首页 > 最新文献

Human Mutation最新文献

英文 中文
Correction to “Macrocephaly and Digital Anomalies Expand the Phenotypic Spectrum of PGAP2 Variants in Hyperphosphatasia with Impaired Intellectual Development Syndrome 3 (HPMRS3)” 更正“大头畸形和数字异常扩大了高磷酸症伴智力发育障碍综合征3 (HPMRS3)中PGAP2变异的表型谱”
IF 3.7 2区 医学 Q2 GENETICS & HEREDITY Pub Date : 2025-10-28 DOI: 10.1155/humu/9836575

S. Susgun, A. Ben-Mahmoud, F. Rüschendorf, et al., “Macrocephaly and Digital Anomalies Expand the Phenotypic Spectrum of PGAP2 Variants in Hyperphosphatasia with Impaired Intellectual Development Syndrome 3 (HPMRS3),” Human Mutation 2024 (2024): 5518289, https://doi.org/10.1155/2024/5518289.

In the article titled “Macrocephaly and Digital Anomalies Expand the Phenotypic Spectrum of PGAP2 Variants in Hyperphosphatasia with Impaired Intellectual Development Syndrome 3 (HPMRS3),” author “Solveig Schulz” was affiliated to “Zentrum für Humangenetik, Tübingen, Germany,” which is incorrect. The correct affiliation for this author appears below:

“Synlab Praxis Humangenetik, Jena, Germany”

We apologize for this error.

S. Susgun, A. Ben-Mahmoud, F. r schendorf, et al.,“巨头畸形和数字异常扩大了高磷酸酶血症伴智力发育障碍综合征3 (HPMRS3)中PGAP2变异的表型谱,”Human Mutation 2024 (2024):5518289, https://doi.org/10.1155/2024/5518289.In这篇题为“巨头畸形和数字异常扩大了高磷酸化与智力发育障碍综合征3 (HPMRS3)中PGAP2变异的表型谱”的文章,作者“Solveig Schulz”隶属于“德国宾根人类基因中心”,这是不正确的。该作者的正确归属如下:“Synlab Praxis Humangenetik, Jena, Germany”我们为这个错误道歉。
{"title":"Correction to “Macrocephaly and Digital Anomalies Expand the Phenotypic Spectrum of PGAP2 Variants in Hyperphosphatasia with Impaired Intellectual Development Syndrome 3 (HPMRS3)”","authors":"","doi":"10.1155/humu/9836575","DOIUrl":"https://doi.org/10.1155/humu/9836575","url":null,"abstract":"<p>S. Susgun, A. Ben-Mahmoud, F. Rüschendorf, et al., “Macrocephaly and Digital Anomalies Expand the Phenotypic Spectrum of <i>PGAP2</i> Variants in Hyperphosphatasia with Impaired Intellectual Development Syndrome 3 (HPMRS3),” <i>Human Mutation</i> 2024 (2024): 5518289, https://doi.org/10.1155/2024/5518289.</p><p>In the article titled “Macrocephaly and Digital Anomalies Expand the Phenotypic Spectrum of <i>PGAP2</i> Variants in Hyperphosphatasia with Impaired Intellectual Development Syndrome 3 (HPMRS3),” author “Solveig Schulz” was affiliated to “Zentrum für Humangenetik, Tübingen, Germany,” which is incorrect. The correct affiliation for this author appears below:</p><p>“Synlab Praxis Humangenetik, Jena, Germany”</p><p>We apologize for this error.</p>","PeriodicalId":13061,"journal":{"name":"Human Mutation","volume":"2025 1","pages":""},"PeriodicalIF":3.7,"publicationDate":"2025-10-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1155/humu/9836575","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145406711","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
TCIRG1 as a Novel Prognostic Biomarker Triggering Immune Infiltration in Renal Clear Cell Carcinoma: An Integrative Study of Single-Cell and Bulk Data TCIRG1作为触发肾透明细胞癌免疫浸润的新型预后生物标志物:单细胞和大量数据的综合研究
IF 3.7 2区 医学 Q2 GENETICS & HEREDITY Pub Date : 2025-10-24 DOI: 10.1155/humu/1839494
Wei Ye, Honghao Yang, Xincheng Yi, Shaoyi Zhang, Siyu Wang, Zongming Jia, Jin Zang
<div> <section> <h3> Background</h3> <p>Tumor microenvironment (TME) is a significant factor regulating the malignant phenotype and drug resistance of kidney renal clear cell carcinoma (KIRC). The identification of biomarker signatures mediating immune infiltration in TME is of significance for prognostic assessment and personalized therapy of KIRC.</p> </section> <section> <h3> Methods</h3> <p>The gene set associated with immune cell populations in KIRC TME was extracted from the single-cell dataset GSE139555 using high-dimensional weighted coexpression network analysis (hdWGCNA). The bulk data from TCGA-KIRC were integrated to screen significant signatures in KIRC prognosis through Cox regression, and a combination of 101 machine learning algorithms was compared to prioritize feature genes for the construction of a novel prognostic model. Finally, LightGBM and XGBoost algorithms identified TCIRG1 as a key model feature and a novel biomarker in KIRC for experimental characterization using western blot, immunohistochemistry, multiple immunofluorescence (mIHC), subcutaneous tumor formation in nude mice, and Transwell assays.</p> </section> <section> <h3> Results</h3> <p>Single-cell data showed that the monocyte population varied most significantly in KIRC samples, and 150 candidate genes from monocytes were identified based on hdWGCNA. By integrating bulk TCGA-KIRC data and Cox regression, 15 prognosis-related genes were extracted as candidates for machine learning–powered training using 101 algorithm combinations, and nine genes were prioritized as feature variables to establish a prognostic model with good predictive performance on the overall survival of KIRC patients. Finally, TCIRG1 was identified as a novel biomarker signature from the prognostic model, and ultimately, by combining LightGBM and XGBoost algorithms, TCIRG1 was identified as a key characteristic signal for experimental validation and functional studies. Immunohistochemistry, cellular, and animal experiments showed that TCIRG1 expression was significantly elevated in KIRC samples, and its high expression was closely associated with adverse clinicopathological features. mIHC results demonstrated a significant positive correlation between TCIRG1 expression and immune cell infiltration in the KIRC TME, particularly with Treg cells.</p> </section> <section> <h3> Conclusions</h3> <p>TCIRG1 was identified and validated as a novel prognostic biomarker triggering immune infiltration in KIRC. The mechanisms and translational prospects of TCIRG1 in KIRC management will be explored in future work.</p>
肿瘤微环境(Tumor microenvironment, TME)是调控肾透明细胞癌(KIRC)恶性表型和耐药的重要因素。鉴定TME中介导免疫浸润的生物标志物特征对KIRC的预后评估和个性化治疗具有重要意义。方法采用高维加权共表达网络分析(high-dimensional weighted coexpression network analysis, hdWGCNA)从单细胞数据集GSE139555中提取与KIRC TME免疫细胞群相关的基因集。整合来自TCGA-KIRC的大量数据,通过Cox回归筛选KIRC预后的重要特征,并比较101种机器学习算法的组合,以优先考虑特征基因,以构建新的预后模型。最后,LightGBM和XGBoost算法将TCIRG1确定为KIRC的关键模型特征和新的生物标志物,用于western blot、免疫组织化学、多重免疫荧光(mIHC)、裸鼠皮下肿瘤形成和Transwell实验表征。结果单细胞数据显示,KIRC样本中单核细胞群体的变化最为显著,并基于hdWGCNA从单核细胞中鉴定出150个候选基因。通过整合大量TCGA-KIRC数据和Cox回归,提取15个预后相关基因作为101种算法组合的机器学习训练候选基因,并将9个基因优先作为特征变量,建立对KIRC患者总体生存具有良好预测性能的预后模型。最后,TCIRG1被鉴定为预后模型中的一个新的生物标志物特征,最终,通过结合LightGBM和XGBoost算法,TCIRG1被鉴定为实验验证和功能研究的关键特征信号。免疫组织化学、细胞和动物实验均显示,TCIRG1在KIRC样本中表达显著升高,其高表达与不良的临床病理特征密切相关。mIHC结果显示,TCIRG1表达与KIRC TME中免疫细胞浸润呈显著正相关,尤其是与Treg细胞。结论TCIRG1是KIRC中触发免疫浸润的一种新的预后生物标志物。TCIRG1在KIRC管理中的作用机制和翻译前景将在今后的工作中进一步探讨。
{"title":"TCIRG1 as a Novel Prognostic Biomarker Triggering Immune Infiltration in Renal Clear Cell Carcinoma: An Integrative Study of Single-Cell and Bulk Data","authors":"Wei Ye,&nbsp;Honghao Yang,&nbsp;Xincheng Yi,&nbsp;Shaoyi Zhang,&nbsp;Siyu Wang,&nbsp;Zongming Jia,&nbsp;Jin Zang","doi":"10.1155/humu/1839494","DOIUrl":"https://doi.org/10.1155/humu/1839494","url":null,"abstract":"&lt;div&gt;\u0000 \u0000 &lt;section&gt;\u0000 \u0000 &lt;h3&gt; Background&lt;/h3&gt;\u0000 \u0000 &lt;p&gt;Tumor microenvironment (TME) is a significant factor regulating the malignant phenotype and drug resistance of kidney renal clear cell carcinoma (KIRC). The identification of biomarker signatures mediating immune infiltration in TME is of significance for prognostic assessment and personalized therapy of KIRC.&lt;/p&gt;\u0000 &lt;/section&gt;\u0000 \u0000 &lt;section&gt;\u0000 \u0000 &lt;h3&gt; Methods&lt;/h3&gt;\u0000 \u0000 &lt;p&gt;The gene set associated with immune cell populations in KIRC TME was extracted from the single-cell dataset GSE139555 using high-dimensional weighted coexpression network analysis (hdWGCNA). The bulk data from TCGA-KIRC were integrated to screen significant signatures in KIRC prognosis through Cox regression, and a combination of 101 machine learning algorithms was compared to prioritize feature genes for the construction of a novel prognostic model. Finally, LightGBM and XGBoost algorithms identified TCIRG1 as a key model feature and a novel biomarker in KIRC for experimental characterization using western blot, immunohistochemistry, multiple immunofluorescence (mIHC), subcutaneous tumor formation in nude mice, and Transwell assays.&lt;/p&gt;\u0000 &lt;/section&gt;\u0000 \u0000 &lt;section&gt;\u0000 \u0000 &lt;h3&gt; Results&lt;/h3&gt;\u0000 \u0000 &lt;p&gt;Single-cell data showed that the monocyte population varied most significantly in KIRC samples, and 150 candidate genes from monocytes were identified based on hdWGCNA. By integrating bulk TCGA-KIRC data and Cox regression, 15 prognosis-related genes were extracted as candidates for machine learning–powered training using 101 algorithm combinations, and nine genes were prioritized as feature variables to establish a prognostic model with good predictive performance on the overall survival of KIRC patients. Finally, TCIRG1 was identified as a novel biomarker signature from the prognostic model, and ultimately, by combining LightGBM and XGBoost algorithms, TCIRG1 was identified as a key characteristic signal for experimental validation and functional studies. Immunohistochemistry, cellular, and animal experiments showed that TCIRG1 expression was significantly elevated in KIRC samples, and its high expression was closely associated with adverse clinicopathological features. mIHC results demonstrated a significant positive correlation between TCIRG1 expression and immune cell infiltration in the KIRC TME, particularly with Treg cells.&lt;/p&gt;\u0000 &lt;/section&gt;\u0000 \u0000 &lt;section&gt;\u0000 \u0000 &lt;h3&gt; Conclusions&lt;/h3&gt;\u0000 \u0000 &lt;p&gt;TCIRG1 was identified and validated as a novel prognostic biomarker triggering immune infiltration in KIRC. The mechanisms and translational prospects of TCIRG1 in KIRC management will be explored in future work.&lt;/p&gt;\u0000 ","PeriodicalId":13061,"journal":{"name":"Human Mutation","volume":"2025 1","pages":""},"PeriodicalIF":3.7,"publicationDate":"2025-10-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1155/humu/1839494","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145366942","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Enhanced ICOS Signaling Between Dendritic Cells and T Cells Characterizes the Immune Landscape of Human Cholangiocarcinoma 树突状细胞和T细胞之间增强的ICOS信号传导表征了人胆管癌的免疫景观
IF 3.7 2区 医学 Q2 GENETICS & HEREDITY Pub Date : 2025-10-23 DOI: 10.1155/humu/9981470
Meiying Zhu, Yuou Li, Xiaolong Tang, Xinjian Wan, Zunqiang Zhou

