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Arhant G, Lachkar S, Thiebaut PA, Marguet F, Lamy A, Thiberville L, Salaün M, Guisier F, Sabourin JC, Piton N. Detection of Tumor DNA in Bronchoscopic Fluids in Peripheral NSCLC: A Proof-of-Concept Study. JTO Clin Res Rep 2024; 5:100596. [PMID: 38328474 PMCID: PMC10847031 DOI: 10.1016/j.jtocrr.2023.100596] [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: 05/25/2023] [Revised: 10/07/2023] [Accepted: 10/14/2023] [Indexed: 02/09/2024] Open
Abstract
Introduction DNA genotyping from plasma is a useful tool for molecular characterization of NSCLC. Nevertheless, the false-negative rate justifies the development of methods with higher sensitivity, especially in difficult-to-reach peripheral lung tumors. Methods We aimed at comparing molecular analysis from the supernatant of guide sheath flush fluid collected during radial-EndoBronchial UltraSound (r-EBUS) bronchoscopy with plasma sampling and tumor biopsies in patients with peripheral NSCLC. The DNA was genotyped using high-throughput sequencing or the COBAS mutation test. There were 65 patients with peripheral lung tumors subjected to concomitant sampling of guide sheath flush supernatant, plasma tumor DNA, and tumor biopsy and cytology using r-EBUS. There were 33 patients (including 24 newly diagnosed with having NSCLC) with an identifiable tumor mutation in the primary lesion selected for the comparative analysis. Results Guide sheath flush-based genotyping yielded a mutation detection rate of 61.8% (17 of 24 mutated EGFR, one of two ERBB2, one of one KRAS, one of one MAP2K, one of four MET, and zero of one STK11), compared with 33% in plasma-based genotyping (p = 0.0151). Furthermore, in eight of 34 r-EBUS without tumor cells on microscopic examination, we were able to detect the mutation in four paired guide sheath flush supernatant, compared with only two in paired plasma. Conclusion The detection of tumor DNA in the supernatant of guide sheath flush fluid collected during r-EBUS bronchoscopy represents a sensitive and complementary method for genotyping NSCLC.
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Affiliation(s)
- Gwenaëlle Arhant
- Department of Pathology, Normandie Univ, UNIROUEN, Institut national de la santé et de la recherche médicale (INSERM) U1245, CHU Rouen, Rouen, France
| | - Samy Lachkar
- Department of Pneumology, CHU Rouen, Rouen, France
| | - Pierre-Alain Thiebaut
- Department of Pathology, Normandie Univ, UNIROUEN, Institut national de la santé et de la recherche médicale (INSERM) U1245, CHU Rouen, Rouen, France
| | - Florent Marguet
- Department of Pathology, Normandie Univ, UNIROUEN, Institut national de la santé et de la recherche médicale (INSERM) U1245, CHU Rouen, Rouen, France
| | - Aude Lamy
- Department of Pathology, Normandie Univ, UNIROUEN, Institut national de la santé et de la recherche médicale (INSERM) U1245, CHU Rouen, Rouen, France
| | - Luc Thiberville
- Department of Pneumology, CHU Rouen, Rouen, France
- Department of Pneumology, Normandie Univ, UNIROUEN, LITIS Lab QuantIF team EA4108, CHU Rouen, and Institut national de la santé et de la recherche médicale (INSERM) CIC-CRB 1404, Rouen, France
| | - Mathieu Salaün
- Department of Pneumology, CHU Rouen, Rouen, France
- Department of Pneumology, Normandie Univ, UNIROUEN, LITIS Lab QuantIF team EA4108, CHU Rouen, and Institut national de la santé et de la recherche médicale (INSERM) CIC-CRB 1404, Rouen, France
| | - Florian Guisier
- Department of Pneumology, CHU Rouen, Rouen, France
- Department of Pneumology, Normandie Univ, UNIROUEN, LITIS Lab QuantIF team EA4108, CHU Rouen, and Institut national de la santé et de la recherche médicale (INSERM) CIC-CRB 1404, Rouen, France
| | - Jean-Christophe Sabourin
- Department of Pathology, Normandie Univ, UNIROUEN, Institut national de la santé et de la recherche médicale (INSERM) U1245, CHU Rouen, Rouen, France
| | - Nicolas Piton
- Department of Pathology, Normandie Univ, UNIROUEN, Institut national de la santé et de la recherche médicale (INSERM) U1245, CHU Rouen, Rouen, France
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Turner SA, Abou Shaar R, Yang Z. The basics of commonly used molecular techniques for diagnosis, and application of molecular testing in cytology. Diagn Cytopathol 2023; 51:83-94. [PMID: 36345929 PMCID: PMC10098847 DOI: 10.1002/dc.25067] [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: 08/09/2022] [Revised: 10/11/2022] [Accepted: 10/16/2022] [Indexed: 11/11/2022]
Abstract
Molecular diagnostics has expanded to become the standard of care for a variety of solid tumor types. With limited diagnostic material, it is often desirable to use cytological preparations to provide rapid and accurate molecular results. This review covers important pre-analytic considerations and limitations, and a description of common techniques that the modern cytopathologist should understand when ordering and interpreting molecular tests in practice.
