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Leiro-Fernandez V, De Chiara L, Rodríguez-Girondo M, Botana-Rial M, Valverde D, Núñez-Delgado M, Fernández-Villar A. Methylation Assessment for the Prediction of Malignancy in Mediastinal Adenopathies Obtained by Endobronchial Ultrasound-Guided Transbronchial Needle Aspiration in Patients with Lung Cancer. Cancers (Basel) 2019; 11:cancers11101408. [PMID: 31547177 PMCID: PMC6826358 DOI: 10.3390/cancers11101408] [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: 08/19/2019] [Revised: 09/13/2019] [Accepted: 09/18/2019] [Indexed: 12/11/2022] Open
Abstract
The evaluation of mediastinal lymph nodes is critical for the correct staging of patients with lung cancer (LC). Endobronchial ultrasound-guided transbronchial needle aspiration (EBUS-TBNA) is a minimally invasive technique for mediastinal staging, though unfortunately lymph node micrometastasis is often missed by cytological analysis. The aim of this study was to evaluate the predictive capacity of methylation biomarkers and provide a classification rule for predicting malignancy in false negative EBUS-TBNA samples. The study included 112 patients with a new or suspected diagnosis of LC that were referred to EBUS-TBNA. Methylation of p16/INK4a, MGMT, SHOX2, E-cadherin, DLEC1, and RASSF1A was quantified by nested methylation-specific qPCR in 218 EBUS-TBNA lymph node samples. Cross-validated linear regression models were evaluated to predict malignancy. According to EBUS-TBNA and final diagnosis, 90 samples were true positives for malignancy, 110 were true negatives, and 18 were false negatives. MGMT, SHOX2, and E-cadherin were the methylation markers that better predicted malignancy. The model including sex, age, short axis diameter and standard uptake value of adenopathy, and SHOX2 showed 82.7% cross-validated sensitivity and 82.4% specificity for the detection of malignant lymphadenopathies among negative cytology samples. Our results suggest that the predictive model approach proposed can complement EBUS-TBNA for mediastinal staging.
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Affiliation(s)
- Virginia Leiro-Fernandez
- Pulmonary Department, Hospital Álvaro Cunqueiro, Vigo Health Area, 36312 Vigo, Spain; (M.B.-R.); (M.N.-D.); (A.F.-V.)
- NeumoVigoI+i Research Group, Vigo Biomedical Research Institute (IBIV), 36312 Vigo, Spain
- Correspondence: (L.D.C.); (V.L.-F.)
| | - Loretta De Chiara
- Department of Biochemistry, Genetics and Immunology, Biomedical Research Center (CINBIO), University of Vigo, 36310 Vigo, Spain;
- Correspondence: (L.D.C.); (V.L.-F.)
| | - Mar Rodríguez-Girondo
- Department of Medical Statistics and Bioinformatics, Leiden University Medical Center, 2300 RC Leiden, The Netherlands;
- SiDOR Research Group, Biomedical Research Center (CINBIO), University of Vigo, 36310 Vigo, Spain
| | - Maribel Botana-Rial
- Pulmonary Department, Hospital Álvaro Cunqueiro, Vigo Health Area, 36312 Vigo, Spain; (M.B.-R.); (M.N.-D.); (A.F.-V.)
- NeumoVigoI+i Research Group, Vigo Biomedical Research Institute (IBIV), 36312 Vigo, Spain
| | - Diana Valverde
- Department of Biochemistry, Genetics and Immunology, Biomedical Research Center (CINBIO), University of Vigo, 36310 Vigo, Spain;
| | - Manuel Núñez-Delgado
- Pulmonary Department, Hospital Álvaro Cunqueiro, Vigo Health Area, 36312 Vigo, Spain; (M.B.-R.); (M.N.-D.); (A.F.-V.)
- NeumoVigoI+i Research Group, Vigo Biomedical Research Institute (IBIV), 36312 Vigo, Spain
| | - Alberto Fernández-Villar
- Pulmonary Department, Hospital Álvaro Cunqueiro, Vigo Health Area, 36312 Vigo, Spain; (M.B.-R.); (M.N.-D.); (A.F.-V.)
