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Corrigendum to “Structural and functional analysis of SOX9 mutations in disorders of sex development (DSD): Integration of clinical data and in silico modeling” [Human Gene, Volume 46 (2025), Article 201461]. “性发育障碍(DSD)中SOX9突变的结构和功能分析:临床数据和计算机建模的整合”[人类基因,46卷(2025),文章201461]的更正。
IF 0.7 Q4 GENETICS & HEREDITY Pub Date : 2026-02-01 Epub Date: 2025-11-14 DOI: 10.1016/j.humgen.2025.201512
Fatou Diop Gueye , Mama Sy Diallo , Arame Ndiaye , Mame Venus Gueye , Ndiaga Diop , Adji Dieynaba Diallo , Rokhaya Ndiaye , Oumar Faye
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引用次数: 0
A novel autosomal dominant variant in TMC1 and rare autosomal recessive variants in GJB2, SLC26A4 caused congenital hearing loss in Vietnamese children 一种新的TMC1常染色体显性变异和罕见的GJB2、SLC26A4常染色体隐性变异导致越南儿童先天性听力损失
IF 0.7 Q4 GENETICS & HEREDITY Pub Date : 2025-12-01 Epub Date: 2025-09-14 DOI: 10.1016/j.humgen.2025.201480
Phuong Nhung Vu , Hai Ha Nguyen , Thi Huyen Thuong Ma , Thi Bich Ngoc Tran , Thi Kim Phuong Doan , Thi Lan Anh Luong , Tien Truong Dang , Dang Ton Nguyen

Background

Hearing loss in children can lead to consequences such as failure in speech, language, education and poor quality of life. This study investigated five Vietnamese families, one with all three children and others with one child suffered from congenital hearing loss to identify genetic cause of the disease.

Methods and results

Whole exome sequencing was performed for one proband of each family. Subsequently, Sanger sequencing was used for validation the genetic variants in the patients as well as other family members including parents and siblings. A novel variant in TMC1 (c.2209C > T) was detected in the affected child of family 1, which arose as a de novo mutation. In all three affected children of family 2, compound heterozygous variants were detected in SLC26A4 (c.754 T > C, c.1229C > T). In the affected children of family 4 and 5, compound heterozygous of GJB2 (c.109G > A, c.428G > A) and a homozygous deletion in GJB2 (c.235delC) were detected, respectively. In family 3, two genetic variants identified in deafness causing genes MYO7A (c.4795C > T) and MYO15A (c.7547C > T) of the patient in heterozygous state. Sangger sequencing identified only one pathogenic variant in each parent of family 2, 4 and 5. Similarly, existence of double heterozygote in MYO7A/MYO15A was not identified in the parents and remaining unaffected child in family 3.

Conclusions

This study contributed to expand genetic variants spectrum in Vietnamese hearing loss pediatrics. Identifying the genetic causes is crucial for early management of hearing loss patients and giving genetic counseling for further pregnancies of high-risk couples.
儿童听力损失可导致诸如言语、语言、教育和生活质量低下等后果。本研究调查了五个越南家庭,其中一个家庭有三个孩子,另一个家庭有一个孩子患有先天性听力损失,以确定该疾病的遗传原因。方法与结果对每个家族1个先证者进行全外显子组测序。随后,Sanger测序用于验证患者以及其他家庭成员(包括父母和兄弟姐妹)的遗传变异。在家族1的患病儿童中检测到一种新的TMC1变异(c.2209C >; T),这是一种新生突变。在家族2的所有3例患儿中,均检测到SLC26A4的复合杂合变异体(c.754)T >; C, C .1229C >; T)。家族4和家族5患儿分别检测到GJB2复合杂合基因(c.109G >; A, c.428G >; A)和GJB2纯合基因缺失(c.235delC)。在家族3中,在杂合状态患者的致聋基因MYO7A (c.4795C >; T)和MYO15A (c.7547C >; T)中鉴定出两个遗传变异。桑格测序仅在家族2、4和5的每个亲本中发现一个致病变异。同样,在父母和家庭3中未发现MYO7A/MYO15A双杂合子的存在。结论本研究有助于扩大越南听力损失儿科的遗传变异谱。确定遗传原因对于听力损失患者的早期管理和为高危夫妇的进一步怀孕提供遗传咨询至关重要。
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引用次数: 0
The LEPR gene: A multifaceted regulator of energy homeostasis, obesity pathogenesis, and metabolic health LEPR基因:能量稳态、肥胖发病机制和代谢健康的多方面调节因子
IF 0.7 Q4 GENETICS & HEREDITY Pub Date : 2025-12-01 Epub Date: 2025-09-25 DOI: 10.1016/j.humgen.2025.201486
Isar Sharma , Nishutosh , Kritika Bakshi , Ritu Mahajan , Nisha Kapoor

Background & Aim

This review examines the leptin-LEPR axis and its role in regulating energy balance and obesity. The LEPR gene provides the essential instructions for synthesizing the leptin receptor, a protein of paramount importance within the neuroendocrine system that orchestrates energy balance. Leptin, an adipokine secreted primarily by adipose tissue, functions as a critical signal reflecting the body's energy stores. It modulates appetite and energy expenditure by binding to its cognate receptor, which is predominantly expressed in the hypothalamus.