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Affiliation(s)
- Scott A Turner
- Department of Pathology, Virginia Commonwealth University, Richmond, Virginia, USA
| | - Rand Abou Shaar
- Department of Pathology, Virginia Commonwealth University, Richmond, Virginia, USA
| | - Zhongbo Yang
- Department of Pathology, Roswell Park Comprehensive Cancer Center, Buffalo, New York, USA
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Li G, Liu D, Flandrin P, Zhang Y, Lambert C, Mallouk N, Cottier M. Tumor-Derived Exosomal RNA From Fine-Needle Aspiration Supernatant as a Novel Liquid Biopsy for Molecular Diagnosis of Cancer. PATHOLOGY AND ONCOLOGY RESEARCH 2022; 28:1610344. [PMID: 35991837 PMCID: PMC9388727 DOI: 10.3389/pore.2022.1610344] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/02/2022] [Accepted: 07/06/2022] [Indexed: 11/15/2022]
Abstract
Background: We hypothesized that the fine needle aspiration (FNA) supernatant from tumor might contain tumor-derived exosomes. The objective of this pilot study was to test if tumor-derived exosomal RNA could be found in FNA supernatants for molecular diagnosis of cancer. Methods: 10 FNA samples from pancreatic tumor were included. After the routine recuperation of cellular material by centrifugation, the cell-free Cytolyt liquid was collected instead of being discarded. 10 ml Cytolyt was used to isolate the exosomes. Transmission electronic microscopy (TEM) was used to examine the presence of exosomes. The exosomal marker CD63 was analyzed by flow cytometry. The exosomal RNA was extracted. RT-qPCR was performed to detect the GAPDH and the tumor marker of glypican 1 gene expression. Results: TEM confirmed the presence of exosomes from FNA supernatants. Flow cytometry showed a strong positive expression of exosome marker CD63. The concentration of exosomal RNA ranged from 18.81 to 354.75 ng/μl with an average of 81.76 ng/μl. The average exosomal RNA quantity was 1390.01 ng (range from 319.77 to 6030.75 ng) with an average 260/280 ratio of 2.12. GAPDH was detectable in all samples. Exosomal glypican 1 was detected in all samples of pancreatic ductal adenorcarcinomas (3/3) and absent from benign cystic samples (3/3). Furthermore, exosomal glypican 1 was positive in one sample with a non-contributive cytology and in one sample in which no malignant cell was found. Conclusion: This is the first report that the supernatants from FNA biopsy may contain tumor-derived exosomal RNA. These tumor-derived exosomes from FNA may provide a new liquid biopsy for the molecular diagnosis of cancer.
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Affiliation(s)
- Guorong Li
- Department of Digestive Surgery and Urology, North Hospital, CHU Saint-Etienne, Saint-Etienne, France
- *Correspondence: Dongdong Liu, ; Guorong Li,
| | - Dongdong Liu
- Department of Laboratory Science, The Second Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou, China
- *Correspondence: Dongdong Liu, ; Guorong Li,
| | - Pascale Flandrin
- Laboratory of Molecular Biology, North Hospital, CHU Saint-Etienne, Saint-Etienne, France
| | - Yang Zhang
- Guangzhou HopeTech Biological Technology Co., Ltd., Guangzhou, China
| | - Claude Lambert
- Section of Flow Cytometry, Immunology Laboratory, North Hospital, CHU Saint-Etienne, Saint-Etienne, France
| | - Nora Mallouk
- Center of Electronic Microscopy, CMES, Faculty of Medicine, University Jean Monnet, Saint-Etienne, France
| | - Michèle Cottier
- Laboratory of Cytopathology, North Hospital, CHU Saint-Etienne, Saint-Etienne, France
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Ruff HM, Lou SK, Hahn E, Grenier S, Stockley TL, Boerner SL. Molecular yield and cytomorphologic assessment of fine needle aspiration specimen supernatants. J Am Soc Cytopathol 2022; 11:142-153. [PMID: 35305954 DOI: 10.1016/j.jasc.2022.02.004] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2021] [Revised: 01/21/2022] [Accepted: 02/15/2022] [Indexed: 06/14/2023]
Abstract
INTRODUCTION Cytology samples are frequently relied upon for the diagnosis of advanced cancer such as lung cancer. As the recommendations for solid malignancies biomarker testing continue to expand, it becomes increasingly important to efficiently utilize limited specimens to minimize the need for additional sampling and its associated risks and costs. MATERIALS AND METHODS We performed molecular testing on fresh or CytoLyt-fixed supernatants derived from fine needle aspirates (FNAs) and compared its performance against the clinical specimen (including formalin-fixed paraffin-embedded cell blocks, residual PreservCyt and fresh samples). Supernatants were assessed for cellularity using Field-stained Cytospin (CS) preparations. RESULTS There was overall almost perfect agreement (41/45 cases, K = 0.822) and substantial to almost perfect agreement in molecular testing results of clinically actionable variants between fresh (20/23 cases, Κ = 0.742) and CytoLyt-fixed (21/22 cases, Κ = 0.908) and its clinical specimen counterpart. Interestingly, CS examination of the supernatants revealed viable tumor cells. Centrifugation for 1 minute at 300 rpm is optimal for overall or tumor cellularity recovery. Delayed molecular testing after 3, 4 and 7 days at 4 degrees Celsius showed identical molecular results. CONCLUSIONS We validated the use of supernatants derived from FNA cytology samples as a substrate for molecular testing using next-generation sequencing and other molecular techniques.
