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Hu L, Ji YY, Zhu P, Lu RQ. Mutation-Selected Amplification droplet digital PCR: A new single nucleotide variant detection assay for TP53 R249S mutant in tumor and plasma samples. Anal Chim Acta 2024; 1318:342929. [PMID: 39067934 DOI: 10.1016/j.aca.2024.342929] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2024] [Revised: 06/21/2024] [Accepted: 06/30/2024] [Indexed: 07/30/2024]
Abstract
The early detection of gene mutations in physiological and pathological processes is a powerful approach to guide decisions in precision medicine. However, detecting low-copy mutant DNA from clinical samples poses a challenge due to the enrichment of wild-type DNA backgrounds. In this study, we devised a novel strategy, named Mutation-Selected Amplification droplet digital PCR (MSA-ddPCR), to quantitatively analyze single nucleotide variants (SNVs) at low variant allele frequencies (VAFs). Using TP53R249S (a hotspot mutation associated with hepatocellular carcinoma) as a model, we optimized the concentration ratio of primers, the annealing temperature and nucleic acid amplification modifiers. Subsequently, we evaluated the linear range and precision of MSA-ddPCR by detecting TP53R249S and TP53wild-type (TP53WT) plasmid DNA, respectively. MSA-ddPCR demonstrated superior ability to discriminate between mutant DNA and wild-type DNA compared to traditional TaqMan-MGB PCR. We further applied MSA-ddPCR to analyze the TP53R249S mutation in 20 plasma samples and 15 formalin-fixed paraffin-embedded (FFPE) tissue samples, and assessed the agreement rates between MSA-ddPCR and amplicon high-throughput sequencing. The results showed that the limit of blanks of MSA-ddPCR are 0.449 copies μL-1 in the FAM channel and 0.452 copies μL-1 in the VIC channel. MSA-ddPCR could accurately quantify VAFs as low as 0.01 %, surpassing existing PCR and next-generation sequencing (NGS) methods. In the detection of clinical samples, a high correlation was found between MSA-ddPCR and amplicon high-throughput sequencing. Additionally, MSA-ddPCR outperformed sequencing methods in terms of detection time and simplicity of data analysis. MSA-ddPCR can be easily implemented into clinical practice and serve as a robust tool for detecting mutant genes due to its high sensitivity and accuracy.
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Affiliation(s)
- Ling Hu
- Department of Clinical Laboratory, Fudan University Shanghai Cancer Center, Department of Oncology, Shanghai Medical School, Fudan University, Shanghai, 20032, China
| | - Yuan-Ye Ji
- Department of Medical Laboratory, Ningbo No.2 Hospital, Ningbo, 315010, China
| | - Peng Zhu
- Department of Medical Laboratory, Ningbo No.2 Hospital, Ningbo, 315010, China; Ningbo Institute of Life and Health Industry, University of Chinese Academy of Sciences, Ningbo, 315010, China.
| | - Ren-Quan Lu
- Department of Clinical Laboratory, Fudan University Shanghai Cancer Center, Department of Oncology, Shanghai Medical School, Fudan University, Shanghai, 20032, China.
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Ntzifa A, Marras T, Georgoulias V, Lianidou E. Liquid biopsy for the management of NSCLC patients under osimertinib treatment. Crit Rev Clin Lab Sci 2024; 61:347-369. [PMID: 38305080 DOI: 10.1080/10408363.2024.2302116] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2023] [Revised: 10/23/2023] [Accepted: 01/02/2024] [Indexed: 02/03/2024]
Abstract
Therapeutic management of NSCLC patients is quite challenging as they are mainly diagnosed at a late stage of disease, and they present a high heterogeneous molecular profile. Osimertinib changed the paradigm shift in treatment of EGFR mutant NSCLC patients achieving significantly better clinical outcomes. To date, osimertinib is successfully administered not only as first- or second-line treatment, but also as adjuvant treatment while its efficacy is currently investigated during neoadjuvant treatment or in stage III, unresectable EGFR mutant NSCLC patients. However, resistance to osimertinib may occur due to clonal evolution, under the pressure of the targeted therapy. The utilization of liquid biopsy as a minimally invasive tool provides insight into molecular heterogeneity of tumor clonal evolution and potent resistance mechanisms which may help to develop more suitable therapeutic approaches. Longitudinal monitoring of NSCLC patients through ctDNA or CTC analysis could reveal valuable information about clinical outcomes during osimertinib treatment. Therefore, several guidelines suggest that liquid biopsy in addition to tissue biopsy should be considered as a standard of care in the advanced NSCLC setting. This practice could significantly increase the number of NSCLC patients that will eventually benefit from targeted therapies, such as EGFR TKIs.
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Affiliation(s)
- Aliki Ntzifa
- Analysis of Circulating Tumor Cells Lab, Lab of Analytical Chemistry, Department of Chemistry, National and Kapodistrian University of Athens, Athens, Greece
| | - Theodoros Marras
- Analysis of Circulating Tumor Cells Lab, Lab of Analytical Chemistry, Department of Chemistry, National and Kapodistrian University of Athens, Athens, Greece
| | - Vasilis Georgoulias
- First Department of Medical Oncology, Metropolitan General Hospital of Athens, Cholargos, Greece
| | - Evi Lianidou
- Analysis of Circulating Tumor Cells Lab, Lab of Analytical Chemistry, Department of Chemistry, National and Kapodistrian University of Athens, Athens, Greece
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3
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Küçükosmanoglu A, van der Borden CL, de Boer LEA, Verhaak R, Noske D, Wurdinger T, Radonic T, Westerman BA. Oncogenic composite mutations can be predicted by co-mutations and their chromosomal location. Mol Oncol 2024. [PMID: 38757376 DOI: 10.1002/1878-0261.13636] [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: 12/14/2022] [Revised: 06/23/2023] [Accepted: 03/12/2024] [Indexed: 05/18/2024] Open
Abstract
Genetic heterogeneity in tumors can show a remarkable selectivity when two or more independent genetic events occur in the same gene. This phenomenon, called composite mutation, points toward a selective pressure, which frequently causes therapy resistance to mutation-specific drugs. Since composite mutations have been described to occur in sub-clonal populations, they are not always captured through biopsy sampling. Here, we provide a proof of concept to predict composite mutations to anticipate which patients might be at risk for sub-clonally driven therapy resistance. We found that composite mutations occur in 5% of cancer patients, mostly affecting the PIK3CA, EGFR, BRAF, and KRAS genes, which are common precision medicine targets. Furthermore, we found a strong and significant relationship between the frequencies of composite mutations with commonly co-occurring mutations in a non-composite context. We also found that co-mutations are significantly enriched on the same chromosome. These observations were independently confirmed using cell line data. Finally, we show the feasibility of predicting compositive mutations based on their co-mutations (AUC 0.62, 0.81, 0.82, and 0.91 for EGFR, PIK3CA, KRAS, and BRAF, respectively). This prediction model could help to stratify patients who are at risk of developing therapy resistance-causing mutations.
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Affiliation(s)
- Asli Küçükosmanoglu
- Department of Neurosurgery, Brain Tumor Center Amsterdam, Amsterdam University Medical Center, Cancer Center Amsterdam, The Netherlands
| | - Carolien L van der Borden
- Department of Neurosurgery, Brain Tumor Center Amsterdam, Amsterdam University Medical Center, Cancer Center Amsterdam, The Netherlands
| | - Lisanne E A de Boer
- Department of Neurosurgery, Brain Tumor Center Amsterdam, Amsterdam University Medical Center, Cancer Center Amsterdam, The Netherlands
| | - Roel Verhaak
- Department of Neurosurgery, Brain Tumor Center Amsterdam, Amsterdam University Medical Center, Cancer Center Amsterdam, The Netherlands
- Department of Computational Biology, The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
| | - David Noske
- Department of Neurosurgery, Brain Tumor Center Amsterdam, Amsterdam University Medical Center, Cancer Center Amsterdam, The Netherlands
| | - Tom Wurdinger
- Department of Neurosurgery, Brain Tumor Center Amsterdam, Amsterdam University Medical Center, Cancer Center Amsterdam, The Netherlands
| | - Teodora Radonic
- Department of Pathology, Amsterdam University Medical Center, Cancer Center Amsterdam, The Netherlands
| | - Bart A Westerman
- Department of Neurosurgery, Brain Tumor Center Amsterdam, Amsterdam University Medical Center, Cancer Center Amsterdam, The Netherlands
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Masuda T, Miura S, Sato Y, Tachihara M, Bessho A, Nakamura A, Miyawaki T, Yoshimine K, Mori M, Shiraishi H, Hamai K, Haratani K, Maeda S, Tabata E, Kitagawa C, Tanizaki J, Imai T, Nogami S, Yamamoto N, Nakagawa K, Hattori N. Significance of micro-EGFR T790M mutations on EGFR-tyrosine kinase inhibitor efficacy in non-small cell lung cancer. Sci Rep 2023; 13:19729. [PMID: 37957228 PMCID: PMC10643699 DOI: 10.1038/s41598-023-45337-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2023] [Accepted: 10/18/2023] [Indexed: 11/15/2023] Open
Abstract
Small amounts of epidermal growth factor receptor (EGFR) T790M mutation (micro-T790M), which is detected using droplet digital PCR (ddPCR) but not conventional PCR, in formalin-fixed and paraffin-embedded (FFPE) samples have been investigated as a predictive factor for the efficacy of EGFR-tyrosine kinase inhibitors (TKIs). However, the predictive value of micro-T790M remains controversial, possibly owing to the failure to examine artificial T790M in FFPE specimens. Therefore, we examined the predictive value of micro-T790M in first-generation (1G), second-generation (2G), and third-generation (3G) EGFR-TKI efficacy using a new method to exclude FFPE-derived artificial mutations in our retrospective cohort. The primary objective was time to treatment failure (TTF) of 1G, 2G, and 3G EGFR-TKIs according to micro-T790M status. In total, 315 patients with EGFR-positive non-small cell lung cancer treated with 1G, 2G, and 3G EGFR-TKIs were included in this study. The proportion of patients positive for micro-T790M in the 1G, 2G, and 3G EGFR-TKI groups was 48.2%, 47.1%, and 47.6%, respectively. In the micro-T790M-positive group, the TTF was significantly longer in the 2G and 3G EGFR-TKI groups than in the 1G TKI group. No differences in the micro-T790M-negative group were observed. Micro-T790M status detected using ddPCR, eliminating false positives, may be a valuable predictor of EGFR-TKI efficacy.
