Institute of Medical Biochemistry and Laboratory Diagnostics, First Faculty of Medicine and General University Hospital in Prague, Charles University, Kateřinská 32, 12108, Prague, Czech Republic.
4th Department of Internal Medicine, First Faculty of Medicine and General University Hospital in Prague, Charles University, U Nemocnice 499/2, 12808, Prague, Czech Republic.
Sci Rep. 2021 Oct 22;11(1):20924. doi: 10.1038/s41598-021-00425-0.
The patatin-like phospholipase domain containing 3 (PNPLA3) gene (viz. its I148M variant) is one of the key players in the pathogenesis of nonalcoholic fatty liver disease (NAFLD). We have identified a novel insertion/deletion variant of 1114 bp, localized in the second intron of the PNPLA3 gene, which corresponds to the 3' terminal sequence of the long-interspersed element (LINE-1). DNA analysis of 122 NAFLD patients and 167 control subjects as well as RNA analysis of 19 liver biopsies revealed that the novel variant is very common (frequency = 0.41), fully linked to the clinically important I148M variant, and clinically silent. Although the LINE-1 insertion does not seem to have any biological effect, it can impede genotyping of the I148M variant. If insertion prevents the attachment of the diagnostic primer, then the non-insertion allele will be selectively amplified; and thus the frequency of the 148M "risk" allele will be significantly overestimated due to the complete linkage of the LINE-1 insertion and the 148I allele of the PNPLA3 gene. Therefore, our findings underline the importance of careful design and consistent documentation of the methodology, including primer sequences. Critical revisions of the results of some studies that have already been reported may therefore be needed.
载脂蛋白 patatin 样磷脂酶结构域 3（PNPLA3）基因（即其 I148M 变体）是导致非酒精性脂肪性肝病（NAFLD）的关键因素之一。我们在 PNPLA3 基因的第二内含子中发现了一个新的 1114bp 缺失/插入变体，该变体对应长散布元件（LINE-1）的 3'末端序列。对 122 名 NAFLD 患者和 167 名对照者的 DNA 分析以及 19 例肝活检的 RNA 分析显示，该新变体非常常见（频率为 0.41），与临床上重要的 I148M 变体完全连锁，且临床意义不明。虽然 LINE-1 插入似乎没有任何生物学效应，但它会阻碍 I148M 变体的基因分型。如果插入阻止了诊断引物的附着，那么非插入等位基因将被选择性扩增；因此，由于 LINE-1 插入与 PNPLA3 基因的 148I 等位基因完全连锁，148M“风险”等位基因的频率将被显著高估。因此，我们的发现强调了仔细设计和一致记录方法（包括引物序列）的重要性。因此，可能需要对已经报道的一些研究的结果进行关键性修订。
