1
|
Santini D, Botticelli A, Galvano A, Iuliani M, Incorvaia L, Gristina V, Taffon C, Foderaro S, Paccagnella E, Simonetti S, Fazio F, Scagnoli S, Pomati G, Pantano F, Perrone G, De Falco E, Russo A, Spinelli GP. Network approach in liquidomics landscape. J Exp Clin Cancer Res 2023; 42:193. [PMID: 37542343 PMCID: PMC10401883 DOI: 10.1186/s13046-023-02743-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2023] [Accepted: 06/27/2023] [Indexed: 08/06/2023] Open
Abstract
Tissue-based biopsy is the present main tool to explore the molecular landscape of cancer, but it also has many limits to be frequently executed, being too invasive with the risk of side effects. These limits and the ability of cancer to constantly evolve its genomic profile, have recently led to the need of a less invasive and more accurate alternative, such as liquid biopsy. By searching Circulating Tumor Cells and residues of their nucleic acids or other tumor products in body fluids, especially in blood, but also in urine, stools and saliva, liquid biopsy is becoming the future of clinical oncology. Despite the current lack of a standardization for its workflows, that makes it hard to be reproduced, liquid biopsy has already obtained promising results for cancer screening, diagnosis, prognosis, and risk of recurrence.Through a more accessible molecular profiling of tumors, it could become easier to identify biomarkers predictive of response to treatment, such as EGFR mutations in non-small cell lung cancer and KRAS mutations in colorectal cancer, or Microsatellite Instability and Mismatch Repair as predictive markers of pembrolizumab response.By monitoring circulating tumor DNA in longitudinal repeated sampling of blood we could also predict Minimal Residual Disease and the risk of recurrence in already radically resected patients.In this review we will discuss about the current knowledge of limitations and strengths of the different forms of liquid biopsies for its inclusion in normal cancer management, with a brief nod to their newest biomarkers and its future implications.
Collapse
Affiliation(s)
- Daniele Santini
- Oncologia Medica A, Policlinico Umberto 1, La Sapienza Università Di Roma, Rome, Italy
| | - Andrea Botticelli
- Oncologia Medica A, Policlinico Umberto 1, La Sapienza Università Di Roma, Rome, Italy
| | - Antonio Galvano
- Section of Medical Oncology, Department of Surgical, Oncological and Oral Sciences, University of Palermo, Palermo, Italy
| | - Michele Iuliani
- Medical Oncology, Fondazione Policlinico Universitario Campus Bio-Medico, Department of Medicine and Surgery, Università Campus Bio-Medico Di Roma, Selcetta, Italy
| | - Lorena Incorvaia
- Section of Medical Oncology, Department of Surgical, Oncological and Oral Sciences, University of Palermo, Palermo, Italy
| | - Valerio Gristina
- Section of Medical Oncology, Department of Surgical, Oncological and Oral Sciences, University of Palermo, Palermo, Italy
| | - Chiara Taffon
- Anatomical Pathology Operative Research Unit, Fondazione Policlinico Universitario Campus Bio-Medico, Rome, Italy
- Department of Medicine and Surgery, Research Unit of Anatomical Pathology, Università Campus Bio-Medico Di Roma, Rome, Italy
| | - Simone Foderaro
- Medical Oncology, Fondazione Policlinico Universitario Campus Bio-Medico, Department of Medicine and Surgery, Università Campus Bio-Medico Di Roma, Selcetta, Italy
| | - Elisa Paccagnella
- Department of Medical Surgical Sciences and Biotechnologies, Sapienza University of Rome, C.So Della Repubblica 79, 04100, Latina, Italy
| | - Sonia Simonetti
- Medical Oncology, Fondazione Policlinico Universitario Campus Bio-Medico, Department of Medicine and Surgery, Università Campus Bio-Medico Di Roma, Selcetta, Italy
| | - Federico Fazio
- UOC Oncologia Territoriale, Polo Pontino, La Sapienza Università Di Roma, Latina, Italy.
| | - Simone Scagnoli
- Oncologia Medica A, Policlinico Umberto 1, La Sapienza Università Di Roma, Rome, Italy
| | | | - Francesco Pantano
- Medical Oncology, Fondazione Policlinico Universitario Campus Bio-Medico, Department of Medicine and Surgery, Università Campus Bio-Medico Di Roma, Selcetta, Italy
| | - Giuseppe Perrone
- Anatomical Pathology Operative Research Unit, Fondazione Policlinico Universitario Campus Bio-Medico, Rome, Italy
- Department of Medicine and Surgery, Research Unit of Anatomical Pathology, Università Campus Bio-Medico Di Roma, Rome, Italy
| | - Elena De Falco
- Department of Medical Surgical Sciences and Biotechnologies, Sapienza University of Rome, C.So Della Repubblica 79, 04100, Latina, Italy
- Mediterranea Cardiocentro, 80122, Naples, Italy
| | - Antonio Russo
- Section of Medical Oncology, Department of Surgical, Oncological and Oral Sciences, University of Palermo, Palermo, Italy
| | - Gian Paolo Spinelli
- UOC Oncologia Territoriale, Polo Pontino, La Sapienza Università Di Roma, Latina, Italy
| |
Collapse
|
2
|
Shin J, Jung C. Improving the Accuracy of Single-Nucleotide Variant Diagnosis Using On-Off Discriminating Primers. BIOSENSORS 2023; 13:380. [PMID: 36979592 PMCID: PMC10046569 DOI: 10.3390/bios13030380] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/05/2023] [Revised: 03/05/2023] [Accepted: 03/09/2023] [Indexed: 06/18/2023]
Abstract
Early detection of rare mutations through liquid biopsy can provide real-time information related to cancer diagnosis, prognosis, and treatment outcomes. Cell-free DNA samples used in liquid biopsies contain single-nucleotide variants (SNVs) with a variant allele frequency (VAF) of approximately ≤1%. Droplet digital polymerase chain reaction (ddPCR) is considered the gold standard of sequencing using liquid samples, generating amplicons from samples containing mutations with 0.001-0.005% VAF; however, it requires expensive equipment and time-consuming protocols. Therefore, various PCR methods for discriminating SNVs have been developed; nonetheless, non-specific amplification cannot be avoided even in the absence of mutations, which hampers the accurate diagnosis of SNVs. In this study, we introduce single-nucleotide variant on-off discrimination-PCR (Soo-PCR), a highly accurate and practical method that uses a 3'-end tailing primer for the on-off discrimination of low-abundance mutant-type targets, including SNVs. Soo-PCR minimizes the chance of incorrect judgments owing to its high discriminating power. Cancer markers, such as KRAS G12D, EGFR L858R, and EGFR T790M mutations, containing 0.1% VAF, were clearly detected in under 2 h with a high reliability comparable with that of ddPCR. This new method serves as a practical approach to accurately detect and evaluate low-abundance mutations in a user-friendly manner.
Collapse
|
3
|
Enzymatic Methods for Mutation Detection in Cancer Samples and Liquid Biopsies. Int J Mol Sci 2023; 24:ijms24020923. [PMID: 36674433 PMCID: PMC9865676 DOI: 10.3390/ijms24020923] [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: 11/27/2022] [Revised: 12/28/2022] [Accepted: 12/29/2022] [Indexed: 01/06/2023] Open
Abstract
Low-level tumor somatic DNA mutations in tissue and liquid biopsies obtained from cancer patients can have profound implications for development of metastasis, prognosis, choice of treatment, follow-up, or early cancer detection. Unless detected, such low-frequency DNA alterations can misinform patient management decisions or become missed opportunities for personalized medicine. Next-generation sequencing technologies and digital-PCR can resolve low-level mutations but require access to specialized instrumentation, time, and resources. Enzymatic-based approaches to detection of low-level mutations provide a simple, straightforward, and affordable alternative to enrich and detect such alterations and is broadly available to low-resource laboratory settings. This review summarizes the traditional uses of enzymatic mutation detection and describes the latest exciting developments, potential, and applications with specific reference to the field of liquid biopsy in cancer.
Collapse
|
4
|
Fang X, Yu S, Jiang Y, Xiang Y, Lu K. Circulating tumor DNA detection in MRD assessment and diagnosis and treatment of non-small cell lung cancer. Front Oncol 2022; 12:1027664. [PMID: 36387176 PMCID: PMC9646858 DOI: 10.3389/fonc.2022.1027664] [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: 08/25/2022] [Accepted: 10/11/2022] [Indexed: 11/24/2022] Open
Abstract
Circulating tumor DNA (ctDNA) has contributed immensely to the management of hematologic malignancy and is now considered a valuable detection tool for solid tumors. ctDNA can reflect the real-time tumor burden and be utilized for analyzing specific cancer mutations via liquid biopsy which is a non-invasive procedure that can be used with a relatively high frequency. Thus, many clinicians use ctDNA to assess minimal residual disease (MRD) and it serves as a prognostic and predictive biomarker for cancer therapy, especially for non-small cell lung cancer (NSCLC). Advanced methods have been developed to detect ctDNA, and recent clinical trials have shown the rationality and feasibility of ctDNA for identifying mutations and guiding treatments in NSCLC. Here, we have reviewed recently developed ctDNA detection methods and the importance of sequence analyses of ctDNA in NSCLC.
Collapse
|
5
|
cyy-287, a novel pyrimidine-2,4-diamine derivative, inhibits tumor growth of EGFR-driven non-small cell lung cancer via the ERK pathway. Acta Biochim Biophys Sin (Shanghai) 2022; 54:1540-1551. [PMID: 36239356 PMCID: PMC9828441 DOI: 10.3724/abbs.2022139] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
In recent decades, EGFR-targeted tyrosine kinase inhibitors (TKIs) have been proven to be an effective therapy for EGFR-mutant non-small cell lung cancer (NSCLC). However, resistance to EGFR-TKIs limits their clinical application. In the present study, we investigate the antitumor effect and underlying mechanism of a novel pyrimidine-2,4-diamine derivative, cyy-287, in NSCLC. We find that cyy-287 has a high affinity for lung tissue and inhibits the proliferation of NSCLC cells. Interestingly, the significant suppression of migration and induction of apoptosis by cyy-287 are only observed in EGFR-driven but not in EGFR-wild-type (wt) cells. According to the RNA sequencing and KEGG enrichment analysis results, cyy-287 markedly inhibits the MAPK pathway in EGFR-driven PC9 cells, and western blot analysis results further indicate that cyy-287 selectively blocks the ERK pathway in EGFR-driven cells. Meanwhile, apoptosis induced by cyy-287 could be partially reversed by ERK pathway inhibition. Further experiment indicates that cyy-287 inhibits the EGFR pathway in both EGFR-driven and EGFR-overexpressing cells. Interestingly, it only induces apoptosis in EGFR-driven cells, not in EGFR-overexpressing cells. The growth of EGFR-driven cells is suppressed by cyy-287 in vivo, with fewer side effects. Our results suggest that cyy-287 may be a potential therapeutic drug with promising antitumor effects against NSCLC.
Collapse
|
6
|
Wu Y, Biswas D, Swanton C. Impact of cancer evolution on immune surveillance and checkpoint inhibitor response. Semin Cancer Biol 2022; 84:89-102. [PMID: 33631295 PMCID: PMC9253787 DOI: 10.1016/j.semcancer.2021.02.013] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Revised: 02/18/2021] [Accepted: 02/19/2021] [Indexed: 12/21/2022]
Abstract
Intratumour heterogeneity (ITH) is pervasive across all cancers studied and may provide the evolving tumour multiple routes to escape immune surveillance. Immune checkpoint inhibitors (CPIs) are rapidly becoming standard of care for many cancers. Here, we discuss recent work investigating the influence of ITH on patient response to immune checkpoint inhibitor (CPI) therapy. At its simplest, ITH may confound the diagnostic accuracy of predictive biomarkers used to stratify patients for CPI therapy. Furthermore, ITH is fuelled by mechanisms of genetic instability that can both engage immune surveillance and drive immune evasion. A greater appreciation of the interplay between ITH and the immune system may hold the key to increasing the proportion of patients experiencing durable responses from CPI therapy.
Collapse
Affiliation(s)
- Yin Wu
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, NW1 1AT, UK; Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, Paul O'Gorman Building, London, WC1E 6DD, UK; Peter Gorer Department of Immunobiology, School of Immunology & Microbial Sciences, King's College London, London, SE1 9RT, UK
| | - Dhruva Biswas
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, NW1 1AT, UK; Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, Paul O'Gorman Building, London, WC1E 6DD, UK; Bill Lyons Informatics Centre, University College London Cancer Institute, Paul O'Gorman Building, London, WC1E 6DD, UK
| | - Charles Swanton
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, NW1 1AT, UK; Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, Paul O'Gorman Building, London, WC1E 6DD, UK.
| |
Collapse
|
7
|
Duffy MJ, Crown J. Circulating Tumor DNA as a Biomarker for Monitoring Patients with Solid Cancers: Comparison with Standard Protein Biomarkers. Clin Chem 2022; 68:1381-1390. [PMID: 35962648 DOI: 10.1093/clinchem/hvac121] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2022] [Accepted: 06/21/2022] [Indexed: 12/20/2022]
Abstract
BACKGROUND Protein-based biomarkers are widely used in monitoring patients with diagnosed cancer. These biomarkers however, lack specificity for cancer and have poor sensitivity in detecting early recurrences and monitoring therapy effectiveness. Emerging data suggest that the use of circulating tumor DNA (ctDNA) has several advantages over standard biomarkers. CONTENT Following curative-intent surgery for cancer, the presence of ctDNA is highly predictive of early disease recurrence, while in metastatic cancer an early decline in ctDNA following the initiation of treatment is predictive of good outcome. Compared with protein biomarkers, ctDNA provides greater cancer specificity and sensitivity for detecting early recurrent/metastatic disease. Thus, in patients with surgically resected colorectal cancer, multiple studies have shown that ctDNA is superior to carcinoembryonic antigen (CEA) in detecting residual disease and early recurrence. Similarly, in breast cancer, ctDNA was shown to be more accurate than carbohydrate antigen 15-3 (CA 15-3) in detecting early recurrences. Other advantages of ctDNA over protein biomarkers in monitoring cancer patients include a shorter half-life in plasma and an ability to predict likely response to specific therapies and identify mechanisms of therapy resistance. However, in contrast to proteins, ctDNA biomarkers are more expensive to measure, less widely available, and have longer turnaround times for reporting. Furthermore, ctDNA assays are less well standardized. SUMMARY Because of their advantages, it is likely that ctDNA measurements will enter clinical use in the future, where they will complement existing biomarkers and imaging in managing patients with cancer. Hopefully, these combined approaches will lead to a better outcome for patients.
Collapse
Affiliation(s)
- Michael J Duffy
- UCD School of Medicine, Conway Institute of Biomolecular and Biomedical Research, University College Dublin, Dublin, Ireland.,UCD Clinical Research Centre, St. Vincent's University Hospital, Dublin, Ireland
| | - John Crown
- Department of Medical Oncology, St Vincent's University Hospital, Dublin, Ireland
| |
Collapse
|
8
|
Pre-PCR Mutation-Enrichment Methods for Liquid Biopsy Applications. Cancers (Basel) 2022; 14:cancers14133143. [PMID: 35804916 PMCID: PMC9264780 DOI: 10.3390/cancers14133143] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2022] [Revised: 06/20/2022] [Accepted: 06/23/2022] [Indexed: 01/25/2023] Open
Abstract
Liquid biopsy is having a remarkable impact on healthcare- and disease-management in the context of personalized medicine. Circulating free DNA (cfDNA) is one of the most instructive liquid-biopsy-based biomarkers and harbors valuable information for diagnostic, predictive, and prognostic purposes. When it comes to cancer, circulating DNA from the tumor (ctDNA) has a wide range of applications, from early cancer detection to the early detection of relapse or drug resistance, and the tracking of the dynamic genomic make-up of tumor cells. However, the detection of ctDNA remains technically challenging, due, in part, to the low frequency of ctDNA among excessive circulating cfDNA originating from normal tissues. During the past three decades, mutation-enrichment methods have emerged to boost sensitivity and enable facile detection of low-level mutations. Although most developed techniques apply mutation enrichment during or following initial PCR, there are a few techniques that allow mutation selection prior to PCR, which provides advantages. Pre-PCR enrichment techniques can be directly applied to genomic DNA and diminish the influence of PCR errors that can take place during amplification. Moreover, they have the capability for high multiplexity and can be followed by established mutation detection and enrichment technologies without changes to their established procedures. The first approaches for pre-PCR enrichment were developed by employing restriction endonucleases directly on genomic DNA in the early 1990s. However, newly developed pre-PCR enrichment methods provide higher sensitivity and versatility. This review describes the available pre-PCR enrichment methods and focuses on the most recently developed techniques (NaME-PrO, UVME, and DEASH/MAESTRO), emphasizing their applications in liquid biopsies.
