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Heymann JJ, D'Ambrosio D, Dombrowski KS, Desai N, Illei PB. Pulmonary Cytopathology: Current and Future Impact on Patient Care. Surg Pathol Clin 2024; 17:395-410. [PMID: 39129139 DOI: 10.1016/j.path.2024.06.002] [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] [Indexed: 08/13/2024]
Abstract
Small biopsies of lung are routinely obtained by many methods, including several that result in cytologic specimens. Because lung cancer is often diagnosed at a stage for which primary resection is not an option, it is critical that all diagnostic, predictive, and prognostic information be derived from such small biopsy specimens. As the number of available diagnostic and predictive markers expands, cytopathologists must familiarize themselves with current requirements for specimen acquisition, handling, results reporting, and molecular and other ancillary testing, all of which are reviewed here.
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Affiliation(s)
- Jonas J Heymann
- Department of Pathology and Laboratory Medicine, New York-Presbyterian Hospital-Weill Cornell Medicine, 1300 York Avenue, New York, NY 10065, USA.
| | - Danielle D'Ambrosio
- Department of Pathology, New York University Grossman School of Medicine, 560 First Avenue, New York, NY 10016, USA
| | - Katya S Dombrowski
- Department of Pathology, The Johns Hopkins University School of Medicine, 600 North Wolfe Street, Baltimore, MD 21287, USA
| | - Niyati Desai
- Department of Pathology and Cell Biology, New York-Presbyterian Hospital-Columbia University Irving Medical Center, 630 West 168th Street, New York, NY 10032, USA
| | - Peter B Illei
- Department of Pathology, The Johns Hopkins University School of Medicine, 600 North Wolfe Street, Baltimore, MD 21287, USA
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Abe H, Kawahara A, Akiba J, Yamaguchi R. Advances in diagnostic liquid-based cytology. Cytopathology 2024. [PMID: 38837293 DOI: 10.1111/cyt.13405] [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: 01/29/2024] [Revised: 05/09/2024] [Accepted: 05/20/2024] [Indexed: 06/07/2024]
Abstract
Liquid-based cytology (LBC) has changed the landscape of gynaecological cytology. A growing demand exists for LBC in diagnostic cytology, particularly for ancillary testing, such as immunocytochemistry and molecular testing. Ancillary testing solely based on conventional preparation (CP) methods remains challenging. Recently, the increased demand for specialist testing and minimally invasive techniques, such as endoscopic ultrasonography fine-needle aspiration, to obtain cellular samples has led to an increasing demand for ancillary testing on cytology LBC supernatant, slides and cell block (CB). This facilitates the diagnosis and prognosis in cytology samples enabling personalized treatment. An understanding of the history and future prospects of LBC is crucial for its application in routine diagnostics by cytopathologists and cytotechnologists. In this review, we initiated an internet search using the keyword 'liquid-based cytology', and we conducted a literature review to discuss the usefulness of combined diagnosis of LBC and CP, immunocytochemistry and molecular testing and assessed the quality of nucleic acids in diagnostic LBC. High-quality and cell-rich diagnostic LBC surpassed the CP method alone in terms of reliability and versatility of ancillary testing in cytological diagnosis. Conclusively, diagnostic LBC lends itself to various new technologies and is expected to continue evolving with innovations in the future.
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Affiliation(s)
- Hideyuki Abe
- Department of Diagnostic Pathology, Kurume University Hospital, Kurume, Japan
| | - Akihiko Kawahara
- Department of Diagnostic Pathology, Kurume University Hospital, Kurume, Japan
| | - Jun Akiba
- Department of Diagnostic Pathology, Kurume University Hospital, Kurume, Japan
| | - Rin Yamaguchi
- Department of Diagnostic Pathology, Nagasaki University Hospital, Nagasaki, Japan
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Jager L, Jennings LJ, Dittmann D, Blanco J, Choy B, Nayar R. Supernatant fluid from endobronchial ultrasound-guided transbronchial needle aspiration for rapid next-generation sequencing. J Am Soc Cytopathol 2024:S2213-2945(24)00043-7. [PMID: 38797657 DOI: 10.1016/j.jasc.2024.04.007] [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: 03/05/2024] [Revised: 04/25/2024] [Accepted: 04/28/2024] [Indexed: 05/29/2024]
Abstract
INTRODUCTION There is an increasing demand to optimize the workflow and maximize tissue available for next-generation sequencing (NGS) for non-small cell carcinoma. We looked at transbronchial needle endobronchial ultrasound-guided bronchoscopy with transbronchial needle aspiration samples and evaluated the performance of supernatant (SN) fluid processed from a dedicated aspirate collected for NGS testing. MATERIALS AND METHODS Nineteen samples were collected and processed using a new workflow. Five aspirates were collected in formalin. One additional dedicated pass was collected fresh and centrifuged. The resulting cell pellet was added to formalin for cell block (CB) processing. DNA and RNA were extracted from concentrated SN for targeted testing using the Oncomine Precision Assay (Thermo Scientific, Waltham, MA). NGS results from the corresponding CB samples were used as "controls" for comparison. RESULTS Thirty-one mutations were detected in SN (Table 1). The most frequently mutated genes were TP53 (35%), EGFR (23%), KRAS (13%), CTNNB1 (6%), and ERBB2 (6%). There was 100% concordance between the mutations detected in SN and corresponding CBs with comparable variant allele frequencies. Turnaround time of NGS results was 1 day for SN compared to 4-10 days for CB. CONCLUSIONS We were able to demonstrate the usefulness of SN for reliable rapid molecular results. We successfully incorporated the workflow for tissue handling and processing among our clinical, cytopathology, and molecular teams. Molecular results were available at the same time as the cytologic diagnosis, allowing for timely reporting of a comprehensive diagnosis. This approach is particularly useful in patients with advanced disease requiring urgent management.
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Affiliation(s)
- Lucy Jager
- Department of Pathology, Northwestern University Feinberg School of Medicine, Northwestern Memorial Hospital, Chicago, Illinois.
| | - Lawrence J Jennings
- Department of Pathology, Northwestern University Feinberg School of Medicine, Northwestern Memorial Hospital, Chicago, Illinois
| | - David Dittmann
- Department of Pathology, Northwestern University Feinberg School of Medicine, Northwestern Memorial Hospital, Chicago, Illinois
| | - Jayjay Blanco
- Department of Pathology, Northwestern University Feinberg School of Medicine, Northwestern Memorial Hospital, Chicago, Illinois
| | - Bonnie Choy
- Department of Pathology, Northwestern University Feinberg School of Medicine, Northwestern Memorial Hospital, Chicago, Illinois
| | - Ritu Nayar
- Department of Pathology, Northwestern University Feinberg School of Medicine, Northwestern Memorial Hospital, Chicago, Illinois
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Fernandes SPM, Vilarinho AS, Frutuoso A, Teixeira C, Silva RAAP. Application of CytoPath®Easy Vials in Cervical Cancer Screening: Self-Sampling Approach. J Cytol 2024; 41:67-74. [PMID: 38779609 PMCID: PMC11108033 DOI: 10.4103/joc.joc_108_23] [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: 06/23/2023] [Revised: 12/03/2023] [Accepted: 01/31/2024] [Indexed: 05/25/2024] Open
Abstract
Context CytoPath®Easy kit (DiaPath S.p.A.) offers a major advantage compared to other commercially available kits available for the screening of cervical cancer, as it does not require additional equipment for sample processing. Using this methodology, collected epithelial cells are immersed in a preservative liquid before setting as a thin layer on a slide via gravity sedimentation. Aims To evaluate the suitability of the CytoPath®Easy kit for the processing of cervical samples, detection of pre-neoplastic lesions, and nucleic preservation and extraction for HR-HPV diagnosis. Materials and Methods A total of 242 self-sampled cervical specimens were utilized, with 192 collected in CytoPath®Easy vials and 50 collected and processed using the ThinPrepTM for comparative analysis. The samples underwent processing, Papanicolaou staining, and microscopic evaluation for morphological parameters. The extracted nucleic acids were assessed for purity and integrity, and the detection of high-risk human papillomavirus (HR-HPV) was carried out using the Alinitym HR HPV system kit (Abbott Laboratórios Lda). Results Both methods demonstrated effective performance, enabling the morphological assessment of the cervical epithelium. Statistical analysis indicated that ThinPrepTM yielded significantly better results in terms of cellularity. Conversely, CytoPath®Easy exhibited superior performance in terms of the quantity of extracted DNA and its degree of purification. Concerning the time consumed during processing, both methods were comparable, with the CytoPath®Easy methodology standing out for its cost-effectiveness, as it does not necessitate additional instruments and consumables. Conclusions The novel CytoPath®Easy methodology proves effective in preserving both nucleic acids and cell morphology characteristics, two crucial features for cervical cancer screening.
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Affiliation(s)
- Sílvia P. M. Fernandes
- School of Health (ESS), Polytechnic Institute of Porto, Rua Dr. António Bernardino de Almeida, 400, 4200-072 Porto, Portugal, Rua Dr. António Bernardino de Almeida, 400, 4200-072 Porto, Portugal
- Área Técnico-Científica de Anatomia Patológica, Citológica e Tanatológica, School of Health (ESS), Rua Dr. António Bernardino de Almeida, 400, 4200-072 Porto, Portugal
- Center for Translational Health and Medical Biotechnology Research (TBIO)/Health Research Network (RISE-Health), ESS, Polytechnic of Porto, R. Dr. António Bernardino de Almeida, 400, 4200-072, Porto, Portugal
- REQUIMTE/LAVQ, ESS, Polytechnic of Porto, R. Dr. António Bernardino de Almeida, 400, 4200-072, Porto, Portugal
| | - Ana Sofia Vilarinho
- School of Health (ESS), Polytechnic Institute of Porto, Rua Dr. António Bernardino de Almeida, 400, 4200-072 Porto, Portugal, Rua Dr. António Bernardino de Almeida, 400, 4200-072 Porto, Portugal
| | - Amaro Frutuoso
- School of Health (ESS), Polytechnic Institute of Porto, Rua Dr. António Bernardino de Almeida, 400, 4200-072 Porto, Portugal, Rua Dr. António Bernardino de Almeida, 400, 4200-072 Porto, Portugal
- Área Técnico-Científica de Anatomia Patológica, Citológica e Tanatológica, School of Health (ESS), Rua Dr. António Bernardino de Almeida, 400, 4200-072 Porto, Portugal
- Serviço de Anatomia Patológica, Hospital Pedro Hispano, Unidade Local de Saúde de Matosinhos, Rua Dr. Eduardo Torres, 4464-513, Matosinhos, Portugal
| | - Cidália Teixeira
- Serviço de Anatomia Patológica, Hospital Pedro Hispano, Unidade Local de Saúde de Matosinhos, Rua Dr. Eduardo Torres, 4464-513, Matosinhos, Portugal
| | - Regina Augusta A. P. Silva
- School of Health (ESS), Polytechnic Institute of Porto, Rua Dr. António Bernardino de Almeida, 400, 4200-072 Porto, Portugal, Rua Dr. António Bernardino de Almeida, 400, 4200-072 Porto, Portugal
- Área Técnico-Científica de Anatomia Patológica, Citológica e Tanatológica, School of Health (ESS), Rua Dr. António Bernardino de Almeida, 400, 4200-072 Porto, Portugal
- REQUIMTE/LAVQ, ESS, Polytechnic of Porto, R. Dr. António Bernardino de Almeida, 400, 4200-072, Porto, Portugal
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Zarabi SK, Zhai L, Cheng YW. A Challenging Correlation between Tumor Cellularity and Somatic Variant Allele Fraction in Lung and Colorectal Cancers-Specimens of Low Tumor Percentage Should Be Analyzed with Caution. Biomolecules 2024; 14:168. [PMID: 38397405 PMCID: PMC10887151 DOI: 10.3390/biom14020168] [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: 11/06/2023] [Revised: 01/26/2024] [Accepted: 01/27/2024] [Indexed: 02/25/2024] Open
Abstract
Background and aims: The percentage of tumor cells (tumor cellularity) in a cancerous tissue has been assumed to correlate with the variant allele fraction (VAF) of an identified pathogenic variant. Many laboratories use the tumor cellularity as part of a quality criteria for specimen processing and clinical reporting. However, a systematic study of such correlation has yet to be shown. We performed a relatively large-scale study to determine whether pathologist-estimated tumor cellularity is correlated with next-generation sequencing (NGS)-derived VAF. Materials and Methods: A total of 1511 non-small cell lung cancer (NSCLC) and colorectal cancer (CRC) specimens, including formalin-fixed paraffin-embedded (FFPE) and fine needle aspirated (FNA) tissues, were analyzed by cancer hotspot NGS. For a given specimen, pathogenic variants of BRAF, EGFR, KRAS, and NRAS were identified and the determined VAFs were correlated with the corresponding tissue tumor cellularity. Results: The coefficient of determination R-squared (R2) values were calculated for each correlation. All R2 values were lower than 0.25, indicating poor correlations. Pathogenic variants were found, not uncommonly, in tumor specimens that carried 10% or lower tumor cellularity. There were no apparent differences of R2 values between the FFPE and FNA specimens. Conclusion: In both NSCLC and CRC, the lack of linear relationship between tumor cellularity and VAF was found across a wide range of tumor cell percentages. Caution should be used when using tumor cellularity to triage specimens for NGS testing. The tumor cellularity should be considered in relation to the limit of detection of the specific assay for the proper interpretation of a negative test result.
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Affiliation(s)
- Samaneh K. Zarabi
- Department of Pathology, Stony Brook University Hospital, New York, NY 11794, USA
| | - Lidong Zhai
- Department of Laboratory Medicine, Robert J. Tomsich Pathology and Laboratory Medicine Institute, Cleveland Clinic, Cleveland, OH 44195, USA
| | - Yu-Wei Cheng
- Department of Laboratory Medicine, Robert J. Tomsich Pathology and Laboratory Medicine Institute, Cleveland Clinic, Cleveland, OH 44195, USA
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Rather MA, Agarwal D, Bhat TA, Khan IA, Zafar I, Kumar S, Amin A, Sundaray JK, Qadri T. Bioinformatics approaches and big data analytics opportunities in improving fisheries and aquaculture. Int J Biol Macromol 2023; 233:123549. [PMID: 36740117 DOI: 10.1016/j.ijbiomac.2023.123549] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2022] [Revised: 01/30/2023] [Accepted: 01/31/2023] [Indexed: 02/05/2023]
Abstract
Aquaculture has witnessed an excellent growth rate during the last two decades and offers huge potential to provide nutritional as well as livelihood security. Genomic research has contributed significantly toward the development of beneficial technologies for aquaculture. The existing high throughput technologies like next-generation technologies generate oceanic data which requires extensive analysis using appropriate tools. Bioinformatics is a rapidly evolving science that involves integrating gene based information and computational technology to produce new knowledge for the benefit of aquaculture. Bioinformatics provides new opportunities as well as challenges for information and data processing in new generation aquaculture. Rapid technical advancements have opened up a world of possibilities for using current genomics to improve aquaculture performance. Understanding the genes that govern economically relevant characteristics, necessitates a significant amount of additional research. The various dimensions of data sources includes next-generation DNA sequencing, protein sequencing, RNA sequencing gene expression profiles, metabolic pathways, molecular markers, and so on. Appropriate bioinformatics tools are developed to mine the biologically relevant and commercially useful results. The purpose of this scoping review is to present various arms of diverse bioinformatics tools with special emphasis on practical translation to the aquaculture industry.