Cholangiocarcinoma exhibits a complex tumor microenvironment, yet the cellular interactions governing its progression remain poorly understood. Here, through integrated analysis of two independent single-cell RNA sequencing datasets comprising both complete tissue and immune-focused profiling, we comprehensively mapped the cellular landscape and intercellular communication networks in human cholangiocarcinoma. Our analysis revealed significant remodeling of immune cell compositions and interaction patterns in the tumor microenvironment. Notably, we identified enhanced ICOS signaling between dendritic cells and T cells as a prominent feature of cholangiocarcinoma. Using CellChat analysis, we demonstrated that tumor-associated dendritic cells, particularly plasmacytoid DCs, exhibit stronger ICOS-mediated communication with T cells compared to their counterparts in normal tissues. Functional validation experiments confirmed that tumor-conditioned dendritic cells upregulate ICOSL expression and promote CD8+ T-cell activation through the ICOS–ICOSL axis, as evidenced by increased CD69 and CD25 expression. This activation was specifically abolished by ICOSL blockade, establishing the functional significance of this pathway. Our findings provide novel insights into tumor-immune interactions in cholangiocarcinoma and suggest the ICOS–ICOSL axis as a potential therapeutic target for immunotherapy.

胆管癌表现出复杂的肿瘤微环境,但控制其进展的细胞相互作用仍然知之甚少。在这里,通过对两个独立的单细胞RNA测序数据集的综合分析,包括完整的组织和免疫聚焦分析,我们全面绘制了人类胆管癌的细胞景观和细胞间通讯网络。我们的分析揭示了肿瘤微环境中免疫细胞组成和相互作用模式的显著重塑。值得注意的是,我们发现树突状细胞和T细胞之间的ICOS信号增强是胆管癌的一个突出特征。使用CellChat分析,我们证明了肿瘤相关的树突状细胞,特别是浆细胞样树突状细胞,与正常组织中的对应细胞相比,表现出更强的icos介导的与T细胞的通信。功能验证实验证实,肿瘤条件下的树突状细胞通过ICOS-ICOSL轴上调ICOSL表达,促进CD8+ t细胞活化,CD69和CD25表达增加。这种激活被ICOSL阻断特异性地消除,从而确立了该通路的功能意义。我们的研究结果为胆管癌的肿瘤-免疫相互作用提供了新的见解,并提示ICOS-ICOSL轴是免疫治疗的潜在治疗靶点。
{"title":"Enhanced ICOS Signaling Between Dendritic Cells and T Cells Characterizes the Immune Landscape of Human Cholangiocarcinoma","authors":"Meiying Zhu,&nbsp;Yuou Li,&nbsp;Xiaolong Tang,&nbsp;Xinjian Wan,&nbsp;Zunqiang Zhou","doi":"10.1155/humu/9981470","DOIUrl":"https://doi.org/10.1155/humu/9981470","url":null,"abstract":"<p>Cholangiocarcinoma exhibits a complex tumor microenvironment, yet the cellular interactions governing its progression remain poorly understood. Here, through integrated analysis of two independent single-cell RNA sequencing datasets comprising both complete tissue and immune-focused profiling, we comprehensively mapped the cellular landscape and intercellular communication networks in human cholangiocarcinoma. Our analysis revealed significant remodeling of immune cell compositions and interaction patterns in the tumor microenvironment. Notably, we identified enhanced ICOS signaling between dendritic cells and T cells as a prominent feature of cholangiocarcinoma. Using CellChat analysis, we demonstrated that tumor-associated dendritic cells, particularly plasmacytoid DCs, exhibit stronger ICOS-mediated communication with T cells compared to their counterparts in normal tissues. Functional validation experiments confirmed that tumor-conditioned dendritic cells upregulate ICOSL expression and promote CD8+ T-cell activation through the ICOS–ICOSL axis, as evidenced by increased CD69 and CD25 expression. This activation was specifically abolished by ICOSL blockade, establishing the functional significance of this pathway. Our findings provide novel insights into tumor-immune interactions in cholangiocarcinoma and suggest the ICOS–ICOSL axis as a potential therapeutic target for immunotherapy.</p>","PeriodicalId":13061,"journal":{"name":"Human Mutation","volume":"2025 1","pages":""},"PeriodicalIF":3.7,"publicationDate":"2025-10-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1155/humu/9981470","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145366716","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Identification of Novel Modifier Genes Associated With Pain in Cystic Fibrosis: An In Silico Gene Discovery 与囊性纤维化疼痛相关的新型修饰基因的鉴定:一项计算机基因发现
IF 3.7 2区 医学 Q2 GENETICS & HEREDITY Pub Date : 2025-10-19 DOI: 10.1155/humu/7570437
Anastasia Ward, Ramil Mauleon, Chee Y. Ooi, Nedeljka Rosic