Collapse
|
9
|
Nkosi D, Miller CA, Jajosky AN, Oltvai ZN. Incidental discovery of acute myeloid leukemia during liquid biopsy of a lung cancer patient. Cold Spring Harb Mol Case Stud 2022; 8:mcs.a006201. [PMID: 35732498 PMCID: PMC9235846 DOI: 10.1101/mcs.a006201] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2022] [Accepted: 04/25/2022] [Indexed: 11/25/2022] Open
Abstract
Liquid biopsy is considered an alternative to standard next-generation sequencing (NGS) of solid tumor samples when biopsy tissue is inadequate for testing or when testing of a peripheral blood sample is preferred. A common assumption of liquid biopsies is that the NGS data obtained on circulating cell-free DNA is a high-fidelity reflection of what would be found by solid tumor testing. Here, we describe a case that challenges this widely held assumption. A patient diagnosed with lung carcinoma showed pathogenic IDH1 and TP53 mutations by liquid biopsy NGS at an outside laboratory. Subsequent in-house NGS of a metastatic lymph node fine-needle aspiration (FNA) sample revealed two pathogenic EGFR mutations. Morphologic and immunophenotypic assessment of the patient's blood sample identified acute myeloid leukemia, with in-house NGS confirming and identifying pathogenic IDH1, TP53, and BCOR mutations, respectively. This case, together with a few similar reports, demonstrates that caution is needed when interpreting liquid biopsy NGS results, especially if they are inconsistent with the presumptive diagnosis. Our case suggests that routine parallel sequencing of peripheral white blood cells would substantially increase the fidelity of the obtained liquid biopsy results.
Collapse
Affiliation(s)
- Dingani Nkosi
- Department of Pathology and Laboratory Medicine, University of Rochester School of Medicine and Dentistry, Rochester, New York 14642, USA
| | - Caroline A Miller
- Department of Pathology and Laboratory Medicine, University of Rochester School of Medicine and Dentistry, Rochester, New York 14642, USA
| | - Audrey N Jajosky
- Department of Pathology and Laboratory Medicine, University of Rochester School of Medicine and Dentistry, Rochester, New York 14642, USA
| | - Zoltán N Oltvai
- Department of Pathology and Laboratory Medicine, University of Rochester School of Medicine and Dentistry, Rochester, New York 14642, USA
| |
Collapse
|
10
|
Nuclease-Assisted, Multiplexed Minor-Allele Enrichment: Application in Liquid Biopsy of Cancer. METHODS IN MOLECULAR BIOLOGY (CLIFTON, N.J.) 2022; 2394:433-451. [PMID: 35094339 DOI: 10.1007/978-1-0716-1811-0_22] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
The use of next-generation sequencing (NGS) to profile genomic variation of individual cancer species is revolutionizing the practice of clinical oncology. In liquid biopsy of cancer, sequencing of circulating-free DNA (cfDNA) is gradually applied to all stages of cancer diagnosis and treatment, serving as complement or replacement of tissue biopsies. However, analysis of cfDNA obtained from blood draws still faces technical obstacles due in part to an excess of wild-type DNA originating from normal tissues and hematopoietic cells. The resulting low-level mutation abundance often falls below routine NGS detection sensitivity and limits reliable mutation identification that meets clinical sensitivity and specificity standards. Despite sample preparation advances that reduce sequencing error rates via use of unique molecular identifiers (molecular barcodes) and error-suppression algorithms, excessive amounts of sequencing are still required to detect mutations at allelic frequency levels below 1%. This requirement reduces throughput and increases cost.In this chapter, we describe a sensitive multiplex mutation detection method that enriches mutation-containing DNA during sample preparation, prior to sequencing, thereby increasing signal-to-noise ratios and providing low-level mutation detection without excessive sequencing depth. We couple targeted next-generation sequencing with wild-type DNA removal using Nuclease-assisted Minor-allele Enrichment using Probe Overlap, NaME-PrO, a recently developed method to eliminate wild-type sequences from multiple targets simultaneously. A step by step guide to library preparation and data analysis are provided as well as some precautions during the sample handling.
Collapse
|
11
|
Kolesar J, Peh S, Thomas L, Baburaj G, Mukherjee N, Kantamneni R, Lewis S, Pai A, Udupa KS, Kumar An N, Rangnekar VM, Rao M. Integration of liquid biopsy and pharmacogenomics for precision therapy of EGFR mutant and resistant lung cancers. Mol Cancer 2022; 21:61. [PMID: 35209919 PMCID: PMC8867675 DOI: 10.1186/s12943-022-01534-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Accepted: 02/07/2022] [Indexed: 11/22/2022] Open
Abstract
The advent of molecular profiling has revolutionized the treatment of lung cancer by comprehensively delineating the genomic landscape of the epidermal growth factor receptor (EGFR) gene. Drug resistance caused by EGFR mutations and genetic polymorphisms of drug metabolizing enzymes and transporters impedes effective treatment of EGFR mutant and resistant lung cancer. This review appraises current literature, opportunities, and challenges associated with liquid biopsy and pharmacogenomic (PGx) testing as precision therapy tools in the management of EGFR mutant and resistant lung cancers. Liquid biopsy could play a potential role in selection of precise tyrosine kinase inhibitor (TKI) therapies during different phases of lung cancer treatment. This selection will be based on the driver EGFR mutational status, as well as monitoring the development of potential EGFR mutations arising during or after TKIs treatment, since some of these new mutations may be druggable targets for alternative TKIs. Several studies have identified the utility of liquid biopsy in the identification of EGFR driver and acquired resistance with good sensitivities for various blood-based biomarkers. With a plethora of sequencing technologies and platforms available currently, further evaluations using randomized controlled trials (RCTs) in multicentric, multiethnic and larger patient cohorts could enable optimization of liquid-based assays for the detection of EGFR mutations, and support testing of CYP450 enzymes and drug transporter polymorphisms to guide precise dosing of EGFR TKIs.
Collapse
Affiliation(s)
- Jill Kolesar
- Department of Pharmacy Practice & Science, University of Kentucky, Lexington, KY, 40536, USA
| | - Spencer Peh
- Department of Pharmacy Practice & Science, University of Kentucky, Lexington, KY, 40536, USA
| | - Levin Thomas
- Department of Pharmacy Practice, Manipal College of Pharmaceutical Sciences, Manipal Academy of Higher Education, Manipal, Karnataka, 576104, India
| | - Gayathri Baburaj
- Department of Pharmacy Practice, Manipal College of Pharmaceutical Sciences, Manipal Academy of Higher Education, Manipal, Karnataka, 576104, India
| | - Nayonika Mukherjee
- Department of Pharmacy Practice, Manipal College of Pharmaceutical Sciences, Manipal Academy of Higher Education, Manipal, Karnataka, 576104, India
| | - Raveena Kantamneni
- Department of Pharmacy Practice, Manipal College of Pharmaceutical Sciences, Manipal Academy of Higher Education, Manipal, Karnataka, 576104, India
| | - Shirley Lewis
- Department of Radiotherapy and Oncology, Kasturba Medical College, Manipal Comprehensive Cancer Care Centre, Manipal Academy of Higher Education, Manipal, Karnataka, 576104, India
| | - Ananth Pai
- Department of Medical Oncology, Kasturba Medical College, Manipal Comprehensive Cancer Care Centre, Manipal Academy of Higher Education, Manipal, Karnataka, 576104, India
| | - Karthik S Udupa
- Department of Medical Oncology, Kasturba Medical College, Manipal Comprehensive Cancer Care Centre, Manipal Academy of Higher Education, Manipal, Karnataka, 576104, India
| | - Naveena Kumar An
- Department of Surgical Oncology, Kasturba Medical College, Manipal Comprehensive Cancer Care Centre, Manipal Academy of Higher Education, Manipal, Karnataka, 576104, India
| | - Vivek M Rangnekar
- Markey Cancer Centre and Department of Radiation Medicine, University of Kentucky, Lexington, KY, 40536, USA
| | - Mahadev Rao
- Department of Pharmacy Practice, Manipal College of Pharmaceutical Sciences, Manipal Academy of Higher Education, Manipal, Karnataka, 576104, India.
| |
Collapse
|
12
|
Dong N, Wang W, Lin S. Sensitive detection of T790M mutations in lung cancer biopsies using a PCR-based lateral flow assay. Anal Biochem 2022; 637:114476. [PMID: 34800430 DOI: 10.1016/j.ab.2021.114476] [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: 09/06/2021] [Revised: 11/14/2021] [Accepted: 11/15/2021] [Indexed: 11/27/2022]
Abstract
T790 M point mutations in EGFR exon 20 are regarded as the most common cause of resistance to epidermal growth factor receptor tyrosine kinase inhibitor treatment. In this study, a PCR-based lateral flow assay (PCR-LFA) was developed to detect T790 M mutations in human genomic DNA. Detection sensitivity was determined using DNA at different mutant to wild-type ratios. The limit of detection of mutant alleles was 15 copies per reaction. The sensitivity of detection of these mutations in 40 formalin-fixed paraffin-embedded tissue biopsies from non-small cell lung cancer patients was analyzed using PCR-LFA and amplification refractory mutation system (ARMS) PCR. Our assay provided the same information as ARMS PCR for 95% (38/40) of the samples. T790 M mutations were detected in 15 (37.5%) and 13 samples using our assay and ARMS PCR, respectively. Droplet digital PCR confirmed the presence of T790 M mutations in the two discordant samples. These results indicate that PCR-LFA is more sensitive than ARMS PCR for clinical screening of these mutations.
Collapse
Affiliation(s)
- Ningning Dong
- The First Affiliated Hospital of Zhengzhou University; Zhengzhou, 450000, China.
| | - Wenjia Wang
- The First Affiliated Hospital of Zhengzhou University; Zhengzhou, 450000, China
| | - Shan Lin
- The First Affiliated Hospital of Zhengzhou University; Zhengzhou, 450000, China
| |
Collapse
|
13
|
Leong KW, Yu F, Makrigiorgos GM. Mutation enrichment in human DNA samples via UV-mediated cross-linking. Nucleic Acids Res 2021; 50:e32. [PMID: 34904676 PMCID: PMC8989544 DOI: 10.1093/nar/gkab1222] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2021] [Revised: 10/28/2021] [Accepted: 11/30/2021] [Indexed: 12/13/2022] Open
Abstract
Detection of low-level DNA mutations can reveal recurrent, hotspot genetic changes of clinical relevance to cancer, prenatal diagnostics, organ transplantation or infectious diseases. However, the high excess of wild-type (WT) alleles, which are concurrently present, often hinders identification of salient genetic changes. Here, we introduce UV-mediated cross-linking minor allele enrichment (UVME), a novel approach that incorporates ultraviolet irradiation (∼365 nm UV) DNA cross-linking either before or during PCR amplification. Oligonucleotide probes matching the WT target sequence and incorporating a UV-sensitive 3-cyanovinylcarbazole nucleoside modification are employed for cross-linking WT DNA. Mismatches formed with mutated alleles reduce DNA binding and UV-mediated cross-linking and favor mutated DNA amplification. UV can be applied before PCR and/or at any stage during PCR to selectively block WT DNA amplification and enable identification of traces of mutated alleles. This enables a single-tube PCR reaction directly from genomic DNA combining optimal pre-amplification of mutated alleles, which then switches to UV-mediated mutation enrichment-based DNA target amplification. UVME cross-linking enables enrichment of mutated KRAS and p53 alleles, which can be screened directly via Sanger sequencing, high-resolution melting, TaqMan genotyping or digital PCR, resulting in the detection of mutation allelic frequencies of 0.001–0.1% depending on the endpoint detection method. UV-mediated mutation enrichment provides new potential for mutation enrichment in diverse clinical samples.
Collapse
Affiliation(s)
- Ka Wai Leong
- Department of Radiation Oncology, Dana-Farber Cancer Institute and Brigham and Women's Hospital, Harvard Medical School, 450 Brookline Avenue, Boston, MA 02115, USA
| | - Fangyan Yu
- Department of Radiation Oncology, Dana-Farber Cancer Institute and Brigham and Women's Hospital, Harvard Medical School, 450 Brookline Avenue, Boston, MA 02115, USA
| | - G Mike Makrigiorgos
- Department of Radiation Oncology, Dana-Farber Cancer Institute and Brigham and Women's Hospital, Harvard Medical School, 450 Brookline Avenue, Boston, MA 02115, USA
| |
Collapse
|
14
|
Sarkar M, Nath A, Kumer A, Mallik C, Akter F, Moniruzzaman M, Ali M. Synthesis, molecular docking screening, ADMET and dynamics studies of synthesized 4-(4-methoxyphenyl)-8-methyl-3,4,5,6,7,8-hexahydroquinazolin-2(1H)-one and quinazolinone derivatives. J Mol Struct 2021. [DOI: 10.1016/j.molstruc.2021.130953] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
|
15
|
Villa M, Sharma GG, Manfroni C, Cortinovis D, Mologni L. New Advances in Liquid Biopsy Technologies for Anaplastic Lymphoma Kinase (ALK)-Positive Cancer. Cancers (Basel) 2021; 13:5149. [PMID: 34680298 PMCID: PMC8534237 DOI: 10.3390/cancers13205149] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2021] [Revised: 10/07/2021] [Accepted: 10/11/2021] [Indexed: 02/06/2023] Open
Abstract
Cancer cells are characterized by high genetic instability, that favors tumor relapse. The identification of the genetic causes of relapse can direct next-line therapeutic choices. As tumor tissue rebiopsy at disease progression is not always feasible, noninvasive alternative methods are being explored. Liquid biopsy is emerging as a non-invasive, easy and repeatable tool to identify specific molecular alterations and monitor disease response during treatment. The dynamic follow-up provided by this analysis can provide useful predictive information and allow prompt therapeutic actions, tailored to the genetic profile of the recurring disease, several months before radiographic relapse. Oncogenic fusion genes are particularly suited for this type of analysis. Anaplastic Lymphoma Kinase (ALK) is the dominant driver oncogene in several tumors, including Anaplastic Large-Cell Lymphoma (ALCL), Non-Small Cell Lung Cancer (NSCLC) and others. Here we review recent findings in liquid biopsy technologies, including ctDNA, CTCs, exosomes, and other markers that can be investigated from plasma samples, in ALK-positive cancers.
Collapse
Affiliation(s)
- Matteo Villa
- Department of Medicine and Surgery, University of Milano-Bicocca, 20900 Monza, Italy; (M.V.); (G.G.S.); (C.M.)
| | - Geeta G. Sharma
- Department of Medicine and Surgery, University of Milano-Bicocca, 20900 Monza, Italy; (M.V.); (G.G.S.); (C.M.)
- Department of Hematology & Hematopoietic Cell Transplantation, City of Hope National Medical Center, 1500 E Duarte Rd, Duarte, CA 91010, USA
| | - Chiara Manfroni
- Department of Medicine and Surgery, University of Milano-Bicocca, 20900 Monza, Italy; (M.V.); (G.G.S.); (C.M.)
| | - Diego Cortinovis
- Department of Oncology, San Gerardo Hospital, 20900 Monza, Italy;
| | - Luca Mologni
- Department of Medicine and Surgery, University of Milano-Bicocca, 20900 Monza, Italy; (M.V.); (G.G.S.); (C.M.)
| |
Collapse
|
16
|
Circulating tumor DNA in lung cancer: real-time monitoring of disease evolution and treatment response. Chin Med J (Engl) 2021; 133:2476-2485. [PMID: 32960843 PMCID: PMC7575184 DOI: 10.1097/cm9.0000000000001097] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Lung cancer is one of the leading causes of all cancer-related deaths. Circulating tumor DNA (ctDNA) is released from apoptotic and necrotic tumor cells. Several sensitive techniques have been invented and adapted to quantify ctDNA genomic alterations. Applications of ctDNA in lung cancer include early diagnosis and detection, prognosis prediction, detecting mutations and structural alterations, minimal residual disease, tumor mutational burden, and tumor evolution tracking. Compared to surgical biopsy and radiographic imaging, the advantages of ctDNA are that it is a non-invasive procedure, allows real-time monitoring, and has relatively high sensitivity and specificity. Given the massive research on non-small cell lung cancer, attention should be paid to small cell lung cancer.
