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Oh HJ, Imam-Aliagan AB, Kim YB, Kim HJ, Izaguirre IA, Sung CK, Yim H. Clinical applications of circulating biomarkers in non-small cell lung cancer. Front Cell Dev Biol 2024; 12:1449232. [PMID: 39239557 PMCID: PMC11375801 DOI: 10.3389/fcell.2024.1449232] [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: 06/14/2024] [Accepted: 08/12/2024] [Indexed: 09/07/2024] Open
Abstract
Despite recent advances in cancer diagnostics and treatment, the mortality associated with lung cancer is still the highest in the world. Late-stage diagnosis, often accompanied by metastasis, is a major contributor to the high mortality rates, emphasizing the urgent need for reliable and readily accessible diagnostic tools that can detect biomarkers unique to lung cancer. Circulating factors, such as circulating tumor DNA and extracellular vesicles, from liquid biopsy have been recognized as diagnostic or prognostic markers in lung cancer. Numerous clinical studies are currently underway to investigate the potential of circulating tumor DNA, circulating tumor RNA, exosomes, and exosomal microRNA within the context of lung cancer. Those clinical studies aim to address the poor diagnostics and limited treatment options for lung cancer, with the ultimate goal of developing clinical markers and personalized therapies. In this review, we discuss the roles of each circulating factor, its current research status, and ongoing clinical studies of circulating factors in non-small cell lung cancer. Additionally, we discuss the circulating factors specifically found in lung cancer stem cells and examine approved diagnostic assays designed to detect circulating biomarkers in lung cancer patients.
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Affiliation(s)
- Hyun-Ji Oh
- Department of Pharmacy, College of Pharmacy, Hanyang University, Ansan, Gyeonggi-do, Republic of Korea
| | - Abdulhamid B Imam-Aliagan
- Department of Biological and Health Sciences, College of Arts and Sciences, Texas A&M University-Kingsville, Kingsville, TX, United States
| | - Yeo-Bin Kim
- Department of Pharmacy, College of Pharmacy, Hanyang University, Ansan, Gyeonggi-do, Republic of Korea
| | - Hyun-Jin Kim
- Department of Pharmacy, College of Pharmacy, Hanyang University, Ansan, Gyeonggi-do, Republic of Korea
| | - Issac A Izaguirre
- Department of Biological and Health Sciences, College of Arts and Sciences, Texas A&M University-Kingsville, Kingsville, TX, United States
| | - Chang K Sung
- Department of Biological and Health Sciences, College of Arts and Sciences, Texas A&M University-Kingsville, Kingsville, TX, United States
| | - Hyungshin Yim
- Department of Pharmacy, College of Pharmacy, Hanyang University, Ansan, Gyeonggi-do, Republic of Korea
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Evans M, Kendall T. Practical considerations for pathological diagnosis and molecular profiling of cholangiocarcinoma: an expert review for best practices. Expert Rev Mol Diagn 2024; 24:393-408. [PMID: 38752560 DOI: 10.1080/14737159.2024.2353696] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2024] [Accepted: 05/07/2024] [Indexed: 05/22/2024]
Abstract
INTRODUCTION Advances in precision medicine have expanded access to targeted therapies and demand for molecular profiling of cholangiocarcinoma (CCA) patients in routine clinical practice. However, pathologists face challenges in establishing a definitive intrahepatic CCA (iCCA) diagnosis while preserving sufficient tissue for molecular profiling. Additionally, they frequently face challenges in optimal tissue handling to preserve nucleic acid integrity. AREAS COVERED This article first identifies the challenges in establishing a definitive diagnosis of iCCA in a lesional liver biopsy while preserving sufficient tissue for molecular profiling. Then, the authors explore the clinical value of molecular profiling, the basic principles of single gene and next-generation sequencing (NGS) techniques, and the challenges in tissue sampling for genomic testing. They also propose an algorithm for best practice in tissue management for molecular profiling of CCA. EXPERT OPINION Several practical challenges face pathologists during tissue sampling and processing for molecular profiling. Optimized tissue processing, careful tissue handling, and selection of appropriate approaches to molecular testing are essential to ensure that the highest possible quality of diagnostic information is provided in the greatest proportion of cases.
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Affiliation(s)
- Matt Evans
- Cellular Pathologist, University Hospital Southampton NHS Foundation Trust, Southampton, UK
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3
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Alexander GE, Lin W, Ortega FE, Ramaiah M, Jung B, Ji L, Revenkova E, Shah P, Croisetiere C, Berman JR, Eubank L, Naik G, Brooks J, Mich A, Shojaee S, Ronaghi N, Chawla H, Hou X, Liu Q, Yakym CJAV, Moradi PW, Halks-Miller M, Aravanis AM, Parpart-Li S, Hunkapiller N. Analytical validation of a multi-cancer early detection test with cancer signal origin using a cell-free DNA-based targeted methylation assay. PLoS One 2023; 18:e0283001. [PMID: 37058491 PMCID: PMC10104288 DOI: 10.1371/journal.pone.0283001] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2022] [Accepted: 02/28/2023] [Indexed: 04/15/2023] Open
Abstract
The analytical validation is reported for a targeted methylation-based cell-free DNA multi-cancer early detection test designed to detect cancer and predict the cancer signal origin (tissue of origin). A machine-learning classifier was used to analyze the methylation patterns of >105 genomic targets covering >1 million methylation sites. Analytical sensitivity (limit of detection [95% probability]) was characterized with respect to tumor content by expected variant allele frequency and was determined to be 0.07%-0.17% across five tumor cases and 0.51% for the lymphoid neoplasm case. Test specificity was 99.3% (95% confidence interval, 98.6-99.7%). In the reproducibility and repeatability study, results were consistent in 31/34 (91.2%) pairs with cancer and 17/17 (100%) pairs without cancer; between runs, results were concordant for 129/133 (97.0%) cancer and 37/37 (100%) non-cancer sample pairs. Across 3- to 100-ng input levels of cell-free DNA, cancer was detected in 157/182 (86.3%) cancer samples but not in any of the 62 non-cancer samples. In input titration tests, cancer signal origin was correctly predicted in all tumor samples detected as cancer. No cross-contamination events were observed. No potential interferent (hemoglobin, bilirubin, triglycerides, genomic DNA) affected performance. The results of this analytical validation study support continued clinical development of a targeted methylation cell-free DNA multi-cancer early detection test.
