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Wei H, Teng F, Wang X, Hou X, Wang H, Wang H, Sun H, Zhou X. Identification of a prognosis-related gene signature and ceRNA regulatory networks in lung adenocarcinoma. Heliyon 2024; 10:e28084. [PMID: 38601687 PMCID: PMC11004716 DOI: 10.1016/j.heliyon.2024.e28084] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2023] [Revised: 02/23/2024] [Accepted: 03/12/2024] [Indexed: 04/12/2024] Open
Abstract
The ceRNA network, consisting of both noncoding RNA and protein-coding RNA, governs the occurrence, progression, metastasis, and infiltration of lung adenocarcinoma. Signatures comprising multiple genes can effectively determine survival stratification and prognosis of patients with lung adenocarcinoma. To explore the mechanisms of lung adenocarcinoma progression and identify potential biological targets, we carried out systematic bioinformatics analyses of the genetic profiles of lung adenocarcinoma, such as weighted gene co-expression network analysis (WGCNA), differential expression (DE) assessment, univariate and multivariate Cox proportional hazard regression models, ceRNA modulatory networks generated using the ENCORI and miRcode databases, nomogram models, ROC curve assessment, and Kaplan-Meier survival curve analysis. The ceRNA network encompassed 37 nodes, comprising 12 mRNAs, 22 lncRNAs, and three miRNAs. Simultaneously, we performed integration analysis using the 12 genes from the ceRNA network. Our findings revealed that the signature established by these 12 genes serves as an adverse element in lung adenocarcinoma, contributing to unfavorable patient prognosis. To ensure the credibility of our results, we used in vitro experiments for further verification. In conclusion, our study delved into the potential mechanisms underlying lung adenocarcinoma via the ceRNA regulatory network, specifically focusing on the PIF1 and has-miR-125a-5p axis. Additionally, a signature comprising 12 genes was identified as a biomarker related to the prognosis of lung adenocarcinoma.
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Affiliation(s)
- Hong Wei
- In-Patient Ultrasound Department, The Second Affiliated Hospital of Harbin Medical University, Harbin, 150081, China
| | - Fei Teng
- In-Patient Ultrasound Department, The Second Affiliated Hospital of Harbin Medical University, Harbin, 150081, China
| | - XiaoLei Wang
- In-Patient Ultrasound Department, The Second Affiliated Hospital of Harbin Medical University, Harbin, 150081, China
| | - XiuJuan Hou
- In-Patient Ultrasound Department, The Second Affiliated Hospital of Harbin Medical University, Harbin, 150081, China
| | - HongBo Wang
- In-Patient Ultrasound Department, The Second Affiliated Hospital of Harbin Medical University, Harbin, 150081, China
| | - Hong Wang
- In-Patient Ultrasound Department, The Second Affiliated Hospital of Harbin Medical University, Harbin, 150081, China
| | - Hui Sun
- In-Patient Ultrasound Department, The Second Affiliated Hospital of Harbin Medical University, Harbin, 150081, China
| | - XianLi Zhou
- In-Patient Ultrasound Department, The Second Affiliated Hospital of Harbin Medical University, Harbin, 150081, China
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Boichuk S, Dunaev P, Skripova V, Galembikova A, Bikinieva F, Shagimardanova E, Gazizova G, Deviatiiarov R, Valeeva E, Mikheeva E, Vasilyeva M, Kopnin P, Strelnikov V, Kiyamova R. Unraveling the Mechanisms of Sensitivity to Anti-FGF Therapies in Imatinib-Resistant Gastrointestinal Stromal Tumors (GIST) Lacking Secondary KIT Mutations. Cancers (Basel) 2023; 15:5354. [PMID: 38001614 PMCID: PMC10670741 DOI: 10.3390/cancers15225354] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2023] [Revised: 11/03/2023] [Accepted: 11/06/2023] [Indexed: 11/26/2023] Open
Abstract
We showed previously that inhibition of KIT signaling in GISTs activates FGFR-signaling pathway rendering cancer cells resistant to receptor tyrosine kinase inhibitor (RTKi) imatinib mesylate (IM) (Gleevec) despite of absence of secondary KIT mutations and thereby illustrating a rationale for the combined (e.g., KIT- and FGFR-targeted) therapies. We show here that long-term culture of IM-resistant GISTs (GIST-R1) with IM substantially down-regulates KIT expression and induces activation of the FGFR-signaling cascade, evidenced by increased expression of total and phosphorylated forms of FGFR1 and 2, FGF-2, and FRS-2, the well-known adaptor protein of the FGF-signaling cascade. This resulted in activation of both AKT- and MAPK-signaling pathways shown on mRNA and protein levels, and rendered cancer cells highly sensitive to pan-FGFR-inhibitors (BGJ 398, AZD 4547, and TAS-120). Indeed, we observed a significant decrease of IC50 values for BGJ 398 in the GIST subclone (GIST-R2) derived from GIST-R1 cells continuously treated with IM for up to 12 months. An increased sensitivity of GIST-R2 cells to FGFR inhibition was also revealed on the xenograft models, illustrating a substantial (>70%) decrease in tumor size in BGJ 398-treated animals when treated with this pan-FGFR inhibitor. Similarly, an increased intra-tumoral apoptosis as detected by immunohistochemical (IHC)-staining for cleaved caspase-3 on day 5 of the treatment was found. As expected, both BGJ 398 and IM used alone lacked the pro-apoptotic and growth-inhibitory activities on GIST-R1 xenografts, thereby revealing their resistance to these TKis when used alone. Important, the knockdown of FGFR2, and, in much less content, FGF-2, abrogated BGJ 398's activity against GIST-R2 cells both in vitro and in vivo, thereby illustrating the FGF-2/FGFR2-signaling axis in IM-resistant GISTs as a primary molecular target for this RTKi. Collectively, our data illustrates that continuous inhibition of KIT signaling in IM-resistant GISTs lacking secondary KIT mutations induced clonal heterogeneity of GISTs and resulted in accumulation of cancer cells with overexpressed FGF-2 and FGFR1/2, thereby leading to activation of FGFR-signaling. This in turn rendered these cells extremely sensitive to the pan-FGFR inhibitors used in combination with IM, or even alone, and suggests a rationale to re-evaluate the effectiveness of FGFR-inhibitors in order to improve the second-line therapeutic strategies for selected subgroups of GIST patients (e.g., IM-resistant GISTs lacking secondary KIT mutations and exhibiting the activation of the FGFR-signaling pathway).
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Affiliation(s)
- Sergei Boichuk
- Department of Pathology, Kazan State Medical University, Kazan 420012, Russia; (P.D.); (A.G.); (F.B.); (E.M.)
- Department of Radiotherapy and Radiology, Russian Medical Academy of Continuous Professional Education, Moscow 127051, Russia
- Central Research Laboratory, Kazan State Medical University, Kazan 420012, Russia;
- Biomarker Research Laboratory, Institute of Fundamental Medicine and Biology, Kazan Federal University, Kazan 420008, Russia; (V.S.); (R.K.)
| | - Pavel Dunaev
- Department of Pathology, Kazan State Medical University, Kazan 420012, Russia; (P.D.); (A.G.); (F.B.); (E.M.)
| | - Vera Skripova
- Biomarker Research Laboratory, Institute of Fundamental Medicine and Biology, Kazan Federal University, Kazan 420008, Russia; (V.S.); (R.K.)
| | - Aigul Galembikova
- Department of Pathology, Kazan State Medical University, Kazan 420012, Russia; (P.D.); (A.G.); (F.B.); (E.M.)
| | - Firyuza Bikinieva
- Department of Pathology, Kazan State Medical University, Kazan 420012, Russia; (P.D.); (A.G.); (F.B.); (E.M.)
| | - Elena Shagimardanova
- Regulatory Genomics Research Center, Institute of Fundamental Medicine and Biology, Kazan Federal University, Kazan 420008, Russia; (E.S.); (G.G.); (R.D.)
- LIFT—Life Improvement by Future Technologies Institute, Moscow 121205, Russia
- Loginov Moscow Clinical Scientific Center, Moscow 111123, Russia
| | - Guzel Gazizova
- Regulatory Genomics Research Center, Institute of Fundamental Medicine and Biology, Kazan Federal University, Kazan 420008, Russia; (E.S.); (G.G.); (R.D.)
| | - Ruslan Deviatiiarov
- Regulatory Genomics Research Center, Institute of Fundamental Medicine and Biology, Kazan Federal University, Kazan 420008, Russia; (E.S.); (G.G.); (R.D.)
- LIFT—Life Improvement by Future Technologies Institute, Moscow 121205, Russia
| | - Elena Valeeva
- Central Research Laboratory, Kazan State Medical University, Kazan 420012, Russia;
| | - Ekaterina Mikheeva
- Department of Pathology, Kazan State Medical University, Kazan 420012, Russia; (P.D.); (A.G.); (F.B.); (E.M.)
| | - Maria Vasilyeva
- Cytogenetics Laboratory, Carcinogenesis Institute, N.N. Blokhin National Medical Research Center of Oncology, Moscow 115478, Russia; (M.V.); (P.K.)
| | - Pavel Kopnin
- Cytogenetics Laboratory, Carcinogenesis Institute, N.N. Blokhin National Medical Research Center of Oncology, Moscow 115478, Russia; (M.V.); (P.K.)
| | - Vladimir Strelnikov
- Epigenetics Laboratory, Research Centre for Medical Genetics, Moscow 115522, Russia;
| | - Ramziya Kiyamova
- Biomarker Research Laboratory, Institute of Fundamental Medicine and Biology, Kazan Federal University, Kazan 420008, Russia; (V.S.); (R.K.)
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Stephan-Falkenau S, Streubel A, Mairinger T, Blum TG, Kollmeier J, Mairinger FD, Bauer T, Pfannschmidt J, Hollmann M, Wessolly M. Integrated Clinical, Molecular and Immunological Characterization of Pulmonary Sarcomatoid Carcinomas Reveals an Immune Escape Mechanism That May Influence Therapeutic Strategies. Int J Mol Sci 2023; 24:10558. [PMID: 37445733 DOI: 10.3390/ijms241310558] [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: 05/22/2023] [Revised: 06/16/2023] [Accepted: 06/21/2023] [Indexed: 07/15/2023] Open
Abstract
Pulmonary sarcomatoid carcinoma (PSC) has highly aggressive biological behaviour and poor clinical outcomes, raising expectations for new therapeutic strategies. We characterized 179 PSC by immunohistochemistry, next-generation sequencing and in silico analysis using a deep learning algorithm with respect to clinical, immunological and molecular features. PSC was more common in men, older ages and smokers. Surgery was an independent factor (p < 0.01) of overall survival (OS). PD-L1 expression was detected in 82.1% of all patients. PSC patients displaying altered epitopes due to processing mutations showed another PD-L1-independent immune escape mechanism, which also significantly influenced OS (p < 0.02). The effect was also maintained when only advanced tumour stages were considered (p < 0.01). These patients also showed improved survival with a significant correlation for immunotherapy (p < 0.05) when few or no processing mutations were detected, although this should be interpreted with caution due to the small number of patients studied. Genomic alterations for which there are already approved drugs were present in 35.4% of patients. Met exon 14 skipping was found more frequently (13.7%) and EGFR mutations less frequently (1.7%) than in other NSCLC. In summary, in addition to the divergent genomic landscape of PSC, the specific immunological features of this prognostically poor subtype should be considered in therapy stratification.
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Affiliation(s)
- Susann Stephan-Falkenau
- Institute for Tissue Diagnostics, MVZ at Helios Klinikum Emil von Behring, 14165 Berlin, Germany
| | - Anna Streubel
- Institute for Tissue Diagnostics, MVZ at Helios Klinikum Emil von Behring, 14165 Berlin, Germany
| | - Thomas Mairinger
- Institute for Tissue Diagnostics, MVZ at Helios Klinikum Emil von Behring, 14165 Berlin, Germany
| | - Torsten-Gerriet Blum
- Department of Pneumology, Heckeshorn Lung Clinic, Helios Klinikum Emil von Behring, 14165 Berlin, Germany
| | - Jens Kollmeier
- Department of Pneumology, Heckeshorn Lung Clinic, Helios Klinikum Emil von Behring, 14165 Berlin, Germany
| | - Fabian D Mairinger
- Institute of Pathology, University Hospital Essen, University of Duisburg-Essen, 45147 Essen, Germany
- German Cancer Consortium (DKTK), Partner Site University Hospital Essen, 45147 Essen, Germany
| | - Torsten Bauer
- Department of Pneumology, Heckeshorn Lung Clinic, Helios Klinikum Emil von Behring, 14165 Berlin, Germany
| | - Joachim Pfannschmidt
- Department of Thoracic Surgery, Heckeshorn Lung Clinic, Helios Klinikum Emil von Behring, 14165 Berlin, Germany
| | - Manuel Hollmann
- Institute for Tissue Diagnostics, MVZ at Helios Klinikum Emil von Behring, 14165 Berlin, Germany
| | - Michael Wessolly
- Institute of Pathology, University Hospital Essen, University of Duisburg-Essen, 45147 Essen, Germany
- German Cancer Consortium (DKTK), Partner Site University Hospital Essen, 45147 Essen, Germany
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Fielding DI, Dalley AJ, Singh M, Nandakumar L, Lakis V, Chittoory H, Fairbairn D, Patch AM, Kazakoff SH, Ferguson K, Bashirzadeh F, Bint M, Pahoff C, Son JH, Hodgson A, Sharma S, Waddell N, Lakhani SR, Hartel G, Nones K, Simpson PT. Evaluating Diff-Quik cytology smears for large-panel mutation testing in lung cancer-Predicting DNA content and success with low-malignant-cellularity samples. Cancer Cytopathol 2023. [PMID: 36938641 DOI: 10.1002/cncy.22690] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2022] [Revised: 12/13/2022] [Accepted: 12/20/2022] [Indexed: 03/21/2023]
Abstract
BACKGROUND Cytology smears are commonly collected during endobronchial ultrasound-guided transbronchial needle aspiration (EBUS TBNA) procedures but are rarely used for molecular testing. Studies are needed to demonstrate their great potential, in particular for the prediction of malignant cell DNA content and for utility in molecular diagnostics using large gene panels. METHODS A prospective study was performed on samples from 66 patients with malignant lymph nodes who underwent EBUS TBNA. All patients had air-dried, Diff-Quik cytology smears and formalin-fixed, paraffin-embedded cell blocks collected for cytopathology and molecular testing. One hundred eighty-five smears were evaluated by microscopy to estimate malignant cell percentage and abundance and to calculate smear size and were subjected to DNA extraction. DNA from 56 smears from 27 patients was sequenced with the TruSight Oncology 500 assay (Illumina). RESULTS Each microscopy parameter had a significant effect on the DNA yield. An algorithm was developed that predicted a >50-ng DNA yield of a smear with an area under the curve of 0.86. Fifty DNA samples (89%) with varying malignant yields were successfully sequenced. Low-malignant-cell content (<25%) and smear area (<15%) were the main reasons for failure. All standard-of-care mutations were detected in replicate smears from individual patients, regardless of malignant cell content. Tier 1/2 mutations were discovered in two cases where standard-of-care specimens were inadequate for sequencing. Smears were scored for tumor mutation burden. CONCLUSIONS Microscopy of Diff-Quik smears can triage samples for comprehensive panel sequencing, which highlights smears as an excellent alternative to traditional testing with cell blocks.