Background

Cystic fibrosis (CF) is the most common life-shortening monogenic autosomal recessive disease in Caucasians with diverse and extensive comorbidities. Where the majority of studies have focused on the respiratory and digestive systems, there has been a paucity of research focusing on pain, even though people living with CF have reported a high prevalence and increased severity of pain. Many studies have identified the complex relationship between genotype and phenotype, and growing evidence suggests that the phenotypic variation observed not only depends on the variations in the CF transmembrane conductance regulator (CFTR) gene but also on modifier genes. Gene modifiers (GMs) have been reported to affect many organs or systems in CF. However, there have been no studies on how GMs may influence pain. Therefore, this study is aimed at highlighting potential modifier genes that may affect pain perception in CF and possible responses to therapeutics.

Methods

The bioinformatics workflow adopted includes database and literature mining, pathway enrichment analysis, protein–protein interactions evaluation and drug–gene network investigation.

Results

We identified seven potential pain modifiers in CF, including chymotrypsin C (CTRC), serine protease inhibitor Kazal-Type 1 (SPINK1), tumour necrosis factor (TNF), ATP-binding cassette subfamily B Member 1 (ABCB1), protease serine 1 (PRSS1) and transforming growth factor beta 1 (TGFB1) interacting with the CFTR gene. The analysis of the biochemical pathways indicates that signal transduction and the immune system are likely to be involved in pain processes. The specific GMs, TNF and ABCB1, are found to be within the central hub genes, indicating their potential influence on the pain pathways in CF.

Conclusions

This in silico analysis highlights potential genes and biochemical pathways implicated in pain pathways that could significantly impact pain perception in people living with CF and their response to prescribed therapies. Further functional analyses are needed to include CF participants and provide a physiological relevance on how genetic polymorphisms of identified GMs may impact their pain phenotype or profile.

囊性纤维化(CF)是白种人中最常见的缩短寿命的单基因常染色体隐性疾病,具有多种多样的合并症。大多数研究都集中在呼吸和消化系统上,而对疼痛的研究却很少,尽管CF患者的发病率很高,疼痛的严重程度也在增加。许多研究已经发现基因型和表型之间的复杂关系,越来越多的证据表明,所观察到的表型变异不仅取决于CF跨膜传导调节基因(CFTR)的变异,还取决于修饰基因的变异。基因修饰因子(GMs)已被报道影响CF的许多器官或系统,然而,还没有关于基因修饰因子如何影响疼痛的研究。因此,本研究旨在突出潜在的修饰基因,这些修饰基因可能影响CF患者的疼痛感知以及对治疗方法的可能反应。方法采用数据库和文献挖掘、途径富集分析、蛋白相互作用评价和药物-基因网络调查等生物信息学工作流程。结果我们确定了CF中7种潜在的疼痛调节剂,包括凝乳胰蛋白酶C (CTRC)、丝氨酸蛋白酶抑制剂kazal - 1 (SPINK1)、肿瘤坏死因子(TNF)、atp结合盒B亚家族成员1 (ABCB1)、蛋白酶丝氨酸1 (PRSS1)和与CFTR基因相互作用的转化生长因子β 1 (TGFB1)。生物化学途径分析表明,信号转导和免疫系统可能参与疼痛过程。特异性GMs, TNF和ABCB1,被发现在中心枢纽基因中,表明它们对CF疼痛通路的潜在影响。结论该计算机分析突出了与疼痛通路相关的潜在基因和生化途径,这些基因和生化途径可能显著影响CF患者的疼痛感知及其对处方治疗的反应。进一步的功能分析需要包括CF参与者,并提供关于已鉴定的gm的遗传多态性如何影响其疼痛表型或特征的生理学相关性。
{"title":"Identification of Novel Modifier Genes Associated With Pain in Cystic Fibrosis: An In Silico Gene Discovery","authors":"Anastasia Ward,&nbsp;Ramil Mauleon,&nbsp;Chee Y. Ooi,&nbsp;Nedeljka Rosic","doi":"10.1155/humu/7570437","DOIUrl":"https://doi.org/10.1155/humu/7570437","url":null,"abstract":"<div>\u0000 \u0000 <section>\u0000 \u0000 <h3> Background</h3>\u0000 \u0000 <p>Cystic fibrosis (CF) is the most common life-shortening monogenic autosomal recessive disease in Caucasians with diverse and extensive comorbidities. Where the majority of studies have focused on the respiratory and digestive systems, there has been a paucity of research focusing on pain, even though people living with CF have reported a high prevalence and increased severity of pain. Many studies have identified the complex relationship between genotype and phenotype, and growing evidence suggests that the phenotypic variation observed not only depends on the variations in the CF transmembrane conductance regulator (<i>CFTR</i>) gene but also on modifier genes. Gene modifiers (GMs) have been reported to affect many organs or systems in CF. However, there have been no studies on how GMs may influence pain. Therefore, this study is aimed at highlighting potential modifier genes that may affect pain perception in CF and possible responses to therapeutics.</p>\u0000 </section>\u0000 \u0000 <section>\u0000 \u0000 <h3> Methods</h3>\u0000 \u0000 <p>The bioinformatics workflow adopted includes database and literature mining, pathway enrichment analysis, protein–protein interactions evaluation and drug–gene network investigation.</p>\u0000 </section>\u0000 \u0000 <section>\u0000 \u0000 <h3> Results</h3>\u0000 \u0000 <p>We identified seven potential pain modifiers in CF, including chymotrypsin C (<i>CTRC</i>), serine protease inhibitor Kazal-Type 1 (<i>SPINK1</i>), tumour necrosis factor (<i>TNF</i>), ATP-binding cassette subfamily B Member 1 (<i>ABCB1</i>), protease serine 1 (<i>PRSS1</i>) and transforming growth factor beta 1 (<i>TGFB1</i>) interacting with the <i>CFTR</i> gene. The analysis of the biochemical pathways indicates that signal transduction and the immune system are likely to be involved in pain processes. The specific GMs, <i>TNF</i> and <i>ABCB1</i>, are found to be within the central hub genes, indicating their potential influence on the pain pathways in CF.</p>\u0000 </section>\u0000 \u0000 <section>\u0000 \u0000 <h3> Conclusions</h3>\u0000 \u0000 <p>This in silico analysis highlights potential genes and biochemical pathways implicated in pain pathways that could significantly impact pain perception in people living with CF and their response to prescribed therapies. Further functional analyses are needed to include CF participants and provide a physiological relevance on how genetic polymorphisms of identified GMs may impact their pain phenotype or profile.</p>\u0000 </section>\u0000 </div>","PeriodicalId":13061,"journal":{"name":"Human Mutation","volume":"2025 1","pages":""},"PeriodicalIF":3.7,"publicationDate":"2025-10-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1155/humu/7570437","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145317619","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Prediction of Immunotherapy Response and Prognostic Outcomes for Patients With Ovarian Cancer Using PANoptosis-Related Genes 利用panoptoosis相关基因预测卵巢癌患者的免疫治疗反应和预后
IF 3.7 2区 医学 Q2 GENETICS & HEREDITY Pub Date : 2025-10-16 DOI: 10.1155/humu/7108361
Lei Zhang, Bo Yang, Huiting Xiao, Lu Sun, Wenting He, Ying Chen

