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Chronic Granulomatous Disease: Clinical and Molecular Characterization of Brazilian Patients. 慢性肉芽肿病:巴西患者的临床和分子特征。
IF 2.2 4区 医学 Q2 BIOTECHNOLOGY & APPLIED MICROBIOLOGY Pub Date : 2026-02-01 DOI: 10.1002/jgm.70086
Leonardo Martinello da Rosa, Martha Braun da Rosa, Mariana de Sampaio Leite Jobim Wilson, Ida Vanessa Doederlein Schwartz, Fernanda Sperb-Ludwig

Chronic granulomatous disease (CGD) is a rare inborn error of immunity caused by defects in components of the NADPH oxidase that impair the elimination of infectious microorganisms. Individuals affected by CGD become more susceptible to recurrent and severe infections. Six male patients from Southern Brazil were clinically and genetically analyzed through data collection from medical records and massively parallel sequencing by a panel for the following genes: CYBB, CYBA, NCF1, NCF2, and NCF4 and whole genome sequencing analysis. The gene-scan technique was used to identify the GT deletion in NCF1. The most common affected organs were the lungs, skin, and lymph nodes; the most common clinical manifestations were recurrent pneumonia, cutaneous involvement, lymph node manifestations, and failure to thrive. Four patients were identified with variants in CYBB: p.Cys257Ser, which is novel; p.Cys257Arg; p.Arg157Ter; and p.Trp483Ter. Both missense variants damage the loop E in gp91phox, a region with functional and structural relevance for the protein. Functional studies show the expression absence of the protein in patients with the variant p.Arg157Ter. The variant p.Trp483Ter is predicted to undergo nonsense mRNA-mediated decay. The GT deletion in NCF1 was identified in two siblings from consanguineous parents: one homozygous and the other apparently heterozygous for the deletion, both with a clinical diagnosis of CGD. Variant analysis in this gene is particularly challenging due to the presence of pseudogenes. A hypothesis for this genotypic discrepancy is the occurrence of a second type of pseudogene lacking the GT deletion, which may have arisen in one parent and been transmitted to the patient observed as heterozygous, being misinterpreted in the analyses as a functional NCF1 sequence.

慢性肉芽肿病(CGD)是一种罕见的先天性免疫错误,由NADPH氧化酶的成分缺陷引起,损害了传染性微生物的消除。受CGD影响的个体变得更容易复发和严重感染。来自巴西南部的6名男性患者通过从医疗记录中收集的数据和由一个小组对以下基因(CYBB、CYBA、NCF1、NCF2和NCF4)进行大规模平行测序和全基因组测序分析进行临床和遗传学分析。采用基因扫描技术对NCF1基因的GT缺失进行鉴定。最常见的受累器官是肺、皮肤和淋巴结;最常见的临床表现是复发性肺炎、皮肤受累、淋巴结表现和不能茁壮成长。4例患者被鉴定出CYBB变异:p.Cys257Ser,这是新的;p.Cys257Arg;p.Arg157Ter;和p.Trp483Ter。两种错义变异体都破坏gp91phox中的环E,这是一个与该蛋白在功能和结构上相关的区域。功能研究表明,在p.a g157ter变异患者中缺乏该蛋白的表达。预测变异p.Trp483Ter会经历无义mrna介导的衰变。在来自近亲父母的两个兄弟姐妹中发现了NCF1的GT缺失:一个是纯合的,另一个是明显的杂合的缺失,两者都有CGD的临床诊断。由于假基因的存在,该基因的变异分析尤其具有挑战性。这种基因型差异的一种假设是,出现了第二种缺乏GT缺失的假基因,这种假基因可能出现在亲本中的一方,并传播给了观察到的杂合子患者,在分析中被误解为功能性NCF1序列。
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引用次数: 0
Single-Cell RNA Sequencing and Network Pharmacology Reveal the Potential Role of Oxidative Phosphorylation Inactivation in Diagnosing and Treating Chronic Tendon Injuries. 单细胞RNA测序和网络药理学揭示氧化磷酸化失活在诊断和治疗慢性肌腱损伤中的潜在作用。
IF 2.2 4区 医学 Q2 BIOTECHNOLOGY & APPLIED MICROBIOLOGY Pub Date : 2026-02-01 DOI: 10.1002/jgm.70085
Jie-Jie Niu, Long Wang, Jia-Chen Qi, Gui-Jun Lu

Background: Chronic tendon injuries, characterized by persistent pain, reduced flexibility, and impaired function, pose a significant clinical challenge. Current therapeutic strategies for these injuries are limited. This study highlighted the crucial role of OXPHOS in maintaining tendon homeostasis and suggested potential therapeutic strategies targeting the OXPHOS pathway.