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Affiliation(s)
- David I Fielding
- Department of Thoracic Medicine, Royal Brisbane and Women's Hospital, Brisbane, Queensland, Australia
- UQ Centre for Clinical Research, Faculty of Medicine, University of Queensland, Brisbane, Queensland, Australia
| | - Andrew J Dalley
- UQ Centre for Clinical Research, Faculty of Medicine, University of Queensland, Brisbane, Queensland, Australia
| | - Mahendra Singh
- UQ Centre for Clinical Research, Faculty of Medicine, University of Queensland, Brisbane, Queensland, Australia
- Pathology Queensland, Royal Brisbane and Women's Hospital, Brisbane, Queensland, Australia
| | - Lakshmy Nandakumar
- Pathology Queensland, Royal Brisbane and Women's Hospital, Brisbane, Queensland, Australia
| | - Vanessa Lakis
- QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
| | - Haarika Chittoory
- UQ Centre for Clinical Research, Faculty of Medicine, University of Queensland, Brisbane, Queensland, Australia
| | - David Fairbairn
- Pathology Queensland, Royal Brisbane and Women's Hospital, Brisbane, Queensland, Australia
| | - Ann-Marie Patch
- QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
| | - Stephen H Kazakoff
- QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
| | - Kaltin Ferguson
- UQ Centre for Clinical Research, Faculty of Medicine, University of Queensland, Brisbane, Queensland, Australia
| | - Farzad Bashirzadeh
- Department of Thoracic Medicine, Royal Brisbane and Women's Hospital, Brisbane, Queensland, Australia
| | - Michael Bint
- Department of Thoracic Medicine, Sunshine Coast University Hospital, Birtinya, Queensland, Australia
| | - Carl Pahoff
- Department of Respiratory Medicine, Gold Coast University Hospital, Southport, Queensland, Australia
| | - Jung Hwa Son
- Department of Thoracic Medicine, Royal Brisbane and Women's Hospital, Brisbane, Queensland, Australia
| | - Alan Hodgson
- Pathology Queensland, Royal Brisbane and Women's Hospital, Brisbane, Queensland, Australia
| | - Sowmya Sharma
- QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
- ACL Pathology, Bellavista, New South Wales, Australia
| | - Nicola Waddell
- QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
| | - Sunil R Lakhani
- UQ Centre for Clinical Research, Faculty of Medicine, University of Queensland, Brisbane, Queensland, Australia
- Pathology Queensland, Royal Brisbane and Women's Hospital, Brisbane, Queensland, Australia
| | - Gunter Hartel
- QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
| | - Katia Nones
- QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
- School of Biomedical Sciences, University of Queensland, St Lucia, Queensland, Australia
| | - Peter T Simpson
- UQ Centre for Clinical Research, Faculty of Medicine, University of Queensland, Brisbane, Queensland, Australia
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Fernández Aceñero MJ, Díaz Del Arco C, Dinarés C, Labiano T, Tejerina E, Bernabé MJ, Forcen E, Saiz-Pardo M, Pérez P, Lozano MD. Overview and update on molecular testing in non-small cell lung carcinoma utilizing endobronchial ultrasound-guided transbronchial needle aspiration (EBUS-TBNA) samples. Diagn Cytopathol 2023; 51:26-35. [PMID: 35899869 DOI: 10.1002/dc.25019] [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: 05/31/2022] [Revised: 07/12/2022] [Accepted: 07/18/2022] [Indexed: 12/13/2022]
Abstract
Lung carcinoma remains one of the most frequent and aggressive human neoplasms. Fortunately, in the last decades, the increasing knowledge of the molecular mechanisms leading to cancer development has allowed the use of targeted therapies with improvement of prognosis in many patients. Clinical management has also changed after the introduction of endobronchialultrasonographic bronchoscopy that allows a conservative staging of lung tumors, avoiding the need of mediastinoscopy for lymph node staging. Lung pathologists and cytopathologists are facing the challenge of giving the more comprehensive prognostic and predictive information with ever smaller tissue or cytological samples. The aim of this review is to summarize the molecular testing for non-small cell lung carcinoma and how pathologists can contribute to the patient's outcome with a conscious management of biological samples.
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Affiliation(s)
| | | | - Carme Dinarés
- Department of Surgical Pathology, Valld'Hebron, Barcelona, Spain
| | - Tania Labiano
- Department of Surgical Pathology, Clínica Universitaria of Navarra, Pamplona, Spain
| | - Eva Tejerina
- Department of Surgical Pathology, Clínica Puerta de Hierro, Madrid, Spain
| | - Mª José Bernabé
- Department of Pneumology, Hospital Clínico San Carlos, Madrid, Spain
| | - Elena Forcen
- Department of Pneumology, Hospital Clínico San Carlos, Madrid, Spain
| | - Melchor Saiz-Pardo
- Departments of Surgical Pathology, Hospital Clínico San Carlos, Madrid, Spain
| | - Pablo Pérez
- Departments of Surgical Pathology, Hospital Clínico San Carlos, Madrid, Spain
| | - Maria D Lozano
- Department of Surgical Pathology, Clínica Universitaria of Navarra, Pamplona, Spain
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Expert opinion on NSCLC small specimen biomarker testing - Part 2: Analysis, reporting, and quality assessment. Virchows Arch 2022; 481:351-366. [PMID: 35857103 PMCID: PMC9297263 DOI: 10.1007/s00428-022-03344-1] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2021] [Revised: 05/16/2022] [Accepted: 05/18/2022] [Indexed: 10/31/2022]
Abstract
The diagnostic work-up for non-small cell lung cancer (NSCLC) requires biomarker testing to guide therapy choices. This article is the second of a two-part series. In Part 1, we summarised evidence-based recommendations for obtaining and processing small specimen samples (i.e. pre-analytical steps) from patients with advanced NSCLC. Here, in Part 2, we summarise evidence-based recommendations relating to analytical steps of biomarker testing (and associated reporting and quality assessment) of small specimen samples in NSCLC. As the number of biomarkers for actionable (genetic) targets and approved targeted therapies continues to increase, simultaneous testing of multiple actionable oncogenic drivers using next-generation sequencing (NGS) becomes imperative, as set forth in European Society for Medical Oncology guidelines. This is particularly relevant in advanced NSCLC, where tissue specimens are typically limited and NGS may help avoid tissue exhaustion compared with sequential biomarker testing. Despite guideline recommendations, significant discrepancies in access to NGS persist across Europe, primarily due to reimbursement constraints. The use of increasingly complex testing methods also has implications for the reporting of results. Molecular testing reports should include clinical interpretation with additional commentary on sample adequacy as appropriate. Molecular tumour boards are recommended to facilitate the interpretation of complex genetic information arising from NGS, and to collaboratively determine the optimal treatment for patients with NSCLC. Finally, whichever testing modality is employed, it is essential that adequate internal and external validation and quality control measures are implemented.
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Koh J, Shin SA, Lee JA, Jeon YK. Lymphoproliferative disorder involving body fluid: diagnostic approaches and roles of ancillary studies. J Pathol Transl Med 2022; 56:173-186. [PMID: 35843627 PMCID: PMC9288893 DOI: 10.4132/jptm.2022.05.16] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2022] [Accepted: 05/16/2022] [Indexed: 11/17/2022] Open
Abstract
Lymphocyte-rich effusions represent benign reactive process or neoplastic condition. Involvement of lymphoproliferative disease in body cavity is not uncommon, and it often causes diagnostic challenge. In this review, we suggest a practical diagnostic approach toward lymphocyte-rich effusions, share representative cases, and discuss the utility of ancillary tests. Cytomorphologic features favoring neoplastic condition include high cellularity, cellular atypia/pleomorphism, monomorphic cell population, and frequent apoptosis, whereas lack of atypia, polymorphic cell population, and predominance of small T cells usually represent benign reactive process. Involvement of non-hematolymphoid malignant cells in body fluid should be ruled out first, followed by categorization of the samples into either small/medium-sized cell dominant or large-sized cell dominant fluid. Small/medium-sized cell dominant effusions require ancillary tests when either cellular atypia or history/clinical suspicion of lymphoproliferative disease is present. Large-sized cell dominant effusions usually suggest neoplastic condition, however, in the settings of initial presentation or low overall cellularity, ancillary studies are helpful for more clarification. Ancillary tests including immunocytochemistry, in situ hybridization, clonality test, and next-generation sequencing can be performed using cytologic preparations. Throughout the diagnostic process, proper review of clinical history, cytomorphologic examination, and application of adequate ancillary tests are key elements for successful diagnosis.
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Affiliation(s)
- Jiwon Koh
- Department of Pathology, Seoul National University Hospital, Seoul National University College of Medicine, Seoul, Korea
| | - Sun Ah Shin
- Department of Pathology, Seoul National University Hospital, Seoul National University College of Medicine, Seoul, Korea
- Department of Pathology, National Cancer Center, Goyang, Korea
| | - Ji Ae Lee
- Department of Pathology, Seoul National University Hospital, Seoul National University College of Medicine, Seoul, Korea
| | - Yoon Kyung Jeon
- Department of Pathology, Seoul National University Hospital, Seoul National University College of Medicine, Seoul, Korea
- Cancer Research Institute, Seoul National University, Seoul, Korea
- Corresponding Author: Yoon Kyung Jeon, MD, PhD, Department of Pathology, Seoul National University Hospital, Seoul National University College of Medicine, 101 Daehak-ro, Jongno-gu, Seoul 03080, Korea Tel: +82-2-740-8323, Fax: +82-2-743-5530, E-mail:
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FFPE-Based NGS Approaches into Clinical Practice: The Limits of Glory from a Pathologist Viewpoint. J Pers Med 2022; 12:jpm12050750. [PMID: 35629172 PMCID: PMC9146170 DOI: 10.3390/jpm12050750] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2022] [Revised: 04/29/2022] [Accepted: 05/03/2022] [Indexed: 01/02/2023] Open
Abstract
The introduction of next-generation sequencing (NGS) in the molecular diagnostic armamentarium is deeply changing pathology practice and laboratory frameworks. NGS allows for the comprehensive molecular characterization of neoplasms, in order to provide the best treatment to oncologic patients. On the other hand, NGS raises technical issues and poses several challenges in terms of education, infrastructures and costs. The aim of this review is to give an overview of the main NGS sequencing platforms that can be used in current molecular diagnostics and gain insights into the clinical applications of NGS in precision oncology. Hence, we also focus on the preanalytical, analytical and interpretative issues raised by the incorporation of NGS in routine pathology diagnostics.
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Sakai T, Udagawa H, Kirita K, Nomura S, Itotani R, Tamiya Y, Sugimoto A, Ota T, Naito T, Izumi H, Nosaki K, Ikeda T, Zenke Y, Matsumoto S, Yoh K, Niho S, Nakai T, Ishii G, Goto K. Comparison of the efficiency of endobronchial ultrasound-guided transbronchial needle aspiration using a 22G needle versus 25G needle for the diagnosis of lymph node metastasis in patients with lung cancer: a prospective randomized, crossover study. Transl Lung Cancer Res 2021; 10:3745-3758. [PMID: 34733625 PMCID: PMC8512458 DOI: 10.21037/tlcr-21-480] [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: 06/09/2021] [Accepted: 08/24/2021] [Indexed: 12/25/2022]
Abstract
Background Endobronchial ultrasound-guided transbronchial needle aspiration (EBUS-TBNA) is generally performed for the diagnosis of hilar/mediastinal lymph node metastasis in patients with lung cancer. Recently, a 25-gauge (G) needle became available, but robust evidence of its usefulness in routine clinical practice is still lacking. Methods A prospective randomized crossover trial was performed, in which patients with suspected hilar/mediastinal lymph node metastasis of lung cancer underwent EBUS-TBNA. The primary endpoint was the rate of yield histology specimens containing malignant cells. Results From December 2018 to February 2020, 102 patients were randomly assigned to EBUS-TBNA using a 22G needle first, followed by a 25G needle (n=50) or EBUS-TBNA using a 25G needle first, followed by a 22G needle (n=52). There was no difference in the diagnostic yield of malignancy between the histology specimens obtained by using the 22G and 25G needles (75% vs. 75%, respectively, P=0.37). The sizes of the tissue samples (16.4 vs. 4.9 mm2, respectively) and number of malignant cells in the tissue samples (626 vs. 400, respectively) were both significantly higher when using the 22G needle than when using the 25G needle. Conclusions No significant difference in the diagnostic yield between the 22G and 25G needles was observed for the diagnosis of lymph node metastasis of lung cancer, suggesting that needles of either gauge could be used for the biopsy. However, we would recommend use of the 22G needle, because it provided larger specimens and specimens containing larger numbers of malignant cells. Trial Registration University hospital Medical Information Network Clinical Trial Registry (ID: UMIN000036680).