Materials & methods

The authors comprehensively examined a wide range of studies to detail the function of the LEPR gene and the complex intracellular signalling pathways it initiates. The focus was on understanding how dysfunctions, from rare genetic mutations to common acquired leptin resistance, disrupt these homeostatic mechanisms.

Results

The review confirms that when leptin binds to its receptor, it initiates a complex cascade of intracellular signalling pathways. These include the Janus kinase 2 (JAK2)/signal transducer and activator of transcription 3 (STAT3) and phosphatidylinositol 3 kinase (PI3K)/Akt pathways. Dysfunction of the leptin-LEPR axis, whether stemming from rare genetic mutations leading to congenital leptin receptor deficiency or the more prevalent acquired leptin resistance observed in common obesity, severely disrupts these intricate homeostatic mechanisms. Such disruptions invariably manifest as profound hyperphagia (excessive hunger) and severe obesity.

Conclusion

A comprehensive understanding of the LEPR axis and its intricate signalling networks is therefore fundamental for elucidating the pathophysiology of obesity and for the development of effective therapeutic strategies.
背景与目的本文综述了瘦素- lepr轴及其在调节能量平衡和肥胖中的作用。LEPR基因为瘦素受体的合成提供了必要的指令,瘦素受体是神经内分泌系统中最重要的蛋白质,负责协调能量平衡。瘦素是一种主要由脂肪组织分泌的脂肪因子,是反映身体能量储存的关键信号。它通过结合其主要在下丘脑表达的同源受体来调节食欲和能量消耗。材料和方法作者全面检查了广泛的研究,详细介绍了LEPR基因的功能和它所启动的复杂的细胞内信号通路。研究的重点是了解从罕见的基因突变到常见的获得性瘦素抵抗等功能障碍是如何破坏这些体内平衡机制的。结果该综述证实,当瘦素与其受体结合时,它启动了一个复杂的细胞内信号通路级联。其中包括Janus kinase 2 (JAK2)/信号转导和转录激活因子3 (STAT3)和磷脂酰肌醇3激酶(PI3K)/Akt通路。无论是由于罕见的基因突变导致先天性瘦素受体缺乏,还是在常见肥胖中观察到的更普遍的获得性瘦素抵抗,瘦素- lepr轴的功能障碍都严重破坏了这些复杂的体内平衡机制。这种破坏总是表现为严重的贪食(过度饥饿)和严重的肥胖。因此,全面了解LEPR轴及其复杂的信号网络对于阐明肥胖的病理生理和制定有效的治疗策略至关重要。
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引用次数: 0
Role of the translocon-associated protein (TRAP)/signal sequence receptor (SSR) complex in the pathogenesis of human diseases 转座子相关蛋白(TRAP)/信号序列受体(SSR)复合物在人类疾病发病机制中的作用
IF 0.7 Q4 GENETICS & HEREDITY Pub Date : 2025-12-01 Epub Date: 2025-11-07 DOI: 10.1016/j.humgen.2025.201510
Darshika Amarakoon, Seong-Ho Lee
The translocon-associated protein/signal sequence receptor (TRAP/SSR) complex, an integral membrane protein complex of the endoplasmic reticulum (ER), has emerged as a critical regulator of co-translational protein translocation, protein secretion, and cellular homeostasis. Despite its fundamental role, research on the TRAP/SSR complex in human diseases remains limited, focusing mainly on its involvement in cancer, diabetes, neurodegenerative and spinal disorders, and hepatitis B virus infection. This review summarizes recent advances in understanding TRAP/SSR function in disease pathogenesis, highlighting its pro-tumorigenic activity, regulation of insulin biosynthesis and secretion, and potential as a biomarker for early diagnosis of neurodegenerative and spine-related disorders. Furthermore, the TRAP/SSR complex facilitates the translocation and secretion of the hepatitis B e antigen, emphasizing its role in viral pathogenesis. However, substantial research gaps persist due to the novelty of this field, and the molecular mechanisms underlying TRAP/SSR-mediated disease regulation remain incompletely understood. Therefore, future investigations should aim to elucidate the mechanistic links between TRAP/SSR dysfunction and diverse pathological conditions, including metabolic, neurodegenerative, infectious, and malignant diseases. Defining disease-specific downstream effectors and interactions with ER stress pathways – particularly the unfolded protein response and ER-associated degradation – will be critical to clarifying its contribution to cellular homeostasis and disease progression. The development of targeted therapeutic strategies to modulate TRAP/SSR activity, supported by integrative multi-omics and structural biology approaches, may ultimately enable the translation of these insights into diagnostic and therapeutic applications.
