1
|
Diks J, Tang Z, Altan M, Anderson S, Chen H, Rashid A, Yang RK, Routbort MJ, Patel KP, Toruner GA, Medeiros LJ, Tang G, Luthra R, Roy-Chowdhuri S. Detection of clinically actionable gene fusions by next-generation sequencing-based RNA sequencing of non-small cell lung cancer cytology specimens: A single-center experience with comparison to fluorescence in situ hybridization. Cancer Cytopathol 2024; 132:41-49. [PMID: 37747438 DOI: 10.1002/cncy.22766] [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: 07/18/2023] [Revised: 08/13/2023] [Accepted: 08/14/2023] [Indexed: 09/26/2023]
Abstract
BACKGROUND Genomic profiling is needed to identify actionable alterations in non-small cell lung cancer (NSCLC). Panel-based testing such as next-generation sequencing (NGS) is often preferred to interrogate multiple alterations simultaneously. In this study, we evaluate the utility of an RNA-based NGS assay to detect genomic alterations in NSCLC cytology specimens and compare these results to fluorescence in situ hybridization (FISH) testing. METHODS A retrospective review was performed of 264 NSCLC cytology specimens that were concurrently tested for gene fusions by RNA-based NGS and ALK, RET, and/or ROS1 by FISH. RESULTS Genomic alterations were detected in 29 cases by NGS, including ALK, RET, ROS1, NTRK, NUTM1, and FGFR3 fusions and MET exon 14 skipping alterations. Of the 20 cases with ALK, RET, and ROS1 fusions detected by NGS, 16 (80%) were concordant with the corresponding FISH results. Three cases showed discordance, where EML4::ALK (n = 2) and SLC34A2::ROS1 (n = 1) fusions were not detected by the corresponding FISH assay; one case with EZR::ROS1 was inadequate for FISH. No gene fusions were detected in 181 cases by NGS and 54 cases failed testing. The concordance rates for detecting ALK, RET, and ROS1 fusions using NGS and FISH were 97%, 100%, and 99.5%, respectively. CONCLUSION RNA-based NGS can be used to detect gene fusions in NSCLC cytology cases with high concordance with FISH results. However, RNA-based NGS may have high failure rates and therefore a low threshold for reflexing inadequate cases to an orthogonal testing method is essential for comprehensive genomic profiling.
Collapse
Affiliation(s)
- John Diks
- Department of Pathology, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Zhenya Tang
- Department of Hematopathology, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Mehmet Altan
- Department of Thoracic/Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Sarah Anderson
- Department of Thoracic/Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Hui Chen
- Department of Pathology, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Asif Rashid
- Department of Pathology, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Richard Kenneth Yang
- Department of Pathology, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Mark J Routbort
- Department of Hematopathology, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Keyur P Patel
- Department of Hematopathology, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Gokce A Toruner
- Department of Hematopathology, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - L Jeffrey Medeiros
- Department of Hematopathology, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Guilin Tang
- Department of Hematopathology, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Rajyalakshmi Luthra
- Department of Hematopathology, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Sinchita Roy-Chowdhuri
- Department of Pathology, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| |
Collapse
|
2
|
Brenner C, Sanders C, Vokuhl C. [Receptor tyrosine kinase- fusions in paediatric spindle cell tumors]. PATHOLOGIE (HEIDELBERG, GERMANY) 2023; 44:357-365. [PMID: 37819532 DOI: 10.1007/s00292-023-01228-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 08/17/2023] [Indexed: 10/13/2023]
Abstract
Pediatric spindle cell tumors are rare and often difficult to diagnose due to a similar morphology and a non-specific immunohistochemical profile. Genetic characterization of these lesions has been constantly improving, which has led to the identification of new subgroups that were partly included in the WHO classification. Receptor tyrosine kinase fusions play a special role in these tumors and their verification has diagnostic relevance and can be an option for target-oriented therapies. In the case of pediatric spindle cell tumors, genetic fusions form especially with NTRK1‑3, ALK, RET, and ROS1. Overall, pediatric tumors with receptor tyrosine kinase fusions are predominantly low-grade tumors, which are often subdivided into the group of intermediate-malign tumors.
Collapse
Affiliation(s)
- Christiane Brenner
- Sektion Kinderpathologie, Institut für Pathologie, Universitätsklinikum Bonn, Venusberg-Campus 1, 53127, Bonn, Deutschland.
| | - Christine Sanders
- Institut für Pathologie, Universitätsklinikum Bonn, Bonn, Deutschland
| | - Christian Vokuhl
- Sektion Kinderpathologie, Institut für Pathologie, Universitätsklinikum Bonn, Venusberg-Campus 1, 53127, Bonn, Deutschland
| |
Collapse
|
3
|
Toruner GA. Low level ALK FISH positive results should be approached with caution and confirmed by an orthogonal method. Transl Lung Cancer Res 2023; 12:1361-1363. [PMID: 37577303 PMCID: PMC10413031 DOI: 10.21037/tlcr-23-265] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2023] [Accepted: 05/30/2023] [Indexed: 08/15/2023]
|
4
|
Wei S, Talarchek JN, Huang M, Gong Y, Du F, Ehya H, Flieder DB, Patchefsky AS, Wasik MA, Pei J. Cell block-based RNA next generation sequencing for detection of gene fusions in lung adenocarcinoma: An institutional experience. Cytopathology 2023; 34:28-34. [PMID: 36062384 DOI: 10.1111/cyt.13175] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2022] [Revised: 08/23/2022] [Accepted: 08/31/2022] [Indexed: 12/14/2022]
Abstract
OBJECTIVE Targeted therapy is an important part of the treatment of lung adenocarcinoma. Tests for EGFR mutation, ALK, ROS1, RET and NTRK gene fusions are needed to make a treatment decision. These gene fusions are traditionally detected by fluorescence in situ hybridisation (FISH) or immunohistochemistry. In this study, we investigated whether gene fusions in pulmonary adenocarcinoma could be accurately detected by RNA next-generation sequencing (RNA-NGS) and whether cytology cell blocks could be used effectively for this test. METHODS Archived cytological specimens of lung adenocarcinoma submitted for RNA sequencing between 2019 and 2022 at Fox Chase Cancer Center were retrospectively retrieved. Hybrid capture-based targeted RNA next generation sequencing was used, which covers 507 fusion genes, including ALK, ROS1, RET and NTRKs, irrespective of their partner genes. DNA NGS, FISH and chromosomal microarray analysis were used to confirm the results of the RNA-NGS. RESULTS A total of 129 lung adenocarcinoma cytology specimens were submitted for molecular testing. Eight of 129 (6.2%) cases were excluded from RNA sequencing as their cell blocks contained inadequate numbers of tumour cells. One case (0.8%) failed to yield adequate RNA. The overall success rate was 93% (120/129). Ten of 120 (8.3%) cytology cases were positive for gene fusions, including 7 ALK, 2 ROS1 fusion genes, and 1 RET fusion gene. Twenty-two cell block cases were also tested for ALK fusion genes using FISH. However, 11 of 22 (50%) failed the testing due to inadequate material. CONCLUSIONS Cytology cell blocks can be used as the main source of material for molecular testing for lung cancer. Detection of gene fusions by RNA-based NGS on cell blocks is convenient and reliable in daily practice.
Collapse
Affiliation(s)
- Shuanzeng Wei
- Department of Pathology, Fox Chase Cancer Center, Philadelphia, Pennsylvania, USA
| | | | - Min Huang
- Department of Pathology, Fox Chase Cancer Center, Philadelphia, Pennsylvania, USA
| | - Yulan Gong
- Department of Pathology, Fox Chase Cancer Center, Philadelphia, Pennsylvania, USA
| | - Fang Du
- Department of Pathology, Fox Chase Cancer Center, Philadelphia, Pennsylvania, USA
| | - Hormoz Ehya
- Department of Pathology, Fox Chase Cancer Center, Philadelphia, Pennsylvania, USA
| | - Douglas B Flieder
- Department of Pathology, Fox Chase Cancer Center, Philadelphia, Pennsylvania, USA
| | - Arthur S Patchefsky
- Department of Pathology, Fox Chase Cancer Center, Philadelphia, Pennsylvania, USA
| | - Mariusz A Wasik
- Department of Pathology, Fox Chase Cancer Center, Philadelphia, Pennsylvania, USA
| | - Jianming Pei
- Department of Pathology, Fox Chase Cancer Center, Philadelphia, Pennsylvania, USA
| |
Collapse
|
5
|
Athanasopoulou K, Daneva GN, Boti MA, Dimitroulis G, Adamopoulos PG, Scorilas A. The Transition from Cancer "omics" to "epi-omics" through Next- and Third-Generation Sequencing. LIFE (BASEL, SWITZERLAND) 2022; 12:life12122010. [PMID: 36556377 PMCID: PMC9785810 DOI: 10.3390/life12122010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/02/2022] [Revised: 11/25/2022] [Accepted: 11/30/2022] [Indexed: 12/05/2022]
Abstract
Deciphering cancer etiopathogenesis has proven to be an especially challenging task since the mechanisms that drive tumor development and progression are far from simple. An astonishing amount of research has revealed a wide spectrum of defects, including genomic abnormalities, epigenomic alterations, disturbance of gene transcription, as well as post-translational protein modifications, which cooperatively promote carcinogenesis. These findings suggest that the adoption of a multidimensional approach can provide a much more precise and comprehensive picture of the tumor landscape, hence serving as a powerful tool in cancer research and precision oncology. The introduction of next- and third-generation sequencing technologies paved the way for the decoding of genetic information and the elucidation of cancer-related cellular compounds and mechanisms. In the present review, we discuss the current and emerging applications of both generations of sequencing technologies, also referred to as massive parallel sequencing (MPS), in the fields of cancer genomics, transcriptomics and proteomics, as well as in the progressing realms of epi-omics. Finally, we provide a brief insight into the expanding scope of sequencing applications in personalized cancer medicine and pharmacogenomics.
Collapse
|
6
|
Ding Y, Sun C, Su W, Miao C, He X, Wang JS, Zhang ZH. Detecting anaplastic lymphoma kinase (ALK) gene rearrangements with next-generation sequencing remains a reliable approach in patients with non-small-cell lung cancer. Virchows Arch 2022; 481:405-419. [PMID: 35624360 DOI: 10.1007/s00428-022-03339-y] [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: 01/05/2022] [Revised: 04/12/2022] [Accepted: 05/12/2022] [Indexed: 11/24/2022]
Abstract
Next-generation sequencing (NGS) is rapidly becoming routine in clinical oncology practice to identify therapeutic biomarkers, including gene rearrangements in anaplastic lymphoma kinase (ALK). Our study investigated the concordance of ALK positivity evaluated by DNA-based NGS with orthogonal ALK testing methods such as fluorescence in situ hybridization (FISH), immunohistochemistry (IHC), and RNA-based NGS (RNA-NGS). Thirty-eight patients with lung adenocarcinoma who were detected with ALK rearrangements using DNA-NGS and also had adequate tissue samples submitted for FISH, IHC, and RNA-NGS, were included in this study. Of the 38 patients, RNA samples from 3 patients failed quality control for RNA-NGS. The concordance of ALK positivity was calculated relative to DNA-NGS results. The concordance rates were 97.1% (34/35) for RNA-NGS, 94.7% (36/38) for IHC, and 97.4% (37/38) for FISH. DNA-NGS detected single ALK rearrangements in 14 (35.0%) patients and complex ALK rearrangements in 26 (65.0%). RNA-NGS detected only single transcripts of the primary ALK fusions. A novel LANCL1-ALK (L7:A20) detected using DNA-NGS was detected as EML4-ALK (E13:A20) transcripts using RNA-NGS. Interestingly, patients with single ALK rearrangements were more likely to be detected with atypical isolated red signals (p < 0.001), while patients with complex ALK rearrangements were more likely to be detected with atypical split red and green signals less than 2 signal diameters apart (p < 0.001). Our study highlights the reliability of NGS in the accurate detection of specific ALK fusion variants and concomitant mutations that are crucial for individualized treatment decisions in patients with lung cancer.
Collapse
Affiliation(s)
- Ying Ding
- Department of Pathology, the First Affiliated Hospital of Nanjing Medical University, Nanjing, 210029, China
| | - Chang Sun
- The First School of Clinical Medicine, Nanjing Medical University, Nanjing, 210029, China
| | - Wei Su
- The First School of Clinical Medicine, Nanjing Medical University, Nanjing, 210029, China
| | - Chen Miao
- Department of Pathology, the First Affiliated Hospital of Nanjing Medical University, Nanjing, 210029, China
| | - Xiao He
- Department of Pathology, the First Affiliated Hospital of Nanjing Medical University, Nanjing, 210029, China
| | - Jin-Song Wang
- Department of Pathology, Nanjing First Hospital, Nanjing Medical University, Nanjing, 210000, China
| | - Zhi-Hong Zhang
- Department of Pathology, the First Affiliated Hospital of Nanjing Medical University, Nanjing, 210029, China.
| |
Collapse
|
7
|
Conde E, Rojo F, Gómez J, Enguita AB, Abdulkader I, González A, Lozano D, Mancheño N, Salas C, Salido M, Salido-Ruiz E, de Álava E. Molecular diagnosis in non-small-cell lung cancer: expert opinion on ALK and ROS1 testing. J Clin Pathol 2022; 75:145-153. [PMID: 33875457 PMCID: PMC8862096 DOI: 10.1136/jclinpath-2021-207490] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2021] [Revised: 03/22/2021] [Accepted: 03/24/2021] [Indexed: 01/09/2023]
Abstract
The effectiveness of targeted therapies with tyrosine kinase inhibitors in non-small-cell lung cancer (NSCLC) depends on the accurate determination of the genomic status of the tumour. For this reason, molecular analyses to detect genetic rearrangements in some genes (ie, ALK, ROS1, RET and NTRK) have become standard in patients with advanced disease. Since immunohistochemistry is easier to implement and interpret, it is normally used as the screening procedure, while fluorescence in situ hybridisation (FISH) is used to confirm the rearrangement and decide on ambiguous immunostainings. Although FISH is considered the most sensitive method for the detection of ALK and ROS1 rearrangements, the interpretation of results requires detailed guidelines. In this review, we discuss the various technologies available to evaluate ALK and ROS1 genomic rearrangements using these techniques. Other techniques such as real-time PCR and next-generation sequencing have been developed recently to evaluate ALK and ROS1 gene rearrangements, but some limitations prevent their full implementation in the clinical setting. Similarly, liquid biopsies have the potential to change the treatment of patients with advanced lung cancer, but further research is required before this technology can be applied in routine clinical practice. We discuss the technical requirements of laboratories in the light of quality assurance programmes. Finally, we review the recent updates made to the guidelines for the determination of molecular biomarkers in patients with NSCLC.
