PKHD1L1是一种参与立体纤毛外衣的基因,可导致常染色体隐性非综合征性听力损失。

IF 3.8 2区 生物学 Q2 GENETICS & HEREDITY
Human Genetics Pub Date : 2024-03-01 Epub Date: 2024-03-09 DOI:10.1007/s00439-024-02649-2
Shelby E Redfield, Pedro De-la-Torre, Mina Zamani, Hanjun Wang, Hina Khan, Tyler Morris, Gholamreza Shariati, Majid Karimi, Margaret A Kenna, Go Hun Seo, Hongen Xu, Wei Lu, Sadaf Naz, Hamid Galehdari, Artur A Indzhykulian, A Eliot Shearer, Barbara Vona
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引用次数: 0

摘要

即使进行了最先进的基因检测,仍有大量患者无法确诊,因此鉴定与非综合征性听力损失相关的基因是一项至关重要的工作。PKHD1L1 是耳蜗毛细胞立体纤毛膜形成所必需的基因,突变后会导致小鼠和斑马鱼听力损失。我们试图确定 PKHD1L1 的双叶变体是否也会导致人类听力损失。我们对四个常染色体隐性非综合征感音神经性听力损失家族的 DNA 进行了外显子组测序。在PKHD1L1中发现了复杂合子p.[(Gly129Ser)];p.[(Gly1314Val)]和p.[(Gly605Arg)];p[(Leu2818TyrfsTer5)]、同源错义p.(His2479Gln)和无义p.(Arg3381Ter)变体,这些变体通过硅致病性预测方法被预测为具有损伤性。我们使用纯化的重组 PKHD1L1 蛋白片段对这两种错义变体进行了体外功能分析。然后,我们评估了其中一个家族中存在和不存在错义变体的蛋白质热力学稳定性,并对另一个变体进行了迷你基因拼接检测。我们使用 AlphaFold2 进行了硅分子建模,并进行了蛋白质序列比对分析,以进一步探索变体对结构的潜在影响。体外功能评估表明,工程化的 PKHD1L1 p.(Gly129Ser) 和 p.(Gly1314Val) 突变体构建体显著降低了表达蛋白片段的折叠和结构稳定性,为这些变异体的致病性提供了进一步的证据。对位于第 17 号外显子边界的 c.1813G>A p.(Gly605Arg) 变体进行的迷你基因检测发现,外显子跳过导致了 48 个氨基酸的框内缺失。硅学分子建模揭示了可能表明 PKHD1L1 蛋白质失稳的关键结构特征。多种证据表明,PKHD1L1 与非综合征性轻中度至重度感音神经性听力损失有关。对轻中度听力损失患者进行 PKHD1L1 检测可能会发现更多的受影响家庭。
本文章由计算机程序翻译,如有差异,请以英文原文为准。

PKHD1L1, a gene involved in the stereocilia coat, causes autosomal recessive nonsyndromic hearing loss.

PKHD1L1, a gene involved in the stereocilia coat, causes autosomal recessive nonsyndromic hearing loss.

Identification of genes associated with nonsyndromic hearing loss is a crucial endeavor given the substantial number of individuals who remain without a diagnosis after even the most advanced genetic testing. PKHD1L1 was established as necessary for the formation of the cochlear hair-cell stereociliary coat and causes hearing loss in mice and zebrafish when mutated. We sought to determine if biallelic variants in PKHD1L1 also cause hearing loss in humans. Exome sequencing was performed on DNA of four families segregating autosomal recessive nonsyndromic sensorineural hearing loss. Compound heterozygous p.[(Gly129Ser)];p.[(Gly1314Val)] and p.[(Gly605Arg)];p[(Leu2818TyrfsTer5)], homozygous missense p.(His2479Gln) and nonsense p.(Arg3381Ter) variants were identified in PKHD1L1 that were predicted to be damaging using in silico pathogenicity prediction methods. In vitro functional analysis of two missense variants was performed using purified recombinant PKHD1L1 protein fragments. We then evaluated protein thermodynamic stability with and without the missense variants found in one of the families and performed a minigene splicing assay for another variant. In silico molecular modeling using AlphaFold2 and protein sequence alignment analysis were carried out to further explore potential variant effects on structure. In vitro functional assessment indicated that both engineered PKHD1L1 p.(Gly129Ser) and p.(Gly1314Val) mutant constructs significantly reduced the folding and structural stabilities of the expressed protein fragments, providing further evidence to support pathogenicity of these variants. Minigene assay of the c.1813G>A p.(Gly605Arg) variant, located at the boundary of exon 17, revealed exon skipping leading to an in-frame deletion of 48 amino acids. In silico molecular modeling exposed key structural features that might suggest PKHD1L1 protein destabilization. Multiple lines of evidence collectively associate PKHD1L1 with nonsyndromic mild-moderate to severe sensorineural hearing loss. PKHD1L1 testing in individuals with mild-moderate hearing loss may identify further affected families.

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来源期刊
Human Genetics
Human Genetics 生物-遗传学
CiteScore
10.80
自引率
3.80%
发文量
94
审稿时长
1 months
期刊介绍: Human Genetics is a monthly journal publishing original and timely articles on all aspects of human genetics. The Journal particularly welcomes articles in the areas of Behavioral genetics, Bioinformatics, Cancer genetics and genomics, Cytogenetics, Developmental genetics, Disease association studies, Dysmorphology, ELSI (ethical, legal and social issues), Evolutionary genetics, Gene expression, Gene structure and organization, Genetics of complex diseases and epistatic interactions, Genetic epidemiology, Genome biology, Genome structure and organization, Genotype-phenotype relationships, Human Genomics, Immunogenetics and genomics, Linkage analysis and genetic mapping, Methods in Statistical Genetics, Molecular diagnostics, Mutation detection and analysis, Neurogenetics, Physical mapping and Population Genetics. Articles reporting animal models relevant to human biology or disease are also welcome. Preference will be given to those articles which address clinically relevant questions or which provide new insights into human biology. Unless reporting entirely novel and unusual aspects of a topic, clinical case reports, cytogenetic case reports, papers on descriptive population genetics, articles dealing with the frequency of polymorphisms or additional mutations within genes in which numerous lesions have already been described, and papers that report meta-analyses of previously published datasets will normally not be accepted. The Journal typically will not consider for publication manuscripts that report merely the isolation, map position, structure, and tissue expression profile of a gene of unknown function unless the gene is of particular interest or is a candidate gene involved in a human trait or disorder.
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