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Affiliation(s)
- Mohd Ashraf Rather
- Division of Fish Genetics and Biotechnology, Faculty of Fisheries Ganderbal, Sher-e- Kashmir University of Agricultural Science and Technology, Kashmir, India.
| | - Deepak Agarwal
- Institute of Fisheries Post Graduation Studies OMR Campus, Vaniyanchavadi, Chennai, India
| | | | - Irfan Ahamd Khan
- Division of Fish Genetics and Biotechnology, Faculty of Fisheries Ganderbal, Sher-e- Kashmir University of Agricultural Science and Technology, Kashmir, India
| | - Imran Zafar
- Department of Bioinformatics and Computational Biology, Virtual University Punjab, Pakistan
| | - Sujit Kumar
- Department of Bioinformatics and Computational Biology, Virtual University Punjab, Pakistan
| | - Adnan Amin
- Postgraduate Institute of Fisheries Education and Research Kamdhenu University, Gandhinagar-India University of Kurasthra, India; Department of Aquatic Environmental Management, Faculty of Fisheries Rangil- Ganderbel -SKUAST-K, India
| | - Jitendra Kumar Sundaray
- ICAR-Central Institute of Freshwater Aquaculture, Kausalyaganga, Bhubaneswar, Odisha 751002, India
| | - Tahiya Qadri
- Division of Food Science and Technology, SKUAST-K, Shalimar, India
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NSCLC in the Era of Targeted and Immunotherapy: What Every Pulmonologist Must Know. Diagnostics (Basel) 2023; 13:diagnostics13061117. [PMID: 36980426 PMCID: PMC10047174 DOI: 10.3390/diagnostics13061117] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2023] [Revised: 02/28/2023] [Accepted: 03/14/2023] [Indexed: 03/18/2023] Open
Abstract
The treatment of non-small cell lung cancer has dramatically changed over the last decade through the use of targeted therapies and immunotherapies. Implementation of these treatment regimens relies on detailed knowledge regarding each tumor’s specific genomic profile, underscoring the necessity of obtaining superior diagnostic tissue specimens. While these treatment approaches are commonly utilized in the metastatic setting, approval among earlier-stage disease will continue to rise, highlighting the importance of early and comprehensive biomarker testing at the time of diagnosis for all patients. Pulmonologists play an integral role in the diagnosis and staging of non-small cell lung cancer via sophisticated tissue sampling techniques. This multifaceted review will highlight current indications for the use of targeted therapies and immunotherapies in non-small cell lung cancer and will outline the quality of various diagnostic approaches and subsequent success of tissue biomarker testing. Pulmonologist-specific methods, including endobronchial ultrasound and guided bronchoscopy, will be examined as well as other modalities such as CT-guided transthoracic biopsy and more.
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Next-Generation Sequencing Analysis of Pancreatic Cancer Using Residual Liquid Cytology Specimens from Endoscopic Ultrasound—Guided Fine-Needle Biopsy: A Prospective Comparative Study with Tissue Specimens. Diagnostics (Basel) 2023; 13:diagnostics13061078. [PMID: 36980386 PMCID: PMC10047095 DOI: 10.3390/diagnostics13061078] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2023] [Revised: 03/03/2023] [Accepted: 03/09/2023] [Indexed: 03/14/2023] Open
Abstract
This study evaluated the feasibility and clinical utility of liquid-based cytology (LBC) specimens via endoscopic ultrasound–guided fine-needle biopsy (EUS-FNB) for next-generation sequencing (NGS) of pancreatic cancer (PC). We prospectively evaluated the performance of DNA extraction and NGS using EUS-FNB samples obtained from PC. Thirty-three consecutive patients with PC who underwent EUS-FNB at our hospital were enrolled. DNA samples were obtained from 96.8% of the patients. When stratified with a variant allele frequency (VAF) > 10% tumor burden, the NGS success rate was 76.7% (n = 23) in formalin-fixed paraffin-embedded (FFPE), 83.3% (n = 25) in LBC, and 76.7% (n = 23) in frozen samples. The overall NGS success rate was 86.7% (n = 26) using FFPE, LBC, or frozen samples. The detection rates for the main mutated genes were as follows: 86.7% for KRAS, 73.3% for TP53, 66.7% for CDKN2A, 36.7% for SMAD4, and 16.7% for ARID1A. LBC had the highest median value of VAF (23.5%) for KRAS and TP53. PC mutation analysis using NGS was successfully performed using LBC compared with FFPE and frozen samples. This approach provides an alternative and affordable source of molecular testing materials.
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He C, Zhao J, Long Y, Yang H, Dong J, Liu H, Hu Z, Yang M, Huo D, Hou C. An ultrasensitive electrochemical biosensor for microRNA-21 detection via AuNPs/GAs and Y-shaped DNA dual-signal amplification strategy. Chem Commun (Camb) 2023; 59:350-353. [PMID: 36514997 DOI: 10.1039/d2cc06329h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Herein, a gold nanoparticles/graphene aerogels (AuNPs/GAs) modified electrochemical biosensor with catalytic hairpin assembly (CHA) and Y-shaped DNA nanostructure dual-signal amplification approaches for ultrasensitive microRNA-21 (miR-21) detection was successfully constructed, which displayed an ultra-wide detection linear range from 5 fM to 50 nM, as well as a relatively low detection limit (LOD) of 14.70 aM (S/N = 3). Furthermore, the sensing strategy had excellent specificity among highly homologous miRNA family members and exhibited satisfactory analytical performance for miRNA detection.
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Affiliation(s)
- Congjuan He
- Key Laboratory for Biorheological Science and Technology of Ministry of Education, State and Local Joint Engineering Laboratory for Vascular Implants, Bioengineering College of Chongqing University, Chongqing 400044, P. R. China.
| | - Jiaying Zhao
- Key Laboratory for Biorheological Science and Technology of Ministry of Education, State and Local Joint Engineering Laboratory for Vascular Implants, Bioengineering College of Chongqing University, Chongqing 400044, P. R. China.
| | - Yanyi Long
- Key Laboratory for Biorheological Science and Technology of Ministry of Education, State and Local Joint Engineering Laboratory for Vascular Implants, Bioengineering College of Chongqing University, Chongqing 400044, P. R. China.
| | - Huisi Yang
- Key Laboratory for Biorheological Science and Technology of Ministry of Education, State and Local Joint Engineering Laboratory for Vascular Implants, Bioengineering College of Chongqing University, Chongqing 400044, P. R. China.
| | - Jiangbo Dong
- Key Laboratory for Biorheological Science and Technology of Ministry of Education, State and Local Joint Engineering Laboratory for Vascular Implants, Bioengineering College of Chongqing University, Chongqing 400044, P. R. China.
| | - Huan Liu
- Chongqing Institute for Food and Drug Control, Chongqing 401121, P. R. China
| | - Zhikun Hu
- Key Laboratory for Biorheological Science and Technology of Ministry of Education, State and Local Joint Engineering Laboratory for Vascular Implants, Bioengineering College of Chongqing University, Chongqing 400044, P. R. China.
| | - Mei Yang
- Key Laboratory for Biorheological Science and Technology of Ministry of Education, State and Local Joint Engineering Laboratory for Vascular Implants, Bioengineering College of Chongqing University, Chongqing 400044, P. R. China.
| | - Danqun Huo
- Key Laboratory for Biorheological Science and Technology of Ministry of Education, State and Local Joint Engineering Laboratory for Vascular Implants, Bioengineering College of Chongqing University, Chongqing 400044, P. R. China. .,National Facility for Translational Medicine, Shanghai Jiao Tong University, Shanghai, 200240, P. R. China
| | - Changjun Hou
- Key Laboratory for Biorheological Science and Technology of Ministry of Education, State and Local Joint Engineering Laboratory for Vascular Implants, Bioengineering College of Chongqing University, Chongqing 400044, P. R. China. .,Chongqing Key Laboratory of Bio-perception & Intelligent Information Processing, School of Microelectronics and Communication Engineering, Chongqing University, Chongqing, 400044, P. R. China
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Das R, Jakubowski MA, Spildener J, Cheng YW. Identification of Novel MET Exon 14 Skipping Variants in Non-Small Cell Lung Cancer Patients: A Prototype Workflow Involving in Silico Prediction and RT-PCR. Cancers (Basel) 2022; 14:cancers14194814. [PMID: 36230737 PMCID: PMC9563401 DOI: 10.3390/cancers14194814] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Revised: 09/11/2022] [Accepted: 09/22/2022] [Indexed: 11/16/2022] Open
Abstract
Background and aims: The MET exon 14 skipping (METex14) is an oncogenic driver mutation that provides a therapeutic opportunity in non-small cell lung cancer (NSCLCs) patients. This event often results from sequence changes at the MET canonical splicing sites. We characterize two novel non-canonical splicing site variants of MET that produce METex14. Materials and Methods: Two variants were identified in three advanced-stage NSCLC patients in a next-generation sequencing panel. The potential impact on splicing was predicted using in silico tools. METex14 mutation was confirmed using reverse transcription (RT)-PCR and a Sanger sequencing analysis on RNA extracted from stained cytology smears. Results: The interrogated MET (RefSeq ID NM_000245.3) variants include a single nucleotide substitution, c.3028+3A>T, in intron 14 and a deletion mutation, c.3012_3028del, in exon 14. The in silico prediction analysis exhibited reduced splicing strength in both variants compared with the MET normal transcript. The RT-PCR and subsequent Sanger sequencing analyses confirmed METex14 skipping in all three patients carrying these variants. Conclusion: This study reveals two non-canonical MET splice variants that cause exon 14 skipping, concurrently also proposes a clinical workflow for the classification of such non-canonical splicing site variants detected by routine DNA-based NGS test. It shows the usefulness of in silico prediction to identify potential METex14 driver mutation and exemplifies the opportunity of routine cytology slides for RNA-based testing.
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Affiliation(s)
| | | | | | - Yu-Wei Cheng
- Correspondence: ; Tel.: +1-216-445-0757; Fax: +1-216-445-0681
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Yokoyama S, Iwaya H, Akahane T, Hamada T, Higashi M, Hashimoto S, Tanoue S, Ohtsuka T, Ido A, Tanimoto A. Sequential evaluation of
MUC
promoter methylation using next‐generation sequencing‐based custom‐made panels in liquid‐based cytology specimens of pancreatic cancer. Diagn Cytopathol 2022; 50:499-507. [DOI: 10.1002/dc.25022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2022] [Accepted: 07/12/2022] [Indexed: 11/06/2022]
Affiliation(s)
- Sieya Yokoyama
- Department of Pathology Kagoshima University Graduate School of Medical and Dental Sciences Kagoshima Japan
| | - Hiromichi Iwaya
- Digestive and Lifestyle Diseases Kagoshima University Graduate School of Medical and Dental Sciences Kagoshima Japan
| | - Toshiaki Akahane
- Department of Pathology Kagoshima University Graduate School of Medical and Dental Sciences Kagoshima Japan
- Center for Human Genome and Gene Analysis Kagoshima University Hospital Kagoshima Japan
| | - Taiji Hamada
- Department of Pathology Kagoshima University Graduate School of Medical and Dental Sciences Kagoshima Japan
| | - Michiyo Higashi
- Unit of Surgical Pathology Kagoshima University Hospital Kagoshima Japan
| | - Shinichi Hashimoto
- Digestive and Lifestyle Diseases Kagoshima University Graduate School of Medical and Dental Sciences Kagoshima Japan
| | - Shiroh Tanoue
- Digestive and Lifestyle Diseases Kagoshima University Graduate School of Medical and Dental Sciences Kagoshima Japan
| | - Takao Ohtsuka
- Department of Digestive Surgery, Breast and Thyroid Surgery Kagoshima University Graduate School of Medical and Dental Sciences Kagoshima Japan
| | - Akio Ido
- Digestive and Lifestyle Diseases Kagoshima University Graduate School of Medical and Dental Sciences Kagoshima Japan
| | - Akihide Tanimoto
- Department of Pathology Kagoshima University Graduate School of Medical and Dental Sciences Kagoshima Japan
- Center for Human Genome and Gene Analysis Kagoshima University Hospital Kagoshima Japan
- Unit of Surgical Pathology Kagoshima University Hospital Kagoshima Japan
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FFPE-Based NGS Approaches into Clinical Practice: The Limits of Glory from a Pathologist Viewpoint. J Pers Med 2022; 12:jpm12050750. [PMID: 35629172 PMCID: PMC9146170 DOI: 10.3390/jpm12050750] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2022] [Revised: 04/29/2022] [Accepted: 05/03/2022] [Indexed: 01/02/2023] Open
Abstract
The introduction of next-generation sequencing (NGS) in the molecular diagnostic armamentarium is deeply changing pathology practice and laboratory frameworks. NGS allows for the comprehensive molecular characterization of neoplasms, in order to provide the best treatment to oncologic patients. On the other hand, NGS raises technical issues and poses several challenges in terms of education, infrastructures and costs. The aim of this review is to give an overview of the main NGS sequencing platforms that can be used in current molecular diagnostics and gain insights into the clinical applications of NGS in precision oncology. Hence, we also focus on the preanalytical, analytical and interpretative issues raised by the incorporation of NGS in routine pathology diagnostics.
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Nakano S, Kawamoto Y, Komatsu Y, Saito R, Ito K, Yamamura T, Harada K, Yuki S, Kawakubo K, Sugiura R, Kato S, Hirata K, Hirata H, Nakajima M, Furukawa R, Takishin Y, Nagai K, Yokota I, Ota KH, Nakaoka S, Kuwatani M, Sakamoto N. Analysis of the Pancreatic Cancer Microbiome Using Endoscopic Ultrasound-Guided Fine-Needle Aspiration-Derived Samples. Pancreas 2022; 51:351-357. [PMID: 35695806 PMCID: PMC9257056 DOI: 10.1097/mpa.0000000000002028] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/20/2021] [Accepted: 04/29/2022] [Indexed: 12/10/2022]
Abstract
OBJECTIVES Most previous studies have analyzed bacteria in tumors using resected pancreatic cancer (PC) tissues, because it is difficult to obtain tissue samples from unresectable advanced PC. We aimed to determine whether minimal tissue obtained by endoscopic ultrasound-guided fine-needle aspiration is useful for microbiome analysis. METHODS Thirty PC and matched duodenal and stomach tissues (N = 90) were prospectively collected from 30 patients who underwent endoscopic ultrasound-guided fine-needle aspiration. Bacterial DNA was extracted, and 16S rRNA sequencing was performed. The primary outcome was the success rate of bacterial detection in tumors. Bacterial diversity and structure were investigated. RESULTS The bacterial detection rates were 80%, 100%, and 97% in PC, gastric, and duodenal samples, respectively. Pancreatic cancer tissues showed a lower α-diversity and a significantly different microbial structure than stomach and duodenal tissues. Proteobacteria were more abundant, whereas Firmicutes, Bacteroidetes, and Fusobacteria were less abundant in PC tissues than in stomach and duodenal tissues. Acinetobacter was more abundant in PC tissues than in stomach and duodenal tissues, and Delftia was more frequently detected in resectable PC. CONCLUSIONS Endoscopic ultrasound-guided fine-needle aspiration samples were valuable for PC microbiome analysis, revealing that the bacterial composition of PC is different from that of the stomach and duodenum.