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Affiliation(s)
- Takeshi Masuda
- Department of Respiratory Medicine, Hiroshima University Hospital, Hiroshima, 734-8551, Japan
| | - Satoru Miura
- Department of Internal Medicine, Niigata Cancer Center Hospital, 2-15-3 Kawagishi-cho, Niigata, 951-8566, Japan.
| | - Yuki Sato
- Department of Respiratory Medicine, Kobe City Medical Center General Hospital, Kobe, 650-0047, Japan
| | - Motoko Tachihara
- Division of Respiratory Medicine, Department of Internal Medicine, Kobe University Graduate School of Medicine, Kobe, 650-0017, Japan
| | - Akihiro Bessho
- Department of Respiratory Medicine, Japanese Red Cross Okayama Hospital, Okayama, 700-8607, Japan
| | - Atsushi Nakamura
- Department of Pulmonary Medicine, Sendai Kousei Hospital, Sendai, 980-0873, Japan
| | - Taichi Miyawaki
- Division of Thoracic Oncology, Shizuoka Cancer Center, Shunto-gun, 411-8777, Japan
| | - Kohei Yoshimine
- Department of Respiratory Medicine, Iizuka Hospital, Iizuka, 820-8505, Japan
| | - Masahide Mori
- Department of Thoracic Oncology, National Hospital Organization, Osaka Toneyama Medical Center, Toyonaka, 560-8552, Japan
| | - Hideaki Shiraishi
- Department of Respiratory Medicine, Mitsui Memorial Hospital, Tokyo, 101-8643, Japan
| | - Kosuke Hamai
- Department of Respiratory Medicine, Hiroshima Prefectural Hospital, Hiroshima, 734-8530, Japan
| | - Koji Haratani
- Department of Medical Oncology, Kindai University Faculty of Medicine, Osakasayama, 589-8511, Japan
| | - Sumiko Maeda
- Department of General Thoracic Surgery, Dokkyo Medical University, Shimotsuga-gun, 321-0293, Japan
| | - Eriko Tabata
- Department of Respiratory Medicine, Ikeda City Hospital, Ikeda, 563-8510, Japan
| | - Chiyoe Kitagawa
- Department of Respiratory Medicine and Medical Oncology, National Hospital Organization Nagoya Medical Center, Nagoya, 460-0001, Japan
| | - Junko Tanizaki
- Department of Medical Oncology, Kishiwada City Hospital, Kishiwada, 596-8501, Japan
| | - Takumi Imai
- Department of Medical Statistics, Osaka Metropolitan University Graduate School of Medicine, Osaka, 558-8585, Japan
| | - Shohei Nogami
- Department of Genome Analysis, LSI Medience Corporation, Tokyo, 174-8555, Japan
| | - Nobuyuki Yamamoto
- Department of Internal Medicine III, Wakayama Medical University, Wakayama, 641-8509, Japan
| | - Kazuhiko Nakagawa
- Department of Medical Oncology, Kindai University Faculty of Medicine, Osakasayama, 589-8511, Japan
| | - Noboru Hattori
- Department of Respiratory Medicine, Hiroshima University Hospital, Hiroshima, 734-8551, Japan
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Chougule A, Chandrani P, Noronha V, Pange P, Kale S, Nikam A, Nambiar K, Marchande D, Durve A, Gupta V, Jagtap V, Tiwrekar P, Menon N, Joshi A, Kaushal R, Pai T, Patil VM, Dutt A, Banavali SD, Prabhash K. Real-World Evidence of EGFR Targeted Therapy in NSCLC- A Brief Report of Decade Long Single Center Experience. JTO Clin Res Rep 2023; 4:100566. [PMID: 38033811 PMCID: PMC10682910 DOI: 10.1016/j.jtocrr.2023.100566] [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: 01/06/2023] [Revised: 08/10/2023] [Accepted: 08/20/2023] [Indexed: 12/02/2023] Open
Abstract
The significance of EGFR targeted therapy in the lung adenocarcinoma is paramount. Several controlled clinical trials have reported considerable survival of EGFR mutation positive patients on receiving the EGFR tyrosine kinase inhibitor (TKI). However, the real-world evidence of benefits of EGFR TKI would be further useful to understand how the designated therapeutic regimen benefits the patients. In this study, we report a decade long real-world evidence of EGFR molecular testing in lung cancer at Tata Memorial Hospital (Mumbai, India). Laboratory and hospital records containing basic demographic details, clinical characteristics, treatment regimen, survival outcome were collected retrospectively. Statistical association and survival analysis were performed using the R programming. The cohort includes 9,053 lung cancer patients tested for EGFR mutations during 2011 to 2019. Baseline T790M and compound mutations were the only mutations observed co-occurring while all other EGFR mutations were mutually exclusive. Furthermore, the baseline T790M were also observed to be associated with TTF1 positivity, smoking and local metastasis. Overall survival of the patients harboring co-occurring compound mutations was significantly lesser than the other EGFR positive patients. Overall, our study suggests that EGFR TKI may provide real-world benefit to the lung cancer patients harboring mutually exclusive EGFR mutations. On the other hand, further systematic study is essential to develop better therapeutic regimen for co-occurring baseline EGFR T790M and other compound mutations.
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Affiliation(s)
- Anuradha Chougule
- Medical Oncology Molecular Laboratory, Tata Memorial Centre, Mumbai, India
| | - Pratik Chandrani
- Medical Oncology Molecular Laboratory, Tata Memorial Centre, Mumbai, India
- Homi Bhabha National Institute, Training School Complex, Mumbai, India
- Centre for Computational Biology, Bioinformatics and Crosstalk Laboratory, ACTREC, Tata Memorial Centre, Navi Mumbai, India
| | - Vanita Noronha
- Homi Bhabha National Institute, Training School Complex, Mumbai, India
- Department of Medical Oncology, Tata Memorial Centre, Mumbai, India
| | - Priyanka Pange
- Medical Oncology Molecular Laboratory, Tata Memorial Centre, Mumbai, India
| | - Shrutikaa Kale
- Medical Oncology Molecular Laboratory, Tata Memorial Centre, Mumbai, India
| | - Ankita Nikam
- Medical Oncology Molecular Laboratory, Tata Memorial Centre, Mumbai, India
| | - Kavya Nambiar
- Medical Oncology Molecular Laboratory, Tata Memorial Centre, Mumbai, India
| | - Dipika Marchande
- Medical Oncology Molecular Laboratory, Tata Memorial Centre, Mumbai, India
| | - Arpana Durve
- Medical Oncology Molecular Laboratory, Tata Memorial Centre, Mumbai, India
| | - Vinod Gupta
- Medical Oncology Molecular Laboratory, Tata Memorial Centre, Mumbai, India
| | - Vinita Jagtap
- Medical Oncology Molecular Laboratory, Tata Memorial Centre, Mumbai, India
| | - Priyanka Tiwrekar
- Medical Oncology Molecular Laboratory, Tata Memorial Centre, Mumbai, India
| | - Nandini Menon
- Homi Bhabha National Institute, Training School Complex, Mumbai, India
- Department of Medical Oncology, Tata Memorial Centre, Mumbai, India
| | - Amit Joshi
- Homi Bhabha National Institute, Training School Complex, Mumbai, India
- Department of Medical Oncology, Tata Memorial Centre, Mumbai, India
| | - Rajeev Kaushal
- Homi Bhabha National Institute, Training School Complex, Mumbai, India
- Department of Pathology, Tata Memorial Centre, Mumbai, India
| | - Trupti Pai
- Homi Bhabha National Institute, Training School Complex, Mumbai, India
- Department of Pathology, Tata Memorial Centre, Mumbai, India
| | - Vijay Maruti Patil
- Homi Bhabha National Institute, Training School Complex, Mumbai, India
- Department of Medical Oncology, Tata Memorial Centre, Mumbai, India
| | - Amit Dutt
- Homi Bhabha National Institute, Training School Complex, Mumbai, India
- Integrated Genomics Laboratory, Advanced Centre for Treatment, Research and Education in Cancer, Tata Memorial Centre, Navi Mumbai, India
| | - Shripad Dinanath Banavali
- Homi Bhabha National Institute, Training School Complex, Mumbai, India
- Department of Medical Oncology, Tata Memorial Centre, Mumbai, India
| | - Kumar Prabhash
- Homi Bhabha National Institute, Training School Complex, Mumbai, India
- Department of Medical Oncology, Tata Memorial Centre, Mumbai, India
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Rare mutation-dominant compound EGFR-positive NSCLC is associated with enriched kinase domain-resided variants of uncertain significance and poor clinical outcomes. BMC Med 2023; 21:73. [PMID: 36829178 PMCID: PMC9960474 DOI: 10.1186/s12916-023-02768-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/14/2022] [Accepted: 02/02/2023] [Indexed: 02/26/2023] Open
Abstract
BACKGROUND Compound epidermal growth factor receptor (EGFR) mutations are less responsive to tyrosine kinase inhibitors (TKIs) than single EGFR mutations in non-small cell lung cancer (NSCLC). However, the detailed clinical characteristics and prognosis of various compound EGFR mutations remain to be elucidated. METHODS We retrospectively studied the next-generation sequencing (NGS) data of treatment-naïve tumors from 1025 NSCLC patients with compound EGFR mutations, which were sub-categorized into different combinations of common mutations (19-Del and EGFR exon 21 p.L858R), rare mutations, and variants of uncertain significance (VUSs). Prognosis and drug resistance to first-line TKIs were analyzed in 174 and 95 patients, respectively. RESULTS Compound EGFR mutations were enriched with EGFR exon 21 p.L858R and rare mutations, but not 19-Del (P < 0.001). The common + rare and rare + rare subtypes had fewer concurrent mutations in the PI3K pathway (P = 0.032), while the rare + rare and common + VUSs subtypes showed increased association with smoking- and temozolomide-related mutational signatures, respectively (P < 0.001). The rare mutation-dominant subtypes (rare + VUSs and rare + rare) had the worst clinical outcomes to first-line TKIs (P < 0.001), which was further confirmed using an external cohort (P = 0.0066). VUSs in the rare + VUSs subtype selectively reside in the EGFR kinase domain (P < 0.001), implying these tumors might select additional mutations to disrupt the regulation/function of the kinase domain. CONCLUSIONS Different subtypes of compound EGFR mutations displayed distinct clinical features and genetic architectures, and rare mutation-dominant compound EGFR mutations were associated with enriched kinase domain-resided VUSs and poor clinical outcomes. Our findings help better understand the oncogenesis of compound EGFR mutations and forecast prognostic outcomes of personalized treatments.
