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Effect of waterpipe smoking and its cessation on metabolic biomarkers and a novel biomarker omentin-1.
IF 2 4区 医学 Q3 BIOTECHNOLOGY & APPLIED MICROBIOLOGY Pub Date : 2025-03-19 DOI: 10.1080/1354750X.2025.2479664
Hiba A Yousif, Mohammed A Hami

Background and objective: Waterpipe smoking (WPS) has increased globally and may lead to various metabolic disorders. However, its long-term effects and cessation impact on metabolic biomarkers and omentin-1 remain unclear. This study aims to evaluate the impact of WPS and its cessation on metabolic biomarkers and omentin-1 levels and explore their correlations.

Materials and methods: 90 individuals were categorized into three groups (non-smokers, waterpipe smokers and cessation of waterpipe smokers). FBS and lipid profiles including TC, TG and HDL were measured using the Cobas 6000 c501 system, while FI was analyzed with the Cobas 6000 c601 system. Omentin-1 concentrations were determined using the enzyme-linked immunosorbent assay (ELISA) with a human omentin ELISA kit.

Results: FI, HOMA-IR and lipid profiles were significantly elevated in WPS and cessation groups. Omentin-1 and DBP levels significantly decreased in both groups compared to non-smokers. Increased WPS duration leads to reduced BMI, WC and DBP, while cessation duration decreases FBS and SBP. A negative association was identified among omentin-1 with FBS and O2.

Conclusion: WPS and its cessation adversely affect metabolic health, reducing omentin-1 levels and increasing the risk of metabolic disorders. Over time, cessation improves specific biochemical markers, highlighting the need for public health awareness.

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引用次数: 0
Early warning system for player recovery? A series of case studies illustrating the application of individualised adaptive reference ranges in the longitudinal blood monitoring of English Premier League soccer players.
IF 2 4区 医学 Q3 BIOTECHNOLOGY & APPLIED MICROBIOLOGY Pub Date : 2025-03-19 DOI: 10.1080/1354750X.2025.2473724
Diarmuid Daniels, Davood Roshan, Nathan A Lewis, John Newell, Georgie Bruinvels, Paul Catterson, Jamie Harley, Micheal Newell, Andrew Barr, Charles R Pedlar

Blood biomarkers can provide objective insight into a player's physiological state of recovery. Individualised approaches to biomarker monitoring may be of higher potential value in assessing player health and recovery compared to population-based reference ranges. We aimed to explore the application of individualised adaptive reference ranges (IARR) in English Premier League (EPL) soccer players using a POC biomarker for C-Reactive Protein (CRP) as a marker of inflammation. Using historical data collected from players' CRP values during the 2019-2020 season, we evaluated the effectiveness of static and IARR in identifying abnormal values and reported sensitivity and specificity at a 5% significance level. Our analysis confirmed that monitoring with IARR is more effective in identifying true abnormalities compared to population-based static reference ranges, particularly when the intra-individual variability is considerably lower than inter-individual variability. The application of IARR for blood monitoring data could assist the practitioner in identifying periods where a player may require performance (e.g. workload management and recovery practices) or medical support from the multi-disciplinary team. However, IARR serve more as an early warning system than a diagnostic tool. Thus, significant care is needed to prevent misuse and misinterpretation when implementing this strategy in real-world settings.

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引用次数: 0
The Ischemia-Modified Albumin Test: New Tricks for an Old Dog?
IF 2 4区 医学 Q3 BIOTECHNOLOGY & APPLIED MICROBIOLOGY Pub Date : 2025-03-18 DOI: 10.1080/1354750X.2025.2481407
Alan H B Wu
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引用次数: 0
A systematic review of first-trimester blood biomarkers associated with preterm prelabor rupture of the fetal membranes.
IF 2 4区 医学 Q3 BIOTECHNOLOGY & APPLIED MICROBIOLOGY Pub Date : 2025-03-06 DOI: 10.1080/1354750X.2025.2475474
Mille Kirk, Josephine RothEkmann, Martin Overgaard, Charlotte K Ekelund, Hanne K Hegaard, Line Rode