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Affiliation(s)
- Shintaro Nakano
- From the Department of Gastroenterology and Hepatology, Hokkaido University Graduate School of Medicine
- Division of Cancer Center, Hokkaido University Hospital, Sapporo
| | | | - Yoshito Komatsu
- Division of Cancer Center, Hokkaido University Hospital, Sapporo
| | - Rika Saito
- From the Department of Gastroenterology and Hepatology, Hokkaido University Graduate School of Medicine
- Division of Cancer Center, Hokkaido University Hospital, Sapporo
| | - Ken Ito
- From the Department of Gastroenterology and Hepatology, Hokkaido University Graduate School of Medicine
- Division of Cancer Center, Hokkaido University Hospital, Sapporo
| | - Takahiro Yamamura
- From the Department of Gastroenterology and Hepatology, Hokkaido University Graduate School of Medicine
| | - Kazuaki Harada
- From the Department of Gastroenterology and Hepatology, Hokkaido University Graduate School of Medicine
| | - Satoshi Yuki
- From the Department of Gastroenterology and Hepatology, Hokkaido University Graduate School of Medicine
| | - Kazumichi Kawakubo
- From the Department of Gastroenterology and Hepatology, Hokkaido University Graduate School of Medicine
| | - Ryo Sugiura
- Department of Gastroenterology and Hepatology, Hakodate Municipal Hospital, Hakodate
| | - Shin Kato
- Department of Gastroenterology, Sapporo City General Hospital
| | - Koji Hirata
- Department of Gastroenterology, Sapporo Hokuyu Hospital
| | - Hajime Hirata
- From the Department of Gastroenterology and Hepatology, Hokkaido University Graduate School of Medicine
| | | | - Ryutaro Furukawa
- From the Department of Gastroenterology and Hepatology, Hokkaido University Graduate School of Medicine
| | - Yunosuke Takishin
- From the Department of Gastroenterology and Hepatology, Hokkaido University Graduate School of Medicine
| | - Kousuke Nagai
- From the Department of Gastroenterology and Hepatology, Hokkaido University Graduate School of Medicine
| | - Isao Yokota
- Department of Biostatistics, Hokkaido University Graduate School of Medicine
| | - Keisuke H. Ota
- Laboratory of Mathematical Biology, Hokkaido University Graduate School of Life Science
| | - Shinji Nakaoka
- Laboratory of Mathematical Biology, Hokkaido University Faculty of Advanced Life Science, Sapporo, Japan
| | - Masaki Kuwatani
- From the Department of Gastroenterology and Hepatology, Hokkaido University Graduate School of Medicine
| | - Naoya Sakamoto
- From the Department of Gastroenterology and Hepatology, Hokkaido University Graduate School of Medicine
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14
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Sekita‐Hatakeyama Y, Fujii T, Nishikawa T, Mitoro A, Sawai M, Itami H, Morita K, Uchiyama T, Takeda M, Sho M, Yoshiji H, Hatakeyama K, Ohbayashi C. Evaluation and diagnostic value of next-generation sequencing analysis of residual liquid-based cytology specimens of pancreatic masses. Cancer Cytopathol 2022; 130:202-214. [PMID: 34665935 PMCID: PMC9297882 DOI: 10.1002/cncy.22525] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2021] [Revised: 09/21/2021] [Accepted: 10/01/2021] [Indexed: 12/12/2022]
Abstract
BACKGROUND Liquid-based cytology (LBC) is a widely used method for processing specimens obtained by endoscopic biopsy. This study evaluated next-generation sequencing (NGS) analysis of LBC specimens to improve the diagnostic accuracy of pancreatic lesions. METHODS Upon the diagnosis of a suspected pancreatic mass, LBC residues were used retrospectively. The quantity and quality of DNA extracted from residual LBC samples were evaluated, and an NGS analysis targeting 6 genes (KRAS, GNAS, TP53, CDKN2A, SMAD4, and PIK3CA) was performed. RESULTS The library was prepared from LBC specimens taken from 52 cases: 44 were successful, and 8 preparations failed. An analysis of DNA quantity and quality suggested that the success or failure of NGS implementation depended on both properties. The final diagnosis was achieved by a combination of the pathological analysis of the surgical excision or biopsy material with clinical information. Among the 33 cases of pancreatic ductal adenocarcinoma (PDAC), KRAS, TP53, CDKN2A, and SMAD4 mutations were identified in 31 (94%), 16 (48%), 3 (9%), and 2 (6%), respectively. Among the 11 benign cases, only a KRAS mutation was identified in 1 case. On the basis of NGS results, 18 of 33 PDACs (55%) were classified as highly dysplastic or more, and 10 of 11 benign lesions were evaluated as nonmalignant, which was consistent with the final diagnosis. CONCLUSIONS NGS analysis using LBC specimens from which DNA of appropriate quantity and quality has been extracted could contribute to improving the assessment of pancreatic tumor malignancies and the application of molecular-targeted drugs.
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Affiliation(s)
| | - Tomomi Fujii
- Department of Diagnostic PathologyNara Medical UniversityKashiharaJapan
| | - Takeshi Nishikawa
- Department of Diagnostic PathologyNara Medical UniversityKashiharaJapan
| | - Akira Mitoro
- Department of GastroenterologyNara Medical UniversityKashiharaJapan
| | - Masayoshi Sawai
- Department of GastroenterologyMinami‐Nara General Medical CenterOyodo‐ChoJapan
| | - Hiroe Itami
- Department of Diagnostic PathologyNara Medical UniversityKashiharaJapan
| | - Kouhei Morita
- Department of Diagnostic PathologyNara Medical UniversityKashiharaJapan
| | - Tomoko Uchiyama
- Department of Diagnostic PathologyNara Medical UniversityKashiharaJapan
| | - Maiko Takeda
- Department of Diagnostic PathologyNara Medical UniversityKashiharaJapan
| | - Masayuki Sho
- Department of SurgeryNara Medical UniversityKashiharaJapan
| | - Hitoshi Yoshiji
- Department of GastroenterologyNara Medical UniversityKashiharaJapan
| | - Kinta Hatakeyama
- Department of Diagnostic PathologyNara Medical UniversityKashiharaJapan
- Department of PathologyNational Cerebral and Cardiovascular CenterSuitaJapan
| | - Chiho Ohbayashi
- Department of Diagnostic PathologyNara Medical UniversityKashiharaJapan
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15
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Marshall T, Kalanjeri S, Almeida FA. Lung cancer staging, the established role of bronchoscopy. Curr Opin Pulm Med 2022; 28:17-30. [PMID: 34720099 DOI: 10.1097/mcp.0000000000000843] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
PURPOSE OF REVIEW Lung cancer is the leading cause of cancer-related deaths worldwide. In the absence of distant metastases, accurate mediastinal nodal staging determines treatment approaches to achieve most favourable outcomes for patients. Mediastinal staging differentiates N0/N1 disease from N2/N3 in surgical candidates. Likewise, presence of nodal involvement in nonsurgical candidates who are being considered for stereotactic body radiation therapy is also critical. This review article seeks to discuss the current options available for mediastinal staging in nonsmall cell lung cancer (NSCLC), particularly the role of bronchoscopy. RECENT FINDINGS Although several techniques are available to stage the mediastinum, bronchoscopy with EBUS-TBNA with or without EUS-FNA appears to be superior in most clinical situations based on its ability to concomitantly diagnose and stage at once, safety, accessibility to the widest array of lymph node stations, cost and low risk of complications. However, training and experience are required to achieve consistent diagnostic accuracy with EBUS-TBNA. SUMMARY EBUS-TBNA with or without EUS-FNA is considered the modality of choice in the diagnosis and staging of NSCLC in both surgical and nonsurgical candidates.
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Affiliation(s)
- Tanya Marshall
- Department of Internal Medicine, Cleveland Clinic Akron General, Akron, Ohio
| | - Satish Kalanjeri
- Pulmonary and Critical Care Medicine, Harry S. Truman Memorial Veterans Hospital
- Pulmonary and Critical Care Medicine, University of Missouri School of Medicine, Columbia, Missouri
| | - Francisco Aecio Almeida
- Department of Pulmonary Medicine, Respiratory Institute, Cleveland Clinic, Cleveland, Ohio, USA
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16
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Ma Y, Huang D, Li X, Cheng W, Huang X, Feng H, Zhu F, Zeng X, Zhao S. GADD45B induced the enhancing of cell viability and proliferation in radiotherapy and increased the radioresistance of HONE1 cells. OPEN CHEM 2021. [DOI: 10.1515/chem-2021-0105] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
Abstract
This study aimed to investigate the key role and mechanism of GADD45B in the radiation resistance of nasopharyngeal carcinoma (NPC) cell lines. Radiotherapy-resistant HONE1 (HONE1-R) cells with stable genetic radioresistance were cultured under continuous radiation stimulation. CCK-8 and clone formation assays were used to verify the radioresistance of the cell line. Transcriptome sequencing was used to identify the most important differential signaling pathway in the cell line. Quantitative reverse transcription polymerase chain reaction (qRT-PCR) and Western blot analysis were used to verify the sequencing results. GADD45B-siRNA was used to knock down the key gene so as to verify the downstream gene expression and analyze its mechanism. The transcriptome analysis showed that 702 genes were upregulated and 772 genes were downregulated in the HONE1-R cell lines. The core differential signaling pathway was mitogen-activated protein kinase (MAPK) signaling pathway, and the core differential gene was GADD45B. After GADD45B was knocked down, the cell viability and proliferation ability of HONE1-R cell lines significantly decreased under radiation, and the expression of cyclin B1 and p-CDK1 decreased significantly. MAPK is the core signaling pathway in radioresistance of NPC. GADD45B plays an important role by affecting cell viability and proliferation in NPC radioresistance. GADD45B is a potential target of radioresistance in NPC.
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Affiliation(s)
- Yanning Ma
- Department of Radiotherapy, Shunde Hospital of Southern Medical University , No. 1, Jiazi Road, Lichun Village, Lunjiao Street, Shunde District, Guangdong Province , Foshan City , 528000 , P. R. China
| | - Dongheng Huang
- Department of Oncology, People’s Hospital of Yangjiang , Yangjiang , Guangdong, 529500 , P. R. China
| | - Xingtong Li
- Department of Radiotherapy, Shunde Hospital of Southern Medical University , No. 1, Jiazi Road, Lichun Village, Lunjiao Street, Shunde District, Guangdong Province , Foshan City , 528000 , P. R. China
| | - Wanqin Cheng
- Department of Radiotherapy, Shunde Hospital of Southern Medical University , No. 1, Jiazi Road, Lichun Village, Lunjiao Street, Shunde District, Guangdong Province , Foshan City , 528000 , P. R. China
| | - Xiaomin Huang
- Department of Radiotherapy, Shunde Hospital of Southern Medical University , No. 1, Jiazi Road, Lichun Village, Lunjiao Street, Shunde District, Guangdong Province , Foshan City , 528000 , P. R. China
| | - Huiyi Feng
- Department of Radiotherapy, Shunde Hospital of Southern Medical University , No. 1, Jiazi Road, Lichun Village, Lunjiao Street, Shunde District, Guangdong Province , Foshan City , 528000 , P. R. China
| | - Fengying Zhu
- Department of Radiotherapy, Shunde Hospital of Southern Medical University , No. 1, Jiazi Road, Lichun Village, Lunjiao Street, Shunde District, Guangdong Province , Foshan City , 528000 , P. R. China
| | - Xiaokang Zeng
- Department of Central Laboratory, Shunde Hospital of Southern Medical University , No. 1 Jiazi Road, Lichun Village, Lunjiao Street, Shunde District, Guangdong Province , Foshan City , 528000 , P. R. China
| | - Shufen Zhao
- Department of Radiotherapy, Shunde Hospital of Southern Medical University , No. 1, Jiazi Road, Lichun Village, Lunjiao Street, Shunde District, Guangdong Province , Foshan City , 528000 , P. R. China
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17
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Chua TH, Chuah KL. Concordance of Cytological Specimens with Histological Tissue for Detection of Epidermal Growth Factor Receptor Mutation in Non-Small Cell Lung Cancer: A Systematic Review. Acta Cytol 2021; 66:61-71. [PMID: 34706365 DOI: 10.1159/000519380] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2021] [Accepted: 08/31/2021] [Indexed: 11/19/2022]
Abstract
INTRODUCTION There is increasing need for more testing in non-small cell lung cancer given the introduction of newer targeted therapies. Cytological specimens including conventional smears (CS), cell blocks (CB), and liquid-based cytology (LBC) are an alternative to histologic tissue (HT) specimens in detecting EGFR mutations, but the concordance of these 2 specimens is yet to be determined. The aim of the present systematic review is to determine the concordance rates between different cytologic specimens with HT in detecting EGFR mutations. METHODS PubMed, Cochrane Library, and Google Scholar were utilized in the primary search, along with reference lists of electronically retrieved full-text articles. Concordance rates were pooled together if 2 or more studies reporting the same type of cytologic specimen were available. RESULTS Overall, 15 studies were included in this review, with 13 studies included in the pooled analysis. There was an overall concordance rate of 92.8% in 593 paired cytologic and HT specimens, with LBC having the highest concordance rate of 96.0%, followed by CS and CB, each with a concordance rate of 95.8%, although the concordance rate of CS and/or CB was lower at 90.6% with a larger pool of studies. LBC was found to have a significantly higher concordance rate than CS and/or CB. CONCLUSION Cytological specimens have a high concordance rate in detecting EGFR mutations, when compared to HT. LBC has shown superior concordance rates compared to CS and CB. Cytological specimens should be considered as an additional and alternative source of diagnostic material for EGFR testing.
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Affiliation(s)
- Tzy Harn Chua
- Department of Pathology, Tan Tock Seng Hospital, Singapore, Singapore
| | - Khoon Leong Chuah
- Department of Pathology, Tan Tock Seng Hospital, Singapore, Singapore
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18
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Tawfik OW, Subramanian J, Caughron S, Mana P, Ewing E, Aboudara M, Borsa J, Schafer L, Saettele T, Jonnalagadda S. Challenges in Pathology Specimen Processing in the New Era of Precision Medicine. Arch Pathol Lab Med 2021; 146:603-610. [PMID: 34424953 DOI: 10.5858/arpa.2021-0089-oa] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/15/2021] [Indexed: 11/06/2022]
Abstract
CONTEXT.— Precision therapies for patients with driver mutations can offer deep and durable responses that correlate with diagnosis, metastasis prognosis, and improvement in survival. Such targeted therapies will continue to increase, pushing us to change our traditional approaches. We needed to search for new tools to effectively integrate technological advancements into our practices because of their capability to improve the efficiency and accuracy of our diagnostic and treatment approaches. Perhaps nothing is as relevant as identifying and implementing new workflows for processing pathologic specimens and for improving communication of critical laboratory information to and from clinicians for appropriate care of patients in an efficient and timely manner. OBJECTIVES.— To define the gold standard in delivering the best care for patients, to identify gaps in the process, and to identify potential solutions that would improve our process, including gaps related to knowledge, skills, attitudes, and practices. DESIGN.— We assembled a team across disciplines to systematically perform a gap analysis study to clarify the discrepancy between the current reality in pathology specimen processing and the desired optimal situation to deliver the results intended for patient care. RESULTS.— A practical collaborative workflow for specimen management seeking the cooperation of the stakeholders in each medical discipline to provide guidelines in specimen collection, delivery, processing, and reporting of results with the ultimate goal of improving patients' outcomes is provided. CONCLUSIONS.— New tools are required to effectively integrate data-driven approaches in specimen processing to meet the new demands.
