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Balázs Z, Balermpas P, Ivanković I, Willmann J, Gitchev T, Bryant A, Guckenberger M, Krauthammer M, Andratschke N. Longitudinal cell-free DNA characterization by low-coverage whole-genome sequencing in patients undergoing high-dose radiotherapy. Radiother Oncol 2024; 197:110364. [PMID: 38834154 DOI: 10.1016/j.radonc.2024.110364] [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: 01/07/2024] [Revised: 05/23/2024] [Accepted: 05/28/2024] [Indexed: 06/06/2024]
Abstract
BACKGROUND AND PURPOSE Current radiotherapy guidelines rely heavily on imaging-based monitoring. Liquid biopsy monitoring promises to complement imaging by providing frequent systemic information about the tumor. In particular, cell-free DNA (cfDNA) sequencing offers a tumor-agnostic approach, which lends itself to monitoring heterogeneous cohorts of cancer patients. METHODS We collected plasma cfDNA from oligometastatic patients (OMD) and head-and-neck cancer patients (SCCHN) at six time points before, during, and after radiotherapy, and compared them to the plasma samples of healthy and polymetastatic volunteers. We performed low-pass (on average 7x) whole-genome sequencing on 93 plasma cfDNA samples and correlated copy number alterations and fragment length distributions to clinical and imaging findings. RESULTS We observed copy number alterations in 4/7 polymetastatic cancer patients, 1/7 OMD and 1/7 SCCHN patients, these patients' imaging showed progression following radiotherapy. Using unsupervised learning, we identified cancer-specific fragment length features that showed a strong correlation with copy number-based tumor fraction estimates. In 4/4 HPV-positive SCCHN patient samples, we detected viral DNA that enabled the monitoring of very low tumor fraction samples. CONCLUSIONS Our results indicate that an elevated tumor fraction is associated with tumor aggressiveness and systemic tumor spread. This information may be used to adapt treatment strategies. Further, we show that by detecting specific sequences such as viral DNA, the sensitivity of detecting cancer from cell-free DNA sequencing data can be greatly increased.
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Affiliation(s)
- Zsolt Balázs
- Department of Quantitative Biomedicine, University of Zurich, Zurich, Switzerland; Department of Biomedical Informatics, University Hospital Zurich, University of Zurich, Zurich, Switzerland
| | - Panagiotis Balermpas
- Department of Radiation Oncology, University Hospital of Zurich, University of Zurich, Zurich, Switzerland
| | - Ivna Ivanković
- Department of Quantitative Biomedicine, University of Zurich, Zurich, Switzerland; Department of Biomedical Informatics, University Hospital Zurich, University of Zurich, Zurich, Switzerland
| | - Jonas Willmann
- Department of Radiation Oncology, University Hospital of Zurich, University of Zurich, Zurich, Switzerland
| | - Todor Gitchev
- Department of Quantitative Biomedicine, University of Zurich, Zurich, Switzerland; Department of Biomedical Informatics, University Hospital Zurich, University of Zurich, Zurich, Switzerland
| | - Asher Bryant
- Center for Cancer Research, National Cancer Institute, National Institutes of Health, Rockville, MD, USA
| | - Matthias Guckenberger
- Department of Radiation Oncology, University Hospital of Zurich, University of Zurich, Zurich, Switzerland
| | - Michael Krauthammer
- Department of Quantitative Biomedicine, University of Zurich, Zurich, Switzerland; Department of Biomedical Informatics, University Hospital Zurich, University of Zurich, Zurich, Switzerland.
| | - Nicolaus Andratschke
- Department of Radiation Oncology, University Hospital of Zurich, University of Zurich, Zurich, Switzerland.
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2
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Antonouli S, Di Nisio V, Daponte N, Daponte AI, Daponte A. Cervical Cancer Genetic Profile through Circulating Tumor DNA: What Can We Learn from Blood? Biomolecules 2024; 14:825. [PMID: 39062539 PMCID: PMC11275054 DOI: 10.3390/biom14070825] [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: 05/19/2024] [Revised: 07/06/2024] [Accepted: 07/08/2024] [Indexed: 07/28/2024] Open
Abstract
Cervical cancer (CC) is one of the deadliest gynecological cancers worldwide. Human papillomavirus is the main etiological agent responsible for the initiation and development of most CC cases. The standard method utilized for CC screening in the global population is the cytological Pap smear test. Despite its effective validity in detecting precancerous lesions and its response to layer stages of this disease, greater screening and diagnostic reliability are needed, as well as an improvement in specificity and sensitivity. In this context, the use of liquid biopsies, like blood, for the isolation of circulating tumor DNA (ctDNA) in CC screening, diagnosis, prognosis, and surveillance could fill the gaps that still exist. In the present review, we aim to study the literature in order to collect knowledge on blood-based liquid biopsy based on descriptions of its precious molecular content and its utilization as a potential tool for CC patients' management. We will mainly focus on the important role of the novel ctDNA and the unique possibilities to additionally use HPV-ctDNA in CC at various stages of clinical application.
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Affiliation(s)
- Sevastiani Antonouli
- Department of Obstetrics and Gynaecology, Faculty of Medicine, School of Health Sciences, University of Thessaly, 41500 Larisa, Greece; (S.A.); (N.D.)
| | - Valentina Di Nisio
- Department of Gynecology and Reproductive Medicine, Karolinska University Hospital, Huddinge, 141 86 Stockholm, Sweden;
- Division of Obstetrics and Gynecology, Department of Clinical Science, Intervention and Technology, Karolinska Institutet, Huddinge, 171 77 Stockholm, Sweden
| | - Nikoletta Daponte
- Department of Obstetrics and Gynaecology, Faculty of Medicine, School of Health Sciences, University of Thessaly, 41500 Larisa, Greece; (S.A.); (N.D.)
| | - Athina-Ioanna Daponte
- Second Department of Dermatology-Venereology, Aristotle University School of Medicine, 54124 Thessaloniki, Greece;
| | - Alexandros Daponte
- Department of Obstetrics and Gynaecology, Faculty of Medicine, School of Health Sciences, University of Thessaly, 41500 Larisa, Greece; (S.A.); (N.D.)
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3
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Till JE, McDaniel L, Chang C, Long Q, Pfeiffer SM, Lyman JP, Padrón LJ, Maurer DM, Yu JX, Spencer CN, Gherardini PF, Da Silva DM, LaVallee TM, Abbott C, Chen RO, Boyle SM, Bhagwat N, Cannas S, Sagreiya H, Li W, Yee SS, Abdalla A, Wang Z, Yin M, Ballinger D, Wissel P, Eads J, Karasic T, Schneider C, O'Dwyer P, Teitelbaum U, Reiss KA, Rahma OE, Fisher GA, Ko AH, Wainberg ZA, Wolff RA, O'Reilly EM, O'Hara MH, Cabanski CR, Vonderheide RH, Carpenter EL. Circulating KRAS G12D but not G12V is associated with survival in metastatic pancreatic ductal adenocarcinoma. Nat Commun 2024; 15:5763. [PMID: 38982051 PMCID: PMC11233636 DOI: 10.1038/s41467-024-49915-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2023] [Accepted: 06/18/2024] [Indexed: 07/11/2024] Open
Abstract
While high circulating tumor DNA (ctDNA) levels are associated with poor survival for multiple cancers, variant-specific differences in the association of ctDNA levels and survival have not been examined. Here we investigate KRAS ctDNA (ctKRAS) variant-specific associations with overall and progression-free survival (OS/PFS) in first-line metastatic pancreatic ductal adenocarcinoma (mPDAC) for patients receiving chemoimmunotherapy ("PRINCE", NCT03214250), and an independent cohort receiving standard of care (SOC) chemotherapy. For PRINCE, higher baseline plasma levels are associated with worse OS for ctKRAS G12D (log-rank p = 0.0010) but not G12V (p = 0.7101), even with adjustment for clinical covariates. Early, on-therapy clearance of G12D (p = 0.0002), but not G12V (p = 0.4058), strongly associates with OS for PRINCE. Similar results are obtained for the SOC cohort, and for PFS in both cohorts. These results suggest ctKRAS G12D but not G12V as a promising prognostic biomarker for mPDAC and that G12D clearance could also serve as an early biomarker of response.
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Affiliation(s)
- Jacob E Till
- Abramson Cancer Center of the University of Pennsylvania, Philadelphia, PA, USA
| | | | - Changgee Chang
- Indiana University School of Medicine, Indianapolis, IN, USA
| | - Qi Long
- Abramson Cancer Center of the University of Pennsylvania, Philadelphia, PA, USA
| | | | - Jaclyn P Lyman
- Parker Institute for Cancer Immunotherapy, San Francisco, CA, USA
| | - Lacey J Padrón
- Parker Institute for Cancer Immunotherapy, San Francisco, CA, USA
| | - Deena M Maurer
- Parker Institute for Cancer Immunotherapy, San Francisco, CA, USA
| | - Jia Xin Yu
- Parker Institute for Cancer Immunotherapy, San Francisco, CA, USA
| | | | | | - Diane M Da Silva
- Parker Institute for Cancer Immunotherapy, San Francisco, CA, USA
| | | | | | | | | | - Neha Bhagwat
- Abramson Cancer Center of the University of Pennsylvania, Philadelphia, PA, USA
| | - Samuele Cannas
- Abramson Cancer Center of the University of Pennsylvania, Philadelphia, PA, USA
| | - Hersh Sagreiya
- Abramson Cancer Center of the University of Pennsylvania, Philadelphia, PA, USA
| | - Wenrui Li
- Abramson Cancer Center of the University of Pennsylvania, Philadelphia, PA, USA
| | - Stephanie S Yee
- Abramson Cancer Center of the University of Pennsylvania, Philadelphia, PA, USA
| | - Aseel Abdalla
- Abramson Cancer Center of the University of Pennsylvania, Philadelphia, PA, USA
| | - Zhuoyang Wang
- Abramson Cancer Center of the University of Pennsylvania, Philadelphia, PA, USA
| | - Melinda Yin
- Abramson Cancer Center of the University of Pennsylvania, Philadelphia, PA, USA
| | - Dominique Ballinger
- Abramson Cancer Center of the University of Pennsylvania, Philadelphia, PA, USA
| | - Paul Wissel
- Abramson Cancer Center of the University of Pennsylvania, Philadelphia, PA, USA
| | - Jennifer Eads
- Abramson Cancer Center of the University of Pennsylvania, Philadelphia, PA, USA
| | - Thomas Karasic
- Abramson Cancer Center of the University of Pennsylvania, Philadelphia, PA, USA
| | - Charles Schneider
- Abramson Cancer Center of the University of Pennsylvania, Philadelphia, PA, USA
| | - Peter O'Dwyer
- Abramson Cancer Center of the University of Pennsylvania, Philadelphia, PA, USA
| | - Ursina Teitelbaum
- Abramson Cancer Center of the University of Pennsylvania, Philadelphia, PA, USA
| | - Kim A Reiss
- Abramson Cancer Center of the University of Pennsylvania, Philadelphia, PA, USA
| | | | | | - Andrew H Ko
- University of California, San Francisco, San Francisco, CA, USA
| | - Zev A Wainberg
- University of California, Los Angeles, Los Angeles, CA, USA
| | - Robert A Wolff
- The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | | | - Mark H O'Hara
- Abramson Cancer Center of the University of Pennsylvania, Philadelphia, PA, USA
| | | | | | - Erica L Carpenter
- Abramson Cancer Center of the University of Pennsylvania, Philadelphia, PA, USA.
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Nguyen TH, Doan NNT, Tran TH, Huynh LAK, Doan PL, Nguyen THH, Nguyen VTC, Nguyen GTH, Nguyen HN, Giang H, Tran LS, Phan MD. Tissue of origin detection for cancer tumor using low-depth cfDNA samples through combination of tumor-specific methylation atlas and genome-wide methylation density in graph convolutional neural networks. J Transl Med 2024; 22:618. [PMID: 38961476 PMCID: PMC11223394 DOI: 10.1186/s12967-024-05416-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2024] [Accepted: 06/19/2024] [Indexed: 07/05/2024] Open
Abstract
BACKGROUND Cell free DNA (cfDNA)-based assays hold great potential in detecting early cancer signals yet determining the tissue-of-origin (TOO) for cancer signals remains a challenging task. Here, we investigated the contribution of a methylation atlas to TOO detection in low depth cfDNA samples. METHODS We constructed a tumor-specific methylation atlas (TSMA) using whole-genome bisulfite sequencing (WGBS) data from five types of tumor tissues (breast, colorectal, gastric, liver and lung cancer) and paired white blood cells (WBC). TSMA was used with a non-negative least square matrix factorization (NNLS) deconvolution algorithm to identify the abundance of tumor tissue types in a WGBS sample. We showed that TSMA worked well with tumor tissue but struggled with cfDNA samples due to the overwhelming amount of WBC-derived DNA. To construct a model for TOO, we adopted the multi-modal strategy and used as inputs the combination of deconvolution scores from TSMA with other features of cfDNA. RESULTS Our final model comprised of a graph convolutional neural network using deconvolution scores and genome-wide methylation density features, which achieved an accuracy of 69% in a held-out validation dataset of 239 low-depth cfDNA samples. CONCLUSIONS In conclusion, we have demonstrated that our TSMA in combination with other cfDNA features can improve TOO detection in low-depth cfDNA samples.
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Affiliation(s)
| | | | - Trung Hieu Tran
- Medical Genetics Institute, Gene Solutions, Ho Chi Minh, Vietnam
| | - Le Anh Khoa Huynh
- Medical Genetics Institute, Gene Solutions, Ho Chi Minh, Vietnam
- Department of Biostatistics, School of Medicine, Virginia Commonwealth University, Richmond, USA
| | - Phuoc Loc Doan
- Medical Genetics Institute, Gene Solutions, Ho Chi Minh, Vietnam
| | | | | | | | | | - Hoa Giang
- Medical Genetics Institute, Gene Solutions, Ho Chi Minh, Vietnam
| | - Le Son Tran
- Medical Genetics Institute, Gene Solutions, Ho Chi Minh, Vietnam
| | - Minh Duy Phan
- Medical Genetics Institute, Gene Solutions, Ho Chi Minh, Vietnam.
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Marinello A, Tagliamento M, Pagliaro A, Conci N, Cella E, Vasseur D, Remon J, Levy A, Dall'Olio FG, Besse B. Circulating tumor DNA to guide diagnosis and treatment of localized and locally advanced non-small cell lung cancer. Cancer Treat Rev 2024; 129:102791. [PMID: 38963991 DOI: 10.1016/j.ctrv.2024.102791] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2024] [Revised: 06/15/2024] [Accepted: 06/22/2024] [Indexed: 07/06/2024]
Abstract
Liquid biopsy is a minimally invasive method for biomarkers detection in body fluids, particularly in blood, which offers an elevated and growing number of clinical applications in oncology. As a result of the improvement in the techniques for DNA analysis, above all next-generation sequencing (NGS) assays, circulating tumor DNA (ctDNA) has become the most informing tumor-derived material for most types of cancer, including non-small cell lung cancer (NSCLC). Although ctDNA concentration is higher in patients with advanced tumors, it can be detected even in patients with early-stage disease. Therefore, numerous clinical applications of ctDNA in the management of early-stage lung cancer are emerging, such as lung cancer screening, the identification of minimal residual disease (MRD), and the prediction of relapse before radiologic progression. Moreover, a high number of clinical trials are ongoing to better define the impact of ctDNA evaluation in this setting. Aim of this review is to offer a comprehensive overview of the most relevant implementations in using ctDNA for the management of early-stage lung cancer, addressing available data, technical aspects, limitations, and future perspectives.