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Faisal Hamdi AI, How SH, Islam MK, Lim JCW, Stanslas J. Adaptive therapy to circumvent drug resistance to tyrosine kinase inhibitors in cancer: is it clinically relevant? Expert Rev Anticancer Ther 2022; 22:1309-1323. [PMID: 36376248 DOI: 10.1080/14737140.2022.2147671] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
INTRODUCTION Cancer is highly adaptable and is constantly evolving against current targeted therapies such as tyrosine kinase inhibitors. Despite advances in recent decades, the emergence of drug resistance to tyrosine kinase inhibitors constantly hampers therapeutic efficacy of cancer treatment. Continuous therapy versus intermittent clinical regimen has been a debate in drug administration of cancer patients. An ecologically-inspired shift in cancer treatment known as 'adaptive therapy' intends to improve the drug administration of drugs to cancer patients that can delay emergence of drug resistance. AREAS COVERED We discuss improved understanding of the concept of drug resistance, the basis of continuous therapy, intermittent clinical regimens, and adaptive therapy will be reviewed. In addition, we discuss how adaptive therapy provides guidance for future cancer treatment. EXPERT OPINION The current understanding of drug resistance in cancer leads to poor prognosis and limited treatment options in patients. Fighting drug resistance mutants is constantly followed by new forms of resistance. In most reported cases, continuous therapy leads to drug resistance and an intermittent clinical regimen vaguely delays it. However, adaptive therapy, conceptually, exploits multiple parameters that can suppress the growth of drug resistance and provides safe treatment for cancer patients in the future.
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Affiliation(s)
- Amir Imran Faisal Hamdi
- Pharmacotherapeutics Unit, Department of Medicine, Universiti Putra MalaysiaMedicine, 43400, Serdang, Malaysia
| | - Soon Hin How
- Kuliyyah of Medicine, International Islamic University Malaysia, Kuantan Campus, Kuliyyah of Medicine, 25200, Kuantan, Malaysia
| | | | - Jonathan Chee Woei Lim
- Pharmacotherapeutics Unit, Department of Medicine, Universiti Putra MalaysiaMedicine, 43400, Serdang, Malaysia
| | - Johnson Stanslas
- Pharmacotherapeutics Unit, Department of Medicine, Universiti Putra MalaysiaMedicine, 43400, Serdang, Malaysia
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EGFR T751_I759delinsN Mutation in Exon19 Detected by NGS but Not by Real-Time PCR in a Heavily-Treated Patient with NSCLC. Int J Mol Sci 2022; 23:ijms232113451. [PMID: 36362239 PMCID: PMC9654563 DOI: 10.3390/ijms232113451] [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: 09/27/2022] [Revised: 11/01/2022] [Accepted: 11/02/2022] [Indexed: 11/06/2022] Open
Abstract
The detection of driver gene mutations can determine appropriate treatment strategies for non-small cell lung cancer (NSCLC) by identifying the presence of an effective druggable target. Mutations in the gene encoding the epidermal growth factor receptor (EGFR) are common driver mutations in NSCLC that can be effectively targeted by the use of EGFR tyrosine kinase inhibitors (EGFR-TKIs). However, without the detection of driver mutations, appropriate therapeutic decisions cannot be made. The most commonly applied methods for detecting driver gene mutations are assays based on polymerase chain reaction (PCR). However, the underlying mechanism of PCR-based assays limits the detection of rare mutations. Therefore, patients harboring rare mutations may not receive optimal treatment. We report a heavily-treated patient with NSCLC who harbored a T751_I759delinsN mutation in exon 19 of EGFR that was not detected by real-time PCR but was successfully detected by next-generation sequencing (NGS). The detection of a driver mutation using NGS resulted in the administration of targeted therapy, leading to favorable progression-free survival for the patient. Our report highlights the importance and potential of routine NGS testing among NSCLC patients for whom traditional assays fail to detect driver mutations when determining treatment options.
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Guo Q, Wang L, Liang X, Zhao M, Huang X, Xu W, Lou J, Qiao L. Comparative analysis of QS3D versus droplet digital PCR for quantitative measures of EGFR T790M mutation from identical plasma. Heliyon 2022; 8:e11339. [PMID: 36387507 PMCID: PMC9647353 DOI: 10.1016/j.heliyon.2022.e11339] [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] [Received: 12/06/2021] [Revised: 07/07/2022] [Accepted: 10/25/2022] [Indexed: 11/09/2022] Open
Abstract
Objectives The capacity of QuantStudio™ 3D (QS3D) and droplet digital PCR (dPCR) for the detection of plasma Epidermal Growth Factor Receptor (EGFR) mutations have been widely reported. Few comparative studies on the quantitative test of the identical DNA material, however, are carried out. Here we compared the performance of the two methods in detecting EGFR T790M mutation in cell-free DNA (cfDNA) from the same lung cancer patients. Methods We recruited 72 non-small cell lung cancer (NSCLC) patients who initially respond to tyrosine kinase inhibitor treatment but subsequently developed resistance. Two tubes of 10mL anticoagulant blood were collected and cfDNA was isolated from plasma. Identical cfDNA samples were analyzed for T790M mutation using QS3D and droplet dPCR in parallel. Results T790M mutation was detected in 15 and 21 cfDNA samples by QS3D and droplet digital PCR, respectively. The 6 discordant samples showed low mutation abundance (∼0.1%) and the discrepancy is caused by the stricter threshold settings for QS3D dPCR. The overall agreement between the two methods was 91.7% (66/72). The median allele frequencies for QS3D dPCR and droplet dPCR to detect T790M mutation was 2.01% and 2.62%, respectively. There was no significance in mutation abundance detected by both methods. Both methods are highly correlated with allele frequencies and copy numbers in T790M wild type and mutant, with R2 of 0.98, 0.92 and 0.95, respectively. Conclusion Our study demonstrated that QS3D dPCR are highly consistent with droplet PCR for quantitative determination of EGFR T790M mutation in plasma cfDNA.
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Simarro J, Pérez-Simó G, Mancheño N, Ansotegui E, Muñoz-Núñez CF, Gómez-Codina J, Juan Ó, Palanca S. Technical Validation and Clinical Implications of Ultrasensitive PCR Approaches for EGFR-Thr790Met Mutation Detection in Pretreatment FFPE Samples and in Liquid Biopsies from Non-Small Cell Lung Cancer Patients. Int J Mol Sci 2022; 23:ijms23158526. [PMID: 35955661 PMCID: PMC9369170 DOI: 10.3390/ijms23158526] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Revised: 07/29/2022] [Accepted: 07/30/2022] [Indexed: 02/04/2023] Open
Abstract
In pretreatment tumor samples of EGFR-mutated non-small cell lung cancer (NSCLC) patients, EGFR-Thr790Met mutation has been detected in a variable prevalence by different ultrasensitive assays with controversial prognostic value. Furthermore, its detection in liquid biopsy (LB) samples remains challenging, being hampered by the shortage of circulating tumor DNA (ctDNA). Here, we describe the technical validation and clinical implications of a real-time PCR with peptide nucleic acid (PNA-Clamp) and digital droplet PCR (ddPCR) for EGFR-Thr790Met detection in diagnosis FFPE samples and in LB. Limit of blank (LOB) and limit of detection (LOD) were established by analyzing negative and low variant allele frequency (VAF) FFPE and LB specimens. In a cohort of 78 FFPE samples, both techniques showed an overall agreement (OA) of 94.20%. EGFR-Thr790Met was detected in 26.47% of cases and was associated with better progression-free survival (PFS) (16.83 ± 7.76 vs. 11.47 ± 1.83 months; p = 0.047). In LB, ddPCR was implemented in routine diagnostics under UNE-EN ISO 15189:2013 accreditation, increasing the detection rate of 32.43% by conventional methods up to 45.95%. During follow-up, ddPCR detected EGFR-Thr790Met up to 7 months before radiological progression. Extensively validated ultrasensitive assays might decipher the utility of pretreatment EGFR-Thr790Met and improve its detection rate in LB studies, even anticipating radiological progression.
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Affiliation(s)
- Javier Simarro
- Molecular Biology Unit, Service of Clinical Analysis, Hospital Universitario y Politécnico La Fe, 46026 Valencia, Spain; (J.S.); (G.P.-S.)
- Clinical and Translational Cancer Research Group, Instituto de Investigación Sanitaria La Fe (IIS La Fe), 46026 Valencia, Spain
| | - Gema Pérez-Simó
- Molecular Biology Unit, Service of Clinical Analysis, Hospital Universitario y Politécnico La Fe, 46026 Valencia, Spain; (J.S.); (G.P.-S.)
- Clinical and Translational Cancer Research Group, Instituto de Investigación Sanitaria La Fe (IIS La Fe), 46026 Valencia, Spain
| | - Nuria Mancheño
- Pathology Department, Hospital Universitario y Politécnico La Fe, 46026 Valencia, Spain;
| | - Emilio Ansotegui
- Pulmonology Department, Hospital Universitario y Politécnico La Fe, 46026 Valencia, Spain;
| | | | - José Gómez-Codina
- Medical Oncology Department, Hospital Universitario y Politécnico La Fe, 46026 Valencia, Spain; (J.G.-C.); (Ó.J.)
| | - Óscar Juan
- Medical Oncology Department, Hospital Universitario y Politécnico La Fe, 46026 Valencia, Spain; (J.G.-C.); (Ó.J.)
| | - Sarai Palanca
- Molecular Biology Unit, Service of Clinical Analysis, Hospital Universitario y Politécnico La Fe, 46026 Valencia, Spain; (J.S.); (G.P.-S.)
