1
|
Nambirajan A, Sood R, Khatoon W, Malik PS, Mohan A, Jain D. Concordance of Immunohistochemistry and Fluorescence In Situ Hybridization in the Detection of Anaplastic Lymphoma Kinase (ALK) and Ros Proto-oncogene 1 (ROS1) Gene Rearrangements in Non-Small Cell Lung Carcinoma: A 4.5-Year Experience Highlighting Challenges and Pitfalls. Arch Pathol Lab Med 2024; 148:928-937. [PMID: 38054562 DOI: 10.5858/arpa.2023-0229-oa] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/31/2023] [Indexed: 12/07/2023]
Abstract
CONTEXT.— ALK and ROS1 rearrangements are essential biomarkers to be tested in advanced lung adenocarcinomas. While D5F3 Ventana assay is a companion diagnostic for anaplastic lymphoma kinase-targeted therapy, immunohistochemistry is only a screening tool for detecting ROS1 rearrangement. Confirmation by cytogenetic or molecular techniques is necessary. OBJECTIVE.— To evaluate the utility of ALK and ROS1 fluorescence in situ hybridization as a complement to immunohistochemistry in routine predictive biomarker testing algorithms. DESIGN.— The study was ambispective, spanning 4.5 years during which lung adenocarcinoma samples were subjected to EGFR mutation testing by real-time polymerase chain reaction and ALK/ROS1 rearrangement testing by immunohistochemistry (Ventana D5F3 assay for anaplastic lymphoma kinase protein; manual assay with D4D6 clone for Ros proto-oncogene 1 protein). Fluorescence in situ hybridization was performed in all anaplastic lymphoma kinase equivocal and Ros proto-oncogene 1 immunopositive cases. RESULTS.— Of 1874 samples included, EGFR mutations were detected in 27% (481 of 1796). Anaplastic lymphoma kinase immunohistochemistry was positive in 10% (174 of 1719) and equivocal in 3% (58 of 1719) of samples tested. ALK fluorescence in situ hybridization showed 81% (77 of 95) concordance with immunohistochemistry. Ros proto-oncogene 1 immunopositivity was noted in 13% (190 of 1425) of cases, with hybridization-confirmed rearrangements in 19.3% (26 of 135) of samples, all of which showed diffuse, strong- to moderate-intensity, cytoplasmic staining in tumor cells. Ros proto-oncogene 1 protein overexpression without rearrangement was significantly common in EGFR-mutant and ALK-rearranged adenocarcinomas. CONCLUSIONS.— Immunostaining is a robust method for ALK-rearrangement testing, with fluorescence in situ hybridization adding value in the rare equivocal stained case. ROS1-rearrangement testing is more cost-effective if immunohistochemistry is followed by fluorescence in situ hybridization after excluding EGFR-mutant and ALK-rearranged adenocarcinomas.
Collapse
Affiliation(s)
- Aruna Nambirajan
- From the Departments of Pathology (Nambirajan, Sood, Khatoon, Jain), Medical Oncology (Malik), and Pulmonary, Critical Care and Sleep Medicine (Mohan), All India Institute of Medical Sciences (AIIMS), New Delhi, India
| | - Ridhi Sood
- From the Departments of Pathology (Nambirajan, Sood, Khatoon, Jain), Medical Oncology (Malik), and Pulmonary, Critical Care and Sleep Medicine (Mohan), All India Institute of Medical Sciences (AIIMS), New Delhi, India
| | - Warisa Khatoon
- From the Departments of Pathology (Nambirajan, Sood, Khatoon, Jain), Medical Oncology (Malik), and Pulmonary, Critical Care and Sleep Medicine (Mohan), All India Institute of Medical Sciences (AIIMS), New Delhi, India
| | - Prabhat Singh Malik
- From the Departments of Pathology (Nambirajan, Sood, Khatoon, Jain), Medical Oncology (Malik), and Pulmonary, Critical Care and Sleep Medicine (Mohan), All India Institute of Medical Sciences (AIIMS), New Delhi, India
| | - Anant Mohan
- From the Departments of Pathology (Nambirajan, Sood, Khatoon, Jain), Medical Oncology (Malik), and Pulmonary, Critical Care and Sleep Medicine (Mohan), All India Institute of Medical Sciences (AIIMS), New Delhi, India
| | - Deepali Jain
- From the Departments of Pathology (Nambirajan, Sood, Khatoon, Jain), Medical Oncology (Malik), and Pulmonary, Critical Care and Sleep Medicine (Mohan), All India Institute of Medical Sciences (AIIMS), New Delhi, India
| |
Collapse
|
2
|
Koduru P, Chen W, Fuda F, Kaur G, Awan F, John S, Garcia R, Gagan J. RNASeq Analysis for Accurate Identification of Fusion Partners in Tumor Specific Translocations Detected by Standard FISH Probes in Hematologic Malignancies. CLINICAL PATHOLOGY (THOUSAND OAKS, VENTURA COUNTY, CALIF.) 2024; 17:2632010X241230262. [PMID: 38371338 PMCID: PMC10874141 DOI: 10.1177/2632010x241230262] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/18/2023] [Accepted: 01/17/2024] [Indexed: 02/20/2024]
Abstract
Background Fluorescence labeled DNA probes and in situ hybridization methods had shorter turn round time for results revolutionized their clinical application. Signals obtained from these probes are highly specific, yet they can produce fusion signals not necessarily representing fusion of actual genes due to other genes included in the probe design. In this study we evaluated discordance between cytogenetic, FISH and RNAseq results in 3 different patients with hematologic malignancies and illustrated the need to perform next generation sequencing (NGS) or RNASeq to accurately interpret FISH results. Methods Bone marrow or peripheral blood karyotypes and FISH were performed to detect recurring translocations associated with hematologic malignancies in clinical samples routinely referred to our clinical cytogenetics laboratory. When required, NGS was performed on DNA and RNA libraries to detect somatic alterations and gene fusions in some of these specimens. Discordance in results between these methods is further evaluated. Results For a patient with plasma cell leukemia standard FGFR3 / IGH dual fusion FISH assay detected fusion that was interpreted as FGFR3-positive leukemia, whereas NGS/RNASeq detected NSD2::IGH. For a pediatric acute lymphoblastic leukemia patient, a genetic diagnosis of PDGFRB-positive ALL was rendered because the PDGFRB break-apart probe detected clonal rearrangement, whereas NGS detected MEF2D::CSF1R. A MYC-positive B-prolymphocytic leukemia was rendered for another patient with a cytogenetically identified t(8;14) and MYC::IGH by FISH, whereas NGS detected a novel PVT1::RCOR1 not previously reported. Conclusions These are 3 cases in a series of several other concordant results, nevertheless, elucidate limitations when interpreting FISH results in clinical applications, particularly when other genes are included in probe design. In addition, when the observed FISH signals are atypical, this study illustrates the necessity to perform complementary laboratory assays, such as NGS and/or RNASeq, to accurately identify fusion genes in tumorigenic translocations.
Collapse
Affiliation(s)
- Prasad Koduru
- Departments of Pathology, UT Southwestern Medical Center, Dallas, TX, USA
| | - Weina Chen
- Departments of Pathology, UT Southwestern Medical Center, Dallas, TX, USA
| | - Franklin Fuda
- Departments of Pathology, UT Southwestern Medical Center, Dallas, TX, USA
| | - Gurbakhash Kaur
- Internal Medicine (Division of Oncology), UT Southwestern Medical Center, Dallas, TX, USA
| | - Farrukh Awan
- Internal Medicine (Division of Oncology), UT Southwestern Medical Center, Dallas, TX, USA
| | - Samuel John
- Pediatrics, UT Southwestern Medical Center, Dallas, TX, USA
| | - Rolando Garcia
- Departments of Pathology, UT Southwestern Medical Center, Dallas, TX, USA
| | - Jeffrey Gagan
- Departments of Pathology, UT Southwestern Medical Center, Dallas, TX, USA
| |
Collapse
|
3
|
Sztankovics D, Krencz I, Moldvai D, Dankó T, Nagy Á, Nagy N, Bedics G, Rókusz A, Papp G, Tőkés AM, Pápay J, Sápi Z, Dezső K, Bödör C, Sebestyén A. Novel RICTOR amplification harbouring entities: FISH validation of RICTOR amplification in tumour tissue after next-generation sequencing. Sci Rep 2023; 13:19610. [PMID: 37949943 PMCID: PMC10638425 DOI: 10.1038/s41598-023-46927-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2023] [Accepted: 11/07/2023] [Indexed: 11/12/2023] Open
Abstract
Alterations in mTOR signalling molecules, including RICTOR amplification, have been previously described in many cancers, particularly associated with poor prognosis. In this study, RICTOR copy number variation (CNV) results of diagnostic next-generation sequencing (NGS) were analysed in 420 various human malignant tissues. RICTOR amplification was tested by Droplet Digital PCR (ddPCR) and validated using the "gold standard" fluorescence in situ hybridisation (FISH). Additionally, the consequences of Rictor protein expression were also studied by immunohistochemistry. RICTOR amplification was presumed in 37 cases with CNV ≥ 3 by NGS, among these, 16 cases (16/420; 3.8%) could be validated by FISH, however, ddPCR confirmed only 11 RICTOR-amplified cases with lower sensitivity. Based on these, neither NGS nor ddPCR could replace traditional FISH in proof of RICTOR amplification. However, NGS could be beneficial to highlight potential RICTOR-amplified cases. The obtained results of the 14 different tumour types with FISH-validated RICTOR amplification demonstrate the importance of RICTOR amplification in a broad spectrum of tumours. The newly described RICTOR-amplified entities could initiate further collaborative studies with larger cohorts to analyse the prevalence of RICTOR amplification in rare diseases. Finally, our and further work could help to improve and expand future therapeutic opportunities for mTOR-targeted therapies.
