Monoallelic expression in melanoma

Lee Silcock, Hakeem Almabrazi, Younes Mokrab, Puthen V. Jithesh, Muna Al-Hashmi, Nicola James, Rebecca Mathew, Valentina Mattei, Davide Bedognetti, Francesca Lessi, Ramzi Temanni, Barbara Seliger, Rashid J. Al-Ali, Francesco M. Marincola, Ena Wang, Sara Tomei

Research output: Contribution to journalArticle

Abstract

Background: Monoallelic expression (MAE) is a frequent genomic phenomenon in normal tissues, however its role in cancer is yet to be fully understood. MAE is defined as the expression of a gene that is restricted to one allele in the presence of a diploid heterozygous genome. Constitutive MAE occurs for imprinted genes, odorant receptors and random X inactivation. Several studies in normal tissues have showed MAE in approximately 5-20% of the cases. However, little information exists on the MAE rate in cancer. In this study we assessed the presence and rate of MAE in melanoma. The genetic basis of melanoma has been studied in depth over the past decades, leading to the identification of mutations/genetic alterations responsible for melanoma development. Methods: To examine the role of MAE in melanoma we used 15 melanoma cell lines and compared their RNA-seq data with genotyping data obtained by the parental TIL (tumor infiltrating lymphocytes). Genotyping was performed using the Illumina HumanOmni1 beadchip. The RNA-seq library preparation and sequencing was performed using the Illumina TruSeq Stranded Total RNA Human Kit and subsequently sequenced using a HiSeq 2500 according to manufacturer’s guidelines. By comparing genotyping data with RNA-seq data, we identified SNPs in which DNA genotypes were heterozygous and corresponding RNA genotypes were homozygous. All homozygous DNA genotypes were removed prior to the analysis. To confirm the validity to detect MAE, we examined heterozygous DNA genotypes from X chromosome of female samples as well as for imprinted and olfactory receptor genes and confirmed MAE. Results: MAE was detected in all 15 cell lines although to a different rate. When looking at the B-allele frequencies we found a preferential pattern of complete monoallelic expression rather then differential monoallelic expression across the 15 melanoma cell lines. As some samples showed high differences in the homozygous and heterozygous call rate, we looked at the single chromosomes and showed that MAE may be explained by underlying large copy number imbalances in some instances. Interestingly these regions included genes known to play a role in melanoma initiation and progression. Nevertheless, some chromosome regions showed MAE without CN imbalances suggesting that additional mechanisms (including epigenetic silencing) may explain MAE in melanoma. Conclusion: The biological implications of MAE are yet to be realized. Nevertheless, our findings suggest that MAE is a common phenomenon in melanoma cell lines. Further analyses are currently being undertaken to evaluate whether MAE is gene/pathway specific and to understand whether MAE can be employed by cancers to achieve a more aggressive phenotype.

Original languageEnglish
Article number112
JournalJournal of translational medicine
Volume17
Issue number1
DOIs
Publication statusPublished - 5 Apr 2019

Fingerprint

Melanoma
Genes
RNA
Chromosomes
Cells
Odorant Receptors
DNA
Genotype
Cell Line
Tissue
Lymphocytes
Gene expression
Tumors
Tumor-Infiltrating Lymphocytes
Gene Expression
X Chromosome Inactivation
Neoplasms
X Chromosome
Diploidy
Gene Frequency

Keywords

  • Melanoma
  • Monoallelic expression
  • RNA-seq

ASJC Scopus subject areas

  • Biochemistry, Genetics and Molecular Biology(all)

Cite this

Monoallelic expression in melanoma. / Silcock, Lee; Almabrazi, Hakeem; Mokrab, Younes; Jithesh, Puthen V.; Al-Hashmi, Muna; James, Nicola; Mathew, Rebecca; Mattei, Valentina; Bedognetti, Davide; Lessi, Francesca; Temanni, Ramzi; Seliger, Barbara; Al-Ali, Rashid J.; Marincola, Francesco M.; Wang, Ena; Tomei, Sara.

In: Journal of translational medicine, Vol. 17, No. 1, 112, 05.04.2019.