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Affiliation(s)
- Heather M Ruff
- Laboratory Medicine Program, Department of Laboratory Medicine and Pathobiology, University Health Network, Toronto, Ontario, Canada; Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada
| | - Si Kei Lou
- Laboratory Medicine Program, Department of Laboratory Medicine and Pathobiology, University Health Network, Toronto, Ontario, Canada; Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada.
| | - Elan Hahn
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada
| | - Sylvie Grenier
- Laboratory Medicine Program, Department of Laboratory Medicine and Pathobiology, University Health Network, Toronto, Ontario, Canada
| | - Tracy L Stockley
- Laboratory Medicine Program, Department of Laboratory Medicine and Pathobiology, University Health Network, Toronto, Ontario, Canada; Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada
| | - Scott L Boerner
- Laboratory Medicine Program, Department of Laboratory Medicine and Pathobiology, University Health Network, Toronto, Ontario, Canada; Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada
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Tafoya M, Judd A, Chiotti K, Dearen K, Jiron K, Chabot-Richards D, Broehm CJ. Performance of a 50-gene next generation sequencing panel with post-centrifuge supernatant cytology fluid in non-small-cell lung cancer. Diagn Cytopathol 2021; 49:1173-1178. [PMID: 34339108 DOI: 10.1002/dc.24844] [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: 05/23/2021] [Revised: 07/19/2021] [Accepted: 07/22/2021] [Indexed: 11/07/2022]
Abstract
BACKGROUND Liquid based cytology (LBC) specimens are increasingly utilized for molecular analysis, as results are comparable to molecular analysis performed on traditional specimens (biopsy or cell block). However, there are few studies demonstrating the long-term viability of DNA in LBC samples. METHODS In this study, a 50-gene next generation sequencing (NGS) panel was performed on DNA isolated from post-centrifuged supernatant LBC samples of cases of non-small-cell lung carcinoma. Comparison was made to results of an identical NGS panel performed on a concurrent clinical sample (biopsy or cell block). Quality parameters including DNA concentration, total reads, amplicons with reads under 450 and 350, and variant allele fraction were also compared. For a subset of LBC samples, DNA was isolated after being held for varying extended lengths of time after collection (up to 41 days) at 5°C and results compared. RESULTS Results of NGS mutation analysis were concordant between LBC samples and clinical samples. DNA concentration was on average higher in the LBC samples compared to the clinical samples. The remaining metrics were more variable, but illustrated the adequacy of LBC samples for NGS testing. DNA isolated from LBC samples held for longer periods of time was of good concentration. NGS analysis was successfully performed on all samples, with concordance with results of clinical samples. CONCLUSION DNA isolated directly from LBC fluid is suitable for NGS analysis. DNA is also stable in LBC preservative for extended periods of time before isolation and NGS analysis can subsequently be successfully performed.
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Affiliation(s)
- Marissa Tafoya
- Department of Pathology, University of New Mexico Hospital, Albuquerque, New Mexico, USA
| | - Andrew Judd
- Department of Pathology, University of New Mexico Hospital, Albuquerque, New Mexico, USA
| | - Kelsey Chiotti
- TriCore Reference Laboratories, Albuquerque, New Mexico, USA
| | - Karen Dearen
- TriCore Reference Laboratories, Albuquerque, New Mexico, USA
| | - Kassandra Jiron
- TriCore Reference Laboratories, Albuquerque, New Mexico, USA
| | - Devon Chabot-Richards
- Department of Pathology, University of New Mexico Hospital, Albuquerque, New Mexico, USA
| | - Cory J Broehm
- Department of Pathology, University of New Mexico Hospital, Albuquerque, New Mexico, USA
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Durin L, Pradines A, Basset C, Ulrich B, Keller L, Dongay V, Favre G, Mazieres J, Guibert N. Liquid Biopsy of Non-Plasma Body Fluids in Non-Small Cell Lung Cancer: Look Closer to the Tumor! Cells 2020; 9:cells9112486. [PMID: 33207539 PMCID: PMC7698102 DOI: 10.3390/cells9112486] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2020] [Revised: 11/11/2020] [Accepted: 11/13/2020] [Indexed: 12/19/2022] Open
Abstract
Liquid biopsy is a rapidly emerging field due to an increasing number of oncogenic drivers and a better understanding of resistance mechanisms to targeted therapies in non-small cell lung cancer (NSCLC). The sensitivity of the most widely used blood-based assays is, however, limited in particular in cases of low tumor volume where shed of tumor-derived material can be limited. A negative result thus requires biopsy confirmation using minimally invasive sampling procedures that can result in small specimens, which are often not suitable for genotyping. Liquid biopsy is not limited to plasma, and tumor DNA circulating in other body fluids such as urine, pleural fluid, cerebrospinal fluid, or cytology specimen-derived supernatant can be exploited. In comparison to cell blocks, these fluids in close contact to the tumor may contain a more abundant and less analytically demanding tumor DNA. In this review, we discuss the potential applications of circulating tumor DNA derived from cytology samples in NSCLC, from early stage (screening, nodule characterization) to metastatic disease.