Collapse
Affiliation(s)
- Dániel Sztankovics
- Department of Pathology and Experimental Cancer Research, Semmelweis University, Üllői út 26, 1085, Budapest, Hungary
| | - Ildikó Krencz
- Department of Pathology and Experimental Cancer Research, Semmelweis University, Üllői út 26, 1085, Budapest, Hungary
| | - Dorottya Moldvai
- Department of Pathology and Experimental Cancer Research, Semmelweis University, Üllői út 26, 1085, Budapest, Hungary
| | - Titanilla Dankó
- Department of Pathology and Experimental Cancer Research, Semmelweis University, Üllői út 26, 1085, Budapest, Hungary
| | - Ákos Nagy
- Department of Pathology and Experimental Cancer Research, Semmelweis University, Üllői út 26, 1085, Budapest, Hungary
- HCEMM-SE Molecular Oncohematology Research Group, Department of Pathology and Experimental Cancer Research, Semmelweis University, Üllői út 26, 1085, Budapest, Hungary
| | - Noémi Nagy
- Department of Pathology and Experimental Cancer Research, Semmelweis University, Üllői út 26, 1085, Budapest, Hungary
- HCEMM-SE Molecular Oncohematology Research Group, Department of Pathology and Experimental Cancer Research, Semmelweis University, Üllői út 26, 1085, Budapest, Hungary
| | - Gábor Bedics
- Department of Pathology and Experimental Cancer Research, Semmelweis University, Üllői út 26, 1085, Budapest, Hungary
- HCEMM-SE Molecular Oncohematology Research Group, Department of Pathology and Experimental Cancer Research, Semmelweis University, Üllői út 26, 1085, Budapest, Hungary
| | - András Rókusz
- Department of Pathology and Experimental Cancer Research, Semmelweis University, Üllői út 26, 1085, Budapest, Hungary
| | - Gergő Papp
- Department of Pathology and Experimental Cancer Research, Semmelweis University, Üllői út 26, 1085, Budapest, Hungary
| | - Anna-Mária Tőkés
- Department of Pathology, Forensic and Insurance Medicine, Semmelweis University, Üllői út 93, 1091, Budapest, Hungary
| | - Judit Pápay
- Department of Pathology and Experimental Cancer Research, Semmelweis University, Üllői út 26, 1085, Budapest, Hungary
| | - Zoltán Sápi
- Department of Pathology and Experimental Cancer Research, Semmelweis University, Üllői út 26, 1085, Budapest, Hungary
| | - Katalin Dezső
- Department of Pathology and Experimental Cancer Research, Semmelweis University, Üllői út 26, 1085, Budapest, Hungary
| | - Csaba Bödör
- Department of Pathology and Experimental Cancer Research, Semmelweis University, Üllői út 26, 1085, Budapest, Hungary
- HCEMM-SE Molecular Oncohematology Research Group, Department of Pathology and Experimental Cancer Research, Semmelweis University, Üllői út 26, 1085, Budapest, Hungary
| | - Anna Sebestyén
- Department of Pathology and Experimental Cancer Research, Semmelweis University, Üllői út 26, 1085, Budapest, Hungary.
| |
Collapse
|
4
|
Clavé S, Jackson JB, Salido M, Kames J, Gerding KMR, Verner EL, Kong EF, Weingartner E, Gibert J, Hardy-Werbin M, Rocha P, Riera X, Torres E, Hernandez J, Cerqueira G, Nichol D, Simmons J, Taus Á, Pijuan L, Bellosillo B, Arriola E. Comprehensive NGS profiling to enable detection of ALK gene rearrangements and MET amplifications in non-small cell lung cancer. Front Oncol 2023; 13:1225646. [PMID: 37927472 PMCID: PMC10623306 DOI: 10.3389/fonc.2023.1225646] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2023] [Accepted: 08/28/2023] [Indexed: 11/07/2023] Open
Abstract
Introduction Next-generation sequencing (NGS) is currently widely used for biomarker studies and molecular profiling to identify concurrent alterations that can lead to the better characterization of a tumor's molecular landscape. However, further evaluation of technical aspects related to the detection of gene rearrangements and copy number alterations is warranted. Methods There were 12 ALK rearrangement-positive tumor specimens from patients with non-small cell lung cancer (NSCLC) previously detected via fluorescence in situ hybridization (FISH), immunohistochemistry (IHC), and an RNA-based NGS assay, and 26 MET high gene copy number (GCN) cases detected by FISH, selected for this retrospective study. All 38 pre-characterized cases were reassessed utilizing the PGDx™ elio™ tissue complete assay, a 505 gene targeted NGS panel, to evaluate concordance with these conventional diagnostic techniques. Results The detection of ALK rearrangements using the DNA-based NGS assay demonstrated excellent sensitivity with the added benefit of characterizing gene fusion partners and genomic breakpoints. MET copy number alterations were also detected; however, some discordances were observed likely attributed to differences in algorithm, reporting thresholds and gene copy number state. TMB was also assessed by the assay and correlated to the presence of NSCLC driver alterations and was found to be significantly lower in cases with NGS-confirmed canonical driver mutations compared with those without (p=0.0019). Discussion Overall, this study validates NGS as an accurate approach for detecting structural variants while also highlighting the need for further optimization to enable harmonization across methodologies for amplifications.
Collapse
Affiliation(s)
- Sergi Clavé
- Pathology Department, Hospital del Mar, Barcelona, Spain
- Cancer Research Program, Hospital del Mar Medical Research Institute, Barcelona, Spain
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Madrid, Spain
| | | | - Marta Salido
- Pathology Department, Hospital del Mar, Barcelona, Spain
- Cancer Research Program, Hospital del Mar Medical Research Institute, Barcelona, Spain
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Madrid, Spain
| | - Jacob Kames
- Personal Genome Diagnostics (PGDx/Labcorp), Baltimore, MD, United States
| | | | - Ellen L. Verner
- Personal Genome Diagnostics (PGDx/Labcorp), Baltimore, MD, United States
| | - Eric F. Kong
- Personal Genome Diagnostics (PGDx/Labcorp), Baltimore, MD, United States
| | | | - Joan Gibert
- Cancer Research Program, Hospital del Mar Medical Research Institute, Barcelona, Spain
| | - Max Hardy-Werbin
- Cancer Research Program, Hospital del Mar Medical Research Institute, Barcelona, Spain
- Medical Oncology Department, Hospital del Mar, Barcelona, Spain
| | - Pedro Rocha
- Cancer Research Program, Hospital del Mar Medical Research Institute, Barcelona, Spain
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Madrid, Spain
- Medical Oncology Department, Hospital del Mar, Barcelona, Spain
| | - Xènia Riera
- Pathology Department, Hospital del Mar, Barcelona, Spain
- Cancer Research Program, Hospital del Mar Medical Research Institute, Barcelona, Spain
| | - Erica Torres
- Pathology Department, Hospital del Mar, Barcelona, Spain
| | - James Hernandez
- Personal Genome Diagnostics (PGDx/Labcorp), Baltimore, MD, United States
| | - Gustavo Cerqueira
- Personal Genome Diagnostics (PGDx/Labcorp), Baltimore, MD, United States
| | - Donna Nichol
- Personal Genome Diagnostics (PGDx/Labcorp), Baltimore, MD, United States
| | - John Simmons
- Personal Genome Diagnostics (PGDx/Labcorp), Baltimore, MD, United States
| | - Álvaro Taus
- Cancer Research Program, Hospital del Mar Medical Research Institute, Barcelona, Spain
- Medical Oncology Department, Hospital del Mar, Barcelona, Spain
| | - Lara Pijuan
- Pathology Department, Hospital del Mar, Barcelona, Spain
| | - Beatriz Bellosillo
- Pathology Department, Hospital del Mar, Barcelona, Spain
- Cancer Research Program, Hospital del Mar Medical Research Institute, Barcelona, Spain
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Madrid, Spain
| | - Edurne Arriola
- Cancer Research Program, Hospital del Mar Medical Research Institute, Barcelona, Spain
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Madrid, Spain
- Medical Oncology Department, Hospital del Mar, Barcelona, Spain
| |
Collapse
|
5
|
Sará L, Clavijo AS, Niño-Torres JD, Solarte LM, Vergara A, Moreno OM, Rodríguez JL, Rojas A. Discordant results for ALK based on immunohistochemistry versus fluorescence in situ hybridization in a cohort of patients diagnosed with lung adenocarcinoma. REVISTA ESPAÑOLA DE PATOLOGÍA 2023; 56:88-96. [PMID: 37061247 DOI: 10.1016/j.patol.2023.02.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/05/2023] [Accepted: 02/01/2023] [Indexed: 03/17/2023]
Abstract
INTRODUCTION Anaplastic lymphoma kinase (ALK) rearrangement located on the short arm of chromosome 2, region 2 and band 3 is frequent in lung cancer patients who respond to targeted therapies with ALK inhibitors Therefore, their identification has become a standard diagnostic test in patients with advanced NSCLS, as such chromosomal alterations may lead to the activation of important signalling pathways involved in cell survival and proliferation. METHODS To investigate the ALK gene status, we performed FISH and IHC assays in 18 lung adenocarcinoma patients, 12 women and 6 men, aged between 29 and 85 years. Paraffin-embedded samples were analyzed in the Pathology Department of the Hospital Universitario San Ignacio. RESULTS Results between the two techniques in 5 patients showed discordant patterns, being positive for FISH and negative for IHC. The borderline to define ALK positivity was set at 15%, These results present experimental evidence that the techniques differ in specific situations. CONCLUSIONS Our findings show that it is advisable to investigate the ALK gene status in patients with suspected lung cancer using both FISH and IHC in combination.