- Clinical and Translational Cancer Research Group, Instituto de Investigación Sanitaria La Fe (IIS La Fe), 46026 Valencia, Spain
- Biochemistry and Molecular Biology Department, Universidad de Valencia, 46010 Valencia, Spain
- Correspondence: ; Tel.: +34-961-244586
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11
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The Presence of EGFR T790M in TKI-Naïve Lung Cancer Samples of Patients Who Developed a T790M-Positive Relapse on First or Second Generation TKI Is Rare. Cancers (Basel) 2022; 14:cancers14143511. [PMID: 35884570 PMCID: PMC9320221 DOI: 10.3390/cancers14143511] [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: 05/30/2022] [Revised: 07/14/2022] [Accepted: 07/16/2022] [Indexed: 02/05/2023] Open
Abstract
EGFR-mutated non-small cell lung cancer (NSCLC) patients can be effectively treated with tyrosine kinase inhibitors (TKI) but frequently present with an EGFR T790M resistance mutation at relapse. We aimed to screen for T790M in pre-treatment formalin-fixed and paraffin-embedded (FFPE) tissue samples of patients with a confirmed T790M mutation at progression. We analyzed 33 pre-treatment DNA samples of NSCLC patients who progressed upon TKI between 2013 to 2019. To establish storage-time dependent formalin fixation-induced background levels for C>T mutations, we analyzed DNA isolated from archival (stored >1 year, n = 22) and recently generated (stored <1 month, n = 11) FFPE samples and included DNA isolated from white blood cells (WBC) (n = 24) as controls. DNA samples were analyzed by droplet digital (dd)PCR, and positivity was defined by outlier detection according to Grubb’s criterion. The T790M background allele frequency levels were 0.160% in DNA isolated from archival-FFPE, 0.100% in fresh FFPE, and 0.035% in WBC. Progression-free survival (PFS) time of the single T790M positive patient was 9 months, while T790M negative patients had a median PFS of 10 months (range 2−27). Proper storage time matched FFPE control samples are essential for reliable detection of T790M mutation at low VAF. The presence of EGFR T790M mutations in pre-TKI samples is rare, even in patients who progressed with EGFR T790M mutations.
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Alen BO, Estévez-Pérez LS, Hermida-Romero MT, Reguera-Arias A, García-Campelo R, de la Torre-Bravos M, Concha Á. Molecular Targets in Lung Cancer: Study of the Evolution of Biomarkers Associated with Treatment with Tyrosine Kinase Inhibitors—Has NF1 Tumor Suppressor a Key Role in Acquired Resistance? Cancers (Basel) 2022; 14:cancers14143323. [PMID: 35884384 PMCID: PMC9313361 DOI: 10.3390/cancers14143323] [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: 05/25/2022] [Revised: 07/04/2022] [Accepted: 07/05/2022] [Indexed: 02/05/2023] Open
Abstract
Simple Summary Resistance to tyrosine kinase inhibitors in patients with EGFR-mutated non-small cell lung cancer is crucial in the development of the disease. Detecting the mechanisms of this resistance is fundamental in lung cancer research, so we evaluated the presence of EGFR mutations in circulating free DNA in plasma of patients with NSCLC under oncological treatment. We studied the role of EGFR and other driver mutations in their involvement in acquired resistance to treatment with EGFR-TKIs and we analyzed the role of liquid biopsy as a non-invasive diagnostic method. Our results showed that liquid biopsy is a very useful tool monitoring the evolution of the disease and the resistance to TKIs. The detection of other concomitant mutations in driver genes is also key in this regard, so we found that alterations in the NFI tumor suppressor gene could be playing a role in disease progression and resistance to targeted therapies. Abstract The application to clinical practice of liquid biopsy in patients with lung cancer has led to an advance in the diagnosis and monitoring of the disease. Detection of alterations in EGFR genes related to TKI treatment in EGFR-mutated non-small cell lung cancer patients is a routine method in pathology laboratories. The primary objective of this work was to analyze the presence of EGFR mutations in cfDNA of 86 patients with lung cancer undergoing oncological treatment related to response to treatment with TKIs. Secondarily, we evaluated the dynamics of EGFR mutations, the presence of the T790M alteration and its relationship with drug resistance and analyzed by NGS molecular alterations in cfDNA of patients with discordant progression. Our results demonstrate that understanding the mutational status of patients treated with TKIs over time is essential to monitor disease progression. In this context, liquid biopsy is a fundamental key. In addition, it is not only necessary to detect EGFR mutations, but also other concomitant mutations that would be influencing the development of the disease. In this sense, we have discovered that mutations in the NF1 tumor suppressor gene could be exerting an as yet unknown function in lung cancer.
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Affiliation(s)
- Begoña O. Alen
- Department of Anatomical Pathology, University Hospital Complex A Coruña, 15006 A Coruña, Spain; (M.T.H.-R.); (A.R.-A.); (Á.C.)
- Molecular Biology Area, Department of Anatomical Pathology, University Hospital Complex A Coruña, 15006 A Coruña, Spain
- Correspondence: (B.O.A.); (L.S.E.-P.); Tel.: +34-981-178-000 (B.O.A.); +34-981-178-000 (L.S.E.-P.)
| | - Lara S. Estévez-Pérez
- Department of Anatomical Pathology, University Hospital Complex A Coruña, 15006 A Coruña, Spain; (M.T.H.-R.); (A.R.-A.); (Á.C.)
- Molecular Biology Area, Department of Anatomical Pathology, University Hospital Complex A Coruña, 15006 A Coruña, Spain
- Correspondence: (B.O.A.); (L.S.E.-P.); Tel.: +34-981-178-000 (B.O.A.); +34-981-178-000 (L.S.E.-P.)
| | - María Teresa Hermida-Romero
- Department of Anatomical Pathology, University Hospital Complex A Coruña, 15006 A Coruña, Spain; (M.T.H.-R.); (A.R.-A.); (Á.C.)
| | - Ana Reguera-Arias
- Department of Anatomical Pathology, University Hospital Complex A Coruña, 15006 A Coruña, Spain; (M.T.H.-R.); (A.R.-A.); (Á.C.)
| | | | | | - Ángel Concha
- Department of Anatomical Pathology, University Hospital Complex A Coruña, 15006 A Coruña, Spain; (M.T.H.-R.); (A.R.-A.); (Á.C.)
- Molecular Biology Area, Department of Anatomical Pathology, University Hospital Complex A Coruña, 15006 A Coruña, Spain
- Biobank of A Coruña, Instituto de Investigación Biomédica A Coruña (INIBIC), 15006 A Coruña, Spain
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13
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Luan Z, Zhao Y, Wang Y, Ma C, Shi C. ccelerated cycling PCR: A novel tool for rapid, sensitive and specific detection of single-nucleotide mutation within 30 min. METHODS IN MICROBIOLOGY 2022; 199:106527. [PMID: 35753510 DOI: 10.1016/j.mimet.2022.106527] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/10/2022] [Revised: 06/18/2022] [Accepted: 06/21/2022] [Indexed: 11/29/2022]
Abstract
Rapid detection of single-nucleotide mutations (SNMs) has played a vital role for point-of-care testing. We herein first introduced accelerated thermal cycling into conventional allele-specific qPCR (AS-qPCR), named accelerated cycling PCR (AC-PCR) to achieve rapid and sensitive detection of SNM. It could simultaneously detect 10 copies of H. pylori DNA and identify its clarithromycin-resistance genotype within 30 min, and showed 100-fold enhanced specificity than AS-qPCR. Therefore, AC-PCR shows great potential in clinical diagnosis for drug-resistance mutation or genotyping analysis.
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Affiliation(s)
- Zhixian Luan
- Qingdao Nucleic Acid Rapid Testing International Science and Technology Cooperation Base, College of Life Sciences, Department of Pathogenic Biology, School of Basic Medicine, and Department of Clinical Laboratory, The Affiliated Hospital of Qingdao University, Qingdao University, Qingdao, 266071, Shandong, China
| | - Yan Zhao
- Qingdao Nucleic Acid Rapid Testing International Science and Technology Cooperation Base, College of Life Sciences, Department of Pathogenic Biology, School of Basic Medicine, and Department of Clinical Laboratory, The Affiliated Hospital of Qingdao University, Qingdao University, Qingdao, 266071, Shandong, China
| | - Yanling Wang
- Qingdao Nucleic Acid Rapid Testing International Science and Technology Cooperation Base, College of Life Sciences, Department of Pathogenic Biology, School of Basic Medicine, and Department of Clinical Laboratory, The Affiliated Hospital of Qingdao University, Qingdao University, Qingdao, 266071, Shandong, China
| | - Cuiping Ma
- Key Laboratory of Optic-electric Sensing and Analytical Chemistry for Life Science, MOE, Shandong Provincial Key Laboratory of Biochemical Engineering, Qingdao Nucleic Acid Rapid Detection Engineering Research Center, College of Marine Science and Biological Engineering, Qingdao University of Science and Technology, Qingdao 266042, China
| | - Chao Shi
- Qingdao Nucleic Acid Rapid Testing International Science and Technology Cooperation Base, College of Life Sciences, Department of Pathogenic Biology, School of Basic Medicine, and Department of Clinical Laboratory, The Affiliated Hospital of Qingdao University, Qingdao University, Qingdao, 266071, Shandong, China.
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14
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Zhang L, Coffin J, Formenti K, Chu Q, Izevbaye I. Application of liquid biopsy-based targeted capture sequencing analysis to improve the precision treatment of non-small cell lung cancer by tyrosine kinase inhibitors. BMJ Open Respir Res 2022; 9:9/1/e001154. [PMID: 35091437 PMCID: PMC8804681 DOI: 10.1136/bmjresp-2021-001154] [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: 11/16/2021] [Accepted: 01/07/2022] [Indexed: 11/04/2022] Open
Abstract
BACKGROUND Targeted therapy of patients with non-small cell lung cancer (NSCLC) who harbour sensitising mutations by tyrosine kinase inhibitors (TKIs) has been found more effective than traditional chemotherapies. However, target genes status (eg, epidermal growth factor receptor (EGFR) TKIs sensitising and resistant mutations) need to be tested for choosing appropriate TKIs. This study is to investigate the performance of a liquid biopsy-based targeted capture sequencing assay on the molecular analysis of NSCLC. METHODS Plasma samples from patients with NSCLC who showed resistance to the first/second-generation EGFR TKIs treatment were collected. The AVENIO ctDNA Expanded Kit is a 77 pan-cancer genes detection assay that was used for detecting EGFR TKIs resistance-associated gene mutations. Through comparison of the EGFR gene testing results from the Cobas EGFR Mutation Test v2, and UltraSEEK Lung Panel, the effectiveness of the targeted capture sequencing assay was verified. RESULTS A total of 24 plasma cell-free DNA (cfDNA) samples were tested by the targeted capture sequencing assay. 33.3% (8/24) cfDNA samples were positive for EGFR exon 20 p.T790M which leads to EGFR dependent TKIs resistance. 8.3% (2/24) and 4.2% (1/24) samples were positive for mesenchymal-epithelial transition gene amplification and B-Raf proto-oncogene, serine/threonine kinase exon 15 p.V600E mutations which lead to EGFR independent TKIs resistance. The median value of the p.T790M variant allele fraction and variant copy numbers was 2% and 36.10 copies/mL plasma, respectively. The next-generation sequencing test showed higher than 90% concordance with either MassArray or qPCR-based methods for detecting either EGFR TKIs sensitising or resistance mutations. CONCLUSION The targeted capture sequencing test can support comprehensive molecular analysis needed for TKIs treatment, which is promising to be clinically applied for the improved precision treatment of NSCLC.