Preterm prelabor rupture of the fetal membranes (PPROM) increases the risk of neonatal mortality and morbidity. The etiology behind the condition is multifactorial but believed to result from an overactivation of inflammatory pathways. This systematic review aimed to synthesize the literature behind first-trimester biomarkers associated with PPROM and compare it to literature within the same area for preterm birth.A search strategy was performed in PubMed, Embase, and CINAHL from 1993-2024 resulting in 14,889 articles screened by two independent authors and presented according to PRISMA guidelines. The biomarkers from the included articles were categorized into four medical headings: The immune system, metabolism and endocrinology, hematology, and reproduction. Biomarkers associated with PPROM were primarily related to the immune system.C-reactive protein (CRP) and white blood cells (WBC) were often investigated for an association with PPROM but displayed divergent results of varying quality. Decreased concentrations of placental growth factor (PlGF) were associated with PPROM and spontaneous preterm birth, potentially highlighting a shared etiology, making soluble fms-like tyrosine kinase-1 (sFlt-1) interesting to investigate as well. Most biomarkers were examined in single studies, providing limited data to make significant conclusions about each biomarker. This review encourages further investigation of CRP, WBC, PlGF, and sFlt-1.

早产胎膜早破(PPROM)会增加新生儿死亡和发病的风险。该病症的病因是多因素的,但据信是炎症通路过度激活所致。本系统性综述旨在综合与早产儿窒息相关的第一胎生物标志物的文献,并将其与早产儿同一领域的文献进行比较。收录文章中的生物标志物分为四个医学标题:免疫系统、新陈代谢和内分泌学、血液学和生殖。C反应蛋白(CRP)和白细胞(WBC)经常被用于调查与胎盘早剥相关性,但结果却各不相同,质量也参差不齐。胎盘生长因子(PlGF)浓度的降低与PPROM和自发性早产有关,可能突显了共同的病因,因此可溶性酪氨酸激酶-1(sFlt-1)也值得研究。大多数生物标志物都是在单项研究中检测的,提供的数据有限,无法对每个生物标志物做出重要结论。本综述鼓励进一步研究 CRP、WBC、PlGF 和 sFlt-1。
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引用次数: 0
The association between systemic inflammation markers and the risk of incident dilated cardiomyopathy: a prospective study of 351,148 participants. 全身炎症指标与扩张型心肌病发病风险之间的关系:一项针对 351 148 名参与者的前瞻性研究。
IF 2 4区 医学 Q3 BIOTECHNOLOGY & APPLIED MICROBIOLOGY Pub Date : 2025-03-01 Epub Date: 2025-02-14 DOI: 10.1080/1354750X.2025.2461694
Xihang Fu, Xiaodie Li, Xinxin Gao, Qianlin Zuo, Lin Wang, Hua Peng, Jing Wu

Background: The role of systemic inflammation in the development and progression of cardiovascular diseases has been attractive, but its association with incident dilated cardiomyopathy (DCM) is rarely investigated. This study aimed to systematically investigate the association between various inflammatory markers and DCM incidence.

Methods: The data were derived from the UK Biobank database. Systemic inflammation markers in this study encompassed peripheral immune cell counts and their ratios and the low-grade inflammation score (INFLA-score). The Cox proportional hazards regression, restricted cubic splines model, and segmented regression were adopted to assess the association between systemic inflammation markers and DCM incidence. Additionally, the subgroup Cox analysis stratified across sex was also performed.

Results: A total of 351,148 participants were enrolled in this study, and 377 subjects developed DCM during a mean follow-up of 12.21 years. The positive association between C-reactive protein (CRP), neutrophil-to-lymphocyte ratio (NLR), and CRP-to-lymphocyte ratio (CLR) and DCM incident risk was found (CRP: HR = 1.190, P = 0.001; NLR: HR = 1.315, P = 0.033; CLR: HR = 1.206, P < 0.001), while the lymphocyte-to-monocyte ratio (LMR) was negatively associated with DCM incident risk (HR = 0.756; P = 0.033). Furthermore, the increased risk of DCM incidence was significantly and nonlinearly correlated with the reduction of platelet count (HR = 0.543; P = 0.002). In the subgroup analysis, sex-specific inflammation markers related to DCM development were noticed.

Conclusions: The study has underlined that multiple inflammation markers were significantly associated with the risk of incident DCM, which would provide evidence for the aetiological study of DCM.

