Alterations in the genetic material that not only affect individual DNA bases (so-called point mutations), but which lead to comprehensive and far-reaching chromosomal rearrangements have been known for quite some time. Chromosomal rearrangements encompass deletions, inversions, duplications, amplifications and translocations. However, the extent to which such structural variations are associated with human cancer has only come to the fore due to the systematic sequencing of entire human genes.

Dr. Jan Korbel’s research group at the European Molecular Biology Laboratory (EMBL) uses a combination of experimental and computational approaches to study the dynamics of the genome and the structural variations associated with cancer. Korbel’s group is part of the “1000 Genomes Consortium” which aims to establish a complete catalogue of human genetic variation across human populations around the world. Using state-of-the-art “next-generation sequencing” (NGS), the researchers from Heidelberg are working on producing an integrated map of the DNA of two-thousand individuals in order to gain insights into the mechanisms that lead to genomic structural variations and mutation hotspots. Korbel and his team are also part of the International Cancer Genome Consortium (ICGC) where they work with scientists from the German Cancer Research Center (DKFZ) and Heidelberg University Hospital with the goal of elucidating the genomic changes present in many types of cancer. They discovered mechanisms which only a few years ago were unimaginable.

Medulloblastoma is a highly malignant primary brain tumour that mainly affects children. It is the second most common cause of childhood deaths in developed countries after car accidents. Using genetic tests, Prof. Dr. Andreas Kulozik of the Department of Oncology in the Centre for Paediatrics and Adolescent Medicine at Heidelberg University Hospital found that a little girl and her brother who had highly aggressive tumours shared the same mutation in the gene p53. Moreover, the siblings had the mutation in all their cells, not just the cancerous ones. This meant that the mutation was inherited from their parents, rather than acquired later by the cells that formed the tumour.

When the scientists in Korbel’s team at the EMBL studied the girl’s sequences in closer detail, they found a genomic chaos that they had never come across before: a chromosome had somehow exploded into countless small pieces and stitched back together in a haphazard way; some pieces were missing and others were in the wrong order. While cells with such massive DNA damage would be expected to have undergone apoptosis (i.e. programmed cell death), this was obviously not the case here. This phenomenon had previously been described and named “chromothripsis” (“chromo” for chromosome and “thripsis” – the Greek word for “shattered into pieces”). As part of the ICGC PedBrain Tumour project, Korbel’s team had previously sequenced the whole genome of medulloblastomas along with the teams of Dr. Stefan Pfister and Prof. Dr. Peter Lichter at the DKFZ. Korbel and his co-workers then went on to study 98 medulloblastoma patients and found that chromothripsis occurred in all patients with a heritable p53 mutation, but did not occur in tumour samples with intact p53.

It has been known for many decades that the p53 protein (named after its molecular weight of around 53 kDa), which is encoded by the p53 gene, suppresses tumour growth. It is also known that p53 helps to protect chromosome telomeres from eroding. If p53, which is generally described as “the guardian of the genome”, finds too many mistakes it can push the cell into apoptosis (programmed cell death) or senescence in order to prevent it from dividing.

At the annual meeting of the National Genome Research Network at the DKFZ in December 2012, Jan Korbel presented his view on the relationship between the observed p53 mutations, chromothripsis and the development of medulloblastoma. Korbel and his colleagues speculate that in cases where p53 was faulty and telomeres damaged, chromosomes would stick together and get pulled in opposite directions during mitosis. At some point the strain would be too much and  the chromosome would shatter, just like a bead necklace that has been overstretched. In the attempt made by the cellular DNA repair machinery to put the chromosome back together, bits of genetic material would be left out and others put together in the wrong order. Korbel further speculated that defective p53 is no longer able to exert its role as guardian of the genome with the result that the incorrect rearrangement of chromosomes following chromothripsis would go unnoticed. As a result, oncogenes may be activated, leading to uncontrolled cell division and tumour development. 

The researchers’ discovery has immediate clinical implications. “If a patient’s tumour cells show signs of chromothripsis, we now know that we should look for an inherited p53 mutation,” said Pfister going on to explain that an inherited p53 mutation could make standard cancer treatments backfire since cytostatic drugs and radiotherapy, which kill cancer cells by damaging their DNA, can also affect other cells in the body. If cells are harbouring defective p53, i.e. heritable p53 mutations, the patient’s repair system cannot react to DNA damage and healthy cells might become cancerous, causing secondary tumours. Doctors therefore need to decide whether to choose therapies that are less intensive and cause less DNA damage.

Korbel estimates that around two to three percent of all cancer cases are the result of chromothripsis. The researchers have already found evidence of a relationship between heritable p53 mutations and chromothripsis in acute myeloid leukaemia.

The researchers have also identified cancer-inducing structural genomic variations in prostate cancer. Prostate cancer is the second most common cancer in Germany and the second most frequent cause of death in men after lung cancer. Prostate cancer occurs mainly in older men. In around two percent of cases, the cancer also occurs in men under 50. In another ICGC research project (“The genomes of early-onset prostate cancers”) carried out in cooperation with research groups from Heidelberg, Berlin and Hamburg (see BIOPRO article of 19th November 2012; Uncovering the genetics of prostate cancer), Korbel and his team found that these early-onset prostate cancers are triggered by a different mechanism from that which causes the disease in older men. Early-onset tumours harbour relatively few genomic variations. However, this small number leads to far-reaching structural alterations of the chromosomes.

The researchers found that crucial exchanges of long DNA segments between chromosomes can cause genes that are normally independent to become tightly linked (fusion genes). The researchers also found that the majority of these genes is usually activated by androgen hormones (male sex hormones) such as testosterone. Through these rearrangements, these genes become connected to cancer genes or strong promoters, resulting in fusion genes that can be activated by male sex hormones, so that otherwise inactive genes with the potential to cause cancer are switched on.

Prostate cancer in young patients appears to be specifically triggered by male sex hormones and involves genetic mutations that distinguish this cancer from prostate cancers in older patients. There are obviously two different mechanisms, one that triggers prostate cancer in young people, and one that triggers prostate cancers in older patients. To substantiate the hypothesis that androgens trigger the mechanism leading to prostate cancer in younger patients, the researchers determined the level of testosterone receptors in 10,000 prostate cancer biopsies and found that men over 50 had lower levels of androgen hormone receptors than younger patients with the same disease. This said, the role of male sex hormones in the development of cancer gradually decreases with age.

Professor Holger Sültmann of the DKFZ, the spokesperson of the ICGC prostate genome project, assumes that this appears to be the first time ever that an age-related mechanism that triggers cancer development was found. The finding supports the researchers’ conclusion that androgens trigger the mechanism that leads to prostate cancer in younger patients, and not in older ones. Further research is needed to obtain information on the medical impact of testosterone levels in men. The researchers hope that their findings on the cause of prostate cancer will promote the development of new strategies to diagnose, prevent and individually treat this cancer.

References:
Joachim Weischenfeldt et al.: Integrative genomic analyses reveal androgen-driven somatic alteration landscape in early-onset prostate cancer. Cancer Cell 23(2), 159-170; 2013.

Genome Sequencing of Pediatric Medulloblastoma Links Catastrophic DNA Rearrangements with TP53 Mutations, CELL 2012 Jan 20; 148(1):59-71