1
|
Cheong TC, Jang A, Wang Q, Leonardi GC, Ricciuti B, Alessi JV, Di Federico A, Awad MM, Lehtinen MK, Harris MH, Chiarle R. Mechanistic patterns and clinical implications of oncogenic tyrosine kinase fusions in human cancers. Nat Commun 2024; 15:5110. [PMID: 38877018 PMCID: PMC11178778 DOI: 10.1038/s41467-024-49499-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2024] [Accepted: 06/04/2024] [Indexed: 06/16/2024] Open
Abstract
Tyrosine kinase (TK) fusions are frequently found in cancers, either as initiating events or as a mechanism of resistance to targeted therapy. Partner genes and exons in most TK fusions are followed typical recurrent patterns, but the underlying mechanisms and clinical implications of these patterns are poorly understood. By developing Functionally Active Chromosomal Translocation Sequencing (FACTS), we discover that typical TK fusions involving ALK, ROS1, RET and NTRK1 are selected from pools of chromosomal rearrangements by two major determinants: active transcription of the fusion partner genes and protein stability. In contrast, atypical TK fusions that are rarely seen in patients showed reduced protein stability, decreased downstream oncogenic signaling, and were less responsive to inhibition. Consistently, patients with atypical TK fusions were associated with a reduced response to TKI therapies. Our findings highlight the principles of oncogenic TK fusion formation and selection in cancers, with clinical implications for guiding targeted therapy.
Collapse
Affiliation(s)
- Taek-Chin Cheong
- Department of Pathology, Boston Children's Hospital and Harvard Medical School, Boston, MA, 02115, USA.
| | - Ahram Jang
- Department of Pathology, Boston Children's Hospital and Harvard Medical School, Boston, MA, 02115, USA
- Division of Endocrinology, Diabetes, and Metabolism, Department of Medicine, Beth Israel Deaconess Medical Center, Boston, MA, 02115, USA
| | - Qi Wang
- Department of Pathology, Boston Children's Hospital and Harvard Medical School, Boston, MA, 02115, USA
| | - Giulia C Leonardi
- Department of Pathology, Boston Children's Hospital and Harvard Medical School, Boston, MA, 02115, USA
- Department of Biomedical and Biotechnological Sciences, University of Catania, 95123, Catania, Italy
| | - Biagio Ricciuti
- Lowe Center for Thoracic Oncology, Dana-Farber Cancer Institute, Boston, MA, 02115, USA
| | - Joao V Alessi
- Lowe Center for Thoracic Oncology, Dana-Farber Cancer Institute, Boston, MA, 02115, USA
| | | | - Mark M Awad
- Lowe Center for Thoracic Oncology, Dana-Farber Cancer Institute, Boston, MA, 02115, USA
| | - Maria K Lehtinen
- Department of Pathology, Boston Children's Hospital and Harvard Medical School, Boston, MA, 02115, USA
| | - Marian H Harris
- Department of Pathology, Boston Children's Hospital and Harvard Medical School, Boston, MA, 02115, USA
| | - Roberto Chiarle
- Department of Pathology, Boston Children's Hospital and Harvard Medical School, Boston, MA, 02115, USA.
- Department of Molecular Biotechnology and Health Sciences, University of Torino, Torino, 10126, Italy.
- Division of Hematopathology, IEO European Institute of Oncology IRCCS, 20141, Milan, Italy.
| |
Collapse
|
2
|
Xia W, Yang J, Li H, Li L, Liu J. Comparing Genomic Profiles of ALK Fusion-Positive and ALK Fusion-Negative Nonsmall Cell Lung Cancer Patients. Glob Med Genet 2024; 11:175-186. [PMID: 38873557 PMCID: PMC11175831 DOI: 10.1055/s-0044-1787301] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2024] Open
Abstract
Background Anaplastic lymphoma kinase ( ALK ) fusion events account for 3 to 7% of genetic alterations in patients with nonsmall cell lung cancer (NSCLC). This study aimed to explore the landscape of ALK fusion-positive and ALK fusion-negative in a large cohort of NSCLC patients. Methods The formalin-fixed paraffin-embedded specimens of NSCLC patients who underwent next-generation sequencing from 2020 to 2023 in Yinfeng Gene Technology Co., Ltd. Clinical laboratory were included in this study. Results In the current study, a total of 180 (3.20%) patients tested positive for ALK fusions in 5,622 NSCLC samples. Within the ALK -positive cohort, a total of 228 ALK fusions were identified. Furthermore, five novel ALK fusion partners, including DAB1-ALK , KCMF1-ALK , KIF13A-ALK , LOC643770-ALK , and XDH-ALK were identified. In cases with ALK fusion-positive, TP53 alterations were the most prevalent (26.3%), followed by CDKN2A (8.4%), epidermal growth factor receptor ( EGFR , 5.6%), and ALK (5.6%). By contrast, EGFR alterations were most prevalent (51%) in patients with ALK fusion-negative NSCLC, followed by TP53 (42.7%), KRAS (11.6%), and CDKN2A (11.3%). A total of 10 cases where ALK fusion co-occurred with EGFR mutations were also identified. Notably, the ALK fusion positivity rate was higher in younger patients ( p < 0.0001) and in female patients ( p = 0.0429). Additionally, positive ALK test results were more prevalent in patients with high programmed death-ligand 1 expression, especially when applying a 50% cutoff. Conclusions Collectively, these findings offer valuable genomic insights that could inform the personalized clinical care of patients with NSCLC harboring ALK fusions within the context of precision medicine.
Collapse
Affiliation(s)
- Wenchao Xia
- Department of Thoracic Surgery, Tianjin Chest Hospital, Tianjin, People's Republic of China
| | - Jing Yang
- Department of Pathogenic Biology, Logistics University of Chinese People's Armed Police Force, Tianjin, People's Republic of China
| | - Hongbin Li
- Department of Oncology, Rongcheng County People's Hospital, Baoding, People's Republic of China
| | - Ling Li
- Department of Medicine, Yinfeng Gene Technology Co., Ltd., Jinan, People's Republic of China
| | - Jinfeng Liu
- Department of Thoracic Surgery, The First Hospital of Hebei Medical University, Shijiazhuang, People's Republic of China
| |
Collapse
|
3
|
Chiarle R, Cheong TC, Jang A, Wang Q, Leonardi G, Ricciuti B, Alessi J, Federico AD, Awad M, Lehtinen M, Harris M. Mechanistic patterns and clinical implications of oncogenic tyrosine kinase fusions in human cancers. RESEARCH SQUARE 2024:rs.3.rs-3782958. [PMID: 38313284 PMCID: PMC10836111 DOI: 10.21203/rs.3.rs-3782958/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/06/2024]
Abstract
Tyrosine kinase (TK) fusions are frequently found in cancers, either as initiating events or as a mechanism of resistance to targeted therapy. Partner genes and exons in most TK fusions are typical and recurrent, but the underlying mechanisms and clinical implications of these patterns are poorly understood. Here, we investigated structures of > 8,000 kinase fusions and explore their generative mechanisms by applying newly developed experimental framework integrating high-throughput genome-wide gene fusion sequencing and clonal selection called Functionally Active Chromosomal Translocation Sequencing (FACTS). We discovered that typical oncogenic TK fusions recurrently seen in patients are selected from large pools of chromosomal rearrangements spontaneously occurring in cells based on two major determinants: active transcription of the fusion partner genes and protein stability. In contrast, atypical TK fusions that are rarely seen in patients showed reduced protein stability, decreased downstream oncogenic signaling, and were less responsive to inhibition. Consistently, patients with atypical TK fusions were associated with a reduced response to TKI therapies, as well as a shorter progression-free survival (PFS) and overall survival (OS) compared to patients with typical TK fusions. These findings highlight the principles of oncogenic TK fusion formation and their selection in cancers, with clinical implications for guiding targeted therapy.
Collapse
Affiliation(s)
| | | | - Ahram Jang
- Boston Children's Hospital and Harvard Medical School
| | - Qi Wang
- Boston Children's Hospital and Harvard Medical School
| | | | | | | | | | | | | | - Marian Harris
- Boston Children's Hospital and Harvard Medical School
| |
Collapse
|
4
|
Preobrazhenskaya EV, Suleymanova AM, Bizin IV, Zagrebin FA, Romanko AA, Saitova ES, Mulkidzhan RS, Imyanitov EN. Spectrum of kinase gene rearrangements in a large series of paediatric inflammatory myofibroblastic tumours. Histopathology 2023. [PMID: 37071060 DOI: 10.1111/his.14912] [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: 12/30/2022] [Revised: 02/24/2023] [Accepted: 03/20/2023] [Indexed: 04/19/2023]
Abstract
INTRODUCTION Inflammatory myofibroblastic tumours (IMTs), being an exceptionally rare category of paediatric neoplasms, often contain druggable gene rearrangements involving tyrosine kinases. METHODS AND RESULTS This study presents a large consecutive series of IMTs which were analysed for the presence of translocations by the PCR test for 5'/3'-end ALK, ROS1, RET, NTRK1, NTRK2 and NTRK3 unbalanced expression, variant-specific PCR for 47 common gene fusions and NGS TruSight RNA fusion panel. Kinase gene rearrangements were detected in 71 of 82 (87%) IMTs (ALK: n = 47; ROS1: n = 20; NTRK3: n = 3; PDGFRb: n = 1). The test for unbalanced expression had 100% reliability in identifying tumours with ALK fusions, but failed to reveal ROS1 rearrangements in eight of 20 (40%) ROS1-driven IMTs; however, ROS1 alterations were detectable by variant-specific PCR in 19 of 20 (95%) cases. ALK rearrangements were particularly common in patients below 1 year of age (10 of 11 (91%) versus 37 of 71 (52%), P = 0.039). ROS1 fusions occurred more often in lung IMTs than in tumours of other organs (14 of 35 (40%) versus six of 47 (13%), P = 0.007). Among 11 IMTs with no kinase gene rearrangement identified, one tumour demonstrated ALK activation via gene amplification and overexpression, and another neoplasm carried COL1A1::USP6 translocation. CONCLUSIONS PCR-based pipeline provides a highly efficient and non-expensive alternative for molecular testing of IMTs. IMTs with no detectable rearrangements need further studies.