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Affiliation(s)
- Tetsuya Sakai
- Department of Thoracic Oncology, National Cancer Center Hospital East, Kashiwa, Japan
| | - Hibiki Udagawa
- Department of Thoracic Oncology, National Cancer Center Hospital East, Kashiwa, Japan
| | - Keisuke Kirita
- Department of Thoracic Oncology, National Cancer Center Hospital East, Kashiwa, Japan
| | - Shogo Nomura
- Biostatistics Division, Center for Research Administration and Support, National Cancer Center, Kashiwa, Japan
| | - Ryo Itotani
- Department of Thoracic Oncology, National Cancer Center Hospital East, Kashiwa, Japan
| | - Yutaro Tamiya
- Department of Thoracic Oncology, National Cancer Center Hospital East, Kashiwa, Japan
| | - Akira Sugimoto
- Department of Thoracic Oncology, National Cancer Center Hospital East, Kashiwa, Japan
| | - Takahiro Ota
- Department of Thoracic Oncology, National Cancer Center Hospital East, Kashiwa, Japan
| | - Tomoyuki Naito
- Department of Thoracic Oncology, National Cancer Center Hospital East, Kashiwa, Japan
| | - Hiroki Izumi
- Department of Thoracic Oncology, National Cancer Center Hospital East, Kashiwa, Japan
| | - Kaname Nosaki
- Department of Thoracic Oncology, National Cancer Center Hospital East, Kashiwa, Japan
| | - Takaya Ikeda
- Department of Thoracic Oncology, National Cancer Center Hospital East, Kashiwa, Japan
| | - Yoshitaka Zenke
- Department of Thoracic Oncology, National Cancer Center Hospital East, Kashiwa, Japan
| | - Shingo Matsumoto
- Department of Thoracic Oncology, National Cancer Center Hospital East, Kashiwa, Japan
| | - Kiyotaka Yoh
- Department of Thoracic Oncology, National Cancer Center Hospital East, Kashiwa, Japan
| | - Seiji Niho
- Department of Thoracic Oncology, National Cancer Center Hospital East, Kashiwa, Japan
| | - Tokiko Nakai
- Department of Pathology and Clinical Laboratories, National Cancer Center Hospital East, Kashiwa, Japan
| | - Genichiro Ishii
- Department of Pathology and Clinical Laboratories, National Cancer Center Hospital East, Kashiwa, Japan
| | - Koichi Goto
- Department of Thoracic Oncology, National Cancer Center Hospital East, Kashiwa, Japan
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10
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Mutations in Epigenetic Regulation Genes in Gastric Cancer. Cancers (Basel) 2021; 13:cancers13184586. [PMID: 34572812 PMCID: PMC8467700 DOI: 10.3390/cancers13184586] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2021] [Revised: 09/08/2021] [Accepted: 09/09/2021] [Indexed: 12/24/2022] Open
Abstract
Simple Summary Epigenetic mechanisms, such as DNA methylation/demethylation, covalent modifications of histone proteins, and chromatin remodeling, create specific patterns of gene expression. Epigenetic deregulations are associated with oncogenesis, relapse of the disease and metastases, and can serve as a useful clinical marker. We assessed the clinical relevance of integrity of the genes coding for epigenetic regulator proteins by mutational profiling of 25 genes in 135 gastric cancer (GC) samples. Overall, mutations in the epigenetic regulation genes were found to be significantly associated with reduced overall survival of patients in the group with metastases and in the group with tumors with signet ring cells. We have also discovered mutual exclusivity of somatic mutations in the KMT2D, KMT2C, ARID1A, and CHD7 genes in our cohort. Our results suggest that mutations in epigenetic regulation genes may be valuable clinical markers and deserve further exploration in independent cohorts. Abstract We have performed mutational profiling of 25 genes involved in epigenetic processes on 135 gastric cancer (GC) samples. In total, we identified 79 somatic mutations in 49/135 (36%) samples. The minority (n = 8) of mutations was identified in DNA methylation/demethylation genes, while the majority (n = 41), in histone modifier genes, among which mutations were most commonly found in KMT2D and KMT2C. Somatic mutations in KMT2D, KMT2C, ARID1A and CHD7 were mutually exclusive (p = 0.038). Mutations in ARID1A were associated with distant metastases (p = 0.03). The overall survival of patients in the group with metastases and in the group with tumors with signet ring cells was significantly reduced in the presence of mutations in epigenetic regulation genes (p = 0.036 and p = 0.041, respectively). Separately, somatic mutations in chromatin remodeling genes correlate with low survival rate of patients without distant metastasis (p = 0.045) and in the presence of signet ring cells (p = 0.0014). Our results suggest that mutations in epigenetic regulation genes may be valuable clinical markers and deserve further exploration in independent cohorts.
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11
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Grant J, Stanley A, Balbi K, Gerrard G, Bennett P. Performance evaluation of the Biocartis Idylla EGFR Mutation Test using pre-extracted DNA from a cohort of highly characterised mutation positive samples. J Clin Pathol 2021; 75:241-249. [PMID: 33514586 DOI: 10.1136/jclinpath-2020-207338] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2020] [Revised: 01/11/2021] [Accepted: 01/12/2021] [Indexed: 12/16/2022]
Abstract
AIMS Targeted therapies for non-small cell lung carcinoma (NSCLC) rely on the detection of specific genomic lesions, such as mutations within the epidermal growth factor receptor (EGFR) gene. The Biocartis Idylla platform and single-use EGFR mutation test cartridge is CE-IVD for use with formalin-fixed paraffin embedded (FFPE) tumour material, but can also function off-scope using extracted DNA as input material. This can expand the utility of the platform and potentially conserve valuable tissue. METHODS We sought to evaluate the performance of this system to detect known EGFR mutations using extracted DNA at different input levels. 130 next generation sequencing-characterised NSCLC cases possessing EGFR mutations that were theoretically detectable by the Idylla system were selected. Replicate analyses were performed using the Idylla EGFR test with up to three different DNA input levels (20 ng, 50 ng and 250 ng). RESULTS Considering only variants within the test manufacturer's specified scope, the Idylla EGFR test generated concordant findings for 90.77% of cases at 20 ng DNA input, 98.46% at 50 ng input and 100% at 250 ng input. Analyses with discordant findings all generated control quantification cycle (CQ) values greater than 23. Very low CQ values were associated with EGFR gene amplification. CONCLUSIONS The Idylla EGFR Mutation Test can be used at least as well with pre-extracted DNA than with direct FFPE input. In cases with control CQ >23, reanalysis with an increased DNA input should ideally be undertaken. If this is not possible, the risk of false negative calls may be mitigated by manual review of the quantitative PCR data and/or by reflexing to alternative analysis options.
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Affiliation(s)
- Jack Grant
- Sarah Cannon Molecular Diagnostics, HCA Healthcare UK, London, UK
| | - Anne Stanley
- Sarah Cannon Molecular Diagnostics, HCA Healthcare UK, London, UK
| | - Kevin Balbi
- Sarah Cannon Molecular Diagnostics, HCA Healthcare UK, London, UK
| | - Gareth Gerrard
- Sarah Cannon Molecular Diagnostics, HCA Healthcare UK, London, UK.,Faculty of Medicine, Imperial College London, London, UK
| | - Philip Bennett
- Sarah Cannon Molecular Diagnostics, HCA Healthcare UK, London, UK
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12
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Murphy SJ, Harris FR, Smadbeck JB, Serla V, Karagouga G, Johnson SH, Kosari F, Pierson KE, Bungum AO, Edell ES, Mansfield AS, Wigle DA, Kipp BR, Vasmatzis G, Aubry MC. Optimizing clinical cytology touch preparations for next generation sequencing. Genomics 2020; 112:5313-5323. [PMID: 33144219 DOI: 10.1016/j.ygeno.2020.10.031] [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: 07/20/2020] [Revised: 10/14/2020] [Accepted: 10/28/2020] [Indexed: 12/26/2022]
Abstract
Intraoperative diagnosis is routinely performed on cytology touch preparations (TPs) from core needle biopsies (CNBs). Current interest promotes their utility as an important source of patient tissue for clinical genomic testing. Herein we present whole genome structural variant analysis (SVA) from mate-pair sequencing (MPseq) and whole exome sequencing (WES) mutation calling in DNA directly whole genome amplified (WGA) from TPs. Chromosomal copy changes and somatic DNA junction detection from MPseq of TPs were highly consistent with associated CNBs and bulk resected tissues in all cases. While increased frequency coverage noise from limitations of amplification of limited sample input was significant, this was effectively compensated by natural tumor enrichment during the TP process, which also enhanced variant detection and loss of heterozygosity evaluations from WES. This novel TP methodology enables expanded utility of frequently limited CNB for both clinical and research genomic testing.
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Affiliation(s)
- Stephen J Murphy
- Center for Individualized Medicine, Bio-marker Discovery Program, Mayo Clinic, Rochester, MN, United States.
| | - Faye R Harris
- Center for Individualized Medicine, Bio-marker Discovery Program, Mayo Clinic, Rochester, MN, United States
| | - James B Smadbeck
- Center for Individualized Medicine, Bio-marker Discovery Program, Mayo Clinic, Rochester, MN, United States
| | - Vishnu Serla
- Center for Individualized Medicine, Bio-marker Discovery Program, Mayo Clinic, Rochester, MN, United States; Departments of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, United States
| | - Giannoula Karagouga
- Center for Individualized Medicine, Bio-marker Discovery Program, Mayo Clinic, Rochester, MN, United States
| | - Sarah H Johnson
- Center for Individualized Medicine, Bio-marker Discovery Program, Mayo Clinic, Rochester, MN, United States
| | - Farhad Kosari
- Center for Individualized Medicine, Bio-marker Discovery Program, Mayo Clinic, Rochester, MN, United States
| | - Karlyn E Pierson
- Departments of Thoracic Surgery, Mayo Clinic, Rochester, MN, United States
| | - Aaron O Bungum
- Departments of Pulmonary and Critical Care Medicine, Mayo Clinic, Rochester, MN, United States
| | - Eric S Edell
- Departments of Pulmonary and Critical Care Medicine, Mayo Clinic, Rochester, MN, United States
| | | | - Dennis A Wigle
- Departments of Thoracic Surgery, Mayo Clinic, Rochester, MN, United States
| | - Benjamin R Kipp
- Departments of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, United States
| | - George Vasmatzis
- Center for Individualized Medicine, Bio-marker Discovery Program, Mayo Clinic, Rochester, MN, United States.
| | - Marie Christine Aubry
- Departments of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, United States.
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13
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Genomic profiling in oncology clinical practice. Clin Transl Oncol 2020; 22:1430-1439. [PMID: 31981077 DOI: 10.1007/s12094-020-02296-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2019] [Accepted: 01/08/2020] [Indexed: 02/04/2023]
Abstract
The development of high-throughput technologies such as next-generation sequencing for DNA sequencing together with the decrease in their cost has led to the progressive introduction of genomic profiling in our daily practice in oncology. Nowadays, genomic profiling is part of genetic counseling, cancer diagnosis, molecular characterization, and as a biomarker of prognosis and response to treatment. Furthermore, germline or somatic genomic characterization of the tumor may provide new treatment opportunities for patients with cancer. In this review, we will summarize the clinical applications and limitations of genomic profiling in oncology clinical practice, focusing on next-generation sequencing.
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14
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Nemtsova MV, Kalinkin AI, Kuznetsova EB, Bure IV, Alekseeva EA, Bykov II, Khorobrykh TV, Mikhaylenko DS, Tanas AS, Kutsev SI, Zaletaev DV, Strelnikov VV. Clinical relevance of somatic mutations in main driver genes detected in gastric cancer patients by next-generation DNA sequencing. Sci Rep 2020; 10:504. [PMID: 31949278 PMCID: PMC6965114 DOI: 10.1038/s41598-020-57544-3] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2019] [Accepted: 12/31/2019] [Indexed: 12/14/2022] Open
Abstract
Somatic mutation profiling in gastric cancer (GC) enables main driver mutations to be identified and their clinical and prognostic value to be evaluated. We investigated 77 tumour samples of GC by next-generation sequencing (NGS) with the Ion AmpliSeq Hotspot Panel v2 and a custom panel covering six hereditary gastric cancer predisposition genes (BMPR1A, SMAD4, CDH1, TP53, STK11 and PTEN). Overall, 47 somatic mutations in 14 genes were detected; 22 of these mutations were novel. Mutations were detected most frequently in the CDH1 (13/47) and TP53 (12/47) genes. As expected, somatic CDH1 mutations were positively correlated with distant metastases (p = 0.019) and tumours with signet ring cells (p = 0.043). These findings confirm the association of the CDH1 mutations with diffuse GC type. TP53 mutations were found to be significantly associated with a decrease in overall survival in patients with Lauren diffuse-type tumours (p = 0.0085), T3-T4 tumours (p = 0.037), and stage III-IV tumours (p = 0.013). Our results confirm that the detection of mutations in the main driver genes may have a significant prognostic value for GC patients and provide an independent GC-related set of clinical and molecular genetic data.
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Affiliation(s)
- Marina V Nemtsova
- Medical Genetics Laboratory, I.M. Sechenov First Moscow State Medical University, Moscow, 119991, Russian Federation.,Epigenetics Laboratory, Research Centre for Medical Genetics, Moscow, 115522, Russian Federation
| | - Alexey I Kalinkin
- Epigenetics Laboratory, Research Centre for Medical Genetics, Moscow, 115522, Russian Federation
| | - Ekaterina B Kuznetsova
- Medical Genetics Laboratory, I.M. Sechenov First Moscow State Medical University, Moscow, 119991, Russian Federation.,Epigenetics Laboratory, Research Centre for Medical Genetics, Moscow, 115522, Russian Federation
| | - Irina V Bure
- Medical Genetics Laboratory, I.M. Sechenov First Moscow State Medical University, Moscow, 119991, Russian Federation
| | - Ekaterina A Alekseeva
- Medical Genetics Laboratory, I.M. Sechenov First Moscow State Medical University, Moscow, 119991, Russian Federation.,Epigenetics Laboratory, Research Centre for Medical Genetics, Moscow, 115522, Russian Federation
| | - Igor I Bykov
- Department No. 1, Medical Faculty, Faculty Surgery, I.M. Sechenov First Moscow State Medical University, Moscow, 119991, Russian Federation
| | - Tatiana V Khorobrykh
- Department No. 1, Medical Faculty, Faculty Surgery, I.M. Sechenov First Moscow State Medical University, Moscow, 119991, Russian Federation
| | - Dmitry S Mikhaylenko
- Medical Genetics Laboratory, I.M. Sechenov First Moscow State Medical University, Moscow, 119991, Russian Federation.,Epigenetics Laboratory, Research Centre for Medical Genetics, Moscow, 115522, Russian Federation.,N.A. Lopatkin Research Institute of Urology and Interventional Radiology - branch of the National Medical Research Radiologiсal Center, Moscow, 105425, Russian Federation
| | - Alexander S Tanas
- Epigenetics Laboratory, Research Centre for Medical Genetics, Moscow, 115522, Russian Federation
| | - Sergey I Kutsev
- Epigenetics Laboratory, Research Centre for Medical Genetics, Moscow, 115522, Russian Federation
| | - Dmitry V Zaletaev
- Medical Genetics Laboratory, I.M. Sechenov First Moscow State Medical University, Moscow, 119991, Russian Federation.,Epigenetics Laboratory, Research Centre for Medical Genetics, Moscow, 115522, Russian Federation
| | - Vladimir V Strelnikov
- Epigenetics Laboratory, Research Centre for Medical Genetics, Moscow, 115522, Russian Federation.
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15
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Ling B, Liao X, Huang Y, Liang L, Jiang Y, Pang Y, Qi G. Identification of prognostic markers of lung cancer through bioinformatics analysis and in vitro experiments. Int J Oncol 2020; 56:193-205. [PMID: 31789390 PMCID: PMC6910184 DOI: 10.3892/ijo.2019.4926] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2019] [Accepted: 10/15/2019] [Indexed: 12/15/2022] Open
Abstract
Lung cancer is one of the most common types of cancer worldwide. Understanding the molecular mechanisms underlying the development and progression of lung cancer may improve early diagnosis, treatment and prognosis. The aim of the present study was to examine the pathogenesis of lung cancer and to identify potentially novel biomarkers. Gene expression datasets of patients with lung cancer were obtained from the Gene Expression Omnibus. Genes which were most closely associated with lung cancer (core genes) were screened by weighted gene co‑expression network analysis. In vitro cell based experiments were further utilized to verify the effects of the core genes on the proliferation of lung cancer cells, adhesion between cells and the matrix, and the associated metabolic pathways. Based on WGCNA screening, two gene modules and five core genes closely associated with lung cancer, including immunoglobulin superfamily member 10 (IGSF10) from the turquoise module, and ribonucleotide reductase regulatory subunit M2, protein regulator of cytokinesis 1, kinesin family member (KIF)14 and KIF2C from the brown module were identified as relevant. Survival analysis and differential gene expression analysis showed that there were significant differences in IGSF10 expression levels between the healthy controls and patients with lung cancer. In patients with lung cancer, IGSF10 expression was decreased, and the overall survival time of patients with lung cancer was significantly shortened. An MTT and colony formation assay showed that IGSF10‑knockout significantly increased proliferation of lung cancer cells, and Transwell assays and adhesion experiments further suggested that the adhesion between cells and the matrix was significantly increased in IGSF10‑knockout cells. Gene Set Enrichment Analysis showed that the expression level of IGSF10 was significantly associated with the activation of the integrin‑β1/focal adhesion kinase (FAK) pathway. Western blotting revealed that knockout of IGSF10 resulted in the activation of the integrin‑β1/FAK pathway, as the protein expression levels of integrin‑β1, phosphorylated (p)‑FAK and p‑AKT were significantly upregulated. Activation of the integrin‑β1/FAK pathway, following knockout of IGSF10, affected the proliferation and adhesion of lung cancer cells. Therefore, IGSF10 my serve as a potential prognostic marker of lung cancer.