Collapse
Affiliation(s)
- Esther Conde
- Department of Pathology and Laboratory of Therapeutic Targets & CIBERONC, HM Hospitales, Madrid, Spain
| | - Federico Rojo
- Department of Pathology, Hospital Universitario Fundacion Jiménez Díaz, Madrid, Spain
| | - Javier Gómez
- Department of Pathology, Hospital Universitario Marques de Valdecilla, Santander, Cantabria, Spain,Instituto de Investigación Sanitaria Valdecilla IDIVAL, Universidad de Cantabria, Santander, Cantabria, Spain
| | - Ana Belén Enguita
- Department of Pathology, Clínica Dermatológica Internacional, Madrid, Spain
| | - Ihab Abdulkader
- Department of Pathology, Complexo Hospitalario Universitario de Santiago de Compostela, Santiago de Compostela, Galicia, Spain
| | - Ana González
- Department of Pathology, Hospital Álvaro Cunqueiro, Vigo, Spain
| | - Dolores Lozano
- Department of Pathology, Clinica Universidad de Navarra, Pamplona, Navarra, Spain
| | - Nuria Mancheño
- Department of Pathology, La Fe University and Polytechnic Hospital, Valencia, Comunidad Valenciana, Spain
| | - Clara Salas
- Department of Pathology, Hospital Universitario Puerta del Hierro Majadahonda, Majadahonda, Madrid, Spain
| | - Marta Salido
- Department of Pathology, Hospital del Mar, Barcelona, Spain
| | - Eduardo Salido-Ruiz
- Department of Pathology, Hospital Universitario de Canarias, La Laguna, Canarias, Spain
| | - Enrique de Álava
- Department of Pathology, Hospital Universitario Virgen del Rocío, Sevilla, Spain
| |
Collapse
|
8
|
Ambrosini-Spaltro A, Farnedi A, Calistri D, Rengucci C, Prisinzano G, Chiadini E, Capelli L, Angeli D, Bennati C, Valli M, De Luca G, Caruso D, Ulivi P, Rossi G. The role of next-generation sequencing in detecting gene FUSIONS with KNOWN and UNKNOWN partners: A single-center experience with methodologies' integration. Hum Pathol 2022; 123:20-30. [PMID: 35181377 DOI: 10.1016/j.humpath.2022.02.005] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/10/2021] [Revised: 02/02/2022] [Accepted: 02/08/2022] [Indexed: 12/22/2022]
Abstract
AIMS Next-generation sequencing (NGS) is becoming a new gold standard for determining molecular predictive biomarkers. This study aimed to evaluate the reliability of NGS in detecting gene fusions, focusing on comparing gene fusions with known and unknown partners. METHODS We collected all gene fusions from a consecutive case series using an amplicon-based DNA/RNA NGS platform and subdivided them into two groups: gene fusions with known partners and gene fusions with unknown partners. Gene fusions involving ALK, ROS1 and RET were also examined by immunohistochemistry (IHC) and/or fluorescent in situ hybridization (FISH). RESULTS Overall, 1174 malignancies underwent NGS analysis. NGS detected gene fusions in 67 cases (5.7%), further subdivided into 43 (64.2%) with known partners and 24 (35.8%) with unknown partners. Gene fusions were predominantly found in non-small cell lung carcinomas (52/67, 77.6%). Gene fusions with known partners frequently involved ALK (20/43, 46.5%) and MET (9/43, 20.9%), while gene fusions with unknown partners mostly involved RET (18/24, 75.0%). FISH/IHC confirmed rearrangement status in most (89.3%) of the gene fusions with known partners, but in only one (4.8%) of the gene fusions with unknown partners, with a significant difference (p<0.001). In 17 patients undergoing targeted therapy, the log-rank test revealed that the overall survival was higher in the known partner group than in the unknown partner group (p=0.002). CONCLUSIONS NGS is a reliable method for detecting gene fusions with known partners, but it is less accurate in identifying gene fusions with unknown partners, for which further analyses (such as FISH) are required.
Collapse
Affiliation(s)
| | - Anna Farnedi
- Pathology Unit, Morgagni-Pierantoni Hospital, Forlì, AUSL Romagna, Italy
| | - Daniele Calistri
- Biosciences Laboratory, IRCCS Istituto Romagnolo per Lo Studio Dei Tumori (IRST) "Dino Amadori", Meldola, Italy
| | - Claudia Rengucci
- Biosciences Laboratory, IRCCS Istituto Romagnolo per Lo Studio Dei Tumori (IRST) "Dino Amadori", Meldola, Italy
| | - Giovanna Prisinzano
- Biosciences Laboratory, IRCCS Istituto Romagnolo per Lo Studio Dei Tumori (IRST) "Dino Amadori", Meldola, Italy
| | - Elisa Chiadini
- Biosciences Laboratory, IRCCS Istituto Romagnolo per Lo Studio Dei Tumori (IRST) "Dino Amadori", Meldola, Italy
| | - Laura Capelli
- Biosciences Laboratory, IRCCS Istituto Romagnolo per Lo Studio Dei Tumori (IRST) "Dino Amadori", Meldola, Italy
| | - Davide Angeli
- Unit of Biostatistics and Clinical Trials, IRCCS Istituto Romagnolo per Lo Studio Dei Tumori (IRST) "Dino Amadori", Meldola, Italy
| | - Chiara Bennati
- Oncology Unit, Santa Maria Delle Croci Hospital, Ravenna, AUSL Romagna, Italy
| | - Mirca Valli
- Pathology Unit, Infermi Hospital, Rimini, AUSL Romagna, Italy
| | | | - Dora Caruso
- Pathology Unit, Santa Maria Delle Croci Hospital, Ravenna, AUSL Romagna, Italy
| | - Paola Ulivi
- Biosciences Laboratory, IRCCS Istituto Romagnolo per Lo Studio Dei Tumori (IRST) "Dino Amadori", Meldola, Italy
| | - Giulio Rossi
- Pathology Unit, Department of Oncology, Fondazione Poliambulanza, Brescia, Italy
| |
Collapse
|
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
|
Wang X, Wang J, Luo X, Lu J, Wang L, Li Q, Wang EH. Diagnosis of NUT Carcinoma Despite False-Negative Next-Generation Sequencing Results: A Case Report and Literature Review. Onco Targets Ther 2021; 14:4621-4633. [PMID: 34475768 PMCID: PMC8407784 DOI: 10.2147/ott.s327722] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2021] [Accepted: 08/18/2021] [Indexed: 12/23/2022] Open
Abstract
Nuclear protein in testis (NUT) carcinoma (NC) is a poorly differentiated malignant tumor with a poor prognosis, which is caused by the NUTM1 gene rearrangement. Positive staining of NUT using immunohistochemistry (IHC) or gene rearrangement of NUTM1 revealed by genetic analysis, such as fluorescence in situ hybridization (FISH) or next-generation sequencing (NGS), are important strategies used for accurate diagnosis. In the current study, we present a case of NC in an 18-year-old man who had a chief complaint of nasal congestion, nasal bleeding, and anosmia. Magnetic resonance imaging revealed a mass in the nasal cavity and nasal septum. The initial pathological diagnosis was basaloid squamous cell carcinoma. Based on the tumor location and abrupt keratinization, further genetic tests were performed, and NC was diagnosed using FISH, which was further verified by IHC. However, neither DNA-based NGS nor RNA-based NGS revealed the NUTM1 gene rearrangement. Using this case as a basis, we have reviewed the related literature, compared the common diagnostic methods of NC, and discussed the advantages and limitations of current tools employed for molecular analysis of the gene fusion.
Collapse
Affiliation(s)
- Xi Wang
- Department of Pathology, The First Affiliated Hospital and College of Basic Medical Sciences, China Medical University, Shenyang, 110001, People's Republic of China
| | - Jinping Wang
- Department of Pathology, The First Affiliated Hospital and College of Basic Medical Sciences, China Medical University, Shenyang, 110001, People's Republic of China
| | - Xue Luo
- Department of Pathology, The First Affiliated Hospital and College of Basic Medical Sciences, China Medical University, Shenyang, 110001, People's Republic of China
| | - Jinxi Lu
- Department of Pathology, The First Affiliated Hospital and College of Basic Medical Sciences, China Medical University, Shenyang, 110001, People's Republic of China
| | - Liang Wang
- Department of Pathology, The First Affiliated Hospital and College of Basic Medical Sciences, China Medical University, Shenyang, 110001, People's Republic of China
| | - Qingchang Li
- Department of Pathology, The First Affiliated Hospital and College of Basic Medical Sciences, China Medical University, Shenyang, 110001, People's Republic of China
| | - En-Hua Wang
- Department of Pathology, The First Affiliated Hospital and College of Basic Medical Sciences, China Medical University, Shenyang, 110001, People's Republic of China
| |
Collapse
|
12
|
Next Generation Sequencing Technology in Lung Cancer Diagnosis. BIOLOGY 2021; 10:biology10090864. [PMID: 34571741 PMCID: PMC8467994 DOI: 10.3390/biology10090864] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 07/27/2021] [Revised: 08/26/2021] [Accepted: 08/31/2021] [Indexed: 12/29/2022]
Abstract
Simple Summary Lung cancer is still one of the most commonly diagnosed and deadliest cancers in the world. Its diagnosis at an early stage is highly necessary and will improve the standard of care of this disease. The aim of this article is to review the importance and applications of next generation sequencing in lung cancer diagnosis. As observed in many studies, next generation sequencing has been proven as a very helpful tool in the early detection of different types of cancers, including lung cancer, and has been used in the clinic, mainly due to its many advantages, such as low cost, speed, efficacy, low quantity usage of biological samples, and diversity. Abstract Lung cancer is still one of the most commonly diagnosed cancers, and one of the deadliest. The high death rate is mainly due to the late stage of diagnosis and low response rate to therapy. Previous and ongoing research studies have tried to discover new reliable and useful cbiomarkers for the diagnosis and prognosis of lung cancer. Next generation sequencing has become an essential tool in cancer diagnosis, prognosis, and evaluation of the treatment response. This article aims to review the leading research and clinical applications in lung cancer diagnosis using next generation sequencing. In this scope, we identified the most relevant articles that present the successful use of next generation sequencing in identifying biomarkers for early diagnosis correlated to lung cancer diagnosis and treatment. This technique can be used to evaluate a high number of biomarkers in a short period of time and from small biological samples, which makes NGS the preferred technique to develop clinical tests for personalized medicine using liquid biopsy, the new trend in oncology.
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
|
Abstract
Inflammatory myofibroblastic tumor is a mesenchymal neoplasm, commonly seen in the lung and abdominopelvic region of children. The authors present an 8-month-old female with a 2-month history of left-sided proptosis. Examination was significant for left-sided proptosis, a left exotropia and hypotropia, left supraduction and adduction deficits, and left optic disc elevation. MRI imaging revealed an extraconal left superomedial orbital mass with globe displacement and proptosis. Left anterior orbitotomy with excisional biopsy showed a solid mass composed of an infiltrative proliferation of bland spindle cells in a variably myxoid background with associated perivascular lymphoplasmacytic infiltration. Immunohistochemistry was positive for ALK-1 and CD34 and demonstrated focal positivity for S100. Fluorescence in-situ hybridization showed an additional copy of the 3'ALK gene (46%) in interphase cells examined. Next generation targeted sequencing found a DCTN1/ALK fusion. Findings were consistent with inflammatory myofibroblastic tumor. To the authors' knowledge, this is one of the largest primary orbital inflammatory myofibroblastic tumors in the youngest reported patient.
Collapse
|
15
|
Belli C, Penault-Llorca F, Ladanyi M, Normanno N, Scoazec JY, Lacroix L, Reis-Filho JS, Subbiah V, Gainor JF, Endris V, Repetto M, Drilon A, Scarpa A, André F, Douillard JY, Curigliano G. ESMO recommendations on the standard methods to detect RET fusions and mutations in daily practice and clinical research. Ann Oncol 2021; 32:337-350. [PMID: 33455880 DOI: 10.1016/j.annonc.2020.11.021] [Citation(s) in RCA: 69] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2020] [Revised: 11/26/2020] [Accepted: 11/28/2020] [Indexed: 12/17/2022] Open
Abstract
Aberrant activation of RET is a critical driver of growth and proliferation in diverse solid tumours. Multikinase inhibitors (MKIs) showing anti-RET activities have been tested in RET-altered tumours with variable results. The low target specificity with consequent increase in side-effects and off-target toxicities resulting in dose reduction and drug discontinuation are some of the major issues with MKIs. To overcome these issues, new selective RET inhibitors such as pralsetinib (BLU-667) and selpercatinib (LOXO-292) have been developed in clinical trials, with selpercatinib recently approved by the Food and Drug Administration (FDA). The results of these trials showed marked and durable antitumour activity and manageable toxicity profiles in patients with RET-altered tumours. The European Society for Medical Oncology (ESMO) Translational Research and Precision Medicine Working Group (TR and PM WG) launched a collaborative project to review the available methods for the detection of RET gene alterations, their potential applications and strategies for the implementation of a rational approach for the detection of RET fusion genes and mutations in human malignancies. We present here recommendations for the routine clinical detection of targetable RET rearrangements and mutations.
Collapse
Affiliation(s)
- C Belli
- Division of Early Drug Development for Innovative Therapies, European Institute of Oncology IRCCS, Milan, Italy
| | - F Penault-Llorca
- University Clermont Auvergne, INSERM U1240, Centre Jean Perrin, Department of BioPathology, Clermont-Ferrand, France
| | - M Ladanyi
- Department of Pathology and Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, USA
| | - N Normanno
- Cell Biology and Biotherapy Unit, Istituto Nazionale Tumori "Fondazione G. Pascale"-IRCCS, Naples, Italy
| | - J-Y Scoazec
- AMMICa, CNRS-UMS 3655 and INSERM-US23, Gustave Roussy, Villejuif, France; Department of Pathology and Translational Research, Gustave Roussy Cancer Centre, Villejuif, France
| | - L Lacroix
- Translational Research Laboratory and Biobank, Gustave Roussy, Villejuif, France; Inserm U981, Gustave Roussy, Villejuif, France; Department of Medical Biology and Pathology, Gustave Roussy, Villejuif, France
| | - J S Reis-Filho
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, USA
| | - V Subbiah
- The University of Texas MD Anderson Cancer Center, Houston, USA
| | - J F Gainor
- Massachusetts General Hospital, Boston, USA
| | - V Endris
- Institute of Pathology, Heidelberg University Hospital, Heidelberg, Germany
| | - M Repetto
- Division of Early Drug Development for Innovative Therapies, European Institute of Oncology IRCCS, Milan, Italy; Department of Oncology and Hemato-Oncology, University of Milan, Milan, Italy
| | - A Drilon
- Division of Solid Tumor Oncology, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, USA; Department of Medicine, Memorial Sloan Kettering Cancer Center, Weill Cornell Medical College, New York, USA
| | - A Scarpa
- ARC-Net Research Centre and Department of Diagnostics and Public Health - Section of Pathology, University of Verona, Verona, Italy
| | - F André
- Gustave Roussy Cancer Center, Villejuif, France
| | - J-Y Douillard
- Scientific and Medical Division, European Society for Medical Oncology, Lugano, Switzerland
| | - G Curigliano
- Division of Early Drug Development for Innovative Therapies, European Institute of Oncology IRCCS, Milan, Italy; Department of Oncology and Hemato-Oncology, University of Milan, Milan, Italy.
| |
Collapse
|
16
|
Ramani NS, Patel KP, Routbort MJ, Alvarez H, Broaddus R, Chen H, Rashid A, Lazar A, San Lucas FA, Yao H, Manekia J, Dang H, Barkoh BA, Medeiros LJ, Luthra R, Roy-Chowdhuri S. Factors Impacting Clinically Relevant RNA Fusion Assays Using Next-Generation Sequencing. Arch Pathol Lab Med 2021; 145:1405-1412. [PMID: 33493304 DOI: 10.5858/arpa.2020-0415-oa] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/06/2020] [Indexed: 11/06/2022]
Abstract
CONTEXT.— RNA-based next-generation sequencing (NGS) assays are being used with increasing frequency for comprehensive molecular profiling of solid tumors. OBJECTIVE.— To evaluate factors that might impact clinical assay performance. DESIGN.— A 4-month retrospective review of cases analyzed by a targeted RNA-based NGS assay to detect fusions was performed. RNA extraction was performed from formalin-fixed, paraffin-embedded tissue sections and/or cytology smears of 767 cases, including 493 in-house and 274 outside referral cases. The types of samples included 422 core needle biopsy specimens (55%), 268 resection specimens (35%), and 77 cytology samples (10%). RESULTS.— Successful NGS fusion testing was achieved in 697 specimens (90.9%) and correlated positively with RNA yield (P < .001) and negatively with specimen necrosis (P = .002), decalcification (P < .001), and paraffin block age of more than 2 years (P = .001). Of the 697 cases that were successfully sequenced, 50 (7.2%) had clinically relevant fusions. The testing success rates and fusion detection rates were similar between core needle biopsy and cytology samples. In contrast, RNA fusion testing was often less successful using resection specimens (P = .007). Testing success was independent of the tumor percentage in the specimen, given that at least 20% tumor cellularity was present. CONCLUSIONS.— The success of RNA-based NGS testing is multifactorial and is influenced by RNA quality and quantity. Identification of preanalytical factors affecting RNA quality and yield can improve NGS testing success rates.
