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Nakazawa M, Harada G, Ghanem P, Bubie A, Kiedrowski LA, Murray JC, Marrone KA, Scott SC, Houseknecht S, Falcon CJ, Evans P, Feliciano J, Hann CL, Ettinger DS, Smith KN, Anagnostou V, Forde PM, Brahmer JR, Levy B, Drilon A, Lam VK. Impact of Tumor-intrinsic Molecular Features on Survival and Acquired Tyrosine Kinase Inhibitor Resistance in ALK-positive NSCLC. CANCER RESEARCH COMMUNICATIONS 2024; 4:786-795. [PMID: 38407352 PMCID: PMC10939006 DOI: 10.1158/2767-9764.crc-24-0065] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/05/2024] [Revised: 02/17/2024] [Accepted: 02/19/2024] [Indexed: 02/27/2024]
Abstract
While tyrosine kinase inhibitors (TKI) have shown remarkable efficacy in anaplastic lymphoma kinase (ALK) fusion-positive advanced non-small cell lung cancer (NSCLC), clinical outcomes vary and acquired resistance remains a significant challenge. We conducted a retrospective study of patients with ALK-positive NSCLC who had clinico-genomic data independently collected from two academic institutions (n = 309). This was paired with a large-scale genomic cohort of patients with ALK-positive NSCLC who underwent liquid biopsies (n = 1,118). Somatic co-mutations in TP53 and loss-of-function alterations in CDKN2A/B were most commonly identified (24.1% and 22.5%, respectively in the clinical cohort), each of which was independently associated with inferior overall survival (HR: 2.58; 95% confidence interval, CI: 1.62-4.09 and HR: 1.93; 95% CI: 1.17-3.17, respectively). Tumors harboring EML4-ALK variant 3 (v3) were not associated with specific co-alterations but were more likely to develop ALK resistance mutations, particularly G1202R and I1171N (OR: 4.11; P < 0.001 and OR: 2.94; P = 0.026, respectively), and had inferior progression-free survival on first-line TKI (HR: 1.52; 95% CI: 1.03-2.25). Non-v3 tumors were associated with L1196M resistance mutation (OR: 4.63; P < 0.001). EML4-ALK v3 and somatic co-alterations in TP53 and CDKN2A/B are associated with inferior clinical outcomes. v3 status is also associated with specific patterns of clinically important ALK resistance mutations. These tumor-intrinsic features may inform rational selection and optimization of first-line and consolidative therapy. SIGNIFICANCE In a large-scale, contemporary cohort of patients with advanced ALK-positive NSCLC, we evaluated molecular characteristics and their impact on acquired resistance mutations and clinical outcomes. Our findings that certain ALK variants and co-mutations are associated with differential survival and specific TKI-relevant resistance patterns highlight potential molecular underpinnings of the heterogenous response to ALK TKIs and nominate biomarkers that may inform patient selection for first-line and consolidative therapies.
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Affiliation(s)
- Mari Nakazawa
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Guilherme Harada
- Memorial Sloan Kettering Cancer Center and Weill Cornell Medical Center, New York, New York
| | - Paola Ghanem
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | | | | | - Joseph C. Murray
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Kristen A. Marrone
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Susan C. Scott
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Stefanie Houseknecht
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Christina J. Falcon
- Memorial Sloan Kettering Cancer Center and Weill Cornell Medical Center, New York, New York
| | - Patrick Evans
- Memorial Sloan Kettering Cancer Center and Weill Cornell Medical Center, New York, New York
| | - Josephine Feliciano
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Christine L. Hann
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - David S. Ettinger
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Kellie N. Smith
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Valsamo Anagnostou
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Patrick M. Forde
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Julie R. Brahmer
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Benjamin Levy
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | | | - Vincent K. Lam
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland
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Qiu T, Zhi X, Ren S. Recent advance of next-generation sequencing in patients with lung cancer. Expert Rev Mol Diagn 2023; 23:959-970. [PMID: 37750512 DOI: 10.1080/14737159.2023.2260755] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2023] [Accepted: 09/15/2023] [Indexed: 09/27/2023]
Abstract
INTRODUCTION Precision medicine based on the driver genes mutation status is the current systemic therapeutic paradigm in patients with lung cancer. Next-generation sequencing (NGS) has emerged as a powerful platform for molecular diagnosis by virtue of high-throughput and massively parallel sequencing. Liquid biopsy also enabled the dynamic monitoring and comprehensive profiling of lung cancer in a noninvasive manner. However, challenges remain in the field of technology and clinical applications, especially in the era of immunotherapy. AREAS COVERED Here, we update the role of NGS in the context of lung cancer screening, molecular diagnosis, predictive and prognostic biomarkers, and guiding personalized treatment. EXPERT OPINION The NGS application for actable genomic alternation has greatly changed the therapeutic landscape in patients with lung cancer including perioperative setting and advanced stage. Meanwhile, emerging evidence has shown the potential of other applications such as early screening and detection, and MRD. However, challenges remain such as the lack of standardized protocols across different platforms and bioinformatics analysis pipelines, and the complexity of interpreting and leveraging numerous genomic mutation messages for therapy selection. Future research is needed to overcome these challenges and expand the applications of NGS to other aspects such as immunotherapy.
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Affiliation(s)
- Tianyu Qiu
- Department of Medical Oncology, Shanghai Pulmonary Hospital, School of Medicine, Tongji University, Shanghai, China
| | - Xinxin Zhi
- Department of Medical Oncology, Shanghai Pulmonary Hospital, School of Medicine, Tongji University, Shanghai, China
| | - Shengxiang Ren
- Department of Medical Oncology, Shanghai Pulmonary Hospital, School of Medicine, Tongji University, Shanghai, China
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Wang Q, Wang Y, Zhang X, Fang C, Qian X, Li Y. Efficacy of erlotinib in NSCLC harboring rare EGFR extracellular domain mutation (T263P) and common mutations: Case report and literature review. Front Oncol 2022; 12:954026. [PMID: 36212397 PMCID: PMC9539819 DOI: 10.3389/fonc.2022.954026] [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: 05/26/2022] [Accepted: 08/29/2022] [Indexed: 11/13/2022] Open
Abstract
The epidermal growth factor receptor (EGFR) typically contains an extracellular domain (ECD), a transmembrane (TM) domain, and an intracellular kinase (KD) domain. ECD mutations of EGFR in NSCLC may affect its normal function and intrinsic resistance to tyrosine kinase inhibitors (TKIs) and the effectiveness of drugs for these patients is unsatisfactory. Recently, we found an EGFR T263P mutation located at the ECD, which has never been reported in Chinese non-small cell lung cancer (NSCLC). Hence, we reported that a patient with advanced lung adenocarcinoma harboring the EGFR T263P mutation, L858R mutation and MET amplification was resistant to osimertinib but significantly benefited from erlotinib and capmatinib treatment. This patient achieved a partial response and had progression-free survival (PFS) for more than 19 months. In summary, we are the first researchers to report in detail on a Chinese patient carrying the T263P mutation and summarize all the ECD mutations in NSCLC. We believe this finding will enlighten us to treat patients with EGFR ECD mutations and more patients deserve further study.
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Affiliation(s)
- Qian Wang
- Department of Medical Oncology, The First Affiliated Hospital of Nanchang University, Nanchang, China
- Medical Innovation Center, The First Affiliated Hospital of Nanchang University, Nanchang, China
| | - Yong Wang
- Department of Medical Oncology, The First Affiliated Hospital of Nanchang University, Nanchang, China
- Medical Innovation Center, The First Affiliated Hospital of Nanchang University, Nanchang, China
| | - Xinwei Zhang
- Department of Medical Oncology, The First Affiliated Hospital of Nanchang University, Nanchang, China
- Medical Innovation Center, The First Affiliated Hospital of Nanchang University, Nanchang, China
| | - Chen Fang
- Department of Medical Oncology, The First Affiliated Hospital of Nanchang University, Nanchang, China
- Medical Innovation Center, The First Affiliated Hospital of Nanchang University, Nanchang, China
| | - Xiaoying Qian
- Department of Medical Oncology, The First Affiliated Hospital of Nanchang University, Nanchang, China
- Medical Innovation Center, The First Affiliated Hospital of Nanchang University, Nanchang, China
| | - Yong Li
- Department of Medical Oncology, The First Affiliated Hospital of Nanchang University, Nanchang, China
- *Correspondence: Yong Li,
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Lin MT, Zheng G, Rodriguez E, Tseng LH, Parini V, Xian R, Zou Y, Gocke CD, Eshleman JR. Double PIK3CA Alterations and Parallel Evolution in Colorectal Cancers. Am J Clin Pathol 2022; 157:244-251. [PMID: 34519764 DOI: 10.1093/ajcp/aqab119] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2021] [Accepted: 06/11/2021] [Indexed: 11/12/2022] Open
Abstract
OBJECTIVES To demonstrate clinicopathologic features and evaluate the clonality of double PIK3CA alterations in colorectal cancers (CRCs). METHODS Clonality was examined in 13 CRCs with double PIK3CA alterations (1.7% of CRCs or 9.6% of PIK3CA-mutated CRCs). Multiregional analyses were performed to confirm subclonal PIK3CA alterations. RESULTS PIK3CA alterations were detected within exon 9 (51%), exon 20 (23%), exon 1 (15%), and exon 7 (6.0%). CRCs with exon 7 alterations showed a significantly higher incidence of double PIK3CA alterations. Most double PIK3CA alterations consisted of a hotpsot alteration and an uncommon alteration; they were often clonal and present within a single tumor population. Multiregional analyses of CRCs with predicted subclonal double-alterations revealed multiclonal CRCs with divergent PIK3CA variant status originating from a common APC- and KRAS-mutated founder lineage of adenoma. CONCLUSIONS The findings supported multiclonal CRCs resulting from parallel evolution during the progression from adenoma to adenocarcinoma within the mitogen-activated protein kinase pathway, as previously demonstrated, or the mammalian target of rapamycin pathway. Further studies are warranted to elucidate clinical significance and potential targeted therapy for CRC patients with double PIK3CA alterations and impacts on clinical decision-making in patients with multiclonal CRCs harboring divergent PIK3CA mutational status.
