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Wang Z, Wang H, Zhou Y, Li L, Lyu M, Wu C, He T, Tan L, Zhu Y, Guo T, Wu H, Zhang H, Sun Y. An individualized protein-based prognostic model to stratify pediatric patients with papillary thyroid carcinoma. Nat Commun 2024; 15:3560. [PMID: 38671151 PMCID: PMC11053152 DOI: 10.1038/s41467-024-47926-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2023] [Accepted: 04/12/2024] [Indexed: 04/28/2024] Open
Abstract
Pediatric papillary thyroid carcinomas (PPTCs) exhibit high inter-tumor heterogeneity and currently lack widely adopted recurrence risk stratification criteria. Hence, we propose a machine learning-based objective method to individually predict their recurrence risk. We retrospectively collect and evaluate the clinical factors and proteomes of 83 pediatric benign (PB), 85 pediatric malignant (PM) and 66 adult malignant (AM) nodules, and quantify 10,426 proteins by mass spectrometry. We find 243 and 121 significantly dysregulated proteins from PM vs. PB and PM vs. AM, respectively. Function and pathway analyses show the enhanced activation of the inflammatory and immune system in PM patients compared with the others. Nineteen proteins are selected to predict recurrence using a machine learning model with an accuracy of 88.24%. Our study generates a protein-based personalized prognostic prediction model that can stratify PPTC patients into high- or low-recurrence risk groups, providing a reference for clinical decision-making and individualized treatment.
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Affiliation(s)
- Zhihong Wang
- Department of Thyroid Surgery, The First Hospital of China Medical University, Shenyang, China
| | - He Wang
- School of Medicine, School of Life Sciences, Westlake University, Hangzhou, China
- Westlake Center for Intelligent Proteomics, Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, China
- Research Center for Industries of the Future, Westlake University, Hangzhou, China
| | - Yan Zhou
- School of Medicine, School of Life Sciences, Westlake University, Hangzhou, China
- Westlake Center for Intelligent Proteomics, Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, China
- Research Center for Industries of the Future, Westlake University, Hangzhou, China
| | - Lu Li
- School of Medicine, School of Life Sciences, Westlake University, Hangzhou, China
- Westlake Center for Intelligent Proteomics, Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, China
- Research Center for Industries of the Future, Westlake University, Hangzhou, China
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, China
| | - Mengge Lyu
- School of Medicine, School of Life Sciences, Westlake University, Hangzhou, China
- Westlake Center for Intelligent Proteomics, Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, China
- Research Center for Industries of the Future, Westlake University, Hangzhou, China
| | - Chunlong Wu
- Westlake Omics (Hangzhou) Biotechnology Co., Ltd., Hangzhou, China
| | - Tianen He
- School of Medicine, School of Life Sciences, Westlake University, Hangzhou, China
- Westlake Center for Intelligent Proteomics, Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, China
- Research Center for Industries of the Future, Westlake University, Hangzhou, China
| | - Lingling Tan
- Westlake Omics (Hangzhou) Biotechnology Co., Ltd., Hangzhou, China
| | - Yi Zhu
- School of Medicine, School of Life Sciences, Westlake University, Hangzhou, China
- Westlake Center for Intelligent Proteomics, Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, China
- Research Center for Industries of the Future, Westlake University, Hangzhou, China
| | - Tiannan Guo
- School of Medicine, School of Life Sciences, Westlake University, Hangzhou, China
- Westlake Center for Intelligent Proteomics, Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, China
- Research Center for Industries of the Future, Westlake University, Hangzhou, China
| | - Hongkun Wu
- Department of Hepatobiliary and Pancreatic Surgery, the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China.
- Zhejiang Provincial Key Laboratory of Pancreatic Disease, Hangzhou, China.
| | - Hao Zhang
- Department of Thyroid Surgery, The First Hospital of China Medical University, Shenyang, China.
| | - Yaoting Sun
- School of Medicine, School of Life Sciences, Westlake University, Hangzhou, China.
- Westlake Center for Intelligent Proteomics, Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, China.
- Research Center for Industries of the Future, Westlake University, Hangzhou, China.
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2
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Wang Z, Ji X, Zhang H, Sun W. Clinical and molecular features of progressive papillary thyroid microcarcinoma. Int J Surg 2024; 110:2313-2322. [PMID: 38241301 PMCID: PMC11019976 DOI: 10.1097/js9.0000000000001117] [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: 08/22/2023] [Accepted: 01/09/2024] [Indexed: 01/21/2024]
Abstract
In recent decades, the prevalence of thyroid cancer has risen substantially, with papillary thyroid microcarcinoma (PTMC) constituting over 50% of cases. Although most PTMCs exhibit indolent growth and a favorable prognosis, some present an increased risk of recurrence and an unfavorable prognosis due to high-risk characteristics such as lymph node metastasis, extrathyroidal extension, and distant metastasis. The early identification of clinically progressing PTMC remains elusive. In this review, the authors summarize findings from PTMC progression-related literature, highlighting that factors such as larger tumor size, cervical lymph node metastasis, extrathyroidal extension, younger age, higher preoperative serum thyroid-stimulating hormone levels, family history, and obesity positively correlate with PTMC progression. The role of multifocality in promoting PTMC progression; however, remains contentious. Furthermore, recent studies have shed light on the impact of mutations, such as BRAF and TERT mutations, on PTMC progression. Researchers have identified several mRNAs, noncoding RNAs, and proteins associated with various features of PTMC progression. Some studies propose that peripheral and tumor tissue-infiltrating immune cells could serve as biomarkers for the clinical progression of PTMC. Collectively, these clinical and molecular features offer a rationale for the early detection and the development of precision theranostic strategies of clinically progressive PTMC.