Collapse
|
6
|
Rossi S, Marinello A, Pagliaro A, Franceschini D, Navarria P, Finocchiaro G, Toschi L, Scorsetti M, Santoro A. Current treatment approaches for brain metastases in ALK/ ROS1/ NTRK-positive non-small-cell lung cancer. Expert Rev Anticancer Ther 2023; 23:29-41. [PMID: 36548111 DOI: 10.1080/14737140.2023.2162044] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
INTRODUCTION Oncogene-addicted non-small cell lung cancer (NSCLC) patients present a high incidence of CNS metastases either at diagnosis or during the course of the disease. In this case, patients present with worse prognosis and are often excluded from clinical trials unless brain metastases are pre-treated or clinically stable. AREAS COVERED As a result of the discovery of several oncogenic drivers in ALK/ROS1/NTRK-positive NSCLC, targeted agents have been tested in several trials. We evaluate and compare the intracranial efficacy of available targeted agents in ALK/ROS1/NTRK-positive NSCLC based on subgroup analysis from pivotal trials. EXPERT OPINION Last-generation ALK inhibitors have shown slightly superior intracranial activity but pivotal trials do not consider the same endpoints for intracranial efficacy, therefore data are not comparable. Local treatments for BM including surgical resection, stereotactic radiosurgery (SRS) and WBRT, should be integrated with systemic therapies basing on specific criteria like presence of oligoprogression or symptomatic progression.
Collapse
Affiliation(s)
- Sabrina Rossi
- Medical Oncology and Hematology Unit, IRCCS Humanitas Research Hospital, Milan, Italy
| | - Arianna Marinello
- Department of Biomedical Sciences, Humanitas University, Milan, Italy
| | - Arianna Pagliaro
- Department of Biomedical Sciences, Humanitas University, Milan, Italy
| | - Davide Franceschini
- Department of Radiotherapy and Radiosurgery, IRCCS Humanitas Research Hospital, Milan, Italy
| | - Pierina Navarria
- Department of Radiotherapy and Radiosurgery, IRCCS Humanitas Research Hospital, Milan, Italy
| | - Giovanna Finocchiaro
- Medical Oncology and Hematology Unit, IRCCS Humanitas Research Hospital, Milan, Italy
| | - Luca Toschi
- Medical Oncology and Hematology Unit, IRCCS Humanitas Research Hospital, Milan, Italy
| | - Marta Scorsetti
- Department of Biomedical Sciences, Humanitas University, Milan, Italy.,Department of Radiotherapy and Radiosurgery, IRCCS Humanitas Research Hospital, Milan, Italy
| | - Armando Santoro
- Medical Oncology and Hematology Unit, IRCCS Humanitas Research Hospital, Milan, Italy.,Department of Biomedical Sciences, Humanitas University, Milan, Italy
| |
Collapse
|
7
|
Zhao R, Guo L, Zhang B, Zhao J, Xiang C, Chen S, Shao J, Zhu L, Ye M, Han Y. Identification and therapeutic evaluation of ALK rearrangements in non-small-cell lung cancer. J Pathol Clin Res 2022; 8:538-549. [PMID: 35848751 PMCID: PMC9535099 DOI: 10.1002/cjp2.289] [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: 01/02/2022] [Revised: 06/17/2022] [Accepted: 06/23/2022] [Indexed: 12/29/2022]
Abstract
This study aimed to present a comprehensive assessment of anaplastic lymphoma kinase (ALK) rearrangements evaluated by DNA/RNA-based next-generation sequencing (NGS) and Ventana immunohistochemistry (IHC) in patients with non-small-cell lung cancer (NSCLC) and to evaluate the therapeutic outcomes of ALK tyrosine kinase inhibitor (TKI) treatment. We investigated ALK gene fusions in 14,894 patients with NSCLC using Ventana IHC and NGS, including 12,533 cases detected via DNA-based NGS and 2,361 cases using RNA-based NGS. The overall percentage agreement (OPA), positive percentage agreement (PPA), and negative percentage agreement (NPA) were calculated when comparing the results between NGS and IHC. The therapeutic responses to ALK-TKIs were also evaluated. In total, 3.50% (439/12,533) of specimens were NGS ALK-positive (NGS-p) in the DNA-based NGS cohort and 3.63% (455/12,533) were IHC ALK-positive (IHC-p). The OPA of NGS was 99.60%, whereas its PPA and NPA were 92.75 and 99.86%, respectively. In the adenocarcinoma (ADC) subcohort, the PPA was 95.69%. In the RNA-based NGS cohort, 2.20% (52/2,361) of specimens were NGS-p and 2.63% (62/2,361) were IHC-p. The OPA of NGS was 99.49%; its PPA and NPA were 82.26 and 99.96%, respectively. Thirteen patients with discordant results received ALK-TKI treatment. In the seven NGS-p/IHC-negative (IHC-n) patients, the overall response rate (ORR) was 85.4% (6/7) and the disease control rate (DCR) was 100%. In the six NGS-negative/IHC-p patients, the ORR was 66.7% (4/6) and the DCR was 100%. In summary, a high concordance of ALK gene fusion detected via NGS and IHC was observed in this study. DNA-based NGS had a higher OPA, PPA, and PPA in the ADC subcohort, whereas RNA-based NGS had a higher NPA. Overall, the results suggest that the combination of NGS and IHC can improve the accuracy of ALK fusion detection; hence, a result determination algorithm for clinical detection of ALK gene fusion was also proposed.
Collapse
Affiliation(s)
- Ruiying Zhao
- Department of Pathology, Shanghai Chest HospitalShanghai Jiao Tong UniversityShanghaiPR China
| | - Lianying Guo
- Department of Pathology, Shanghai Chest HospitalShanghai Jiao Tong UniversityShanghaiPR China
| | - Bo Zhang
- Department of Pulmonary, Shanghai Chest HospitalShanghai Jiao Tong UniversityShanghaiPR China
| | - Jikai Zhao
- Department of Pathology, Shanghai Chest HospitalShanghai Jiao Tong UniversityShanghaiPR China
| | - Chan Xiang
- Department of Pathology, Shanghai Chest HospitalShanghai Jiao Tong UniversityShanghaiPR China
| | - Shengnan Chen
- Department of Pathology, Shanghai Chest HospitalShanghai Jiao Tong UniversityShanghaiPR China
| | - Jinchen Shao
- Department of Pathology, Shanghai Chest HospitalShanghai Jiao Tong UniversityShanghaiPR China
| | - Lei Zhu
- Department of Pathology, Shanghai Chest HospitalShanghai Jiao Tong UniversityShanghaiPR China
| | - Min Ye
- Department of Pathology, Shanghai Chest HospitalShanghai Jiao Tong UniversityShanghaiPR China
| | - Yuchen Han
- Department of Pathology, Shanghai Chest HospitalShanghai Jiao Tong UniversityShanghaiPR China
| |
Collapse
|
8
|
Steeghs EM, Groen HJ, Schuuring E, Aarts MJ, Damhuis RA, Voorham QJ, consortium PATH, Ligtenberg MJ, Grünberg K. Mutation-tailored treatment selection in non-small cell lung cancer patients in daily clinical practice. Lung Cancer 2022; 167:87-97. [DOI: 10.1016/j.lungcan.2022.04.001] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2022] [Revised: 03/28/2022] [Accepted: 04/01/2022] [Indexed: 12/13/2022]
|
9
|
Canterbury CR, Fernandes H, Crapanzano JP, Murty VV, Mansukhani MM, Shu CA, Szabolcs M, Saqi A. ALK Gene Rearrangements in Lung Adenocarcinomas: Concordance of Immunohistochemistry, Fluorescence In Situ Hybridization, RNA In Situ Hybridization, and RNA Next-Generation Sequencing Testing. JTO Clin Res Rep 2021; 2:100223. [PMID: 34746883 PMCID: PMC8552107 DOI: 10.1016/j.jtocrr.2021.100223] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2021] [Revised: 08/05/2021] [Accepted: 08/29/2021] [Indexed: 11/29/2022] Open
Abstract
Introduction The 2018 updated molecular testing guidelines for patients with advanced lung cancer incorporated ALK immunohistochemistry (IHC) analysis as an equivalent to fluorescence in situ hybridization (FISH) method recommended in 2013. Nevertheless, no specific recommendation for alternative methods was proposed owing to insufficient data. The aim of this study was to compare the results of ALK IHC, FISH, RNA next-generation sequencing (NGS), and RNA in situ hybridization (ISH) with available clinical data. Methods A search for lung carcinomas with ALK testing by greater than or equal to one modality (i.e., ALK IHC, FISH, NGS) was performed; a subset underwent RNA ISH. When available, clinical data were recorded. Results The results were concordant among all performed testing modalities in 86 of 90 cases (95.6%). Of the four discordant cases, two were ALK positive by FISH but negative by IHC, RNA NGS, and RNA ISH. The remaining two cases failed RNA NGS testing, one was IHC negative, FISH positive, RNA ISH negative and the second was IHC positive, FISH positive, RNA ISH equivocal. RNA NGS identified one rare and one novel ALK fusion. Sufficient therapy data were available in 10 cases treated with tyrosine kinase inhibitors; three had disease progression, including one with discordant results (FISH positive, RNA NGS negative, IHC negative, RNA ISH negative) and two with concordant ALK positivity among all modalities. Conclusions Our results reveal high concordance among IHC, RNA NGS, and RNA ISH. In cases of discordance with available RNA NGS, FISH result was positive whereas IHC and ISH results were negative. On the basis of our data, multimodality testing is recommended to identify discrepant results and patients (un)likely to respond to tyrosine kinase inhibitors.