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Affiliation(s)
- Ming-Tseh Lin
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Gang Zheng
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Department of Pathology and Laboratory Medicine, Mayo Clinic, Rochester, MN, USA
| | - Erika Rodriguez
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Li-Hui Tseng
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Graduate Institute of Medical Genomics and Proteomics, National Taiwan University, Taipei, Taiwan
| | - Vamsi Parini
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Rena Xian
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Ying Zou
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Christopher D Gocke
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - James R Eshleman
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
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Wang HL, Wang HR, Liang Y, Hu AN, Enguita FJ, Zhou XG, Dong J. Hsa_circ_0006571 promotes spinal metastasis through sponging microRNA-138 to regulate sirtuin 1 expression in lung adenocarcinoma. Transl Lung Cancer Res 2020; 9:2411-2427. [PMID: 33489803 PMCID: PMC7815347 DOI: 10.21037/tlcr-20-1250] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Background Circular RNAs (circRNAs) are known to participate in lung cancer. However, their role in spinal metastasis (SM) of lung adenocarcinoma remains elusive. In this study, we determined that hsa_circ_0006571 serves as a sponge for miR-138, which targets sirtuin 1 (Sirt1) in the development of SM. Methods A human circRNA microarray was performed to compare SM and lung adenocarcinoma samples. The expression of hsa_circ_0006571 and miR-138 was determined using quantitative polymerase chain reaction (qPCR) in vitro and in vivo. Cell proliferation was performed by Cell Counting Kit-8 (CCK-8) and apoptosis was analyzed by Annexin V/PI staining. RNA-pulldown and RNA immunoprecipitation (RIP) were used to analyze the interaction between hsa_circ_0006571. Tumor metastasis was determined through a xenograft experiment in vivo. Results Hsa_circ_0006571 was observed to be significantly upregulated in SM tissues through circRNA microarray and qPCR. We detected a lower expression of miR-138 in SM tissues compared with lung adenocarcinoma. Hsa_circ_0006571 silencing suppressed lung cancer cell proliferation and migration while promoting apoptosis. Hsa_circ_0006571 interacted with miR-138 to promote expression of Sirt1, leading to activation of epithelial-mesenchymal transition (EMT). Xenograft experiments showed that downregulation of hsa_circ_0006571 delayed the SM of lung adenocarcinoma cells via the miR-138-Sirt1 axis. Conclusions Hsa_circ_0006571 promoted tumor cell migration and invasion via the miR-138/Sirt1 pathway. Our observations indicate that circRNAs are possible novel therapeutic targets for SM of lung adenocarcinoma.
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Affiliation(s)
- Hou-Lei Wang
- Department of Orthopaedic Surgery, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Hui-Ren Wang
- Department of Orthopaedic Surgery, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Yun Liang
- Department of Orthopaedic Surgery, Zhongshan Hospital, Fudan University, Shanghai, China
| | - An-Nan Hu
- Department of Orthopaedic Surgery, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Francisco J Enguita
- Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, Lisboa, Portugal
| | - Xiao-Gang Zhou
- Department of Orthopaedic Surgery, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Jian Dong
- Department of Orthopaedic Surgery, Zhongshan Hospital, Fudan University, Shanghai, China
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Concomitant Rare KRAS and BRAF Mutations in Lung Adenocarcinoma: A Case Report. JOURNAL OF MOLECULAR PATHOLOGY 2020. [DOI: 10.3390/jmp1010006] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
In July 2020, an active smoker, 63-year old man was admitted to the oncology unit of A.O.R.N. Sant’Anna e San Sebastiano (Caserta, Italy). Chest radiology highlighted right pleural effusion. Total-body CT scanning revealed a solid lesion with lobulated contours in the apical segment of the upper right lobe. The patient’s oncologist requested a molecular assessment of EGFR, ALK, ROS1, BRAF, and KRAS, as well as an evaluation of PD-L1 expression level. To this end, we carried out NGS analysis, on DNA extracted from cytospins, by adopting a custom-designed NGS panel (SiRe®). Overall, no actionable mutations in the tested genes were identified. Conversely, concomitant BRAF exon 11 p.G469A and a KRAS exon 4 p.A146T mutations were detected. Owing to the limited data on the presence of KRAS exon 4 p.A146T point mutation in lung adenocarcinoma patients, a further molecular confirmatory analysis was carried out with a dedicated KRAS cartridge on a fully automated real time polymerase chain reaction. When DNA was extracted from the TTF-1 positive tumor cell slide, the same KRAS alteration was observed. Unfortunately, the patient died in August 2020 before having the chance to start any type of treatment.
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Wang H, Hu A, Liang Y, Wang K, Zhou X, Dong J. Genome-wide analysis of long non-coding RNA expression profile in lung adenocarcinoma compared to spinal metastasis. ANNALS OF TRANSLATIONAL MEDICINE 2020; 8:1516. [PMID: 33313261 PMCID: PMC7729335 DOI: 10.21037/atm-20-7046] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Background Long non-coding RNAs (lncRNAs) play important roles in tumor metastasis. The aim of the present study was to investigate their expression profile and potential functions in spinal metastasis (SM) of lung adenocarcinoma. Methods We conducted lncRNA and mRNA expression in lung adenocarcinoma and its SM tissue using microarray analysis. Quantitative reverse-transcriptase polymerase chain reaction (qRT-PCR) revealed 10 differentially expressed lncRNAs. Gene ontology and pathway analysis were performed to test the gene effect. Possible target genes of lncRNAs were predicted based on precise algorithms. Results Microarray analysis found many significantly differentially expressed lncRNAs and mRNAs in lung adenocarcinoma compared with SM. qRT-PCR results aligned with those of the microarray analysis. The expression level of 10 lncRNAs showed the same trend (P<0.05). Biologic pathways known to be involved in cancer were identified among the differentially expressed mRNAs; these include cell adhesion molecules (related to 42 genes), focal adhesion (related to 31 genes), cytokine-cytokine receptor interaction (related to 48 genes), and extracellular matrix-receptor interaction (related to 23 genes). About 9,458 lncRNAs were found to have cis- or trans-genes. A total of 2,317 cis target genes were discovered to be abnormally expressed and could be regulated by lncRNAs in SM of lung adenocarcinoma. Conclusions Our results offer a genome-wide differential expression of lncRNA in lung adenocarcinoma and SM, as well as laying the foundation for further investigations of lncRNAs correlated with lung adenocarcinoma metastasis.
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Affiliation(s)
- Houlei Wang
- Department of Orthopaedic Surgery, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Annan Hu
- Department of Orthopaedic Surgery, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Yun Liang
- Department of Orthopaedic Surgery, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Ketao Wang
- Department of Orthopaedic Surgery, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Xiaogang Zhou
- Department of Orthopaedic Surgery, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Jian Dong
- Department of Orthopaedic Surgery, Zhongshan Hospital, Fudan University, Shanghai, China
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Suda K, Sakai K, Obata K, Ohara S, Fujino T, Koga T, Hamada A, Soh J, Nishio K, Mitsudomi T. Inter- and Intratumor Heterogeneity of EGFR Compound Mutations in Non-Small Cell Lung Cancers: Analysis of Five Cases. Clin Lung Cancer 2020; 22:e141-e145. [PMID: 33051123 DOI: 10.1016/j.cllc.2020.09.009] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2020] [Revised: 09/01/2020] [Accepted: 09/10/2020] [Indexed: 01/10/2023]
Abstract
BACKGROUND Several clinical and preclinical studies suggest that non-small cell lung cancers (NSCLCs) with EGFR compound mutations were associated with lower efficacies of first-generation EGFR inhibitors than tumors with single EGFR mutation. Some researchers hypothesize that EGFR mutation status is heterogeneous in such tumors and that second-generation EGFR inhibitors may eliminate cancer cells with uncommon EGFR mutations from tumors with EGFR compound mutations. However, this hypothesis is currently unproven; therefore, we performed the current study to determine if tumor cells with EGFR compound mutations are present in heterogeneous or homogeneous manners. PATIENTS AND METHODS Multiregion analysis was performed for surgically resected primary NSCLC tumors with EGFR compound mutations to examine the intratumor heterogeneity of EGFR compound mutations. In addition, we evaluated the intertumor heterogeneity of EGFR compound mutations using 2 pleural disseminations obtained from a patient with NSCLC at exploratory thoracotomy and 9 primary or metastatic lesions obtained from 2 autopsied NSCLC patients. Digital polymerase chain reaction, target sequencing, or direct sequencing were used to detect EGFR mutations. RESULTS This study included 5 NSCLC cases; their compound mutations were L858R+S768I, G719X+S768I, G719A+R776H, L858R+E709G, and L858R+I759M. Noncancerous pulmonary tissues from each patient did not harbor EGFR mutations, which revealed that all mutations were somatic. We did not detect any intra- or intertumor heterogeneity in these EGFR compound mutations. CONCLUSION No intra- or intertumor heterogeneity was observed for EGFR compound mutations. Our results indicate that both EGFR mutations were truncal and selective elimination of cancer cells with uncommon EGFR mutations is unrealistic.