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Affiliation(s)
- Lei Zhang
- Department of Laboratory Medicine and Pathology, University of Alberta, Edmonton, Alberta, Canada
| | - John Coffin
- Department of Laboratory Medicine and Pathology, University of Alberta, Edmonton, Alberta, Canada
| | - Kim Formenti
- Department of Laboratory Medicine and Pathology, University of Alberta, Edmonton, Alberta, Canada
| | - Quincy Chu
- Cross Cancer Institute, Alberta Health Services, Edmonton, Alberta, Canada
| | - Iyare Izevbaye
- Department of Laboratory Medicine and Pathology, University of Alberta, Edmonton, Alberta, Canada
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15
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Batra U, Nathany S, Sharma M, Jain P, Dhanda S, Singh H, Jain A, Mehta A. EGFR detection by liquid biopsy: ripe for clinical usage. Future Oncol 2021; 18:85-92. [PMID: 34704813 DOI: 10.2217/fon-2021-0620] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Introduction: With the International Association for the Study of Lung Cancer (IASLC) recommendations promoting liquid biopsy as a primary detection tool, a new era of research has begun. The authors aimed to study the concordance of plasma genotyping platforms against the tissue gold standard. Methods: 184 patients with non-small cell lung cancer underwent EGFR genotyping using Cobas, droplet digital polymerase chain reaction (ddPCR) and Therascreen assays from 2019-2020. Results: Of 184 cases, 70 were positive by Cobas, 51 by ddPCR and 69 by Therascreen. The sensitivity of Cobas was 97.1% and the sensitivity of ddPCR was 71%. Receiver operating characteristic analysis showed an area under the curve of 0.977 for Cobas and 0.846 for ddPCR. Conclusion: In line with the FLAURA trial of osimertinib making its way to first-line and given the IASLC recommendations, it is important to understand the attributes of these tests to initiate appropriate treatment.
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Affiliation(s)
- Ullas Batra
- Medical Oncology, Rajiv Gandhi Cancer Institute & Research Centre, New Delhi 110085, India
| | - Shrinidhi Nathany
- Molecular Diagnostics, Rajiv Gandhi Cancer Institute & Research Centre, New Delhi 110085, India
| | - Mansi Sharma
- Medical Oncology, Rajiv Gandhi Cancer Institute & Research Centre, New Delhi 110085, India
| | - Parveen Jain
- Medical Oncology, Rajiv Gandhi Cancer Institute & Research Centre, New Delhi 110085, India
| | - Surender Dhanda
- Molecular Diagnostics, Rajiv Gandhi Cancer Institute & Research Centre, New Delhi 110085, India
| | - Harkirat Singh
- Medical Oncology, Rajiv Gandhi Cancer Institute & Research Centre, New Delhi 110085, India
| | - Arpit Jain
- Medical Oncology, Rajiv Gandhi Cancer Institute & Research Centre, New Delhi 110085, India
| | - Anurag Mehta
- Laboratory Services, Molecular Diagnostics & Research, Rajiv Gandhi Cancer Institute & Research Centre, New Delhi 110085, India
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16
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Stitz R, Buder A, Silye R, Baumgartner B, Pühringer F, Filipits M, Oberndorfer E, Heitzer E. Validation of a next-generation sequencing assay for the detection of EGFR mutations in cell-free circulating tumor DNA. Exp Mol Pathol 2021; 123:104685. [PMID: 34560086 DOI: 10.1016/j.yexmp.2021.104685] [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] [Received: 08/04/2021] [Revised: 09/06/2021] [Accepted: 09/17/2021] [Indexed: 11/27/2022]
Abstract
Detection of EGFR mutations from blood plasma represents a gentle, non-invasive alternative to rebiopsy and can therefore be used for therapy monitoring of non-small-cell lung cancer (NSCLC) patients. The aim of this project was to investigate whether the Reveal ctDNA™ 28 NGS assay (ArcherDX, Boulder, CO), has a comparable sensitivity and specificity to droplet digital PCR (ddPCR, gold-standard) and is therefore suitable for therapy monitoring of progressing lung cancer patients. First, we validated the NGS assay with a commercially available reference material (SeraCare, Massachusetts, US). Using an input of 22 ng, a sensitivity of 96% and a specificity of 100% could be achieved for variant allele frequencies (VAF) of 0.5%. For variants at a VAF of 0.1% the sensitivity was substantially reduced. Next, 28 plasma samples from 16 patients were analyzed and results were compared to existing ddPCR data. This comparative analysis of patient samples revealed a concordance of 91% between NGS and ddPCR. These results confirm that the Reveal ctDNA™ 28 NGS assay can be used for therapy monitoring of patients under TKI therapy. However, due to the slightly superior sensitivity of ddPCR, a combination of NGS (with broad coverage of a large number of genomic loci) and ddPCR (with targeted highly sensitive detection of specific mutations) might be the ideal approach.
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Affiliation(s)
- Regina Stitz
- Institute of Pathology, Salzkammergutklinikum Vöcklabruck, Vöcklabruck, Austria
| | - Anna Buder
- Institute of Cancer Research, Department of Medicine I, Comprehensive Cancer Center, Medical Center of Vienna, Vienna, Austria
| | - Rene Silye
- Institute of Pathology, Salzkammergutklinikum Vöcklabruck, Vöcklabruck, Austria
| | - Bernhard Baumgartner
- Department of Pulmonary Medicine, Salzkammergutklinikum Vöcklabruck, Vöcklabruck, Austria
| | - Franz Pühringer
- Institute of Pathology, Salzkammergutklinikum Vöcklabruck, Vöcklabruck, Austria
| | - Martin Filipits
- Institute of Cancer Research, Department of Medicine I, Comprehensive Cancer Center, Medical Center of Vienna, Vienna, Austria
| | - Eva Oberndorfer
- Institute of Pathology, Salzkammergutklinikum Vöcklabruck, Vöcklabruck, Austria
| | - Ellen Heitzer
- Institute of Human Genetics, Diagnostic and Research Center for Molecular BioMedicine, Medical University of Graz, Graz, Austria.
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17
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Pasini L, Notarangelo M, Vagheggini A, Burgio MA, Crinò L, Chiadini E, Prochowski AI, Delmonte A, Ulivi P, D'Agostino VG. Unveiling mutational dynamics in non-small cell lung cancer patients by quantitative EGFR profiling in vesicular RNA. Mol Oncol 2021; 15:2423-2438. [PMID: 33942501 PMCID: PMC8410558 DOI: 10.1002/1878-0261.12976] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2021] [Revised: 04/08/2021] [Accepted: 04/30/2021] [Indexed: 12/15/2022] Open
Abstract
The mutational status of the epidermal growth factor receptor (EGFR) guides the stratification of non‐small cell lung cancer (NSCLC) patients for treatment with tyrosine kinase inhibitors (TKIs). A liquid biopsy test on cell‐free DNA is recommended as a clinical decision‐supporting tool, although it has limited sensitivity. Here, we comparatively investigated the extracellular vesicle (EV)‐RNA as an independent source for multidimensional and longitudinal EGFR profiling in a cohort of 27 NSCLC patients. We introduced and validated a new rapid, highly specific EV‐RNA test with wild‐type (WT) and mutant‐sensitive probes (E746‐A750del, L858R, and T790M). We included a cohort of 20 NSCLC patients with EGFR WT tumor tissues and systematically performed molecular EV‐RNA and circulating tumor DNA analyses with clinical data statistics and biophysical profiles of EVs. At the single‐patient level, we detected variegated tumor heterogeneity dynamics supported by combinations of driver EGFR mutations. EV‐RNA‐based mutation analysis showed an unprecedented sensitivity of over 90%. The resistance‐associated mutation T790M frequently pre‐existed at baseline with a gained EV‐transcript copy number at progression, while the general mutational burden was mostly decreasing during the intermediate follow‐up. The biophysical profile of EVs and the quantitative assessment of T790M revealed an association with tumor size determined by the sum of the longest diameters in target lesions. Vesicular RNA provides a validated tool suitable for use in clinical practice to investigate the dynamics of common driver EGFR mutations in NSCLC patients receiving TKIs.
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Affiliation(s)
- Luigi Pasini
- Bioscience Laboratory, IRCCS Istituto Romagnolo per lo Studio dei Tumori (IRST) "Dino Amadori", Meldola, Italy
| | - Michela Notarangelo
- Laboratory of Biotechnology and Nanomedicine, Department of Cellular, Computational and Integrative Biology (CIBIO), University of Trento, Italy
| | - Alessandro Vagheggini
- Unit of Biostatistics, IRCCS Istituto Romagnolo per lo Studio dei Tumori (IRST) "Dino Amadori", Meldola, Italy
| | - Marco Angelo Burgio
- Medical Oncology Unit, IRCCS Istituto Romagnolo per lo Studio dei Tumori (IRST) "Dino Amadori", Meldola, Italy
| | - Lucio Crinò
- Medical Oncology Unit, IRCCS Istituto Romagnolo per lo Studio dei Tumori (IRST) "Dino Amadori", Meldola, Italy
| | - Elisa Chiadini
- Bioscience Laboratory, IRCCS Istituto Romagnolo per lo Studio dei Tumori (IRST) "Dino Amadori", Meldola, Italy
| | - Andrea Iamurri Prochowski
- Radiology Unit, IRCCS Istituto Romagnolo per lo Studio dei Tumori (IRST) "Dino Amadori", Meldola, Italy
| | - Angelo Delmonte
- Medical Oncology Unit, IRCCS Istituto Romagnolo per lo Studio dei Tumori (IRST) "Dino Amadori", Meldola, Italy
| | - Paola Ulivi
- Bioscience Laboratory, IRCCS Istituto Romagnolo per lo Studio dei Tumori (IRST) "Dino Amadori", Meldola, Italy
| | - Vito Giuseppe D'Agostino
- Laboratory of Biotechnology and Nanomedicine, Department of Cellular, Computational and Integrative Biology (CIBIO), University of Trento, Italy
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18
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Cortiula F, Pasello G, Follador A, Nardo G, Polo V, Scquizzato E, Conte AD, Miorin M, Giovanis P, D’Urso A, Girlando S, Settanni G, Picece V, Veccia A, Corvaja C, Indraccolo S, De Maglio G. A Multi-Center, Real-Life Experience on Liquid Biopsy Practice for EGFR Testing in Non-Small Cell Lung Cancer (NSCLC) Patients. Diagnostics (Basel) 2020; 10:diagnostics10100765. [PMID: 32998450 PMCID: PMC7601690 DOI: 10.3390/diagnostics10100765] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2020] [Revised: 09/24/2020] [Accepted: 09/27/2020] [Indexed: 02/07/2023] Open
Abstract
Background: circulating tumor DNA (ctDNA) is a source of tumor genetic material for EGFR testing in NSCLC. Real-word data about liquid biopsy (LB) clinical practice are lacking. The aim of the study was to describe the LB practice for EGFR detection in North Eastern Italy. Methods: we conducted a multi-regional survey on ctDNA testing practices in lung cancer patients. Results: Median time from blood collection to plasma separation was 50 min (20–120 min), median time from plasma extraction to ctDNA analysis was 24 h (30 min–5 days) and median turnaround time was 24 h (6 h–5 days). Four hundred and seventy five patients and 654 samples were tested. One hundred and ninety-two patients were tested at diagnosis, with 16% EGFR mutation rate. Among the 283 patients tested at disease progression, 35% were T790M+. Main differences in LB results between 2017 and 2018 were the number of LBs performed for each patient at disease progression (2.88 vs. 1.2, respectively) and the percentage of T790M+ patients (61% vs. 26%).
