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Sun J, Chang J, Guo Z, Sun H, Xu J, Liu X, Sun W. Proteomics Analysis of Renal Cell Line Caki-2 with AFMID Overexpression and Potential Biomarker Discovery in Urine. J Proteome Res 2024. [PMID: 39213636 DOI: 10.1021/acs.jproteome.4c00431] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/04/2024]
Abstract
Aromatic caninurine formamase (AFMID) is an enzyme involved in the tryptophan pathway, metabolizing N-formylkynurenine to kynurenine. AFMID had been found significantly downregulated in clear cell renal cell carcinoma (ccRCC) in both tissue and urine samples. Although ccRCC is characterized by a typical Warburg-like phenotype, mitochondrial dysfunction, and elevated fat deposition, it is unknown whether AFMID plays a role in tumorigenesis and the development of ccRCC. In the present study, AFMID overexpression had inhibitory effects for ccRCC cells, decreasing the rate of cell proliferation. Quantitative proteomics showed that AFMID overexpression altered cellular signaling pathways involved in cell growth and cellular metabolism pathways, including lipid metabolism and inositol phosphate metabolism. Further urine proteomic analysis indicated that cellular function dysfunction with AFMID overexpression could be reflected in the urine. The activity of predicted upregulators DDX58, TREX1, TGFB1, SMARCA4, and TNF in ccRCC cells and urine showed opposing change trends. Potential urinary biomarkers were tentatively discovered and further validated using an independent cohort. The protein panel of APOC3, UMOD, and CILP achieved an AUC value of 0.862 for the training cohort and 0.883 for the validation cohort. The present study is of significance in terms of highlighting various aspects of pathway changes associated with AFMID enzymes, discovering potential specific biomarkers for potential patient diagnosis, and therapeutic targeting.
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Affiliation(s)
- Jiameng Sun
- Core Instrument Facility, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences, School of Basic Medicine, Peking Union Medical College, 5 Dong Dan San Tiao, Beijing 100005, China
| | - Jinchun Chang
- National Institute of Biological Sciences,7 Science Park Road ZGC Life Science Park, Beijing 102206, China
- School of Health, Quanzhou Medical College, No. 2 Anji Road, Luojiang District, Quanzhou City, Fujian Province 362011, China
| | - Zhengguang Guo
- Core Instrument Facility, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences, School of Basic Medicine, Peking Union Medical College, 5 Dong Dan San Tiao, Beijing 100005, China
| | - Haidan Sun
- Core Instrument Facility, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences, School of Basic Medicine, Peking Union Medical College, 5 Dong Dan San Tiao, Beijing 100005, China
| | - Jiyu Xu
- Core Instrument Facility, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences, School of Basic Medicine, Peking Union Medical College, 5 Dong Dan San Tiao, Beijing 100005, China
| | - Xiaoyan Liu
- Core Instrument Facility, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences, School of Basic Medicine, Peking Union Medical College, 5 Dong Dan San Tiao, Beijing 100005, China
| | - Wei Sun
- Core Instrument Facility, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences, School of Basic Medicine, Peking Union Medical College, 5 Dong Dan San Tiao, Beijing 100005, China
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Yang G, Yin Q, Wang W, Xu S, Liu H. Prognostic role of CRABP2 in lung cancer: a meta-analysis. J Cardiothorac Surg 2024; 19:366. [PMID: 38915108 PMCID: PMC11194904 DOI: 10.1186/s13019-024-02887-5] [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: 06/20/2023] [Accepted: 06/15/2024] [Indexed: 06/26/2024] Open
Abstract
BACKGROUND The prognostic value of cellular retinoic acid-binding protein 2 (CRABP2), in lung cancer patients remains to be uncertained. Therefore, our research attempted to assess the relationship between CRABP2 and survival analysis in lung cancer patients through meta-analysis. METHOD Related literature retrieved from Cochrane Library, Ovid, Embase, PubMed, the CNKI, and the Web of Science. The latest update of the search was May 1, 2023. The outcome indicators included as effective measures in the study were hazard ratio (HR), and 95% confidence interval (CI). The Stata 12.0 software was used to analyze the data. RESULTS A total of4 studies were finally enrolled in our meta-analysis. The increased plasma level of CRABP2 predicted poor OS in lung cancer patient with a combined HR of 1.14 (95% CI: 1.00-1.30), and were not associated with poor PFS with combined HR: 1.15% CI: 0.63-2.09) in lung cancer patients. CONCLUSIONS Our meta-analysis found the increased plasma level of CRABP2 was associated with poor OS independently in NSCLC patients. The plasma CRABP2 level may be an indicator of biological aggressiveness of the tumor. Our research was promising regarding the feasibility and utility of plasma CRABP2 as a novel prognostic biomarker in NSCLC, and the findings warrant further investigation.
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Affiliation(s)
- Guang Yang
- Department of Thoracic Surgery, The First Hospital of Hebei Medical University, No. 89 Donggang Street, Yuhua District, Shijiazhuang, 050031, Hebei Province, People's Republic of China
| | - Qifan Yin
- Department of Thoracic Surgery, Hebei Provincal General Hospital, No.348,West He-Ping Road, XinHua District, Shijiazhuang, 050051, Hebei Province, People's Republic of China
| | - Wenhao Wang
- Department of Thoracic Surgery, The First Hospital of Hebei Medical University, No. 89 Donggang Street, Yuhua District, Shijiazhuang, 050031, Hebei Province, People's Republic of China
| | - Siwei Xu
- Department of Thoracic Surgery, The First Hospital of Hebei Medical University, No. 89 Donggang Street, Yuhua District, Shijiazhuang, 050031, Hebei Province, People's Republic of China
| | - Huining Liu
- Department of Thoracic Surgery, The First Hospital of Hebei Medical University, No. 89 Donggang Street, Yuhua District, Shijiazhuang, 050031, Hebei Province, People's Republic of China.
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3
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Liu J, Chang X, Qian L, Chen S, Xue Z, Wu J, Luo D, Huang B, Fan J, Guo T, Nie X. Proteomics-Derived Biomarker Panel Facilitates Distinguishing Primary Lung Adenocarcinomas With Intestinal or Mucinous Differentiation From Lung Metastatic Colorectal Cancer. Mol Cell Proteomics 2024; 23:100766. [PMID: 38608841 PMCID: PMC11092395 DOI: 10.1016/j.mcpro.2024.100766] [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: 09/12/2023] [Revised: 03/07/2024] [Accepted: 04/09/2024] [Indexed: 04/14/2024] Open
Abstract
The diagnosis of primary lung adenocarcinomas with intestinal or mucinous differentiation (PAIM) remains challenging due to the overlapping histomorphological, immunohistochemical (IHC), and genetic characteristics with lung metastatic colorectal cancer (lmCRC). This study aimed to explore the protein biomarkers that could distinguish between PAIM and lmCRC. To uncover differences between the two diseases, we used tandem mass tagging-based shotgun proteomics to characterize proteomes of formalin-fixed, paraffin-embedded tumor samples of PAIM (n = 22) and lmCRC (n = 17).Then three machine learning algorithms, namely support vector machine (SVM), random forest, and the Least Absolute Shrinkage and Selection Operator, were utilized to select protein features with diagnostic significance. These candidate proteins were further validated in an independent cohort (PAIM, n = 11; lmCRC, n = 19) by IHC to confirm their diagnostic performance. In total, 105 proteins out of 7871 proteins were significantly dysregulated between PAIM and lmCRC samples and well-separated two groups by Uniform Manifold Approximation and Projection. The upregulated proteins in PAIM were involved in actin cytoskeleton organization, platelet degranulation, and regulation of leukocyte chemotaxis, while downregulated ones were involved in mitochondrial transmembrane transport, vasculature development, and stem cell proliferation. A set of ten candidate proteins (high-level expression in lmCRC: CDH17, ATP1B3, GLB1, OXNAD1, LYST, FABP1; high-level expression in PAIM: CK7 (an established marker), NARR, MLPH, S100A14) was ultimately selected to distinguish PAIM from lmCRC by machine learning algorithms. We further confirmed using IHC that the five protein biomarkers including CDH17, CK7, MLPH, FABP1 and NARR were effective biomarkers for distinguishing PAIM from lmCRC. Our study depicts PAIM-specific proteomic characteristics and demonstrates the potential utility of new protein biomarkers for the differential diagnosis of PAIM and lmCRC. These findings may contribute to improving the diagnostic accuracy and guide appropriate treatments for these patients.
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Affiliation(s)
- Jiaying Liu
- Department of Pathology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Xiaona Chang
- Department of Pathology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Liujia Qian
- Center for ProtTalks, Westlake Laboratory of Life Sciences and Biomedicine, Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, Zhejiang, China; Institute of Basic Medical Sciences, Westlake Institute for Advanced Study, Hangzhou, Zhejiang, China; Research Center for Industries of the Future, Westlake University, Hangzhou, Zhejiang, China
| | - Shuo Chen
- Department of Pathology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Zhangzhi Xue
- Center for ProtTalks, Westlake Laboratory of Life Sciences and Biomedicine, Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, Zhejiang, China; Institute of Basic Medical Sciences, Westlake Institute for Advanced Study, Hangzhou, Zhejiang, China; Research Center for Industries of the Future, Westlake University, Hangzhou, Zhejiang, China
| | - Junhua Wu
- Department of Pathology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Danju Luo
- Department of Pathology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Bo Huang
- Department of Pathology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Jun Fan
- Department of Pathology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Tiannan Guo
- Center for ProtTalks, Westlake Laboratory of Life Sciences and Biomedicine, Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, Zhejiang, China; Institute of Basic Medical Sciences, Westlake Institute for Advanced Study, Hangzhou, Zhejiang, China; Research Center for Industries of the Future, Westlake University, Hangzhou, Zhejiang, China.
| | - Xiu Nie
- Department of Pathology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China.
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Jiang F, Zhao J, Sun J, Chen W, Zhao Y, Zhou S, Yuan S, Timofeeva M, Law PJ, Larsson SC, Chen D, Houlston RS, Dunlop MG, Theodoratou E, Li X. Impact of ambient air pollution on colorectal cancer risk and survival: insights from a prospective cohort and epigenetic Mendelian randomization study. EBioMedicine 2024; 103:105126. [PMID: 38631091 PMCID: PMC11035091 DOI: 10.1016/j.ebiom.2024.105126] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2023] [Revised: 03/20/2024] [Accepted: 04/04/2024] [Indexed: 04/19/2024] Open
Abstract
BACKGROUND This study investigates the associations between air pollution and colorectal cancer (CRC) risk and survival from an epigenomic perspective. METHODS Using a newly developed Air Pollutants Exposure Score (APES), we utilized a prospective cohort study (UK Biobank) to investigate the associations of individual and combined air pollution exposures with CRC incidence and survival, followed by an up-to-date systematic review with meta-analysis to verify the associations. In epigenetic two-sample Mendelian randomization analyses, we examine the associations between genetically predicted DNA methylation related to air pollution and CRC risk. Further genetic colocalization and gene-environment interaction analyses provided different insights to disentangle pathogenic effects of air pollution via epigenetic modification. FINDINGS During a median 12.97-year follow-up, 5767 incident CRC cases among 428,632 participants free of baseline CRC and 533 deaths in 2401 patients with CRC were documented in the UK Biobank. A higher APES score was associated with an increased CRC risk (HR, 1.03, 95% CI = 1.01-1.06; P = 0.016) and poorer survival (HR, 1.13, 95% CI = 1.03-1.23; P = 0.010), particularly among participants with insufficient physical activity and ever smokers (Pinteraction > 0.05). A subsequent meta-analysis of seven observational studies, including UK Biobank data, corroborated the association between PM2.5 exposure (per 10 μg/m3 increment) and elevated CRC risk (RR,1.42, 95% CI = 1.12-1.79; P = 0.004; I2 = 90.8%). Genetically predicted methylation at PM2.5-related CpG site cg13835894 near TMBIM1/PNKD and cg16235962 near CXCR5, and NO2-related cg16947394 near TMEM110 were associated with an increased CRC risk. Gene-environment interaction analysis confirmed the epigenetic modification of aforementioned CpG sites with CRC risk and survival. INTERPRETATION Our study suggests the association between air pollution and CRC incidence and survival, underscoring the possible modifying roles of epigenomic factors. Methylation may partly mediate pathogenic effects of air pollution on CRC, with annotation to epigenetic alterations in protein-coding genes TMBIM1/PNKD, CXCR5 and TMEM110. FUNDING Xue Li is supported by the Natural Science Fund for Distinguished Young Scholars of Zhejiang Province (LR22H260001), the National Nature Science Foundation of China (No. 82204019) and Healthy Zhejiang One Million People Cohort (K-20230085). ET is supported by a Cancer Research UK Career Development Fellowship (C31250/A22804). MGD is supported by the MRC Human Genetics Unit Centre Grant (U127527198).
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Affiliation(s)
- Fangyuan Jiang
- Department of Big Data in Health Science, School of Public Health and the Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Jianhui Zhao
- Department of Big Data in Health Science, School of Public Health and the Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Jing Sun
- Department of Big Data in Health Science, School of Public Health and the Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Wenxi Chen
- Department of Big Data in Health Science, School of Public Health and the Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Yuyuan Zhao
- Department of Big Data in Health Science, School of Public Health and the Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Siyun Zhou
- Department of Big Data in Health Science, School of Public Health and the Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Shuai Yuan
- Unit of Cardiovascular and Nutritional Epidemiology, Institute of Environmental Medicine, Karolinska Institute, Stockholm, Sweden
| | - Maria Timofeeva
- Danish Institute for Advanced Study (DIAS), Epidemiology, Biostatistics and Biodemography Research Unit, Institute of Public Health, University of Southern Denmark, Odense, Denmark
| | - Philip J Law
- Division of Genetics and Epidemiology, Institute of Cancer Research, London, UK
| | - Susanna C Larsson
- Unit of Cardiovascular and Nutritional Epidemiology, Institute of Environmental Medicine, Karolinska Institute, Stockholm, Sweden; Unit of Medical Epidemiology, Department of Surgical Sciences, Uppsala, Sweden
| | - Dong Chen
- Department of Colorectal Surgery, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310003, Zhejiang Province, China
| | - Richard S Houlston
- Division of Genetics and Epidemiology, Institute of Cancer Research, London, UK
| | - Malcolm G Dunlop
- Cancer Research UK Edinburgh Centre, Medical Research Council Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK
| | - Evropi Theodoratou
- Cancer Research UK Edinburgh Centre, Medical Research Council Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK; Centre for Global Health, Usher Institute, The University of Edinburgh, Edinburgh, UK
| | - Xue Li
- Department of Big Data in Health Science, School of Public Health and the Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China.