Method: This study utilized both bulk-sequencing (bulk-seq) and single-cell RNA sequencing (scRNA-seq) to analyze the heterogeneity in tenocytes, vascular endothelial cells, tendon-derived stem cells, adipocytes, and neurons from both non-lesional and lesional tendons. Key oxidative phosphorylation (OXPHOS)-related genes, such as COX15, COX4I1, COX5B, COX7A1, COX8A, NDUFA12, NDUFA5, NDUFB10, NDUFB3, NDUFC1, NDUFS1, and NDUFS4, were found to be significantly downregulated in lesional tendons compared with non-lesional ones, indicating impaired energy metabolism. This reduction in OXPHOS activity may contribute to increased necroptosis in chronic tendon injuries. Furthermore, bisphenol A and valproic acid were found to activate OXPHOS-related genes.

Results: The findings highlighted the crucial role of OXPHOS in maintaining tendon homeostasis and demonstrated potential therapeutic strategies targeting the OXPHOS pathway, such as bisphenol A and valproic acid, to enhance healing in chronic tendon conditions.

Conclusion: The crucial role of OXPHOS in maintaining tendon homeostasis underscores its potential as a therapeutic target, reflecting that strategies aimed at modulating the OXPHOS pathway may provide promising treatment options. Chronic tendon injuries present a major clinical challenge with limited treatments. This study investigated the molecular mechanisms underlying these injuries using bulk and single-cell RNA sequencing. We identified significant downregulation of oxidative phosphorylation (OXPHOS)-related genes in lesional tendons across multiple cell types, contributing to increased necroptosis. In vitro experiments and molecular docking revealed that valproic acid activates OXPHOS and inhibits necroptosis. These findings highlight the critical role of mitochondrial function in tendon homeostasis and suggest valproic acid as a promising therapeutic candidate for treating chronic tendon injuries by restoring OXPHOS activity.

背景:慢性肌腱损伤以持续疼痛、柔韧性降低和功能受损为特征,是一项重大的临床挑战。目前对这些损伤的治疗策略是有限的。这项研究强调了OXPHOS在维持肌腱稳态中的关键作用,并提出了针对OXPHOS通路的潜在治疗策略。方法:本研究采用大量测序(bulk-seq)和单细胞RNA测序(scRNA-seq)分析非病变和病变肌腱的肌腱细胞、血管内皮细胞、肌腱源性干细胞、脂肪细胞和神经元的异质性。关键氧化磷酸化(OXPHOS)相关基因,如COX15、COX4I1、COX5B、COX7A1、COX8A、NDUFA12、NDUFA5、NDUFB10、NDUFB3、NDUFC1、NDUFS1、NDUFS4在病变肌腱中与非病变肌腱相比显著下调,表明能量代谢受损。这种OXPHOS活性的降低可能导致慢性肌腱损伤中坏死下垂的增加。此外,双酚A和丙戊酸还能激活oxphos相关基因。结果:研究结果强调了OXPHOS在维持肌腱稳态中的关键作用,并展示了针对OXPHOS通路的潜在治疗策略,如双酚A和丙戊酸,以促进慢性肌腱疾病的愈合。结论:OXPHOS在维持肌腱稳态中的关键作用强调了其作为治疗靶点的潜力,反映了旨在调节OXPHOS通路的策略可能提供有希望的治疗选择。慢性肌腱损伤目前是一个主要的临床挑战与有限的治疗。本研究利用大量和单细胞RNA测序研究了这些损伤的分子机制。我们发现,在多种细胞类型的病变肌腱中,氧化磷酸化(OXPHOS)相关基因显著下调,导致坏死坏死增加。体外实验和分子对接显示丙戊酸能激活OXPHOS,抑制坏死下垂。这些发现强调了线粒体功能在肌腱稳态中的关键作用,并表明丙戊酸是通过恢复OXPHOS活性来治疗慢性肌腱损伤的有希望的治疗候选药物。
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引用次数: 0
CXCL14 Promotes Ovarian Cancer Progression and Autophagy Through the IKBKE/NF-κB Pathway CXCL14通过IKBKE/NF-κB通路促进卵巢癌进展和自噬。
IF 2.2 4区 医学 Q2 BIOTECHNOLOGY & APPLIED MICROBIOLOGY Pub Date : 2026-01-22 DOI: 10.1002/jgm.70084
Yan Lingling, Rao Yanqiu, Zhu Xuchao, Liu Menbing, Liu Jiangang