- NeumoVigoI+i Research Group, Vigo Biomedical Research Institute (IBIV), 36312 Vigo, Spain
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Gleeson FC, Kipp BR, Voss JS, Campion MB, Minot DM, Tu ZJ, Klee EW, Graham RP, Lazaridis KN, Henry MR, Levy MJ. Frequency of mitogen-activated protein kinase and phosphoinositide 3-kinase signaling pathway pathogenic alterations in EUS-FNA sampled malignant lymph nodes in rectal cancer with theranostic potential. Gastrointest Endosc 2015; 82:550-6.e1. [PMID: 25887718 DOI: 10.1016/j.gie.2015.01.050] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/19/2014] [Accepted: 01/24/2015] [Indexed: 12/31/2022]
Abstract
BACKGROUND Targeted next-generation sequencing has the potential to stratify a tumor by molecular subtype and aid the development of a biomarker profile for prognostic risk stratification and theranostic potential. OBJECTIVE To assess the frequency and distribution of pathogenic alterations in malignant lymph node cytology specimens. DESIGN Multigene molecular profiling of archived malignant EUS-FNA lymph node cytology specimens using the Ion Ampliseq Cancer Hotspot Panel v2, which targets at least 2855 possible mutations within 50 cancer-associated genes. SETTING Single tertiary referral center. PATIENTS Sporadic, treatment naive, locally advanced primary rectal cancer by EUS-FNA (n = 76) who subsequently completed neoadjuvant therapy with on-site oncologic surgery. MAIN OUTCOME MEASUREMENTS The frequency and distribution of pathogenic alterations in malignant lymph node cytology specimens by the mitogen-activated protein kinase (MAPK) or phosphoinositide 3-kinase (PI3K) signaling pathways, by KRAS or NRAS wild-type lymph node status, by extramesenteric lymph node status, and by a complete pathologic response status. RESULTS Eleven patients (14.5%) were 50-gene panel wild-type. Sixty-five patients had 139 pathogenic alterations (2 [1-3] per patient) in 13 of 50 evaluated genes. The following represent a spectrum of identified alterations: TP53 (n = 52; 68.4%), APC (n = 36; 47.4%), KRAS (n = 22; 28.9%), FBXW7 (n = 8; 10.5%), NRAS (n = 6; 7.9%), PIK3CA (n = 4; 5.3%), SMAD4 (n = 3; 3.9%), and BRAF (n = 3; 3.9%). Pathogenic alterations were identified in the MAPK and PI3K signaling pathways in 41% and 5% of patients, respectively. LIMITATIONS Findings were limited to a 50 cancer-associated gene analysis. CONCLUSIONS Molecular EUS lymph node assessments using cancer "hotspot" panels can identify pathogenic alteration frequency and distribution and have theranostic potential for individualized patient care.
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Affiliation(s)
- Ferga C Gleeson
- Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, Minnesota, USA
| | - Benjamin R Kipp
- Department of Anatomic Pathology, Mayo Clinic, Rochester, Minnesota, USA
| | - Jesse S Voss
- Department of Anatomic Pathology, Mayo Clinic, Rochester, Minnesota, USA
| | - Michael B Campion
- Department of Anatomic Pathology, Mayo Clinic, Rochester, Minnesota, USA
| | - Douglas M Minot
- Department of Anatomic Pathology, Mayo Clinic, Rochester, Minnesota, USA
| | - Zheng J Tu
- Division of Biomedical Statics and Informatics, Department of Health Sciences Research, Mayo Clinic, Rochester, Minnesota, USA
| | - Eric W Klee
- Division of Biomedical Statics and Informatics, Department of Health Sciences Research, Mayo Clinic, Rochester, Minnesota, USA
| | - Rondell P Graham
- Department of Anatomic Pathology, Mayo Clinic, Rochester, Minnesota, USA
| | - Konstantinos N Lazaridis
- Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, Minnesota, USA; Center for Individualized Medicine, Mayo Clinic, Rochester, Minnesota, USA
| | - Michael R Henry
- Department of Anatomic Pathology, Mayo Clinic, Rochester, Minnesota, USA
| | - Michael J Levy
- Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, Minnesota, USA
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Gleeson FC, Kipp BR, Voss JS, Campion MB, Minot DM, Tu ZJ, Klee EW, Sciallis AP, Graham RP, Lazaridis KN, Henry MR, Levy MJ. Endoscopic ultrasound fine-needle aspiration cytology mutation profiling using targeted next-generation sequencing: personalized care for rectal cancer. Am J Clin Pathol 2015; 143:879-88. [PMID: 25972331 DOI: 10.1309/ajcpu3j7fgayqbrl] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
OBJECTIVES In an era of precision medicine, our aim was to determine the frequency and theranostic potential of mutations identified in malignant lymph nodes (LNs) sampled by endoscopic ultrasound fine-needle aspiration (EUS FNA) of patients with rectal cancer by targeted next-generation sequencing (NGS). METHODS The NGS Ion AmpliSeq Cancer Hotspot Panel v2 (Life Technologies, Carlsbad, CA) and MiSeq (Illumina, San Diego, CA) sequencers were used to sequence and assess for 2,800 or more possible mutations in 50 established cancer-associated genes. RESULTS Among 102 patients, 89% had 194 pathogenic alterations identified in 19 genes. The identification of KRAS, NRAS, or BRAF mutations suggests that 42% are likely nonresponders to anti-epidermal growth factor receptor therapy. Among KRAS, NRAS, or BRAF wild-type patients, alterations in eight genes linked to alternative therapies were identified in 44%. CONCLUSIONS Our data demonstrate the successful ability to apply a single multiplex test to allow multigene mutation detection from malignant LN cytology specimen DNA collected by EUS FNA.