Collapse
Affiliation(s)
- Carleigh R Canterbury
- Department of Pathology and Cell Biology, Columbia University Medical Center, New York, New York
| | - Helen Fernandes
- Department of Pathology and Cell Biology, Columbia University Medical Center, New York, New York
| | - John P Crapanzano
- Department of Pathology and Cell Biology, Columbia University Medical Center, New York, New York
| | - Vundavalli V Murty
- Department of Pathology and Cell Biology, Columbia University Medical Center, New York, New York
| | - Mahesh M Mansukhani
- Department of Pathology and Cell Biology, Columbia University Medical Center, New York, New York
| | - Catherine A Shu
- Division of Hematology/Oncology, Department of Medicine, Columbia University Medical Center, New York, New York
| | - Matthias Szabolcs
- Department of Pathology and Cell Biology, Columbia University Medical Center, New York, New York
| | - Anjali Saqi
- Department of Pathology and Cell Biology, Columbia University Medical Center, New York, New York
| |
Collapse
|
10
|
Pisapia P, Pepe F, Sgariglia R, Nacchio M, Russo G, Gragnano G, Conticelli F, Salatiello M, De Luca C, Girolami I, Eccher A, Iaccarino A, Bellevicine C, Vigliar E, Malapelle U, Troncone G. Methods for actionable gene fusion detection in lung cancer: now and in the future. Pharmacogenomics 2021; 22:833-847. [PMID: 34525844 DOI: 10.2217/pgs-2021-0048] [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] [Indexed: 12/28/2022] Open
Abstract
Although gene fusions occur rarely in non-small-cell lung cancer (NSCLC) patients, they represent a relevant target in treatment decision algorithms. To date, immunohistochemistry and fluorescence in situ hybridization are the two principal methods used in clinical trials. However, using these methods in routine clinical practice is often impractical and time consuming because they can only analyze single genes and the quantity of tissue material is often insufficient. Thus, novel technologies, able to test multiple genes in a single run with minimal sample input, are being under investigation. Here, we discuss the utility of next-generation sequencing and nCounter technologies in detecting simultaneous gene fusions in NSCLC patients.
Collapse
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
| | - Gianluca Gragnano
- 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
| | - Caterina De Luca
- 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 & Diagnostics, University & Hospital Trust of Verona, Verona, Italy
| | - Antonino Iaccarino
- Department of Public Health, University of Naples Federico II, Naples, 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
| |
Collapse
|
11
|
Concordance Analysis of ALK Gene Fusion Detection Methods in Patients with Non-Small-Cell Lung Cancer from Chile, Brazil, and Peru. J Mol Diagn 2021; 23:1127-1137. [PMID: 34186175 DOI: 10.1016/j.jmoldx.2021.05.018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2019] [Revised: 05/08/2021] [Accepted: 05/27/2021] [Indexed: 11/23/2022] Open
Abstract
About 4% to 7% of the non-small-cell lung cancer patients have anaplastic lymphoma kinase (ALK) rearrangements, and specific targeted therapies improve patients' outcomes significantly. ALK gene fusions are detected by immunohistochemistry or fluorescent in situ hybridization as gold standards in South America. Next-generation sequencing-based assays are a reliable alternative, able to perform simultaneous detection of multiple events from a single sample. We analyzed 4240 non-small-cell lung cancer samples collected in 37 hospitals from Chile, Brazil, and Peru, where ALK rearrangements were determined as part of their standard of care (SofC) using either immunohistochemistry or fluorescent in situ hybridization. A subset of 1450 samples was sequenced with the Oncomine Focus Assay (OFA), and the concordance with the SofC tests was measured. An orthogonal analysis was performed using a real-time quantitative PCR echinoderm microtubule-associated protein-like 4-ALK fusion detection kit. ALK fusion prevalence is similar for Chile (3.67%; N = 2142), Brazil (4.05%; N = 1013), and Peru (4.59%; N = 675). Although a comparison between OFA and SofC assays showed similar sensitivity, OFA had significantly higher specificity and higher positive predictive value, which opens new opportunities for a more specific determination of ALK gene rearrangements.
Collapse
|
12
|
Zhou H, Xu B, Xu J, Zhu G, Guo Y. Novel MRPS9-ALK Fusion Mutation in a Lung Adenocarcinoma Patient: A Case Report. Front Oncol 2021; 11:670907. [PMID: 34168990 PMCID: PMC8217641 DOI: 10.3389/fonc.2021.670907] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2021] [Accepted: 05/10/2021] [Indexed: 12/25/2022] Open
Abstract
Anaplastic lymphoma kinase (ALK) rearrangements account for approximately 5-6% of non-small-cell lung cancer (NSCLC) patients. In this study, a case of lung adenocarcinoma harboring a novel MRPS9-ALK fusion is reported. The patient responded well to the first and second generation of ALK-tyrosine kinase inhibitors (ALK-TKIs) (crizotinib then alectinib), as her imaging findings and clinical symptoms significantly improved. At last follow-up, over 21 months of overall survival (OS) has been achieved since ALK-TKI treatment. The progression-free survival (PFS) is already ten months since alectinib. The adverse effects were manageable. The case presented here provides first clinical evidence of the efficacy of ALK-TKIs in NSCLC patients with MRPS9-ALK fusion.
Collapse
Affiliation(s)
- Huamiao Zhou
- Department of Oncology, Zhejiang Provincial Hospital of Traditional Chinese Medicine, Hangzhou, China
| | - Binyue Xu
- The First School of Clinical Medicine, Zhejiang Chinese Medical University, Hangzhou, China
| | - Jili Xu
- The First School of Clinical Medicine, Zhejiang Chinese Medical University, Hangzhou, China
| | - Guomeng Zhu
- Department of Oncology, Zhejiang Provincial Hospital of Traditional Chinese Medicine, Hangzhou, China
| | - Yong Guo
- Department of Oncology, Zhejiang Provincial Hospital of Traditional Chinese Medicine, Hangzhou, China
| |
Collapse
|
13
|
Batra U, Nathany S, Sharma M, Pasricha S, Bansal A, Jain P, Mehta A. IHC versus FISH versus NGS to detect ALK gene rearrangement in NSCLC: all questions answered? J Clin Pathol 2021; 75:405-409. [PMID: 33753563 DOI: 10.1136/jclinpath-2021-207408] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2021] [Revised: 02/19/2021] [Accepted: 02/22/2021] [Indexed: 11/04/2022]
Abstract
AIMS Anaplastic lymphoma kinase (ALK) rearranged non-small cell lung carcinoma (NSCLC) is a distinct molecular subtype and rapid approval of ALK tyrosine kinase inhibitors (TKIs) has necessitated rapid and sensitive diagnostic modalities for the detection of this alteration. Gene rearrangements can be identified using many techniques including fluorescence in situ hybridisation (FISH), reverse transcriptase-PCR, next-generation sequencing (NGS) and immunohistochemistry (IHC) for fusion oncoprotein expression. We aimed to determine the concordance between IHC, FISH and NGS for ALK biomarker detection, and determine differences in sensitivity, and survival outcomes. METHODS We analysed the concordance between IHC using D5F3 monoclonal antibody, FISH (break-apart) and NGS using a custom panel containing 71 different ALK variants. RESULTS Among 71 cases included in this study, FISH was evaluable in 58 cases. The concordance of ALK IHC with FISH was 75.9% and that with NGS was 84.5%. The sensitivities of FISH and NGS were 75.6% and 87.5%, respectively. The median progression-free survival of ALK IHC-positive and FISH-negative group was 5.5 months and that of both positive was 9.97 months. CONCLUSION Although NGS offers a better throughput and visualisation, IHC still remains the quintessential screening tool in upfront diagnosis of ALK rearranged NSCLC.
Collapse
Affiliation(s)
- Ullas Batra
- Medical Oncology, Rajiv Gandhi Cancer Institute and Research Centre, New Delhi, India
| | - Shrinidhi Nathany
- Molecular Diagnostics, Rajiv Gandhi Cancer Institute and Research Centre, New Delhi, India
| | - Mansi Sharma
- Medical Oncology, Rajiv Gandhi Cancer Institute and Research Centre, New Delhi, India
| | - Sunil Pasricha
- Pathology, Rajiv Gandhi Cancer Institute and Research Centre, New Delhi, India
| | - Abhishek Bansal
- Radiology, Rajiv Gandhi Cancer Institute and Research Centre, New Delhi, India
| | - Parveen Jain
- Medical Oncology, Rajiv Gandhi Cancer Institute and Research Centre, New Delhi, India
| | - Anurag Mehta
- Laboratory Services, Transfusion Medicine and Research, Rajiv Gandhi Cancer Institute and Research Centre, New Delhi, India
| |
Collapse
|
14
|
De Luca C, Pepe F, Iaccarino A, Pisapia P, Righi L, Listì A, Greco L, Gragnano G, Campione S, De Dominicis G, Pagni F, Sgariglia R, Nacchio M, Tufano R, Conticelli F, Vigliar E, Bellevicine C, Cortinovis DL, Novello S, Molina-Vila MA, Rosell R, Troncone G, Malapelle U. RNA-Based Assay for Next-Generation Sequencing of Clinically Relevant Gene Fusions in Non-Small Cell Lung Cancer. Cancers (Basel) 2021; 13:cancers13010139. [PMID: 33406752 PMCID: PMC7796105 DOI: 10.3390/cancers13010139] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2020] [Revised: 12/28/2020] [Accepted: 01/02/2021] [Indexed: 02/07/2023] Open
Abstract
Gene fusions represent novel predictive biomarkers for advanced non-small cell lung cancer (NSCLC). In this study, we validated a narrow NGS gene panel able to cover therapeutically-relevant gene fusions and splicing events in advanced-stage NSCLC patients. To this aim, we first assessed minimal complementary DNA (cDNA) input and the limit of detection (LoD) in different cell lines. Then, to evaluate the feasibility of applying our panel to routine clinical samples, we retrospectively selected archived lung adenocarcinoma histological and cytological (cell blocks) samples. Overall, our SiRe RNA fusion panel was able to detect all fusions and a splicing event harbored in a RNA pool diluted up to 2 ng/µL. It also successfully analyzed 46 (95.8%) out of 48 samples. Among these, 43 (93.5%) out of 46 samples reproduced the same results as those obtained with conventional techniques. Intriguingly, the three discordant results were confirmed by a CE-IVD automated real-time polymerase chain reaction (RT-PCR) analysis (Easy PGX platform, Diatech Pharmacogenetics, Jesi, Italy). Based on these findings, we conclude that our new SiRe RNA fusion panel is a valid and robust tool for the detection of clinically relevant gene fusions and splicing events in advanced NSCLC.