Ovarian cancer remains a leading cause of gynecological malignancy-related deaths, necessitating the identification of novel molecular pathways driving tumor progression. Utilizing a data-driven approach, we conducted bioinformatic analyses of TCGA and GEO datasets, identifying a significant upregulation of CXCL14 in ovarian cancer tissues, which correlates with poor patient survival. Functional assays demonstrated that overexpression of CXCL14 enhances ovarian cancer cell proliferation, invasion, and autophagy. Mechanistically, CXCL14 activates the canonical NF-κB signaling pathway by inducing phosphorylation and degradation of IκBα, leading to phosphorylation and nuclear translocation of p65. Importantly, we identified IKBKE as a critical kinase mediating CXCL14-induced activation of the canonical NF-κB pathway through phosphorylation of IκBα. Knockdown of IKBKE effectively attenuates CXCL14-driven NF-κB activation, thereby suppressing cell proliferation, invasion, and autophagy. In vivo, CXCL14 overexpression markedly enhances ovarian tumor growth, accompanied by increased levels of IKBKE and phosphorylated p65. These findings elucidate a novel regulatory axis, CXCL14/IKBKE/NF-κB, in ovarian cancer progression, highlighting CXCL14 as a potential therapeutic target for ovarian cancer treatment.

卵巢癌仍然是妇科恶性肿瘤相关死亡的主要原因,因此有必要确定驱动肿瘤进展的新分子途径。利用数据驱动的方法,我们对TCGA和GEO数据集进行了生物信息学分析,发现CXCL14在卵巢癌组织中显著上调,这与患者生存率低相关。功能分析表明,过表达CXCL14可增强卵巢癌细胞的增殖、侵袭和自噬。在机制上,CXCL14通过诱导i -κB α的磷酸化和降解,激活典型的NF-κB信号通路,导致p65的磷酸化和核易位。重要的是,我们发现IKBKE是通过磷酸化i -κB α介导cxcl14诱导的典型NF-κB通路激活的关键激酶。IKBKE的下调可有效减弱cxcl14驱动的NF-κB活化,从而抑制细胞增殖、侵袭和自噬。在体内,CXCL14过表达显著促进卵巢肿瘤生长,同时IKBKE和磷酸化p65水平升高。这些发现阐明了一个新的调控轴CXCL14/IKBKE/NF-κB在卵巢癌进展中的作用,强调了CXCL14作为卵巢癌治疗的潜在靶点。
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引用次数: 0
miRNA-Directed Anticancer Strategies: The Emerging Role of Natural Products in Ovarian Cancer mirna导向的抗癌策略:天然产物在卵巢癌中的新作用。
IF 2.2 4区 医学 Q2 BIOTECHNOLOGY & APPLIED MICROBIOLOGY Pub Date : 2026-01-11 DOI: 10.1002/jgm.70080
Rasha Abu-Khudir, Shaza H. Aly, Nehal I. Rizk, Rabab S. Hamad, Heba M. Midan, Mai A. Abd-Elmawla, Sherif S. Abdel Mageed, Ahmed I. Abulsoud, Mohamed Bakr Zaki, Osama A. Mohammed, Ahmed E. Elesawy, Walaa A. El-Dakroury, Ahmed S. Doghish

Ovarian cancer (OC) is still one of the most serious gynecologic malignancies in the world. It is characterized by a significant likelihood of recurrence and resistance to conventional therapies and a lack of efficient screening techniques. MicroRNAs (miRNAs) are small, noncoding RNA molecules that exert pivotal functions in modulating gene expression. miRNAs are improperly regulated in OC, contributing to tumor onset, progression, metastasis, and resistance to chemotherapeutics. As a result, miRNAs are promising therapeutic targets for the treatment of OC. Recently, natural products derived from plants and other sources have drawn more interest because of their potential to modulate miRNA expression. A variety of bioactive substances, such as curcumin, quercetin, and others, have shown the ability to either promote tumor-suppressing miRNAs or suppress tumor-promoting miRNAs. These substances have a great deal of promise for improving the effectiveness of traditional chemotherapy, lowering adverse effects, and providing more individualized treatment plans. Additionally, their capacity to target several miRNAs implicated in cancer-related pathways offers a multimodal strategy for treating OC. We can upgrade the potential therapeutic options for OC and other cancers by exploring novel natural products with miRNA-modulating effects. However, further research is needed to clinically translate miRNA-based therapeutics employing natural compounds, especially in the areas of safety, bioavailability, and drug delivery methods. This review emphasized the implications of miRNAs in OC, the impact of natural products on miRNA regulations, and the potential for incorporating these natural substances into clinical practice for individualized and successful OC treatments.