Background

Ovarian cancer (OC) is a lethal malignancy often diagnosed at a late stage with frequent recurrence and immunotherapy resistance. PANoptosis is a novel programmed cell death regulating tumors and immunity. We constructed a prognostic model based on PANoptosis-related genes (PRGs) and evaluated its value for predicting immunotherapy response and survival in OC.

Methods

PRGs linked to OC prognosis were identified from public databases, followed by using the STRING database to develop a protein–protein interaction (PPI) network. The LASSO and multivariate Cox regression analyses were used to construct a risk model, and its predictive value was verified by survival analysis, receiver operator characteristic (ROC) curve, and nomogram. Next, we analyzed the immune microenvironment by combining CIBERSORT, MCP-counter, and ssGSEA algorithms and assessed the response of patients in different risk groups to immunotherapy using TIDE with immune phenotype score (IPS) methods. GSEA was performed to evaluate the activation status of biological pathways between patients in different risk groups. Finally, we verified the expression and potential biological functions of the key genes using quantitative reverse transcription-PCR (qRT-PCR), CCK-8, scratch, and transwell assays.

Results

A PANoptosis-related risk model for OC was constructed based on eight genes (PIK3CG, CAMK2A, CD38, NFKB1, PSMA4, PSMA8, PSMB1, and STAT4). The model could accurately evaluate the prognostic outcomes for OC patients, showing a high stability across different datasets. High-risk patients had lower immune cell infiltration, elevated TIDE, and reduced IPS, which suggested weaker immunotherapy responsiveness and therefore a worse prognosis. In addition, pathway analysis showed that the high-risk group was mainly enriched in tumor progression–related pathways. In vitro, PIK3CG, CAMK2A, NFKB1, PSMA4, and PSMB1 were upregulated in OC cell lines, and knockdown of PIK3CG notably suppressed the proliferative, migratory, and invasive capabilities of OC cells.

Conclusion

The PRG model established in this study may contribute to the assessment of immunotherapeutic response and prognosis for OC patients.

背景卵巢癌(OC)是一种晚期诊断的致命恶性肿瘤,经常复发和免疫治疗耐药。PANoptosis是一种调节肿瘤和免疫的新型程序性细胞死亡。我们构建了一个基于panoptoosis相关基因(PRGs)的预后模型,并评估了其预测OC免疫治疗反应和生存的价值。方法从公共数据库中识别与OC预后相关的PRGs,然后利用STRING数据库建立蛋白-蛋白相互作用(PPI)网络。采用LASSO和多变量Cox回归分析构建风险模型,并通过生存分析、ROC曲线和nomogram验证其预测价值。接下来,我们结合CIBERSORT、MCP-counter和ssGSEA算法分析了免疫微环境,并使用TIDE结合免疫表型评分(IPS)方法评估了不同风险组患者对免疫治疗的反应。采用GSEA评估不同风险组患者生物通路的激活状态。最后,我们利用定量逆转录pcr (qRT-PCR)、CCK-8、scratch和transwell实验验证了关键基因的表达和潜在的生物学功能。结果基于PIK3CG、CAMK2A、CD38、NFKB1、PSMA4、PSMA8、PSMB1、STAT4 8个基因构建了OC pantoposis相关风险模型。该模型可以准确评估OC患者的预后,在不同的数据集上表现出很高的稳定性。高危患者免疫细胞浸润较低,TIDE升高,IPS降低,提示免疫治疗反应性较弱,预后较差。此外,通路分析显示高危组主要富集肿瘤进展相关通路。在体外实验中,PIK3CG、CAMK2A、NFKB1、PSMA4和PSMB1在OC细胞系中表达上调,PIK3CG的下调显著抑制OC细胞的增殖、迁移和侵袭能力。结论本研究建立的PRG模型可用于评估卵巢癌患者的免疫治疗反应和预后。
{"title":"Prediction of Immunotherapy Response and Prognostic Outcomes for Patients With Ovarian Cancer Using PANoptosis-Related Genes","authors":"Lei Zhang,&nbsp;Bo Yang,&nbsp;Huiting Xiao,&nbsp;Lu Sun,&nbsp;Wenting He,&nbsp;Ying Chen","doi":"10.1155/humu/7108361","DOIUrl":"https://doi.org/10.1155/humu/7108361","url":null,"abstract":"<div>\u0000 \u0000 <section>\u0000 \u0000 <h3> Background</h3>\u0000 \u0000 <p>Ovarian cancer (OC) is a lethal malignancy often diagnosed at a late stage with frequent recurrence and immunotherapy resistance. PANoptosis is a novel programmed cell death regulating tumors and immunity. We constructed a prognostic model based on PANoptosis-related genes (PRGs) and evaluated its value for predicting immunotherapy response and survival in OC.</p>\u0000 </section>\u0000 \u0000 <section>\u0000 \u0000 <h3> Methods</h3>\u0000 \u0000 <p>PRGs linked to OC prognosis were identified from public databases, followed by using the STRING database to develop a protein–protein interaction (PPI) network. The LASSO and multivariate Cox regression analyses were used to construct a risk model, and its predictive value was verified by survival analysis, receiver operator characteristic (ROC) curve, and nomogram. Next, we analyzed the immune microenvironment by combining CIBERSORT, MCP-counter, and ssGSEA algorithms and assessed the response of patients in different risk groups to immunotherapy using TIDE with immune phenotype score (IPS) methods. GSEA was performed to evaluate the activation status of biological pathways between patients in different risk groups. Finally, we verified the expression and potential biological functions of the key genes using quantitative reverse transcription-PCR (qRT-PCR), CCK-8, scratch, and transwell assays.</p>\u0000 </section>\u0000 \u0000 <section>\u0000 \u0000 <h3> Results</h3>\u0000 \u0000 <p>A PANoptosis-related risk model for OC was constructed based on eight genes (<i>PIK3CG</i>, <i>CAMK2A</i>, <i>CD38</i>, <i>NFKB1</i>, <i>PSMA4</i>, <i>PSMA8</i>, <i>PSMB1</i>, and <i>STAT4</i>). The model could accurately evaluate the prognostic outcomes for OC patients, showing a high stability across different datasets. High-risk patients had lower immune cell infiltration, elevated TIDE, and reduced IPS, which suggested weaker immunotherapy responsiveness and therefore a worse prognosis. In addition, pathway analysis showed that the high-risk group was mainly enriched in tumor progression–related pathways. In vitro, <i>PIK3CG</i>, <i>CAMK2A</i>, <i>NFKB1</i>, <i>PSMA4</i>, and <i>PSMB1</i> were upregulated in OC cell lines, and knockdown of <i>PIK3CG</i> notably suppressed the proliferative, migratory, and invasive capabilities of OC cells.</p>\u0000 </section>\u0000 \u0000 <section>\u0000 \u0000 <h3> Conclusion</h3>\u0000 \u0000 <p>The PRG model established in this study may contribute to the assessment of immunotherapeutic response and prognosis for OC patients.</p>\u0000 </section>\u0000 </div>","PeriodicalId":13061,"journal":{"name":"Human Mutation","volume":"2025 1","pages":""},"PeriodicalIF":3.7,"publicationDate":"2025-10-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1155/humu/7108361","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145317439","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Novel Algorithm for Monogenic Noninvasive Prenatal Testing With Highly Similar Parental Pathogenic Haplotypes: A Representative Case of Congenital Adrenal Hyperplasia Pedigree 具有高度相似亲本致病单倍型的单基因无创产前检测新算法:一个先天性肾上腺增生家系的代表性病例
IF 3.7 2区 医学 Q2 GENETICS & HEREDITY Pub Date : 2025-10-13 DOI: 10.1155/humu/9990873
Wenjing Zhou, Fulin Liu, Shaojun Li, Di Wu, Jiyun Yang