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Chen Y, Zeng C, Zhang X, Hua Q. ALOX5AP is an Indicator for High CD8 Lymphocyte Infiltration and "Hot" Tumor Microenvironment in Osteosarcoma: A Bioinformatic Study. Biochem Genet 2023; 61:2363-2381. [PMID: 37041365 DOI: 10.1007/s10528-023-10374-0] [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: 01/08/2023] [Accepted: 03/29/2023] [Indexed: 04/13/2023]
Abstract
Little progress has been made in the treatment and prognosis of osteosarcoma in the past 40 years. Tumor microenvironment (TME) plays a critical role in the progression of osteosarcoma. This study aims to determine immune-associated prognostic biomarkers for osteosarcoma patients. With the help of analytical tools including ESTIMATE, differential gene expression, LASSO, and univariate cox and multivariate cox regression analysis, osteosarcoma gene expression data from Gene Expression Omnibus (GEO) databases were investigated. Following the establishment of a prognostic risk score model, internal and external validations using the GEO and TARGET databases were carried out. A total of 44 and 55 samples respectively in the GSE21257 and the TARGET databases were included. Our analysis found 93 differentially expressed genes (DEGs) between the high and low-ImmuneScore groups. Through univariate cox and LASSO analysis, ALOX5AP was identified as an indicator of TME in osteosarcomas. ALOX5AP was then used to construct a prognostic risk model. Internal and external verification revealed that higher expression of ALOX5AP was correlated with lower risk. Through the CIBERSORT algorithm, the level of CD8 T cells was found to negatively correlate with the risk score. This study revealed that ALOX5AP is an indicator for predicting high CD8 lymphocyte infiltration and "hot" tumor microenvironment in osteosarcomas. Thus, ALOX5AP has the potential to act as a biomarker for effective immunotherapies in osteosarcoma patients.
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Affiliation(s)
- Yongjun Chen
- Department of Spine Surgery, Zhongshan Hospital Xiamen University, Xiamen University, 201-209 Hubin South Road, Xiamen, Fujian, 361004, People's Republic of China
| | - Cheng Zeng
- Shanghai Synyi Medical Technology Co., Ltd, Shanghai, 201203, People's Republic of China
| | - Xue Zhang
- Shanghai Synyi Medical Technology Co., Ltd, Shanghai, 201203, People's Republic of China
| | - Qiang Hua
- Department of Spine Surgery, Zhongshan Hospital Xiamen University, Xiamen University, 201-209 Hubin South Road, Xiamen, Fujian, 361004, People's Republic of China.
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Chen XY, Wen XM, Zhao W, Chu MQ, Gu Y, Huang HH, Yuan Q, Xu ZJ, Qian J, Lin J. ALOX5AP is a new prognostic indicator in acute myeloid leukemia. Discov Oncol 2023; 14:210. [PMID: 37994961 PMCID: PMC10667204 DOI: 10.1007/s12672-023-00826-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/02/2023] [Accepted: 11/10/2023] [Indexed: 11/24/2023] Open
Abstract
BACKGROUND The overexpression of ALOX5AP has been observed in many types of cancer and has been identified as an oncogene. However, its role in acute myeloid leukemia (AML) has not been extensively studied. This study aimed to identify the expression and methylation patterns of ALOX5AP in bone marrow (BM) samples of AML patients, and further explore its clinical significance. METHODS Eighty-two de novo AML patients and 20 healthy donors were included in the study. Meanwhile, seven public datasets from Gene Expression Omnibus (GEO) and The Cancer Genome Atlas (TCGA) were included to confirm the alteration of ALOX5AP. Receiver operating characteristic (ROC) curve analysis was applied to determine the discriminative capacity of ALOX5AP expression to discriminate AML. The prognostic value of ALOX5AP was identified by the Kaplan-Meier method and log-rank test. It was further validated in four independent cohorts (n = 1186). Significantly different genes associated with ALOX5AP expression were subsequently compared by LinkedOmics, and Metascape database. RESULTS The level of ALOX5AP expression was significantly increased in bone marrow cells of AML patients compared with healthy donors (P < 0.05). ROC curve analysis suggested that ALOX5AP expression might be a potential biomarker to discriminate AML from controls. ALOX5AP overexpression was associated with decreased overall survival (OS) in AML according to the TCGA data (P = 0.006), which was validated by other four independent cohorts. DNA methylation levels of ALOX5AP were significantly lower in AML patients compared to normal samples (P < 0.05), as confirmed in the Diseasemeth database and the independent cohort GSE63409. ALOX5AP level was positively associated with genes with proleukemic effects such as PAX2, HOX family, SOX11, H19, and microRNAs that act as oncogenes in leukemia, such as miR125b, miR-93, miR-494, miR-193b, while anti-leukemia-related genes and tumor suppressor microRNAs such as miR-582, miR-9 family and miR-205 were negatively correlated. CONCLUSION ALOX5AP overexpression, associated with its hypomethylation, predicts poorer prognosis in AML.
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Affiliation(s)
- Xin-Yi Chen
- Laboratory Center, Affiliated People's Hospital of Jiangsu University, Zhenjiang, Jiangsu, China
- Zhenjiang Clinical Research Center of Hematology, Zhenjiang, Jiangsu, China
| | - Xiang-Mei Wen
- Laboratory Center, Affiliated People's Hospital of Jiangsu University, Zhenjiang, Jiangsu, China
- Zhenjiang Clinical Research Center of Hematology, Zhenjiang, Jiangsu, China
| | - Wei Zhao
- Zhenjiang Clinical Research Center of Hematology, Zhenjiang, Jiangsu, China
- Department of Hematology, Affiliated People's Hospital of Jiangsu University, Zhenjiang, Jiangsu, China
| | - Ming-Qiang Chu
- Zhenjiang Clinical Research Center of Hematology, Zhenjiang, Jiangsu, China
- Department of Hematology, Affiliated People's Hospital of Jiangsu University, Zhenjiang, Jiangsu, China
| | - Yu Gu
- Zhenjiang Clinical Research Center of Hematology, Zhenjiang, Jiangsu, China
- Department of Hematology, Affiliated People's Hospital of Jiangsu University, Zhenjiang, Jiangsu, China
| | - Hai-Hui Huang
- Laboratory Center, Affiliated People's Hospital of Jiangsu University, Zhenjiang, Jiangsu, China
- Zhenjiang Clinical Research Center of Hematology, Zhenjiang, Jiangsu, China
| | - Qian Yuan
- Zhenjiang Clinical Research Center of Hematology, Zhenjiang, Jiangsu, China
- Department of Hematology, Affiliated People's Hospital of Jiangsu University, Zhenjiang, Jiangsu, China
| | - Zi-Jun Xu
- Laboratory Center, Affiliated People's Hospital of Jiangsu University, Zhenjiang, Jiangsu, China.
- Zhenjiang Clinical Research Center of Hematology, Zhenjiang, Jiangsu, China.
| | - Jun Qian
- Zhenjiang Clinical Research Center of Hematology, Zhenjiang, Jiangsu, China.
- Department of Hematology, Affiliated People's Hospital of Jiangsu University, Zhenjiang, Jiangsu, China.
| | - Jiang Lin
- Laboratory Center, Affiliated People's Hospital of Jiangsu University, Zhenjiang, Jiangsu, China.
- Zhenjiang Clinical Research Center of Hematology, Zhenjiang, Jiangsu, China.
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Jiang Y, Zhang Y, Ju C, Zhang R, Li H, Chen F, Zhu Y, Shen S, Wei Y. A cross-disorder study to identify causal relationships, shared genetic variants, and genes across 21 digestive disorders. iScience 2023; 26:108238. [PMID: 37965154 PMCID: PMC10641500 DOI: 10.1016/j.isci.2023.108238] [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: 04/19/2023] [Revised: 06/26/2023] [Accepted: 10/13/2023] [Indexed: 11/16/2023] Open
Abstract
Digestive disorders are a significant contributor to the global burden of disease and seriously affect human quality of life. Research has already confirmed the presence of pleiotropic genetic loci among digestive disorders, and studies have explored shared genetic factors among pan-cancers, including various malignant digestive disorders. However, most cross-phenotype studies within the digestive tract system have been limited to a few traits, with no systematic coverage of common benign and malignant digestive disorders. Here, we analyzed data from the UK Biobank to investigate 21 digestive disorders, exploring the genetic correlations and causal relationships between diseases, as well as the common genetic factors and potential biological pathways driving these relationships. Our findings confirmed the extensive genetic correlation and causal relationship between digestive disorders, providing important insights into the genetic etiology, causality, disease prevention, and clinical treatment of diseases.
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Affiliation(s)
- Yue Jiang
- Clinical Stem Cell Center, The Affiliated Drum Tower Hospital of Nanjing University Medical School, Nanjing 210008, China
| | - Yihong Zhang
- Laboratory Medicine Center, The Second Affiliated Hospital of Nanjing Medical University, Nanjing 210011, China
| | - Can Ju
- Department of Biostatistics, School of Public Health, Center of Global Health, Nanjing Medical University, Nanjing 211166, China
| | - Ruyang Zhang
- Department of Biostatistics, School of Public Health, Center of Global Health, Nanjing Medical University, Nanjing 211166, China
| | - Hui Li
- Department of Gastroenterology, The Affiliated Hospital of Integrated Traditional Chinese and Western Medicine, Nanjing University of Chinese Medicine, Nanjing 210028, China
| | - Feng Chen
- Department of Biostatistics, School of Public Health, Center of Global Health, Nanjing Medical University, Nanjing 211166, China
| | - Yefei Zhu
- Laboratory Medicine Center, The Second Affiliated Hospital of Nanjing Medical University, Nanjing 210011, China
| | - Sipeng Shen
- Department of Biostatistics, School of Public Health, Center of Global Health, Nanjing Medical University, Nanjing 211166, China
| | - Yongyue Wei
- Peking University Center for Public Health and Epidemic Preparedness and Response, Key Laboratory of Epidemiology of Major Diseases (Peking University), Ministry of Education, Beijing 100191, China
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Lin X, Dong Y, Gu Y, Wei F, Peng J, Su Y, Wang Y, Yang C, Neira SV, Kapoor A, Tang D. Taxifolin Inhibits the Growth of Non-Small-Cell Lung Cancer via Downregulating Genes Displaying Novel and Robust Associations with Immune Evasion Factors. Cancers (Basel) 2023; 15:4818. [PMID: 37835514 PMCID: PMC10571863 DOI: 10.3390/cancers15194818] [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: 08/24/2023] [Revised: 09/25/2023] [Accepted: 09/28/2023] [Indexed: 10/15/2023] Open
Abstract
Using an LL2 cell-based syngeneic mouse LC model, taxifolin suppressed allografts along with the appearance of 578 differentially expressed genes (DEGs). These DEGs were associated with enhancement of processes related to the extracellular matrix and lymphocyte chemotaxis as well as the reduction in pathways relevant to cell proliferation. From these DEGs, we formulated 12-gene (TxflSig) and 7-gene (TxflSig1) panels; both predicted response to ICB (immune checkpoint blockade) therapy more effectively in non-small-cell lung cancer (NSCLC) than numerous well-established ICB biomarkers, including PD-L1. In both panels, the mouse counterparts of ITGAL, ITGAX, and TMEM119 genes were downregulated by taxifolin. They were strongly associated with immune suppression in LC, evidenced by their robust correlations with the major immunosuppressive cell types (MDSC, Treg, and macrophage) and multiple immune checkpoints in NSCLC and across multiple human cancer types. ITGAL, ITGAX, and IIT (ITGAL-ITGAX-TMEM119) effectively predicted NSCLC's response to ICB therapy; IIT stratified the mortality risk of NSCLC. The stromal expressions of ITGAL and ITGAX, together with tumor expression of TMEM119 in NSCLC, were demonstrated. Collectively, we report multiple novel ICB biomarkers-TxflSig, TxflSig1, IIT, ITGAL, and ITGAX-and taxifolin-derived attenuation of immunosuppressive activities in NSCLC, suggesting the inclusion of taxifolin in ICB therapies for NSCLC.
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Affiliation(s)
- Xiaozeng Lin
- Department of Surgery, McMaster University, Hamilton, ON L8S 4K1, Canada; (X.L.); (Y.D.); (Y.G.); (J.P.); (Y.S.); (S.V.N.); (A.K.)
- Urological Cancer Center for Research and Innovation (UCCRI), St Joseph’s Hospital, Hamilton, ON L8N 4A6, Canada
- The Research Institute of St Joe’s Hamilton, St Joseph’s Hospital, Hamilton, ON L8N 4A6, Canada
| | - Ying Dong
- Department of Surgery, McMaster University, Hamilton, ON L8S 4K1, Canada; (X.L.); (Y.D.); (Y.G.); (J.P.); (Y.S.); (S.V.N.); (A.K.)
- Urological Cancer Center for Research and Innovation (UCCRI), St Joseph’s Hospital, Hamilton, ON L8N 4A6, Canada
- The Research Institute of St Joe’s Hamilton, St Joseph’s Hospital, Hamilton, ON L8N 4A6, Canada
| | - Yan Gu
- Department of Surgery, McMaster University, Hamilton, ON L8S 4K1, Canada; (X.L.); (Y.D.); (Y.G.); (J.P.); (Y.S.); (S.V.N.); (A.K.)
- Urological Cancer Center for Research and Innovation (UCCRI), St Joseph’s Hospital, Hamilton, ON L8N 4A6, Canada
- The Research Institute of St Joe’s Hamilton, St Joseph’s Hospital, Hamilton, ON L8N 4A6, Canada
| | - Fengxiang Wei
- The Genetics Laboratory, Longgang District Maternity and Child Healthcare Hospital of Shenzhen City, Longgang District, Shenzhen 518174, China;
| | - Jingyi Peng
- Department of Surgery, McMaster University, Hamilton, ON L8S 4K1, Canada; (X.L.); (Y.D.); (Y.G.); (J.P.); (Y.S.); (S.V.N.); (A.K.)
- Urological Cancer Center for Research and Innovation (UCCRI), St Joseph’s Hospital, Hamilton, ON L8N 4A6, Canada
- The Research Institute of St Joe’s Hamilton, St Joseph’s Hospital, Hamilton, ON L8N 4A6, Canada
| | - Yingying Su
- Department of Surgery, McMaster University, Hamilton, ON L8S 4K1, Canada; (X.L.); (Y.D.); (Y.G.); (J.P.); (Y.S.); (S.V.N.); (A.K.)
- Urological Cancer Center for Research and Innovation (UCCRI), St Joseph’s Hospital, Hamilton, ON L8N 4A6, Canada
- The Research Institute of St Joe’s Hamilton, St Joseph’s Hospital, Hamilton, ON L8N 4A6, Canada
| | - Yanjun Wang
- Jilin Jianwei Songkou Biotechnology Co., Ltd., Changchun 510664, China;
| | - Chengzhi Yang
- Benda International Inc., Ottawa, ON K1X 0C1, Canada;
| | - Sandra Vega Neira
- Department of Surgery, McMaster University, Hamilton, ON L8S 4K1, Canada; (X.L.); (Y.D.); (Y.G.); (J.P.); (Y.S.); (S.V.N.); (A.K.)