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Affiliation(s)
- Gregory E. Alexander
- GRAIL, LLC, A Subsidiary of Illumina, Inc., Currently Held Separate from Illumina, Inc., Under the Terms of the Interim Measures Order of the European Commission Dated 29 October 2021, Menlo Park, California, United States of America
| | - Wendy Lin
- GRAIL, LLC, A Subsidiary of Illumina, Inc., Currently Held Separate from Illumina, Inc., Under the Terms of the Interim Measures Order of the European Commission Dated 29 October 2021, Menlo Park, California, United States of America
| | - Fabian E. Ortega
- GRAIL, LLC, A Subsidiary of Illumina, Inc., Currently Held Separate from Illumina, Inc., Under the Terms of the Interim Measures Order of the European Commission Dated 29 October 2021, Menlo Park, California, United States of America
| | - Madhuvanthi Ramaiah
- GRAIL, LLC, A Subsidiary of Illumina, Inc., Currently Held Separate from Illumina, Inc., Under the Terms of the Interim Measures Order of the European Commission Dated 29 October 2021, Menlo Park, California, United States of America
| | - Byoungsok Jung
- GRAIL, LLC, A Subsidiary of Illumina, Inc., Currently Held Separate from Illumina, Inc., Under the Terms of the Interim Measures Order of the European Commission Dated 29 October 2021, Menlo Park, California, United States of America
| | - Lijuan Ji
- GRAIL, LLC, A Subsidiary of Illumina, Inc., Currently Held Separate from Illumina, Inc., Under the Terms of the Interim Measures Order of the European Commission Dated 29 October 2021, Menlo Park, California, United States of America
| | - Ekaterina Revenkova
- GRAIL, LLC, A Subsidiary of Illumina, Inc., Currently Held Separate from Illumina, Inc., Under the Terms of the Interim Measures Order of the European Commission Dated 29 October 2021, Menlo Park, California, United States of America
| | - Payal Shah
- GRAIL, LLC, A Subsidiary of Illumina, Inc., Currently Held Separate from Illumina, Inc., Under the Terms of the Interim Measures Order of the European Commission Dated 29 October 2021, Menlo Park, California, United States of America
| | - Christian Croisetiere
- GRAIL, LLC, A Subsidiary of Illumina, Inc., Currently Held Separate from Illumina, Inc., Under the Terms of the Interim Measures Order of the European Commission Dated 29 October 2021, Menlo Park, California, United States of America
| | - Jennifer R. Berman
- GRAIL, LLC, A Subsidiary of Illumina, Inc., Currently Held Separate from Illumina, Inc., Under the Terms of the Interim Measures Order of the European Commission Dated 29 October 2021, Menlo Park, California, United States of America
| | - Lane Eubank
- GRAIL, LLC, A Subsidiary of Illumina, Inc., Currently Held Separate from Illumina, Inc., Under the Terms of the Interim Measures Order of the European Commission Dated 29 October 2021, Menlo Park, California, United States of America
| | - Gunjan Naik
- GRAIL, LLC, A Subsidiary of Illumina, Inc., Currently Held Separate from Illumina, Inc., Under the Terms of the Interim Measures Order of the European Commission Dated 29 October 2021, Menlo Park, California, United States of America
| | - Jacqueline Brooks
- GRAIL, LLC, A Subsidiary of Illumina, Inc., Currently Held Separate from Illumina, Inc., Under the Terms of the Interim Measures Order of the European Commission Dated 29 October 2021, Menlo Park, California, United States of America
| | - Andrea Mich
- GRAIL, LLC, A Subsidiary of Illumina, Inc., Currently Held Separate from Illumina, Inc., Under the Terms of the Interim Measures Order of the European Commission Dated 29 October 2021, Menlo Park, California, United States of America
| | - Seyedmehdi Shojaee
- GRAIL, LLC, A Subsidiary of Illumina, Inc., Currently Held Separate from Illumina, Inc., Under the Terms of the Interim Measures Order of the European Commission Dated 29 October 2021, Menlo Park, California, United States of America
| | - Neda Ronaghi
- GRAIL, LLC, A Subsidiary of Illumina, Inc., Currently Held Separate from Illumina, Inc., Under the Terms of the Interim Measures Order of the European Commission Dated 29 October 2021, Menlo Park, California, United States of America
| | - Hemanshi Chawla
- GRAIL, LLC, A Subsidiary of Illumina, Inc., Currently Held Separate from Illumina, Inc., Under the Terms of the Interim Measures Order of the European Commission Dated 29 October 2021, Menlo Park, California, United States of America
| | - Xinyi Hou
- GRAIL, LLC, A Subsidiary of Illumina, Inc., Currently Held Separate from Illumina, Inc., Under the Terms of the Interim Measures Order of the European Commission Dated 29 October 2021, Menlo Park, California, United States of America
| | - Qinwen Liu
- GRAIL, LLC, A Subsidiary of Illumina, Inc., Currently Held Separate from Illumina, Inc., Under the Terms of the Interim Measures Order of the European Commission Dated 29 October 2021, Menlo Park, California, United States of America
| | - Christopher-James A. V. Yakym
- GRAIL, LLC, A Subsidiary of Illumina, Inc., Currently Held Separate from Illumina, Inc., Under the Terms of the Interim Measures Order of the European Commission Dated 29 October 2021, Menlo Park, California, United States of America