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Affiliation(s)
- Lucile Durin
- Pulmonology Department, Hôpital Larrey, University Hospital of Toulouse, 31059 Toulouse, France; (L.D.); (V.D.); (J.M.)
| | - Anne Pradines
- Cancer Research Centre of Toulouse (CRCT), Inserm, National Scientific Research Centre (CNRS), 31100 Toulouse, France; (A.P.); (L.K.); (G.F.)
- Medical Laboratory, Claudius Regaud Institute, Toulouse University Cancer Institute (IUCT-O), 31100 Toulouse, France
| | - Céline Basset
- Cytology Department, Toulouse University Cancer Institute (IUCT-O), 31100 Toulouse, France;
| | - Bryan Ulrich
- Emory University School of Medicine, Atlanta, GA 30322, USA;
| | - Laura Keller
- Cancer Research Centre of Toulouse (CRCT), Inserm, National Scientific Research Centre (CNRS), 31100 Toulouse, France; (A.P.); (L.K.); (G.F.)
- Medical Laboratory, Claudius Regaud Institute, Toulouse University Cancer Institute (IUCT-O), 31100 Toulouse, France
| | - Vincent Dongay
- Pulmonology Department, Hôpital Larrey, University Hospital of Toulouse, 31059 Toulouse, France; (L.D.); (V.D.); (J.M.)
| | - Gilles Favre
- Cancer Research Centre of Toulouse (CRCT), Inserm, National Scientific Research Centre (CNRS), 31100 Toulouse, France; (A.P.); (L.K.); (G.F.)
- Medical Laboratory, Claudius Regaud Institute, Toulouse University Cancer Institute (IUCT-O), 31100 Toulouse, France
- University of Toulouse III—Paul Sabatier, 31062 Toulouse, France
| | - Julien Mazieres
- Pulmonology Department, Hôpital Larrey, University Hospital of Toulouse, 31059 Toulouse, France; (L.D.); (V.D.); (J.M.)
- Cancer Research Centre of Toulouse (CRCT), Inserm, National Scientific Research Centre (CNRS), 31100 Toulouse, France; (A.P.); (L.K.); (G.F.)
- University of Toulouse III—Paul Sabatier, 31062 Toulouse, France
| | - Nicolas Guibert
- Pulmonology Department, Hôpital Larrey, University Hospital of Toulouse, 31059 Toulouse, France; (L.D.); (V.D.); (J.M.)
- Cancer Research Centre of Toulouse (CRCT), Inserm, National Scientific Research Centre (CNRS), 31100 Toulouse, France; (A.P.); (L.K.); (G.F.)
- University of Toulouse III—Paul Sabatier, 31062 Toulouse, France
- Correspondence: ; Tel.: +33-567771836
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Heymann JJ, Siddiqui MT. Ancillary Techniques in Cytologic Specimens Obtained from Solid Lesions of the Pancreas: A Review. Acta Cytol 2019; 64:103-123. [PMID: 30970350 DOI: 10.1159/000497153] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2018] [Accepted: 01/22/2019] [Indexed: 12/21/2022]
Abstract
Advanced methods of molecular characterization have elucidated the genetic, epigenetic, and proteomic alterations associated with the broad spectrum of pancreatic disease, particularly neoplasia. Next-generation sequencing, in particular, has revealed the genomic diversity among pancreatic ductal adenocarcinoma, neuroendocrine and acinar tumors, solid pseudopapillary neoplasm, and other pancreatico-biliary neoplasms. Differentiating these entities from one another by morphologic analysis alone may be challenging, especially when examining the small quantities of diagnostic material inherent to cytologic specimens. In order to enhance the sensitivity and specificity of pancreatic cytomorphology, multiple diagnostic, prognostic, and predictive ancillary tests have been and continue to be developed. Although a great number of such tests have been developed for evaluation of specimens collected from cystic lesions and strictures, ancillary techniques also play a significant role in the evaluation of cytologic specimens obtained from solid lesions of the pancreas. Furthermore, while some tests have been developed to differentiate diagnostic entities from one another, others have been developed to simply identify dysplasia and malignancy. Ancillary studies are particularly important in the subset of cases for which cytomorphologic analysis provides a result that is equivocal or insufficient to guide clinical management. Selection of appropriate ancillary testing modalities requires familiarity with both their methodology and the molecular basis of the pancreatic diseases for which testing is being performed.