背景:全身性炎症在心血管疾病的发生和发展中的作用很有吸引力,但其与扩张型心肌病(DCM)发病率的关系却很少被研究。本研究旨在系统调查各种炎症标志物与扩张型心肌病发病率之间的关系:方法:数据来自英国生物库数据库。本研究中的全身炎症指标包括外周免疫细胞计数及其比率和低度炎症评分(INFLA-score)。采用 Cox 比例危险回归、限制性立方样条模型和分段回归来评估全身炎症标志物与 DCM 发病率之间的关系。此外,还进行了按性别分层的亚组 Cox 分析:结果:共有 351 148 人参与了这项研究,其中 377 人在平均 12.21 年的随访期间患上了 DCM。研究发现,C反应蛋白(CRP)、中性粒细胞与淋巴细胞比值(NLR)和CRP与淋巴细胞比值(CLR)与DCM发病风险呈正相关(CRP:HR = 1.190,P = 0.001;NLR:HR = 1.315,P = 0.033;CLR:HR = 1.206,P = 0.033)。此外,DCM发病风险的增加与血小板计数的减少呈显著非线性相关(HR = 0.543; P = 0.002)。在亚组分析中发现,与DCM发病有关的炎症标记物具有性别特异性:该研究强调,多种炎症标志物与DCM发病风险显著相关,这将为DCM的病因学研究提供证据。
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引用次数: 0
Serum autoantibody-based biomarkers for prognosis in early-stage lung cancer patients with surgical resection. 基于血清自身抗体的生物标志物对手术切除早期肺癌患者预后的影响。
IF 2 4区 医学 Q3 BIOTECHNOLOGY & APPLIED MICROBIOLOGY Pub Date : 2025-03-01 Epub Date: 2025-02-14 DOI: 10.1080/1354750X.2025.2456023
Panpan Jiang, Kaili Wang, Yaqin Wei, Haonan Chen, Xueqin Cai, Yan Hua, Ming Li

Background: Lung cancer is the cancer with the highest morbidity and mortality in the world. With the increasing diagnosis rate of patients with early-stage lung cancer, surgery treatment becomes an option for more patients. However, there is a lack of effective indicators to assess the risk of recurrence after lung cancer surgery.

Methods: We collected levels of serum autoantibodies and evaluated their roles as biomarkers especially for postoperative recurrence of lung cancer. In vitro experiments including antibody-dependent cellular cytotoxicity (ADCC), antibody-dependent cellular phagocytosis (ADCP) and complement-dependent cytotoxicity (CDC) were performed to explore the functions of serum autoantibodies.

Results: Our study demonstrated that serum autoantibody-positive patients with early-stage lung cancer had a longer postoperative progression period. The levels of serum autoantibodies in patients with lung cancer were higher than that in patients with benign lung diseases. But all the serum autoantibodies had no difference between patients with stage I and II. In addition, the results of in vitro experiments indicated that serum autoantibodies can mediate immune responses and enhance anti-tumour effects.

Conclusion: This study proposed effective biomarkers for prognosis in lung cancer patients after surgery which is critical to reduce the recurrence.

背景:肺癌是世界上发病率和死亡率最高的癌症。随着早期肺癌患者诊断率的提高,手术治疗成为更多患者的选择。然而,目前缺乏评估肺癌手术后复发风险的有效指标。方法:我们收集血清自身抗体水平,并评估其作为生物标志物的作用,特别是在肺癌术后复发。通过体外实验,包括抗体依赖性细胞毒性(ADCC)、抗体依赖性细胞吞噬(ADCP)和补体依赖性细胞毒性(CDC),探讨血清自身抗体的功能。结果:我们的研究表明血清自身抗体阳性的早期肺癌患者有较长的术后进展期。肺癌患者血清自身抗体水平高于肺部良性疾病患者。但所有的血清自身抗体在I期和II期患者之间没有差异。此外,体外实验结果表明,血清自身抗体可介导免疫反应,增强抗肿瘤作用。结论:本研究为肺癌患者术后预后提供了有效的生物标志物,对减少复发至关重要。
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引用次数: 0
Systemic fluoride levels in toenails as biomarkers of exposure and their association with the severity of dental fluorosis in Mexican schoolchildren - a cross-sectional study.
IF 2 4区 医学 Q3 BIOTECHNOLOGY & APPLIED MICROBIOLOGY Pub Date : 2025-03-01 Epub Date: 2025-02-24 DOI: 10.1080/1354750X.2025.2456657
Jesús Lavalle-Carrasco, Nelly Molina-Frechero, Elizabeth Hernández-Pérez, Leonor Sánchez-Pérez, Sandra López-Verdín, Ronell Bologna-Molina