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Affiliation(s)
- Kenichi Suda
- Division of Thoracic Surgery, Department of Surgery, Kindai University Faculty of Medicine, Osaka-Sayama, Japan
| | - Kazuko Sakai
- Department of Genome Biology, Kindai University Faculty of Medicine, Osaka-Sayama, Japan
| | - Keiko Obata
- Division of Thoracic Surgery, Department of Surgery, Kindai University Faculty of Medicine, Osaka-Sayama, Japan
| | - Shuta Ohara
- Division of Thoracic Surgery, Department of Surgery, Kindai University Faculty of Medicine, Osaka-Sayama, Japan
| | - Toshio Fujino
- Division of Thoracic Surgery, Department of Surgery, Kindai University Faculty of Medicine, Osaka-Sayama, Japan
| | - Takamasa Koga
- Division of Thoracic Surgery, Department of Surgery, Kindai University Faculty of Medicine, Osaka-Sayama, Japan
| | - Akira Hamada
- Division of Thoracic Surgery, Department of Surgery, Kindai University Faculty of Medicine, Osaka-Sayama, Japan
| | - Junichi Soh
- Division of Thoracic Surgery, Department of Surgery, Kindai University Faculty of Medicine, Osaka-Sayama, Japan
| | - Kazuto Nishio
- Department of Genome Biology, Kindai University Faculty of Medicine, Osaka-Sayama, Japan
| | - Tetsuya Mitsudomi
- Division of Thoracic Surgery, Department of Surgery, Kindai University Faculty of Medicine, Osaka-Sayama, Japan.
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Clonal Origin Evaluated by Trunk and Branching Drivers and Prevalence of Mutations in Multiple Lung Tumor Nodules. Mol Diagn Ther 2020; 24:461-472. [DOI: 10.1007/s40291-020-00471-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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10
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Ham-Karim HA, Ebili HO, Manger K, Fadhil W, Ahmad NS, Richman SD, Ilyas M. Targeted Next-Generation Sequencing Validates the Use of Diagnostic Biopsies as a Suitable Alternative to Resection Material for Mutation Screening in Colorectal Cancer. Mol Diagn Ther 2020; 23:383-393. [PMID: 30741375 DOI: 10.1007/s40291-019-00388-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
BACKGROUND Mutation testing in the context of neoadjuvant therapy must be performed on biopsy samples. Given the issue of tumour heterogeneity, this raises the question of whether the biopsies are representative of the whole tumour. Here we have compared the mutation profiles of colorectal biopsies with their matched resection specimens. METHODS We performed next-generation sequencing (NGS) analysis on 25 paired formalin-fixed, paraffin-embedded colorectal cancer biopsy and primary resection samples. DNA was extracted and analysed using the TruSight tumour kit, allowing the interrogation of 26 cancer driver genes. Samples were run on an Illumina MiSeq. Mutations were validated using quick-multiplex-consensus (QMC)-polymerase chain reaction (PCR) in conjunction with high resolution melting (HRM). The paired biopsy and resection tumour samples were assessed for presence or absence of mutations, mutant allele frequency ratios, and allelic imbalance status. RESULTS A total of 81 mutations were detected, in ten of the 26 genes in the TruSight kit. Two of the 25 paired cases were wild-type across all genes. The mutational profiles, allelic imbalance status, and mutant allele frequency ratios of the paired biopsy and resection samples were highly concordant (88.75-98.85%), with all but three (3.7%) of the mutations identified in the resection specimens also being present in the biopsy specimens. All 81 mutations were confirmed by QMC-PCR and HRM analysis, although four low-level mutations required a co-amplification at lower denaturation temperature (COLD)-PCR protocol to enrich for the mutant alleles. CONCLUSIONS Diagnostic biopsies are adequate and reliable materials for molecular testing by NGS. The use of biopsies for molecular screening will enhance targeted neoadjuvant therapy.
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Affiliation(s)
- Hersh A Ham-Karim
- Division of Pathology, School of Medicine, Queen's Medical Centre, University of Nottingham, Nottingham, NG7 2UH, UK.,Department of Medical Laboratory Sciences, College of Health Sciences, Komar University of Science and Technology, Chaq-Chaq-Qualaraisi, Sulaimani, Iraq
| | - Henry Okuchukwu Ebili
- Division of Pathology, School of Medicine, Queen's Medical Centre, University of Nottingham, Nottingham, NG7 2UH, UK. .,Department of Morbid Anatomy and Histopathology, Olabisi Onabanjo University, Ago-Iwoye, Nigeria.
| | - Kirsty Manger
- Centre for Medical Genetics, Nottingham University Hospitals NHS Trust, City Hospital Campus, Nottingham, UK
| | - Wakkas Fadhil
- Division of Pathology, School of Medicine, Queen's Medical Centre, University of Nottingham, Nottingham, NG7 2UH, UK
| | - Narmeen S Ahmad
- Clinical Oncology, University of Nottingham, City Hospital Campus, Nottingham, UK.,Kurdistan Institution for Strategic Studies and Scientific Research, Qirga, Sulaimani, KRG, Iraq
| | - Susan D Richman
- Department of Pathology and Tumour Biology, Leeds Institute of Cancer and Pathology, Wellcome Trust Brenner Building, St James University Hospital, Leeds, UK
| | - Mohammad Ilyas
- Division of Pathology, School of Medicine, Queen's Medical Centre, University of Nottingham, Nottingham, NG7 2UH, UK
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11
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Rodriguez EF, De Marchi F, Lokhandwala PM, Belchis D, Xian R, Gocke CD, Eshleman JR, Illei P, Li MT. IDH1 and IDH2 mutations in lung adenocarcinomas: Evidences of subclonal evolution. Cancer Med 2020; 9:4386-4394. [PMID: 32333643 PMCID: PMC7300411 DOI: 10.1002/cam4.3058] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2019] [Revised: 03/24/2020] [Accepted: 03/30/2020] [Indexed: 12/19/2022] Open
Abstract
Background Selective IDH1 and IDH2 inhibitors have been approved for targeted therapy of acute myeloid leukemia. Clinical trials for solid tumors with IDH1 and IDH2 (IDH1/2) mutations are ongoing. Reports of IDH1/2‐mutated non–small cell lung cancers (NSCLCs), however, are limited. Methods We evaluated IDH1/2 mutations in 1,924 NSCLC specimens (92% adenocarcinoma) using a next‐generation sequencing assay. Results Retrospective quality assessments identified false detection of IDH1 c.395G>A (p.R132H) resulting from cytosine deamination (C:G→T:A) artifact in one specimen. IDH1/2 mutations were detected in 9 (0.5%) adenocarcinomas taken by fine‐needle aspiration (n = 3), thoracentesis (n = 2) or core biopsy (n = 4). All nine adenocarcinomas showed high‐grade features. Extensive clear cell change, however, was not observed. High expression (50% or greater) of PD‐L1 was observed in two of five specimens examined. IDH1/2 mutations were associated with old age, smoking history, and coexisting KRAS mutation. Lower than expected variant allele frequency of IDH1/2 mutants and coexistence of IDH1/2 mutations with known trunk drivers in the BRAF, EGFR, and KRAS genes suggest they could be branching drivers leading to subclonal evolution in lung adenocarcinomas. Multiregional analysis of an adenocarcinoma harboring two IDH2 mutations revealed parallel evolution originating from a KRAS‐mutated lineage, further supporting subclonal evolution promoted by IDH1/2 mutations. Conclusions IDH1/2 mutations in NSCLCs are uncommon. They occur in adenocarcinomas with high‐grade features and may be branching drivers leading to subclonal evolution. Accumulation of more IDH1/2‐mutated NSCLCs is needed to clarify their clinicopathological characteristics and implications for targeted therapy.
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Affiliation(s)
- Erika F Rodriguez
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Federico De Marchi
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Parvez M Lokhandwala
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Deborah Belchis
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Rena Xian
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD, USA.,Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Christopher D Gocke
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD, USA.,Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - James R Eshleman
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD, USA.,Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Peter Illei
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Ming-Tseh Li
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
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12
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Tseng LH, De Marchi F, Pallavajjalla A, Rodriguez E, Xian R, Belchis D, Gocke CD, Eshleman JR, Illei P, Lin MT. Clinical Validation of Discordant Trunk Driver Mutations in Paired Primary and Metastatic Lung Cancer Specimens. Am J Clin Pathol 2019; 152:570-581. [PMID: 31264684 DOI: 10.1093/ajcp/aqz077] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
OBJECTIVES To propose an operating procedure for validation of discordant trunk driver mutations. METHODS Concordance of trunk drivers was examined by next-generation sequencing in 15 patients with two to three metastatic lung cancers and 32 paired primary and metastatic lung cancers. RESULTS Tissue identity was confirmed by genotyping 17 single-nucleotide polymorphisms within the panel. All except three pairs showed concordant trunk drivers. Quality assessment conducted in three primary and metastatic pairs with discordant trunk drivers indicates metastasis from a synchronous or remote lung primary in two patients. Review of literature revealed high discordant rates of EGFR and KRAS mutations, especially when Sanger sequencing was applied to examine primary and lymph node metastatic tumors. CONCLUSIONS Trunk driver mutations are highly concordant in primary and metastatic tumors. Discordance of trunk drivers, once confirmed, may suggest a second primary cancer. Guidelines are recommended to establish standard operating procedures for validation of discordant trunk drivers.