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Affiliation(s)
- Jonas J Heymann
- Division of Cytopathology, Department of Pathology and Laboratory Medicine, New York-Presbyterian Hospital-Weill Cornell Medical College, New York, New York, USA,
| | - Momin T Siddiqui
- Division of Cytopathology, Department of Pathology and Laboratory Medicine, New York-Presbyterian Hospital-Weill Cornell Medical College, New York, New York, USA
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Janaki N, Harbhajanka A, Michael CW, Bomeisl P, Wasman J, Atchley M, Miskiewicz K, Alouani D, Sadri N. Comparison of cytocentrifugation supernatant fluid and formalin‐fixed paraffin‐embedded tissue for targeted next‐generation sequencing. Cancer Cytopathol 2019; 127:297-305. [DOI: 10.1002/cncy.22126] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2018] [Revised: 03/08/2019] [Accepted: 03/11/2019] [Indexed: 01/09/2023]
Affiliation(s)
- Nafiseh Janaki
- Department of Pathology University Hospitals Cleveland Medical Center Cleveland Ohio
- Department of Pathology Case Western Reserve University School of Medicine Cleveland Ohio
| | - Aparna Harbhajanka
- Department of Pathology University Hospitals Cleveland Medical Center Cleveland Ohio
- Department of Pathology Case Western Reserve University School of Medicine Cleveland Ohio
| | - Claire W. Michael
- Department of Pathology University Hospitals Cleveland Medical Center Cleveland Ohio
- Department of Pathology Case Western Reserve University School of Medicine Cleveland Ohio
| | - Phillip Bomeisl
- Department of Pathology University Hospitals Cleveland Medical Center Cleveland Ohio
- Department of Pathology Case Western Reserve University School of Medicine Cleveland Ohio
| | - Jay Wasman
- Department of Pathology University Hospitals Cleveland Medical Center Cleveland Ohio
- Department of Pathology Case Western Reserve University School of Medicine Cleveland Ohio
| | - Maureen Atchley
- Department of Pathology University Hospitals Cleveland Medical Center Cleveland Ohio
| | - Kristina Miskiewicz
- Department of Pathology University Hospitals Cleveland Medical Center Cleveland Ohio
| | - David Alouani
- Department of Pathology University Hospitals Cleveland Medical Center Cleveland Ohio
- Department of Pathology Case Western Reserve University School of Medicine Cleveland Ohio
| | - Navid Sadri
- Department of Pathology University Hospitals Cleveland Medical Center Cleveland Ohio
- Department of Pathology Case Western Reserve University School of Medicine Cleveland Ohio
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Huang M, Wei S. Overview of Molecular Testing of Cytology Specimens. Acta Cytol 2019; 64:136-146. [PMID: 30917368 DOI: 10.1159/000497187] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2018] [Accepted: 01/23/2019] [Indexed: 12/15/2022]
Abstract
OBJECTIVE Utilizing cytology specimens for molecular testing has attracted increasing attention in the era of personalized medicine. Cytology specimens are clinically easier to access. The samples can be quickly and completely fixed in a very short time of fixation before tissue degradation occurs, compared to hours or days of fixation in surgical pathology specimens. In addition, cytology specimens can be fixed without formalin, which can significantly damage DNA and RNA. All these factors contribute to the superb quality of DNA and RNA in cytology specimens for molecular tests. STUDY DESIGN We summarize the most pertinent information in the literature regarding molecular testing in the field of cytopathology. RESULTS The first part focuses on the types of cytological specimens that can be used for molecular testing, including the advantages and limitations. The second section describes the common molecular tests and their clinical application. CONCLUSION Various types of cytology specimens are suitable for many molecular tests, which may require additional clinical laboratory validation.