| | - Patriss Wais Moradi
- GRAIL, LLC, A Subsidiary of Illumina, Inc., Currently Held Separate from Illumina, Inc., Under the Terms of the Interim Measures Order of the European Commission Dated 29 October 2021, Menlo Park, California, United States of America
| | - Meredith Halks-Miller
- GRAIL, LLC, A Subsidiary of Illumina, Inc., Currently Held Separate from Illumina, Inc., Under the Terms of the Interim Measures Order of the European Commission Dated 29 October 2021, Menlo Park, California, United States of America
| | - Alexander M. Aravanis
- GRAIL, LLC, A Subsidiary of Illumina, Inc., Currently Held Separate from Illumina, Inc., Under the Terms of the Interim Measures Order of the European Commission Dated 29 October 2021, Menlo Park, California, United States of America
| | - Sonya Parpart-Li
- GRAIL, LLC, A Subsidiary of Illumina, Inc., Currently Held Separate from Illumina, Inc., Under the Terms of the Interim Measures Order of the European Commission Dated 29 October 2021, Menlo Park, California, United States of America
| | - Nathan Hunkapiller
- GRAIL, LLC, A Subsidiary of Illumina, Inc., Currently Held Separate from Illumina, Inc., Under the Terms of the Interim Measures Order of the European Commission Dated 29 October 2021, Menlo Park, California, United States of America
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Di Sario G, Rossella V, Famulari ES, Maurizio A, Lazarevic D, Giannese F, Felici C. Enhancing clinical potential of liquid biopsy through a multi-omic approach: A systematic review. Front Genet 2023; 14:1152470. [PMID: 37077538 PMCID: PMC10109350 DOI: 10.3389/fgene.2023.1152470] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2023] [Accepted: 03/20/2023] [Indexed: 04/05/2023] Open
Abstract
In the last years, liquid biopsy gained increasing clinical relevance for detecting and monitoring several cancer types, being minimally invasive, highly informative and replicable over time. This revolutionary approach can be complementary and may, in the future, replace tissue biopsy, which is still considered the gold standard for cancer diagnosis. "Classical" tissue biopsy is invasive, often cannot provide sufficient bioptic material for advanced screening, and can provide isolated information about disease evolution and heterogeneity. Recent literature highlighted how liquid biopsy is informative of proteomic, genomic, epigenetic, and metabolic alterations. These biomarkers can be detected and investigated using single-omic and, recently, in combination through multi-omic approaches. This review will provide an overview of the most suitable techniques to thoroughly characterize tumor biomarkers and their potential clinical applications, highlighting the importance of an integrated multi-omic, multi-analyte approach. Personalized medical investigations will soon allow patients to receive predictable prognostic evaluations, early disease diagnosis, and subsequent ad hoc treatments.
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Langerhans Cell Histiocytosis-Associated Pulmonary Adenocarcinoma: A Word of Caution during Molecular Determinations. JOURNAL OF MOLECULAR PATHOLOGY 2022. [DOI: 10.3390/jmp3040024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Background: Smoking habit is a common cause of pulmonary Langerhans cell histiocytosis (PLCH) and lung cancer and both diseases may coexist in the lung and share genetic alterations, such as V600E BRAF mutations. We collected a small series of three cases of PLCH-associated lung adenocarcinoma in order to evaluate the molecular setup in both components and underline the critical role of careful tissue selection for predictive molecular driver testing. Methods: Three cases of PLCH-associated adenocarcinoma were collected from consultation files. Clinical data from referring physicians and clinical data were obtained. The surgical biopsies were tested by immunohistochemistry and molecular analysis after separate dissection of adenocarcinoma cells and Langerhans histiocytes. Results: There were three active smoking men with a median age at diagnosis of 60.6 years. PLCH was disclosed at imaging during work-up for suspected lung cancer. Molecular analysis revealed KRAS (G12C and G13C) mutations in two cases and V600E BRAF mutation in one case of PLCH. Immunostaining with the V600E BRAF mutation specific primary antibody VE1 correctly recognized BRAF-mutated LCH. One case was wild-type in both diseases. Two similar cases were found in the literature, one of which showed a discrepant KRAS (G12D) mutation in adenocarcinoma and a V600E BRAF mutation in LCH; Conclusions: This case series of PLCH-associated adenocarcinoma underline the possibility to disclose identical genetic alterations in co-existing benign and malignant pathologies, then potentially creating erroneous interpretation of molecular analysis leading to inadequate therapeutic options in case of incorrect diagnostic recognition and inappropriate selection of both components through microdissection.
