Bladder cancer (BLCA) is a common and difficult-to-manage disease worldwide. Most common type of BLCA is urothelial carcinoma (UC). Fibrillin 2 (FBN2) was first discovered while studying Marfan syndrome, and its encoded products are associated with elastin fibres. To date, the role of FBN2 in BLCA remains unclear. The authors first downloaded data from The Cancer Genome Atlas (TCGA) and Gene Expression Omnibus (GEO). The patients were divided into high FBN2 expression and low FBN2 expression groups, and the survival curve, clinical characteristics, tumour microenvironment (TME), and immune cell differences were analysed between the two groups. Then, the differentially expressed genes (DEGs) were filtered, and functional enrichment for DEGs was performed. Finally, chemotherapy drug susceptibility analysis based on the high and low FBN2 groups was conducted. The authors found upregulated expression of FBN2 in BLCA and proved that FBN2 could be an independent prognostic factor for BLCA. TME analysis showed that the expression of FBN2 affects several aspects of the TME. The upregulated expression of FBN2 was associated with a high stromal score, which may lead to immunosuppression and be detrimental to immunotherapy. In addition, the authors found that NK cells resting, macrophage M0 infiltration, and other phenomena of immune cell infiltration appeared in the high expression group of FBN2. The high expression of FBN2 was related to the high sensitivity of some chemotherapy drugs. The authors systematically investigated the effects and mechanisms of FBN2 on BLCA and provided a new understanding of the role of FBN2 as a risk factor and TME influencer in BLCA.
{"title":"A comprehensive analysis of FBN2 in bladder cancer: A risk factor and the tumour microenvironment influencer","authors":"Zechao Lu, Zeguang Lu, Yongchang Lai, Haobin Zhou, Zhibiao Li, Wanyan Cai, Zeyao Xu, Hongcheng Luo, Yushu Chen, Jianyu Li, Jishen Zhang, Zhaohui He, Fucai Tang","doi":"10.1049/syb2.12067","DOIUrl":"10.1049/syb2.12067","url":null,"abstract":"<p>Bladder cancer (BLCA) is a common and difficult-to-manage disease worldwide. Most common type of BLCA is urothelial carcinoma (UC). Fibrillin 2 (FBN2) was first discovered while studying Marfan syndrome, and its encoded products are associated with elastin fibres. To date, the role of FBN2 in BLCA remains unclear. The authors first downloaded data from The Cancer Genome Atlas (TCGA) and Gene Expression Omnibus (GEO). The patients were divided into high FBN2 expression and low FBN2 expression groups, and the survival curve, clinical characteristics, tumour microenvironment (TME), and immune cell differences were analysed between the two groups. Then, the differentially expressed genes (DEGs) were filtered, and functional enrichment for DEGs was performed. Finally, chemotherapy drug susceptibility analysis based on the high and low FBN2 groups was conducted. The authors found upregulated expression of FBN2 in BLCA and proved that FBN2 could be an independent prognostic factor for BLCA. TME analysis showed that the expression of FBN2 affects several aspects of the TME. The upregulated expression of FBN2 was associated with a high stromal score, which may lead to immunosuppression and be detrimental to immunotherapy. In addition, the authors found that NK cells resting, macrophage M0 infiltration, and other phenomena of immune cell infiltration appeared in the high expression group of FBN2. The high expression of FBN2 was related to the high sensitivity of some chemotherapy drugs. The authors systematically investigated the effects and mechanisms of FBN2 on BLCA and provided a new understanding of the role of FBN2 as a risk factor and TME influencer in BLCA.</p>","PeriodicalId":50379,"journal":{"name":"IET Systems Biology","volume":null,"pages":null},"PeriodicalIF":2.3,"publicationDate":"2023-06-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://ietresearch.onlinelibrary.wiley.com/doi/epdf/10.1049/syb2.12067","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10044794","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Glioblastoma is a grade IV pernicious neoplasm occurring in the supratentorial region of brain. As its causes are largely unknown, it is essential to understand its dynamics at the molecular level. This necessitates the identification of better diagnostic and prognostic molecular candidates. Blood-based liquid biopsies are emerging as a novel tool for cancer biomarker discovery, guiding the treatment and improving its early detection based on their tumour origin. There exist previous studies focusing on the identification of tumour-based biomarkers for glioblastoma. However, these biomarkers inadequately represent the underlying pathological state and incompletely illustrate the tumour because of non-recursive nature of this approach to monitor the disease. Also, contrary to the tumour biopsies, liquid biopsies are non-invasive and can be performed at any interval during the disease span to surveil the disease. Therefore, in this study, a unique dataset of blood-based liquid biopsies obtained primarily from tumour-educated blood platelets (TEP) is utilised. This RNA-seq data from ArrayExpress is acquired comprising human cohort with 39 glioblastoma subjects and 43 healthy subjects. Canonical and machine learning approaches are applied for identification of the genomic biomarkers for glioblastoma and their crosstalks. In our study, 97 genes appeared enriched in 7 oncogenic pathways (RAF-MAPK, P53, PRC2-EZH2, YAP conserved, MEK-MAPK, ErbB2 and STK33 signalling pathways) using GSEA, out of which 17 have been identified participating actively in crosstalks. Using PCA, 42 genes are found enriched in 7 pathways (cytoplasmic