Collapse
|
17
|
Cucchiara F, Petrini I, Romei C, Crucitta S, Lucchesi M, Valleggi S, Scavone C, Capuano A, De Liperi A, Chella A, Danesi R, Del Re M. Combining liquid biopsy and radiomics for personalized treatment of lung cancer patients. State of the art and new perspectives. Pharmacol Res 2021; 169:105643. [PMID: 33940185 DOI: 10.1016/j.phrs.2021.105643] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/11/2021] [Revised: 04/22/2021] [Accepted: 04/22/2021] [Indexed: 12/11/2022]
Abstract
Lung cancer has become a paradigm for precision medicine in oncology, and liquid biopsy (LB) together with radiomics may have a great potential in this scenario. They are both minimally invasive, easy to perform, and can be repeated during patient's follow-up. Also, increasing evidence suggest that LB and radiomics may provide an efficient way to screen and diagnose tumors at an early stage, including the monitoring of any change in the tumor molecular profile. This could allow treatment optimization, improvement of patients' quality of life, and healthcare-related costs reduction. Latest reports on lung cancer patients suggest a combination of these two strategies, along with cutting-edge data analysis, to decode valuable information regarding tumor type, aggressiveness, progression, and response to treatment. The approach seems more compatible with clinical practice than the current standard, and provides new diagnostic companions being able to suggest the best treatment strategy compared to conventional methods. To implement radiomics and liquid biopsy directly into clinical practice, an artificial intelligence (AI)-based system could help to link patients' clinical data together with tumor molecular profiles and imaging characteristics. AI could also solve problems and limitations related to LB and radiomics methodologies. Further work is needed, including new health policies and the access to large amounts of high-quality and well-organized data, allowing a complementary and synergistic combination of LB and imaging, to provide an attractive choice e in the personalized treatment of lung cancer.
Collapse
Affiliation(s)
- Federico Cucchiara
- Unit of Clinical Pharmacology and Pharmacogenetics, Department of Clinical and Experimental Medicine, University Hospital of Pisa, Pisa, Italy
| | - Iacopo Petrini
- Unit of Pneumology, Department of Translational Research and New Technologies in Medicine, University Hospital of Pisa, Pisa, Italy
| | - Chiara Romei
- Unit II of Radio-diagnostics, Department of Diagnostic and Imaging, University Hospital of Pisa, Pisa, Italy
| | - Stefania Crucitta
- Unit of Clinical Pharmacology and Pharmacogenetics, Department of Clinical and Experimental Medicine, University Hospital of Pisa, Pisa, Italy
| | - Maurizio Lucchesi
- Unit of Pneumology, Department of Translational Research and New Technologies in Medicine, University Hospital of Pisa, Pisa, Italy
| | - Simona Valleggi
- Unit of Pneumology, Department of Translational Research and New Technologies in Medicine, University Hospital of Pisa, Pisa, Italy
| | - Cristina Scavone
- Department of Experimental Medicine, University of Campania Luigi Vanvitelli, Naples, Italy
| | - Annalisa Capuano
- Department of Experimental Medicine, University of Campania Luigi Vanvitelli, Naples, Italy
| | - Annalisa De Liperi
- Unit II of Radio-diagnostics, Department of Diagnostic and Imaging, University Hospital of Pisa, Pisa, Italy
| | - Antonio Chella
- Unit of Pneumology, Department of Translational Research and New Technologies in Medicine, University Hospital of Pisa, Pisa, Italy
| | - Romano Danesi
- Unit of Clinical Pharmacology and Pharmacogenetics, Department of Clinical and Experimental Medicine, University Hospital of Pisa, Pisa, Italy.
| | - Marzia Del Re
- Unit of Clinical Pharmacology and Pharmacogenetics, Department of Clinical and Experimental Medicine, University Hospital of Pisa, Pisa, Italy
| |
Collapse
|
18
|
Pinzani P, D'Argenio V, Del Re M, Pellegrini C, Cucchiara F, Salvianti F, Galbiati S. Updates on liquid biopsy: current trends and future perspectives for clinical application in solid tumors. Clin Chem Lab Med 2021; 59:1181-1200. [PMID: 33544478 DOI: 10.1515/cclm-2020-1685] [Citation(s) in RCA: 54] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2020] [Accepted: 01/20/2021] [Indexed: 01/19/2023]
Abstract
Despite advances in screening and therapeutics cancer continues to be one of the major causes of morbidity and mortality worldwide. The molecular profile of tumor is routinely assessed by surgical or bioptic samples, however, genotyping of tissue has inherent limitations: it represents a single snapshot in time and it is subjected to spatial selection bias owing to tumor heterogeneity. Liquid biopsy has emerged as a novel, non-invasive opportunity of detecting and monitoring cancer in several body fluids instead of tumor tissue. Circulating tumor cells (CTCs), circulating tumor DNA (ctDNA), RNA (mRNA and microRNA), microvesicles, including exosomes and tumor "educated platelets" were recently identified as a source of genomic information in cancer patients which could reflect all subclones present in primary and metastatic lesions allowing sequential monitoring of disease evolution. In this review, we summarize the currently available information concerning liquid biopsy in breast cancer, colon cancer, lung cancer and melanoma. These promising issues still need to be standardized and harmonized across laboratories, before fully adopting liquid biopsy approaches into clinical practice.
Collapse
Affiliation(s)
- Pamela Pinzani
- Department of Experimental and Clinical Biomedical Sciences "Mario Serio", University of Florence, Florence, Italy
| | - Valeria D'Argenio
- Department of Human Sciences and Quality of Life Promotion, San Raffaele Open University, Rome, Italy.,CEINGE-Biotecnologie Avanzate, Naples, Italy
| | - Marzia Del Re
- Clinical Pharmacology and Pharmacogenetics Unit, Department of Clinical and Experimental Medicine, University of Pisa, Pisa, Italy
| | - Cristina Pellegrini
- Department of Biotechnological and Applied Clinical Sciences, University of L'Aquila, L'Aquila, Italy
| | - Federico Cucchiara
- Clinical Pharmacology and Pharmacogenetics Unit, Department of Clinical and Experimental Medicine, University of Pisa, Pisa, Italy
| | - Francesca Salvianti
- Department of Experimental and Clinical Biomedical Sciences "Mario Serio", University of Florence, Florence, Italy
| | - Silvia Galbiati
- Diabetes Research Institute, IRCCS Ospedale San Raffaele, Milan, Italy
| |
Collapse
|
19
|
Cucchiara F, Del Re M, Valleggi S, Romei C, Petrini I, Lucchesi M, Crucitta S, Rofi E, De Liperi A, Chella A, Russo A, Danesi R. Integrating Liquid Biopsy and Radiomics to Monitor Clonal Heterogeneity of EGFR-Positive Non-Small Cell Lung Cancer. Front Oncol 2020; 10:593831. [PMID: 33489892 PMCID: PMC7819134 DOI: 10.3389/fonc.2020.593831] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2020] [Accepted: 10/30/2020] [Indexed: 12/19/2022] Open
Abstract
Background EGFR-positive Non-small Cell Lung Cancer (NSCLC) is a dynamic entity and tumor progression and resistance to tyrosine kinase inhibitors (TKIs) arise from the accumulation, over time and across different disease sites, of subclonal genetic mutations. For instance, the occurrence of EGFR T790M is associated with resistance to gefitinib, erlotinib, and afatinib, while EGFR C797S causes osimertinib to lose activity. Sensitive technologies as radiomics and liquid biopsy have great potential to monitor tumor heterogeneity since they are both minimally invasive, easy to perform, and can be repeated over patient’s follow-up, enabling the extraction of valuable information. Yet, to date, there are no reported cases associating liquid biopsy and radiomics during treatment. Case presentation In this case series, seven patients with metastatic EGFR-positive NSCLC have been monitored during target therapy. Plasma-derived cell free DNA (cfDNA) was analyzed by a digital droplet PCR (ddPCR), while radiomic analyses were performed using the validated LifeX® software on computed tomography (CT)-images. The dynamics of EGFR mutations in cfDNA was compared with that of radiomic features. Then, for each EGFR mutation, a radiomic signature was defines as the sum of the most predictive features, weighted by their corresponding regression coefficients for the least absolute shrinkage and selection operator (LASSO) model. The receiver operating characteristic (ROC) curves were computed to estimate their diagnostic performance. The signatures achieved promising performance on predicting the presence of EGFR mutations (R2 = 0.447, p <0.001 EGFR activating mutations R2 = 0.301, p = 0.003 for T790M; and R2 = 0.354, p = 0.001 for activating plus resistance mutations), confirmed by ROC analysis. Conclusion To our knowledge, these are the first cases to highlight a potentially promising strategy to detect clonal heterogeneity and ultimately identify patients at risk of progression during treatment. Together, radiomics and liquid biopsy could detect the appearance of new mutations and therefore suggest new therapeutic management.
Collapse
Affiliation(s)
- Federico Cucchiara
- Clinical Pharmacology and Pharmacogenetics Unit, Department of Clinical and Experimental Medicine, University of Pisa, Pisa, Italy
| | - Marzia Del Re
- Clinical Pharmacology and Pharmacogenetics Unit, Department of Clinical and Experimental Medicine, University of Pisa, Pisa, Italy
| | - Simona Valleggi
- Pneumology Unit, Cardiovascular and Thoracic Department, Azienda Ospedaliero-Universitaria Pisana, Pisa, Italy
| | - Chiara Romei
- Radiology Unit 2, Department of Diagnostics and Imaging, Azienda Ospedaliero-Universitaria Pisana, Pisa, Italy
| | - Iacopo Petrini
- Pneumology Unit, Cardiovascular and Thoracic Department, Azienda Ospedaliero-Universitaria Pisana, Pisa, Italy.,Department of Translational Research and New Technologies in Medicine and Surgery, University of Pisa, Pisa, Italy
| | - Maurizio Lucchesi
- Pneumology Unit, Cardiovascular and Thoracic Department, Azienda Ospedaliero-Universitaria Pisana, Pisa, Italy
| | - Stefania Crucitta
- Clinical Pharmacology and Pharmacogenetics Unit, Department of Clinical and Experimental Medicine, University of Pisa, Pisa, Italy
| | - Eleonora Rofi
- Clinical Pharmacology and Pharmacogenetics Unit, Department of Clinical and Experimental Medicine, University of Pisa, Pisa, Italy
| | - Annalisa De Liperi
- Radiology Unit 2, Department of Diagnostics and Imaging, Azienda Ospedaliero-Universitaria Pisana, Pisa, Italy
| | - Antonio Chella
- Pneumology Unit, Cardiovascular and Thoracic Department, Azienda Ospedaliero-Universitaria Pisana, Pisa, Italy
| | - Antonio Russo
- Section of Medical Oncology, Department of Surgical, Oncological and Stomatological Sciences, University of Palermo, Palermo, Italy
| | - Romano Danesi
- Clinical Pharmacology and Pharmacogenetics Unit, Department of Clinical and Experimental Medicine, University of Pisa, Pisa, Italy
| |
Collapse
|
20
|
Belloum Y, Janning M, Mohme M, Simon R, Kropidlowski J, Sartori A, Irwin D, Westphal M, Lamszus K, Loges S, Riethdorf S, Pantel K, Wikman H. Discovery of Targetable Genetic Alterations in NSCLC Patients with Different Metastatic Patterns Using a MassARRAY-Based Circulating Tumor DNA Assay. Cells 2020; 9:E2337. [PMID: 33105541 PMCID: PMC7690267 DOI: 10.3390/cells9112337] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2020] [Revised: 10/15/2020] [Accepted: 10/19/2020] [Indexed: 12/14/2022] Open
Abstract
Circulating tumor DNA (ctDNA) has shown great promise as a minimally invasive liquid biopsy for personalized cancer diagnostics especially among metastatic patients. Here, we used a novel sensitive assay to detect clinically relevant mutations in ctDNA in blood plasma from metastatic non-small cell lung cancer (NSCLC) patients, including patients with a limited oligo-brain metastatic disease. We analyzed 66 plasma samples from 56 metastatic NSCLC patients for 74 hotspot mutations in five genes commonly mutated in NSCLC using a novel MassARRAY-based lung cancer panel with a turnaround time of only 3 days. Mutations in plasma DNA could be detected in 28 out of 56 patients (50.0%), with a variant allele frequency (VAF) ranging between 0.1% and 5.0%. Mutations were detected in 50.0% of patients with oligo-brain metastatic disease, although the median VAF was lower (0.4%) compared to multi-brain metastatic patients (0.9%) and patients with extra-cranial metastatic progression (1.2%). We observed an overall concordance of 86.4% (n = 38/44) for EGFR status between plasma and tissue. The MassARRAY technology can detect clinically relevant mutations in plasma DNA from metastatic NSCLC patients including patients with limited, oligo-brain metastatic disease.
Collapse
Affiliation(s)
- Yassine Belloum
- Department of Tumor Biology, University Medical Center Hamburg-Eppendorf, 20246 Hamburg, Germany; (Y.B.); (M.J.); (J.K.); (S.L.); (S.R.); (K.P.)
| | - Melanie Janning
- Department of Tumor Biology, University Medical Center Hamburg-Eppendorf, 20246 Hamburg, Germany; (Y.B.); (M.J.); (J.K.); (S.L.); (S.R.); (K.P.)
- Department of Oncology, Hematology and Bone Marrow Transplantation with Section Pneumology, University Medical Center Hamburg-Eppendorf, 20246 Hamburg, Germany
- Division of Personalized Medical Oncology, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
- Department of Personalized Oncology, University Hospital Mannheim, University of Heidelberg, 68167 Mannheim, Germany
| | - Malte Mohme
- Department of Neurosurgery, University Medical Center Hamburg-Eppendorf, 20246 Hamburg, Germany; (M.M.); (M.W.); (K.L.)
| | - Ronald Simon
- Institute of Pathology, University Medical Center Hamburg-Eppendorf, 20246 Hamburg, Germany;
| | - Jolanthe Kropidlowski
- Department of Tumor Biology, University Medical Center Hamburg-Eppendorf, 20246 Hamburg, Germany; (Y.B.); (M.J.); (J.K.); (S.L.); (S.R.); (K.P.)
| | | | - Darryl Irwin
- Agena Bioscience GmbH, 22761 Hamburg, Germany; (A.S.); (D.I.)
| | - Manfred Westphal
- Department of Neurosurgery, University Medical Center Hamburg-Eppendorf, 20246 Hamburg, Germany; (M.M.); (M.W.); (K.L.)
| | - Katrin Lamszus
- Department of Neurosurgery, University Medical Center Hamburg-Eppendorf, 20246 Hamburg, Germany; (M.M.); (M.W.); (K.L.)
| | - Sonja Loges
- Department of Tumor Biology, University Medical Center Hamburg-Eppendorf, 20246 Hamburg, Germany; (Y.B.); (M.J.); (J.K.); (S.L.); (S.R.); (K.P.)
