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Genomic and Glycolytic Entropy Are Reliable Radiogenomic Heterogeneity Biomarkers for Non-Small Cell Lung Cancer. Int J Mol Sci 2023; 24:ijms24043988. [PMID: 36835402 PMCID: PMC9959107 DOI: 10.3390/ijms24043988] [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: 12/29/2022] [Revised: 02/08/2023] [Accepted: 02/15/2023] [Indexed: 02/18/2023] Open
Abstract
Radiogenomic heterogeneity features in 18F-fluorodeoxyglucose positron emission tomography (18F-FDG PET) have become popular in non-small cell lung cancer (NSCLC) research. However, the reliabilities of genomic heterogeneity features and of PET-based glycolytic features in different image matrix sizes have yet to be thoroughly tested. We conducted a prospective study with 46 NSCLC patients to assess the intra-class correlation coefficient (ICC) of different genomic heterogeneity features. We also tested the ICC of PET-based heterogeneity features from different image matrix sizes. The association of radiogenomic features with clinical data was also examined. The entropy-based genomic heterogeneity feature (ICC = 0.736) is more reliable than the median-based feature (ICC = -0.416). The PET-based glycolytic entropy was insensitive to image matrix size change (ICC = 0.958) and remained reliable in tumors with a metabolic volume of <10 mL (ICC = 0.894). The glycolytic entropy is also significantly associated with advanced cancer stages (p = 0.011). We conclude that the entropy-based radiogenomic features are reliable and may serve as ideal biomarkers for research and further clinical use for NSCLC.
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Martin D, Smith SC, Chesney A, Jackson-Cook C, Pillappa R. Too Sensitive or Just Right? Am J Clin Pathol 2022; 158:283-290. [PMID: 35482487 DOI: 10.1093/ajcp/aqac043] [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: 10/27/2021] [Accepted: 03/14/2022] [Indexed: 11/13/2022] Open
Abstract
OBJECTIVES To compare the performance of the rabbit monoclonal antihuman CD246 antibody (D5F3 clone) with the established ALK1 clone for immunohistochemical assessment of anaplastic large cell lymphoma (ALCL). METHODS Archival cases of ALCL (n = 27) were assessed immunohistochemically by use of ALK1 and D5F3 clones under standard Clinical Laboratory Improvement Amendments-compliant conditions. The intensity of cytoplasmic staining (0 = none; 1 = faint; 2 = moderate; 3+ = strong) and proportion of neoplastic cells (0%, <5%, 5%-50%, >50%) were evaluated and compared with clinical ALK break-apart fluorescence in situ hybridization (FISH) assays. RESULTS Nine ALCL specimens were positive for ALK expression by ALK1 staining (33%; 1 = 1+; 0 = 2+; 8 = 3+), while 14 were positive by D5F3 staining (48%; 3 = 1+; 1 = 2+; 10 = 3+). Across the cohort, D5F3 staining showed a significantly greater proportion of cells staining positive (P = .02) and greater intensity (P = .03). Of 3 cases positive for D5F3 only with FISH results, none showed rearrangements, although 1 showed copy number gains at the ALK locus in a subset of cells. CONCLUSIONS Overall, D5F3 showed greater stain intensity and proportion staining than ALK1 in ALK-positive ALCL cases, which is especially helpful in limited samples. Caution and consideration of orthogonal ALK testing types is recommended, especially for cases with weak or focal staining.
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Affiliation(s)
- Dana Martin
- Department of Pathology, Virginia Commonwealth University (VCU) School of Medicine, Richmond, VA, USA
| | - Steven C Smith
- Department of Pathology, Virginia Commonwealth University (VCU) School of Medicine, Richmond, VA, USA
- Department of Surgery, Virginia Commonwealth University (VCU) School of Medicine, Richmond, VA, USA
| | - Alden Chesney
- Department of Pathology, Virginia Commonwealth University (VCU) School of Medicine, Richmond, VA, USA
| | - Colleen Jackson-Cook
- Department of Pathology, Virginia Commonwealth University (VCU) School of Medicine, Richmond, VA, USA
- Department of Human and Molecular Genetics, VCU Health, Richmond, VA, USA
| | - Raghavendra Pillappa
- Department of Pathology, Virginia Commonwealth University (VCU) School of Medicine, Richmond, VA, USA
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Pinsolle J, McLeer-Florin A, Giaj Levra M, de Fraipont F, Emprou C, Gobbini E, Toffart AC. Translating Systems Medicine Into Clinical Practice: Examples From Pulmonary Medicine With Genetic Disorders, Infections, Inflammations, Cancer Genesis, and Treatment Implication of Molecular Alterations in Non-small-cell Lung Cancers and Personalized Medicine. Front Med (Lausanne) 2019; 6:233. [PMID: 31737634 PMCID: PMC6828737 DOI: 10.3389/fmed.2019.00233] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2019] [Accepted: 10/03/2019] [Indexed: 12/30/2022] Open
Abstract
Non-small-cell lung cancers (NSCLC) represent 85% of all lung cancers, with adenocarcinoma as the most common subtype. Since the 2000's, the discovery of molecular alterations including epidermal growth factor receptor (EGFR) mutations and anaplastic lymphoma kinase (ALK) rearrangements together with the development of specific tyrosine kinase inhibitors (TKIs) has facilitated the development of personalized medicine in the management of this disease. This review focuses on the biology of molecular alterations in NSCLC as well as the diagnostic tools and therapeutic alternatives available for each targetable alteration. Rapid and sensitive methods are essential to detect gene alterations, using tumor tissue biopsies or liquid biopsies. Massive parallel sequencing or Next Generation Sequencing (NGS) allows to simultaneously analyze numerous genes from relatively low amounts of DNA. The detection of oncogenic fusions can be conducted using fluorescence in situ hybridization, reverse-transcription polymerase chain reaction, immunohistochemistry, or NGS. EGFR mutations, ALK and ROS1 rearrangements, MET (MET proto-oncogenereceptor tyrosine kinase), BRAF (B-Raf proto-oncogen serine/threonine kinase), NTRK (neurotrophic tropomyosin receptor kinase), and RET (ret proto-oncogene) alterations are described with their respective TKIs, either already authorized or still in development. We have herein paid particular attention to the mechanisms of resistance to EGFR and ALK-TKI. As a wealth of diagnostic tools and personalized treatments are currently under development, a close collaboration between molecular biologists, pathologists, and oncologists is crucial.
