Cancer Genetics and Epigenetics

Manuel Perucho

In our group we study tumours from the intestinal tract (i.e. colon, and stomach) that sometimes develop when the cell machinery preserving the integrity of the genome, rather like computer spelling programs that detect errors and correct them, is not working properly. When these corrector genes (mutators) are inactivated, the mutations that occur in all normal cells accumulate in large numbers because they are not repaired. This originates a remarkable genomic instability and cancer eventually develops when mutations occur in some cancer genes, such as the oncogenes and tumour suppressor genes. Some of the mutator genes are not inactivated by mutations (mutator mutations) but by epigenetic silencing. This results as a consequence of the disintegration of the epigenetic code, an unexplored process that is strongly associated to aging. These studies have clinical applications. For instance, many hereditary colon tumours originate by mutations in mutator genes that are transmitted from generation to generation. Molecular diagnosis of the deficient mutator genes determines which members of these families will be affected in the future. Identification of tumours with this kind of genomic instability is also useful to detect familial cancer patients and to predict survival.

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Molecular mechanisms for gastrointestinal cancer pathogenesis

Our research aims to understand better the mechanisms of genomic instability as a "remote control", and cancer epigenetics as an "ultraremote control" mechanisms underlying tumorigenesis.Using unbiased DNA fingerprinting aproaches we obtained panoramic views of the genetic and epigenetic disruption of the genome in cancer. A picture is emerging from these studies in which epigenetic alterations precede and determine the occurrence of genetic alterations in gastrointestinal tumorigenesis:

  • In tumors with microsatellite instability (MSI), gradual and age-associated CpG island hypermethylation underlies the manifestation of the mutator phenotype when the DNA mismatch repair gene MLH1 becomes epigenetically silenced.
  • In MSI negative tumors, a gradual increase in DNA hypomethylation during aging may underlie genome disruption accompanying tumor progression. This "wear & tear" model proposes that the loss of methylation relentlessly spreads throughout the chromosomes leading to mitotic errors when certain chromosomal regions are hit, followed by genomic damage and ultimately cancer development.

Epigenetic biomarkers for cancer susceptibility and metastatic spread

We are currently analyzing the impact of the alterations in patterns of DNA methylation in genome disruption and studying the applications of these epigenetic somatic alterations for gastrointestinal cancer diagnosis and prognosis. Specifically we are studying the epigenomics of proteolysis and the applications of epigenetic alterations in several members of the metalloproteinase gene family as biomarkers for defining individuals at high risk for field cancerization.  Also, these studies should yield tools predictive for metastatic homing tendency of primary colorectal cancers, and diagnostic for distinguishing primary ovarian cancers from metastatic gastrointestinal tumors.

DNA demethylation, predictive for the development of multiple colon cancers

Some colon cancer patients present synchronous cancers (multiple simultaneous cancers) at diagnosis and others develop later additional primary (metachronous) cancers, but the risk factors are unknown for nonhereditary colon cancer. We have discovered that high levels of DNA demethylation in non-cancerous mucosa from patients who underwent primary colon cancer resection was predictive for metachronous neoplasms. The levels of demethylation would serve as a prognostic biomarker that would allow for improved identification of individuals at high risk for the development of metachronous colorectal cancer. This would consequently lead to increased efficiency of surveillance and prognosis.

Genomics and epigenomics of colorectal cancer prediction

In addition, we are starting new projects to discover cancer susceptibilty and resistance genes by using genomic and epigenomic approaches. Genome Wide Association Study (GWAS) preliminary study with Spanish cases and controls confirmed some of the loci previously reported as colorectal cancer susceptibilty genes and identified novel single loci associated to increased risk.

Exome deep sequencing and methylation profiling together with array CGH approaches will integrate the genomic and epigenomic somatic alterations underlying gastrointestinal cancer, providing novel diagnostic and prognostic markers that could not be obtained by any of the individual approaches in isolation.

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Manuel Perucho

(+34) 93 554 3050 extn: 3061