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Xiu D, Mo Y, Liu C, Hu Y, Wang Y, Zhao Y, Guo T, Cheng K, Huang C, Liu L, Cheng M. Integrative Nomogram of Computed Tomography Radiomics, Clinical, and Tumor Immune Features for Analysis of Disease-Free Survival of NSCLC Patients with Surgery. JOURNAL OF ONCOLOGY 2023; 2023:8607062. [PMID: 36866239 PMCID: PMC9974282 DOI: 10.1155/2023/8607062] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/22/2022] [Revised: 08/10/2022] [Accepted: 11/25/2022] [Indexed: 02/23/2023]
Abstract
To improve prognosis of cancer patients and determine the integrative value for analysis of disease-free survival prediction, a clinic investigation was performed involving with 146 non-small cell lung cancer (NSCLC) patients (83 men and 73 women; mean age: 60.24 years ± 8.637) with a history of surgery. Their computed tomography (CT) radiomics, clinical records, and tumor immune features were firstly obtained and analyzed in this study. Histology and immunohistochemistry were also performed to establish a multimodal nomogram through the fitting model and cross-validation. Finally, Z test and decision curve analysis (DCA) were performed to evaluate and compare the accuracy and difference of each model. In all, seven radiomics features were selected to construct the radiomics score model. The clinicopathological and immunological factors model, including T stage, N stage, microvascular invasion, smoking quantity, family history of cancer, and immunophenotyping. The C-index of the comprehensive nomogram model on the training set and test set was 0.8766 and 0.8426 respectively, which was better than that of the clinicopathological-radiomics model (Z test, P =0.041<0.05), radiomics model and clinicopathological model (Z test, P =0.013<0.05 and P =0.0097<0.05). Integrative nomogram based on computed tomography radiomics, clinical and immunophenotyping can be served as effective imaging biomarker to predict DFS of hepatocellular carcinoma after surgical resection.
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Affiliation(s)
- Dianhui Xiu
- Department of Radiology, China-Japan Union Hospital of Jilin University, Changchun 130021, China
| | - Yan Mo
- Deepwise AI Lab, Beijing Deepwise & League of PHD Technology Co. Ltd., Beijing 100080, China
| | - Chaohui Liu
- Deepwise AI Lab, Beijing Deepwise & League of PHD Technology Co. Ltd., Beijing 100080, China
| | - Yu Hu
- Department of Pathology, China-Japan Union Hospital of Jilin University, Changchun 130021, China
| | - Yanjing Wang
- Department of Radiology, China-Japan Union Hospital of Jilin University, Changchun 130021, China
| | - Yiming Zhao
- Department of Radiology, China-Japan Union Hospital of Jilin University, Changchun 130021, China
| | - Tiantian Guo
- Department of Radiology, China-Japan Union Hospital of Jilin University, Changchun 130021, China
| | - Kailiang Cheng
- Department of Radiology, China-Japan Union Hospital of Jilin University, Changchun 130021, China
| | - Chencui Huang
- Deepwise AI Lab, Beijing Deepwise & League of PHD Technology Co. Ltd., Beijing 100080, China
| | - Lin Liu
- Department of Radiology, China-Japan Union Hospital of Jilin University, Changchun 130021, China
| | - Min Cheng
- Department of Radiology, China-Japan Union Hospital of Jilin University, Changchun 130021, China
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Öberg K. Molecular Genomic Blood Biomarkers for Neuroendocrine Tumors: The Long and Winding Road from Berzelius and Bence Jones to a Neuroendocrine Destination. Neuroendocrinology 2021; 111:297-303. [PMID: 32380502 DOI: 10.1159/000508488] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/19/2020] [Accepted: 05/06/2020] [Indexed: 12/13/2022]
Affiliation(s)
- Kjell Öberg
- Department of Endocrine Oncology, University Hospital, Uppsala, Sweden,
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Malczewska A, Kos-Kudła B, Kidd M, Drozdov I, Bodei L, Matar S, Oberg K, Modlin IM. The clinical applications of a multigene liquid biopsy (NETest) in neuroendocrine tumors. Adv Med Sci 2020; 65:18-29. [PMID: 31841822 PMCID: PMC7453408 DOI: 10.1016/j.advms.2019.10.002] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2019] [Revised: 09/19/2019] [Accepted: 10/18/2019] [Indexed: 02/07/2023]
Abstract