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Affiliation(s)
- Min Huang
- Department of Pathology, Fox Chase Cancer Center, Philadelphia, Pennsylvania, USA
| | - Shuanzeng Wei
- Department of Pathology, Fox Chase Cancer Center, Philadelphia, Pennsylvania, USA,
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Nishino M. Sustainable cytopathology in the precision medicine era: Exploring new sources for molecular testing in thyroid cytology specimens. Cancer Cytopathol 2019; 127:143-145. [PMID: 30707506 DOI: 10.1002/cncy.22107] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2019] [Accepted: 01/17/2019] [Indexed: 01/19/2023]
Affiliation(s)
- Michiya Nishino
- Department of Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, Massachusetts
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11
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Ye W, Hannigan B, Zalles S, Mehrotra M, Barkoh BA, Williams MD, Cabanillas ME, Edeiken-Monroe B, Hu P, Duose D, Wistuba II, Medeiros LJ, Stewart J, Luthra R, Roy-Chowdhuri S. Centrifuged supernatants from FNA provide a liquid biopsy option for clinical next-generation sequencing of thyroid nodules. Cancer Cytopathol 2019; 127:146-160. [PMID: 30620446 DOI: 10.1002/cncy.22098] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2018] [Revised: 12/05/2018] [Accepted: 12/05/2018] [Indexed: 12/21/2022]
Abstract
BACKGROUND Molecular testing is recommended as an adjunct to improve the preoperative diagnosis of fine-needle aspiration (FNA) of thyroid nodules. Centrifuged supernatants from FNA samples, which are typically discarded, have recently emerged as a novel liquid-based biopsy for molecular testing. This study evaluates the use of thyroid FNA supernatants for detecting clinically relevant mutations. METHODS Supernatants from thyroid FNA samples (n = 156) were evaluated. A 50-gene next-generation sequencing (NGS) assay was used, and mutation analysis results from a subset of samples were further compared with those of paired FNA smears and/or cell blocks. RESULTS All 156 samples yielded adequate DNA (median, 135 ng; range, 11-3180 ng), and 129 of these samples (83%) were successfully sequenced by NGS. The most frequently detected somatic mutations included BRAF and RAS mutations, which were followed by RET, TP53, PTEN, CDKN2A, and PIK3CA mutations. Eleven of 31 cases with an indeterminate cytologic diagnosis and 9 of 12 cases that were suspicious for malignancy had somatic mutations, including the BRAF V600E mutation, which is highly definitive for papillary thyroid carcinoma (PTC). Seven of the 9 indeterminate and suspicious cases with the BRAF V600E mutation had surgical follow-up, and they were all confirmed to be PTC. A comparison of the mutation profiles derived from supernatants with those of paired smears and/or cell blocks in a small subset of cases (n = 8) showed 100% concordance. CONCLUSIONS This study provides evidence that FNA supernatants can be used as a surrogate for thyroid molecular testing to improve diagnostic accuracy in indeterminate nodules, provide prognostic/predictive information, and improve overall patient management.
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Affiliation(s)
- Wenrui Ye
- Diagnostic Genetics, School of Health Professions, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Brette Hannigan
- Diagnostic Genetics, School of Health Professions, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Stephanie Zalles
- Diagnostic Genetics, School of Health Professions, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Meenakshi Mehrotra
- Department of Hematopathology, Division of Pathology and Laboratory Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Bedia A Barkoh
- Department of Hematopathology, Division of Pathology and Laboratory Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Michelle D Williams
- Department of Pathology, Division of Pathology and Laboratory Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Maria E Cabanillas
- Department of Endocrine Neoplasia and Hormonal Disorders, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Beth Edeiken-Monroe
- Department of Diagnostic Radiology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Peter Hu
- Diagnostic Genetics, School of Health Professions, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Dzifa Duose
- Department of Translational Molecular Pathology, Division of Pathology and Laboratory Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Ignacio I Wistuba
- Department of Translational Molecular Pathology, Division of Pathology and Laboratory Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - L Jeffrey Medeiros
- Department of Hematopathology, Division of Pathology and Laboratory Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - John Stewart
- Department of Pathology, Division of Pathology and Laboratory Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Rajyalakshmi Luthra
- Department of Hematopathology, Division of Pathology and Laboratory Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Sinchita Roy-Chowdhuri
- Department of Pathology, Division of Pathology and Laboratory Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas
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Roy‐Chowdhuri S. Molecular testing of residual cytology samples: Rethink, reclaim, repurpose. Cancer Cytopathol 2018; 127:15-17. [DOI: 10.1002/cncy.22076] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2018] [Revised: 09/19/2018] [Accepted: 09/24/2018] [Indexed: 12/19/2022]
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Roy-Chowdhuri S, Mehrotra M, Bolivar AM, Kanagal-Shamanna R, Barkoh BA, Hannigan B, Zalles S, Ye W, Duose D, Broaddus R, Staerkel G, Wistuba I, Medeiros LJ, Luthra R. Salvaging the supernatant: next generation cytopathology for solid tumor mutation profiling. Mod Pathol 2018; 31:1036-1045. [PMID: 29463880 DOI: 10.1038/s41379-018-0006-x] [Citation(s) in RCA: 54] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2017] [Revised: 11/27/2017] [Accepted: 12/03/2017] [Indexed: 12/25/2022]
Abstract
With the expanding role of targeted therapy in patients with solid tumors, pathologists face the daunting task of having to maximize limited volume tissue obtained by fine needle aspiration for a variety of molecular tests. While most molecular studies on fine needle aspiration samples have been reported using cellular material, recent studies have shown that a substantial amount of DNA can be retrieved from the supernatant fluid of aspirate needle rinses after cell pelleting for cytospin or cell block preparations. In routine clinical workflow, the supernatant is discarded; however this fluid may provide a complementary source of DNA for tumor mutational profiling. In this study, we evaluated the post-centrifuged supernatant from 25 malignant and 10 benign fine needle aspiration needle rinses. The mean and median DNA yields from the supernatants were 445 ng and 176.4 ng (range, 15.1-2958 ng), respectively. Next generation sequencing using the Ion AmpliSeq Cancer Hotspot Panel v2 detected somatic mutations in all 25 malignant samples. No mutations were detected in any of the benign samples tested. When available, mutations detected in the supernatant fluid were compared to the next generation sequencing analysis performed on a prior or concurrent surgical specimen from the same patient and showed 100% concordance. In a subset of cases (n = 19) mutations in EGFR, KRAS, BRAF, PIK3CA, and NRAS were successfully confirmed by droplet digital PCR, providing an orthogonal platform for mutation analysis. In summary, in this study we show that post centrifuged supernatants from fine needle aspiration needle rinses can provide a robust substrate for expanded mutation profiling by next generation sequencing, as well as hotspot mutation testing by droplet digital PCR. The ability to detect somatic mutations from otherwise discarded supernatant fluids offers the ability to triage and effectively utilize limited volume fine needle aspiration samples when multiple molecular tests are requested, without the need to re-biopsy for additional tissue samples.