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Kucharczyk T, Krawczyk P, Kowalski DM, Płużański A, Kubiatowski T, Kalinka E. RET Proto-Oncogene-Not Such an Obvious Starting Point in Cancer Therapy. Cancers (Basel) 2022; 14:5298. [PMID: 36358717 PMCID: PMC9657474 DOI: 10.3390/cancers14215298] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2022] [Revised: 10/13/2022] [Accepted: 10/14/2022] [Indexed: 11/26/2023] Open
Abstract
Mutations and fusions of RET (rearranged during transfection) gene are detected in a few common types of tumors including thyroid or non-small cells lung cancers. Multiple kinase inhibitors (MKIs) do not show spectacular effectiveness in patients with RET-altered tumors. Hence, recently, two novel RET-specific inhibitors were registered in the US and in Europe. Selpercatinib and pralsetinib showed high efficacy in clinical trials, with fewer adverse effects, in comparison to previously used MKIs. However, the effectiveness of these new drugs may be reduced by the emergence of resistance mutations in RET gene and activation of different activating signaling pathways. This review presents the function of the normal RET receptor, types of molecular disturbances of the RET gene in patients with various cancers, methods of detecting these abnormalities, and the effectiveness of modern anticancer therapies (ranging from immunotherapies, through MKIs, to RET-specific inhibitors).
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Affiliation(s)
- Tomasz Kucharczyk
- Chair and Department of Pneumonology, Oncology and Allergology, Medical University of Lublin, 20-059 Lublin, Poland
| | - Paweł Krawczyk
- Chair and Department of Pneumonology, Oncology and Allergology, Medical University of Lublin, 20-059 Lublin, Poland
| | - Dariusz M. Kowalski
- Department of Lung and Thoracic Tumours, Maria Skłodowskiej-Curie National Research Institute, 02-718 Warsaw, Poland
| | - Adam Płużański
- Department of Lung and Thoracic Tumours, Maria Skłodowskiej-Curie National Research Institute, 02-718 Warsaw, Poland
| | - Tomasz Kubiatowski
- Oncology and Immunology Clinic, Warmian-Masurian Cancer Center of the Ministry of the Interior and Administration’s Hospital, 10-228 Olsztyn, Poland
| | - Ewa Kalinka
- Department of Oncology, Polish Mother’s Memorial Hospital-Research Institute, 90-302 Lodz, Poland
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7
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Seki Y, Yoshida T, Kohno T, Masuda K, Okuma Y, Goto Y, Horinouchi H, Yamamoto N, Kuwano K, Ohe Y. Liquid biopsy for the detection of resistance mutations to ROS1 and RET inhibitors in non-small lung cancers: A case series study. Respir Investig 2022; 60:852-856. [PMID: 36089506 DOI: 10.1016/j.resinv.2022.08.002] [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: 06/18/2022] [Revised: 07/20/2022] [Accepted: 08/02/2022] [Indexed: 11/28/2022]
Abstract
Liquid biopsy can identify gene alterations that are associated with resistance to fusion gene-targeted treatments. In this study, we present three cases of advanced non-small cell lung cancer (NSCLC) harboring gene fusions; cell-free DNA (cfDNA) was used to assess the resistance mutations. A patient with MET amplification underwent RET-fusion NSCLC treatment with selpercatinib. A patient with ROS1 G2032R underwent ROS1-fusion NSCLC treatment with crizotinib. A patient who underwent ROS1-fusion NSCLC treatment with crizotinib harbored no somatic mutations. This case series shows that cfDNA analysis can identify potentially actionable genomic alterations, after disease progression, in targeted therapy for fusion genes. TRIAL REGISTRATION: The study was registered in the UMIN Clinical Trial Registry (UMIN 000017581).
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Affiliation(s)
- Yoshitaka Seki
- Division of Respirology, Department of Internal Medicine, The Jikei University Katsushika Medical Center; Division of Genome Biology, National Cancer Center Research Institute, Chuo-ku, Tokyo, Japan.
| | - Tatsuya Yoshida
- Division of Thoracic Oncology, National Cancer, Center Hospital, Tokyo, Japan
| | - Takashi Kohno
- Division of Genome Biology, National Cancer Center Research Institute, Chuo-ku, Tokyo, Japan
| | - Ken Masuda
- Division of Thoracic Oncology, National Cancer, Center Hospital, Tokyo, Japan
| | - Yusuke Okuma
- Division of Thoracic Oncology, National Cancer, Center Hospital, Tokyo, Japan
| | - Yasushi Goto
- Division of Thoracic Oncology, National Cancer, Center Hospital, Tokyo, Japan
| | - Hidehito Horinouchi
- Division of Thoracic Oncology, National Cancer, Center Hospital, Tokyo, Japan
| | - Noboru Yamamoto
- Division of Thoracic Oncology, National Cancer, Center Hospital, Tokyo, Japan
| | - Kazuyoshi Kuwano
- Division of Respiratory Diseases, Department of Internal Medicine, The Jikei University School of Medicine, Japan
| | - Yuichiro Ohe
- Division of Thoracic Oncology, National Cancer, Center Hospital, Tokyo, Japan
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8
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Mauri G, Vitiello PP, Sogari A, Crisafulli G, Sartore-Bianchi A, Marsoni S, Siena S, Bardelli A. Liquid biopsies to monitor and direct cancer treatment in colorectal cancer. Br J Cancer 2022; 127:394-407. [PMID: 35264786 PMCID: PMC9346106 DOI: 10.1038/s41416-022-01769-8] [Citation(s) in RCA: 43] [Impact Index Per Article: 21.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2021] [Revised: 02/02/2022] [Accepted: 02/17/2022] [Indexed: 12/15/2022] Open
Abstract
Colorectal cancer (CRC) is one of the most prevalent and deadly cancers worldwide. Despite recent improvements in treatment and prevention, most of the current therapeutic options are weighted by side effects impacting patients' quality of life. Better patient selection towards systemic treatments represents an unmet clinical need. The recent multidisciplinary and molecular advancements in the treatment of CRC patients demand the identification of efficient biomarkers allowing to personalise patient care. Currently, core tumour biopsy specimens represent the gold-standard biological tissue to identify such biomarkers. However, technical feasibility, tumour heterogeneity and cancer evolution are major limitations of this single-snapshot approach. Genotyping circulating tumour DNA (ctDNA) has been addressed as potentially overcoming such limitations. Indeed, ctDNA has been retrospectively demonstrated capable of identifying minimal residual disease post-surgery and post-adjuvant treatment, as well as spotting druggable molecular alterations for tailoring treatments in metastatic disease. In this review, we summarise the available evidence on ctDNA applicability in CRC. Then, we review ongoing clinical trials assessing how liquid biopsy can be used interventionally to guide therapeutic choice in localised, locally advanced and metastatic CRC. Finally, we discuss how its widespread could transform CRC patients' management, dissecting its limitations while suggesting improvement strategies.