- Department of Oncology, Hematology and Bone Marrow Transplantation with Section Pneumology, University Medical Center Hamburg-Eppendorf, 20246 Hamburg, Germany
- Division of Personalized Medical Oncology, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
- Department of Personalized Oncology, University Hospital Mannheim, University of Heidelberg, 68167 Mannheim, Germany
| | - Sabine Riethdorf
- Department of Tumor Biology, University Medical Center Hamburg-Eppendorf, 20246 Hamburg, Germany; (Y.B.); (M.J.); (J.K.); (S.L.); (S.R.); (K.P.)
| | - Klaus Pantel
- Department of Tumor Biology, University Medical Center Hamburg-Eppendorf, 20246 Hamburg, Germany; (Y.B.); (M.J.); (J.K.); (S.L.); (S.R.); (K.P.)
| | - Harriet Wikman
- Department of Tumor Biology, University Medical Center Hamburg-Eppendorf, 20246 Hamburg, Germany; (Y.B.); (M.J.); (J.K.); (S.L.); (S.R.); (K.P.)
| |
Collapse
|
21
|
Song H, Liu D, Dong S, Zeng L, Wu Z, Zhao P, Zhang L, Chen ZS, Zou C. Epitranscriptomics and epiproteomics in cancer drug resistance: therapeutic implications. Signal Transduct Target Ther 2020; 5:193. [PMID: 32900991 PMCID: PMC7479143 DOI: 10.1038/s41392-020-00300-w] [Citation(s) in RCA: 53] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2020] [Revised: 07/18/2020] [Accepted: 07/28/2020] [Indexed: 12/24/2022] Open
Abstract
Drug resistance is a major hurdle in cancer treatment and a key cause of poor prognosis. Epitranscriptomics and epiproteomics are crucial in cell proliferation, migration, invasion, and epithelial–mesenchymal transition. In recent years, epitranscriptomic and epiproteomic modification has been investigated on their roles in overcoming drug resistance. In this review article, we summarized the recent progress in overcoming cancer drug resistance in three novel aspects: (i) mRNA modification, which includes alternative splicing, A-to-I modification and mRNA methylation; (ii) noncoding RNAs modification, which involves miRNAs, lncRNAs, and circRNAs; and (iii) posttranslational modification on molecules encompasses drug inactivation/efflux, drug target modifications, DNA damage repair, cell death resistance, EMT, and metastasis. In addition, we discussed the therapeutic implications of targeting some classical chemotherapeutic drugs such as cisplatin, 5-fluorouridine, and gefitinib via these modifications. Taken together, this review highlights the importance of epitranscriptomic and epiproteomic modification in cancer drug resistance and provides new insights on potential therapeutic targets to reverse cancer drug resistance.
Collapse
Affiliation(s)
- Huibin Song
- Shenzhen People's Hospital (The Second Clinical Medical College, Jinan University; The First Affiliated Hospital, Southern University of Science and Technology), Shenzhen, 518001, Guangdong, China
| | - Dongcheng Liu
- Shenzhen People's Hospital (The Second Clinical Medical College, Jinan University; The First Affiliated Hospital, Southern University of Science and Technology), Shenzhen, 518001, Guangdong, China
| | - Shaowei Dong
- Shenzhen People's Hospital (The Second Clinical Medical College, Jinan University; The First Affiliated Hospital, Southern University of Science and Technology), Shenzhen, 518001, Guangdong, China
| | - Leli Zeng
- College of Pharmacy and Health Sciences, St. John's University, Queens, 11439 New York, USA.,Tomas Lindahl Nobel Laureate Laboratory, Research Centre, The Seventh Affiliated Hospital, Sun Yat-sen University, Shenzhen, 518107, Guangdong, China
| | - Zhuoxun Wu
- College of Pharmacy and Health Sciences, St. John's University, Queens, 11439 New York, USA
| | - Pan Zhao
- Shenzhen People's Hospital (The Second Clinical Medical College, Jinan University; The First Affiliated Hospital, Southern University of Science and Technology), Shenzhen, 518001, Guangdong, China
| | - Litu Zhang
- Department of Research, Affiliated Tumor Hospital of Guangxi Medical University, Nanning, 530021, Guangxi, China
| | - Zhe-Sheng Chen
- College of Pharmacy and Health Sciences, St. John's University, Queens, 11439 New York, USA.
| | - Chang Zou
- Shenzhen People's Hospital (The Second Clinical Medical College, Jinan University; The First Affiliated Hospital, Southern University of Science and Technology), Shenzhen, 518001, Guangdong, China. .,Shenzhen Public Service Platform on Tumor Precision Medicine and Molecular Diagnosis, Shenzhen, 518001, Guangdong, China.
| |
Collapse
|
22
|
Wang N, Zhang X, Wang F, Zhang M, Sun B, Yin W, Deng S, Wan Y, Lu W. The Diagnostic Accuracy of Liquid Biopsy in EGFR-Mutated NSCLC: A Systematic Review and Meta-Analysis of 40 Studies. SLAS Technol 2020; 26:42-54. [PMID: 32659150 DOI: 10.1177/2472630320939565] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Epidermal growth factor receptor (EGFR) mutations are the most common carcinogenic driver mutations in non-small-cell lung cancer (NSCLC) patients, while invasive tissue biopsy has certain inherent defects. PubMed, Ovid Medline, Embase, and the Cochrane Library were systematically searched on January 4, 2020, using the keywords "liquid biopsy," "EGFR," and "NSCLC." The pooled sensitivity and specificity of EGFR mutations in paired tissue and blood were calculated. The accuracy was assessed by receiver operating characteristic curve. The meta-regression of the subgroup was performed to analyze the heterogeneity. Hazard ratio (HR) and 95% confidence interval (CI) were combined for evaluating the impact of EGFR mutation in tissue and liquid blood biopsy. A total of 40 studies with 5,995 patients were involved in the study. The pooled sensitivity was 68% (95% CI = 60-75%), and the specificity was 98% (95% CI = 95-99%). The diagnostic odds ratio was 88 (95% CI = 40-195), and the area under the curve was 0.91 (95% CI = 0.88-0.93). In the meta-regression, the sensitivity and specificity remain lower in the Asian studies than non-Asian studies (sensitivity: 66% vs. 73%, P = 0.04; specificity: 96% vs. 97%, P = 0.03, respectively). The EGFR mutation was associated with a better progression-free survival than wild type in both tissue (HR = 0.54, 95% CI = 0.34-0.85, P = 0.007) and blood (HR = 0.81, 95% CI = 0.71-0.92, P = 0.001) detection. Peripheral blood liquid biopsy had a better specificity for detecting EGFR mutation in NSCLC patients, while tissue biopsy still needs to be undertaken for negative blood biopsy patients due to its lower sensitivity.
Collapse
Affiliation(s)
- Naiqun Wang
- Hospital Infection Management Department, The People's Hospital of Yichun City, Yichun, Jiangxi, China
| | - Xiaolian Zhang
- Laboratory Department, The People's Hospital of Yichun City, Yichun, Jiangxi, China
| | - Feilong Wang
- Thoracic Surgery Department, Jining No. 1 People's Hospital, Jining, Shandong, China
| | - Min Zhang
- Department of Stomatology, Affiliated Hospital of Jining Medical University, Jining, Shandong, China
| | - Bo Sun
- Thoracic Surgery Department, Jining No. 1 People's Hospital, Jining, Shandong, China
| | - Weihua Yin
- Oncology Department, The People's Hospital of Yichun City, Yichun, Jiangxi, China
| | - Shaorong Deng
- Blood Transfusion Department, The People's Hospital of Yichun City, Yichun, Jiangxi, China
| | - Ying Wan
- Thoracic Surgery Department, Jining No. 1 People's Hospital, Jining, Shandong, China
| | - Wei Lu
- Thoracic Surgery Department, Jining No. 1 People's Hospital, Jining, Shandong, China
| |
Collapse
|
23
|
Kim P, Li H, Wang J, Zhao Z. Landscape of drug-resistance mutations in kinase regulatory hotspots. Brief Bioinform 2020; 22:5854404. [PMID: 32510566 DOI: 10.1093/bib/bbaa108] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2020] [Revised: 04/23/2020] [Accepted: 05/05/2020] [Indexed: 12/13/2022] Open
Abstract
More than 48 kinase inhibitors (KIs) have been approved by Food and Drug Administration. However, drug-resistance (DR) eventually occurs, and secondary mutations have been found in the previously targeted primary-mutated cancer cells. Cancer and drug research communities recognize the importance of the kinase domain (KD) mutations for kinasopathies. So far, a systematic investigation of kinase mutations on DR hotspots has not been done yet. In this study, we systematically investigated four types of representative mutation hotspots (gatekeeper, G-loop, αC-helix and A-loop) associated with DR in 538 human protein kinases using large-scale cancer data sets (TCGA, ICGC, COSMIC and GDSC). Our results revealed 358 kinases harboring 3318 mutations that covered 702 drug resistance hotspot residues. Among them, 197 kinases had multiple genetic variants on each residue. We further computationally assessed and validated the epidermal growth factor receptor mutations on protein structure and drug-binding efficacy. This is the first study to provide a landscape view of DR-associated mutation hotspots in kinase's secondary structures, and its knowledge will help the development of effective next-generation KIs for better precision medicine.
Collapse
|
24
|
Circulating tumour DNA: A new biomarker to monitor resistance in NSCLC patients treated with EGFR-TKIs. Biochim Biophys Acta Rev Cancer 2020; 1873:188363. [PMID: 32275933 DOI: 10.1016/j.bbcan.2020.188363] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2020] [Revised: 04/03/2020] [Accepted: 04/03/2020] [Indexed: 12/24/2022]
Abstract
Targeted molecular therapies have markedly improved the therapeutic management of lung cancer, while the discovery of epidermal growth factor receptor tyrosine kinase inhibitors (EGFR-TKIs) has revolutionized the treatment of non-small cell lung cancer (NSCLC). However, the clinical benefit of targeted therapies is limited by the eventual emergence of resistance. Identifying and monitoring the underlying mechanism of EGFR-TKI resistance could lead to more precise therapy and advances in treatment. Presently, tissue biopsy remains the gold standard for genotyping but it is limited by sampling bias, lack of available tissue, and potential complications. Analysis of circulating tumour DNA (ctDNA) may overcome the current limitations of tissue biopsies and provide a comprehensive landscape of the resistance mechanisms in a minimally invasive manner. Well-developed, analytically valid detection technologies are prerequisites for integrating ctDNA detection into clinical cancer management. Here, we provide an overview of available methodologies for ctDNA detection and we also discuss the potential clinical applications of ctDNA to monitor the resistance mechanisms.
Collapse
|
25
|
Li H, Wang J, Zhang G, Li Y, Lin L, Yang H, Zhou J, Zhang L, Lv D. Detection of plasma T790M mutation after the first generation EGFR-TKI resistance of non-small cell lung cancer in the real world. J Thorac Dis 2020; 12:550-557. [PMID: 32274120 PMCID: PMC7138969 DOI: 10.21037/jtd.2019.12.122] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Background The epidermal growth factor receptor (EGFR) gene has been identified as the driving gene of non-small cell lung cancer (NSCLC), and EGFR-tyrosine kinase inhibitor (TKI) has shown efficacy, but acquired resistance is inevitable. It has been confirmed that the secondary EGFR Thr790Met (T790M) mutation accounts for about 50% of the mechanisms of acquired resistance to EGFR-TKI. The third-generation of EGFR-TKI has significantly efficacy in advanced T790M-positive NSCLC patients. Therefore, it is necessary to detect the status of T790M in patients with acquired resistance after first generation EGFR-TKI. The objective of this study was to investigate the positive rate of plasma test T790M mutation and its relationship with different clinical characteristics, and the frequency of T790M mutation in advanced EGFR-mutant NSCLC patients with acquired resistance after firstline EGFR-TKI treatment. Methods Patients from a single clinical center (Taizhou hospital) were recruited prospectively from September 2017 to June 2018. The eligibility criteria of the trial included the following: (I) aged 18 years or older, histologically confirmed NSCLC stage IIIB/st and EGFR mutation positive; (II) progressive disease (PD) after first generation EGFR-TKI by RECIST v1.1, with PFS>3 months; (III) no third generation TKI treatment. All patients signed informed consent, had 10 mL of blood drawn, and were evaluated for the presence of T790M gene by amplification refractory mutation system (ARMS). The study was approved by the Ethics Committee of Taizhou Hospital (ethical batch number: 201637). Results A total of 189 patients were included in the analysis. The overall T790M mutation rate of plasma detection was 36.51% (69/189). The positive rate of T790M mutation after the failure of first generation EGFR-TKI treatment was not correlated with the patient’s age, sex, and the type of first generation TKI drugs. However, it was related to the mutation type of EGFR in baseline and the mode of progression according to reports by Wu et al. The frequency of T790M mutation among patients with initial exon 19 deletion mutation, exon 21 L858R point mutation, and other mutations were 45.45%, 26.19% and 33.33%, respectively. The mutation rate of T790M in 19del mutant patients was higher than that of L858R mutation and other mutations (P=0.026). The frequency of T790M mutation in local progression patients was 50% after the first generation TKI was resistant to drug treatment: in gradual progression it was 26.92%, and in dramatic progression it was 38.10%. The frequency of T790M mutation of patients with local progression was significantly higher (P=0.031). Conclusions The patients with EGFR mutations after the first generation of EGFR-TKI-acquired resistance of NSCLC were evaluated for their plasma EGFR mutation status, and the overall T790M mutation rate of was 36.51%. The frequency of T790M mutation with initial mutation of 19 del was higher than that of L858R mutation and other mutations, and local progression was higher than that in patients with gradual progression and dramatic progression.
Collapse
Affiliation(s)
- Haiyan Li
- Pulmonary Medicine, Affiliated Taizhou Hospital of Zhejiang Province of Wenzhou Medical University, Taizhou 317000, China
| | - Jinwei Wang
- Functional Inspection Section, Affiliated Taizhou Hospital of Zhejiang Province of Wenzhou Medical University, Taizhou 317000, China
| | - Guojing Zhang
- Oncology Department, Wenzhou Geriatric Hospital, Wenzhou 325600, China
| | - Yuping Li
- Pulmonary Medicine, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou 325000, China
| | - Ling Lin
- Pulmonary Medicine, Affiliated Taizhou Hospital of Zhejiang Province of Wenzhou Medical University, Taizhou 317000, China
| | - Haihua Yang
- Radiation Oncology, Laboratory of Cellular and Molecular Radiation Oncology, Radiation Oncology Institute of Enze Medical Health Academy, Affiliated Taizhou Hospital of Zhejiang Province of Wenzhou Medical University, Taizhou 317000, China
| | - Jingjing Zhou
- Pathology Department, Affiliated Taizhou Hospital of Zhejiang Province of Wenzhou Medical University, Taizhou 317000, China
| | - Lingna Zhang
- Pathology Department, Affiliated Taizhou Hospital of Zhejiang Province of Wenzhou Medical University, Taizhou 317000, China
| | - Dongqing Lv
- Pulmonary Medicine, Affiliated Taizhou Hospital of Zhejiang Province of Wenzhou Medical University, Taizhou 317000, China
| |
Collapse
|
26
|
Chen G, Bao Y, Weng Q, Zhao Y, Lu X, Fu L, Chen L, Liu Z, Zhang X, Liang G. Compound 15c, a Novel Dual Inhibitor of EGFR L858R/T790M and FGFR1, Efficiently Overcomes Epidermal Growth Factor Receptor-Tyrosine Kinase Inhibitor Resistance of Non-Small-Cell Lung Cancers. Front Pharmacol 2020; 10:1533. [PMID: 31998131 PMCID: PMC6965315 DOI: 10.3389/fphar.2019.01533] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2019] [Accepted: 11/27/2019] [Indexed: 11/16/2022] Open
Abstract
In the past decades, epidermal growth factor receptor-tyrosine kinase inhibitors (EGFR-TKIs) had been proved as an effective treatment strategy for the patients with EGFR-mutated non-small-cell lung cancer (NSCLC). However, the tolerance for the EGFR-TKI always occurred after continuous administration for a period of time and limiting the application of these drugs. Activation of FGFR1 signaling pathway was one of the important escape mechanisms for EGFR-TKI resistant in NSCLC. Here, a novel dual inhibitor of EGFRL858R/T790M and FGFR1, compound15c, was found and can efficiently overcame the EGFR-TKI resistance via its simultaneous inhibition of their kinase activities. Comparison with EGFRL858R/T790M and FGFR1 inhibitor treatment alone or combined revealed that the inhibition of EGFRL858R/T790M and FGFR1 activity by 15c was responsible for surmounting the intrinsic EGFR-TKI resistance in EGFRL858R/T790M-mutated H1975 cells and the acquired resistance in Afatinib-tolerant PC9 cells (AFA-PC9). Flow Cytometry and Caspase3 activity analysis assay showed that 15c induced significant the early apoptosis of H1975 cells. Xenograft tumor formation in BALB/c mice induced by a H1975 cells was suppressed by 15c treatment, with no changes in animal body weight. Generally, 15c may act as a new-generation EGFR-TKI for the therapy of NSCLC patients suffering a resistance to current TKI.