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Affiliation(s)
- Li-Hui Tseng
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD
- Department of Medical Genetics, National Taiwan University Hospital, Taipei
| | - Federico De Marchi
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD
| | - Aparna Pallavajjalla
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD
| | - Erika Rodriguez
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD
| | - Rena Xian
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD
| | - Deborah Belchis
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD
| | - Christopher D Gocke
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD
- Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, MD
| | - James R Eshleman
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD
- Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, MD
| | - Peter Illei
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD
| | - Ming-Tseh Lin
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD
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13
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Simarro J, Murria R, Pérez-Simó G, Llop M, Mancheño N, Ramos D, Juan ID, Barragán E, Laiz B, Cases E, Ansótegui E, Gómez-Codina J, Aparicio J, Salvador C, Juan Ó, Palanca S. Development, Implementation and Assessment of Molecular Diagnostics by Next Generation Sequencing in Personalized Treatment of Cancer: Experience of a Public Reference Healthcare Hospital. Cancers (Basel) 2019; 11:E1196. [PMID: 31426418 PMCID: PMC6721584 DOI: 10.3390/cancers11081196] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2019] [Revised: 08/12/2019] [Accepted: 08/13/2019] [Indexed: 02/07/2023] Open
Abstract
The establishment of precision medicine in cancer patients requires the study of several biomarkers. Single-gene testing approaches are limited by sample availability and turnaround time. Next generation sequencing (NGS) provides an alternative for detecting genetic alterations in several genes with low sample requirements. Here we show the implementation to routine diagnostics of a NGS assay under International Organization for Standardization (UNE-EN ISO 15189:2013) accreditation. For this purpose, 106 non-small cell lung cancer (NSCLC) and 102 metastatic colorectal cancer (mCRC) specimens were selected for NGS analysis with Oncomine Solid Tumor (ThermoFisher). In NSCLC the most prevalently mutated gene was TP53 (49%), followed by KRAS (31%) and EGFR (13%); in mCRC, TP53 (50%), KRAS (48%) and PIK3CA (16%) were the most frequently mutated genes. Moreover, NGS identified actionable genetic alterations in 58% of NSCLC patients, and 49% of mCRC patients did not harbor primary resistance mechanisms to anti-EGFR treatment. Validation with conventional approaches showed an overall agreement >90%. Turnaround time and cost analysis revealed that NGS implementation is feasible in the public healthcare context. Therefore, NGS is a multiplexed molecular diagnostic tool able to overcome the limitations of current molecular diagnosis in advanced cancer, allowing an improved and economically sustainable molecular profiling.
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Affiliation(s)
- Javier Simarro
- Molecular Biology Unit, Service of Clinical Analysis, University and Polytechnic La Fe Hospital, 46026 Valencia, Spain
- Clinical and Translational Cancer Research Group, Health Research Institute La Fe, 46026 Valencia, Spain
| | - Rosa Murria
- Molecular Biology Unit, Service of Clinical Analysis, University and Polytechnic La Fe Hospital, 46026 Valencia, Spain
- Clinical and Translational Cancer Research Group, Health Research Institute La Fe, 46026 Valencia, Spain
| | - Gema Pérez-Simó
- Molecular Biology Unit, Service of Clinical Analysis, University and Polytechnic La Fe Hospital, 46026 Valencia, Spain
- Clinical and Translational Cancer Research Group, Health Research Institute La Fe, 46026 Valencia, Spain
| | - Marta Llop
- Molecular Biology Unit, Service of Clinical Analysis, University and Polytechnic La Fe Hospital, 46026 Valencia, Spain
| | - Nuria Mancheño
- Department of Pathology, University and Polytechnic La Fe Hospital, 46026 Valencia, Spain
| | - David Ramos
- Department of Pathology, University and Polytechnic La Fe Hospital, 46026 Valencia, Spain
| | - Inmaculada de Juan
- Molecular Biology Unit, Service of Clinical Analysis, University and Polytechnic La Fe Hospital, 46026 Valencia, Spain
- Clinical and Translational Cancer Research Group, Health Research Institute La Fe, 46026 Valencia, Spain
| | - Eva Barragán
- Molecular Biology Unit, Service of Clinical Analysis, University and Polytechnic La Fe Hospital, 46026 Valencia, Spain
| | - Begoña Laiz
- Molecular Biology Unit, Service of Clinical Analysis, University and Polytechnic La Fe Hospital, 46026 Valencia, Spain
| | - Enrique Cases
- Department of Pulmonology, University and Polytechnic La Fe Hospital, 46026 Valencia, Spain
| | - Emilio Ansótegui
- Department of Pulmonology, University and Polytechnic La Fe Hospital, 46026 Valencia, Spain
| | - José Gómez-Codina
- Clinical and Translational Cancer Research Group, Health Research Institute La Fe, 46026 Valencia, Spain
- Department of Medical Oncology, University and Polytechnic La Fe Hospital, 46026 Valencia, Spain
| | - Jorge Aparicio
- Clinical and Translational Cancer Research Group, Health Research Institute La Fe, 46026 Valencia, Spain
- Department of Medical Oncology, University and Polytechnic La Fe Hospital, 46026 Valencia, Spain
| | - Carmen Salvador
- Clinical and Translational Cancer Research Group, Health Research Institute La Fe, 46026 Valencia, Spain
- Department of Medical Oncology, University and Polytechnic La Fe Hospital, 46026 Valencia, Spain
| | - Óscar Juan
- Department of Medical Oncology, University and Polytechnic La Fe Hospital, 46026 Valencia, Spain
| | - Sarai Palanca
- Molecular Biology Unit, Service of Clinical Analysis, University and Polytechnic La Fe Hospital, 46026 Valencia, Spain.
- Clinical and Translational Cancer Research Group, Health Research Institute La Fe, 46026 Valencia, Spain.
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14
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Kage H, Kohsaka S, Shinozaki-Ushiku A, Hiraishi Y, Sato J, Nagayama K, Ushiku T, Takai D, Nakajima J, Miyagawa K, Aburatani H, Mano H, Nagase T. Small lung tumor biopsy samples are feasible for high quality targeted next generation sequencing. Cancer Sci 2019; 110:2652-2657. [PMID: 31222846 PMCID: PMC6676108 DOI: 10.1111/cas.14112] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2019] [Revised: 06/17/2019] [Accepted: 06/19/2019] [Indexed: 12/30/2022] Open
Abstract
Next‐generation sequencing (NGS) has been implemented in clinical oncology to analyze multiple genes and to guide therapy. In patients with advanced lung cancer, small biopsies such as computed tomography‐guided needle biopsy (CTNB), endobronchial ultrasound‐guided transbronchial needle aspiration (EBUS‐TBNA) and transbronchial biopsy (TBB) are less invasive and are preferable to resection to make a pathological diagnosis. However, the quality of DNA/RNA and NGS from small lung tumor biopsy samples is unknown. Between April 2017 and March 2018, 107 consecutive samples were obtained from thoracic tumors or metastatic sites for targeted NGS analysis. Fifteen samples were obtained through CTNB, 11 through EBUS‐TBNA, 11 through TBB and 70 through surgical resection. All samples were formalin‐fixed and paraffin‐embedded. DNA and RNA quality was measured using the ddCq method and the percentage of RNA fragments above 200 nucleotides (DV200), respectively. Our custommade probes were designed to capture exon sequences of 464 cancer‐related genes and transcripts of 463 genes. DNA and RNA yield from the 3 biopsy methods were similar, and less than the yield obtained from resected samples. The quality of DNA and RNA was similar across all methods. Overall, 12 of 15 CTNB samples (80%), all 11 EBUS‐TBNA samples, and 9 of 11 TBB samples (82%) underwent successful NGS assays from DNA. NGS analysis from RNA was successful in all 12 CTNB samples, 9 of 11 EBUS‐TBNA samples (82%), and 8 of 11 TBB samples (73%). CTNB, EBUS‐TBNA and TBB mostly resulted in adequate DNA and RNA quality and enabled high‐quality targeted NGS analysis.
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Affiliation(s)
- Hidenori Kage
- Department of Respiratory Medicine, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Shinji Kohsaka
- Division of Cellular Signaling, National Cancer Center Research Institute, Tokyo, Japan
| | - Aya Shinozaki-Ushiku
- Department of Pathology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Yoshihisa Hiraishi
- Department of Respiratory Medicine, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Jiro Sato
- Department of Radiology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Kazuhiro Nagayama
- Department of Thoracic Surgery, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Tetsuo Ushiku
- Department of Pathology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Daiya Takai
- Department of Clinical Laboratory, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Jun Nakajima
- Department of Thoracic Surgery, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Kiyoshi Miyagawa
- Laboratory of Molecular Radiology, Center for Disease Biology and Integrative Medicine, The University of Tokyo, Tokyo, Japan
| | - Hiroyuki Aburatani
- Genome Science Laboratory, Research Center for Advanced Science and Technology, The University of Tokyo, Tokyo, Japan
| | - Hiroyuki Mano
- Division of Cellular Signaling, National Cancer Center Research Institute, Tokyo, Japan
| | - Takahide Nagase
- Department of Respiratory Medicine, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
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15
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Cao W, Yan C, Wang H, Tang T, Wang H, Liu D. Validity of an NGS-based multiple gene panel in identifying actionable mutations for patients with NSCLC in a Chinese hospital. Oncol Lett 2019; 17:5425-5434. [PMID: 31186761 PMCID: PMC6507321 DOI: 10.3892/ol.2019.10265] [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: 02/14/2018] [Accepted: 03/19/2019] [Indexed: 11/09/2022] Open
Abstract
Non-small cell lung cancer (NSCLC) is the most common type of lung cancer. A number of targeted therapies have been approved for clinical use or are in clinical trials. Next generation sequencing (NGS) is widely applied in the identification of actionable genomic alterations and enables personalized cancer therapy for patients. Several multiple-gene panels are available in China for the practice of precision medicine-based cancer therapy. However, the efficiency of these panels requires evaluation. The current study investigated 23 NSCLC samples using a custom designed panel of complete coding regions of ~180 cancer driver genes (FD-180) and whole exome sequencing for control samples, obtained from white blood cell samples. The results obtained suggested that actionable mutations with available targeted therapeutic options were identified in 69.6% of cases, including 60.9% of therapeutic targets recommended by the National Comprehensive Cancer Network guidelines. Furthermore, 8.7% of patients had a gene mutation that potentially qualified them for clinical trials or associated off-label therapies. As such, the results obtained in the current study demonstrated the reliability of the targeted NGS panel and its potential use for identifying actionable gene alterations and designing personalized therapies for patients with NSCLC.