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Affiliation(s)
- Gianluca Mauri
- IFOM-FIRC Institute of Molecular Oncology, Milan, Italy
- Department of Oncology and Hemato-Oncology, Università degli Studi di Milano, Milan, Italy
| | - Pietro Paolo Vitiello
- Candiolo Cancer Institute, FPO-IRCCS, 10060, Candiolo, TO, Italy
- Department of Oncology, University of Torino, 10060, Candiolo, TO, Italy
| | - Alberto Sogari
- Candiolo Cancer Institute, FPO-IRCCS, 10060, Candiolo, TO, Italy
- Department of Oncology, University of Torino, 10060, Candiolo, TO, Italy
| | - Giovanni Crisafulli
- Candiolo Cancer Institute, FPO-IRCCS, 10060, Candiolo, TO, Italy
- Department of Oncology, University of Torino, 10060, Candiolo, TO, Italy
| | - Andrea Sartore-Bianchi
- Department of Oncology and Hemato-Oncology, Università degli Studi di Milano, Milan, Italy
- Department of Hematology, Oncology, and Molecular Medicine, Grande Ospedale Metropolitano Niguarda, 20162, Milan, Italy
| | | | - Salvatore Siena
- Department of Oncology and Hemato-Oncology, Università degli Studi di Milano, Milan, Italy
- Department of Hematology, Oncology, and Molecular Medicine, Grande Ospedale Metropolitano Niguarda, 20162, Milan, Italy
| | - Alberto Bardelli
- Candiolo Cancer Institute, FPO-IRCCS, 10060, Candiolo, TO, Italy.
- Department of Oncology, University of Torino, 10060, Candiolo, TO, Italy.
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9
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Hundal J, Lopetegui-Lia N, Vredenburgh J. Discovery, Significance, and Utility of JAK2 Mutation in Squamous Cell Carcinoma of the Lung. Cureus 2022; 14:e25913. [PMID: 35844327 PMCID: PMC9279128 DOI: 10.7759/cureus.25913] [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] [Accepted: 06/13/2022] [Indexed: 11/05/2022] Open
Abstract
Lung cancer continues to be the leading cause of cancer-related deaths worldwide. Many studies show lung cancer is a histologically and molecularly heterogeneous group, even within the same histological subtype. Liquid biopsies are a new tool that can identify targetable genomic mutations and impact management. JAK2 p.V617F is a mutation commonly found in myeloproliferative neoplasms but rarely identified in non-small cell lung cancer (NSCLCs). The significance of Janus Kinase (JAK2) mutation in lung cancer is not clearly understood. However, it is thought that it may have a role in treating solid tumors, such as lung cancer. We present two cases of patients diagnosed with NSCLC who were discovered to have JAK2 V617F mutation on liquid biopsy.
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10
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Dziadziuszko R, Hung T, Wang K, Choeurng V, Drilon A, Doebele RC, Barlesi F, Wu C, Dennis L, Skoletsky J, Woodhouse R, Li M, Chang C, Simmons B, Riehl T, Wilson TR. Pre- and post-treatment blood-based genomic landscape of patients with ROS1 or NTRK fusion-positive solid tumours treated with entrectinib. Mol Oncol 2022; 16:2000-2014. [PMID: 35338679 PMCID: PMC9120896 DOI: 10.1002/1878-0261.13214] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2021] [Revised: 01/25/2022] [Accepted: 03/24/2022] [Indexed: 11/08/2022] Open
Abstract
Genomic tumour profiling informs targeted treatment options. Entrectinib is a tyrosine kinase inhibitor with efficacy in NTRK fusion-positive (-fp) solid tumours and ROS1-fp non-small cell lung cancer. FoundationOne® Liquid CDx (F1L CDx), a non-invasive in vitro next-generation sequencing (NGS)-based diagnostic, detects genomic alterations in plasma circulating tumour DNA (ctDNA). We evaluated the clinical validity of F1L CDx as an aid in identifying patients with NTRK-fp or ROS1-fp tumours and assessed the genomic landscape pre- and post-entrectinib treatment. Among evaluable pre-treatment clinical samples (N = 85), positive percentage agreements between F1L CDx and clinical trial assays (CTAs) were 47.4% (NTRK fusions) and 64.5% (ROS1 fusions); positive predictive value was 100% for both. The objective response rate for CTA+ F1L CDx+ patients was 72.2% in both cohorts. The median duration of response significantly differed between F1L CDx+ and F1L CDx- samples in ROS1-fp (5.6 vs. 17.3 months) but not NTRK-fp (9.2 vs. 12.9 months) patients. Fifteen acquired resistance mutations were detected. We conclude that F1L CDx is a clinically valid complement to tissue-based testing to identify patients who may benefit from entrectinib and those with acquired resistance mutations associated with disease progression.