经位点相关蛋白/信号序列受体(TRAP/SSR)复合物是内质网(ER)的完整膜蛋白复合物,已成为共翻译蛋白易位、蛋白分泌和细胞稳态的关键调节因子。尽管TRAP/SSR复合物具有基础作用,但对其在人类疾病中的研究仍然有限,主要集中在其与癌症、糖尿病、神经退行性疾病和脊柱疾病以及乙型肝炎病毒感染的关系上。本文综述了TRAP/SSR在疾病发病机制中的作用,重点介绍了其致瘤活性,胰岛素生物合成和分泌的调节,以及作为神经退行性疾病和脊柱相关疾病早期诊断的生物标志物的潜力。此外,TRAP/SSR复合物促进乙型肝炎e抗原的易位和分泌,强调其在病毒发病中的作用。然而,由于这一领域的新颖性,大量的研究空白仍然存在,并且TRAP/ ssr介导的疾病调节的分子机制仍然不完全清楚。因此,未来的研究应旨在阐明TRAP/SSR功能障碍与多种病理状况(包括代谢性、神经退行性、感染性和恶性疾病)之间的机制联系。明确疾病特异性下游效应物和内质网应激途径的相互作用——特别是未折叠蛋白反应和内质网相关降解——对于阐明其在细胞稳态和疾病进展中的作用至关重要。在综合多组学和结构生物学方法的支持下,开发靶向治疗策略来调节TRAP/SSR活性,最终可能使这些见解转化为诊断和治疗应用。
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引用次数: 0
Knockdown of histone H1–5 gene affects the sensitivity of MRC-5 and HeLa cells to DNA damaging agents 组蛋白H1-5基因敲低影响MRC-5和HeLa细胞对DNA损伤剂的敏感性
IF 0.7 Q4 GENETICS & HEREDITY Pub Date : 2025-12-01 Epub Date: 2025-09-12 DOI: 10.1016/j.humgen.2025.201475
Tigran Harutyunyan , Anzhela Sargsyan , Gohar Tadevosyan , Lily Kalashyan , Rouben Aroutiounian , Galina Hovhannisyan
Linker histone H1.5, encoded by the H1–5 gene, plays a key role in chromatin compaction and genome stability. However, its role in cellular responses to mutagens is still poorly understood. Here, we analyzed the genotoxic effects of the standard genotoxic drugs doxorubicin (DOX) and mitomycin C (MMC) at non-cytotoxic concentrations after 24 h of treatment in normal lung fibroblasts (MRC-5) and cervical carcinoma cells (HeLa) with H1–5 gene knockdown (KD). Using CRISPR-Cas9, we achieved significant repression of H1–5 expression. Alkaline DNA comet assay and cytokinesis-block micronucleus assay showed that H1–5 KD significantly increased spontaneous and mutagen-induced DNA and chromosome damage levels in both cell lines (p < 0.05). Our results suggest that H1–5 gene deficiency makes DNA more susceptible to genotoxic impact while its mechanistic role in occurrence of DNA and chromosome damage requires further elucidation.
由H1-5基因编码的连接蛋白H1.5在染色质压实和基因组稳定性中起关键作用。然而,它在细胞对诱变剂反应中的作用仍然知之甚少。在这里,我们分析了标准基因毒性药物多柔比星(DOX)和丝裂霉素C (MMC)在治疗24小时后的非细胞毒性浓度对正常肺成纤维细胞(MRC-5)和H1-5基因敲低(KD)的宫颈癌细胞(HeLa)的遗传毒性作用。使用CRISPR-Cas9,我们实现了H1-5表达的显著抑制。碱性DNA彗星试验和细胞分裂阻滞微核试验显示,H1-5 KD显著增加了两种细胞系的自发和诱变诱导的DNA和染色体损伤水平(p < 0.05)。我们的研究结果表明,H1-5基因缺失使DNA更容易受到遗传毒性的影响,但其在DNA和染色体损伤发生中的机制有待进一步阐明。
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引用次数: 0
Single-cell transcriptomics exposes an uncharacterized lncRNA governing colorectal cancer metastasis 单细胞转录组学揭示了一种未表征的lncRNA控制结直肠癌转移
IF 0.7 Q4 GENETICS & HEREDITY Pub Date : 2025-12-01 Epub Date: 2025-09-12 DOI: 10.1016/j.humgen.2025.201479
Abbas Heydari Lori , Nahid Askari , Hossein Pourghadamyari
Colorectal cancer (CRC) exhibits significant molecular heterogeneity, with long non-coding RNAs (lncRNAs) playing crucial regulatory roles. This study identifies LncRNA01996 as a key oncogenic driver upregulated in CRC tumors compared to adjacent normal tissues, with expression levels correlating directly with advancing cancer stage (Stage I to IV). Mechanistically, LncRNA01996 stabilizes β-catenin, hyperactivating the Wnt signaling pathway while simultaneously suppressing E-CADHERIN expression a critical factor in maintaining cellular adhesion. This dual action promotes cancer cell invasion and metastasis. Additionally, LncRNA01996 transcriptionally activates MYC, amplifying its oncogenic effects.