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Affiliation(s)
- Arianna Marinello
- Department of Cancer Medicine, Gustave Roussy, Villejuif, France; INSERM Unit 1030 - Molecular Radiotherapy and Therapeutic Innovation, Gustave Roussy, Villejuif, France
| | - Marco Tagliamento
- Department of Cancer Medicine, Gustave Roussy, Villejuif, France; Department of Internal Medicine and Medical Specialties, University of Genova, Genova, Italy.
| | - Arianna Pagliaro
- Department of Cancer Medicine, Gustave Roussy, Villejuif, France; Department of Medical Oncology, IRCCS Istituto Clinico Humanitas, Rozzano, Italy
| | - Nicole Conci
- Department of Medical Oncology, IRCCS Sant'Orsola-Malpighi, Bologna, Italy
| | - Eugenia Cella
- Department of Internal Medicine and Medical Specialties, University of Genova, Genova, Italy
| | - Damien Vasseur
- Department of Medical Biology and Pathology, Gustave Roussy, Villejuif, France
| | - Jordi Remon
- Department of Cancer Medicine, Gustave Roussy, Villejuif, France
| | - Antonin Levy
- Department of Radiotherapy, Gustave Roussy, Villejuif, France
| | | | - Benjamin Besse
- Department of Cancer Medicine, Gustave Roussy, Villejuif, France
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6
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Kato T, Yang JCH, Ahn MJ, Sakai H, Morise M, Chen YM, Han JY, Yang JJ, Zhao J, Hsia TC, Berghoff K, Bruns R, Vioix H, Lang S, Johne A, Le X, Paik PK. Efficacy and safety of tepotinib in Asian patients with advanced NSCLC with MET exon 14 skipping enrolled in VISION. Br J Cancer 2024; 130:1679-1686. [PMID: 38575731 PMCID: PMC11091176 DOI: 10.1038/s41416-024-02615-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2023] [Revised: 01/30/2024] [Accepted: 02/06/2024] [Indexed: 04/06/2024] Open
Abstract
BACKGROUND Tepotinib, a MET inhibitor approved for the treatment of MET exon 14 (METex14) skipping NSCLC, demonstrated durable clinical activity in VISION (Cohort A + C; N = 313): objective response rate (ORR) 51.4% (95% CI: 45.8, 57.1); median duration of response (mDOR) 18.0 months (95% CI: 12.4, 46.4). We report outcomes in Asian patients from VISION (Cohort A + C) (cut-off: November 20, 2022). METHODS Patients with advanced METex14 skipping NSCLC, detected by liquid or tissue biopsy, received tepotinib 500 mg (450 mg active moiety) once daily. PRIMARY ENDPOINT objective response (RECIST 1.1) by independent review. Secondary endpoints included: DOR, progression-free survival (PFS), overall survival (OS), safety, and health-related quality of life (HRQoL). RESULTS Across treatment lines in 106 Asian patients (39.6% female, 43.4% smoking history, 79.2% adenocarcinoma, 47.2% treatment-naive), ORR was 56.6% (95% CI: 46.6, 66.2), mDOR 18.5 months (10.4, ne), mPFS 13.8 months (10.8, 22.0), and mOS 25.5 months (19.3, 36.4). Consistent efficacy observed, regardless of baseline characteristics. HRQoL remained stable during treatment. Treatment-related adverse events (TRAEs) occurred in 95.3% of patients (39.6% Grade ≥3). Most common TRAEs: peripheral edema (62.3%), creatinine increase (38.7%). CONCLUSIONS Tepotinib demonstrated robust and durable efficacy, with a manageable safety profile, in Asian patients with METex14 skipping NSCLC. CLINICAL TRIAL REGISTRATION NCT02864992.
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Affiliation(s)
- Terufumi Kato
- Department of Thoracic Oncology, Kanagawa Cancer Center, Yokohama, Japan
| | - James Chih-Hsin Yang
- Department of Medical Oncology, National Taiwan University Cancer Center, Taipei, Taiwan.
| | - Myung-Ju Ahn
- Division of Hematology Oncology, Department of Medicine, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Republic of Korea
| | - Hiroshi Sakai
- Department of Thoracic Oncology, Saitama Cancer Center, Kitaadachi-gun, Japan
- Department of Thoracic Oncology, Ageo Central General Hospital, Saitama, Japan
| | - Masahiro Morise
- Department of Respiratory Medicine, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Yuh-Min Chen
- Department of Chest Medicine, Taipei Veterans General Hospital, and School of Medicine, National Yang-Ming University, Taipei, Taiwan
| | - Ji-Youn Han
- The Center for Lung Cancer, National Cancer Center, Goyang, Republic of Korea
| | - Jin-Ji Yang
- Department of Oncology, Guangdong Lung Cancer Institute, Guangdong General Hospital and Guangdong Academy of Medical Sciences, Guangzhou, China
| | - Jun Zhao
- Department of Thoracic Oncology, Peking University Cancer Hospital and Institute, Beijing, China
| | - Te-Chun Hsia
- Department of Internal Medicine, China Medical University Hospital, Taichung, Taiwan
| | - Karin Berghoff
- Global Patient Safety, Merck Healthcare KGaA, Darmstadt, Germany
| | - Rolf Bruns
- Department of Biostatistics, Merck Healthcare KGaA, Darmstadt, Germany
| | - Helene Vioix
- Global Evidence and Value Department, Merck Healthcare KGaA, Darmstadt, Germany
| | - Simone Lang
- Global Clinical Development, Merck Healthcare KGaA, Darmstadt, Germany
| | - Andreas Johne
- Global Clinical Development, Merck Healthcare KGaA, Darmstadt, Germany
| | - Xiuning Le
- Department of Thoracic Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Paul K Paik
- Department of Medicine, Weill Cornell Medical College, New York, NY, USA
- Department of Medicine, Thoracic Oncology Service, Memorial Sloan-Kettering Cancer Center, New York, NY, USA
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7
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Ren F, Fei Q, Qiu K, Zhang Y, Zhang H, Sun L. Liquid biopsy techniques and lung cancer: diagnosis, monitoring and evaluation. J Exp Clin Cancer Res 2024; 43:96. [PMID: 38561776 PMCID: PMC10985944 DOI: 10.1186/s13046-024-03026-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2024] [Accepted: 03/24/2024] [Indexed: 04/04/2024] Open
Abstract
Lung cancer stands as the most prevalent form of cancer globally, posing a significant threat to human well-being. Due to the lack of effective and accurate early diagnostic methods, many patients are diagnosed with advanced lung cancer. Although surgical resection is still a potential means of eradicating lung cancer, patients with advanced lung cancer usually miss the best chance for surgical treatment, and even after surgical resection patients may still experience tumor recurrence. Additionally, chemotherapy, the mainstay of treatment for patients with advanced lung cancer, has the potential to be chemo-resistant, resulting in poor clinical outcomes. The emergence of liquid biopsies has garnered considerable attention owing to their noninvasive nature and the ability for continuous sampling. Technological advancements have propelled circulating tumor cells (CTCs), circulating tumor DNA (ctDNA), extracellular vesicles (EVs), tumor metabolites, tumor-educated platelets (TEPs), and tumor-associated antigens (TAA) to the forefront as key liquid biopsy biomarkers, demonstrating intriguing and encouraging results for early diagnosis and prognostic evaluation of lung cancer. This review provides an overview of molecular biomarkers and assays utilized in liquid biopsies for lung cancer, encompassing CTCs, ctDNA, non-coding RNA (ncRNA), EVs, tumor metabolites, TAAs and TEPs. Furthermore, we expound on the practical applications of liquid biopsies, including early diagnosis, treatment response monitoring, prognostic evaluation, and recurrence monitoring in the context of lung cancer.
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Affiliation(s)
- Fei Ren
- Department of Geriatrics, The First Hospital of China Medical University, Shen Yang, 110000, China
| | - Qian Fei
- Department of Oncology, Shengjing Hospital of China Medical University, Shen Yang, 110000, China
| | - Kun Qiu
- Thoracic Surgery, The First Hospital of China Medical University, Shen Yang, 110000, China
| | - Yuanjie Zhang
- Thoracic Surgery, The First Hospital of China Medical University, Shen Yang, 110000, China
| | - Heyang Zhang
- Department of Hematology, The First Hospital of China Medical University, Shen Yang, 110000, China.
| | - Lei Sun
- Thoracic Surgery, The First Hospital of China Medical University, Shen Yang, 110000, China.
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8
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Zhong J, Jiang H, Liu X, Liao H, Xie F, Shao B, Jia S, Li H. Variant allele frequency in circulating tumor DNA correlated with tumor disease burden and predicted outcomes in patients with advanced breast cancer. Breast Cancer Res Treat 2024; 204:617-629. [PMID: 38183515 PMCID: PMC10959836 DOI: 10.1007/s10549-023-07210-9] [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: 10/10/2023] [Accepted: 11/29/2023] [Indexed: 01/08/2024]
Abstract
PURPOSE In patients with first-line advanced breast cancer (ABC), the correlation between ctDNA variant allele frequency (VAF) and tumor disease burden, and its prognostic value remains poorly investigated. METHODS This study included patients with ABC diagnosed at Peking University Cancer Hospital who performed ctDNA test before receiving first-line treatment. Baseline plasma samples were collected for assessing ctDNA alterations and VAF with next-generation sequencing. The sum of tumor target lesion diameters (SLD) was measured with imaging methods according to RECIST 1.1 criteria. RESULTS The final cohort included 184 patients. The median age of the cohort was 49.4 (IQR: 42.3-56.8) years. The median VAF was 15.6% (IQR: 5.4%-33.7%). VAF showed positive correlation with SLD in patients with relatively large tumor lesions (r = 0.314, p = 0.003), but not in patients with small tumor lesions (p = 0.226). VAF was associated with multiple metastasis sites (p = 0.001). Multivariate Cox regression analysis showed that high VAF was associated with shorter overall survival (OS) (HR: 3.519, 95% confidence interval (CI): 2.149-5.761), and first-line progression-free survival (PFS) (HR: 2.352, 95%CI: 1.462-3.782). Combined VAF and SLD improved prediction performance, both median OS and PFS of patients in VAF(H)/SLD(H) group were significantly longer than VAF(L)/SLD(L) group (mOS: 49.3 vs. 174.1 months; mPFS: 9.6 vs. 25.3 months). CONCLUSION ctDNA VAF associated with tumor disease burden, and was a prognostic factor for patients with ABC. A combination of ctDNA test and radiographic imaging might enhance tumor burden evaluation, and improve prognosis stratification in patients with ABC.
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Affiliation(s)
- Jianxin Zhong
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Department of Breast Oncology, Peking University Cancer Hospital & Institute, Beijing, China
| | - Hanfang Jiang
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Department of Breast Oncology, Peking University Cancer Hospital & Institute, Beijing, China
| | - Xiaoran Liu
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Department of Breast Oncology, Peking University Cancer Hospital & Institute, Beijing, China
| | - Hao Liao
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Department of Breast Oncology, Peking University Cancer Hospital & Institute, Beijing, China
| | - Feng Xie
- Huidu Shanghai Medical Sciences, Shanghai, China
| | - Bin Shao
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Department of Breast Oncology, Peking University Cancer Hospital & Institute, Beijing, China.
| | - Shidong Jia
- Huidu Shanghai Medical Sciences, Shanghai, China.
| | - Huiping Li
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Department of Breast Oncology, Peking University Cancer Hospital & Institute, Beijing, China.
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9
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Galant N, Nicoś M, Kuźnar-Kamińska B, Krawczyk P. Variant Allele Frequency Analysis of Circulating Tumor DNA as a Promising Tool in Assessing the Effectiveness of Treatment in Non-Small Cell Lung Carcinoma Patients. Cancers (Basel) 2024; 16:782. [PMID: 38398173 PMCID: PMC10887123 DOI: 10.3390/cancers16040782] [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: 01/22/2024] [Revised: 02/06/2024] [Accepted: 02/07/2024] [Indexed: 02/25/2024] Open
Abstract
Despite the different possible paths of treatment, lung cancer remains one of the leading causes of death in oncological patients. New tools guiding the therapeutic process are under scientific investigation, and one of the promising indicators of the effectiveness of therapy in patients with NSCLC is variant allele frequency (VAF) analysis. VAF is a metric characterized as the measurement of the specific variant allele proportion within a genomic locus, and it can be determined using methods based on NGS or PCR. It can be assessed using not only tissue samples but also ctDNA (circulating tumor DNA) isolated from liquid biopsy. The non-invasive characteristic of liquid biopsy enables a more frequent collection of material and increases the potential of VAF analysis in monitoring therapy. Several studies have been performed on patients with NSCLC to evaluate the possibility of VAF usage. The research carried out so far demonstrates that the evaluation of VAF dynamics may be useful in monitoring tumor progression, remission, and recurrence during or after treatment. Moreover, the use of VAF analysis appears to be beneficial in making treatment decisions. However, several issues require better understanding and standardization before VAF testing can be implemented in clinical practice. In this review, we discuss the difficulties in the application of ctDNA VAF analysis in clinical routine, discussing the diagnostic and methodological challenges in VAF measurement in liquid biopsy. We highlight the possible applications of VAF-based measurements that are under consideration in clinical trials in the monitoring of personalized treatments for patients with NSCLC.
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Affiliation(s)
- Natalia Galant
- Department of Pneumonology, Oncology and Allergology, Medical University of Lublin, 20-059 Lublin, Poland
| | - Marcin Nicoś
- Department of Pneumonology, Oncology and Allergology, Medical University of Lublin, 20-059 Lublin, Poland
| | - Barbara Kuźnar-Kamińska
- Department of Pulmonology, Allergology and Respiratory Oncology, Poznan University of Medical Sciences, 61-710 Poznan, Poland;
| | - Paweł Krawczyk
- Department of Pneumonology, Oncology and Allergology, Medical University of Lublin, 20-059 Lublin, Poland
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10
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Wen J, Yu JZ, Liu C, Ould Ismail AAO, Ma W. Exploring the Molecular Tumor Microenvironment and Translational Biomarkers in Brain Metastases of Non-Small-Cell Lung Cancer. Int J Mol Sci 2024; 25:2044. [PMID: 38396722 PMCID: PMC10889194 DOI: 10.3390/ijms25042044] [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: 12/05/2023] [Revised: 01/17/2024] [Accepted: 02/01/2024] [Indexed: 02/25/2024] Open
Abstract
Brain metastases represent a significant clinical challenge in the treatment of non-small-cell lung cancer (NSCLC), often leading to a severe decline in patient prognosis and survival. Recent advances in imaging and systemic treatments have increased the detection rates of brain metastases, yet clinical outcomes remain dismal due to the complexity of the metastatic tumor microenvironment (TME) and the lack of specific biomarkers for early detection and targeted therapy. The intricate interplay between NSCLC tumor cells and the surrounding TME in brain metastases is pivotal, influencing tumor progression, immune evasion, and response to therapy. This underscores the necessity for a deeper understanding of the molecular underpinnings of brain metastases, tumor microenvironment, and the identification of actionable biomarkers that can inform multimodal treatment approaches. The goal of this review is to synthesize current insights into the TME and elucidate molecular mechanisms in NSCLC brain metastases. Furthermore, we will explore the promising horizon of emerging biomarkers, both tissue- and liquid-based, that hold the potential to radically transform the treatment strategies and the enhancement of patient outcomes.