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Affiliation(s)
| | | | - Hao Zhang
- Department of Thyroid Surgery, The First Hospital of China Medical University, Shenyang, Liaoning Province, People’s Republic of China
| | - Wei Sun
- Department of Thyroid Surgery, The First Hospital of China Medical University, Shenyang, Liaoning Province, People’s Republic of China
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3
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Liu T, Ji W, Cheng X, Lv L, Yu X, Wang N, Li M, Hu T, Shi Z. Revealing a Novel Methylated Integrin Alpha-8 Related to Extracellular Matrix and Anoikis Resistance Using Proteomic Analysis in the Immune Microenvironment of Lung Adenocarcinoma. Mol Biotechnol 2024:10.1007/s12033-024-01114-9. [PMID: 38514598 DOI: 10.1007/s12033-024-01114-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2023] [Accepted: 02/07/2024] [Indexed: 03/23/2024]
Abstract
Genomic epigenetics of extracellular matrix (ECM) play an important role in lung adenocarcinoma (LUAD). Our study identified a signature of potential prognostic genes associated with ECM and constructed immune risk-related prognosis model in LUAD. We downloaded mRNAs transcriptome data, miRNAs expression data, and clinical patient information for LUAD based on The Cancer Genome Atlas. "Limma, clusterProfiler, ggplot2" R packages and GSEA were used to analyze meaningful genes and explore potential biological function. A competing endogenous RNA network was constructed to reveal the mechanism of ECM-related genes. Combined with clinical LUAD patients' characteristics, univariate and multivariate Cox regression analyses were used to build prognostic immune risk model. Next, we calculated AUC value of ROC curve, and explored survival probability of different risk groups. A total of 2966 mRNAs were differently expressed in LUAD samples and normal samples. Function enrichment analyses proved mRNAs were associated with many tumor pathways, such as cell adhesion, vascular smooth muscle contraction, and cell cycle. There were 18 mRNAs related to ECM receptor signaling pathway, and 7 mRNAs expressions were correlated with EGFR expression, but only 5mRNAs were associated with the long-term prognosis. Based on Integrin alpha-8 (ITGA8) molecule, we identified potential 3 miRNAs from several databases. The promoter of ITGA8 was higher-methylated and lower-expressed in LUAD. And lower-expressed group has poor prognosis for patients. 66 immunomodulators related to ITGA8 were performed to construct immune correlation prediction model (p < 0.05). Comprehensive analyses of ITGA8 revealed it combined focal adhesion kinase to activate PI3K/AKT signaling pathway to influence the occurrence and development of LUAD. A novel immune prognostic model about ITGA8 was constructed and verified in LUAD patients. Combined with non-coding genes and genomic epigenetics, identification of potential biomarkers provided new light on therapeutic strategy for clinical patients.
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Affiliation(s)
- Tingting Liu
- Department of Respiratory and Critical Care Medicine, The First Affiliated Hospital of Xian Jiaotong University, Xian, Shanxi, China
| | - Wen Ji
- Department of Respiratory and Critical Care Medicine, The First Affiliated Hospital of Xian Jiaotong University, Xian, Shanxi, China
| | - Xue Cheng
- Department of Respiratory and Critical Care Medicine, The First Affiliated Hospital of Xian Jiaotong University, Xian, Shanxi, China
| | - Lin Lv
- Department of Respiratory and Critical Care Medicine, The First Affiliated Hospital of Xian Jiaotong University, Xian, Shanxi, China
| | - Xiaohui Yu
- Department of Respiratory and Critical Care Medicine, The First Affiliated Hospital of Xian Jiaotong University, Xian, Shanxi, China
| | - Na Wang
- Department of Respiratory and Critical Care Medicine, The First Affiliated Hospital of Xian Jiaotong University, Xian, Shanxi, China
| | - Mengcong Li
- Department of Respiratory and Critical Care Medicine, The First Affiliated Hospital of Xian Jiaotong University, Xian, Shanxi, China
| | - Tinghua Hu
- Department of Respiratory and Critical Care Medicine, The First Affiliated Hospital of Xian Jiaotong University, Xian, Shanxi, China
| | - Zhihong Shi
- Department of Respiratory and Critical Care Medicine, The First Affiliated Hospital of Xian Jiaotong University, Xian, Shanxi, China.
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4
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Liu W, Zhu J, Wu Z, Yin Y, Wu Q, Wu Y, Zheng J, Wang C, Chen H, Qazi TJ, Wu J, Zhang Y, Liu H, Yang J, Lu D, Zhang X, Ai Z. Insight of novel biomarkers for papillary thyroid carcinoma through multiomics. Front Oncol 2023; 13:1269751. [PMID: 37795451 PMCID: PMC10546062 DOI: 10.3389/fonc.2023.1269751] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2023] [Accepted: 09/05/2023] [Indexed: 10/06/2023] Open
Abstract
Introduction The overdiagnosing of papillary thyroid carcinoma (PTC) in China necessitates the development of an evidence-based diagnosis and prognosis strategy in line with precision medicine. A landscape of PTC in Chinese cohorts is needed to provide comprehensiveness. Methods 6 paired PTC samples were employed for whole-exome sequencing, RNA sequencing, and data-dependent acquisition mass spectrum analysis. Weighted gene co-expression network analysis and protein-protein interactions networks were used to screen for hub genes. Moreover, we verified the hub genes' diagnostic and prognostic potential using online databases. Logistic regression was employed to construct a diagnostic model, and we evaluated its efficacy and specificity based on TCGA-THCA and GEO datasets. Results The basic multiomics landscape of PTC among local patients were drawn. The similarities and differences were compared between the Chinese cohort and TCGA-THCA cohorts, including the identification of PNPLA5 as a driver gene in addition to BRAF mutation. Besides, we found 572 differentially expressed genes and 79 differentially expressed proteins. Through integrative analysis, we identified 17 hub genes for prognosis and diagnosis of PTC. Four of these genes, ABR, AHNAK2, GPX1, and TPO, were used to construct a diagnostic model with high accuracy, explicitly targeting PTC (AUC=0.969/0.959 in training/test sets). Discussion Multiomics analysis of the Chinese cohort demonstrated significant distinctions compared to TCGA-THCA cohorts, highlighting the unique genetic characteristics of Chinese individuals with PTC. The novel biomarkers, holding potential for diagnosis and prognosis of PTC, were identified. Furthermore, these biomarkers provide a valuable tool for precise medicine, especially for immunotherapeutic or nanomedicine based cancer therapy.