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Affiliation(s)
| | | | - Yuanhe Huang
- Basic Medical Sciences, Youjiang Medical University for Nationalities, Baise, Guangxi 533000
| | | | - Yan Jiang
- Medical College, Guangxi University, Nanning, Guangxi 530004
| | - Yaqin Pang
- College of Public Health and Management, Youjiang Medical University for Nationalities, Baise, Guangxi 533000, P.R. China
| | - Guangzi Qi
- College of Public Health and Management, Youjiang Medical University for Nationalities, Baise, Guangxi 533000, P.R. China
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16
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Targeted Gene Next-Generation Sequencing Panel in Patients with Advanced Lung Adenocarcinoma: Paving the Way for Clinical Implementation. Cancers (Basel) 2019; 11:cancers11091229. [PMID: 31443496 PMCID: PMC6770536 DOI: 10.3390/cancers11091229] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2019] [Revised: 08/04/2019] [Accepted: 08/15/2019] [Indexed: 12/24/2022] Open
Abstract
Identification of targetable molecular changes is essential for selecting appropriate treatment in patients with advanced lung adenocarcinoma. Methods: In this study, a Sanger sequencing plus Fluorescence In Situ Hybridization (FISH) sequential approach was compared with a Next-Generation Sequencing (NGS)-based approach for the detection of actionable genomic mutations in an experimental cohort (EC) of 117 patients with advanced lung adenocarcinoma. Its applicability was assessed in small biopsies and cytology specimens previously tested for epidermal growth factor receptor (EGFR) and anaplastic lymphoma kinase (ALK) mutational status, comparing the molecular changes identified and the impact on clinical outcomes. Subsequently, an NGS-based approach was applied and tested in an implementation cohort (IC) in clinical practice. Using Sanger and FISH, patients were classified as EGFR-mutated (n = 22, 18.8%), ALK-mutated (n = 9, 7.7%), and unclassifiable (UC) (n = 86, 73.5%). Retesting the EC with NGS led to the identification of at least one gene variant in 56 (47.9%) patients, totaling 68 variants among all samples. Still, in the EC, combining NGS plus FISH for ALK, patients were classified as 23 (19.7%) EGFR; 20 (17.1%) KRAS; five (4.3%) B-Raf proto-oncogene (BRAF); one (0.9%) Erb-B2 Receptor Tyrosine Kinase 2 (ERBB2); one (0.9%) STK11; one (0.9%) TP53, and nine (7.7%) ALK mutated. Only 57 (48.7%) remained genomically UC, reducing the UC rate by 24.8%. Fourteen (12.0%) patients presented synchronous alterations. Concordance between NGS and Sanger for EGFR status was very high (κ = 0.972; 99.1%). In the IC, a combined DNA and RNA NGS panel was used in 123 patients. Genomic variants were found in 79 (64.2%). In addition, eight (6.3%) EML4-ALK, four (3.1%), KIF5B-RET, four (3.1%) CD74-ROS1, one (0.8%) TPM3-NTRK translocations and three (2.4%) exon 14 skipping MET Proto-Oncogene (MET) mutations were detected, and 36% were treatable alterations. Conclusions: This study supports the use of NGS as the first-line test for genomic profiling of patients with advanced lung adenocarcinoma.
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17
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Lee JH, Ahn BK, Baik SS, Lee KH. Comprehensive Analysis of Somatic Mutations in Colorectal Cancer With Peritoneal Metastasis. In Vivo 2019; 33:447-452. [PMID: 30804124 DOI: 10.21873/invivo.11493] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2018] [Revised: 01/23/2019] [Accepted: 01/28/2019] [Indexed: 01/13/2023]
Abstract
BACKGROUND To analyze for genetic mutations which may presage peritoneal metastasis by using targeted next-generation sequencing (NGS). MATERIALS AND METHODS Formalin-fixed, paraffin-embedded primary tumor specimens were obtained from 10 patients with small obstructing colorectal cancer and peritoneal metastasis (group A) and five with large non-obstructing colorectal cancer and no recurrence (group B). DNA was extracted for the sequencing of 409 cancer genes. The distribution of genetic mutations was compared between the two groups to find genetic mutations related to peritoneal metastasis. RESULTS When the samples were sorted based on similarity of gene expression by hierarchical clustering analysis, the samples were well divided between the two study groups. Mutations in AT-rich interactive domain-containing protein 1A (ARID1A), polycystic kidney and hepatic disease 1 (PKHD1), ubiquitin-protein ligase E3 component n-recognin 5 (UBR5), paired box 5 (PAX5), tumor protein p53 (TP53), additional sex combs like 1 (ASXL1) and androgen receptor (AR) genes were detected more frequently in group A. CONCLUSION A number of somatic mutations presumed to be relevant to colorectal cancer with peritoneal metastasis were identified in our study by NGS.
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Affiliation(s)
- Ju-Hee Lee
- Department of Surgery, Dongguk University Medical Center, Gyeongju, Republic of Korea
| | - Byung Kyu Ahn
- Department of Surgery, Hanyang University College of Medicine, Seoul, Republic of Korea
| | - Seung Sam Baik
- Department of Pathology, Hanyang University College of Medicine, Seoul, Republic of Korea
| | - Kang Hong Lee
- Department of Surgery, Hanyang University College of Medicine, Seoul, Republic of Korea
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18
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Nicolè L, Cappello F, Cappellesso R, VandenBussche CJ, Fassina A. MicroRNA profiling in serous cavity specimens: Diagnostic challenges and new opportunities. Cancer Cytopathol 2019; 127:493-500. [DOI: 10.1002/cncy.22143] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2018] [Revised: 04/12/2019] [Accepted: 04/15/2019] [Indexed: 12/16/2022]
Affiliation(s)
- Lorenzo Nicolè
- Surgical Pathology and Cytopathology Unit, Department of Medicine University of Padua Padua Italy
| | | | - Rocco Cappellesso
- Surgical Pathology and Cytopathology Unit, Department of Medicine University of Padua Padua Italy
| | - Christopher J. VandenBussche
- Department of Pathology Johns Hopkins University School of Medicine Baltimore Maryland
- Department of Oncology Johns Hopkins University School of Medicine Baltimore Maryland
| | - Ambrogio Fassina
- Surgical Pathology and Cytopathology Unit, Department of Medicine University of Padua Padua Italy
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19
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Khoueiry P, Fakhri G, Akel R, El Assaad M, Mahfouz R, Khuri F, Chami H, Petersen J, Viet S, Davies G, Kadara H, Tfayli A. Deep targeted sequencing analysis of hot spot mutations in non-small cell lung cancer patients from the Middle Eastern population. J Thorac Dis 2019; 11:2383-2391. [PMID: 31372275 DOI: 10.21037/jtd.2019.05.74] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Background The overall 5-year survival of lung cancer remains dismal despite the current treatment regimens. Testing for driver mutations has become routine practice for oncologists due to the presence of targeted therapy readily available for patients. Deep targeted sequencing through next generation sequencing (NGS) is an adequate methodology to detect mutations at multi-genetic levels. The molecular pathology of non-small cell lung cancer (NSCLC) is poorly understood in the Middle East and, to date, no other reports have been published on deep targeted sequencing of lung adenocarcinoma (LUAD) tissues. Methods Deep targeted sequencing using TruSeq Amplicon Cancer panel of 48 genes was performed on 85 formalin-fixed paraffin-embedded tissues from patients with LUAD who were treatment-naive at the time of the collection. Variants with an allele frequency higher than 10% were retained. Results Variant calling identified a total of 2,455 variants of which missense mutations were the most frequent (75.6%). All of our samples showed at least one mutation in one of the 10 most commonly mutated genes with FLT3 being the gene with the highest mutation rate (67%). TP53, KRAS and STK11 were the second, third and fourth most commonly mutated genes, respectively while EGFR mutation rate reached 22.4%. Conclusions To the best of our knowledge, this is the first hot spot profiling study on patients from this area. The frequencies of mutated genes presented in our study showed similarity to other reported outcomes. At least one mutation was detected in our cohort of LUAD.
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Affiliation(s)
- Pierre Khoueiry
- Department of Biochemistry and Molecular Genetics, American University of Beirut, Beirut, Lebanon
| | - Ghina Fakhri
- Division of Hematology and Oncology, Department of Internal Medicine, American University of Beirut Medical Center, Beirut, Lebanon
| | - Reem Akel
- Division of Hematology and Oncology, Department of Internal Medicine, American University of Beirut Medical Center, Beirut, Lebanon
| | - Majd El Assaad
- Division of Hematology and Oncology, Department of Internal Medicine, American University of Beirut Medical Center, Beirut, Lebanon
| | - Rami Mahfouz
- Department of Pathology and Laboratory Medicine, American University of Beirut Medical Center, Beirut, Lebanon
| | - Fadlo Khuri
- Division of Hematology and Oncology, Department of Internal Medicine, American University of Beirut Medical Center, Beirut, Lebanon
| | - Hassan Chami
- Division of Pulmonary and Critical Care, Department of Internal Medicine, American University of Beirut Medical Center, Beirut, Lebanon
| | - Jason Petersen
- Avera Institute for Human Genetics, Sioux Falls, South Dakota 57108, USA
| | - Sarah Viet
- Avera Institute for Human Genetics, Sioux Falls, South Dakota 57108, USA
| | - Gareth Davies
- Avera Institute for Human Genetics, Sioux Falls, South Dakota 57108, USA
| | - Humam Kadara
- Department of Biochemistry and Molecular Genetics, American University of Beirut, Beirut, Lebanon
| | - Arafat Tfayli
- Division of Hematology and Oncology, Department of Internal Medicine, American University of Beirut Medical Center, Beirut, Lebanon
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20
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Yu GH, Glaser LJ, Gustafson KS. Role of Ancillary Techniques in Fluid Cytology. Acta Cytol 2019; 64:52-62. [PMID: 31018204 DOI: 10.1159/000496568] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2018] [Accepted: 01/02/2019] [Indexed: 01/11/2023]
Abstract
The cytologic evaluation of serous effusions may be challenging for a number of reasons. Distinction of benign, reactive conditions from malignancy represents the main focus when examining these specimens. The morphologic diagnosis of malignancy may be difficult due to the relative paucity of abnormal cells. In other situations, cellularity is not an issue, but the ability to confidently identify a second, foreign (i.e., tumor) population within a background mesothelial cells on the basis of cytomorphologic features alone may pose problems. Cases with definitive morphologic evidence of malignancy may require additional studies in order to determine the tumor subtype and, in the case of carcinoma, the primary site of origin. Cases in which a definitive and precise diagnosis of malignancy is made may be optimal candidates for further molecular testing in order to gain prognostic information and guide personal therapeutic decisions. Finally, while an inflammatory or infectious condition can be suggested on the basis of cellular components and associated background elements, the identification of causative agent(s) may be difficult without additional studies. In all of these situations, the use of ancillary studies and techniques is critical; their utility and appropriate application are the subject of this review.
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Affiliation(s)
- Gordon H Yu
- Hospital of the University of Pennsylvania, Department of Pathology and Laboratory Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, USA,
| | - Laurel J Glaser
- Hospital of the University of Pennsylvania, Department of Pathology and Laboratory Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, USA
| | - Karen S Gustafson
- Hospital of the University of Pennsylvania, Department of Pathology and Laboratory Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, USA
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21
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Guerini-Rocco E, Passaro A, Casadio C, De Luca VM, Guarize J, de Marinis F, Vacirca D, Barberis M. Acquired Resistance to Tyrosine Kinase Inhibitors in Non-Small Cell Lung Cancers: The Role of Next-Generation Sequencing on Endobronchial Ultrasound-Guided Transbronchial Needle Aspiration Samples. Arch Pathol Lab Med 2019; 142:465-473. [PMID: 29565206 DOI: 10.5858/arpa.2017-0158-ra] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
CONTEXT - Molecular testing is essential for the diagnostic workup of patients with advanced non-small cell lung cancers. Cytology specimens from minimally invasive procedures, such as endobronchial ultrasound-guided transbronchial needle aspiration, are often the only available samples for these patients. The implementation of molecular diagnostic testing, and in particular next-generation sequencing-based testing, on these cytologic specimens is currently an evolving field for lung cytopathology. The application of these molecular analyses on tyrosine kinase inhibitor-resistant non-small cell lung cancers raises unique technical, biologic, and clinical challenges. OBJECTIVE - To provide an overview of the implementation of next-generation sequencing analysis on endobronchial ultrasound-guided transbronchial needle aspiration samples to detect the molecular aberrations underneath the phenomenon of acquired resistance in patients with non-small cell lung cancers progressing while on the EGFR/ALK tyrosine kinase inhibitor treatment. DATA SOURCES - Peer-reviewed original articles, review articles, and published guidelines and expert opinion reports were reviewed, together with our single-center experience. CONCLUSIONS - Next-generation sequencing analyses and the endobronchial ultrasound-guided transbronchial needle aspiration procedure may represent a valuable strategy to address the unique requirements of molecular testing on tyrosine kinase inhibitor-resistant non-small cell lung cancers.
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Affiliation(s)
| | | | | | | | | | | | | | - Massimo Barberis
- From the Divisions of Pathology (Drs Guerini-Rocco, Casadio, Midolo De Luca, and Barberis, and Mr Vacirca), Thoracic Oncology (Drs Passaro and de Marinis), and Thoracic Surgery (Dr Guarize), European Institute of Oncology, Milan, Italy
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22
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Balla A, Hampel KJ, Sharma MK, Cottrell CE, Sidiropoulos N. Comprehensive Validation of Cytology Specimens for Next-Generation Sequencing and Clinical Practice Experience. J Mol Diagn 2018; 20:812-821. [DOI: 10.1016/j.jmoldx.2018.06.001] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2017] [Revised: 05/31/2018] [Accepted: 06/21/2018] [Indexed: 12/29/2022] Open
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Abstract
Effusion cytology plays multiple roles in the management of benign and malignant disease, from primary diagnosis to tissue allocation for ancillary diagnostic studies and biomarker testing of therapeutic targets. This article summarizes recent advances in pleural effusion cytology, with a focus on the practical application of immunohistochemical markers, cytogenetic techniques, flow cytometry, and molecular techniques for the diagnosis and management of primary and secondary neoplasms of the pleura.