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Affiliation(s)
- Jiexi Wen
- Department of Pathology and Laboratory Medicine, Dartmouth-Hitchcock Medical Center, Geisel School of Medicine at Dartmouth, Lebanon, NH 03756, USA
| | - Jie-Zeng Yu
- Division of Hematology/Oncology, Department of Medicine, University of California at San Francisco, San Francisco, CA 94143, USA
| | - Catherine Liu
- School of Medicine and Dentistry, University of Rochester, Rochester, NY 14642, USA
| | - A. Aziz O. Ould Ismail
- Department of Pathology and Laboratory Medicine, Dartmouth-Hitchcock Medical Center, Geisel School of Medicine at Dartmouth, Lebanon, NH 03756, USA
| | - Weijie Ma
- Department of Pathology and Laboratory Medicine, Dartmouth-Hitchcock Medical Center, Geisel School of Medicine at Dartmouth, Lebanon, NH 03756, USA
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11
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Tran HT, Heeke S, Sujit S, Vokes N, Zhang J, Aminu M, Lam VK, Vaporciyan A, Swisher SG, Godoy MCB, Cascone T, Sepesi B, Gibbons DL, Wu J, Heymach JV. Circulating tumor DNA and radiological tumor volume identify patients at risk for relapse with resected, early-stage non-small-cell lung cancer. Ann Oncol 2024; 35:183-189. [PMID: 37992871 PMCID: PMC11233158 DOI: 10.1016/j.annonc.2023.11.008] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2023] [Revised: 11/01/2023] [Accepted: 11/15/2023] [Indexed: 11/24/2023] Open
Abstract
BACKGROUND Predicting relapse and overall survival (OS) in early-stage non-small-cell lung cancer (NSCLC) patients remains challenging. Therefore, we hypothesized that detection of circulating tumor DNA (ctDNA) can identify patients with increased risk of relapse and that integrating radiological tumor volume measurement along with ctDNA detectability improves prediction of outcome. PATIENTS AND METHODS We analyzed 366 serial plasma samples from 85 patients who underwent surgical resections and assessed ctDNA using a next-generation sequencing liquid biopsy assay, and measured tumor volume using a computed tomography-based three-dimensional annotation. RESULTS Our results showed that patients with detectable ctDNA at baseline or after treatment and patients who did not clear ctDNA after treatment had a significantly worse clinical outcome. Integrating radiological analysis allowed the stratification in risk groups prognostic of clinical outcome as confirmed in an independent cohort of 32 patients. CONCLUSIONS Our findings suggest ctDNA and radiological monitoring could be valuable tools for guiding follow-up care and treatment decisions for early-stage NSCLC patients.
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Affiliation(s)
- H T Tran
- Department of Thoracic Head & Neck Medical Oncology
| | - S Heeke
- Department of Thoracic Head & Neck Medical Oncology
| | - S Sujit
- Department of Imaging Physics, The University of Texas MD Anderson Cancer Center, Houston
| | - N Vokes
- Department of Thoracic Head & Neck Medical Oncology
| | - J Zhang
- Department of Thoracic Head & Neck Medical Oncology
| | - M Aminu
- Department of Imaging Physics, The University of Texas MD Anderson Cancer Center, Houston
| | - V K Lam
- Department of Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins, Baltimore
| | - A Vaporciyan
- Department of Thoracic and Cardiovascular Surgery
| | - S G Swisher
- Department of Thoracic and Cardiovascular Surgery
| | - M C B Godoy
- Department of Thoracic Imaging, The University of Texas MD Anderson Cancer Center, Houston, USA
| | - T Cascone
- Department of Thoracic Head & Neck Medical Oncology
| | - B Sepesi
- Department of Thoracic Head & Neck Medical Oncology
| | - D L Gibbons
- Department of Thoracic Head & Neck Medical Oncology
| | - J Wu
- Department of Thoracic Head & Neck Medical Oncology; Department of Imaging Physics, The University of Texas MD Anderson Cancer Center, Houston
| | - J V Heymach
- Department of Thoracic Head & Neck Medical Oncology.
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12
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Roque R, Ribeiro IP, Figueiredo-Dias M, Gourley C, Carreira IM. Current Applications and Challenges of Next-Generation Sequencing in Plasma Circulating Tumour DNA of Ovarian Cancer. BIOLOGY 2024; 13:88. [PMID: 38392306 PMCID: PMC10886635 DOI: 10.3390/biology13020088] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/16/2023] [Revised: 01/25/2024] [Accepted: 01/27/2024] [Indexed: 02/24/2024]
Abstract
Circulating tumour DNA (ctDNA) facilitates longitudinal study of the tumour genome, which, unlike tumour tissue biopsies, globally reflects intratumor and intermetastatis heterogeneity. Despite its costs, next-generation sequencing (NGS) has revolutionised the study of ctDNA, ensuring a more comprehensive and multimodal approach, increasing data collection, and introducing new variables that can be correlated with clinical outcomes. Current NGS strategies can comprise a tumour-informed set of genes or the entire genome and detect a tumour fraction as low as 10-5. Despite some conflicting studies, there is evidence that ctDNA levels can predict the worse outcomes of ovarian cancer (OC) in both early and advanced disease. Changes in those levels can also be informative regarding treatment efficacy and tumour recurrence, capable of outperforming CA-125, currently the only universally utilised plasma biomarker in high-grade serous OC (HGSOC). Qualitative evaluation of sequencing shows that increasing copy number alterations and gene variants during treatment may correlate with a worse prognosis in HGSOC. However, following tumour clonality and emerging variants during treatment poses a more unique opportunity to define treatment response, select patients based on their emerging resistance mechanisms, like BRCA secondary mutations, and discover potential targetable variants. Sequencing of tumour biopsies and ctDNA is not always concordant, likely as a result of clonal heterogeneity, which is better captured in the plasma samples than it is in a large number of biopsies. These incoherences may reflect tumour clonality and reveal the acquired alterations that cause treatment resistance. Cell-free DNA methylation profiles can be used to distinguish OC from healthy individuals, and NGS methylation panels have been shown to have excellent diagnostic capabilities. Also, methylation signatures showed promise in explaining treatment responses, including BRCA dysfunction. ctDNA is evolving as a promising new biomarker to track tumour evolution and clonality through the treatment of early and advanced ovarian cancer, with potential applicability in prognostic prediction and treatment selection. While its role in HGSOC paves the way to clinical applicability, its potential interest in other histological subtypes of OC remains unknown.
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Affiliation(s)
- Ricardo Roque
- Cytogenetics and Genomics Laboratory, Institute of Cellular and Molecular Biology, Faculty of Medicine, University of Coimbra, 3004-504 Coimbra, Portugal
- Centre of Investigation on Environment Genetics and Oncobiology (CIMAGO), Institute for Clinical and Biomedical Research (iCBR), Faculty of Medicine, University of Coimbra, 3004-504 Coimbra, Portugal
- Portuguese Institute of Oncology of Coimbra, 3000-075 Coimbra, Portugal
| | - Ilda Patrícia Ribeiro
- Cytogenetics and Genomics Laboratory, Institute of Cellular and Molecular Biology, Faculty of Medicine, University of Coimbra, 3004-504 Coimbra, Portugal
- Centre of Investigation on Environment Genetics and Oncobiology (CIMAGO), Institute for Clinical and Biomedical Research (iCBR), Faculty of Medicine, University of Coimbra, 3004-504 Coimbra, Portugal
| | - Margarida Figueiredo-Dias
- Faculty of Medicine, Gynecology Department, University of Coimbra, 3004-504 Coimbra, Portugal
- Coimbra Academic and Clinical Centre, 3000-370 Coimbra, Portugal
- Gynecology Department, Hospital University Centre of Coimbra, 3004-561 Coimbra, Portugal
| | - Charlie Gourley
- Nicola Murray Centre for Ovarian Cancer Research, Cancer Research UK Scotland Centre, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh EH4 2XU, UK
| | - Isabel Marques Carreira
- Cytogenetics and Genomics Laboratory, Institute of Cellular and Molecular Biology, Faculty of Medicine, University of Coimbra, 3004-504 Coimbra, Portugal
- Centre of Investigation on Environment Genetics and Oncobiology (CIMAGO), Institute for Clinical and Biomedical Research (iCBR), Faculty of Medicine, University of Coimbra, 3004-504 Coimbra, Portugal
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Li C, Shao J, Li P, Feng J, Li J, Wang C. Circulating tumor DNA as liquid biopsy in lung cancer: Biological characteristics and clinical integration. Cancer Lett 2023; 577:216365. [PMID: 37634743 DOI: 10.1016/j.canlet.2023.216365] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2023] [Revised: 08/22/2023] [Accepted: 08/23/2023] [Indexed: 08/29/2023]
Abstract
Lung cancer maintains high morbidity and mortality rate globally despite significant advancements in diagnosis and treatment in the era of precision medicine. Pathological analysis of tumor tissue, the current gold standard for lung cancer diagnosis, is intrusive and intrinsically confined to evaluating the limited amount of tissues that could be physically extracted. However, tissue biopsy has several limitations, including the invasiveness of the procedure and difficulty in obtaining samples for patients at advanced stages., there Additionally,has been no major breakthrough in tumor biomarkers with high specificity and sensitivity, particularly for early-stage lung cancer. Liquid biopsy has been considered a feasible auxiliary tool for tearly dianosis, evaluating treatment responses and monitoring prognosis of lung cancer. Circulating tumor DNA (ctDNA), an ideal biomarker of liquid biopsy, has emerged as one of the most reliable tools for monitoring tumor processes at molecular levels. Herein, this review focuses on tumor heterogeneity to elucidate the superiority of liquid biopsy and retrospectively discussdeciphersolution. We systematically elaborate ctDNA biological characteristics, introduce methods for ctDNA detection, and discuss the current role of plasma ctDNA in lung cancer management. Finally, we summarize the drawbacks of ctDNA analysis and highlight its potential clinical application in lung cancer.
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Affiliation(s)
- Changshu Li
- Department of Pulmonary and Critical Care Medicine, Med-X Center for Manufacturing, Frontiers Science Center for Disease-Related Molecular Network, State Key Laboratory of Respiratory Health and Multimorbidity, West China School of Medicine, West China Hospital, Sichuan University, Chengdu, China
| | - Jun Shao
- Department of Pulmonary and Critical Care Medicine, Med-X Center for Manufacturing, Frontiers Science Center for Disease-Related Molecular Network, State Key Laboratory of Respiratory Health and Multimorbidity, West China School of Medicine, West China Hospital, Sichuan University, Chengdu, China
| | - Peiyi Li
- Department of Anesthesiology, West China Hospital, Sichuan University, Chengdu, China
| | - Jiaming Feng
- West China School of Medicine, Sichuan University, Chengdu, China
| | - Jingwei Li
- Department of Pulmonary and Critical Care Medicine, Med-X Center for Manufacturing, Frontiers Science Center for Disease-Related Molecular Network, State Key Laboratory of Respiratory Health and Multimorbidity, West China School of Medicine, West China Hospital, Sichuan University, Chengdu, China
| | - Chengdi Wang
- Department of Pulmonary and Critical Care Medicine, Med-X Center for Manufacturing, Frontiers Science Center for Disease-Related Molecular Network, State Key Laboratory of Respiratory Health and Multimorbidity, West China School of Medicine, West China Hospital, Sichuan University, Chengdu, China.
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14
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Garon EB, Reck M, Nishio K, Heymach JV, Nishio M, Novello S, Paz-Ares L, Popat S, Aix SP, Graham H, Butts BD, Visseren-Grul C, Nakagawa K. Ramucirumab plus erlotinib versus placebo plus erlotinib in previously untreated EGFR-mutated metastatic non-small-cell lung cancer (RELAY): exploratory analysis of next-generation sequencing results. ESMO Open 2023; 8:101580. [PMID: 37390764 PMCID: PMC10485403 DOI: 10.1016/j.esmoop.2023.101580] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2023] [Revised: 04/12/2023] [Accepted: 05/08/2023] [Indexed: 07/02/2023] Open
Abstract
BACKGROUND Ramucirumab plus erlotinib (RAM + ERL) demonstrated superior progression-free survival (PFS) over placebo + ERL (PBO + ERL) in the phase III RELAY study of patients with epidermal growth factor receptor (EGFR)-mutated metastatic non-small-cell lung cancer (EGFR+ mNSCLC; NCT02411448). Next-generation sequencing (NGS) was used to identify clinically relevant alterations in circulating tumor DNA (ctDNA) and explore their impact on treatment outcomes. PATIENTS AND METHODS Eligible patients with EGFR+ mNSCLC were randomized 1 : 1 to ERL (150 mg/day) plus RAM (10 mg/kg)/PBO every 2 weeks. Liquid biopsies were to be prospectively collected at baseline, cycle 4 (C4), and postdiscontinuation follow-up. EGFR and co-occurring/treatment-emergent (TE) genomic alterations in ctDNA were analyzed using Guardant360 NGS platform. RESULTS In those with valid baseline samples, detectable activating EGFR alterations in ctDNA (aEGFR+) were associated with shorter PFS [aEGFR+: 12.7 months (n = 255) versus aEGFR-: 22.0 months (n = 131); hazard ratio (HR) = 1.87, 95% confidence interval (CI) 1.42-2.51]. Irrespective of detectable/undetectable baseline aEGFR, RAM + ERL was associated with longer PFS versus PBO + ERL [aEGFR+: median PFS (mPFS) = 15.2 versus 11.1 months, HR = 0.63, 95% CI 0.46-0.85; aEGFR-: mPFS = 22.1 versus 19.2 months, HR = 0.80, 95% CI 0.49-1.30]. Baseline alterations co-occurring with aEGFR were identified in 69 genes, most commonly TP53 (43%), EGFR (other than aEGFR; 25%), and PIK3CA (10%). PFS was longer in RAM + ERL, irrespective of baseline co-occurring alterations. Clearance of baseline aEGFR by C4 was associated with longer PFS (mPFS = 14.1 versus 7.0 months, HR = 0.481, 95% CI 0.33-0.71). RAM + ERL improved PFS outcomes, irrespective of aEGFR mutation clearance. TE gene alterations were most commonly in EGFR [T790M (29%), other (19%)] and TP53 (16%). CONCLUSIONS Baseline aEGFR alterations in ctDNA were associated with shorter mPFS. RAM + ERL was associated with improved PFS outcomes, irrespective of detectable/undetectable aEGFR, co-occurring baseline alterations, or aEGFR+ clearance by C4. aEGFR+ clearance by C4 was associated with improved PFS outcomes. Monitoring co-occurring alterations and aEGFR+ clearance may provide insights into mechanisms of EGFR tyrosine kinase inhibitor resistance and the patients who may benefit from intensified treatment schedules.