Collapse
Affiliation(s)
- Caterina De Luca
- Department of Public Health, University of Naples Federico II, 80131 Naples, Italy; (C.D.L.); (F.P.); (A.I.); (P.P.); (L.G.); (G.G.); (R.S.); (M.N.); (F.C.); (E.V.); (C.B.); (U.M.)
| | - Francesco Pepe
- Department of Public Health, University of Naples Federico II, 80131 Naples, Italy; (C.D.L.); (F.P.); (A.I.); (P.P.); (L.G.); (G.G.); (R.S.); (M.N.); (F.C.); (E.V.); (C.B.); (U.M.)
| | - Antonino Iaccarino
- Department of Public Health, University of Naples Federico II, 80131 Naples, Italy; (C.D.L.); (F.P.); (A.I.); (P.P.); (L.G.); (G.G.); (R.S.); (M.N.); (F.C.); (E.V.); (C.B.); (U.M.)
| | - Pasquale Pisapia
- Department of Public Health, University of Naples Federico II, 80131 Naples, Italy; (C.D.L.); (F.P.); (A.I.); (P.P.); (L.G.); (G.G.); (R.S.); (M.N.); (F.C.); (E.V.); (C.B.); (U.M.)
| | - Luisella Righi
- Department of Oncology, San Luigi University Hospital, University of Turin, 10043 Orbassano, Italy; (L.R.); (A.L.)
| | - Angela Listì
- Department of Oncology, San Luigi University Hospital, University of Turin, 10043 Orbassano, Italy; (L.R.); (A.L.)
| | - Lorenza Greco
- Department of Public Health, University of Naples Federico II, 80131 Naples, Italy; (C.D.L.); (F.P.); (A.I.); (P.P.); (L.G.); (G.G.); (R.S.); (M.N.); (F.C.); (E.V.); (C.B.); (U.M.)
| | - Gianluca Gragnano
- Department of Public Health, University of Naples Federico II, 80131 Naples, Italy; (C.D.L.); (F.P.); (A.I.); (P.P.); (L.G.); (G.G.); (R.S.); (M.N.); (F.C.); (E.V.); (C.B.); (U.M.)
| | - Severo Campione
- Anatomic Pathology, A.O.R.N. Antonio Cardarelli, 80131 Naples, Italy; (S.C.); (G.D.D.); (S.N.)
| | - Gianfranco De Dominicis
- Anatomic Pathology, A.O.R.N. Antonio Cardarelli, 80131 Naples, Italy; (S.C.); (G.D.D.); (S.N.)
| | - Fabio Pagni
- Department of Medicine and Surgery, San Gerardo Hospital, University of Milano-Bicocca, 20900 Monza, Italy; (F.P.); (D.L.C.)
| | - Roberta Sgariglia
- Department of Public Health, University of Naples Federico II, 80131 Naples, Italy; (C.D.L.); (F.P.); (A.I.); (P.P.); (L.G.); (G.G.); (R.S.); (M.N.); (F.C.); (E.V.); (C.B.); (U.M.)
| | - Mariantonia Nacchio
- Department of Public Health, University of Naples Federico II, 80131 Naples, Italy; (C.D.L.); (F.P.); (A.I.); (P.P.); (L.G.); (G.G.); (R.S.); (M.N.); (F.C.); (E.V.); (C.B.); (U.M.)
| | - Rossella Tufano
- CEINGE Biotecnologie Avanzate, Via Gaetano Salvatore 486, 80131 Naples, Italy;
| | - Floriana Conticelli
- Department of Public Health, University of Naples Federico II, 80131 Naples, Italy; (C.D.L.); (F.P.); (A.I.); (P.P.); (L.G.); (G.G.); (R.S.); (M.N.); (F.C.); (E.V.); (C.B.); (U.M.)
| | - Elena Vigliar
- Department of Public Health, University of Naples Federico II, 80131 Naples, Italy; (C.D.L.); (F.P.); (A.I.); (P.P.); (L.G.); (G.G.); (R.S.); (M.N.); (F.C.); (E.V.); (C.B.); (U.M.)
| | - Claudio Bellevicine
- Department of Public Health, University of Naples Federico II, 80131 Naples, Italy; (C.D.L.); (F.P.); (A.I.); (P.P.); (L.G.); (G.G.); (R.S.); (M.N.); (F.C.); (E.V.); (C.B.); (U.M.)
| | - Diego Luigi Cortinovis
- Department of Medicine and Surgery, San Gerardo Hospital, University of Milano-Bicocca, 20900 Monza, Italy; (F.P.); (D.L.C.)
| | - Silvia Novello
- Anatomic Pathology, A.O.R.N. Antonio Cardarelli, 80131 Naples, Italy; (S.C.); (G.D.D.); (S.N.)
| | | | - Rafael Rosell
- Cancer Biology and Precision Medicine Program Catalan Institute of Oncology, Germans Trias i Pujol Health Sciences Institute and Hospital Badalona, 08916 Barcelona, Spain;
| | - Giancarlo Troncone
- Department of Public Health, University of Naples Federico II, 80131 Naples, Italy; (C.D.L.); (F.P.); (A.I.); (P.P.); (L.G.); (G.G.); (R.S.); (M.N.); (F.C.); (E.V.); (C.B.); (U.M.)
- Correspondence: ; Fax: +39-(011)-0817-463-679
| | - Umberto Malapelle
- Department of Public Health, University of Naples Federico II, 80131 Naples, Italy; (C.D.L.); (F.P.); (A.I.); (P.P.); (L.G.); (G.G.); (R.S.); (M.N.); (F.C.); (E.V.); (C.B.); (U.M.)
| |
Collapse
|
15
|
Kumar M, Kumar K, Singh HP, Nair S, Patel A, Kumar A, Soni S. Discordance between Fluorescence In Situ Hybridization and Immunohistochemistry Analysis of Anaplastic Lymphoma Kinase Rearrangement in Indian Patients with Non-Small Cell Lung Cancer. South Asian J Cancer 2020; 9:109-114. [PMID: 33354554 PMCID: PMC7745737 DOI: 10.1055/s-0040-1721191] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022] Open
Abstract
Aims This study aims to evaluate the incidence of anaplastic lymphoma kinase (ALK) mutation in nonsmall cell lung cancer (NSCLC) incorporating fluorescence in situ hybridization (FISH) and immunohistochemistry (IHC) methods and to look for any discordance. Methods We evaluated 101 samples obtained from an enriched cohort of NSCLCs patients from the Army Hospital Research and Referral, New Delhi, India, between November 2016 and November 2018. IHC was performed using the highly-sensitive D5F3 rabbit monoclonal primary antibody. FISH was performed with dual-color, break-apart probe (ZytoLight SPEC) on formalin-fixed, and paraffin-embedded tissue. Discordance between IHC and FISH for ALK rearrangements was evaluated. Pearson correlation coefficient ( r ) was performed to identify any association of ALK presence (by IHC and FISH) with smoking brain metastasis, programmed death-ligand (PD-L1) expression, pleural effusion, and histopathological subtype. Results A total of 7.92% (8/101) cases tested by IHC and 9.9% (10/101) cases tested by FISH were positive for ALK rearrangement. Of 93 ALK IHC-negative cases, 4 were ALK FISH-positive, whereas of 91 ALK FISH-negative cases, 4 were ALK IHC-positive cases. The correlation analysis demonstrated no or very weak correlation in ALK mutations by IHC or FISH with smoking, brain metastasis, PD-L1 expression, pleural effusion, and histopathological examination, except a weak positive correlation ( r = 0.33) observed between brain metastasis and ALK rearrangement identified by FISH. Conclusions Our study demonstrated a somewhat similar incidence of ALK FISH-positive cases and ALK IHC-positive cases, though the incidence was numerically higher for ALK-FISH method.