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Affiliation(s)
- Wei Liu
- Department of Surgery (Thyroid & Breast), Zhongshan Hospital, Fudan University, Shanghai, China
| | - Junkan Zhu
- Department of Surgery (Thyroid & Breast), Zhongshan Hospital, Fudan University, Shanghai, China
- School of Basic Medical Sciences, Fudan University, Shanghai, China
| | - Zhen Wu
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai, China
| | - Yongxiang Yin
- Department of Pathology, Wuxi Maternal and Child Health Care Hospital, Womens Hospital of Jiangnan University, Jiangnan University, Jiangsu, China
| | - Qiao Wu
- Department of Surgery (Thyroid & Breast), Zhongshan Hospital, Fudan University, Shanghai, China
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai, China
| | - Yiming Wu
- Shanghai WeHealth BioMedical Technology Co., Ltd., Shanghai, China
| | - Jiaojiao Zheng
- Department of Surgery (Thyroid & Breast), Zhongshan Hospital, Fudan University, Shanghai, China
| | - Cong Wang
- Department of Surgery (Thyroid & Breast), Zhongshan Hospital, Fudan University, Shanghai, China
- Department of General Surgery, Zhongshan Hospital (Xiamen), Fudan University, Xiamen, China
- Xiamen Clinical Research Center for Cancer Therapy, Xiamen, China
| | - Hongyan Chen
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai, China
| | - Talal Jamil Qazi
- Department of Biomedical Engineering, Balochistan University of Engineering and Technology, Khuzdar, Pakistan
| | - Jun Wu
- Chinese Academy of Sciences Center for Excellence in Molecular Cell Science, Cell Bank, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai, China
| | - Yuqing Zhang
- Chinese Academy of Sciences Center for Excellence in Molecular Cell Science, Cell Bank, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai, China
| | - Houbao Liu
- Department of General Surgery, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Jingmin Yang
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai, China
- Shanghai WeHealth BioMedical Technology Co., Ltd., Shanghai, China
- National Health Commission Key Laboratory of Birth Defects and Reproductive Health, Chongqing Population and Family Planning Science and Technology Research Institute, Chongqing, China
| | - Daru Lu
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai, China
- National Health Commission Key Laboratory of Birth Defects and Reproductive Health, Chongqing Population and Family Planning Science and Technology Research Institute, Chongqing, China
| | - Xumin Zhang
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai, China
| | - Zhilong Ai
- Department of Surgery (Thyroid & Breast), Zhongshan Hospital, Fudan University, Shanghai, China
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5
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Clements CM, Henen MA, Vögeli B, Shellman YG. The Structural Dynamics, Complexity of Interactions, and Functions in Cancer of Multi-SAM Containing Proteins. Cancers (Basel) 2023; 15:3019. [PMID: 37296980 PMCID: PMC10252437 DOI: 10.3390/cancers15113019] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2023] [Revised: 05/25/2023] [Accepted: 05/30/2023] [Indexed: 06/12/2023] Open
Abstract
SAM domains are crucial mediators of diverse interactions, including those important for tumorigenesis or metastasis of cancers, and thus SAM domains can be attractive targets for developing cancer therapies. This review aims to explore the literature, especially on the recent findings of the structural dynamics, regulation, and functions of SAM domains in proteins containing more than one SAM (multi-SAM containing proteins, MSCPs). The topics here include how intrinsic disorder of some SAMs and an additional SAM domain in MSCPs increase the complexity of their interactions and oligomerization arrangements. Many similarities exist among these MSCPs, including their effects on cancer cell adhesion, migration, and metastasis. In addition, they are all involved in some types of receptor-mediated signaling and neurology-related functions or diseases, although the specific receptors and functions vary. This review also provides a simple outline of methods for studying protein domains, which may help non-structural biologists to reach out and build new collaborations to study their favorite protein domains/regions. Overall, this review aims to provide representative examples of various scenarios that may provide clues to better understand the roles of SAM domains and MSCPs in cancer in general.
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Affiliation(s)
- Christopher M. Clements
- Department of Dermatology, School of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA;
| | - Morkos A. Henen
- Department of Biochemistry and Molecular Genetics, School of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA; (M.A.H.); (B.V.)
| | - Beat Vögeli
- Department of Biochemistry and Molecular Genetics, School of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA; (M.A.H.); (B.V.)
| | - Yiqun G. Shellman
- Department of Dermatology, School of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA;
- Charles C. Gates Regenerative Medicine and Stem Cell Biology Institute, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
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6
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Mehmood A, Nawab S, Jin Y, Kaushik AC, Wei DQ. Mutational Impacts on the N and C Terminal Domains of the MUC5B Protein: A Transcriptomics and Structural Biology Study. ACS OMEGA 2023; 8:3726-3735. [PMID: 36743039 PMCID: PMC9893249 DOI: 10.1021/acsomega.2c04871] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Accepted: 11/18/2022] [Indexed: 06/18/2023]
Abstract
Cholangiocarcinoma (CCA) involves various epithelial tumors historically linked with poor prognosis because of its aggressive sickness course, delayed diagnosis, and limited efficacy of typical chemotherapy in its advanced stages. In-depth molecular profiling has exposed a varied scenery of genomic alterations as CCA's oncogenic drivers. Previous studies have mainly focused on commonly occurring TP53 and KRAS alterations, but there is limited research conducted to explore other vital genes involved in CCA. We retrieved data from The Cancer Genome Atlas (TCGA) to hunt for additional CCA targets and plotted a mutational landscape, identifying key genes and their frequently expressed variants. Next, we performed a survival analysis for all of the top genes to shortlist the ones with better significance. Among those genes, we observed that MUC5B has the most significant p-value of 0.0061. Finally, we chose two missense mutations at different positions in the vicinity of MUC5B N and C terminal domains. These mutations were further subjected to molecular dynamics (MD) simulation, which revealed noticeable impacts on the protein structure. Our study not only reveals one of the highly mutated genes with enhanced significance in CCA but also gives insights into the influence of its variants. We believe these findings are a good asset for understanding CCA from genomics and structural biology perspectives.
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Affiliation(s)
- Aamir Mehmood
- Department
of Bioinformatics and Biological Statistics, School of Life Sciences
and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, P. R. China
| | - Sadia Nawab
- State
Key Laboratory of Microbial Metabolism and School of Life Sciences
and Biotechnology, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, P. R. China
| | - Yifan Jin
- Department
of Bioinformatics and Biological Statistics, School of Life Sciences
and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, P. R. China
| | - Aman Chandra Kaushik
- Department
of Bioinformatics and Biological Statistics, School of Life Sciences
and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, P. R. China
| | - Dong-Qing Wei
- State
Key Laboratory of Microbial Metabolism, Shanghai-Islamabad-Belgrade
Joint Innovation Center on Antibacterial Resistances, Joint International
Research Laboratory of Metabolic & Developmental Sciences and
School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200030, P. R. China
- Zhongjing
Research and Industrialization Institute of Chinese Medicine, Zhongguancun Scientific Park, Meixi, Nanyang, Henan 473006, P. R. China
- Peng
Cheng Laboratory, Vanke
Cloud City Phase I Building 8, Xili Street, Nanshan
District, Shenzhen, Guangdong 518055, P. R. China
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7
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Yao JM, Zhao JY, Lv FF, Yang XB, Wang HJ. A Potential Nine-lncRNAs Signature Identification and Nomogram Diagnostic Model Establishment for Papillary Thyroid Cancer. Pathol Oncol Res 2022; 28:1610012. [PMID: 35280112 PMCID: PMC8906208 DOI: 10.3389/pore.2022.1610012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2021] [Accepted: 01/19/2022] [Indexed: 12/24/2022]
Abstract
The purpose of our current study was to establish a long non-coding RNA(lncRNA) signature and assess its prognostic and diagnostic power in papillary thyroid cancer (PTC). LncRNA expression profiles were obtained from the Cancer Genome Atlas (TCGA). The key module and hub lncRNAs related to PTC were determined by weighted gene co-expression network analysis (WGCNA) and LASSO Cox regression analyses, respectively. Functional enrichment analyses, including Gene Ontology and Kyoto Encyclopedia of Genes and Genomes (KEGG) and gene set enrichment analysis were implemented to analyze the possible biological processes and signaling pathways of hub lncRNAs. Associations between key lncRNA expressions and tumor-infiltrating immune cells were identified using the TIMER website, and proportions of immune cells in high/low risk score groups were compared. Kaplan-Meier Plotter was used to evaluate the prognostic significance of hub genes in PTC. A diagnostic model was conducted with logistic regression analysis, and its diagnostic performance was assessed by calibration/receiver operating characteristic curves and principal component analysis. A nine-lncRNAs signature (SLC12A5-AS1, LINC02028, KIZ-AS1, LINC02019, LINC01877, LINC01444, LINC01176, LINC01290, and LINC00581) was established in PTC, which has significant diagnostic and prognostic power. Functional enrichment analyses elucidated the regulatory mechanism of the nine-lncRNAs signature in the development of PTC. This signature and expressions of nine hub lncRNAs were correlated with the distributions of tumor infiltrating immune cells. A diagnostic nomogram was also established for PTC. By comparing with the published models with less than or equal to nine lncRNAs, our signature showed a preferable performace for prognosis prediction. In conclusion, our present research established an innovative nine-lncRNAs signature and a six-lncRNAs nomogram that might act as a potential indicator for PTC prognosis and diagnosis, which could be conducive to the PTC treatment.