- Urological Cancer Center for Research and Innovation (UCCRI), St Joseph’s Hospital, Hamilton, ON L8N 4A6, Canada
- The Research Institute of St Joe’s Hamilton, St Joseph’s Hospital, Hamilton, ON L8N 4A6, Canada
| | - Anil Kapoor
- Department of Surgery, McMaster University, Hamilton, ON L8S 4K1, Canada; (X.L.); (Y.D.); (Y.G.); (J.P.); (Y.S.); (S.V.N.); (A.K.)
- Urological Cancer Center for Research and Innovation (UCCRI), St Joseph’s Hospital, Hamilton, ON L8N 4A6, Canada
- The Research Institute of St Joe’s Hamilton, St Joseph’s Hospital, Hamilton, ON L8N 4A6, Canada
| | - Damu Tang
- Department of Surgery, McMaster University, Hamilton, ON L8S 4K1, Canada; (X.L.); (Y.D.); (Y.G.); (J.P.); (Y.S.); (S.V.N.); (A.K.)
- Urological Cancer Center for Research and Innovation (UCCRI), St Joseph’s Hospital, Hamilton, ON L8N 4A6, Canada
- The Research Institute of St Joe’s Hamilton, St Joseph’s Hospital, Hamilton, ON L8N 4A6, Canada
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9
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Xu N, Yu Y, Duan C, Wei J, Sun W, Jiang C, Jian B, Cao W, Jia L, Ma X. Quantitative proteomics identifies and validates urinary biomarkers of rhabdomyosarcoma in children. Clin Proteomics 2023; 20:10. [PMID: 36918772 PMCID: PMC10012572 DOI: 10.1186/s12014-023-09401-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Accepted: 03/02/2023] [Indexed: 03/16/2023] Open
Abstract
BACKGROUND Rhabdomyosarcoma (RMS) is the most common soft tissue sarcoma with poor prognosis in children. The 5-year survival rate for early RMS has improved, whereas it remains unsatisfactory for advanced patients. Urine can rapidly reflect changes in the body and identify low-abundance proteins. Early screening of tumor markers through urine in RMS allows for earlier treatment, which is associated with better outcomes. METHODS RMS patients under 18 years old, including those newly diagnosed and after surgery, were enrolled. Urine samples were collected at the time points of admission and after four cycles of chemotherapy during follow-up. Then, a two-stage workflow was established. (1) In the discovery stage, differential proteins (DPs) were initially identified in 43 RMS patients and 12 healthy controls (HCs) using a data-independent acquisition method. (2) In the verification stage, DPs were further verified as biomarkers in 54 RMS patients and 25 HCs using parallel reaction monitoring analysis. Furthermore, a receiver operating characteristic (ROC) curve was used to construct the protein panels for the diagnosis of RMS. Gene Ontology (GO) and Ingenuity Pathway Analysis (IPA) software were used to perform bioinformatics analysis. RESULTS A total of 251 proteins were significantly altered in the discovery stage, most of which were enriched in the head, neck and urogenital tract, consistent with the most common sites of RMS. The most overrepresented biological processes from GO analysis included immunity, inflammation, tumor invasion and neuronal damage. Pathways engaging the identified proteins revealed 33 common pathways, including WNT/β-catenin signaling and PI3K/AKT signaling. Finally, 39 proteins were confirmed as urinary biomarkers for RMS, and a diagnostic panel composed of 5 candidate proteins (EPS8L2, SPARC, HLA-DRB1, ACAN, and CILP) was constructed for the early screening of RMS (AUC: 0.79, 95%CI = 0.66 ~ 0.92). CONCLUSIONS These findings provide novel biomarkers in urine that are easy to translate into clinical diagnosis of RMS and illustrate the value of global and targeted urine proteomics to identify and qualify candidate biomarkers for noninvasive molecular diagnosis.
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Affiliation(s)
- Na Xu
- Medical Oncology Department, Pediatric Oncology Center, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, Beijing Key Laboratory of Pediatric Hematology Oncology, Key Laboratory of Major Diseases in Children, Ministry of Education, No. 56 Nalishi Road, Beijing, 100045, China.,Department of Pediatrics, Beijing Friendship Hospital, Capital Medical University, Beijing, China
| | - Yuncui Yu
- Clinical Research Center, Department of Pharmacy, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, Beijing, No. 56 Nanlishi Road, Beijing, 100045, China
| | - Chao Duan
- Medical Oncology Department, Pediatric Oncology Center, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, Beijing Key Laboratory of Pediatric Hematology Oncology, Key Laboratory of Major Diseases in Children, Ministry of Education, No. 56 Nalishi Road, Beijing, 100045, China
| | - Jing Wei
- Clinical Research Center, Department of Pharmacy, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, Beijing, No. 56 Nanlishi Road, Beijing, 100045, China
| | - Wei Sun
- Proteomics Research Center, Core Facility of Instruments, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Chiyi Jiang
- Medical Oncology Department, Pediatric Oncology Center, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, Beijing Key Laboratory of Pediatric Hematology Oncology, Key Laboratory of Major Diseases in Children, Ministry of Education, No. 56 Nalishi Road, Beijing, 100045, China
| | - Binglin Jian
- Medical Oncology Department, Pediatric Oncology Center, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, Beijing Key Laboratory of Pediatric Hematology Oncology, Key Laboratory of Major Diseases in Children, Ministry of Education, No. 56 Nalishi Road, Beijing, 100045, China
| | - Wang Cao
- Clinical Research Center, Department of Pharmacy, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, Beijing, No. 56 Nanlishi Road, Beijing, 100045, China
| | - Lulu Jia
- Clinical Research Center, Department of Pharmacy, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, Beijing, No. 56 Nanlishi Road, Beijing, 100045, China.
| | - Xiaoli Ma
- Medical Oncology Department, Pediatric Oncology Center, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, Beijing Key Laboratory of Pediatric Hematology Oncology, Key Laboratory of Major Diseases in Children, Ministry of Education, No. 56 Nalishi Road, Beijing, 100045, China.
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10
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Zhu X, Liu X, Qiu X, Niu Z, Dong W, Song Y. Prognostic roles of a novel basement membranes-related gene signature in lung adenocarcinoma. Front Genet 2023; 14:1100560. [PMID: 36845403 PMCID: PMC9946986 DOI: 10.3389/fgene.2023.1100560] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2022] [Accepted: 01/31/2023] [Indexed: 02/11/2023] Open
Abstract
Background: The basement membranes (BMs) are involved in tumor progression, while few comprehensive analyses to date are performed on the role of BM-related gene signatures in lung adenocarcinoma (LUAD). Thus, we aimed to develop a novel prognostic model in LUAD based on BMs-related gene profiling. Methods: The LUAD BMs-related gene profiling and corresponding clinicopathological data were obtained from the basement membrane BASE, The Cancer Genome Atlas (TCGA) and gene expression omnibus (GEO) databases. The Cox regression and least absolute shrinkage and selection operator (LASSO) methods were used to construct a BMs-based risk signature. The concordance index (C-index), receiver operating characteristic (ROC), and calibration curves were generated to evaluate the nomogram. The GSE72094 dataset was used to validate prediction of the signature. The differences in functional enrichment, immune infiltration, and drug sensitivity analyses were compared based on risk score. Results: In TCGA training cohort, 10 BMs-related genes were found, (e.g., ACAN, ADAMTS15, ADAMTS8, BCAN, etc). The signal signature based on these 10 genes was categorized into high- and low-risk groups regarding survival differences (p < 0.001). Multivariable analysis showed that the signature of combined 10 BMs-related genes was an independent prognostic predictor. Such a prognostic value of BMs-based signature in validation cohort of the GSE72094 were further verified. The GEO verification, C-index, and ROC curve showed that the nomogram had accurate prediction performance. The functional analysis suggested that BMs were mainly enriched in extracellular matrix-receptor (ECM-receptor) interaction. Moreover, the BMs-based model was correlated with immune checkpoint. Conclusion: This study identified BMs-based risk signature genes and demonstrated their ability to predict prognosis and guide personalized treatment of patients with LUAD.
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Affiliation(s)
- Xingzhuang Zhu
- Department of Oncology, Qingdao University, Qingdao, China,Department of Radiation Oncology, Yantai Yuhuangding Hospital, Affiliated Hospital of Qingdao University, Yantai, China
| | - Xiaoyan Liu
- Department of Radiation Oncology, Yantai Yuhuangding Hospital, Affiliated Hospital of Qingdao University, Yantai, China
| | - Xiaowen Qiu
- Department of Oncology, Binzhou Medical University, Yantai, China
| | - Zihao Niu
- Ministry of Education Key Laboratory of Otolaryngology Head and Neck Surgery, Department of Otolaryngology Head and Neck Surgery, Beijing Tongren Hospital, Capital Medical University, Beijing, China
| | - Wei Dong
- Department of Radiation Oncology, Yantai Yuhuangding Hospital, Affiliated Hospital of Qingdao University, Yantai, China
| | - Yipeng Song
- Department of Radiation Oncology, Yantai Yuhuangding Hospital, Affiliated Hospital of Qingdao University, Yantai, China,*Correspondence: Yipeng Song,
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11
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Zhang S, Liu D, Ning X, Zhang X, Lu Y, Zhang Y, Li A, Gao Z, Wang Z, Zhao X, Chen S, Cai Z. A Signature Constructed Based on the Integrin Family Predicts Prognosis and Correlates with the Tumor Microenvironment of Patients with Lung Adenocarcinoma. J Environ Pathol Toxicol Oncol 2023; 42:59-77. [PMID: 36749090 DOI: 10.1615/jenvironpatholtoxicoloncol.2022046232] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
As an important element in regulating the tumor microenvironment (TME), integrin plays a key role in tumor progression. This study aimed to establish prognostic signatures to predict the overall survival and identify the immune landscape of patients with lung adenocarcinoma based on integrins. The Cancer Genome Atlas-Lung Adenocarcinoma (TCGA-LUAD) and Gene Expression Omnibus datasets were used to obtain information on mRNA levels and clinical factors (GSE72094). The least absolute shrinkage and selection operator (LASSO) model was used to create a prediction model that included six integrin genes. The nomogram, risk score, and time-dependent receiver operating characteristic analysis all revealed that the signatures had a good prognostic value. The gene signatures may be linked to carcinogenesis and TME, according to a gene set enrichment analysis. The immunological and stromal scores were computed using the ESTIMATE algorithm, and the data revealed, the low-risk group had a higher score. We discovered that the B lymphocytes, plasma, CD4+ T, dendritic, and mast cells were much higher in the group with low-risk using the CiberSort. Inflammatory processes and several HLA family genes were upregulated in the low-risk group. The low-risk group with a better prognosis is more sensitive to immune checkpoint inhibitor medication, according to immunophenoscore (IPS) research. We found that the patients in the high-risk group were more susceptible to chemotherapy than other group patients, according to the prophetic algorithm. The gene signatures could accurately predict the prognosis, identify the immune status of patients with lung adenocarcinoma, and provide guidance for therapy.
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Affiliation(s)
- Shusen Zhang
- Department of Pulmonary and Critical Care Medicine, Affiliated Xing Tai People Hospital of Hebei Medical University, Xingtai, Hebei, China; The First Department of Pulmonary and Critical Care Medicine, The Second Hospital of Hebei Medical University, Shijiazhuang, Hebei, China; Hebei Province Xingtai People's Hospital Postdoctoral Workstation, Xingtai, Hebei, China; Postdoctoral Mobile Station, Hebei Medical University, Shijiazhuang, Hebei, China
| | - Dengxiang Liu
- Department of Oncology, Affiliated Xing Tai People Hospital of Hebei Medical University, Xingtai, Hebei, China
| | - Xuecong Ning
- Department of Pulmonary and Critical Care Medicine, Affiliated Xing Tai People Hospital of Hebei Medical University, Xingtai, Hebei, China
| | - Xiaochong Zhang
- Department of Oncology, Affiliated Xing Tai People Hospital of Hebei Medical University, Xingtai, Hebei, China
| | - Yuanyuan Lu
- Department of Anesthesiology, Affiliated Xing Tai People Hospital of Hebei Medical University, Xingtai, Hebei, China
| | - Yang Zhang
- Department of Pulmonary and Critical Care Medicine, Affiliated Xing Tai People Hospital of Hebei Medical University, Xingtai, Hebei, China
| | - Aimin Li
- Department of Pulmonary and Critical Care Medicine, Affiliated Xing Tai People Hospital of Hebei Medical University, Xingtai, Hebei, China
| | - Zhiguo Gao
- Department of Pulmonary and Critical Care Medicine, Affiliated Xing Tai People Hospital of Hebei Medical University, Xingtai, Hebei, China
| | - Zhihua Wang
- Department of Pulmonary and Critical Care Medicine, Affiliated Xing Tai People Hospital of Hebei Medical University, Xingtai, Hebei, China
| | - Xiaoling Zhao
- Department of Oncology, Affiliated Xing Tai People Hospital of Hebei Medical University, Xingtai, Hebei, China
| | - Shubo Chen
- Hebei Province Xingtai People's Hospital Postdoctoral Workstation, Xingtai, Hebei, China; Department of Oncology, Affiliated Xing Tai People Hospital of Hebei Medical University, Xingtai, Hebei, China
| | - Zhigang Cai
- The First Department of Pulmonary and Critical Care Medicine, The Second Hospital of Hebei Medical University, Shijiazhuang, Hebei, China; Department of Oncology, Affiliated Xing Tai People Hospital of Hebei Medical University, Xingtai, Hebei, China
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12
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Wang X, Tang X, Gu J, Sun Z, Yang S, Mu Y, Guan M, Chen K, Liu W, Ruan H, Xu J. CEACAM6 serves as a biomarker for leptomeningeal metastasis in lung adenocarcinoma. Cancer Med 2023; 12:4521-4529. [PMID: 36082960 PMCID: PMC9972070 DOI: 10.1002/cam4.5221] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2022] [Revised: 07/25/2022] [Accepted: 08/14/2022] [Indexed: 11/05/2022] Open
Abstract
BACKGROUND AND AIMS Diagnosis of leptomeningeal metastasis (LM) is challenging. In our previous study, CEACAM6 mRNA was found to be highly expressed in the circulating tumor cells of cerebrospinal fluid (CSF) from patients with lung adenocarcinoma with LM (LUAD-LM). The aim of this study was to identify whether CEACAM6 could be used as a biomarker for LUAD-LM. MATERIALS AND METHODS The level of CEACAM6 was determined by enzyme-linked immunosorbent assay (ELISA) in CSF from 40 LUAD-LM and 44 normal controls, and additional serum samples from 138 LUAD patients, including 12 LUAD-LM patients, and 30 healthy controls. Carcinoembryonic antigen (CEA), cytokeratin 19 fragment (CYFRA 21-1) and neuron-specific enolase (NSE) levels in the CSF and sera were detected by chemiluminescent immunoassay. Receiver operating characteristic curve was plotted to evaluate the diagnostic performance for LUAD-LM. RESULTS CSF CEACAM6 level was higher in LUAD-LM than that in normal controls. In serum, LUAD patients had a higher level of CAECAM6 than healthy controls, and LM patients had the highest level among them. Serum CEACAM6 had a higher AUC than CEA in differentiating LM from non-LM in LUAD patients (0.95 vs. 0.64, p < 0.001). CONCLUSION CEACAM6 may serve as a potential biomarker in diagnosing LUAD-LM.