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Affiliation(s)
- E B Garon
- David Geffen School of Medicine at University of California Los Angeles/TRIO-US Network, Los Angeles, USA.
| | - M Reck
- LungenClinic, Airway Research Center North (ARCN), German Center for Lung Research (DZL), Grosshansdorf, Germany
| | - K Nishio
- Department of Medical Oncology, Kindai University, Osaka, Japan
| | - J V Heymach
- Department of Thoracic/Head & Neck Medical Oncology, University of Texas, MD Anderson Cancer Center, Houston, USA; Department of Cancer Biology, University of Texas, MD Anderson Cancer Center, Houston, USA
| | - M Nishio
- Department of Thoracic Medical Oncology, Cancer Institute Hospital, Japanese Foundation for Cancer Research, Tokyo, Japan
| | - S Novello
- Department of Oncology, AOU San Luigi, University of Turin, Turin, Italy
| | - L Paz-Ares
- Medical Oncology Department, Hospital Universitario Doce de Octubre, Madrid, Spain
| | - S Popat
- Royal Marsden NHS Trust, London, UK
| | - S Ponce Aix
- Hospital Universitario 12 de Octubre, Madrid, Spain
| | - H Graham
- Eli Lilly and Company, Indianapolis, USA
| | - B D Butts
- Eli Lilly and Company, Indianapolis, USA
| | | | - K Nakagawa
- Department of Medical Oncology, Kindai University Faculty of Medicine, Osaka, Japan
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15
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Ottestad AL, Johansen H, Halvorsen TO, Dai HY, Wahl SGF, Emdal EF, Grønberg BH. Associations between detectable circulating tumor DNA and tumor glucose uptake measured by 18F-FDG PET/CT in early-stage non-small cell lung cancer. BMC Cancer 2023; 23:646. [PMID: 37434111 PMCID: PMC10334612 DOI: 10.1186/s12885-023-11147-z] [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: 03/15/2023] [Accepted: 07/03/2023] [Indexed: 07/13/2023] Open
Abstract
BACKGROUND The low level of circulating tumor DNA (ctDNA) in the blood is a well-known challenge for the application of liquid biopsies in early-stage non-small cell lung cancer (NSCLC) management. Studies of metastatic NSCLC indicate that ctDNA levels are associated with tumor metabolic activity as measured by 18F-fluorodeoxyglucose positron emission tomography (18F-FDG PET/CT). This study investigated this association in NSCLC patients considered for potentially curative treatment and explored whether the two methods provide independent prognostic information. METHOD Patients with stage I-III NSCLC who had routinely undergone an 18F-FDG PET/CT scan and exploratory ctDNA analyses were included. Tumor glucose uptake was measured by maximum standardized uptake value (SUVmax), metabolic tumor volume (MTV), and total lesion glycolysis (TLG) from the 18F-FDG PET/CT scans. ctDNA detectability and quantity, using variant allele frequency, were estimated by tumor-informed ctDNA analyses. RESULTS In total, 63 patients (median age 70 years, 60% women, and 90% adenocarcinoma) were included. The tumor glucose uptake (SUVmax, MTV, and TLG) was significantly higher in patients with detectable ctDNA (n = 19, p < 0.001). The ctDNA quantity correlated with MTV (Spearman's ρ = 0.53, p = 0.021) and TLG (Spearman's ρ = 0.56, p = 0.013) but not with SUVmax (Spearman's ρ = 0.034, p = 0.15). ctDNA detection was associated with shorter OS independent of MTV (HR: 2.70, 95% CI: 1.07-6.82, p = 0.035) and TLG (HR: 2.63, 95% CI: 1.06-6.51, p = 0.036). Patients with high tumor glucose uptake and detectable ctDNA had shorter overall survival and progression-free survival than those without detectable ctDNA, though these associations were not statistically significant (p > 0.05). CONCLUSION There was a positive correlation between plasma ctDNA quantity and MTV and TLG in early-stage NSCLC patients. Despite the correlation, the results indicated that ctDNA detection was a negative prognostic factor independent of MTV and TLG.
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Affiliation(s)
- Anine Larsen Ottestad
- Department of Clinical and Molecular Medicine, Faculty of Medicine and Health Sciences, Norwegian University of Science and Technology (NTNU), Trondheim, 7030, Norway.
- Department of Oncology, St. Olavs Hospital, Trondheim University Hospital, Trondheim, 7030, Norway.
| | - Håkon Johansen
- Department of Radiology and Nuclear Medicine, St. Olavs Hospital, Trondheim University Hospital, Trondheim, 7030, Norway
| | - Tarje Onsøien Halvorsen
- Department of Clinical and Molecular Medicine, Faculty of Medicine and Health Sciences, Norwegian University of Science and Technology (NTNU), Trondheim, 7030, Norway
- Department of Oncology, St. Olavs Hospital, Trondheim University Hospital, Trondheim, 7030, Norway
| | - Hong Yan Dai
- Department of Clinical and Molecular Medicine, Faculty of Medicine and Health Sciences, Norwegian University of Science and Technology (NTNU), Trondheim, 7030, Norway
- Department of Pathology, Clinic of Laboratory Medicine, St. Olavs Hospital, Trondheim University Hospital, Trondheim, 7030, Norway
| | - Sissel Gyrid Freim Wahl
- Department of Clinical and Molecular Medicine, Faculty of Medicine and Health Sciences, Norwegian University of Science and Technology (NTNU), Trondheim, 7030, Norway
- Department of Pathology, Clinic of Laboratory Medicine, St. Olavs Hospital, Trondheim University Hospital, Trondheim, 7030, Norway
| | - Elisabeth Fritzke Emdal
- Department of Pathology, Clinic of Laboratory Medicine, St. Olavs Hospital, Trondheim University Hospital, Trondheim, 7030, Norway
| | - Bjørn Henning Grønberg
- Department of Clinical and Molecular Medicine, Faculty of Medicine and Health Sciences, Norwegian University of Science and Technology (NTNU), Trondheim, 7030, Norway
- Department of Oncology, St. Olavs Hospital, Trondheim University Hospital, Trondheim, 7030, Norway
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Cai P, Yang B, Zhao J, Ye P, Yang D. Detection of KRAS mutation using plasma samples in non-small-cell lung cancer: a systematic review and meta-analysis. Front Oncol 2023; 13:1207892. [PMID: 37483491 PMCID: PMC10357383 DOI: 10.3389/fonc.2023.1207892] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2023] [Accepted: 06/20/2023] [Indexed: 07/25/2023] Open
Abstract
Background The aim of this study was to investigate the diagnostic accuracy of KRAS mutation detection using plasma sample of patients with non-small cell lung cancer (NSCLC). Methods Databases of Pubmed, Embase, Cochrane Library, and Web of Science were searched for studies detecting KRAS mutation in paired tissue and plasma samples of patients with NSCLC. Data were extracted from each eligible study and analyzed using MetaDiSc and STATA. Results After database searching and screening of the studies with pre-defined criteria, 43 eligible studies were identified and relevant data were extracted. After pooling the accuracy data from 3341 patients, the pooled sensitivity, specificity and diagnostic odds ratio were 71%, 94%, and 59.28, respectively. Area under curve of summary receiver operating characteristic curve was 0.8883. Subgroup analysis revealed that next-generation sequencing outperformed PCR-based techniques in detecting KRAS mutation using plasma sample of patients with NSCLC, with sensitivity, specificity, and diagnostic odds ratio of 73%, 94%, and 82.60, respectively. Conclusion Compared to paired tumor tissue sample, plasma sample showed overall good performance in detecting KRAS mutation in patients with NSCLC, which could serve as good surrogate when tissue samples are not available.
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Affiliation(s)
- Peiling Cai
- Department of Anatomy and Histology, School of Preclinical Medicine, Chengdu University, Chengdu, China
| | - Bofan Yang
- School of Clinical Medicine, Chengdu University, Chengdu, China
| | - Jiahui Zhao
- School of Clinical Medicine, Chengdu University, Chengdu, China
| | - Peng Ye
- Department of Anatomy and Histology, School of Preclinical Medicine, Chengdu University, Chengdu, China
| | - Dongmei Yang
- Clinical Laboratory & Clinical Research and Translational Center, Second People’s Hospital of Yibin City-West China Yibin Hospital, Sichuan University, Yibin, China
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Cohen SA, Liu MC, Aleshin A. Practical recommendations for using ctDNA in clinical decision making. Nature 2023; 619:259-268. [PMID: 37438589 DOI: 10.1038/s41586-023-06225-y] [Citation(s) in RCA: 14] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2022] [Accepted: 05/16/2023] [Indexed: 07/14/2023]
Abstract
The continuous improvement in cancer care over the past decade has led to a gradual decrease in cancer-related deaths. This is largely attributed to improved treatment and disease management strategies. Early detection of recurrence using blood-based biomarkers such as circulating tumour DNA (ctDNA) is being increasingly used in clinical practice. Emerging real-world data shows the utility of ctDNA in detecting molecular residual disease and in treatment-response monitoring, helping clinicians to optimize treatment and surveillance strategies. Many studies have indicated ctDNA to be a sensitive and specific biomarker for recurrence. However, most of these studies are largely observational or anecdotal in nature, and peer-reviewed data regarding the use of ctDNA are mainly indication-specific. Here we provide general recommendations on the clinical utility of ctDNA and how to interpret ctDNA analysis in different treatment settings, especially in patients with solid tumours. Specifically, we provide an understanding around the implications, strengths and limitations of this novel biomarker and how to best apply the results in clinical practice.
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Affiliation(s)
- Stacey A Cohen
- Fred Hutchinson Cancer Center, Seattle, WA, USA.
- University of Washington, Seattle, WA, USA.
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Condoluci A, Rossi D. Special issue on circulating tumor DNA: Introductory editorial. Semin Hematol 2023; 60:125-131. [PMID: 37620237 DOI: 10.1053/j.seminhematol.2023.08.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2023] [Accepted: 08/13/2023] [Indexed: 08/26/2023]
Affiliation(s)
- Adalgisa Condoluci
- Clinic of Hematology, Oncology Institute of Southern Switzerland, Ente Ospedaliero Cantonale, Bellinzona, Switzerland; Laboratory of Experimental Hematology, Institute of Oncology Research, Bellinzona, Switzerland; Università della Svizzera Italiana, Lugano, Switzerland
| | - Davide Rossi
- Clinic of Hematology, Oncology Institute of Southern Switzerland, Ente Ospedaliero Cantonale, Bellinzona, Switzerland; Laboratory of Experimental Hematology, Institute of Oncology Research, Bellinzona, Switzerland; Università della Svizzera Italiana, Lugano, Switzerland; Faculty of Biomedical Sciences, Università della Svizzera Italiana, Lugano, Switzerland.
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19
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Raei N, Safaralizadeh R, Latifi-Navid S. Clinical application of circulating tumor DNA in metastatic cancers. Expert Rev Mol Diagn 2023; 23:1209-1220. [PMID: 37797209 DOI: 10.1080/14737159.2023.2268008] [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: 04/07/2023] [Accepted: 10/04/2023] [Indexed: 10/07/2023]
Abstract
INTRODUCTION Advances in genomics have facilitated the application of cell-free DNA (cfDNA) and circulating tumor DNA (ctDNA) in phase II and phase III clinical trials. The various mutations of cfDNA/ctDNA have been correlated with clinical features. Advances in next-generation sequencing (NGS) and digital droplet PCR have paved the way for identifying cfDNA/ctDNA mutations. AREAS COVERED Herein, the biology of ctDNA and its function in clinical application in metastasis, which may lead to improved clinical management of metastatic cancer patients, are comprehensively reviewed. EXPERT OPINION Metastatic cancer ctDNA shows the greatest frequency of mutations in TP53, HER-2, KRAS, and EGFR genes (alteration frequency of > 50%). Therefore, identifying key mutations frequently present in metastatic cancers can help identify patients with pre-malignant tumors before cancer progression. Studying ctDNA can help determine the prognosis and select appropriate treatments for affected patients. Nevertheless, the obstacles to detecting and analyzing ctDNA should be addressed before translation into routine practice. Also, more clinical trials should be conducted to study the significance of ctDNA in commonly diagnosed malignancies. Given the recent advances in personalized anti-neoplastic treatments, further studies are needed to detect a panel of ctDNA and patient-specific ctDNA for various cancers.
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Affiliation(s)
- Negin Raei
- Digestive Disease Research Center, Ardabil University of Medical Sciences, Ardabil, Iran
- Department of Biology, Faculty of Natural Sciences, University of Tabriz, Tabriz, Iran
| | - Reza Safaralizadeh
- Department of Biology, Faculty of Natural Sciences, University of Tabriz, Tabriz, Iran
| | - Saeid Latifi-Navid
- Department of Biology, Faculty of Sciences, University of Mohaghegh Ardabili, Ardabil, Iran
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Maansson CT, Andersen ER, Ulhoi MP, Meldgaard P, Sorensen BS. DNAfusion: an R/Bioconductor package for increased sensitivity of detecting gene fusions in liquid biopsies. BMC Bioinformatics 2023; 24:131. [PMID: 37016288 PMCID: PMC10074784 DOI: 10.1186/s12859-023-05259-3] [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: 10/28/2022] [Accepted: 03/28/2023] [Indexed: 04/06/2023] Open
Abstract
BACKGROUND EML4-ALK gene fusions are oncogenic drivers in non-small cell lung cancer (NSCLC), and liquid biopsies containing EML4-ALK fragments can be used to study tumor dynamics using next-generation sequencing (NGS). However, the sensitivity of EML4-ALK detection varies between pipelines and analysis tools. RESULTS We developed an R/Bioconductor package, DNAfusion, which can be applied to BAM files generated by commercially available NGS pipelines, such as AVENIO. Forty-eight blood samples from a training cohort consisting of 41 stage IV EML4-ALK-positive NSCLC patients and seven healthy controls were used to develop DNAfusion. DNAfusion detected EML4-ALK in significantly more samples (sensitivity = 61.0%) compared to AVENIO (sensitivity = 36.6%). The newly identified EML4-ALK-positive patients were verified using droplet digital PCR. DNAfusion was subsequently validated in a blinded validation cohort comprising 24 EML4-ALK-positive and 24 EML4-ALK-negative stage IV NSCLC patients. DNAfusion detected significantly more EML4-ALK individuals in the validation cohort (sensitivity = 62.5%) compared to AVENIO (sensitivity = 29.2%). DNAfusion demonstrated a specificity of 100% in both the training and validation cohorts. CONCLUSION Here we present DNAfusion, which increases the sensitivity of EML4-ALK detection in liquid biopsies and can be implemented downstream of commercially available NGS pipelines. The simplistic method of operating the R package makes it easy to implement in the clinical setting, enabling wider expansion of NGS-based diagnostics.
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Affiliation(s)
- Christoffer Trier Maansson
- Department of Clinical Biochemistry, Faculty of Health, Aarhus University Hospital, Palle Juul-Jensens Boulevard 69, 8200, Århus N, Denmark
- Department of Clinical Medicine, Aarhus University, Århus N, Denmark
| | - Emma Roger Andersen
- Department of Clinical Biochemistry, Faculty of Health, Aarhus University Hospital, Palle Juul-Jensens Boulevard 69, 8200, Århus N, Denmark
- Department of Clinical Medicine, Aarhus University, Århus N, Denmark
| | - Maiken Parm Ulhoi
- Department of Clinical Biochemistry, Faculty of Health, Aarhus University Hospital, Palle Juul-Jensens Boulevard 69, 8200, Århus N, Denmark
- Department of Clinical Medicine, Aarhus University, Århus N, Denmark
- Department of Oncology, Aarhus University Hospital, Århus N, Denmark
| | - Peter Meldgaard
- Department of Clinical Medicine, Aarhus University, Århus N, Denmark
- Department of Oncology, Aarhus University Hospital, Århus N, Denmark
| | - Boe Sandahl Sorensen
- Department of Clinical Biochemistry, Faculty of Health, Aarhus University Hospital, Palle Juul-Jensens Boulevard 69, 8200, Århus N, Denmark.