Clinically, high LncRNA01996 expression is linked to aggressive tumor features, elevated serum markers (CEA, CA19–9), and shorter overall survival in patients. These findings were consistent across patient tissues, cell lines (SW480, SKM), and single-cell RNA sequencing data, confirming its role in diverse CRC microenvironments.
In summary, LncRNA01996 drives CRC progression by dysregulating Wnt/β-catenin signaling, disrupting cell adhesion, and amplifying MYC-driven malignancy. Its strong association with advanced disease and poor outcomes positions LncRNA01996 as a promising prognostic biomarker and a compelling therapeutic target for intercepting CRC metastasis.
结直肠癌(CRC)表现出明显的分子异质性,其中长链非编码rna (lncRNAs)发挥着至关重要的调控作用。本研究确定LncRNA01996是CRC肿瘤中与邻近正常组织相比上调的关键致癌驱动因子,其表达水平与癌症进展(I期至IV期)直接相关。从机制上讲,LncRNA01996稳定β-catenin,过度激活Wnt信号通路,同时抑制E-CADHERIN的表达,这是维持细胞粘附的关键因素。这种双重作用促进了癌细胞的侵袭和转移。此外,LncRNA01996转录激活MYC,放大其致癌作用。在临床上,LncRNA01996的高表达与侵袭性肿瘤特征、血清标志物(CEA、CA19-9)升高和患者总生存期缩短有关。这些发现在患者组织、细胞系(SW480、SKM)和单细胞RNA测序数据中是一致的,证实了其在不同CRC微环境中的作用。总之,LncRNA01996通过失调Wnt/β-catenin信号、破坏细胞粘附和放大myc驱动的恶性肿瘤来驱动结直肠癌的进展。LncRNA01996与晚期疾病和不良预后的强烈关联使其成为一种有前景的预后生物标志物和阻断结直肠癌转移的令人信服的治疗靶点。
{"title":"Single-cell transcriptomics exposes an uncharacterized lncRNA governing colorectal cancer metastasis","authors":"Abbas Heydari Lori ,&nbsp;Nahid Askari ,&nbsp;Hossein Pourghadamyari","doi":"10.1016/j.humgen.2025.201479","DOIUrl":"10.1016/j.humgen.2025.201479","url":null,"abstract":"<div><div>Colorectal cancer (CRC) exhibits significant molecular heterogeneity, with long non-coding RNAs (lncRNAs) playing crucial regulatory roles. This study identifies <em>LncRNA01996</em> as a key oncogenic driver upregulated in CRC tumors compared to adjacent normal tissues, with expression levels correlating directly with advancing cancer stage (Stage I to IV). Mechanistically, <em>LncRNA01996</em> stabilizes β-catenin, hyperactivating the Wnt signaling pathway while simultaneously suppressing <em>E-CADHERIN</em> expression a critical factor in maintaining cellular adhesion. This dual action promotes cancer cell invasion and metastasis. Additionally, <em>LncRNA01996</em> transcriptionally activates MYC, amplifying its oncogenic effects.</div><div>Clinically, high <em>LncRNA01996</em> expression is linked to aggressive tumor features, elevated serum markers (CEA, CA19–9), and shorter overall survival in patients. These findings were consistent across patient tissues, cell lines (SW480, SKM), and single-cell RNA sequencing data, confirming its role in diverse CRC microenvironments.</div><div>In summary, <em>LncRNA01996</em> drives CRC progression by dysregulating Wnt/β-catenin signaling, disrupting cell adhesion, and amplifying <em>MYC</em>-driven malignancy. Its strong association with advanced disease and poor outcomes positions <em>LncRNA01996</em> as a promising prognostic biomarker and a compelling therapeutic target for intercepting CRC metastasis.</div></div>","PeriodicalId":29686,"journal":{"name":"Human Gene","volume":"46 ","pages":"Article 201479"},"PeriodicalIF":0.7,"publicationDate":"2025-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145094986","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Mapping the transcriptional architecture of glioblastoma at the single-cell level: Decoding heterogeneity, angiogenesis, and mesenchymal shifts 在单细胞水平上绘制胶质母细胞瘤的转录结构:解码异质性、血管生成和间质转移
IF 0.7 Q4 GENETICS & HEREDITY Pub Date : 2025-12-01 Epub Date: 2025-08-19 DOI: 10.1016/j.humgen.2025.201467
Naureen Mallick, Reaz Uddin