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Affiliation(s)
- Francesco Cortiula
- Dipartimento di Oncologia, Azienda Sanitaria Universitaria Friuli Centrale, 33100 Udine, Italy; (A.F.); (C.C.)
- Dipartimento di Medicina (DAME), Università degli Studi di Udine, 33100 Udine, Italy
- Correspondence: (F.C.); (S.I.)
| | - Giulia Pasello
- Oncologia Medica 2, Istituto Oncologico Veneto IOV IRCCS, 35128 Padova, Italy;
| | - Alessandro Follador
- Dipartimento di Oncologia, Azienda Sanitaria Universitaria Friuli Centrale, 33100 Udine, Italy; (A.F.); (C.C.)
| | - Giorgia Nardo
- U.O.C. Immunologia e Diagnostica Molecolare Oncologica, Istituto Oncologico Veneto IOV IRCCS, 35128 Padova, Italy;
| | - Valentina Polo
- Dipartimento di Oncologia, AULSS 2 Marca Trevigiana, Ospedale Ca’ Foncello, 31100 Treviso, Italy;
| | - Elisa Scquizzato
- Dipartimento interaziendale di Anatomia Patologica, ULSS 2 Marca Trevigiana, 31100 Treviso, Italy;
| | - Alessandro Del Conte
- S.O.C. Oncologia Medica e dei Tumori Immunocorrelati, Centro di Riferimento Oncologico (CRO) IRCCS, 33081 Aviano, Italy;
| | - Marta Miorin
- SSD Genetica medica, Azienda Sanitaria Friuli Occidentale, Presidio Ospedaliero di Pordenone, 33170 Pordenone, Italy;
| | - Petros Giovanis
- U.O.C. Oncologia, ULSS1 Dolomiti, Presidio Ospedaliero di Feltre, 32032 Feltre, Italy;
| | - Alessandra D’Urso
- U.O.C. Anatomia Patologica, ULSS1 Dolomiti, Presidio Ospedaliero di Feltre, 32032 Feltre, Italy;
| | - Salvator Girlando
- U.O. Anatomia Patologica, Ospedale Santa Chiara, 38122 Trento, Italy;
| | - Giulio Settanni
- Servizio di Anatomia-Istologia Patologica, IRCCS Ospedale Sacro Cuore Don Calabria, 37024 Negrar, Italy;
| | - Vincenzo Picece
- Dipartimento di Oncologia Medica, IRCCS Ospedale Sacro Cuore Don Calabria, 37024 Negrar, Italy;
| | - Antonello Veccia
- U.O. Oncologia Medica, Ospedale Santa Chiara, 38122 Trento, Italy;
| | - Carla Corvaja
- Dipartimento di Oncologia, Azienda Sanitaria Universitaria Friuli Centrale, 33100 Udine, Italy; (A.F.); (C.C.)
- Dipartimento di Medicina (DAME), Università degli Studi di Udine, 33100 Udine, Italy
| | - Stefano Indraccolo
- U.O.C. Immunologia e Diagnostica Molecolare Oncologica, Istituto Oncologico Veneto IOV IRCCS, 35128 Padova, Italy;
- Correspondence: (F.C.); (S.I.)
| | - Giovanna De Maglio
- SOC Anatomia Patologica, Azienda Sanitaria UniversitariaFriuli Centrale, 33100 Udine, Italy;
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19
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Zhao C, Jiang T, Li J, Wang Y, Su C, Chen X, Ren S, Li X, Zhou C. The impact of EGFR exon 19 deletion subtypes on clinical outcomes in non-small cell lung cancer. Transl Lung Cancer Res 2020; 9:1149-1158. [PMID: 32953493 PMCID: PMC7481579 DOI: 10.21037/tlcr-19-359] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Background The study investigated the resistant pattern and clinical outcomes of epidermal growth factor receptor (EGFR) exon 19 deletion (19del) subtypes to tyrosine kinase inhibitors (TKIs) in non-small cell lung cancer (NSCLC). Methods Two hundred eight treatment naive NSCLC patients detected as EGFR 19del using amplification-refractory mutation system (ARMS) were included. DNA sequencing was used to detect the subtypes. Clinicopathological features as well as patients’ outcomes treated with first-line EGFR-TKIs were analyzed. Results Thirteen EGFR 19del subtypes were confirmed in 181 samples (87.0%). Among these, delE746_A750 was the most frequent subtype (130/181, 71.8%). delE746_A750 and deletions starting from E746 were frequently found in female (P=0.003 and P=0.013, respectively) and never smokers (P=0.002 and P=0.014, respectively) than non-delE746_A750 and deletions starting from L747 patients, respectively. T790M was more frequently occurred in delE746_A750 than non-delE746_A750 (P=0.001) and deletions starting from E746 than L747 patients (P=0.006) after first-line EGFR-TKIs resistance. Patients harboring deletions starting from L747 with insertions had significantly shorter progression-free survival (PFS) than deletions starting from L747 without insertion (8.3 vs. 15.0 m, P=0.017), or all other patients (8.3 vs. 12.6 m, P=0.027). Different 19del subtypes with T790M mutation had similar PFS when treated with osimertinib (P=0.102). Conclusions Patients with EGFR 19del subtypes had different clinicopathological features, and resistant pattern when treated with first-line TKIs. Patients harboring deletions starting from L747 with insertions had inferior outcomes than other subtypes.
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Affiliation(s)
- Chao Zhao
- Department of Lung Cancer and Immunology, Shanghai Pulmonary Hospital, Tongji University, Shanghai, China
| | - Tao Jiang
- Department of Medical Oncology, Shanghai Pulmonary Hospital, Tongji University, Shanghai, China
| | - Jiayu Li
- Department of Medical Oncology, Shanghai Pulmonary Hospital, Tongji University, Shanghai, China
| | - Yan Wang
- Department of Medical Oncology, Shanghai Pulmonary Hospital, Tongji University, Shanghai, China
| | - Chunxia Su
- Department of Medical Oncology, Shanghai Pulmonary Hospital, Tongji University, Shanghai, China
| | - Xiaoxia Chen
- Department of Medical Oncology, Shanghai Pulmonary Hospital, Tongji University, Shanghai, China
| | - Shengxiang Ren
- Department of Medical Oncology, Shanghai Pulmonary Hospital, Tongji University, Shanghai, China
| | - Xuefei Li
- Department of Lung Cancer and Immunology, Shanghai Pulmonary Hospital, Tongji University, Shanghai, China
| | - Caicun Zhou
- Department of Medical Oncology, Shanghai Pulmonary Hospital, Tongji University, Shanghai, China
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20
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Pender A, Hughesman C, Law E, Kristanti A, McNeil K, Wong S, Tucker T, Bosdet I, Young S, Laskin J, Karsan A, Yip S, Ho C. EGFR circulating tumour DNA testing: identification of predictors of ctDNA detection and implications for survival outcomes. Transl Lung Cancer Res 2020; 9:1084-1092. [PMID: 32953487 PMCID: PMC7481591 DOI: 10.21037/tlcr-19-581] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Background EGFR T790M testing is the standard of care for activating EGFR mutation (EGFRm) non-small cell lung cancer (NSCLC) progressing on 1st/2nd generation TKIs to select patients for osimertinib. Despite sensitive assays, detection of circulating tumour deoxyribonucleic acid (ctDNA) is variable and influenced by clinical factors. The number and location of sites of progressive disease at time of testing were reviewed to explore the effect on EGFR ctDNA detection. The prognostic value of EGFR ctDNA detection on survival outcomes was assessed. Methods Following extraction of cell-free DNA from plasma using the QIAamp Circulating Nucleic Acid Kit, custom droplet digital polymerase chair reaction (ddPCR) assays were used to assess EGFR ctDNA using the Bio-Rad QX200 system. The ddPCR assay has a limit of detection of ≤0.15% variant allele fraction. Baseline characteristics and imaging reports at time of EGFR ctDNA testing were reviewed retrospectively for a 1 year period. Results The study included 177 patients who had an EGFR ctDNA test. Liver (aOR 3.13) or bone (aOR 2.76) progression or 3–5 sites of progression (aOR 2.22) were predictive of EGFR ctDNA detection. The median OS from first ctDNA test after multiple testing iterations was 12.3 m undetectable EGFR ctDNA, 7.6 m for original EGFR mutation only and 24.1 m with T790M (P=0.001). Conclusions Patients with liver or bone progression and 3–5 progressing sites are more likely to have informative EGFR ctDNA testing. Detection of EGFR ctDNA is a negative prognostic indicator in the absence of a T790M resistance mutation, potentially reflecting the disease burden in the absence of targeted therapy options.