Collapse
Affiliation(s)
- Gaozhi Chen
- Chemical Biology Research Center, School of Pharmaceutical Sciences, Wenzhou Medical University, Wenzhou, China.,Engineering Laboratory of Zhejiang Province for Pharmaceutical Development of Growth Factors, Biomedical Collaborative Innovation Center of Wenzhou, Wenzhou, China
| | - Yuyan Bao
- Department of Pharmacy, Sanmen People's Hospital of Zhejiang, Sanmen, China
| | - Qiaoyou Weng
- Key Laboratory of Imaging Diagnosis and Minimally Invasive Intervention, The Fifth Affiliated Hospital of Wenzhou Medical University, Lishui, China
| | - Yingxin Zhao
- Chemical Biology Research Center, School of Pharmaceutical Sciences, Wenzhou Medical University, Wenzhou, China
| | - Xiaoyao Lu
- Chemical Biology Research Center, School of Pharmaceutical Sciences, Wenzhou Medical University, Wenzhou, China
| | - Lili Fu
- Chemical Biology Research Center, School of Pharmaceutical Sciences, Wenzhou Medical University, Wenzhou, China
| | - Lingfeng Chen
- Chemical Biology Research Center, School of Pharmaceutical Sciences, Wenzhou Medical University, Wenzhou, China
| | - Zhiguo Liu
- Chemical Biology Research Center, School of Pharmaceutical Sciences, Wenzhou Medical University, Wenzhou, China
| | - Xiaomin Zhang
- Department of Pharmacy, Sanmen People's Hospital of Zhejiang, Sanmen, China
| | - Guang Liang
- Chemical Biology Research Center, School of Pharmaceutical Sciences, Wenzhou Medical University, Wenzhou, China
| |
Collapse
|
27
|
Pathophysiology of ctDNA Release into the Circulation and Its Characteristics: What Is Important for Clinical Applications. Recent Results Cancer Res 2020; 215:163-180. [PMID: 31605229 DOI: 10.1007/978-3-030-26439-0_9] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
The clinical implications of being able to accurately detect tumor-derived DNA in the circulation, termed circulating tumor DNA (ctDNA), could be enormous. Already, a plethora of clinical applications is under validation that include detection of minimal residual disease and predicting recurrence, monitoring response and resistance to treatment, identifying targets for therapies, and early detection. ctDNA is only a fraction of the total cell-free DNA (cfDNA) which confounds its detection and sometimes conceals its properties. To use ctDNA as a cancer biomarker with confidence, we need to understand its nature. Its characteristics, including size, half-life, and amount, are critical for the development of tests for its detection and discrimination from the rest of the cfDNA. Technological advances have enabled the detection and quantification of individual fragments of cfDNA, which is pivotal for clinical applications. Understanding the causes, the source of and the mechanisms of release of ctDNA are important for the interpretation of test results. Despite the many advances in understanding the nature and biology of ctDNA, we do not yet have a clear appreciation of the processes that govern its presence and levels in the circulation. ctDNA is not detectable in the blood of every cancer patient, and there is not a directly proportional relationship to tumor type, size, or stage. It is not clear if the lack of correlation with these specific clinical parameters is strictly due to technical or biological challenges. Better understanding of the pathophysiology of ctDNA is therefore important for the improvement of clinical applications and interpretation of their results.
Collapse
|
28
|
Liquid Biopsy in Non-Small Cell Lung Cancer: Highlights and Challenges. Cancers (Basel) 2019; 12:cancers12010017. [PMID: 31861557 PMCID: PMC7017364 DOI: 10.3390/cancers12010017] [Citation(s) in RCA: 71] [Impact Index Per Article: 14.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2019] [Revised: 12/16/2019] [Accepted: 12/17/2019] [Indexed: 12/14/2022] Open
Abstract
Non-small cell lung cancer is one leading cause of death worldwide, and patients would greatly benefit from an early diagnosis. Since targeted and immunotherapies have emerged as novel approaches for more tailored treatments, repeated assessments of the tumor biology have become pivotal to drive clinical decisions. Currently, tumor tissue biopsy is the gold standard to investigate potentially actionable biomarkers, but this procedure is invasive and may prove inadequate to represent the whole malignancy. In this regard, liquid biopsy represents a minimally invasive and more comprehensive option for early detection and investigation of this tumor. Today, cell-free DNA is the only approved circulating marker to select patients for a targeted therapy. Conversely, the other tumor-derived markers (i.e., circulating tumor cells, miRNAs, exosomes, and tumor educated platelets) are still at a pre-clinical phase, although they show promising results for their application in screening programs or as prognostic/predictive biomarkers. The main challenges for their clinical translation are the lack of reliable cutoffs and, especially for miRNAs, the great variability among the studies. Moreover, no established tool has been approved for circulating tumor cells and exosome isolation. Finally, large prospective clinical trials are mandatory to provide evidence of their clinical utility.
Collapse
|
29
|
Jiang F, Yang X, He X, Yang M. Circulating DNA, a Potentially Sensitive and Specific Diagnostic Tool for Future Medicine. Dose Response 2019; 17:1559325819891010. [PMID: 31827416 PMCID: PMC6886285 DOI: 10.1177/1559325819891010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2019] [Revised: 10/21/2019] [Accepted: 10/24/2019] [Indexed: 11/28/2022] Open
Abstract
Liquid biopsy has the great potential of detecting early diseases before deterioration and is valued for screening abnormalities at early stage. In oncology, circulating DNA derived from shed cancer cells reflects the tissue of origin, so it could be used to locate tissue sites during early screening. However, the heterogenous parameters of different types limit the clinical application, making it inaccessible to encompass all the cancer types. Instead, for reproducible scenario as pregnancy, fetal cell-free DNA has been well utilized for screening aneuploidies. Noninvasive and convenient as is, it would be of great value in the next decades far more than early diagnosis. This review recapitulates the discovery and development of tumor and fetal cell-free DNA. The common factors are also present that could be taken into consideration when collecting, transporting, and preserving samples. Meanwhile, several protocols used for purifying cell-free DNA, either classic ones or through commercial kits, are compared carefully. In addition, the development of technologies for analyzing cell-free DNA have been summarized and discussed in detail, especially some up-to-date approaches. At the end, the potential prospect of circulating DNA is bravely depicted. In summary, although there would be a lot of efforts before it’s prevalent, cell-free DNA remains a promising tool in point-of-care diagnostic medicine.
Collapse
Affiliation(s)
- Fan Jiang
- Department of Rehabilitation Medicine, The First People's Hospital of Wenling, Wenzhou Medical University, Wenling, Zhejiang, China
| | - Xiaoxiao Yang
- Department of Rehabilitation Medicine, The First People's Hospital of Wenling, Wenzhou Medical University, Wenling, Zhejiang, China
| | - Xiping He
- Department of Rehabilitation Medicine, The First People's Hospital of Wenling, Wenzhou Medical University, Wenling, Zhejiang, China
| | - Mingming Yang
- Department of Radiation Oncology, University of Texas Southwestern Medical Center, Dallas, TX, USA
| |
Collapse
|
30
|
Vasan N, Baselga J, Hyman DM. A view on drug resistance in cancer. Nature 2019; 575:299-309. [PMID: 31723286 DOI: 10.1038/s41586-019-1730-1] [Citation(s) in RCA: 1228] [Impact Index Per Article: 245.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2019] [Accepted: 09/23/2019] [Indexed: 12/11/2022]
Abstract
The problem of resistance to therapy in cancer is multifaceted. Here we take a reductionist approach to define and separate the key determinants of drug resistance, which include tumour burden and growth kinetics; tumour heterogeneity; physical barriers; the immune system and the microenvironment; undruggable cancer drivers; and the many consequences of applying therapeutic pressures. We propose four general solutions to drug resistance that are based on earlier detection of tumours permitting cancer interception; adaptive monitoring during therapy; the addition of novel drugs and improved pharmacological principles that result in deeper responses; and the identification of cancer cell dependencies by high-throughput synthetic lethality screens, integration of clinico-genomic data and computational modelling. These different approaches could eventually be synthesized for each tumour at any decision point and used to inform the choice of therapy.
Collapse
Affiliation(s)
- Neil Vasan
- Memorial Sloan Kettering Cancer Center, New York, NY, USA.,Weill Cornell Medical College, New York, NY, USA
| | - José Baselga
- Memorial Sloan Kettering Cancer Center, New York, NY, USA.,Weill Cornell Medical College, New York, NY, USA.,AstraZeneca, Gaithersburg, MD, USA
| | - David M Hyman
- Memorial Sloan Kettering Cancer Center, New York, NY, USA. .,Weill Cornell Medical College, New York, NY, USA.
| |
Collapse
|
31
|
Westover D, Zugazagoitia J, Cho BC, Lovly CM, Paz-Ares L. Mechanisms of acquired resistance to first- and second-generation EGFR tyrosine kinase inhibitors. Ann Oncol 2019; 29:i10-i19. [PMID: 29462254 DOI: 10.1093/annonc/mdx703] [Citation(s) in RCA: 419] [Impact Index Per Article: 83.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Patients with non-small-cell lung cancer (NSCLC) whose tumours harbour activating mutations within the epidermal growth factor receptor (EGFR) frequently derive significant clinical and radiographic benefits from treatment with EGFR tyrosine kinase inhibitors (TKIs). As such, prospective identification of EGFR mutations is now the standard of care worldwide. However, acquired therapeutic resistance to these agents invariably develops. Over the past 10 years, great strides have been made in defining the molecular mechanisms of EGFR TKI resistance in an effort to design rational strategies to overcome this acquired drug resistance. Approximately 60% of patients with acquired resistance to the EGFR TKIs (erlotinib, gefitinib, and afatinib) develop a new mutation within the drug target. This mutation-T790M-has been shown to alter drug binding and enzymatic activity of the mutant EGF receptor. Less common mechanisms of acquired resistance include MET amplification, ERBB2 amplification, transformation to small-cell lung cancer, and others. Here, we present a condensed overview of the literature on EGFR-mutant NSCLC, paying particular attention to mechanisms of drug resistance, recent clinical trial results, and novel strategies for identifying and confronting drug resistance, while also striving to identify gaps in current knowledge. These advances are rapidly altering the treatment landscape for EGFR-mutant NSCLC, expanding the armamentarium of available therapies to maximize patient benefit.
Collapse
Affiliation(s)
- D Westover
- Department of Medicine, Vanderbilt University Medical Center, Nashville, USA
| | - J Zugazagoitia
- Medical Oncology Department, Hospital Universitario 12 de Octubre, Madrid.,Instituto de Investigación i + 12, Madrid.,Lung Cancer Group, Clinical Research Program, CNIO, Madrid.,Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Spain
| | - B C Cho
- Division of Medical Oncology, Department of Internal Medicine, Yonsei Cancer Center, Yonsei University College of Medicine, Seoul, Korea
| | - C M Lovly
- Department of Medicine, Vanderbilt University Medical Center, Nashville, USA.,Department of Cancer Biology.,Vanderbilt-Ingram Cancer Center, Vanderbilt University Medical Center, Nashville, USA
| | - L Paz-Ares
- Medical Oncology Department, Hospital Universitario 12 de Octubre, Madrid.,Instituto de Investigación i + 12, Madrid.,Lung Cancer Group, Clinical Research Program, CNIO, Madrid.,Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Spain.,Complutense University, Madrid, Spain
| |
Collapse
|
32
|
Lu YT, Delijani K, Mecum A, Goldkorn A. Current status of liquid biopsies for the detection and management of prostate cancer. Cancer Manag Res 2019; 11:5271-5291. [PMID: 31239778 PMCID: PMC6559244 DOI: 10.2147/cmar.s170380] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2019] [Accepted: 04/18/2019] [Indexed: 12/14/2022] Open
Abstract
In recent years, new therapeutic options have become available for prostate cancer (PC) patients, generating an urgent need for better biomarkers to guide the choice of therapy and monitor treatment response. Liquid biopsies, including circulating tumor cells (CTCs), circulating nucleic acids, and exosomes, have been developed as minimally invasive assays allowing oncologists to monitor PC patients with real-time cellular or molecular information. While CTC counts remain the most extensively validated prognostic biomarker to monitor treatment response, recent advances demonstrate that CTC morphology and androgen receptor characterization can provide additional information to guide the choice of treatment. Characterization of cell-free DNA (cfDNA) is another rapidly emerging field with novel technologies capable of monitoring the evolution of treatment relevant alterations such as those in DNA damage repair genes for poly (ADP-ribose) polymerase (PARP) inhibition. In addition, several new liquid biopsy fields are emerging, including the characterization of heterogeneity, CTC RNA sequencing, the culture and xenografting of CTCs, and the characterization of extracellular vesicles (EVs) and circulating microRNAs. This review describes the clinical utilization of liquid biopsies in the management of PC patients and emerging liquid biopsy technologies with the potential to advance personalized cancer therapy.
Collapse
Affiliation(s)
- Yi-Tsung Lu
- Division of Medical Oncology, Department of Medicine, Keck School of Medicine and Translational and Clinical Science Program, USC Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, CA, USA
| | - Kevin Delijani
- Division of Medical Oncology, Department of Medicine, Keck School of Medicine and Translational and Clinical Science Program, USC Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, CA, USA
| | - Andrew Mecum
- Division of Medical Oncology, Department of Medicine, Keck School of Medicine and Translational and Clinical Science Program, USC Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, CA, USA
| | - Amir Goldkorn
- Division of Medical Oncology, Department of Medicine, Keck School of Medicine and Translational and Clinical Science Program, USC Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, CA, USA
| |
Collapse
|
33
|
Assi H, Tfayli A, Assaf N, Daya SA, Bidikian AH, Kawsarani D, Fermanian P, Zaatari G, Mahfouz R. Prevalence of T790M mutation among TKI-therapy resistant Lebanese lung cancer patients based on liquid biopsy analysis: a first report from a major tertiary care center. Mol Biol Rep 2019; 46:3671-3676. [PMID: 31147859 DOI: 10.1007/s11033-019-04797-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2019] [Accepted: 04/03/2019] [Indexed: 01/16/2023]
Abstract
Lung adenocarcinoma patients have variable prognosis due to many factors. Detection of epidermal growth factor receptor (EGFR) activating mutations is one of the factors that implies the need for initiating a first-line EGFR tyrosine kinase inhibitor (TKI) treatment. However, T790M resistance mutation emergence during treatment accounts for most EGFR-TKI drug resistance. The traditional sample taken for T790M mutation analysis is tissue biopsy, but its numerous disadvantages have introduced liquid biopsy as a preferred method for testing. We studied the prevalence of T790M mutation among pulmonary adenocarcinoma patients in Lebanese patients based on liquid biopsy testing the circulating tumor DNA (ctDNA). We have reviewed the laboratory charts of 52 patients who developed resistance on treatment and referred to AUBMC for EGFR T790M Liquid Biopsy to analyze the mutational analysis results for EGFR T790M. In total, 82.6% of the tested lung cancer patients were positive for a specific EGFR mutation. Among these patients, a total 26.9% were positive for T790M, which is comparable to the international prevalence of this mutation. However, for those cases who developed resistance with circulating DNA showing an EGFR mutation, 50% were positive for T790M that is also comparable to the international literature. This is the first report from Lebanon to discuss the prevalence of T790M mutation using liquid biopsy among Lebanese population. An important landmark molecular epidemiology study that will be a reference to all oncologists in Lebanon and the region in assessing the potential for targeted therapy options in the country. In addition, the data will be of an asset to the building international literature related to this disease.