ribosomal proteins, translation factors, electron transport chain, ribosome, Huntington's disease, primary immunodeficiency pathways, and interferon type I signalling pathway) harbouring tumour when altered, out of which 25 actively participate in crosstalks. All the 14 pathways foster well-known cancer hallmarks and the identified DEGs can serve as genomic biomarkers, not only for the diagnosis and prognosis of Glioblastoma but also in providing a molecular foothold for oncogenic decision making in order to fathom the disease dynamics. Moreover, SNP analysis for the identified DEGs is performed to investigate their roles in disease dynamics in an elaborated manner. These results suggest that TEPs are capable of providing disease insights just like tumour cells with an advantage of being extracted anytime during the course of disease in order to monitor it.
{"title":"Identification of genomic biomarkers and their pathway crosstalks for deciphering mechanistic links in glioblastoma","authors":"Darrak Moin Quddusi, Naim Bajcinca","doi":"10.1049/syb2.12066","DOIUrl":"10.1049/syb2.12066","url":null,"abstract":"<p>Glioblastoma is a grade IV pernicious neoplasm occurring in the supratentorial region of brain. As its causes are largely unknown, it is essential to understand its dynamics at the molecular level. This necessitates the identification of better diagnostic and prognostic molecular candidates. Blood-based liquid biopsies are emerging as a novel tool for cancer biomarker discovery, guiding the treatment and improving its early detection based on their tumour origin. There exist previous studies focusing on the identification of tumour-based biomarkers for glioblastoma. However, these biomarkers inadequately represent the underlying pathological state and incompletely illustrate the tumour because of non-recursive nature of this approach to monitor the disease. Also, contrary to the tumour biopsies, liquid biopsies are non-invasive and can be performed at any interval during the disease span to surveil the disease. Therefore, in this study, a unique dataset of blood-based liquid biopsies obtained primarily from tumour-educated blood platelets (TEP) is utilised. This RNA-seq data from ArrayExpress is acquired comprising human cohort with 39 glioblastoma subjects and 43 healthy subjects. Canonical and machine learning approaches are applied for identification of the genomic biomarkers for glioblastoma and their crosstalks. In our study, 97 genes appeared enriched in 7 oncogenic pathways (RAF-MAPK, P53, PRC2-EZH2, YAP conserved, MEK-MAPK, ErbB2 and STK33 signalling pathways) using GSEA, out of which 17 have been identified participating actively in crosstalks. Using PCA, 42 genes are found enriched in 7 pathways (cytoplasmic ribosomal proteins, translation factors, electron transport chain, ribosome, Huntington's disease, primary immunodeficiency pathways, and interferon type I signalling pathway) harbouring tumour when altered, out of which 25 actively participate in crosstalks. All the 14 pathways foster well-known cancer hallmarks and the identified DEGs can serve as genomic biomarkers, not only for the diagnosis and prognosis of Glioblastoma but also in providing a molecular foothold for oncogenic decision making in order to fathom the disease dynamics. Moreover, SNP analysis for the identified DEGs is performed to investigate their roles in disease dynamics in an elaborated manner. These results suggest that TEPs are capable of providing disease insights just like tumour cells with an advantage of being extracted anytime during the course of disease in order to monitor it.</p>","PeriodicalId":50379,"journal":{"name":"IET Systems Biology","volume":null,"pages":null},"PeriodicalIF":2.3,"publicationDate":"2023-06-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://ietresearch.onlinelibrary.wiley.com/doi/epdf/10.1049/syb2.12066","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10046688","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Several bioinformatics studies have been performed on high-throughput expression data to determine the cellular pathways and hub genes affected by Gastric cancer (GC). However, these studies differ in using a healthy tissue or normal tissue adjacent to the tumour (NAT) as calibrator tissues. This study was designed to find how using healthy or NAT tissues as calibrator tissues could affect pathway enrichment data and hub genes in GC. Two gene expression datasets with NAT tissues (GSE79973 and GSE118916) and one dataset with healthy tissues (GSE54129) were downloaded and processed by the limma package to screen the differentially expressed genes (DEGs). Kyoto Encyclopedia of Genes and Genomes (KEGG) and gene ontology (GO) enrichment analysis were performed by the Enrichr online tool. Protein-protein interaction network construction, module analysis, and hub genes selection were performed by Cytoscape software, Molecular Complex Detection plugin, and cytoHubba plugin, respectively. The gene expression profiling interactive analysis web server was used to analyse RNA sequencing expression data from The Cancer Genome Atlas Program. The Kaplan—Meier plotter was used to perform survival analysis. Our results showed that some KEGG and GO pathways were shared between studies with NAT and the study with healthy tissues. However, some terms, especially inflammation-related terms, were missed when NAT tissues were used as calibrator tissues. Also, only FN1 and COL1A1 are common hub genes between DEGs of the studies with NAT and healthy tissues. Since hub genes are usually extracted and suggested as candidate targets for GC diagnosis, prognosis, or treatment, selecting healthy or NAT tissues may affect the hub genes selection.