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Affiliation(s)
- Ossama William Tawfik
- The Department of Pathology (Tawfik, Caughron, Mana, Ewing), Saint Luke's Health System, Kansas City, Missouri.,MAWD Pathology Group, Kansas City, Kansas (Tawfik, Caughron, Mana, Ewing)
| | - Janakiraman Subramanian
- From the Division of Oncology (Subramanian, Schafer), Saint Luke's Health System, Kansas City, Missouri.,The Department of Medicine (Subramanian), niversity of Missouri, Kansas City
| | - Samuel Caughron
- The Department of Pathology (Tawfik, Caughron, Mana, Ewing), Saint Luke's Health System, Kansas City, Missouri.,MAWD Pathology Group, Kansas City, Kansas (Tawfik, Caughron, Mana, Ewing)
| | - Pradip Mana
- The Department of Pathology (Tawfik, Caughron, Mana, Ewing), Saint Luke's Health System, Kansas City, Missouri.,MAWD Pathology Group, Kansas City, Kansas (Tawfik, Caughron, Mana, Ewing)
| | - Eric Ewing
- The Department of Pathology (Tawfik, Caughron, Mana, Ewing), Saint Luke's Health System, Kansas City, Missouri.,MAWD Pathology Group, Kansas City, Kansas (Tawfik, Caughron, Mana, Ewing)
| | - Matthew Aboudara
- Division of Pulmonology (Aboudara, Saettele), Saint Luke's Health System, Kansas City, Missouri
| | - John Borsa
- Department of Radiology (Borsa), Saint Luke's Health System, Kansas City, Missouri.,Department of Radiology (Borsa), niversity of Missouri, Kansas City
| | - Liudmila Schafer
- From the Division of Oncology (Subramanian, Schafer), Saint Luke's Health System, Kansas City, Missouri
| | - Timothy Saettele
- Division of Pulmonology (Aboudara, Saettele), Saint Luke's Health System, Kansas City, Missouri
| | - Sreeni Jonnalagadda
- Division of Gastroenterology, in the Department of Medicine, (Jonnalagadda), Saint Luke's Health System, Kansas City, Missouri
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19
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Akahane T, Kitazono I, Kobayashi Y, Nishida-Kirita Y, Yamaguchi T, Yanazume S, Tabata K, Kobayashi H, Tanimoto A. Direct next-generation sequencing analysis using endometrial liquid-based cytology specimens for rapid cancer genomic profiling. Diagn Cytopathol 2021; 49:1078-1085. [PMID: 34319014 DOI: 10.1002/dc.24841] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2021] [Revised: 07/13/2021] [Accepted: 07/20/2021] [Indexed: 11/08/2022]
Abstract
BACKGROUND Genomic examination of cytology specimens is often performed on cell blocks or conventional smears rather than on liquid-based cytology (LBC) specimens. Since LBC specimens preserve high-quality DNA, cancer genome profiling using next-generation sequencing (NGS) is also attainable from residual LBC specimens. One of the advantages of using LBC specimens for NGS is that it allows direct extraction of DNA from residual specimens, avoiding a sacrifice of smear slides and minimizing genomic profiling processing time. METHODS Endometrial LBC specimens were subjected to NGS analysis to validate the practicality of rapid cancer genomic profiling in a pathology laboratory. The extracted DNA was subjected to NGS using a customized cancer gene panel comprising 56 genes and 17 microsatellite regions. The workflow strategy was defined, and the processing time estimated for specimen sampling, cell counting, NGS run, and genome profiling. RESULTS NGS analysis of most LBC specimens revealed somatic mutations, tumor mutation burden, and microsatellite instability, which were almost identical to those obtained from formalin-fixed paraffin-embedded tissues. The processing time for direct NGS analysis and cancer genomic profiling of the residual LBC specimens was approximately 5 days. CONCLUSION The residual LBC specimens collected using endometrial cytology were verified to carry a high tumor fraction for NGS analysis and could serve as an alternate source for rapid molecular classification and diagnosis of endometrial cancers, as a routine process in a pathology laboratory.
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Affiliation(s)
- Toshiaki Akahane
- Department of Pathology, Kagoshima University Graduate School of Medical and Dental Sciences, Kagoshima, Japan.,Center for Human Genome and Gene Analysis, Kagoshima University Hospital, Japan
| | - Ikumi Kitazono
- Unit of Surgical Pathology, Kagoshima University Hospital, Kagoshima, Japan
| | - Yusuke Kobayashi
- Advanced Cancer Medicine for Gynecologic Cancer, Kagoshima University Graduate School of Medical and Dental Sciences, Kagoshima, Japan
| | | | - Tomomi Yamaguchi
- Department of Pathology, Laboratory of Cancer Medical Science, Hokuto Hospital, Obihiro, Japan
| | - Shintaro Yanazume
- Department of Obstetrics and Gynecology, Kagoshima University Graduate School of Medical and Dental Sciences, Kagoshima, Japan
| | - Kazuhiro Tabata
- Department of Pathology, Kagoshima University Graduate School of Medical and Dental Sciences, Kagoshima, Japan
| | - Hiroaki Kobayashi
- Advanced Cancer Medicine for Gynecologic Cancer, Kagoshima University Graduate School of Medical and Dental Sciences, Kagoshima, Japan.,Department of Obstetrics and Gynecology, Kagoshima University Graduate School of Medical and Dental Sciences, Kagoshima, Japan
| | - Akihide Tanimoto
- Department of Pathology, Kagoshima University Graduate School of Medical and Dental Sciences, Kagoshima, Japan.,Center for Human Genome and Gene Analysis, Kagoshima University Hospital, Japan.,Unit of Surgical Pathology, Kagoshima University Hospital, Kagoshima, Japan
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20
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Testing EGFR with Idylla on Cytological Specimens of Lung Cancer: A Review. Int J Mol Sci 2021; 22:ijms22094852. [PMID: 34063720 PMCID: PMC8125729 DOI: 10.3390/ijms22094852] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2021] [Revised: 04/30/2021] [Accepted: 04/30/2021] [Indexed: 12/14/2022] Open
Abstract
The current standard of care for advanced non-small-cell lung cancer is based on detecting actionable mutations that can benefit from targeted therapy. Comprehensive genetic tests can have long turn-around times, and because EGFR mutations are the most prevalent actionable mutation, a quick detection would enable a prompt initiation of targeted therapy. Furthermore, the scarcity of diagnostic material means that sometimes only cytologic material is available. The Idylla™ EGFR assay is a real-time PCR–based method able to detect 51 EGFR mutations in 2.5 h. Idylla is validated for use only on FFPE sections, but some researchers described their experiences with cytological material. We reviewed the relevant literature, finding four articles describing 471 cases and many types of cytological input material: smears, cell-block sections, suspensions, and extracted DNA. The sensitivity, specificity, and limit of detection appear comparable to those obtained with histological input material, with one exception: the usage of scraped stained smears as input may reduce the accuracy of the test. In conclusion, usage of cytological material as input to the Idylla EGFR test is possible. A workflow where common mutations are tested first and fast, leaving rarer mutations for subsequent comprehensive profiling, seems the most effective approach.
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21
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Pisapia P, Pepe F, Sgariglia R, Nacchio M, Russo G, Conticelli F, Girolami I, Eccher A, Bellevicine C, Vigliar E, Malapelle U, Troncone G. Next generation sequencing in cytology. Cytopathology 2021; 32:588-595. [PMID: 33792981 PMCID: PMC8451925 DOI: 10.1111/cyt.12974] [Citation(s) in RCA: 36] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2020] [Revised: 02/02/2021] [Accepted: 03/06/2021] [Indexed: 12/17/2022]
Abstract
The application of next generation sequencing (NGS) technology to cytological samples has significantly modified molecular cytopathology practice. Cytological samples represent a valid source of high-quality DNA for NGS analysis, especially for predicting patients' response to targeted treatments and for refining the risk of malignancy in indeterminate cytological diagnoses. However, several pre-analytical factors may influence the reliability of NGS clinical analysis. Here, we briefly review the challenges of NGS in cytology practice, focusing on those pre-analytical factors that may negatively affect NGS success rates and routine diagnostic applications. Finally, we address the future directions of the field.
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Affiliation(s)
- Pasquale Pisapia
- Department of Public Health, University of Naples Federico II, Naples, Italy
| | - Francesco Pepe
- Department of Public Health, University of Naples Federico II, Naples, Italy
| | - Roberta Sgariglia
- Department of Public Health, University of Naples Federico II, Naples, Italy
| | - Mariantonia Nacchio
- Department of Public Health, University of Naples Federico II, Naples, Italy
| | - Gianluca Russo
- Department of Public Health, University of Naples Federico II, Naples, Italy
| | - Floriana Conticelli
- Department of Public Health, University of Naples Federico II, Naples, Italy
| | - Ilaria Girolami
- Division of Pathology, Central Hospital Bolzano, Bolzano, Italy
| | - Albino Eccher
- Department of Pathology and Diagnostics, University and Hospital Trust of Verona, Verona, Italy
| | - Claudio Bellevicine
- Department of Public Health, University of Naples Federico II, Naples, Italy
| | - Elena Vigliar
- Department of Public Health, University of Naples Federico II, Naples, Italy
| | - Umberto Malapelle
- Department of Public Health, University of Naples Federico II, Naples, Italy
| | - Giancarlo Troncone
- Department of Public Health, University of Naples Federico II, Naples, Italy
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22
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Pisapia P, Pepe F, Iaccarino A, Sgariglia R, Nacchio M, Conticelli F, Salatiello M, Tufano R, Russo G, Gragnano G, Girolami I, Eccher A, Malapelle U, Troncone G. Next Generation Sequencing in Cytopathology: Focus on Non-Small Cell Lung Cancer. Front Med (Lausanne) 2021; 8:633923. [PMID: 33644101 PMCID: PMC7904874 DOI: 10.3389/fmed.2021.633923] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2020] [Accepted: 01/19/2021] [Indexed: 12/12/2022] Open
Abstract
Molecular cytopathology is a rapidly evolving field embracing both conventional microscopy and molecular pathology. Its growing popularity stems from the fact that in many types of advanced cancers, including non small cell lung cancer (NSCLC), cytological samples often constitute the only available specimens for morphomolecular analysis. Indeed, non formalin fixed and paraffin embedded (FFPE) cytological samples feature a higher quality of extracted nucleic acids than histological specimens. However, because of the growing complexity of molecular testing, several efforts should be made to validate the analytical performance of the wide array of currently available molecular technologies, including next generation sequencing (NGS). This technology has the terrific advantage of allowing simultaneous detection of scores of predictive biomarkers even in low-input DNA/RNA specimens. Here, we briefly review the role of the modern cytopathologist in the morphomolecular diagnosing of advanced stage NSCLC and the adoption of NGS in conventional cytopreparations (cell blocks, direct smears, and liquid-based cytology) and supernatants.
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Affiliation(s)
- Pasquale Pisapia
- Department of Public Health, University of Naples Federico II, Naples, Italy
| | - Francesco Pepe
- Department of Public Health, University of Naples Federico II, Naples, Italy
| | - Antonino Iaccarino
- Department of Public Health, University of Naples Federico II, Naples, Italy
| | - Roberta Sgariglia
- Department of Public Health, University of Naples Federico II, Naples, Italy
| | - Mariantonia Nacchio
- Department of Public Health, University of Naples Federico II, Naples, Italy
| | - Floriana Conticelli
- Department of Public Health, University of Naples Federico II, Naples, Italy
| | - Maria Salatiello
- Department of Public Health, University of Naples Federico II, Naples, Italy
| | | | - Gianluca Russo
- Department of Public Health, University of Naples Federico II, Naples, Italy
| | - Gianluca Gragnano
- Department of Public Health, University of Naples Federico II, Naples, Italy
| | - Ilaria Girolami
- Division of Pathology, Central Hospital Bolzano, Bolzano, Italy
| | - Albino Eccher
- Department of Pathology and Diagnostics, University and Hospital Trust of Verona, Verona, Italy
| | - Umberto Malapelle
- Department of Public Health, University of Naples Federico II, Naples, Italy
| | - Giancarlo Troncone
- Department of Public Health, University of Naples Federico II, Naples, Italy
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23
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Liang H, Li C, Zhao Y, Zhao S, Huang J, Cai X, Cheng B, Xiong S, Li J, Wang W, Zhu C, Li W, He J, Liang W. Concomitant Mutations in EGFR 19Del/L858R Mutation and Their Association with Response to EGFR-TKIs in NSCLC Patients. Cancer Manag Res 2020; 12:8653-8662. [PMID: 32982456 PMCID: PMC7509478 DOI: 10.2147/cmar.s255967] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2020] [Accepted: 08/08/2020] [Indexed: 11/23/2022] Open
Abstract
Objective Differences in efficacy of epidermal growth factor receptor-tyrosine kinase inhibitors (EGFR-TKI) have been observed between non-small cell lung cancer (NSCLC) patients with 19 exon deletion (19Del) and L858R mutation. We explored whether the total number or pattern of concomitant mutations of 19Del and L858R may explain their different sensitivities. Patients and Methods This study contained the mutational profiles of EGFR-mutated NSCLC patients from two cohorts: Guangzhou (G1) and database (G2). Concomitant mutation status and EGFR-TKI response information were retrieved. Results A total of 403 patients covered 283 genes in the G1 and 803 patients with a different gene set in the G2 were included. Similar prevalence of total concomitant mutation number was observed in both G1 (19Del 32.48% vs L858R 30.45%; P=0.68) and G2 (19Del 74.9% vs L858R 73.2%; P=0.65) cohorts. Only HGF/c-Met pathway same more related to L858R mutation. EGFR-TKI response information was recorded for 134 patients in the G2 cohort. 19Del showed a higher objective response (OR) rate compared with L858R, regardless of concomitant mutations. Compared to patients with OR, non-OR patients had more concomitant mutations, both in 19Del (53.8% vs 83.3%; P=0.021) and L858R (51.4% vs 77.8%; P=0.029). In particular, total concomitant mutations (OR=0.27; P=0.03), sensitive EGFR mutations (OR=2.21; P=0.04), and T790M (OR=0.244; P=0.02) significantly affected the TKI response. Conclusion Concomitant mutations were widespread in 19Del and L858R and were associated with poorer OR to EGFR-TKIs. However, 19Del and L858R had similar numbers and patterns of concomitant mutations, which might not explain the different sensitivity to EGFR-TKI.
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Affiliation(s)
- Hengrui Liang
- Department of Thoracic Surgery and Oncology, The First Affiliated Hospital of Guangzhou Medical University, State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, Guangzhou, People's Republic of China
| | - Caichen Li
- Department of Thoracic Surgery and Oncology, The First Affiliated Hospital of Guangzhou Medical University, State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, Guangzhou, People's Republic of China
| | - Yi Zhao
- Department of Thoracic Surgery and Oncology, The First Affiliated Hospital of Guangzhou Medical University, State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, Guangzhou, People's Republic of China
| | - Shen Zhao
- Department of Medical Oncology, Sun Yat-Sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou, People's Republic of China
| | - Jun Huang
- Department of Thoracic Surgery and Oncology, The First Affiliated Hospital of Guangzhou Medical University, State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, Guangzhou, People's Republic of China
| | - Xiuyu Cai
- Department of Medical Oncology, Sun Yat-Sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou, People's Republic of China.,Department of General Internal Medicine, Sun Yat-Sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou, People's Republic of China
| | - Bo Cheng
- Department of Thoracic Surgery and Oncology, The First Affiliated Hospital of Guangzhou Medical University, State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, Guangzhou, People's Republic of China
| | - Shan Xiong
- Department of Thoracic Surgery and Oncology, The First Affiliated Hospital of Guangzhou Medical University, State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, Guangzhou, People's Republic of China
| | - Jianfu Li
- Department of Thoracic Surgery and Oncology, The First Affiliated Hospital of Guangzhou Medical University, State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, Guangzhou, People's Republic of China
| | - Wei Wang
- Department of Thoracic Surgery and Oncology, The First Affiliated Hospital of Guangzhou Medical University, State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, Guangzhou, People's Republic of China
| | - Changbin Zhu
- BGI Genomics, BGI-Shenzhen, Shenzhen 518083, People's Republic of China
| | - Weiwei Li
- BGI-Guangzhou Medical Laboratory, BGI-Shenzhen, Guangzhou 510006, People's Republic of China
| | - Jianxing He
- Department of Thoracic Surgery and Oncology, The First Affiliated Hospital of Guangzhou Medical University, State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, Guangzhou, People's Republic of China
| | - Wenhua Liang
- Department of Thoracic Surgery and Oncology, The First Affiliated Hospital of Guangzhou Medical University, State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, Guangzhou, People's Republic of China
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24
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Characteristics and response to crizotinib in lung cancer patients with MET amplification detected by next-generation sequencing. Lung Cancer 2020; 149:17-22. [PMID: 32949827 DOI: 10.1016/j.lungcan.2020.08.021] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2019] [Revised: 06/23/2020] [Accepted: 08/30/2020] [Indexed: 01/13/2023]
Abstract
OBJECTIVES Mesenchymal-epithelial transition (MET) amplification is a rare gene alteration in lung cancer. The aim of this study was to investigate the clinical characteristics of MET amplification in lung cancer and the response to crizotinib by subsets of patients with MET amplification detected by next-generation sequencing (NGS). PATIENTS AND METHODS We collected NGS sequencing data for patients with MET amplification in our institution from January 2018 to April 2019. The efficacy of crizotinib in MET amplification was retrospectively analyzed. RESULTS A total of 2694 patients received NGS tests, 3.27 % (82/2507) of patients had primary MET amplification, and acquired MET amplification accounted for 16.04 % (30/187) of re-biopsy patients. Only 19 patients received monotherapy with crizotinib. In survival analysis, ten patients with copy number greater than 4 (CN > 4) had longer median PFS (mPFS) (4.76 months; 95 %CI: 1.67-7.85 months) compared with other nine patients (CN ≤ 4) (2.10 months; 95 %CI: 1.53-2.68 months; P = 0.063), but failed to get a statistical significance. No significant differences were observed between median PFS (mPFS) of the patients with primary and acquired MET amplification (4.04 months vs 2.76 months; P = 0.310). CONCLUSIONS Primary and acquired MET amplification were detected in 3.27 % and 16.04 % of lung cancer patients, respectively. Patients with CN > 4 seemed to have longer PFS after crizotinib treatment. No significant differences in PFS were observed between patients with primary and acquired MET amplification.