卵巢癌(OC)仍然是世界上最严重的妇科恶性肿瘤之一。它的特点是复发的可能性很大,对常规治疗有抵抗力,缺乏有效的筛查技术。MicroRNAs (miRNAs)是一种小的非编码RNA分子,在调节基因表达中发挥关键作用。在卵巢癌中,mirna被不正确地调节,导致肿瘤的发生、进展、转移和对化疗药物的耐药性。因此,mirna是治疗OC的有希望的治疗靶点。最近,来自植物和其他来源的天然产物因其调节miRNA表达的潜力而引起了更多的兴趣。多种生物活性物质,如姜黄素、槲皮素等,已经显示出促进肿瘤抑制mirna或抑制肿瘤促进mirna的能力。这些物质在提高传统化疗的有效性、降低不良反应和提供更个性化的治疗方案方面有很大的希望。此外,它们靶向与癌症相关途径相关的几种mirna的能力为治疗OC提供了一种多模式策略。我们可以通过探索具有mirna调节作用的新型天然产物来升级卵巢癌和其他癌症的潜在治疗选择。然而,需要进一步的研究来临床转化使用天然化合物的基于mirna的治疗方法,特别是在安全性,生物利用度和给药方法方面。这篇综述强调了miRNA在OC中的意义,天然产物对miRNA调控的影响,以及将这些天然物质纳入临床实践以个体化和成功治疗OC的潜力。
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引用次数: 0
MicroRNAs as Key Regulators and Potential Biomarkers in Vitiligo Pathogenesis MicroRNAs作为白癜风发病机制的关键调控因子和潜在生物标志物
IF 2.2 4区 医学 Q2 BIOTECHNOLOGY & APPLIED MICROBIOLOGY Pub Date : 2026-01-08 DOI: 10.1002/jgm.70083
Ahmed S. Doghish, Nehal I. Rizk, Osama A. Mohammed, Mohamed Hemdan, Khaled M. Alam-Eldein, Mohamed Salah Basiouny, Khaled Abuelhaded, Hend H. Mohamed, Abanoub A. S. Shaker, Moaz M. Elshafey, Alaa Adel Abo Ella, Reda M. Mansour

Vitiligo involves melanocyte loss, potentially due to oxidative stress, immune dysfunction, and genetics. This article examines microRNAs (miRNAs), noncoding RNAs crucial for gene expression regulation, as they act as molecular switches that can activate or deactivate genes upon translation. It identifies modified miRNA levels in the skin, blood, immune cells, and exosomes of vitiligo patients. These miRNAs are essential for melanocyte viability and for modulating oxidative stress and immunological responses. Specific miRNAs may function as diagnostic or prognostic biomarkers. The review offers an in-depth comprehension of the crucial functions of miRNAs in development.

白癜风涉及黑素细胞的损失,可能是由于氧化应激、免疫功能障碍和遗传。本文研究了microRNAs (miRNAs),一种对基因表达调控至关重要的非编码rna,因为它们作为分子开关,可以在翻译时激活或灭活基因。它鉴定了白癜风患者皮肤、血液、免疫细胞和外泌体中修饰的miRNA水平。这些mirna对黑素细胞的活力和调节氧化应激和免疫反应至关重要。特异的mirna可作为诊断或预后的生物标志物。这篇综述提供了对mirna在发育中的关键功能的深入理解。
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引用次数: 0
(−)-Epicatechin Regulates Radioresistance in Lung Adenocarcinoma Through ALKBH5 Downregulation of FOXM1 (-)-表儿茶素通过ALKBH5下调FOXM1调控肺腺癌放射耐药
IF 2.2 4区 医学 Q2 BIOTECHNOLOGY & APPLIED MICROBIOLOGY Pub Date : 2026-01-07 DOI: 10.1002/jgm.70082
Hongying Xu, Jie Xia, Anao Wu, Sihan Zhou, Huahua Zhou, Shixian Wu, Meifang Huang