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Affiliation(s)
- Christin M Lepus
- Department of Pathology, Brigham and Women's Hospital, 75 Francis Street, Boston, MA 02115, USA
| | - Marina Vivero
- Department of Pathology, Brigham and Women's Hospital, 75 Francis Street, Boston, MA 02115, USA.
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24
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Roy-Chowdhuri S, Mehrotra M, Bolivar AM, Kanagal-Shamanna R, Barkoh BA, Hannigan B, Zalles S, Ye W, Duose D, Broaddus R, Staerkel G, Wistuba I, Medeiros LJ, Luthra R. Salvaging the supernatant: next generation cytopathology for solid tumor mutation profiling. Mod Pathol 2018; 31:1036-1045. [PMID: 29463880 DOI: 10.1038/s41379-018-0006-x] [Citation(s) in RCA: 54] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2017] [Revised: 11/27/2017] [Accepted: 12/03/2017] [Indexed: 12/25/2022]
Abstract
With the expanding role of targeted therapy in patients with solid tumors, pathologists face the daunting task of having to maximize limited volume tissue obtained by fine needle aspiration for a variety of molecular tests. While most molecular studies on fine needle aspiration samples have been reported using cellular material, recent studies have shown that a substantial amount of DNA can be retrieved from the supernatant fluid of aspirate needle rinses after cell pelleting for cytospin or cell block preparations. In routine clinical workflow, the supernatant is discarded; however this fluid may provide a complementary source of DNA for tumor mutational profiling. In this study, we evaluated the post-centrifuged supernatant from 25 malignant and 10 benign fine needle aspiration needle rinses. The mean and median DNA yields from the supernatants were 445 ng and 176.4 ng (range, 15.1-2958 ng), respectively. Next generation sequencing using the Ion AmpliSeq Cancer Hotspot Panel v2 detected somatic mutations in all 25 malignant samples. No mutations were detected in any of the benign samples tested. When available, mutations detected in the supernatant fluid were compared to the next generation sequencing analysis performed on a prior or concurrent surgical specimen from the same patient and showed 100% concordance. In a subset of cases (n = 19) mutations in EGFR, KRAS, BRAF, PIK3CA, and NRAS were successfully confirmed by droplet digital PCR, providing an orthogonal platform for mutation analysis. In summary, in this study we show that post centrifuged supernatants from fine needle aspiration needle rinses can provide a robust substrate for expanded mutation profiling by next generation sequencing, as well as hotspot mutation testing by droplet digital PCR. The ability to detect somatic mutations from otherwise discarded supernatant fluids offers the ability to triage and effectively utilize limited volume fine needle aspiration samples when multiple molecular tests are requested, without the need to re-biopsy for additional tissue samples.
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Affiliation(s)
- Sinchita Roy-Chowdhuri
- Department of Pathology, Division of Pathology and Laboratory Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.
| | - Meenakshi Mehrotra
- Department of Hematopathology, Division of Pathology and Laboratory Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Ana Maria Bolivar
- Diagnostic Genetics, School of Health Professions, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Rashmi Kanagal-Shamanna
- Department of Hematopathology, Division of Pathology and Laboratory Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Bedia A Barkoh
- Department of Hematopathology, Division of Pathology and Laboratory Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Brette Hannigan
- Diagnostic Genetics, School of Health Professions, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Stephanie Zalles
- Diagnostic Genetics, School of Health Professions, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Wenrui Ye
- Diagnostic Genetics, School of Health Professions, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Dzifa Duose
- Department of Translational Molecular Pathology, Division of Pathology and Laboratory Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Russell Broaddus
- Department of Pathology, Division of Pathology and Laboratory Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Gregg Staerkel
- Department of Pathology, Division of Pathology and Laboratory Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Ignacio Wistuba
- Department of Translational Molecular Pathology, Division of Pathology and Laboratory Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - L Jeffrey Medeiros
- Department of Hematopathology, Division of Pathology and Laboratory Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Rajyalakshmi Luthra
- Department of Hematopathology, Division of Pathology and Laboratory Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.,Department of Translational Molecular Pathology, Division of Pathology and Laboratory Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
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25
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Zhang Y, Li J, Hua P, Liu N, Li Q, Zhu X, Jiang L, Zheng K, Su X. Targeted next-generation sequencing in cytology specimens for molecular profiling of lung adenocarcinoma. INTERNATIONAL JOURNAL OF CLINICAL AND EXPERIMENTAL PATHOLOGY 2018; 11:3647-3655. [PMID: 31949745 PMCID: PMC6962840] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 04/24/2018] [Accepted: 05/27/2018] [Indexed: 06/10/2023]
Abstract
AIMS Molecular profiling is important for cancer diagnosis and treatment. For many advanced stage lung cancer patients, cytology specimens may be the only materials available for molecular testing. The aim of this study is to evaluate the utility of Next-Generation Sequencing (NGS) of cytology specimens for the molecular profiling of lung adenocarcinoma. METHODS NGS was performed on cell blocks of pleural effusions and fine-needle aspiration (FNA) samples of lung adenocarcinoma to determine the mutation status of EGFR, KRAS, PIK3CA, BRAF, ALK, PDGFRA, and DDR2. Then, quantitative Real-Time PCR (qPCR) was performed and the results were compared to those of NGS. Next, NGS was performed on available histological specimens from the same patients. Last, DNA Quality Index analysis was performed to further explore the applicability of using cytology samples as the source for NGS. RESULTS NGS detected mutations in EGFR, PIK3CA, and KRAS. NGS and qPCR results showed high concordance. NGS exhibited advantages over qPCR in detecting non-hotspot mutations and providing accurate information for allele sequence and mutation frequency. NGS of cytological and histological samples from the same patients showed high concordance. DNA Quality Index analysis showed that DNA extracted from cell blocks of pleural fluid was of similar quality compared to FFPE tissue blocks. CONCLUSIONS NGS can be successfully performed on both FNA and pleural fluid samples from lung adenocarcinomas. The high quality DNA of FFPE cell block of pleural effusion makes it the first choice for molecular profiling, especially when cytology specimens are the only available samples for molecular profiling.
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Affiliation(s)
- Yuan Zhang
- Department of Pathology, West China Hospital of Sichuan UniversityChengdu, China
- Chengdu Women and Children’s Central HospitalChengdu, China
| | - Jinnan Li
- Department of Pathology, West China Hospital of Sichuan UniversityChengdu, China
| | - Ping Hua
- Chengdu Women and Children’s Central HospitalChengdu, China
| | - Nian Liu
- Department of Pathology, West China Hospital of Sichuan UniversityChengdu, China
| | - Qiyuan Li
- Department of Pathology, West China Hospital of Sichuan UniversityChengdu, China
| | - Xianglan Zhu
- Department of Pathology, West China Hospital of Sichuan UniversityChengdu, China
| | - Lili Jiang
- Department of Pathology, West China Hospital of Sichuan UniversityChengdu, China
| | - Ke Zheng
- Department of Pathology, West China Hospital of Sichuan UniversityChengdu, China
| | - Xueying Su
- Department of Pathology, West China Hospital of Sichuan UniversityChengdu, China
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Lüsebrink J, Pieper M, Tillmann RL, Brockmann M, Schildgen O, Schildgen V. Pre-clinical validation of a next generation sequencing testing panel. Exp Mol Pathol 2018; 104:170-174. [DOI: 10.1016/j.yexmp.2018.04.001] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2017] [Revised: 03/09/2018] [Accepted: 04/02/2018] [Indexed: 12/13/2022]
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27
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Turner SR, Buonocore D, Desmeules P, Rekhtman N, Dogan S, Lin O, Arcila ME, Jones DR, Huang J. Feasibility of endobronchial ultrasound transbronchial needle aspiration for massively parallel next-generation sequencing in thoracic cancer patients. Lung Cancer 2018; 119:85-90. [PMID: 29656758 PMCID: PMC5905717 DOI: 10.1016/j.lungcan.2018.03.003] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2017] [Revised: 02/23/2018] [Accepted: 03/06/2018] [Indexed: 01/17/2023]
Abstract
INTRODUCTION Next-generation sequencing (NGS) allows for the identification of a growing number of therapeutic and prognostic molecular targets. However, NGS typically requires greater quantities of DNA than traditional molecular testing does. Endobronchial ultrasound transbronchial needle aspiration (EBUS-TBNA) is a minimally invasive procedure used to sample central thoracic lesions, but it is not well established whether this technique provides sufficient material for NGS. METHODS We performed a retrospective review of EBUS-TBNA at our institution (3/1/14-9/28/16). NGS was performed using a comprehensive hybrid-capture based assay (MSK-IMPACT) that detects >340 gene mutations. Samples found to be diagnostic for malignancy and for which MSK-IMPACT had been attempted were identified. Pathologic and clinical data were obtained from the medical record, and the results of MSK-IMPACT were examined. RESULTS In total, 784 EBUS-TBNA procedures were performed during the study period. MSK-IMPACT was requested for 115 malignant samples and was successful for 99 (86.1%), identifying an average of 12.7 mutations at a mean coverage depth of 806X. NGS was performed on paraffin-embedded cell blocks in 93 cases (93.9%) and on cell-free DNA in needle rinse fluid in 6 cases. The success rate of the assay improved significantly from the first third of cases (76.3%), to 92.3% for the final one-third of cases (p < 0.05). CONCLUSIONS EBUS-TBNA reliably provided adequate tissue for hybrid capture NGS, and is a suitable option for comprehensive NGS testing in patients with thoracic malignancies.
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Affiliation(s)
- Simon R Turner
- Thoracic Surgery, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY, USA
| | - Darren Buonocore
- Pathology Services, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY, USA
| | - Patrice Desmeules
- Pathology Services, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY, USA
| | - Natasha Rekhtman
- Pathology Services, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY, USA
| | - Snjezana Dogan
- Pathology Services, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY, USA
| | - Oscar Lin
- Pathology Services, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY, USA
| | - Maria E Arcila
- Pathology Services, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY, USA
| | - David R Jones
- Thoracic Surgery, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY, USA
| | - James Huang
- Thoracic Surgery, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY, USA.
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28
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Clinical characteristics of non-small cell lung cancer harboring mutations in exon 20 of EGFR or HER2. Oncotarget 2018; 9:21132-21140. [PMID: 29765525 PMCID: PMC5940408 DOI: 10.18632/oncotarget.24958] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2017] [Accepted: 03/15/2018] [Indexed: 12/26/2022] Open
Abstract
Unlike common epidermal growth factor receptor gene (EGFR) mutations that confer sensitivity to tyrosine kinase inhibitors (TKIs) in non-small cell lung cancer (NSCLC), mutations in exon 20 of either EGFR or the human EGFR2 gene (HER2) are associated with insensitivity to EGFR-TKIs, with treatment options for patients with such mutations being limited. Clinical characteristics, outcome of EGFR-TKI or nivolumab treatment, and the presence of coexisting mutations were reviewed for NSCLC patients with exon-20 mutations of EGFR or HER2 as detected by routine application of an amplicon-based next-generation sequencing panel. Between July 2013 and June 2017, 206 patients with pathologically confirmed lung cancer were screened for genetic alterations including HER2 and EGFR mutations. Ten patients harbored HER2 exon-20 insertions (one of whom also carried an exon-19 deletion of EGFR), and 12 patients harbored EGFR exon-20 mutations. Five of the 13 patients with EGFR mutations were treated with EGFR-TKIs, two of whom manifested a partial response, two stable disease, and one progressive disease. Among the seven patients treated with nivolumab, one patient manifested a partial response, three stable disease, and three progressive disease, with most (86%) of these patients discontinuing treatment as a result of disease progression within 4 months. The H1047R mutation of PIK3CA detected in one patient was the only actionable mutation coexisting with the exon-20 mutations of EGFR or HER2. Potentially actionable mutations thus rarely coexist with exon-20 mutations of EGFR or HER2, and EGFR-TKIs and nivolumab show limited efficacy in patients with such exon-20 mutations.
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29
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D'Haene N, Fontanges Q, De Nève N, Blanchard O, Melendez B, Delos M, Dehou MF, Maris C, Nagy N, Rousseau E, Vandenhove J, Gilles A, De Prez C, Verset L, Van Craynest MP, Demetter P, Van Laethem JL, Salmon I, Le Mercier M. Clinical application of targeted next-generation sequencing for colorectal cancer patients: a multicentric Belgian experience. Oncotarget 2018; 9:20761-20768. [PMID: 29755687 PMCID: PMC5945518 DOI: 10.18632/oncotarget.25099] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2017] [Accepted: 03/17/2018] [Indexed: 01/14/2023] Open
Abstract
International guidelines made RAS (KRAS and NRAS) status a prerequisite for the use of anti-EGFR agents for metastatic colorectal cancer (CRC) patients. Daily, new data emerges on the theranostic and prognostic role of molecular biomarkers; this is a strong incentive for a validated, sensitive, and broadly available molecular screening test. Next-generation sequencing (NGS) has begun to supplant other technologies for genomic profiling. We report here our 2 years of clinical practice using NGS results to guide therapeutic decisions. The Ion Torrent AmpliSeq colon/lung cancer panel, which allows mutation detection in 22 cancer-related genes, was prospectively used in clinical practice (BELAC ISO 15189 accredited method). The DNA of 741 formalin-fixed paraffin-embedded CRC tissues, including primary tumors and metastasis, was obtained from 14 different Belgian institutions and subjected to targeted NGS. Of the tumors tested, 98% (727) were successfully sequenced and 89% (650) harbored at least one mutation. KRAS, BRAF and NRAS mutations were found in 335 (46%), 78 (11%) and 32 (4%) samples, respectively. These mutation frequencies were consistent with those reported in public databases. Moreover, mutations and amplifications in potentially actionable genes were identified in 464 samples (64%), including mutations in PIK3CA (14%), ERBB2 (0.4%), AKT1 (0.6%), and MAP2K1 (0.1%), as well as amplifications of ERBB2 (0.3%) and EGFR (0.3%). The median turnaround time between reception of the sample in the laboratory and report release was 8 calendar days. Overall, the AmpliSeq colon/lung cancer panel was successfully applied in daily practice and provided reliable clinically relevant information for CRC patients.