Collapse
Affiliation(s)
- Nisha S Ramani
- From the Departments of Pathology (Ramani, Broaddus, Chen, Rashid, Lazar, Roy-Chowdhuri)
| | - Keyur P Patel
- Hematopathology (Patel, Routbort, Alvarez, San Lucas, Manekia, Dang, Barkoh, Medeiros, Luthra)
| | - Mark J Routbort
- Hematopathology (Patel, Routbort, Alvarez, San Lucas, Manekia, Dang, Barkoh, Medeiros, Luthra)
| | - Hector Alvarez
- Hematopathology (Patel, Routbort, Alvarez, San Lucas, Manekia, Dang, Barkoh, Medeiros, Luthra)
| | - Russell Broaddus
- From the Departments of Pathology (Ramani, Broaddus, Chen, Rashid, Lazar, Roy-Chowdhuri)
| | - Hui Chen
- From the Departments of Pathology (Ramani, Broaddus, Chen, Rashid, Lazar, Roy-Chowdhuri)
| | - Asif Rashid
- From the Departments of Pathology (Ramani, Broaddus, Chen, Rashid, Lazar, Roy-Chowdhuri)
| | - Alex Lazar
- From the Departments of Pathology (Ramani, Broaddus, Chen, Rashid, Lazar, Roy-Chowdhuri)
| | - Francis A San Lucas
- Hematopathology (Patel, Routbort, Alvarez, San Lucas, Manekia, Dang, Barkoh, Medeiros, Luthra)
| | - Hui Yao
- and Bioinformatics and Computational Biology (Yao), The University of Texas MD Anderson Cancer Center, Houston. Broaddus is currently with the Department of Pathology and Laboratory Medicine, University of North Carolina School of Medicine, Chapel Hill
| | - Jawad Manekia
- Hematopathology (Patel, Routbort, Alvarez, San Lucas, Manekia, Dang, Barkoh, Medeiros, Luthra)
| | - Hyvan Dang
- Hematopathology (Patel, Routbort, Alvarez, San Lucas, Manekia, Dang, Barkoh, Medeiros, Luthra)
| | - Bedia A Barkoh
- Hematopathology (Patel, Routbort, Alvarez, San Lucas, Manekia, Dang, Barkoh, Medeiros, Luthra)
| | - L Jeffrey Medeiros
- Hematopathology (Patel, Routbort, Alvarez, San Lucas, Manekia, Dang, Barkoh, Medeiros, Luthra)
| | - Rajyalakshmi Luthra
- Hematopathology (Patel, Routbort, Alvarez, San Lucas, Manekia, Dang, Barkoh, Medeiros, Luthra)
| | - Sinchita Roy-Chowdhuri
- From the Departments of Pathology (Ramani, Broaddus, Chen, Rashid, Lazar, Roy-Chowdhuri)
| |
Collapse
|
17
|
Kang J, Zhang XC, Chen HJ, Zhong WZ, Xu Y, Su J, Zhou Q, Tu HY, Wang Z, Xu CR, Yang XN, Chen ZH, Wu X, Zhang X, Shao Y, Wu YL, Yang JJ. Complex ALK Fusions Are Associated With Better Prognosis in Advanced Non-Small Cell Lung Cancer. Front Oncol 2020; 10:596937. [PMID: 33363027 PMCID: PMC7759679 DOI: 10.3389/fonc.2020.596937] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2020] [Accepted: 11/10/2020] [Indexed: 12/27/2022] Open
Abstract
Background Echinoderm microtubule-associated protein-like 4 (EML4) is the canonical anaplastic lymphoma kinase (ALK) fusion partner in non-small cell lung cancer (NSCLC), and ALK-positive patients showed promising responses to ALK tyrosine kinase inhibitors (TKIs). However, studies that comprehensively investigate ALK TKI treatment in patients with different ALK fusion patterns are still lacking. Methods Ninety-eight ALK-positive patients with advanced NSCLC were retrospectively studied for their response to crizotinib and subsequent treatments. Comprehensive genomic profiling (CGP) was conducted to divide patients into different groups based on their ALK fusion patterns. Non-canonical ALK fusions were validated using RNA-sequencing. Results 54.1% of patients had pure canonical EML4-ALK fusions, 19.4% carried only non-canonical ALK fusions, and 26.5% harbored complex ALK fusions with coexisting canonical and non-canonical ALK fusions. The objective response rate and median progression-free survival to crizotinib treatment tended to be better in the complex ALK fusion group. Notably, patients with complex ALK fusions had significantly improved overall survival after crizotinib treatment (p = 0.012), especially when compared with the pure canonical EML4-ALK fusion group (p = 0.010). The complex ALK fusion group also tended to respond better to next-generation ALK TKIs, which were used as later-line therapies. Most identified non-canonical ALK fusions were likely to be expressed in tumors, and some of them formed canonical EML4-ALK transcripts during mRNA maturation. Conclusion Our results suggest NSCLC patients with complex ALK fusions could potentially have better treatment outcomes to ALK TKIs therapy. Also, diagnosis using CGP is of great value to identify novel ALK fusions and predict prognosis.
Collapse
Affiliation(s)
- Jin Kang
- Division of Pulmonary Oncology, Guangdong Lung Cancer Institute, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou, China
| | - Xu-Chao Zhang
- Division of Pulmonary Oncology, Guangdong Lung Cancer Institute, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou, China.,Medical Research Center, Guangdong Provincial People's Hospital and Guangdong Academy of Medical Sciences, The Second School of Clinical Medicine, Southern Medical University, Guangzhou, China.,Guangdong Lung Cancer Institute, Guangdong Provincial Key Laboratory of Translational Medicine in Lung Cancer, Guangdong Provincial People's Hospital & Guangdong Academy of Medical Sciences, School of Medicine, South China University of Technology, Guangzhou, China
| | - Hua-Jun Chen
- Division of Pulmonary Oncology, Guangdong Lung Cancer Institute, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou, China
| | - Wen-Zhao Zhong
- Division of Pulmonary Oncology, Guangdong Lung Cancer Institute, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou, China
| | - Yang Xu
- Translational Medicine Research Institute, Geneseeq Technology Inc., Toronto, ON, Canada
| | - Jian Su
- Division of Pulmonary Oncology, Guangdong Lung Cancer Institute, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou, China
| | - Qing Zhou
- Division of Pulmonary Oncology, Guangdong Lung Cancer Institute, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou, China
| | - Hai-Yan Tu
- Division of Pulmonary Oncology, Guangdong Lung Cancer Institute, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou, China
| | - Zhen Wang
- Division of Pulmonary Oncology, Guangdong Lung Cancer Institute, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou, China
| | - Chong-Rui Xu
- Division of Pulmonary Oncology, Guangdong Lung Cancer Institute, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou, China
| | - Xue-Ning Yang
- Division of Pulmonary Oncology, Guangdong Lung Cancer Institute, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou, China
| | - Zhi-Hong Chen
- Division of Pulmonary Oncology, Guangdong Lung Cancer Institute, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou, China
| | - Xue Wu
- Translational Medicine Research Institute, Geneseeq Technology Inc., Toronto, ON, Canada
| | - Xian Zhang
- Nanjing Geneseeq Technology Inc., Nanjing, China
| | - Yang Shao
- Nanjing Geneseeq Technology Inc., Nanjing, China.,School of Public Health, Nanjing Medical University, Nanjing, China
| | - Yi-Long Wu
- Division of Pulmonary Oncology, Guangdong Lung Cancer Institute, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou, China.,Medical Research Center, Guangdong General Hospital and Guangdong Academy of Medical Sciences, Guangzhou, China
| | - Jin-Ji Yang
- Division of Pulmonary Oncology, Guangdong Lung Cancer Institute, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou, China
| |
Collapse
|
18
|
Mok T, Peters S, Camidge DR, Noé J, Gadgeel S, Ignatius Ou SH, Kim DW, Konopa K, Pozzi E, Liu T, Loftin IR, Williams C, Shaw AT. Outcomes According to ALK Status Determined by Central IHC or FISH in Patients with ALK-Positive NSCLC Enrolled in the Phase III ALEX Study. J Thorac Oncol 2020; 16:S1556-0864(20)30815-7. [PMID: 34756882 DOI: 10.1016/j.jtho.2020.10.007] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2020] [Revised: 09/18/2020] [Accepted: 10/04/2020] [Indexed: 01/05/2023]
Abstract
INTRODUCTION We retrospectively examined progression-free survival (PFS) and response by ALK fluorescence in-situ hybridization (FISH) status in patients with advanced ALK immunohistochemistry (IHC)-positive non-small-cell lung cancer (NSCLC) in the ALEX study. METHODS 303 treatment-naïve patients were randomized to receive twice-daily alectinib 600 mg or crizotinib 250 mg. ALK status was assessed centrally using Ventana ALK (D5F3) CDx IHC and Vysis ALK Break Apart FISH Probe Kit. Primary endpoint: investigator-assessed PFS. Secondary endpoints of interest: objective response rate (ORR) and duration. RESULTS Investigator-assessed PFS was significantly prolonged with alectinib versus crizotinib in ALK IHC-positive/FISH-positive tumors (n = 203, 67%) (HR 0.37, 95% CI: 0.25-0.56) and ALK IHC-positive/FISH-uninformative tumors (n = 61, 20%) (HR 0.39, 95% CI: 0.20-0.78), but not ALK IHC-positive/FISH-negative tumors (n = 39, 13%) (HR 1.33, 95% CI: 0.6-3.2). ORRs were higher with alectinib versus crizotinib in ALK IHC-positive/FISH-positive tumors 90.6% versus 81.4%; stratified odds ratio [OR] 2.22, 95% CI: 0.97-5.07) and ALK IHC-positive/FISH-uninformative tumors (96.0% versus 75.0%; OR 9.29, 95% CI: 1.05-81.88), but not ALK IHC-positive/FISH-negative tumors (28.6% versus 44.4%; OR 0.45, 95% CI: 0.12-1.74). Next-generation sequencing (NGS) was performed in 35/39 patients with ALK IHC-positive/FISH-negative tumors; no ALK fusion was identified in 20/35 (57.1%) patients by NGS, but 10/20 (50.0%) had partial response/stable disease. CONCLUSION Outcomes of patients with ALK IHC-positive/FISH-positive and ALK IHC-positive/FISH-uninformative NSCLC were similar to the overall ALEX population. These results suggest that Ventana ALK IHC is a standard testing method for selecting patients for treatment with alectinib.
Collapse
Affiliation(s)
- Tony Mok
- State Key Laboratory of Translational Oncology, Chinese University of Hong Kong, Hong Kong.
| | | | | | | | - Shirish Gadgeel
- Department of Internal Medicine, Division of Hematology and Oncology, University of Michigan, Ann Arbor, Michigan
| | | | - Dong-Wan Kim
- Seoul National University Hospital, Seoul, South Korea
| | - Krzysztof Konopa
- Department of Oncology and Radiotherapy, Medical University of Gdansk, Gdansk, Poland
| | | | - Ting Liu
- F. Hoffmann-La Roche Ltd, Basel, Switzerland
| | | | | | - Alice T Shaw
- Massachusetts General Hospital, Boston, Massachusetts
| |
Collapse
|
19
|
Bleker de Oliveira M, Koshkin V, Liu G, Krylov SN. Analytical Challenges in Development of Chemoresistance Predictors for Precision Oncology. Anal Chem 2020; 92:12101-12110. [PMID: 32790291 DOI: 10.1021/acs.analchem.0c02644] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Chemoresistance, i.e., tumor insensitivity to chemotherapy, shortens life expectancy of cancer patients. Despite the availability of new treatment options, initial systemic regimens for solid tumors are dominated by a set of standard chemotherapy drugs, and alternative therapies are used only when a patient has demonstrated chemoresistance clinically. Chemoresistance predictors use laboratory parameters measured on tissue samples to predict the patient's response to chemotherapy and help to avoid application of chemotherapy to chemoresistant patients. Despite thousands of publications on putative chemoresistance predictors, there are only about a dozen predictors that are sufficiently accurate for precision oncology. One of the major reasons for inaccuracy of predictors is inaccuracy of analytical methods utilized to measure their laboratory parameters: an inaccurate method leads to an inaccurate predictor. The goal of this study was to identify analytical challenges in chemoresistance-predictor development and suggest ways to overcome them. Here we describe principles of chemoresistance predictor development via correlating a clinical parameter, which manifests disease state, with a laboratory parameter. We further classify predictors based on the nature of laboratory parameters and analyze advantages and limitations of different predictors using the reliability of analytical methods utilized for measuring laboratory parameters as a criterion. Our eventual focus is on predictors with known mechanisms of reactions involved in drug resistance (drug extrusion, drug degradation, and DNA damage repair) and using rate constants of these reactions to establish accurate and robust laboratory parameters. Many aspects and conclusions of our analysis are applicable to all types of disease biomarkers built upon the correlation of clinical and laboratory parameters.
Collapse
Affiliation(s)
- Mariana Bleker de Oliveira
- Department of Chemistry and Centre for Research on Biomolecular Interactions, York University, Toronto M3J 1P3, Canada
| | - Vasilij Koshkin
- Department of Chemistry and Centre for Research on Biomolecular Interactions, York University, Toronto M3J 1P3, Canada
| | - Geoffrey Liu
- Department of Medicine, Medical Oncology, Princess Margaret Cancer Centre, Toronto M5G 2M9, Canada
| | - Sergey N Krylov
- Department of Chemistry and Centre for Research on Biomolecular Interactions, York University, Toronto M3J 1P3, Canada
| |
Collapse
|
20
|
Comparison of Large, Medium, and Small Solid Tumor Gene Panels for Detection of Clinically Actionable Mutations in Cancer. Target Oncol 2020; 15:523-530. [PMID: 32770442 DOI: 10.1007/s11523-020-00743-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
BACKGROUND Next-generation sequencing of gene panels has supplanted single-gene testing for cancer molecular diagnostics in many laboratories. Considerations for the optimal number of genes to assess in a panel depend on the purpose of the testing. OBJECTIVE To address the optimal size for the identification of clinically actionable variants in different-sized solid tumor sequencing panels. PATIENTS AND METHODS Sequencing results from 480 patients with a large, 315 gene, panel were compared against coverage of a medium, 161 gene, and small, 50 gene, panel. RESULTS The large panel detected a total of 2072 sequence variants in 480 patient specimens; 61 (12.7%) contained variants for which there is therapy approved by the US Food and Drug Administration, 89 (18.5%) had variants associated with an off-label therapy, and 312 (65.0%) contained variants eligible for a genomically matched clinical trial. The small panel covered only 737 of the 2072 variants (35.5%) and somewhat fewer therapy-related variants (on-label 88.5%, off-label 60.7%). The medium-size panel included 1354 of the 2072 (65.3%) variants reported by the large panel. All 318 patients with a clinically actionable variant would have been identified by the medium panel. CONCLUSIONS The results demonstrate that a carefully designed medium size gene panel is as effective as a large panel for the detection of clinically actionable variants and can be run by most molecular pathology laboratories.