- Department of Clinical Medicine, Aarhus University, Århus N, Denmark.
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21
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Clinical implications of ctDNA for EGFR-TKIs as first-line treatment in NSCLC. J Cancer Res Clin Oncol 2023; 149:1211-1220. [PMID: 35380256 DOI: 10.1007/s00432-022-03952-z] [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: 12/10/2021] [Accepted: 02/07/2022] [Indexed: 12/15/2022]
Abstract
PURPOSE This study aimed to explore the clinical implications of ctDNA for epidermal growth factor receptor-tyrosine kinase inhibitors (EGFR-TKIs) as the first-line treatment in EGFR-mutated (EGFRm) non-small cell lung cancer (NSCLC) in real-world settings. METHODS A total of 122 patients with NSCLC who underwent tissue and liquid next generation sequencing (NGS) tests were included. 66 patients with detected EGFR mutation in both tumor-tissue and plasma were included into the EGFRt+, p+ group, and 56 patients with EGFR mutation detected only in tumor-tissue were included into the EGFRt+, p- group. The differences in clinical characteristics, concomitant mutations and prognosis between the two groups were compared. RESULTS The detection rate of the EGFRt+, p+ group was 54.1% (66/122). EGFRt+, p+ in the NGS test was particularly relevant to the size of tumors, liver metastasis, bone metastasis and TP53 mutation. In patients with TP53 mutation in ctDNA, the detection rate of EGFR mutation in ctDNA was up to 91.3%. EGFRt+, p+ could be an independent prognostic factor for first-line EGFR-TKIs treatment. Combination therapy seems to be a promising approach to improve the outcome for EGFRt+, p+ (P = 0.017, HR 0.509 [95% CI 0.288-0.897]). Moreover, the combination of TP53 mutated status and EGFRm status in plasma showed a better completion of risk stratification for PFS (Log-rank P < 0.001). CONCLUSIONS Co-detection of EGFR mutation in tumor tissue and plasma is an independent prognostic factor for first-line EGFR-TKIs treatment. Moreover, combination therapy could be a promising approach to improve the outcome for these patients.
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22
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Impact of Whole Genome Doubling on Detection of Circulating Tumor DNA in Colorectal Cancer. Cancers (Basel) 2023; 15:cancers15041136. [PMID: 36831479 PMCID: PMC9954709 DOI: 10.3390/cancers15041136] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2022] [Revised: 02/03/2023] [Accepted: 02/07/2023] [Indexed: 02/12/2023] Open
Abstract
OBJECTIVE Circulating tumor DNA (ctDNA) is a candidate biomarker of cancer with practice-changing potential in the detection of both early and residual disease. Disease stage and tumor size affect the probability of ctDNA detection, whereas little is known about the influence of other tumor characteristics on ctDNA detection. This study investigates the impact of tumor cell whole-genome doubling (WGD) on the detection of ctDNA in plasma collected preoperatively from newly diagnosed colorectal cancer (CRC) patients. METHODS WGD was estimated from copy numbers derived from whole-exome sequencing (WES) data of matched tumor and normal DNA from 833 Danish CRC patients. To explore if tumor WGD status impacts ctDNA detection, we applied tumor-informed ctDNA analysis to preoperative plasma samples from all patients. RESULTS Patients with WGD+ tumors had 53% increased odds of being ctDNA positive (OR = 1.53, 95%CI: 1.12-2.09). After stratification for UICC stage, the association persisted for Stage I (OR = 2.44, 95%CI: 1.22-5.03) and Stage II (OR = 1.76, 95%CI: 1.11-2.81) but not for Stage III (OR = 0.83, 95%CI: 0.44-1.53) patients. CONCLUSION The presence of WGD significantly increases the probability of detecting ctDNA, particularly for early-stage disease. In patients with more advanced disease, the benefit of WGD on ctDNA detection is less pronounced, consistent with increased DNA shedding from these tumors, making ctDNA detection less dependent on the amount of ctDNA released per tumor cell.
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23
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Zhang J, Zhou N, Deng H, Chen X, Chen Q, Wang Q, Sun L, Wen Y, Cao X, Luo Z, Zhang J, Zhu W, Guo L. Prognostic value of circulating tumor DNA using target next-generation sequencing in extensive-stage small-cell lung cancer. Lung Cancer 2023; 178:11-19. [PMID: 36758321 DOI: 10.1016/j.lungcan.2023.01.015] [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: 12/02/2022] [Revised: 01/27/2023] [Accepted: 01/30/2023] [Indexed: 02/04/2023]
Abstract
BACKGROUND Chemotherapy remains the mainstay of treatment for small-cell lung cancer (SCLC). Liquid biopsies provide a convenient and non-invasive detection method for monitoring disease progression in patients with SCLC. METHODS We performed next-generation sequencing of 159 plasma samples from 69 patients with extensive-stage (ES)-SCLC. Circulating tumor (ct)DNA levels were quantified in haploid genome equivalents per mL (hGE/mL). MuTect2 was used to detect single nucleotide variants and short insertions/deletions. The "enrichKEGG" function in the "clusterProfiler" R package was used to enrich the mutated genes that only appeared during disease progression. RESULTS In our cohort, 66 of 69 (95.7%) plasma samples at the time of diagnosis had detectable somatic mutations; TP53 (89%) and RB1(56%) were the most frequent mutations, as well as copy number variations in some common SCLC-related genes such as RB1. Combination ctDNA and tissue testing improved the overall detection rate of actionable mutations from 19.4% to 26.9% compared with that of tissue detection alone. In addition, ctDNA levels changed dynamically during the course of treatment and were significantly associated with decreased progression-free survival. Notably, actionable mutations were detected at the time of diagnosis and during disease progression. CONCLUSIONS Our study revealed a dynamic somatic mutation profile through continuous ctDNA detection and confirmed that ctDNA levels can reflect tumor burden and predict PFS in patients with extensive stage-SCLC. Furthermore, we demonstrated that plasma ctDNA assays can provide real-time information on somatic mutations for potential targeted therapies for SCLC.
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Affiliation(s)
- Jiexia Zhang
- Guangzhou Institute of Respiratory Disease, State Key Laboratory of Respiratory Disease, Department of Respiration, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Ningning Zhou
- Department of Medical Oncology, Sun Yat-Sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou, China
| | - Huojin Deng
- Department of Pulmonary and Critical Care Medicine, Zhujiang Hospital, Southern Medical University, Guangzhou, China
| | - Xin Chen
- Department of Pulmonary and Critical Care Medicine, Zhujiang Hospital, Southern Medical University, Guangzhou, China
| | - Qunqing Chen
- Department of Cardiothoracic Surgery, Zhujiang Hospital, Southern Medical University, Guangzhou, China
| | - Qiongyao Wang
- Department of Oncology, Zhujiang Hospital, Southern Medical University, Guangzhou, China
| | - Lei Sun
- Department of Oncology, Zhujiang Hospital, Southern Medical University, Guangzhou, China
| | - Yang Wen
- Department of Pathology, Zhujiang Hospital, Southern Medical University, Guangzhou, China
| | - Xiaolong Cao
- Department of Oncology, Zhujiang Hospital, Southern Medical University, Guangzhou, China
| | - Zhiqiang Luo
- Department of Thoracic Surgery, Maoming People's Hospital, Maoming, Guangdong, China
| | - Jian Zhang
- Department of Oncology, Zhujiang Hospital, Southern Medical University, Guangzhou, China
| | - Weiliang Zhu
- Department of Oncology, Zhujiang Hospital, Southern Medical University, Guangzhou, China
| | - Linlang Guo
- Department of Pathology, Zhujiang Hospital, Southern Medical University, Guangzhou, China.
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Matsubara N, de Bono J, Olmos D, Procopio G, Kawakami S, Ürün Y, van Alphen R, Flechon A, Carducci MA, Choi YD, Hotte SJ, Korbenfeld E, Kramer G, Agarwal N, Chi KN, Dearden S, Gresty C, Kang J, Poehlein C, Harrington EA, Hussain M. Olaparib Efficacy in Patients with Metastatic Castration-resistant Prostate Cancer and BRCA1, BRCA2, or ATM Alterations Identified by Testing Circulating Tumor DNA. Clin Cancer Res 2023; 29:92-99. [PMID: 36318705 PMCID: PMC9811154 DOI: 10.1158/1078-0432.ccr-21-3577] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2021] [Revised: 12/17/2021] [Accepted: 10/28/2022] [Indexed: 11/16/2022]
Abstract
PURPOSE The phase III PROfound study (NCT02987543) evaluated olaparib versus abiraterone or enzalutamide (control) in metastatic castration-resistant prostate cancer (mCRPC) with tumor homologous recombination repair (HRR) gene alterations. We present exploratory analyses on the use of circulating tumor DNA (ctDNA) testing as an additional method to identify patients with mCRPC with HRR gene alterations who may be eligible for olaparib treatment. PATIENTS AND METHODS Plasma samples collected during screening in PROfound were retrospectively sequenced using the FoundationOne®Liquid CDx test for BRCA1, BRCA2 (BRCA), and ATM alterations in ctDNA. Only patients from Cohort A (BRCA/ATM alteration positive by tissue testing) were evaluated. We compared clinical outcomes, including radiographic progression-free survival (rPFS) between the ctDNA subgroup and Cohort A. RESULTS Of the 181 (73.9%) Cohort A patients who gave consent for plasma sample ctDNA testing, 139 (76.8%) yielded a result and BRCA/ATM alterations were identified in 111 (79.9%). Of these, 73 patients received olaparib and 38 received control. Patients' baseline demographics and characteristics, and the prevalence of HRR alterations were comparable with the Cohort A intention-to-treat (ITT) population. rPFS was longer in the olaparib group versus control [median 7.4 vs. 3.5 months; hazard ratio (HR), 0.33; 95% confidence interval (CI), 0.21-0.53; nominal P < 0.0001], which is consistent with Cohort A ITT population (HR, 0.34; 95% CI, 0.25-0.47). CONCLUSIONS When tumor tissue testing is not feasible or has failed, ctDNA testing may be a suitable alternative to identify patients with mCRPC carrying BRCA/ATM alterations who may benefit from olaparib treatment.
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Affiliation(s)
- Nobuaki Matsubara
- National Cancer Center Hospital East, Chiba, Japan
- Corresponding Author: Nobuaki Matsubara, National Cancer Center Hospital East, 6-5-1, Kashiwanoha, 104-0045 Kashiwa, Chiba, Japan. Phone: 814-7133-1111; Fax: 814-7134-6922; E-mail:
| | - Johann de Bono
- The Institute of Cancer Research and Royal Marsden, London, United Kingdom
| | - David Olmos
- Spanish National Cancer Research Centre (CNIO), Madrid, Spain
- Instituto de Investigación Biomédica de Málaga (IBIMA), Málaga, Spain
| | - Giuseppe Procopio
- Medical Oncology Dept, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | - Satoru Kawakami
- Department of Urology, Saitama Medical Center, Saitama Medical University, Saitama, Japan
| | - Yüksel Ürün
- Department of Medical Oncology, Ankara University, Ankara, Turkey
| | - Robbert van Alphen
- Department of Oncology, Elisabeth Tweesteden Hospital, Tilburg, the Netherlands
| | - Aude Flechon
- Cancérologie Médicale, Centre Léon-Bérard, Lyon Cedex, France
| | | | - Young Deuk Choi
- Department of Urology, Yonsei University Severance Hospital, Seoul, Republic of South Korea
| | | | | | | | - Neeraj Agarwal
- Huntsman Cancer Institute, University of Utah (NCI-CCC), Salt Lake City, Utah
| | - Kim N. Chi
- University of British Columbia, Vancouver, Canada
| | | | | | | | | | | | - Maha Hussain
- Robert H. Lurie Comprehensive Cancer Center, Northwestern University Feinberg School of Medicine, Chicago, Illinois
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25
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Chen R, Li J, Fujimoto J, Hong L, Hu X, Quek K, Tang M, Mitra A, Behrens C, Chow CW, Jiang P, Little LD, Gumbs C, Song X, Zhang J, Tan D, Heymach JV, Wistuba I, Futreal PA, Gibbons DL, Byers LA, Zhang J, Reuben A. Immunogenomic intertumor heterogeneity across primary and metastatic sites in a patient with lung adenocarcinoma. J Exp Clin Cancer Res 2022; 41:172. [PMID: 35546239 PMCID: PMC9092788 DOI: 10.1186/s13046-022-02361-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2021] [Accepted: 04/10/2022] [Indexed: 11/10/2022] Open
Abstract
Abstract
Background
Lung cancer is the leading cause of cancer death, partially owing to its extensive heterogeneity. The analysis of intertumor heterogeneity has been limited by an inability to concurrently obtain tissue from synchronous metastases unaltered by multiple prior lines of therapy.
Methods
In order to study the relationship between genomic, epigenomic and T cell repertoire heterogeneity in a rare autopsy case from a 32-year-old female never-smoker with left lung primary late-stage lung adenocarcinoma (LUAD), we did whole-exome sequencing (WES), DNA methylation and T cell receptor (TCR) sequencing to characterize the immunogenomic landscape of one primary and 19 synchronous metastatic tumors.
Results
We observed heterogeneous mutation, methylation, and T cell patterns across distinct metastases. Only TP53 mutation was detected in all tumors suggesting an early event while other cancer gene mutations were later events which may have followed subclonal diversification. A set of prevalent T cell clonotypes were completely excluded from left-side thoracic tumors indicating distinct T cell repertoire profiles between left-side and non left-side thoracic tumors. Though a limited number of predicted neoantigens were shared, these were associated with homology of the T cell repertoire across metastases. Lastly, ratio of methylated neoantigen coding mutations was negatively associated with T-cell density, richness and clonality, suggesting neoantigen methylation may partially drive immunosuppression.
Conclusions
Our study demonstrates heterogeneous genomic and T cell profiles across synchronous metastases and how restriction of unique T cell clonotypes within an individual may differentially shape the genomic and epigenomic landscapes of synchronous lung metastases.
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26
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Smolkova B, Kataki A, Earl J, Ruz-Caracuel I, Cihova M, Urbanova M, Buocikova V, Tamargo S, Rovite V, Niedra H, Schrader J, Kohl Y. Liquid biopsy and preclinical tools for advancing diagnosis and treatment of patients with pancreatic neuroendocrine neoplasms. Crit Rev Oncol Hematol 2022; 180:103865. [DOI: 10.1016/j.critrevonc.2022.103865] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2022] [Accepted: 10/31/2022] [Indexed: 11/06/2022] Open
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27
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Sivars L, Palsdottir K, Crona Guterstam Y, Falconer H, Hellman K, Tham E. The current status of cell‐free human papillomavirus
DNA
as a biomarker in cervical cancer and other
HPV
‐associated tumors: A review. Int J Cancer 2022; 152:2232-2242. [PMID: 36274628 DOI: 10.1002/ijc.34333] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2022] [Revised: 09/28/2022] [Accepted: 10/10/2022] [Indexed: 12/24/2022]
Abstract
Tumor cells release fragments of their DNA into the circulation, so called cell-free tumor DNA (ctDNA), allowing for analysis of tumor DNA in a simple blood test, that is, liquid biopsy. Cervical cancer is one of the most common malignancies among women worldwide and high-risk human papillomavirus (HR-HPV) is the cause of the majority of cases. HR-HPV integrates into the host genome and is often present in multiple copies per cell and should thus also be released as ctDNA. Such ctHPV DNA is therefore a possible biomarker in cervical cancer. In this review, we first give a background on ctDNA in general and then a comprehensive review of studies on ctHPV DNA in cervical cancer and pre-malignant lesions that may develop in cervical cancer. Furthermore, studies on ctHPV DNA in other HPV related malignancies (eg, head-and-neck and anogenital cancers) are briefly reviewed. We conclude that detection of ctHPV DNA in plasma from patients with cervical cancer is feasible, although optimized protocols and ultra-sensitive techniques are required for sufficient sensitivity. Results from retrospective studies in both cervical cancer and other HPV-related malignancies suggests that ctHPV DNA is a promising prognostic biomarker, for example, for detecting relapses early. This paves the way for larger, preferably prospective studies investigating the clinical value of ctHPV DNA as a biomarker in cervical cancer. However, there are conflicting results whether ctHPV DNA can be found in blood from patients with pre-malignant lesions and further studies are needed to fully elucidate this question.