Collapse
Affiliation(s)
- Manish Kumar
- Department of Medical Oncology, Army Hospital Research and Referral, New Delhi, India
| | - Kishore Kumar
- Department of Medical Oncology, Command Hospital Air Force, Bengaluru, Karnataka, India
| | - Harinder Pal Singh
- Department of Medical Oncology, Army Hospital Research and Referral, New Delhi, India
| | - Suresh Nair
- Department of Medical Oncology, Army Hospital Research and Referral, New Delhi, India
| | - Amol Patel
- Department of Medical Oncology, Army Hospital Research and Referral, New Delhi, India
| | - Ashok Kumar
- Department of Radiation Oncology, Army Hospital Research and Referral, New Delhi, India
| | - Sneha Soni
- Community Medicine, Rama Medical College, Hapur, Uttar Pradesh, India
| |
Collapse
|
16
|
Strong ALK and PD-L1 positive IHC expression related ALK amplification in an advanced lung sarcomatoid carcinoma: A therapeutic trap? Lung Cancer 2020; 152:94-97. [PMID: 33360808 DOI: 10.1016/j.lungcan.2020.12.022] [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: 11/12/2020] [Revised: 12/06/2020] [Accepted: 12/15/2020] [Indexed: 11/23/2022]
Abstract
OBJECTIVES Immunohistochemistry (IHC) is considered as a screening method for ALK rearrangement thanks to its excellent sensitivity. Strong marking on immunohistochemistry give the go-ahead to start ALK tyrosine kinase inhibitors (ALK TKI). Lack of therapeutic response may then lead to the suspicion of molecular alterations other than ALK rearrangements. METHODS We present a patient with strong ALK and PD-L1 positive IHC expression lung sarcomatoid carcinoma with initial life-threatening disease progression after beginning ALK TKI. We also review the literature to summarize ALK amplification clinical features and therapeutic management in lung cancers. RESULTS Fluorescence in situ Hybridization (FISH) revealed ALK amplification on the initial anatomopathological samples. Lack of ALK rearrangement and strong PD-L1 positive IHC expression led to the initiation of immune checkpoint inhibitor (ICI) as a second line of treatment, with an excellent response. CONCLUSION We demonstrated that IHC positive test, in these cases, must be interpreted with caution. FISH analysis has to be recommended to confirm IHC results in case of unusual phenotype, such as smoker or lung cancer other than adenocarcinoma. Although lung carcinoma with ALK rearrangement seems to be not sensitive to ICI, further investigations should be conducted on other types of ALK molecular alterations. ALK amplifications, as observed in the present case, should not be an impediment to taking into account the PD-L1 marking for the initiation of treatment by immunotherapy.
Collapse
|
17
|
Kastnerova L, Martinek P, Grossmann P, Steiner P, Vanecek T, Kyclova J, Ferak I, Zalud R, Slehobr O, Svajdler P, Sulc M, Bradamante M, Banik M, Hadravsky L, Sticova E, Hajkova V, Ptakova N, Michal M, Kazakov DV. A Clinicopathological Study of 29 Spitzoid Melanocytic Lesions With ALK Fusions, Including Novel Fusion Variants, Accompanied by Fluorescence In Situ Hybridization Analysis for Chromosomal Copy Number Changes, and Both TERT Promoter and Next-Generation Sequencing Mutation Analysis. Am J Dermatopathol 2020; 42:578-592. [PMID: 32701692 DOI: 10.1097/dad.0000000000001632] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
ALK-fused spitzoid neoplasms represent a distinctive group of melanocytic lesions. To date, few studies addressed genetic and chromosomal alterations in these lesions beyond the ALK rearrangements. Our objective was to study genetic alterations, including ALK gene fusions, telomerase reverse transcriptase promoter (TERT-p) mutations, chromosomal copy number changes, and mutations in other genes. We investigated 29 cases of Spitz lesions (11 Spitz nevi and 18 atypical Spitz tumors), all of which were ALK immunopositive. There were 16 female and 13 male patients, with age ranging from 1 to 43 years (mean, 18.4 years). The most common location was the lower extremity. Microscopically, all neoplasms were polypoid or dome shaped with a plexiform, predominantly dermally located proliferation of fusiform to spindled melanocytes with mild to moderate pleomorphism. The break-apart test for ALK was positive in 17 of 19 studied cases. ALK fusions were detected in 23 of 26 analyzable cases by Archer FusionPlex Solid Tumor Kit. In addition to the previously described rearrangements, 3 novel fusions, namely, KANK1-ALK, MYO5A-ALK, and EEF2-ALK, were found. Fluorescence in situ hybridization for copy number changes yielded one case with the loss of RREB1 among 21 studied cases. TERT-p hotspot mutation was found in 1 of 23 lesions. The mutation analysis of 271 cancer-related genes using Human Comprehensive Cancer Panel was performed in 4 cases and identified in each case mutations in several genes with unknown significance, except for a pathogenic variant in the BLM gene. Our study confirms that most ALK fusion spitzoid neoplasms can be classified as atypical Spitz tumors, which occurs in young patients with acral predilection and extends the spectrum of ALK fusions in spitzoid lesions, including 3 hitherto unreported fusions. TERT-p mutations and chromosomal copy number changes involving 6p25 (RRB1), 11q13 (CCND1), 6p23 (MYB), 9p21 (CDKN2A), and 8q24 (MYC) are rare in these lesions. The significance of mutation in other genes remains unknown.
Collapse
Affiliation(s)
- Liubov Kastnerova
- Sikl's Department of Pathology, Medical Faculty in Pilsen, Charles University in Prague, Pilsen, Czech Republic
- Bioptical Laboratory, Pilsen, Czech Republic
| | - Petr Martinek
- Sikl's Department of Pathology, Medical Faculty in Pilsen, Charles University in Prague, Pilsen, Czech Republic
- Bioptical Laboratory, Pilsen, Czech Republic
| | - Petr Grossmann
- Sikl's Department of Pathology, Medical Faculty in Pilsen, Charles University in Prague, Pilsen, Czech Republic
- Bioptical Laboratory, Pilsen, Czech Republic
| | - Petr Steiner
- Sikl's Department of Pathology, Medical Faculty in Pilsen, Charles University in Prague, Pilsen, Czech Republic
- Bioptical Laboratory, Pilsen, Czech Republic
| | - Tomas Vanecek
- Sikl's Department of Pathology, Medical Faculty in Pilsen, Charles University in Prague, Pilsen, Czech Republic
- Bioptical Laboratory, Pilsen, Czech Republic
| | - Jitka Kyclova
- Department of Pathology, University Hospital, Brno, Czech Republic
| | - Ivan Ferak
- Agel Laboratory, Novy Jicin, Czech Republic
| | - Radim Zalud
- Department of Pathology, Regional Hospital, Kolin, Czech Republic
| | - Ondrej Slehobr
- Department of Pathology, Regional Hospital, Kolin, Czech Republic
| | - Peter Svajdler
- Department of Pathology, L. Pausteur University Hospital, Kosice, Czech Republic
| | - Miroslav Sulc
- Pathology Laboratory Chomutov, Chomutov, Czech Republic
| | | | - Martin Banik
- Department of Pathology, Regional Hospital, Karlovy Vary, Czech Republic
| | - Ladislav Hadravsky
- Department of Pathology, 1st Faculty of Medicine and General University Hospital, Charles University in Prague, Czech Republic; and
| | - Eva Sticova
- Clinical and Transplant Pathology Centre, Institute for Clinical and Experimental Medicine, Prague, Czech Republic
| | | | | | - Michal Michal
- Sikl's Department of Pathology, Medical Faculty in Pilsen, Charles University in Prague, Pilsen, Czech Republic
- Bioptical Laboratory, Pilsen, Czech Republic
| | - Dmitry V Kazakov
- Sikl's Department of Pathology, Medical Faculty in Pilsen, Charles University in Prague, Pilsen, Czech Republic
- Bioptical Laboratory, Pilsen, Czech Republic
| |
Collapse
|
18
|
Zeng L, Li Y, Xu Q, Jiang W, Lizaso A, Mao X, Zhang Y, Yang N, Wang Z. Comparison of Next-Generation Sequencing and Ventana Immunohistochemistry in Detecting ALK Rearrangements and Predicting the Efficacy of First-Line Crizotinib in Patients with Advanced Non-Small Cell Lung Cancer. Onco Targets Ther 2020; 13:7101-7109. [PMID: 32801744 PMCID: PMC7398878 DOI: 10.2147/ott.s265974] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2020] [Accepted: 07/09/2020] [Indexed: 01/17/2023] Open
Abstract
Introduction Reliable diagnostic approaches to detect ALK rearrangement are critical for selecting patients eligible for crizotinib therapy. This study aimed to compare next-generation sequencing (NGS) and Ventana immunohistochemistry (IHC) in evaluating ALK rearrangements and evaluate their impact on first-line crizotinib efficacy. Patients and Methods A total of 472 NSCLC patients were identified as ALK-positive by NGS and/or IHC between March 2014 and February 2020. The concordance of ALK detection, overall response rate (ORR), and progression-free survival (PFS) were analyzed for 319 patients who received front-line crizotinib. Results First-line crizotinib (n=319) significantly prolonged PFS in comparison with chemotherapy (n=46; 12.0 vs 6.8 months; p<0.0001). Of the 76 crizotinib-treated patients whose ALK status was assessed by both NGS and IHC, 78.9% of the patients had concordant ALK status (NGS-positive/IHC-positive), 18.4% patients were NGS-positive but IHC-negative, and 2 patients were IHC-positive but NGS-negative. Different detection assays confer no statistical difference in ORR and PFS with first-line crizotinib. The ORR in NGS only, IHC only, and both NGS and IHC was 84.3%, 90.1%, and 88.1%, respectively, while PFS was 11.4, 13.0, and 11.0 months, respectively. The ORR in NGS-positive/IHC-positive and NGS-positive/IHC-negative patients was 85.4% and 92.8%, respectively. Compared to NGS-positive/IHC-positive patients, those with NGS-positive/IHC-negative results had a trend of shorter PFS but statistical significance was not reached (mPFS, 5.9 months vs 11.5 months, p=0.43). Conclusion Our results demonstrate that ALK status detected by NGS and/or IHC is reliable in identifying patients with ALK-positive NSCLC who will benefit from ALK inhibitor therapy.