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Affiliation(s)
- Nicky D'Haene
- Department of Pathology, Erasme Hospital, Université Libre de Bruxelles, Brussels, Belgium
| | - Quitterie Fontanges
- Department of Pathology, Erasme Hospital, Université Libre de Bruxelles, Brussels, Belgium
| | - Nancy De Nève
- Department of Pathology, Erasme Hospital, Université Libre de Bruxelles, Brussels, Belgium
| | - Oriane Blanchard
- Department of Pathology, Erasme Hospital, Université Libre de Bruxelles, Brussels, Belgium
| | - Barbara Melendez
- Department of Pathology, Erasme Hospital, Université Libre de Bruxelles, Brussels, Belgium
| | - Monique Delos
- Department of Pathology, CHU UCL Namur, Yvoir, Belgium
| | | | - Calliope Maris
- Department of Pathology, Erasme Hospital, Université Libre de Bruxelles, Brussels, Belgium.,Department of Pathology, Braine l´Alleud Waterloo Hospital, Braine l´Alleud, Belgium
| | - Nathalie Nagy
- Department of Pathology, Charleroi University Hospital, Charleroi, Belgium
| | | | | | - André Gilles
- Department of Pathology, EPICURA Hospital, Frameries, Belgium
| | - Carine De Prez
- Department of Pathology, Brugmann University Hospital, Brussels, Belgium
| | - Laurine Verset
- Department of Pathology, Erasme Hospital, Université Libre de Bruxelles, Brussels, Belgium.,CurePath, Jumet, Belgium
| | | | - Pieter Demetter
- Department of Pathology, Erasme Hospital, Université Libre de Bruxelles, Brussels, Belgium
| | - Jean-Luc Van Laethem
- Department of Oncology, Erasme Hospital, Université Libre de Bruxelles, Brussels, Belgium
| | - Isabelle Salmon
- Department of Pathology, Erasme Hospital, Université Libre de Bruxelles, Brussels, Belgium
| | - Marie Le Mercier
- Department of Pathology, Erasme Hospital, Université Libre de Bruxelles, Brussels, Belgium
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30
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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.
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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
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31
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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: 333] [Impact Index Per Article: 55.5] [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.
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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
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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.
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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
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Fassan M. Molecular Diagnostics in Pathology: Time for a Next-Generation Pathologist? Arch Pathol Lab Med 2018; 142:313-320. [DOI: 10.5858/arpa.2017-0269-ra] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/29/2023]
Abstract
Context.—Comprehensive molecular investigations of mainstream carcinogenic processes have led to the use of effective molecular targeted agents in most cases of solid tumors in clinical settings.Objective.—To update readers regarding the evolving role of the pathologist in the therapeutic decision-making process and the introduction of next-generation technologies into pathology practice.Data Sources.—Current literature on the topic, primarily sourced from the PubMed (National Center for Biotechnology Information, Bethesda, Maryland) database, were reviewed.Conclusions.—Adequate evaluation of cytologic-based and tissue-based predictive diagnostic biomarkers largely depends on both proper pathologic characterization and customized processing of biospecimens. Moreover, increased requests for molecular testing have paralleled the recent, sharp decrease in tumor material to be analyzed—material that currently comprises cytology specimens or, at minimum, small biopsies in most cases of metastatic/advanced disease. Traditional diagnostic pathology has been completely revolutionized by the introduction of next-generation technologies, which provide multigene, targeted mutational profiling, even in the most complex of clinical cases. Combining traditional and molecular knowledge, pathologists integrate the morphological, clinical, and molecular dimensions of a disease, leading to a proper diagnosis and, therefore, the most-appropriate tailored therapy.
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Affiliation(s)
- Matteo Fassan
- From the Department of Medicine, Surgical Pathology and Cytopathology Unit, University of Padua, Padua, Italy
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Rachiglio AM, Esposito Abate R, Sacco A, Pasquale R, Fenizia F, Lambiase M, Morabito A, Montanino A, Rocco G, Romano C, Nappi A, Iaffaioli RV, Tatangelo F, Botti G, Ciardiello F, Maiello MR, De Luca A, Normanno N. Limits and potential of targeted sequencing analysis of liquid biopsy in patients with lung and colon carcinoma. Oncotarget 2018; 7:66595-66605. [PMID: 27448974 PMCID: PMC5341823 DOI: 10.18632/oncotarget.10704] [Citation(s) in RCA: 68] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2016] [Accepted: 05/29/2016] [Indexed: 12/12/2022] Open
Abstract
The circulating free tumor DNA (ctDNA) represents an alternative, minimally invasive source of tumor DNA for molecular profiling. Targeted sequencing with next generation sequencing (NGS) can assess hundred mutations starting from a low DNA input. We performed NGS analysis of ctDNA from 44 patients with metastatic non-small-cell lung carcinoma (NSCLC) and 35 patients with metastatic colorectal carcinoma (CRC). NGS detected EGFR mutations in 17/22 plasma samples from EGFR-mutant NSCLC patients (sensitivity 77.3%). The concordance rate between tissue and plasma in NSCLC was much lower for other mutations such as KRAS that, based on the allelic frequency and the fraction of neoplastic cells, were likely to be sub-clonal. NGS also identified EGFR mutations in plasma samples from two patients with EGFR wild type tumor tissue. Both mutations were confirmed by droplet digital PCR (ddPCR) in both plasma and tissue samples. In CRC, the sensitivity of the NGS plasma analysis for RAS mutations was 100% (6/6) in patients that had not resection of the primary tumor before blood drawing, and 46.2% (6/13) in patients with primary tumor resected before enrollment. Our study showed that NGS is a suitable method for plasma testing. However, its clinical sensitivity is significantly affected by the presence of the primary tumor and by the heterogeneity of driver mutations.
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Affiliation(s)
- Anna Maria Rachiglio
- Laboratory of Pharmacogenomics, CROM-Istituto Nazionale Tumori "Fondazione G. Pascale"-IRCCS, Naples, Italy
| | - Riziero Esposito Abate
- Laboratory of Pharmacogenomics, CROM-Istituto Nazionale Tumori "Fondazione G. Pascale"-IRCCS, Naples, Italy
| | - Alessandra Sacco
- Laboratory of Pharmacogenomics, CROM-Istituto Nazionale Tumori "Fondazione G. Pascale"-IRCCS, Naples, Italy
| | - Raffaella Pasquale
- Laboratory of Pharmacogenomics, CROM-Istituto Nazionale Tumori "Fondazione G. Pascale"-IRCCS, Naples, Italy
| | - Francesca Fenizia
- Laboratory of Pharmacogenomics, CROM-Istituto Nazionale Tumori "Fondazione G. Pascale"-IRCCS, Naples, Italy
| | - Matilde Lambiase
- Laboratory of Pharmacogenomics, CROM-Istituto Nazionale Tumori "Fondazione G. Pascale"-IRCCS, Naples, Italy
| | - Alessandro Morabito
- Thoraco-Pulmonary, Medical Oncology, Istituto Nazionale Tumori "Fondazione G. Pascale"-IRCCS, Naples, Italy
| | - Agnese Montanino
- Thoraco-Pulmonary, Medical Oncology, Istituto Nazionale Tumori "Fondazione G. Pascale"-IRCCS, Naples, Italy
| | - Gaetano Rocco
- Thoracic Surgery, Istituto Nazionale Tumori "Fondazione G. Pascale"-IRCCS, Naples, Italy
| | - Carmen Romano
- Gastro-Intestinal Medical Oncology, Istituto Nazionale Tumori "Fondazione G. Pascale"-IRCCS, Naples, Italy
| | - Anna Nappi
- Gastro-Intestinal Medical Oncology, Istituto Nazionale Tumori "Fondazione G. Pascale"-IRCCS, Naples, Italy
| | - Rosario Vincenzo Iaffaioli
- Gastro-Intestinal Medical Oncology, Istituto Nazionale Tumori "Fondazione G. Pascale"-IRCCS, Naples, Italy
| | - Fabiana Tatangelo
- Surgical Pathology Unit, Istituto Nazionale Tumori "Fondazione G. Pascale"-IRCCS, Naples, Italy
| | - Gerardo Botti
- Surgical Pathology Unit, Istituto Nazionale Tumori "Fondazione G. Pascale"-IRCCS, Naples, Italy
| | - Fortunato Ciardiello
- Department of Clinical and Experimental Medicine 'F. Magrassi' - Medical Oncology, Seconda Università degli Studi di Napoli, Napoli, Italy
| | - Monica R Maiello
- Cell Biology and Biotherapy Unit, Istituto Nazionale Tumori "Fondazione G. Pascale"-IRCCS, Naples, Italy
| | - Antonella De Luca
- Cell Biology and Biotherapy Unit, Istituto Nazionale Tumori "Fondazione G. Pascale"-IRCCS, Naples, Italy
| | - Nicola Normanno
- Laboratory of Pharmacogenomics, CROM-Istituto Nazionale Tumori "Fondazione G. Pascale"-IRCCS, Naples, Italy.,Cell Biology and Biotherapy Unit, Istituto Nazionale Tumori "Fondazione G. Pascale"-IRCCS, Naples, Italy
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Abraham J, Singh S, Joshi S. Liquid biopsy - emergence of a new era in personalized cancer care. ACTA ACUST UNITED AC 2018. [DOI: 10.1186/s41241-018-0053-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
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The next generation of metastatic melanoma: uncovering the genetic variants for anti-BRAF therapy response. Oncotarget 2018; 7:25135-49. [PMID: 26863566 PMCID: PMC5041894 DOI: 10.18632/oncotarget.7175] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2015] [Accepted: 01/24/2016] [Indexed: 12/12/2022] Open
Abstract
Metastatic melanoma (MM) is a highly aggressive cancer with a median overall survival of 6-9 months, notwithstanding the numerous efforts in development of new therapeutic approaches. To this aim we tested the clinical applicability of the Ion Torrent Personal Genome Machine to simultaneously screen MM patients in order to individuate new or already known SNPs and mutations able to predict the duration of response to BRAF inhibitors. An Ampliseq Custom Panel, including 11 crucial full length genes involved in melanoma carcinogenesis and therapy response pathways, was created and used to analyze 25 MM patients. We reported BRAFV600 and NRASQ61 mutations in 68% and 24% of samples, respectively. Moreover, we more frequently identified the following alterations related to BRAF status: PIK3CAI391M (44%) and KITD737N (36%) mutations, CTLA4T17A (52%), MC1RV60L (32%) and MITFS473A (60%) polymorphisms. Considering the progression free survival (PFS), statistical analyses showed that BRAFV600 patients without any of these more frequent alterations had a higher median PFS. Protein structure changes seem to be due to these variants by in silico analysis. In conclusion, a Next-Generation Sequencing approach with custom panel may provide new information to evaluate tumor-specific therapeutic susceptibility and individual prognosis to improve the care of MM patients.
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Stoy SP, Segal JP, Mueller J, Furtado LV, Vokes EE, Patel JD, Murgu S. Feasibility of Endobronchial Ultrasound-guided Transbronchial Needle Aspiration Cytology Specimens for Next Generation Sequencing in Non-small-cell Lung Cancer. Clin Lung Cancer 2017; 19:230-238.e2. [PMID: 29277564 DOI: 10.1016/j.cllc.2017.11.010] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2017] [Revised: 11/20/2017] [Accepted: 11/25/2017] [Indexed: 01/13/2023]
Abstract
INTRODUCTION Next generation sequencing (NGS) testing of lung cancer is recommended by guidelines, and endobronchial ultrasound (EBUS)-guided transbronchial needle aspiration (TBNA) often provides the only material available for testing. Previous studies have demonstrated successful NGS testing on cell block samples obtained by EBUS; however, cytology smears provide a more reliable sample with better DNA quality for testing. In this study, we aimed to determine the success rate of OncoScreen (50 gene) and OncoPlus (1213 gene) panel NGS testing of cytology samples obtained by EBUS utilizing 22- and 25-gauge needles. METHODS Fifty-four patients underwent EBUS-TBNA of lung cancer for which NGS testing was requested. Data was analyzed for needle gauge, cytologic assessment, NGS test success, and sample type (cytology smear or cell block) used for testing. RESULTS Eighty-five NGS tests were ordered on 54 samples. Overall, 95.3% of samples had successful testing. OncoScreen and OncoPlus panels were successful 98.0% and 91.4% of the time, respectively. Cytology smears provided testing material for 85% of the tests. OncoScreen testing was successful in 97.5% and 100% of the 22- and 25-gauge samples, respectively (P = 1.00). OncoPlus testing was successful in 91.3% and 100% of the 22- and 25-gauge samples, respectively (P = 1.00). CONCLUSIONS NGS can be reliably performed on cytology smears obtained from EBUS-TBNA. The size of the needle does not seem to affect the success rate of small or large panel NGS tests.
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Affiliation(s)
- Sean P Stoy
- Department of Medicine, University of Chicago Medicine and Biological Sciences, Chicago, IL
| | - Jeremy P Segal
- Department of Pathology, University of Chicago Medicine and Biological Sciences, Chicago, IL
| | - Jeffrey Mueller
- Department of Pathology, University of Chicago Medicine and Biological Sciences, Chicago, IL
| | - Larissa V Furtado
- Department of Pathology, University of Utah School of Medicine, Salt Lake City, UT
| | - Everett E Vokes
- Department of Medicine, University of Chicago Medicine and Biological Sciences, Chicago, IL
| | - Jyoti D Patel
- Department of Medicine, University of Chicago Medicine and Biological Sciences, Chicago, IL
| | - Septimiu Murgu
- Department of Medicine, University of Chicago Medicine and Biological Sciences, Chicago, IL.
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38
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Sibinga Mulder BG, Mieog JSD, Farina Sarasqueta A, Handgraaf HJM, Vasen HFA, Swijnenburg RJ, Luelmo SAC, Feshtali S, Inderson A, Vahrmeijer AL, Bonsing BA, Wezel TV, Morreau H. Diagnostic value of targeted next-generation sequencing in patients with suspected pancreatic or periampullary cancer. J Clin Pathol 2017; 71:246-252. [DOI: 10.1136/jclinpath-2017-204607] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2017] [Revised: 07/07/2017] [Accepted: 07/07/2017] [Indexed: 01/04/2023]
Abstract
AimsRadiological imaging and morphological assessment of cytology material have limitations for preoperative classification of pancreatic or periampullary lesions, often resulting in surgical resection without definitive diagnosis. Our prospective study aims to define the diagnostic value of targeted next-generation sequencing (NGS) of DNA from cytology material.MethodsPatients with a suspect pancreatic or periampullary lesion underwent standard diagnostic evaluation including preoperative morphological cytology assessment. Treatment options for suspect lesions were surgical exploration with possible resection, follow-up or palliation. The cytology samples were analysed with NGS, in which 50 genes were sequenced for the presence of pathogenic variants. The NGS results were integrated with the clinical information during multidisciplinary team meetings, and changes in the treatment plan were scored. Diagnostic accuracy of NGS analysis (malignancy vs benign disease) was calculated.ResultsNGS results of the cytology samples were confirmed in the resection specimens of the first 10 included patients. The integration of the NGS results led to a change in treatment plan in 7 out of 70 patients (from exploration to follow-up, n=4; from follow-up to exploration and resection, n=2; from palliation to resection, n=1). In four patients, the NGS results were contradictory, but did not affect the treatment plan. In the remaining 59 patients, NGS analysis supported the initial treatment plan. The diagnostic accuracy of NGS analysis was 94% (sensitivity=93%; specificity=100%).ConclusionsNGS can change the treatment plan in a significant portion of patients with suspect pancreatic or periampullary lesions. Application of NGS can optimise treatment selection and diminish unnecessary surgeries.