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Affiliation(s)
- Rafal Dziadziuszko
- Department of Oncology and RadiotherapyMedical University of GdańskGdańskPoland
| | - Tiffany Hung
- Oncology Biomarker DepartmentGenentech, Inc.South San FranciscoCAUSA
| | - Kun Wang
- BiostatisticsFoundation Medicine Inc.CambridgeMAUSA
| | - Voleak Choeurng
- Oncology BiostatisticsGenentech, Inc.South San FranciscoCAUSA
| | - Alexander Drilon
- Early Drug Development ServiceMemorial Sloan Kettering Cancer Center, and Weill Cornell Medical CollegeNew YorkNYUSA
| | | | - Fabrice Barlesi
- The National Centre for Scientific Research (CNRS)The National Institute of Health and Medical Research (INSERM)Aix Marseille UniversityMarseilleFrance
- Medical OncologyGustave RoussyVillejuifFrance
| | - Charlie Wu
- Oncology Biomarker DepartmentGenentech, Inc.South San FranciscoCAUSA
| | - Lucas Dennis
- Franchise DevelopmentFoundation Medicine Inc.CambridgeMAUSA
| | - Joel Skoletsky
- Companion Diagnostics DevelopmentFoundation Medicine Inc.CambridgeMAUSA
| | - Ryan Woodhouse
- Regulatory AffairsFoundation Medicine Inc.CambridgeMAUSA
| | - Meijuan Li
- Biometrics and BiomarkersFoundation Medicine Inc.CambridgeMAUSA
| | - Ching‐Wei Chang
- Oncology BiostatisticsGenentech, Inc.South San FranciscoCAUSA
| | - Brian Simmons
- Product Development OncologyGenentech, Inc.South San FranciscoCAUSA
| | - Todd Riehl
- Product Development OncologyGenentech, Inc.South San FranciscoCAUSA
| | - Timothy R. Wilson
- Oncology Biomarker DepartmentGenentech, Inc.South San FranciscoCAUSA
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Bonosi L, Ferini G, Giammalva GR, Benigno UE, Porzio M, Giovannini EA, Musso S, Gerardi RM, Brunasso L, Costanzo R, Paolini F, Graziano F, Scalia G, Umana GE, Di Bonaventura R, Sturiale CL, Iacopino DG, Maugeri R. Liquid Biopsy in Diagnosis and Prognosis of High-Grade Gliomas; State-of-the-Art and Literature Review. Life (Basel) 2022; 12:life12030407. [PMID: 35330158 PMCID: PMC8950809 DOI: 10.3390/life12030407] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2022] [Revised: 03/05/2022] [Accepted: 03/08/2022] [Indexed: 12/31/2022] Open
Abstract
Gliomas, particularly high-grade gliomas, represent the most common and aggressive tumors of the CNS and are still burdened by high mortality and a very poor prognosis, regardless of the type of therapy. Their diagnosis and monitoring rely on imaging techniques and direct biopsy of the pathological tissue; however, both procedures have inherent limitations. To address these limitations, liquid biopsies have been proposed in this field. They could represent an innovative tool that could help clinicians in the early diagnosis, monitoring, and prognosis of these tumors. Furthermore, the rapid development of next-generation sequencing (NGS) technologies has led to a significant reduction in sequencing cost, with improved accuracy, providing a molecular profile of cancer and leading to better survival results and less disease burden. This paper focuses on the current clinical application of liquid biopsy in the early diagnosis and prognosis of cancer, introduces NGS-related methods, reviews recent progress, and summarizes challenges and future perspectives.
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Affiliation(s)
- Lapo Bonosi
- Neurosurgical Clinic, AOUP “Paolo Giaccone”, Post Graduate Residency Program in Neurologic Surgery, Department of Biomedicine Neurosciences and Advanced Diagnostics, School of Medicine, University of Palermo, 90127 Palermo, Italy; (G.R.G.); (U.E.B.); (M.P.); (E.A.G.); (S.M.); (R.M.G.); (L.B.); (R.C.); (F.P.); (D.G.I.); (R.M.)
- Correspondence: ; Tel.: +39-0916554656
| | - Gianluca Ferini
- Department of Radiation Oncology, REM Radioterapia srl, 95125 Catania, Italy;
| | - Giuseppe Roberto Giammalva
- Neurosurgical Clinic, AOUP “Paolo Giaccone”, Post Graduate Residency Program in Neurologic Surgery, Department of Biomedicine Neurosciences and Advanced Diagnostics, School of Medicine, University of Palermo, 90127 Palermo, Italy; (G.R.G.); (U.E.B.); (M.P.); (E.A.G.); (S.M.); (R.M.G.); (L.B.); (R.C.); (F.P.); (D.G.I.); (R.M.)
| | - Umberto Emanuele Benigno
- Neurosurgical Clinic, AOUP “Paolo Giaccone”, Post Graduate Residency Program in Neurologic Surgery, Department of Biomedicine Neurosciences and Advanced Diagnostics, School of Medicine, University of Palermo, 90127 Palermo, Italy; (G.R.G.); (U.E.B.); (M.P.); (E.A.G.); (S.M.); (R.M.G.); (L.B.); (R.C.); (F.P.); (D.G.I.); (R.M.)
| | - Massimiliano Porzio
- Neurosurgical Clinic, AOUP “Paolo Giaccone”, Post Graduate Residency Program in Neurologic Surgery, Department of Biomedicine Neurosciences and Advanced Diagnostics, School of Medicine, University of Palermo, 90127 Palermo, Italy; (G.R.G.); (U.E.B.); (M.P.); (E.A.G.); (S.M.); (R.M.G.); (L.B.); (R.C.); (F.P.); (D.G.I.); (R.M.)
