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Loss of heterozygosity: what is it good for?

Ryland GL, Doyle MA, Goode D, Boyle SE, Choong DY, Rowley SM, Li J, Australian Ovarian Cancer Study GroupBowtell DD, Tothill RW, Campbell IG, Gorringe KL - BMC Med Genomics (2015)

Bottom Line: Modified two-hit hypothesis: reduction to homozygosity of low penetrance germline predisposition alleles.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.

View Article: PubMed Central - PubMed

Affiliation: Cancer Genetics Laboratory, Peter MacCallum Cancer Centre, East Melbourne, Victoria, Australia. georgina.ryland@petermac.org.

ABSTRACT

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.

No MeSH data available.


Related in: MedlinePlus

Methylation. a Frequency of probes on the HM27 methylation array that have high (value > 0.75), intermediate (0.25-0.75) and low (<0.25) methylation associated with LOH in a sample, comparing all autosomes (no difference between LOH and no LOH) and chromosome X (more low methylation probes in LOH regions). b Considering only probes that were significantly different between LOH and no LOH, the frequency of significant probes where the mean methylation ratio (LOH/no LOH) was increased (>1.5, higher in LOH) or decreased (<0.75, higher in no LOH). c Percentage of significant methylation probes that are located in regions where the majority (>2/3) of LOH is either copy number loss, neutral or neither. Only regions with at least 20 % LOH were included
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Fig2: Methylation. a Frequency of probes on the HM27 methylation array that have high (value > 0.75), intermediate (0.25-0.75) and low (<0.25) methylation associated with LOH in a sample, comparing all autosomes (no difference between LOH and no LOH) and chromosome X (more low methylation probes in LOH regions). b Considering only probes that were significantly different between LOH and no LOH, the frequency of significant probes where the mean methylation ratio (LOH/no LOH) was increased (>1.5, higher in LOH) or decreased (<0.75, higher in no LOH). c Percentage of significant methylation probes that are located in regions where the majority (>2/3) of LOH is either copy number loss, neutral or neither. Only regions with at least 20 % LOH were included

Mentions: Somatic gene mutation is not the only mechanism of biallelic inactivation. Some TSGs can be inactivated through a combination of LOH and promoter hypermethylation, for example MLH1. This methylation can be acquired somatically or may be a consequence of imprinting. We assessed this possibility using TCGA ovarian cancer methylation data. Globally, we observed that there was no enrichment for methylation in regions of LOH – in samples with LOH at a locus, on average 12.7 % of genes were strongly methylated (probe value of >0.75), whereas 13.65 % of genes were strongly methylated when there was no LOH, (Fig. 2a). CNL-LOH was less likely to have strongly methylated genes than CNN-LOH (12.3 % vs 12.9 %, p < 0.0001, Chi-squared test). However, when we analysed the X chromosome separately, we found that samples with any LOH were more likely to have low methylation levels (45.3 % of genes had a probe value of <0.25, compared to 35.5 % in samples without LOH, p < 0.0001 Chi-squared test).Fig. 2


Loss of heterozygosity: what is it good for?

Ryland GL, Doyle MA, Goode D, Boyle SE, Choong DY, Rowley SM, Li J, Australian Ovarian Cancer Study GroupBowtell DD, Tothill RW, Campbell IG, Gorringe KL - BMC Med Genomics (2015)

Methylation. a Frequency of probes on the HM27 methylation array that have high (value > 0.75), intermediate (0.25-0.75) and low (<0.25) methylation associated with LOH in a sample, comparing all autosomes (no difference between LOH and no LOH) and chromosome X (more low methylation probes in LOH regions). b Considering only probes that were significantly different between LOH and no LOH, the frequency of significant probes where the mean methylation ratio (LOH/no LOH) was increased (>1.5, higher in LOH) or decreased (<0.75, higher in no LOH). c Percentage of significant methylation probes that are located in regions where the majority (>2/3) of LOH is either copy number loss, neutral or neither. Only regions with at least 20 % LOH were included
© Copyright Policy - open-access
Related In: Results  -  Collection

License 1 - License 2
Show All Figures
getmorefigures.php?uid=PMC4522148&req=5

Fig2: Methylation. a Frequency of probes on the HM27 methylation array that have high (value > 0.75), intermediate (0.25-0.75) and low (<0.25) methylation associated with LOH in a sample, comparing all autosomes (no difference between LOH and no LOH) and chromosome X (more low methylation probes in LOH regions). b Considering only probes that were significantly different between LOH and no LOH, the frequency of significant probes where the mean methylation ratio (LOH/no LOH) was increased (>1.5, higher in LOH) or decreased (<0.75, higher in no LOH). c Percentage of significant methylation probes that are located in regions where the majority (>2/3) of LOH is either copy number loss, neutral or neither. Only regions with at least 20 % LOH were included
Mentions: Somatic gene mutation is not the only mechanism of biallelic inactivation. Some TSGs can be inactivated through a combination of LOH and promoter hypermethylation, for example MLH1. This methylation can be acquired somatically or may be a consequence of imprinting. We assessed this possibility using TCGA ovarian cancer methylation data. Globally, we observed that there was no enrichment for methylation in regions of LOH – in samples with LOH at a locus, on average 12.7 % of genes were strongly methylated (probe value of >0.75), whereas 13.65 % of genes were strongly methylated when there was no LOH, (Fig. 2a). CNL-LOH was less likely to have strongly methylated genes than CNN-LOH (12.3 % vs 12.9 %, p < 0.0001, Chi-squared test). However, when we analysed the X chromosome separately, we found that samples with any LOH were more likely to have low methylation levels (45.3 % of genes had a probe value of <0.25, compared to 35.5 % in samples without LOH, p < 0.0001 Chi-squared test).Fig. 2

Bottom Line: Modified two-hit hypothesis: reduction to homozygosity of low penetrance germline predisposition alleles.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.

View Article: PubMed Central - PubMed

Affiliation: Cancer Genetics Laboratory, Peter MacCallum Cancer Centre, East Melbourne, Victoria, Australia. georgina.ryland@petermac.org.

ABSTRACT

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.

No MeSH data available.


Related in: MedlinePlus