Will we cure cancer by sequencing thousands of genomes?

Molecular Cytogenetics20136:57

DOI: 10.1186/1755-8166-6-57

Received: 4 September 2013

Accepted: 6 November 2013

Published: 13 December 2013

Abstract

The promise to understand cancer and develop efficacious therapies by sequencing thousands of cancers has not occurred. Mutations in specific genes termed oncogenes and tumor suppressor genes are extremely heterogeneous amongst the same type of cancer as well as between cancers. They provide little selective advantage to the cancer and in functional tests have yet to be shown to be sufficient for transformation. Here I discuss the karyotyptic theory of cancer and ask if it is time for a new approach to understanding and ultimately treating cancer.

Keywords

Cancer genome Cancer Karyotype Oncogenes Tumor suppressor genes

“We can carry on and sequence every piece of DNA that ever existed, but I don’t think we will find any Achilles heels.”- James Watson, Cancer World 2013

Background

By 2005 hundreds of gene mutations had been identified in individual cancers, it was unclear however, how prevalent these gene mutations were in cancers and which were specific to a certain type of cancer, if any. To answer these questions it was proposed to sequence thousands of cancers [1].

Main text

The first and most consistent finding from cancer sequencing studies has been that most cancers do not share the same mutations; they are so-called “hills” on the mutational landscape [2] (Figure 1). Sequencing acute myeloid leukemia (AML) from a single patient revealed 10 non-synonymous mutations in protein coding genes yet when 187 other AML patients were screened none of the same mutations were found [3]. Lung cancer sequencing showed that only 4 out of 623 genes analyzed were in more than 10% of tumors [4]. One of the most promising candidates for a cancer-specific mutation from sequencing studies, isocitrate dehydrogenase (IDH1) [5], was found to be mutated in only 12% of glioblastoma multiforme [6] and 8% of AML [7]. In addition to the intertumor mutational heterogeneity there exists widespread intratumor mutational heterogeneity with the majority of mutations not shared across different regions of the same tumor [8] (Figure 1).
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Figure 1

(A) The cancer genome landscape adapted from Salk et. al.[9] and Wood et. al.[2]. The cancer genome landscape illustrates that the same type of cancer does not share most mutations. The peaks correspond to how frequently a specific gene is mutated in a particular type of cancer. Large peaks, termed “mountains” indicate gene mutations that occur frequently amongst the same type of cancer while small peaks, termed “hills” indicate infrequent gene mutations. (B) In addition to intertumor mutational heterogeneity there exists widespread intratumor mutational heterogeneity. Within a tumor some mutations are present in the majority of single cells, depicted here as “trees”, while other mutations exist only subclonally amongst a tumor, depicted here as “seedlings”.

Consistent with these findings the effects of mutations in oncogenes and tumor suppressors are now thought to be small. Indeed, modeling the effects of mutations in oncogenes and tumor suppressor genes indicate they provide very little selective advantage to the cancer, a “surprisingly small” 0.4% [10]. Functional tests of oncogenes and tumor suppressor genes further call into question the role these mutations play in carcinogenesis. Initial tests of oncogenes and tumor suppressor genes as transforming agents were largely performed in a mouse cell line NIH/3T3, which is considered a model for normal cells. Yet, this line has ~70 chromosomes instead of 40 [11], becomes transformed with a mere change in culturing conditions [12], can lose the postulated initiating oncogenes without change in carcinogenicity [13], and above all is by itself tumorigenic [14, 15]. Despite these well-documented caveats NIH/3T3 cells are still used for transformation assays by scientists [16]. It may be argued that other lines, such as the human embryonic kidney 293 cell line (HEK293) and mammary epithelial cell line MCF10A have been successfully used to identify oncogenes and tumor suppressor genes as transforming agents. These lines, however, are prone to transformation and are known to have abnormal karyotypes [17]. Indeed, transformation by oncogenes, such as ras, are typically only successful when they are activated by viral promoters reaching levels of expression hundreds of fold higher than what is ever actually seen in cancer and in which the karyotypes are altered [18, 19]. Even then, only after long latencies of many cell generations will minute fractions of transfected cells ever transform into cancer [2022]. The consistent finding that mutations in cancer are largely heterogeneous has been hard to reconcile with the idea that only mutations in specific genes are the cause of cancer—as some sequencing studies suggest [23].