Noninvasive prenatal testing (NIPT) has been widely used in various monogenic recessive disorders based on relative haplotype dosage (RHDO) analysis. We accepted a congenital adrenal hyperplasia (CAH) pedigree with highly similar parental pathogenic haplotypes. The initial monogenic NIPT attempt was unsuccessful due to a paucity of informative single-nucleotide polymorphisms (SNPs), prompting improvement of the current method. With a refined algorithm that deduces the fetal genotype based on dosage changes at SNPs located on a specific parental haplotype, while also effectively sidestepping allele bias introduced by hybrid capture, monogenic NIPT was successfully carried out in this family, yielding results consistent with invasive prenatal diagnosis. Theoretically, this algorithm can be employed in scenarios involving consanguineous marriages or when parents share a highly homologous haplotype, thereby broadening its applicability. Detailed methodology is described, and the advantages of our algorithm are discussed.

基于相对单倍型剂量(RHDO)分析的无创产前检测(NIPT)已广泛应用于各种单基因隐性疾病。我们接受了一个先天性肾上腺增生(CAH)的家系,具有高度相似的亲本致病单倍型。由于缺乏信息丰富的单核苷酸多态性(snp),最初的单基因NIPT尝试失败,促使当前方法的改进。通过一种基于特定亲本单倍型上snp的剂量变化推断胎儿基因型的改进算法,同时有效地避免了杂交捕获带来的等位基因偏倚,在该家庭中成功进行了单基因NIPT,结果与有创产前诊断一致。理论上,该算法可用于近亲婚姻或父母具有高度同源单倍型的情况,从而扩大了其适用性。详细描述了算法的方法,并讨论了算法的优点。
{"title":"Novel Algorithm for Monogenic Noninvasive Prenatal Testing With Highly Similar Parental Pathogenic Haplotypes: A Representative Case of Congenital Adrenal Hyperplasia Pedigree","authors":"Wenjing Zhou,&nbsp;Fulin Liu,&nbsp;Shaojun Li,&nbsp;Di Wu,&nbsp;Jiyun Yang","doi":"10.1155/humu/9990873","DOIUrl":"https://doi.org/10.1155/humu/9990873","url":null,"abstract":"<p>Noninvasive prenatal testing (NIPT) has been widely used in various monogenic recessive disorders based on relative haplotype dosage (RHDO) analysis. We accepted a congenital adrenal hyperplasia (CAH) pedigree with highly similar parental pathogenic haplotypes. The initial monogenic NIPT attempt was unsuccessful due to a paucity of informative single-nucleotide polymorphisms (SNPs), prompting improvement of the current method. With a refined algorithm that deduces the fetal genotype based on dosage changes at SNPs located on a specific parental haplotype, while also effectively sidestepping allele bias introduced by hybrid capture, monogenic NIPT was successfully carried out in this family, yielding results consistent with invasive prenatal diagnosis. Theoretically, this algorithm can be employed in scenarios involving consanguineous marriages or when parents share a highly homologous haplotype, thereby broadening its applicability. Detailed methodology is described, and the advantages of our algorithm are discussed.</p>","PeriodicalId":13061,"journal":{"name":"Human Mutation","volume":"2025 1","pages":""},"PeriodicalIF":3.7,"publicationDate":"2025-10-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1155/humu/9990873","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145316847","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
AIF1L as a Ferroptosis-Linked Biomarker in Microsatellite States–Driven Colorectal Cancer: Functional and Diagnostic Insights From Multiomics Analysis AIF1L作为微卫星状态驱动的结直肠癌中的铁凋亡相关生物标志物:多组学分析的功能和诊断见解
IF 3.7 2区 医学 Q2 GENETICS & HEREDITY Pub Date : 2025-10-10 DOI: 10.1155/humu/6663166
Yuanyuan Qin, Hongli Zhou, Lingyan Zhu, Wenting Li, Zequn Jiang, Li Li, Mianhua Wu

Background

Microsatellite instability (MSI) serves as a crucial biomarker for immune checkpoint blockade therapy in colorectal cancer (CRC). However, only around 40% of MSI CRC patients benefit from ICB. Investigating the mechanisms underlying MSI CRC, particularly its association with cell death and the immune microenvironment, can provide insights to improve immunotherapy efficacy.

Methods

Transcriptomic and clinical data of MSI CRC patients were collected from TCGA and GEO databases. Differential expression analysis, weighted gene coexpression network analysis, and Cox regression models were employed to identify five cell death–related prognostic genes (POU4F1, AIF1L, SLC18A1, INSL4, and HOXC6). Single-cell analysis, immune infiltration analysis, and in vitro and in vivo experiments were conducted to validate their roles in MSI CRC.

Results

The five-gene risk model effectively stratified high- and low-risk groups and predicted survival differences (AUC > 0.6). AIF1L exhibited elevated expression in MSI-H groups and demonstrated a significant correlation with ferroptosis and immune cell infiltration. In vitro experiments showed that AIF1L boosted cell proliferation and migration via modulating ferroptosis, showing correspondence with in vivo experiments. Moreover, enrichment analysis revealed that AIF1L participated in immune-related signaling pathways, potentially impacting the tumor microenvironment and patient prognosis.

Conclusion

AIF1L may regulate MSI CRC progression by promoting ferroptosis, serving as a prospective biomarker for prognosis and a therapeutic target for personalized therapy. This study uncovers new mechanisms in MSI CRC and provides a foundation for optimizing immunotherapy, though further investigation into its specific roles is needed.