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Affiliation(s)
- Xueying Wang
- Department of Laboratory Medicine, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Xuemei Tang
- Central Laboratory, Huashan Hospital, Fudan University, Shanghai, China
| | - Jiahui Gu
- Department of Laboratory Medicine, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Ziwei Sun
- Department of Laboratory Medicine, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Shengrui Yang
- Department of Laboratory Medicine, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Yuan Mu
- Department of Laboratory Medicine, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China.,Branch of National Clinical Research Center for Laboratory Medicine, Nanjing, China
| | - Ming Guan
- Central Laboratory, Huashan Hospital, Fudan University, Shanghai, China.,Department of Laboratory Medicine, Huashan Hospital, Fudan University, Shanghai, China
| | - Kun Chen
- Department of Laboratory Medicine, Huashan Hospital, Fudan University, Shanghai, China
| | - Wei Liu
- School of Internet of Things Engineering, Wuxi University, Wuxi, China
| | - Haoyu Ruan
- Department of Laboratory Medicine, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China.,Branch of National Clinical Research Center for Laboratory Medicine, Nanjing, China
| | - Jian Xu
- Department of Laboratory Medicine, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China.,Branch of National Clinical Research Center for Laboratory Medicine, Nanjing, China
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13
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Hartung NM, Mainka M, Pfaff R, Kuhn M, Biernacki S, Zinnert L, Schebb NH. Development of a quantitative proteomics approach for cyclooxygenases and lipoxygenases in parallel to quantitative oxylipin analysis allowing the comprehensive investigation of the arachidonic acid cascade. Anal Bioanal Chem 2023; 415:913-933. [PMID: 36683060 PMCID: PMC9883352 DOI: 10.1007/s00216-022-04489-3] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2022] [Revised: 12/07/2022] [Accepted: 12/14/2022] [Indexed: 01/24/2023]
Abstract
Oxylipins derived from the cyclooxygenase (COX) and lipoxygenase (LOX) pathways of the arachidonic acid (ARA) cascade are essential for the regulation of the inflammatory response and many other physiological functions. Comprehensive analytical methods comprised of oxylipin and protein abundance analysis are required to fully understand mechanisms leading to changes within these pathways. Here, we describe the development of a quantitative multi-omics approach combining liquid chromatography tandem mass spectrometry-based targeted oxylipin metabolomics and proteomics. As the first targeted proteomics method to cover these pathways, it enables the quantitative analysis of all human COX (COX-1 and COX-2) and relevant LOX pathway enzymes (5-LOX, 12-LOX, 15-LOX, 15-LOX-2, and FLAP) in parallel to the analysis of 239 oxylipins with our targeted oxylipin metabolomics method from a single sample. The detailed comparison between MRM3 and classical MRM-based detection in proteomics showed increased selectivity for MRM3, while MRM performed better in terms of sensitivity (LLOQ, 16-122 pM vs. 75-840 pM for the same peptides), linear range (up to 1.5-7.4 μM vs. 4-368 nM), and multiplexing capacities. Thus, the MRM mode was more favorable for this pathway analysis. With this sensitive multi-omics approach, we comprehensively characterized oxylipin and protein patterns in the human monocytic cell line THP-1 and differently polarized primary macrophages. Finally, the quantification of changes in protein and oxylipin levels induced by lipopolysaccharide stimulation and pharmaceutical treatment demonstrates its usefulness to study molecular modes of action involved in the modulation of the ARA cascade.
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Affiliation(s)
- Nicole M Hartung
- Chair of Food Chemistry, Faculty of Mathematics and Natural Sciences, University of Wuppertal, Gaußstr. 20, 42119, Wuppertal, Germany
| | - Malwina Mainka
- Chair of Food Chemistry, Faculty of Mathematics and Natural Sciences, University of Wuppertal, Gaußstr. 20, 42119, Wuppertal, Germany
| | - Rebecca Pfaff
- Chair of Food Chemistry, Faculty of Mathematics and Natural Sciences, University of Wuppertal, Gaußstr. 20, 42119, Wuppertal, Germany
| | - Michael Kuhn
- Chair of Food Chemistry, Faculty of Mathematics and Natural Sciences, University of Wuppertal, Gaußstr. 20, 42119, Wuppertal, Germany
| | - Sebastian Biernacki
- Chair of Food Chemistry, Faculty of Mathematics and Natural Sciences, University of Wuppertal, Gaußstr. 20, 42119, Wuppertal, Germany
| | - Lilli Zinnert
- Chair of Food Chemistry, Faculty of Mathematics and Natural Sciences, University of Wuppertal, Gaußstr. 20, 42119, Wuppertal, Germany
| | - Nils Helge Schebb
- Chair of Food Chemistry, Faculty of Mathematics and Natural Sciences, University of Wuppertal, Gaußstr. 20, 42119, Wuppertal, Germany.
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14
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The Tumorigenic Effect of the High Expression of Ladinin-1 in Lung Adenocarcinoma and Its Potential as a Therapeutic Target. Molecules 2023; 28:molecules28031103. [PMID: 36770773 PMCID: PMC9919345 DOI: 10.3390/molecules28031103] [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: 11/05/2022] [Revised: 01/04/2023] [Accepted: 01/10/2023] [Indexed: 01/24/2023] Open
Abstract
The oncogenic role of Ladinin-1 (LAD1), an anchoring filament protein, is largely unknown. In this study, we conducted a series of studies on the oncogenic role of LAD1 in lung adenocarcinoma (LUAD). Firstly, we analyzed the aberrant expression of LAD1 in LUAD and its correlation with patient survival, tumor immune infiltration, and the activation of cancer signaling pathways. Furthermore, the relationship between LAD1 expression and K-Ras and EGF signaling activation, tumor cell proliferation, migration, and colony formation was studied by gene knockout/knockout methods. We found that LAD1 was frequently overexpressed in LUAD, and high LAD1 expression predicts a poor prognosis. LAD1 exhibits promoter hypomethylation in LUAD, which may contribute to its mRNA upregulation. Single-sample gene set enrichment analysis (ssGSEA) showed that acquired immunity was negatively correlated with LAD1 expression, which was verified by the downregulated GO terms of "Immunoglobulin receptor binding" and "Immunoglobulin complex circulating" in the LAD1 high-expression group through Gene Set Variation Analysis (GSVA). Notably, the Ras-dependent signature was the most activated signaling in the LAD1 high-expression group, and the phosphorylation of downstream effectors, such as ERK and c-jun, was strongly inhibited by LAD1 deficiency. Moreover, we demonstrated that LAD1 depletion significantly inhibited the proliferation, migration, and cell-cycle progression of LUAD cells and promoted sensitivity to Gefitinib, K-Ras inhibitor, and paclitaxel treatments. We also confirmed that LAD1 deficiency remarkably retarded tumor growth in the xenograft model. Conclusively, LAD1 is a critical prognostic biomarker for LUAD and has potential as an intervention target.
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15
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Ni L, Li P, Li M, Huang S, Dang N. SERPINB8 and furin regulate ITGAX expression and affect the proliferation and invasion of melanoma cells. Exp Dermatol 2023; 32:24-29. [PMID: 36134483 DOI: 10.1111/exd.14677] [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: 04/07/2022] [Revised: 09/14/2022] [Accepted: 09/18/2022] [Indexed: 01/12/2023]
Abstract
In the past 10 years, the systemic treatment of advanced melanoma has undergone tremendous changes through the development of targeted therapy. However, there is still a long way to go. This study aims to characterize the function and interaction of ITGAX, SERPINB8 and furin in BRAF V600E mutant melanoma. Differentially expressed genes related to BRAF V600E mutation and BRAFi treatment were obtained by analysing GSE141484 and GSE22838. two kinds of BRAFi (Vemurafenib, 10 μM; Dabrafenib, 1 μM) were used to treat A375 and 1205Lu cells, respectively. The expression of ITGAX, SERPINB8 and Furin in A375 and 1205Lu cells was down-regulated by specific siRNAs, and cell proliferation, clone formation and invasion were detected by CCK-8, colony formation and transwell assays. The physical binding of furin and SERPINB8 was detected by immunoprecipitation. BRAFi treatment down-regulated the ITGAX and SERPINB8 expression and did not change furin expression. Knockdown of ITGAX and SERPINB8 both inhibited the proliferation and invasion of A375 and 1205Lu cells. Knocking down SERPINB8 down-regulated the expression of ITGAX. Furin knockdown and inhibitors all up-regulated the protein level of ITGAX. SERPINB8 can physically bind to furin. In summary, SERPINB8 and furin regulate the expression of ITGAX in melanoma cells, and ITGAX significantly promotes the proliferation and invasion of melanoma cells.
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Affiliation(s)
- Li Ni
- Department of Dermatology, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, Shandong, China
| | - Pin Li
- Science and Technology Innovation Center, Shandong First Medical University & Shandong Academy of Medical Sciences, Jinan, Shandong, China
| | - Mingming Li
- Department of Dermatology, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, Shandong, China
| | - Shuhong Huang
- Science and Technology Innovation Center, Shandong First Medical University & Shandong Academy of Medical Sciences, Jinan, Shandong, China
- Institute of Basic Medicine, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, Shandong, China
| | - Ningning Dang
- Department of Dermatology, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, Shandong, China
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16
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Chang CY, Huang YC, Chiang HH, Wu YY, Wu KL, Chang YY, Liu LX, Tsai YM, Hsu YL. Ladinin 1 Shortens Survival via Promoting Proliferation and Enhancing Invasiveness in Lung Adenocarcinoma. Int J Mol Sci 2022; 24:431. [PMID: 36613882 PMCID: PMC9820746 DOI: 10.3390/ijms24010431] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2022] [Revised: 12/13/2022] [Accepted: 12/13/2022] [Indexed: 12/29/2022] Open
Abstract
Lung cancer is one of the deadliest cancers worldwide, including in Taiwan. The poor prognosis of the advanced lung cancer lies in delayed diagnosis and non-druggable targets. It is worth paying more attention to these ongoing issues. Public databases and an in-house cohort were used for validation. The KM plotter was utilized to discover the clinical significance. GSEA and GSVA were adopted for a functional pathway survey. Molecular biological methods, including proliferation, migration, and the EMT methods, were used for verification. Based on public databases, the increased expression of Ladinin 1 (LAD1) was presented in tumor and metastatic sites. Furthermore, an in-house cohort revealed a higher intensity of LAD1 in tumor rather than in normal parts. The greater the expression of LAD1 was, the shorter the duration of lung adenocarcinoma (LUAD) patient survival. Moreover, the association of B3GNT3 with LAD1 affected the survival of LUAD patients. Functional analyses using GSEA and GSVA revealed the associations with survival, migration, invasion, and EMT. Biologic functions supported the roles of LAD1 in proliferation via the cell cycle and migration in EMT. This study reveals that LAD1 plays a major role in regulating proliferation and migration in lung cancer and impacts survival in LUAD. It is worth investing in further studies and in the development of drugs targeting LAD1.
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Affiliation(s)
- Chao-Yuan Chang
- Graduate Institute of Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung 807, Taiwan
- Department of Anatomy, Kaohsiung Medical University, Kaohsiung 807, Taiwan
| | - Yung-Chi Huang
- Graduate Institute of Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung 807, Taiwan
- Drug Development and Value Creation Research Center, Kaohsiung Medical University, Kaohsiung 807, Taiwan
| | - Hung-Hsing Chiang
- Division of Thoracic Surgery, Department of Surgery, Kaohsiung Medical University Hospital, Kaohsiung Medical University, Kaohsiung 807, Taiwan
| | - Yu-Yuan Wu
- School of Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung 807, Taiwan
| | - Kuan-Li Wu
- Graduate Institute of Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung 807, Taiwan
- Drug Development and Value Creation Research Center, Kaohsiung Medical University, Kaohsiung 807, Taiwan
- Division of Pulmonary and Critical Care Medicine, Kaohsiung Medical University Hospital, Kaohsiung Medical University, Kaohsiung 807, Taiwan
| | - Yung-Yun Chang
- Division of Pulmonary and Critical Care Medicine, Kaohsiung Medical University Hospital, Kaohsiung Medical University, Kaohsiung 807, Taiwan
- Division of General Medicine, Kaohsiung Medical University Hospital, Kaohsiung Medical University, Kaohsiung 807, Taiwan
| | - Lian-Xiu Liu
- Graduate Institute of Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung 807, Taiwan
| | - Ying-Ming Tsai
- Graduate Institute of Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung 807, Taiwan
- Drug Development and Value Creation Research Center, Kaohsiung Medical University, Kaohsiung 807, Taiwan
- Division of Pulmonary and Critical Care Medicine, Kaohsiung Medical University Hospital, Kaohsiung Medical University, Kaohsiung 807, Taiwan
| | - Ya-Ling Hsu
- Graduate Institute of Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung 807, Taiwan
- Drug Development and Value Creation Research Center, Kaohsiung Medical University, Kaohsiung 807, Taiwan
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17
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Duan L, Shan W, Bo G, Lu G, Guo L. Qualitative (and Quantitative) Values of the Lung-RADS and Computed Tomography in Diagnosing Solitary Pulmonary Nodules. Diagnostics (Basel) 2022; 12:diagnostics12112699. [PMID: 36359542 PMCID: PMC9689942 DOI: 10.3390/diagnostics12112699] [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: 10/06/2022] [Revised: 10/30/2022] [Accepted: 10/31/2022] [Indexed: 11/09/2022] Open
Abstract
Background: Lung-RADS classification and CT signs can both help in the differential diagnosis of SPNs. The purpose of this study was to investigate the diagnostic value of these two methods and the combination of the two methods for solitary pulmonary nodules (SPNs). Methods: A total of 296 cases of SPNs were retrospectively analyzed. All the SPNs were classified according to the Lung-RADS grading version 1.1. The scores of each lesion were calculated according to their CT signs. Imaging features, such as the size and margin of the lesions, pleural traction, spiculation, lobulation, bronchial cutoff, air bronchogram, vacuoles, tumor vasculature, and cavity signs, were analyzed. The imaging results were compared with the pathology examination findings. Receiver operating characteristic (ROC) curves were applied to compare the values of the different methods in differentially diagnosing benign and malignant SPNs. Results: The sensitivity, specificity, and accuracy of Lung-RADS grading for diagnosing SPNs were 34.0%, 94.4%, and 47.6%, respectively. The area under the ROC curve (AUC) was 0.600 (p < 0.001). The sensitivity, specificity, and accuracy of the CT sign scores were 56.3%, 70.0%, and 60.5%, respectively, and the AUC was 0.657 (p < 0.001). The sensitivity, specificity, and accuracy of the combination of the two methods for diagnosing SPNs were 93.2%, 61.1%, and 83.5%, and the AUC was 0.777 (p < 0.001). Conclusion: The combination of Lung-RADS classification and CT signs significantly improved the differential diagnosis of SPNs.