Collapse
Affiliation(s)
- Liang Zeng
- Department of Medical Oncology, The First Affiliated Hospital of Soochow University, Suzhou 215006, People's Republic of China.,Department of Medical Oncology, Lung Cancer and Gastrointestinal Unit, Hunan Cancer Hospital/The Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha 410013, People's Republic of China
| | - Yizhi Li
- Department of Medical Oncology, Lung Cancer and Gastrointestinal Unit, Hunan Cancer Hospital/The Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha 410013, People's Republic of China
| | - Qinqin Xu
- Department of Medical Oncology, Qinghai Provincial People's Hospital, Xining, People's Republic of China
| | - Wenjuan Jiang
- Department of Medical Oncology, Lung Cancer and Gastrointestinal Unit, Hunan Cancer Hospital/The Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha 410013, People's Republic of China
| | - Analyn Lizaso
- Department of Medical Affairs, Burning Rock Biotech, Guangzhou, 510300, People's Republic of China
| | - Xinru Mao
- Department of Medical Affairs, Burning Rock Biotech, Guangzhou, 510300, People's Republic of China
| | - Yongchang Zhang
- Department of Medical Oncology, Lung Cancer and Gastrointestinal Unit, Hunan Cancer Hospital/The Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha 410013, People's Republic of China
| | - Nong Yang
- Department of Medical Oncology, Lung Cancer and Gastrointestinal Unit, Hunan Cancer Hospital/The Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha 410013, People's Republic of China
| | - Zhenxing Wang
- Department of Medical Oncology, The First Affiliated Hospital of Soochow University, Suzhou 215006, People's Republic of China
| |
Collapse
|
19
|
Barua S, Wang G, Mansukhani M, Hsiao S, Fernandes H. Key considerations for comprehensive validation of an RNA fusion NGS panel. Pract Lab Med 2020; 21:e00173. [PMID: 32613069 PMCID: PMC7322345 DOI: 10.1016/j.plabm.2020.e00173] [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: 10/14/2019] [Revised: 04/19/2020] [Accepted: 05/28/2020] [Indexed: 12/28/2022] Open
Abstract
Objectives Validation of RNA-based NGS assays for the detection of therapeutically targetable gene fusions is challenging. Here, we report systematic validation and quality control monitoring of our targeted fusion panel for the detection of 17 clinically relevant fusion transcripts across several tumor types. We implemented this RNA Fusion Panel as a reflex test for tumors lacking DNA driver mutations. Design Forty-four formalin-fixed, paraffin-embedded (FFPE) or fresh-frozen lung, brain, soft tissue and skin tumors were used to determine the accuracy of the assay. Additional fusion-positive specimens and a calibrated reference standard were used to establish the precision, reproducibility and sensitivity of the assay. All aspects of the validation, including quality control metrics, were performed according to New York State guidelines. Results For the RNA fusion panel, accuracy, reproducibility and precision studies were above 99%. Reproducibility and sensitivity studies with the reference standard were helpful in identifying inconsistencies. The limit of detection for most RNA fusion transcripts was 50 copies. Application of the RNA fusion assay as a reflex test to 450 tumor samples lacking DNA driver mutations resulted in a 10% increase in diagnostic yield with minimal additional processing time. Conclusions The validated RNA fusion panel provides clinical utility in therapy selection for patients with solid tumors. By using a sequential testing approach, the RNA fusion assay complements the DNA hotspot assay in identifying clinically relevant variants across many tumor types with minimal additional increase in processing time. RNA fusion NGS panel uses anchored multiplex PCR to detect known and novel fusions. Pre- and post-sequencing quality control increases accuracy of results. Sequential testing of RNA, on samples without DNA variants is practical and cost-effective. Detection of novel RNA fusions expands the therapeutic landscape of tumors.
Collapse
Affiliation(s)
- Subit Barua
- Department of Pathology and Cell Biology, Columbia University Medical Center, New York, USA
| | - Gary Wang
- Department of Pathology and Cell Biology, Columbia University Medical Center, New York, USA
| | - Mahesh Mansukhani
- Department of Pathology and Cell Biology, Columbia University Medical Center, New York, USA
| | - Susan Hsiao
- Department of Pathology and Cell Biology, Columbia University Medical Center, New York, USA
| | - Helen Fernandes
- Department of Pathology and Cell Biology, Columbia University Medical Center, New York, USA
| |
Collapse
|
20
|
|
21
|
Peng R, Zhang R, Zhang J, Tan P, Han Y, Zhang K, Lin G, Xie J, Li J. Continual Improvement of the Reliability of EML4-ALK Rearrangement Detection in Non-Small-Cell Lung Cancer: A Long-Term Comparison of ALK Detection in China. J Mol Diagn 2020; 22:876-884. [PMID: 32302779 DOI: 10.1016/j.jmoldx.2020.03.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2019] [Revised: 10/24/2019] [Accepted: 03/30/2020] [Indexed: 12/01/2022] Open
Abstract
The results of EML4-ALK testing are critical to manage ALK tyrosine kinase receptor inhibitor treatment. Thus, the accurate detection of ALK rearrangement is increasingly becoming a matter of serious concern. To address this issue, a long-term EML4-ALK proficiency testing (PT) scheme was launched in China in 2015, serving as an educational tool for assessing and improving the testing quality of EML4-ALK fusion detection. Responses across 20 different PT samples interrogating three different variants and wild-type samples were collected between 2015 and 2019. Performance was analyzed by evaluating the detection methods, kits, and pre-analytic practices used to further display the landscape of changing conditions of the reliability of EML4-ALK testing. During the 5 years, 3224 results reported from 988 laboratories were evaluated, with an overall error rate of 5.36%. Along with an increasing number of participating laboratories, the error rate within each of the different methods showed a significantly downward trend over the years. No obvious differences in the error rates were found regarding the testing methods or kit manufacturers. Moreover, the individual performance of the laboratories improved when they participated in more PT scheme rounds. The data demonstrated that the performance of individual Chinese laboratories for EML4-ALK testing continuously improved over time by participating PT schemes, regardless of their method. However, care must be taken in standardized operations and validations.
Collapse
Affiliation(s)
- Rongxue Peng
- National Center for Clinical Laboratories, Beijing Hospital, National Center of Gerontology, Beijing, China; Beijing Engineering Research Center of Laboratory Medicine, Beijing Hospital, Beijing, China
| | - Rui Zhang
- National Center for Clinical Laboratories, Beijing Hospital, National Center of Gerontology, Beijing, China; Beijing Engineering Research Center of Laboratory Medicine, Beijing Hospital, Beijing, China
| | - Jiawei Zhang
- National Center for Clinical Laboratories, Beijing Hospital, National Center of Gerontology, Beijing, China; Beijing Engineering Research Center of Laboratory Medicine, Beijing Hospital, Beijing, China; Graduate School, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, China
| | - Ping Tan
- National Center for Clinical Laboratories, Beijing Hospital, National Center of Gerontology, Beijing, China; Beijing Engineering Research Center of Laboratory Medicine, Beijing Hospital, Beijing, China; Graduate School, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, China
| | - Yanxi Han
- National Center for Clinical Laboratories, Beijing Hospital, National Center of Gerontology, Beijing, China; Beijing Engineering Research Center of Laboratory Medicine, Beijing Hospital, Beijing, China
| | - Kuo Zhang
- National Center for Clinical Laboratories, Beijing Hospital, National Center of Gerontology, Beijing, China; Beijing Engineering Research Center of Laboratory Medicine, Beijing Hospital, Beijing, China
| | - Guigao Lin
- National Center for Clinical Laboratories, Beijing Hospital, National Center of Gerontology, Beijing, China; Beijing Engineering Research Center of Laboratory Medicine, Beijing Hospital, Beijing, China
| | - Jiehong Xie
- National Center for Clinical Laboratories, Beijing Hospital, National Center of Gerontology, Beijing, China; Beijing Engineering Research Center of Laboratory Medicine, Beijing Hospital, Beijing, China
| | - Jinming Li
- National Center for Clinical Laboratories, Beijing Hospital, National Center of Gerontology, Beijing, China; Beijing Engineering Research Center of Laboratory Medicine, Beijing Hospital, Beijing, China; Graduate School, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, China.
| |
Collapse
|
22
|
Brisudova A, Skarda J. Gene rearrangement detection by next-generation sequencing in patients with non-small cell lung carcinoma. Biomed Pap Med Fac Univ Palacky Olomouc Czech Repub 2020; 164:127-132. [PMID: 32284620 DOI: 10.5507/bp.2020.015] [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: 11/11/2019] [Accepted: 03/19/2020] [Indexed: 11/23/2022] Open
Abstract
Non-small cell lung carcinoma (NSCLC) is the leading cause of cancer-related deaths worldwide. Various molecular markers in NSCLC patients have been developed, including gene rearrangements, currently used in therapeutic strategies. With increasing number of these molecular biomarkers of NSCLC, there is a demand for highly efficient methods for detecting mutations and translocations in treatable targets. Those currently available U.S. Food and Drug Administration (FDA) approved approaches, for example imunohistochemisty (IHC) and fluorescence in situ hybridization (FISH), are inadequate, due to sufficient quantity of material and long time duration. Next-generation massive parallel sequencing (NGS), with the ability to perform and capture data from millions of sequencing reactions simultaneously could resolve the problem. Thanks to gradual NGS introduction into clinical laboratories, screening time should be considerably shorter, which is very important for patients with advanced NSCLC. Moreover, only a minimum sample input is needed for achieving adequate results. NGS was compared to the current detection methods of ALK, ROS1, c-RET and c-MET rearrangements in NSCLC and a significant match, between IHC, FISH and NGS results, was found. Recent available researches have been carried out on a small numbers of patients. Verifying these results on larger patients cohort is important. This review sumarizes the literature on this subject and compares current possibilities of predictive gene rearrangements detection in patients with NSCLC.