Research output: Contribution to journalArticle

Silcock, L, Almabrazi, H, Mokrab, Y, Jithesh, PV, Al-Hashmi, M, James, N, Mathew, R, Mattei, V, Bedognetti, D, Lessi, F, Temanni, R, Seliger, B, Al-Ali, RJ, Marincola, FM, Wang, E & Tomei, S 2019, 'Monoallelic expression in melanoma', Journal of translational medicine, vol. 17, no. 1, 112. https://doi.org/10.1186/s12967-019-1863-x
Silcock, Lee ; Almabrazi, Hakeem ; Mokrab, Younes ; Jithesh, Puthen V. ; Al-Hashmi, Muna ; James, Nicola ; Mathew, Rebecca ; Mattei, Valentina ; Bedognetti, Davide ; Lessi, Francesca ; Temanni, Ramzi ; Seliger, Barbara ; Al-Ali, Rashid J. ; Marincola, Francesco M. ; Wang, Ena ; Tomei, Sara. / Monoallelic expression in melanoma. In: Journal of translational medicine. 2019 ; Vol. 17, No. 1.
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abstract = "Background: Monoallelic expression (MAE) is a frequent genomic phenomenon in normal tissues, however its role in cancer is yet to be fully understood. MAE is defined as the expression of a gene that is restricted to one allele in the presence of a diploid heterozygous genome. Constitutive MAE occurs for imprinted genes, odorant receptors and random X inactivation. Several studies in normal tissues have showed MAE in approximately 5-20{\%} of the cases. However, little information exists on the MAE rate in cancer. In this study we assessed the presence and rate of MAE in melanoma. The genetic basis of melanoma has been studied in depth over the past decades, leading to the identification of mutations/genetic alterations responsible for melanoma development. Methods: To examine the role of MAE in melanoma we used 15 melanoma cell lines and compared their RNA-seq data with genotyping data obtained by the parental TIL (tumor infiltrating lymphocytes). Genotyping was performed using the Illumina HumanOmni1 beadchip. The RNA-seq library preparation and sequencing was performed using the Illumina TruSeq Stranded Total RNA Human Kit and subsequently sequenced using a HiSeq 2500 according to manufacturer’s guidelines. By comparing genotyping data with RNA-seq data, we identified SNPs in which DNA genotypes were heterozygous and corresponding RNA genotypes were homozygous. All homozygous DNA genotypes were removed prior to the analysis. To confirm the validity to detect MAE, we examined heterozygous DNA genotypes from X chromosome of female samples as well as for imprinted and olfactory receptor genes and confirmed MAE. Results: MAE was detected in all 15 cell lines although to a different rate. When looking at the B-allele frequencies we found a preferential pattern of complete monoallelic expression rather then differential monoallelic expression across the 15 melanoma cell lines. As some samples showed high differences in the homozygous and heterozygous call rate, we looked at the single chromosomes and showed that MAE may be explained by underlying large copy number imbalances in some instances. Interestingly these regions included genes known to play a role in melanoma initiation and progression. Nevertheless, some chromosome regions showed MAE without CN imbalances suggesting that additional mechanisms (including epigenetic silencing) may explain MAE in melanoma. Conclusion: The biological implications of MAE are yet to be realized. Nevertheless, our findings suggest that MAE is a common phenomenon in melanoma cell lines. Further analyses are currently being undertaken to evaluate whether MAE is gene/pathway specific and to understand whether MAE can be employed by cancers to achieve a more aggressive phenotype.",
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AU - Silcock, Lee

AU - Almabrazi, Hakeem

AU - Mokrab, Younes

AU - Jithesh, Puthen V.

AU - Al-Hashmi, Muna

AU - James, Nicola

AU - Mathew, Rebecca

AU - Mattei, Valentina

AU - Bedognetti, Davide

AU - Lessi, Francesca

AU - Temanni, Ramzi

AU - Seliger, Barbara

AU - Al-Ali, Rashid J.

AU - Marincola, Francesco M.

AU - Wang, Ena

AU - Tomei, Sara

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N2 - Background: Monoallelic expression (MAE) is a frequent genomic phenomenon in normal tissues, however its role in cancer is yet to be fully understood. MAE is defined as the expression of a gene that is restricted to one allele in the presence of a diploid heterozygous genome. Constitutive MAE occurs for imprinted genes, odorant receptors and random X inactivation. Several studies in normal tissues have showed MAE in approximately 5-20% of the cases. However, little information exists on the MAE rate in cancer. In this study we assessed the presence and rate of MAE in melanoma. The genetic basis of melanoma has been studied in depth over the past decades, leading to the identification of mutations/genetic alterations responsible for melanoma development. Methods: To examine the role of MAE in melanoma we used 15 melanoma cell lines and compared their RNA-seq data with genotyping data obtained by the parental TIL (tumor infiltrating lymphocytes). Genotyping was performed using the Illumina HumanOmni1 beadchip. The RNA-seq library preparation and sequencing was performed using the Illumina TruSeq Stranded Total RNA Human Kit and subsequently sequenced using a HiSeq 2500 according to manufacturer’s guidelines. By comparing genotyping data with RNA-seq data, we identified SNPs in which DNA genotypes were heterozygous and corresponding RNA genotypes were homozygous. All homozygous DNA genotypes were removed prior to the analysis. To confirm the validity to detect MAE, we examined heterozygous DNA genotypes from X chromosome of female samples as well as for imprinted and olfactory receptor genes and confirmed MAE. Results: MAE was detected in all 15 cell lines although to a different rate. When looking at the B-allele frequencies we found a preferential pattern of complete monoallelic expression rather then differential monoallelic expression across the 15 melanoma cell lines. As some samples showed high differences in the homozygous and heterozygous call rate, we looked at the single chromosomes and showed that MAE may be explained by underlying large copy number imbalances in some instances. Interestingly these regions included genes known to play a role in melanoma initiation and progression. Nevertheless, some chromosome regions showed MAE without CN imbalances suggesting that additional mechanisms (including epigenetic silencing) may explain MAE in melanoma. Conclusion: The biological implications of MAE are yet to be realized. Nevertheless, our findings suggest that MAE is a common phenomenon in melanoma cell lines. Further analyses are currently being undertaken to evaluate whether MAE is gene/pathway specific and to understand whether MAE can be employed by cancers to achieve a more aggressive phenotype.

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