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Affiliation(s)
- Lizhen Duan
- Department of Medical Imaging, The Affiliated Huai’an No.1 People’s Hospital of Nanjing Medical University, Huai’an 223300, China
| | - Wenli Shan
- Department of Medical Imaging, The Affiliated Huai’an No.1 People’s Hospital of Nanjing Medical University, Huai’an 223300, China
| | - Genji Bo
- Department of Medical Imaging, The Affiliated Huai’an No.1 People’s Hospital of Nanjing Medical University, Huai’an 223300, China
| | - Guangming Lu
- Department of Medical Imaging, The Affiliated Jinling Hospital, Medical School of Nanjing University, Nanjing 210002, China
| | - Lili Guo
- Department of Medical Imaging, The Affiliated Huai’an No.1 People’s Hospital of Nanjing Medical University, Huai’an 223300, China
- Correspondence: ; Tel.: +86-13651549848
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18
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Kuo HCD, Wu R, Sarwar MS, Zheng M, Wang C, Sargsyan D, Suh N, Kong ANT. DNA Methylome and Transcriptome Study of Triterpenoid CDDO in TPA-Mediated Skin Carcinogenesis Model. AAPS J 2022; 24:115. [PMID: 36324037 DOI: 10.1208/s12248-022-00763-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2022] [Accepted: 10/19/2022] [Indexed: 11/06/2022] Open
Abstract
Overexposure to ultraviolet radiation and environmental carcinogens drive skin cancer development through redox imbalance and gene mutation. Antioxidants such as triterpenoids have exhibited anti-oxidative and anti-inflammatory potentials to alleviate skin carcinogenesis. This study investigated the methylome and transcriptome altered by tumor promoter 12-O-tetradecanoylphorbol-13-acetate (TPA) or TPA with 2-cyano 2,3-dioxoolean-1,9-dien-28-oic acid (CDDO). The results show that CDDO blocks TPA-induced transformation dose dependently. Several differential expressed genes (DEGs) involved in skin cell transformation, while counteracted by CDDO, were revealed by differential expression analysis including Lyl1, Lad1, and Dennd2d. In CpG methylomic profiles, the differentially methylated regions (DMRs) in the promoter region altered by TPA while showing the opposite methylation status in the CDDO treatment group were identified. The correlation between DNA methylation and RNA expression has been established and DMRs showing inverse correlation were further studied as potential therapeutic targets. From the CpG methylome and transcriptome results, CDDO significantly restored gene expression of NAD(P)H:quinone oxidoreductase 1 (Nqo1) inhibited by TPA by decreasing their promoter CpG methylation. Ingenuity Pathways Analysis (IPA) shows that CDDO neutralized the effect of TPA through modulating cell cycles, cell migration, and inflammatory and immune response regulatory pathways. Notably, Tumor Necrosis Factor Receptor 2 (TNFR2) signaling was significantly downregulated by CDDO potentially contributing to prevention of TPA-induced cell transformation. Overall, incorporating the transcriptome, CpG methylome, and signaling pathway network, we reveal potential therapeutic targets and pathways by which CDDO could reverse TPA-induced carcinogenesis. The results could be useful for future human study and targets development for skin cancer.
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Affiliation(s)
- Hsiao-Chen Dina Kuo
- Department of Pharmaceutics, Center for Phytochemical Epigenome Studies, Ernest Mario School of Pharmacy, Rutgers, The State University of New Jersey, 160 Frelinghuysen Road, NJ, 08854, Piscataway, USA.,Graduate Program of Pharmaceutical Sciences, Ernest Mario School of Pharmacy, Rutgers, The State University of New Jersey, NJ, Piscataway, USA
| | - Renyi Wu
- Department of Pharmaceutics, Center for Phytochemical Epigenome Studies, Ernest Mario School of Pharmacy, Rutgers, The State University of New Jersey, 160 Frelinghuysen Road, NJ, 08854, Piscataway, USA
| | - Md Shahid Sarwar
- Department of Pharmaceutics, Center for Phytochemical Epigenome Studies, Ernest Mario School of Pharmacy, Rutgers, The State University of New Jersey, 160 Frelinghuysen Road, NJ, 08854, Piscataway, USA
| | - Meinizi Zheng
- Department of Statistics and Biostatistics, Rutgers, The State University of New Jersey, NJ, 08854, Piscataway, USA
| | - Chao Wang
- Department of Pharmaceutics, Center for Phytochemical Epigenome Studies, Ernest Mario School of Pharmacy, Rutgers, The State University of New Jersey, 160 Frelinghuysen Road, NJ, 08854, Piscataway, USA
| | - Davit Sargsyan
- Department of Pharmaceutics, Center for Phytochemical Epigenome Studies, Ernest Mario School of Pharmacy, Rutgers, The State University of New Jersey, 160 Frelinghuysen Road, NJ, 08854, Piscataway, USA.,Graduate Program of Pharmaceutical Sciences, Ernest Mario School of Pharmacy, Rutgers, The State University of New Jersey, NJ, Piscataway, USA
| | - Nanjoo Suh
- Department of Chemical Biology, Ernest Mario School of Pharmacy, Rutgers, The State University of New Jersey, NJ, Piscataway, USA.,Rutgers Cancer Institute of New Jersey, NJ, New Brunswick, USA
| | - Ah-Ng Tony Kong
- Department of Pharmaceutics, Center for Phytochemical Epigenome Studies, Ernest Mario School of Pharmacy, Rutgers, The State University of New Jersey, 160 Frelinghuysen Road, NJ, 08854, Piscataway, USA.
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19
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Abbasian MH, Ardekani AM, Sobhani N, Roudi R. The Role of Genomics and Proteomics in Lung Cancer Early Detection and Treatment. Cancers (Basel) 2022; 14:5144. [PMID: 36291929 PMCID: PMC9600051 DOI: 10.3390/cancers14205144] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2022] [Revised: 10/10/2022] [Accepted: 10/18/2022] [Indexed: 08/17/2023] Open
Abstract
Lung cancer is the leading cause of cancer-related death worldwide, with non-small-cell lung cancer (NSCLC) being the primary type. Unfortunately, it is often diagnosed at advanced stages, when therapy leaves patients with a dismal prognosis. Despite the advances in genomics and proteomics in the past decade, leading to progress in developing tools for early diagnosis, targeted therapies have shown promising results; however, the 5-year survival of NSCLC patients is only about 15%. Low-dose computed tomography or chest X-ray are the main types of screening tools. Lung cancer patients without specific, actionable mutations are currently treated with conventional therapies, such as platinum-based chemotherapy; however, resistances and relapses often occur in these patients. More noninvasive, inexpensive, and safer diagnostic methods based on novel biomarkers for NSCLC are of paramount importance. In the current review, we summarize genomic and proteomic biomarkers utilized for the early detection and treatment of NSCLC. We further discuss future opportunities to improve biomarkers for early detection and the effective treatment of NSCLC.
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Affiliation(s)
- Mohammad Hadi Abbasian
- Department of Medical Genetics, National Institute of Genetic Engineering and Biotechnology (NIGEB), Tehran 1497716316, Iran
| | - Ali M. Ardekani
- Department of Medical Biotechnology, National Institute of Genetic Engineering and Biotechnology (NIGEB), Tehran 1497716316, Iran
| | - Navid Sobhani
- Department of Medicine, Section of Epidemiology and Population Sciences, Baylor College of Medicine, Houston, TX 77030, USA
| | - Raheleh Roudi
- Department of Radiology, Molecular Imaging Program at Stanford, Stanford University, Stanford, CA 94305, USA
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20
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Liu JY, Liu LP, Li Z, Luo YW, Liang F. The role of cuproptosis-related gene in the classification and prognosis of melanoma. Front Immunol 2022; 13:986214. [PMID: 36341437 PMCID: PMC9632664 DOI: 10.3389/fimmu.2022.986214] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2022] [Accepted: 09/28/2022] [Indexed: 11/29/2022] Open
Abstract
Background Melanoma, as one of the most aggressive and malignant cancers, ranks first in the lethality rate of skin cancers. Cuproptosis has been shown to paly a role in tumorigenesis, However, the role of cuproptosis in melanoma metastasis are not clear. Studying the correlation beteen the molecular subtypes of cuproptosis-related genes (CRGs) and metastasis of melanoma may provide some guidance for the prognosis of melanoma. Methods We collected 1085 melanoma samples in The Cancer Genome Atlas(TCGA) and Gene Expression Omnibus(GEO) databases, constructed CRGs molecular subtypes and gene subtypes according to clinical characteristics, and investigated the role of CRGs in melanoma metastasis. We randomly divide the samples into train set and validation set according to the ratio of 1:1. A prognostic model was constructed using data from the train set and then validated on the validation set. We performed tumor microenvironment analysis and drug sensitivity analyses for high and low risk groups based on the outcome of the prognostic model risk score. Finally, we established a metastatic model of melanoma. Results According to the expression levels of 12 cuproptosis-related genes, we obtained three subtypes of A1, B1, and C1. Among them, C1 subtype had the best survival outcome. Based on the differentially expressed genes shared by A1, B1, and C1 genotypes, we obtained the results of three gene subtypes of A2, B2, and C2. Among them, the B2 group had the best survival outcome. Then, we constructed a prognostic model consisting of 6 key variable genes, which could more accurately predict the 1-, 3-, and 5-year overall survival rates of melanoma patients. Besides, 98 drugs were screened out. Finally, we explored the role of cuproptosis-related genes in melanoma metastasis and established a metastasis model using seven key genes. Conclusions In conclusion, CRGs play a role in the metastasis and prognosis of melanoma, and also provide new insights into the underlying pathogenesis of melanoma.
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Affiliation(s)
- Jin-Ya Liu
- Department of Plastic Surgery, The Third Xiangya Hospital of Central South University, Changsha, China
| | - Le-Ping Liu
- Department of Blood Transfusion, The Third Xiangya Hospital of Central South University, Changsha, China,Department of Pediatrics, The Third Xiangya Hospital, Central South University, Changsha, China
| | - Ze Li
- Department of Hematology and Critical Care Medicine, The Third Xiangya Hospital, Central South University, Changsha, China
| | - Yan-Wei Luo
- Department of Blood Transfusion, The Third Xiangya Hospital of Central South University, Changsha, China,*Correspondence: Fang Liang, ; Yan-Wei Luo,
| | - Fang Liang
- Department of Hematology and Critical Care Medicine, The Third Xiangya Hospital, Central South University, Changsha, China,*Correspondence: Fang Liang, ; Yan-Wei Luo,
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21
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Kussrow A, Kammer MN, Massion PP, Webster R, Bornhop DJ. Assay Performance of a Label-Free, Solution-Phase CYFRA 21-1 Determination. ACS OMEGA 2022; 7:31916-31923. [PMID: 36120008 PMCID: PMC9476196 DOI: 10.1021/acsomega.2c02763] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
CYFRA 21.1, a cytokeratin fragment of epithelial origin, has long been a valuable blood-based biomarker. As with most biomarkers, the clinical diagnostic value of CYFRA 21.1 is dependent on the quantitative performance of the assay. Looking toward translation, it is shown here that a free-solution assay (FSA) coupled with a compensated interferometric reader (CIR) can be used to provide excellent analytical performance in quantifying CYFRA 21.1 in patient serum samples. This report focuses on the analytical performance of the high-sensitivity (hs)-CYFRA 21.1 assay in the context of quantifying the biomarker in two indeterminate pulmonary nodule (IPN) patient cohorts totaling 179 patients. Each of the ten assay calibrations consisted of 6 concentrations, each run as 7 replicates (e.g., 10 × 6 × 7 data points) and were performed on two different instruments by two different operators. Coefficients of variation (CVs) for the hs-CYFRA 21.1 analytical figures of merit, limit of quantification (LOQ) of ca. 60 pg/mL, B max, initial slope, probe-target binding affinity, and reproducibility of quantifying an unknown were found to range from 2.5 to 8.3%. Our results demonstrate the excellent performance of our FSA-CIR hs-CYFRA 21-1 assay and a proof of concept for potentially redefining the performance characteristics of this existing important candidate biomarker.
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Affiliation(s)
- Amanda
K. Kussrow
- Department
of Chemistry and The Vanderbilt Institute for Chemical Biology, Vanderbilt University, Nashville, Tennessee 37235, United States
| | - Michael N. Kammer
- Division
of Allergy, Pulmonary and Critical Care Medicine and Vanderbilt-Ingram
Cancer Center, Vanderbilt University, Nashville, Tennessee 37235, United States
| | - Pierre P. Massion
- Division
of Allergy, Pulmonary and Critical Care Medicine and Vanderbilt-Ingram
Cancer Center, Vanderbilt University, Nashville, Tennessee 37235, United States
| | - Rebekah Webster
- Department
of Chemistry and The Vanderbilt Institute for Chemical Biology, Vanderbilt University, Nashville, Tennessee 37235, United States
| | - Darryl J. Bornhop
- Department
of Chemistry and The Vanderbilt Institute for Chemical Biology, Vanderbilt University, Nashville, Tennessee 37235, United States
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22
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MicroRNA-146a promotes proliferation, migration, and invasion of HepG2 via regulating FLAP. Cancer Cell Int 2022; 22:149. [PMID: 35410355 PMCID: PMC8996575 DOI: 10.1186/s12935-022-02568-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2022] [Accepted: 04/01/2022] [Indexed: 12/24/2022] Open
Abstract
Abnormal expression of 5-Lipoxygenase Activating Protein (FLAP) has been detected in many tumor cells. MicroRNAs (miRNAs) negatively regulate gene expression post-transcriptionally by binding to the 3'–untranslated region (3'–UTR) of the target mRNA sequences and have been shown to be involved in various types of cancers. Herein, we aimed to demonstrate the expression of miR-146a and FLAP in human HCC tissues and liver cancer cell lines. We demonstrated that miR-146a expression is overexpressed, while FLAP protein and mRNA are suppressed in hepatocellular carcinoma tissues and HepG2 cells compared to para-carcinoma tissues and HL–7702 cells. Dual luciferase reporter gene assay showed that miR-146a-5p can directly target FLAP mRNA. Knockdown of miR-146a also resulted in increased FLAP expression of cancer cells. Additionally, miR-146a silencing or restoration of FLAP led to a reduction of HepG2 cell proliferation, cell cycle progression, migration, and invasion. This study showed that miR-146a has a stimulatory role in HepG2 cells and promotes HepG2 cell migration and invasion by targeting FLAP mRNA. Thus, miR-146a may be a tumor promoter and a potential therapeutic target for the treatment of HCC patients.