Glioblastoma (GBM), a grade IV glioma, is the most aggressive and fatal primary brain tumor, accounting for 48 % of all Central Nervous System tumors. Despite advancements in therapeutic strategies, GBM remains highly resistant to treatment, with a median survival time of just 14 months. This study aimed to identify molecular signature genes associated with GBM heterogeneity using scRNA-seq datasets from 10× Genomics. Two scRNA-seq datasets were processed through the Cell Ranger pipeline, followed by quality control, normalization, and scaling. After data integration using R, Principal Component Analysis was performed, and clusters were visualized using UMAP. A total of 2772 DEGs were identified, of which 95 DEGs met the threshold of logFC≥4 and p-adj ≤ 0.05. These DEGs were significantly enriched in angiogenesis and the PI3K signaling pathway, associated with poor prognosis. Principal Component Analysis revealed 15 principal components, with the first four accounting for the greatest variance. UMAP clustering identified 13 distinct cell clusters, which were annotated using the HPCA reference dataset, revealing enrichment in astrocytes, immune cells, and other tumor-associated cell types. A PPI network was constructed using the STRING database and visualized in Cytoscape, leading to the identification of three mesenchymal hub genes—KDA, PDGFRB, and CXCL12—as key angiogenic markers in GBM. The identified DEGs and hub genes were further validated using GEPIA2 and GSEA. This study provides novel insights into GBM heterogeneity and angiogenic biomarkers, potentially guiding future therapeutic strategies. Nevertheless, additional experimental validation is required to fully understand their role in GBM pathogenesis.
胶质母细胞瘤(GBM)是一种四级胶质瘤,是最具侵袭性和致命性的原发性脑肿瘤,占所有中枢神经系统肿瘤的48%。尽管治疗策略取得了进步,但GBM仍然对治疗具有高度耐药性,中位生存时间仅为14个月。本研究旨在利用10x Genomics的scRNA-seq数据集,鉴定与GBM异质性相关的分子特征基因。通过Cell Ranger流水线处理两个scRNA-seq数据集,然后进行质量控制、归一化和缩放。使用R进行数据整合后,进行主成分分析,并使用UMAP对聚类进行可视化。共鉴定出2772个deg,其中95个deg符合logFC≥4和p-adj≤0.05的阈值。这些deg在血管生成和PI3K信号通路中显著富集,与预后不良相关。主成分分析揭示了15个主成分,其中前四个主成分的方差最大。UMAP聚类鉴定出13个不同的细胞簇,使用HPCA参考数据集进行注释,揭示了星形胶质细胞、免疫细胞和其他肿瘤相关细胞类型的富集。使用STRING数据库构建PPI网络,并在Cytoscape中可视化,从而鉴定出三个间充质中心基因- kda, PDGFRB和cxcl12 -作为GBM的关键血管生成标志物。使用GEPIA2和GSEA进一步验证鉴定的DEGs和hub基因。这项研究为GBM异质性和血管生成生物标志物提供了新的见解,可能指导未来的治疗策略。然而,要充分了解它们在GBM发病机制中的作用,还需要进一步的实验验证。
{"title":"Mapping the transcriptional architecture of glioblastoma at the single-cell level: Decoding heterogeneity, angiogenesis, and mesenchymal shifts","authors":"Naureen Mallick,&nbsp;Reaz Uddin","doi":"10.1016/j.humgen.2025.201467","DOIUrl":"10.1016/j.humgen.2025.201467","url":null,"abstract":"<div><div>Glioblastoma (GBM), a grade IV glioma, is the most aggressive and fatal primary brain tumor, accounting for 48 % of all Central Nervous System tumors. Despite advancements in therapeutic strategies, GBM remains highly resistant to treatment, with a median survival time of just 14 months. This study aimed to identify molecular signature genes associated with GBM heterogeneity using scRNA-seq datasets from 10× Genomics. Two scRNA-seq datasets were processed through the Cell Ranger pipeline, followed by quality control, normalization, and scaling. After data integration using R, Principal Component Analysis was performed, and clusters were visualized using UMAP. A total of 2772 DEGs were identified, of which 95 DEGs met the threshold of logFC≥4 and p-adj ≤ 0.05. These DEGs were significantly enriched in angiogenesis and the PI3K signaling pathway, associated with poor prognosis. Principal Component Analysis revealed 15 principal components, with the first four accounting for the greatest variance. UMAP clustering identified 13 distinct cell clusters, which were annotated using the HPCA reference dataset, revealing enrichment in astrocytes, immune cells, and other tumor-associated cell types. A PPI network was constructed using the STRING database and visualized in Cytoscape, leading to the identification of three mesenchymal hub genes—KDA, PDGFRB, and CXCL12—as key angiogenic markers in GBM. The identified DEGs and hub genes were further validated using GEPIA2 and GSEA. This study provides novel insights into GBM heterogeneity and angiogenic biomarkers, potentially guiding future therapeutic strategies. Nevertheless, additional experimental validation is required to fully understand their role in GBM pathogenesis.