Collapse
|
21
|
Bruno R, Fontanini G. Next Generation Sequencing for Gene Fusion Analysis in Lung Cancer: A Literature Review. Diagnostics (Basel) 2020; 10:diagnostics10080521. [PMID: 32726941 PMCID: PMC7460167 DOI: 10.3390/diagnostics10080521] [Citation(s) in RCA: 84] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2020] [Revised: 07/16/2020] [Accepted: 07/18/2020] [Indexed: 02/07/2023] Open
Abstract
Gene fusions have a pivotal role in non-small cell lung cancer (NSCLC) precision medicine. Several techniques can be used, from fluorescence in situ hybridization and immunohistochemistry to next generation sequencing (NGS). Although several NGS panels are available, gene fusion testing presents more technical challenges than other variants. This is a PubMed-based narrative review aiming to summarize NGS approaches for gene fusion analysis and their performance on NSCLC clinical samples. The analysis can be performed at DNA or RNA levels, using different target enrichment (hybrid-capture or amplicon-based) and sequencing chemistries, with both custom and commercially available panels. DNA sequencing evaluates different alteration types simultaneously, but large introns and repetitive sequences can impact on the performance and it does not discriminate between expressed and unexpressed gene fusions. RNA-based targeted approach analyses and quantifies directly fusion transcripts and is more accurate than DNA panels on tumor tissue, but it can be limited by RNA quality and quantity. On liquid biopsy, satisfying data have been published on circulating tumor DNA hybrid-capture panels. There is not a perfect method for gene fusion analysis, but NGS approaches, though still needing a complete standardization and optimization, present several advantages for the clinical practice.
Collapse
Affiliation(s)
- Rossella Bruno
- Unit of Pathological Anatomy, University Hospital of Pisa, Via Roma 67, 56126 Pisa, Italy;
| | - Gabriella Fontanini
- Department of Surgical, Medical, Molecular Pathology and Critical Area, University of Pisa, Via Savi 10, 56126 Pisa, Italy
- Correspondence:
| |
Collapse
|
22
|
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
|
23
|
|
24
|
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
|
25
|
Chen HF, Wang WX, Xu CW, Huang LC, Li XF, Lan G, Zhai ZQ, Zhu YC, Du KQ, Lei L, Fang MY. A novel SOS1-ALK fusion variant in a patient with metastatic lung adenocarcinoma and a remarkable response to crizotinib. Lung Cancer 2020; 142:59-62. [PMID: 32114282 DOI: 10.1016/j.lungcan.2020.02.012] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2020] [Revised: 02/16/2020] [Accepted: 02/19/2020] [Indexed: 11/24/2022]
Abstract
OBJECTIVES Transforming anaplastic lymphoma kinase (ALK) gene rearrangements are well known as a unique subset of non-small cell lung cancer (NSCLC) with mutations other than EGFR. Currently, crizotinib is the standard first-line treatment for ALK-positive NSCLC. MATERIALS AND METHODS With advances in detection methods, more and more uncommon ALK fusion partners have been identified. Herein we present a novel SOS1-ALK fusion and the efficacy of crizotinib in an advanced NSCLC patient harboring this type of fusion. RESULTS A 52-year-old Chinese man had left upper lobe primary NSCLC and synchronous multiple lung metastases (cT2N3M1, stage IV). The ultrasound-guided fine-needle aspiration cytology of palpable left supraclavicular lymph nodes and the results of immunohistochemistry staining supported the diagnosis of metastatic lung adenocarcinoma. Using a next-generation sequencing assay (NGS), we showed that the tumor had a SOS1-ALK fusion which the breakpoints was (S2, A20) rather than other actionable mutations. Therefore, the patient received first-line crizotinib and experienced a remarkable tumor response and has tolerated crizotinib well until this writing. CONCLUSION Considering this rare SOS1-ALK fusion and remarkable response to an ALK-inhibitor, it is important to be aware of the presence of SOS1-ALK fusions in patients with advanced NSCLC to better guide targeted therapy. Precision methods, such as NGS for oncogenic alteration detection, should also be encouraged in clinical practice.
Collapse
Affiliation(s)
- Hua-Fei Chen
- Department of Thoracic Disease Diagnosis and Treatment Center, Zhejiang Rongjun Hospital,The Third Affiliated Hospital of Jiaxing University, Jiaxing Zhejiang 314000, People's Republic of China
| | - Wen-Xian Wang
- Department of Chemotherapy, Zhejiang Cancer Hospital, Hangzhou Zhejiang 310022, People's Republic of China
| | - Chun-Wei Xu
- Department of Pathology, Fujian Cancer Hospital, Fujian Medical University Cancer Hospital, Fuzhou Fujian 350014, People's Republic of China.
| | - Li-Chao Huang
- Department of Thoracic Disease Diagnosis and Treatment Center, Zhejiang Rongjun Hospital,The Third Affiliated Hospital of Jiaxing University, Jiaxing Zhejiang 314000, People's Republic of China
| | - Xiao-Feng Li
- Department of Thoracic Disease Diagnosis and Treatment Center, Zhejiang Rongjun Hospital,The Third Affiliated Hospital of Jiaxing University, Jiaxing Zhejiang 314000, People's Republic of China
| | - Gang Lan
- Department of Thoracic Disease Diagnosis and Treatment Center, Zhejiang Rongjun Hospital,The Third Affiliated Hospital of Jiaxing University, Jiaxing Zhejiang 314000, People's Republic of China
| | - Zhan-Qiang Zhai
- Department of Thoracic Disease Diagnosis and Treatment Center, Zhejiang Rongjun Hospital,The Third Affiliated Hospital of Jiaxing University, Jiaxing Zhejiang 314000, People's Republic of China
| | - You-Cai Zhu
- Department of Thoracic Disease Diagnosis and Treatment Center, Zhejiang Rongjun Hospital,The Third Affiliated Hospital of Jiaxing University, Jiaxing Zhejiang 314000, People's Republic of China
| | - Kai-Qi Du
- Department of Thoracic Disease Diagnosis and Treatment Center, Zhejiang Rongjun Hospital,The Third Affiliated Hospital of Jiaxing University, Jiaxing Zhejiang 314000, People's Republic of China
| | - Lei Lei
- Department of Chemotherapy, Zhejiang Cancer Hospital, Hangzhou Zhejiang 310022, People's Republic of China.
| | - Mei-Yu Fang
- Department of Chemotherapy, Zhejiang Cancer Hospital, Hangzhou Zhejiang 310022, People's Republic of China
| |
Collapse
|
26
|
Toruner GA, Tang Z, Tang G, Medeiros LJ, Hu S. Low ALK FISH positive metastatic non-small cell lung cancer (NSCLC) patients have shorter progression-free survival after treatment with ALK inhibitors. Cancer Genet 2019; 241:57-60. [PMID: 31870845 DOI: 10.1016/j.cancergen.2019.12.003] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2019] [Revised: 12/05/2019] [Accepted: 12/10/2019] [Indexed: 12/18/2022]
Abstract
ALK FISH assay guides clinical decision to initiate therapy with ALK inhibitors in patients with stage IV non-small cells lung cancer (NSCLC). In this single institution retrospective study, we investigated the association between the strength of ALK positivity and progression-free survival (PFS) We screened 4,829 patients tested for ALK rearrangement by FISH from 01/06/2012 to 06/30/2018 and included 66 stage IV NSCLC ALK positive patients, who were ALK inhibitor naïve, received an ALK inhibitor, and been followed at least 10 months to the study. The median PFS for cases high positive cases [≥=50% positive nuclei; n = 49] and low positive cases [16-49% positive nuclei; n = 17] is 16 months and 4 months respectively, and the hazard ratio is 2.89 [95 CI 1.34-6.2] (p = 0.0068). When cases are stratified according to cut-off ≥=30% positive nuclei, the median PFS for cases above (n = 55) and below the cut-off (n = 11) is 12 and 3 months, respectively and the hazard ratio is 9.60 [95 CI 2.63-35.04] (p < 0.0001) Patients with low FISH positive results have shorter PFS. Although a biological reason is plausible, false positivity may be a contributing factor. For low positive results, confirmation of the FISH result with an orthogonal technology is warranted.
Collapse
Affiliation(s)
- Gokce A Toruner
- Section of Clinical Cytogenetics, Department of Hematopathology, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Boulevard, Houston, TX 77030-4009, United States.
| | - Zhenya Tang
- Section of Clinical Cytogenetics, Department of Hematopathology, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Boulevard, Houston, TX 77030-4009, United States
| | - Guilin Tang
- Section of Clinical Cytogenetics, Department of Hematopathology, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Boulevard, Houston, TX 77030-4009, United States
| | - L Jeffrey Medeiros
- Section of Clinical Cytogenetics, Department of Hematopathology, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Boulevard, Houston, TX 77030-4009, United States
| | - Shimin Hu
- Section of Clinical Cytogenetics, Department of Hematopathology, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Boulevard, Houston, TX 77030-4009, United States
| |
Collapse
|
27
|
Zhou X, Shou J, Sheng J, Xu C, Ren S, Cai X, Chu Q, Wang W, Zhen Q, Zhou Y, Li W, Pan H, Li H, Sun T, Cheng H, Wang H, Lou F, Rao C, Cao S, Pan H, Fang Y. Molecular and clinical analysis of Chinese patients with anaplastic lymphoma kinase (ALK)-rearranged non-small cell lung cancer. Cancer Sci 2019; 110:3382-3390. [PMID: 31444835 PMCID: PMC6778633 DOI: 10.1111/cas.14177] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2019] [Revised: 08/08/2019] [Accepted: 08/15/2019] [Indexed: 12/17/2022] Open
Abstract
Anaplastic lymphoma kinase (ALK) fusions have been recognized as a therapeutic target in non‐small cell lung cancer (NSCLC). However, molecular signatures and clinical characteristics of the Chinese population with ALK‐rearranged NSCLC are not well elucidated. In the present study, we carried out targeted next‐generation sequencing on tissue and plasma ctDNA samples in 1688 patients with NSCLC. Overall, ALK fusions were detected in 70 patients (4.1%), and the frequencies of ALK fusions detected in tissue and plasma samples were 5.1% and 3.3%, respectively. Additionally, the prevalence of breakpoint locations for EML4‐ALK fusions in ctDNA was significantly correlated with that in tumor tissues (R2 = .91, P = .045). According to age, the incidence rates of ALK fusions among young (age <45 years), middle‐aged (between 45 and 70 years) and elderly (>70 years) patients were significantly different (P < .001). In 70 ALK‐rearranged cases, coexistence of epidermal growth factor receptor (EGFR) alterations and ALK fusions was detected in 12 cases (17.1%) and EGFR mutations tended to coexist with non‐EML4‐ALK rearrangements. Notably, novel ALK fusion partners, including TRIM66,SWAP70,WNK3,ERC1,TCF12 and FBN1 were identified in the present study. Among EML4‐ALK fusion variants, patients with variant V1 were younger than patients with variant V3 (P = .023), and TP53 mutations were more frequently concurrent with variant V3 compared with variant V1 (P = .009). In conclusion, these findings provide new insights into the molecular‐clinical profiles of patients with ALK‐rearranged NSCLC that may improve the treatment strategy of this population.
Collapse
Affiliation(s)
- Xiaoyun Zhou
- Department of Medical Oncology, Sir Run Run Shaw Hospital, Zhejiang University, Hangzhou, China
| | - Jiawei Shou
- Department of Medical Oncology, Sir Run Run Shaw Hospital, Zhejiang University, Hangzhou, China
| | - Jin Sheng
- Department of Medical Oncology, Sir Run Run Shaw Hospital, Zhejiang University, Hangzhou, China
| | - Chunwei Xu
- Department of Pathology, Fujian Cancer Hospital, Fujian Medical University, Fuzhou, China
| | - Shengxiang Ren
- Department of Medical Oncology, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai, China
| | - Xiuyu Cai
- Sun Yet-Sen University Cancer Center, Guangzhou, China
| | - Qian Chu
- Department of Oncology, Tongji Hospital of Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Wenxian Wang
- Department of Chemotherapy, Zhejiang Cancer Hospital, Hangzhou, China
| | - Qinhong Zhen
- Department of Medical Oncology, Quzhou People's Hospital, Quzhou, China
| | - Yuefen Zhou
- Department of Medical Oncology, Lishui Municipal Central Hospital, Lishui, China
| | - Wenfeng Li
- Department of Medical Oncology, First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
| | - Hong Pan
- Department of Medical Oncology, Sir Run Run Shaw Hospital, Zhejiang University, Hangzhou, China
| | - Hongsen Li
- Department of Medical Oncology, Sir Run Run Shaw Hospital, Zhejiang University, Hangzhou, China
| | - Tao Sun
- Department of Surgery, University of Chicago, Chicago, USA
| | | | - Huina Wang
- Acornmed Biotechnology Co., Ltd., Beijing, China
| | - Feng Lou
- Acornmed Biotechnology Co., Ltd., Beijing, China
| | - Chuangzhou Rao
- Department of Radiation and Chemotherapy, Hwamei Hospital, University of Chinese Academy of Sciences, Ningbo, China
| | - Shanbo Cao
- Acornmed Biotechnology Co., Ltd., Beijing, China
| | - Hongming Pan
- Department of Medical Oncology, Sir Run Run Shaw Hospital, Zhejiang University, Hangzhou, China
| | - Yong Fang
- Department of Medical Oncology, Sir Run Run Shaw Hospital, Zhejiang University, Hangzhou, China
| |
Collapse
|
28
|
Abstract
OPINION STATEMENT There has been rapid progress in the use of targeted therapies for ALK-positive which has led to improve dramatically PFS and OS in the metastatic ALK-rearranged NSCLC patients. There are several molecules now available (crizotinib, ceritinib, brigatinib, alectinib, and lorlatinib) and others in development. Such an improvement in treatment efficacy has even more highlighted the importance of an adequate identification of ALK alterations. Efficient and easily accessible testing tools are required to identify eligible patients in a timely fashion. Different methods for detecting ALK+ NSCLC patients are now available, with fluorescence in situ hybridization (FISH) and immunohistochemistry (IHC) currently representing validated diagnostic techniques for the initial assessment of ALK status. Furthermore the widespread use of next-generation sequencing to detect other possible different activating mutations has allowed to identify individual ALK fusion variants. Several more expensive and time-consuming methods are also available nowadays which have the advantage to detect even rarer uncommon ALK fusion variants and mutations in tumour or blood samples. A review of the evolving testing-treatment landscape is needed to highlight the importance of properly diagnosing and treating this group of patients.
Collapse
|
29
|
Mendoza DP, Stowell J, Muzikansky A, Shepard JAO, Shaw AT, Digumarthy SR. Computed Tomography Imaging Characteristics of Non-Small-Cell Lung Cancer With Anaplastic Lymphoma Kinase Rearrangements: A Systematic Review and Meta-Analysis. Clin Lung Cancer 2019; 20:339-349. [PMID: 31164317 DOI: 10.1016/j.cllc.2019.05.006] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2019] [Revised: 04/14/2019] [Accepted: 05/02/2019] [Indexed: 02/06/2023]
Abstract
INTRODUCTION Several studies have suggested that non-small-cell lung cancer (NSCLC) patients who harbor anaplastic lymphoma kinase (ALK) rearrangement might have different imaging features compared with those without the rearrangement. The goal of this work was to systematically investigate the computed tomography (CT) imaging features of ALK-rearranged NSCLC. MATERIALS AND METHODS We searched published studies that investigated CT imaging features of ALK-rearranged NSCLC compared with ALK-negative, including epidermal growth factor receptor (EGFR)-mutant and ALK/EGFR-negative, NSCLC. We extracted clinicopathologic characteristics and CT imaging features of patients in the included studies. Features were compared and tested in the form of odds ratios (ORs) or weighted mean differences at a 95% confidence interval. RESULTS Twelve studies with 2210 patients with NSCLC were included. Compared with ALK-negative NSCLC, ALK-rearranged NSCLC was more likely to be solid (OR, 2.37; P < .001) and less likely to have cavitation (OR, 0.45; P = .002). In advanced stages, patients with ALK-rearranged NSCLC, compared with EGFR-mutant NSCLC, were more likely to have lymphadenopathy (OR, 3.47; P < .001), pericardial metastasis (OR, 2.18; P = .04), pleural metastasis (OR, 2.07; P = .004), and lymphangitic carcinomatosis (OR, 3.41; P = .02), but less likely to have lung metastasis (OR, 0.52; P = .003). Compared with ALK/EGFR-negative NSCLC, ALK-rearranged NSCLC was more likely to have lymphangitic carcinomatosis (OR, 3.88; P = .03), pleural metastasis (OR, 1.89; P = .02), and pleural effusion (OR, 2.94; P = .003). CONCLUSION ALK-rearranged NSCLC has imaging features that are different compared with EGFR-mutant and ALK/EGFR-negative NSCLC. These imaging features might provide clues as to the presence of ALK rearrangement and help in the selection of patients who might benefit from expedited molecular testing or repeat testing after a negative assay.