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25
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Matsuo Y, Yamashita K, Yoshida T, Satoh Y. Method for preservation of DNA stability of liquid-based cytology specimens from a lung adenocarcinoma cell line. Virchows Arch 2020; 478:507-516. [PMID: 32869115 DOI: 10.1007/s00428-020-02919-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2020] [Revised: 08/06/2020] [Accepted: 08/24/2020] [Indexed: 01/07/2023]
Abstract
Liquid-based cytology (LBC) specimens of lung adenocarcinoma have the potential to be widely used for genetic analysis. However, formaldehyde contained in some LBC preservation solutions can cause DNA fragmentation during specimen storage, rendering the samples unsuitable for molecular analysis. To investigate a novel preservation technique for improved DNA stability, which was evaluated by mutation analysis of epidermal growth factor receptor (EGFR) gene in human lung adenocarcinoma cell lines. Cells were fixed in CytoRich Red preservation solution. After 30 min of fixation, cells were either stored using the conventional method (suspended in preservation solution) or washed in phosphate-buffered saline and stored as a cell pellet (newly proposed method). The effect of storage was evaluated after 5, 7, and 9 days of storage at ambient temperature. The cell pellet group was also tested after 14 and 28 days. Specifically, we evaluated the DNA stability, DNA yield, and sample suitability for polymerase chain reaction (PCR), and EGFR mutation detection. The DNA yields and degree of stability from the cell pellet group were higher than those from the suspension group at every time point examined. PCR amplification from the cell pellet group was successful up to day 28. Mutation detection using the Cycleave PCR method indicated that the Ct values of the cell pellet group were significantly lower than those of the suspension group. Storing LBC specimens as a cell pellet post-fixation can maintain the DNA quality for a longer period than the conventional method, making it a promising strategy for molecular analysis.
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Affiliation(s)
- Yukiko Matsuo
- Department of Thoracic Surgery, Kitasato University School of Medicine, 1-15-1 Kitasato, Minami-Ku, Sagamihara, Kanagawa, 252-0374, Japan
| | - Kazuya Yamashita
- Department of Pathology, Kitasato University Hospital, Sagamihara, Japan
| | - Tsutomu Yoshida
- Department of Pathology, Kitasato University Hospital, Sagamihara, Japan.,Department of Pathology, Kitasato University School of Medicine, Sagamihara, Japan
| | - Yukitoshi Satoh
- Department of Thoracic Surgery, Kitasato University School of Medicine, 1-15-1 Kitasato, Minami-Ku, Sagamihara, Kanagawa, 252-0374, Japan.
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26
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Sauter JL, Chen Y, Alex D, Balassanian R, Cuda J, Flanagan MB, Griffith CC, Illei P, Johnson DN, McGrath CM, Randolph ML, Reynolds JP, Spiczka AJ, van Zante A, VanderLaan PA. Results from the 2019 American Society of Cytopathology survey on rapid onsite evaluation (ROSE)-part 2: subjective views among the cytopathology community. J Am Soc Cytopathol 2020; 9:570-578. [PMID: 32861593 DOI: 10.1016/j.jasc.2020.06.010] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2020] [Revised: 06/24/2020] [Accepted: 06/26/2020] [Indexed: 12/16/2022]
Abstract
INTRODUCTION This study aims to improve understanding of the cytopathology community's perspective regarding the value of rapid onsite evaluation (ROSE) in clinical practice. MATERIALS AND METHODS The American Society of Cytopathology membership was surveyed in 2019 to obtain subjective data on the cytopathology community's perceptions regarding ROSE. Comments were categorized by major themes and attitudes and analyzed by respondent's role in laboratory, practice size, and practice setting (Fisher's exact and χ2 tests). RESULTS A total of 541 responses were received from 255 cytopathologists/pathologists, 261 cytotechnologists, 19 trainees, and 6 others (as previously reported). Reasons for which cytopathology personnel provide this service aligned with their perceptions of why clinicians request ROSE. A minority of respondents, disproportionally from high volume centers, felt ROSE is unnecessary. Overall attitude regarding ROSE was generally positive. There were no significant differences in attitude regarding ROSE according to role in laboratory or practice size, but respondents from academic centers provided a significantly higher percentage of positive comments than those in private or community practice. Although survey respondents generally felt that ROSE is valuable to patient care, they also highlighted several challenges, including staffing, time commitment, and inadequate reimbursement. Implementation of telecytology was felt to potentially alleviate some of these challenges. CONCLUSIONS Survey results show that the cytology community views ROSE favorably, practices vary considerably, and there is a perceived need for improved reimbursement. Data from this study may be used to identify areas that warrant additional research to clarify the clinical value of ROSE.
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Affiliation(s)
- Jennifer L Sauter
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York.
| | - Yigu Chen
- Department of Pathology, Beth Israel Deaconess Medical Center and Harvard Medical School, Boston, Massachusetts
| | - Deepu Alex
- Department of Pathology and Laboratory Medicine, British Columbia Cancer Agency, Vancouver, Canada
| | - Ronald Balassanian
- Department of Pathology, University of California San Francisco, San Francisco, California
| | - Jackie Cuda
- Department of Pathology, University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania
| | - Melina B Flanagan
- Department of Pathology, Anatomy, and Laboratory Medicine, West Virginia University, Morgantown, West Virginia
| | - Christopher C Griffith
- Robert J. Tomsich Pathology and Laboratory Medicine Institute, Cleveland Clinic, Cleveland, Ohio
| | - Peter Illei
- Department of Pathology, Johns Hopkins Medical Institutions, Baltimore, Maryland
| | - Daniel N Johnson
- Department of Pathology, Northwestern University Feinberg School of Medicine, Chicago, Illinois
| | - Cindy M McGrath
- Department of Pathology and Laboratory Medicine, University of Pennsylvania Medical Center and Perelman School of Medicine, Philadelphia, Pennsylvania
| | - Melissa L Randolph
- Department of Pathology and Laboratory Medicine, Indiana University School of Medicine, Indianapolis, Indiana
| | - Jordan P Reynolds
- Robert J. Tomsich Pathology and Laboratory Medicine Institute, Cleveland Clinic, Cleveland, Ohio
| | - Amy J Spiczka
- American Society for Clinical Pathology, Chicago, Illinois
| | - Annemieke van Zante
- Department of Pathology, University of California San Francisco, San Francisco, California
| | - Paul A VanderLaan
- Department of Pathology, Beth Israel Deaconess Medical Center and Harvard Medical School, Boston, Massachusetts
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27
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Fulmer CG, Park K, Dilcher T, Ho M, Mirabelli S, Alperstein S, Hissong EM, Pittman M, Siddiqui M, Heymann JJ, Yantiss RK, Borczuk AC, Fernandes H, Sigel C, Song W, Mosquera JM, Rao R. Next-generation sequencing of residual cytologic fixative preserved DNA from pancreatic lesions: A pilot study. Cancer Cytopathol 2020; 128:840-851. [PMID: 32598087 DOI: 10.1002/cncy.22315] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2020] [Revised: 05/01/2020] [Accepted: 05/21/2020] [Indexed: 12/12/2022]
Abstract
BACKGROUND Endoscopic ultrasound-guided fine needle aspiration (EUS-FNA) is a sensitive and specific tool in the risk stratification of pancreatic lesions, including cysts. The sensitivity and specificity of EUS-FNA has been shown to improve when cytology is combined with next-generation sequencing (NGS). Ideally, fresh cyst fluid is used for NGS. In this pilot study, we explore the possibility of sequencing DNA derived from residual alcohol-fixed pancreatic aspirates. METHODS Residual cytologic fixatives (n = 42) from 39 patients who underwent EUS-FNA for pancreatic lesions were collected along with demographics, imaging, and laboratory studies. Samples were designated as nonneoplastic/nonmucinous benign (NB), mucinous cyst (MC), pancreatic ductal adenocarcinoma (PDAC), or well-differentiated neuroendocrine tumor (NET) on the basis of cytopathologic evaluation and sequenced on the Oncomine platform (ThermoFisher Scientific, Waltham, Massachusetts). RESULTS Ten of 14 (71.4%) MCs exhibited clinically significant variants, including KRAS, GNAS, and TP53. Ten of 15 (66.7%) PDACs had KRAS alterations, and 9 of 15 (60%) showed variants in TP53. No variants were detected in any NETs. Only 1 of 9 (11.1%) NB aspirates showed variants in KRAS and MAP2K. Sequencing of formalin-fixed, paraffin-embedded tissue revealed variants identical to those detected in fixative-derived DNA in 4 of 5 cases (80%). CONCLUSION Residual DNA from alcohol-fixed aspirates are an underutilized source for NGS. Sequencing residual fixative-derived DNA has the potential to be integrated into the workup of pancreatic aspirates, possibly impacting management.
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Affiliation(s)
- Clifton G Fulmer
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, New York.,Robert J. Tomsich Pathology and Laboratory Medicine Institute, The Cleveland Clinic, Cleveland, Ohio
| | - Kyung Park
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, New York
| | - Thomas Dilcher
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, New York
| | - Mai Ho
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, New York
| | - Susanna Mirabelli
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, New York
| | - Susan Alperstein
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, New York
| | - Erika M Hissong
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, New York
| | - Meredith Pittman
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, New York
| | - Momin Siddiqui
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, New York
| | - Jonas J Heymann
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, New York
| | - Rhonda K Yantiss
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, New York
| | - Alain C Borczuk
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, New York
| | - Helen Fernandes
- Department of Pathology and Cell Biology, Columbia University Irving Medical Center, New York, New York
| | - Carlie Sigel
- Department of Pathology, The Memorial Sloan Kettering Cancer Center, New York, New York
| | - Wei Song
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, New York
| | - Juan Miguel Mosquera
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, New York.,Englander Institute for Precision Medicine, Weill Cornell Medicine, New York, New York
| | - Rema Rao
- The Leopold G. Koss Division of Cytology, The Albert Einstein College of Medicine/Montefiore Medical Center, Bronx, New York
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28
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Yamaguchi T, Akahane T, Harada O, Kato Y, Aimono E, Takei H, Tasaki T, Noguchi H, Nishihara H, Kamata H, Tanimoto A. Next-generation sequencing in residual liquid-based cytology specimens for cancer genome analysis. Diagn Cytopathol 2020; 48:965-971. [PMID: 32511899 DOI: 10.1002/dc.24511] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2020] [Revised: 05/12/2020] [Accepted: 05/19/2020] [Indexed: 12/11/2022]
Abstract
BACKGROUND Cancer genome profiling of cytology specimens using next-generation sequencing (NGS) requires adequate and good-quality DNA. Genomic examination of cytology samples was conventionally performed on cell block (CB) or smear specimens than on residual liquid-based cytology (LBC) specimens, which are high-quality DNA sources even after long-term storage. METHODS We estimated tumor fractions of 37 residual LBC specimens, including 30 fine needle aspiration (FNA) samples from the thyroid (12 papillary thyroid carcinomas and two malignant lymphomas), lymph node (13 metastatic carcinomas and one malignant lymphoma), and breast cancer (one phyllodes tumor and one invasive ductal carcinoma), two pancreatic carcinoma samples, and five liquid (ascites, pleural effusion, and cerebrospinal fluid) samples. The DNA was extracted from all samples and subjected to NGS using a customized cancer gene panel comprising 28 cancer-related genes. RESULTS NGS analysis revealed somatic mutations corresponding to pathological diagnosis with adequate variant allele frequency (VAF) in 24 LBC specimens, which had significantly higher tumor fraction (72.5% ± 4.9%). Ten cases, including the five fluid samples, had very small tumor fractions (7.5% ± 2.3%) to obtain sufficient VAF. Other two samples had high tumor fractions but showed very low VAF, indicating the presence of fusion genes. The remaining one sample yielded no DNA recovery. CONCLUSION The residual LBC specimens collected by FNA from the thyroid gland and lymph node were verified to carry high tumor fraction and could serve as an alternate source for molecular testing to screen and diagnose cancers without the use of CB or smears.
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Affiliation(s)
- Tomomi Yamaguchi
- Department of Pathology, Laboratory of Cancer Medical Science, Hokuto Hospital, Obihiro, Hokkaido, Japan
| | - Toshiaki Akahane
- Department of Pathology, Kagoshima University Graduate School of Medical and Dental Sciences, Kagoshima, Japan.,Center for Human Genome and Gene Analysis, Kagoshima University Hospital, Kagoshima, Japan
| | - Ohi Harada
- Department of Pathology, Laboratory of Cancer Medical Science, Hokuto Hospital, Obihiro, Hokkaido, Japan
| | - Yasutaka Kato
- Department of Biology and Genetics, Laboratory of Cancer Medical Science, Hokuto Hospital, Obihiro, Hokkaido, Japan
| | - Eriko Aimono
- Keio Cancer Center, Keio University School of Medicine, Shinjuku-ku, Tokyo, Japan
| | - Hidehiro Takei
- Department of Diagnostic Pathology, Asahikawa Medical University, Asahikawa, Hokkaido, Japan
| | - Takashi Tasaki
- Department of Pathology, Kagoshima University Graduate School of Medical and Dental Sciences, Kagoshima, Japan
| | - Hirotsugu Noguchi
- Department of Pathology, Kagoshima University Graduate School of Medical and Dental Sciences, Kagoshima, Japan
| | - Hiroshi Nishihara
- Department of Biology and Genetics, Laboratory of Cancer Medical Science, Hokuto Hospital, Obihiro, Hokkaido, Japan.,Keio Cancer Center, Keio University School of Medicine, Shinjuku-ku, Tokyo, Japan
| | - Hajime Kamata
- Department of Neurosurgery, Hokuto Hospital, Obihiro, Hokkaido, Japan
| | - Akihide Tanimoto
- Department of Pathology, Kagoshima University Graduate School of Medical and Dental Sciences, Kagoshima, Japan.,Center for Human Genome and Gene Analysis, Kagoshima University Hospital, Kagoshima, Japan
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29
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Sung S, Heymann JJ, Crapanzano JP, Moreira AL, Shu C, Bulman WA, Saqi A. Lung cancer cytology and small biopsy specimens: diagnosis, predictive biomarker testing, acquisition, triage, and management. J Am Soc Cytopathol 2020; 9:332-345. [PMID: 32591241 DOI: 10.1016/j.jasc.2020.04.014] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2020] [Revised: 04/17/2020] [Accepted: 04/22/2020] [Indexed: 02/07/2023]
Abstract
In the 21st century, there has been a dramatic shift in the management of advanced-stage lung carcinoma, and this has coincided with an increasing use of minimally invasive tissue acquisition methods. Both have had significant downstream effects on cytology and small biopsy specimens. Current treatments require morphologic, immunohistochemical, and/or genotypical subtyping of non-small cell lung carcinoma. To meet these objectives, standardized classification of cytology and small specimen diagnoses, immunohistochemical algorithms, and predictive biomarker testing guidelines have been developed. This review provides an overview of current classification, biomarker testing, methods of small specimen acquisition and triage, clinical management strategies, and emerging technologies.