微卫星不稳定性(Microsatellite instability, MSI)是结直肠癌(CRC)免疫检查点阻断治疗的重要生物标志物。然而,只有约40%的MSI结直肠癌患者受益于ICB。研究MSI结直肠癌的机制,特别是其与细胞死亡和免疫微环境的关联,可以为提高免疫治疗效果提供见解。方法从TCGA和GEO数据库中收集MSI结直肠癌患者的转录组学和临床资料。采用差异表达分析、加权基因共表达网络分析和Cox回归模型鉴定5个细胞死亡相关预后基因(POU4F1、AIF1L、SLC18A1、INSL4和HOXC6)。通过单细胞分析、免疫浸润分析、体外和体内实验验证其在MSI CRC中的作用。结果五基因风险模型有效地划分了高、低风险组,并预测了生存差异(AUC > 0.6)。AIF1L在MSI-H组中表达升高,与铁下垂和免疫细胞浸润有显著相关性。体外实验表明,AIF1L通过调节铁下垂促进细胞增殖和迁移,与体内实验结果一致。此外,富集分析显示AIF1L参与免疫相关信号通路,可能影响肿瘤微环境和患者预后。结论AIF1L可能通过促进铁下垂来调节MSI结直肠癌的进展,可作为预测预后的生物标志物和个体化治疗的靶点。本研究揭示了MSI结直肠癌的新机制,为优化免疫治疗提供了基础,但需要进一步研究其具体作用。
{"title":"AIF1L as a Ferroptosis-Linked Biomarker in Microsatellite States–Driven Colorectal Cancer: Functional and Diagnostic Insights From Multiomics Analysis","authors":"Yuanyuan Qin,&nbsp;Hongli Zhou,&nbsp;Lingyan Zhu,&nbsp;Wenting Li,&nbsp;Zequn Jiang,&nbsp;Li Li,&nbsp;Mianhua Wu","doi":"10.1155/humu/6663166","DOIUrl":"https://doi.org/10.1155/humu/6663166","url":null,"abstract":"<div>\u0000 \u0000 <section>\u0000 \u0000 <h3> Background</h3>\u0000 \u0000 <p>Microsatellite instability (MSI) serves as a crucial biomarker for immune checkpoint blockade therapy in colorectal cancer (CRC). However, only around 40% of MSI CRC patients benefit from ICB. Investigating the mechanisms underlying MSI CRC, particularly its association with cell death and the immune microenvironment, can provide insights to improve immunotherapy efficacy.</p>\u0000 </section>\u0000 \u0000 <section>\u0000 \u0000 <h3> Methods</h3>\u0000 \u0000 <p>Transcriptomic and clinical data of MSI CRC patients were collected from TCGA and GEO databases. Differential expression analysis, weighted gene coexpression network analysis, and Cox regression models were employed to identify five cell death–related prognostic genes (POU4F1, AIF1L, SLC18A1, INSL4, and HOXC6). Single-cell analysis, immune infiltration analysis, and in vitro and in vivo experiments were conducted to validate their roles in MSI CRC.</p>\u0000 </section>\u0000 \u0000 <section>\u0000 \u0000 <h3> Results</h3>\u0000 \u0000 <p>The five-gene risk model effectively stratified high- and low-risk groups and predicted survival differences (AUC &gt; 0.6). AIF1L exhibited elevated expression in MSI-H groups and demonstrated a significant correlation with ferroptosis and immune cell infiltration. In vitro experiments showed that AIF1L boosted cell proliferation and migration via modulating ferroptosis, showing correspondence with in vivo experiments. Moreover, enrichment analysis revealed that AIF1L participated in immune-related signaling pathways, potentially impacting the tumor microenvironment and patient prognosis.</p>\u0000 </section>\u0000 \u0000 <section>\u0000 \u0000 <h3> Conclusion</h3>\u0000 \u0000 <p>AIF1L may regulate MSI CRC progression by promoting ferroptosis, serving as a prospective biomarker for prognosis and a therapeutic target for personalized therapy. This study uncovers new mechanisms in MSI CRC and provides a foundation for optimizing immunotherapy, though further investigation into its specific roles is needed.</p>\u0000 </section>\u0000 </div>","PeriodicalId":13061,"journal":{"name":"Human Mutation","volume":"2025 1","pages":""},"PeriodicalIF":3.7,"publicationDate":"2025-10-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1155/humu/6663166","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145272553","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
One-Sided Matching Portal (OSMP): A Tool to Facilitate Rare Disease Patient Matchmaking 单方面匹配门户(OSMP):一个工具,以促进罕见疾病患者配对
IF 3.7 2区 医学 Q2 GENETICS & HEREDITY Pub Date : 2025-10-09 DOI: 10.1155/humu/5941599
Matthew Osmond, E. Magda Price, Orion J. Buske, Mackenzie Frew, Madeline Couse, Taila Hartley, Conor Klamann, Hannah G. B. H. Le, Jenny Xu, Delvin So, Anjali Jain, Kevin Lu, Kevin Mo, Hannah Wyllie, Erika Wall, Hannah G. Driver, Warren A. Cheung, Ana S. A. Cohen, Emily G. Farrow, Isabelle Thiffault, Care4Rare Canada Consortium, Andrei L. Turinsky, Tomi Pastinen, Michael Brudno, Kym M. Boycott

Background

Genomic matchmaking—the process of identifying individuals with overlapping phenotypes and rare variants in the same gene—is an important tool facilitating gene discoveries for unsolved rare genetic disease (RGD) patients. Current approaches are two-sided, meaning both patients being matched must have the same candidate gene flagged. This limits the number of RGD patients eligible for matchmaking. One-sided matchmaking, in which a gene of interest is queried in the genome-wide sequencing data of RGD patients, would make matchmaking possible for previously undiscoverable individuals. However, platforms and workflows for this approach have not been well established.

Result

We released a beta version of the One-Sided Matching Portal (OSMP), a platform capable of performing one-sided matchmaking queries across thousands of participants stored in genomic databases. The OSMP returns variant-level and participant-level information on each variant occurrence (VO) identified in a queried gene. A workflow for one-sided matchmaking was developed so that researchers could prioritize the many VOs returned from a given query. This workflow was tested through pilot studies where two sets of genes were queried in over 2500 individuals: 130 genes that were newly associated with disease in OMIM and 178 novel candidate genes that were not associated with a disease-gene association in OMIM. These pilots returned a large number of initial VOs (12,872 and 20,308, respectively); however, the workflow filtered out over 99.8% of these VOs prior to review by a participant’s clinician. Filters on participant-level information, including variant zygosity, participant phenotype, and whether a variant was also present in unaffected participants, were effective at reducing the number of false positive matches.

Conclusion

As demonstrated through the two pilot studies, one-sided matchmaking queries can be efficiently performed using the OSMP. The availability of variant-level and participant-level data is key to ensuring this approach is practical for researchers.