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Affiliation(s)
- Wei Cao
- Department of Cardiothoracic Surgery, The Second Hospital of Anhui Medical University, Hefei, Anhui 230601, P.R. China
| | - Chenghai Yan
- First Dimension Biosciences (Suzhou) Co., Ltd., Industrial Park, Suzhou, Jiangsu 215126, P.R. China
| | - Hailong Wang
- First Dimension Biosciences (Suzhou) Co., Ltd., Industrial Park, Suzhou, Jiangsu 215126, P.R. China
| | - Tom Tang
- First Dimension Biosciences (Suzhou) Co., Ltd., Industrial Park, Suzhou, Jiangsu 215126, P.R. China
| | - Haifeng Wang
- First Dimension Biosciences (Suzhou) Co., Ltd., Industrial Park, Suzhou, Jiangsu 215126, P.R. China
| | - Dujuan Liu
- First Dimension Biosciences (Suzhou) Co., Ltd., Industrial Park, Suzhou, Jiangsu 215126, P.R. China
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16
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Kurzrock R, Ball DW, Zahurak ML, Nelkin BD, Subbiah V, Ahmed S, O'Connor A, Karunsena E, Parkinson RM, Bishop JA, Ha Y, Sharma R, Gocke CD, Zinner R, Rudek MA, Sherman SI, Azad NS. A Phase I Trial of the VEGF Receptor Tyrosine Kinase Inhibitor Pazopanib in Combination with the MEK Inhibitor Trametinib in Advanced Solid Tumors and Differentiated Thyroid Cancers. Clin Cancer Res 2019; 25:5475-5484. [PMID: 31186313 DOI: 10.1158/1078-0432.ccr-18-1881] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2018] [Revised: 11/16/2018] [Accepted: 06/07/2019] [Indexed: 12/20/2022]
Abstract
PURPOSE Differentiated thyroid cancer (DTC) responds to VEGF receptor inhibitors. VEGF signals through RAS/RAF/MEK signaling. We evaluated the safety and efficacy of the VEGF receptor inhibitor pazopanib and MEK inhibitor trametinib in advanced solid tumors and DTC. PATIENTS AND METHODS Patients with advanced solid tumors were enrolled in a phase I, multicenter trial with a DTC expansion cohort. Patients received pazopanib 400-800 mg and trametinib 1-2 mg daily. Efficacy in the expansion cohort was assessed with objective response (OR) at 6 months of treatment. RESULTS Twenty-six patients were enrolled in five dose levels. MTD was not reached; the recommended phase II dose was pazopanib 800 mg orally and trametinib 2 mg orally every day. There was one dose-limiting toxicity on dose level 1 with grade 3 fatigue and muscle weakness. Common grade 3 adverse events were elevated transaminases (19%), diarrhea (15%), hypertension (12%), and fatigue (8%). Thirteen patients were enrolled in the DTC cohort; OR was 33% (95% confidence interval, 9.9, 65.1%) and median progression-free survival was 10.7 months. The cohort was terminated after planned interim analysis suggested insufficiently increased activity against the historical control of pazopanib alone. Reduction in tumor diameter negatively correlated with p-ERK change in tumor (Spearman ρ = -0.71; P = 0.05). NRAS mutation was associated with response (Fisher exact P = 0.008). CONCLUSIONS Pazopanib + trametinib was tolerable at full single-agent doses with clinical activity in DTC but did not achieve the prespecified response rate target.
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Affiliation(s)
- Razelle Kurzrock
- The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Douglas W Ball
- The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University, Baltimore, Maryland.,Division of Diabetes Endocrinology and Metabolism, Johns Hopkins University, Baltimore Maryland
| | - Marianna L Zahurak
- The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University, Baltimore, Maryland
| | - Barry D Nelkin
- The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University, Baltimore, Maryland
| | - Vivek Subbiah
- The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Shabina Ahmed
- Division of Diabetes Endocrinology and Metabolism, Johns Hopkins University, Baltimore Maryland
| | - Ashley O'Connor
- The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University, Baltimore, Maryland
| | - Enusha Karunsena
- The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University, Baltimore, Maryland
| | - Rose M Parkinson
- The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University, Baltimore, Maryland
| | - Justin A Bishop
- Department of Pathology, Johns Hopkins University, School of Medicine, Baltimore, Maryland
| | - Yoonji Ha
- The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University, Baltimore, Maryland
| | - Rajni Sharma
- Department of Pathology, Johns Hopkins University, School of Medicine, Baltimore, Maryland
| | - Christopher D Gocke
- The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University, Baltimore, Maryland
| | - Ralph Zinner
- The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Michelle A Rudek
- The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University, Baltimore, Maryland
| | - Steven I Sherman
- The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Nilofer S Azad
- The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University, Baltimore, Maryland.
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17
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Falla-Martinez JC, Espinosa D, Baena JC, Rodriguez LX, Sua LF, Zambrano AR. An endothelial growth factor receptor compound mutation of T790M substitution with exon 19 deletion in a previously untreated patient: a case report. J Med Case Rep 2019; 13:144. [PMID: 31088573 PMCID: PMC6518648 DOI: 10.1186/s13256-019-2075-y] [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: 08/03/2018] [Accepted: 04/08/2019] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Endothelial growth factor receptor (EGFR) mutations are an essential driver of personalized therapy for patients with lung cancer and are detected in approximately 15% of Caucasian and 50% of Asian patients. EGFR tyrosine kinase inhibitors have been developed and used for this set of patients. T790M mutation in exon 20 is usually associated with secondary resistance to EGFR tyrosine kinase inhibitors therapy but is also present in treatment-naïve patients. The frequency for baseline T790M mutation varies from 4 to 35% according to the detection method used. Newer techniques have yielded higher rates, but concerns about false-positive results have been raised. Compound mutations account for 4-14% of all EGFR-mutated tumors, with no studies yet to provide a frequency rate for T790M + 19 deletion association due to the small number of cases. However, there are reports that pretreatment T790M + L858R association is significantly more frequent compared to T790M + exon 19 deletion mutations. Diagnostic challenges, current knowledge on the subject, and therapeutic decisions are discussed. CASE PRESENTATION We present the case of a 43-year-old Hispanic woman, a treatment-naïve patient, with metastasized lung cancer adenocarcinoma harboring a T790M deletion along with the classic 19 mutation. The initial symptoms were monoparesis of her left leg, associated with hyperreflexia, and hypoesthesia. In the absence of third-generation tyrosine kinase inhibitors, a platinum-based therapy was initiated with no response and she died 4 months after diagnosis. CONCLUSIONS Osimertinib seems to be a suitable therapy for treatment-naïve patients with sensitizing and resistant compound EGFR mutations. More studies regarding the clinical characteristics of these patients and the appropriate management of this condition are needed to provide the highest standard of care.
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Affiliation(s)
- Juan C Falla-Martinez
- Hematology-Oncology department, Fundacion Valle del Lili, Carrera 98 No. 18-49, Fundacion Valle del Lili, Cali, Colombia
| | - Daniela Espinosa
- Internal Medicine department, Fundacion Valle del Lili, Carrera 98 No. 18-49, Cali, Colombia
| | - Juan C Baena
- Hematology-Oncology department, Fundacion Valle del Lili, Carrera 98 No. 18-49, Fundacion Valle del Lili, Cali, Colombia
| | - Lisa X Rodriguez
- Human Genetics department, Fundacion Valle del Lili, Carrera 98 No. 18-49, Cali, Colombia
| | - Luz F Sua
- Pathology department, Fundacion Valle del Lili, Carrera 98 No. 18-49, Cali, Colombia
| | - Angela R Zambrano
- Hematology-Oncology department, Fundacion Valle del Lili, Carrera 98 No. 18-49, Fundacion Valle del Lili, Cali, Colombia.
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18
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Namba K, Tomida S, Matsubara T, Takahashi Y, Kurihara E, Ogoshi Y, Yoshioka T, Takeda T, Torigoe H, Sato H, Shien K, Yamamoto H, Soh J, Tsukuda K, Toyooka S. Application of amplicon-based targeted sequencing with the molecular barcoding system to detect uncommon minor EGFR mutations in patients with treatment-naïve lung adenocarcinoma. BMC Cancer 2019; 19:175. [PMID: 30808329 PMCID: PMC6390598 DOI: 10.1186/s12885-019-5374-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2018] [Accepted: 02/18/2019] [Indexed: 11/10/2022] Open
Abstract
Background In lung cancer, epidermal growth factor receptor (EGFR) tyrosine kinase inhibitor sensitizing mutations co-existing with rare minor EGFR mutations are known as compound mutations. These minor EGFR mutations can lead to acquired resistance after EGFR tyrosine kinase inhibitor treatment, so determining the mutation status of patients is important. However, using amplicon-based targeted deep sequencing based on next-generation sequencing to characterize mutations is prone to sequencing error. We therefore assessed the benefit of incorporating molecular barcoding with high-throughput sequencing to investigate genomic heterogeneity in treatment-naïve patients who have undergone resection of their non-small cell lung cancer (NSCLC) EGFR mutations. Methods We performed amplicon-based targeted sequencing with the molecular barcoding system (MBS) to detect major common EGFR mutations and uncommon minor mutations at a 0.5% allele frequency in fresh–frozen lung cancer samples. Results Profiles of the common mutations of EGFR identified by MBS corresponded with the results of clinical testing in 63 (98.4%) out of 64 cases. Uncommon mutations of EGFR were detected in seven cases (10.9%). Among the three types of major EGFR mutations, patients with the G719X mutation had a significantly higher incidence of compound mutations than those with the L858R mutation or exon 19 deletion (p = 0.0052). This was validated in an independent cohort from the Cancer Genome Atlas dataset (p = 0.018). Conclusions Our findings demonstrate the feasibility of using the MBS to establish an accurate NSCLC patient genotype. This work will help understand the molecular basis of EGFR compound mutations in NSCLC, and could aid the development of new treatment modalities. Electronic supplementary material The online version of this article (10.1186/s12885-019-5374-1) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Kei Namba
- Departments of Thoracic, Breast and Endocrinological Surgery, Okayama University Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, 2-5-1 Shikata-cho, Kita-ku, Okayama City, 700-8558, Japan
| | - Shuta Tomida
- Department of Biobank, Okayama University Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, 2-5-1 Shikata-cho, Kita-ku, Okayama City, 700-8558, Japan.