Collapse
Affiliation(s)
- Aneta Brisudova
- Department of Clinical and Molecular Pathology, Faculty of Medicine and Dentistry, Palacky University Olomouc, Czech Republic
| | - Jozef Skarda
- Department of Clinical and Molecular Pathology, Faculty of Medicine and Dentistry, Palacky University Olomouc, Czech Republic
| |
Collapse
|
23
|
Smuk G, Pajor G, Szuhai K, Morreau H, Kocsmár I, Kocsmár É, Pajor L, Kajtár B, Sárosi V, Lotz G, Tornóczky T. Attenuated isolated 3' signal: A highly challenging therapy relevant ALK FISH pattern in NSCLC. Lung Cancer 2020; 143:80-85. [PMID: 32272316 DOI: 10.1016/j.lungcan.2020.03.007] [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: 10/12/2019] [Revised: 01/14/2020] [Accepted: 03/08/2020] [Indexed: 11/17/2022]
Abstract
OBJECTIVES Targeted therapies in the management of patients with lung cancer provide significantly better outcome compared to chemotherapy. Detection of the anaplastic lymphoma kinase (ALK) gene rearrangement has great predictive value for treatment with small molecule tyrosine kinase inhibitor (crizotinib and alectinib commonly). Fluorescent in situ hybridisation (FISH) assay is a basic diagnostic test designed for detecting ALK gene rearrangements. Although being considered as gold standard method by IASLC's guideline, it is often regarded as difficult and error prone. Our aim was to examine a unique atypical ALK FISH pattern, revealed during a systematic large-scale monitoring, which carries the great risk of misinterpretation, hence may result in loss of patients eligible for targeted therapy. MATERIALS AND METHODS Tissue and cytology samples from nearly one thousand patients with advanced stage non-small cell lung cancer (NSCLC, n = 996) were routinely examined by ALK FISH and immunohistochemistry (Ventana ALK-D5F3-CDx assay). Anchored Multiplex PCR based Next Generation Sequencing (AMP-NGS) was used to detect fusion gene transcripts in ambiguous cases. RESULTS Fifty-nine (5,9%) of the cases were positive with ALK FISH test. Three cases showed atypical pattern with a significantly reduced sized red (3') signal and complete loss of green signals. Digital signal measurement confirmed this finding, showing consistent attenuation of 3' signals throughout the tumours. In all three cases AMP-NGS and ALK IHC verified the presence of a fusion gene and expressed oncoprotein, respectively. CONCLUSION Approximately 5% of the 59 ALK positive cases exhibited atypical attenuated isolated 3' signal pattern. The immunohistochemistry and AMP-NGS examinations helped to clarify the presence of oncoprotein and the fusion gene, respectively. Our results emphasize the importance of extensive exploration of the genetic background of any unexpected FISH finding to avoid false diagnosis. This enables clinicians to indicate the adequate therapy with higher efficiency for patients suffering from NSCLC.
Collapse
Affiliation(s)
- Gábor Smuk
- Department of Pathology, Medical School and Clinical Center, University of Pécs, Hungary
| | - Gábor Pajor
- Department of Pathology, Medical School and Clinical Center, University of Pécs, Hungary
| | - Károly Szuhai
- Department of Cell and Chemical Biology, Leiden University Medical Center, Netherlands
| | - Hans Morreau
- Department of Pathology, Leiden University Medical Center, Netherlands
| | - Ildikó Kocsmár
- 2nd Department of Pathology, Faculty of Medicine, Semmelweis University, Hungary
| | - Éva Kocsmár
- 2nd Department of Pathology, Faculty of Medicine, Semmelweis University, Hungary
| | - László Pajor
- Department of Pathology, Medical School and Clinical Center, University of Pécs, Hungary
| | - Béla Kajtár
- Department of Pathology, Medical School and Clinical Center, University of Pécs, Hungary
| | - Veronika Sárosi
- 1st Department of Internal Medicine, Medical School and Clinical Center, University of Pécs, Hungary
| | - Gábor Lotz
- 2nd Department of Pathology, Faculty of Medicine, Semmelweis University, Hungary
| | - Tamás Tornóczky
- Department of Pathology, Medical School and Clinical Center, University of Pécs, Hungary.
| |
Collapse
|
24
|
Canale M, Pasini L, Bronte G, Delmonte A, Cravero P, Crinò L, Ulivi P. Role of liquid biopsy in oncogene-addicted non-small cell lung cancer. Transl Lung Cancer Res 2019; 8:S265-S279. [PMID: 31857950 DOI: 10.21037/tlcr.2019.09.15] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
The discovery of actionable oncogene in non-small cell lung cancer (NSCLC) allowed the identification of a subgroup of patients who benefit from targeted tyrosine kinase inhibitors more than others. Mutations in the epidermal growth factor receptor (EGFR), translocations in the anaplastic lymphoma kinase (ALK) and rearrangements in the ROS proto-oncogene 1 (ROS1) must be identified in tumor tissue to guide the proper treatment choice. Liquid biopsy is based on the analysis of tumor materials released in the circulation. Liquid biopsy can be complementary to tissue biopsy, both at baseline and at progression, especially in the detection of somatic gene alterations emerging during the treatment with tyrosine kinase inhibitors (TKIs). Particularly, circulating DNA is used to find mutations in driver oncogenes, while circulating tumor cells, extracellular vesicles (EVs) and cell-free microRNAs (cfmiRNAs) are still under investigation. To help the unbiased use of liquid biopsy in the choice of the appropriate therapy, some recommendations were delivered by expert panels. Currently, analysis of EGFR mutations in cell-free DNA (cfDNA) is recommended at baseline when tissue biopsy harbors scarce tumor cells, and at progression before performing tissue biopsy; liquid biopsy analysis for other oncogenic drivers is not indicated in the clinical practice.
Collapse
Affiliation(s)
- Matteo Canale
- Biosciences Laboratory, Istituto Scientifico Romagnolo per lo Studio e la Cura dei Tumori (IRST) IRCCS, Meldola, Italy
| | - Luigi Pasini
- Biosciences Laboratory, Istituto Scientifico Romagnolo per lo Studio e la Cura dei Tumori (IRST) IRCCS, Meldola, Italy
| | - Giuseppe Bronte
- Department of Medical Oncology, Istituto Scientifico Romagnolo per lo Studio e la Cura dei Tumori (IRST) IRCCS, Meldola, Italy
| | - Angelo Delmonte
- Department of Medical Oncology, Istituto Scientifico Romagnolo per lo Studio e la Cura dei Tumori (IRST) IRCCS, Meldola, Italy
| | - Paola Cravero
- Department of Medical Oncology, Istituto Scientifico Romagnolo per lo Studio e la Cura dei Tumori (IRST) IRCCS, Meldola, Italy
| | - Lucio Crinò
- Department of Medical Oncology, Istituto Scientifico Romagnolo per lo Studio e la Cura dei Tumori (IRST) IRCCS, Meldola, Italy
| | - Paola Ulivi
- Biosciences Laboratory, Istituto Scientifico Romagnolo per lo Studio e la Cura dei Tumori (IRST) IRCCS, Meldola, Italy
| |
Collapse
|
25
|
Guyard A, Charpy C, Théou-Anton N, Cremades A, Grassin F, Bourgogne A, Leroy K, Pujals A, Copie-Bergman C, Chouaid C, Mansuet-Lupo A. Isolated 5' Signals Are an Atypical Pattern To Be Considered as Positive for ALK Rearrangement: A Brief Report of Three Cases and Review of the Literature. Transl Oncol 2019; 12:784-787. [PMID: 30909092 PMCID: PMC6434406 DOI: 10.1016/j.tranon.2019.02.015] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2019] [Revised: 02/21/2019] [Accepted: 02/21/2019] [Indexed: 12/01/2022] Open
Abstract
Anaplastic lymphoma kinase (ALK) rearrangement is reported in 3% to 8% of patients with lung adenocarcinoma and can be detected by fluorescent in situ hybridization (FISH) or indirectly by immunohistochemistry. In FISH assay, isolated 5′ signal (loss of 3′ signal) is usually considered negative. We report three young nonsmoking patients with stage IV lung adenocarcinoma. Strong ALK expression in tumor cells detected by immunohistochemistry was observed in all cases, but FISH revealed an isolated 5′ signal pattern. Massive parallel “next-generation” sequencing was performed in two patients and confirmed ALK rearrangement. The three patients were treated and responded to crizotinib after 14, 10, and 31 months.
Collapse
Affiliation(s)
- Alice Guyard
- Department of Pathology, HUPC, Hôpital Cochin, Assistance Publique-Hôpitaux de Paris, Paris 75014, France
| | - Cécile Charpy
- Department of Pathology, Hôpital Henri Mondor, Assistance Publique-Hôpitaux de Paris, 94010, Créteil, France
| | - Nathalie Théou-Anton
- Department of Genetic, Hôpital Bichat-Claude Bernard, Assistance Publique-Hôpitaux de Paris, 75877, Paris, France
| | - Anne Cremades
- Department of Pathology, Hôpital Bégin, 94160, Saint Mandé, France
| | | | - Anaïs Bourgogne
- Department of Pathology, Centre Intercommunal de Créteil, 94000 Créteil, France
| | - Karen Leroy
- Department of Genetic and Molecular Biology, HUPC, Hôpital Cochin, Assistance Publique-Hôpitaux de Paris, Paris 75014, France
| | - Anaïs Pujals
- Department of Pathology, Hôpital Henri Mondor, Assistance Publique-Hôpitaux de Paris, 94010, Créteil, France
| | - Christiane Copie-Bergman
- Department of Pathology, Hôpital Henri Mondor, Assistance Publique-Hôpitaux de Paris, 94010, Créteil, France
| | - Christos Chouaid
- Department of Pneumology, Centre Intercommunal de Créteil, 94000 Créteil, France
| | - Audrey Mansuet-Lupo
- Department of Pathology, HUPC, Hôpital Cochin, Assistance Publique-Hôpitaux de Paris, Paris 75014, France.
| |
Collapse
|