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Affiliation(s)
- Alexandra Pender
- Department of Medical Oncology, Royal Free London NHS Foundation Trust and North Middlesex University Hospital, London, UK
| | - Curtis Hughesman
- Cancer Genetics & Genomics Laboratory, BC Cancer, Vancouver, Canada
| | - Elaine Law
- Cancer Genetics & Genomics Laboratory, BC Cancer, Vancouver, Canada
| | - Amadea Kristanti
- Cancer Genetics & Genomics Laboratory, BC Cancer, Vancouver, Canada
| | - Kelly McNeil
- Cancer Genetics & Genomics Laboratory, BC Cancer, Vancouver, Canada
| | - Selina Wong
- Department of Medical Oncology, BC Cancer, Vancouver, Canada
| | - Tracy Tucker
- Cancer Genetics & Genomics Laboratory, BC Cancer, Vancouver, Canada
| | - Ian Bosdet
- Cancer Genetics & Genomics Laboratory, BC Cancer, Vancouver, Canada
| | - Sean Young
- Cancer Genetics & Genomics Laboratory, BC Cancer, Vancouver, Canada
| | - Janessa Laskin
- Department of Medical Oncology, BC Cancer, Vancouver, Canada.,University of British Columbia, Vancouver, Canada
| | - Aly Karsan
- University of British Columbia, Vancouver, Canada.,Department of Pathology and Laboratory Medicine, BC Cancer, Vancouver, Canada
| | - Stephen Yip
- Cancer Genetics & Genomics Laboratory, BC Cancer, Vancouver, Canada.,University of British Columbia, Vancouver, Canada.,Department of Pathology and Laboratory Medicine, BC Cancer, Vancouver, Canada
| | - Cheryl Ho
- Department of Medical Oncology, BC Cancer, Vancouver, Canada.,University of British Columbia, Vancouver, Canada
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21
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He Q, Zhu X, Shi X, Lin C, Jin Y, Yan J, He J, Yu X. cfDNA changes for monitoring of targeted therapy in a primary EGFR mutation lung adenocarcinoma. Transl Lung Cancer Res 2020; 9:807-810. [PMID: 32676342 PMCID: PMC7354132 DOI: 10.21037/tlcr-20-442] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Affiliation(s)
- Qiong He
- Institute of Cancer and Basic Medicine (ICBM), Chinese Academy of Sciences, Hangzhou 310022, China.,Department of Medical Oncology, Cancer Hospital of the University of Chinese Academy of Sciences, Hangzhou 310022, China.,Department of Medical Oncology, Zhejiang Cancer Hospital, Hangzhou 310022, China
| | - Xian Zhu
- Department of Cardiovascular Surgery, The Second Affiliated Hospital of Zhejiang University School of Medicine, Hangzhou 310022, China
| | - Xun Shi
- Institute of Cancer and Basic Medicine (ICBM), Chinese Academy of Sciences, Hangzhou 310022, China.,Department of Medical Oncology, Cancer Hospital of the University of Chinese Academy of Sciences, Hangzhou 310022, China.,Department of Medical Oncology, Zhejiang Cancer Hospital, Hangzhou 310022, China
| | - Chen Lin
- Institute of Cancer and Basic Medicine (ICBM), Chinese Academy of Sciences, Hangzhou 310022, China.,Department of Medical Oncology, Cancer Hospital of the University of Chinese Academy of Sciences, Hangzhou 310022, China.,Department of Medical Oncology, Zhejiang Cancer Hospital, Hangzhou 310022, China
| | - Yin Jin
- Institute of Cancer and Basic Medicine (ICBM), Chinese Academy of Sciences, Hangzhou 310022, China.,Department of Medical Oncology, Cancer Hospital of the University of Chinese Academy of Sciences, Hangzhou 310022, China.,Department of Medical Oncology, Zhejiang Cancer Hospital, Hangzhou 310022, China
| | - Junrong Yan
- Nanjing Geneseeq Technology Inc., Nanjing 210032, China
| | - Jiachen He
- Nanjing Geneseeq Technology Inc., Nanjing 210032, China
| | - Xinmin Yu
- Institute of Cancer and Basic Medicine (ICBM), Chinese Academy of Sciences, Hangzhou 310022, China.,Department of Medical Oncology, Cancer Hospital of the University of Chinese Academy of Sciences, Hangzhou 310022, China.,Department of Medical Oncology, Zhejiang Cancer Hospital, Hangzhou 310022, China
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22
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Serrano MJ, Exposito-Hernández J, Guerrero R, Lopez-Hidalgo J, Aguilar M, Lorente JA, de Álava E, Garrido-Navas MC. From precision medicine to imprecision medicine through limited diagnostic ability to detect low allelic frequency mutations. Transl Lung Cancer Res 2020; 9:180-183. [PMID: 32420057 PMCID: PMC7225138 DOI: 10.21037/tlcr.2020.03.07] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- María José Serrano
- GENYO, Centre for Genomics and Oncological Research (Pfizer/University of Granada/Andalusian Regional Government), PTS Granada, Granada, Spain.,Integral Oncology Division, Virgen de las Nieves University Hospital, Granada, Spain.,Department of Pathological Anatomy, Faculty of Medicine, Campus de Ciencias de la Salud, University of Granada, Granada, Spain
| | | | - Rosa Guerrero
- Integral Oncology Division, Virgen de las Nieves University Hospital, Granada, Spain
| | | | - Mariano Aguilar
- Department of Pathological Anatomy, Faculty of Medicine, Campus de Ciencias de la Salud, University of Granada, Granada, Spain
| | - Jose A Lorente
- GENYO, Centre for Genomics and Oncological Research (Pfizer/University of Granada/Andalusian Regional Government), PTS Granada, Granada, Spain.,Laboratory of Genetic Identification, Department of Legal Medicine, University of Granada, Granada, Spain
| | - Enrique de Álava
- Institute of Biomedicine of Sevilla (IBiS), Virgen del Rocio University Hospital/CSIC/University of Sevilla/CIBERONC, Seville, Spain.,Department of Normal and Pathological Cytology and Histology, School of Medicine, University of Seville, Seville, Spain
| | - M Carmen Garrido-Navas
- GENYO, Centre for Genomics and Oncological Research (Pfizer/University of Granada/Andalusian Regional Government), PTS Granada, Granada, Spain
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23
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Zhou J, Zhou F, Xie H, Wu Y, Zhao J, Su C. An advanced non-small cell lung cancer patient with epidermal growth factor receptor sensitizing mutation responded to toripalimab in combination with chemotherapy after resistance to osimertinib: a case report. Transl Lung Cancer Res 2020; 9:354-359. [PMID: 32420075 PMCID: PMC7225156 DOI: 10.21037/tlcr.2020.02.09] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
The clinical activity and favorable toxicity profile of osimertinib has led it to be approved not only for advanced non-small cell lung cancer (NSCLC) patients with T790M-positive tumors when first, or second-generation epidermal growth factor receptor-tyrosine kinase inhibitor (EGFR-TKI) treatment fails, but also for untreated advanced NSCLC patients with EGFR sensitizing mutation, so how to manage patients who get acquired resistance to osimertinib has becoming an emerging clinical challenge. This presentation would report a case of an advanced NSCLC patient with EGFR 19DEL who received combination therapy of toripalimab and chemotherapy after resistance to first line osimertinib therapy and achieved a PFS benefit of over 8 months. This case highlighted that immune checkpoint blockade combined chemotherapy might be a new possibility for advanced NSCLC patients with acquired resistance to osimertinib.
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Affiliation(s)
- Juan Zhou
- Department of Medical Oncology, Shanghai Pulmonary Hospital & Thoracic Cancer Institute, Tongji University School of Medicine, Shanghai 200433, China
| | - Fei Zhou
- Department of Medical Oncology, Shanghai Pulmonary Hospital & Thoracic Cancer Institute, Tongji University School of Medicine, Shanghai 200433, China
| | - Huikang Xie
- Department of Pathology, Shanghai Pulmonary Hospital & Thoracic Cancer Institute, Tongji University School of Medicine, Shanghai 200433, China
| | - Yan Wu
- Department of Medical Oncology, Shanghai Pulmonary Hospital & Thoracic Cancer Institute, Tongji University School of Medicine, Shanghai 200433, China
| | - Jing Zhao
- Department of Medical Oncology, Shanghai Pulmonary Hospital & Thoracic Cancer Institute, Tongji University School of Medicine, Shanghai 200433, China
| | - Chunxia Su
- Department of Medical Oncology, Shanghai Pulmonary Hospital & Thoracic Cancer Institute, Tongji University School of Medicine, Shanghai 200433, China
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24
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Shen FF, Guo W, Tian RF, Guo Y, Yang YL, Song X. Long-term survival with targeted therapy in an advanced non-small cell lung cancer patient based on genetic profiling. Transl Lung Cancer Res 2020; 9:373-378. [PMID: 32420078 PMCID: PMC7225131 DOI: 10.21037/tlcr.2020.01.21] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Abstract
Non-small cell lung cancer (NSCLC) is a profoundly devastating disease that is the leading cause of cancer-related death worldwide. With the rapid development of next-generation sequencing (NGS), which has supplied the ability to decode tumors at the DNA level, so that targeted therapy plays a crucial role in improving NSCLC survival. We first reported a 32-year-old Chinese female patient received the ninth-line treatment, who was initially diagnosed with advanced NSCLC with EGFR 19 deletion. The patient had a satisfactory clinical response to initial gefitinib treatment. Subsequently, an EGFR T790M mutation was detected from plasma-derived circulating tumor DNA (ctDNA) by ddPCR after disease progression, while NGS did not. Osimertinib was still tried but had no therapeutic effect. Then the disease even progressed on the administration of chemotherapy and gefitinib in succession. Rebiopsy for NGS detection was performed, and gefitinib plus anlotinib/vemurafenib were tried. And then, gefitinib plus crizotinib were administrated for MET amplification after the third biopsy. Furthermore, chemotherapy combined with immunotherapy was performed due to the PD-L1 positive expression. Up to now, osimertinib treatment was undertaken to base on an EGFR exon 20 T790M mutation using NGS-based genotyping in cerebrospinal fluid (CSF) ctDNA. Tumor genome dynamic monitoring can identify tumor driving genes and drug resistance mechanisms to guide tumor treatment. This study found that the total survival time of advanced NSCLC patients was more than four years after chemoradiotherapy and targeted therapy, indicating the significance of dynamic monitoring of gene alterations for cancer treatment.