Lung adenocarcinoma (LUAD), a major subtype of non–small-cell lung cancer, exhibits high incidence and mortality rates. Radiotherapy is a critical treatment modality for LUAD, yet its efficacy is often compromised by radiotherapy resistance. (−)-Epicatechin (EC), a natural flavanol derived from Fagopyrum cymosum, has been reported to enhance radiosensitivity in various cancers. However, its specific role and underlying mechanisms in LUAD radiotherapy resistance remain unclear. In this study, we established radiotherapy-resistant cell lines A549R and NCI-H520R by repeatedly irradiating A549 and NCI-H520 cells with gradient doses of X-rays. Furthermore, a xenograft tumor model was constructed by subcutaneously inoculating A549R cells into the left dorsal region of nude mice. The results demonstrated that the forkhead box M1 (FOXM1)—a key oncoprotein implicated in lung cancer proliferation, invasion, and therapy resistance—was significantly upregulated in LUAD tissues and radiotherapy-resistant A549R cells. Knockdown of FOXM1 enhanced radiosensitivity in A549R cells, promoted radiation-induced apoptosis, and suppressed cell proliferation. EC effectively potentiated the radiotherapy response of A549R cells in vitro and attenuated radiotherapy resistance while inhibiting tumor growth in vivo. Mechanistically, EC downregulated ALKBH5, an m6A demethylase known to participate in cancer biology by regulating mRNA demethylation, thereby promoting m6A methylation of FOXM1 mRNA and subsequently suppressing FOXM1 expression, ultimately mitigating radiotherapy resistance in LUAD. This study reveals a novel mechanism by which EC enhances radiosensitivity in LUAD via the ALKBH5/FOXM1 axis, offering a potential therapeutic strategy to overcome radiotherapy resistance in LUAD.

肺腺癌(LUAD)是一种非小细胞肺癌的主要亚型,具有很高的发病率和死亡率。放疗是LUAD的一种重要治疗方式,但其疗效往往受到放疗耐药性的影响。(-)-表儿茶素(EC)是一种从荞麦中提取的天然黄烷醇,据报道可增强各种癌症的放射敏感性。然而,其在LUAD放疗耐药中的具体作用和潜在机制尚不清楚。在本研究中,我们通过梯度剂量的x射线反复照射A549和NCI-H520R细胞,建立了放射治疗耐药细胞系A549R和NCI-H520R。在裸鼠左背区皮下接种A549R细胞,建立异种移植瘤模型。结果表明,叉头盒M1 (FOXM1)是参与肺癌增殖、侵袭和治疗抵抗的关键癌蛋白,在LUAD组织和放疗抵抗的A549R细胞中显著上调。FOXM1敲低可增强A549R细胞的放射敏感性,促进辐射诱导的细胞凋亡,抑制细胞增殖。EC在体外有效增强A549R细胞的放疗反应,在体内抑制肿瘤生长的同时减弱放疗抵抗。在机制上,EC下调ALKBH5,一种已知通过调节mRNA去甲基化参与癌症生物学的m6A去甲基化酶,从而促进FOXM1 mRNA的m6A甲基化,随后抑制FOXM1的表达,最终减轻LUAD患者的放疗耐药。本研究揭示了EC通过ALKBH5/FOXM1轴增强LUAD放射敏感性的新机制,为克服LUAD放射耐药提供了潜在的治疗策略。
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引用次数: 0
Anisomycin Induces Senescence and Death of Ovarian Cancer Stem Cells Through the MicroRNA-340/SENP6/SUMOylation Pathway 大霉素通过MicroRNA-340/SENP6/SUMOylation途径诱导卵巢癌干细胞衰老和死亡
IF 2.2 4区 医学 Q2 BIOTECHNOLOGY & APPLIED MICROBIOLOGY Pub Date : 2026-01-06 DOI: 10.1002/jgm.70081
Lian Yang, Ye Xia, Zeyu Cui, Yanchen Lai, Yongyi Huang, Ying Xiong, Juan Chen, Te Liu

Ovarian cancer remains a leading cause of gynecologic cancer mortality, in part due to the persistence of ovarian cancer stem cells (OCSCs) that drive tumor recurrence, metastasis, and drug resistance. Anisomycin, a natural antibiotic derived from Streptomyces coelicolor, has previously been shown to exert antitumor effects, but the mechanisms by which it targets OCSCs remain unclear. In this study, primary human OCSCs were isolated and treated with anisomycin to investigate its biological and molecular effects. Cell proliferation, apoptosis, migration, and colony formation were assessed in vitro, and tumorigenicity was evaluated in xenograft mouse models. Transcriptomic, biochemical, and molecular assays were performed to identify downstream pathways. Anisomycin treatment markedly inhibited proliferation and promoted senescence and cell death of OCSCs. Mechanistically, anisomycin induced upregulation of microRNA-340, which in turn suppressed the deSUMOylating enzyme SENP6. This repression increased SUMOylation of key senescence-related proteins, including p53 and p16, leading to stabilization of their expression and enforcement of cell-cycle arrest. Overexpression of microRNA-340 reproduced these effects, both in vitro and in vivo, confirming its central role in mediating anisomycin activity. Bioinformatic analyses further revealed that expression of SENP6 and senescence-associated genes correlated with disease progression and patient survival in ovarian cancer cohorts. These findings identify a previously unrecognized epigenetic mechanism by which anisomycin induces senescence and death in OCSCs, suggesting that targeting the microRNA-340/SENP6/SUMOylation pathway may represent a promising therapeutic approach.