PURPOSE There are few effective biomarkers for neuroendocrine tumors. Precision oncology strategies have provided liquid biopsies for real-time and tailored decision-making. This has led to the development of the first neuroendocrine tumor liquid biopsy (the NETest). The NETest represents a transcriptomic signature of neuroendocrine tumor (NETs) that captures tumor biology and disease activity. The data have direct clinical application in terms of identifying residual disease, disease progress and the efficacy of treatment. In this overview we assess the available published information on the metrics and clinical efficacy of the NETest. MATERIAL AND METHODS Published data on the NETest have been collated and analyzed to understand the clinical application of this multianalyte biomarker in NETs. RESULTS NETest assay has been validated as a standardized and reproducible clinical laboratory measurement. It is not affected by demographic characteristics, or acid suppressive medication. Clinical utility of the NETest has been documented in gastroenteropancreatic, bronchopulmonary NETs, in paragangliomas and pheochromocytomas. The test facilitates accurate diagnosis of a NET disease, and real-time monitoring of the disease status (stable/progressive disease). It predicts aggressive tumor behavior, identifies operative tumor resection, and efficacy of the medical treatment (e.g. somatostatin analogues), or peptide receptor radionuclide therapy (PRRT). NETest metrics and clinical applications out-perform standard biomarkers like chromogranin A. CONCLUSIONS The NETest exhibits clinically competent metrics as an effective biomarker for neuroendocrine tumors. Measurement of NET transcripts in blood is a significant advance in neuroendocrine tumor management and demonstrates that blood provides a viable source to identify and monitor tumor status.
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Affiliation(s)
- Anna Malczewska
- Department of Endocrinology and Neuroendocrine Tumors, Medical University of Silesia, Katowice, Poland.
| | - Beata Kos-Kudła
- Department of Endocrinology and Neuroendocrine Tumors, Medical University of Silesia, Katowice, Poland
| | - Mark Kidd
- Wren Laboratories, Branford, CT, USA
| | | | - Lisa Bodei
- Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | | | - Kjell Oberg
- Department of Endocrine Oncology, University Hospital, Uppsala, Sweden
| | - Irvin M Modlin
- Gastroenterological Surgery, Yale University School of Medicine, New Haven, CT, USA
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Pavel M, Jann H, Prasad V, Drozdov I, Modlin IM, Kidd M. NET Blood Transcript Analysis Defines the Crossing of the Clinical Rubicon: When Stable Disease Becomes Progressive. Neuroendocrinology 2017; 104:170-182. [PMID: 27078712 DOI: 10.1159/000446025] [Citation(s) in RCA: 68] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/11/2016] [Accepted: 04/05/2016] [Indexed: 12/13/2022]
Abstract
BACKGROUND/AIMS A key issue in gastroenteropancreatic neuroendocrine tumors (GEP-NETs) is early identification and prediction of disease progression. Clinical evaluation and imaging are limited due to the lack of sensitivity and disease indolence. We assessed the NETest as a predictive and prognostic marker of progression in a long-term follow-up study. METHODS GEP-NETs (n = 34) followed for a median 4 years (2.2-5.4) were evaluated. WHO tumor grade/stage grade 1: n = 17, grade 2: n = 14, grade 3: n = 1 (for 2, no grade was available); 31 (91%) were stage IV. Baseline and longitudinal imaging and blood biomarkers were available in all, and progression was defined per standard clinical protocols (RECIST 1.0). The NETest was measured by quantitative PCR of blood and multianalyte algorithmic analysis (disease activity scaled 0-100% with low <40% and high activity risk cutoffs >80%); chromogranin A (CgA) was measured by radioimmunoassay (normal <150 µg/l); progression-free survival (PFS) was analyzed by Cox proportional-hazard regression and Kaplan-Meier analysis. RESULTS At baseline, 100% were NETest positive, and CgA was elevated in 50%. The only baseline variable (Cox modeling) associated with PFS was NETest (hazard ratio = 1.022, 95% confidence interval = 1.005-1.04; p < 0.012). Using Kaplan-Meier analyses, the baseline NETest (>80%) was significantly associated (p = 0.01) with disease progression (median PFS 0.68 vs. 2.78 years with <40% levels). The NETest was more informative (96%) than CgA changes (<under>></under>25%) in consistently predicting disease alterations (40%, p < 2 × 10-5, χ2 = 18). The NETest had an earlier time point change than imaging (1.02 ± 0.15 years). Baseline NETest levels >40% in stable disease were 100% prognostic of disease progression versus CgA (χ2 = 5, p < 0.03). Baseline NETest values <40% accurately (100%) predicted stability over 5 years (p = 0.05, χ2 = 3.8 vs. CgA). CONCLUSION The NETest correlated with a well-differentiated GEP-NET clinical status. The NETest has predictive and prognostic utility for GEP-NETs identifying clinically actionable alterations ∼1 year before image-based evidence of progression.