Introduction: Elevated fluoride (F-) exposure during childhood produces dental fluorosis (DF). Nails have been used for monitoring systemic F- in relation to DF. The aim of this study was to evaluate F- levels in toenails in association with DF severity in Mexican schoolchildren.

Materials and methods: 120 schoolchildren from nonendemic areas (NEAs) and endemic F- areas (EAs) were screened for DF via the Thylstrup and Fejerskov index (TFI). Toenails were collected to quantify systemic F-. The associations between the biomarker, DF severity, tap water intake, sex, and age were analyzed.

Results: The mean F- in toenails in the NEAs and EAs were 0.63 ± 0.43 and 2.72 ± 1.38 mg/kg, respectively (p < 0.001). A positive correlation was observed between the biomarker and DF severity (rs = 0.755, p < 0.001). Tap water consumption and the biomarker were associated with DF severity (p < 0.001). Within TFI7-8 the mean F- level was higher in those ages 10-11 than in those ages 8-9 (p < 0.05).

Conclusion: Systemic F- levels in toenails are associated with DF severity in Mexican schoolchildren from both the NEAs and the EAs, which reflects the ability of the biomarker to accurately record the exposure to the compound in relation to clinical damage.

{"title":"Systemic fluoride levels in toenails as biomarkers of exposure and their association with the severity of dental fluorosis in Mexican schoolchildren - a cross-sectional study.","authors":"Jesús Lavalle-Carrasco, Nelly Molina-Frechero, Elizabeth Hernández-Pérez, Leonor Sánchez-Pérez, Sandra López-Verdín, Ronell Bologna-Molina","doi":"10.1080/1354750X.2025.2456657","DOIUrl":"10.1080/1354750X.2025.2456657","url":null,"abstract":"<p><strong>Introduction: </strong>Elevated fluoride (F<sup>-</sup>) exposure during childhood produces dental fluorosis (DF). Nails have been used for monitoring systemic F<sup>-</sup> in relation to DF. The aim of this study was to evaluate F<sup>-</sup> levels in toenails in association with DF severity in Mexican schoolchildren.</p><p><strong>Materials and methods: </strong>120 schoolchildren from nonendemic areas (NEAs) and endemic F<sup>-</sup> areas (EAs) were screened for DF via the Thylstrup and Fejerskov index (TFI). Toenails were collected to quantify systemic F<sup>-</sup>. The associations between the biomarker, DF severity, tap water intake, sex, and age were analyzed.</p><p><strong>Results: </strong>The mean F<sup>-</sup> in toenails in the NEAs and EAs were 0.63 ± 0.43 and 2.72 ± 1.38 mg/kg, respectively (p < 0.001). A positive correlation was observed between the biomarker and DF severity (r<sub>s</sub> = 0.755, p < 0.001). Tap water consumption and the biomarker were associated with DF severity (p < 0.001). Within TFI7-8 the mean F<sup>-</sup> level was higher in those ages 10-11 than in those ages 8-9 (p < 0.05).</p><p><strong>Conclusion: </strong>Systemic F<sup>-</sup> levels in toenails are associated with DF severity in Mexican schoolchildren from both the NEAs and the EAs, which reflects the ability of the biomarker to accurately record the exposure to the compound in relation to clinical damage.</p>","PeriodicalId":8921,"journal":{"name":"Biomarkers","volume":" ","pages":"140-146"},"PeriodicalIF":2.0,"publicationDate":"2025-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143439765","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Dynamine 3 as a diagnostic and prognostic biomarker in pancreatic cancer: Implications for early detection and targeted therapy.
