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Gong B, Lababidi S, Kusko R, Bouri K, Prezek S, Thovarai V, Prasanna A, Maier EJ, Golkaram M, Sun X, Kyriakidis K, Kitajima JP, Ebrahim Sahraeian SM, Guo Y, Johanson E, Jones W, Tong W, Xu J. Towards accurate indel calling for oncopanel sequencing through an international pipeline competition at precisionFDA. Sci Rep 2024; 14:8165. [PMID: 38589653 PMCID: PMC11001604 DOI: 10.1038/s41598-024-58573-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2023] [Accepted: 04/01/2024] [Indexed: 04/10/2024] Open
Abstract
Accurately calling indels with next-generation sequencing (NGS) data is critical for clinical application. The precisionFDA team collaborated with the U.S. Food and Drug Administration's (FDA's) National Center for Toxicological Research (NCTR) and successfully completed the NCTR Indel Calling from Oncopanel Sequencing Data Challenge, to evaluate the performance of indel calling pipelines. Top performers were selected based on precision, recall, and F1-score. The performance of many other pipelines was close to the top performers, which produced a top cluster of performers. The performance was significantly higher in high confidence regions and coding regions, and significantly lower in low complexity regions. Oncopanel capture and other issues may have occurred that affected the recall rate. Indels with higher variant allele frequency (VAF) may generally be called with higher confidence. Many of the indel calling pipelines had good performance. Some of them performed generally well across all three oncopanels, while others were better for a specific oncopanel. The performance of indel calling can further be improved by restricting the calls within high confidence intervals (HCIs) and coding regions, and by excluding low complexity regions (LCR) regions. Certain VAF cut-offs could be applied according to the applications.
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Affiliation(s)
- Binsheng Gong
- Division of Bioinformatics and Biostatistics, Office of Research, National Center for Toxicological Research, Office of the Chief Scientist, Office of the Commissioner, U.S. Food and Drug Administration, Jefferson, AR, 72079, USA
| | - Samir Lababidi
- Health Informatics Staff, Office of Data, Analytics, and Research, Office of Digital Transformation, Office of the Commissioner, U.S. Food and Drug Administration, Silver Spring, MD, 20993, USA
| | - Rebecca Kusko
- Cellino Biotech, 750 Main Street, Cambridge, MA, 02143, USA
| | - Khaled Bouri
- Office of Regulatory Science and Innovation, Office of the Chief Scientist, Office of the Commissioner, U.S. Food and Drug Administration, Silver Spring, MD, 20993, USA
| | | | | | | | | | | | | | | | | | | | - Yunfei Guo
- Roche Sequencing Solutions, Santa Clara, CA, 95050, USA
| | - Elaine Johanson
- Health Informatics Staff, Office of Data, Analytics, and Research, Office of Digital Transformation, Office of the Commissioner, U.S. Food and Drug Administration, Silver Spring, MD, 20993, USA
| | - Wendell Jones
- Q squared Solutions Genomics, 2400 Elis Road, Durham, NC, 27703, USA
| | - Weida Tong
- Division of Bioinformatics and Biostatistics, Office of Research, National Center for Toxicological Research, Office of the Chief Scientist, Office of the Commissioner, U.S. Food and Drug Administration, Jefferson, AR, 72079, USA
| | - Joshua Xu
- Division of Bioinformatics and Biostatistics, Office of Research, National Center for Toxicological Research, Office of the Chief Scientist, Office of the Commissioner, U.S. Food and Drug Administration, Jefferson, AR, 72079, USA.