</div></div>","PeriodicalId":29686,"journal":{"name":"Human Gene","volume":"46 ","pages":"Article 201467"},"PeriodicalIF":0.7,"publicationDate":"2025-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144887251","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Deciphering the risk of missense mutation rs137854486 (W1925R) of FN1 in papillary thyroid cancer: A computational and molecular dynamics approach 解读乳头状甲状腺癌中FN1错义突变rs137854486 (W1925R)的风险:计算和分子动力学方法
IF 0.7 Q4 GENETICS & HEREDITY Pub Date : 2025-12-01 Epub Date: 2025-09-22 DOI: 10.1016/j.humgen.2025.201484
Febby Payva , Remya James , Amrisa Pavithra E. , Padmashree Das , Santhy K.S.
Papillary thyroid cancer (PTC) accounts for more than 85 % of all thyroid cancers. Three transcriptomic datasets of PTC, one each from humans (GSE138198), transgenic mice (GSE58689), and cell lines (GSE6339), were analysed for differentially expressed genes (DEGs). Seventy-three common DEGs were binned into significant pathways associated with cancer and immunity, for which gene ontology studies at the biological process, molecular function, and cellular component levels were performed. Protein–protein interaction (PPI) network construction and analysis of modules identified fibronectin 1 (FN1) as the critical hub gene in the pathophysiology of PTC. Survival analysis, immune infiltration analysis, and co-expression analysis of the hub genes were conducted to confirm their relationship with PTC prognosis. Analysis of four missense variants V692E, T817A, T817P and W1925R of FN1 associated with PTC, followed by structural analysis and molecular dynamics simulation, validated that the missense mutation rs137854486 (W1925R) of FN1 is significant in the tumorigenesis of PTC. FoldX predicted a significant positive ΔΔG (9.85646) value for W1925R, portraying substantial destabilization of FN1. The root mean square deviation (RMSD), root mean square fluctuation (RMSF), and radius of gyration (Rg) values of the W1925R mutant indicate significant structural deviations in the protein, resulting in increased flexibility and reduced stability. Increased flexibility, particularly in regions critical for protein function, could affect the biological activity of the protein, with a crucial influence on the pathophysiology of PTC.
乳头状甲状腺癌(PTC)占所有甲状腺癌的85%以上。分别来自人(GSE138198)、转基因小鼠(GSE58689)和细胞系(GSE6339)的3个PTC转录组学数据集分析差异表达基因(DEGs)。73个常见的deg被归类为与癌症和免疫相关的重要途径,并在生物过程、分子功能和细胞成分水平上进行了基因本体论研究。蛋白-蛋白相互作用(Protein-protein interaction, PPI)网络构建及模块分析表明,纤连蛋白1 (fibronectin, FN1)是PTC病理生理中的关键枢纽基因。通过生存分析、免疫浸润分析和枢纽基因共表达分析,证实其与PTC预后的关系。对与PTC相关的FN1的4个错义变异V692E、T817A、T817P和W1925R进行分析,并进行结构分析和分子动力学模拟,验证了FN1的错义突变rs137854486 (W1925R)在PTC的肿瘤发生中具有重要意义。FoldX预测W1925R的显著阳性ΔΔG(9.85646)值,描绘了FN1的大量不稳定。W1925R突变体的均方根偏差(RMSD)、均方根波动(RMSF)和旋转半径(Rg)值表明,该蛋白存在明显的结构偏差,导致柔韧性增加,稳定性降低。灵活性的增加,特别是在蛋白质功能的关键区域,可能影响蛋白质的生物活性,对PTC的病理生理有重要影响。
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引用次数: 0
LiqBiMark: An advanced bioinformatics pipeline for integrative transcriptomic analysis and identification of non-invasive prognostic biomarkers using GEO datasets LiqBiMark:一个先进的生物信息学管道,用于整合转录组学分析和使用GEO数据集鉴定非侵入性预后生物标志物
IF 0.7 Q4 GENETICS & HEREDITY Pub Date : 2025-12-01 Epub Date: 2025-09-29 DOI: 10.1016/j.humgen.2025.201490
Amir Mohammad Mazhari , Farshad Safaei , Mahsa Torkamanian-Afshar , Ali Najafi