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Hwang DH, Garcia EP, Ducar MD, Cibas ES, Sholl LM. Next-generation sequencing of cytologic preparations: An analysis of quality metrics. Cancer Cytopathol 2017; 125:786-794. [DOI: 10.1002/cncy.21897] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2017] [Revised: 06/25/2017] [Accepted: 06/26/2017] [Indexed: 01/08/2023]
Affiliation(s)
- David H. Hwang
- Department of Pathology; Brigham and Women's Hospital and Harvard Medical School; Boston Massachusetts
| | - Elizabeth P. Garcia
- Center for Advanced Molecular Diagnostics; Brigham and Women's Hospital and Harvard Medical School; Boston Massachusetts
| | - Matthew D. Ducar
- Center for Cancer Genome Discovery; Dana-Farber Cancer Institute; Boston Massachusetts
| | - Edmund S. Cibas
- Department of Pathology; Brigham and Women's Hospital and Harvard Medical School; Boston Massachusetts
| | - Lynette M. Sholl
- Department of Pathology; Brigham and Women's Hospital and Harvard Medical School; Boston Massachusetts
- Center for Advanced Molecular Diagnostics; Brigham and Women's Hospital and Harvard Medical School; Boston Massachusetts
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40
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Lindquist KE, Karlsson A, Levéen P, Brunnström H, Reuterswärd C, Holm K, Jönsson M, Annersten K, Rosengren F, Jirström K, Kosieradzki J, Ek L, Borg Å, Planck M, Jönsson G, Staaf J. Clinical framework for next generation sequencing based analysis of treatment predictive mutations and multiplexed gene fusion detection in non-small cell lung cancer. Oncotarget 2017; 8:34796-34810. [PMID: 28415793 PMCID: PMC5471012 DOI: 10.18632/oncotarget.16276] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2016] [Accepted: 03/01/2017] [Indexed: 12/26/2022] Open
Abstract
Precision medicine requires accurate multi-gene clinical diagnostics. We describe the implementation of an Illumina TruSight Tumor (TST) clinical NGS diagnostic framework and parallel validation of a NanoString RNA-based ALK, RET, and ROS1 gene fusion assay for combined analysis of treatment predictive alterations in non-small cell lung cancer (NSCLC) in a regional healthcare region of Sweden (Scandinavia). The TST panel was clinically validated in 81 tumors (99% hotspot mutation concordance), after which 533 consecutive NSCLCs were collected during one-year of routine clinical analysis in the healthcare region (~90% advanced stage patients). The NanoString assay was evaluated in 169 of 533 cases. In the 533-sample cohort 79% had 1-2 variants, 12% >2 variants and 9% no detected variants. Ten gene fusions (five ALK, three RET, two ROS1) were detected in 135 successfully analyzed cases (80% analysis success rate). No ALK or ROS1 FISH fusion positive case was missed by the NanoString assay. Stratification of the 533-sample cohort based on actionable alterations in 11 oncogenes revealed that 66% of adenocarcinomas, 13% of squamous carcinoma (SqCC) and 56% of NSCLC not otherwise specified harbored ≥1 alteration. In adenocarcinoma, 10.6% of patients (50.3% if including KRAS) could potentially be eligible for emerging therapeutics, in addition to the 15.3% of patients eligible for standard EGFR or ALK inhibitors. For squamous carcinoma corresponding proportions were 4.4% (11.1% with KRAS) vs 2.2%. In conclusion, multiplexed NGS and gene fusion analyses are feasible in NSCLC for clinical diagnostics, identifying notable proportions of patients potentially eligible for emerging molecular therapeutics.
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Affiliation(s)
| | - Anna Karlsson
- Division of Oncology and Pathology, Department of Clinical Sciences Lund, Lund University, Medicon Village, Lund SE 22381, Sweden
| | - Per Levéen
- Department of Pathology, Regional Laboratories Region Skåne, Lund SE 22185, Sweden
| | - Hans Brunnström
- Department of Pathology, Regional Laboratories Region Skåne, Lund SE 22185, Sweden
- Division of Oncology and Pathology, Department of Clinical Sciences Lund, Lund University, Lund SE 22185, Sweden
| | - Christel Reuterswärd
- Division of Oncology and Pathology, Department of Clinical Sciences Lund, Lund University, Medicon Village, Lund SE 22381, Sweden
| | - Karolina Holm
- Division of Oncology and Pathology, Department of Clinical Sciences Lund, Lund University, Medicon Village, Lund SE 22381, Sweden
| | - Mats Jönsson
- Division of Oncology and Pathology, Department of Clinical Sciences Lund, Lund University, Medicon Village, Lund SE 22381, Sweden
| | - Karin Annersten
- Division of Oncology and Pathology, Department of Clinical Sciences Lund, Lund University, Medicon Village, Lund SE 22381, Sweden
| | - Frida Rosengren
- Division of Oncology and Pathology, Department of Clinical Sciences Lund, Lund University, Medicon Village, Lund SE 22381, Sweden
| | - Karin Jirström
- Department of Pathology, Regional Laboratories Region Skåne, Lund SE 22185, Sweden
- Division of Oncology and Pathology, Department of Clinical Sciences Lund, Lund University, Lund SE 22185, Sweden
| | - Jaroslaw Kosieradzki
- Department of Respiratory Medicine and Allergology, Skane University Hospital, Lund SE22185, Sweden
| | - Lars Ek
- Department of Respiratory Medicine and Allergology, Skane University Hospital, Lund SE22185, Sweden
| | - Åke Borg
- Division of Oncology and Pathology, Department of Clinical Sciences Lund, Lund University, Medicon Village, Lund SE 22381, Sweden
- CREATE Health Strategic Center for Translational Cancer Research, Lund University, Medicon Village, Lund SE 22381, Sweden
| | - Maria Planck
- Division of Oncology and Pathology, Department of Clinical Sciences Lund, Lund University, Medicon Village, Lund SE 22381, Sweden
- Department of Oncology, Skåne University Hospital, Lund SE 22381, Sweden
| | - Göran Jönsson
- Division of Oncology and Pathology, Department of Clinical Sciences Lund, Lund University, Medicon Village, Lund SE 22381, Sweden
- CREATE Health Strategic Center for Translational Cancer Research, Lund University, Medicon Village, Lund SE 22381, Sweden
| | - Johan Staaf
- Division of Oncology and Pathology, Department of Clinical Sciences Lund, Lund University, Medicon Village, Lund SE 22381, Sweden
- CREATE Health Strategic Center for Translational Cancer Research, Lund University, Medicon Village, Lund SE 22381, Sweden
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Calvayrac O, Pradines A, Pons E, Mazières J, Guibert N. Molecular biomarkers for lung adenocarcinoma. Eur Respir J 2017; 49:49/4/1601734. [PMID: 28381431 DOI: 10.1183/13993003.01734-2016] [Citation(s) in RCA: 82] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2016] [Accepted: 12/28/2016] [Indexed: 12/28/2022]
Abstract
The identification of oncogenic driver alterations that underlie sensitivity to small inhibitors has led to growing interest in identifying additional targetable oncogenes in nonsmall cell lung cancer. Although the therapeutic impact of the discovery of these alterations has now been widely demonstrated, the epidemiological data associated with each of these biomarkers remain insufficiently studied. In this review, we discuss the techniques used to discover each of these candidate oncogenes, their prevalence in nonsmall cell lung cancer, and briefly outline the epidemiological features of the major oncogenes and ways in which their identification can determine therapeutic strategies.
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Affiliation(s)
- Olivier Calvayrac
- Inserm, Centre de Recherche en Cancérologie de Toulouse, CRCT UMR-1037, Toulouse, France
| | - Anne Pradines
- Inserm, Centre de Recherche en Cancérologie de Toulouse, CRCT UMR-1037, Toulouse, France.,Institut Universitaire du Cancer, Toulouse, France.,Institut Claudius Regaud, IUCT-Oncopole, Laboratoire de Biologie Médicale Oncologique, Toulouse, France
| | - Elvire Pons
- Inserm, Centre de Recherche en Cancérologie de Toulouse, CRCT UMR-1037, Toulouse, France.,Institut Claudius Regaud, IUCT-Oncopole, Laboratoire de Biologie Médicale Oncologique, Toulouse, France
| | - Julien Mazières
- Inserm, Centre de Recherche en Cancérologie de Toulouse, CRCT UMR-1037, Toulouse, France .,Institut Universitaire du Cancer, Toulouse, France.,Hôpital Larrey, Centre Hospitalier Universitaire, Université Paul Sabatier, Toulouse, France
| | - Nicolas Guibert
- Inserm, Centre de Recherche en Cancérologie de Toulouse, CRCT UMR-1037, Toulouse, France.,Institut Universitaire du Cancer, Toulouse, France.,Hôpital Larrey, Centre Hospitalier Universitaire, Université Paul Sabatier, Toulouse, France
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42
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Stoy S, Murgu S. The use of endobronchial ultrasound guided transbronchial needle aspiration specimens for next generation sequencing in non-small cell lung cancer: a clinical perspective. J Thorac Dis 2017; 9:E398-E401. [PMID: 28523189 DOI: 10.21037/jtd.2017.03.169] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Affiliation(s)
- Sean Stoy
- University of Chicago Medical Center, Chicago, IL, USA
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43
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Baum JE, Zhang P, Hoda RS, Geraghty B, Rennert H, Narula N, Fernandes HD. Accuracy of next-generation sequencing for the identification of clinically relevant variants in cytology smears in lung adenocarcinoma. Cancer Cytopathol 2017; 125:398-406. [PMID: 28272845 DOI: 10.1002/cncy.21844] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2016] [Revised: 01/25/2017] [Accepted: 01/26/2017] [Indexed: 12/30/2022]
Abstract
BACKGROUND Minimally invasive diagnostic procedures such as needle-core biopsy and fine-needle aspiration provide adequate material for molecular analyses. Advances in precision oncology are trending toward the interrogation of limited amounts of genomic material to guide clinical and therapeutic decisions. The aim of this study was to investigate the minimum cellularity needed on cytologic smears for the identification of clinically relevant variants with next-generation sequencing (NGS). METHODS Thirty cases of cytologically diagnosed, resection-proven primary lung adenocarcinoma were identified. Nineteen of the 30 cases were known to harbor actionable variants. One Diff-Quik (DQ)-stained slide and 1 Papanicolaou (Pap)-stained slide were selected from each case. Cases were categorized as containing fewer than 100 tumor cells, 100 to 500 tumor cells, or more than 500 tumor cells. NGS was performed on the Ion Torrent platform. RESULTS NGS was successfully performed on all cell blocks and on 90% of the smears. Paired DQ and Pap smears showed similar cellularity, and cases that differed in cellularity were within 1 category of each other. The cases with more than 100 tumor cells had a 93% success rate; this was significantly different from the situation for cases with fewer than 100 tumor cells, which were successfully sequenced only 67% of the time. Overall, NGS was able to provide clinically relevant information for 83% of DQ smears and for 90% of Pap smears tested. CONCLUSIONS The data show a significantly higher likelihood of successful NGS with cytologic smears with more than 100 tumor cells. There was a trend for a higher NGS success rate with Pap smears versus DQ smears. Cancer Cytopathol 2017;125:398-406. © 2017 American Cancer Society.
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Affiliation(s)
- Jordan E Baum
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, New York
| | - Pan Zhang
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, New York
| | - Rana S Hoda
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, New York
| | - Brian Geraghty
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, New York
| | - Hanna Rennert
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, New York
| | - Navneet Narula
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, New York
| | - Helen D Fernandes
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, New York
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44
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Lee HY, Lee SH, Won JK, Lee DS, Kwon NJ, Choi SM, Lee J, Lee CH, Lee SM, Yim JJ, Yoo CG, Kim YW, Han SK, Park YS. Analysis of Fifty Hotspot Mutations of Lung Squamous Cell Carcinoma in Never-smokers. J Korean Med Sci 2017; 32:415-420. [PMID: 28145643 PMCID: PMC5290099 DOI: 10.3346/jkms.2017.32.3.415] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/11/2016] [Accepted: 11/11/2016] [Indexed: 01/08/2023] Open
Abstract
Smoking is the major risk factor for lung squamous cell carcinoma (SCC), although a small number of lung SCCs occurs in never-smokers. The purpose of this study was to compare 50 hotspot mutations of lung SCCs between never-smokers and smokers. We retrospectively reviewed the medical records of patients newly diagnosed with lung SCC between January 1, 2011 and December 31, 2013 in the Seoul National University Hospital. Formalin-fixed, paraffin-embedded tumor samples were used for analysis of hotspot mutations. Fifty cancer-related genes in never-smokers were compared to those in ever-smokers. Of 379 lung SCC patients, 19 (5.0%) were never-smokers. The median age of these 19 patients was 67 years (interquartile range 57-73 years), and 10 of these patients were women (52.5%). The incidence rates of stage I, II, III, and IV disease in this group were 26.4%, 5.3%, 31.6%, and 36.8%, respectively, and sequencing was performed successfully in 14 cases. In the 26 lung SCC tumor samples (12 from never-smokers and 14 from ever-smokers) sequenced using personal genome machine, the most common mutations were in TP53 (75.0%), RAS (66.7%), and STK11 (33.3%), but mutations were also found in EGFR, KIT, and PTEN. The distribution of hotspot mutations in never-smokers was similar to that in ever-smokers. There was no significant difference in overall survival between the 2 groups. The 50 hotspot mutations of lung SCC in never-smokers were similar to those of ever-smokers.
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Affiliation(s)
- Ha Youn Lee
- Division of Pulmonary and Critical Care Medicine, Department of Internal Medicine, Seoul National University Hospital, Seoul, Korea
- Department of Internal Medicine, Seoul National University College of Medicine, Seoul, Korea
| | - Se Hoon Lee
- Department of Internal Medicine, Seoul National University College of Medicine, Seoul, Korea
- Cancer Research Institute, Seoul National University College of Medicine, Seoul, Korea
| | - Jae Kyung Won
- Department of Pathology, Seoul National University College of Medicine, Seoul, Korea
| | - Dong Soo Lee
- Department of Nuclear Medicine, Seoul National University College of Medicine, Seoul, Korea
| | | | - Sun Mi Choi
- Division of Pulmonary and Critical Care Medicine, Department of Internal Medicine, Seoul National University Hospital, Seoul, Korea
- Department of Internal Medicine, Seoul National University College of Medicine, Seoul, Korea
| | - Jinwoo Lee
- Division of Pulmonary and Critical Care Medicine, Department of Internal Medicine, Seoul National University Hospital, Seoul, Korea
- Department of Internal Medicine, Seoul National University College of Medicine, Seoul, Korea
| | - Chang Hoon Lee
- Division of Pulmonary and Critical Care Medicine, Department of Internal Medicine, Seoul National University Hospital, Seoul, Korea
- Department of Internal Medicine, Seoul National University College of Medicine, Seoul, Korea
| | - Sang Min Lee
- Division of Pulmonary and Critical Care Medicine, Department of Internal Medicine, Seoul National University Hospital, Seoul, Korea
- Department of Internal Medicine, Seoul National University College of Medicine, Seoul, Korea
| | - Jae Joon Yim
- Division of Pulmonary and Critical Care Medicine, Department of Internal Medicine, Seoul National University Hospital, Seoul, Korea
- Department of Internal Medicine, Seoul National University College of Medicine, Seoul, Korea
| | - Chul Gyu Yoo
- Division of Pulmonary and Critical Care Medicine, Department of Internal Medicine, Seoul National University Hospital, Seoul, Korea
- Department of Internal Medicine, Seoul National University College of Medicine, Seoul, Korea
| | - Young Whan Kim
- Division of Pulmonary and Critical Care Medicine, Department of Internal Medicine, Seoul National University Hospital, Seoul, Korea
- Department of Internal Medicine, Seoul National University College of Medicine, Seoul, Korea
| | - Sung Koo Han
- Division of Pulmonary and Critical Care Medicine, Department of Internal Medicine, Seoul National University Hospital, Seoul, Korea
- Department of Internal Medicine, Seoul National University College of Medicine, Seoul, Korea
| | - Young Sik Park
- Division of Pulmonary and Critical Care Medicine, Department of Internal Medicine, Seoul National University Hospital, Seoul, Korea
- Department of Internal Medicine, Seoul National University College of Medicine, Seoul, Korea.