IF 2 4区 医学 Q3 BIOTECHNOLOGY & APPLIED MICROBIOLOGY Pub Date : 2025-03-01 Epub Date: 2025-02-04 DOI: 10.1080/1354750X.2025.2458104
Fatih Yay, Hasan Çağrı Yıldırım, Fatih Kuş, Şuayib Yalçın
<p><strong>Background: </strong>Dynamins are defined as a group of molecules with GTPase activity. Among them, DNM3 has gained recognition in oncology for its tumor suppressor role. Based on this, the aim of this study is to investigate the effects of the DNM3 gene in patients diagnosed with pancreatic cancer using bioinformatics databases.</p><p><strong>Materials and methods: </strong>For differential gene expression analysis, TCGA TARGET GTEx study on the UCSC Xena and GEO datasets were utilized; for the analysis of changes in gene expression according to clinical and pathological characteristics, UALCAN was employed; for Overall Survival (OS) analysis, Kaplan-Meier Plotter was used; for gene alteration analysis, cBioPortal was utilized; for immune cell infiltration analysis, Tumor Immune Estimation Resource (TIMER) and TIMER2.0 were employed; for enrichment analyses Enrichr was used; for Gene Set Correlation Enrichment Analysis Gscore was used on GSE15471; for essentiality of DNM3 gene in pancratic cancer cell lines DepMap was used; and for the detection of miRNAs, miRDB was utilized; ENCORI was used for gene-miRNA correlation and miRNA prognosis analyses.</p><p><strong>Results: </strong>In the pancreatic adenocarcinoma (PAAD) cohort, DNM3 gene expression was higher in tumor samples, and there was no significant difference in expression among cancer stages. High levels of DNM3 gene expression were associated with longer OS in PAAD. A weak positive correlation was observed between DNM3 gene expression and B-Cell and CD4+ T Cell infiltrations, while a moderate positive correlation was found with CD8+ T Cell, Macrophage, Neutrophil, and Dendritic Cell infiltrations in TIMER. NK cell by QUANTISEQ, CD 4+ T Cell by TIMER, T cell regulatory (Tregs) by CIBERSORT-ABS infiltrations were positively associated with DNM3 gene expression and decreased risk in prognosis. Common lymphoid progenitor by XCELL and MDSC by TIDE infiltrations were negatively associated with DNM3 gene expression and increased risk of prognosis. Macrophage M1 by QUANTISEQ was positively associated with DNM3 gene expression and increased risk in prognosis. DNM3 gene appears to be associated with various pathways related to inflammation and the immune system. Amplification of the DNM3 gene was detected in 5 out of 175 patients. Enrichment was observed in pathways such as bacterial invasion of epithelial cells, endocytosis, endocrine and other factor-regulated calcium reabsorption, synaptic vesicle cycle, and phospholipase D signaling pathway. According to Gscore, DNM3 gene was associated with Fc epsilon RI signaling pathway, HALLMARK MTORC1 SIGNALING, HALLMARK EPITHELIAL MESENCHYMAL TRANSITION gene sets. According to ENCORI, DNM3 gene was negatively correlated with hsa-miR-203a-3p and increased expression of this miRNA was associated with adverse prognosis in PAAD.</p><p><strong>Conclusions: </strong>The DNM3 gene may play a tumor suppressor role in pancreatic cancer, similar to its r