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23
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Mechanism of Synsepalum dulcificum Daniell. Inhibiting Lung Adenocarcinoma. EVIDENCE-BASED COMPLEMENTARY AND ALTERNATIVE MEDICINE 2022; 2022:5242179. [PMID: 35190747 PMCID: PMC8858071 DOI: 10.1155/2022/5242179] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/23/2021] [Accepted: 01/12/2022] [Indexed: 12/24/2022]
Abstract
Objective: Synsepalum dulcificum Daniell. (SD) is a natural plant fruit and is famous for containing miraculin. It has been reported that SD can be used as an adjuvant treatment to correct patients' loss of taste during the antitumor process, but the effect of SD itself as an antitumor is not clear. In this study, we investigated the mechanism of action of SD on lung adenocarcinoma using network pharmacology. Materials and Methods. The components of SD were identified by liquid chromatography-mass spectrometry, and then the compounds that affect tumor immunity of SD were screened and the related targets were predicted by TCMIO database. At the same time, the results were associated with lung adenocarcinoma targets included in the MalaCards and CTD databases, so as to construct a compound-target action network diagram and explore the mechanism of SD in the treatment of lung adenocarcinoma. In in vitro experiments, cell viability was determined and western blotting was used to detect the related expression of action targets to determine the therapeutic effect of SD. Results. In this experiment, 335 chemical components were identified in SD, and 107 components were related to tumor immunity. After screening by ADME, it was found that 11 compounds might be inhaled into the human body and affect the growth of lung adenocarcinoma. In vitro experiments showed that SD could inhibit the growth of lung adenocarcinoma A549 cells. SD could reduce the expression of PCNA (P < 0.05) and significantly increase the expression of Caspase-3 (P < 0.05). The results of further experiments showed that SD could significantly reduce the phosphorylation of EGFR (P < 0.05), and SD could also effectively inhibit the expression of JAK and STAT3 phosphorylation (P < 0.01) and inhibit the expression of PI3K and AKT phosphorylation (P < 0.01). Conclusion. SD can inhibit the growth of lung adenocarcinoma A549 cells and the potential mechanism was found to be the inhibition of EGFR/JAK/STAT3 and EGFR/PI3K/AKT signaling pathway, and the substance basis for SD to exert antitumor effect may be catechin, taxifolin, betaine, epigallocatechin gallate, erucamide, guanosine, kaempferol, lanosterol, morin, oleanolic acid, and quercetin.
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24
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Serafini FL, Lanuti P, Delli Pizzi A, Procaccini L, Villani M, Taraschi AL, Pascucci L, Mincuzzi E, Izzi J, Chiacchiaretta P, Buca D, Catitti G, Bologna G, Simeone P, Pieragostino D, Caulo M. Diagnostic Impact of Radiological Findings and Extracellular Vesicles: Are We Close to Radiovesicolomics? BIOLOGY 2021; 10:biology10121265. [PMID: 34943180 PMCID: PMC8698452 DOI: 10.3390/biology10121265] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/01/2021] [Revised: 11/29/2021] [Accepted: 11/30/2021] [Indexed: 11/23/2022]
Abstract
Simple Summary Over the years, diagnostic tests such as in radiology and flow cytometry have become more and more powerful in the constant struggle against different pathologies, some of which are life-threatening. The possibility of using these “weapons” in a conjugated manner could result in higher healing and prevention rates, and a decrease in late diagnosis diseases. Different correlations among pathologies, extracellular vesicles (EVs), and radiological findings were recently demonstrated by many authors. Together with the increasing importance of “omics” sciences, and artificial intelligence in this new century, the perspective of a new research field called “radiovesicolomics” could be the missing link, enabling a different approach to disease diagnosis and treatment. Abstract Currently, several pathologies have corresponding and specific diagnostic and therapeutic branches of interest focused on early and correct detection, as well as the best therapeutic approach. Radiology never ceases to develop newer technologies in order to give patients a clear, safe, early, and precise diagnosis; furthermore, in the last few years diagnostic imaging panoramas have been extended to the field of artificial intelligence (AI) and machine learning. On the other hand, clinical and laboratory tests, like flow cytometry and the techniques found in the “omics” sciences, aim to detect microscopic elements, like extracellular vesicles, with the highest specificity and sensibility for disease detection. If these scientific branches started to cooperate, playing a conjugated role in pathology diagnosis, what could be the results? Our review seeks to give a quick overview of recent state of the art research which investigates correlations between extracellular vesicles and the known radiological features useful for diagnosis.
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Affiliation(s)
- Francesco Lorenzo Serafini
- Department of Neuroscience, Imaging and Clinical Sciences, University “G. d’Annunzio”, 66100 Chieti, Italy; (F.L.S.); (L.P.); (M.V.); (A.L.T.); (L.P.); (E.M.); (J.I.); (P.C.); (M.C.)
| | - Paola Lanuti
- Department of Medicine and Aging Sciences, University “G. d’Annunzio”, 66100 Chieti, Italy; (P.L.); (D.B.); (G.C.); (G.B.); (P.S.)
- Center for Advanced Studies and Technology (CAST), University “G. d’Annunzio”, 66100 Chieti, Italy;
| | - Andrea Delli Pizzi
- Institute of Advanced Biomedical Technologies (ITAB), University “G. d’Annunzio”, 66100 Chieti, Italy
- Department of Innovative Technologies in Medicine & Dentistry, University “G. d’Annunzio”, 66100 Chieti, Italy
- Correspondence:
| | - Luca Procaccini
- Department of Neuroscience, Imaging and Clinical Sciences, University “G. d’Annunzio”, 66100 Chieti, Italy; (F.L.S.); (L.P.); (M.V.); (A.L.T.); (L.P.); (E.M.); (J.I.); (P.C.); (M.C.)
| | - Michela Villani
- Department of Neuroscience, Imaging and Clinical Sciences, University “G. d’Annunzio”, 66100 Chieti, Italy; (F.L.S.); (L.P.); (M.V.); (A.L.T.); (L.P.); (E.M.); (J.I.); (P.C.); (M.C.)
| | - Alessio Lino Taraschi
- Department of Neuroscience, Imaging and Clinical Sciences, University “G. d’Annunzio”, 66100 Chieti, Italy; (F.L.S.); (L.P.); (M.V.); (A.L.T.); (L.P.); (E.M.); (J.I.); (P.C.); (M.C.)
| | - Luca Pascucci
- Department of Neuroscience, Imaging and Clinical Sciences, University “G. d’Annunzio”, 66100 Chieti, Italy; (F.L.S.); (L.P.); (M.V.); (A.L.T.); (L.P.); (E.M.); (J.I.); (P.C.); (M.C.)
| | - Erica Mincuzzi
- Department of Neuroscience, Imaging and Clinical Sciences, University “G. d’Annunzio”, 66100 Chieti, Italy; (F.L.S.); (L.P.); (M.V.); (A.L.T.); (L.P.); (E.M.); (J.I.); (P.C.); (M.C.)
| | - Jacopo Izzi
- Department of Neuroscience, Imaging and Clinical Sciences, University “G. d’Annunzio”, 66100 Chieti, Italy; (F.L.S.); (L.P.); (M.V.); (A.L.T.); (L.P.); (E.M.); (J.I.); (P.C.); (M.C.)
| | - Piero Chiacchiaretta
- Department of Neuroscience, Imaging and Clinical Sciences, University “G. d’Annunzio”, 66100 Chieti, Italy; (F.L.S.); (L.P.); (M.V.); (A.L.T.); (L.P.); (E.M.); (J.I.); (P.C.); (M.C.)
- Institute of Advanced Biomedical Technologies (ITAB), University “G. d’Annunzio”, 66100 Chieti, Italy
| | - Davide Buca
- Department of Medicine and Aging Sciences, University “G. d’Annunzio”, 66100 Chieti, Italy; (P.L.); (D.B.); (G.C.); (G.B.); (P.S.)
- Center for Advanced Studies and Technology (CAST), University “G. d’Annunzio”, 66100 Chieti, Italy;
| | - Giulia Catitti
- Department of Medicine and Aging Sciences, University “G. d’Annunzio”, 66100 Chieti, Italy; (P.L.); (D.B.); (G.C.); (G.B.); (P.S.)
- Center for Advanced Studies and Technology (CAST), University “G. d’Annunzio”, 66100 Chieti, Italy;
| | - Giuseppina Bologna
- Department of Medicine and Aging Sciences, University “G. d’Annunzio”, 66100 Chieti, Italy; (P.L.); (D.B.); (G.C.); (G.B.); (P.S.)
- Center for Advanced Studies and Technology (CAST), University “G. d’Annunzio”, 66100 Chieti, Italy;
| | - Pasquale Simeone
- Department of Medicine and Aging Sciences, University “G. d’Annunzio”, 66100 Chieti, Italy; (P.L.); (D.B.); (G.C.); (G.B.); (P.S.)
- Center for Advanced Studies and Technology (CAST), University “G. d’Annunzio”, 66100 Chieti, Italy;
| | - Damiana Pieragostino
- Center for Advanced Studies and Technology (CAST), University “G. d’Annunzio”, 66100 Chieti, Italy;
- Department of Innovative Technologies in Medicine & Dentistry, University “G. d’Annunzio”, 66100 Chieti, Italy
| | - Massimo Caulo
- Department of Neuroscience, Imaging and Clinical Sciences, University “G. d’Annunzio”, 66100 Chieti, Italy; (F.L.S.); (L.P.); (M.V.); (A.L.T.); (L.P.); (E.M.); (J.I.); (P.C.); (M.C.)
- Institute of Advanced Biomedical Technologies (ITAB), University “G. d’Annunzio”, 66100 Chieti, Italy
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25
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Li J, Wang Z, Tie C. High expression of ladinin-1 (LAD1) predicts adverse outcomes: a new candidate docetaxel resistance gene for prostatic cancer (PCa). Bioengineered 2021; 12:5749-5759. [PMID: 34516317 PMCID: PMC8806705 DOI: 10.1080/21655979.2021.1968647] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022] Open
Abstract
Docetaxel resistance is one of the major obstacles that undermine the treatment outcome of PCa. Exploring molecular mechanisms associated with docetaxel resistance could provide insights into the formulation of novel strategies enhancing the efficacy of PCa treatment. Ladinin-1 (LAD1) is an anchoring filament protein in basement membranes, which contributes to the association of the epithelial cells with the underlying mesenchyme. LAD1 has been implicated in the progression of different cancers. However, its role in PCa remains to be investigated. In the present study, we found that LAD1 was highly expressed in docetaxel-resistant PCa cells, while its expression was significantly suppressed in tumor samples after docetaxel treatment. Moreover, the expression level of LAD1 in PCa tissues was significantly higher than that of normal tissue, and high expression level of LAD1 was significantly associated with adverse outcomes of PCa patients. Finally, high expression of LAD1 in PCa tissue was also correlated with the expression level of genes involving in tumor cell proliferation and invasive behaviors. Collectively, our data suggest that LAD1 may serve as a potential prognostic factor in PCa patients.
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Affiliation(s)
- Jianping Li
- Department of Urology, The Second Affiliated Hospital of Xi'an Jiaotong University, China
| | - Ziming Wang
- Department of Urology, The Second Affiliated Hospital of Xi'an Jiaotong University, China
| | - Chong Tie
- Department of Urology, The Second Affiliated Hospital of Xi'an Jiaotong University, China
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26
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Ma L, Xiu G, Muscat J, Sinha R, Sun D, Xiu G. Comparative proteomic analysis of exhaled breath condensate between lung adenocarcinoma and CT-detected benign pulmonary nodule patients. Cancer Biomark 2021; 34:163-174. [PMID: 34334381 DOI: 10.3233/cbm-203269] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
BACKGROUND Lung cancer is the leading cause of cancer mortality worldwide. The collection of exhaled breath condensate (EBC) is a non-invasive method that may have enormous potential as a biomarker for the early detection of lung cancer. OBJECTIVE To investigate the proteomic differences of EBC between lung cancer and CT-detected benign nodule patients, and determine whether these proteins could be potential biomarkers. METHODS Proteomic analysis was performed on individual samples from 10 lung cancer patients and 10 CT-detected benign nodule patients using data-independent acquisition (DIA) mass spectrometry. RESULTS A total of 1,254 proteins were identified, and 21 proteins were differentially expressed in the lung adenocarcinoma group compared to the benign nodule group (p< 0.05). The GO analysis showed that most of these proteins were involved in neutrophil-related biological processes, and the KEGG analysis showed these proteins were mostly annotated to pyruvate and propanoate metabolism. Through protein-protein interactions (PPIs) analysis, ME1 and LDHB contributed most to the interaction-network of these proteins. CONCLUSION Significantly differentially expressed proteins were detected between lung cancer and the CT-detected benign nodule group from EBC samples, and these proteins might serve as potential novel biomarkers of EBC for early lung cancer detection.
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Affiliation(s)
- Lin Ma
- State Environmental Protection Key Lab of Environmental Risk Assessment and Control on Chemical Processes, School of Resources and Environmental Engineering, East China University of Science and Technology, Shanghai, China.,Department of Public Health Sciences, The Pennsylvania State University College of Medicine, Penn State Hershey Medical Center, PA, USA
| | | | - Joshua Muscat
- Department of Public Health Sciences, The Pennsylvania State University College of Medicine, Penn State Hershey Medical Center, PA, USA
| | - Raghu Sinha
- Department of Biochemistry and Molecular Biology Penn State Hershey Medical Center, PA, USA
| | - Dongxiao Sun
- Department of Pharmacology, Mass Spectrometry Core Facility, The Pennsylvania State University, PA, USA
| | - Guangli Xiu
- State Environmental Protection Key Lab of Environmental Risk Assessment and Control on Chemical Processes, School of Resources and Environmental Engineering, East China University of Science and Technology, Shanghai, China
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Ye X, An L, Wang X, Zhang C, Huang W, Sun C, Li R, Ma H, Wang H, Gao M. ALOX5AP Predicts Poor Prognosis by Enhancing M2 Macrophages Polarization and Immunosuppression in Serous Ovarian Cancer Microenvironment. Front Oncol 2021; 11:675104. [PMID: 34094977 PMCID: PMC8172172 DOI: 10.3389/fonc.2021.675104] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2021] [Accepted: 04/29/2021] [Indexed: 12/20/2022] Open
Abstract
Background Serous ovarian cancer (SOC) is a highly lethal gynecological malignancy with poor prognosis. Given the importance of the immune-related tumor microenvironment (TME) in ovarian cancer, investigating tumor-immune interactions and identifying novel prognostic and therapeutic targets in SOC is a promising avenue of research. ALOX5AP (Arachidonate 5-Lipoxygenase Activating Protein) is a key enzyme in converting arachidonic acid to leukotriene: a crucial immune-modulating lipid mediator. However, the role of ALOX5AP in SOC has yet to be studied. Methods ALOX5AP expression patterns across ovarian cancer and their normal tissue counterparts were cross-checked using public microarray and RNA-seq analyses and then validated in clinical samples by qRT-PCR. Kaplan-Meier survival analysis was performed in multiple independent SOC patient cohorts. Univariate and multivariate Cox regression analysis were then employed to identify clinical risk parameters associated with survival, and a genomic-clinicopathologic nomogram was built. Gene enrichment, immune infiltration, and immunosuppressor correlation analyses were then evaluated. Results ALOX5AP mRNA levels in SOC tissues were significantly upregulated compared to normal tissues. Elevated ALOX5AP was markedly associated with poor overall survival and progression-free survival in multiple SOC patient cohorts as well as with adverse clinicopathological features, including lymphatic invasion, unsatisfactory cytoreductive surgery, rapid relapse after primary treatment, and platinum non-responsiveness. A predictive nomogram, which integrated ALOX5AP expression and two independent prognosis factors (primary therapy outcome and tumor residual), was conducted to predict the 3-year and 5-year survival rate of SOC patients. Mechanistically, functional and pathway enrichment analyses revealed that ALOX5AP was primarily involved in immune response and regulation. Further exploration demonstrated that ALOX5AP was highly expressed in the immunoreactive subtype of ovarian cancer and closely related to immunocyte infiltration, especially M2 macrophage polarization. Additionally, ALOX5AP was enriched in the C4 (lymphocyte depleted) immune subtype of SOC and associated with crucial immune-repressive receptors in the tumor microenvironment at the genomic level. Conclusions ALOX5AP expression indicates a worse survival outcome and has the potential to be utilized as a prognostic predictor for SOC patients. Given the availability of well-studied ALOX5AP inhibitors, this study has immediate clinical implications for the exploitation of ALOX5AP as an immunotherapeutic target in SOC.