Collapse
Affiliation(s)
- Elena V Preobrazhenskaya
- Department of Tumor Growth Biology, N.N. Petrov Institute of Oncology, Saint-Petersburg, Russia
- Department of Medical Genetics, St.-Petersburg Pediatric Medical University, Saint-Petersburg, Russia
| | - Amina M Suleymanova
- Institute of Pediatric Oncology, N.N. Blokhin National Medical Research Center of Oncology, Moscow, Russia
| | - Ilya V Bizin
- Department of Tumor Growth Biology, N.N. Petrov Institute of Oncology, Saint-Petersburg, Russia
| | - Fyodor A Zagrebin
- Department of Tumor Growth Biology, N.N. Petrov Institute of Oncology, Saint-Petersburg, Russia
| | - Alexandr A Romanko
- Department of Medical Genetics, St.-Petersburg Pediatric Medical University, Saint-Petersburg, Russia
| | - Evgeniya S Saitova
- Department of Tumor Growth Biology, N.N. Petrov Institute of Oncology, Saint-Petersburg, Russia
| | - Rimma S Mulkidzhan
- Department of Tumor Growth Biology, N.N. Petrov Institute of Oncology, Saint-Petersburg, Russia
| | - Evgeny N Imyanitov
- Department of Tumor Growth Biology, N.N. Petrov Institute of Oncology, Saint-Petersburg, Russia
- Department of Medical Genetics, St.-Petersburg Pediatric Medical University, Saint-Petersburg, Russia
| |
Collapse
|
5
|
Zhai X, Liu Y, Liang Z, Wang W, Qin T, Liu SV, Um SW, Luo F, Liu J. Classical ALK G1202R resistance mutation was identified in a lung adenocarcinoma patient with rare LOC388942-ALK fusion after sequential treatment with ALK-TKIs and anlotinib: a case report. ANNALS OF TRANSLATIONAL MEDICINE 2022; 10:1180. [PMID: 36467355 PMCID: PMC9708479 DOI: 10.21037/atm-22-5194] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/16/2022] [Accepted: 11/07/2022] [Indexed: 07/30/2023]
Abstract
BACKGROUND Anaplastic lymphoma kinase (ALK)-positive non-small cell lung cancer (NSCLC) is a heterogeneous disease. To date, more than ninety ALK fusions in lung cancer have been found. Here, we report for the first time a rare LOC388942-ALK fusion in NSCLC was sensitive to crizotinib but resistant to the sequential ceritinib and alectinib and acquired classical ALK G1202R resistance mutation after long-term treatment with anlotinib. This case highlights dynamic monitoring of gene alteration using next-generation sequencing (NGS) is necessary during the anti-tumor process. CASE DESCRIPTION A 55-year-old male, with no history of smoking history and no family history of cancer, was found malignant pleural effusion and multiple metastasis nodules in the left lung. He was histopathologically diagnosed with ALK-positive cT4N0M1a adenocarcinoma in June 2016. NGS of the tumor identified a rare LOC388942-ALK fusion (L intergenic: A 20, 1.41%). Then, the patient was treated with chemotherapy, crizotinib, ceritinib, alectinib, and anlotinib sequentially. The patient achieved partial response (PR) to chemotherapy and crizotinib. No evidence of a secondary resistant molecular event was found after resistance to crizotinib, ceritinib, or Alectinib. After 8 months of alectinib treatment, the tumor gradually enlarged again. Anlotinib was followed for 13 months. Thirteen months later, new lesions in the lower lobe of the right lung appeared and increased gradually, indicating definite progression of the tumor. Classical ALK G1202R resistance mutations was detected using cfDNA NGS. The patient refused to receive lorlatinib targeting G1202R resistance mutations and continued with anlotinib. He dead in August 2022, achieving 5-year overall survival (OS). CONCLUSIONS Distinct ALK fusions in NSCLC have different cancer biology, leading to different response to ALK tyrosine kinase inhibitors (ALK-TKIs), even developed different resistance mechanism. Reporting the clinical details of rare ALK fusions in NSCLC is necessary to guide the treatment for clinicians and researchers.
Collapse
Affiliation(s)
- Xiaoqian Zhai
- Lung Cancer Center & Institute, West China Hospital, Sichuan University, Chengdu, China
| | - Yanyang Liu
- Lung Cancer Center & Institute, West China Hospital, Sichuan University, Chengdu, China
| | - Zuoyu Liang
- Pathology Department, West China Hospital, Sichuan University, Chengdu, China
| | - Weiya Wang
- Pathology Department, West China Hospital, Sichuan University, Chengdu, China
| | - Tian Qin
- Burning Rock Biotech, Guangzhou, China
| | - Stephen V. Liu
- Department of Medicine, Georgetown University, Washington, DC, USA
| | - Sang-Won Um
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Feng Luo
- Lung Cancer Center & Institute, West China Hospital, Sichuan University, Chengdu, China
| | - Jiewei Liu
- Lung Cancer Center & Institute, West China Hospital, Sichuan University, Chengdu, China
| |
Collapse
|
6
|
Yang H, Li H, Fang Y, Li Z, Zhu J, Liu H, Lu C, Zhang X, Ma T, Zhang C. A non-functional 5' ALK fusion validated at the RNA level as a classical EML4-ALK that responds well to the novel ALK inhibitor ensartinib: A case report. Front Med (Lausanne) 2022; 9:979032. [PMID: 36275795 PMCID: PMC9582288 DOI: 10.3389/fmed.2022.979032] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2022] [Accepted: 09/14/2022] [Indexed: 11/21/2022] Open
Abstract
Background Currently, many targeted drugs are approved for treatment of ALK fusion non-small cell lung cancer. However, it has been previously assumed that patients with 5′ non-oncogenic kinase (5′ NOK) fusion detected by DNA next-generation sequencing (NGS) would not benefit from ALK inhibitors because of lack of an intact kinase domain. Case description A novel 5′ NOK fusion form, ALK-CYP27C1 (A19:C5), was detected by DNA NGS in surgical tissue specimens of a patient with recurrent lung adenosquamous carcinoma. The patient achieved 29 months of progression-free survival with ensartinib treatment. The results of RNA NGS from the same operative tissue identified EML4-ALK (E13:A20) fusion variant type I. Conclusion This is the first case to provide real-world evidence of effective treatment of a patient with the 5′ NOK fusion form at the DNA level but functional EML4-ALK at the RNA level, illustrating the need for RNA testing in 5′ NOK patients.
Collapse
Affiliation(s)
- Hong Yang
- Department of Oncology, Inner Mongolia People’s Hospital, Hohhot, China
| | - Haojing Li
- Department of Oncology, Inner Mongolia People’s Hospital, Hohhot, China
| | - Yu Fang
- Department of Translational Medicine, Genetron Health (Beijing) Technology, Co., Ltd., Beijing, China
| | - Zhijun Li
- Department of Oncology, Inner Mongolia People’s Hospital, Hohhot, China
| | - Jianhua Zhu
- Department of Translational Medicine, Genetron Health (Beijing) Technology, Co., Ltd., Beijing, China
| | - Huan Liu
- Department of Oncology, Inner Mongolia Medical University, Hohhot, China
| | - Chao Lu
- Department of Oncology, Inner Mongolia Medical University, Hohhot, China
| | - Xiaoyan Zhang
- Department of Translational Medicine, Genetron Health (Beijing) Technology, Co., Ltd., Beijing, China,*Correspondence: Xiaoyan Zhang,
| | - Tonghui Ma
- Department of Translational Medicine, Genetron Health (Beijing) Technology, Co., Ltd., Beijing, China,Tonghui Ma,
| | - Cuiying Zhang
- Department of Oncology, Inner Mongolia People’s Hospital, Hohhot, China,Cuiying Zhang,
| |
Collapse
|
7
|
Comparison between Immunocytochemistry, FISH and NGS for ALK and ROS1 Rearrangement Detection in Cytological Samples. Int J Mol Sci 2022; 23:ijms231810556. [PMID: 36142468 PMCID: PMC9502752 DOI: 10.3390/ijms231810556] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2022] [Revised: 08/30/2022] [Accepted: 09/06/2022] [Indexed: 11/29/2022] Open
Abstract
The detection of ROS1 and ALK rearrangements is performed for advanced-stage non-small cell lung cancer. Several techniques can be used on cytological samples, such as immunocytochemistry (ICC), fluorescence in situ hybridization (FISH) and, more recently, next-generation sequencing (NGS), which is gradually becoming the gold standard. We performed a retrospective study to compare ALK and ROS1 rearrangement results from immunocytochemistry, FISH and NGS methods from 131 cytological samples. Compared to NGS, the sensitivity and specificity of ICC were 0.79 and 0.91, respectively, for ALK, and 1 and 0.87 for ROS1. Regarding FISH, the sensitivity and specificity were both at 1 for ALK and ROS1 probes. False-positive cases obtained by ICC were systematically corrected by FISH. When using ICC and FISH techniques, results are very close to NGS. The false-positive cases obtained by ICC are corrected by FISH, and the true-positive cases are confirmed. NGS has the potential to improve the detection of ALK and ROS1 rearrangements in cytological samples; however, the cost of this technique is still much higher than the sequential use of ICC and FISH.