An alternative theory of cancer

All cancers display at least one numerical or structural chromosome aberration [24, 25]. Analysis of chromosomal gains and losses across many cancers have revealed predominant karyotypic patterns in cancer, to the extent that cancer types can be clustered based on karyotypes [2629] (Figure 2). The non-random gains and losses of chromosomes illustrate the importance of aneuploidy in carcinogenesis. These observations, along with the fact that aneuploidy is a prognostic indicator of patient survival [24], have led to the proposal that aneuploidy causes cancer [20, 21, 3036]. Still, such karyotypic patterns and aneuploidy in general have been proposed to merely reflect the gain and loss of cancer genes [27, 37, 38]. To test this hypothesis I compared the frequency a chromosome is gained or lost to the number of cancer genes per chromosome. If cancer karyotypes were selected for solely on cancer genes we would expect the number of cancer genes to relate to the frequency a chromosome is gained or lost.
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Figure 2

Chromosome arm-level somatic copy-number alterations (SCNAs) identified in 26 different cancer types by Beroukhim et. al.[27]. SCNAs are displayed across all autosomes where red and blue indicate gain and loss respectively. Different cancer types are organized by unsupervised hierarchical clustering.

The cancer gene census currently lists a total of 507 cancer genes [39]. Analysis of 19,003 solid cancers reported in the Mitelman Database revealed 35,021 chromosome losses and 21,268 gains [25, 38]. Organizing these cancer genes by chromosome and comparing them to how frequently they are lost or gained in cancer shows that there is no relationship between the number of cancer genes on a chromosome and the frequency that chromosome is gained or lost (Figure 3). The gain or loss of a single chromosome is thus not simply the gain or loss of a cancer gene. Indeed, a single trisomy induces complex gene expression changes across the entire genome [40, 41]. Such karyotypic patterns then must represent the selection of the entire karyotype, given that a gain or loss of a chromosome affects the entire genome.
http://static-content.springer.com/image/art%3A10.1186%2F1755-8166-6-57/MediaObjects/13039_2013_Article_445_Fig3_HTML.jpg
Figure 3

The frequency a chromosome is gained or lost in cancer does not merely reflect the gain and loss of cancer genes. The numbers in circles are human chromosome numbers. The number of cancer genes per chromosome is compared to the frequency of chromosome gain (A), chromosome loss (B), and chromosome gain and loss (C) in 19,003 cancers as reported in The Mitelman Database [25].

Conclusion

If the karyotype is central to carcinogenesis and not individual genes, will we cure cancer by sequencing thousands of genomes or is it time for a new approach?