| | - Evier Andrea Giovannini
- Neurosurgical Clinic, AOUP “Paolo Giaccone”, Post Graduate Residency Program in Neurologic Surgery, Department of Biomedicine Neurosciences and Advanced Diagnostics, School of Medicine, University of Palermo, 90127 Palermo, Italy; (G.R.G.); (U.E.B.); (M.P.); (E.A.G.); (S.M.); (R.M.G.); (L.B.); (R.C.); (F.P.); (D.G.I.); (R.M.)
| | - Sofia Musso
- Neurosurgical Clinic, AOUP “Paolo Giaccone”, Post Graduate Residency Program in Neurologic Surgery, Department of Biomedicine Neurosciences and Advanced Diagnostics, School of Medicine, University of Palermo, 90127 Palermo, Italy; (G.R.G.); (U.E.B.); (M.P.); (E.A.G.); (S.M.); (R.M.G.); (L.B.); (R.C.); (F.P.); (D.G.I.); (R.M.)
| | - Rosa Maria Gerardi
- Neurosurgical Clinic, AOUP “Paolo Giaccone”, Post Graduate Residency Program in Neurologic Surgery, Department of Biomedicine Neurosciences and Advanced Diagnostics, School of Medicine, University of Palermo, 90127 Palermo, Italy; (G.R.G.); (U.E.B.); (M.P.); (E.A.G.); (S.M.); (R.M.G.); (L.B.); (R.C.); (F.P.); (D.G.I.); (R.M.)
| | - Lara Brunasso
- Neurosurgical Clinic, AOUP “Paolo Giaccone”, Post Graduate Residency Program in Neurologic Surgery, Department of Biomedicine Neurosciences and Advanced Diagnostics, School of Medicine, University of Palermo, 90127 Palermo, Italy; (G.R.G.); (U.E.B.); (M.P.); (E.A.G.); (S.M.); (R.M.G.); (L.B.); (R.C.); (F.P.); (D.G.I.); (R.M.)
| | - Roberta Costanzo
- Neurosurgical Clinic, AOUP “Paolo Giaccone”, Post Graduate Residency Program in Neurologic Surgery, Department of Biomedicine Neurosciences and Advanced Diagnostics, School of Medicine, University of Palermo, 90127 Palermo, Italy; (G.R.G.); (U.E.B.); (M.P.); (E.A.G.); (S.M.); (R.M.G.); (L.B.); (R.C.); (F.P.); (D.G.I.); (R.M.)
| | - Federica Paolini
- Neurosurgical Clinic, AOUP “Paolo Giaccone”, Post Graduate Residency Program in Neurologic Surgery, Department of Biomedicine Neurosciences and Advanced Diagnostics, School of Medicine, University of Palermo, 90127 Palermo, Italy; (G.R.G.); (U.E.B.); (M.P.); (E.A.G.); (S.M.); (R.M.G.); (L.B.); (R.C.); (F.P.); (D.G.I.); (R.M.)
| | - Francesca Graziano
- Unit of Neurosurgery, Garibaldi Hospital, 95124 Catania, Italy; (F.G.); (G.S.)
| | - Gianluca Scalia
- Unit of Neurosurgery, Garibaldi Hospital, 95124 Catania, Italy; (F.G.); (G.S.)
| | - Giuseppe Emmanuele Umana
- Trauma Center, Gamma Knife Center, Department of Neurosurgery, Cannizzaro Hospital, 95125 Catania, Italy;
| | - Rina Di Bonaventura
- Department of Neurosurgery, Fondazione Policlinico Universitario “A. Gemelli” IRCCS, Università Cattolica del Sacro Cuore, 00168 Rome, Italy; (R.D.B.); (C.L.S.)
| | - Carmelo Lucio Sturiale
- Department of Neurosurgery, Fondazione Policlinico Universitario “A. Gemelli” IRCCS, Università Cattolica del Sacro Cuore, 00168 Rome, Italy; (R.D.B.); (C.L.S.)
| | - Domenico Gerardo Iacopino
- Neurosurgical Clinic, AOUP “Paolo Giaccone”, Post Graduate Residency Program in Neurologic Surgery, Department of Biomedicine Neurosciences and Advanced Diagnostics, School of Medicine, University of Palermo, 90127 Palermo, Italy; (G.R.G.); (U.E.B.); (M.P.); (E.A.G.); (S.M.); (R.M.G.); (L.B.); (R.C.); (F.P.); (D.G.I.); (R.M.)
| | - Rosario Maugeri
- Neurosurgical Clinic, AOUP “Paolo Giaccone”, Post Graduate Residency Program in Neurologic Surgery, Department of Biomedicine Neurosciences and Advanced Diagnostics, School of Medicine, University of Palermo, 90127 Palermo, Italy; (G.R.G.); (U.E.B.); (M.P.); (E.A.G.); (S.M.); (R.M.G.); (L.B.); (R.C.); (F.P.); (D.G.I.); (R.M.)