Collapse
|
8
|
A novel intergenic region ALK fusion is targetable by alectinib in a non-small cell lung cancer patient with brain metastasis. Anticancer Drugs 2022; 33:1182-1185. [PMID: 35946559 PMCID: PMC9575568 DOI: 10.1097/cad.0000000000001363] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
Anaplastic lymphoma kinase (ALK) rearrangement defines a unique nonsmall cell lung cancer (NSCLC) molecular subtype, of which the patients could potentially benefit from anti-ALK therapies. So far, the outcomes of the canonical echinoderm microtubule-associated protein-like (EML-ALK) patients subjected to ALK inhibitors are well established. However, given the increasing complexity of ALK fusion partners, as detected by high-throughput sequencing, the responses of those with rare ALK fusion events remain to be explored. Here, we report a lung adenocarcinoma patient with brain metastasis harboring an ARHGAP5 downstream intergenic region ALK fusion, as detected by using DNA-based next-generation sequencing, who experienced a partial response to alectinib treatment. While whole- transcriptome RNA sequencing (RNA-seq) failed to identify potential ALK fusion transcripts, subsequent targeted deep RNA-seq revealed the expression of EML4-ALK transcripts in the tumor tissue. Given the increasing application of the ALK-tyrosine kinase inhibitors (TKIs), it is extremely crucial to define the patients who could be suitable for this treatment in clinic. The present case has provided supporting evidence that noncanonical ALK rearrangements on the genomic level are often functionally relevant and targetable by ALK-TKI, particularly in cases with sub-optimal quantity and quality for RNA validation.
Collapse
|
9
|
Zhao R, Guo L, Zhang B, Zhao J, Xiang C, Chen S, Shao J, Zhu L, Ye M, Han Y. Identification and therapeutic evaluation of ALK rearrangements in non-small-cell lung cancer. J Pathol Clin Res 2022; 8:538-549. [PMID: 35848751 PMCID: PMC9535099 DOI: 10.1002/cjp2.289] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2022] [Revised: 06/17/2022] [Accepted: 06/23/2022] [Indexed: 12/29/2022]
Abstract
This study aimed to present a comprehensive assessment of anaplastic lymphoma kinase (ALK) rearrangements evaluated by DNA/RNA-based next-generation sequencing (NGS) and Ventana immunohistochemistry (IHC) in patients with non-small-cell lung cancer (NSCLC) and to evaluate the therapeutic outcomes of ALK tyrosine kinase inhibitor (TKI) treatment. We investigated ALK gene fusions in 14,894 patients with NSCLC using Ventana IHC and NGS, including 12,533 cases detected via DNA-based NGS and 2,361 cases using RNA-based NGS. The overall percentage agreement (OPA), positive percentage agreement (PPA), and negative percentage agreement (NPA) were calculated when comparing the results between NGS and IHC. The therapeutic responses to ALK-TKIs were also evaluated. In total, 3.50% (439/12,533) of specimens were NGS ALK-positive (NGS-p) in the DNA-based NGS cohort and 3.63% (455/12,533) were IHC ALK-positive (IHC-p). The OPA of NGS was 99.60%, whereas its PPA and NPA were 92.75 and 99.86%, respectively. In the adenocarcinoma (ADC) subcohort, the PPA was 95.69%. In the RNA-based NGS cohort, 2.20% (52/2,361) of specimens were NGS-p and 2.63% (62/2,361) were IHC-p. The OPA of NGS was 99.49%; its PPA and NPA were 82.26 and 99.96%, respectively. Thirteen patients with discordant results received ALK-TKI treatment. In the seven NGS-p/IHC-negative (IHC-n) patients, the overall response rate (ORR) was 85.4% (6/7) and the disease control rate (DCR) was 100%. In the six NGS-negative/IHC-p patients, the ORR was 66.7% (4/6) and the DCR was 100%. In summary, a high concordance of ALK gene fusion detected via NGS and IHC was observed in this study. DNA-based NGS had a higher OPA, PPA, and PPA in the ADC subcohort, whereas RNA-based NGS had a higher NPA. Overall, the results suggest that the combination of NGS and IHC can improve the accuracy of ALK fusion detection; hence, a result determination algorithm for clinical detection of ALK gene fusion was also proposed.
Collapse
Affiliation(s)
- Ruiying Zhao
- Department of Pathology, Shanghai Chest HospitalShanghai Jiao Tong UniversityShanghaiPR China
| | - Lianying Guo
- Department of Pathology, Shanghai Chest HospitalShanghai Jiao Tong UniversityShanghaiPR China
| | - Bo Zhang
- Department of Pulmonary, Shanghai Chest HospitalShanghai Jiao Tong UniversityShanghaiPR China
| | - Jikai Zhao
- Department of Pathology, Shanghai Chest HospitalShanghai Jiao Tong UniversityShanghaiPR China
| | - Chan Xiang
- Department of Pathology, Shanghai Chest HospitalShanghai Jiao Tong UniversityShanghaiPR China
| | - Shengnan Chen
- Department of Pathology, Shanghai Chest HospitalShanghai Jiao Tong UniversityShanghaiPR China
| | - Jinchen Shao
- Department of Pathology, Shanghai Chest HospitalShanghai Jiao Tong UniversityShanghaiPR China
| | - Lei Zhu
- Department of Pathology, Shanghai Chest HospitalShanghai Jiao Tong UniversityShanghaiPR China
| | - Min Ye
- Department of Pathology, Shanghai Chest HospitalShanghai Jiao Tong UniversityShanghaiPR China
| | - Yuchen Han
- Department of Pathology, Shanghai Chest HospitalShanghai Jiao Tong UniversityShanghaiPR China
| |
Collapse
|
10
|
Characterizing kinase intergenic-breakpoint rearrangements in a large-scale lung cancer population and real-world clinical outcomes. ESMO Open 2022; 7:100405. [PMID: 35305401 PMCID: PMC9058911 DOI: 10.1016/j.esmoop.2022.100405] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2021] [Revised: 01/12/2022] [Accepted: 01/19/2022] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND Kinase gene fusions are strong driver mutations in neoplasia; however, kinase intergenic-breakpoint rearrangements (IGRs) confound the detection of such fusions and of targeted treatments. We aim to provide an overview of kinase IGRs in a large lung cancer cohort and examine real-world survival outcomes of patients with such fusions. METHODS Mutational profiles analyzed using targeted next-generation sequencing of 425 cancer-related genes between June 2016 and July 2019 were retrospectively reviewed. Patients' demographic data, clinical characteristics, and survivals were analyzed. RNA sequencing or immunohistochemical assays were carried out to verify chimeric fusion products. RESULTS We identified 3411 patients with kinase fusions from a cohort of 30 450 patients with lung cancer, and 624 kinase IGR events were identified in 538 of the 3411 patients. The most frequently identified kinase genes included anaplastic lymphoma kinase (ALK), RET proto-oncogene (RET), ROS proto-oncogene 1 (ROS1), Erb-B2 receptor tyrosine kinase 2/3 (ERBB2/3), and epidermal growth factor receptor (EGFR). Our data showed that most (67%) kinase IGRs occurred on the same chromosome and kinase domains remained intact at the 3'-end. Approximately 3% (19/624) of the kinase IGRs had one genomic breakpoint located in gene promoter regions, including nine fusion events involving ALK, RET, ROS1, EGFR, ERBB2, or fibroblast growth factor receptor 3 (FGFR3). Among the 538 patients with kinase IGRs, 167 (31%) lacked oncogenic driver mutations, among which 28 received targeted therapies in real-world practice. Notably, three ALK IGR patients who harbored no canonical oncogenic aberrations were confirmed with an EML4-ALK chimeric fusion product by RNA sequencing and/or ALK immunohistochemical assays. One patient demonstrated a favorable clinical outcome after 14 months on crizotinib. An additional two patients who had ROS1 IGRs demonstrated a clinical benefit after 13 and 19 months on crizotinib, respectively. CONCLUSION A large real-world lung cancer cohort with kinase IGRs was comprehensively analyzed for their molecular characteristics. The data indicated the potential oncogenic function of kinase IGRs and their outcomes following the administration of targeted therapies.