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Affiliation(s)
- Xiang Ye
- Department of Geriatric Medicine, Qilu Hospital of Shandong University, Jinan, China.,Key Laboratory of Experimental Teratology of Ministry of Education, Department of Medical Genetics, School of Basic Medical Sciences, Cheeloo College of Medicine, Shandong University, Jinan, China
| | - Limei An
- Health Management Division, Rizhao Central Hospital, Rizhao, China
| | - Xiangxiang Wang
- Department of Obstetrics and Gynecology, Central Hospital Affiliated to Shandong First Medical University, Jinan, China
| | - Chenyi Zhang
- Department of Obstetrics and Gynecology, Gynecology Oncology Key Laboratory, Qilu Hospital of Shandong University, Jinan, China
| | - Wenqian Huang
- Department of Obstetrics and Gynecology, Gynecology Oncology Key Laboratory, Qilu Hospital of Shandong University, Jinan, China
| | - Chenggong Sun
- Department of Obstetrics and Gynecology, Gynecology Oncology Key Laboratory, Qilu Hospital of Shandong University, Jinan, China
| | - Rongrong Li
- Department of Obstetrics and Gynecology, Gynecology Oncology Key Laboratory, Qilu Hospital of Shandong University, Jinan, China
| | - Hanlin Ma
- Department of Obstetrics and Gynecology, Gynecology Oncology Key Laboratory, Qilu Hospital of Shandong University, Jinan, China
| | - Hongyan Wang
- Department of Obstetrics and Gynecology, Gynecology Oncology Key Laboratory, Qilu Hospital of Shandong University, Jinan, China
| | - Min Gao
- Department of Obstetrics and Gynecology, Gynecology Oncology Key Laboratory, Qilu Hospital of Shandong University, Jinan, China
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Moon B, Yang SJ, Park SM, Lee SH, Song KS, Jeong EJ, Park M, Kim JS, Yeom YI, Kim JA. LAD1 expression is associated with the metastatic potential of colorectal cancer cells. BMC Cancer 2020; 20:1180. [PMID: 33267790 PMCID: PMC7709356 DOI: 10.1186/s12885-020-07660-0] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2020] [Accepted: 11/18/2020] [Indexed: 12/28/2022] Open
Abstract
BACKGROUND Anchoring filament protein ladinin-1 (LAD1) was related to the aggressive progression of breast, lung, laryngeal and thyroid cancers. However, the association of LAD1 with colorectal cancer remained unknown. Here, to determine the relationship of LAD1 with colorectal cancer progression, we explored the effect of LAD1 loss on the malignant features of colorectal cancer cells. METHODS We constructed LAD1-depleted cell lines and examined the effect of LAD1 deficiency on the phenotypic and molecular features of colorectal cancer cells in vitro. The function of LAD1 in metastasis in vivo was examined by establishing a spleen-to-liver metastasis mouse model. LAD1 protein expression in colorectal cancer patient specimens was assessed by immunohistochemistry of tumor microarrays. RESULTS We found that LAD1 was abundant in most colorectal cancer cells. In addition, high expression of LAD1 significantly correlated with poor patient outcome. LAD1 depletion inhibited the migration and invasion of two different colorectal cancer cell lines, SW620 and Caco-2, without affecting their proliferation. In addition, LAD1 loss led to defects in liver metastasis of SW620 cells in the mouse model. Immunohistochemistry of colorectal cancer tissues revealed LAD1 enrichment in metastatic tissues compared to that in primary tumor and normal tissues. CONCLUSION These results suggest that LAD1 expression is associated with the metastatic progression of colorectal cancer by promoting the migration and invasion of cancer cells.
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Affiliation(s)
- Byul Moon
- Personalized Genomic Medicine Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, 34141, South Korea
- Department of Functional Genomics, KRIBB School of Bioscience, University of Science and Technology, Daejeon, 34113, South Korea
| | - Suk-Jin Yang
- Personalized Genomic Medicine Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, 34141, South Korea
- Present address: Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Seong Min Park
- Personalized Genomic Medicine Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, 34141, South Korea
- Present address: Translational Research Branch, Research Institute, National Cancer Center, Goyang, 10408, South Korea
| | - Sang-Hyun Lee
- Biotherapeutics Translational Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, 34141, South Korea
| | - Kyu Sang Song
- Department of Pathology, Chungnam National University College of Medicine, Daejeon, 34134, South Korea
| | - Eun-Jeong Jeong
- Biotherapeutics Translational Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, 34141, South Korea
- Department of Biological Science, College of Natural Sciences, Wonkwang University, Iksan, 54538, South Korea
| | - Mijin Park
- Personalized Genomic Medicine Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, 34141, South Korea
- Department of Functional Genomics, KRIBB School of Bioscience, University of Science and Technology, Daejeon, 34113, South Korea
| | - Jang-Seong Kim
- Department of Functional Genomics, KRIBB School of Bioscience, University of Science and Technology, Daejeon, 34113, South Korea
- Biotherapeutics Translational Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, 34141, South Korea
| | - Young Il Yeom
- Personalized Genomic Medicine Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, 34141, South Korea
- Department of Functional Genomics, KRIBB School of Bioscience, University of Science and Technology, Daejeon, 34113, South Korea
| | - Jung-Ae Kim
- Personalized Genomic Medicine Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, 34141, South Korea.
- Department of Functional Genomics, KRIBB School of Bioscience, University of Science and Technology, Daejeon, 34113, South Korea.
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Cainap C, Pop LA, Balacescu O, Cainap SS. Early diagnosis and screening in lung cancer. Am J Cancer Res 2020; 10:1993-2009. [PMID: 32774997 PMCID: PMC7407360] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2020] [Accepted: 06/25/2020] [Indexed: 06/11/2023] Open
Abstract
Lung cancer is the third most diagnosed cancer, but the first cause of cancer-related deaths worldwide. This rather high death rate is due mainly to the fact that most patients are diagnosed with advanced-stage cancer, for which the conventional treatment does not work. The most used screening method for lung cancer is a low-dose CT scan, but it is recommended for specific age populations and it also started different debates on its advantages for lung cancer diagnosis. Over the year, several new techniques have been developed that are less invasive, have lower side effect, and can be implemented at all types of populations. This article aimed to present the advantages and disadvantages of using several methods for lung cancer diagnosis, including analysis of volatile organic compounds, exhaled breath condensate analysis and specific genomic approaches.
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Affiliation(s)
- Calin Cainap
- Department of Oncology, “Iuliu Hatieganu” University of Medicine and PharmacyCluj-Napoca, Romania
- Prof. Dr. Ion Chiricuta Institute of OncologyCluj-Napoca, Romania
| | - Laura A Pop
- Research Center for Functional Genomics, Biomedicine and Translational Medicine, University of Medicine and Pharmacy Iuliu HatieganuCluj-Napoca, Romania
| | - Ovidiu Balacescu
- Department of Functional Genomics and Experimental Pathology, Prof. Dr. Ion Chiricuta Institute of OncologyCluj-Napoca, Romania
| | - Simona S Cainap
- Department of Pediatric Cardiology, Emergency County Hospital for Children, Pediatric Clinic no 2Cluj-Napoca, Romania
- Department of Mother and Child, “Iuliu Hatieganu” University of Medicine and PharmacyCluj-Napoca, Romania
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Gasparri R, Sedda G, Noberini R, Bonaldi T, Spaggiari L. Clinical Application of Mass Spectrometry-Based Proteomics in Lung Cancer Early Diagnosis. Proteomics Clin Appl 2020; 14:e1900138. [PMID: 32418314 DOI: 10.1002/prca.201900138] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2019] [Revised: 04/06/2020] [Indexed: 12/18/2022]
Abstract
The current knowledge on proteomic biomarker analysis for the early diagnosis of lung cancer is summarized, underlining the diversity among the results and the current interest in translating research results into clinical practice. A MEDLINE/PubMed literature search to retrieve all the papers published in the last 10 years is performed. Proteomics studies on lung cancer have gathered evidence on the potential role of biomarkers in early diagnosis. Although promising, none of them have proved to be sufficiently reliable to achieve validation. Future research should evolve toward a multipanel analysis of proteins, considering the possibility that individual biomarkers might not be specific enough to diagnose lung cancer, but could be related to oncological conditions.
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Affiliation(s)
- Roberto Gasparri
- Department of Thoracic Surgery, IEO, European Institute of Oncology IRCCS, Via Giuseppe Ripamonti 435, Milan, 20141, Italy
| | - Giulia Sedda
- Department of Thoracic Surgery, IEO, European Institute of Oncology IRCCS, Via Giuseppe Ripamonti 435, Milan, 20141, Italy
| | - Roberta Noberini
- Department of Experimental Oncology, IEO, European Institute of Oncology IRCCS, Via Adamello 16, Milan, 20139, Italy
| | - Tiziana Bonaldi
- Department of Experimental Oncology, IEO, European Institute of Oncology IRCCS, Via Adamello 16, Milan, 20139, Italy
| | - Lorenzo Spaggiari
- Department of Thoracic Surgery, IEO, European Institute of Oncology IRCCS, Via Giuseppe Ripamonti 435, Milan, 20141, Italy.,Department of Oncology and Hemato-Oncology, University of Milan, Via Festa del Perdono, Milan, 7 - 20122, Italy
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31
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Li M, Jin X, Li H, Wu G, Wang S, Yang C, Deng S. Key genes with prognostic values in suppression of osteosarcoma metastasis using comprehensive analysis. BMC Cancer 2020; 20:65. [PMID: 31992246 PMCID: PMC6988291 DOI: 10.1186/s12885-020-6542-z] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2019] [Accepted: 01/14/2020] [Indexed: 12/17/2022] Open
Abstract
BACKGROUND Osteosarcoma is a primary malignant tumor originating from mesenchymal tissue, with a poor distant metastasis prognosis. The molecular mechanisms of osteosarcoma metastasis are extremely complicated. METHODS A public data series (GSE21257) was used to identify differentially expressed genes (DEGs) in osteosarcoma patients that did, or did not, develop metastases. Functional enrichment analysis, a protein-protein interaction network, and survival analysis of DEGs were performed. DEGs with a prognostic value were considered as candidate genes and their functional predictions, different expression in normal and malignant tissues, and immune infiltration were analyzed. RESULTS The DEGs were mainly enriched in the immune response. Three candidate genes (ALOX5AP, CD74, and FCGR2A) were found, all of which were expressed at higher levels in lungs and lymph nodes than in matched cancer tissues and were probably expressed in the microenvironment. CONCLUSIONS Candidate genes can help us understand the molecular mechanisms underlying osteosarcoma metastasis and provide targets for future research.
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Affiliation(s)
- Mi Li
- Department of Orthopedics, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China
| | - Xin Jin
- Department of Digestive Surgical Oncology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022, China
| | - Hao Li
- Department of Orthopedics, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China
| | - Gang Wu
- Cancer Center, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022, China
| | - Shanshan Wang
- Cancer Center, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022, China
| | - Caihong Yang
- Department of Orthopedics, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China.
| | - Sisi Deng
- Cancer Center, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022, China.
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Li W, Li M, Cao X, Han H, Kong F, Yue X. Comparative analysis of whey proteins in donkey colostrum and mature milk using quantitative proteomics. Food Res Int 2019; 127:108741. [PMID: 31882075 DOI: 10.1016/j.foodres.2019.108741] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2019] [Revised: 09/30/2019] [Accepted: 10/02/2019] [Indexed: 11/28/2022]
Abstract
Donkey milk is attracting increasing attention as a nutritional milk source similar to human milk. In this study, we carried out qualitative and quantitative analysis of the donkey whey proteome using a label-free proteomic approach, combined with parallel reaction monitoring (PRM) as a validation method. A total of 300 whey proteins were identified in donkey colostrum (DC) and donkey mature (DM) milk, of which 18 were differentially expressed (P < 0.05) between the two types of milk. Gene ontology (GO) analysis showed that differentially and uniquely expressed proteins were mainly involved in cellular processes, response to stimulus, metabolic processes, and biological regulation. Their molecular functions included binding, catalytic activity, and molecular functional regulation, and their main annotated areas of origin were the cell, cell-part, and the extracellular region. Most differentially and uniquely expressed proteins were linked with malaria, systemic lupus erythematosus, or antigen processing and presentation. Our results provide insight into the complexity of the donkey whey proteome and molecular evidence for nutritional differences between different lactation stages.
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Affiliation(s)
- Weixuan Li
- College of Food Science, Shenyang Agricultural University, Shenyang, Liaoning Province, China
| | - Mohan Li
- College of Food Science, Shenyang Agricultural University, Shenyang, Liaoning Province, China
| | - Xueyan Cao
- College of Food Science, Shenyang Agricultural University, Shenyang, Liaoning Province, China
| | - Hongjiao Han
- College of Food Science, Shenyang Agricultural University, Shenyang, Liaoning Province, China
| | - Fanhua Kong
- College of Food Science, Shenyang Agricultural University, Shenyang, Liaoning Province, China
| | - Xiqing Yue
- College of Food Science, Shenyang Agricultural University, Shenyang, Liaoning Province, China.
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Al Nasrallah N, Sears CR. Biomarkers in Pulmonary Nodule Diagnosis: Is It Time to Put Away the Biopsy Needle? Chest 2019; 154:467-468. [PMID: 30195336 DOI: 10.1016/j.chest.2018.04.032] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2018] [Revised: 04/13/2018] [Accepted: 04/16/2018] [Indexed: 12/26/2022] Open
Affiliation(s)
- Nawar Al Nasrallah
- Division of Pulmonary, Critical Care, Sleep and Occupational Medicine, Indiana University School of Medicine, Indianapolis, IN
| | - Catherine R Sears
- Division of Pulmonary, Critical Care, Sleep and Occupational Medicine, Indiana University School of Medicine, Indianapolis, IN.