卵巢癌仍然是妇科癌症死亡率的主要原因,部分原因是卵巢癌干细胞(OCSCs)的持续存在导致肿瘤复发、转移和耐药。大霉素是一种从彩色链霉菌中提取的天然抗生素,先前已被证明具有抗肿瘤作用,但其靶向OCSCs的机制尚不清楚。本研究分离了原代人OCSCs,并用大霉素处理,研究其生物学和分子效应。在体外评估了细胞增殖、凋亡、迁移和集落形成,并在异种移植小鼠模型中评估了致瘤性。进行转录组学、生化和分子分析以确定下游途径。大霉素处理明显抑制OCSCs的增殖,促进细胞衰老和死亡。从机制上讲,大霉素诱导了microRNA-340的上调,从而抑制了去氧化酶SENP6。这种抑制增加了关键衰老相关蛋白的SUMOylation,包括p53和p16,导致它们的表达稳定和细胞周期阻滞的实施。在体外和体内,microRNA-340的过表达都再现了这些效应,证实了其在介导大霉素活性中的核心作用。生物信息学分析进一步揭示,在卵巢癌队列中,SENP6和衰老相关基因的表达与疾病进展和患者生存相关。这些发现发现了一种以前未被认识到的表观遗传机制,即大霉素诱导OCSCs衰老和死亡,这表明靶向microRNA-340/SENP6/SUMOylation途径可能是一种很有前景的治疗方法。
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引用次数: 0
Multi-Omics Analysis Reveals the Molecular Subtypes and Confirmed the GREM1 as the Core Gene 多组学分析揭示了分子亚型,确认GREM1为核心基因。
IF 2.2 4区 医学 Q2 BIOTECHNOLOGY & APPLIED MICROBIOLOGY Pub Date : 2026-01-06 DOI: 10.1002/jgm.70067
Zhen-Qing Li, Hui-Rong Huang, Ke-Rong Zhai, Bin Li

Research on molecular classification of lung cancer based on transcriptomic features has achieved remarkable progress. The complementary information provided by distinct molecular profiles has motivated the integration of multi-omics datasets to refine the classification system for lung cancer. In this study, we employed a computational pipeline incorporating 10 clustering algorithms to integrate multi-omics datasets from lung adenocarcinoma (LUAD) patients, combined with 10 machine learning methods, leading to the identification of high-resolution molecular subtypes and the development of a consensus machine learning–driven signature (CMLS) with robust predictive performance. Our findings reveal that the CS1 subtype is associated with more favorable prognosis and enhanced immune responsiveness. Furthermore, a CMLS model constructed from 26 core genes demonstrated strong prognostic predictive power. Patients with high CMLS scores exhibited lower infiltration of CD8+ T cells, poorer survival, and diminished response to immunotherapy. In contrast, the low-CMLS group showed improved clinical outcomes, greater responsiveness to immunotherapy, and a tendency toward an immunologically “hot” tumor phenotype. Integrated multi-omics analysis indicated that Gremlin-1 (GREM1) acts as a key regulator within the differential screening–selected gene aberrant in neuroblastoma (DAN) family genes–mediated transforming growth factor-beta (TGF-β) signaling pathway. In conclusion, our data establish a molecular classifier that stratifies patients into distinct score groups, with those in the low-CMLS group potentially benefiting from treatment with pilaralisib.