Collapse
|
11
|
Ma JW, Li M. Molecular typing of lung adenocarcinoma with computed tomography and CT image-based radiomics: a narrative review of research progress and prospects. Transl Cancer Res 2022; 10:4217-4231. [PMID: 35116717 PMCID: PMC8797562 DOI: 10.21037/tcr-21-1037] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2021] [Accepted: 09/03/2021] [Indexed: 12/21/2022]
Abstract
Objective The purpose of this paper was to perform a narrative review of current research evidence on conventional computed tomography (CT) imaging features and CT image-based radiomic features for predicting gene mutations in lung adenocarcinoma and discuss how to translate the research findings to guide future practice. Background Lung cancer, especially lung adenocarcinoma, is the leading cause of cancer-related deaths. With advances in the diagnosis and treatment of lung adenocarcinoma with the emergence of molecular testing, the prediction of oncogenes and even drug resistance gene mutations have become key to individualized and precise clinical treatment in order to prolong survival and improve quality of life. The progress of imageological examination includes the development of CT and radiomics are promising quantitative methods for predicting different gene mutations in lung adenocarcinoma, especially common mutations, such as epidermal growth factor receptor (EGFR) mutation, anaplastic lymphoma kinase (ALK) mutation and Kirsten rat sarcoma viral oncogene (KRAS) mutation. Methods The PubMed electronic database was searched along with a set of terms specific to lung adenocarcinoma, radiomics (including texture analysis), CT, computed tomography, EGFR, ALK, KRAS, rearranging transfection (RET) rearrangement and c-ros oncogene 1 (ROS-1), v-raf murine sarcoma viral oncogene homolog B1 (BRAF), and human epidermal growth factor receptor 2 (HER2) mutations et al. This review has been reported in compliance with the Narrative Review checklist guidelines. From each full-text article, information was extracted regarding a set of terms above. Conclusions Research on the application of conventional CT features and CT image-based radiomic features for predicting the gene mutation status of lung adenocarcinoma is still in a preliminary stage. Noninvasively determination of mutation status in lung adenocarcinoma before targeted therapy with conventional CT features and CT image-based radiomic features remains both hopes and challenges. Before radiomics could be applied in clinical practice, more work needs to be done.
Collapse
Affiliation(s)
- Jing-Wen Ma
- Department of Diagnostic Radiology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Meng Li
- Department of Diagnostic Radiology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| |
Collapse
|
12
|
Hao J, Wang J, Wei P, Liu J, Su P, Xing A, Jing H. Anaplastic lymphoma kinase fusion protein expression is associated with a favorable prognosis in resected invasive mucinous lung adenocarcinoma: A retrospective study from two Chinese tertiary hospitals. J Cancer Res Ther 2022; 18:445-451. [DOI: 10.4103/jcrt.jcrt_2334_21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
|
13
|
Pisapia P, Pepe F, Sgariglia R, Nacchio M, Russo G, Gragnano G, Conticelli F, Salatiello M, De Luca C, Girolami I, Eccher A, Iaccarino A, Bellevicine C, Vigliar E, Malapelle U, Troncone G. Methods for actionable gene fusion detection in lung cancer: now and in the future. Pharmacogenomics 2021; 22:833-847. [PMID: 34525844 DOI: 10.2217/pgs-2021-0048] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
Although gene fusions occur rarely in non-small-cell lung cancer (NSCLC) patients, they represent a relevant target in treatment decision algorithms. To date, immunohistochemistry and fluorescence in situ hybridization are the two principal methods used in clinical trials. However, using these methods in routine clinical practice is often impractical and time consuming because they can only analyze single genes and the quantity of tissue material is often insufficient. Thus, novel technologies, able to test multiple genes in a single run with minimal sample input, are being under investigation. Here, we discuss the utility of next-generation sequencing and nCounter technologies in detecting simultaneous gene fusions in NSCLC patients.
Collapse
Affiliation(s)
- Pasquale Pisapia
- Department of Public Health, University of Naples Federico II, Naples, Italy
| | - Francesco Pepe
- Department of Public Health, University of Naples Federico II, Naples, Italy
| | - Roberta Sgariglia
- Department of Public Health, University of Naples Federico II, Naples, Italy
| | - Mariantonia Nacchio
- Department of Public Health, University of Naples Federico II, Naples, Italy
| | - Gianluca Russo
- Department of Public Health, University of Naples Federico II, Naples, Italy
| | - Gianluca Gragnano
- Department of Public Health, University of Naples Federico II, Naples, Italy
| | - Floriana Conticelli
- Department of Public Health, University of Naples Federico II, Naples, Italy
| | - Maria Salatiello
- Department of Public Health, University of Naples Federico II, Naples, Italy
| | - Caterina De Luca
- Department of Public Health, University of Naples Federico II, Naples, Italy
| | - Ilaria Girolami
- Division of Pathology, Central Hospital Bolzano, Bolzano, Italy
| | - Albino Eccher
- Department of Pathology & Diagnostics, University & Hospital Trust of Verona, Verona, Italy
| | - Antonino Iaccarino
- Department of Public Health, University of Naples Federico II, Naples, Italy
| | - Claudio Bellevicine
- Department of Public Health, University of Naples Federico II, Naples, Italy
| | - Elena Vigliar
- Department of Public Health, University of Naples Federico II, Naples, Italy
| | - Umberto Malapelle
- Department of Public Health, University of Naples Federico II, Naples, Italy
| | - Giancarlo Troncone
- Department of Public Health, University of Naples Federico II, Naples, Italy
| |
Collapse
|
14
|
Zhao R, Yao F, Xiang C, Zhao J, Shang Z, Guo L, Ding W, Ma S, Yu A, Shao J, Zhu L, Han Y. Identification of NTRK gene fusions in lung adenocarcinomas in the Chinese population. J Pathol Clin Res 2021; 7:375-384. [PMID: 33768710 PMCID: PMC8185368 DOI: 10.1002/cjp2.208] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2020] [Revised: 02/09/2021] [Accepted: 02/14/2021] [Indexed: 12/30/2022]
Abstract
The molecular profile of neurotrophic tyrosine kinase receptor (NTRK) gene fusions in lung adenocarcinoma (LUAD) is not fully understood. Next-generation sequencing (NGS) and pan-tyrosine kinase receptor (TRK) immunohistochemistry (IHC) are powerful tools for NTRK fusion detection. In this study, a total of 4,619 LUAD formalin-fixed, paraffin-embedded tissues were collected from patients who underwent biopsy or resection at the Shanghai Chest Hospital during 2017-2019. All specimens were screened for NTRK1 rearrangements using DNA-based NGS. Thereafter, the cases with NTRK1 rearrangements and cases negative for common driver mutations were analyzed for NTRK1/2/3 fusions using total nucleic acid (TNA)-based NGS and pan-TRK IHC. Overall, four NTRK1/2 fusion events were identified, representing 0.087% of the original sample set. At the DNA level, seven NTRK1 rearrangements were identified, while only two TPM3-NTRK1 fusions were confirmed on TNA-based NGS as functional. In addition, two NTRK2 fusions (SQSTM1-NTRK2 and KIF5B-NTRK2) were identified by TNA-based NGS in 350 'pan-negative' cases. Two patients harboring NTRK1/2 fusions were diagnosed with invasive adenocarcinoma, while the other two were diagnosed with adenocarcinoma in situ and minimally invasive adenocarcinoma. All four samples with NTRK fusions were positive for the expression of pan-TRK. The two samples with NTRK2 fusions showed cytoplasmic staining alone, while the other two samples with NTRK1 fusions exhibited both cytoplasmic and membranous staining. In summary, functional NTRK fusions are found in early-stage LUAD; however, they are extremely rare. According to this study's results, they are independent oncogenic drivers, mutually exclusive with other driver mutations. We demonstrated that NTRK rearrangement analysis using a DNA-based approach should be verified with an RNA-based assay.