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Affiliation(s)
- Lars Sivars
- Department of Molecular Medicine and Surgery, Karolinska Institutet Stockholm Sweden
| | - Kolbrun Palsdottir
- Department of Women's and Children's Health Karolinska Instituet Stockholm Sweden
- Department of Gynaecologic Cancer, Theme Cancer Karolinska University Hospital Stockholm Sweden
| | - Ylva Crona Guterstam
- Department of Clinical Science, Intervention and Technology Karolinska Institutet Stockholm Sweden
- Department of Gynaecology and Reproductive Medicine Karolinska University Hospital Huddinge Sweden
| | - Henrik Falconer
- Department of Women's and Children's Health Karolinska Instituet Stockholm Sweden
- Department of Gynaecologic Cancer, Theme Cancer Karolinska University Hospital Stockholm Sweden
| | - Kristina Hellman
- Department of Women's and Children's Health Karolinska Instituet Stockholm Sweden
- Department of Gynaecologic Cancer, Theme Cancer Karolinska University Hospital Stockholm Sweden
| | - Emma Tham
- Department of Molecular Medicine and Surgery, Karolinska Institutet Stockholm Sweden
- Department of Clinical Genetics Karolinska University Hospital Stockholm Sweden
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Palmieri M, Zulato E, Wahl SGF, Guibert N, Frullanti E. Diagnostic accuracy of circulating free DNA testing for the detection of KRAS mutations in non-small cell lung cancer: A systematic review and meta-analysis. Front Genet 2022; 13:1015161. [PMID: 36386815 PMCID: PMC9640997 DOI: 10.3389/fgene.2022.1015161] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2022] [Accepted: 10/11/2022] [Indexed: 11/25/2022] Open
Abstract
Kirsten rat sarcoma viral oncogene homolog (KRAS) gene encodes a GTPase that acts as a molecular switch for intracellular signal transduction, promoting cell growth and proliferation. Mutations in the KRAS gene represent important biomarkers for NSCLC targeted therapy. However, detection of KRAS mutations in tissues has shown some limitations. During the last years, analyses of circulating free DNA (cfDNA) has emerged as an alternative and minimally invasive, approach to investigate tumor molecular changes. Here, we assessed the diagnostic performance of cfDNA analysis, compared to tissues through a meta-analysis and systematic review of existing literature. From 561 candidate papers, we finally identified 40 studies, including 2,805 NSCLC patients. We extracted values relating to the number of true-positive, false-positive, false-negative, and true-negative. Pooled sensitivity, specificity, positive likelihood ratio, negative likelihood ratio, and diagnostic odds ratio, each with 95% CI, were calculated. A summary receiver operating characteristic curve and the area under curve (AUC) were used to evaluate the overall diagnostic performance. The pooled sensitivity was 0.71 (95% CI 0.68–0.74) and the specificity was 0.93 (95% CI 0.92–0.94). The diagnostic odds ratio was 35.24 (95% CI 24.88–49.91) and the area under the curve was 0.92 (SE = 0.094). These results provide evidence that detection of KRAS mutation using cfDNA testing is of adequate diagnostic accuracy thus offering to the clinicians a new promising screening test for NSCLC patients.
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Affiliation(s)
- Maria Palmieri
- Med Biotech Hub and Competence Center, Department of Medical Biotechnologies, University of Siena, Siena, Italy
| | - Elisabetta Zulato
- Basic and Translational Oncology Unit, Istituto Oncologico Veneto IOV—IRCCS, Padova, Italy
| | - Sissel Gyrid Freim Wahl
- Department of Pathology, St. Olavs Hospital, Trondheim University Hospital, Trondheim, Norway
- Department of Clinical and Molecular Medicine, NTNU, Norwegian University of Technology and Science, Trondheim, Norway
| | - Nicolas Guibert
- Thoracic Oncology Department, Larrey Hospital, University Hospital of Toulouse, Toulouse, France
- Inserm, Centre de Recherche en Cancérologie de Toulouse, CRCT UMR-1037, Toulouse, France
- University of Toulouse III (Paul Sabatier), Toulouse, France
| | - Elisa Frullanti
- Med Biotech Hub and Competence Center, Department of Medical Biotechnologies, University of Siena, Siena, Italy
- *Correspondence: Elisa Frullanti,
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Liquid Biopsy and the Translational Bridge from the TIME to the Clinic. Cells 2022; 11:cells11193114. [PMID: 36231076 PMCID: PMC9563580 DOI: 10.3390/cells11193114] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2022] [Revised: 09/09/2022] [Accepted: 09/28/2022] [Indexed: 11/16/2022] Open
Abstract
Research and advancing understanding of the tumor immune microenvironment (TIME) is vital to optimize and direct more effective cancer immune therapy. Pre-clinical bench research is vital to better understand the genomic interplay of the TIME and immune therapy responsiveness. However, a vital key to effective translational cancer research is having a bridge of translation to bring that understanding from the bench to the bedside. Without that bridge, research into the TIME will lack an efficient and effective translation into the clinic and cancer treatment decision making. As a clinical oncologist, the purpose of this commentary is to emphasize the importance of researching and improving clinical utility of the bridge, as well as the TIME research itself.
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30
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Xie S, Liu Q. Case report: Different mechanisms of drug resistance in a synchronous multiple primary lung cancer patient after EGFR-TKI treatment. Front Oncol 2022; 12:977065. [PMID: 36249035 PMCID: PMC9557219 DOI: 10.3389/fonc.2022.977065] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2022] [Accepted: 09/16/2022] [Indexed: 11/30/2022] Open
Abstract
Non-small-cell lung cancer (NSCLC) is the most common cancer in the world. In recent years, the incidence of synchronous multiple primary lung cancer (SMPLC) has gradually increased. Surgery is the preferred method to treat these patients. The management of SMPLC patients who cannot tolerate surgical treatment is controversial. We report a rare case in which a 70-year-old Chinese woman with no history of smoking had three primary lung adenocarcinoma lesions. Two lesions had epidermal growth factor receptor (EGFR) exon 19 deletion mutations, and one lesion had the L858R mutation. After first-generation EGFR–tyrosine kinase inhibitor (TKI) treatment, the three lesions all showed a good response until disease progression. After the corresponding drug treatments were given based on the different drug resistance mechanisms, good responsiveness was shown in each lessions. This case suggests that in the treatment of SMPLC, it is necessary to learn the molecular-biological information of each lesion due to the differences thereof, and a targeted treatment regimen should be developed on this basis.
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31
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Mack PC, Miao J, Redman MW, Moon J, Goldberg SB, Herbst RS, Melnick MA, Walther Z, Hirsch FR, Politi K, Kelly K, Gandara DR. Circulating Tumor DNA Kinetics Predict Progression-Free and Overall Survival in EGFR TKI-Treated Patients with EGFR-Mutant NSCLC (SWOG S1403). Clin Cancer Res 2022; 28:3752-3760. [PMID: 35713632 PMCID: PMC9444942 DOI: 10.1158/1078-0432.ccr-22-0741] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2022] [Revised: 05/04/2022] [Accepted: 06/15/2022] [Indexed: 01/26/2023]
Abstract
PURPOSE Dynamic changes in circulating tumor DNA (ctDNA) are under investigation as an early indicator of treatment outcome. EXPERIMENTAL DESIGN Serial plasma ctDNA (baseline, 8 weeks, and at progression) was prospectively incorporated into the SWOG S1403 clinical trial of afatinib ± cetuximab in tyrosine kinase inhibitor-naïve, EGFR mutation tissue-positive non-small cell lung cancer. RESULTS EGFR mutations were detected in baseline ctDNA in 77% (82/106) of patients, associated with the presence of brain and/or liver metastases and M1B stage. Complete clearance of EGFR mutations in ctDNA by 8 weeks was associated with a significantly decreased risk of progression, compared with those with persistent ctDNA at Cycle 3 Day 1 [HR, 0.23; 95% confidence interval (CI), 0.12-0.45; P < 0.0001], with a median progression-free survival (PFS) of 15.1 (95% CI, 10.6-17.5) months in the group with clearance of ctDNA versus 4.6 (1.7-7.5) months in the group with persistent ctDNA. Clearance was also associated with a decreased risk of death (HR, 0.44; 95% CI, 0.21-0.90), P = 0.02; median overall survival (OS): 32.6 (23.5-not estimable) versus 15.6 (4.9-28.3) months. CONCLUSIONS Plasma clearance of mutant EGFR ctDNA at 8 weeks was highly and significantly predictive of PFS and OS, outperforming RECIST response for predicting long-term benefit.
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Affiliation(s)
- Philip C. Mack
- Center for Thoracic Oncology, Tisch Cancer Institute, Mount Sinai Health System, New York City, NY
| | - Jieling Miao
- SWOG Statistical Center and Clinical Biostatistics, Fred Hutchinson Cancer Research Center, Seattle, WA
| | - Mary W. Redman
- SWOG Statistical Center and Clinical Biostatistics, Fred Hutchinson Cancer Research Center, Seattle, WA
| | - James Moon
- SWOG Statistical Center and Clinical Biostatistics, Fred Hutchinson Cancer Research Center, Seattle, WA
| | - Sarah B. Goldberg
- Department of Internal Medicine (Section of Medical Oncology), Yale School of Medicine, New Haven, CT
| | - Roy S. Herbst
- Department of Internal Medicine (Section of Medical Oncology), Yale School of Medicine, New Haven, CT
| | - Mary Ann Melnick
- Department of Internal Medicine (Section of Medical Oncology), Yale School of Medicine, New Haven, CT
| | - Zenta Walther
- Department of Pathology, Yale School of Medicine, New Haven, CT
| | - Fred R. Hirsch
- Center for Thoracic Oncology, Tisch Cancer Institute, Mount Sinai Health System, New York City, NY
| | - Katerina Politi
- Department of Pathology, Yale School of Medicine, New Haven, CT
| | - Karen Kelly
- Division of Hematology/Oncology, University of California at Davis, Sacramento, CA
| | - David R. Gandara
- Division of Hematology/Oncology, University of California at Davis, Sacramento, CA
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Sánchez-Herrero E, Serna-Blasco R, Robado de Lope L, González-Rumayor V, Romero A, Provencio M. Circulating Tumor DNA as a Cancer Biomarker: An Overview of Biological Features and Factors That may Impact on ctDNA Analysis. Front Oncol 2022; 12:943253. [PMID: 35936733 PMCID: PMC9350013 DOI: 10.3389/fonc.2022.943253] [Citation(s) in RCA: 26] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2022] [Accepted: 06/16/2022] [Indexed: 11/13/2022] Open
Abstract
Cancer cells release nucleic acids, freely or associated with other structures such as vesicles into body fluids, including blood. Among these nucleic acids, circulating tumor DNA (ctDNA) has emerged as a minimally invasive biomarker for tumor molecular profiling. However, certain biological characteristics of ctDNA are still unknown. Here, we provide an overview of the current knowledge about ctDNA biological features, including size and structure as well as the mechanisms of ctDNA shedding and clearance, and the physio-pathological factors that determine ctDNA levels. A better understanding of ctDNA biology is essential for the development of new methods that enable the analysis of ctDNA.
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Affiliation(s)
- Estela Sánchez-Herrero
- Liquid Biopsy Laboratory. Biomedical Sciences Research Institute Puerta de Hierro-Majadahonda, Majadahonda, Spain
- +D Department, Atrys Health, Barcelona, Spain
| | - Roberto Serna-Blasco
- Liquid Biopsy Laboratory. Biomedical Sciences Research Institute Puerta de Hierro-Majadahonda, Majadahonda, Spain
| | - Lucia Robado de Lope
- Liquid Biopsy Laboratory. Biomedical Sciences Research Institute Puerta de Hierro-Majadahonda, Majadahonda, Spain
| | | | - Atocha Romero
- Liquid Biopsy Laboratory. Biomedical Sciences Research Institute Puerta de Hierro-Majadahonda, Majadahonda, Spain
- Medical Oncology Department, Hospital Universitario Puerta de Hierro-Majadahonda, Majadahonda, Spain
- *Correspondence: Atocha Romero, ; orcid.org/0000-0002-1634-7397
| | - Mariano Provencio
- Liquid Biopsy Laboratory. Biomedical Sciences Research Institute Puerta de Hierro-Majadahonda, Majadahonda, Spain
- Medical Oncology Department, Hospital Universitario Puerta de Hierro-Majadahonda, Majadahonda, Spain
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Elamin YY, Robichaux JP, Carter BW, Altan M, Tran H, Gibbons DL, Heeke S, Fossella FV, Lam VK, Le X, Negrao MV, Nilsson MB, Patel A, Vijayan RSK, Cross JB, Zhang J, Byers LA, Lu C, Cascone T, Feng L, Luthra R, San Lucas FA, Mantha G, Routbort M, Blumenschein G, Tsao AS, Heymach JV. Poziotinib for EGFR exon 20-mutant NSCLC: Clinical efficacy, resistance mechanisms, and impact of insertion location on drug sensitivity. Cancer Cell 2022; 40:754-767.e6. [PMID: 35820397 PMCID: PMC9667883 DOI: 10.1016/j.ccell.2022.06.006] [Citation(s) in RCA: 45] [Impact Index Per Article: 22.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/21/2021] [Revised: 04/14/2022] [Accepted: 06/14/2022] [Indexed: 02/06/2023]
Abstract
We report a phase II study of 50 advanced non-small cell lung cancer (NSCLC) patients with point mutations or insertions in EGFR exon 20 treated with poziotinib (NCT03066206). The study achieved its primary endpoint, with confirmed objective response rates (ORRs) of 32% and 31% by investigator and blinded independent review, respectively, with a median progression-free survival of 5.5 months. Using preclinical studies, in silico modeling, and molecular dynamics simulations, we found that poziotinib sensitivity was highly dependent on the insertion location, with near-loop insertions (amino acids A767 to P772) being more sensitive than far-loop insertions, an observation confirmed clinically with ORRs of 46% and 0% observed in near versus far-loop, respectively (p = 0.0015). Putative mechanisms of acquired resistance included EGFR T790M, MET amplifications, and epithelial-to-mesenchymal transition (EMT). Our data demonstrate that poziotinib is active in EGFR exon 20-mutant NSCLC, although this activity is influenced by insertion location.