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Affiliation(s)
- Julian Pinsolle
- Department of Pneumology, CHU Grenoble Alpes, Grenoble, France
- Medicine Faculty, Université Grenoble Alpes, Grenoble, France
| | - Anne McLeer-Florin
- Medicine Faculty, Université Grenoble Alpes, Grenoble, France
- Departement of Pathological Anatomy and Cytology, Pôle de Biologie et Pathologie, CHU Grenoble Alpes, Grenoble, France
- UGA/INSERM U1209/CNRS 5309-Institute for Advanced Biosciences - Université Grenoble Alpes, Grenoble, France
| | - Matteo Giaj Levra
- Department of Pneumology, CHU Grenoble Alpes, Grenoble, France
- Department of Biochemistry, Molecular Biology and Environmental Toxicology, CHU Grenoble Alpes, Grenoble, France
| | - Florence de Fraipont
- UGA/INSERM U1209/CNRS 5309-Institute for Advanced Biosciences - Université Grenoble Alpes, Grenoble, France
- Department of Biochemistry, Molecular Biology and Environmental Toxicology, CHU Grenoble Alpes, Grenoble, France
| | - Camille Emprou
- Medicine Faculty, Université Grenoble Alpes, Grenoble, France
- Departement of Pathological Anatomy and Cytology, Pôle de Biologie et Pathologie, CHU Grenoble Alpes, Grenoble, France
| | - Elisa Gobbini
- Department of Pneumology, CHU Grenoble Alpes, Grenoble, France
- Cancer Research Center Lyon, Centre Léon Bérard, Lyon, France
| | - Anne-Claire Toffart
- Department of Pneumology, CHU Grenoble Alpes, Grenoble, France
- Medicine Faculty, Université Grenoble Alpes, Grenoble, France
- UGA/INSERM U1209/CNRS 5309-Institute for Advanced Biosciences - Université Grenoble Alpes, Grenoble, France
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Genomic heterogeneity of ALK fusion breakpoints in non-small-cell lung cancer. Mod Pathol 2018; 31:791-808. [PMID: 29327716 DOI: 10.1038/modpathol.2017.181] [Citation(s) in RCA: 60] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2017] [Revised: 10/24/2017] [Accepted: 10/26/2017] [Indexed: 01/06/2023]
Abstract
In lung adenocarcinoma, canonical EML4-ALK inversion results in a fusion protein with a constitutively active ALK kinase domain. Evidence of ALK rearrangement occurs in a minority (2-7%) of lung adenocarcinoma, and only ~60% of these patients will respond to targeted ALK inhibition by drugs such as crizotinib and ceritinib. Clinically, targeted anti-ALK therapy is often initiated based on evidence of an ALK genomic rearrangement detected by fluorescence in situ hybridization (FISH) of interphase cells in formalin-fixed, paraffin-embedded tissue sections. At the genomic level, however, ALK rearrangements are heterogeneous, with multiple potential breakpoints in EML4, and alternate fusion partners. Using next-generation sequencing of DNA and RNA together with ALK immunohistochemistry, we comprehensively characterized genomic breakpoints in 33 FISH-positive lung adenocarcinomas. Of these 33 cases, 29 (88%) had detectable DNA level ALK rearrangements involving EML4, KIF5B, or non-canonical partners including ASXL2, ATP6V1B1, PRKAR1A, and SPDYA. A subset of 12 cases had material available for RNA-Seq. Of these, eight of eight (100%) cases with DNA rearrangements showed ALK fusion transcripts from RNA-Seq; three of four cases (75%) without detectable DNA rearrangements were similarly negative by RNA-Seq, and one case was positive by RNA-Seq but negative by DNA next-generation sequencing. By immunohistochemistry, 17 of 19 (89%) tested cases were clearly positive for ALK protein expression; the remaining cases had no detectable DNA level rearrangement or had a non-canonical rearrangement not predicted to form a fusion protein. Survival analysis of patients treated with targeted ALK inhibitors demonstrates a significant difference in mean survival between patients with next-generation sequencing confirmed EML4-ALK rearrangements, and those without (20.6 months vs 5.4 months, P<0.01). Together, these data demonstrate abundant genomic heterogeneity among ALK-rearranged lung adenocarcinoma, which may account for differences in treatment response with targeted ALK inhibitors.