Collapse
Affiliation(s)
- Ruiying Zhao
- Department of Pathology, Shanghai Chest HospitalShanghai Jiao Tong UniversityShanghaiPR China
| | - Feng Yao
- Department of Thoracic Surgery, Shanghai Chest HospitalShanghai Jiao Tong UniversityShanghaiPR China
| | - Chan Xiang
- Department of Pathology, Shanghai Chest HospitalShanghai Jiao Tong UniversityShanghaiPR China
| | - Jikai Zhao
- Department of Pathology, Shanghai Chest HospitalShanghai Jiao Tong UniversityShanghaiPR China
| | - Zhanxian Shang
- Department of Pathology, Shanghai Chest HospitalShanghai Jiao Tong UniversityShanghaiPR China
| | - Lianying Guo
- Department of Pathology, Shanghai Chest HospitalShanghai Jiao Tong UniversityShanghaiPR China
| | - Wenjie Ding
- Department of Pathology, Shanghai Chest HospitalShanghai Jiao Tong UniversityShanghaiPR China
| | - Shengji Ma
- Department of Pathology, Shanghai Chest HospitalShanghai Jiao Tong UniversityShanghaiPR China
| | - Anbo Yu
- Department of Pathology, Shanghai Chest HospitalShanghai Jiao Tong UniversityShanghaiPR China
| | - Jinchen Shao
- Department of Pathology, Shanghai Chest HospitalShanghai Jiao Tong UniversityShanghaiPR China
| | - Lei Zhu
- Department of Pathology, Shanghai Chest HospitalShanghai Jiao Tong UniversityShanghaiPR China
| | - Yuchen Han
- Department of Pathology, Shanghai Chest HospitalShanghai Jiao Tong UniversityShanghaiPR China
| |
Collapse
|
15
|
Li Y, Tan Y, Hu S, Xie J, Yan Z, Zhang X, Zong Y, Han-Zhang H, Li Q, Li C. Targeted Sequencing Analysis of Predominant Histological Subtypes in Resected Stage I Invasive Lung Adenocarcinoma. J Cancer 2021; 12:3222-3229. [PMID: 33976731 PMCID: PMC8100815 DOI: 10.7150/jca.51405] [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: 08/02/2020] [Accepted: 03/15/2021] [Indexed: 01/11/2023] Open
Abstract
Objective: Lung adenocarcinoma (LADC) is classified into five main histological subtypes with distinct clinicopathologic characteristics: lepidic-predominant adenocarcinoma (LPA), acinar-predominant adenocarcinoma (APA), papillary-predominant adenocarcinoma (PPA), micropapillary-predominant adenocarcinoma (MPA) and solid-predominant adenocarcinoma (SPA). However, the mutational profiles of predominant histological subtypes have not been well defined. In this study, we aimed to reveal the genomic landscape of 5 main histological subtypes. Patients and Methods: We performed next-generation sequencing (NGS) in a cohort of 86 stage I invasive adenocarcinoma (IAC) patients, using a customized panel including 168 cancer-associated genes. Results: Our analysis identified a total of 302 genomic alterations. Five subtypes showed different mutation profiles with LPA, APA, PPA, MPA and SPA had an average mutation rate of 1.95 (range: 0-5), 2.56 (range: 1-6), 3.5 (range: 1-7), 3.75 (range: 1-8) and 6.05 (range: 2-12), respectively (p=4.17e-06). Driver mutations occurred in 96.55% (83/86) of all patients. EGFR (73.3%), KRAS (9.3%), ALK (4.7%) and MET (4.7%) are the most commonly mutated lung cancer driver genes, TP53 is the top mutated tumor suppressor gene. SPA patients harbored more driver mutations and higher frequency of TP53 than LPA patients. Interestingly, LRP1B mutations, which has been reported to be associated with high tumor mutation burden and better response to immunotherapy, were only detected from 5 SPA patients (p=0.001). No patients from other four cohorts harbored LRP1B mutations. Conclusions: We revealed distinctive mutation landscape of the 5 major histological subtypes of LADC, evident by distinctive average mutation rate with SPA and LPA having the highest and lowest average mutation rate, respectively. SPA patients showed higher mutation rate of LRP1B and higher rates for PD-L1 positivity, indicating that SPA patients may have better response to immunotherapy.
Collapse
Affiliation(s)
- Yan Li
- Department of Respiratory Medicine, The Third Affiliated Hospital of Soochow University, 185 Juqian Road, Changzhou, China
- Department of Respiratory Medicine, The Affiliated Hospital of Xuzhou Medical University, 99 Huaihai Road, Xuzhou, China
| | - Yan Tan
- Department of Pathology, The Third Affiliated Hospital of Soochow University, 185 Juqian Road, Changzhou, China
| | - Song Hu
- Department of Respiratory Medicine, The Third Affiliated Hospital of Soochow University, 185 Juqian Road, Changzhou, China
| | - Jun Xie
- Department of Respiratory Medicine, The Third Affiliated Hospital of Soochow University, 185 Juqian Road, Changzhou, China
| | - Zhantao Yan
- Department of Pathology, The Third Affiliated Hospital of Soochow University, 185 Juqian Road, Changzhou, China
| | - Xian Zhang
- Department of Respiratory Medicine, The Third Affiliated Hospital of Soochow University, 185 Juqian Road, Changzhou, China
| | - Yun Zong
- Department of Respiratory Medicine, The Third Affiliated Hospital of Soochow University, 185 Juqian Road, Changzhou, China
| | - Han Han-Zhang
- Burning Rock Biotech, Guangzhou, Guangdong, 510300, China
| | - Qing Li
- Department of Pathology, The Third Affiliated Hospital of Soochow University, 185 Juqian Road, Changzhou, China
| | - Chong Li
- Department of Respiratory Medicine, The Third Affiliated Hospital of Soochow University, 185 Juqian Road, Changzhou, China
| |
Collapse
|
16
|
Li D, Ding L, Ran W, Huang Y, Li G, Wang C, Xiao Y, Wang X, Lin D, Xing X. Status of 10 targeted genes of non-small cell lung cancer in eastern China: A study of 884 patients based on NGS in a single institution. Thorac Cancer 2020; 11:2580-2589. [PMID: 32729257 PMCID: PMC7471050 DOI: 10.1111/1759-7714.13577] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2020] [Revised: 06/26/2020] [Accepted: 06/28/2020] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND The status of targeted genes and the association between targeted genes and clinicopathological features in Chinese lung cancer patients remains to be elucidated. METHODS The status of 10 targeted genes was evaluated by next-generation sequencing (NGS) in 884 non-small cell lung cancer (NSCLC) patients. The relationship between gene alterations and clinicopathological characters was analyzed. RESULTS Overall, 684 (77.4%) patients harbored gene alterations, and EGFR (510, 57.7%) was found to be the most common type of mutation followed by KRAS (91, 10.3%), HER2 (38, 4.3%), PIK3CA (32, 3.6%), ALK (21, 2.4%), BRAF (10, 1.1%), ROS1 (5, 0.6%), RET (5, 0.6%), MET (4, 0.5%) and NRAS (1, 0.1%). Gene alterations were more frequent in females, non-smokers and adenocarcinoma (P < 0.001). EGFR mutations were associated with women, non-smokers, normal level of serum tumor markers, and adenocarcinoma (P < 0.001). Patients without lymph node metastasis (P = 0.012), or early stage disease (P < 0.001) exhibited a higher EGFR mutation rate. KRAS mutations tended to arise in men (P < 0.001), smokers (P < 0.001) and patients with higher levels of serum tumor markers (P = 0.048). A mucus-producing component was associated with KRAS (P < 0.001), ROS1 (P = 0.033) and ALK (P < 0.001) alterations. ALK and ROS1 rearrangements were more frequent in micropapillary structures (P = 0.004, P = 0.012). BRAF mutation was associated with advanced disease patients and micropapillary structure (P < 0.001). PIK3CA mutation was more likely to be found in elderly patients (P = 0.014). Some patients had synchronous gene alterations, including EGFR/PIK3CA, EGFR/HER2, HER2/KRAS, EGFR/KRAS, EGFR/ROS1, EGFR/NRAS, KRAS/PIK3CA, KRAS/PIK3CA/HER2. CONCLUSIONS Most patients had at least one genetic alteration, and individual patients harbored synchronous mutation. Each gene alteration had unique clinicopathological characteristics. KEY POINTS SIGNIFICANT FINDINGS OF THE STUDY: This study revealed the frequency and distribution of 10 targeted gene abnormalities and their association with clinicopathological parameters of Chinese non-small cell lung cancer (NSCLC) patients in eastern China. WHAT THIS STUDY ADDS Some rare synchronous mutations were detected in our study by next-generation sequencing (NGS).
Collapse
Affiliation(s)
- Dan Li
- Department of PathologyThe Affiliated Hospital of Qingdao UniversityQingdaoChina
| | - Li Ding
- Medical Affairs DepartmentThe Affiliated Hospital of Qingdao UniversityQingdaoChina
| | - Wenwen Ran
- Department of PathologyThe Affiliated Hospital of Qingdao UniversityQingdaoChina
| | - Yan Huang
- Department of Human ResourcesThe Affiliated Hospital of Qingdao UniversityQingdaoChina
| | - Guangqi Li
- Department of PathologyThe Affiliated Hospital of Qingdao UniversityQingdaoChina
| | - Chengqin Wang
- Department of PathologyThe Affiliated Hospital of Qingdao UniversityQingdaoChina
| | - Yujing Xiao
- Department of PathologyThe Affiliated Hospital of Qingdao UniversityQingdaoChina
| | - Xiaonan Wang
- Department of PathologyThe Affiliated Hospital of Qingdao UniversityQingdaoChina
| | - Dongliang Lin
- Department of PathologyThe Affiliated Hospital of Qingdao UniversityQingdaoChina
| | - Xiaoming Xing
- Department of PathologyThe Affiliated Hospital of Qingdao UniversityQingdaoChina
| |
Collapse
|
17
|
Chen B, Yang L, Zhang R, Luo W, Li W. Radiomics: an overview in lung cancer management-a narrative review. ANNALS OF TRANSLATIONAL MEDICINE 2020; 8:1191. [PMID: 33241040 PMCID: PMC7576016 DOI: 10.21037/atm-20-4589] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Radiomics is a novel approach for optimizing the analysis massive data from medical images to provide auxiliary guidance in clinical issues. Quantitative feature extraction is one of the critical steps of radiomics. The association between radiomics features and the clinicopathological information of diseases can be identified by several statistics methods. For instance, although significant progress has been made in the field of lung cancer, too many questions remain, especially for the individualized decisions. Radiomics offers a new tool to encode the characteristics of lung cancer which is the leading cause of cancer-related deaths worldwide. Here, we reviewed the workflow and clinical utility of radiomics in lung cancer management, including pulmonary nodules detection, classification, histopathology and genetics evaluation, clinical staging, therapy response, and prognosis prediction. Most of these studies showed positive results, indicating the potential value of radiomics in clinical practice. The implementation of radiomics is both feasible and invaluable, and has aided clinicians in ascertaining the nature of a disease with greater precision. However, it should be noted that radiomics in its current state cannot completely replace the work of therapists or tissue examination. The potential future trends of this modality were also remarked. More efforts are needed to overcome the limitations identified above in order to facilitate the widespread application of radiomics in the reasonably near future.