Collapse
Affiliation(s)
- Dexter P Mendoza
- Department of Radiology, Massachusetts General Hospital, Boston, MA
| | - Justin Stowell
- Department of Radiology, Massachusetts General Hospital, Boston, MA
| | - Alona Muzikansky
- Biostatistics Center, Massachusetts General Hospital, Boston, MA
| | | | - Alice T Shaw
- Massachusetts General Hospital Cancer Center and Department of Medicine, Massachusetts General Hospital, Boston, MA
| | | |
Collapse
|
30
|
Lin C, Shi X, Yang S, Zhao J, He Q, Jin Y, Yu X. Comparison of ALK detection by FISH, IHC and NGS to predict benefit from crizotinib in advanced non-small-cell lung cancer. Lung Cancer 2019; 131:62-68. [PMID: 31027700 DOI: 10.1016/j.lungcan.2019.03.018] [Citation(s) in RCA: 66] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2018] [Revised: 10/28/2018] [Accepted: 03/19/2019] [Indexed: 01/06/2023]
Abstract
PURPOSE Anaplastic lymphoma kinase (ALK) is now a validated kinase target in non-small cell lung cancer (NSCLC). We implemented three ALK laboratory methodologies: fluorescence in situ hybridization (FISH), immunohistochemistry (IHC) and next-generation sequencing (NGS) to detect EML4-ALK fusions and compared the predictive value for Crizotinib efficacy in ALK-positive patients. METHODS 55 ALK positive patients confirmed by at least one method were enrolled in the present study, of whom 45 cases were assessed by FISH, IHC and NGS concurrently, and another 10 cases only received IHC and NGS assessment for ALK status. RESULTS IHC presented the uppermost positive rate (94.5%), followed by NGS (92.7%) and FISH(82.4%), among which IHC and NGS had the highest concordance rate of 87.3%. No difference was detected in ORR, DCR and PFS of ALK positive cases defined in three groups. Notably, NGS positive patients were correlated with a higher DCR and longer PFS compared to NGS negative cases (P = 0.02 and P = 0.09), while FISH and IHC status were not distinguishing in predicting the outcome of Crizotinib. TP53 concurrent mutation might reduce responsiveness to Crizotinib and worsen prognosis in ALK-rearranged NSCLC. CONCLUSION FISH present a certain false-negative rate although considered the gold standard. Ventana-D5F3 IHC is qualified as a screening tool, while NGS positive may predict clinical benefit of Crizotinib more accurately, allowing efficient test for specific variants and concurrent genomic alterations.
Collapse
Affiliation(s)
- Chen Lin
- Department of Medical Oncology, Zhejiang Cancer Hospital, China
| | - Xun Shi
- Department of Medical Oncology, Zhejiang Cancer Hospital, China
| | - Shao Yang
- Nanjing Geneseeq Technology Inc., Nangjing, China
| | - Jun Zhao
- Department of Medical Oncology, Zhejiang Cancer Hospital, China
| | - Qiong He
- Department of Medical Oncology, Zhejiang Cancer Hospital, China
| | - Ying Jin
- Department of Medical Oncology, Zhejiang Cancer Hospital, China; Zhejiang Key Laboratory of Radiation Oncology, China.
| | - Xinmin Yu
- Department of Medical Oncology, Zhejiang Cancer Hospital, China; Zhejiang Key Laboratory of Diagnosis and Treatment Technology of Thoracic Oncology, China.
| |
Collapse
|
31
|
Next-generation Sequencing for ALK and ROS1 Rearrangement Detection in Patients With Non-small-cell Lung Cancer: Implications of FISH-positive Patterns. Clin Lung Cancer 2019; 20:e421-e429. [PMID: 30898567 DOI: 10.1016/j.cllc.2019.02.008] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2018] [Revised: 02/13/2019] [Accepted: 02/17/2019] [Indexed: 01/12/2023]
Abstract
BACKGROUND Detection of ALK and ROS1 gene rearrangements in non-small-cell lung cancer is required for directing patient care. Although fluorescence in situ hybridization (FISH) and immunohistochemistry have been established as gold standard methods, next-generation sequencing (NGS) platforms are called to be at least equally successful. Comparison of these methods for translation into daily use is currently under investigation. PATIENTS AND METHODS Forty non-small-cell lung cancer paraffin-embedded samples with previous ALK (n = 33) and ROS1 (n = 7) FISH results were examined with the Oncomine Focus Assay and tested for ALK and ROS1 immunoreactivity. Clinical implications of concurrent molecular alterations and concordance between methods were evaluated. RESULTS NGS was successful in 32 (80%) cases: 25 ALK and 7 ROS1. Few concomitant alterations were detected: 1 ALK rearranged case had an ALK p.L1196M-resistant mutation, 4 had CDK4, MYC, and/or ALK amplifications, and 1 ROS1 rearranged case showed a FGFR4 amplification. Comparison between techniques revealed 5 (16%) discordant cases that had lower progression-free survival than concordant cases: 7.6 (95% confidence interval, 2.2-13) versus 19.4 (95% confidence interval, 10.1-28.6). Remarkably, 4 of these cases had isolated 3' signal FISH pattern (P = .026). CONCLUSION Our data support that the identification of 3' isolated signal FISH pattern in ALK and ROS1 cases might suggest a false-positive result. NGS seems a reliable technique to assess ALK and ROS1 rearrangements, offering the advantage over immunohistochemistry of detecting other molecular alterations with potential therapeutic implications.
Collapse
|
32
|
Herbreteau G, Vallée A, Charpentier S, Normanno N, Hofman P, Denis MG. Circulating free tumor DNA in non-small cell lung cancer (NSCLC): clinical application and future perspectives. J Thorac Dis 2019; 11:S113-S126. [PMID: 30775034 DOI: 10.21037/jtd.2018.12.18] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Major advances in the treatment of non-small cell lung cancer (NSCLC) patients have been obtained during the last decade. Molecular testing of tumor samples is therefore mandatory in routine clinical practice. Tumor DNA is also present as cell-free molecules in blood, which is therefore a very useful and convenient source of tumor DNA. In this review, we discuss pre-analytical and analytical aspects of circulating tumor DNA (ctDNA) analysis. We also describe the use of ctDNA analysis in routine clinical practice, and discuss the potential use of ctDNA monitoring both to identify minimal residual disease and as a potential tool to early identify patients' response to treatment.
Collapse
Affiliation(s)
- Guillaume Herbreteau
- Department of Biochemistry, Nantes University Hospital, 9 quai Moncousu, F-44093 Nantes Cedex, France
| | - Audrey Vallée
- Department of Biochemistry, Nantes University Hospital, 9 quai Moncousu, F-44093 Nantes Cedex, France
| | - Sandrine Charpentier
- Department of Biochemistry, Nantes University Hospital, 9 quai Moncousu, F-44093 Nantes Cedex, France
| | - Nicola Normanno
- Cell Biology and Biotherapy Unit, Istituto Nazionale Tumori, IRCCS, "Fondazione G. Pascale", Naples, Italy
| | - Paul Hofman
- Laboratory of Clinical and Experimental Pathology, Inserm U1081/CNRS 7284, Université Côte d'Azur, CHU Nice and FHU OncoAge, and Hospital-Integrated Biobank (BB-0033-00025), Pasteur Hospital, Nice, France
| | - Marc G Denis
- Department of Biochemistry, Nantes University Hospital, 9 quai Moncousu, F-44093 Nantes Cedex, France
| |
Collapse
|
33
|
Abstract
INTRODUCTION Anaplastic lymphoma kinase (ALK) is one of the most attractive molecular targets for the treatment of patients with non-small-cell lung cancer. Treatment with ALK inhibitors is recognized as the standard-of-care for patients with ALK gene rearrangements, but it is important to appropriately select patients who will benefit from such treatment. Areas covered: In this article, we review the evidence regarding ALK testing. Immunohistochemistry (IHC), fluorescence in situ hybridization (FISH), and reverse transcription polymerase chain reaction (RT-PCR) are the representative methods for detecting ALK gene fusions. Among these diagnostic modalities, IHC in particular exhibits high sensitivity and specificity for the detection of ALK fusions when appropriately applied and interpreted. Expert commentary: Discrepancies have been reported between the results of IHC and FISH. However, it was revealed that patients with IHC-positivity and FISH-negativity may respond to alectinib, indicating that IHC can be used as a stand-alone method from a clinical standpoint for the identification of patients eligible for treatment with ALK inhibitors. In addition, differences between ALK variants have been reported to affect the prognosis and efficacy of ALK inhibitor-based treatments, and RT-PCR will likely increase in importance as a complementary tool.
Collapse
Affiliation(s)
- Yuka Kozuma
- a Department of Thoracic Oncology , National Kyushu Cancer Center , Fukuoka , Japan.,b Department of Surgery and Sciences, Graduate School of Medical Sciences , Kyushu University , Fukuoka , Japan
| | - Gouji Toyokawa
- b Department of Surgery and Sciences, Graduate School of Medical Sciences , Kyushu University , Fukuoka , Japan
| | - Takashi Seto
- a Department of Thoracic Oncology , National Kyushu Cancer Center , Fukuoka , Japan
| |
Collapse
|
34
|
Grocholski S, Banerji S, Qing G, Dawe DE. Benefit of crizotinib in a lung cancer patient with discordant ALK testing results. Cancer Treat Res Commun 2018; 15:13-16. [PMID: 30207282 DOI: 10.1016/j.ctarc.2018.02.002] [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: 04/23/2017] [Revised: 02/12/2018] [Accepted: 02/19/2018] [Indexed: 11/16/2022]
Abstract
Crizotinib is a first line treatment for patients with non-small cell lung cancer (NSCLC) harboring translocations in anaplastic lymphoma kinase (ALK). The current gold standard for determining ALK status is fluorescence in-situ hybridisation (FISH), but immunohistochemistry (IHC) is becoming increasingly popular due to lower cost. There are currently few reports on clinical outcomes with crizotinib therapy in patients who have tested negative by FISH and positive by IHC. A 53 year old lifelong non-smoking, physically active male with newly diagnosed Stage IV NSCLC presented with shortness of breath on exertion one month prior to referral. Staging CT scan failed to show a discreet lung lesion, but the left lower lobe was collapsed due to pleural effusion. Pleural fluid showed adenocarcinoma and IHC was positive for an ALK mutation, while FISH was negative. Pre-treatment PET-CT showed hypermetabolic, enlarged lymph nodes in the mediastinum and retroperitoneum. Partially due to patient concerns about cytotoxic chemotherapy toxicity, crizotinib therapy was instituted. Repeat CT conducted two months after crizotinib initiation showed a decrease in lymphadenopathy at all sites compared to the PET-CT. Furthermore, the patient showed clinical improvement, with less drainage through his PleurX catheter and stability of his excellent performance status. After 12 months on crizotinib CT showed ongoing improvement in lymphadenopathy. His bloodwork has been stable, and he denies significant drug toxicity. This case illustrates a sustained response to crizotinib therapy in a patient with an ALK translocation identified by IHC, but with negative FISH testing. The literature suggests that the population with these discordant results could be up to 19% of ALK positive NSCLC. Patients in this subgroup who are receiving crizotinib should be identified and outcome data pooled. However, in the interim, oncologists may wish to consider targeted therapy for these discordant patients.
Collapse
Affiliation(s)
- Steven Grocholski
- Rady Faculty of Health Sciences, Department of Internal Medicine, University of Manitoba, Winnipeg, MB, Canada
| | - Shantanu Banerji
- Rady Faculty of Health Sciences, Department of Internal Medicine, University of Manitoba, Winnipeg, MB, Canada; Cancer Care Manitoba, Department of Hematology and Medical Oncology, Winnipeg, MB, Canada
| | - Gefei Qing
- Rady Faculty of Health Sciences, Department of Pathology, University of Manitoba, Winnipeg, MB, Canada
| | - David E Dawe
- Rady Faculty of Health Sciences, Department of Internal Medicine, University of Manitoba, Winnipeg, MB, Canada; Cancer Care Manitoba, Department of Hematology and Medical Oncology, Winnipeg, MB, Canada.
| |
Collapse
|
35
|
Mehrad M, Roy S, LaFramboise WA, Petrosko P, Miller C, Incharoen P, Dacic S. KRAS mutation is predictive of outcome in patients with pulmonary sarcomatoid carcinoma. Histopathology 2018; 73:207-214. [PMID: 29489023 DOI: 10.1111/his.13505] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2017] [Accepted: 02/24/2018] [Indexed: 12/31/2022]
Abstract
AIMS Pulmonary sarcomatoid carcinoma (PSC) is a poorly differentiated non-small-cell lung carcinoma (NSCLC) with aggressive behaviour. This study aimed to evaluate the prognostic clinicopathological and genetic characteristics of PSCs. METHODS AND RESULTS Fifty-three cases of surgically treated PSCs were selected, 23 of which were subjected to mutation and copy number variation analysis using the 50-gene Ion AmpliSeq Cancer Panel. The majority of the patients were male (32 of 53, 60.3%) and smokers (51 of 53, 96.2%). Overall, 25 (47.1%) patients died within 2-105 months (mean = 22.7 months, median = 15 months) after diagnosis, and 28 were alive 3-141 months (mean = 38.7 months, median = 21.5 months) after diagnosis. Five-year overall survival was 12.5%. KRAS codon 12/13 mutation in adenocarcinomas (P = 0.01), age more than 70 years (P = 0.008) and tumour size ≥4.0 cm (P = 0.02) were associated strongly with worse outcome. TP53 (17 of 23, 74.0%) and KRAS codon 12 of 13 mutations (10 of 23, 43.4%) were the most common genetic alterations. Potentially actionable variants were identified including ATM (four of 23, 17.3%), MET, FBXW7 and EGFR (two of 23, 8.7%), AKT1, KIT, PDGFRA, HRAS, JAK3 and SMAD4 (one of 23, 4.3%). MET exon 14 skipping and missense mutations were identified in two (11.1%) cases with adenocarcinoma histology. Copy number analysis showed loss of RB1 (three of 23, 13%) and ATM (two of 23, 8.7%). Copy number gains were seen in EGFR (two of 23, 13.0%) and in one (4.3%) of each PIK3CA, KRAS, MET and STK11. CONCLUSIONS Potentially targetable mutations can be identified in a subset of PSC, although most tumours harbour currently untargetable prognostically adverse TP53 and KRAS mutations.