{"title":"Dynamine 3 as a diagnostic and prognostic biomarker in pancreatic cancer: Implications for early detection and targeted therapy.","authors":"Fatih Yay, Hasan Çağrı Yıldırım, Fatih Kuş, Şuayib Yalçın","doi":"10.1080/1354750X.2025.2458104","DOIUrl":"10.1080/1354750X.2025.2458104","url":null,"abstract":"&lt;p&gt;&lt;strong&gt;Background: &lt;/strong&gt;Dynamins are defined as a group of molecules with GTPase activity. Among them, DNM3 has gained recognition in oncology for its tumor suppressor role. Based on this, the aim of this study is to investigate the effects of the DNM3 gene in patients diagnosed with pancreatic cancer using bioinformatics databases.&lt;/p&gt;&lt;p&gt;&lt;strong&gt;Materials and methods: &lt;/strong&gt;For differential gene expression analysis, TCGA TARGET GTEx study on the UCSC Xena and GEO datasets were utilized; for the analysis of changes in gene expression according to clinical and pathological characteristics, UALCAN was employed; for Overall Survival (OS) analysis, Kaplan-Meier Plotter was used; for gene alteration analysis, cBioPortal was utilized; for immune cell infiltration analysis, Tumor Immune Estimation Resource (TIMER) and TIMER2.0 were employed; for enrichment analyses Enrichr was used; for Gene Set Correlation Enrichment Analysis Gscore was used on GSE15471; for essentiality of DNM3 gene in pancratic cancer cell lines DepMap was used; and for the detection of miRNAs, miRDB was utilized; ENCORI was used for gene-miRNA correlation and miRNA prognosis analyses.&lt;/p&gt;&lt;p&gt;&lt;strong&gt;Results: &lt;/strong&gt;In the pancreatic adenocarcinoma (PAAD) cohort, DNM3 gene expression was higher in tumor samples, and there was no significant difference in expression among cancer stages. High levels of DNM3 gene expression were associated with longer OS in PAAD. A weak positive correlation was observed between DNM3 gene expression and B-Cell and CD4+ T Cell infiltrations, while a moderate positive correlation was found with CD8+ T Cell, Macrophage, Neutrophil, and Dendritic Cell infiltrations in TIMER. NK cell by QUANTISEQ, CD 4+ T Cell by TIMER, T cell regulatory (Tregs) by CIBERSORT-ABS infiltrations were positively associated with DNM3 gene expression and decreased risk in prognosis. Common lymphoid progenitor by XCELL and MDSC by TIDE infiltrations were negatively associated with DNM3 gene expression and increased risk of prognosis. Macrophage M1 by QUANTISEQ was positively associated with DNM3 gene expression and increased risk in prognosis. DNM3 gene appears to be associated with various pathways related to inflammation and the immune system. Amplification of the DNM3 gene was detected in 5 out of 175 patients. Enrichment was observed in pathways such as bacterial invasion of epithelial cells, endocytosis, endocrine and other factor-regulated calcium reabsorption, synaptic vesicle cycle, and phospholipase D signaling pathway. According to Gscore, DNM3 gene was associated with Fc epsilon RI signaling pathway, HALLMARK MTORC1 SIGNALING, HALLMARK EPITHELIAL MESENCHYMAL TRANSITION gene sets. According to ENCORI, DNM3 gene was negatively correlated with hsa-miR-203a-3p and increased expression of this miRNA was associated with adverse prognosis in PAAD.&lt;/p&gt;&lt;p&gt;&lt;strong&gt;Conclusions: &lt;/strong&gt;The DNM3 gene may play a tumor suppressor role in pancreatic cancer, similar to its r","PeriodicalId":8921,"journal":{"name":"Biomarkers","volume":" ","pages":"147-166"},"PeriodicalIF":2.0,"publicationDate":"2025-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143027789","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Differential gene expression analysis and machine learning identified structural, TFs, cytokine and glycoproteins, including SOX2, TOP2A, SPP1, COL1A1, and TIMP1 as potential drivers of lung cancer.
IF 2 4区 医学 Q3 BIOTECHNOLOGY & APPLIED MICROBIOLOGY Pub Date : 2025-03-01 Epub Date: 2025-02-10 DOI: 10.1080/1354750X.2025.2461698
Syed Naseer Ahmad Shah, Rafat Parveen