Collapse
Affiliation(s)
- Bojiang Chen
- Department of Respiratory and Critical Care Medicine, West China Hospital of Sichuan University, Chengdu, China
| | - Lan Yang
- Department of Respiratory and Critical Care Medicine, West China Hospital of Sichuan University, Chengdu, China
| | - Rui Zhang
- Department of Respiratory and Critical Care Medicine, West China Hospital of Sichuan University, Chengdu, China
| | - Wenxin Luo
- Department of Respiratory and Critical Care Medicine, West China Hospital of Sichuan University, Chengdu, China
| | - Weimin Li
- Department of Respiratory and Critical Care Medicine, West China Hospital of Sichuan University, Chengdu, China
| |
Collapse
|
18
|
Schrock AB, Madison R, Rosenzweig M, Allen JM, Erlich RL, Wang SY, Chidiac T, Reddy VS, Riess JW, Yassa AE, Shakir A, Miller VA, Alexander BM, Venstrom J, McGregor K, Ali SM. Patients with NSCLCs Harboring Internal Inversions or Deletion Rearrangements of the ALK Gene Have Durable Responses to ALK Kinase Inhibitors. LUNG CANCER-TARGETS AND THERAPY 2020; 11:33-39. [PMID: 32368168 PMCID: PMC7184117 DOI: 10.2147/lctt.s239675] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/22/2019] [Accepted: 03/24/2020] [Indexed: 12/24/2022]
Abstract
Background ALK fusions are targetable drivers in non-small-cell lung cancer (NSCLC). However, patients with NSCLC harboring ALK rearrangements without a fusion partner identified in DNA have also been shown to respond to ALK inhibitors. We aimed to characterize complex ALK variants that may predict sensitivity to multiple approved ALK inhibitors. Methods Comprehensive genomic profiling (CGP) of DNA isolated from formalin-fixed paraffin-embedded (FFPE) tumor tissue or blood-based circulating tumor DNA was performed for 39,159 NSCLC patients during routine clinical care. For a subset of cases, RNA sequencing was performed, and prior ALK test results and clinical treatment information were collected from treating physicians. Results We queried the Foundation Medicine NSCLC database and identified ALK internal inversions, as well as internal deletions, as the sole ALK rearrangements in 6 (0.02%) and 3 (0.01%) of cases, respectively. In cases with ALK internal inversions, RNA testing identified an EML4-ALK fusion in 2/2 cases evaluated, and 3/3 patients treated with ALK inhibitors had durable responses. A single patient with an ALK internal deletion and clinical data available responded to multiple ALK inhibitors. RNA data available for a subset of non-NSCLC cases suggest that ALK internal deletions removing a portion of the N-terminus are drivers themselves and do not result in ALK fusions. Fluorescence in situ hybridization (FISH) results were inconsistent for both classes of DNA events. Conclusion Rare internal inversions of ALK appear to be indicative of ALK fusions, which can be detected in RNA, and response to ALK inhibitors in patients with NSCLC. In contrast, ALK internal deletions are not associated with ALK fusions in RNA but likely represent targetable drivers themselves. These data suggest that CGP of DNA should be supplemented with immunohistochemistry or RNA-based testing to further resolve these events and match patients to effective therapies.
Collapse
Affiliation(s)
- Alexa B Schrock
- Foundation Medicine, Department of Clinical Development, Cambridge, MA, USA
| | - Russell Madison
- Foundation Medicine, Department of Clinical Development, Cambridge, MA, USA
| | - Mark Rosenzweig
- Foundation Medicine, Department of Translational Oncology and Clinical Reporting, Cambridge, MA, USA
| | - Justin M Allen
- Foundation Medicine, Department of Translational Oncology and Clinical Reporting, Cambridge, MA, USA
| | - Rachel L Erlich
- Foundation Medicine, Department of Translational Oncology and Clinical Reporting, Cambridge, MA, USA
| | - Siao-Yi Wang
- Loyola University Medical Cancer, Department of Hematology and Oncology, Maywood, IL, USA
| | - Tarek Chidiac
- Zangmeister Cancer Center, Department of Hematology and Oncology, Columbus, OH, USA
| | - Vodur Suresh Reddy
- Cancer Care Specialists, Department of Hematology and Oncology, Reno, NV, USA
| | - Jonathan W Riess
- UC Davis Comprehensive Cancer Center, Department of Hematology and Oncology Sacramento, CA, USA
| | - Ahmet Ersin Yassa
- UC Davis Comprehensive Cancer Center, Department of Hematology and Oncology Sacramento, CA, USA
| | - Abdur Shakir
- Sarah Bush Lincoln Health System, Department of Medical Oncology, Mattoon, IL, USA
| | - Vincent A Miller
- Foundation Medicine, Department of Clinical Development, Cambridge, MA, USA
| | - Brian M Alexander
- Foundation Medicine, Department of Clinical Development, Cambridge, MA, USA
| | - Jeffrey Venstrom
- Foundation Medicine, Department of Clinical Development, Cambridge, MA, USA
| | - Kimberly McGregor
- Foundation Medicine, Department of Clinical Development, Cambridge, MA, USA
| | - Siraj M Ali
- Foundation Medicine, Department of Clinical Development, Cambridge, MA, USA
| |
Collapse
|
19
|
Song L, Zhu Z, Mao L, Li X, Han W, Du H, Wu H, Song W, Jin Z. Clinical, Conventional CT and Radiomic Feature-Based Machine Learning Models for Predicting ALK Rearrangement Status in Lung Adenocarcinoma Patients. Front Oncol 2020; 10:369. [PMID: 32266148 PMCID: PMC7099003 DOI: 10.3389/fonc.2020.00369] [Citation(s) in RCA: 45] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2020] [Accepted: 03/03/2020] [Indexed: 12/25/2022] Open
Abstract
Objectives: To predict the anaplastic lymphoma kinase (ALK) mutations in lung adenocarcinoma patients non-invasively with machine learning models that combine clinical, conventional CT and radiomic features. Methods: This retrospective study included 335 lung adenocarcinoma patients who were randomly divided into a primary cohort (268 patients; 90 ALK-rearranged; and 178 ALK wild-type) and a test cohort (67 patients; 22 ALK-rearranged; and 45 ALK wild-type). One thousand two hundred and eighteen quantitative radiomic features were extracted from the semi-automatically delineated volume of interest (VOI) of the entire tumor using both the original and the pre-processed non-enhanced CT images. Twelve conventional CT features and seven clinical features were also collected. Normalized features were selected using a sequential of the F-test-based method, the density-based spatial clustering of applications with noise (DBSCAN) method, and the recursive feature elimination (RFE) method. Selected features were then used to build three predictive models (radiomic, radiological, and integrated models) for the ALK-rearranged phenotype by a soft voting classifier. Models were evaluated in the test cohort using the area under the receiver operating characteristic curve (AUC), accuracy, sensitivity, and specificity, and the performances of three models were compared using the DeLong test. Results: Our results showed that the addition of clinical information and conventional CT features significantly enhanced the validation performance of the radiomic model in the primary cohort (AUC = 0.83–0.88, P = 0.01), but not in the test cohort (AUC = 0.80–0.88, P = 0.29). The majority of radiomic features associated with ALK mutations reflected information around and within the high-intensity voxels of lesions. The presence of the cavity and left lower lobe location were new imaging phenotypic patterns in association with ALK-rearranged tumors. Current smoking was strongly correlated with non-ALK-mutated lung adenocarcinoma. Conclusions: Our study demonstrates that radiomics-derived machine learning models can potentially serve as a non-invasive tool to identify ALK mutation of lung adenocarcinoma.