Collapse
Affiliation(s)
- Mitra Mehrad
- Department of Pathology, Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Somak Roy
- Department of Pathology, University of Pittsburgh Medical Center, Pittsburgh, PA, USA
| | - William A LaFramboise
- Department of Pathology, University of Pittsburgh Medical Center, Pittsburgh, PA, USA
| | - Patti Petrosko
- Department of Pathology, University of Pittsburgh Medical Center, Pittsburgh, PA, USA
| | - Caitlyn Miller
- Department of Pathology, University of Pittsburgh Medical Center, Pittsburgh, PA, USA
| | | | - Sanja Dacic
- Department of Pathology, University of Pittsburgh Medical Center, Pittsburgh, PA, USA
| |
Collapse
|
36
|
Xu CW, Wang WX, Chen YP, Chen Y, Liu W, Zhong LH, Chen FF, Zhuang W, Song ZB, Chen XH, Huang YJ, Guan YF, Yi X, Lv TF, Zhu WF, Lu JP, Wang XJ, Shi Y, Lin XD, Chen G, Song Y. Simultaneous VENTANA IHC and RT-PCR testing of ALK status in Chinese non-small cell lung cancer patients and response to crizotinib. J Transl Med 2018; 16:93. [PMID: 29642919 PMCID: PMC5896026 DOI: 10.1186/s12967-018-1468-9] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2017] [Accepted: 03/31/2018] [Indexed: 11/19/2022] Open
Abstract
Background ALK rearrangement-advanced NSCLC patients respond to crizotinib. ALK rearrangement is currently determined with RT-PCR. VENTANA IHC is a standard method to identify ALK protein overexpression in NSCLC; however, VENTANA IHC has rarely been used to determine the response to crizotinib in Chinese patients with NSCLC and ALK overexpression. To better clarify the clinical implication of VENTANA IHC to detect ALK rearrangements, we conducted this study to analyze VENTANA IHC and RT-PCR in a large cohort of Chinese patients with NSCLC undergoing screening for ALK rearrangements. Methods A total of 1720 patients with NSCLC who had ALK rearrangements detected by VENTANA IHC and/or RT-PCR were included in this analysis. We compared the efficacy and survival of ALK-positive patients detected by VENTANA IHC and RT-PCR. We used NGS to identify patients in whom the two methods were inconsistent. Results Among 1720 patients, 187 (10.87%) were shown to be ALK-positive by VENTANA IHC and/or RT-PCR, and 66 received crizotinib treatment. We identified 10.27% (172/1674) of patients as ALK-positive by the VENTANA IHC method, and 12.73% (41/322) of patients had ALK rearrangements by the RT-PCR method. Twenty-nine of 276 (10.51%) ALK-positive patients were simultaneously analyzed using VENTANA IHC and RT-PCR. The overall response rates were 65.90% (29/44) by VENTANA IHC and 55.88% (19/34) by RT-PCR. The disease control rates were 86.36% (38/44) by VENTANA IHC and 76.47% (26/34) by RT-PCR. In contrast, the median progression-free survival for VENTANA IHC and RT-PCR was 8.5 and 9.2 months, respectively. The VENTANA IHC and RT-PCR results obtained for 6 of 17 ALK-positive patients were inconsistent based on NGS; specifically, 4 patients had EML4-ALK fusions, 2 patients had non EML4-ALK fusions, 1 patient had a KCL1-ALK fusion, and one patient had a FBXO36-ALK fusion. Conclusions VENTANA IHC is a reliable and rapid screening tool used in routine pathologic laboratories for the identification of suitable candidates for ALK-targeted therapy. VENTANA IHC has moderate sensitivity and a slightly higher association with response to therapy with ALK inhibitors, and some VENTANA IHC-positive, but RT-PCR-negative cases may benefit from crizotinib.
Collapse
Affiliation(s)
- Chun-Wei Xu
- Department of Pathology, Fujian Cancer Hospital, Fujian Medical University Cancer Hospital, No 420, Fuma Road, Fuzhou, 350014, Fujian, People's Republic of China
| | - Wen-Xian Wang
- Department of Chemotherapy, Zhejiang Cancer Hospital, Hangzhou, 310022, Zhejiang, People's Republic of China
| | - Yan-Ping Chen
- Department of Pathology, Fujian Cancer Hospital, Fujian Medical University Cancer Hospital, No 420, Fuma Road, Fuzhou, 350014, Fujian, People's Republic of China
| | - Yu Chen
- Department of Medical Oncology, Fujian Cancer Hospital, Fujian Medical University Cancer Hospital, Fuzhou, 350014, Fujian, People's Republic of China
| | - Wei Liu
- Department of Pathology, Fujian Cancer Hospital, Fujian Medical University Cancer Hospital, No 420, Fuma Road, Fuzhou, 350014, Fujian, People's Republic of China
| | - Li-Hua Zhong
- Department of Pathology, Fujian Cancer Hospital, Fujian Medical University Cancer Hospital, No 420, Fuma Road, Fuzhou, 350014, Fujian, People's Republic of China
| | - Fang-Fang Chen
- Department of Pathology, Fujian Cancer Hospital, Fujian Medical University Cancer Hospital, No 420, Fuma Road, Fuzhou, 350014, Fujian, People's Republic of China
| | - Wu Zhuang
- Department of Medical Oncology, Fujian Cancer Hospital, Fujian Medical University Cancer Hospital, Fuzhou, 350014, Fujian, People's Republic of China
| | - Zheng-Bo Song
- Department of Chemotherapy, Zhejiang Cancer Hospital, Hangzhou, 310022, Zhejiang, People's Republic of China
| | - Xiao-Hui Chen
- Department of Thoracic Surgery, Fujian Cancer Hospital, Fujian Medical University Cancer Hospital, Fuzhou, 350014, Fujian, People's Republic of China
| | - Yun-Jian Huang
- Department of Medical Oncology, Fujian Cancer Hospital, Fujian Medical University Cancer Hospital, Fuzhou, 350014, Fujian, People's Republic of China
| | - Yan-Fang Guan
- Geneplus-Beijing, Beijing, 102200, People's Republic of China
| | - Xin Yi
- Geneplus-Beijing, Beijing, 102200, People's Republic of China
| | - Tang-Feng Lv
- Department of Respiratory Medicine, Jinling Hospital, Nanjing, 210002, Jiangsu, People's Republic of China
| | - Wei-Feng Zhu
- Department of Pathology, Fujian Cancer Hospital, Fujian Medical University Cancer Hospital, No 420, Fuma Road, Fuzhou, 350014, Fujian, People's Republic of China
| | - Jian-Ping Lu
- Department of Pathology, Fujian Cancer Hospital, Fujian Medical University Cancer Hospital, No 420, Fuma Road, Fuzhou, 350014, Fujian, People's Republic of China
| | - Xiao-Jiang Wang
- Department of Pathology, Fujian Cancer Hospital, Fujian Medical University Cancer Hospital, No 420, Fuma Road, Fuzhou, 350014, Fujian, People's Republic of China
| | - Yi Shi
- Department of Pathology, Fujian Cancer Hospital, Fujian Medical University Cancer Hospital, No 420, Fuma Road, Fuzhou, 350014, Fujian, People's Republic of China
| | - Xian-Dong Lin
- Department of Pathology, Fujian Cancer Hospital, Fujian Medical University Cancer Hospital, No 420, Fuma Road, Fuzhou, 350014, Fujian, People's Republic of China
| | - Gang Chen
- Department of Pathology, Fujian Cancer Hospital, Fujian Medical University Cancer Hospital, No 420, Fuma Road, Fuzhou, 350014, Fujian, People's Republic of China.
| | - Yong Song
- Department of Respiratory Medicine, Jinling Hospital, Nanjing, 210002, Jiangsu, People's Republic of China
| |
Collapse
|
37
|
Lindeman NI, Cagle PT, Aisner DL, Arcila ME, Beasley MB, Bernicker EH, Colasacco C, Dacic S, Hirsch FR, Kerr K, Kwiatkowski DJ, Ladanyi M, Nowak JA, Sholl L, Temple-Smolkin R, Solomon B, Souter LH, Thunnissen E, Tsao MS, Ventura CB, Wynes MW, Yatabe Y. Updated Molecular Testing Guideline for the Selection of Lung Cancer Patients for Treatment With Targeted Tyrosine Kinase Inhibitors: Guideline From the College of American Pathologists, the International Association for the Study of Lung Cancer, and the Association for Molecular Pathology. Arch Pathol Lab Med 2018; 142:321-346. [PMID: 29355391 DOI: 10.5858/arpa.2017-0388-cp] [Citation(s) in RCA: 515] [Impact Index Per Article: 85.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
CONTEXT - In 2013, an evidence-based guideline was published by the College of American Pathologists, the International Association for the Study of Lung Cancer, and the Association for Molecular Pathology to set standards for the molecular analysis of lung cancers to guide treatment decisions with targeted inhibitors. New evidence has prompted an evaluation of additional laboratory technologies, targetable genes, patient populations, and tumor types for testing. OBJECTIVE - To systematically review and update the 2013 guideline to affirm its validity; to assess the evidence of new genetic discoveries, technologies, and therapies; and to issue an evidence-based update. DESIGN - The College of American Pathologists, the International Association for the Study of Lung Cancer, and the Association for Molecular Pathology convened an expert panel to develop an evidence-based guideline to help define the key questions and literature search terms, review abstracts and full articles, and draft recommendations. RESULTS - Eighteen new recommendations were drafted. The panel also updated 3 recommendations from the 2013 guideline. CONCLUSIONS - The 2013 guideline was largely reaffirmed with updated recommendations to allow testing of cytology samples, require improved assay sensitivity, and recommend against the use of immunohistochemistry for EGFR testing. Key new recommendations include ROS1 testing for all adenocarcinoma patients; the inclusion of additional genes ( ERBB2, MET, BRAF, KRAS, and RET) for laboratories that perform next-generation sequencing panels; immunohistochemistry as an alternative to fluorescence in situ hybridization for ALK and/or ROS1 testing; use of 5% sensitivity assays for EGFR T790M mutations in patients with secondary resistance to EGFR inhibitors; and the use of cell-free DNA to "rule in" targetable mutations when tissue is limited or hard to obtain.
Collapse
Affiliation(s)
- Neal I Lindeman
- From the Departments of Pathology (Drs Lindeman and Sholl) and Medicine (Dr Kwiatkowski), Brigham and Women's Hospital, Boston, Massachusetts; the Cancer Center (Dr Bernicker) and the Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, Texas (Dr Cagle); the Department of Pathology, University of Colorado School of Medicine, Denver (Dr Aisner); the Diagnostic and Molecular Pathology Laboratory (Dr Arcila) and the Molecular Diagnostics Service (Dr Ladanyi), Memorial Sloan Kettering Cancer Center, New York, New York; the Department of Pathology & Medicine, Pulmonary, Critical Care and Sleep Medicine, New York, New York (Dr Beasley); the Pathology and Laboratory Quality Center, College of American Pathologists, Northfield, Illinois (Mss Colasacco and Ventura); the Department of Pathology, University of Pittsburgh, Pittsburgh, Pennsylvania (Dr Dacic); the Department of Medicine and Pathology, University of Colorado, Denver (Dr Hirsch); the Department of Pathology, University of Aberdeen, Aberdeen, Scotland (Dr Kerr); the Department of Molecular Pathology, Roswell Park Cancer Institute, Buffalo, New York (Dr Nowak); the Clinical and Scientific Affairs Division, Association for Molecular Pathology, Bethesda, Maryland (Dr Temple-Smolkin); the Molecular Therapeutics and Biomarkers Laboratory, Peter Maccallum Cancer Center, Melbourne, Australia (Dr Solomon); the Department of Pathology, VU University Medical Center, Amsterdam, the Netherlands (Dr Thunnissen); the Department of Laboratory Medicine and Pathobiology, Princess Margaret Cancer Center, Toronto, Ontario, Canada (Dr Tsao); Scientific Affairs, International Association for the Study of Lung Cancer, Aurora, Colorado (Dr Wynes); and the Department of Pathology and Molecular Diagnostics, Aichi Cancer Center, Nagoya, Japan (Dr Yatabe). Dr Souter is in private practice in Wellanport, Ontario, Canada
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
38
|
Lindeman NI, Cagle PT, Aisner DL, Arcila ME, Beasley MB, Bernicker EH, Colasacco C, Dacic S, Hirsch FR, Kerr K, Kwiatkowski DJ, Ladanyi M, Nowak JA, Sholl L, Temple-Smolkin R, Solomon B, Souter LH, Thunnissen E, Tsao MS, Ventura CB, Wynes MW, Yatabe Y. Updated Molecular Testing Guideline for the Selection of Lung Cancer Patients for Treatment With Targeted Tyrosine Kinase Inhibitors: Guideline From the College of American Pathologists, the International Association for the Study of Lung Cancer, and the Association for Molecular Pathology. J Thorac Oncol 2018; 13:323-358. [PMID: 29396253 DOI: 10.1016/j.jtho.2017.12.001] [Citation(s) in RCA: 326] [Impact Index Per Article: 54.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/29/2017] [Indexed: 12/15/2022]
Abstract
CONTEXT In 2013, an evidence-based guideline was published by the College of American Pathologists, the International Association for the Study of Lung Cancer, and the Association for Molecular Pathology to set standards for the molecular analysis of lung cancers to guide treatment decisions with targeted inhibitors. New evidence has prompted an evaluation of additional laboratory technologies, targetable genes, patient populations, and tumor types for testing. OBJECTIVE To systematically review and update the 2013 guideline to affirm its validity; to assess the evidence of new genetic discoveries, technologies, and therapies; and to issue an evidence-based update. DESIGN The College of American Pathologists, the International Association for the Study of Lung Cancer, and the Association for Molecular Pathology convened an expert panel to develop an evidence-based guideline to help define the key questions and literature search terms, review abstracts and full articles, and draft recommendations. RESULTS Eighteen new recommendations were drafted. The panel also updated 3 recommendations from the 2013 guideline. CONCLUSIONS The 2013 guideline was largely reaffirmed with updated recommendations to allow testing of cytology samples, require improved assay sensitivity, and recommend against the use of immunohistochemistry for EGFR testing. Key new recommendations include ROS1 testing for all adenocarcinoma patients; the inclusion of additional genes (ERBB2, MET, BRAF, KRAS, and RET) for laboratories that perform next-generation sequencing panels; immunohistochemistry as an alternative to fluorescence in situ hybridization for ALK and/or ROS1 testing; use of 5% sensitivity assays for EGFR T790M mutations in patients with secondary resistance to EGFR inhibitors; and the use of cell-free DNA to "rule in" targetable mutations when tissue is limited or hard to obtain.
Collapse
Affiliation(s)
- Neal I Lindeman
- Department of Pathology, Brigham and Women's Hospital, Boston, Massachusetts.
| | - Philip T Cagle
- Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, Texas
| | - Dara L Aisner
- Department of Pathology, University of Colorado School of Medicine, Denver, New York
| | - Maria E Arcila
- Diagnostic and Molecular Pathology Laboratory, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Mary Beth Beasley
- Department of Pathology & Medicine, Pulmonary, Critical Care and Sleep Medicine, New York, New York
| | | | - Carol Colasacco
- Pathology and Laboratory Quality Center, College of American Pathologists, Northfield, Illinois
| | - Sanja Dacic
- Department of Pathology, University of Pittsburgh, Pittsburgh, Pennsylvania
| | - Fred R Hirsch
- Department of Medicine and Pathology, University of Colorado, Denver, New York
| | - Keith Kerr
- Department of Pathology, University of Aberdeen, Aberdeen, Scotland
| | | | - Marc Ladanyi
- Molecular Diagnostics Service, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Jan A Nowak
- Department of Molecular Pathology, Roswell Park Cancer Institute, Buffalo, New York
| | - Lynette Sholl
- Department of Pathology, Brigham and Women's Hospital, Boston, Massachusetts
| | - Robyn Temple-Smolkin
- Clinical and Scientific Affairs Division, Association for Molecular Pathology, Bethesda, Maryland
| | - Benjamin Solomon
- Molecular Therapeutics and Biomarkers Laboratory, Peter Maccallum Cancer Center, Melbourne, Australia
| | | | - Erik Thunnissen
- Department of Pathology, VU University Medical Center, Amsterdam, the Netherlands
| | - Ming S Tsao
- Department of Laboratory Medicine and Pathobiology, Princess Margaret Cancer Center, Toronto, Ontario, Canada
| | - Christina B Ventura
- Pathology and Laboratory Quality Center, College of American Pathologists, Northfield, Illinois
| | - Murry W Wynes
- Scientific Affairs, International Association for the Study of Lung Cancer, Aurora, Colorado
| | - Yasushi Yatabe
- Department of Pathology and Molecular Diagnostics, Aichi Cancer Center, Nagoya, Japan
| |
Collapse
|
39
|
Lindeman NI, Cagle PT, Aisner DL, Arcila ME, Beasley MB, Bernicker EH, Colasacco C, Dacic S, Hirsch FR, Kerr K, Kwiatkowski DJ, Ladanyi M, Nowak JA, Sholl L, Temple-Smolkin R, Solomon B, Souter LH, Thunnissen E, Tsao MS, Ventura CB, Wynes MW, Yatabe Y. Updated Molecular Testing Guideline for the Selection of Lung Cancer Patients for Treatment With Targeted Tyrosine Kinase Inhibitors: Guideline From the College of American Pathologists, the International Association for the Study of Lung Cancer, and the Association for Molecular Pathology. J Mol Diagn 2018; 20:129-159. [PMID: 29398453 DOI: 10.1016/j.jmoldx.2017.11.004] [Citation(s) in RCA: 215] [Impact Index Per Article: 35.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/29/2017] [Indexed: 02/07/2023] Open
Abstract
CONTEXT In 2013, an evidence-based guideline was published by the College of American Pathologists, the International Association for the Study of Lung Cancer, and the Association for Molecular Pathology to set standards for the molecular analysis of lung cancers to guide treatment decisions with targeted inhibitors. New evidence has prompted an evaluation of additional laboratory technologies, targetable genes, patient populations, and tumor types for testing. OBJECTIVE To systematically review and update the 2013 guideline to affirm its validity; to assess the evidence of new genetic discoveries, technologies, and therapies; and to issue an evidence-based update. DESIGN The College of American Pathologists, the International Association for the Study of Lung Cancer, and the Association for Molecular Pathology convened an expert panel to develop an evidence-based guideline to help define the key questions and literature search terms, review abstracts and full articles, and draft recommendations. RESULTS Eighteen new recommendations were drafted. The panel also updated 3 recommendations from the 2013 guideline. CONCLUSIONS The 2013 guideline was largely reaffirmed with updated recommendations to allow testing of cytology samples, require improved assay sensitivity, and recommend against the use of immunohistochemistry for EGFR testing. Key new recommendations include ROS1 testing for all adenocarcinoma patients; the inclusion of additional genes (ERBB2, MET, BRAF, KRAS, and RET) for laboratories that perform next-generation sequencing panels; immunohistochemistry as an alternative to fluorescence in situ hybridization for ALK and/or ROS1 testing; use of 5% sensitivity assays for EGFR T790M mutations in patients with secondary resistance to EGFR inhibitors; and the use of cell-free DNA to "rule in" targetable mutations when tissue is limited or hard to obtain.
