Loss of heterozygosity: what is it good for?

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 Ovarian tumour cohort
A tumour cohort (n = 86) comprising a variety of histological subtypes including serous (n = 45), endometrioid (n = 28), mucinous (n = 7) and clear cell (n = 6) were obtained through the Australia Ovarian Cancer Study, the Peter MacCallum Cancer Centre Tissue Bank, or from patients presenting to hospitals in the south of England [8].

Background

Loss of heterozygosity (LOH) is a common genetic event in cancer development, and is known to be involved in the somatic loss of wild-type alleles in many inherited cancer syndromes. The wider involvement of LOH in cancer is assumed to relate to unmasking a somatically mutated tumour suppressor gene through loss of the wild type allele.

Methods

We analysed 86 ovarian carcinomas for mutations in 980 genes selected on the basis of their location in common regions of LOH.

Results

We identified 36 significantly mutated genes, but these could only partly account for the quanta of LOH in the samples. Using our own and TCGA data we then evaluated five possible models to explain the selection for non-random accumulation of LOH in ovarian cancer genomes: 1. Classic two-hit hypothesis: high frequency biallelic genetic inactivation of tumour suppressor genes. 2. Epigenetic two-hit hypothesis: biallelic inactivation through methylation and LOH. 3. Multiple alternate-gene biallelic inactivation: low frequency gene disruption. 4. Haplo-insufficiency: Single copy gene disruption. 5. Modified two-hit hypothesis: reduction to homozygosity of low penetrance germline predisposition alleles. We determined that while high-frequency biallelic gene inactivation under model 1 is rare, regions of LOH (particularly copy-number neutral LOH) are enriched for deleterious mutations and increased promoter methylation, while copy-number loss LOH regions are likely to contain under-expressed genes suggestive of haploinsufficiency. Reduction to homozygosity of cancer predisposition SNPs may also play a minor role.

Conclusion

It is likely that selection for regions of LOH depends on its effect on multiple genes. Selection for copy number neutral LOH may better fit the classic two-hit model whereas selection for copy number loss may be attributed to its effect on multi-gene haploinsufficiency. LOH mapping alone is unlikely to be successful in identifying novel tumour suppressor genes; a combined approach may be more effective. 

 

Conclusion (full text section)

The broader relevance of LOH in cancer has been debated for some time [5], [31] although many of the criticisms stemmed from technical issues that are being overcome by newer methodologies. Our initial assumption for this study was that we would detect high-frequency mutated genes in the minimal peak regions of LOH we had defined by LOH mapping using these newer methodologies; i.e. a classic two-hit model. However, the biology of LOH does not support this assumption and with large-scale tumour studies it is now possible to explore the many possibilities for the functional significance of this genetic event as summarised in Table 3. We suggest that the non-random patterns of LOH detected in cancer are a result of multiple different mechanisms operating to affect multiple genes, which may differ from tumour to tumour yet collectively play a role in the development of the tumorigenic phenotype. It is worth noting the differences in CNL-LOH versus CNN- LOH, with the latter appearing more relevant for selection of deleterious mutations and methylation, in contrast to global changes in gene expression. Identifying the specific driver genes targeted in a particular cancer remains a challenge given the multiple possible reasons for selection of an LOH event.