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Li Z, Liu Y, Guo P, Wei Y. Construction and validation of a novel angiogenesis pattern to predict prognosis and immunotherapy efficacy in colorectal cancer. Aging (Albany NY) 2023; 15:12413-12450. [PMID: 37938164 PMCID: PMC10683615 DOI: 10.18632/aging.205189] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2023] [Accepted: 10/02/2023] [Indexed: 11/09/2023]
Abstract
BACKGROUND Evidence suggests that the tumor microenvironment (TME) affects the tumor active response to immunotherapy. Tumor angiogenesis is closely related to the TME. Nonetheless, the effects of angiogenesis on the TME of colorectal cancer (CRC) remain unknown. METHODS We comprehensively assessed the angiogenesis patterns in CRC based on 36 angiogenesis-related genes (ARGs). Subsequently, we evaluated the prognostic values and therapeutic sensitivities of angiogenesis patterns using multiple methods. We then performed the machine learning algorithm and functional experiments to identify the prognostic key ARGs. Ultimately, the regulation of gut microbiota on the expression of ARGs was further investigated by using whole genome sequencing. RESULTS Two angiogenesis clusters were identified and angiogenesis cluster B was characterized by increased stromal and immunity activation with unfavorable odds of survival. Further, an ARG_score including 9 ARGs to predict recurrence-free survival (RFS) was established and its predominant predictive ability was confirmed. The low ARG_score patients were characterized by a high mutation burden, high microsatellite instability, and immune activation with better prognosis. Moreover, patients with high KLK10 expression were associated with a hot tumor immune microenvironment, poorer immune checkpoint blocking treatment, and shorter survival. The in vitro experiments also indicated that Fusobacterium nucleatum (F.n) infection significantly induced KLK10 expression in CRC. CONCLUSIONS The quantification of angiogenesis patterns could contribute to predict TME characteristics, prognosis, and individualized immunotherapy strategies. Furthermore, our findings suggest that F.n may influence CRC progression through ARGs, which could serve as a clinical biomarker and therapeutic target for F.n-infected CRC patients.
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Affiliation(s)
- Zhiyong Li
- Department of Emergency Surgery, Peking University People’s Hospital, Xicheng, Beijing 100044, China
| | - Yang Liu
- Department of Pancreatic and Gastrointestinal Surgery Division, Ningbo Second Hospital, Ningbo, Zhejiang 315010, China
| | - Peng Guo
- Department of Emergency Surgery, Peking University People’s Hospital, Xicheng, Beijing 100044, China
- Department of Emergency Medicine, Peking University People’s Hospital, Xicheng, Beijing 100044, China
- Laboratory of Surgery Oncology, Peking University People’s Hospital, Xicheng, Beijing 100044, China
| | - Yunwei Wei
- Department of Pancreatic and Gastrointestinal Surgery Division, Ningbo Second Hospital, Ningbo, Zhejiang 315010, China
- Ningbo Key Laboratory of Intestinal Microecology and Human Major Diseases, Ningbo, Zhejiang 315010, China
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Huang Q, Yan J, Jiang Q, Guo F, Mo L, Deng T. Construction of a pyroptosis-related lncRNAs signature for predicting prognosis and immunotherapy response in glioma. Medicine (Baltimore) 2023; 102:e32793. [PMID: 36820554 PMCID: PMC9907962 DOI: 10.1097/md.0000000000032793] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/12/2023] Open
Abstract
Recent studies have proved that pyroptosis-related long non-coding RNAs (PRlncRNAs) are closely linked to tumor progression, prognosis, and immunity. Here, we systematically evaluated the correlation of PRlncRNAs with glioma prognosis. This study included 3 glioma cohorts (The Cancer Genome Atlas, Chinese Glioma Genome Atlas, and Gravendeel). Through Pearson correlation analysis, PRlncRNAs were screened from these 3 cohorts. Univariate Cox regression analysis was then carried out to determine the prognostic PRlncRNAs. A pyroptosis-related lncRNAs signature (PRLS) was then built by least absolute shrinkage and selection operator and multivariate Cox analyses. We systematically evaluated the correlation of the PRLS with the prognosis, immune features, and tumor mutation burden in glioma. A total of 14 prognostic PRlncRNAs overlapped in all cohorts and were selected as candidate lncRNAs. Based on The Cancer Genome Atlas cohort, a PRLS containing 7 PRlncRNAs was built. In all cohorts, the PRLS was proved to be a good predictor of glioma prognosis, with a higher risk score related to a poorer prognosis. We observed obvious differences in the immune microenvironment, immune cell infiltration level, and immune checkpoint expression in low- and high-risk subgroups. Compared with low-risk cases, high-risk cases had lower Tumor Immune Dysfunction and Exclusion scores and greater tumor mutation burden, indicating that high-risk cases can be more sensitive to immunotherapy. A nomogram combining PRLS and clinical parameters was constructed, which showed more robust and accurate predictive power. In conclusion, the PRLS is a potentially useful indicator for predicting prognosis and response to immunotherapy in glioma. Our findings may provide a useful insight into clinically individualized treatment strategies for patients.