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Affiliation(s)
- Sinchita Roy-Chowdhuri
- Department of Pathology, Division of Pathology and Laboratory Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.
| | - Meenakshi Mehrotra
- Department of Hematopathology, Division of Pathology and Laboratory Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Ana Maria Bolivar
- Diagnostic Genetics, School of Health Professions, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Rashmi Kanagal-Shamanna
- Department of Hematopathology, Division of Pathology and Laboratory Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Bedia A Barkoh
- Department of Hematopathology, Division of Pathology and Laboratory Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Brette Hannigan
- Diagnostic Genetics, School of Health Professions, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Stephanie Zalles
- Diagnostic Genetics, School of Health Professions, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Wenrui Ye
- Diagnostic Genetics, School of Health Professions, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Dzifa Duose
- Department of Translational Molecular Pathology, Division of Pathology and Laboratory Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Russell Broaddus
- Department of Pathology, Division of Pathology and Laboratory Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Gregg Staerkel
- Department of Pathology, Division of Pathology and Laboratory Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Ignacio Wistuba
- Department of Translational Molecular Pathology, Division of Pathology and Laboratory Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - L Jeffrey Medeiros
- Department of Hematopathology, Division of Pathology and Laboratory Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Rajyalakshmi Luthra
- Department of Hematopathology, Division of Pathology and Laboratory Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.,Department of Translational Molecular Pathology, Division of Pathology and Laboratory Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
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Gonda TA, Viterbo D, Gausman V, Kipp C, Sethi A, Poneros JM, Gress F, Park T, Khan A, Jackson SA, Blauvelt M, Toney N, Finkelstein SD. Mutation Profile and Fluorescence In Situ Hybridization Analyses Increase Detection of Malignancies in Biliary Strictures. Clin Gastroenterol Hepatol 2017; 15:913-919.e1. [PMID: 28017843 DOI: 10.1016/j.cgh.2016.12.013] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/09/2016] [Revised: 12/09/2016] [Accepted: 12/12/2016] [Indexed: 02/07/2023]
Abstract
BACKGROUND & AIMS It is a challenge to detect malignancies in biliary strictures. Various sampling methods are available to increase diagnostic yield, but these require additional procedure time and expertise. We evaluated the combined accuracy of fluorescence in situ hybridization (FISH) and polymerase chain reaction-based DNA mutation profiling (MP) of specimens collected using standard brush techniques. METHODS We performed a prospective study of 107 consecutive patients treated for biliary strictures by endoscopic retrograde cholangiopancreatography from June 2012 through June 2014. We performed routine cytology and FISH analyses on cells collected by standard brush techniques, and analyzed supernatants for point mutations in KRAS and loss-of-heterozygosity mutations in tumor-suppressor genes at 10 loci (MP analysis was performed at Interpace Diagnostics). Strictures were determined to be nonmalignant based on repeat image analysis or laboratory test results 12 months after the procedure. Malignant strictures were identified based on subsequent biopsy or cytology analyses, pathology analyses of samples collected during surgery, or death from biliary malignancy. We determined the sensitivity and specificity with which FISH and MP analyses detected malignancies using the exact binomial test. RESULTS Our final analysis included 100 patients; 41% had biliary malignancies. Cytology analysis identified patients with malignancies with 32% sensitivity and 100% specificity. Addition of FISH or MP results to cytology results increased the sensitivity of detection to 51% (P < .01) without reducing specificity. The combination of cytology, MP, and FISH analyses detected malignancies with 73% sensitivity (P < .001). FISH identified an additional 9 of the 28 malignancies not detected by cytology analysis, and MP identified an additional 8 malignancies. FISH and MP together identified 17 of the 28 malignancies not detected by cytology analysis. CONCLUSIONS Addition of FISH and mutation analyses to cytology analysis significantly increased the level of sensitivity with which we detected malignancy in biliary strictures, with 100% specificity. These techniques can be performed using standard brush samples collected during endoscopic retrograde cholangiopancreatography, with mutations detected in free DNA in supernatant fluid of samples. The tests are complementary and therefore should be used sequentially in the diagnostic evaluation of biliary strictures.
