference of Tumor Evolution during Chemotherapy by Computational Modeling and In Situ Analysis of Genetic and Phenotypic Cellular Diversity. Cell Rep. 6, 514–527 (2014).

18. Andor, N., Harness, J. V., Müller, S., Mewes, H. W. & Petritsch, C. EXPANDS: expanding ploidy and allele frequency on nested subpopulations. Bioinforma. Oxf. Engl. 30, 50–60 (2014).

19. Allen, B., Kon, M. & Bar-Yam, Y. A new phylogenetic diversity measure generalizing the shannon index and its application to phyllostomid bats. Am. Nat. 174, 236–243 (2009).

20. Roylance, R. et al. Relationship of extreme chromosomal instability with long-term survival in a retrospective analysis of primary breast cancer. Cancer Epidemiol. Biomark. Prev. Publ. Am. Assoc. Cancer Res. Cosponsored Am. Soc. Prev. Oncol. 20, 2183–2194 (2011).

21. Szathmáry, E. & Smith, J. M. The major evolutionary transitions. Nature 374, 227–232 (1995).

22. Biebricher, C. K. & Eigen, M. The error threshold. Virus Res. 107, 117–127 (2005).

Citation Format: Noemi Andor, Trevor A. Graham, Claudia Petritsch, Hanlee P. Ji*, Carlo C. Maley*. Pan-cancer analysis of the etiology and consequences of intra-tumor heterogeneity. [abstract]. In: Proceedings of the AACR Special Conference on Translation of the Cancer Genome; Feb 7-9, 2015; San Francisco, CA. Philadelphia (PA): AACR; Cancer Res 2015;75(22 Suppl 1):Abstract nr PR03.