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Affiliation(s)
- Qianrong Huang
- Department of Neurosurgery, Guangxi Medical University Cancer Hospital, Nanning, Guangxi, PR China
| | - Jun Yan
- Department of Neurosurgery, Guangxi Medical University Cancer Hospital, Nanning, Guangxi, PR China
| | - Qian Jiang
- Department of Neurosurgery, Guangxi Medical University Cancer Hospital, Nanning, Guangxi, PR China
| | - Fangzhou Guo
- Department of Neurosurgery, Guangxi Medical University Cancer Hospital, Nanning, Guangxi, PR China
| | - Ligen Mo
- Department of Neurosurgery, Guangxi Medical University Cancer Hospital, Nanning, Guangxi, PR China
| | - Teng Deng
- Department of Neurosurgery, Guangxi Medical University Cancer Hospital, Nanning, Guangxi, PR China
- * Correspondence: Teng Deng, Department of Neurosurgery, Guangxi Medical University Cancer Hospital, No. 71 Hedi Road, Qingxiu District, Nanning, Guangxi 530021, PR China (e-mail: )
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Sun Z, Zhao Y, Wei Y, Ding X, Tan C, Wang C. Identification and validation of an anoikis-associated gene signature to predict clinical character, stemness, IDH mutation, and immune filtration in glioblastoma. Front Immunol 2022; 13:939523. [PMID: 36091049 PMCID: PMC9452727 DOI: 10.3389/fimmu.2022.939523] [Citation(s) in RCA: 34] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2022] [Accepted: 08/05/2022] [Indexed: 11/13/2022] Open
Abstract
BackgroundGlioblastoma (GBM) is the most prominent and aggressive primary brain tumor in adults. Anoikis is a specific form of programmed cell death that plays a key role in tumor invasion and metastasis. The presence of anti-anoikis factors is associated with tumor aggressiveness and drug resistance.MethodsThe non-negative matrix factorization algorithm was used for effective dimension reduction for integrated datasets. Differences in the tumor microenvironment (TME), stemness indices, and clinical characteristics between the two clusters were analyzed. Difference analysis, weighted gene coexpression network analysis (WGCNA), univariate Cox regression, and least absolute shrinkage and selection operator regression were leveraged to screen prognosis-related genes and construct a risk score model. Immunohistochemistry was performed to evaluate the expression of representative genes in clinical specimens. The relationship between the risk score and the TME, stemness, clinical traits, and immunotherapy response was assessed in GBM and pancancer.ResultsTwo definite clusters were identified on the basis of anoikis-related gene expression. Patients with GBM assigned to C1 were characterized by shortened overall survival, higher suppressive immune infiltration levels, and lower stemness indices. We further constructed a risk scoring model to quantify the regulatory patterns of anoikis-related genes. The higher risk score group was characterized by a poor prognosis, the infiltration of suppressive immune cells and a differentiated phenotype, whereas the lower risk score group exhibited the opposite effects. In addition, patients in the lower risk score group exhibited a higher frequency of isocitrate dehydrogenase (IDH) mutations and a more sensitive response to immunotherapy. Drug sensitivity analysis was performed, revealing that the higher risk group may benefit more from drugs targeting the PI3K/mTOR signaling pathway.ConclusionWe revealed potential relationships between anoikis-related genes and clinical features, TME, stemness, IDH mutation, and immunotherapy and elucidated their therapeutic value.