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Affiliation(s)
- Fang-Fang Shen
- Department of Respiratory Medicine, Shanxi Provincial Cancer Hospital, Taiyuan 030001, China
| | - Wei Guo
- Department of Respiratory Medicine, Shanxi Provincial Cancer Hospital, Taiyuan 030001, China
| | - Rui-Fen Tian
- Department of Respiratory Medicine, Shanxi Provincial Cancer Hospital, Taiyuan 030001, China
| | - Yi Guo
- Department of Respiratory Medicine, Shanxi Provincial Cancer Hospital, Taiyuan 030001, China
| | - Yan-Li Yang
- Department of Respiratory Medicine, Shanxi Provincial Cancer Hospital, Taiyuan 030001, China
| | - Xia Song
- Department of Respiratory Medicine, Shanxi Provincial Cancer Hospital, Taiyuan 030001, China
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25
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Ma S, He Z, Fu H, Wang L, Wu X, Zhang Z, Wang Q. Dynamic changes of acquired T790M mutation and small cell lung cancer transformation in a patient with EGFR-mutant adenocarcinoma after first- and third-generation EGFR-TKIs: a case report. Transl Lung Cancer Res 2020; 9:139-143. [PMID: 32206560 PMCID: PMC7082284 DOI: 10.21037/tlcr.2020.01.07] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
Epithelial growth factor receptor (EGFR) T790M mutation and small cell lung cancer (SCLC) transformation are well-known resistance mechanisms acquired during treatment with EGFR tyrosine kinase inhibitors (TKIs). Various mechanisms sometimes coexist in patients. Here, we report a 57-year-old female diagnosed with stage IV lung adenocarcinoma, who harbored an EGFR exon 19 deletion mutation. This patient initially received gefitinib and progressed after 14 months. A repeat biopsy was performed, and the original EGFR exon 19 deletion and acquired exon 20 T790M mutation were identified. Then, pemetrexed plus carboplatin was administered as second-line and osimertinib as third-line treatment. Rapid progression and mixed response were observed after 2 months on osimertinib, with stable disease of the primary lung lesion but rapid growth of a right lower chest mass. The progressive chest lesion underwent biopsy, and the SCLC transformation was revealed. Furthermore, the patient was treated with etoposide and cisplatin, and she achieved disease control for 4 months. A fourth biopsy both for the primary lung lesion and the chest mass were finally conducted. Interestingly, the histopathology of the two different lesions showed adenocarcinoma and SCLC, respectively. The patient then rapidly suffered brain metastasis, and no EGFR mutations were detected in her cerebrospinal fluid (CSF). Overall survival (OS) of the patient was 29 months. This patient experienced concomitant resistance mechanisms of T790M mutation and SCLC transformation, which might have resulted from intra-tumor heterogeneity and drug-induced selection. Ultimately, this case reminds us that repeat biopsies are essential for patients receiving EGFR-TKIs in order to make appropriate treatment decisions according to the diverse mechanisms of acquired resistance.
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Affiliation(s)
- Shuxiang Ma
- Department of Internal Medicine, Henan Cancer Hospital, Affiliated Cancer Hospital of Zhengzhou University, Zhengzhou 450008, China
| | - Zhen He
- Department of Internal Medicine, Henan Cancer Hospital, Affiliated Cancer Hospital of Zhengzhou University, Zhengzhou 450008, China
| | - Hongyong Fu
- Department of Internal Medicine, Henan Cancer Hospital, Affiliated Cancer Hospital of Zhengzhou University, Zhengzhou 450008, China
| | - Lili Wang
- Department of Internal Medicine, Henan Cancer Hospital, Affiliated Cancer Hospital of Zhengzhou University, Zhengzhou 450008, China
| | - Xuan Wu
- Department of Internal Medicine, Henan Cancer Hospital, Affiliated Cancer Hospital of Zhengzhou University, Zhengzhou 450008, China
| | - Zhe Zhang
- Department of Internal Medicine, Henan Cancer Hospital, Affiliated Cancer Hospital of Zhengzhou University, Zhengzhou 450008, China
| | - Qiming Wang
- Department of Internal Medicine, Henan Cancer Hospital, Affiliated Cancer Hospital of Zhengzhou University, Zhengzhou 450008, China
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26
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Zheng Y, Zhou M, Arulananda S, Um SW, Li H. Management of non-small cell lung cancer with resistance to epidermal growth factor receptor tyrosine kinase inhibitor: case discussion. J Thorac Dis 2020; 12:159-164. [PMID: 32274080 PMCID: PMC7138979 DOI: 10.21037/jtd.2020.01.65] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Yuyan Zheng
- Department of Thoracic Surgery, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Min Zhou
- Department of Respiratory Medicine, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Surein Arulananda
- Department of Medical Oncology, Olivia Newton-John Cancer and Wellness Centre, Heidelberg, Australia
| | - Sang-Won Um
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, South Korea
| | - Hecheng Li
- Department of Thoracic Surgery, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
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27
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Bessi S, Pepe F, Ottaviantonio M, Pisapia P, Malapelle U, Troncone G, Biancalani M. Comparison between two different next generation sequencing platforms for clinical relevant gene mutation test in solid tumours. J Clin Pathol 2020; 73:602-604. [PMID: 32060075 DOI: 10.1136/jclinpath-2019-206422] [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: 12/30/2019] [Revised: 01/15/2020] [Accepted: 01/16/2020] [Indexed: 11/03/2022]
Abstract
In the present study, we analysed 44 formalin fixed paraffin embedded (FFPE) from different solid tumours by adopting two different next generation sequencing platforms: GeneReader (QIAGEN, Hilden, Germany) and Ion Torrent (Thermo Fisher Scientific, Waltham, Massachusetts, USA). We highlighted a 100% concordance between the platforms. In addition, focusing on variant detection, we evaluated a very good agreement between the two tests (Cohen's kappa=0.84) and, when taking into account variant allele fraction value for each variant, a very high concordance was obtained (Pearson's r=0.94). Our results underlined the high performance rate of GeneReader on FFPE samples and its suitability in routine molecular predictive practice.
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Affiliation(s)
- Silvia Bessi
- Azienda USL Toscana Centro, Complex Unit of Pathological Anatomy Empoli-Prato, S. Stefano Hospital, Prato, Italy
| | - Francesco Pepe
- Department of Public Health, University of Naples Federico II, Naples, Italy
| | - Marco Ottaviantonio
- Azienda USL Toscana Centro, Complex Unit of Pathological Anatomy Empoli-Prato, S. Stefano Hospital, Prato, Italy
| | - Pasquale Pisapia
- 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
| | - Mauro Biancalani
- Azienda USL Toscana Centro, Complex Unit of Pathological Anatomy Empoli-Prato, S. Stefano Hospital, Prato, Italy
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28
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Zhu C, Zhuang W, Chen L, Yang W, Ou WB. Frontiers of ctDNA, targeted therapies, and immunotherapy in non-small-cell lung cancer. Transl Lung Cancer Res 2020; 9:111-138. [PMID: 32206559 PMCID: PMC7082279 DOI: 10.21037/tlcr.2020.01.09] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Non-small-cell lung cancer (NSCLC), a main subtype of lung cancer, is one of the most common causes of cancer death in men and women worldwide. Circulating tumor DNA (ctDNA), tyrosine kinase inhibitors (TKIs) and immunotherapy have revolutionized both our understanding of NSCLC, from its diagnosis to targeted NSCLC therapies, and its treatment. ctDNA quantification confers convenience and precision to clinical decision making. Furthermore, the implementation of TKI-based targeted therapy and immunotherapy has significantly improved NSCLC patient quality of life. This review provides an update on the methods of ctDNA detection and its impact on therapeutic strategies; therapies that target epidermal growth factor receptor (EGFR) and anaplastic lymphoma kinase (ALK) using TKIs such as osimertinib and lorlatinib; the rise of various resistant mechanisms; and the control of programmed cell death-1 (PD-1), programmed cell death ligand-1 (PD-L1), and cytotoxic T-lymphocyte antigen-4 (CTLA-4) by immune checkpoint inhibitors (ICIs) in immunotherapy; blood tumor mutational burden (bTMB) calculated by ctDNA assay as a novel biomarker for immunotherapy. However, NSCLC patients still face many challenges. Further studies and trials are needed to develop more effective drugs or therapies to treat NSCLC.
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Affiliation(s)
- Chennianci Zhu
- Zhejiang Provincial Key Laboratory of Silkworm Bioreactor and Biomedicine, College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou 310018, China
| | - Weihao Zhuang
- Zhejiang Provincial Key Laboratory of Silkworm Bioreactor and Biomedicine, College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou 310018, China
| | - Limin Chen
- Zhejiang Provincial Key Laboratory of Silkworm Bioreactor and Biomedicine, College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou 310018, China
| | - Wenyu Yang
- Zhejiang Provincial Key Laboratory of Silkworm Bioreactor and Biomedicine, College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou 310018, China
| | - Wen-Bin Ou
- Zhejiang Provincial Key Laboratory of Silkworm Bioreactor and Biomedicine, College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou 310018, China
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29
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Liu L, Lizaso A, Mao X, Yang N, Zhang Y. Rechallenge with erlotinib in osimertinib-resistant lung adenocarcinoma mediated by driver gene loss: a case report. Transl Lung Cancer Res 2020; 9:144-147. [PMID: 32206561 PMCID: PMC7082283 DOI: 10.21037/tlcr.2020.01.10] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
The efficacy and safety of osimertinib have been demonstrated in several clinical trials; however, acquired resistance is an inevitable problem associated with most targeted drugs. Based on previous findings, the mechanism of osimertinib resistance is equivocal, and there is still no consensus on the most optimal treatment strategy after developing resistance, especially for patients detected with no actionable driver mutation. Here, we report the efficacy of erlotinib rechallenge in a patient with advanced lung adenocarcinoma following osimertinib resistance mediated by driver gene loss. Following osimertinib resistance, targeted sequencing of both blood and tissue samples revealed the disappearance of both EGFR exon 19 deletion and T790M. Erlotinib was then re-administered, achieving partial response for 26 months at least. Our case provides clinical evidence supporting the efficacy of erlotinib rechallenges in overcoming osimertinib resistance mediated by driver gene loss, which may translate into novel treatment strategies for lung cancer patients following development of resistance to osimertinib.
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Affiliation(s)
- Lingli Liu
- Department of Medical Oncology, Lung Cancer and Gastrointestinal Unit, Hunan Cancer Hospital/The Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha 410013, China.,Graduate Schools, University of South China, Hengyang 421001, China
| | | | - Xinru Mao
- Burning Rock Biotech, Guangzhou 510300, China
| | - Nong Yang
- Department of Medical Oncology, Lung Cancer and Gastrointestinal Unit, Hunan Cancer Hospital/The Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha 410013, China
| | - Yongchang Zhang
- Department of Medical Oncology, Lung Cancer and Gastrointestinal Unit, Hunan Cancer Hospital/The Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha 410013, China
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