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Affiliation(s)
- Simon Sung
- Columbia University Medical Center, Department of Pathology & Cell Biology, New York, New York.
| | - Jonas J Heymann
- Department of Pathology and Laboratory Medicine, New York-Presbyterian Hospital-Weill Cornell Medical College, New York, New York
| | - John P Crapanzano
- Columbia University Medical Center, Department of Pathology & Cell Biology, New York, New York
| | - Andre L Moreira
- Department of Pathology, New York University Langone Health, New York, New York
| | - Catherine Shu
- Department of Medicine, Hematology & Oncology, Columbia University Medical Center, New York, New York
| | - William A Bulman
- Department of Medicine, Pulmonary, Columbia University Medical Center, New York, New York
| | - Anjali Saqi
- Columbia University Medical Center, Department of Pathology & Cell Biology, New York, New York
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30
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A Novel Approach for the Genetic Analysis of Biliary Tract Cancer Specimens Obtained Through Endoscopic Ultrasound-Guided Fine Needle Aspiration Using Targeted Amplicon Sequencing. Clin Transl Gastroenterol 2020; 10:e00022. [PMID: 30908307 PMCID: PMC6445609 DOI: 10.14309/ctg.0000000000000022] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Biliary tract cancer (BTC) is an aggressive malignant tumor, and biomarker-based clinical trials for this cancer are currently ongoing. Endoscopic ultrasound–guided fine needle aspiration (EUS-FNA) is a safe procedure and enables pathological diagnoses; however, it is uncertain whether a tiny tumor sample of BTC obtained through EUS-FNA can be analyzed for diverse genetic alterations in the development and tolerance of BTC. Thus, we aimed to verify the feasibility of genetic analyses with EUS-FNA samples of BTC.
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31
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Heymann JJ, Yoxtheimer LM, Park HJ, Fernandez EM, Facey KE, Alperstein SA, Tran HV, Baek I, Scognamiglio T, Rennert H, Siddiqui MT, Song W. Preanalytic variables in quality and quantity of nucleic acids extracted from FNA specimens of thyroid gland nodules collected in CytoLyt: Cellularity and storage time. Cancer Cytopathol 2020; 128:656-672. [PMID: 32267620 DOI: 10.1002/cncy.22270] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2019] [Revised: 03/06/2020] [Accepted: 03/10/2020] [Indexed: 12/20/2022]
Abstract
BACKGROUND Morphologic and genetic analysis of thyroid nodules may be performed from a single vial. Preanalytic variables that affect nucleic acid extracted from a single vial are evaluated. METHODS Thyroid fine-needle aspiration (FNA) specimens collected in CytoLyt were evaluated. A ThinPrep slide was prepared. Extracted nucleic acids were analyzed using Oncomine Comprehensive Panel, version 2, after Ion AmpliSeq library preparation. A pathologist and a cytotechnologist enumerated specimen cellularity. RESULTS Fifty-six samples were collected from 55 nodules in 53 patients. Bethesda category correlated with cellularity (P = .01), and storage time (median, 43 days; range, 7-77 days) was longer for specimens in categories II and III than for those in categories IV and VI (P = .01). The mean specimen DNA concentration was 4.5 ng/µL (range, 0-23.8 ng/µL), and 25 (45%) had concentrations >3.3 ng/µL. The mean specimen RNA concentration was 4.8 ng/µL (range, 0-42.4 ng/µL), and 31 (55%) had concentrations >1.4 ng/µL. Nucleic acid quantity increased with epithelial cellularity. Storage time weakly correlated with the quantity of extracted DNA, independent of cellularity, but not extracted RNA. Greater proportions of cell-free DNA and lesser proportions of long, intact RNA fragments were extracted from a subset of samples with longer storage time. Among 15 single nucleotide variants, the median mutant allelic fraction was 15.1%. One false-negative result was identified. Five specimens subsequently determined to harbor a genetic alteration failed quality metrics. CONCLUSIONS Cellularity and storage time affect the quantity and quality of nucleic acid extracted from thyroid FNA specimens collected in CytoLyt. Further investigation will serve to quantify the magnitude of such effects and to elucidate other contributing factors.
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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
| | - Lorene M Yoxtheimer
- Department of Pathology and Laboratory Medicine, Tulane University School of Medicine, New Orleans, Louisiana
| | - Hyeon Jin Park
- Clinical Genomics Laboratory, Department of Pathology and Laboratory Medicine, New York-Presbyterian Hospital-Weill Cornell Medical College, New York, New York.,Caryl and Israel Englander Institute for Precision Medicine, New York-Presbyterian Hospital-Weill Cornell Medical College, New York, New York
| | - Evan M Fernandez
- Caryl and Israel Englander Institute for Precision Medicine, New York-Presbyterian Hospital-Weill Cornell Medical College, New York, New York
| | - Kirk E Facey
- Division of Cytopathology, Department of Pathology and Laboratory Medicine, New York-Presbyterian Hospital-Weill Cornell Medical College, New York, New York
| | - Susan A Alperstein
- Division of Cytopathology, Department of Pathology and Laboratory Medicine, New York-Presbyterian Hospital-Weill Cornell Medical College, New York, New York
| | - Hung V Tran
- Clinical Genomics Laboratory, Department of Pathology and Laboratory Medicine, New York-Presbyterian Hospital-Weill Cornell Medical College, New York, New York.,Caryl and Israel Englander Institute for Precision Medicine, New York-Presbyterian Hospital-Weill Cornell Medical College, New York, New York
| | - Inji Baek
- Clinical Genomics Laboratory, Department of Pathology and Laboratory Medicine, New York-Presbyterian Hospital-Weill Cornell Medical College, New York, New York.,Caryl and Israel Englander Institute for Precision Medicine, New York-Presbyterian Hospital-Weill Cornell Medical College, New York, New York
| | - Theresa Scognamiglio
- Division of Head and Neck Pathology, Department of Pathology and Laboratory Medicine, New York-Presbyterian Hospital-Weill Cornell Medical College, New York, New York
| | - Hanna Rennert
- Division of Molecular and Genomic Pathology, Department of Pathology and Laboratory Medicine, New York-Presbyterian Hospital-Weill Cornell Medical College, New York, New York
| | - Momin T Siddiqui
- Division of Cytopathology, Department of Pathology and Laboratory Medicine, New York-Presbyterian Hospital-Weill Cornell Medical College, New York, New York
| | - Wei Song
- Clinical Genomics Laboratory, Department of Pathology and Laboratory Medicine, New York-Presbyterian Hospital-Weill Cornell Medical College, New York, New York.,Caryl and Israel Englander Institute for Precision Medicine, New York-Presbyterian Hospital-Weill Cornell Medical College, New York, New York
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Tanaka R, Ohtsuka K, Ogura W, Arai N, Yoshida T, Nakazato Y, Tachibana K, Takata S, Fujiwara M, Kamma H, Shibahara J, Kondo H. Subtyping and EGFR mutation testing from blocks of cytological materials, based on liquid-based cytology for lung cancer at bronchoscopic examinations. Diagn Cytopathol 2020; 48:516-523. [PMID: 32125777 DOI: 10.1002/dc.24397] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2019] [Revised: 01/13/2020] [Accepted: 02/20/2020] [Indexed: 12/12/2022]
Abstract
BACKGROUND Liquid-based cytology (LBC) allows immunohistochemistry (IHC), fluorescence in situ hybridization, and molecular testing to be performed in fixed cell materials. We examined the feasibility of subtyping and EGFR mutation testing of bronchoscopic samples from patients with lung cancer using cell blocks (CB) based on LBC fixation (LBC-CB). METHODS We included 35 consecutive patients with peripheral lung nodules who underwent endobronchial ultrasonography with a guide sheath in our hospital. Thirty of these patients were diagnosed with lung cancer by obtaining cytological samples. Cytological subtyping was performed with IHC using LBC-CB, and the Cobas EGFR Mutation Test ver. 2 was performed using extracted genomic DNA from the LBC-CB, formalin-fixed paraffin-embedded (FFPE) tissue, and matched plasma. RESULTS Of the 30 cases, 25 were classified cytomorphologically as adenocarcinoma (ADC, n = 17) and squamous-cell carcinoma (SQCC, n = 8). The remaining five cases were classified by IHC as favor ADC (n = 3) and favor SQCC (n = 2) according to the WHO criteria. In the final ADC group (n = 20), EGFR mutations on the LBC-CB were identified in eight cases (40%; 1 exon 19 deletion, 6 L858R, and 1 L861Q). Mutations in FFPE samples were identified in seven cases (35%) at the same site in each case. Plasma EGFR mutations were identified in four cases (20%) at the same site. The CB detection rate was higher than for FFPE and plasma. CONCLUSION LBC-CB is suitable for subtyping and EGFR mutation testing in lung cancers.
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Affiliation(s)
- Ryota Tanaka
- Department of Surgery, Kyorin University School of Medicine, Tokyo, Japan
| | - Kouki Ohtsuka
- Department of Clinical Laboratory, Kyorin University School of Medicine, Tokyo, Japan
| | - Wataru Ogura
- Department of Clinical Laboratory, Kyorin University School of Medicine, Tokyo, Japan
| | - Nobuaki Arai
- Department of Surgery, Kyorin University School of Medicine, Tokyo, Japan
| | - Tsutomu Yoshida
- Department of Surgery, Kyorin University School of Medicine, Tokyo, Japan
| | - Yoko Nakazato
- Department of Surgery, Kyorin University School of Medicine, Tokyo, Japan
| | - Keisei Tachibana
- Department of Surgery, Kyorin University School of Medicine, Tokyo, Japan
| | - Saori Takata
- Department of Respiratory Medicine, Kyorin University School of Medicine, Tokyo, Japan
| | - Masachika Fujiwara
- Department of Pathology, Kyorin University School of Medicine, Tokyo, Japan
| | - Hiroshi Kamma
- Department of Pathology, Kyorin University School of Medicine, Tokyo, Japan
| | - Junji Shibahara
- Department of Pathology, Kyorin University School of Medicine, Tokyo, Japan
| | - Haruhiko Kondo
- Department of Surgery, Kyorin University School of Medicine, Tokyo, Japan
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Zheng C, Li X, Ren Y, Yin Z, Zhou B. Coexisting EGFR and TP53 Mutations in Lung Adenocarcinoma Patients Are Associated With COMP and ITGB8 Upregulation and Poor Prognosis. Front Mol Biosci 2020; 7:30. [PMID: 32175330 PMCID: PMC7056714 DOI: 10.3389/fmolb.2020.00030] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2019] [Accepted: 02/11/2020] [Indexed: 12/24/2022] Open
Abstract
The heterogeneity of lung adenocarcinoma is driven by key mutations in oncogenes. To determine the gene expression, single nucleotide polymorphisms, and co-mutations participating in the initiation and progression of lung adenocarcinoma, we comprehensively analyzed the data of 491 patients from The Cancer Genome Atlas. Using log-rank and Kruskal-Wallis analysis, Oncoprint, Kaplan-Meier survival plots, and a nomogram, we found that EGFRL858R with co-mutation TP53 was significant prognostic determinant versus that with co-wild TP53 (hazard ratio, 2.77, P = 0.012). Further gene co-expression network and functional enrichment analysis indicated that co-mutation of EGFRL858R/TP53 increases the expression of COMP and ITGB8, which are involved in extracellular matrix organization and cell surface receptor signaling pathways, thus contributing to poor prognosis in lung adenocarcinoma. Validation was performed using three GEO profiles along with colony formation and CCK-8 assays for proliferation, transwell and wound-healing for migration in transfected H1299 and A549 cell lines. To the best of our knowledge, these results are the first to indicate that patients harboring the co-mutation of EGFRL858R/TP53 show increased expression of COMP and ITGB8, which participate in extracellular matrix dysfunction and can be used as prognostic biomarkers in patients with lung adenocarcinoma.
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Affiliation(s)
- Chang Zheng
- Department of Clinical Epidemiology, First Affiliated Hospital of China Medical University, Shenyang, China.,Department of Epidemiology, School of Public Health, China Medical University, Shenyang, China
| | - Xuelian Li
- Department of Epidemiology, School of Public Health, China Medical University, Shenyang, China
| | - Yangwu Ren
- Department of Epidemiology, School of Public Health, China Medical University, Shenyang, China
| | - Zhihua Yin
- Department of Epidemiology, School of Public Health, China Medical University, Shenyang, China
| | - Baosen Zhou
- Department of Clinical Epidemiology, First Affiliated Hospital of China Medical University, Shenyang, China
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Nishikawa T, Fujii T, Tatsumi S, Sugimoto A, Sekita-Hatakeyama Y, Shimada K, Yamazaki M, Hatakeyama K, Ohbayashi C. Molecular Analysis of Liquid-Based Cytological Specimen Using Virtually Positive Sputum with Adenocarcinoma Cells. Diagnostics (Basel) 2020; 10:diagnostics10020084. [PMID: 32033355 PMCID: PMC7168204 DOI: 10.3390/diagnostics10020084] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2020] [Revised: 01/29/2020] [Accepted: 02/03/2020] [Indexed: 12/12/2022] Open
Abstract
Liquid-based cytology (LBC) analysis of sputum is a useful diagnostic and prognostic tool for detecting lung cancer. DNA and RNA derived from lung cancer cells can be used for this diagnosis. However, the quality of cytological material is not always adequate for molecular analysis due to the effect of formalin in the commercially available fixation kits. In this study, we examined DNA and RNA extraction methods for LBC analysis with formalin fixation, using lung carcinoma cell lines and sputum. The human non-small cell lung cancer cell lines were fixed with LBC fixation reagents, such as CytoRich red preservative. Quantification of thyroid transcription factor-1 (TTF-1) and actin mRNA, epidermal growth factor receptor (EGFR) DNA in HCC827, H1975, and H1299 cells, and mutation analysis of EGFR in HCC827 and H1975 cells were performed by quantitative PCR (qPCR) and fluorescence resonance energy transfer (FRET)-based preferential homoduplex formation assay (F-PHFA) method, respectively. mRNA and DNA extracted from cell lines using RNA and/or DNA extraction kits for formalin-fixed paraffin-embedded (FFPE) fixed with various LBC solutions were efficiently detected by qPCR. The detection limit of EGFR mutations was at a rate of 5% mutated positive cells in LBC. The detection limit of the EGFR exon 19 deletion in HCC827 was detected in more than 1.5% of the positive cells in sputum. In contrast, the detection limit of the T790M/L858R mutation in H1975 was detected in more than 13% of the positive cells. We also detected EGFR mutations using next generation sequencing (NGS). The detection limit of NGS for EGFR mutation was lower than that of the F-PHFA method. Furthermore, more than 0.1% of positive cells could be cytomorphologically detected. Our results demonstrate that LBC systems are powerful tools for cytopathological and genetic analyses. However, careful attention should be paid to the incidence of false negative results in the genetic analysis of EGFR mutations detected by LBC.