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Affiliation(s)
- Ferga C. Gleeson
- Divison of Gastroenterology and Hepatology, Mayo Clinic, Rochester, MN
| | | | - Jesse S. Voss
- Department of Anatomic Pathology, Mayo Clinic, Rochester, MN
| | | | | | - Zheng J. Tu
- Division of Biomedical Statistics and Informatics, Department of Health Sciences Research, Mayo Clinic, Rochester, MN
| | - Eric W. Klee
- Division of Biomedical Statistics and Informatics, Department of Health Sciences Research, Mayo Clinic, Rochester, MN
| | | | | | - Konstantinos N. Lazaridis
- Divison of Gastroenterology and Hepatology, Mayo Clinic, Rochester, MN
- Center for Individualized Medicine, Mayo Clinic, Rochester, MN
| | | | - Michael J. Levy
- Divison of Gastroenterology and Hepatology, Mayo Clinic, Rochester, MN
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Gleeson FC, Kipp BR, Kerr SE, Voss JS, Lazaridis KN, Katzka DA, Levy MJ. Characterization of endoscopic ultrasound fine-needle aspiration cytology by targeted next-generation sequencing and theranostic potential. Clin Gastroenterol Hepatol 2015; 13:37-41. [PMID: 25424571 DOI: 10.1016/j.cgh.2014.10.017] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/22/2014] [Accepted: 10/22/2014] [Indexed: 02/07/2023]
Abstract
Determination of tumor genetic architecture based on tissue analysis yields important information on signaling pathways involved in cancer pathogenesis and plays a growing role in choosing the optimal medical management of malignancies. Specifically, the advent of next-generation sequencing has led to a rapidly evolving era of relatively inexpensive, high-throughput DNA sequencing of tumors. One such example is multiplexed tumor genotyping (ie, panel testing) of more than 2800 mutations across 50 commonly mutated cancer-associated genes. This resulting mutational landscape shows medically actionable pathogenic alterations to optimize antitumor therapy. We recently assessed the performance and outcome of targeted next-generation sequencing with archived endoscopic ultrasound fine-needle aspirates across a broad range of primary and metastatic sites with encouraging accuracy. As a result, endoscopic ultrasound has the potential to move from a test for diagnosis or confirmation of malignancy, to one in which it could facilitate the personalization of cancer-directed therapy.
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Affiliation(s)
- Ferga C Gleeson
- Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, Minnesota.