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Affiliation(s)
- Zhongzheng Sun
- Department of Neurosurgery, The Second Hospital of Shandong University, Jinan, China
| | - Yongquan Zhao
- Department of Neurosurgery, Dongying City District People’s Hospital, Dongying, China
| | - Yan Wei
- Department of Neurology, The Second Hospital of Shandong University, Jinan, China
| | - Xuan Ding
- Department of Neurosurgery, The Second Hospital of Shandong University, Jinan, China
| | - Chenyang Tan
- Department of Neurosurgery, The Second Hospital of Shandong University, Jinan, China
| | - Chengwei Wang
- Department of Neurosurgery, The Second Hospital of Shandong University, Jinan, China
- *Correspondence: Chengwei Wang,
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Li XY, Ma WN, Su LX, Shen Y, Zhang L, Shao Y, Wang D, Wang Z, Wen MZ, Yang XT. Association of Angiogenesis Gene Expression With Cancer Prognosis and Immunotherapy Efficacy. Front Cell Dev Biol 2022; 10:805507. [PMID: 35155426 PMCID: PMC8826089 DOI: 10.3389/fcell.2022.805507] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2021] [Accepted: 01/03/2022] [Indexed: 11/13/2022] Open
Abstract
Background: Several new blood vessels are formed during the process of tumor development. These new blood vessels provide nutrients and water for tumour growth, while spreading tumour cells to distant areas and forming new metastases in different parts of the body. The available evidence suggests that tumour angiogenesis is closely associated with the tumour microenvironment and is regulated by a variety of pro-angiogenic factors and/or angiogenic inhibitors.Methods: In the present study, a comprehensive characterization of angiogenesis genes expression was performed in a pan-cancer analysis across the 33 human cancer types. Further, genetic data from several public databases were also used in the current study. An angiogenesis score was assigned to The Cancer Genome Atlas (TCGA) pan-cancer data, with one angiogenesis score as per sample for each tumour.Results: It was found that angiogenesis genes vary across cancer types, and are associated with a number of genomic and immunological features. Further, it was noted that macrophages and iTreg infiltration were generally higher in tumours with high angiogenesis scores, whereas lymphocytes and B cells showed the opposite trend. Notably, NK cells showed significantly different correlations among cancer types. Furthermore, results of the present study showed that a high angiogenesis score was associated with poor survival and aggressive types of cancer in most of the cancer types.Conclusion: In conclusion, the current study evidently showed that the expression of angiogenesis genes is a key feature of tumour biology that has a major impact on prognosis of patient with cancers.
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Affiliation(s)
- Xin-yu Li
- Department of Interventional Therapy, Shanghai Ninth People’s Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Department of Neurosurgery, Shanghai Ninth People’s Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Wei-Ning Ma
- Department of Pediatrics, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Li-xin Su
- Department of Interventional Therapy, Shanghai Ninth People’s Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Yuchen Shen
- Department of Interventional Therapy, Shanghai Ninth People’s Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Liming Zhang
- Department of Interventional Therapy, Shanghai Ninth People’s Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Yuhao Shao
- Department of Interventional Therapy, Shanghai Ninth People’s Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Deming Wang
- Department of Interventional Therapy, Shanghai Ninth People’s Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Zhenfeng Wang
- Department of Interventional Therapy, Shanghai Ninth People’s Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Ming-Zhe Wen
- Department of Interventional Therapy, Shanghai Ninth People’s Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Xi-tao Yang
- Department of Interventional Therapy, Shanghai Ninth People’s Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- *Correspondence: Xi-tao Yang,
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BOP1 Used as a Novel Prognostic Marker and Correlated with Tumor Microenvironment in Pan-Cancer. JOURNAL OF ONCOLOGY 2021; 2021:3603030. [PMID: 34603446 PMCID: PMC8481050 DOI: 10.1155/2021/3603030] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Revised: 08/24/2021] [Accepted: 09/04/2021] [Indexed: 01/18/2023]
Abstract
Previous studies have indicated the important role of block of proliferation 1 (BOP1) in the progression of several malignant tumors; no comprehensive pan-cancer analysis of BOP1 has been performed. Here, we aim to systematically identify the expression, prognostic value, and potential immunological functions of BOP1 in 33 malignancies. We obtained the gene expression data and clinical information from multiple public databases to assess the expression level and prognostic value of BOP1 in 33 cancers. We also analyzed the relationship between BOP1 expression and DNA methylation, tumor microenvironment (TME), microsatellite instability (MSI), tumor mutational burden (TMB), and immune checkpoints. Moreover, we conducted gene set enrichment analysis (GSEA) to investigate the biological function and signal transduction pathways of BOP1 in different types of tumors. Finally, we validated the expression of BOP1 in lung cancer cell line and detected the influence of BOP1 on lung cancer cell migration and the expression of epithelial-mesenchymal transition- (EMT-) related genes. Collectively, our findings elucidated that BOP1 has the potential to be a promising molecular prognostic biomarker for predicting poor survival in various malignant tumors, as well as a cancer-promoting gene involved in tumorigenesis and tumor immunity.
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