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Affiliation(s)
- Takeshi Nishikawa
- Department of Diagnostic Pathology, Nara Medical University School of Medicine, 840 Shijo-cho, Kashihara, Nara 634-8521, Japan; (T.N.); (S.T.); (A.S.); (Y.S.-H.); (K.H.); (C.O.)
| | - Tomomi Fujii
- Department of Diagnostic Pathology, Nara Medical University School of Medicine, 840 Shijo-cho, Kashihara, Nara 634-8521, Japan; (T.N.); (S.T.); (A.S.); (Y.S.-H.); (K.H.); (C.O.)
- Correspondence: ; Tel.: +81-744-22-3051 (ext. 4307); Fax: +81-744-23-5687
| | - Shigenobu Tatsumi
- Department of Diagnostic Pathology, Nara Medical University School of Medicine, 840 Shijo-cho, Kashihara, Nara 634-8521, Japan; (T.N.); (S.T.); (A.S.); (Y.S.-H.); (K.H.); (C.O.)
| | - Aya Sugimoto
- Department of Diagnostic Pathology, Nara Medical University School of Medicine, 840 Shijo-cho, Kashihara, Nara 634-8521, Japan; (T.N.); (S.T.); (A.S.); (Y.S.-H.); (K.H.); (C.O.)
| | - Yoko Sekita-Hatakeyama
- Department of Diagnostic Pathology, Nara Medical University School of Medicine, 840 Shijo-cho, Kashihara, Nara 634-8521, Japan; (T.N.); (S.T.); (A.S.); (Y.S.-H.); (K.H.); (C.O.)
| | - Keiji Shimada
- Department of Diagnostic Pathology, Nara City Hospital, Nara 630-8305, Japan;
| | - Masaharu Yamazaki
- Department of Central Clinical Laboratory, Nara Medical University Hospital, Nara 634-8521, Japan;
| | - Kinta Hatakeyama
- Department of Diagnostic Pathology, Nara Medical University School of Medicine, 840 Shijo-cho, Kashihara, Nara 634-8521, Japan; (T.N.); (S.T.); (A.S.); (Y.S.-H.); (K.H.); (C.O.)
| | - Chiho Ohbayashi
- Department of Diagnostic Pathology, Nara Medical University School of Medicine, 840 Shijo-cho, Kashihara, Nara 634-8521, Japan; (T.N.); (S.T.); (A.S.); (Y.S.-H.); (K.H.); (C.O.)
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Wu W, Cao Z, Zhang W, Zhang L, Hou L, Wu C. Comparison of the SuperARMS and ARMS for detecting EGFR mutations in liquid-based cytology specimens from NSCLC patients. Diagn Pathol 2020; 15:9. [PMID: 32005253 PMCID: PMC6995041 DOI: 10.1186/s13000-019-0910-5] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2019] [Accepted: 11/26/2019] [Indexed: 12/18/2022] Open
Abstract
BACKGROUND Non-surgical cytological specimens are adequate not only for accurate histological subtyping but also for molecular profiling. A modified amplification refractory mutation system polymerase chain reaction (ARMS PCR), known as SuperARMS PCR, was improved by optimizing the primers designation, which provides a higher sensitivity and specificity approach for free plasma DNA detection. It is unclear whether SuperARMS PCR detects epidermal growth factor receptor (EGFR) mutations in cytology samples. The aim of this study was to compare the EGFR mutations detected by ARMS PCR and SuperARMS PCR in cytology samples derived from advanced non-small cell lung cancer (NSCLC) patients. METHODS From March 2016 to March 2018, a total of 234 cytological samples were obtained from primary or metastatic lesions of NSCLC, including 144 fine-needle aspirations (FNAs), 36 endobroncheal ultrasonography (EBUS) FNAs, 36 transbronchial needle aspirations (TBNAs) and 18 pleural effusion (PLEs). EGFR mutations were simultaneously detected using an ADx-ARMS EGFR kit (Amoy Diagnostics CO., ltd., Xiamen, China) and an ADx-SuperARMS EGFR kit (Amoy Diagnostics CO., ltd., Xiamen, China). Digital droplet PCR (ddPCR) and next-generation sequencing (NGS) were further used to verify the EGFR mutant inconsistent samples. RESULTS All of the 234 patients with advanced or recurrent NSCLC were diagnosed and assessed by two cytopathologists, and their EGFR mutation statuses were successfully detected by ARMS and SuperARMS. Importantly, the SuperARMS and ARMS methods showed a highly concordant result of 94.0% (220/234) (95%CI: 85.0, 95.0%). The positive rate of the SuperARMS was higher than the ARMS in the cytology samples for EGFR detection (46.2% vs. 40.2%). The specific EGFR mutation sites in 16 samples (6.8%) were not completely consistent between the SuperARMS and ARMS. A total of 14 patients showed EGFR mutations when detected by SuperARMS, but by ARMS there were EGFR wild-type. Two patients were detected as having one more EGFR mutation site by SuperARMS than by ARMS. ddPCR and NGS were used to further confirm the EGFR mutations in these inconsistent samples. Eight samples had the same mutation results as the SuperARMS, and 6 samples were not verified because the remaining DNA was insufficient. A total of 78 EGFR mutation patients received Tyrosine Kinase Inhibitor (TKI) treatment. The overall objective response rate (ORR) was 88.5% (69/78) for EGFR TKI treatment. CONCLUSION SuperARMS showed a high sensitivity and specificity for EGFR detection and thus, is expected to become a routine test in the clinic to be used as a widely available, easy-to-operate and sensitive method for EGFR mutation detection in liquid-based cytology samples.
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Affiliation(s)
| | | | - Wei Zhang
- Department of Pathology, Shanghai Pulmonary Hospital, Tongji University School of Medicine, 200433, Shanghai, People's Republic of China
| | - Liping Zhang
- Department of Pathology, Shanghai Pulmonary Hospital, Tongji University School of Medicine, 200433, Shanghai, People's Republic of China
| | - Likun Hou
- Department of Pathology, Shanghai Pulmonary Hospital, Tongji University School of Medicine, 200433, Shanghai, People's Republic of China
| | - Chunyan Wu
- Department of Pathology, Shanghai Pulmonary Hospital, Tongji University School of Medicine, 200433, Shanghai, People's Republic of China.
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EGFR mutation genotyping and ALK status determination in liquid-based cytology samples of non-small cell lung cancer. Virchows Arch 2019; 476:753-762. [DOI: 10.1007/s00428-019-02692-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2019] [Revised: 09/23/2019] [Accepted: 10/14/2019] [Indexed: 02/07/2023]
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Smolle E, Leithner K, Olschewski H. Oncogene addiction and tumor mutational burden in non-small-cell lung cancer: Clinical significance and limitations. Thorac Cancer 2019; 11:205-215. [PMID: 31799812 PMCID: PMC6997016 DOI: 10.1111/1759-7714.13246] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2019] [Revised: 10/23/2019] [Accepted: 10/25/2019] [Indexed: 12/25/2022] Open
Abstract
Lung cancer incidence has increased worldwide over the past decades, with non-small cell lung cancer (NSCLC) accounting for the vast majority (85%) of lung cancer specimens. It is estimated that lung cancer causes about 1.7 million global deaths per year worldwide. Multiple trials have been carried out, with the aim of finding new effective treatment options. Lately, special focus has been placed on immune checkpoint (PD1/PD-L1) inhibitors which impact the tumor immune microenvironment. Tumor mutational burden (TMB) has been found to predict response to immune checkpoint inhibitors. Conversely, recent studies have weakened the significance of TMB as a predictor of response to therapy and survival. In this review article, we discuss the significance of TMB, as well as possible limitations. Furthermore, we give a concise overview of mutations frequently found in NSCLC, and discuss the significance of oncogene addiction in lung cancer as an essential driver of tumorigenesis and tumor progression.
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Affiliation(s)
- Elisabeth Smolle
- Division of Pulmonology, Department of Internal Medicine, Medical University of Graz, Graz, Austria
| | - Katharina Leithner
- Division of Pulmonology, Department of Internal Medicine, Medical University of Graz, Graz, Austria
| | - Horst Olschewski
- Division of Pulmonology, Department of Internal Medicine, Medical University of Graz, Graz, Austria
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Fine-needle aspiration of the liver: a 10-year single institution retrospective review. Hum Pathol 2019; 92:25-31. [DOI: 10.1016/j.humpath.2019.07.007] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/03/2019] [Revised: 07/12/2019] [Accepted: 07/19/2019] [Indexed: 01/23/2023]
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39
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Cheng YW, Stefaniuk C, Jakubowski MA. Real-time PCR and targeted next-generation sequencing in the detection of low level EGFR mutations: Instructive case analyses. Respir Med Case Rep 2019; 28:100901. [PMID: 31367517 PMCID: PMC6656700 DOI: 10.1016/j.rmcr.2019.100901] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2019] [Revised: 06/26/2019] [Accepted: 07/07/2019] [Indexed: 12/25/2022] Open
Abstract
Background Allele specific real-time PCR and next-generation sequencing (NGS) are widely used to detect somatic mutation in non-small cell lung cancer (NSCLC). Both methods commonly use formalin-fixed paraffin-embedded (FFPE) tissues as diagnostic materials. Real-time PCR has the advantage of being easy to use and more tolerant of variable DNA quality, but has limited multiplex capability. NGS, in contrast, allows simultaneous analysis of many genomic loci while revealing the exact sequence changes; it is, however, more technically demanding and more expensive to employed. A challenge for both platforms is the varied limit of detection (LoD) for target genomic loci, even within the same gene. The variability of detection sensitivity may be problematic if well-known actionable somatic mutations are missed. Cases We compared LoDs between real-time PCR and targeted NGS tests for some commonly observed EGFR mutations in NSCLC specimens. Conclusions The FDA-approved real-time PCR test was superior to the NGS in detecting low level EGFR exon 19 deletion (near 1% variant allele fraction (VAF)). The cancer hotspot NGS detects low level EGFR c.2369C > T, p.T790M (2–5% VAF) better than the FDA-approved real-time PCR method. We conclude that the real-time PCR and hotspot NGS methods have complementary strengths in accurately determining clinically important EGFR mutations in NSCLC.
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Affiliation(s)
- Yu-Wei Cheng
- Molecular Pathology Section, Department of Laboratory Medicine, Robert J. Tomsich Pathology and Laboratory Medicine Institute, Cleveland Clinic, Cleveland, OH, USA
| | - Catherine Stefaniuk
- Molecular Pathology Section, Department of Laboratory Medicine, Robert J. Tomsich Pathology and Laboratory Medicine Institute, Cleveland Clinic, Cleveland, OH, USA.,Department of Pathology and Laboratory Medicine, University of Cincinnati Medical Center, Cincinnati, OH, USA
| | - Maureen A Jakubowski
- Molecular Pathology Section, Department of Laboratory Medicine, Robert J. Tomsich Pathology and Laboratory Medicine Institute, Cleveland Clinic, Cleveland, OH, USA
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McHugh KE, Dermawan JK, Cheng YW, Cruise M, Sohal DPS, Reynolds JP. Molecular testing in metastatic colorectal adenocarcinoma cytology cell pellets. Diagn Cytopathol 2019; 47:1132-1137. [PMID: 31290252 DOI: 10.1002/dc.24275] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2019] [Revised: 06/05/2019] [Accepted: 06/25/2019] [Indexed: 01/22/2023]
Abstract
BACKGROUND Mutational status for KRAS, NRAS, and BRAF genes should be performed on all colorectal carcinoma (CRC) specimens in order to guide targeted therapy selection for metastatic disease. Mutations are typically assessed via polymerase chain reaction and/or next generation sequencing (NGS) on formalin-fixed paraffin-embedded tissues. With minimally invasive diagnostic methodologies, the cytology cell pellet obtained by fine-needle aspiration (FNA) can serve as an alternative source of tumor deoxyribonucleic acid. METHODS An electronic record review of the cytopathology files (CoPathPlus, Cerner Corp., North Kansas City, Missouri) from September 1, 2015 through December 31, 2018 was conducted. All cytology specimens obtained via FNA and diagnosed as metastatic CRC on which NGS was performed were included. NGS for KRAS, NRAS, and BRAF mutations using the AmpliSeq Cancer Hotspot Panel v2.0 kit (Thermo Fisher Scientific, Waltham, Massachusetts) was performed on cytology cell pellets. RESULTS Forty-eight cases were identified. Forty-six of 48 specimens (96%) were adequate for molecular testing. Of those adequate specimens, proportion of malignant cells in the sample ranged from 5% to 95% (mean 46%). Twenty-seven of 48 cases (56%) were positive for clinically relevant mutations. Twenty-four of 27 cases (89%) were positive for KRAS mutations, with exon 2 most frequently involved (22/24 cases, 92%). Two of 27 cases (7%) were positive for NRAS mutations and one case (1/27, 4%) was positive for a BRAF mutation involving codon 594. CONCLUSION Mutational analysis performed on cytology cell pellets serves as a useful means of gathering clinically actionable information on tumor mutation status in metastatic CRC.
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Affiliation(s)
- Kelsey E McHugh
- Robert J. Tomsich Pathology and Laboratory Medicine Institute, Cleveland Clinic, Cleveland, Ohio
| | - Josephine K Dermawan
- Robert J. Tomsich Pathology and Laboratory Medicine Institute, Cleveland Clinic, Cleveland, Ohio
| | - Yu-Wei Cheng
- Robert J. Tomsich Pathology and Laboratory Medicine Institute, Cleveland Clinic, Cleveland, Ohio
| | - Michael Cruise
- Robert J. Tomsich Pathology and Laboratory Medicine Institute, Cleveland Clinic, Cleveland, Ohio
| | - Davendra P S Sohal
- Department of Hematology and Medical Oncology, Taussig Cancer Institute, Cleveland Clinic, Cleveland, Ohio
| | - Jordan P Reynolds
- Robert J. Tomsich Pathology and Laboratory Medicine Institute, Cleveland Clinic, Cleveland, Ohio
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Akahane T, Yamaguchi T, Kato Y, Yokoyama S, Hamada T, Nishida Y, Higashi M, Nishihara H, Suzuki S, Ueno S, Tanimoto A. Comprehensive validation of liquid-based cytology specimens for next-generation sequencing in cancer genome analysis. PLoS One 2019; 14:e0217724. [PMID: 31199826 PMCID: PMC6568385 DOI: 10.1371/journal.pone.0217724] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2019] [Accepted: 05/07/2019] [Indexed: 12/20/2022] Open
Abstract
In addition to conventional cytology, liquid-based cytology (LBC) is also used for immunocytochemistry and gene analysis. However, an appropriate method to obtain high quality DNA for next-generation sequencing (NGS) using LBC specimens remains controversial. We determined the optimal conditions for fixation with an alcohol-based fixative for LBC and DNA extraction using cultured cancer cell lines and clinical specimens. The extracted DNA was processed for NGS after the DNA quality was confirmed based on the DNA concentration and degree of degradation. The optimal conditions for cultured cells to obtain high quality DNA were to fix the cells at a density of 6 × 103 or 2 × 104 cells/mL and to use the magnetic bead-based DNA extraction method. Even after storing the fixed cells for 90 days, DNA extracted using the above and other extraction kits, including membrane-based methods, did not undergo degradation. Furthermore, 5-year-old residual LBC samples demonstrated high DNA quality that was suitable for NGS. Furthermore, a cancer genome panel analysis was successfully performed with DNA extracted from cultured cells fixed at 6 × 103 cells/mL for 90 days, and with DNA from residual LBC samples even after 1 year of storage. Residual LBC samples may be a useful source of DNA for clinical NGS to promote genome-based cancer medicine.
