Cellular reprogramming: clues to establishing, and targeting, the cancer epigenome.

25 Nov 2009

The VI plenary session of Wednesday, November 18, at the AACR-NCI-EORTC conference in Boston, was chaired by Peter A. Hones (USC/Norris Comprehensive Cancer Center, Los Angeles, CA) and focused on cellular reprogramming in cancer, and on research aimed at targeting the cancer epigenome.

Stephen B. Baylin, (Johns Hopkins University School of Medicine, Baltimore, MD, USA) discussed the role played by cell stress - at the levels of aging, chronic injury, and inflammation- in tumorigenesis. More and more evidence is accumulating to prove the point that cell stress not only damages DNA, but also creates massive chromatic alterations, partly in response to DNA damage, which set up a favourable situation for the selection of mutated, resistant cells.

Hundreds of genes become vulnerable after chromatin remodelling, among which epigenetic gatekeepers such p16, p19, secreted frizzled protein, nuclear proteins gata 4 and5, Apc, and Sox genes. Alterations at the level of these genes give rise to preinvasive, self-renewing cells. Indeed, the process of cell reprogramming at the chromatin level, in which cell stress is only one of the causative factors, sets up a 'perfect' platform (from the tumour point of view) for the selection of subsequent mutations such as kras and c-myc, in a subpopulation of self-renewing tumor initiating cells.


Recently, Cedar and co-authors established a new model for de novo methylation in cancer, which was illustrated by Baylin (Cedar et al, Nat Rev Cancer 2009). Several studies have shown in the past that cancer cells are subject to abnormal de novo methylation compared with their normal counterparts. Early experiments that concentrated on individual gene promoters indicated that cancer-associated DNA methylation was restricted to tumour suppressor genes, and these findings gave rise to the theory that these methylation patterns are generated through a process of selection. More recently however, with the advent of microarray methodologies, it has become possible to examine global patterns of de novo methylation in cancer, and these studies now show that a large number of CpG islands can become de novo methylated at an early stage of tumourigenesis. Although these CpG islands remain largely unmethylated during normal development, there seems to be some trigger that causes them to undergo de novo methylation in cancer.

Therefore, when trying to translate this new model from the bench to the bedside, investigators should keep in mind that the so-called epigenetic 'therapies' should not be aimed at targeting individual genes (as earlier models predicted), but at targeting programs of genes which become de novo methylated in cancer. The goal should be the correction of pathways which are deregulated in cancer, such as the Wnt pathway, the Notch pathways, and the pathways involved in cell cycle regulation, apoptosis, adhesion and migration.


One of the first examples of this translation from the bench to the clinic is the recent study by Brock and coauthors, who investigated the association between gene methylation and recurrence of non small cell lung cancer (NSCLC) (Brock et al, 2008). Indeed, despite optimal and early surgical treatment of non-small-cell lung cancer, many patients die of recurrent NSCLC. Therefore, there is an urgent need of better biomarkers which can predict the disease free survival of stage I NSCLC.  The trial recruited fifty-one patients with stage I NSCLC who underwent curative resection but who had a recurrence within 40 months after resection (case patients), who were matched on the basis of age, NSCLC stage, sex, and date of surgery to 116 patients with stage I NSCLC, who underwent curative resection but who did not have a recurrence within 40 months after resection (controls). The study showed that promoter methylation of the cyclin-dependent kinase inhibitor 2A gene p16, the H-cadherin gene CDH13, the Ras association domain family 1 gene RASSF1A, and the adenomatous polyposis coli gene APC in tumours and in histologically tumour-negative lymph nodes was associated with tumor recurrence, independently of NSCLC stage, age, sex, race, smoking history, and histologic characteristics of the tumor. Therefore, DNA hypermethylation markers could be a possible promising answer to the need of better biomarkers in NSCLC, as the results of this translational study pointed out.


Peter Jones, chairman of the session and last speaker, focused on the dramatic changes that affect the methylation status of Cpg islands in prostate cancer. Prostate cancer is a paradigmatic example of a 'rampant epichange' - as Jones put it -, which fits perfectly well within the model proposed by Cedar and coauthors mentioned earlier (Cedar et al, 2009).


Recently, the research group led by Gal-Yam devised a new experimental strategy using customised arrays to investigate this phenonenon and the coordinated patterns of gene expression, DNA methylation, and polycomb marks which differentiate prostate cancer cells from their normal counterparts (Gal-Yam et al, PNAS 2008). The results were astonishing in clearly suggesting two separate silencing mechanisms that act in parallel to reprogram the cancer epigenome.Three major changes in the epigenomic landscape distinguish the two cell types. First, developmentally significant genes containing CpG islands which are silenced by Polycomb repressive complexes (PRCs) in the normal cells acquire DNA methylation silencing and lose their PRC marks. Since these genes are normally silent, this switch does not cause de novo repression, but might significantly reduce epigenetic plasticity. Two other groups of genes are silenced by either de novo DNA methylation without PRC occupancy (5mC reprogramming) or by de novo PRC occupancy without DNA methylation (PRC reprogramming) (Gal-Yam et al, PNAS 2008).


Of course, cancer prostate cell lines in a dish are not the same as cells of a prostate tumor in patients, and the applicability of these observations to prostate tumours (and to cancer cells in general) need to be further investigated. But, as Jones pointed out, the study by Gal-Yam and co-authors stresses the importance of an integrative approach for the characterisation of the cancer epigenome, while demonstrating the benefits of a coherent experimental system to map multiple epigenetic factors.




Cedar H, Bergman Y. Linking DNA methylation and histone modification: patterns and paradigms. Nat Rev Genet. 2009;10(5):295-304.


Brock MV, Hooker CM, Ota-Machida E, et al. DNA methylation markers and early recurrence in stage I lung cancer. N Engl J Med. 2008;358(11):1118-28.


Gal-Yam EN, Egger G, Iniguez L, et al. Frequent switching of Polycomb repressive marks and DNA hypermethylation in the PC3 prostate cancer cell line. PNAS 2008;105(35):12979-84.