Sidra Medicine, Research Branch, Doha, PO, 26999, Qatar.
Fondazione Pisana Per la Scienza, Pisa, Italy.
J Transl Med. 2019 Apr 5;17(1):112. doi: 10.1186/s12967-019-1863-x.
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.
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.
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.
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.
单等位基因表达（MAE）是正常组织中常见的基因组现象，但它在癌症中的作用尚未完全理解。MAE 定义为在存在二倍体杂合基因组的情况下，基因的表达仅限于一个等位基因。组成型 MAE 发生在印迹基因、气味受体和随机 X 失活中。在正常组织中进行的几项研究表明，大约有 5-20%的病例存在 MAE。然而，关于癌症中 MAE 率的信息很少。在这项研究中，我们评估了黑色素瘤中 MAE 的存在和发生率。在过去的几十年中，黑色素瘤的遗传基础已经进行了深入研究，导致确定了导致黑色素瘤发展的突变/遗传改变。
为了研究 MAE 在黑色素瘤中的作用，我们使用了 15 种黑色素瘤细胞系，并将它们的 RNA-seq 数据与通过亲本 TIL（肿瘤浸润淋巴细胞）获得的基因分型数据进行比较。基因分型使用 Illumina HumanOmni1 珠芯片进行。RNA-seq 文库制备和测序使用 Illumina TruSeq stranded Total RNA Human Kit 进行，并按照制造商的指南使用 HiSeq 2500 进行测序。通过将基因分型数据与 RNA-seq 数据进行比较，我们确定了 DNA 基因型为杂合且相应 RNA 基因型为纯合的 SNP。在进行分析之前，所有纯合 DNA 基因型都被删除。为了确认检测 MAE 的有效性，我们还检查了女性样本中 X 染色体上的杂合 DNA 基因型以及印迹和嗅觉受体基因，并证实了 MAE 的存在。
尽管 MAE 的发生率不同，但在所有 15 种细胞系中均检测到 MAE。当观察 B 等位基因频率时，我们发现 15 种黑色素瘤细胞系中存在一种偏爱的完全单等位基因表达模式，而不是差异单等位基因表达模式。由于一些样本在纯合和杂合调用率上显示出很大的差异，我们研究了单个染色体，并表明 MAE 可能是由于某些情况下存在较大的拷贝数失衡引起的。有趣的是，这些区域包括已知在黑色素瘤起始和进展中发挥作用的基因。然而，一些染色体区域显示出 MAE 而没有 CN 失衡，这表明可能存在其他机制（包括表观遗传沉默）来解释黑色素瘤中的 MAE。
MAE 的生物学意义尚未实现。然而，我们的研究结果表明，MAE 是黑色素瘤细胞系中的一种常见现象。目前正在进行进一步的分析，以评估 MAE 是否是基因/途径特异性的，并了解 MAE 是否可以被癌症利用来实现更具侵袭性的表型。