| | - Takehiro Matsubara
- Okayama University Hospital Biobank, Okayama University Hospital, 2-5-1 Shikata-cho, Kita-ku, Okayama City, 700-8558, Japan
| | - Yuta Takahashi
- Departments of Thoracic, Breast and Endocrinological Surgery, Okayama University Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, 2-5-1 Shikata-cho, Kita-ku, Okayama City, 700-8558, Japan
| | - Eisuke Kurihara
- Departments of Thoracic, Breast and Endocrinological Surgery, Okayama University Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, 2-5-1 Shikata-cho, Kita-ku, Okayama City, 700-8558, Japan
| | - Yusuke Ogoshi
- Departments of Thoracic, Breast and Endocrinological Surgery, Okayama University Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, 2-5-1 Shikata-cho, Kita-ku, Okayama City, 700-8558, Japan
| | - Takahiro Yoshioka
- Department of Gastroenterological Surgery, Okayama University Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, 2-5-1 Shikata-cho, Kita-ku, Okayama City, 700-8558, Japan
| | - Tatsuaki Takeda
- Department of Clinical Pharmacy, Okayama University Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, 2-5-1 Shikata-cho, Kita-ku, Okayama City, Okayama, 700-8558, Japan
| | - Hidejiro Torigoe
- Departments of Thoracic, Breast and Endocrinological Surgery, Okayama University Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, 2-5-1 Shikata-cho, Kita-ku, Okayama City, 700-8558, Japan
| | - Hiroki Sato
- Departments of Thoracic, Breast and Endocrinological Surgery, Okayama University Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, 2-5-1 Shikata-cho, Kita-ku, Okayama City, 700-8558, Japan
| | - Kazuhiko Shien
- Departments of Thoracic, Breast and Endocrinological Surgery, Okayama University Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, 2-5-1 Shikata-cho, Kita-ku, Okayama City, 700-8558, Japan
| | - Hiromasa Yamamoto
- Departments of Thoracic, Breast and Endocrinological Surgery, Okayama University Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, 2-5-1 Shikata-cho, Kita-ku, Okayama City, 700-8558, Japan
| | - Junichi Soh
- Departments of Thoracic, Breast and Endocrinological Surgery, Okayama University Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, 2-5-1 Shikata-cho, Kita-ku, Okayama City, 700-8558, Japan
| | - Kazunori Tsukuda
- Departments of Thoracic, Breast and Endocrinological Surgery, Okayama University Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, 2-5-1 Shikata-cho, Kita-ku, Okayama City, 700-8558, Japan
| | - Shinichi Toyooka
- Departments of Thoracic, Breast and Endocrinological Surgery, Okayama University Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, 2-5-1 Shikata-cho, Kita-ku, Okayama City, 700-8558, Japan
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19
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Grosse A, Grosse C, Rechsteiner M, Soltermann A. Analysis of the frequency of oncogenic driver mutations and correlation with clinicopathological characteristics in patients with lung adenocarcinoma from Northeastern Switzerland. Diagn Pathol 2019; 14:18. [PMID: 30744664 PMCID: PMC6371584 DOI: 10.1186/s13000-019-0789-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2018] [Accepted: 02/01/2019] [Indexed: 12/28/2022] Open
Abstract
BACKGROUND Molecular testing of lung adenocarcinoma for oncogenic driver mutations has become standard in pathology practice. The aim of the study was to analyze the EGFR, KRAS, ALK, RET, ROS1, BRAF, ERBB2, MET and PIK3CA mutational status in a representative cohort of Swiss patients with lung adenocarcinoma and to correlate the mutational status with clinicopathological patient characteristics. METHODS All patients who underwent molecular testing of newly diagnosed lung adenocarcinoma during a 4-year period (2014-2018) were included. Molecular analyses were performed with Sanger sequencing (n = 158) and next generation sequencing (n = 311). ALK, ROS1 and RET fusion gene analyses were also performed with fluorescence in situ hybridization and immunohistochemistry/immunocytochemistry. Demographic and clinical data were obtained from the medical records. RESULTS Of 469 patients with informative EGFR mutation analyses, 90 (19.2%) had EGFR mutations. KRAS mutations were present in 33.9% of the patients, while 6.0% of patients showed ALK rearrangement. BRAF, ERBB2, MET and PIK3CA mutations and ROS1 and RET rearrangements were found in 2.6%, 1.9%, 1.9%, 1.5%, 1.7% and 0.8% of the patients, respectively. EGFR mutation was significantly associated with female gender and never smoking status. ALK translocations were more frequent in never smokers, while KRAS mutations were more commonly found in ever smokers. The association between KRAS mutational status and female gender was statistically significant only on multivariate analysis after adjusting for smoking. CONCLUSION The EGFR mutation rate in the current study is among the higher previously reported mutation rates, while the frequencies of KRAS, BRAF, ERBB2 and PIK3CA mutations and ALK, ROS1 and RET rearrangements are similar to the results of previous reports. EGFR and KRAS mutations were significantly associated with gender and smoking. ALK rearrangements showed a significant association with smoking status alone.
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Affiliation(s)
- Alexandra Grosse
- Institute of Pathology and Molecular Pathology, Clinical Pathology, University Hospital Zurich, Rämistrasse 100, 8091, Zurich, Switzerland
| | - Claudia Grosse
- Institute of Pathology, Kepler University Hospital, Krankenhausstraße 9, 4021, Linz, Austria.
| | - Markus Rechsteiner
- Institute of Pathology and Molecular Pathology, Diagnostic Molecular Pathology, University Hospital Zurich, Rämistrasse 100, 8091, Zurich, Switzerland
| | - Alex Soltermann
- Institute of Pathology and Molecular Pathology, Clinical Pathology, University Hospital Zurich, Rämistrasse 100, 8091, Zurich, Switzerland
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20
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Abe M, Watanabe K, Shinozaki-Ushiku A, Ushiku T, Abe T, Fujihara Y, Amano Y, Zong L, Wang CP, Kubo E, Inaki R, Kinoshita N, Yamashita S, Takai D, Ushijima T, Nagase T, Hoshi K. Identification of a metastatic lung adenocarcinoma of the palate mucosa through genetic and histopathological analysis: a rare case report and literature review. BMC Cancer 2019; 19:52. [PMID: 30634950 PMCID: PMC6329170 DOI: 10.1186/s12885-019-5277-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2017] [Accepted: 01/04/2019] [Indexed: 02/08/2023] Open
Abstract
Background Cancers of unknown primary origin (CUPs) are reported to be the 3-4th most common causes of cancer death. Recent years have seen advances in mutational analysis and genomics profiling. These advances could improve accuracy of diagnosis of CUPs and might improve the prognosis of patients with CUPs. Case presentation A 76-year old male with an adenocarcinoma of unknown primary origin in the lung presented with another tumor of the palate mucosa. The tumor cells in the pleural effusion were all negative for immunohistochemical markers (TTF-1 and Napsin A) and lung-specific oncogenic driver alterations (EGFR mutation and ALK translocation). The tumor of the palate mucosa was likewise identified as an adenocarcinoma, and the cells showed cytological similarities with the tumor cells in the pleural effusion; TTF-1, Napsin A, EGFR mutation and ALK translocation were all negative. This result suggested that origins of the tumors of the palate mucosa and in the lung were the same, even though the origin had not yet been determined. Next, we addressed whether the tumor of the palate mucosa was a primary tumor or not. Secretory carcinoma (SC), which is a common type of minor salivary gland tumor (MSGT), was suspected; however, mammaglobin was negative and ETV6-NTRK3 (EN) fusion was not observed. Other MSGTs were excluded based on histological and immunohistochemical findings. Furthermore, an additional examination demonstrated an oncogenic KRAS mutation at codon 12 (p.G12D) in both palate tumor and in pleural effusion. KRAS mutation is known to exist in one-third of lung adenocarcinomas (LUADs), but quite rare in MSGTs. The possibility of metastasis from other organs was considered unlikely from the results of endoscopic and imaging studies. This result indicated that the primary site of the CUP was indeed the lung, and that the tumor of the palate mucosa was a metastasis of the LUAD. Conclusions A tumor of the palate mucosa that showed diagnostic difficulties was determined to be a metastatic LUAD by genomic alterations and histopathological findings. Electronic supplementary material The online version of this article (10.1186/s12885-019-5277-1) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Masanobu Abe
- Department of Oral & Maxillofacial Surgery, University of Tokyo Hospital, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-8655, Japan. .,Division for Health Service Promotion, University of Tokyo, Tokyo, Japan.
| | - Kousuke Watanabe
- Department of Respiratory Medicine, University of Tokyo Hospital, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-8655, Japan.