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Affiliation(s)
- Marianne Pavel
- Department of Hepatology and Gastroenterology, Campus-Virchow-Klinikum, Berlin, Germany
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Oberg K, Krenning E, Sundin A, Bodei L, Kidd M, Tesselaar M, Ambrosini V, Baum RP, Kulke M, Pavel M, Cwikla J, Drozdov I, Falconi M, Fazio N, Frilling A, Jensen R, Koopmans K, Korse T, Kwekkeboom D, Maecke H, Paganelli G, Salazar R, Severi S, Strosberg J, Prasad V, Scarpa A, Grossman A, Walenkamp A, Cives M, Virgolini I, Kjaer A, Modlin IM. A Delphic consensus assessment: imaging and biomarkers in gastroenteropancreatic neuroendocrine tumor disease management. Endocr Connect 2016; 5:174-87. [PMID: 27582247 PMCID: PMC5045519 DOI: 10.1530/ec-16-0043] [Citation(s) in RCA: 68] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/18/2016] [Accepted: 08/31/2016] [Indexed: 12/17/2022]
Abstract
The complexity of the clinical management of neuroendocrine neoplasia (NEN) is exacerbated by limitations in imaging modalities and a paucity of clinically useful biomarkers. Limitations in currently available imaging modalities reflect difficulties in measuring an intrinsically indolent disease, resolution inadequacies and inter-/intra-facility device variability and that RECIST (Response Evaluation Criteria in Solid Tumors) criteria are not optimal for NEN. Limitations of currently used biomarkers are that they are secretory biomarkers (chromogranin A, serotonin, neuron-specific enolase and pancreastatin); monoanalyte measurements; and lack sensitivity, specificity and predictive capacity. None of them meet the NIH metrics for clinical usage. A multinational, multidisciplinary Delphi consensus meeting of NEN experts (n = 33) assessed current imaging strategies and biomarkers in NEN management. Consensus (>75%) was achieved for 78% of the 142 questions. The panel concluded that morphological imaging has a diagnostic value. However, both imaging and current single-analyte biomarkers exhibit substantial limitations in measuring the disease status and predicting the therapeutic efficacy. RECIST remains suboptimal as a metric. A critical unmet need is the development of a clinico-biological tool to provide enhanced information regarding precise disease status and treatment response. The group considered that circulating RNA was better than current general NEN biomarkers and preliminary clinical data were considered promising. It was resolved that circulating multianalyte mRNA (NETest) had clinical utility in both diagnosis and monitoring disease status and therapeutic efficacy. Overall, it was concluded that a combination of tumor spatial and functional imaging with circulating transcripts (mRNA) would represent the future strategy for real-time monitoring of disease progress and therapeutic efficacy.
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Affiliation(s)
| | | | | | - Lisa Bodei
- Memorial Sloan Kettering Cancer CenterNew York, New York, USA
| | - Mark Kidd
- Wren LaboratoriesBranford, Connecticut, USA
| | | | | | | | - Matthew Kulke
- Dana Farber Cancer InstituteBoston, Massachusetts, USA
| | | | | | | | | | - Nicola Fazio
- IEO (European Institute of Oncology)Milan, Italy
| | | | - Robert Jensen
- National Institutes of HealthBethesda, Maryland, USA
| | | | - Tiny Korse
- Netherlands Cancer InstituteAmsterdam, Netherlands
| | | | | | - Giovanni Paganelli
- Instituto Scientifico Romagnolo per lo Studio e la Cura dei TumoriMeldola, Italy
| | | | - Stefano Severi
- Instituto Scientifico Romagnolo per lo Studio e la Cura dei TumoriMeldola, Italy
| | | | | | | | | | | | - Mauro Cives
- H. Lee Moffitt Cancer CenterTampa, Florida, USA
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Wang L, Xu Y, Luo C, Sun J, Zhang J, Lee MW, Bai A, Chen G, Frenz CM, Li Z, Huang W. MAGEA10 gene expression in non-small cell lung cancer and A549 cells, and the affinity of epitopes with the complex of HLA-A(∗)0201 alleles. Cell Immunol 2015; 297:10-8. [PMID: 26058806 DOI: 10.1016/j.cellimm.2015.05.004] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2015] [Revised: 05/11/2015] [Accepted: 05/14/2015] [Indexed: 12/15/2022]
Abstract
MAGEA10, a cancer/testis antigens expressed in tumors but not in normal tissues with the exception of testis and placenta, represents an attractive target for cancer immunotherapy. However, suppressive cytoenvironment and requirement of specific HLA-alleles presentation frequently led to immunotherapy failure. In this study MAGEA10 was scarcely expressed in cancer patients, but enhanced by viili polysaccharides, which indicates a possibility of increasing epitopes presentation. Furthermore the correlation of gene expression with methylation, indicated by R(2) value for MAGEA10 that was 3 times higher than the value for other MAGE genes tested, provides an explanation of why MAGEA10 was highly inhibited, this is also seen by Kaplan-Meier analysis because MAGEA10 did not change the patients' lifespan. By using Molecular-Docking method, 3 MAGEA10 peptides were found binding to the groove position of HLA-A(∗)0210 as same as MAGEA4 peptide co-crystallized with HLA-A(∗)0210, which indicates that they could be promising for HLA-A(∗)0201 presentation in immunotherapy.