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Affiliation(s)
- Jin-Ming Yao
- Department of Endocrinology and Metabology, The First Affiliated Hospital of Shandong First Medical University and Shandong Provincial Qianfoshan Hospital, Jinan, China.,Shandong Key Laboratory of Rheumatic Disease and Translational Medicine, Jinan, China.,Shandong Institute of Nephrology, Jinan, China
| | - Jun-Yu Zhao
- Department of Endocrinology and Metabology, The First Affiliated Hospital of Shandong First Medical University and Shandong Provincial Qianfoshan Hospital, Jinan, China.,Shandong Key Laboratory of Rheumatic Disease and Translational Medicine, Jinan, China.,Shandong Institute of Nephrology, Jinan, China
| | - Fang-Fang Lv
- Department of Endocrinology and Metabology, The 960th hospital of the PLA Joint Logistics Support Force, Jinan, China
| | - Xue-Bo Yang
- Beijing Splinger Institute of Medicine, Jinan, China
| | - Huan-Jun Wang
- Department of Endocrinology and Metabology, The First Affiliated Hospital of Shandong First Medical University and Shandong Provincial Qianfoshan Hospital, Jinan, China.,Shandong Key Laboratory of Rheumatic Disease and Translational Medicine, Jinan, China.,Shandong Institute of Nephrology, Jinan, China
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8
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Yang F, Lian M, Ma H, Feng L, Shen X, Chen J, Fang J. Identification of key genes associated with papillary thyroid microcarcinoma characteristics by integrating transcriptome sequencing and weighted gene co-expression network analysis. Gene 2022; 811:146086. [PMID: 34856364 DOI: 10.1016/j.gene.2021.146086] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2021] [Revised: 11/01/2021] [Accepted: 11/23/2021] [Indexed: 12/24/2022]
Abstract
OBJECTIVE Papillary thyroid microcarcinoma (PTMC) is the most prevalent histological type of thyroid carcinoma. Despite the overall favorable prognosis of PTMC, some cases exhibit aggressive phenotypes. The identification of robust biomarkers may improve early PTMC diagnosis. In this study, we integrated high-throughput transcriptome sequencing, bioinformatic analyses and experimental validation to identify key genes associated with the malignant characteristics of PTMC. METHODS Total RNA was extracted from 24 PTMC samples and 7 non-malignant thyroid tissue samples, followed by RNA sequencing. The differentially expressed genes (DEGs) were identified and used to construct co-expression networks by weighted gene co-expression network analysis (WGCNA). Gene ontology and Kyoto Encyclopedia of Genes and Genomes enrichment analyses were performed, and protein-protein interaction networks were constructed. Key modules and hub genes showing a strong correlation with the malignant characteristics of PTMC were identified and validated. RESULTS The green-yellow and turquoise modules generated by WGCNA were strongly associated with the malignant characteristics of PTMC. Functional enrichment analysis revealed that genes in the green-yellow module participated in cell motility and metabolism, whereas those in the turquoise module participated in several oncogenic biological processes. Nine real hub genes (FHL1, NDRG2, NEXN, SYNM, COL1A1, FN1, LAMC2, POSTN, and TGFBI) were identified and validated at the transcriptional and translational levels. Our preliminary results indicated their diagnostic potentials in PTMC. CONCLUSIONS In this study, we identified key co-expression modules and nine malignancy-related genes with potential diagnostic value in PTMC.
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Affiliation(s)
- Fan Yang
- Department of Otorhinolaryngology Head and Neck Surgery, Beijing Anzhen Hospital, Capital Medical University, Beijing, China, 100029.
| | - Meng Lian
- Department of Otorhinolaryngology Head and Neck Surgery, Beijing Tongren Hospital, Capital Medical University, Beijing, China, 100730
| | - Hongzhi Ma
- Department of Otorhinolaryngology Head and Neck Surgery, Beijing Tongren Hospital, Capital Medical University, Beijing, China, 100730
| | - Ling Feng
- Department of Otorhinolaryngology Head and Neck Surgery, Beijing Tongren Hospital, Capital Medical University, Beijing, China, 100730
| | - Xixi Shen
- Department of Otorhinolaryngology Head and Neck Surgery, Beijing Tongren Hospital, Capital Medical University, Beijing, China, 100730
| | - Jiaming Chen
- Department of Otorhinolaryngology Head and Neck Surgery, Beijing Tongren Hospital, Capital Medical University, Beijing, China, 100730
| | - Jugao Fang
- Department of Otorhinolaryngology Head and Neck Surgery, Beijing Tongren Hospital, Capital Medical University, Beijing, China, 100730; Department of Thyroid Surgery, Beijing Tongren Hospital, Capital Medical University, Beijing, China, 100730.
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9
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Liprins in oncogenic signaling and cancer cell adhesion. Oncogene 2021; 40:6406-6416. [PMID: 34654889 PMCID: PMC8602034 DOI: 10.1038/s41388-021-02048-1] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2021] [Revised: 09/21/2021] [Accepted: 09/28/2021] [Indexed: 12/30/2022]
Abstract
Liprins are a multifunctional family of scaffold proteins, identified by their involvement in several important neuronal functions related to signaling and organization of synaptic structures. More recently, the knowledge on the liprin family has expanded from neuronal functions to processes relevant to cancer progression, including cell adhesion, cell motility, cancer cell invasion, and signaling. These proteins consist of regions, which by prediction are intrinsically disordered, and may be involved in the assembly of supramolecular structures relevant for their functions. This review summarizes the current understanding of the functions of liprins in different cellular processes, with special emphasis on liprins in tumor progression. The available data indicate that liprins may be potential biomarkers for cancer progression and may have therapeutic importance.