| | - Aya Shinozaki-Ushiku
- Department of Pathology, Graduate School of Medicine, the University of Tokyo, Tokyo, Japan
| | - Tetsuo Ushiku
- Department of Pathology, Graduate School of Medicine, the University of Tokyo, Tokyo, Japan
| | - Takahiro Abe
- Department of Oral & Maxillofacial Surgery, University of Tokyo Hospital, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-8655, Japan
| | - Yuko Fujihara
- Department of Oral & Maxillofacial Surgery, University of Tokyo Hospital, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-8655, Japan
| | - Yosuke Amano
- Department of Respiratory Medicine, University of Tokyo Hospital, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-8655, Japan
| | - Liang Zong
- Graduate School of Medicine, the University of Tokyo, Tokyo, Japan.,Department of Gastrointestinal Surgery, Peking University Cancer Hospital & Institute, Beijing, China
| | - Cheng-Ping Wang
- Department of Otolaryngology, National Taiwan University Hospital, Taipei, Taiwan
| | - Emi Kubo
- Division of Epigenomics, National Cancer Center Research Institute, Tokyo, Japan
| | - Ryoko Inaki
- Department of Oral & Maxillofacial Surgery, University of Tokyo Hospital, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-8655, Japan
| | - Naoya Kinoshita
- Department of Oral & Maxillofacial Surgery, University of Tokyo Hospital, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-8655, Japan
| | - Satoshi Yamashita
- Division of Epigenomics, National Cancer Center Research Institute, Tokyo, Japan
| | - Daiya Takai
- Department of Clinical Laboratory, University of Tokyo Hospital, Tokyo, Japan
| | - Toshikazu Ushijima
- Division of Epigenomics, National Cancer Center Research Institute, Tokyo, Japan
| | - Takahide Nagase
- Department of Respiratory Medicine, University of Tokyo Hospital, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-8655, Japan
| | - Kazuto Hoshi
- Department of Oral & Maxillofacial Surgery, University of Tokyo Hospital, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-8655, Japan
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21
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Clinical validation of coexisting driver mutations in colorectal cancers. Hum Pathol 2018; 86:12-20. [PMID: 30481508 DOI: 10.1016/j.humpath.2018.11.014] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/12/2018] [Revised: 11/13/2018] [Accepted: 11/16/2018] [Indexed: 12/17/2022]
Abstract
Mutational profiling is recommended for selecting targeted therapy and predicting prognosis of metastatic colorectal cancer (CRC). Detection of coexisting mutations within the same pathway, which are usually mutually exclusive, raises the concern for potential laboratory errors. In this retrospective study for quality assessment of a next-generation sequencing assay, we examined BRAF, KRAS, and NRAS genes within the mitogen-activated protein kinase (MAPK) pathway and the PIK3CA gene within the phosphatidylinositol 3-kinase (mTOR) pathway in 744 CRC specimens submitted to our clinical diagnostics laboratory. Although coexistence of mutations between the MAPK and mTOR pathways was observed, it rarely occurred within the MAPK pathway. Retrospective quality assessments identified false detection of coexisting activating KRAS and NRAS mutations in 1 specimen and confirmed 2 activating KRAS mutations in 2 specimens and coexisting activating KRAS and NRAS mutations in 2 specimens, but no coexisting activating RAS and BRAF mutations. There were 15 CRCs with a kinase-impaired BRAF mutation, including 3 with a coexisting activating KRAS mutation, which may have therapeutic implications. Multiregional analysis based on different histologic features demonstrated that coexisting KRAS and NRAS mutations may be present in the same or different tumor populations and showed that invasion of adenomas by synchronous adenocarcinomas of different clonal origin may result in detection of coexisting mutations within the MAPK pathway. In this study, we proposed an operating procedure for clinical validation of unexpected coexisting mutations. Further studies are warranted to elucidate the biological significance and clinical implications of coexisting mutations within the MAPK pathway.
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22
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Abstract
Lung cancer diagnosis and ancillary testing are increasingly relying on cytology and small biopsy specimens obtained via minimally invasive means. Paired with traditional immunohistochemical characterization of tumors, biomarker testing and comprehensive genomic profiling are becoming essential steps in the workup of lung cancer to identify targetable alterations and guide optimal therapy selection. Recent advances in immune checkpoint inhibitor therapy have led to an increasingly complex and unresolved landscape for tumor PD-L1 testing. The prevalence and importance of lung cancer cytology specimens are growing, with more required by the cytopathologist in directing the care of patients with lung cancer.
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Affiliation(s)
- Paul A VanderLaan
- Department of Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, 330 Brookline Avenue, Boston, MA 02215, USA.
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23
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De Marchi F, Haley L, Fryer H, Ibrahim J, Beierl K, Zheng G, Gocke CD, Eshleman JR, Belchis D, Illei P, Lin MT. Clinical Validation of Coexisting Activating Mutations Within EGFR, Mitogen-Activated Protein Kinase, and Phosphatidylinositol 3-Kinase Pathways in Lung Cancers. Arch Pathol Lab Med 2018; 143:174-182. [PMID: 30485130 DOI: 10.5858/arpa.2017-0495-oa] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
CONTEXT.— Mutations within the same signature transduction pathway are redundant and, therefore, most are mutually exclusive. Laboratory errors, however, may introduce unexpected coexisting mutations. OBJECTIVE.— To validate coexisting mutations within epidermal growth factor receptor (EGFR), mitogen-activated protein kinase, and phosphatidylinositol 3-kinase pathways. DESIGN.— In this retrospective study for quality assessment of next-generation sequencing in a clinical diagnostics setting, coexisting mutations within EGFR, KRAS, NRAS, BRAF, AKT1, and PIK3CA genes were examined in 1208 non-small cell lung cancers. RESULTS.— EGFR mutations did not coexist with BRAF mutations, neither kinase-activated nor kinase-impaired mutations. There was a low but similar incidence (3.3%-5.1%) of PIK3CA mutations in BRAF-, EGFR-, and KRAS-mutated lung cancers and a rare incidence of coexisting KRAS and EGFR mutations detected in 1 of 1208 lung cancers (0.08%) or 1 of 226 EGFR-mutated lung cancers (0.4%). Coexisting BRAF p.V600E mutation was observed in 3 of 4 AKT1 p.E17K-mutated lung cancers. Mutational profiling of DNA reisolated from subareas with the same or different histomorphology, using an alternative assay, confirmed that coexisting mutations might present within the same (whole or subclonal) population or different populations and clarified that the so-called coexisting activating KRAS and BRAF mutations originally reported in a specimen were indeed present in separate lung nodules submitted in the same block. CONCLUSIONS.— The results supported that EGFR and BRAF mutations are early driver mutations in lung cancers. Guidelines from official organizations to establish standard operating procedures are warranted to validate unexpected coexisting mutations and, if clinically indicated, to determine their presence in the same or different tumor populations.
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Affiliation(s)
- Federico De Marchi
- From the Departments of Pathology (Drs De Marchi, Ibrahim, Zheng, Gocke, Eshleman, Belchis, Illei, and Lin, Ms Haley, Mr Fryer, and Ms Beierl) and Oncology (Drs Gocke and Eshleman), Johns Hopkins University School of Medicine, Baltimore, Maryland; and the Division of Hematology and Bone Marrow Transplantation, Hospital-University of Udine, Udine, Italy (Dr De Marchi)
| | - Lisa Haley
- From the Departments of Pathology (Drs De Marchi, Ibrahim, Zheng, Gocke, Eshleman, Belchis, Illei, and Lin, Ms Haley, Mr Fryer, and Ms Beierl) and Oncology (Drs Gocke and Eshleman), Johns Hopkins University School of Medicine, Baltimore, Maryland; and the Division of Hematology and Bone Marrow Transplantation, Hospital-University of Udine, Udine, Italy (Dr De Marchi)
| | - Henderson Fryer
- From the Departments of Pathology (Drs De Marchi, Ibrahim, Zheng, Gocke, Eshleman, Belchis, Illei, and Lin, Ms Haley, Mr Fryer, and Ms Beierl) and Oncology (Drs Gocke and Eshleman), Johns Hopkins University School of Medicine, Baltimore, Maryland; and the Division of Hematology and Bone Marrow Transplantation, Hospital-University of Udine, Udine, Italy (Dr De Marchi)
| | - Junaid Ibrahim
- From the Departments of Pathology (Drs De Marchi, Ibrahim, Zheng, Gocke, Eshleman, Belchis, Illei, and Lin, Ms Haley, Mr Fryer, and Ms Beierl) and Oncology (Drs Gocke and Eshleman), Johns Hopkins University School of Medicine, Baltimore, Maryland; and the Division of Hematology and Bone Marrow Transplantation, Hospital-University of Udine, Udine, Italy (Dr De Marchi)
| | - Katie Beierl
- From the Departments of Pathology (Drs De Marchi, Ibrahim, Zheng, Gocke, Eshleman, Belchis, Illei, and Lin, Ms Haley, Mr Fryer, and Ms Beierl) and Oncology (Drs Gocke and Eshleman), Johns Hopkins University School of Medicine, Baltimore, Maryland; and the Division of Hematology and Bone Marrow Transplantation, Hospital-University of Udine, Udine, Italy (Dr De Marchi)
| | - Gang Zheng
- From the Departments of Pathology (Drs De Marchi, Ibrahim, Zheng, Gocke, Eshleman, Belchis, Illei, and Lin, Ms Haley, Mr Fryer, and Ms Beierl) and Oncology (Drs Gocke and Eshleman), Johns Hopkins University School of Medicine, Baltimore, Maryland; and the Division of Hematology and Bone Marrow Transplantation, Hospital-University of Udine, Udine, Italy (Dr De Marchi)