| | - Benjamin R Kipp
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota
| | - Sarah E Kerr
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota
| | - Jesse S Voss
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota
| | - Konstantinos N Lazaridis
- Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, Minnesota; Center for Individualized Medicine, Mayo Clinic, Rochester, Minnesota
| | - David A Katzka
- Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, Minnesota
| | - Michael J Levy
- Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, Minnesota
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Gilbert CR, Chen A, Akulian JA, Lee HJ, Wahidi M, Argento AC, Tanner NT, Pastis NJ, Harris K, Sterman D, Toth JW, Chenna PR, Feller-Kopman D, Yarmus L. The use of convex probe endobronchial ultrasound-guided transbronchial needle aspiration in a pediatric population: a multicenter study. Pediatr Pulmonol 2014; 49:807-15. [PMID: 24039186 DOI: 10.1002/ppul.22887] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/17/2013] [Accepted: 06/29/2013] [Indexed: 12/25/2022]
Abstract
INTRODUCTION The presence of intrathoracic lymphadenopathy and mediastinal masses in the pediatric population often presents a diagnostic challenge. With limited minimally invasive methodologies to obtain a diagnosis, invasive sampling via mediastinoscopy or thoracotomy is often pursued. Endobronchial ultrasound transbronchial needle aspiration (EBUS-TBNA) is a minimally invasive, outpatient procedure that has demonstrated significant success in the adult population in the evaluation of such abnormalities. Within the pediatric literature there is limited data regarding the use of EBUS-TBNA. We report the first multicenter review of a pediatric population undergoing EBUS-TBNA procedures identifying the feasibility, safety, utility, and outcomes of this procedure. METHODS All patients of 18 years of age or younger undergoing EBUS-TBNA at six major academic medical centers from the years 2007 through 2013 were reviewed. Data regarding procedural performance, outcomes, and complications were recorded. RESULTS A total of 21 patients meeting the inclusion criteria were identified in six centers. The mean age of the cohort was 13.7 (±4.1) years. EBUS-TBNA provided adequate sampling in 20/21 (95%) of the cases with diagnostic material obtained in 10 (48%) cases. Eight patients (38%) underwent additional surgical procedures to confirm or obtain diagnostic tissue. Within our cohort, 13 patients (62%) were able to avoid invasive surgical biopsy procedures. No procedural or anesthesia related complications were identified. CONCLUSION We report the first multicenter study to date confirming the feasibility and utility of EBUS-TBNA in the pediatric population. Due to the low overall procedural risk of EBUS-TBNA, it should be considered as a potential first line diagnostic option for children presenting with mediastinal or hilar abnormalities but further prospective studies are needed.
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Affiliation(s)
- Christopher R Gilbert
- Department of Pulmonary, Allergy, and Critical Care Medicine, Bronchoscopy and Interventional Pulmonology, Penn State College of Medicine-Milton S. Hershey Medical Center, Hershey, Pennsylvania
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Leiro-Fernández V, De Chiara L, Botana-Rial M, González-Piñeiro A, Tardio-Baiges A, Núñez-Delgado M, Valverde Pérez D, Fernández-Villar A. Viability of lymph node samples obtained by echobronchoscopy in the study of epigenetic alterations in patients with lung cancer. Arch Bronconeumol 2014; 50:213-20. [PMID: 24388707 DOI: 10.1016/j.arbres.2013.11.017] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2013] [Revised: 11/13/2013] [Accepted: 11/18/2013] [Indexed: 12/12/2022]
Abstract
INTRODUCTION The diagnosis of microscopic lymph node metastasis in lung cancer is challenging despite the constant advances in tumor staging. The analysis of the methylation status of certain genes in lymph node samples could improve the diagnostic capability of conventional cyto-histological methods. The aim of this study was to demonstrate the feasibility of methylation studies using cytological lymph node samples. METHODS Prospective study including 88 patients with a diagnosis or strong suspicion of non-small cell lung cancer, in which an echobronchoscopy was performed on mediastinal or hilar lymph nodes for diagnostic and/or staging. DNA was extracted from cytological lymph node samples and sodium bisulfite modification was performed. Methylation studies for p16/INK4a and SHOX2 were accomplished by MS-qPCR and pyrosequencing. RESULTS The methodology used in our study yielded optimal/good DNA quality in 90% of the cases. No differences in DNA concentration were observed with respect to the lymph node biopsied and final diagnosis. Methylation analyses using MS-qPCR and pyrosequencing were not possible in a small number of samples mainly due to low DNA concentration, inadequate purity, fragmentation and/or degradation as a consequence of bisulfite conversion. CONCLUSION Methylation quantification using MS-qPCR and pyrosequencing of cytological lymph node samples obtained using echobronchoscopy is feasible if an appropriate DNA concentration is obtained, notably contributing to the identification of epigenetic biomarkers capable of improving decision-making for the benefit of potentially curable lung cancer patients.