基因组配对是鉴定具有重叠表型和相同基因罕见变异的个体的过程,是促进未解决的罕见遗传病(RGD)患者基因发现的重要工具。目前的方法是双向的,这意味着两个匹配的患者必须有相同的候选基因标记。这限制了符合配对条件的RGD患者的数量。单侧配对,在RGD患者的全基因组测序数据中查询感兴趣的基因,将使以前未发现的个体配对成为可能。然而,这种方法的平台和工作流还没有很好地建立起来。我们发布了单侧配对门户(OSMP)的测试版,该平台能够对存储在基因组数据库中的数千名参与者进行单侧配对查询。OSMP返回在查询的基因中确定的每个变异发生(VO)的变异水平和参与者水平信息。开发了一个单侧匹配的工作流程,以便研究人员可以优先考虑从给定查询返回的许多VOs。该工作流程通过试点研究进行了测试,其中在2500多人中查询了两组基因:130个与OMIM疾病新相关的基因和178个与OMIM疾病基因关联无关的新候选基因。这些飞行员返回了大量初始VOs(分别为12,872和20,308);然而,在参与者的临床医生审查之前,工作流程过滤掉了超过99.8%的这些VOs。筛选参与者水平的信息,包括变异合子,参与者表型,以及是否在未受影响的参与者中也存在变异,可以有效地减少假阳性匹配的数量。通过两个试点研究表明,使用OSMP可以有效地执行单侧配对查询。变量水平和参与者水平数据的可用性是确保该方法对研究人员实用的关键。
{"title":"One-Sided Matching Portal (OSMP): A Tool to Facilitate Rare Disease Patient Matchmaking","authors":"Matthew Osmond,&nbsp;E. Magda Price,&nbsp;Orion J. Buske,&nbsp;Mackenzie Frew,&nbsp;Madeline Couse,&nbsp;Taila Hartley,&nbsp;Conor Klamann,&nbsp;Hannah G. B. H. Le,&nbsp;Jenny Xu,&nbsp;Delvin So,&nbsp;Anjali Jain,&nbsp;Kevin Lu,&nbsp;Kevin Mo,&nbsp;Hannah Wyllie,&nbsp;Erika Wall,&nbsp;Hannah G. Driver,&nbsp;Warren A. Cheung,&nbsp;Ana S. A. Cohen,&nbsp;Emily G. Farrow,&nbsp;Isabelle Thiffault,&nbsp;Care4Rare Canada Consortium,&nbsp;Andrei L. Turinsky,&nbsp;Tomi Pastinen,&nbsp;Michael Brudno,&nbsp;Kym M. Boycott","doi":"10.1155/humu/5941599","DOIUrl":"https://doi.org/10.1155/humu/5941599","url":null,"abstract":"<div>\u0000 \u0000 <section>\u0000 \u0000 <h3> Background</h3>\u0000 \u0000 <p>Genomic matchmaking—the process of identifying individuals with overlapping phenotypes and rare variants in the same gene—is an important tool facilitating gene discoveries for unsolved rare genetic disease (RGD) patients. Current approaches are two-sided, meaning both patients being matched must have the same candidate gene flagged. This limits the number of RGD patients eligible for matchmaking. One-sided matchmaking, in which a gene of interest is queried in the genome-wide sequencing data of RGD patients, would make matchmaking possible for previously undiscoverable individuals. However, platforms and workflows for this approach have not been well established.</p>\u0000 </section>\u0000 \u0000 <section>\u0000 \u0000 <h3> Result</h3>\u0000 \u0000 <p>We released a beta version of the One-Sided Matching Portal (OSMP), a platform capable of performing one-sided matchmaking queries across thousands of participants stored in genomic databases. The OSMP returns variant-level and participant-level information on each variant occurrence (VO) identified in a queried gene. A workflow for one-sided matchmaking was developed so that researchers could prioritize the many VOs returned from a given query. This workflow was tested through pilot studies where two sets of genes were queried in over 2500 individuals: 130 genes that were newly associated with disease in OMIM and 178 novel candidate genes that were not associated with a disease-gene association in OMIM. These pilots returned a large number of initial VOs (12,872 and 20,308, respectively); however, the workflow filtered out over 99.8% of these VOs prior to review by a participant’s clinician. Filters on participant-level information, including variant zygosity, participant phenotype, and whether a variant was also present in unaffected participants, were effective at reducing the number of false positive matches.</p>\u0000 </section>\u0000 \u0000 <section>\u0000 \u0000 <h3> Conclusion</h3>\u0000 \u0000 <p>As demonstrated through the two pilot studies, one-sided matchmaking queries can be efficiently performed using the OSMP. The availability of variant-level and participant-level data is key to ensuring this approach is practical for researchers.</p>\u0000 </section>\u0000 </div>","PeriodicalId":13061,"journal":{"name":"Human Mutation","volume":"2025 1","pages":""},"PeriodicalIF":3.7,"publicationDate":"2025-10-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1155/humu/5941599","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145272309","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Polycystic Ovary Syndrome May Be Associated With a Novel Mitochondrial tRNAAsp Mutation 多囊卵巢综合征可能与线粒体tRNAAsp突变有关
IF 3.7 2区 医学 Q2 GENETICS & HEREDITY Pub Date : 2025-10-07 DOI: 10.1155/humu/6663471
Yu Ding, Xuejiao Yu, Jian Xu, Caijuan Zhang, Jianhang Leng

Polycystic ovary syndrome is a common clinical condition often linked to insulin resistance (IR) and primarily affects women at reproductive age. Previous research has indicated a close association between mitochondrial tRNA (mt-tRNA) mutations and this syndrome; however, the range of mt-tRNA mutations in PCOS-IR remains largely unclear. In this study, we examined mt-tRNA mutations in 302 Han Chinese women with PCOS-IR and 589 control subjects, identifying a novel m.7544C>T mutation potentially related to this syndrome. At the molecular level, the m.7544C>T mutation occurs at a highly conserved nucleotide within the anticodon stem of mt-tRNAAsp, disrupting the 30C-40G base-pairing. Using cybrids cells derived from two individuals carrying this mutation and two controls without it, we observed that the m.7544C>T decreased the steady-state levels of tRNAAsp, altered mitochondrial RNA transcripts, impaired the activities of respiratory chain enzymes and oxygen consumption rates (OCRs), compromised mitochondrial functions, and increased oxidative stress. Overall, our findings strongly suggest that the m.7544C>T mutation contributes to the development of PCOS-IR, offering new insights into the pathophysiology of PCOS-IR driven by tRNA mutation–induced mitochondrial dysfunction and oxidative stress.

多囊卵巢综合征是一种常见的临床疾病,通常与胰岛素抵抗(IR)有关,主要影响育龄妇女。先前的研究表明,线粒体tRNA (mt-tRNA)突变与该综合征密切相关;然而,PCOS-IR中mt-tRNA突变的范围仍不清楚。在这项研究中,我们检测了302名患有PCOS-IR的汉族女性和589名对照受试者的mt-tRNA突变,发现了一种可能与该综合征相关的新型m.7544C>;T突变。在分子水平上,m.7544C>;T突变发生在mt-tRNAAsp反密码子茎中的一个高度保守的核苷酸上,破坏了30C-40G碱基配对。使用来自两个携带该突变的个体和两个不携带该突变的对照组的杂交细胞,我们观察到m.7544C>;T降低了tRNAAsp的稳态水平,改变了线粒体RNA转录,损害了呼吸链酶的活性和氧消耗率(ocr),损害了线粒体功能,并增加了氧化应激。总之,我们的研究结果强烈提示m.7544C>;T突变有助于PCOS-IR的发展,为tRNA突变诱导的线粒体功能障碍和氧化应激驱动PCOS-IR的病理生理学提供了新的见解。
{"title":"Polycystic Ovary Syndrome May Be Associated With a Novel Mitochondrial tRNAAsp Mutation","authors":"Yu Ding,&nbsp;Xuejiao Yu,&nbsp;Jian Xu,&nbsp;Caijuan Zhang,&nbsp;Jianhang Leng","doi":"10.1155/humu/6663471","DOIUrl":"https://doi.org/10.1155/humu/6663471","url":null,"abstract":"<p>Polycystic ovary syndrome is a common clinical condition often linked to insulin resistance (IR) and primarily affects women at reproductive age. Previous research has indicated a close association between mitochondrial tRNA (mt-tRNA) mutations and this syndrome; however, the range of mt-tRNA mutations in PCOS-IR remains largely unclear. In this study, we examined mt-tRNA mutations in 302 Han Chinese women with PCOS-IR and 589 control subjects, identifying a novel m.7544C&gt;T mutation potentially related to this syndrome. At the molecular level, the m.7544C&gt;T mutation occurs at a highly conserved nucleotide within the anticodon stem of mt-tRNA<sup>Asp</sup>, disrupting the 30C-40G base-pairing. Using cybrids cells derived from two individuals carrying this mutation and two controls without it, we observed that the m.7544C&gt;T decreased the steady-state levels of tRNA<sup>Asp</sup>, altered mitochondrial RNA transcripts, impaired the activities of respiratory chain enzymes and oxygen consumption rates (OCRs), compromised mitochondrial functions, and increased oxidative stress. Overall, our findings strongly suggest that the m.7544C&gt;T mutation contributes to the development of PCOS-IR, offering new insights into the pathophysiology of PCOS-IR driven by tRNA mutation–induced mitochondrial dysfunction and oxidative stress.</p>","PeriodicalId":13061,"journal":{"name":"Human Mutation","volume":"2025 1","pages":""},"PeriodicalIF":3.7,"publicationDate":"2025-10-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1155/humu/6663471","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145271804","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Correction to “Prognostic Value of Ubiquitination-Related Genes in Ovarian Cancer and Their Correlation With Tumor Immunity” 更正“卵巢癌泛素化相关基因的预后价值及其与肿瘤免疫的相关性”
IF 3.7 2区 医学 Q2 GENETICS & HEREDITY Pub Date : 2025-10-04 DOI: 10.1155/humu/9879845

S. Zhao, X. Lin, Y. Huang, et al., “Prognostic Value of Ubiquitination-Related Genes in Ovarian Cancer and Their Correlation With Tumor Immunity,” Human Mutation 2025 (2025): 8369299, https://doi.org/10.1155/humu/8369299.