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10
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Assessing mPTC Progression during Active Surveillance: Volume or Diameter Increase? J Clin Med 2021; 10:jcm10184068. [PMID: 34575179 PMCID: PMC8471696 DOI: 10.3390/jcm10184068] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2021] [Revised: 09/02/2021] [Accepted: 09/05/2021] [Indexed: 11/17/2022] Open
Abstract
Active surveillance (AS) is considered an alternative to immediate surgery in micropapillary thyroid carcinoma (mPTC). However, the definition of clinical mPTC progression during AS is controversial. We evaluated changes in tumor size using both tumor diameters and volume in 109 patients with mPTC followed in an AS protocol for a mean period of 31 ± 18 months. At the time of data lock, 19/109 (17.4%) mPTC reached and maintained a volume increase of ≥50%. However, only 3/19 (15.7%) showed progression, according to the diameter increase. The remaining 16 showed a slight diameter growth without reaching the original protocol progression criteria. The mean mPTC growth rate in stable cases was 0.37 mm3/month, while it was significantly greater in the mPTC, which achieved a volume change ≥50% with respect to the other. The two mPTC that developed a significant diameter increase had a growth rate of 41 and 18 mm3/month. Instead, the growth rates of the three mPTC that developed lymph node metastases were 0, 2.5 and 16 mm3/month. The ≥50% volume increase appears to be a too sensitive marker of disease progression, with a downstream higher surgery rate. The assessment of growth rate could distinguish mPTC with high and low growth rates, which would allow us to tailor the algorithm of the evaluations to a more appropriate timing.
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Huang F, Wang L, Jia H. Research trends for papillary thyroid carcinoma from 2010 to 2019: A systematic review and bibliometrics analysis. Medicine (Baltimore) 2021; 100:e26100. [PMID: 34032748 PMCID: PMC8154384 DOI: 10.1097/md.0000000000026100] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/28/2020] [Accepted: 05/06/2021] [Indexed: 01/04/2023] Open
Abstract
BACKGROUND Thyroid carcinoma comprises the fastest rising incidence of carcinomas over the past decade. Papillary thyroid carcinoma (PTC) is the most predominant type of thyroid carcinoma. This study aimed to assess the research trends in the field of PTC. METHODS Publications from January 2010 to December 2019 were retrieved from the Web of Science Core Collection database using Thompson Reuters. Searching strategies were determined according to Medical Subject Heading terms. Different kinds of bibliometrics software, such as HistCite and VOSviewer, and online bibliometrics analysis platforms were utilized to evaluate and visualize the results. RESULTS A total of 8102 publications across 93 countries were identified, with the annual number of publications showing an increasing trend. The United States, China, and South Korea showed their dominant position in PTC publication outputs, H-index, total citations, and international collaborations. Thyroid was the most productive journal. Akira Miyauchi published the most articles, and the most productive institution was Yonsei University. The hotspots keywords proliferation, invasion and metastasis, diagnoses and prognoses, therapeutic resistance, recurrence, and microcarcinomas appeared earlier and were sustained over the last 3 years. CONCLUSIONS This bibliometric study provides a comprehensive analysis delineating the scientific productivity, collaboration, and research hotspots within the PTC field, which will be very helpful when focusing on the direction of research over the next few years.
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Affiliation(s)
- Fengyan Huang
- Epidemiology and Health Statistics, School of Public Health, Cheeloo College of Medicine, Shandong University, 44 Wenhua Xi Road, Jinan, Shandong 250012
| | - Lihua Wang
- Epidemiology and Health Statistics, School of Public Health, Cheeloo College of Medicine, Shandong University, 44 Wenhua Xi Road, Jinan, Shandong 250012
| | - Hongying Jia
- Epidemiology and Health Statistics, School of Public Health, Cheeloo College of Medicine, Shandong University, 44 Wenhua Xi Road, Jinan, Shandong 250012
- The Second Hospital, Cheeloo College of Medicine, Shandong University, 247 Beiyuan Dajie, Jinan, Shandong 250033, PR China
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Jacinto JGP, Häfliger IM, Borel N, Zanolari P, Drögemüller C, Veiga IMB. Clinicopathological and Genomic Characterization of a Simmental Calf with Generalized Bovine Juvenile Angiomatosis. Animals (Basel) 2021; 11:ani11030624. [PMID: 33652974 PMCID: PMC7996833 DOI: 10.3390/ani11030624] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2021] [Revised: 02/19/2021] [Accepted: 02/22/2021] [Indexed: 11/29/2022] Open
Abstract
Simple Summary Vascular anomalies represent a heterogeneous group of rare disorders encompassing both vascular malformations and tumors, which can be congenital or arise shortly after birth. They often pose a diagnostic challenge in human and veterinary medicine, and the referring nomenclature is equivocal. Bovine juvenile angiomatosis (BJA), a clinical condition belonging to this group of disorders, encompasses vascular malformations and tumors arising in calves. Usually, such vascular anomalies are not further investigated on a molecular genetic level, mainly because of a lack of resources and diagnostic tools, as well as the low value and short lifespan of the affected animals. Here we report the clinical, pathological, immunohistochemical, and genetic features of a Simmental calf that displayed multiple cutaneous, subcutaneous, and visceral vascular hamartomas compatible with a generalized form of BJA. Whole-genome sequencing identified six coding variants, including four heterozygous variants in the PREX1, UBE3B, PCDHGA2, and ZSWIM6 genes, which occurred only in the BJA-affected calf and were absent in the global control cohort of more than 4500 cattle. Assuming a germline mutation as etiology, one of these variants might be responsible for the vascular malformations identified in this calf. Abstract Bovine juvenile angiomatosis (BJA) comprises a group of single or multiple proliferative vascular anomalies in the skin and viscera of affected calves. The purpose of this study was to characterize the clinicopathological phenotype of a 1.5-month-old Simmental calf with multiple cutaneous, subcutaneous, and visceral vascular hamartomas, which were compatible with a generalized form of BJA, and to identify genetic cause for this phenotype by whole-genome sequencing (WGS). The calf was referred to the clinics as a result of its failure to thrive and the presence of multiple cutaneous and subcutaneous nodules, some of which bled abundantly following spontaneous rupture. Gross pathology revealed similar lesions at the inner thoracic wall, diaphragm, mediastinum, pericardium, inner abdominal wall, and mesentery. Histologically, variably sized cavities lined by a single layer of plump cells and supported by a loose stroma with occasional acute hemorrhage were observed. Determined by immunochemistry, the plump cells lining the cavities displayed a strong cytoplasmic signal for PECAM-1, von Willebrand factor, and vimentin. WGS revealed six private protein-changing variants affecting different genes present in the calf and absent in more than 4500 control genomes. Assuming a spontaneous de novo mutation event, one of the identified variants found in the PREX1, UBE3B, PCDHGA2, and ZSWIM6 genes may represent a possible candidate pathogenic variant for this rare form of vascular malformation.