Background: Lung cancer is a primary global health concern, responsible for a considerable portion of cancer-related fatalities worldwide. Understanding its molecular complexities is crucial for identifying potential targets for treatment. The goal is to slow disease progression and intervene early to prevent the development of advanced lung cancer cases. Hence, there's an urgent need for new biomarkers that can detect lung cancer in its early stages.

Methods: The study conducted RNA-Seq analysis of lung cancer samples from the publicly available SRA database (NCBI SRP009408), including both control and tumour samples. The genes with differential expression between tumour and healthy tissues were identified using R and Bioconductor. Machine learning (ML) techniques, Random Forest, Lasso, XGBoost, Gradient Boosting and Elastic Net were employed to pinpoint significant genes followed by classifiers, Multilayer Perceptron (MLP), Support Vector Machines (SVM) and k-Nearest Neighbours (k-NN). Gene ontology and pathway analyses were performed on the significant differentially expressed genes (DEGs). The top genes from DEG and machine learning analyses were combined for protein-protein interaction (PPI) analysis, identifying 10 hub genes essential for lung cancer progression.

Results: The integrated analysis of ML and DEGs revealed the significance of specific genes in lung cancer samples, identified the top 5 upregulated genes (COL11A1, TOP2A, SULF1, DIO2, MIR196A2) and the top 5 downregulated genes (PDK4, FOSB, FLYWCH1, CYB5D2, MIR328), along with their associated genes implicated in pathways or co-expression networks were identified. Among the various algorithms employed, Random Forest and XGBoost proved effective in identifying common genes, underscoring their potential significance in lung cancer pathogenesis. The MLP exhibited the highest accuracy in classifying samples using all genes. Additionally, the protein-protein interaction (PPI) analysis identified 10 hub genes that are pivotal in lung cancer pathogenesis: COL1A1, SOX2, SPP1, THBS2, POSTN, COL5A1, COL11A1, TIMP1, TOP2A and PKP1.

Conclusion: The study contributes to the early prediction of lung cancer by identifying potential biomarkers that could enhance early diagnosis and pave the way for practical clinical applications in the future. Integrating DEGs and machine learning-derived significant genes for PPI analysis offers a robust approach to uncovering critical molecular targets for lung cancer treatment.

{"title":"Differential gene expression analysis and machine learning identified structural, TFs, cytokine and glycoproteins, including SOX2, TOP2A, SPP1, COL1A1, and TIMP1 as potential drivers of lung cancer.","authors":"Syed Naseer Ahmad Shah, Rafat Parveen","doi":"10.1080/1354750X.2025.2461698","DOIUrl":"10.1080/1354750X.2025.2461698","url":null,"abstract":"<p><strong>Background: </strong>Lung cancer is a primary global health concern, responsible for a considerable portion of cancer-related fatalities worldwide. Understanding its molecular complexities is crucial for identifying potential targets for treatment. The goal is to slow disease progression and intervene early to prevent the development of advanced lung cancer cases. Hence, there's an urgent need for new biomarkers that can detect lung cancer in its early stages.</p><p><strong>Methods: </strong>The study conducted RNA-Seq analysis of lung cancer samples from the publicly available SRA database (NCBI SRP009408), including both control and tumour samples. The genes with differential expression between tumour and healthy tissues were identified using R and Bioconductor. Machine learning (ML) techniques, Random Forest, Lasso, XGBoost, Gradient Boosting and Elastic Net were employed to pinpoint significant genes followed by classifiers, Multilayer Perceptron (MLP), Support Vector Machines (SVM) and k-Nearest Neighbours (k-NN). Gene ontology and pathway analyses were performed on the significant differentially expressed genes (DEGs). The top genes from DEG and machine learning analyses were combined for protein-protein interaction (PPI) analysis, identifying 10 hub genes essential for lung cancer progression.</p><p><strong>Results: </strong>The integrated analysis of ML and DEGs revealed the significance of specific genes in lung cancer samples, identified the top 5 upregulated genes (COL11A1, TOP2A, SULF1, DIO2, MIR196A2) and the top 5 downregulated genes (PDK4, FOSB, FLYWCH1, CYB5D2, MIR328), along with their associated genes implicated in pathways or co-expression networks were identified. Among the various algorithms employed, Random Forest and XGBoost proved effective in identifying common genes, underscoring their potential significance in lung cancer pathogenesis. The MLP exhibited the highest accuracy in classifying samples using all genes. Additionally, the protein-protein interaction (PPI) analysis identified 10 hub genes that are pivotal in lung cancer pathogenesis: COL1A1, SOX2, SPP1, THBS2, POSTN, COL5A1, COL11A1, TIMP1, TOP2A and PKP1.</p><p><strong>Conclusion: </strong>The study contributes to the early prediction of lung cancer by identifying potential biomarkers that could enhance early diagnosis and pave the way for practical clinical applications in the future. Integrating DEGs and machine learning-derived significant genes for PPI analysis offers a robust approach to uncovering critical molecular targets for lung cancer treatment.</p>","PeriodicalId":8921,"journal":{"name":"Biomarkers","volume":" ","pages":"200-215"},"PeriodicalIF":2.0,"publicationDate":"2025-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143070888","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Differences in biomarkers of potential harm after 2+ years of tobacco heating system use compared to cigarette smoking: a cross-sectional study.
IF 2 4区 医学 Q3 BIOTECHNOLOGY & APPLIED MICROBIOLOGY Pub Date : 2025-03-01 Epub Date: 2025-02-19 DOI: 10.1080/1354750X.2025.2461069
S Michael Ansari, Patrice Leroy, Guillaume de La Bourdonnaye, Sandrine Pouly, Lindsay Reese, Christelle Haziza