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45
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Kamps R, Brandão RD, Bosch BJVD, Paulussen ADC, Xanthoulea S, Blok MJ, Romano A. Next-Generation Sequencing in Oncology: Genetic Diagnosis, Risk Prediction and Cancer Classification. Int J Mol Sci 2017; 18:ijms18020308. [PMID: 28146134 PMCID: PMC5343844 DOI: 10.3390/ijms18020308] [Citation(s) in RCA: 284] [Impact Index Per Article: 40.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2016] [Accepted: 01/19/2017] [Indexed: 12/17/2022] Open
Abstract
Next-generation sequencing (NGS) technology has expanded in the last decades with significant improvements in the reliability, sequencing chemistry, pipeline analyses, data interpretation and costs. Such advances make the use of NGS feasible in clinical practice today. This review describes the recent technological developments in NGS applied to the field of oncology. A number of clinical applications are reviewed, i.e., mutation detection in inherited cancer syndromes based on DNA-sequencing, detection of spliceogenic variants based on RNA-sequencing, DNA-sequencing to identify risk modifiers and application for pre-implantation genetic diagnosis, cancer somatic mutation analysis, pharmacogenetics and liquid biopsy. Conclusive remarks, clinical limitations, implications and ethical considerations that relate to the different applications are provided.
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Affiliation(s)
- Rick Kamps
- Department of Clinical Genetics: GROW-School for Oncology and Developmental Biology, Maastricht University Medical Centre, 6229HX Maastricht, The Netherlands.
| | - Rita D Brandão
- Department of Clinical Genetics: GROW-School for Oncology and Developmental Biology, Maastricht University Medical Centre, 6229HX Maastricht, The Netherlands.
| | - Bianca J van den Bosch
- Department of Clinical Genetics: GROW-School for Oncology and Developmental Biology, Maastricht University Medical Centre, 6229HX Maastricht, The Netherlands.
| | - Aimee D C Paulussen
- Department of Clinical Genetics: GROW-School for Oncology and Developmental Biology, Maastricht University Medical Centre, 6229HX Maastricht, The Netherlands.
| | - Sofia Xanthoulea
- Department of Gynaecology and Obstetrics: GROW-School for Oncology and Developmental Biology, Maastricht University Medical Centre, 6229HX Maastricht, The Netherlands.
| | - Marinus J Blok
- Department of Clinical Genetics: GROW-School for Oncology and Developmental Biology, Maastricht University Medical Centre, 6229HX Maastricht, The Netherlands.
| | - Andrea Romano
- Department of Gynaecology and Obstetrics: GROW-School for Oncology and Developmental Biology, Maastricht University Medical Centre, 6229HX Maastricht, The Netherlands.
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46
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Reynolds JP, Zhou Y, Jakubowski MA, Wang Z, Brainard JA, Klein RD, Farver CF, Almeida FA, Cheng YW. Next-generation sequencing of liquid-based cytology non-small cell lung cancer samples. Cancer Cytopathol 2017; 125:178-187. [PMID: 28085233 DOI: 10.1002/cncy.21812] [Citation(s) in RCA: 43] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2016] [Revised: 10/18/2016] [Accepted: 11/04/2016] [Indexed: 12/25/2022]
Abstract
BACKGROUND The detection of mutated epidermal growth factor receptor (EGFR) in non-small cell lung cancer (NSCLC) with residual cell pellets derived from liquid-based cytology (LBC) samples (eg, endoscopic ultrasound-guided fine-needle aspiration) has been validated with allele-specific polymerase chain reaction. The aim of this study was to validate next-generation sequencing (NGS) technology for detecting gene mutations with residual cell pellets from LBC. METHODS Archived DNA extracted from LBC samples of adenocarcinoma stored in PreservCyt with a known EGFR mutation status was retrieved. Genomic DNA was multiplex-amplified and enriched with Ion AmpliSeq Cancer Hotspot Panel v2 chemistry and the OneTouch 2 instrument; this was followed by semiconductor sequencing on the Ion Personal Genome Machine platform. The mutation hotspots of 6 NSCLC-related genes (BRAF, EGFR, ERBB2, KRAS, MET, and phosphatidylinositol-4,5-bisphosphate 3-kinase catalytic subunit α [PIK3CA]) were analyzed with NextGENe and Torrent Suite bioinformatics tools. RESULTS The commonly identified EGFR sequence changes, including 4 L858R mutations, 3 exon 19 deletions, and 1 exon 20 insertion, were in 100% concordance between the assay platforms. Less common NSCLC variants were also found in the mutation hotspots of ERBB2, KRAS, MET, and PIK3CA genes. CONCLUSIONS NSCLC mutation analysis using NGS can be successfully performed on residual cell pellets derived from LBC samples. This approach allows the simultaneous examination of multiple mutation hotspots in a timely manner to improve patient care. Cancer Cytopathol 2017;125:178-187. © 2016 American Cancer Society.
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Affiliation(s)
- Jordan P Reynolds
- Robert J. Tomsich Pathology and Laboratory Medicine Institute, Cleveland Clinic, Cleveland, Ohio
| | - Yaolin Zhou
- Robert J. Tomsich Pathology and Laboratory Medicine Institute, Cleveland Clinic, Cleveland, Ohio
| | - Maureen A Jakubowski
- Robert J. Tomsich Pathology and Laboratory Medicine Institute, Cleveland Clinic, Cleveland, Ohio
| | - Zhen Wang
- Robert J. Tomsich Pathology and Laboratory Medicine Institute, Cleveland Clinic, Cleveland, Ohio
| | - Jennifer A Brainard
- Robert J. Tomsich Pathology and Laboratory Medicine Institute, Cleveland Clinic, Cleveland, Ohio
| | - Roger D Klein
- Robert J. Tomsich Pathology and Laboratory Medicine Institute, Cleveland Clinic, Cleveland, Ohio
| | - Carol F Farver
- Robert J. Tomsich Pathology and Laboratory Medicine Institute, Cleveland Clinic, Cleveland, Ohio
| | | | - Yu-Wei Cheng
- Robert J. Tomsich Pathology and Laboratory Medicine Institute, Cleveland Clinic, Cleveland, Ohio
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47
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In vivo severity ranking of Ras pathway mutations associated with developmental disorders. Proc Natl Acad Sci U S A 2017; 114:510-515. [PMID: 28049852 DOI: 10.1073/pnas.1615651114] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Germ-line mutations in components of the Ras/MAPK pathway result in developmental disorders called RASopathies, affecting about 1/1,000 human births. Rapid advances in genome sequencing make it possible to identify multiple disease-related mutations, but there is currently no systematic framework for translating this information into patient-specific predictions of disease progression. As a first step toward addressing this issue, we developed a quantitative, inexpensive, and rapid framework that relies on the early zebrafish embryo to assess mutational effects on a common scale. Using this assay, we assessed 16 mutations reported in MEK1, a MAPK kinase, and provide a robust ranking of these mutations. We find that mutations found in cancer are more severe than those found in both RASopathies and cancer, which, in turn, are generally more severe than those found only in RASopathies. Moreover, this rank is conserved in other zebrafish embryonic assays and Drosophila-specific embryonic and adult assays, suggesting that our ranking reflects the intrinsic property of the mutant molecule. Furthermore, this rank is predictive of the drug dose needed to correct the defects. This assay can be readily used to test the strengths of existing and newly found mutations in MEK1 and other pathway components, providing the first step in the development of rational guidelines for patient-specific diagnostics and treatment of RASopathies.
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48
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Mafficini A, Simbolo M, Parisi A, Rusev B, Luchini C, Cataldo I, Piazzola E, Sperandio N, Turri G, Franchi M, Tortora G, Bovo C, Lawlor RT, Scarpa A. BRCA somatic and germline mutation detection in paraffin embedded ovarian cancers by next-generation sequencing. Oncotarget 2016; 7:1076-83. [PMID: 26745875 PMCID: PMC4811444 DOI: 10.18632/oncotarget.6834] [Citation(s) in RCA: 60] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2015] [Accepted: 12/29/2015] [Indexed: 12/21/2022] Open
Abstract
BRCA mutated ovarian cancers respond better to platinum-based therapy and to the recently approved PARP-inhibitors. There is the need for efficient and timely methods to detect both somatic and germline mutations using formalin-fixed paraffin-embedded (FFPE) tissues and commercially available technology. We used a commercial kit exploring all exons and 50bp exon-intron junctions of BRCA1 and BRCA2 genes, and semiconductor next-generation sequencing (NGS) on DNA from 47 FFPE samples of high-grade serous ovarian cancers. Pathogenic mutations were found in 13/47 (28%) cancers: eight in BRCA1 and five in BRCA2. All BRCA1 and two BRCA2 mutations were germline; three BRCA2 mutations were somatic. All mutations were confirmed by Sanger sequencing. To evaluate the performance of the NGS panel, we assessed its capability to detect the 6,953 variants described for BRCA1 and BRCA2 in ClinVar and COSMIC databases using callability analysis. 6,059 (87.1%) variants were identified automatically by the software; 829 (12.0%) required visual verification. The remaining 65 (0.9%) variants were uncallable, and would require 15 Sanger reactions to be resolved. Thus, the sensitivity of the NGS-panel was 99.1%. In conclusion, NGS performed with a commercial kit is highly efficient for detection of germline and somatic mutations in BRCA genes using routine FFPE tissue.
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Affiliation(s)
- Andrea Mafficini
- ARC-Net Research Centre, University and Hospital Trust of Verona, Verona, Italy
| | - Michele Simbolo
- ARC-Net Research Centre, University and Hospital Trust of Verona, Verona, Italy
| | - Alice Parisi
- Department of Pathology & Diagnostics, University and Hospital Trust of Verona, Verona, Italy
| | - Borislav Rusev
- ARC-Net Research Centre, University and Hospital Trust of Verona, Verona, Italy.,Department of Pathology & Diagnostics, University and Hospital Trust of Verona, Verona, Italy
| | - Claudio Luchini
- ARC-Net Research Centre, University and Hospital Trust of Verona, Verona, Italy.,Department of Pathology & Diagnostics, University and Hospital Trust of Verona, Verona, Italy
| | - Ivana Cataldo
- ARC-Net Research Centre, University and Hospital Trust of Verona, Verona, Italy
| | - Elena Piazzola
- Department of Pathology & Diagnostics, University and Hospital Trust of Verona, Verona, Italy
| | - Nicola Sperandio
- ARC-Net Research Centre, University and Hospital Trust of Verona, Verona, Italy
| | - Giona Turri
- Department of Pathology & Diagnostics, University and Hospital Trust of Verona, Verona, Italy
| | - Massimo Franchi
- Department of Gynecology, University and Hospital Trust of Verona, Verona, Italy
| | - Giampaolo Tortora
- Comprehensive Cancer Centre, University and Hospital Trust of Verona, Verona, Italy
| | - Chiara Bovo
- Board of Directors, University and Hospital Trust of Verona, Verona, Italy
| | - Rita T Lawlor
- ARC-Net Research Centre, University and Hospital Trust of Verona, Verona, Italy.,Department of Pathology & Diagnostics, University and Hospital Trust of Verona, Verona, Italy
| | - Aldo Scarpa
- ARC-Net Research Centre, University and Hospital Trust of Verona, Verona, Italy.,Department of Pathology & Diagnostics, University and Hospital Trust of Verona, Verona, Italy
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49
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Serratì S, De Summa S, Pilato B, Petriella D, Lacalamita R, Tommasi S, Pinto R. Next-generation sequencing: advances and applications in cancer diagnosis. Onco Targets Ther 2016; 9:7355-7365. [PMID: 27980425 PMCID: PMC5144906 DOI: 10.2147/ott.s99807] [Citation(s) in RCA: 115] [Impact Index Per Article: 14.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
Technological advances have led to the introduction of next-generation sequencing (NGS) platforms in cancer investigation. NGS allows massive parallel sequencing that affords maximal tumor genomic assessment. NGS approaches are different, and concern DNA and RNA analysis. DNA sequencing includes whole-genome, whole-exome, and targeted sequencing, which focuses on a selection of genes of interest for a specific disease. RNA sequencing facilitates the detection of alternative gene-spliced transcripts, posttranscriptional modifications, gene fusion, mutations/single-nucleotide polymorphisms, small and long noncoding RNAs, and changes in gene expression. Most applications are in the cancer research field, but lately NGS technology has been revolutionizing cancer molecular diagnostics, due to the many advantages it offers compared to traditional methods. There is greater knowledge on solid cancer diagnostics, and recent interest has been shown also in the field of hematologic cancer. In this review, we report the latest data on NGS diagnostic/predictive clinical applications in solid and hematologic cancers. Moreover, since the amount of NGS data produced is very large and their interpretation is very complex, we briefly discuss two bioinformatic aspects, variant-calling accuracy and copy-number variation detection, which are gaining a lot of importance in cancer-diagnostic assessment.
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Affiliation(s)
- Simona Serratì
- Molecular Genetics Laboratory, IRCCS Istituto Tumori Giovanni Paolo II, Bari, Italy
| | - Simona De Summa
- Molecular Genetics Laboratory, IRCCS Istituto Tumori Giovanni Paolo II, Bari, Italy
| | - Brunella Pilato
- Molecular Genetics Laboratory, IRCCS Istituto Tumori Giovanni Paolo II, Bari, Italy
| | - Daniela Petriella
- Molecular Genetics Laboratory, IRCCS Istituto Tumori Giovanni Paolo II, Bari, Italy
| | - Rosanna Lacalamita
- Molecular Genetics Laboratory, IRCCS Istituto Tumori Giovanni Paolo II, Bari, Italy
| | - Stefania Tommasi
- Molecular Genetics Laboratory, IRCCS Istituto Tumori Giovanni Paolo II, Bari, Italy
| | - Rosamaria Pinto
- Molecular Genetics Laboratory, IRCCS Istituto Tumori Giovanni Paolo II, Bari, Italy
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50
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Mino-Kenudson M. Cytological reporting on lung FNA and small biopsy specimens in the era of personalized medicine. Cancer Cytopathol 2016; 125:155-160. [DOI: 10.1002/cncy.21793] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2016] [Revised: 10/10/2016] [Accepted: 10/12/2016] [Indexed: 11/12/2022]
Affiliation(s)
- Mari Mino-Kenudson
- Department of Pathology; Massachusetts General Hospital and Harvard Medical School; Boston Massachusetts
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