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Affiliation(s)
- Joana G. P. Jacinto
- Department of Veterinary Medical Sciences, University of Bologna, 40064 Ozzano Emilia (BO), Italy;
- Institute of Genetics, Vetsuisse Faculty, University of Bern, 3012 Bern, Switzerland;
| | - Irene M. Häfliger
- Institute of Genetics, Vetsuisse Faculty, University of Bern, 3012 Bern, Switzerland;
| | - Nicole Borel
- Institute of Veterinary Pathology, Vetsuisse Faculty, University of Zurich, 8057 Zurich, Switzerland;
| | - Patrik Zanolari
- Clinic for Ruminants, Vetsuisse Faculty, University of Bern, 3012 Bern, Switzerland;
| | - Cord Drögemüller
- Institute of Genetics, Vetsuisse Faculty, University of Bern, 3012 Bern, Switzerland;
- Correspondence: ; Tel.: +41-31-631-2529
| | - Inês M. B. Veiga
- Institute of Animal Pathology, Vetsuisse Faculty, University of Bern, 3012 Bern, Switzerland;
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Zeng H, Huang Y, Chen L, Li H, Ma X. Exploration and validation of the effects of robust co-expressed immune-related genes on immune infiltration patterns and prognosis in laryngeal cancer. Int Immunopharmacol 2020; 85:106622. [PMID: 32485354 DOI: 10.1016/j.intimp.2020.106622] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2020] [Revised: 05/17/2020] [Accepted: 05/18/2020] [Indexed: 02/08/2023]
Abstract
OBJECTIVES Laryngeal cancer is a common malignant tumor that originates from the larynx, yet its molecular mechanisms have not been thoroughly explored. The purpose of this study was to identify and evaluate immune-related genes in laryngeal cancer through gene co-expression networks, which may serve as biomarkers for its immunotherapy. METHODS We applied ESTIMATE to evaluate the immune-infiltration landscape of tumor microenvironment. The co-expression networks were constructed by weighted gene co expression network analysis (WGCNA) and compared with the existing human immune related genes (IRGs) to determine the co-expressed IRGs. GSVA combined with CIBERSORT and ssGSEA illustrated the correlation of hub genes and immune infiltration patterns. TIDE algorithm and Subclass mapping evaluated the function of hub genes in predicting immune function and immunotherapeutic sensitivity. The pRRophetic was employed in the sensitivity prediction of chemotherapeutic drugs. RESULTS A total of 23 co-expressed IRGs were identified and showed robust expression characteristics. These genes were significantly related to immune infiltration patterns, immune function and sensitivity prediction of immunotherapy and chemotherapeutic drugs for laryngeal cancer patients. Genetic alteration in somatic mutation level and related pathways were also revealed. CONCLUSION The 23 co-expressed IRGs may act as immunotherapeutic biomarkers and potential therapeutic targets for laryngeal cancer with certain expression robustness. The molecular mechanisms deserve further investigation, which will guide clinical treatment in the future.
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Affiliation(s)
- Hao Zeng
- Department of Biotherapy, Cancer Center, West China Hospital, Sichuan University, China; State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, and Collaborative Innovation Center for Biotherapy, Chengdu, China
| | - Yeqian Huang
- Department of Biotherapy, Cancer Center, West China Hospital, Sichuan University, China; West China School of Medicine, West China Hospital, Sichuan University, China
| | - Linyan Chen
- Department of Biotherapy, Cancer Center, West China Hospital, Sichuan University, China; State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, and Collaborative Innovation Center for Biotherapy, Chengdu, China
| | - Hui Li
- Department of Biotherapy, Cancer Center, West China Hospital, Sichuan University, China; West China School of Medicine, West China Hospital, Sichuan University, China
| | - Xuelei Ma
- Department of Biotherapy, Cancer Center, West China Hospital, Sichuan University, China; State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, and Collaborative Innovation Center for Biotherapy, Chengdu, China.
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14
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Zhou Q, Li Z, Song L, Mu D, Wang J, Tian L, Liao Y. Whole-exome mutational landscape of metastasis in patient-derived hepatocellular carcinoma cells. Genes Dis 2020; 7:380-391. [PMID: 32884992 PMCID: PMC7452411 DOI: 10.1016/j.gendis.2020.05.003] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2020] [Revised: 04/29/2020] [Accepted: 05/09/2020] [Indexed: 02/06/2023] Open
Abstract
In order to explore the genomic basis for liver cancer metastasis, whole-exome sequencing (WES) was performed on patient-derived hepatocellular carcinoma (HCC) cell lines with differential metastatic potentials and analyzed their clonal evolution relationships. An evolutionary tree based on genomic single nucleotide polymorphism (SNP) was constructed in MegaX software. The WES data showed that the average percentage of heterogeneous mutations in each HCC cell lines was 16.55% (range, 15.38%–18.17%). C: G > T: A and T: A > C: G somatic transitions were the two most frequent substitutions. In these metastatic HCC cell lines, non-silent gene mutations were found in 21.88% of known driver genes and 10 classical signaling pathways. The protein interaction network was constructed by STRING, and hub genes were found in the shared trunk mutation genes and the heterogeneous branch mutations respectively. In cBioPortal database, some of the selected hub genes were found to be associated with poor overall survival (OS) of HCC patients. Among the mutated HCC driver genes, a novel KEAP1 mutation with a homozygous frameshift truncation at the c-terminal Nrf2 binding region was detected and verified in MHCC97-H and HCC97LM3 cells. In conclusion, WES data demonstrate that HCC cell lines from tumor biopsy specimens of the same patient have obtained different metastatic potentials through repeated selection in rodents in vivo, and they do indeed have a genetic relationship at the genomic level.