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MESH Headings
- Aged
- Biopsy, Needle/methods
- Bronchoscopy/methods
- Carcinoma, Non-Small-Cell Lung/chemistry
- Carcinoma, Non-Small-Cell Lung/diagnostic imaging
- Carcinoma, Non-Small-Cell Lung/genetics
- Carcinoma, Non-Small-Cell Lung/secondary
- CpG Islands/genetics
- DNA Methylation
- DNA, Neoplasm/analysis
- DNA, Neoplasm/isolation & purification
- Endosonography
- Feasibility Studies
- Female
- Genes, p16
- Homeodomain Proteins/genetics
- Humans
- Lung Neoplasms/chemistry
- Lung Neoplasms/diagnostic imaging
- Lung Neoplasms/genetics
- Lung Neoplasms/pathology
- Lymph Nodes/pathology
- Lymphatic Metastasis/diagnostic imaging
- Lymphatic Metastasis/pathology
- Male
- Mediastinum
- Middle Aged
- Neoplasm Proteins/genetics
- Prospective Studies
- Sequence Analysis, DNA
- Sulfites/pharmacology
- Ultrasonography, Interventional
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Affiliation(s)
- Virginia Leiro-Fernández
- Servicio de Neumología, Complexo Hospitalario Universitario de Vigo (CHUVI), Vigo, Pontevedra, España
| | - Loretta De Chiara
- Departamento de Bioquímica, Genética e Inmunología, Facultad de Biología, Universidad de Vigo, Vigo, Pontevedra, España
| | - Maribel Botana-Rial
- Servicio de Neumología, Complexo Hospitalario Universitario de Vigo (CHUVI), Vigo, Pontevedra, España
| | - Ana González-Piñeiro
- Servicio de Anatomía Patológica, Complexo Hospitalario Universitario de Vigo (CHUVI), Vigo, Pontevedra, España
| | - Antoni Tardio-Baiges
- Servicio de Anatomía Patológica, Complexo Hospitalario Universitario de Vigo (CHUVI), Vigo, Pontevedra, España
| | - Manuel Núñez-Delgado
- Servicio de Neumología, Complexo Hospitalario Universitario de Vigo (CHUVI), Vigo, Pontevedra, España
| | - Diana Valverde Pérez
- Departamento de Bioquímica, Genética e Inmunología, Facultad de Biología, Universidad de Vigo, Vigo, Pontevedra, España
| | - Alberto Fernández-Villar
- Servicio de Neumología, Complexo Hospitalario Universitario de Vigo (CHUVI), Vigo, Pontevedra, España.
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Spieler P, Rössle M. Respiratory Tract and Mediastinum. ESSENTIALS OF DIAGNOSTIC PATHOLOGY 2012. [PMCID: PMC7122295 DOI: 10.1007/978-3-642-24719-4_2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Normal cytology, abnormal and atypical cells, non-cellular components, and infectious cell changes are largely described together with benign, malignant, and neuroendocrine lesions regarding exfoliative and aspiration cytology of the lung. A separate section broadly addresses diagnostic findings and differential diagnoses in bronchoalveolar washings. The section ‘Fine needle aspiration biopsy of mediastinal disorders’ covers in particular biopsy techniques, accuracy of liquid-based cytology, and the complex lesions of the thymus gland. Cytodiagnostic algorithms of the major benign and malignant pulmonary and mediastinal lesions and their respective differential diagnoses are additionally presented in synoptic setups.
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Affiliation(s)
- Peter Spieler
- Institut für Pathologie, Kantonsspital St. Gallen, Rorschacherstraße 95, 9007 St. Gallen, Switzerland
| | - Matthias Rössle
- Institut für Klinische Pathologie, UniversitätsSpital Zürich, Schmelzbergstraße 12, 8091 Zürich, Switzerland
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Abstract
Technical improvements have made profound changes in diagnostic ultrasound imaging. Some of these changes, such as encoded pulses and receive focusing, occur in the background and are essentially nonadjustable. Others, including harmonics and compounding, are real-time options and are adjustable by the imager. New technologies that offer great promise for improved characterization of lesions include contrast ultrasound and elastography. This article will attempt to update the small animal imager on the clinical applications of these newer technologies.
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Affiliation(s)
- Robert T O'Brien
- Department of Clinical Sciences at the College of Veterinary Medicine, Kansas State University, Manhattan, KS 66506-5601, USA.
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