Declarations

Authors’ Affiliations

(1)
Department of Biological Sciences, Virginia Tech

References

  1. Miklos GLG: The human cancer genome project – one more misstep in the war on cancer. Nat Biotechnol 2005, 23: 535–537. 10.1038/nbt0505-535View Article
  2. Wood LD, Parsons DW, Jones S, Lin J, Sjoblom T, Leary RJ, Shen D, Boca SM, Barber T, Ptak J, et al.: The genomic landscapes of human breast and colorectal cancers. Science 2007, 318(5853):1108–1113. 10.1126/science.1145720View ArticlePubMed
  3. Ley TJ, Mardis ER, Ding L, Fulton B, McLellan MD, Chen K, Dooling D, Dunford-Shore BH, McGrath S, Hickenbotham M, et al.: DNA sequencing of a cytogenetically normal acute myeloid leukaemia genome. Nature 2008, 456(7218):66–72. 10.1038/nature07485PubMed CentralView ArticlePubMed
  4. Weir BA, Woo MS, Getz G, Perner S, Ding L, Beroukhim R, Lin WM, Province MA, Kraja A, Johnson LA, et al.: Characterizing the cancer genome in lung adenocarcinoma. Nature 2007, 450(7171):893–898. 10.1038/nature06358PubMed CentralView ArticlePubMed
  5. Sjoblom T, Jones S, Wood LD, Parsons DW, Lin J, Barber TD, Mandelker D, Leary RJ, Ptak J, Silliman N, et al.: The consensus coding sequences of human breast and colorectal cancers. Science 2006, 314(5797):268–274. 10.1126/science.1133427View ArticlePubMed
  6. Parsons DW, Jones S, Zhang X, Lin JC, Leary RJ, Angenendt P, Mankoo P, Carter H, Siu IM, Gallia GL, et al.: An integrated genomic analysis of human glioblastoma multiforme. Science 2008, 321(5897):1807–1812. 10.1126/science.1164382PubMed CentralView ArticlePubMed
  7. Mardis ER, Ding L, Dooling DJ, Larson DE, McLellan MD, Chen K, Koboldt DC, Fulton RS, Delehaunty KD, McGrath SD, et al.: Recurring mutations found by sequencing an acute myeloid leukemia genome. N Engl J Med 2009, 361(11):1058–1066. 10.1056/NEJMoa0903840PubMed CentralView ArticlePubMed
  8. Gerlinger M, Rowan AJ, Horswell S, Larkin J, Endesfelder D, Gronroos E, Martinez P, Matthews N, Stewart A, Tarpey P, et al.: Intratumor heterogeneity and branched evolution revealed by multiregion sequencing. N Engl J Med 2012, 366(10):883–892. 10.1056/NEJMoa1113205View ArticlePubMed
  9. Salk JJ, Fox EJ, Loeb LA: Mutational heterogeneity in human cancers: origin and consequences. Annu Rev Pathol 2010, 5: 51–75. 10.1146/annurev-pathol-121808-102113PubMed CentralView ArticlePubMed
  10. Bozic I, Antal T, Ohtsuki H, Carter H, Kim D, Chen S, Karchin R, Kinzler KW, Vogelstein B, Nowak MA: Accumulation of driver and passenger mutations during tumor progression. Proc Natl Acad Sci U S A 2010, 107(43):18545–18550. 10.1073/pnas.1010978107PubMed CentralView ArticlePubMed
  11. Denko NC, Giaccia AJ, Stringer JR, Stambrook PJ: The human Ha-ras oncogene induces genomic instability in murine fibroblasts within one cell cycle. Proc Natl Acad Sci U S A 1994, 91(11):5124–5128. 10.1073/pnas.91.11.5124PubMed CentralView ArticlePubMed
  12. Rubin H, Xu K: Evidence for the progressive and adaptive nature of spontaneous transformation in the NIH/3T3 cell line. Proc Natl Acad Sci U S A 1989, 86(6):1860–1864. 10.1073/pnas.86.6.1860PubMed CentralView ArticlePubMed
  13. Gilbert PX, Harris H: The role of the ras oncogene in the formation of tumours. J Cell Sci 1988, 90(Pt 3):433–446.PubMed
  14. Greig RG, Koestler TP, Trainer DL, Corwin SP, Miles L, Kline T, Sweet R, Yokoyama S, Poste G: Tumorigenic and metastatic properties of “normal” and ras-transfected NIH/3 T3 cells. Proc Natl Acad Sci U S A 1985, 82(11):3698–3701. 10.1073/pnas.82.11.3698PubMed CentralView ArticlePubMed
  15. Boone CW, Jacobs JB: Sarcomas routinely produced from putatively nontumorigenic Balb/3T3 and C3H/10/T1/2 cells by subcutaneous inoculation attached to plastic platelets. J Supramol Struct 1976, 5(2):131–137. 10.1002/jss.400050204View ArticlePubMed
  16. Stratton MR: Exploring the Genomes of Cancer Cells: Progress and Promise. Science 2011, 331(6024):1553–1558. 10.1126/science.1204040View ArticlePubMed
  17. Stepanenko AA, Kavsan VM: Immortalization and malignant transformation of eukaryotic cells. TSitologiia i genetika 2012, 46(2):36–75.PubMed
  18. Hua VY, Wang WK, Duesberg PH: Dominant transformation by mutated human ras genes in vitro requires more than 100 times higher expression than is observed in cancers. Proc Natl Acad Sci U S A 1997, 94(18):9614–9619. 10.1073/pnas.94.18.9614PubMed CentralView ArticlePubMed