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Affiliation(s)
- Yasir Y Elamin
- Department of Thoracic/Head and Neck Medical Oncology, The University of Texas M.D. Anderson Cancer Center, Unit 432, PO Box 301402, 1500 Holcombe Boulevard, Houston, TX 77030, USA
| | - Jacqulyne P Robichaux
- Department of Thoracic/Head and Neck Medical Oncology, The University of Texas M.D. Anderson Cancer Center, Unit 432, PO Box 301402, 1500 Holcombe Boulevard, Houston, TX 77030, USA
| | - Brett W Carter
- Department of Thoracic Imaging, The University of Texas M.D. Anderson Cancer Center, Houston, TX 77030, USA
| | - Mehmet Altan
- Department of Thoracic/Head and Neck Medical Oncology, The University of Texas M.D. Anderson Cancer Center, Unit 432, PO Box 301402, 1500 Holcombe Boulevard, Houston, TX 77030, USA
| | - Hai Tran
- Department of Thoracic/Head and Neck Medical Oncology, The University of Texas M.D. Anderson Cancer Center, Unit 432, PO Box 301402, 1500 Holcombe Boulevard, Houston, TX 77030, USA
| | - Don L Gibbons
- Department of Thoracic/Head and Neck Medical Oncology, The University of Texas M.D. Anderson Cancer Center, Unit 432, PO Box 301402, 1500 Holcombe Boulevard, Houston, TX 77030, USA
| | - Simon Heeke
- Department of Thoracic/Head and Neck Medical Oncology, The University of Texas M.D. Anderson Cancer Center, Unit 432, PO Box 301402, 1500 Holcombe Boulevard, Houston, TX 77030, USA
| | - Frank V Fossella
- Department of Thoracic/Head and Neck Medical Oncology, The University of Texas M.D. Anderson Cancer Center, Unit 432, PO Box 301402, 1500 Holcombe Boulevard, Houston, TX 77030, USA
| | - Vincent K Lam
- Department of Thoracic/Head and Neck Medical Oncology, The University of Texas M.D. Anderson Cancer Center, Unit 432, PO Box 301402, 1500 Holcombe Boulevard, Houston, TX 77030, USA; Department of Medicine, Johns Hopkins Sidney Kimmel Cancer Center, Baltimore, MD 21287, USA
| | - Xiuning Le
- Department of Thoracic/Head and Neck Medical Oncology, The University of Texas M.D. Anderson Cancer Center, Unit 432, PO Box 301402, 1500 Holcombe Boulevard, Houston, TX 77030, USA
| | - Marcelo V Negrao
- Department of Thoracic/Head and Neck Medical Oncology, The University of Texas M.D. Anderson Cancer Center, Unit 432, PO Box 301402, 1500 Holcombe Boulevard, Houston, TX 77030, USA
| | - Monique B Nilsson
- Department of Thoracic/Head and Neck Medical Oncology, The University of Texas M.D. Anderson Cancer Center, Unit 432, PO Box 301402, 1500 Holcombe Boulevard, Houston, TX 77030, USA
| | - Anisha Patel
- Department of Dermatology, The University of Texas M.D. Anderson Cancer Center, Houston, TX 77030, USA
| | - R S K Vijayan
- Institute for Applied Cancer Science, The University of Texas M.D. Anderson Cancer Center, Houston, TX 77030, USA
| | - Jason B Cross
- Institute for Applied Cancer Science, The University of Texas M.D. Anderson Cancer Center, Houston, TX 77030, USA
| | - Jianjun Zhang
- Department of Thoracic/Head and Neck Medical Oncology, The University of Texas M.D. Anderson Cancer Center, Unit 432, PO Box 301402, 1500 Holcombe Boulevard, Houston, TX 77030, USA
| | - Lauren A Byers
- Department of Thoracic/Head and Neck Medical Oncology, The University of Texas M.D. Anderson Cancer Center, Unit 432, PO Box 301402, 1500 Holcombe Boulevard, Houston, TX 77030, USA
| | - Charles Lu
- Department of Thoracic/Head and Neck Medical Oncology, The University of Texas M.D. Anderson Cancer Center, Unit 432, PO Box 301402, 1500 Holcombe Boulevard, Houston, TX 77030, USA
| | - Tina Cascone
- Department of Thoracic/Head and Neck Medical Oncology, The University of Texas M.D. Anderson Cancer Center, Unit 432, PO Box 301402, 1500 Holcombe Boulevard, Houston, TX 77030, USA
| | - Lei Feng
- Department of Biostatistics, The University of Texas M.D. Anderson Cancer Center, Houston, TX 77030, USA
| | - Rajyalakshmi Luthra
- Department of Hematopathology, The University of Texas M.D. Anderson Cancer Center, Houston, TX 77030, USA
| | - Francis A San Lucas
- Department of Hematopathology, The University of Texas M.D. Anderson Cancer Center, Houston, TX 77030, USA
| | - Geeta Mantha
- Department of Hematopathology, The University of Texas M.D. Anderson Cancer Center, Houston, TX 77030, USA
| | - Mark Routbort
- Department of Hematopathology, The University of Texas M.D. Anderson Cancer Center, Houston, TX 77030, USA
| | - George Blumenschein
- Department of Thoracic/Head and Neck Medical Oncology, The University of Texas M.D. Anderson Cancer Center, Unit 432, PO Box 301402, 1500 Holcombe Boulevard, Houston, TX 77030, USA
| | - Anne S Tsao
- Department of Thoracic/Head and Neck Medical Oncology, The University of Texas M.D. Anderson Cancer Center, Unit 432, PO Box 301402, 1500 Holcombe Boulevard, Houston, TX 77030, USA
| | - John V Heymach
- Department of Thoracic/Head and Neck Medical Oncology, The University of Texas M.D. Anderson Cancer Center, Unit 432, PO Box 301402, 1500 Holcombe Boulevard, Houston, TX 77030, USA.
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Yan X, Liu C. Clinical application and prospect of MRD evaluation in lung cancer based on ctDNA level: A review. TUMORI JOURNAL 2022:3008916221101927. [PMID: 35815471 DOI: 10.1177/03008916221101927] [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: 11/17/2022]
Abstract
Lung cancer is one of the most malignant cancers in China with a rising incidence rate. Despite the fact that surgical treatment is the only possible cure for lung cancer, its long-term efficacy is compromised by the high level of postoperative local recurrence rate. Minimal residual disease is the leading cause of tumor recurrence, yet the suggested combination of clinical, radiological and serological (carcinoembryonic antigen) tests fails to reveal the underlying residual tissue in all stage I-III lung cancer cases, which makes tumor recurrence surveillance timely. Through monitoring circulating tumor DNA, the minimal residual disease level can be accessed and provide guidance for more precise postoperative personalized treatment, and its scientific feasibility can revolutionize lung cancer therapy. In the present review we summarized the progress of circulating tumor DNA in lung cancer minimal residual disease detection and discussed its application value in guiding precise treatment of lung cancer.
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Affiliation(s)
- Xing Yan
- The Second Affiliated Hospital of Dalian Medical University Thoracic surgery, DaLian, China
| | - Changhong Liu
- The Second Affiliated Hospital of Dalian Medical University Thoracic surgery, DaLian, China
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35
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Hu D, Guo E, Yang B, Qin X, Fu Y, Fan J, Zhuang X, Yao Q, Lu F, Li W, Xiao R, Wu X, Yang X, Wang Z, Liu C, You L, Zang R, Zhou Q, Zhao W, Chen G, Sun C. Mutation profiles in circulating cell‐free
DNA
predict acquired resistance to Olaparib in high‐grade serous ovarian carcinoma. Cancer Sci 2022; 113:2849-2861. [PMID: 35661486 PMCID: PMC9357630 DOI: 10.1111/cas.15456] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2022] [Revised: 04/23/2022] [Accepted: 05/29/2022] [Indexed: 11/30/2022] Open
Affiliation(s)
- Dianxing Hu
- Department of Obstetrics and Gynecology, Tongji Hospital, Tongji Medical College Huazhong University of Science and Technology Wuhan China
| | - Ensong Guo
- Department of Obstetrics and Gynecology, Tongji Hospital, Tongji Medical College Huazhong University of Science and Technology Wuhan China
| | - Bin Yang
- Department of Obstetrics and Gynecology, Tongji Hospital, Tongji Medical College Huazhong University of Science and Technology Wuhan China
| | - Xu Qin
- Department of Stomatology, Tongji Hospital, Tongji Medical College Huazhong University of Science and Technology Wuhan China
| | - Yu Fu
- Department of Obstetrics and Gynecology, Tongji Hospital, Tongji Medical College Huazhong University of Science and Technology Wuhan China
| | - Junpeng Fan
- Department of Obstetrics and Gynecology, Tongji Hospital, Tongji Medical College Huazhong University of Science and Technology Wuhan China
| | - Xucui Zhuang
- Department of Obstetrics and Gynecology, Tongji Hospital, Tongji Medical College Huazhong University of Science and Technology Wuhan China
| | - Qianqian Yao
- Department of Medical Science Shanghai AccuraGen Biotechnology Co., Ltd Shanghai China
| | - Funian Lu
- Department of Obstetrics and Gynecology, Tongji Hospital, Tongji Medical College Huazhong University of Science and Technology Wuhan China
| | - Wenting Li
- Department of Obstetrics and Gynecology, Tongji Hospital, Tongji Medical College Huazhong University of Science and Technology Wuhan China
| | - Rourou Xiao
- Department of Obstetrics and Gynecology, Tongji Hospital, Tongji Medical College Huazhong University of Science and Technology Wuhan China
| | - Xue Wu
- Department of Obstetrics and Gynecology, Tongji Hospital, Tongji Medical College Huazhong University of Science and Technology Wuhan China
| | - Xiaohang Yang
- Department of Obstetrics and Gynecology, Tongji Hospital, Tongji Medical College Huazhong University of Science and Technology Wuhan China
| | - Zizhuo Wang
- Department of Obstetrics and Gynecology, Tongji Hospital, Tongji Medical College Huazhong University of Science and Technology Wuhan China
| | - Chen Liu
- Department of Obstetrics and Gynecology, Tongji Hospital, Tongji Medical College Huazhong University of Science and Technology Wuhan China
| | - Lixin You
- Department of Obstetrics and Gynecology, Tongji Hospital, Tongji Medical College Huazhong University of Science and Technology Wuhan China
| | - Rongyu Zang
- Department of Gynecologic Oncology, Zhongshan Hospital Fudan University Shanghai China
| | - Qi Zhou
- Department of Gynecology Oncology Chongqing University Cancer Hospital Chongqing China
| | - Weidong Zhao
- Department of Gynecologic Oncology Anhui Provincial Cancer Hospital Hefei China
| | - Gang Chen
- Department of Obstetrics and Gynecology, Tongji Hospital, Tongji Medical College Huazhong University of Science and Technology Wuhan China
| | - Chaoyang Sun
- Department of Obstetrics and Gynecology, Tongji Hospital, Tongji Medical College Huazhong University of Science and Technology Wuhan China
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Rehman AU, Khan P, Maurya SK, Siddiqui JA, Santamaria-Barria JA, Batra SK, Nasser MW. Liquid biopsies to occult brain metastasis. Mol Cancer 2022; 21:113. [PMID: 35538484 PMCID: PMC9088117 DOI: 10.1186/s12943-022-01577-x] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Accepted: 04/19/2022] [Indexed: 02/08/2023] Open
Abstract
Brain metastasis (BrM) is a major problem associated with cancer-related mortality, and currently, no specific biomarkers are available in clinical settings for early detection. Liquid biopsy is widely accepted as a non-invasive method for diagnosing cancer and other diseases. We have reviewed the evidence that shows how the molecular alterations are involved in BrM, majorly from breast cancer (BC), lung cancer (LC), and melanoma, with an inception in how they can be employed for biomarker development. We discussed genetic and epigenetic changes that influence cancer cells to breach the blood-brain barrier (BBB) and help to establish metastatic lesions in the uniquely distinct brain microenvironment. Keeping abreast with the recent breakthroughs in the context of various biomolecules detections and identifications, the circulating tumor cells (CTC), cell-free nucleotides, non-coding RNAs, secretory proteins, and metabolites can be pursued in human body fluids such as blood, serum, cerebrospinal fluid (CSF), and urine to obtain potential candidates for biomarker development. The liquid biopsy-based biomarkers can overlay with current imaging techniques to amplify the signal viable for improving the early detection and treatments of occult BrM.
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Affiliation(s)
- Asad Ur Rehman
- Department of Biochemistry and Molecular Biology, University of Nebraska Medical Center, Omaha, NE, 68108, USA
| | - Parvez Khan
- Department of Biochemistry and Molecular Biology, University of Nebraska Medical Center, Omaha, NE, 68108, USA
| | - Shailendra Kumar Maurya
- Department of Biochemistry and Molecular Biology, University of Nebraska Medical Center, Omaha, NE, 68108, USA
| | - Jawed A Siddiqui
- Department of Biochemistry and Molecular Biology, University of Nebraska Medical Center, Omaha, NE, 68108, USA.,Fred and Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, NE, 68108, USA
| | | | - Surinder K Batra
- Department of Biochemistry and Molecular Biology, University of Nebraska Medical Center, Omaha, NE, 68108, USA.,Fred and Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, NE, 68108, USA.,Eppley Institute for Research in Cancer and Allied Diseases, University of Nebraska Medical Center, Omaha, NE-68198, USA
| | - Mohd Wasim Nasser
- Department of Biochemistry and Molecular Biology, University of Nebraska Medical Center, Omaha, NE, 68108, USA. .,Fred and Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, NE, 68108, USA.
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Daily Practice Assessment of KRAS Status in NSCLC Patients: A New Challenge for the Thoracic Pathologist Is Right around the Corner. Cancers (Basel) 2022; 14:cancers14071628. [PMID: 35406400 PMCID: PMC8996900 DOI: 10.3390/cancers14071628] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2022] [Revised: 03/17/2022] [Accepted: 03/18/2022] [Indexed: 12/16/2022] Open
Abstract
Simple Summary RAS mutation is the most frequent oncogenic alteration in human cancers and KRAS is the most frequently mutated, notably in non-small cell lung carcinomas (NSCLC). Various attempts to inhibit KRAS in the past were unsuccessful in these latter tumors. However, recently, several small molecules (AMG510, MRTX849, JNJ-74699157, and LY3499446) have been developed to specifically target KRAS G12C-mutated tumors, which seems promising for patient treatment and should soon be administered in daily practice for non-squamous (NS)-NSCLC. In this context, it will be mandatory to systematically assess the KRAS status in routine clinical practice, at least in advanced NS-NSCLC, leading to new challenges for thoracic oncologists. Abstract KRAS mutations are among the most frequent genomic alterations identified in non-squamous non-small cell lung carcinomas (NS-NSCLC), notably in lung adenocarcinomas. In most cases, these mutations are mutually exclusive, with different genomic alterations currently known to be sensitive to therapies targeting EGFR, ALK, BRAF, ROS1, and NTRK. Recently, several promising clinical trials targeting KRAS mutations, particularly for KRAS G12C-mutated NSCLC, have established new hope for better treatment of patients. In parallel, other studies have shown that NSCLC harboring co-mutations in KRAS and STK11 or KEAP1 have demonstrated primary resistance to immune checkpoint inhibitors. Thus, the assessment of the KRAS status in advanced-stage NS-NSCLC has become essential to setting up an optimal therapeutic strategy in these patients. This stimulated the development of new algorithms for the management of NSCLC samples in pathology laboratories and conditioned reorganization of optimal health care of lung cancer patients by the thoracic pathologists. This review addresses the recent data concerning the detection of KRAS mutations in NSCLC and focuses on the new challenges facing pathologists in daily practice for KRAS status assessment.