一些生物信息学研究已经对高通量表达数据进行了研究,以确定胃癌(GC)影响的细胞途径和中心基因。然而,这些研究在使用健康组织或肿瘤附近的正常组织(NAT)作为校准组织方面有所不同。本研究旨在发现使用健康或NAT组织作为校准组织如何影响GC的途径富集数据和中心基因。下载两个NAT组织的基因表达数据集(GSE79973和GSE118916)和一个健康组织的基因表达数据集(GSE54129),用limma软件包进行处理,筛选差异表达基因(DEGs)。京都基因与基因组百科全书(KEGG)和基因本体(GO)富集分析通过富集在线工具进行。分别使用Cytoscape软件、Molecular Complex Detection插件和cytoHubba插件进行蛋白-蛋白相互作用网络构建、模块分析和枢纽基因选择。基因表达谱交互分析web服务器用于分析来自The Cancer Genome Atlas Program的RNA测序表达数据。使用Kaplan-Meier绘图仪进行生存分析。我们的研究结果表明,在NAT研究和健康组织研究中,一些KEGG和GO通路是共享的。然而,当使用NAT组织作为校准器组织时,遗漏了一些术语,特别是与炎症相关的术语。此外,只有FN1和COL1A1是NAT研究中deg与健康组织之间的共同枢纽基因。由于中心基因通常被提取并建议作为胃癌诊断、预后或治疗的候选靶点,选择健康或NAT组织可能会影响中心基因的选择。
{"title":"Hub genes and pathways in gastric cancer: A comparison between studies that used normal tissues adjacent to the tumour and studies that used healthy tissues as calibrator","authors":"Khadijeh Sadegh, Amirhossein Ahmadi","doi":"10.1049/syb2.12065","DOIUrl":"10.1049/syb2.12065","url":null,"abstract":"<p>Several bioinformatics studies have been performed on high-throughput expression data to determine the cellular pathways and hub genes affected by Gastric cancer (GC). However, these studies differ in using a healthy tissue or normal tissue adjacent to the tumour (NAT) as calibrator tissues. This study was designed to find how using healthy or NAT tissues as calibrator tissues could affect pathway enrichment data and hub genes in GC. Two gene expression datasets with NAT tissues (GSE79973 and GSE118916) and one dataset with healthy tissues (GSE54129) were downloaded and processed by the limma package to screen the differentially expressed genes (DEGs). Kyoto Encyclopedia of Genes and Genomes (KEGG) and gene ontology (GO) enrichment analysis were performed by the Enrichr online tool. Protein-protein interaction network construction, module analysis, and hub genes selection were performed by Cytoscape software, Molecular Complex Detection plugin, and cytoHubba plugin, respectively. The gene expression profiling interactive analysis web server was used to analyse RNA sequencing expression data from The Cancer Genome Atlas Program. The Kaplan—Meier plotter was used to perform survival analysis. Our results showed that some KEGG and GO pathways were shared between studies with NAT and the study with healthy tissues. However, some terms, especially inflammation-related terms, were missed when NAT tissues were used as calibrator tissues. Also, only <i>FN1</i> and <i>COL1A1</i> are common hub genes between DEGs of the studies with NAT and healthy tissues. Since hub genes are usually extracted and suggested as candidate targets for GC diagnosis, prognosis, or treatment, selecting healthy or NAT tissues may affect the hub genes selection.</p>","PeriodicalId":50379,"journal":{"name":"IET Systems Biology","volume":null,"pages":null},"PeriodicalIF":2.3,"publicationDate":"2023-04-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://ietresearch.onlinelibrary.wiley.com/doi/epdf/10.1049/syb2.12065","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9705634","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Chromosomal instability (CIN) is closely associated to the early detection of several clinical tumours. In this study, the authors first established a novel prognostic model of melanoma using the hub genes of CIN, based on the datasets of The cancer genome atlas-skin cutaneous melanoma (TCGA-SKCM) and GSE65904 cohorts. Based on the risk scores of our model, the disease-specific survival (DSS) prognosis was worse in the high-risk group. Combining risk score, stage, age, ulceration, and clark factors, a Nomogram was generated to predict 1, 3, 5-year survival rates, which indicated a good clinical validity. Our finding also showed a correlation between high/low risk and tumour infiltration levels of ‘activated CD8 T cells’ and ‘effector memory CD8 T cells’. Moreover, the authors first performed a CIN-based tumour clustering analysis using TCGA-SKCM cases, and identified two melanoma clusters, which exhibit the distinct DSS prognosis and the tumour-infiltrating levels of CD8 T cells. Taken together, a promising CIN-related prognostic signature and clustering for melanoma cases were first established in our study.