Collapse
Affiliation(s)
- Neal I Lindeman
- Department of Pathology, Brigham and Women's Hospital, Boston, Massachusetts.
| | - Philip T Cagle
- Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, Texas
| | - Dara L Aisner
- Department of Pathology, University of Colorado School of Medicine, Denver, Colorado
| | - Maria E Arcila
- Diagnostic and Molecular Pathology Laboratory, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Mary Beth Beasley
- Department of Pathology & Medicine, Pulmonary, Critical Care and Sleep Medicine, New York, New York
| | - Eric H Bernicker
- Cancer Research Program, Houston Methodist Research Institute, Houston, Texas
| | - Carol Colasacco
- Pathology and Laboratory Quality Center, College of American Pathologists, Northfield, Illinois
| | - Sanja Dacic
- Department of Pathology, University of Pittsburgh, Pittsburgh, Pennsylvania
| | - Fred R Hirsch
- Department of Medicine and Pathology, University of Colorado, Denver, Colorado
| | - Keith Kerr
- Department of Pathology, University of Aberdeen, Aberdeen, Scotland
| | | | - Marc Ladanyi
- Molecular Diagnostics Service, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Jan A Nowak
- Department of Molecular Pathology, Roswell Park Cancer Institute, Buffalo, New York
| | - Lynette Sholl
- Department of Pathology, Brigham and Women's Hospital, Boston, Massachusetts
| | - Robyn Temple-Smolkin
- Clinical and Scientific Affairs Division, Association for Molecular Pathology, Bethesda, Maryland
| | - Benjamin Solomon
- Molecular Therapeutics and Biomarkers Laboratory, Peter Maccallum Cancer Center, Melbourne, Australia
| | | | - Erik Thunnissen
- Department of Pathology, VU University Medical Center, Amsterdam, The Netherlands
| | - Ming S Tsao
- Department of Laboratory Medicine and Pathobiology, Princess Margaret Cancer Center, Toronto, Ontario, Canada
| | - Christina B Ventura
- Pathology and Laboratory Quality Center, College of American Pathologists, Northfield, Illinois
| | - Murry W Wynes
- Scientific Affairs, International Association for the Study of Lung Cancer, Aurora, Colorado
| | - Yasushi Yatabe
- Department of Pathology and Molecular Diagnostics, Aichi Cancer Center, Nagoya, Japan
| |
Collapse
|
40
|
Li TT, Gao X, Gao L, Gan BL, Xie ZC, Zeng JJ, Chen G. Role of upregulated miR-136-5p in lung adenocarcinoma: A study of 1242 samples utilizing bioinformatics analysis. Pathol Res Pract 2018. [PMID: 29526559 DOI: 10.1016/j.prp.2018.02.017] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/09/2023]
Abstract
BACKGROUND It is generally acknowledged that miRNAs play pivotal roles in the initiation and development of cancer. The aim of the current study is to investigate the clinicopathological role of miR-136-5p in lung adenocarcinoma and its underlying molecular mechanism. MATERIALS AND METHODS Data of a cohort of 1242 samples were provided by the Gene Expression Omnibus and The Cancer Genome Atlas to evaluate miR-136-5p expression in lung adenocarcinoma. A comprehensive meta-analysis integrating the expression data from all sources was performed, followed by a summary receiver operating curve plotted to appraise the upregulated expression of miR-136-5p in lung adenocarcinoma. Candidate targets of miR-136-5p were launched by the intersection of differentially expressed genes in The Cancer Genome Atlas and genes predicted by 12 web-based platforms. Then, hub genes were illustrated by a protein-protein interaction network. Furthermore, Kyoto Encyclopedia of Genes and Genomes, Gene Ontology and Protein Analysis Through Evolutionary Relationships analyses of potential target genes were carried out via bioinformatics tools. RESULTS MiR-136-5p expression was upregulated in lung adenocarcinoma versus normal tissues (standard mean difference = 0.43, 95% confidence interval: 0.27-0.58). The summary receiver operating characteristic curve further verified the upregulation of miR-136-5p in lung adenocarcinoma (area under curve = 0.7459). A total of 311 candidate target genes of miR-136-5p were gathered to create a protein-protein interaction network. Molecular mechanism analysis unveiled the potential miR-136-5p target genes participated in cell adhesion molecules, focal adhesion, complement and coagulation cascades and blood coagulation. CONCLUSION MiR-136-5p is overexpressed in lung adenocarcinoma and is involved in the molecular mechanism of lung adenocarcinoma via suppressing the expressions of downstream targets, especially claudin-18, sialophorin and syndecan 2 that participate in cell adhesion.
Collapse
Affiliation(s)
- Tian-Tian Li
- Department of Pathology, First Affiliated Hospital of Guangxi Medical University, 6 Shuangyong Road, Nanning, Guangxi Zhuang Autonomous Region, 530021, PR China
| | - Xiang Gao
- Department of Pathology, First Affiliated Hospital of Guangxi Medical University, 6 Shuangyong Road, Nanning, Guangxi Zhuang Autonomous Region, 530021, PR China
| | - Li Gao
- Department of Pathology, First Affiliated Hospital of Guangxi Medical University, 6 Shuangyong Road, Nanning, Guangxi Zhuang Autonomous Region, 530021, PR China
| | - Bin-Liang Gan
- Department of Pathology, First Affiliated Hospital of Guangxi Medical University, 6 Shuangyong Road, Nanning, Guangxi Zhuang Autonomous Region, 530021, PR China
| | - Zu-Cheng Xie
- Department of Pathology, First Affiliated Hospital of Guangxi Medical University, 6 Shuangyong Road, Nanning, Guangxi Zhuang Autonomous Region, 530021, PR China
| | - Jing-Jing Zeng
- Department of Pathology, First Affiliated Hospital of Guangxi Medical University, 6 Shuangyong Road, Nanning, Guangxi Zhuang Autonomous Region, 530021, PR China.
| | - Gang Chen
- Department of Pathology, First Affiliated Hospital of Guangxi Medical University, 6 Shuangyong Road, Nanning, Guangxi Zhuang Autonomous Region, 530021, PR China
| |
Collapse
|
41
|
Abstract
Alectinib is an ATP-competitive small molecule and a second-generation inhibitor of ALK. EML4-ALK rearrangement is found in 3-5% of patients with NSCLC. The first-generation inhibitor crizotinib has changed the treatment dramatically, though most of the patients show disease progression within one year. Extra-thoracic progress, i.e., CNS metastases is common. The second-generation inhibitor alectinib has shown significant improvement in PFS and a remarkable prolongation of time to CNS progression. Alectinib has received approval as first-line therapy as well as second-line therapy after crizotinib failure. The toxicity profile is favorable compared to crizotinib and chemotherapy.
Collapse
Affiliation(s)
- M Herden
- Department of Haematology, Oncology and Stem Cell Transplantation, University Medical Centre Freiburg, Faculty of Medicine, University of Freiburg, Hugstetter Str. 55, 79106, Freiburg, Germany
| | - Cornelius F Waller
- Department of Haematology, Oncology and Stem Cell Transplantation, University Medical Centre Freiburg, Faculty of Medicine, University of Freiburg, Hugstetter Str. 55, 79106, Freiburg, Germany.
| |
Collapse
|
42
|
ALK fusion variants detection by targeted RNA-next generation sequencing and clinical responses to crizotinib in ALK-positive non-small cell lung cancer. Lung Cancer 2017; 116:15-24. [PMID: 29413046 DOI: 10.1016/j.lungcan.2017.12.004] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2017] [Revised: 12/05/2017] [Accepted: 12/06/2017] [Indexed: 11/22/2022]
Abstract
OBJECTIVES The aim of the present study was firstly to assess in a clinical setting the yields of an amplicon-based parallel RNA sequencing (RNA-seq) assay for ALK fusion transcript variants detection in comparison with immunohistochemistry (IHC) and fluorescent in-situ hybridization (FISH) in a selected population of ALK-positive and ALK-negative non-small cell lung cancer (NSCLC) cases, and secondly to evaluate the impact of the ALK variant on crizotinib efficacy. MATERIALS AND METHODS The cohort used for the assessment of the RNA-seq assay comprised 53 samples initially diagnosed as being ALK-positive based on the results obtained by IHC and/or FISH, and 23 ALK-negative samples. A distinction was made between 'truly' IHC/FISH positive or 'truly' IHC/FISH negative samples, and those for which the IHC and/or FISH were equivocal (IHC) or borderline-positive (FISH). RESULTS On the overall population, RNA-seq sensitivity (Se) and specificity (Spe) were of 80% and 100%, respectively when IHC and FISH were combined. For the 31 'truly positive' samples, Se and Spe of 100% were reached. An ALK status could be assigned by RNA-seq in 10/10 of the equivocal and/or borderline-positive IHC/FISH cases, 2/7 IHC/FISH discordant cases. When crizotinib efficacy was evaluated according to the type of ALK variant, better clinical outcomes were observed in crizotinib-treated patients with EML4-ALK v1/v2/others variants compared to v3a/b variants. CONCLUSION RNA-seq detects ALK rearrangements with a high sensitivity and specificity using only 10 ng of RNA. It appears to be a promising rescue technique for non-clear-cut IHC/FISH cases and also offers a unique opportunity to identify ALK fusion variants and evaluate their predictive value for ALK inhibitors efficacy.
Collapse
|
43
|
Vendrell JA, Taviaux S, Béganton B, Godreuil S, Audran P, Grand D, Clermont E, Serre I, Szablewski V, Coopman P, Mazières J, Costes V, Pujol JL, Brousset P, Rouquette I, Solassol J. Detection of known and novel ALK fusion transcripts in lung cancer patients using next-generation sequencing approaches. Sci Rep 2017; 7:12510. [PMID: 28970558 PMCID: PMC5624911 DOI: 10.1038/s41598-017-12679-8] [Citation(s) in RCA: 73] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2017] [Accepted: 09/04/2017] [Indexed: 12/25/2022] Open
Abstract
Rearrangements of the anaplastic lymphoma kinase (ALK) gene in non-small cell lung cancer (NSCLC) represent a novel molecular target in a small subset of tumors. Although ALK rearrangements are usually assessed by immunohistochemistry (IHC) and fluorescence in situ hybridization (FISH), molecular approaches have recently emerged as relevant alternatives in routine laboratories. Here, we evaluated the use of two different amplicon-based next-generation sequencing (NGS) methods (AmpliSeq and Archer®FusionPlex®) to detect ALK rearrangements, and compared these with IHC and FISH. A total of 1128 NSCLC specimens were screened using conventional analyses, and a subset of 37 (15 ALK-positive, and 22 ALK-negative) samples were selected for NGS assays. Although AmpliSeq correctly detected 25/37 (67.6%) samples, 1/37 (2.7%) and 11/37 (29.7%) specimens were discordant and uncertain, respectively, requiring further validation. In contrast, Archer®FusionPlex® accurately classified all samples and allowed the correct identification of one rare DCTN1-ALK fusion, one novel CLIP1-ALK fusion, and one novel GCC2-ALK transcript. Of particular interest, two out of three patients harboring these singular rearrangements were treated with and sensitive to crizotinib. These data show that Archer®FusionPlex® may provide an effective and accurate alternative to FISH testing for the detection of known and novel ALK rearrangements in clinical diagnostic settings.
Collapse
Affiliation(s)
- Julie A Vendrell
- CHU Montpellier, Arnaud de Villeneuve Hospital, Department of Pathology, Montpellier, Université de Montpellier, Montpellier, France
| | - Sylvie Taviaux
- CHU Montpellier, Arnaud de Villeneuve Hospital, Department of Pathology, Montpellier, Université de Montpellier, Montpellier, France
| | - Benoît Béganton
- Institut de Recherche en Cancérologie de Montpellier (IRCM), INSERM U1194, Université de Montpellier, Institut du Cancer de Montpellier (ICM), Montpellier, France
| | - Sylvain Godreuil
- CHU Montpellier, Arnaud de Villeneuve Hospital, Department of Bacteriology, Université de Montpellier, Montpellier, France
| | - Patricia Audran
- Institut du Cancer de Montpellier (ICM), Department of Biopathology, Montpellier, France
| | - David Grand
- Department of Pathology, Institut Universitaire du Cancer Toulouse Oncopole, CHU de Toulouse, Toulouse, France
| | - Estelle Clermont
- Department of Pathology, Institut Universitaire du Cancer Toulouse Oncopole, CHU de Toulouse, Toulouse, France
| | - Isabelle Serre
- CHU Montpellier, Arnaud de Villeneuve Hospital, Department of Pathology, Montpellier, Université de Montpellier, Montpellier, France
| | - Vanessa Szablewski
- CHU Montpellier, Arnaud de Villeneuve Hospital, Department of Pathology, Montpellier, Université de Montpellier, Montpellier, France
| | - Peter Coopman
- Institut de Recherche en Cancérologie de Montpellier (IRCM), INSERM U1194, Université de Montpellier, Institut du Cancer de Montpellier (ICM), Montpellier, France
| | - Julien Mazières
- Thoracic Oncology Department, Larrey Hospital, University Hospital of Toulouse, Toulouse, France
| | - Valérie Costes
- CHU Montpellier, Arnaud de Villeneuve Hospital, Department of Pathology, Montpellier, Université de Montpellier, Montpellier, France
| | - Jean-Louis Pujol
- CHU Montpellier, Arnaud de Villeneuve Hospital, Department of Thoracic Oncology, Université de Montpellier, Montpellier, France
| | - Pierre Brousset
- Department of Pathology, Institut Universitaire du Cancer Toulouse Oncopole, CHU de Toulouse, Toulouse, France.,Laboratoire d'excellence Labex TOUCAN, Toulouse, France
| | - Isabelle Rouquette
- Department of Pathology, Institut Universitaire du Cancer Toulouse Oncopole, CHU de Toulouse, Toulouse, France
| | - Jérôme Solassol
- CHU Montpellier, Arnaud de Villeneuve Hospital, Department of Pathology, Montpellier, Université de Montpellier, Montpellier, France. .,Institut de Recherche en Cancérologie de Montpellier (IRCM), INSERM U1194, Université de Montpellier, Institut du Cancer de Montpellier (ICM), Montpellier, France.
| |
Collapse
|
44
|
ALK in Non-Small Cell Lung Cancer (NSCLC) Pathobiology, Epidemiology, Detection from Tumor Tissue and Algorithm Diagnosis in a Daily Practice. Cancers (Basel) 2017; 9:cancers9080107. [PMID: 28805682 PMCID: PMC5575610 DOI: 10.3390/cancers9080107] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2017] [Revised: 08/08/2017] [Accepted: 08/10/2017] [Indexed: 12/25/2022] Open
Abstract
Patients with advanced-stage non-small cell lung carcinoma (NSCLC) harboring an ALK rearrangement, detected from a tissue sample, can benefit from targeted ALK inhibitor treatment. Several increasingly effective ALK inhibitors are now available for treatment of patients. However, despite an initial favorable response to treatment, in most cases relapse or progression occurs due to resistance mechanisms mainly caused by mutations in the tyrosine kinase domain of ALK. The detection of an ALK rearrangement is pivotal and can be done using different methods, which have variable sensitivity and specificity depending, in particular, on the quality and quantity of the patient’s sample. This review will first highlight briefly some information regarding the pathobiology of an ALK rearrangement and the epidemiology of patients harboring this genomic alteration. The different methods used to detect an ALK rearrangement as well as their advantages and disadvantages will then be examined and algorithms proposed for detection in daily routine practice.