In the article titled “Prognostic Value of Ubiquitination-Related Genes in Ovarian Cancer and Their Correlation With Tumor Immunity,” there were errors in all the affiliations. The corrected affiliation list appears below:

Shu Zhao,1,2,3,4 Xiaojing Lin,1,3 Yuying Huang,2 Zhongmin Kang,5 Huali Luo,2 Qizhu Zhang,1,3 Qinshan Li,1,2,3 and Mengxing Li5

1Department of Obstetrics and Gynecology, Institute of Precision Medicine of Guizhou Province, Affiliated Hospital of Guizhou Medical University, Guiyang, Guizhou, China

2Department of Clinical Biochemistry, School of Medical Laboratory Science, Guizhou Medical University, Guiyang, Guizhou, China

3Clinical Medical College, Guizhou Medical University, Guiyang, Guizhou, China

4Department of Obstetrics, Guizhou Provincial People’s Hospital, Guiyang, Guizhou, China

5Department of Hematology, Guizhou Province Institute of Hematology, Guizhou Province Laboratory of Hematopoietic Stem Cell Transplantation Centre, Affiliated Hospital of Guizhou Medical University Guiyang, Guizhou, China

We apologize for this error.

赵生,林晓霞,黄毅,等,“泛素化相关基因在卵巢癌中的预后价值及其与肿瘤免疫的相关性”,《人类突变2025》(2025):8369299,https://doi.org/10.1155/humu/8369299.In文章“泛素化相关基因在卵巢癌中的预后价值及其与肿瘤免疫的相关性”,均有错误。正确的隶属关系如下:赵姝,1、2、3、4林晓静,1、3黄玉英,2康忠民,5罗华丽,2张启珠,1、3李钦山,1、2、3,李梦星。中国贵州省贵阳贵州医科大学附属医院贵州省精准医学研究所妇产科2贵州医科大学医学检验学院临床生物化学系,中国贵州省贵阳3临床医学院,4贵州省人民医院产科,贵州省贵阳市;5贵州省血液研究所血液科,贵州省造血干细胞移植中心实验室,贵州医科大学附属医院,贵州省贵阳市。对此错误深表歉意。
{"title":"Correction to “Prognostic Value of Ubiquitination-Related Genes in Ovarian Cancer and Their Correlation With Tumor Immunity”","authors":"","doi":"10.1155/humu/9879845","DOIUrl":"https://doi.org/10.1155/humu/9879845","url":null,"abstract":"<p>S. Zhao, X. Lin, Y. Huang, et al., “Prognostic Value of Ubiquitination-Related Genes in Ovarian Cancer and Their Correlation With Tumor Immunity,” <i>Human Mutation</i> 2025 (2025): 8369299, https://doi.org/10.1155/humu/8369299.</p><p>In the article titled “Prognostic Value of Ubiquitination-Related Genes in Ovarian Cancer and Their Correlation With Tumor Immunity,” there were errors in all the affiliations. The corrected affiliation list appears below:</p><p>Shu Zhao,<sup>1,2,3,4</sup> Xiaojing Lin,<sup>1,3</sup> Yuying Huang,<sup>2</sup> Zhongmin Kang,<sup>5</sup> Huali Luo,<sup>2</sup> Qizhu Zhang,<sup>1,3</sup> Qinshan Li,<sup>1,2,3</sup> and Mengxing Li<sup>5</sup></p><p><i><sup>1</sup>Department of Obstetrics and Gynecology, Institute of Precision Medicine of Guizhou Province, Affiliated Hospital of Guizhou Medical University, Guiyang, Guizhou, China</i></p><p><i><sup>2</sup>Department of Clinical Biochemistry, School of Medical Laboratory Science, Guizhou Medical University, Guiyang, Guizhou, China</i></p><p><i><sup>3</sup>Clinical Medical College, Guizhou Medical University, Guiyang, Guizhou, China</i></p><p><i><sup>4</sup>Department of Obstetrics, Guizhou Provincial People’s Hospital, Guiyang, Guizhou, China</i></p><p><i><sup>5</sup>Department of Hematology, Guizhou Province Institute of Hematology, Guizhou Province Laboratory of Hematopoietic Stem Cell Transplantation Centre, Affiliated Hospital of Guizhou Medical University Guiyang, Guizhou, China</i></p><p>We apologize for this error.</p>","PeriodicalId":13061,"journal":{"name":"Human Mutation","volume":"2025 1","pages":""},"PeriodicalIF":3.7,"publicationDate":"2025-10-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1155/humu/9879845","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145224354","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
期刊
Human Mutation
全部 Acc. Chem. Res. ACS Applied Bio Materials ACS Appl. Electron. Mater. ACS Appl. Energy Mater. ACS Appl. Mater. Interfaces ACS Appl. Nano Mater. ACS Appl. Polym. Mater. ACS BIOMATER-SCI ENG ACS Catal. ACS Cent. Sci. ACS Chem. Biol. ACS Chemical Health & Safety ACS Chem. Neurosci. ACS Comb. Sci. ACS Earth Space Chem. ACS Energy Lett. ACS Infect. Dis. ACS Macro Lett. ACS Mater. Lett. ACS Med. Chem. Lett. ACS Nano ACS Omega ACS Photonics ACS Sens. ACS Sustainable Chem. Eng. ACS Synth. Biol. Anal. Chem. BIOCHEMISTRY-US Bioconjugate Chem. BIOMACROMOLECULES Chem. Res. Toxicol. Chem. Rev. Chem. Mater. CRYST GROWTH DES ENERG FUEL Environ. Sci. Technol. Environ. Sci. Technol. Lett. Eur. J. Inorg. Chem. IND ENG CHEM RES Inorg. Chem. J. Agric. Food. Chem. J. Chem. Eng. Data J. Chem. Educ. J. Chem. Inf. Model. J. Chem. Theory Comput. J. Med. Chem. J. Nat. Prod. J PROTEOME RES J. Am. Chem. Soc. LANGMUIR MACROMOLECULES Mol. Pharmaceutics Nano Lett. Org. Lett. ORG PROCESS RES DEV ORGANOMETALLICS J. Org. Chem. J. Phys. Chem. J. Phys. Chem. A J. Phys. Chem. B J. Phys. Chem. C J. Phys. Chem. Lett. Analyst Anal. Methods Biomater. Sci. Catal. Sci. Technol. Chem. Commun. Chem. Soc. Rev. CHEM EDUC RES PRACT CRYSTENGCOMM Dalton Trans. Energy Environ. Sci. ENVIRON SCI-NANO ENVIRON SCI-PROC IMP ENVIRON SCI-WAT RES Faraday Discuss. Food Funct. Green Chem. Inorg. Chem. Front. Integr. Biol. J. Anal. At. Spectrom. J. Mater. Chem. A J. Mater. Chem. B J. Mater. Chem. C Lab Chip Mater. Chem. Front. Mater. Horiz. MEDCHEMCOMM Metallomics Mol. Biosyst. Mol. Syst. Des. Eng. Nanoscale Nanoscale Horiz. Nat. Prod. Rep. New J. Chem. Org. Biomol. Chem. Org. Chem. Front. PHOTOCH PHOTOBIO SCI PCCP Polym. Chem.
×
引用
GB/T 7714-2015
复制
MLA
复制
APA
复制
导出至
BibTeX EndNote RefMan NoteFirst NoteExpress
×
0
微信
客服QQ
Book学术公众号 扫码关注我们
反馈
×
意见反馈
请填写您的意见或建议
请填写您的手机或邮箱
×
提示
您的信息不完整,为了账户安全,请先补充。
现在去补充
×
提示
您因"违规操作"
具体请查看互助需知
我知道了
×
提示
现在去查看 取消
×
提示
确定
Book学术官方微信
Book学术文献互助
Book学术文献互助群
群 号:604180095
Book学术
文献互助 智能选刊 最新文献 互助须知 联系我们:info@booksci.cn
Book学术提供免费学术资源搜索服务,方便国内外学者检索中英文文献。致力于提供最便捷和优质的服务体验。
Copyright © 2023 Book学术 All rights reserved.
ghs 京公网安备 11010802042870号 京ICP备2023020795号-1