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Affiliation(s)
- Likui Wang
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, PR China.
| | - Yuefang Xu
- Department of pharmacy, First Hospital Affiliated to PLA General Hospital, Beijing 100037, PR China.
| | - Cheng Luo
- Department of Biotechnology, University of Tartu, Riia 23, Tartu 51010, Estonia.
| | - Jian Sun
- Department of Chemistry, The University of Hong Kong, Hong Kong.
| | - Jinlu Zhang
- School of Food Engineering and Biotechnology, Tianjin University of Science and Technology, Tianjin, PR China.
| | - Ming-Wei Lee
- School of Medical Laboratory and Biotechnology, Chung-Shan Medical University, No. 110, Sec. 1, Jianguo N. Rd., Taichung City 402, Taiwan.
| | - Aiping Bai
- Department of Medicine, Beth Israel Deaconess Medical Center, Harvard University, Boston, MA 02215, USA.
| | - Guanhua Chen
- Department of Chemistry, The University of Hong Kong, Hong Kong.
| | - Christopher M Frenz
- Department of Mathematics and Computer Science, Mercy College, Dobbs Ferry, NY, USA.
| | - Zhengguo Li
- School of Life Science, Chongqing University, Chongqing 400030, China.
| | - Wenlin Huang
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, PR China.
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Su Y, Pan L. Identification of logic relationships between genes and subtypes of non-small cell lung cancer. PLoS One 2014; 9:e94644. [PMID: 24743794 PMCID: PMC3990524 DOI: 10.1371/journal.pone.0094644] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2013] [Accepted: 03/18/2014] [Indexed: 11/23/2022] Open
Abstract
Non-small cell lung cancer (NSCLC) has two major subtypes: adenocarcinoma (AC) and squamous cell carcinoma (SCC). The diagnosis and treatment of NSCLC are hindered by the limited knowledge about the pathogenesis mechanisms of subtypes of NSCLC. It is necessary to research the molecular mechanisms related with AC and SCC. In this work, we improved the logic analysis algorithm to mine the sufficient and necessary conditions for the presence states (presence or absence) of phenotypes. We applied our method to AC and SCC specimens, and identified lower and higher logic relationships between genes and two subtypes of NSCLC. The discovered relationships were independent of specimens selected, and their significance was validated by statistic test. Compared with the two earlier methods (the non-negative matrix factorization method and the relevance analysis method), the current method outperformed these methods in the recall rate and classification accuracy on NSCLC and normal specimens. We obtained biomarkers. Among biomarkers, genes have been used to distinguish AC from SCC in practice, and other six genes were newly discovered biomarkers for distinguishing subtypes. Furthermore, NKX2-1 has been considered as a molecular target for the targeted therapy of AC, and other genes may be novel molecular targets. By gene ontology analysis, we found that two biological processes (‘epidermis development’ and ‘cell adhesion’) were closely related with the tumorigenesis of subtypes of NSCLC. More generally, the current method could be extended to other complex diseases for distinguishing subtypes and detecting the molecular targets for targeted therapy.
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Affiliation(s)
- Yansen Su
- Key Laboratory of Image Information Processing and Intelligent Control, School of Automation, Huazhong University of Science and Technology, Wuhan, Hubei, China
- * E-mail: (YS); (LP)
| | - Linqiang Pan
- Key Laboratory of Image Information Processing and Intelligent Control, School of Automation, Huazhong University of Science and Technology, Wuhan, Hubei, China
- * E-mail: (YS); (LP)
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