染色体不稳定性(CIN)与几种临床肿瘤的早期发现密切相关。在本研究中,作者首先基于the cancer genome atlas-skin skin melanoma (TCGA-SKCM)和GSE65904队列的数据集,利用CIN枢纽基因建立了一种新的黑色素瘤预后模型。根据我们模型的风险评分,高危组的疾病特异性生存(DSS)预后较差。结合风险评分、分期、年龄、溃疡、clark等因素,生成Nomogram预测1、3、5年生存率,临床有效性较好。我们的发现还显示了“活化CD8 T细胞”和“效应记忆CD8 T细胞”的高/低风险与肿瘤浸润水平之间的相关性。此外,作者首先使用TCGA-SKCM病例进行了基于cin的肿瘤聚类分析,并确定了两个黑色素瘤簇,它们表现出不同的DSS预后和CD8 T细胞的肿瘤浸润水平。综上所述,我们的研究首次建立了一个有希望的与cin相关的黑色素瘤病例预后特征和聚类。
{"title":"Chromosome instability-associated prognostic signature and cluster investigation for cutaneous melanoma cases","authors":"Ning Liu, Guangjing Liu, Qian Ma, Xiaobing Li","doi":"10.1049/syb2.12064","DOIUrl":"10.1049/syb2.12064","url":null,"abstract":"<p>Chromosomal instability (CIN) is closely associated to the early detection of several clinical tumours. In this study, the authors first established a novel prognostic model of melanoma using the hub genes of CIN, based on the datasets of The cancer genome atlas-skin cutaneous melanoma (TCGA-SKCM) and GSE65904 cohorts. Based on the risk scores of our model, the disease-specific survival (DSS) prognosis was worse in the high-risk group. Combining risk score, stage, age, ulceration, and clark factors, a Nomogram was generated to predict 1, 3, 5-year survival rates, which indicated a good clinical validity. Our finding also showed a correlation between high/low risk and tumour infiltration levels of ‘activated CD8 T cells’ and ‘effector memory CD8 T cells’. Moreover, the authors first performed a CIN-based tumour clustering analysis using TCGA-SKCM cases, and identified two melanoma clusters, which exhibit the distinct DSS prognosis and the tumour-infiltrating levels of CD8 T cells. Taken together, a promising CIN-related prognostic signature and clustering for melanoma cases were first established in our study.</p>","PeriodicalId":50379,"journal":{"name":"IET Systems Biology","volume":null,"pages":null},"PeriodicalIF":2.3,"publicationDate":"2023-04-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://ftp.ncbi.nlm.nih.gov/pub/pmc/oa_pdf/cb/34/SYB2-17-121.PMC10280610.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9709911","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
The traditional blood glucose estimation method requires to take the invasive measurements several times a day. Therefore, it has a high infection risk and the users are suffered from the pain. Moreover, the long term consumable cost is high. Recently, the wearable and non-invasive blood glucose estimation approach has been proposed. However, due to the unreliability of the acquisition device, the presence of the noise and the variations of the acquisition environments, the obtained features and the reference blood glucose values are highly unreliable. Moreover, different subjects have different responses of the infrared light to the blood glucose. To address this issue, a polynomial fitting approach to smooth the obtained features or the reference blood glucose values has been proposed. In particular, the design of the coefficients in the polynomial is formulated as the various optimisation problems. First, the blood glucose values are estimated based on the individual optimisation approaches. Second, the absolute difference values between the estimated blood glucose values and the actual blood glucose values based on each optimisation approach are computed. Third, these absolute difference values for each optimisation approach are sorted in the ascending order. Fourth, for each sorted blood glucose value, the optimisation method corresponding to the minimum absolute difference value is selected. Fifth, the accumulate probability of each selected optimisation method is computed. If the accumulate probability of any selected optimisation method at a point is greater than a threshold value, then the accumulate probabilities of these three selected optimisation methods at that point are reset to zero. A range of the sorted blood glucose values are defined as that with the corresponding boundaries points being the previous reset point and this reset point. Hence, after performing the above procedures for all the sorted reference blood glucose values in the validation set, the regions of the sorted reference blood glucose values and the corresponding optimisation methods in these regions are determined. It is worth noting that the conventional lowpass denoising method was performed in the signal domain (either in the time domain or in the frequency domain), while the authors’ proposed