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Lu Z, Chen Y, Jing X, Hu C. Diagnostic accuracy of MALDI-TOF mass spectrometry for non-small cell lung cancer: a meta-analysis. Biomarkers 2018; 23:245-252. [PMID: 29264950 DOI: 10.1080/1354750x.2017.1420822] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Affiliation(s)
- Zhaolian Lu
- School of Graduate, Second Military Medical University, Shanghai, China
- Department of Laboratory Medicine, General Hospital of Jinan Military Command Region, Jinan, China
| | - Yingjian Chen
- Department of Laboratory Medicine, General Hospital of Jinan Military Command Region, Jinan, China
| | - Xinyan Jing
- School of Graduate, Weifang Medical University, Weifang, China
| | - Chengjin Hu
- Department of Laboratory Medicine, General Hospital of Jinan Military Command Region, Jinan, China
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Huang L, Zhou JG, Yao WX, Tian X, Lv SP, Zhang TY, Jin SH, Bai YJ, Ma H. Systematic review and meta-analysis of the efficacy of serum neuron-specific enolase for early small cell lung cancer screening. Oncotarget 2017; 8:64358-64372. [PMID: 28969076 PMCID: PMC5610008 DOI: 10.18632/oncotarget.17825] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2017] [Accepted: 04/11/2017] [Indexed: 11/25/2022] Open
Abstract
We performed a pooled analysis of the efficacy of serum neuron-specific enolase (NSE) levels for early detection of small cell lung cancer (SCLC) in patients with benign lung diseases and healthy individuals. Comprehensive searches of several databases through September 2016 were conducted. The quality of the included studies was assessed using the Quality Assessment of Diagnostic Accuracy Studies (QUADAS-2) tool. Ultimately, 33 studies containing 9546 samples were included in the review. Pooled sensitivity of NSE for detecting SCLC was 0.688 (95%CI: 0.627-0.743), specificity was 0.921 (95%CI: 0.890-0.944), positive likelihood ratio was 8.744 (95%CI: 6.308-12.121), negative likelihood ratio was 0.339 (95%CI: 0.283- 0.405), diagnostic odds ratio was 25.827 (95%CI: 17.490- 38.136) and area under the curve was 0.88 (95%CI: 0.85- 0.91). Meta-regression indicated that study region was a source of heterogeneity in the sensitivity and joint models, while cut-off level was a source in the joint model. Subgroup analysis showed that enzyme linked immunosorbent assays had the highest sensitivity and radioimmunoassay assays had the highest specificity. The diagnostic performance was better in Europe [sensitivity: 0.740 (95%CI: 0.676-0.795), specificity: 0.932 (95%CI: 0.904-0.953)] than in Asia [sensitivity: 0.590 (95%CI: 0.496- 0.678), specificity: 0.901 (95%CI: 0.819-0.948)]. In Europe, 25 ng/ml is likely the most suitable NSE cut-off level. NSE thus has high diagnostic efficacy when screening for SCLC, though the efficacy differs depending on study region, assay method and cut-off level. In the clinic, NSE measurements should be considered along with clinical symptoms, image results and histopathology.
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Affiliation(s)
- Lang Huang
- Department of Oncology, Affiliated Hospital of Zunyi Medical University, Zunyi 563000, China
| | - Jian-Guo Zhou
- Department of Oncology, Affiliated Hospital of Zunyi Medical University, Zunyi 563000, China
| | - Wen-Xiu Yao
- Department of Oncology, Affiliated Cancer Hospital of Medical School, University of Electronic Science and Technology of China, Sichuan Cancer Hospital and Institute & Cancer, The Second People's Hospital of Sichuan Province, Chengdu 610000, China
| | - Xu Tian
- Chongqing Cancer Hospital and Institute, Chongqing 40030, China
| | - Shui-Ping Lv
- Department of Oncology, Affiliated Hospital of Zunyi Medical University, Zunyi 563000, China
| | - Ting-You Zhang
- Department of Oncology, Affiliated Hospital of Zunyi Medical University, Zunyi 563000, China
| | - Shu-Han Jin
- Department of Cardiology and Endodontics, Affiliated Stomatological Hospital of Zunyi Medical University, Zunyi 563000, China
| | - Yu-Ju Bai
- Department of Oncology, Affiliated Hospital of Zunyi Medical University, Zunyi 563000, China
| | - Hu Ma
- Department of Oncology, Affiliated Hospital of Zunyi Medical University, Zunyi 563000, China
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