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Affiliation(s)
- Toshiaki Akahane
- Department of Pathology, Kagoshima University Graduate School of Medical and Dental Sciences, Kagoshima, Japan
- Center for Human Genome and Gene Analysis, Kagoshima University Hospital, Kagoshima, Japan
| | - Tomomi Yamaguchi
- Department of Pathology, Laboratory of Cancer Medical Science, Hokuto Hospital, Obihiro, Japan
| | - Yasutaka Kato
- Department of Pathology, Laboratory of Cancer Medical Science, Hokuto Hospital, Obihiro, Japan
| | - Seiya Yokoyama
- Department of Pathology, Kagoshima University Graduate School of Medical and Dental Sciences, Kagoshima, Japan
| | - Taiji Hamada
- Department of Pathology, Kagoshima University Graduate School of Medical and Dental Sciences, Kagoshima, Japan
| | - Yukari Nishida
- Department Surgical Pathology, Kagoshima University Hospital, Kagoshima, Japan
| | - Michiyo Higashi
- Department of Pathology, Kagoshima University Graduate School of Medical and Dental Sciences, Kagoshima, Japan
- Department Surgical Pathology, Kagoshima University Hospital, Kagoshima, Japan
| | - Hiroshi Nishihara
- Department of Biology and Genetics, Laboratory of Cancer Medical Science, Hokuto Hospital, Obihiro, Japan
- Keio Cancer Center, Keio University School of Medicine, Tokyo, Japan
| | - Shinsuke Suzuki
- Department of Clinical Cancer Research, Kagoshima University Graduate School of Medical and Dental Sciences, 890–8544 Kagoshima, Japan
- Kagoshima University Hospital Cancer Center, Kagoshima University Hospital, Kagoshima, Japan
| | - Shinichi Ueno
- Department of Clinical Cancer Research, Kagoshima University Graduate School of Medical and Dental Sciences, 890–8544 Kagoshima, Japan
- Kagoshima University Hospital Cancer Center, Kagoshima University Hospital, Kagoshima, Japan
| | - Akihide Tanimoto
- Department of Pathology, Kagoshima University Graduate School of Medical and Dental Sciences, Kagoshima, Japan
- Center for Human Genome and Gene Analysis, Kagoshima University Hospital, Kagoshima, Japan
- Department Surgical Pathology, Kagoshima University Hospital, Kagoshima, Japan
- * E-mail:
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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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The diagnosis of non-small cell lung cancer in the molecular era. Mod Pathol 2019; 32:16-26. [PMID: 30600321 DOI: 10.1038/s41379-018-0156-x] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2018] [Accepted: 08/20/2018] [Indexed: 12/17/2022]
Abstract
Lung carcinoma is the leading cause of cancer mortality for both genders in the United States and throughout the world. Many of these tumors are being diagnosed with minimally invasive means resulting in small samples. There is a need to extract an increasing amount of therapeutic and prognostic information from progressively smaller samples. Collaboration among clinicians and pathologists is needed to produce a comprehensive final diagnosis in patients with lung cancer. This collaboration facilitates triage of small samples for ancillary studies including molecular testing. What follows represents a review of the current required testing for lung cancer specimens, an example of an algorithm currently employed at the Cleveland Clinic so that all required tests can be performed even on the smallest of specimens and suggestions on how pathologists may approach this new era of "doing more with less".
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The utilization of cytologic and small biopsy samples for ancillary molecular testing. Mod Pathol 2019; 32:77-85. [PMID: 30600323 DOI: 10.1038/s41379-018-0138-z] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2018] [Accepted: 07/22/2018] [Indexed: 11/09/2022]
Abstract
There has recently been an increased emphasis on the utilization of cytologic samples and small biopsies for not only diagnostic purposes but also for ancillary testing. In some instances, the ancillary tests contribute to the diagnosis and in other scenarios, they provide prognostic and theranostic information for the management of patients with advanced stage cancer. These ancillary tests include immunohistochemical biomarker analysis, molecular mutation analysis, and cytogenetic tests. Despite the finite nature of the cellular material procured in cytologic and small tissue biopsies, pathologists are tasked with ordering an increasing number of tests using these limited samples. This requires the pathologists to utilize and triage these samples in an optimal fashion so that as much information can be gleaned from a given specimen. This review will focus on the pre-analytic requirements for ancillary molecular and cytogenetic tests in the context of a discussion of the various preparation methods for cytologic and small biopsy specimens. The goal will be to provide the reader with the necessary concepts that can be utilized to develop optimal specimen selection and triage strategies to maximize the chances of effectively utilizing these samples for comprehensive diagnostic and relevant ancillary testing purposes.
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Matsuo Y, Yoshida T, Yamashita K, Satoh Y. Reducing DNA damage by formaldehyde in liquid-based cytology preservation solutions to enable the molecular testing of lung cancer specimens. Cancer Cytopathol 2018; 126:1011-1021. [PMID: 30343520 DOI: 10.1002/cncy.22069] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2018] [Revised: 08/18/2018] [Accepted: 09/11/2018] [Indexed: 12/17/2022]
Abstract
BACKGROUND Liquid-based cytology (LBC) is a useful cytopathological method, and LBC lung adenocarcinoma specimens may be used for genetic analysis in the near future. In the current study, the authors determined whether LBC specimens can be used for epidermal growth factor receptor (EGFR) mutation analysis in human lung adenocarcinoma cell lines. METHODS Genomic DNA was extracted from 3 lung adenocarcinoma cell lines that were fixed in LBC preservation solution using 2 protocols (one for cultured cells and one for tissues) of a DNA extraction kit. Different fixation times were tested for each protocol: 30 minutes, 1 hour, and 1 to 9 days. As controls, cells also were fixed in 10% formalin or 95% ethanol. The authors investigated the effect of fixation time on DNA fragmentation, polymerase chain reaction (PCR) amplification, and EGFR mutation detection. RESULTS The DNA yield of LBC specimens tended to decrease depending on fixation time. When using the DNA extraction protocol for tissues, PCR amplification was successful after 9 days of fixation, although extracted genomic DNA that was fixed for >1 hour demonstrated fragmentation. Mutation analyses using the Cycleave PCR method were successful after 7 days of fixation. The DNA extraction protocol for tissues was appropriate for lung adenocarcinoma cell lines that were stored for >1 day in a preservative solution. The results of the current study demonstrated that EGFR mutations can be detected on day 7 using lung adenocarcinoma cell lines fixed in CytoRich Red preservative. CONCLUSIONS When LBC specimens are used for targeted molecular genetic testing, the appropriate preservative solution and extraction protocol first should be determined.
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Affiliation(s)
- Yukiko Matsuo
- Department of Thoracic Surgery, Kitasato University School of Medicine, Kanagawa, Japan
| | - Tsutomu Yoshida
- Department of Pathology, Kitasato University School of Medicine, Kanagawa, Japan.,Department of Pathology, Kitasato University Hospital, Kanagawa, Japan
| | - Kazuya Yamashita
- Department of Pathology, Kitasato University Hospital, Kanagawa, Japan
| | - Yukitoshi Satoh
- Department of Thoracic Surgery, Kitasato University School of Medicine, Kanagawa, Japan
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Alekseyev YO, Fazeli R, Yang S, Basran R, Maher T, Miller NS, Remick D. A Next-Generation Sequencing Primer-How Does It Work and What Can It Do? Acad Pathol 2018; 5:2374289518766521. [PMID: 29761157 PMCID: PMC5944141 DOI: 10.1177/2374289518766521] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2017] [Revised: 02/14/2018] [Accepted: 02/16/2018] [Indexed: 12/28/2022] Open
Abstract
Next-generation sequencing refers to a high-throughput technology that determines the nucleic acid sequences and identifies variants in a sample. The technology has been introduced into clinical laboratory testing and produces test results for precision medicine. Since next-generation sequencing is relatively new, graduate students, medical students, pathology residents, and other physicians may benefit from a primer to provide a foundation about basic next-generation sequencing methods and applications, as well as specific examples where it has had diagnostic and prognostic utility. Next-generation sequencing technology grew out of advances in multiple fields to produce a sophisticated laboratory test with tremendous potential. Next-generation sequencing may be used in the clinical setting to look for specific genetic alterations in patients with cancer, diagnose inherited conditions such as cystic fibrosis, and detect and profile microbial organisms. This primer will review DNA sequencing technology, the commercialization of next-generation sequencing, and clinical uses of next-generation sequencing. Specific applications where next-generation sequencing has demonstrated utility in oncology are provided.
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Affiliation(s)
- Yuriy O Alekseyev
- Department of Pathology and Laboratory Medicine, Boston University School of Medicine and Boston Medical Center, Boston, MA, USA
| | - Roghayeh Fazeli
- Department of Pathology and Laboratory Medicine, Boston University School of Medicine and Boston Medical Center, Boston, MA, USA
| | - Shi Yang
- Department of Pathology and Laboratory Medicine, Boston University School of Medicine and Boston Medical Center, Boston, MA, USA
| | - Raveen Basran
- Department of Pathology and Laboratory Medicine, Boston University School of Medicine and Boston Medical Center, Boston, MA, USA
| | - Thomas Maher
- Department of Pathology and Laboratory Medicine, Boston University School of Medicine and Boston Medical Center, Boston, MA, USA
| | - Nancy S Miller
- Department of Pathology and Laboratory Medicine, Boston University School of Medicine and Boston Medical Center, Boston, MA, USA
| | - Daniel Remick
- Department of Pathology and Laboratory Medicine, Boston University School of Medicine and Boston Medical Center, Boston, MA, USA
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Xiong Y, Li M, Zhang P, Zhang L, Yang Y. [Study on Genetype in Lung Squamous Carcinoma by High-throughput of
Transcriptome Sequence]. ZHONGGUO FEI AI ZA ZHI = CHINESE JOURNAL OF LUNG CANCER 2018; 20:727-731. [PMID: 29167000 PMCID: PMC5973275 DOI: 10.3779/j.issn.1009-3419.2017.11.01] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
BACKGROUND Recently, there is no effective targeted drug for to the lung squamous carcinoma, the targeted drug for the adenocarcinoma does not benefit for the patients with squamous lung cancer, and researchers have known less targets for this type of patients. The main study herein is to screen and identify the specific key genes for the lung squamous carcinoma that will provide potential novel targets to describe pathogenesis of lung cancer. METHODS Transcript sequence was used to detect the five pairs lung squamous carcinoma and normal lung tissues and bioinformatics was performed to investigate the differential coding genes between them and quantitative PCR was done to validate the key genes expression in lung cancer cell lines. RESULTS The results of transcriptome sequence showed that 534 genes were up-regulated in the tumor tissues compared with the corresponding normal tissues. The top ten increased genes in the tumors were GAGE12J, SPRR3, PRAME, SPRR1A, SPRR2E, MAGEA3, SPRR1B, IL36G and TMPRSS11D. Next, we identified expression of SPRR family in lung cancer cell lines H520, GLC82, A549, H1299 and PC9. And we found higher expression of SPRR family genes in H1299 cells which metastasized to the lymph node. CONCLUSIONS SPRR family genes are identified to be highly expressed in the lung squamous carcinoma by high throughput transcript sequencing. This SPRR family genes are associated with lymph node metastasis that provide novel idea for lung cancer therapy.
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Affiliation(s)
- Ying Xiong
- Department of Thoracic Surgery II, Beijing Cancer Hospital, Key Laboratory of Carcinogenesis and Translational Research
(Ministry of Education/Beijing), Peking University Cancer Hospital and Institute, Beijing 100142, China
| | - Mingzhen Li
- Beijing Center for Physical and Chemical Analysis, Beijing 100089, China
| | - Panpan Zhang
- Department of Thoracic Surgery II, Beijing Cancer Hospital, Key Laboratory of Carcinogenesis and Translational Research
(Ministry of Education/Beijing), Peking University Cancer Hospital and Institute, Beijing 100142, China
| | - Liyi Zhang
- Department of Thoracic Surgery II, Beijing Cancer Hospital, Key Laboratory of Carcinogenesis and Translational Research
(Ministry of Education/Beijing), Peking University Cancer Hospital and Institute, Beijing 100142, China
| | - Yue Yang
- Department of Thoracic Surgery II, Beijing Cancer Hospital, Key Laboratory of Carcinogenesis and Translational Research
(Ministry of Education/Beijing), Peking University Cancer Hospital and Institute, Beijing 100142, China
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Mito JK, Conner JR, Hornick JL, Cibas ES, Qian X. SOX10/keratin dual-color immunohistochemistry: An effective first-line test for the workup of epithelioid malignant neoplasms in FNA and small biopsy specimens. Cancer Cytopathol 2018; 126:179-189. [DOI: 10.1002/cncy.21960] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2017] [Revised: 11/18/2017] [Accepted: 12/01/2017] [Indexed: 12/12/2022]
Affiliation(s)
- Jeffrey K. Mito
- Department of Pathology; Brigham and Women's Hospital, and Harvard Medical School; Boston Massachusetts
| | - James R. Conner
- Department of Pathology; Brigham and Women's Hospital, and Harvard Medical School; Boston Massachusetts
| | - Jason L. Hornick
- Department of Pathology; Brigham and Women's Hospital, and Harvard Medical School; Boston Massachusetts
| | - Edmund S. Cibas
- Department of Pathology; Brigham and Women's Hospital, and Harvard Medical School; Boston Massachusetts
| | - Xiaohua Qian
- Department of Pathology; Brigham and Women's Hospital, and Harvard Medical School; Boston Massachusetts
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Doxtader EE, Cheng YW, Zhang Y. Molecular Testing of Non-Small Cell Lung Carcinoma Diagnosed by Endobronchial Ultrasound-Guided Transbronchial Fine-Needle Aspiration: The Cleveland Clinic Experience. Arch Pathol Lab Med 2018; 143:670-676. [PMID: 29372844 DOI: 10.5858/arpa.2017-0184-ra] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
CONTEXT.— Given the increasing demand for molecular testing of non-small cell lung carcinoma specimens to guide therapeutic decision-making and the trend toward minimally invasive techniques for obtaining diagnostic tissue, cytopathology laboratories must devise strategies to maximize DNA yield for necessary molecular testing. OBJECTIVE.— To describe our experience at Cleveland Clinic with epidermal growth factor receptor (EGFR) mutation testing by next-generation sequencing and anaplastic lymphoma kinase (ALK) gene rearrangement testing by fluorescence in situ hybridization of non-small cell lung carcinomas diagnosed by cytology, with an emphasis on specimens obtained by endobronchial ultrasound-guided transbronchial fine-needle aspiration. DATA SOURCES.— Data sources include a review of the current literature, including published articles from our institution. CONCLUSIONS.— At our institution, liquid-based cytology specimens are the primary resource used for molecular testing of non-small cell lung carcinomas; in most instances, adequate DNA can be extracted from the residual cell pellet for next-generation sequencing, and ThinPrep slides can be used reliably for fluorescence in situ hybridization testing for ALK gene rearrangements. In occasional cases where the cell pellet material is not adequate for molecular testing, cell blocks and/or surgical pathology specimens are secondary options. The cytopathologist's role in specimen handling and triage is essential to ensure that molecular testing can be carried out successfully.
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Affiliation(s)
- Erika E Doxtader
- From the Departments of Pathology (Drs Doxtader and Zhang) and Laboratory Medicine (Dr Cheng), Cleveland Clinic, Cleveland, Ohio
| | - Yu-Wei Cheng
- From the Departments of Pathology (Drs Doxtader and Zhang) and Laboratory Medicine (Dr Cheng), Cleveland Clinic, Cleveland, Ohio
| | - Yaxia Zhang
- From the Departments of Pathology (Drs Doxtader and Zhang) and Laboratory Medicine (Dr Cheng), Cleveland Clinic, Cleveland, Ohio
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