method is performed in the feature space or the reference blood glucose space. Hence, the authors’ proposed method can further improve the reliability of the obtained feature values or the reference blood glucose values so as to improve the accuracy of the blood glucose estimation. Moreover, the individual modelling regression method has been employed here to suppress the effects of different users having different responses of the infrared light to the blood glucose values. The computer numerical simulation results show that the authors’ proposed method yields the mean absolute relative deviation (MARD) at 0.0930 and the percentage of the test data falling in the zo
{"title":"Fusion of various optimisation based feature smoothing methods for wearable and non-invasive blood glucose estimation","authors":"Yiting Wei, Bingo Wing-Kuen Ling, Danni Chen, Yuheng Dai, Qing Liu","doi":"10.1049/syb2.12063","DOIUrl":"10.1049/syb2.12063","url":null,"abstract":"<p>The traditional blood glucose estimation method requires to take the invasive measurements several times a day. Therefore, it has a high infection risk and the users are suffered from the pain. Moreover, the long term consumable cost is high. Recently, the wearable and non-invasive blood glucose estimation approach has been proposed. However, due to the unreliability of the acquisition device, the presence of the noise and the variations of the acquisition environments, the obtained features and the reference blood glucose values are highly unreliable. Moreover, different subjects have different responses of the infrared light to the blood glucose. To address this issue, a polynomial fitting approach to smooth the obtained features or the reference blood glucose values has been proposed. In particular, the design of the coefficients in the polynomial is formulated as the various optimisation problems. First, the blood glucose values are estimated based on the individual optimisation approaches. Second, the absolute difference values between the estimated blood glucose values and the actual blood glucose values based on each optimisation approach are computed. Third, these absolute difference values for each optimisation approach are sorted in the ascending order. Fourth, for each sorted blood glucose value, the optimisation method corresponding to the minimum absolute difference value is selected. Fifth, the accumulate probability of each selected optimisation method is computed. If the accumulate probability of any selected optimisation method at a point is greater than a threshold value, then the accumulate probabilities of these three selected optimisation methods at that point are reset to zero. A range of the sorted blood glucose values are defined as that with the corresponding boundaries points being the previous reset point and this reset point. Hence, after performing the above procedures for all the sorted reference blood glucose values in the validation set, the regions of the sorted reference blood glucose values and the corresponding optimisation methods in these regions are determined. It is worth noting that the conventional lowpass denoising method was performed in the signal domain (either in the time domain or in the frequency domain), while the authors’ proposed method is performed in the feature space or the reference blood glucose space. Hence, the authors’ proposed method can further improve the reliability of the obtained feature values or the reference blood glucose values so as to improve the accuracy of the blood glucose estimation. Moreover, the individual modelling regression method has been employed here to suppress the effects of different users having different responses of the infrared light to the blood glucose values. The computer numerical simulation results show that the authors’ proposed method yields the mean absolute relative deviation (MARD) at 0.0930 and the percentage of the test data falling in the zo","PeriodicalId":50379,"journal":{"name":"IET Systems Biology","volume":null,"pages":null},"PeriodicalIF":2.3,"publicationDate":"2023-03-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://ietresearch.onlinelibrary.wiley.com/doi/epdf/10.1049/syb2.12063","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9703714","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}