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38
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Le X, Hong L, Hensel C, Chen R, Kemp H, Coleman N, Ciunci CA, Liu SV, Negrao MV, Yen J, Xia X, Scheuenpflug J, Stroh C, Juraeva D, Tsao A, Hong D, Raymond V, Paik P, Zhang J, Heymach JV. Landscape and Clonal Dominance of Co-occurring Genomic Alterations in Non-Small-Cell Lung Cancer Harboring MET Exon 14 Skipping. JCO Precis Oncol 2021; 5:PO.21.00135. [PMID: 34957368 PMCID: PMC8694524 DOI: 10.1200/po.21.00135] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Revised: 08/31/2021] [Accepted: 10/15/2021] [Indexed: 12/12/2022] Open
Abstract
MET exon 14 skipping alterations (METex14) comprise a diverse set of actionable oncogene drivers in non–small-cell lung cancer (NSCLC). Recent studies have established the efficacy of tyrosine kinase inhibitors for this patient population. The landscape of co-occurring genetic alterations in METex14 NSCLC and their potential impact to therapeutic sensitivities has not yet been fully described.
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Affiliation(s)
- Xiuning Le
- Department of Thoracic/Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Lingzhi Hong
- Department of Thoracic/Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX.,Department of Oncology, Nanjing First Hospital, Nanjing Medical University, Nanjing, China
| | | | | | - Haley Kemp
- Department of Thoracic/Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Niamh Coleman
- Department of Investigational Cancer Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Christine A Ciunci
- Division of Hematology/Oncology, Department of Medicine, Abramson Cancer Center, University of Pennsylvania, Philadelphia, PA
| | - Stephen V Liu
- Division of Oncology, Department of Medicine, Lombardi Comprehensive Cancer Center of Georgetown University, Washington, DC
| | - Marcelo V Negrao
- Department of Thoracic/Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX
| | | | | | | | | | | | - Anne Tsao
- Department of Thoracic/Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX
| | - David Hong
- Department of Investigational Cancer Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, TX
| | | | - Paul Paik
- Thoracic Oncology, Division of Solid Tumor Oncology, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Jianjun Zhang
- Department of Thoracic/Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX
| | - John V Heymach
- Department of Thoracic/Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX
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van der Laan P, van Houdt WJ, van den Broek D, Steeghs N, van der Graaf WTA. Liquid Biopsies in Sarcoma Clinical Practice: Where Do We Stand? Biomedicines 2021; 9:1315. [PMID: 34680432 PMCID: PMC8533081 DOI: 10.3390/biomedicines9101315] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2021] [Revised: 09/17/2021] [Accepted: 09/22/2021] [Indexed: 12/17/2022] Open
Abstract
Sarcomas are rare tumors of bone and soft tissue with a mesenchymal origin. This uncommon type of cancer is marked by a high heterogeneity, consisting of over 70 subtypes. Because of this broad spectrum, their treatment requires a subtype-specific therapeutic approach. Tissue biopsy is currently the golden standard for sarcoma diagnosis, but it has its limitations. Over the recent years, methods to detect, characterize, and monitor cancer through liquid biopsy have evolved rapidly. The analysis of circulating biomarkers in peripheral blood, such as circulating tumor cells (CTC) or circulating tumor DNA (ctDNA), could provide real-time information on tumor genetics, disease state, and resistance mechanisms. Furthermore, it traces tumor evolution and can assess tumor heterogeneity. Although the first results in sarcomas are encouraging, there are technical challenges that need to be addressed for implementation in clinical practice. Here, we summarize current knowledge about liquid biopsies in sarcomas and elaborate on different strategies to integrate liquid biopsy into sarcoma clinical care.
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Affiliation(s)
- Pia van der Laan
- Department of Surgical Oncology, Netherlands Cancer Institute, 1066 CX Amsterdam, The Netherlands; (P.v.d.L.); (W.J.v.H.)
- Department of Medical Oncology, Netherlands Cancer Institute, 1066 CX Amsterdam, The Netherlands;
| | - Winan J. van Houdt
- Department of Surgical Oncology, Netherlands Cancer Institute, 1066 CX Amsterdam, The Netherlands; (P.v.d.L.); (W.J.v.H.)
| | - Daan van den Broek
- Department of Laboratory Medicine, Netherlands Cancer Institute, 1066 CX Amsterdam, The Netherlands;
| | - Neeltje Steeghs
- Department of Medical Oncology, Netherlands Cancer Institute, 1066 CX Amsterdam, The Netherlands;
| | - Winette T. A. van der Graaf
- Department of Medical Oncology, Netherlands Cancer Institute, 1066 CX Amsterdam, The Netherlands;
- Department of Medical Oncology, Erasmus MC Cancer Institute, Erasmus MC, 3015 GD Rotterdam, The Netherlands
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40
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Hofman P. EGFR Status Assessment for Better Care of Early Stage Non-Small Cell Lung Carcinoma: What Is Changing in the Daily Practice of Pathologists? Cells 2021; 10:2157. [PMID: 34440926 PMCID: PMC8392580 DOI: 10.3390/cells10082157] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2021] [Revised: 08/18/2021] [Accepted: 08/19/2021] [Indexed: 02/08/2023] Open
Abstract
The recent emergence of novel neoadjuvant and/or adjuvant therapies for early stage (I-IIIA) non-small cell lung carcinoma (NSCLC), mainly tyrosine kinase inhibitors (TKIs) targeting EGFR mutations and immunotherapy or chemo-immunotherapy, has suddenly required the evaluation of biomarkers predictive of the efficacy of different treatments in these patients. Currently, the choice of one or another of these treatments mainly depends on the results of immunohistochemistry for PD-L1 and of the status of EGFR and ALK. This new development has led to the setup of different analyses for clinical and molecular pathology laboratories, which have had to rapidly integrate a number of new challenges into daily practice and to establish new organization for decision making. This review outlines the impact of the management of biological samples in laboratories and discusses perspectives for pathologists within the framework of EGFR TKIs in early stage NSCLC.
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Affiliation(s)
- Paul Hofman
- Laboratory of Clinical and Experimental Pathology, CHU Nice, FHU OncoAge, Pasteur Hospital, Université Côte d’Azur, 06108 Nice, France; ; Tel.: +33-492-038-855; Fax: +33-492-8850
- CHU Nice, FHU OncoAge, Hospital-Integrated Biobank BB-0033-00025, Université Côte d’Azur, 06000 Nice, France
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41
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Qvick A, Stenmark B, Carlsson J, Isaksson J, Karlsson C, Helenius G. Liquid biopsy as an option for predictive testing and prognosis in patients with lung cancer. Mol Med 2021; 27:68. [PMID: 34217228 PMCID: PMC8254966 DOI: 10.1186/s10020-021-00331-1] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2021] [Accepted: 06/16/2021] [Indexed: 12/19/2022] Open
Abstract
BACKGROUND The aim of this study was to investigate the clinical value of liquid biopsy as a primary source for variant analysis in lung cancer. In addition, we sought to characterize liquid biopsy variants and to correlate mutational load to clinical data. METHODS Circulating cell-free DNA was extracted from plasma from patients with lung cancer (n = 60) and controls with benign lung disease (n = 16). Variant analysis was performed using the AVENIO ctDNA Surveillance kit and the results were correlated to clinical and variant analysis data from tumor tissue or cytology retrieved from clinical routine diagnostics. RESULTS There were significantly more variants detected in lung cancer cases compared to controls (p = 0.011), but no difference between the histological subgroups of lung cancer was found (p = 0.465). Furthermore, significantly more variants were detected in patients with stage IIIb-IV disease compared to patients with stage I-IIIa (median 7 vs 4, p = 0.017). Plasma cfDNA mutational load was significantly associated with overall survival (p = 0.010). The association persisted when adjusted for stage and ECOG performance status (HR: 3.64, 95% CI 1.37-9.67, p = 0.009). Agreement between tumor and plasma samples significantly differed with stage; patients with stage IIIb-IV disease showed agreement in 88.2% of the cases with clinically relevant variants, compared to zero cases in stage I-IIIa (p = 0.004). Furthermore, one variant in EGFR, two in KRAS, and one in BRAF were detected in plasma but not in tumor samples. CONCLUSION This study concludes that in the vast majority of advanced NSCLC patients a reliable variant analysis can be performed using liquid biopsy from plasma. Furthermore, we found that the number of variants in plasma is associated with prognosis, possibly indicating a strategy for closer follow up on this crucial patient group.
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Affiliation(s)
- Alvida Qvick
- Dept. of Laboratory Medicine, Örebro University Hospital, Södra Grev. Roseng., 701 85 Örebro, Sweden
- Faculty of Medicine and Health, Örebro University, Örebro, Sweden
| | - Bianca Stenmark
- Dept. of Laboratory Medicine, Örebro University Hospital, Södra Grev. Roseng., 701 85 Örebro, Sweden
- Faculty of Medicine and Health, Örebro University, Örebro, Sweden
| | - Jessica Carlsson
- Dept. of Urology, Faculty of Medicine and Health, Örebro University, Örebro, Sweden
| | - Johan Isaksson
- Dept. of Respiratory Medicine, Gävle Hospital, Gävle, Sweden
- Centre for Research and Development Region Gävleborg/Uppsala University, Gävle, Sweden
- Dept. of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden
| | | | - Gisela Helenius
- Dept. of Laboratory Medicine, Örebro University Hospital, Södra Grev. Roseng., 701 85 Örebro, Sweden
- Faculty of Medicine and Health, Örebro University, Örebro, Sweden
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Hofman P. Next-Generation Sequencing with Liquid Biopsies from Treatment-Naïve Non-Small Cell Lung Carcinoma Patients. Cancers (Basel) 2021; 13:2049. [PMID: 33922637 PMCID: PMC8122958 DOI: 10.3390/cancers13092049] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2021] [Revised: 04/11/2021] [Accepted: 04/20/2021] [Indexed: 12/16/2022] Open
Abstract
Recently, the liquid biopsy (LB), a non-invasive and easy to repeat approach, has started to compete with the tissue biopsy (TB) for detection of targets for administration of therapeutic strategies for patients with advanced stages of lung cancer at tumor progression. A LB at diagnosis of late stage non-small cell lung carcinoma (NSCLC) is also being performed. It may be asked if a LB can be complementary (according to the clinical presentation or systematics) or even an alternative to a TB for treatment-naïve advanced NSCLC patients. Nucleic acid analysis with a TB by next-generation sequencing (NGS) is gradually replacing targeted sequencing methods for assessment of genomic alterations in lung cancer patients with tumor progression, but also at baseline. However, LB is still not often used in daily practice for NGS. This review addresses different aspects relating to the use of LB for NGS at diagnosis in advanced NSCLC, including its advantages and limitations.
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Affiliation(s)
- Paul Hofman
- Laboratory of Clinical and Experimental Pathology, Université Côte d’Azur, CHU Nice, FHU OncoAge, Pasteur Hospital, 30 avenue de la voie romaine, BP69, CEDEX 01, 06001 Nice, France; ; Tel.: +33-4-92-03-88-55 or +33-4-92-03-87-49; Fax: +33-4-92-88-50
- Hospital-Integrated Biobank BB-0033-00025, Université Côte d’Azur, CHU Nice, FHU OncoAge, 06001 Nice, France
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Heeke S, Hofman V, Benzaquen J, Otto J, Tanga V, Zahaf K, Allegra M, Long-Mira E, Lassalle S, Marquette CH, Ilie M, Hofman P. Detection of EGFR Mutations From Plasma of NSCLC Patients Using an Automatic Cartridge-Based PCR System. Front Pharmacol 2021; 12:657743. [PMID: 33935776 PMCID: PMC8079969 DOI: 10.3389/fphar.2021.657743] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2021] [Accepted: 03/12/2021] [Indexed: 11/17/2022] Open
Abstract
The introduction of liquid biopsies for the detection of EGFR mutations in non-small cell lung cancer patients (NSCLC) has revolutionized the clinical care. However, liquid biopsies are technically challenging and require specifically trained personnel. To facilitate the implementation of liquid biopsies for the detection of EGFR mutations from plasma, we have assessed a fully automated cartridge-based qPCR test that allows the automatic detection of EGFR mutations directly from plasma. We have analyzed 54 NSCLC patients and compared the results of the cartridge-base device to an FDA-approved assay. Detection of EGFR mutations was comparable but slightly lower in the cartridge-based device for L858R mutations (14/15 detected, 93%) and exon 19 deletions (18/20 detected, 90%). Unfortunately, 8/54 (15%) tests failed but increasing the proteinase K volume helped to recover 3/4 (75%) unsuccessful samples. In summary, the fully automated cartridge-based device allowed the detection of EGFR mutations directly from plasma in NSCLC patients with promising accuracy. However, protocol adjustments are necessary to reduce a high test failure rate.
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Affiliation(s)
- Simon Heeke
- Department of Thoracic H&N Medical Oncology, UT MD Anderson Cancer Center, Houston, TX, United States
| | - Véronique Hofman
- Laboratory of Clinical and Experimental Pathology, Biobank BB-0033-00025, Centre Hospitalier Universitaire Nice, Nice, France.,Team 4 IRCAN, Inserm U1081/CNRS 7284, IRCAN, Nice, France.,FHU Oncoage, Nice, France
| | - Jonathan Benzaquen
- FHU Oncoage, Nice, France.,Pulmonary Department, Pasteur Hospital, Nice, France
| | - Josiane Otto
- FHU Oncoage, Nice, France.,Department of Medical Oncology, Centre Antoine Lacassagne, Nice, France
| | - Virginie Tanga
- Laboratory of Clinical and Experimental Pathology, Biobank BB-0033-00025, Centre Hospitalier Universitaire Nice, Nice, France
| | - Katia Zahaf
- Laboratory of Clinical and Experimental Pathology, Biobank BB-0033-00025, Centre Hospitalier Universitaire Nice, Nice, France
| | - Maryline Allegra
- Laboratory of Clinical and Experimental Pathology, Biobank BB-0033-00025, Centre Hospitalier Universitaire Nice, Nice, France
| | - Elodie Long-Mira
- Laboratory of Clinical and Experimental Pathology, Biobank BB-0033-00025, Centre Hospitalier Universitaire Nice, Nice, France.,Team 4 IRCAN, Inserm U1081/CNRS 7284, IRCAN, Nice, France.,FHU Oncoage, Nice, France
| | - Sandra Lassalle
- Laboratory of Clinical and Experimental Pathology, Biobank BB-0033-00025, Centre Hospitalier Universitaire Nice, Nice, France.,Team 4 IRCAN, Inserm U1081/CNRS 7284, IRCAN, Nice, France.,FHU Oncoage, Nice, France
| | - Charles-Hugo Marquette
- Team 4 IRCAN, Inserm U1081/CNRS 7284, IRCAN, Nice, France.,FHU Oncoage, Nice, France.,Pulmonary Department, Pasteur Hospital, Nice, France
| | - Marius Ilie
- Laboratory of Clinical and Experimental Pathology, Biobank BB-0033-00025, Centre Hospitalier Universitaire Nice, Nice, France.,Team 4 IRCAN, Inserm U1081/CNRS 7284, IRCAN, Nice, France.,FHU Oncoage, Nice, France
| | - Paul Hofman
- Laboratory of Clinical and Experimental Pathology, Biobank BB-0033-00025, Centre Hospitalier Universitaire Nice, Nice, France.,Team 4 IRCAN, Inserm U1081/CNRS 7284, IRCAN, Nice, France.,FHU Oncoage, Nice, France
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