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Sathe G, Na CH, Renuse S, Madugundu AK, Albert M, Moghekar A, Pandey A. Quantitative Proteomic Profiling of Cerebrospinal Fluid to Identify Candidate Biomarkers for Alzheimer's Disease. Proteomics Clin Appl 2019; 13:e1800105. [PMID: 30578620 PMCID: PMC6639119 DOI: 10.1002/prca.201800105] [Citation(s) in RCA: 71] [Impact Index Per Article: 14.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2018] [Revised: 12/17/2018] [Indexed: 12/13/2022]
Abstract
PURPOSE The aim of this study is to identify the potential cerebrospinal fluid (CSF) biomarkers for Alzheimer's disease and to evaluate these markers on independent CSF samples using parallel reaction monitoring (PRM) assays. EXPERIMENTAL DESIGN High-Resolution mass spectrometry and tandem mass tag (TMT) multiplexing technology are employed to identify potential biomarkers for Alzheimer's disease. Some of the identified potential biomarkers are validated using PRM assays. RESULTS A total of 2327 proteins are identified in the CSF of which 139 are observed to be significantly altered in the CSF of AD patients. The proteins altered in AD includes a number of known AD marker such as MAPT, NPTX2, VGF, GFAP, and NCAM1 as well as novel biomarkers such as PKM and YWHAG. These findings are validated in a separate set of CSF specimens from AD dementia patients and controls. NPTX2, in combination with PKM or YWHAG, leads to the best results with AUCs of 0.935 and 0.933, respectively. CONCLUSIONS AND CLINICAL RELEVANCE The proteins that are found to be altered in the CSF of patients with AD could be used for monitoring disease progression and therapeutic response and perhaps also for early detection once they are validated in larger studies.
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Affiliation(s)
- Gajanan Sathe
- Institute of Bioinformatics, International Technology Park, Bangalore 560 066, India
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
- Manipal Academy of Higher Education (MAHE), Manipal 576104, Karnataka, India
| | - Chan Hyun Na
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD, 21205 USA
- Institute for Cell Engineering, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
| | - Santosh Renuse
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
| | - Anil K. Madugundu
- Institute of Bioinformatics, International Technology Park, Bangalore 560 066, India
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
- Manipal Academy of Higher Education (MAHE), Manipal 576104, Karnataka, India
| | - Marilyn Albert
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD, 21205 USA
| | - Abhay Moghekar
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD, 21205 USA
| | - Akhilesh Pandey
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
- Institute for Cell Engineering, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
- Departments of Biological Chemistry, Pathology and Oncology, Johns Hopkins University School of Medicine, Baltimore, MD, 21205 USA
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35
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Tanner NT, Brasher PB, Jett J, Silvestri GA. Effect of a Rule-in Biomarker Test on Pulmonary Nodule Management: A Survey of Pulmonologists and Thoracic Surgeons. Clin Lung Cancer 2019; 21:e89-e98. [PMID: 31732400 DOI: 10.1016/j.cllc.2019.05.004] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2019] [Revised: 03/09/2019] [Accepted: 05/02/2019] [Indexed: 12/26/2022]
Abstract
INTRODUCTION The field of biomarker development is evolving to assist in determining benign from malignant pulmonary nodules. Although a prospective clinical utility would best to show how a biomarker affects patient treatment and outcomes, we sought to begin to understand how the results might alter management by determining how physicians would use the results of a rule-in blood test to manage pulmonary nodules. MATERIALS AND METHODS Pulmonologists and thoracic surgeons in the American College of Chest Physicians clinician database were invited to participate in an online survey. The participant demographic data were collected. Four hypothetical clinical vignettes were presented. The participants accessed the pretest probability (probability of cancer [pCA]) for malignancy and chose the management strategies as the case progressed. The management strategies chosen before and after the result of a rule-in biomarker test were compared and assessed for guideline concordance. RESULTS Of the 455 eligible participants who had opened the survey, 416 (92%) completed it: 332 pulmonologists and 84 thoracic surgeons. Although 91% of the participants were very comfortable managing nodules, depending on the case, 30% to 62% incorrectly assessed the pCA, with 22% to 62% overestimating the risk and 8% to 51% underestimating the risk. After a rule-in blood test result, the clinician change in management moved in the right direction in some cases but, in others, the physicians used the results incorrectly. Pulmonologists and thoracic surgeons differed in the management strategies, with surgeons recommending surgery more often. CONCLUSIONS Although the use of biomarker testing for pulmonary nodule evaluation is promising, without proper physician education, the potential for harm exists. Clinical utility studies are needed to appropriately inform the effect of biomarker use.
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Affiliation(s)
- Nichole T Tanner
- Department of Medicine, Thoracic Oncology Research Group, Medical University of South Carolina, Charleston, SC; HEROIC, Ralph H. Johnson Veterans Affairs Medical Center, Charleston, SC.
| | - Paul Bradley Brasher
- Department of Medicine, Thoracic Oncology Research Group, Medical University of South Carolina, Charleston, SC
| | | | - Gerard A Silvestri
- Department of Medicine, Thoracic Oncology Research Group, Medical University of South Carolina, Charleston, SC
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36
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Calabrese F, Lunardi F, Pezzuto F, Fortarezza F, Vuljan SE, Marquette C, Hofman P. Are There New Biomarkers in Tissue and Liquid Biopsies for the Early Detection of Non-Small Cell Lung Cancer? J Clin Med 2019; 8:jcm8030414. [PMID: 30917582 PMCID: PMC6463117 DOI: 10.3390/jcm8030414] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2019] [Revised: 03/11/2019] [Accepted: 03/21/2019] [Indexed: 02/07/2023] Open
Abstract
Lung cancer is one of the most lethal malignancies worldwide, mainly due to its late diagnoses. The detection of molecular markers on samples provided from routine bronchoscopy including several liquid-based cytology tests (e.g., bronchoaspirate, bronchoalveolar lavage) and/or on easily obtained specimens such as sputum could represent a new approach to improve the sensitivity in lung cancer diagnoses. Recently growing interest has been reported for "noninvasive" liquid biopsy as a valuable source for molecular profiling. Unfortunately, a biomarker and/or composition of biomarkers capable of detecting early-stage lung cancer has yet to be discovered even if in the last few years there has been, through the use of revolutionary new technologies, an explosion of lung cancer biomarkers. Assay sensitivity and specificity need to be improved particularly when new approaches and/or tools are used. We have focused on the most important markers detected in tissue, and on several cytological specimens and liquid biopsies overall.
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Affiliation(s)
- Fiorella Calabrese
- Department of Cardiac, Thoracic, Vascular Sciences and Public Health, University of Padova Medical School, 35121 Padova, Italy.
| | - Francesca Lunardi
- Department of Cardiac, Thoracic, Vascular Sciences and Public Health, University of Padova Medical School, 35121 Padova, Italy.
| | - Federica Pezzuto
- Department of Cardiac, Thoracic, Vascular Sciences and Public Health, University of Padova Medical School, 35121 Padova, Italy.
| | - Francesco Fortarezza
- Department of Cardiac, Thoracic, Vascular Sciences and Public Health, University of Padova Medical School, 35121 Padova, Italy.
| | - Stefania Edith Vuljan
- Department of Cardiac, Thoracic, Vascular Sciences and Public Health, University of Padova Medical School, 35121 Padova, Italy.
| | - Charles Marquette
- University Côte d'Azur, University Nice Hospital, FHU OncoAge, Department of Pneumology, Pasteur Hospital, 06001 Nice, France.
- University Côte d'Azur, CNRS, INSERM, IRCAN, Team 4, FHU OncoAge, 06001 Nice, France.
| | - Paul Hofman
- University Côte d'Azur, CNRS, INSERM, IRCAN, Team 4, FHU OncoAge, 06001 Nice, France.
- University Côte d'Azur, University Nice Hospital, FHU OncoAge, Laboratory of Clinical and Experimental Pathology, Pasteur Hospital, 06001 Nice, France.
- University Côte d'Azur, Biobank (BB-0033-00025), FHU OncoAge, Pasteur Hospital, 06001 Nice, France.
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Gao B, Zhao Y, Li Y, Liu J, Wang L, Li G, Su Z. Prediction of Driver Modules via Balancing Exclusive Coverages of Mutations in Cancer Samples. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2019; 6:1801384. [PMID: 30828525 PMCID: PMC6382311 DOI: 10.1002/advs.201801384] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/19/2018] [Revised: 10/04/2018] [Indexed: 05/07/2023]
Abstract
Mutual exclusivity of cancer driving mutations is a frequently observed phenomenon in the mutational landscape of cancer. The long tail of rare mutations complicates the discovery of mutually exclusive driver modules. The existing methods usually suffer from the problem that only few genes in some identified modules cover most of the cancer samples. To overcome this hurdle, an efficient method UniCovEx is presented via identifying mutually exclusive driver modules of balanced exclusive coverages. UniCovEx first searches for candidate driver modules with a strong topological relationship in signaling networks using a greedy strategy. It then evaluates the candidate modules by considering their coverage, exclusivity, and balance of coverage, using a novel metric termed exclusive entropy of modules, which measures how balanced the modules are. Finally, UniCovEx predicts sample-specific driver modules by solving a minimum set cover problem using a greedy strategy. When tested on 12 The Cancer Genome Atlas datasets of different cancer types, UniCovEx shows a significant superiority over the previous methods. The software is available at: https://sourceforge.net/projects/cancer-pathway/files/.
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Affiliation(s)
- Bo Gao
- School of MathematicsShandong UniversityJinan250100China
- State Key Laboratory of Microbial TechnologyShandong UniversityJinan250100China
| | - Yue Zhao
- IAMMADISNCMISAcademy of Mathematics and Systems ScienceChinese Academy of SciencesBeijing100190China
- School of Mathematical SciencesUniversity of Chinese Academy of SciencesBeijing100049China
| | - Yang Li
- School of MathematicsShandong UniversityJinan250100China
- State Key Laboratory of Microbial TechnologyShandong UniversityJinan250100China
| | - Juntao Liu
- School of MathematicsShandong UniversityJinan250100China
| | - Lushan Wang
- State Key Laboratory of Microbial TechnologyShandong UniversityJinan250100China
| | - Guojun Li
- School of MathematicsShandong UniversityJinan250100China
- State Key Laboratory of Microbial TechnologyShandong UniversityJinan250100China
| | - Zhengchang Su
- Department of Bioinformatics and GenomicsCollege of Computing and InformaticsThe University of North Carolina at Charlotte9201 University City BlvdCharlotteNC28223USA
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38
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Wu JI, Lin YP, Tseng CW, Chen HJ, Wang LH. Crabp2 Promotes Metastasis of Lung Cancer Cells via HuR and Integrin β1/FAK/ERK Signaling. Sci Rep 2019; 9:845. [PMID: 30696915 PMCID: PMC6351595 DOI: 10.1038/s41598-018-37443-4] [Citation(s) in RCA: 47] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2018] [Accepted: 11/30/2018] [Indexed: 01/31/2023] Open
Abstract
Increased Crabp2 levels have been found in various types of cancer, and are associated with poor patients’ survival. Although Crabp2 is found to be overexpressed in lung cancer, its role in metastasis of lung cancer is unclear. In this study, Crabp2 was overexpressed in high-metastatic C10F4 than low-metastatic lung cancer cells. Analysis of clinical samples revealed that high CRABP2 levels were correlated with lymph node metastases, poor overall survival, and increased recurrence. Knockdown of Crabp2 decreased migration, invasion, anoikis resistance, and in vivo metastasis. Crabp2 was co-immunoprecipitated with HuR, and overexpression of Crabp2 increased HuR levels, which promoted integrin β1/FAK/ERK signaling. Inhibition of HuR or integrin β1/FAK/ERK signaling reversed the promoting effect of Crabp2 in migration, invasion, and anoikis resistance. Knockdown of Crabp2 further inhibited the growth of cancer cells as compared with that by gemcitabine or irinotecan alone. The expression of Crabp2 in human lung tumors was correlated with stress marker CHOP. In conclusion, our findings have identified the promoting role of Crabp2 in anoikis resistance and metastasis. CRABP2 may serve as a prognostic marker and targeting CRABP2 may be exploited as a modality to reduce metastasis.
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Affiliation(s)
- Jun-I Wu
- Institute of Molecular and Genomic Medicine, National Health Research Institutes, Miaoli County, Taiwan.,Department of Life Sciences, National Central University, Taoyuan, Taiwan
| | - Yi-Pei Lin
- Institute of Molecular and Genomic Medicine, National Health Research Institutes, Miaoli County, Taiwan.,Institute of Molecular and Cellular Biology, National Taiwan University, Taipei, Taiwan
| | - Chien-Wei Tseng
- Institute of Molecular and Genomic Medicine, National Health Research Institutes, Miaoli County, Taiwan.,Graduate Institute of Integrated Medicine, China Medical University, Taichung, Taiwan
| | - Hui-Jane Chen
- Institute of Molecular and Genomic Medicine, National Health Research Institutes, Miaoli County, Taiwan
| | - Lu-Hai Wang
- Institute of Molecular and Genomic Medicine, National Health Research Institutes, Miaoli County, Taiwan. .,Department of Life Sciences, National Central University, Taoyuan, Taiwan. .,Institute of Molecular and Cellular Biology, National Taiwan University, Taipei, Taiwan. .,Graduate Institute of Integrated Medicine, China Medical University, Taichung, Taiwan. .,Chinese Medical Research Center, China Medical University, Taichung, Taiwan.
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39
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Wang Z, Zhang X. Single Cell Proteomics for Molecular Targets in Lung Cancer: High-Dimensional Data Acquisition and Analysis. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2018; 1068:73-87. [PMID: 29943297 DOI: 10.1007/978-981-13-0502-3_7] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
In the proteomic and genomic era, lung cancer researchers are increasingly under challenge with traditional protein analyzing tools. High output, multiplexed analytical procedures are in demand for disclosing the post-translational modification, molecular interactions and signaling pathways of proteins precisely, specifically, dynamically and systematically, as well as for identifying novel proteins and their functions. This could be better realized by single-cell proteomic methods than conventional proteomic methods. Using single-cell proteomic tools including flow cytometry, mass cytometry, microfluidics and chip technologies, chemical cytometry, single-cell western blotting, the quantity and functions of proteins are analyzed simultaneously. Aside from deciphering disease mechanisms, single-cell proteomic techniques facilitate the identification and screening of biomarkers, molecular targets and promising compounds as well. This review summarized single-cell proteomic tools and their use in lung cancer.
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Affiliation(s)
- Zheng Wang
- Department of Respiratory and Critical Care Medicine, Zhengzhou University People's Hospital, Zhengzhou, China
| | - Xiaoju Zhang
- Department of Respiratory and Critical Care Medicine, Zhengzhou University People's Hospital, Zhengzhou, China. .,Biomedical Research Center, Zhengzhou University People's Hospital, Zhengzhou, China.
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