Collapse
Affiliation(s)
- Lan Song
- Department of Radiology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Zhenchen Zhu
- Department of Radiology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China.,4+4 MD Program, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Li Mao
- Deepwise AI Lab, Deepwise Inc., Beijing, China
| | - Xiuli Li
- Deepwise AI Lab, Deepwise Inc., Beijing, China
| | - Wei Han
- Department of Epidemiology and Biostatistics, Institute of Basic Medicine Sciences, Chinese Academy of Medical Sciences and School of Basic Medicine, Peking Union Medical College, Beijing, China
| | - Huayang Du
- Department of Radiology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Huanwen Wu
- Department of Pathology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Wei Song
- Department of Radiology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Zhengyu Jin
- Department of Radiology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| |
Collapse
|
20
|
Li W, Liu Y, Li W, Chen L, Ying J. Intergenic Breakpoints Identified by DNA Sequencing Confound Targetable Kinase Fusion Detection in NSCLC. J Thorac Oncol 2020; 15:1223-1231. [PMID: 32151779 DOI: 10.1016/j.jtho.2020.02.023] [Citation(s) in RCA: 58] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2020] [Revised: 02/20/2020] [Accepted: 02/21/2020] [Indexed: 10/24/2022]
Abstract
INTRODUCTION Next-generation sequencing (NGS) based on genomic DNA has been widely applied for gene rearrangement detection in patients with NSCLC. However, intergenic-breakpoint fusions, in which one or both genomic breakpoints localize to intergenic regions, confound kinase fusion detection. We evaluated the function of intergenic-breakpoint fusions with multiplex molecular testing approaches. METHODS NSCLCs with intergenic-breakpoint fusion identified by DNA-based NGS were analyzed by RNA-based NGS, immunohistochemistry (IHC), and fluorescence in situ hybridization. RESULTS A total of 26 cases with single intergenic-breakpoint fusion were identified from a large cohort of NSCLCs using DNA-based NGS. Of the 26 cases, RNA-based NGS detected expressed fusion transcripts in 11 cases, but the genomic breakpoint position did not logically predict breakpoint of the fusion transcript in these cases, possibly owing to complex rearrangements (n = 5), alternative splicing (n = 2), and reciprocal rearrangement (n = 4). Nonetheless, no expressed fusion transcript was detected in five cases. Moreover, positive anaplastic lymphoma receptor tyrosine (ALK) finding was observed in three of the remaining 10 cases with IHC but not with RNA-based NGS. Three patients with intergenic-breakpoint ALK fusion with or without RNA-based NGS or IHC confirmation who received crizotinib treatment were found to have partial responses. However, one patient with intergenic-breakpoint ROS1, given the positive fluorescence in situ hybridization result, received crizotinib but developed progressive disease within 1 month, possibly owing to no functional fusion transcript detected by RNA-based NGS. CONCLUSIONS Intergenic-breakpoint fusions detected by DNA sequencing confound kinase fusion detection in NSCLC, as functional fusion transcripts may be generated or not. Additional validation testing using RNA/protein assay should be performed in intergenic-breakpoint fusion cases to guide optimal treatment.
Collapse
Affiliation(s)
- Weihua Li
- Department of Pathology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, People's Republic of China
| | - Yutao Liu
- Department of Medical Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, People's Republic of China
| | - Wenbin Li
- Department of Pathology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, People's Republic of China
| | - Li Chen
- HeliTec Biotechnologies, Shenzhen, Guangdong Province, People's Republic of China
| | - Jianming Ying
- Department of Pathology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, People's Republic of China.
| |
Collapse
|
21
|
Ou SHI, Zhu VW, Nagasaka M. Catalog of 5' Fusion Partners in ALK-positive NSCLC Circa 2020. JTO Clin Res Rep 2020; 1:100015. [PMID: 34589917 PMCID: PMC8474466 DOI: 10.1016/j.jtocrr.2020.100015] [Citation(s) in RCA: 48] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2020] [Accepted: 02/05/2020] [Indexed: 12/17/2022] Open
Abstract
Since the discovery of anaplastic lymphoma kinase fusion-positive (ALK+) NSCLC in 2007, the methods to detect ALK+ NSCLC have evolved and expanded from fluorescence in situ hybridization and immunohistochemistry to next-generation DNA sequencing, targeted RNA sequencing, and whole transcriptome sequencing. As such, the deep sequencing methods have resulted in the expansion of distinct fusion partners identified in ALK+ NSCLC to 90 (one variant PLEKHM2-ALK is found in small cell lung cancer but included in this catalog) by the end of January 2020; about 65 of them (since 2018) and most of the recent novel fusion partners were reported from China. Thirty-four of the distinct fusion partners are located on the short arm of chromosome 2; 28 of these 34 fusion partners are located on 2p21-25, in which ALK is located on 2p23.2-p23.1. Many of these new ALK+ NSCLC fusion variants have responded to ALK tyrosine kinase inhibitors (TKIs). Several of these novel ALK fusion variants were identified as being resistant to EGFR TKIs or as dual 3'ALK fusions. In addition, at least 28 intergenic ALK rearrangements have also been reported, with three of them reported as responding to crizotinib. This review aims to serve as a central source of reference of fusion partners in ALK+ NSCLC for clinicians and scientists. We aim to update and improve the list going forward.
Collapse
Affiliation(s)
- Sai-Hong Ignatius Ou
- Department of Medicine, Division of Hematology-Oncology, Chao Family Comprehensive Cancer Center, University of California Irvine School of Medicine, Orange, California
| | - Viola W. Zhu
- Department of Medicine, Division of Hematology-Oncology, Chao Family Comprehensive Cancer Center, University of California Irvine School of Medicine, Orange, California
| | - Misako Nagasaka
- Department of Oncology, Karmanos Cancer Institute/Wayne State University School of Medicine, Detroit, Michigan
- Department of Advanced Medical Innovations, St. Marianna University Graduate School of Medicine, Kawasaki, Kanagawa, Japan
| |
Collapse
|
22
|
Tian P, Liu Y, Zeng H, Tang Y, Lizaso A, Ye J, Shao L, Li Y. Unique molecular features and clinical outcomes in young patients with non-small cell lung cancer harboring ALK fusion genes. J Cancer Res Clin Oncol 2020; 146:935-944. [PMID: 31894386 DOI: 10.1007/s00432-019-03116-6] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2019] [Accepted: 12/17/2019] [Indexed: 02/08/2023]
Abstract
PURPOSE This study aimed to determine the molecular features and clinical outcomes of young patients with non-small cell lung cancer (NSCLC) harboring ALK fusion genes. METHODS We interrogated the genomic profile of 1652 patients with lung cancer who underwent targeted next-generation sequencing to screen for candidate oncogenic drivers using histological specimens acquired from January 2016 to December 2018. RESULTS ALK fusions were identified in 101 NSCLC patients, and 52 of them were diagnosed before the age of 50 years (52/367, 14.2%). Of the 52 patients with early-onset disease, 22 (42.3%) were male and 43 (82.7%) never smoked; the median patient age was 44 years (range 28-50 years). The most frequently occurring ALK fusion partner was EML4, which was identified in 80.8% (42/52) of young patients. Compared to the older patients, patients with early-onset disease were more likely to harbor EML4-ALK variant 1 (38.5% vs. 14.3%; P = 0.007). We also identified rare ALK fusions, including CHRNA7-ALK, TACR1-ALK, HIP1-ALK, DYSF-ALK and ITGAV-ALK, in patients with early-onset disease, and patients with these fusions responded well to crizotinib treatment. A statistically significant difference was observed in progression-free survival (PFS) between the young patients and older patients who received crizotinib as the first-line therapy (17.5 months vs 9.0 months, P = 0.048). However, the median PFS of young patients harboring concurrent TP53 mutations was only 6.2 months. CONCLUSION Unique genetic characteristics were found in ALK-rearranged NSCLC patients with early disease onset, and these patients responded better to crizotinib and had longer PFS compared to patients with later disease onset. However, patients with concomitant TP53 mutations may not have a significant response to treatment.
Collapse
Affiliation(s)
- Panwen Tian
- Department of Respiratory and Critical Care Medicine, West China Hospital, Sichuan University, No. 37 Guo Xue Alley, Chengdu, 610041, Sichuan, China.,Lung Cancer Treatment Center, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Yujie Liu
- Department of Respiratory and Critical Care Medicine, West China Hospital, Sichuan University, No. 37 Guo Xue Alley, Chengdu, 610041, Sichuan, China
| | - Hao Zeng
- Department of Respiratory and Critical Care Medicine, West China Hospital, Sichuan University, No. 37 Guo Xue Alley, Chengdu, 610041, Sichuan, China
| | - Yuan Tang
- Department of Pathology, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | | | - Junyi Ye
- Burning Rock Biotech, Guangzhou, Guangdong, China
| | - Lin Shao
- Burning Rock Biotech, Guangzhou, Guangdong, China
| | - Yalun Li
- Department of Respiratory and Critical Care Medicine, West China Hospital, Sichuan University, No. 37 Guo Xue Alley, Chengdu, 610041, Sichuan, China.