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Key Words
- BTB, Broad-complex, Tramtrack, and Bric-a-brac
- CDS, coding for amino acids in protein
- CNC, cap’n’collar
- CTR, C-terminal region
- CUL3, Cullin3
- Clonal evolution
- DGR, DC domain harboring six Kelch-repeat domain
- Encyclopedia of genes and genomes (KEGG)
- FA, fatty acid
- GO, Gene Ontology
- Gene ontology (GO)
- Genome-wide association
- HCC, hepatocellular carcinoma
- Hepatocellular carcinoma
- IVR, intervening region
- KEGG, Kyoto Encyclopedia of Genes and Genomes
- Metastatic potentiality
- NTR, N-terminal region
- OS, overall survival
- SNP, single nucleotide polymorphism
- Somatic gene mutation
- WES, whole exome sequencing
- Whole exome sequencing
- bZIP, basic-region leucine zipper
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Affiliation(s)
- Qian Zhou
- Key Laboratory of Molecular Biology on Infectious Diseases, Ministry of Education, Chongqing, China.,Institute for Viral Hepatitis, Chongqing Medical University, Chongqing, China.,Department of Infectious Diseases, Second Affiliated Hospital, Chongqing Medical University, Chongqing, China
| | - Zuli Li
- Key Laboratory of Molecular Biology on Infectious Diseases, Ministry of Education, Chongqing, China.,Institute for Viral Hepatitis, Chongqing Medical University, Chongqing, China.,Department of Infectious Diseases, Second Affiliated Hospital, Chongqing Medical University, Chongqing, China
| | - Linlan Song
- Key Laboratory of Molecular Biology on Infectious Diseases, Ministry of Education, Chongqing, China.,Institute for Viral Hepatitis, Chongqing Medical University, Chongqing, China.,Department of Infectious Diseases, Second Affiliated Hospital, Chongqing Medical University, Chongqing, China
| | - Di Mu
- Key Laboratory of Molecular Biology on Infectious Diseases, Ministry of Education, Chongqing, China.,Institute for Viral Hepatitis, Chongqing Medical University, Chongqing, China.,Department of Infectious Diseases, Second Affiliated Hospital, Chongqing Medical University, Chongqing, China
| | - Jin Wang
- Key Laboratory of Molecular Biology on Infectious Diseases, Ministry of Education, Chongqing, China.,Institute for Viral Hepatitis, Chongqing Medical University, Chongqing, China.,Department of Infectious Diseases, Second Affiliated Hospital, Chongqing Medical University, Chongqing, China
| | - Li Tian
- Key Laboratory of Molecular Biology on Infectious Diseases, Ministry of Education, Chongqing, China.,Institute for Viral Hepatitis, Chongqing Medical University, Chongqing, China.,Department of Infectious Diseases, Second Affiliated Hospital, Chongqing Medical University, Chongqing, China
| | - Yong Liao
- Key Laboratory of Molecular Biology on Infectious Diseases, Ministry of Education, Chongqing, China.,Institute for Viral Hepatitis, Chongqing Medical University, Chongqing, China.,Department of Infectious Diseases, Second Affiliated Hospital, Chongqing Medical University, Chongqing, China
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15
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Song J, Yan T, Qiu W, Fan Y, Yang Z. Clinical Analysis of Risk Factors for Cervical Lymph Node Metastasis in Papillary Thyroid Microcarcinoma: A Retrospective Study of 3686 Patients. Cancer Manag Res 2020; 12:2523-2530. [PMID: 32308489 PMCID: PMC7153998 DOI: 10.2147/cmar.s250163] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2020] [Accepted: 03/24/2020] [Indexed: 12/24/2022] Open
Abstract
Purpose To investigate the risk factors for cervical lymph node metastasis (LNM) in papillary thyroid microcarcinoma (PTMC). Patients and Methods In total, 3686 patients with PTMC who underwent initial surgery in Shanghai Jiao Tong University affiliated Sixth People’s Hospital from January 2010 to December 2019 were retrospectively analyzed. Univariate and multivariate analyses were conducted to identify risk factors associated with cervical LNM. Results Male gender [odds ratio (OR) =1.420, P <0.001], age <55 years (OR =2.128, P <0.001), tumor size >6.5 mm (OR =2.112, P <0.001), lymphovascular invasion (LVI) (OR =2.110, P =0.016), multifocality (OR =1.358, P =0.022), extrathyroidal extension (ETE) (OR =1.598, P <0.001), and lateral LNM (LLNM) (OR =6.383, P <0.001) served as independent risk factors for central LNM (CLNM). Moreover, male gender (OR =1.668, P =0.001), tumor size >6.5 mm (OR =2.223, P <0.001), chronic lymphocytic thyroiditis (OR =1.402, P =0.021), LVI (OR =4.582, P <0.001), ETE (OR =1.393, P=0.023), and CLNM (OR =6.212, P <0.001) served as independent risk factors for LLNM. Furthermore, solitary PTMC with lesions in the upper third of the thyroid gland were more associated with LLNM than lesions in the other regions. Conclusion This study suggests that meticulous evaluation of risk factors associated with LNM is required in order to guide the surgical treatment of PTMC patients in clinical practice.
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Affiliation(s)
- Jianlu Song
- Center of Thyroid and Parathyroid, Department of Thyroid, Parathyroid, Breast and Hernia Surgery, Shanghai Jiao Tong University Affiliated Sixth People's Hospital, Shanghai 200233, People's Republic of China
| | - Ting Yan
- Center of Thyroid and Parathyroid, Department of Thyroid, Parathyroid, Breast and Hernia Surgery, Shanghai Jiao Tong University Affiliated Sixth People's Hospital, Shanghai 200233, People's Republic of China
| | - Wangwang Qiu
- Center of Thyroid and Parathyroid, Department of Thyroid, Parathyroid, Breast and Hernia Surgery, Shanghai Jiao Tong University Affiliated Sixth People's Hospital, Shanghai 200233, People's Republic of China
| | - Youben Fan
- Center of Thyroid and Parathyroid, Department of Thyroid, Parathyroid, Breast and Hernia Surgery, Shanghai Jiao Tong University Affiliated Sixth People's Hospital, Shanghai 200233, People's Republic of China
| | - Zhili Yang
- Center of Thyroid and Parathyroid, Department of Thyroid, Parathyroid, Breast and Hernia Surgery, Shanghai Jiao Tong University Affiliated Sixth People's Hospital, Shanghai 200233, People's Republic of China
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16
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Musolf AM, Moiz BA, Sun H, Pikielny CW, Bossé Y, Mandal D, de Andrade M, Gaba C, Yang P, Li Y, You M, Govindan R, Wilson RK, Kupert EY, Anderson MW, Schwartz AG, Pinney SM, Amos CI, Bailey-Wilson JE. Whole Exome Sequencing of Highly Aggregated Lung Cancer Families Reveals Linked Loci for Increased Cancer Risk on Chromosomes 12q, 7p, and 4q. Cancer Epidemiol Biomarkers Prev 2019; 29:434-442. [PMID: 31826912 DOI: 10.1158/1055-9965.epi-19-0887] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2019] [Revised: 10/15/2019] [Accepted: 12/04/2019] [Indexed: 12/20/2022] Open
Abstract
BACKGROUND Lung cancer kills more people than any other cancer in the United States. In addition to environmental factors, lung cancer has genetic risk factors as well, though the genetic etiology is still not well understood. We have performed whole exome sequencing on 262 individuals from 28 extended families with a family history of lung cancer. METHODS Parametric genetic linkage analysis was performed on these samples using two distinct analyses-the lung cancer only (LCO) analysis, where only patients with lung cancer were coded as affected, and the all aggregated cancers (AAC) analysis, where other cancers seen in the pedigree were coded as affected. RESULTS The AAC analysis yielded a genome-wide significant result at rs61943670 in POLR3B at 12q23.3. POLR3B has been implicated somatically in lung cancer, but this germline finding is novel and is a significant expression quantitative trait locus in lung tissue. Interesting genome-wide suggestive haplotypes were also found within individual families, particularly near SSPO at 7p36.1 in one family and a large linked haplotype spanning 4q21.3-28.3 in a different family. The 4q haplotype contains potential causal rare variants in DSPP at 4q22.1 and PTPN13 at 4q21.3. CONCLUSIONS Regions on 12q, 7p, and 4q are linked to increased cancer risk in highly aggregated lung cancer families, 12q across families and 7p and 4q within a single family. POLR3B, SSPO, DSPP, and PTPN13 are currently the best candidate genes. IMPACT Functional work on these genes is planned for future studies and if confirmed would lead to potential biomarkers for risk in cancer.