Background: Growing evidence indicates that noncombustible products could be a tobacco harm reduction tool for smokers who do not quit. The Tobacco Heating System (THS) emits substantially lower levels of harmful cigarette smoke constituents, and previous randomized clinical studies showed improved levels of biomarkers of potential harm (BoPH) linked to smoking-related disease.

Methods: In this cross-sectional study of healthy participants (n = 982) who (i) smoked cigarettes, (ii) had voluntarily switched from smoking to THS use, or (iii) formerly smoked, blood and urine samples were assayed for nine BoPH. The co-primary endpoints were carboxyhemoglobin, total 4-(methylnitrosamino)-1-(3-pyridyl)-1-butanol, white blood cells, and 8-epi-prostaglandin-F. The key secondary endpoints were high-density lipoprotein cholesterol, soluble intercellular adhesion molecule-1, 11-dehydrothromboxane B2, central vascular augmentation index, and forced expiratory volume in 1 s (%predicted post-bronchodilator).

Results: THS users showed significant favorable differences in all nine BoPH compared to current smokers. Results in THS users were similar to those in former smokers.

Conclusion: Compared to current smokers, healthy participants who voluntarily switched from smoking to THS use for ≥2 years in the real world had favorable differences in BoPH related to oxygen delivery, genotoxicity, inflammation, oxidative stress, lipid metabolism, endothelial function, platelet activation, and cardiovascular and respiratory function. Clinicaltrials.gov Identifier: NCT05385055.

{"title":"Differences in biomarkers of potential harm after 2+ years of tobacco heating system use compared to cigarette smoking: a cross-sectional study.","authors":"S Michael Ansari, Patrice Leroy, Guillaume de La Bourdonnaye, Sandrine Pouly, Lindsay Reese, Christelle Haziza","doi":"10.1080/1354750X.2025.2461069","DOIUrl":"10.1080/1354750X.2025.2461069","url":null,"abstract":"<p><strong>Background: </strong>Growing evidence indicates that noncombustible products could be a tobacco harm reduction tool for smokers who do not quit. The Tobacco Heating System (THS) emits substantially lower levels of harmful cigarette smoke constituents, and previous randomized clinical studies showed improved levels of biomarkers of potential harm (BoPH) linked to smoking-related disease.</p><p><strong>Methods: </strong>In this cross-sectional study of healthy participants (<i>n</i> = 982) who (i) smoked cigarettes, (ii) had voluntarily switched from smoking to THS use, or (iii) formerly smoked, blood and urine samples were assayed for nine BoPH. The co-primary endpoints were carboxyhemoglobin, total 4-(methylnitrosamino)-1-(3-pyridyl)-1-butanol, white blood cells, and 8-epi-prostaglandin-F<sub>2α</sub>. The key secondary endpoints were high-density lipoprotein cholesterol, soluble intercellular adhesion molecule-1, 11-dehydrothromboxane B<sub>2</sub>, central vascular augmentation index, and forced expiratory volume in 1 s (%predicted post-bronchodilator).</p><p><strong>Results: </strong>THS users showed significant favorable differences in all nine BoPH compared to current smokers. Results in THS users were similar to those in former smokers.</p><p><strong>Conclusion: </strong>Compared to current smokers, healthy participants who voluntarily switched from smoking to THS use for ≥2 years in the real world had favorable differences in BoPH related to oxygen delivery, genotoxicity, inflammation, oxidative stress, lipid metabolism, endothelial function, platelet activation, and cardiovascular and respiratory function. Clinicaltrials.gov Identifier: NCT05385055.</p>","PeriodicalId":8921,"journal":{"name":"Biomarkers","volume":" ","pages":"178-191"},"PeriodicalIF":2.0,"publicationDate":"2025-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143062875","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
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