Collapse
Affiliation(s)
- Hazem Assi
- Department of Internal Medicine, American University of Beirut Medical Center, Beirut, Lebanon
| | - Arafat Tfayli
- Department of Internal Medicine, American University of Beirut Medical Center, Beirut, Lebanon
| | - Nada Assaf
- Department of Pathology and Laboratory Medicine, American University of Beirut Medical Center, PO BOX 11-0236, Beirut, Lebanon
| | - Sarah Abou Daya
- Department of Pathology and Laboratory Medicine, American University of Beirut Medical Center, PO BOX 11-0236, Beirut, Lebanon
| | - Aram H Bidikian
- Faculty of Medicine, American University of Beirut, Beirut, Lebanon
| | - Dima Kawsarani
- Department of Pathology and Laboratory Medicine, American University of Beirut Medical Center, PO BOX 11-0236, Beirut, Lebanon
| | - Puzant Fermanian
- Department of Pathology and Laboratory Medicine, American University of Beirut Medical Center, PO BOX 11-0236, Beirut, Lebanon
| | - Ghazi Zaatari
- Department of Pathology and Laboratory Medicine, American University of Beirut Medical Center, PO BOX 11-0236, Beirut, Lebanon
| | - Rami Mahfouz
- Department of Pathology and Laboratory Medicine, American University of Beirut Medical Center, PO BOX 11-0236, Beirut, Lebanon.
| |
Collapse
|
34
|
Garcia J, Wozny AS, Geiguer F, Delherme A, Barthelemy D, Merle P, Tissot C, Jones FS, Johnson C, Xing X, Xu Z, Edelstein DL, Brevet M, Souquet PJ, Rodriguez-Lafrasse C, Payen L, Couraud S. Profiling of circulating tumor DNA in plasma of non-small cell lung cancer patients, monitoring of epidermal growth factor receptor p.T790M mutated allelic fraction using beads, emulsion, amplification, and magnetics companion assay and evaluation in future application in mimicking circulating tumor cells. Cancer Med 2019; 8:3685-3697. [PMID: 31112372 PMCID: PMC6866744 DOI: 10.1002/cam4.2244] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2019] [Revised: 04/12/2019] [Accepted: 04/26/2019] [Indexed: 12/12/2022] Open
Abstract
Cell-free plasma DNA (cfDNA) and mimicking circulating tumor cells (mCTCs) have demonstrated tremendous potential for molecular diagnosis of cancer and have been rapidly implemented in specific settings. However, widespread clinical adoption still faces some obstacles. The purpose was to compare the performance of a BEAMing (beads, emulsion, amplification, and magnetics) assay (OncoBEAM™-epidermal growth factor receptor [EGFR] [Sysmex Inostics]) and a next-generation sequencing assay (NGS; 56G Oncology panel kit, Swift Bioscience) to detect the p.T790M EGFR mutation in cfDNA of non-small cell lung cancer (NSCLC) patients. CfDNA samples (n = 183) were collected within our hospital from patients having a known EGFR sensitizing mutation, and presenting disease progression while under first-line therapy. EGFR mutations were detected using NGS in 42.1% of samples during progression in cfDNA. Testing using the OncoBEAM™-EGFR assay enabled detection of the p.T790M EGFR mutation in 40/183 NSCLC patients (21.8%) versus 20/183 (10.9%), using the NGS assay. Samples that were only positive with the OncoBEAM™-EGFR assay had lower mutant allelic fractions (Mean = 0.1304%; SD ± 0.1463%). In addition, we investigated the detection of p.T790M in mCTCs using H1975 cells. These cells spiked into whole blood were enriched using the ClearCellFX1 microfluidic device. Using the OncoBEAM™-EGFR assay, p.T790M was detected in as few as 1.33 tumoral cells/mL. Overall, these findings highlight the value of using the OncoBEAM™-EGFR to optimize detection of the p.T790M mutation, as well as the complementary clinical value that each of the mutation detection assay offers: NGS enabled the detection of mutations in other oncogenes that may be relevant to secondary resistance mechanisms, whereas the OncoBEAM™-EGFR assay achieved higher sensitivity for detection of clinically actionable mutations.
Collapse
Affiliation(s)
- Jessica Garcia
- Laboratoire de Biochimie et Biologie Moléculaire, Groupe Hospitalier Sud, Hospices Civils de Lyon, Lyon, France.,Cancer Research Center of Lyon, INSERM U1052, CNRS UMR5286, Claude Bernard University, University of Lyon, Lyon, France.,CIRculating CANcer (CIRCAN) program, Hospices Civils de Lyon Cancer institute, Lyon, France.,Laboratoire Commun de Recherche Hospices Civils de Lyon - BioMérieux, Centre Hospitalier Lyon Sud, Hospices Civils de Lyon, Lyon, France
| | - Anne-Sophie Wozny
- Laboratoire de Biochimie et Biologie Moléculaire, Groupe Hospitalier Sud, Hospices Civils de Lyon, Lyon, France.,CIRculating CANcer (CIRCAN) program, Hospices Civils de Lyon Cancer institute, Lyon, France
| | - Florence Geiguer
- Laboratoire de Biochimie et Biologie Moléculaire, Groupe Hospitalier Sud, Hospices Civils de Lyon, Lyon, France.,CIRculating CANcer (CIRCAN) program, Hospices Civils de Lyon Cancer institute, Lyon, France.,Laboratoire Commun de Recherche Hospices Civils de Lyon - BioMérieux, Centre Hospitalier Lyon Sud, Hospices Civils de Lyon, Lyon, France
| | - Aurélia Delherme
- Laboratoire de Biochimie et Biologie Moléculaire, Groupe Hospitalier Sud, Hospices Civils de Lyon, Lyon, France.,CIRculating CANcer (CIRCAN) program, Hospices Civils de Lyon Cancer institute, Lyon, France.,Laboratoire Commun de Recherche Hospices Civils de Lyon - BioMérieux, Centre Hospitalier Lyon Sud, Hospices Civils de Lyon, Lyon, France
| | - David Barthelemy
- Laboratoire de Biochimie et Biologie Moléculaire, Groupe Hospitalier Sud, Hospices Civils de Lyon, Lyon, France.,Cancer Research Center of Lyon, INSERM U1052, CNRS UMR5286, Claude Bernard University, University of Lyon, Lyon, France.,CIRculating CANcer (CIRCAN) program, Hospices Civils de Lyon Cancer institute, Lyon, France.,Laboratoire Commun de Recherche Hospices Civils de Lyon - BioMérieux, Centre Hospitalier Lyon Sud, Hospices Civils de Lyon, Lyon, France
| | - Patrick Merle
- Service de Pneumologie et oncologie thoracique, CHU G Montpied, Clermont-Ferrand, France
| | - Claire Tissot
- Service de Pneumologie et Cancérologie Thoracique, CHU Saint Etienne, Saint-Priest-en-Jarez, France
| | | | | | - Xiaobin Xing
- SOPHiA GENETICS SA, Headquarters, Saint Sulpice, Switzerland
| | - Zhenyu Xu
- SOPHiA GENETICS SA, Headquarters, Saint Sulpice, Switzerland
| | | | - Marie Brevet
- Cancer Research Center of Lyon, INSERM U1052, CNRS UMR5286, Claude Bernard University, University of Lyon, Lyon, France.,CIRculating CANcer (CIRCAN) program, Hospices Civils de Lyon Cancer institute, Lyon, France.,Institut de pathologie multisites des HCL-Site Est, Hospices Civils de Lyon, Lyon, France
| | - Pierre-Jean Souquet
- Service de Pneumologie aigue spécialisée et cancérologie thoracique, Groupement hospitalier sud, Institut de Cancérologie des Hospices Civils de Lyon, Lyon, France
| | - Claire Rodriguez-Lafrasse
- Laboratoire de Biochimie et Biologie Moléculaire, Groupe Hospitalier Sud, Hospices Civils de Lyon, Lyon, France.,UMR CNRS 5822/IN2P3, IPNL, PRISME, Laboratoire de Radiobiologie Cellulaire et Moléculaire, Faculté de Médecine Lyon-Sud, Université Lyon 1, Lyon, France
| | - Léa Payen
- Laboratoire de Biochimie et Biologie Moléculaire, Groupe Hospitalier Sud, Hospices Civils de Lyon, Lyon, France.,Cancer Research Center of Lyon, INSERM U1052, CNRS UMR5286, Claude Bernard University, University of Lyon, Lyon, France.,CIRculating CANcer (CIRCAN) program, Hospices Civils de Lyon Cancer institute, Lyon, France.,Laboratoire Commun de Recherche Hospices Civils de Lyon - BioMérieux, Centre Hospitalier Lyon Sud, Hospices Civils de Lyon, Lyon, France
| | - Sébastien Couraud
- CIRculating CANcer (CIRCAN) program, Hospices Civils de Lyon Cancer institute, Lyon, France.,Service de Pneumologie aigue spécialisée et cancérologie thoracique, Groupement hospitalier sud, Institut de Cancérologie des Hospices Civils de Lyon, Lyon, France.,EMR 3738 Ciblage Thérapeutique en Oncologie, Faculté de médecine Lyon Sud, Université Lyon 1, Université de Lyon, Lyon, France
| |
Collapse
|
35
|
Lyu M, Zhou J, Ning K, Ying B. The diagnostic value of circulating tumor cells and ctDNA for gene mutations in lung cancer. Onco Targets Ther 2019; 12:2539-2552. [PMID: 31040697 PMCID: PMC6454989 DOI: 10.2147/ott.s195342] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
PURPOSE Detecting gene mutations by two competing biomarkers, circulating tumor cells (CTCs) and ctDNA has gradually paved a new diagnostic avenue for personalized medicine. We performed a comprehensive analysis to compare the diagnostic value of CTCs and ctDNA for gene mutations in lung cancer. METHODS Publications were electronically searched in PubMed, Embase, and Web of Science as of July 2018. Pooled sensitivity, specificity, and AUC, each with a 95% CI, were yielded. Subgroup analyses and sensitivity analyses were conducted. Quality assessment of included studies was also performed. RESULTS From 4,283 candidate articles, we identified 47 articles with a total of 7,244 patients for qualitative review and meta-analysis. When detecting EGFR, the CTC and ctDNA groups had pooled sensitivity of 75.4% (95% CI 0.683-0.817) and 67.1% (95% CI 0.647-0.695), respectively. When testing KRAS, pooled sensitivity was 38.7% (95% CI 0.266-0.519) in the CTC group and 65.1% (95% CI 0.558-0.736) in the ctDNA group. The diagnostic performance of ctDNA in testing ALK and BRAF was also evaluated. Heterogeneity among the 47 articles was acceptable. CONCLUSION ctDNA might be a more promising biomarker with equivalent performance to CTCs when detecting EGFR and its detailed subtypes, and superior diagnostic capacity when testing KRAS and ALK. In addition, the diagnostic performance of ctDNA and CTCs depends on the detection methods greatly, and this warrants further studies to explore more sensitive methods.
Collapse
Affiliation(s)
- Mengyuan Lyu
- West China School of Medicine, Sichuan University, Chengdu, Sichuan, People's Republic of China
- Department of Laboratory Medicine, West China Hospital, Sichuan University, Chengdu, Sichuan, People's Republic of China,
| | - Jian Zhou
- West China School of Medicine, Sichuan University, Chengdu, Sichuan, People's Republic of China
- Department of Thoracic Surgery, West China Hospital, Sichuan University, Chengdu, Sichuan, People's Republic of China
| | - Kang Ning
- West China School of Medicine, Sichuan University, Chengdu, Sichuan, People's Republic of China
| | - Binwu Ying
- Department of Laboratory Medicine, West China Hospital, Sichuan University, Chengdu, Sichuan, People's Republic of China,
| |
Collapse
|
36
|
Bronkhorst AJ, Ungerer V, Holdenrieder S. The emerging role of cell-free DNA as a molecular marker for cancer management. BIOMOLECULAR DETECTION AND QUANTIFICATION 2019; 17:100087. [PMID: 30923679 PMCID: PMC6425120 DOI: 10.1016/j.bdq.2019.100087] [Citation(s) in RCA: 313] [Impact Index Per Article: 62.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/21/2018] [Revised: 02/26/2019] [Accepted: 03/11/2019] [Indexed: 02/07/2023]
Abstract
An increasing number of studies demonstrate the potential use of cell-free DNA (cfDNA) as a surrogate marker for multiple indications in cancer, including diagnosis, prognosis, and monitoring. However, harnessing the full potential of cfDNA requires (i) the optimization and standardization of preanalytical steps, (ii) refinement of current analysis strategies, and, perhaps most importantly, (iii) significant improvements in our understanding of its origin, physical properties, and dynamics in circulation. The latter knowledge is crucial for interpreting the associations between changes in the baseline characteristics of cfDNA and the clinical manifestations of cancer. In this review we explore recent advancements and highlight the current gaps in our knowledge concerning each point of contact between cfDNA analysis and the different stages of cancer management.
Collapse
Affiliation(s)
| | | | - Stefan Holdenrieder
- Institute for Laboratory Medicine, German Heart Centre, Technical University Munich, Lazarettstraße. 36, D-80636, Munich, Germany
| |
Collapse
|
37
|
Pantel K, Alix-Panabières C. Liquid biopsy and minimal residual disease — latest advances and implications for cure. Nat Rev Clin Oncol 2019; 16:409-424. [DOI: 10.1038/s41571-019-0187-3] [Citation(s) in RCA: 460] [Impact Index Per Article: 92.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
|
38
|
Monitoring of Response and Resistance in Plasma of EGFR-Mutant Lung Cancer Using Droplet Digital PCR. Methods Mol Biol 2019; 1768:193-207. [PMID: 29717445 DOI: 10.1007/978-1-4939-7778-9_12] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/16/2023]
Abstract
The identification of oncogenic driver mutations has led to the rapid rise of genotype-directed treatments. However, genetic analysis of tumors remains cumbersome and a morbid experience for patients. Noninvasive assessment of tumor genotype, so-called "liquid biopsy," such as plasma genotyping represents a potentially transformative tool. Here we describe a genotyping protocol of cell-free plasma DNA (cfDNA) using Droplet Digital™ PCR (ddPCR™). ddPCR emulsifies DNA into ~20,000 droplets in which PCR is performed to endpoint in each droplet for both mutant and wild-type DNA. Droplets are run through a modified flow cytometer where mutant and wild-type DNA emit different colored signals. The count of these signals upon Poisson distribution analysis allows sensitive quantification of allelic prevalence.
Collapse
|
39
|
Aggarwal C, Thompson JC, Black TA, Katz SI, Fan R, Yee SS, Chien AL, Evans TL, Bauml JM, Alley EW, Ciunci CA, Berman AT, Cohen RB, Lieberman DB, Majmundar KS, Savitch SL, Morrissette JJD, Hwang WT, Elenitoba-Johnson KSJ, Langer CJ, Carpenter EL. Clinical Implications of Plasma-Based Genotyping With the Delivery of Personalized Therapy in Metastatic Non-Small Cell Lung Cancer. JAMA Oncol 2019; 5:173-180. [PMID: 30325992 PMCID: PMC6396811 DOI: 10.1001/jamaoncol.2018.4305] [Citation(s) in RCA: 311] [Impact Index Per Article: 62.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2018] [Accepted: 07/18/2018] [Indexed: 12/27/2022]
Abstract
Importance The clinical implications of adding plasma-based circulating tumor DNA next-generation sequencing (NGS) to tissue NGS for targetable mutation detection in non-small cell lung cancer (NSCLC) have not been formally assessed. Objective To determine whether plasma NGS testing was associated with improved mutation detection and enhanced delivery of personalized therapy in a real-world clinical setting. Design, Setting, and Participants This prospective cohort study enrolled 323 patients with metastatic NSCLC who had plasma testing ordered as part of routine clinical management. Plasma NGS was performed using a 73-gene commercial platform. Patients were enrolled at the Hospital of the University of Pennsylvania from April 1, 2016, through January 2, 2018. The database was locked for follow-up and analyses on January 2, 2018, with a median follow-up of 7 months (range, 1-21 months). Main Outcomes and Measures The number of patients with targetable alterations detected with plasma and tissue NGS; the association between the allele fractions (AFs) of mutations detected in tissue and plasma; and the association of response rate with the plasma AF of the targeted mutations. Results Among the 323 patients with NSCLC (60.1% female; median age, 65 years [range, 33-93 years]), therapeutically targetable mutations were detected in EGFR, ALK, MET, BRCA1, ROS1, RET, ERBB2, or BRAF for 113 (35.0%) overall. Ninety-four patients (29.1%) had plasma testing only at the discretion of the treating physician or patient preference. Among the 94 patients with plasma testing alone, 31 (33.0%) had a therapeutically targetable mutation detected, thus obviating the need for an invasive biopsy. Among the remaining 229 patients who had concurrent plasma and tissue NGS or were unable to have tissue NGS, a therapeutically targetable mutation was detected in tissue alone for 47 patients (20.5%), whereas the addition of plasma testing increased this number to 82 (35.8%). Thirty-six of 42 patients (85.7%) who received a targeted therapy based on the plasma result achieved a complete or a partial response or stable disease. The plasma-based targeted mutation AF had no correlation with depth of Response Evaluation Criteria in Solid Tumors response (r = -0.121; P = .45). Conclusions and Relevance Integration of plasma NGS testing into the routine management of stage IV NSCLC demonstrates a marked increase of the detection of therapeutically targetable mutations and improved delivery of molecularly guided therapy.