  19. Li R, Rasnick D, Duesberg P, Zimonjic D, et al.: Derivation of human tumor cells in vitro without widespread genomic instability. Cancer Res 2001, 61: 8838–8844. Cancer Res 2002, 62(21):6345–6348; discussion 6348–6349
  20. Nicholson JM, Duesberg P: On the karyotypic origin and evolution of cancer cells. Cancer Genet Cytogenet 2009, 194(2):96–110. 10.1016/j.cancergencyto.2009.06.008View ArticlePubMed
  21. Li L, McCormack AA, Nicholson JM, Fabarius A, Hehlmann R, Sachs RK, Duesberg PH: Cancer-causing karyotypes: chromosomal equilibria between destabilizing aneuploidy and stabilizing selection for oncogenic function. Cancer Genet Cytogenet 2009, 188(1):1–25. 10.1016/j.cancergencyto.2008.08.016View ArticlePubMed
  22. Klein A, Li N, Nicholson JM, McCormack AA, Graessmann A, Duesberg P: Transgenic oncogenes induce oncogene-independent cancers with individual karyotypes and phenotypes. Cancer Genet Cytogenet 2010, 200(2):79–99. 10.1016/j.cancergencyto.2010.04.008View ArticlePubMed
  23. Alexandrov LB, Nik-Zainal S, Wedge DC, Aparicio SA, Behjati S, Biankin AV, Bignell GR, Bolli N, Borg A, Borresen-Dale AL, et al.: Signatures of mutational processes in human cancer. Nature 2013, 500(7463):415–421. 10.1038/nature12477PubMed CentralView ArticlePubMed
  24. Schulze S, Petersen I: Gender and ploidy in cancer survival. Cell Oncol (Dordr) 2011, 34(3):199–208. 10.1007/s13402-011-0013-0View Article
  25. Mitelman F, Johansson B, Mertens F: Mitelman Database of Chromosome Aberrations in Cancer 2011. 2011. http://​cgap.​nci.​nih.​gov/​Chromosomes/​Mitelman
  26. Gebhart E, Liehr T: Patterns of genomic imbalances in human solid tumors. Int J Oncol 2000, 16: 383–399.PubMed
  27. Beroukhim R, Mermel CH, Porter D, Wei G, Raychaudhuri S, Donovan J, Barretina J, Boehm JS, Dobson J, Urashima M, et al.: The landscape of somatic copy-number alteration across human cancers. Nature 2010, 463(7283):899–905. 10.1038/nature08822PubMed CentralView ArticlePubMed
  28. Nicholson JM, Cimini D: Cancer karyotypes: survival of the fittest. Frontiers in oncology 2013, 3: 1–19.View Article
  29. Baudis M: Genomic imbalances in 5918 malignant epithelial tumors: an explorative meta-analysis of chromosomal CGH data. BMC Cancer 2007, 7: 226. 10.1186/1471-2407-7-226PubMed CentralView ArticlePubMed
  30. Duesberg P, Mandrioli D, McCormack A, Nicholson JM: Is carcinogenesis a form of speciation? Cell Cycle 2011, 10(13):2100–2114. 10.4161/cc.10.13.16352View ArticlePubMed
  31. Vincent MD: Cancer: beyond speciation. In Advances in cancer research. Edited by: David G. MA: Academic Press; 2011:283–350. Volume 112
  32. Heng HH, Stevens JB, Bremer SW, Ye KJ, Liu G, Ye CJ: The evolutionary mechanism of cancer. J Cell Biochem 2010, 109(6):1072–1084.PubMed
  33. Duesberg P: Chromosomal chaos and cancer. Sci Am 2007, 296(5):52–59. 10.1038/scientificamerican0507-52View ArticlePubMed
  34. Duesberg P, Rasnick D, Li R, Winters L, Rausch C, Hehlmann R: How aneuploidy may cause cancer and genetic instability. Anticancer Res 1999, 19(6A):4887–4906.PubMed
  35. Boveri T: Zur Frage der Entstehung maligner Tumoren. Jena, Germany: Gustav Fischer Verlag; 1914.
  36. Boveri T, Harris H: Concerning the origin of malignant tumours by Theodor Boveri. Translated and annotated by Henry Harris. J Cell Sci 2008, 121(Supplement 1):1–84. 10.1242/jcs.025742View ArticlePubMed
  37. Lengauer C, Kinzler KW, Vogelstein B: Genetic instability in colorectal cancers. Nature 1997, 386: 623–627. 10.1038/386623a0View ArticlePubMed
  38. Duijf PH, Schultz N, Benezra R: Cancer cells preferentially lose small chromosomes. Int J Cancer 2012, 132(10):2316–2326.PubMed CentralView ArticlePubMed
  39. Futreal PA, Coin L, Marshall M, Down T, Hubbard T, Wooster R, Rahman N, Stratton MR: A census of human cancer genes. Nat Rev Cancer 2004, 4(3):177–183. 10.1038/nrc1299PubMed CentralView ArticlePubMed
  40. Upender MB, Habermann JK, McShane LM, Korn EL, Barrett JC, Difilippantonio MJ, Ried T: Chromosome transfer induced aneuploidy results in complex dysregulation of the cellular transcriptome in immortalized and cancer cells. Cancer Res 2004, 64(19):6941–6949. 10.1158/0008-5472.CAN-04-0474View ArticlePubMed
  41. Shapiro BL: Down syndrome - a disruption of homeostasis. Am J Med Genet 1983, 14: 241–269. 10.1002/ajmg.1320140206View ArticlePubMed

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