Background

The Gene Expression Omnibus (GEO) database was established by the National Center for Biotechnology Information (NCBI) to facilitate sharing molecular biology data. This repository hosts numerous datasets related to complex diseases such as cancer, generated by researchers worldwide. One of the most challenging issues is finding non-invasive biomarkers in the vast amount of data deposited in public databases related to a specific type of cancer.

Results

To address this issue, we have designed a Liquid Biopsy Biomarker Discovery (LiqBiMark) pipeline that compares two datasets on the same type of cancer, but with different sample sources, to propose potential biomarker candidates. Additionally, the LiqBiMark generates co-expression networks and conducts clustering analysis.

Conclusions

The pipeline is designed to be accessible even to users with minimal experience, allowing them to obtain results quickly and efficiently.
GEO (Gene Expression Omnibus)数据库是由美国国家生物技术信息中心(NCBI)为促进分子生物学数据共享而建立的。该存储库拥有由世界各地的研究人员生成的与癌症等复杂疾病相关的大量数据集。最具挑战性的问题之一是在与特定类型癌症相关的公共数据库中存储的大量数据中找到非侵入性生物标志物。为了解决这个问题,我们设计了一个液体活检生物标志物发现(Liquid Biopsy Biomarker Discovery, LiqBiMark)管道,该管道比较了同一类型癌症的两个数据集,但具有不同的样本来源,以提出潜在的生物标志物候选物。此外,LiqBiMark生成共表达网络并进行聚类分析。结论:该管道的设计即使对经验最少的用户也是可访问的,使他们能够快速有效地获得结果。
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引用次数: 0
Adiponectin gene polymorphism and TyPE 2 diabetes MellitUS: Contrasting genetic RISKS in overdominant vs recessive and allele models – an updated meta – analysis 脂联素基因多态性与2型糖尿病:显性、隐性和等位基因模型的遗传风险对比——一项最新的荟萃分析
IF 0.7 Q4 GENETICS & HEREDITY Pub Date : 2025-12-01 Epub Date: 2025-08-14 DOI: 10.1016/j.humgen.2025.201463
Santhini Gopalakrishnan , Santhi Priya Sobha , Karpagavel Lakshmanan

Background

Type 2 Diabetes Mellitus (T2DM) is a metabolic disorder and adipokines such as adiponectin plays a crucial role in the development of T2DM. Adiponectin is encoded by APM1/ADIPOQ gene and polymorphism has been associated with T2DM. The present study aims to determine the overall effect of major SNP of adiponectin gene with T2DM risk.

Methods

A through literature search was conducted to identify suitable studies and data was extracted. The association of SNP with T2DM was determined using odds ratio (OR) with 95 % C.I.

Result

Allele contrast and recessive model of rs16861194(−11426 A > G), rs266729(−1137C > G), rs2241766(+45 T > G), rs17300539(−11,391 G > A) and rs822396(−3971 G > A) genotype of the APM1/ADIPOQ gene was associated with reduced T2DM risk. The African and Asian population subgroup demonstrated lower T2DM risk under allele contrast and recessive model of rs16861194 and rs2241766 while Caucasian was associated with reduced risk in recessive model of rs266729. The rs822396 variant demonstrated lower risk under allele contrast and recessive model in Asian subgroup. The rs2241767(+346 A > G) polymorphism was associated with reduced T2DM risk under allele contrast and in subgroup analysis only African population showed significant association. In contrast, the over dominant model was associated with increased T2DM risk in rs16861194, rs266729, rs182052, rs2241766, rs17300539 and rs822396. The African and Asian ethnicity demonstrated an increased risk in over dominant model with rs16861194 and rs2241766 while Asian ethnicity showed significant association under over dominant model in rs182052 and rs822396. The rs3774261(+712 A > G) and rs1501299(+276G > T) showed no association with T2DM risk.

