Complete Loss of HLA Class I Heterozygosity in a Patient with Acute Myeloid Leukemia

Zollikofer, Christine; Ringhoffer, Mark; Kündgen, Lukas; Fürst, Daniel E.; Schrezenmeier, Hubert; Mytilineos, Joannis

doi:10.1016/j.bbmt.2014.11.234

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“…Three of the four genes belong to the HLA family, i.e., HLA-A and HLA-B, and HLA-C, and all revealed a lower allelic heterozygosity in tumor tissues (Figure 5 ). Loss of heterozygosity (LOH) of the HLA loci was reported in many cancers ( Maleno et al, 2002 ; Wang et al, 2006 ; Zollikofer et al, 2014 ). In our case, these loci are heterozygous at the DNA level, while at the mRNA level, one of the copies showed a significantly reduced expression compared to the other one.…”

Section: Resultsmentioning

confidence: 99%

A Genome-Wide Study of Allele-Specific Expression in Colorectal Cancer

Liu

Dong

Li³

2018

Front. Genet.

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Accumulating evidence from small-scale studies has suggested that allele-specific expression (ASE) plays an important role in tumor initiation and progression. However, little is known about genome-wide ASE in tumors. In this study, we conducted a comprehensive analysis of ASE in individuals with colorectal cancer (CRC) on a genome-wide scale. We identified 5.4 thousand genome-wide ASEs of single nucleotide variations (SNVs) from tumor and normal tissues of 59 individuals with CRC. We observed an increased ASE level in tumor samples and the ASEs enriched as hotspots on the genome. Around 63% of the genes located there were previously reported to contain complex regulatory elements, e.g., human leukocyte antigen (HLA), or were implicated in tumor progression. Focussing on the allelic expression of somatic mutations, we found that 37.5% of them exhibited ASE, and genes harboring such somatic mutations, were enriched in important pathways implicated in cancers. In addition, by comparing the expected and observed ASE events in tumor samples, we identified 50 tumor specific ASEs which possibly contributed to the somatic events in the regulatory regions of the genes and significantly enriched known cancer driver genes. By analyzing CRC ASEs from several perspectives, we provided a systematic understanding of how ASE is implicated in both tumor and normal tissues and will be of critical value in guiding ASE studies in cancer.

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Section: Resultsmentioning

confidence: 99%