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Affiliation(s)
- Anthony M Musolf
- Computational and Statistical Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Baltimore, Maryland
| | - Bilal A Moiz
- Computational and Statistical Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Baltimore, Maryland
| | - Haiming Sun
- Computational and Statistical Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Baltimore, Maryland.,Laboratory of Medical Genetics, Harbin Medical University, Harbin, China
| | | | - Yohan Bossé
- Institut universitaire de cardiologie et de pneumologie de Québec, Department of Molecular Medicine, Laval University, Québec, Québec, Canada
| | - Diptasri Mandal
- Department of Genetics, Louisiana State University Health Sciences Center, New Orleans, Louisiana
| | | | - Colette Gaba
- Department of Medicine, University of Toledo Dana Cancer Center, Toledo, Ohio
| | | | - Yafang Li
- Baylor College of Medicine, Houston, Texas
| | - Ming You
- Medical College of Wisconsin, Milwaukee, Wisconsin
| | - Ramaswamy Govindan
- Division of Oncology, Washington University School of Medicine, St. Louis, Missouri
| | - Richard K Wilson
- Institute for Genomic Medicine, Nationwide Children's Hospital, Columbus, Ohio
| | | | | | - Ann G Schwartz
- Karmanos Cancer Institute, Wayne State University, Detroit, Michigan
| | - Susan M Pinney
- Department of Environmental Health, University of Cincinnati College of Medicine, Cincinnati, Ohio
| | | | - Joan E Bailey-Wilson
- Computational and Statistical Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Baltimore, Maryland.
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Zhang B, Wang Q, Fu C, Jiang C, Ma S. Exploration of the immune-related signature and immune infiltration analysis for breast ductal and lobular carcinoma. ANNALS OF TRANSLATIONAL MEDICINE 2019; 7:730. [PMID: 32042746 DOI: 10.21037/atm.2019.11.117] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Background In this study, we aimed to explore the tumour associated immune signature of breast cancer (BC) and conduct integrative analyses with immune infiltrates in BC. Methods We downloaded the transcriptome profiling and clinical data of BC from The Cancer Genome Atlas (TCGA) database. The list of immune-related signatures was from the Innate database. The limma package was utilized to conduct the normalization, and we screened the differential immune signatures in BC. A univariate Cox regression model and the LASSO method were used to find the hub prognostic immune genes. The TAIG risk model was calculated based on the multivariate Cox regression results, and a receiver operating characteristic (ROC) curve was generated to assess the predictive power of TAIG. Moreover, we also conducted a correlation analysis between TAIG and the clinical characteristics. Additionally, we utilized the METABRIC cohort as the validation data set. The TIMER database is a comprehensive resource for performing systematic analyses of immune infiltrates across various malignancies. We evaluated the associations of immune signatures with several immune cells based on TIMER. Furthermore, we used the CIBERSORT algorithm to determine the fractions of immune cells in each sample and compared the differential distributions of immune infiltrates between two TAIG groups using the Wilcoxon rank-sum test. Results A total of 1,178 samples were obtained from the TCGA-BRCA database, but only 1,045 breast tumour samples were matched with complete transcriptome expression data. Meanwhile, we collected a total of 1,094 BC patients from the METABRIC cohort. We found a list of 1,399 differential immune signatures associated with survival, and functional analysis revealed that these genes participated in cytokine-cytokine receptor interactions, Th1 and Th2 cell differentiation and the JAK-STAT signalling pathway. The TAIG risk model was established from the multivariate Cox analysis, and we observed that high TAIG levels correlated with poor survival outcomes based on Kaplan-Meier analysis. The Kruskal-Wallis test suggested that high TAIG levels correlated with high AJCC-TNM stages and advanced pathological stages (P<0.01). We validated the well robustness of TAIG in METABRIC cohort and 5-year AUC reached up to 0.829. Moreover, we further uncovered the associations of hub immune signatures with immune cells and calculated the immune cell fractions in specific tumour samples based on gene signature expression. Last, we used the Wilcoxon rank-sum test to compare the differential immune density in the two groups and found that several immune cells had a significantly lower infiltrating density in the high TAIG groups, including CD8+ T cells (P=0.031), memory resting CD4+ T cells (P=0.026), M0 macrophages (P=0.023), and M2 macrophages (P=0.048). Conclusions In summary, we explored the immune signature of BC and constructed a TAIG risk model to predict prognosis. Moreover, we integrated the identified immune signature with tumour-infiltrating immune cells and found adverse associations between the TAIG levels and immune cell infiltrating density.
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Affiliation(s)
- Bochuan Zhang
- College of Food Science and Technology, Shenyang Agricultural University, Shenyang 110161, China
| | - Qingfeng Wang
- Basic Medical College Liaoning University of Traditional Chinese Medicine, Shenyang 110847, China
| | - Chenghao Fu
- College of Bioscience and Biotechnology, Shenyang Agricultural University, Shenyang 110161, China
| | - Chunying Jiang
- College of Bioscience and Biotechnology, Shenyang Agricultural University, Shenyang 110161, China
| | - Shiliang Ma
- College of Food Science and Technology, Shenyang Agricultural University, Shenyang 110161, China.,College of Bioscience and Biotechnology, Shenyang Agricultural University, Shenyang 110161, China
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