基于转录组学特征的肺癌分子分类研究取得了显著进展。不同分子谱提供的互补信息促使多组学数据集的整合,以完善肺癌的分类系统。在这项研究中,我们采用了包含10种聚类算法的计算管道来整合来自肺腺癌(LUAD)患者的多组学数据集,并结合10种机器学习方法,从而确定了高分辨率的分子亚型,并开发了具有强大预测性能的共识机器学习驱动签名(CMLS)。我们的研究结果表明,CS1亚型与更有利的预后和增强的免疫反应性相关。此外,由26个核心基因构建的CMLS模型显示出较强的预后预测能力。CMLS评分高的患者表现出CD8+ T细胞浸润较低,生存率较差,对免疫治疗的反应减弱。相比之下,低cmls组表现出改善的临床结果,对免疫治疗的反应性更强,并且倾向于免疫“热”肿瘤表型。综合多组学分析表明,在神经母细胞瘤(DAN)家族基因介导的转化生长因子-β (TGF-β)信号通路中,Gremlin-1 (GREM1)在差异筛选基因异常中起关键调节作用。总之,我们的数据建立了一个分子分类器,将患者分为不同的评分组,低cmls组的患者可能受益于pilaralisib治疗。
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引用次数: 0
Tumor Immune Contexture Model Predicts Prognosis and Immunotherapy Response in Gastric Cancer 肿瘤免疫环境模型预测胃癌的预后和免疫治疗反应。
IF 2.2 4区 医学 Q2 BIOTECHNOLOGY & APPLIED MICROBIOLOGY Pub Date : 2025-12-17 DOI: 10.1002/jgm.70065
Jiexuan Wang, Xin Yang, Xuan Dai, Zhiqian Hu, Xinxing Li
<div> <section> <h3> Background</h3> <p>Gastric cancer (GC) is highly heterogeneous, and current prognostic models fail to fully capture tumor immune characteristics, limiting personalized treatment. This study introduces the Tumor Immune Environment Score (TIES), an immune-based prognostic model designed to enhance risk stratification and predict response to immunotherapy.</p> </section> <section> <h3> Methods</h3> <p>Transcriptomic and clinical data from seven GC cohorts, comprising a total of 1487 patients, were analyzed. The training cohort included GSE15459, GSE62254, GSE84433, and GSE13861, while the validation cohort comprised GSE26899, GSE26901, and TCGA-STAD. Immune-related gene signatures were quantified using ssGSEA and subsequently analyzed via LASSO and Cox regression. Clinical applicability was quantified using decision-curve analysis (DCA) and reclassification metrics (category-free NRI/IDI) for TIES versus TIES + pathological stage. Immunotherapy response was assessed using data from GSE183924, and its associations with immune characteristics, molecular alterations, and drug sensitivity were investigated. For experimental confirmation, we established a 12-gene RT-qPCR panel in 30 institutional GC specimens and computed a weighted qPCR surrogate (qTIES).</p> </section> <section> <h3> Results</h3> <p>A high TIES was associated with worse OS (HR = 2.44, <i>p</i> < 0.001) and DFS (HR = 2.25, <i>p</i> < 0.001). TIES was an independent prognostic factor and demonstrated superior predictive accuracy compared to TNM staging (AUC = 0.75–0.79 vs. 0.61–0.64, <i>p</i> < 0.001). Integrating clinical-pathological features with TIES significantly enhanced predictive performance (AUC = 0.75–0.78 vs. 0.61–0.63, <i>p</i> < 0.01). A low TIES was indicative of an immune-inflamed subtype, characterized by a higher TMB (<i>p</i> < 0.01) and a greater likelihood of response to immunotherapy (HR = 0.24, <i>p</i> = 0.014). TIES outperformed TIDE in predicting immunotherapy outcomes, achieving a higher OS C-index (0.780 vs. 0.743) and DFS C-index (0.664 vs. 0.610). At 3 years, TIES + stage yielded a greater net benefit than TIES alone across clinically relevant thresholds (DCA) and improved NRI/IDI.The qPCR panel reproduced axis biology (CSR/TGF-βincreased with NK/Th2 decreased), correlated with pathological stage, stratified OS/DFS by Kaplan–Meier, and showed 3-year discrimination.</p> </section> <section> <h3> Conclusion</h3> <p>TIES represents a robust immune-based prognostic tool for GC, facilitating improved risk stratification and immuno
背景:胃癌(GC)是高度异质性的,目前的预后模型不能完全捕捉肿瘤的免疫特征,限制了个性化治疗。本研究引入了肿瘤免疫环境评分(TIES),这是一种基于免疫的预后模型,旨在加强风险分层和预测对免疫治疗的反应。方法:对7个GC队列共1487例患者的转录组学和临床数据进行分析。训练队列包括GSE15459、GSE62254、GSE84433和GSE13861,验证队列包括GSE26899、GSE26901和TCGA-STAD。使用ssGSEA对免疫相关基因特征进行量化,随后通过LASSO和Cox回归进行分析。采用决策曲线分析(DCA)和TIES与TIES +病理分期的再分类指标(无类别NRI/IDI)对临床适用性进行量化。使用GSE183924的数据评估免疫治疗反应,并研究其与免疫特性、分子改变和药物敏感性的关系。为了实验证实,我们在30个机构GC标本中建立了一个12个基因的RT-qPCR面板,并计算了加权qPCR代理(qTIES)。结果:高TIES与较差的OS相关(HR = 2.44, p)。结论:TIES是一种强大的基于免疫的GC预后工具,有助于改善风险分层和免疫治疗反应预测。将其整合到临床实践中,特别是与临床病理特征相结合,可以增强个性化治疗策略并改善患者预后。
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引用次数: 0
Facilitating Precision Medicine in HCC Patients by Deep Learning–Directed lncRNAs Classification and Ascertaining Causal Markers 以深度学习为导向的lncrna分类和确定病因标志物,促进HCC患者的精准医疗。
IF 2.2 4区 医学 Q2 BIOTECHNOLOGY & APPLIED MICROBIOLOGY Pub Date : 2025-12-17 DOI: 10.1002/jgm.70066
Rashi Jain, Sathish Kumar Mungamuri, Prabha Garg