Collapse
Affiliation(s)
- Charu Aggarwal
- Division of Hematology-Oncology, Department of Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia
- Abramson Cancer Center, University of Pennsylvania Perelman School of Medicine, Philadelphia
| | - Jeffrey C. Thompson
- Division of Pulmonary, Allergy, and Critical Care Medicine, Thoracic Oncology Group, Department of Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia
| | - Taylor A. Black
- Division of Hematology-Oncology, Department of Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia
| | - Sharyn I. Katz
- Department of Radiology, University of Pennsylvania Perelman School of Medicine, Philadelphia
| | - Ryan Fan
- Division of Hematology-Oncology, Department of Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia
| | - Stephanie S. Yee
- Division of Hematology-Oncology, Department of Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia
| | - Austin L. Chien
- Division of Hematology-Oncology, Department of Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia
| | - Tracey L. Evans
- Division of Hematology-Oncology, Department of Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia
- Abramson Cancer Center, University of Pennsylvania Perelman School of Medicine, Philadelphia
| | - Joshua M. Bauml
- Division of Hematology-Oncology, Department of Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia
- Abramson Cancer Center, University of Pennsylvania Perelman School of Medicine, Philadelphia
| | - Evan W. Alley
- Division of Hematology-Oncology, Department of Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia
- Abramson Cancer Center, University of Pennsylvania Perelman School of Medicine, Philadelphia
| | - Christine A. Ciunci
- Division of Hematology-Oncology, Department of Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia
- Abramson Cancer Center, University of Pennsylvania Perelman School of Medicine, Philadelphia
| | - Abigail T. Berman
- Division of Hematology-Oncology, Department of Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia
- Abramson Cancer Center, University of Pennsylvania Perelman School of Medicine, Philadelphia
| | - Roger B. Cohen
- Division of Hematology-Oncology, Department of Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia
- Abramson Cancer Center, University of Pennsylvania Perelman School of Medicine, Philadelphia
| | - David B. Lieberman
- Department of Pathology and Laboratory Medicine, Hospital of the University of Pennsylvania, Philadelphia
| | - Krishna S. Majmundar
- Division of Hematology-Oncology, Department of Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia
| | - Samantha L. Savitch
- Division of Hematology-Oncology, Department of Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia
| | - Jennifer J. D. Morrissette
- Department of Pathology and Laboratory Medicine, Hospital of the University of Pennsylvania, Philadelphia
| | - Wei-Ting Hwang
- Abramson Cancer Center, University of Pennsylvania Perelman School of Medicine, Philadelphia
- Department of Biostatistics, Epidemiology, and Informatics, University of Pennsylvania, Philadelphia
| | | | - Corey J. Langer
- Division of Hematology-Oncology, Department of Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia
- Abramson Cancer Center, University of Pennsylvania Perelman School of Medicine, Philadelphia
| | - Erica L. Carpenter
- Division of Hematology-Oncology, Department of Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia
- Abramson Cancer Center, University of Pennsylvania Perelman School of Medicine, Philadelphia
| |
Collapse
|
40
|
Chen G, Ye L, Han Y, Han P. Retracted Article: MiR-148a agomir based targeting of c-Met and Her-3 is able to attenuate EGFR-T790M mutation driven gefitinib and erlotinib resistance in non-small cell lung cancer cells. RSC Adv 2019; 9:21139-21146. [PMID: 35521334 PMCID: PMC9066016 DOI: 10.1039/c8ra10224d] [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: 12/13/2018] [Accepted: 05/30/2019] [Indexed: 11/21/2022] Open
Abstract
MiR-148a inhibits NSCLC progression. Whether miR-148a would reduce EGFR tyrosine kinase inhibitor (TKI) resistance of NSCLC cells remains underexplored. In this study, 5 NSCLC patients received surgery and gefitinib treatment but developed pleural metastasis. Patients' NSCLC adopted EGFR T790M mutation. 5 naïve and 5 gefitinib-resisting NSCLC cell lines were derived from patients primary and metastatic tumor tissues, and the 5 gefitinib-resisting NSCLC cell lines were trained with erlotinib to establish the erlotinib-resisting cell lines. MiR-148a levels in cells were analyzed by qRT-PCR. miR-148a overexpression was mimicked by agomir treatment. NSCLC cell malignancy was evaluated by cell proliferation, apoptosis, colony formation and transwell invasion assays. Protein levels of c-Met, Her-3 and IGF-1R were assessed by western blotting. miRNA-mRNA interaction was investigated by luciferase reporter assay and AGO2-RIP. Transient overexpression of MET, ERBB3 or IGF1R gene was achieved by plasmid transfection. Results showed that the MiR-148a level was decreased with the development of gefitinib and erlotinib resistance and that there was an increase in malignancy in NSCLC cells in vitro. Treatment with miR-148a agomir significantly enhanced the cytotoxicity of gefitinib and erlotinib to naïve, gefitinib-resisting and erlotinib-resisting NSCLC cells in vitro while reducing their protein levels of c-Met, Her-3 and IGF-1R, the mRNAs of which were verified as direct targets of miR-148a in NSCLC cells. Restoring c-Met or Her-3 protein levels partially reduced the gefitinib and erlotinib sensitizing effect of miR-148a agomir treatment on NSCLC cells. We concluded that MiR-148a attenuated gefitinib and erlotinib resistance in non-small cell lung cancer cells with EGFR T790M mutation by targeting c-Met and Her-3 expression. MiR-148a inhibits NSCLC progression.![]()
Collapse
Affiliation(s)
- Guimin Chen
- Department II of Internal Medicine
- Lin Yi Cancer Hospital
- Linyi
- China
| | - Lei Ye
- Department I of Internal Medicine
- Lin Yi Cancer Hospital
- Linyi
- China
| | - Yufei Han
- Department II of Internal Medicine
- Lin Yi Cancer Hospital
- Linyi
- China
| | - Ping Han
- Department II of Respiration
- Linyi People's Hospital
- Linyi
- China
| |
Collapse
|
41
|
Nishizuka SS, Sato KA, Hachiya T. A Pipeline for ctDNA Detection Following Primary Tumor Profiling Using a Cancer-Related Gene Sequencing Panel. Methods Mol Biol 2019; 1908:229-241. [PMID: 30649732 DOI: 10.1007/978-1-4939-9004-7_16] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Circulating tumor DNA (ctDNA) is emerging as a promising biomarker for cancer diagnosis. However, the system to detect gene mutations with very low frequencies from plasma remains to be established in terms of technical aspects of sequencing technologies and cost for universal use. One strategy is to employ a cancer sequencing panel to detect mutations in a primary tumor in a time- and cost-effective manner, and subsequently assess these mutations with a digital PCR technology from plasma ctDNA. This strategy enables the accurate detection of low frequency mutations (i.e., less than 1% allele frequency) from ctDNA, since both comprehensive coverage of genes and quantitative mutation detection with very low frequencies are required for cancer diagnosis from plasma samples. Here, we present a pipeline can be used to detect mutations from plasma ctDNA with very low allele frequencies using a next-generation sequencing technology for comprehensive coverage of primary tumors and droplet digital PCR for sensitive detection from plasma ctDNA.
Collapse
Affiliation(s)
- Satoshi S Nishizuka
- Division of Biomedical Research and Development, Institute of Biomedical Sciences, Iwate Medical University, Morioka, Iwate, Japan.
| | - Kei A Sato
- Department of Surgery, Iwate Medical University School of Medicine, Morioka, Iwate, Japan
| | - Tsuyoshi Hachiya
- Division of Biomedical Information Analysis, Iwate Tohoku Medical Megabank Organization, Disaster Reconstruction Center, Iwate Medical University, Yahaba, Shiwa, Iwate, Japan
| |
Collapse
|
42
|
Potential clinical applications of circulating cell-free DNA in ovarian cancer patients. Expert Rev Mol Med 2018; 20:e6. [PMID: 30558693 DOI: 10.1017/erm.2018.5] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Circulating cell-free DNA (cfDNA) consists of small fragments of DNA that circulate freely in the bloodstream. In cancer patients, a fraction of cfDNA is derived from tumour cells, therefore containing the same genetic and epigenetic alterations, and is termed circulating cell-free tumour DNA. The potential use of cfDNA, the so-called 'liquid biopsy', as a non-invasive cancer biomarker has recently received a lot of attention. The present review will focus on studies concerning the potential clinical applications of cfDNA in ovarian cancer patients.
Collapse
|
43
|
Complexity of genome sequencing and reporting: Next generation sequencing (NGS) technologies and implementation of precision medicine in real life. Crit Rev Oncol Hematol 2018; 133:171-182. [PMID: 30661654 DOI: 10.1016/j.critrevonc.2018.11.008] [Citation(s) in RCA: 72] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2018] [Accepted: 11/23/2018] [Indexed: 12/17/2022] Open
Abstract
The finalization of the Human Genome Project in 2003 paved the way for a deeper understanding of cancer, favouring a faster progression towards "personalized" medicine. Research in oncology has progressively focused on the sequencing of cancer genomes, to better understand the genetic basis of tumorigenesis and identify actionable alterations to guide cancer therapy. Thanks to the development of next-generation-sequencing (NGS) techniques, sequencing of tumoral DNA is today technically easier, faster and cheaper. Commercially available NGS panels enable the detection of single or global genomic alterations, namely gene mutation and mutagenic burden, both on germline and somatic DNA, potentially predicting the response or resistance to cancer treatments. Profiling of tumor DNA is nowadays a standard in cancer research and treatment. In this review we discuss the history, techniques and applications of NGS in cancer care, under a "personalized tailored therapy" perspective.
Collapse
|
44
|
Gyanchandani R, Kvam E, Heller R, Finehout E, Smith N, Kota K, Nelson JR, Griffin W, Puhalla S, Brufsky AM, Davidson NE, Lee AV. Whole genome amplification of cell-free DNA enables detection of circulating tumor DNA mutations from fingerstick capillary blood. Sci Rep 2018; 8:17313. [PMID: 30470782 PMCID: PMC6251935 DOI: 10.1038/s41598-018-35470-9] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2018] [Accepted: 11/01/2018] [Indexed: 12/25/2022] Open
Abstract
The ability to measure mutations in plasma cell-free DNA (cfDNA) has the potential to revolutionize cancer surveillance and treatment by enabling longitudinal monitoring not possible with solid tumor biopsies. However, obtaining sufficient quantities of cfDNA remains a challenge for assay development and clinical translation; consequently, large volumes of venous blood are typically required. Here, we test proof-of-concept for using smaller volumes via fingerstick collection. Matched venous and fingerstick blood were obtained from seven patients with metastatic breast cancer. Fingerstick blood was separated at point-of-care using a novel paper-based concept to isolate plasma centrifuge-free. Patient cfDNA was then analyzed with or without a new method for whole genome amplification via rolling-circle amplification (WG-RCA). We identified somatic mutations by targeted sequencing and compared the concordance of mutation detection from venous and amplified capillary samples by droplet-digital PCR. Patient mutations were detected with 100% concordance after WG-RCA, although in some samples, allele frequencies showed greater variation likely due to differential amplification or primer inaccessibility. These pilot findings provide physiological evidence that circulating tumor DNA is accessible by fingerstick and sustains presence/absence of mutation detection after whole-genome amplification. Further refinement may enable simpler and less-invasive methods for longitudinal or theranostic surveillance of metastatic cancer.
Collapse
Affiliation(s)
- Rekha Gyanchandani
- Women's Cancer Research Center, Department of Pharmacology and Chemical Biology, UPMC Hillman Cancer Center, Magee Womens Research Institute, Pittsburgh, PA, 15213, USA.,Western Oncolytics, 265 William Pitt Way, Pittsburgh, PA, 15238, USA
| | - Erik Kvam
- GE Global Research, One Research Circle, Niskayuna, NY, 12309, USA.
| | - Ryan Heller
- GE Global Research, One Research Circle, Niskayuna, NY, 12309, USA.,QIAGEN, 100 Cummings Center, Beverly, MA, 01915, USA
| | - Erin Finehout
- GE Global Research, One Research Circle, Niskayuna, NY, 12309, USA.,Terumo BCT, 10811 Collins Ave, Lakewood, CO, 80215, USA
| | - Nicholas Smith
- Women's Cancer Research Center, Department of Pharmacology and Chemical Biology, UPMC Hillman Cancer Center, Magee Womens Research Institute, Pittsburgh, PA, 15213, USA
| | - Karthik Kota
- Department of Medicine, University of Pittsburgh, Pittsburgh, PA, 15213, USA
| | - John R Nelson
- GE Global Research, One Research Circle, Niskayuna, NY, 12309, USA
| | - Weston Griffin
- GE Global Research, One Research Circle, Niskayuna, NY, 12309, USA
| | - Shannon Puhalla
- Women's Cancer Research Center, Department of Pharmacology and Chemical Biology, UPMC Hillman Cancer Center, Magee Womens Research Institute, Pittsburgh, PA, 15213, USA
| | - Adam M Brufsky
- Women's Cancer Research Center, Department of Pharmacology and Chemical Biology, UPMC Hillman Cancer Center, Magee Womens Research Institute, Pittsburgh, PA, 15213, USA
| | - Nancy E Davidson
- Women's Cancer Research Center, Department of Pharmacology and Chemical Biology, UPMC Hillman Cancer Center, Magee Womens Research Institute, Pittsburgh, PA, 15213, USA.,Fred Hutchinson Cancer Research Center, 1100 Fairview Avenue N, Seattle, WA, 98109, USA
| | - Adrian V Lee
- Women's Cancer Research Center, Department of Pharmacology and Chemical Biology, UPMC Hillman Cancer Center, Magee Womens Research Institute, Pittsburgh, PA, 15213, USA.
| |
Collapse
|
45
|
The cornerstone of integrating circulating tumor DNA into cancer management. Biochim Biophys Acta Rev Cancer 2018; 1871:1-11. [PMID: 30419316 DOI: 10.1016/j.bbcan.2018.11.002] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2018] [Revised: 08/23/2018] [Accepted: 11/07/2018] [Indexed: 12/26/2022]
Abstract
Recent circulating tumor DNA (ctDNA) research has demonstrated its potential as a non-invasive biomarker for cancer. However, the deployment of ctDNA assays in routine clinical practice remains challenging owing to variability in analytical approaches and the assessment of clinical significance. A well-developed, analytically valid ctDNA assay is a prerequisite for integrating ctDNA into cancer management, and an appropriate analytical technology is crucial for the development of a ctDNA assay. Other determinants including pre-analytical procedures, test validation, internal quality control (IQC), and continual proficiency testing (PT) are also important for the accuracy of ctDNA assays. In the present review, we will focus on the most widely used ctDNA detection technologies and the key quality management measures used to assure the accuracy of ctDNA assays. The aim of this review is to provide useful information for technology selection during ctDNA assay development and assure a reliable test result in clinical practice.
Collapse
|
46
|
Hughes NP, Xu L, Nielsen CH, Chang E, Hori SS, Natarajan A, Lee S, Kjær A, Kani K, Wang SX, Mallick P, Gambhir SS. A blood biomarker for monitoring response to anti-EGFR therapy. Cancer Biomark 2018; 22:333-344. [PMID: 29689709 DOI: 10.3233/cbm-171149] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
BACKGROUND AND OBJECTIVE To monitor therapies targeted to epidermal growth factor receptors (EGFR) in non-small cell lung cancer (NSCLC), we investigated Peroxiredoxin 6 (PRDX6) as a biomarker of response to anti-EGFR agents. METHODS We studied cells that are sensitive (H3255, HCC827) or resistant (H1975, H460) to gefitinib. PRDX6 was examined with either gefitinib or vehicle treatment using enzyme-linked immunosorbent assays. We created xenograft models from one sensitive (HCC827) and one resistant cell line (H1975) and monitored serum PRDX6 levels during treatment. RESULTS PRDX6 levels in cell media from sensitive cell lines increased significantly after gefitinib treatment vs. vehicle, whereas there was no significant difference for resistant lines. PRDX6 accumulation over time correlated positively with gefitinib sensitivity. Serum PRDX6 levels in gefitinib-sensitive xenograft models increased markedly during the first 24 hours of treatment and then decreased dramatically during the following 48 hours. Differences in serum PRDX6 levels between vehicle and gefitinib-treated animals could not be explained by differences in tumor burden. CONCLUSIONS Our results show that changes in serum PRDX6 during the course of gefitinib treatment of xenograft models provide insight into tumor response and such an approach offers several advantages over imaging-based strategies for monitoring response to anti-EGFR agents.