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Affiliation(s)
- Tamas A Gonda
- Division of Digestive and Liver Disease, Department of Medicine, Columbia University Medical Center, New York, New York.
| | - Domenico Viterbo
- Division of Digestive and Liver Disease, Department of Medicine, Columbia University Medical Center, New York, New York
| | - Valerie Gausman
- Division of Digestive and Liver Disease, Department of Medicine, Columbia University Medical Center, New York, New York
| | - Claudine Kipp
- Division of Digestive and Liver Disease, Department of Medicine, Columbia University Medical Center, New York, New York
| | - Amrita Sethi
- Division of Digestive and Liver Disease, Department of Medicine, Columbia University Medical Center, New York, New York
| | - John M Poneros
- Division of Digestive and Liver Disease, Department of Medicine, Columbia University Medical Center, New York, New York
| | - Frank Gress
- Division of Digestive and Liver Disease, Department of Medicine, Columbia University Medical Center, New York, New York
| | - Tina Park
- Division of Digestive and Liver Disease, Department of Medicine, Columbia University Medical Center, New York, New York
| | - Ali Khan
- Division of Digestive and Liver Disease, Department of Medicine, Columbia University Medical Center, New York, New York
| | - Sara A Jackson
- Interpace Diagnostics Corporation, Pittsburgh, Pennsylvania
| | - Megan Blauvelt
- Interpace Diagnostics Corporation, Pittsburgh, Pennsylvania
| | - Nicole Toney
- Interpace Diagnostics Corporation, Pittsburgh, Pennsylvania
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15
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Alsubai J, Matters GL, McGovern CO, Liao J, Gilius EL, Smith JP. Germline Mutation of the CCK Receptor: A Novel Biomarker for Pancreas Cancer. Clin Transl Gastroenterol 2016; 7:e134. [PMID: 26741064 PMCID: PMC4737870 DOI: 10.1038/ctg.2015.61] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/11/2015] [Accepted: 11/03/2015] [Indexed: 12/18/2022] Open
Abstract
Objectives: Today, genetic biomarkers have been demonstrated to play an important role in identifying at-risk subjects for familial or inherited cancers. We have identified a single-nucleotide polymorphism (SNP) that results in missplicing of the cholecystokinin (CCK) receptor gene and expressing a larger mutated receptor in pancreatic cancer. The purpose of this study was to evaluate the significance and specificity of this SNP as a potential biomarker in patients with pancreatic cancer compared with other gastrointestinal (GI) cancers that also have CCK receptors. Methods: DNA was isolated and genotyped for the CCK receptor SNP from frozen tumor tissue from banked specimens of patients with pancreas, gastric, or colon cancer and from human cancer cell lines. Genotype and allelic frequencies were compared between the cancer cohort and two normal control databases using Fisher's exact test and odds ratio (OR). The Kaplan–Meier method was used to estimate the survival for patients with the CCK-B receptor SNP compared with those with the wild-type genotype. Immunohistochemical staining of cancer cells was done to detect the mutated receptor. Results: Colon and gastric cancer patients had similar genotype frequencies for the CCK receptor SNP as that reported in the normal population. In contrast, the prevalence of the SNP in subjects with pancreatic cancer was twice that of controls and other GI cancers. Survival was adversely affected by the presence of the SNP only in those with pancreatic cancer. Immunoreactivity for the mutated receptor was positive in pancreatic cancer tissues with the SNP but absent in other GI cancers. Conclusions: A SNP of the CCK receptor is significantly increased in patients with pancreatic cancer but not in those with other GI malignancies. Therefore, this SNP may be a potential biomarker for pancreatic cancer.
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Affiliation(s)
- Jelal Alsubai
- Department of Medicine, Pennsylvania State University School of Medicine, Hershey, Pennsylvania, USA
| | - Gail L Matters
- Department of Biochemistry and Molecular Biology, Pennsylvania State University School of Medicine, Hershey, Pennsylvania, USA
| | - Christopher O McGovern
- Department of Biochemistry and Molecular Biology, Pennsylvania State University School of Medicine, Hershey, Pennsylvania, USA
| | - Jiangang Liao
- Department of Public Health Sciences, Pennsylvania State University, College of Medicine, Hershey, Pennsylvania, USA
| | - Evan L Gilius
- The National Cancer Institute, NIH, Bethesda, Maryland, USA
| | - Jill P Smith
- Department of Medicine, Pennsylvania State University School of Medicine, Hershey, Pennsylvania, USA.,Department of Medicine/Gastroenterology Georgetown University School of Medicine, Washington, District of Columbia, USA
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