Collapse
|
45
|
Hout DR, Schweitzer BL, Lawrence K, Morris SW, Tucker T, Mazzola R, Skelton R, McMahon F, Handshoe J, Lesperance M, Karsan A, Saltman DL. Performance of a RT-PCR Assay in Comparison to FISH and Immunohistochemistry for the Detection of ALK in Non-Small Cell Lung Cancer. Cancers (Basel) 2017; 9:cancers9080099. [PMID: 28763012 PMCID: PMC5575602 DOI: 10.3390/cancers9080099] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2017] [Revised: 07/19/2017] [Accepted: 07/29/2017] [Indexed: 12/17/2022] Open
Abstract
Patients with lung cancers harboring an activating anaplastic lymphoma kinase (ALK) rearrangement respond favorably to ALK inhibitor therapy. Fluorescence in situ hybridization (FISH) and immunohistochemistry (IHC) are validated and widely used screening tests for ALK rearrangements but both methods have limitations. The ALK RGQ RT-PCR Kit (RT-PCR) is a single tube quantitative real-time PCR assay for high throughput and automated interpretation of ALK expression. In this study, we performed a direct comparison of formalin-fixed paraffin-embedded (FFPE) lung cancer specimens using all three ALK detection methods. The RT-PCR test (diagnostic cut-off ΔCt of ≤8) was shown to be highly sensitive (100%) when compared to FISH and IHC. Sequencing of RNA detected full-length ALK transcripts or EML4-ALK and KIF5B-ALK fusion variants in discordant cases in which ALK expression was detected by the ALK RT-PCR test but negative by FISH and IHC. The overall specificity of the RT-PCR test for the detection of ALK in cases without full-length ALK expression was 94% in comparison to FISH and sequencing. These data support the ALK RT-PCR test as a highly efficient and reliable diagnostic screening approach to identify patients with non-small cell lung cancer whose tumors are driven by oncogenic ALK.
Collapse
Affiliation(s)
- David R Hout
- Insight Genetics, Inc., Suite 510, 2 International Plaza, Nashville, TN 37217, USA.
| | - Brock L Schweitzer
- Insight Genetics, Inc., Suite 510, 2 International Plaza, Nashville, TN 37217, USA.
| | - Kasey Lawrence
- Insight Genetics, Inc., Suite 510, 2 International Plaza, Nashville, TN 37217, USA.
| | - Stephan W Morris
- Insight Genetics, Inc., Suite 510, 2 International Plaza, Nashville, TN 37217, USA.
| | - Tracy Tucker
- Department of Pathology and Laboratory Medicine, BC Cancer Agency, 675 West 10th Avenue, Vancouver, BC V5Z 1L3, Canada.
| | - Rosetta Mazzola
- Department of Medical Oncology, British Columbia Cancer Agency, VIC 2410 Lee Avenue, Victoria, BC V8R 6V5, Canada.
| | - Rachel Skelton
- Insight Genetics, Inc., Suite 510, 2 International Plaza, Nashville, TN 37217, USA.
| | - Frank McMahon
- Insight Genetics, Inc., Suite 510, 2 International Plaza, Nashville, TN 37217, USA.
| | - John Handshoe
- Insight Genetics, Inc., Suite 510, 2 International Plaza, Nashville, TN 37217, USA.
| | - Mary Lesperance
- Department of Mathematics and Statistics, University of Victoria, Box 1700, STN CSC, Victoria, BC V8W 2Y2, Canada.
| | - Aly Karsan
- Department of Pathology and Laboratory Medicine, BC Cancer Agency, 675 West 10th Avenue, Vancouver, BC V5Z 1L3, Canada.
| | - David L Saltman
- Department of Medical Oncology, British Columbia Cancer Agency, VIC 2410 Lee Avenue, Victoria, BC V8R 6V5, Canada.
| |
Collapse
|
46
|
Shackelford RE, Ansari JM, Wei EX, Alexander JS, Cotelingam J. Anaplastic lymphoma kinase rearrangements in non-small-cell lung cancer: novel applications in diagnostics and treatment. Pharmacogenomics 2017; 18:1179-1192. [PMID: 28745554 DOI: 10.2217/pgs-2017-0098] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
The ALK gene, first identified as an anaplastic large cell lymphoma driver mutation, is dysregulated in nearly 20 different human malignancies, including 3-7% of non-small-cell lung cancers (NSCLC). In NSCLC, ALK commonly fuses with the EML4, forming a constitutively active tyrosine kinase that drives oncogenic progression. Recently, several ALK-inhibiting drugs have been developed that are more effective than standard chemotherapeutic regimens in treating advanced ALK-positive NSCLC. For this reason, molecular diagnostic testing for dysregulated ALK expression is a necessary part of identifying optimal NSCLC treatment options. Here, we review the molecular pathology of ALK-positive NSCLC, ALK molecular diagnostic techniques, ALK-targeted NSCLC treatments, and drug resistance mechanisms to ALK-targeted therapies.
Collapse
Affiliation(s)
| | - Junaid M Ansari
- Department of Molecular & Cellular Physiology, LSU Health Sciences Center, Shreveport, LA 71130, USA
| | - Eric X Wei
- Department of Pathology, LSU Health Shreveport, Shreveport, LA, USA
| | - Jonathan S Alexander
- Department of Molecular & Cellular Physiology, LSU Health Sciences Center, Shreveport, LA 71130, USA
| | - James Cotelingam
- Department of Pathology, LSU Health Shreveport, Shreveport, LA, USA
| |
Collapse
|
47
|
Pisapia P, Lozano MD, Vigliar E, Bellevicine C, Pepe F, Malapelle U, Troncone G. ALK and ROS1 testing on lung cancer cytologic samples: Perspectives. Cancer Cytopathol 2017; 125:817-830. [DOI: 10.1002/cncy.21899] [Citation(s) in RCA: 43] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2017] [Revised: 07/10/2017] [Accepted: 07/10/2017] [Indexed: 12/23/2022]
Affiliation(s)
- Pasquale Pisapia
- Department of Public Health; University of Naples Federico II; Naples Italy
| | - Maria D. Lozano
- Department of Pathology; University Clinic of Navarra; Pamplona Spain
| | - Elena Vigliar
- Department of Public Health; University of Naples Federico II; Naples Italy
| | | | - Francesco Pepe
- 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
|
48
|
Trejo Bittar HE, Luvison A, Miller C, Dacic S. A comparison of ALK gene rearrangement and ALK protein expression in primary lung carcinoma and matched metastasis. Histopathology 2017; 71:269-277. [PMID: 28316074 DOI: 10.1111/his.13215] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2017] [Accepted: 03/15/2017] [Indexed: 11/28/2022]
Abstract
AIMS The 2013 College of American Pathologists, the Association for Molecular Pathology and the International Association for the Study of Lung Cancer guideline for EGFR and ALK testing in lung carcinoma indicates that either the primary tumour or the metastasis is suitable for testing. The heterogeneity of gene mutations has been studied extensively, while similar reports on gene rearrangements are limited. The aim of this study was to determine if ALK status between primary tumour and matched metastasis differs. METHODS AND RESULTS Fifteen ALK fluorescence in-situ hybridization (FISH) rearranged and 19 non-ALK FISH rearranged adenocarcinomas were collected retrospectively based on availability of tissue from a matched metastatic site. Sixty-eight samples were tested by ALK FISH (Vysis ALK break-apart FISH kit) and ALK immunohistochemistry (IHC) (Ventana ALK D5F3 CDx assay). Overall agreement of FISH and IHC was 88%, with IHC showing 100% specificity and 71% sensitivity. Concordance between primary site and metastasis by ALK FISH was seen in 30 cases (88%), and in 32 cases (94%) by ALK IHC. Five discordant cases were found (15%). Three ALK FISH discordant cases had low percentage of ALK FISH-positive tumour cells (average 23%, range: 18-31%) and all were negative by ALK IHC. One IHC discordant case had a high percentage of ALK FISH-positive tumour cells (67%), and was ALK IHC-negative. One FISH discordant case showed ALK FISH- and ALK IHC-positive primary tumour, but ALK FISH- and ALK IHC-negative metastasis. CONCLUSIONS ALK FISH results show more frequent discordances between primary tumour and matched metastases than ALK IHC, due probably to technical challenges and sample quality. This observation indicates that the quality of sample and technical expertise of the laboratory should guide the decision about ALK testing in clinical practice.
Collapse
Affiliation(s)
| | - Alyssa Luvison
- Department of Pathology, University of Pittsburgh Medical Center, Pittsburgh, PA, USA
| | - Caitlyn Miller
- Department of Pathology, University of Pittsburgh Medical Center, Pittsburgh, PA, USA
| | - Sanja Dacic
- Department of Pathology, University of Pittsburgh Medical Center, Pittsburgh, PA, USA
| |
Collapse
|
49
|
Yamamoto G, Kikuchi M, Kobayashi S, Arai Y, Fujiyoshi K, Wakatsuki T, Kakuta M, Yamane Y, Iijima Y, Mizutani H, Nakajima Y, Sudo J, Kinoshita H, Kurimoto F, Akiyama H, Uramoto H, Sakai H, Akagi Y, Akagi K. Routine genetic testing of lung cancer specimens derived from surgery, bronchoscopy and fluid aspiration by next generation sequencing. Int J Oncol 2017; 50:1579-1589. [PMID: 28350094 PMCID: PMC5403533 DOI: 10.3892/ijo.2017.3935] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2016] [Accepted: 02/10/2017] [Indexed: 01/11/2023] Open
Abstract
After the development of EGFR tyrosine kinase inhibitors (TKIs), genetic testing of EGFR became required for effective treatment of lung cancer. Initially, the testing was conducted separately for each mutated region. However, many EGFR mutations have since been identified that determine the efficacy of EGFR-TKIs. Therefore, genetic testing of EGFR by next generation sequencing (NGS) may be a suitable strategy for lung cancer. Here we examined the applicability of the NGS method in regard to sensitivity, time and cost. A total of 939 specimens were obtained from 686 lung cancer patients at our hospital. DNA and RNA were simultaneously extracted from specimens derived from surgery, bronchoscopy, and fluid aspiration. Specimens included cerebrospinal fluid, pleural effusion, abdominal fluid, and pericardial effusion. From RNA, target regions (EGFR, KRAS, ALK fusion and RET fusion) were enriched by RT-PCR and sequenced with MiSeq. From DNA, PCR or PCR-RFLP conventional methods were performed. NGS and conventional methods were carried out routinely per week. Among the total 939 specimens, 38 specimens could not be examined with NGS. Among these, 34 specimens were analyzed by conventional testing with simultaneously extracted DNA. The remaining four specimens could not be tested with either method. Compared with the conventional method, the concordance rate of mutations was 99% (892/901), excluding specimens with NGS failure. The time period required from processing of specimens to results was 4 days, and the cost per sample was sufficiently low. In conclusion, the genetic testing with NGS method was useful for lung cancer treatment. The cost, sensitivity and time were able to tolerate routine examinations.
Collapse
Affiliation(s)
- Gou Yamamoto
- Department of Molecular Diagnosis and Cancer Prevention, Saitama Cancer Center, Ina, Kitaadachi, Saitama 362-0806, Japan
| | - Mari Kikuchi
- Department of Molecular Diagnosis and Cancer Prevention, Saitama Cancer Center, Ina, Kitaadachi, Saitama 362-0806, Japan
| | - Shiho Kobayashi
- Department of Molecular Diagnosis and Cancer Prevention, Saitama Cancer Center, Ina, Kitaadachi, Saitama 362-0806, Japan
| | - Yoshiko Arai
- Department of Molecular Diagnosis and Cancer Prevention, Saitama Cancer Center, Ina, Kitaadachi, Saitama 362-0806, Japan
| | - Kenji Fujiyoshi
- Department of Molecular Diagnosis and Cancer Prevention, Saitama Cancer Center, Ina, Kitaadachi, Saitama 362-0806, Japan
| | - Tomokazu Wakatsuki
- Department of Molecular Diagnosis and Cancer Prevention, Saitama Cancer Center, Ina, Kitaadachi, Saitama 362-0806, Japan
| | - Miho Kakuta
- Department of Molecular Diagnosis and Cancer Prevention, Saitama Cancer Center, Ina, Kitaadachi, Saitama 362-0806, Japan
| | - Yuki Yamane
- Department of Thoracic Oncology, Saitama Cancer Center, Ina, Kitaadachi, Saitama 362-0806, Japan
| | - Yoshihito Iijima
- Department of Thoracic Surgery, Saitama Cancer Center, Ina, Kitaadachi, Saitama 362-0806, Japan
| | - Hideaki Mizutani
- Department of Thoracic Oncology, Saitama Cancer Center, Ina, Kitaadachi, Saitama 362-0806, Japan
| | - Yuki Nakajima
- Department of Thoracic Surgery, Saitama Cancer Center, Ina, Kitaadachi, Saitama 362-0806, Japan
| | - Junko Sudo
- Department of Thoracic Oncology, Saitama Cancer Center, Ina, Kitaadachi, Saitama 362-0806, Japan
| | - Hiroyasu Kinoshita
- Department of Thoracic Surgery, Saitama Cancer Center, Ina, Kitaadachi, Saitama 362-0806, Japan
| | - Futoshi Kurimoto
- Department of Thoracic Oncology, Saitama Cancer Center, Ina, Kitaadachi, Saitama 362-0806, Japan
| | - Hirohiko Akiyama
- Department of Thoracic Surgery, Saitama Cancer Center, Ina, Kitaadachi, Saitama 362-0806, Japan
| | - Hidetaka Uramoto
- Department of Thoracic Surgery, School of Medicine, Kanazawa Medical University, Uchinaka, Kahoku, Ishikawa 920-0293, Japan
| | - Hiroshi Sakai
- Department of Thoracic Oncology, Saitama Cancer Center, Ina, Kitaadachi, Saitama 362-0806, Japan
| | - Yoshito Akagi
- Department of Surgery, Kurume University, Kurume, Fukuoka 830-0011, Japan
| | - Kiwamu Akagi
- Department of Molecular Diagnosis and Cancer Prevention, Saitama Cancer Center, Ina, Kitaadachi, Saitama 362-0806, Japan
| |
Collapse
|