| | - Christopher D Gocke
- From the Departments of Pathology (Drs De Marchi, Ibrahim, Zheng, Gocke, Eshleman, Belchis, Illei, and Lin, Ms Haley, Mr Fryer, and Ms Beierl) and Oncology (Drs Gocke and Eshleman), Johns Hopkins University School of Medicine, Baltimore, Maryland; and the Division of Hematology and Bone Marrow Transplantation, Hospital-University of Udine, Udine, Italy (Dr De Marchi)
| | - James R Eshleman
- From the Departments of Pathology (Drs De Marchi, Ibrahim, Zheng, Gocke, Eshleman, Belchis, Illei, and Lin, Ms Haley, Mr Fryer, and Ms Beierl) and Oncology (Drs Gocke and Eshleman), Johns Hopkins University School of Medicine, Baltimore, Maryland; and the Division of Hematology and Bone Marrow Transplantation, Hospital-University of Udine, Udine, Italy (Dr De Marchi)
| | - Deborah Belchis
- From the Departments of Pathology (Drs De Marchi, Ibrahim, Zheng, Gocke, Eshleman, Belchis, Illei, and Lin, Ms Haley, Mr Fryer, and Ms Beierl) and Oncology (Drs Gocke and Eshleman), Johns Hopkins University School of Medicine, Baltimore, Maryland; and the Division of Hematology and Bone Marrow Transplantation, Hospital-University of Udine, Udine, Italy (Dr De Marchi)
| | - Peter Illei
- From the Departments of Pathology (Drs De Marchi, Ibrahim, Zheng, Gocke, Eshleman, Belchis, Illei, and Lin, Ms Haley, Mr Fryer, and Ms Beierl) and Oncology (Drs Gocke and Eshleman), Johns Hopkins University School of Medicine, Baltimore, Maryland; and the Division of Hematology and Bone Marrow Transplantation, Hospital-University of Udine, Udine, Italy (Dr De Marchi)
| | - Ming-Tseh Lin
- From the Departments of Pathology (Drs De Marchi, Ibrahim, Zheng, Gocke, Eshleman, Belchis, Illei, and Lin, Ms Haley, Mr Fryer, and Ms Beierl) and Oncology (Drs Gocke and Eshleman), Johns Hopkins University School of Medicine, Baltimore, Maryland; and the Division of Hematology and Bone Marrow Transplantation, Hospital-University of Udine, Udine, Italy (Dr De Marchi)
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24
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Cross-platform comparison for the detection of RAS mutations in cfDNA (ddPCR Biorad detection assay, BEAMing assay, and NGS strategy). Oncotarget 2018; 9:21122-21131. [PMID: 29765524 PMCID: PMC5940402 DOI: 10.18632/oncotarget.24950] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2017] [Accepted: 02/27/2018] [Indexed: 01/05/2023] Open
Abstract
CfDNA samples from colon (mCRC) and non-small cell lung cancers (NSCLC) (CIRCAN cohort) were compared using three platforms: droplet digital PCR (ddPCR, Biorad); BEAMing/OncoBEAM™-RAS-CRC (Sysmex Inostics); next-generation sequencing (NGS, Illumina), utilizing the 56G oncology panel (Swift Biosciences). Tissue biopsy and time matched cfDNA samples were collected at diagnosis in the mCRC cohort and during 1st progression in the NSCLC cohort. Excellent matches between cfDNA/FFPE mutation profiles were observed. Detection thresholds were between 0.5-1% for cfDNA samples examined using ddPCR and NGS, and 0.03% with BEAMing. This high level of sensitivity enabled the detection of KRAS mutations in 5/19 CRC patients with negative FFPE profiles. In the mCRC cohort, comparison of mutation results obtained by testing FFPE to those obtained by testing cfDNA by ddPCR resulted in 47% sensitivity, 77% specificity, 70% positive predictive value (PPV) and 55% negative predictive value (NPV). For BEAMing, we observed 93% sensitivity, 69% specificity, 78% PPV and 90% NPV. Finally, sensitivity of NGS was 73%, specificity was 77%, PPV 79% and NPV 71%. Our study highlights the complementarity of different diagnostic approaches and variability of results between OncoBEAM™-RAS-CRC and NGS assays. While the NGS assay provided a larger breadth of coverage of the major targetable alterations of 56 genes in one run, its performance for specific alterations was frequently confirmed by ddPCR results.
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25
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Fumagalli C, Vacirca D, Rappa A, Passaro A, Guarize J, Rafaniello Raviele P, de Marinis F, Spaggiari L, Casadio C, Viale G, Barberis M, Guerini-Rocco E. The long tail of molecular alterations in non-small cell lung cancer: a single-institution experience of next-generation sequencing in clinical molecular diagnostics. J Clin Pathol 2018. [PMID: 29535211 DOI: 10.1136/jclinpath-2018-205032] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
BACKGROUND Molecular profiling of advanced non-small cell lung cancers (NSCLC) is essential to identify patients who may benefit from targeted treatments. In the last years, the number of potentially actionable molecular alterations has rapidly increased. Next-generation sequencing allows for the analysis of multiple genes simultaneously. AIMS To evaluate the feasibility and the throughput of next-generation sequencing in clinical molecular diagnostics of advanced NSCLC. METHODS A single-institution cohort of 535 non-squamous NSCLC was profiled using a next-generation sequencing panel targeting 22 actionable and cancer-related genes. RESULTS 441 non-squamous NSCLC (82.4%) harboured at least one gene alteration, including 340 cases (63.6%) with clinically relevant molecular aberrations. Mutations have been detected in all but one gene (FGFR1) of the panel. Recurrent alterations were observed in KRAS, TP53, EGFR, STK11 and MET genes, whereas the remaining genes were mutated in <5% of the cases. Concurrent mutations were detected in 183 tumours (34.2%), mostly impairing KRAS or EGFR in association with TP53 alterations. CONCLUSIONS The study highlights the feasibility of targeted next-generation sequencing in clinical setting. The majority of NSCLC harboured mutations in clinically relevant genes, thus identifying patients who might benefit from different targeted therapies.
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Affiliation(s)
- Caterina Fumagalli
- Division of Pathology and Laboratory Medicine, European Institute of Oncology, Milan, Italy
| | - Davide Vacirca
- Division of Pathology and Laboratory Medicine, European Institute of Oncology, Milan, Italy
| | - Alessandra Rappa
- Division of Pathology and Laboratory Medicine, European Institute of Oncology, Milan, Italy
| | - Antonio Passaro
- Division of Thoracic Oncology, European Institute of Oncology, Milan, Italy
| | - Juliana Guarize
- Division of Thoracic Surgery, European Institute of Oncology, Milan, Italy
| | | | - Filippo de Marinis
- Division of Thoracic Oncology, European Institute of Oncology, Milan, Italy
| | - Lorenzo Spaggiari
- Division of Thoracic Surgery, European Institute of Oncology, Milan, Italy.,Department of Oncology and Hemato-Oncology, University of Milan, Milan, Italy
| | - Chiara Casadio
- Division of Pathology and Laboratory Medicine, European Institute of Oncology, Milan, Italy
| | - Giuseppe Viale
- Division of Pathology and Laboratory Medicine, European Institute of Oncology, Milan, Italy.,Department of Oncology and Hemato-Oncology, University of Milan, Milan, Italy
| | - Massimo Barberis
- Division of Pathology and Laboratory Medicine, European Institute of Oncology, Milan, Italy
| | - Elena Guerini-Rocco
- Division of Pathology and Laboratory Medicine, European Institute of Oncology, Milan, Italy.,Department of Oncology and Hemato-Oncology, University of Milan, Milan, Italy
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26
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Fumagalli C, Casadio C, Barberis M, Guarize J, Guerini-Rocco E. Letter to the Editor. Clin Lung Cancer 2018; 19:e439-e440. [PMID: 29606366 DOI: 10.1016/j.cllc.2018.03.001] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2018] [Accepted: 03/04/2018] [Indexed: 11/17/2022]
Affiliation(s)
- Caterina Fumagalli
- Division of Pathology and Laboratory Medicine, Istituto Europeo di Oncologia, Milan, Italy
| | - Chiara Casadio
- Division of Pathology and Laboratory Medicine, Istituto Europeo di Oncologia, Milan, Italy
| | - Massimo Barberis
- Division of Pathology and Laboratory Medicine, Istituto Europeo di Oncologia, Milan, Italy.
| | - Juliana Guarize
- Division of Thoracic Surgery, Istituto Europeo di Oncologia, Milan, Italy
| | - Elena Guerini-Rocco
- Division of Pathology and Laboratory Medicine, Istituto Europeo di Oncologia, Milan, Italy; Department of Oncology and Hemato-Oncology, University of Milan, Milan, Italy
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27
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Long-term progression-free survival in an advanced lung adenocarcinoma patient harboring EZR-ROS1 rearrangement: a case report. BMC Pulm Med 2018; 18:13. [PMID: 29361925 PMCID: PMC5781300 DOI: 10.1186/s12890-018-0585-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2017] [Accepted: 01/15/2018] [Indexed: 01/06/2023] Open
Abstract
Background Crizotinib is recommended as first-line therapy in ROS1-driven lung adenocarcinoma. However, the optimal first-line therapy for this subgroup of lung cancer is controversial according to the available clinical data. Case presentation Here, we describe a 57-year-old man who was diagnosed with stage IIIB lung adenocarcinoma and EGFR/KRAS/ALK-negative tumors. The patient received six cycles of pemetrexed plus cisplatin as first-line therapy and then pemetrexed as maintenance treatment, with a progression-free survival (PFS) of 42 months. The patient relapsed and underwent re-biopsy. EZR-ROS1 fusion mutation was detected by next-generation sequencing (NGS). The patient was prescribed crizotinib as second-line therapy and achieved a PFS of 6 months. After disease progression, lorlatinib was administered as third-line therapy, with a favorable response. Conclusions Prolonged PFS in patients receiving pemetrexed chemotherapy might be related to the EZR-ROS1 fusion mutation. Lorlatinib is an optimal choice in patients showing crizotinib resistance.
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