| |
Collapse
|
23
|
Wang S, Ma P, Ma G, Lv Z, Wu F, Guo M, Li Y, Tan Q, Song S, Zhou E, Geng W, Duan Y, Li Y, Jin Y. Value of serum tumor markers for predicting EGFR mutations and positive ALK expression in 1089 Chinese non-small-cell lung cancer patients: A retrospective analysis. Eur J Cancer 2019; 124:1-14. [PMID: 31707279 DOI: 10.1016/j.ejca.2019.10.005] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2019] [Revised: 09/28/2019] [Accepted: 10/01/2019] [Indexed: 12/25/2022]
Abstract
PURPOSE The role of serum tumor markers (STMs) in the modern management of epidermal growth factor receptor (EGFR) and anaplastic lymphoma kinase (ALK) mutations in lung cancer remains poorly described. In this study, we investigated whether STMs could be a valuable noninvasive tool to predict EGFR mutations and ALK positivity in non-small-cell lung cancer (NSCLC) patients. EXPERIMENTAL DESIGN We retrospectively reviewed and included 1089 NSCLC patients who underwent EGFR or ALK mutation testing and STMs measurement prior to treatment. The differences in several clinical characteristics and STMs between the subgroups were analyzed. Multivariate logistic regression analysis was performed to identify predictors of EGFR mutations and ALK positivity. RESULTS EGFR mutations were found more frequently in females (63.11%), never-smokers (59.69%), and those with lung adenocarcinoma (ADC) (53.87%). Negative carbohydrate antigen (CA) 125, ferritin (FERR), squamous cell carcinoma antigen (SCC), and soluble fragment of cytokeratin 19 (CYFRA 21-1) levels were significantly associated with EGFR mutations (p < 0.05). Multivariate analysis demonstrated that ADC, never-smoker status, and negative CA 125 and SCC results were predictors of EGFR mutations (p < 0.05). The receiver operating characteristic (ROC) curve yielded an area under the curve (AUC) of 0.715 (95% confidence interval [CI]: 0.673-0.758) for the combination of the four factors. Positive ALK expression was found more frequently in younger patients (median age: 49 years), females (8.40%), never-smokers (8.82%), and those negative for carcinoembryonic antigen (CEA) (8.02%). Multivariate analysis demonstrated that younger age and never-smoker status were the only independent predictors of ALK positivity (p < 0.05). The ROC curve yielded an AUC of 0.760 (95% CI: 0.677-0.844) for the combination of these two factors. CONCLUSION STMs are associated with mutant EGFR status and could be integrated with other clinical factors to enhance the ability to distinguish EGFR mutation status among NSCLC patients. For ALK-positive patients, younger age and never-smoker status could predict the mutation status, whereas STMs could not.
Collapse
Affiliation(s)
- Sufei Wang
- Department of Respiratory and Critical Care Medicine, NHC Key Laboratory of Pulmonary Diseases, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, 1277 Jiefang Avenue, Wuhan, Hubei, 430022, China
| | - Pei Ma
- Department of Respiratory and Critical Care Medicine, NHC Key Laboratory of Pulmonary Diseases, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, 1277 Jiefang Avenue, Wuhan, Hubei, 430022, China
| | - Guanzhou Ma
- Department of Respiratory and Critical Care Medicine, NHC Key Laboratory of Pulmonary Diseases, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, 1277 Jiefang Avenue, Wuhan, Hubei, 430022, China
| | - Zhilei Lv
- Department of Respiratory and Critical Care Medicine, NHC Key Laboratory of Pulmonary Diseases, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, 1277 Jiefang Avenue, Wuhan, Hubei, 430022, China
| | - Feng Wu
- Department of Respiratory and Critical Care Medicine, NHC Key Laboratory of Pulmonary Diseases, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, 1277 Jiefang Avenue, Wuhan, Hubei, 430022, China
| | - Mengfei Guo
- Department of Respiratory and Critical Care Medicine, NHC Key Laboratory of Pulmonary Diseases, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, 1277 Jiefang Avenue, Wuhan, Hubei, 430022, China
| | - Yumei Li
- Department of Respiratory and Critical Care Medicine, NHC Key Laboratory of Pulmonary Diseases, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, 1277 Jiefang Avenue, Wuhan, Hubei, 430022, China
| | - Qi Tan
- Department of Respiratory and Critical Care Medicine, NHC Key Laboratory of Pulmonary Diseases, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, 1277 Jiefang Avenue, Wuhan, Hubei, 430022, China
| | - Siwei Song
- Department of Respiratory and Critical Care Medicine, NHC Key Laboratory of Pulmonary Diseases, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, 1277 Jiefang Avenue, Wuhan, Hubei, 430022, China
| | - E Zhou
- Department of Respiratory and Critical Care Medicine, NHC Key Laboratory of Pulmonary Diseases, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, 1277 Jiefang Avenue, Wuhan, Hubei, 430022, China
| | - Wei Geng
- Department of Respiratory and Critical Care Medicine, NHC Key Laboratory of Pulmonary Diseases, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, 1277 Jiefang Avenue, Wuhan, Hubei, 430022, China
| | - Yanran Duan
- School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, 13 Hangkong Avenue, Wuhan, Hubei, 430022, China
| | - Yan Li
- Department of Pathology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, 1277 Jiefang Avenue, Wuhan, Hubei, 430022, China.
| | - Yang Jin
- Department of Respiratory and Critical Care Medicine, NHC Key Laboratory of Pulmonary Diseases, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, 1277 Jiefang Avenue, Wuhan, Hubei, 430022, China.
| |
Collapse
|
24
|
Zhou X, Shou J, Sheng J, Xu C, Ren S, Cai X, Chu Q, Wang W, Zhen Q, Zhou Y, Li W, Pan H, Li H, Sun T, Cheng H, Wang H, Lou F, Rao C, Cao S, Pan H, Fang Y. Molecular and clinical analysis of Chinese patients with anaplastic lymphoma kinase (ALK)-rearranged non-small cell lung cancer. Cancer Sci 2019; 110:3382-3390. [PMID: 31444835 PMCID: PMC6778633 DOI: 10.1111/cas.14177] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2019] [Revised: 08/08/2019] [Accepted: 08/15/2019] [Indexed: 12/17/2022] Open
Abstract
Anaplastic lymphoma kinase (ALK) fusions have been recognized as a therapeutic target in non‐small cell lung cancer (NSCLC). However, molecular signatures and clinical characteristics of the Chinese population with ALK‐rearranged NSCLC are not well elucidated. In the present study, we carried out targeted next‐generation sequencing on tissue and plasma ctDNA samples in 1688 patients with NSCLC. Overall, ALK fusions were detected in 70 patients (4.1%), and the frequencies of ALK fusions detected in tissue and plasma samples were 5.1% and 3.3%, respectively. Additionally, the prevalence of breakpoint locations for EML4‐ALK fusions in ctDNA was significantly correlated with that in tumor tissues (R2 = .91, P = .045). According to age, the incidence rates of ALK fusions among young (age <45 years), middle‐aged (between 45 and 70 years) and elderly (>70 years) patients were significantly different (P < .001). In 70 ALK‐rearranged cases, coexistence of epidermal growth factor receptor (EGFR) alterations and ALK fusions was detected in 12 cases (17.1%) and EGFR mutations tended to coexist with non‐EML4‐ALK rearrangements. Notably, novel ALK fusion partners, including TRIM66,SWAP70,WNK3,ERC1,TCF12 and FBN1 were identified in the present study. Among EML4‐ALK fusion variants, patients with variant V1 were younger than patients with variant V3 (P = .023), and TP53 mutations were more frequently concurrent with variant V3 compared with variant V1 (P = .009). In conclusion, these findings provide new insights into the molecular‐clinical profiles of patients with ALK‐rearranged NSCLC that may improve the treatment strategy of this population.
Collapse
Affiliation(s)
- Xiaoyun Zhou
- Department of Medical Oncology, Sir Run Run Shaw Hospital, Zhejiang University, Hangzhou, China
| | - Jiawei Shou
- Department of Medical Oncology, Sir Run Run Shaw Hospital, Zhejiang University, Hangzhou, China
| | - Jin Sheng
- Department of Medical Oncology, Sir Run Run Shaw Hospital, Zhejiang University, Hangzhou, China
| | - Chunwei Xu
- Department of Pathology, Fujian Cancer Hospital, Fujian Medical University, Fuzhou, China
| | - Shengxiang Ren
- Department of Medical Oncology, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai, China
| | - Xiuyu Cai
- Sun Yet-Sen University Cancer Center, Guangzhou, China
| | - Qian Chu
- Department of Oncology, Tongji Hospital of Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Wenxian Wang
- Department of Chemotherapy, Zhejiang Cancer Hospital, Hangzhou, China
| | - Qinhong Zhen
- Department of Medical Oncology, Quzhou People's Hospital, Quzhou, China
| | - Yuefen Zhou
- Department of Medical Oncology, Lishui Municipal Central Hospital, Lishui, China
| | - Wenfeng Li
- Department of Medical Oncology, First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
| | - Hong Pan
- Department of Medical Oncology, Sir Run Run Shaw Hospital, Zhejiang University, Hangzhou, China
| | - Hongsen Li
- Department of Medical Oncology, Sir Run Run Shaw Hospital, Zhejiang University, Hangzhou, China
| | - Tao Sun
- Department of Surgery, University of Chicago, Chicago, USA
| | | | - Huina Wang
- Acornmed Biotechnology Co., Ltd., Beijing, China
| | - Feng Lou
- Acornmed Biotechnology Co., Ltd., Beijing, China
| | - Chuangzhou Rao
- Department of Radiation and Chemotherapy, Hwamei Hospital, University of Chinese Academy of Sciences, Ningbo, China
| | - Shanbo Cao
- Acornmed Biotechnology Co., Ltd., Beijing, China
| | - Hongming Pan
- Department of Medical Oncology, Sir Run Run Shaw Hospital, Zhejiang University, Hangzhou, China
| | - Yong Fang
- Department of Medical Oncology, Sir Run Run Shaw Hospital, Zhejiang University, Hangzhou, China
| |
Collapse
|