Conclusion

The major polymorphism of adiponectin showed increased risk under overdominant model while showed a reduced risk under allele and recessive genetic model.
背景2型糖尿病(T2DM)是一种代谢性疾病,脂联素等脂肪因子在T2DM的发展中起着至关重要的作用。脂联素由APM1/ADIPOQ基因编码,其多态性与T2DM有关。本研究旨在确定脂联素基因主要SNP与T2DM风险的总体影响。方法通过文献检索,筛选合适的研究并提取资料。结果APM1/ADIPOQ基因型rs16861194(- 11426 A >; G)、rs266729(- 1137C >; G)、rs2241766(+45 T >; G)、rs17300539(- 11391 G >; A)和rs822396(- 3971 G >; A)的等位基因对比和隐性模型与T2DM风险降低相关。在rs16861194和rs2241766等位基因对比和隐性模型下,非洲和亚洲人群亚组T2DM风险较低,而在rs266729隐性模型下,高加索人群与T2DM风险降低相关。rs822396变异在等位基因对比和隐性模型下在亚洲亚群中表现出较低的风险。在等位基因对比下,rs2241767(+346 A >; G)多态性与T2DM风险降低相关,在亚组分析中,只有非洲人群显示出显著的相关性。相反,过显性模型与rs16861194、rs266729、rs182052、rs2241766、rs17300539和rs822396的T2DM风险增加相关。非洲和亚洲族裔在rs16861194和rs2241766的过显性模型下风险增加,而亚洲族裔在rs182052和rs822396的过显性模型下风险显著增加。rs3774261(+712 A >; G)和rs1501299(+276G >; T)与T2DM风险无相关性。结论脂联素主多态性在过显性遗传模式下风险增加,在等位基因和隐性遗传模式下风险降低。
{"title":"Adiponectin gene polymorphism and TyPE 2 diabetes MellitUS: Contrasting genetic RISKS in overdominant vs recessive and allele models – an updated meta – analysis","authors":"Santhini Gopalakrishnan ,&nbsp;Santhi Priya Sobha ,&nbsp;Karpagavel Lakshmanan","doi":"10.1016/j.humgen.2025.201463","DOIUrl":"10.1016/j.humgen.2025.201463","url":null,"abstract":"<div><h3>Background</h3><div>Type 2 Diabetes Mellitus (T2DM) is a metabolic disorder and adipokines such as adiponectin plays a crucial role in the development of T2DM. Adiponectin is encoded by APM1/ADIPOQ gene and polymorphism has been associated with T2DM. The present study aims to determine the overall effect of major SNP of adiponectin gene with T2DM risk.</div></div><div><h3>Methods</h3><div>A through literature search was conducted to identify suitable studies and data was extracted. The association of SNP with T2DM was determined using odds ratio (OR) with 95 % C.I.</div></div><div><h3>Result</h3><div>Allele contrast and recessive model of rs16861194(−11426 A &gt; G), rs266729(−1137C &gt; G), rs2241766(+45 T &gt; G), rs17300539(−11,391 G &gt; A) and rs822396(−3971 G &gt; A) genotype of the APM1/ADIPOQ gene was associated with reduced T2DM risk. The African and Asian population subgroup demonstrated lower T2DM risk under allele contrast and recessive model of rs16861194 and rs2241766 while Caucasian was associated with reduced risk in recessive model of rs266729. The rs822396 variant demonstrated lower risk under allele contrast and recessive model in Asian subgroup. The rs2241767(+346 A &gt; G) polymorphism was associated with reduced T2DM risk under allele contrast and in subgroup analysis only African population showed significant association. In contrast, the over dominant model was associated with increased T2DM risk in rs16861194, rs266729, rs182052, rs2241766, rs17300539 and rs822396. The African and Asian ethnicity demonstrated an increased risk in over dominant model with rs16861194 and rs2241766 while Asian ethnicity showed significant association under over dominant model in rs182052 and rs822396. The rs3774261(+712 A &gt; G) and rs1501299(+276G &gt; T) showed no association with T2DM risk.</div></div><div><h3>Conclusion</h3><div>The major polymorphism of adiponectin showed increased risk under overdominant model while showed a reduced risk under allele and recessive genetic model.</div></div>","PeriodicalId":29686,"journal":{"name":"Human Gene","volume":"46 ","pages":"Article 201463"},"PeriodicalIF":0.7,"publicationDate":"2025-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144879614","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
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Human Gene
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