Collapse
Affiliation(s)
- Nicholas P Hughes
- Molecular Imaging Program at Stanford, Department of Radiology, Stanford University School of Medicine, Stanford, CA, USA.,Molecular Imaging Program at Stanford, Department of Radiology, Stanford University School of Medicine, Stanford, CA, USA
| | - Lingyun Xu
- Molecular Imaging Program at Stanford, Department of Radiology, Stanford University School of Medicine, Stanford, CA, USA.,Canary Center at Stanford for Cancer Early Detection, Palo Alto, CA, USA.,Molecular Imaging Program at Stanford, Department of Radiology, Stanford University School of Medicine, Stanford, CA, USA
| | - Carsten H Nielsen
- Molecular Imaging Program at Stanford, Department of Radiology, Stanford University School of Medicine, Stanford, CA, USA.,Department of Clinical Physiology, Nuclear Medicine and PET, Center for Diagnostic Investigations, Rigshospitalet, Copenhagen, Denmark.,Cluster for Molecular Imaging, Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark.,Molecular Imaging Program at Stanford, Department of Radiology, Stanford University School of Medicine, Stanford, CA, USA
| | - Edwin Chang
- Molecular Imaging Program at Stanford, Department of Radiology, Stanford University School of Medicine, Stanford, CA, USA.,Canary Center at Stanford for Cancer Early Detection, Palo Alto, CA, USA.,Molecular Imaging Program at Stanford, Department of Radiology, Stanford University School of Medicine, Stanford, CA, USA
| | - Sharon S Hori
- Molecular Imaging Program at Stanford, Department of Radiology, Stanford University School of Medicine, Stanford, CA, USA.,Canary Center at Stanford for Cancer Early Detection, Palo Alto, CA, USA
| | - Arutselvan Natarajan
- Molecular Imaging Program at Stanford, Department of Radiology, Stanford University School of Medicine, Stanford, CA, USA.,Canary Center at Stanford for Cancer Early Detection, Palo Alto, CA, USA
| | - Samantha Lee
- Canary Center at Stanford for Cancer Early Detection, Palo Alto, CA, USA
| | - Andreas Kjær
- Department of Clinical Physiology, Nuclear Medicine and PET, Center for Diagnostic Investigations, Rigshospitalet, Copenhagen, Denmark.,Cluster for Molecular Imaging, Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Kian Kani
- Lawrence J. Ellison Institute of Transformative Medicine, University of Southern California, Los Angeles, CA, USA
| | - Shan X Wang
- Department of Bioengineering, Stanford University, Stanford, CA, USA.,Department of Materials Science and Engineering, Stanford University, Stanford, CA, USA
| | - Parag Mallick
- Molecular Imaging Program at Stanford, Department of Radiology, Stanford University School of Medicine, Stanford, CA, USA.,Canary Center at Stanford for Cancer Early Detection, Palo Alto, CA, USA
| | - Sanjiv Sam Gambhir
- Molecular Imaging Program at Stanford, Department of Radiology, Stanford University School of Medicine, Stanford, CA, USA.,Canary Center at Stanford for Cancer Early Detection, Palo Alto, CA, USA.,Department of Bioengineering, Stanford University, Stanford, CA, USA.,Department of Materials Science and Engineering, Stanford University, Stanford, CA, USA
| |
Collapse
|
47
|
Tissue or blood: which is more suitable for detection of EGFR mutations in non-small cell lung cancer? Int J Biol Markers 2018; 33:40-48. [PMID: 29552976 DOI: 10.5301/ijbm.5000256] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
BACKGROUND Many studies have evaluated the accuracy of EGFR mutation status in blood against that in tumor tissues as the reference. We conducted this systematic review and meta-analysis to assess whether blood can be used as a substitute for tumor tissue in detecting EGFR mutations. METHODS Investigations that provided data on EGFR mutation status in blood were searched in the databases of Medline, Embase, Ovid Technologies and Web of Science. The detect efficiency of EGFR mutations in paired blood and tissues was compared using a random-effects model of meta-analysis. Pooled sensitivity and specificity and diagnostic accuracy were calculated by receiver operating characteristic curve. RESULTS A total of 19 studies with 2,922 individuals were involved in this meta-analysis. The pooled results showed the positive detection rate of EGFR mutations in lung cancer tissues was remarkably higher than that of paired blood samples (odds ratio [OR] = 1.47, p<0.001). The pooled sensitivity and specificity of blood were 0.65 and 0.91, respectively, and the area under the receiver operating characteristic curve was 0.89. CONCLUSIONS Although blood had a better specificity for detecting EGFR mutations, the absence of blood positivity should not necessarily be construed as confirmed negativity. Patients with negative results for blood should decidedly undergo further biopsies to ascertain EGFR mutations.
Collapse
|
48
|
Attili I, Karachaliou N, Conte P, Bonanno L, Rosell R. Therapeutic approaches for T790M mutation positive non-small-cell lung cancer. Expert Rev Anticancer Ther 2018; 18:1021-1030. [PMID: 30079781 DOI: 10.1080/14737140.2018.1508347] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
INTRODUCTION Epidermal growth factor receptor (EGFR) mutation positive non-small cell lung cancer (NSCLC) is a subset of lung cancer with demonstrated response to targeted therapies. However, resistance to the first targeted approach usually occurs within the first year, and it is associated in 50-60% of cases to the T790M resistance mutation. Areas covered: The review provides an overview on the significance of the presence of the T790M mutation, its detection, treatment options and subsequent mechanisms of resistance. Expert commentary: Osimertinib is the current treatment option for T790M mutation positive NSCLC after progression to first or second-generation EGFR TKIs, with activity also on brain metastasis. However, the scenario is in continuous evolution and results from clinical trials are awaited in first-line setting and in combination strategies.
Collapse
Affiliation(s)
- Ilaria Attili
- a Department of Surgical, Oncological and Gastroenterological Sciences , University of Padova , Padova , Italy
| | - Niki Karachaliou
- b Instituto Oncológico Dr Rosell (IOR) , University Hospital Sagrat Cor , Barcelona , Spain.,c Coyote Research Group, Pangaea Oncology, Laboratory of Molecular Biology , Quirón-Dexeus University Institute , Barcelona , Spain
| | - PierFranco Conte
- a Department of Surgical, Oncological and Gastroenterological Sciences , University of Padova , Padova , Italy
| | - Laura Bonanno
- d Medical Oncology 2 , Istituto Oncologico Veneto, IRCCS , Padova , Italy
| | - Rafael Rosell
- c Coyote Research Group, Pangaea Oncology, Laboratory of Molecular Biology , Quirón-Dexeus University Institute , Barcelona , Spain.,e Institut d'Investigació en Ciències Germans Trias i Pujol , Badalona , Spain.,f Instituto Oncológico Dr Rosell (IOR) , Quirón-Dexeus University Institute , Barcelona , Spain.,g Institut Català d'Oncologia , Hospital Germans Trias i Pujol , Badalona , Spain
| |
Collapse
|
49
|
Song KA, Hosono Y, Turner C, Jacob S, Lochmann TL, Murakami Y, Patel NU, Ham J, Hu B, Powell KM, Coon CM, Windle BE, Oya Y, Koblinski JE, Harada H, Leverson JD, Souers AJ, Hata AN, Boikos S, Yatabe Y, Ebi H, Faber AC. Increased Synthesis of MCL-1 Protein Underlies Initial Survival of EGFR-Mutant Lung Cancer to EGFR Inhibitors and Provides a Novel Drug Target. Clin Cancer Res 2018; 24:5658-5672. [PMID: 30087143 DOI: 10.1158/1078-0432.ccr-18-0304] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2018] [Revised: 06/29/2018] [Accepted: 08/01/2018] [Indexed: 11/16/2022]
Abstract
Purpose: EGFR inhibitors (EGFRi) are effective against EGFR-mutant lung cancers. The efficacy of these drugs, however, is mitigated by the outgrowth of resistant cells, most often driven by a secondary acquired mutation in EGFR, T790M We recently demonstrated that T790M can arise de novo during treatment; it follows that one potential therapeutic strategy to thwart resistance would be identifying and eliminating these cells [referred to as drug-tolerant cells (DTC)] prior to acquiring secondary mutations like T790M Experimental Design: We have developed DTCs to EGFRi in EGFR-mutant lung cancer cell lines. Subsequent analyses of DTCs included RNA-seq, high-content microscopy, and protein translational assays. Based on these results, we tested the ability of MCL-1 BH3 mimetics to combine with EGFR inhibitors to eliminate DTCs and shrink EGFR-mutant lung cancer tumors in vivo Results: We demonstrate surviving EGFR-mutant lung cancer cells upregulate the antiapoptotic protein MCL-1 in response to short-term EGFRi treatment. Mechanistically, DTCs undergo a protein biosynthesis enrichment resulting in increased mTORC1-mediated mRNA translation of MCL-1, revealing a novel mechanism in which lung cancer cells adapt to short-term pressures of apoptosis-inducing kinase inhibitors. Moreover, MCL-1 is a key molecule governing the emergence of early EGFR-mutant DTCs to EGFRi, and we demonstrate it can be effectively cotargeted with clinically emerging MCL-1 inhibitors both in vitro and in vivo Conclusions: Altogether, these data reveal that this novel therapeutic combination may delay the acquisition of secondary mutations, therefore prolonging therapy efficacy. Clin Cancer Res; 24(22); 5658-72. ©2018 AACR.
Collapse
Affiliation(s)
- Kyung-A Song
- Philips Institute for Oral Health Research, VCU School of Dentistry and Massey Cancer Center, Richmond, Virginia
| | - Yasuyuki Hosono
- Division of Molecular Therapeutics, Aichi Cancer Center Research Institute, Nagoya, Japan
| | - Crystal Turner
- Philips Institute for Oral Health Research, VCU School of Dentistry and Massey Cancer Center, Richmond, Virginia
| | - Sheeba Jacob
- Philips Institute for Oral Health Research, VCU School of Dentistry and Massey Cancer Center, Richmond, Virginia
| | - Timothy L Lochmann
- Philips Institute for Oral Health Research, VCU School of Dentistry and Massey Cancer Center, Richmond, Virginia
| | - Yoshiko Murakami
- Department of Pathology and Molecular Diagnostics, Aichi Cancer Center, Nagoya, Japan
| | - Neha U Patel
- Philips Institute for Oral Health Research, VCU School of Dentistry and Massey Cancer Center, Richmond, Virginia
| | - Jungoh Ham
- Philips Institute for Oral Health Research, VCU School of Dentistry and Massey Cancer Center, Richmond, Virginia
| | - Bin Hu
- Department of Pathology, VCU School of Medicine, Richmond, Virginia
| | - Krista M Powell
- Philips Institute for Oral Health Research, VCU School of Dentistry and Massey Cancer Center, Richmond, Virginia
| | - Colin M Coon
- Philips Institute for Oral Health Research, VCU School of Dentistry and Massey Cancer Center, Richmond, Virginia
| | - Brad E Windle
- Philips Institute for Oral Health Research, VCU School of Dentistry and Massey Cancer Center, Richmond, Virginia
| | - Yuko Oya
- Division of Molecular Therapeutics, Aichi Cancer Center Research Institute, Nagoya, Japan
| | | | - Hisashi Harada
- Philips Institute for Oral Health Research, VCU School of Dentistry and Massey Cancer Center, Richmond, Virginia
| | | | | | - Aaron N Hata
- Massachusetts General Hospital Cancer Center and Department of Medicine, Harvard Medical School, Boston, Massachusetts
| | - Sosipatros Boikos
- Division of Hematology, Oncology and Palliative Care, Virginia Commonwealth University, Massey Cancer Center, Richmond, Virginia
| | - Yasushi Yatabe
- Department of Pathology and Molecular Diagnostics, Aichi Cancer Center, Nagoya, Japan.,Precision Medicine Center, Aichi Cancer Center, Nagoya, Japan
| | - Hiromichi Ebi
- Division of Molecular Therapeutics, Aichi Cancer Center Research Institute, Nagoya, Japan. .,Precision Medicine Center, Aichi Cancer Center, Nagoya, Japan
| | - Anthony C Faber
- Philips Institute for Oral Health Research, VCU School of Dentistry and Massey Cancer Center, Richmond, Virginia.
| |
Collapse
|
50
|
Mlika M, Dziri C, Zorgati MM, Ben Khelil M, Mezni F. Liquid Biopsy as Surrogate to Tissue in Lung Cancer for Molecular Profiling: A Meta-Analysis. CURRENT RESPIRATORY MEDICINE REVIEWS 2018; 14:48-60. [PMID: 30271314 PMCID: PMC6128071 DOI: 10.2174/1573398x14666180430144452] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2018] [Revised: 04/25/2018] [Accepted: 04/27/2018] [Indexed: 12/17/2022]
Abstract
Background: The accurate microscopic diagnosis of lung cancer has become insufficient due to the concept of personalized medicine. Tissue samples are used not only for microscopic diagnosis but also for the assessment of the different targets. Biopsies are performed in 80% of the patients and they are not sufficient for molecular diagnosis in 30% of the cases. Liquid biopsy (LB) has been reported as a possible surrogate to tissue samples and has been introduced in the management scheme of the patients since 2014. We aimed to highlight the diagnostic value of liquid biopsy in assessing the molecular profile of non small cell carcinomas in comparison with tissue biopsy. Methods: We retracted eligible articles from PubMed, Embase and Cochrane databases. We calculated the pooled sensitivity (SEN), specificity (SPE), positive likelihood ratio (PLR), negative likelihood ratio (NLR) and diagnostic odds ratio (DOR). A summary receiver operating characteristic curve (SROC) and area under curve (AUC) were used to evaluate the overall diagnostic performance using the Meta-Disc software 5.1.32. The heterogeneity was assessed using I square statistics. A meta-regression was performed in case of heterogeneity. In case of absence of covariates, a sensitivity analysis was done in order to assess publications that induced a statistical bias. Results: 39 eligible studies involving 4782 patients were included. The overall statistical studies showed heterogeneity in the SEN, SPE, PLR, NLR and DOR. No threshold effect was revealed. The meta-regression incorporating the ethnicity, the test, the technique used in tissue and plasma and the use of plasma or serum as covariates showed no impact of these factors. A sensitivity analysis allowed achieving the homogeneity in the SPE and DOR. The overall pooled SEN and SPE were 0.61 and 0.95 respectively. The PLR was 9.51, the NLR was 0.45 and DOR was 24.58. The SROC curve with AUC of 0,93 indicated that the liquid biopsy is capable of identifying wild type samples from mutated ones with a relatively high accuracy. Conclusion: This meta-analysis suggested that detection of molecular mutations by cfDNA is of adequate diagnostic accuracy in association to tissues. The high specificity and the moderate sensitivity highlight the value of LB as a screening test
Collapse
Affiliation(s)
- Mona Mlika
- 1Department of Pathology, Abderrahman Mami Hospital, Ariana, Tunisia; 2University Tunis El Manar, Faculty of Medicine of Tunis, Tunis, Tunisia; 3Department of General Surgery B, Charles Nicolle Hospital, Tunis, Tunisia; 4Medical Center of ABM, Military College, Qatar
| | - Chadli Dziri
- 1Department of Pathology, Abderrahman Mami Hospital, Ariana, Tunisia; 2University Tunis El Manar, Faculty of Medicine of Tunis, Tunis, Tunisia; 3Department of General Surgery B, Charles Nicolle Hospital, Tunis, Tunisia; 4Medical Center of ABM, Military College, Qatar
| | - Mohamed Majdi Zorgati
- 1Department of Pathology, Abderrahman Mami Hospital, Ariana, Tunisia; 2University Tunis El Manar, Faculty of Medicine of Tunis, Tunis, Tunisia; 3Department of General Surgery B, Charles Nicolle Hospital, Tunis, Tunisia; 4Medical Center of ABM, Military College, Qatar
| | - Mehdi Ben Khelil
- 1Department of Pathology, Abderrahman Mami Hospital, Ariana, Tunisia; 2University Tunis El Manar, Faculty of Medicine of Tunis, Tunis, Tunisia; 3Department of General Surgery B, Charles Nicolle Hospital, Tunis, Tunisia; 4Medical Center of ABM, Military College, Qatar
| | - Faouzi Mezni
- 1Department of Pathology, Abderrahman Mami Hospital, Ariana, Tunisia; 2University Tunis El Manar, Faculty of Medicine of Tunis, Tunis, Tunisia; 3Department of General Surgery B, Charles Nicolle Hospital, Tunis, Tunisia; 4Medical Center of ABM, Military College, Qatar
| |
Collapse
|