Background

Hepatocellular carcinoma (HCC) is a deadly disease, ranking as the fifth most prevalent type of cancer worldwide. To advance precision medicine for HCC, it is imperative to identify novel biomarkers that can facilitate its clinical management. Notably, long noncoding RNAs (lncRNAs) have been demonstrated to play pivotal roles in regulating gene expression and driving tumor progression.

Methods

This study harnessed artificial intelligence (AI) to identify novel lncRNA biomarkers using patient data from The Cancer Genome Atlas. A hierarchical composite deep learning (DL) framework was constructed to classify patient samples according to the pathological stages. Explainable AI-based SHapley Additive exPlanations (SHAP) analysis, Kaplan–Meier survival analysis, and biological investigations were performed to identify potential lncRNA biomarkers.

Results

The DL hierarchical composite framework employed three deep neural networks (DNNs) to classify tumorous liver tissue samples from normal samples (Model 1), distinguish between early and advanced disease stages (Model 2), and further assess the pathological stage of HCC progression (Model 3). Model 1 (AU-ROC = 1.000) and Model 2 (AU-ROC = 0.977) exhibited robust predictive capabilities on unseen data. Model 3 (AU-ROC = 0.774) showed lower performance, highlighting the inherent challenges in the data due to the close association of lncRNAs across advanced HCC stages. SHAP analysis revealed the key lncRNAs driving these classifications, providing insights into the molecular mechanisms of HCC progression. Further investigations identified AC010280.2, AC118754.1, DIO3OS, LINC01748, and LINC00659 as potential biomarkers for HCC.

Conclusions

This comprehensive study integrated cutting-edge technologies that pave the way for biomarker discovery, facilitating precision medicine in HCC.

背景:肝细胞癌(HCC)是一种致命的疾病,在世界范围内排名第五。为了推进肝细胞癌的精准医疗,必须寻找新的生物标志物来促进其临床管理。值得注意的是,长链非编码rna (lncRNAs)已被证明在调节基因表达和驱动肿瘤进展中发挥关键作用。方法:本研究利用人工智能(AI)利用来自癌症基因组图谱的患者数据识别新的lncRNA生物标志物。构建了分层复合深度学习框架,根据病理分期对患者样本进行分类。采用可解释的基于人工智能的SHapley加性解释(SHAP)分析、Kaplan-Meier生存分析和生物学调查来鉴定潜在的lncRNA生物标志物。结果:DL分层复合框架利用3个深度神经网络(dnn)将肿瘤肝组织样本与正常样本进行分类(模型1),区分疾病早期和晚期(模型2),并进一步评估HCC进展的病理分期(模型3)。模型1 (AU-ROC = 1.000)和模型2 (AU-ROC = 0.977)对未见数据表现出稳健的预测能力。模型3 (AU-ROC = 0.774)表现较差,由于lncrna在晚期HCC阶段的密切关联,突出了数据中的固有挑战。SHAP分析揭示了驱动这些分类的关键lncrna,为HCC进展的分子机制提供了见解。进一步的研究发现AC010280.2、AC118754.1、DIO3OS、LINC01748和LINC00659是潜在的HCC生物标志物。结论:这项综合性研究整合了尖端技术,为发现生物标志物铺平了道路,促进了HCC的精准医学。
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引用次数: 0
期刊
Journal of Gene Medicine
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