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12
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Qureshi S, Chan N, George M, Ganesan S, Toppmeyer D, Omene C. Immune Checkpoint Inhibitors in Triple Negative Breast Cancer: The Search for the Optimal Biomarker. Biomark Insights 2022; 17:11772719221078774. [PMID: 35221668 PMCID: PMC8874164 DOI: 10.1177/11772719221078774] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2021] [Accepted: 01/04/2022] [Indexed: 12/14/2022] Open
Abstract
Triple negative breast cancer (TNBC) is a high-risk and aggressive malignancy characterized by the absence of estrogen receptors (ER) and progesterone receptors (PR) on the surface of malignant cells, and by the lack of overexpression of human epidermal growth factor 2 (HER2). It has limited therapeutic options compared to other subtypes of breast cancer. There is now a growing body of evidence on the role of immunotherapy in TNBC, however much of the data from clinical trials is conflicting and thus, challenging for clinicians to integrate the data into clinical practice. Landmark phase III trials using immunotherapy in the early-stage neoadjuvant setting concluded that the addition of immunotherapy to chemotherapy improved the pathologic complete response (pCR) rate compared to chemotherapy with placebo while others found no significant improvement in pCR. Phase III trials have investigated the utility of immunotherapy in previously untreated metastatic TNBC, and these studies have similarly arrived at inconsistent conclusions. Some studies showed no benefit while others demonstrated a clinically significant improvement in overall survival in the PD-L1 positive population. It is not yet clear which biomarkers are most useful, and assays for these biomarkers have not been standardized. Given the often serious and severe side effects of immunotherapy, it is important and necessary to identify predictive biomarkers of response and resistance in order to enhance patient selection. In this review, we will discuss both the challenges of traditional biomarkers and the opportunities of emerging biomarkers for patient selection.
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Affiliation(s)
- Sadaf Qureshi
- Department of Medicine, Rutgers Robert Wood Johnson Medical School, Rutgers, The State University of New Jersey, New Brunswick, NJ, USA
| | - Nancy Chan
- Department of Medicine, Rutgers Robert Wood Johnson Medical School, Rutgers, The State University of New Jersey, New Brunswick, NJ, USA
- Rutgers Cancer Institute of New Jersey, Rutgers, The State University of New Jersey, New Brunswick, NJ, USA
| | - Mridula George
- Department of Medicine, Rutgers Robert Wood Johnson Medical School, Rutgers, The State University of New Jersey, New Brunswick, NJ, USA
- Rutgers Cancer Institute of New Jersey, Rutgers, The State University of New Jersey, New Brunswick, NJ, USA
| | - Shridar Ganesan
- Department of Medicine, Rutgers Robert Wood Johnson Medical School, Rutgers, The State University of New Jersey, New Brunswick, NJ, USA
- Rutgers Cancer Institute of New Jersey, Rutgers, The State University of New Jersey, New Brunswick, NJ, USA
| | - Deborah Toppmeyer
- Department of Medicine, Rutgers Robert Wood Johnson Medical School, Rutgers, The State University of New Jersey, New Brunswick, NJ, USA
- Rutgers Cancer Institute of New Jersey, Rutgers, The State University of New Jersey, New Brunswick, NJ, USA
| | - Coral Omene
- Department of Medicine, Rutgers Robert Wood Johnson Medical School, Rutgers, The State University of New Jersey, New Brunswick, NJ, USA
- Rutgers Cancer Institute of New Jersey, Rutgers, The State University of New Jersey, New Brunswick, NJ, USA
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13
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Herath S, Sadeghi Rad H, Radfar P, Ladwa R, Warkiani M, O’Byrne K, Kulasinghe A. The Role of Circulating Biomarkers in Lung Cancer. Front Oncol 2022; 11:801269. [PMID: 35127511 PMCID: PMC8813755 DOI: 10.3389/fonc.2021.801269] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2021] [Accepted: 12/21/2021] [Indexed: 12/12/2022] Open
Abstract
Lung cancer is the leading cause of cancer morbidity and mortality worldwide and early diagnosis is crucial for the management and treatment of this disease. Non-invasive means of determining tumour information is an appealing diagnostic approach for lung cancers as often accessing and removing tumour tissue can be a limiting factor. In recent years, liquid biopsies have been developed to explore potential circulating tumour biomarkers which are considered reliable surrogates for understanding tumour biology in a non-invasive manner. Most common components assessed in liquid biopsy include circulating tumour cells (CTCs), cell-free DNA (cfDNA), circulating tumour DNA (ctDNA), microRNA and exosomes. This review explores the clinical use of circulating tumour biomarkers found in liquid biopsy for screening, early diagnosis and prognostication of lung cancer patients.
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14
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Gonda A, Zhao N, Shah JV, Siebert JN, Gunda S, Inan B, Kwon M, Libutti SK, Moghe PV, Francis NL, Ganapathy V. Extracellular Vesicle Molecular Signatures Characterize Metastatic Dynamicity in Ovarian Cancer. Front Oncol 2021; 11:718408. [PMID: 34868914 PMCID: PMC8637407 DOI: 10.3389/fonc.2021.718408] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2021] [Accepted: 10/29/2021] [Indexed: 01/05/2023] Open
Abstract
BACKGROUND Late-stage diagnosis of ovarian cancer, a disease that originates in the ovaries and spreads to the peritoneal cavity, lowers 5-year survival rate from 90% to 30%. Early screening tools that can: i) detect with high specificity and sensitivity before conventional tools such as transvaginal ultrasound and CA-125, ii) use non-invasive sampling methods and iii) longitudinally significantly increase survival rates in ovarian cancer are needed. Studies that employ blood-based screening tools using circulating tumor-cells, -DNA, and most recently tumor-derived small extracellular vesicles (sEVs) have shown promise in non-invasive detection of cancer before standard of care. Our findings in this study show the promise of a sEV-derived signature as a non-invasive longitudinal screening tool in ovarian cancer. METHODS Human serum samples as well as plasma and ascites from a mouse model of ovarian cancer were collected at various disease stages. Small extracellular vesicles (sEVs) were extracted using a commercially available kit. RNA was isolated from lysed sEVs, and quantitative RT-PCR was performed to identify specific metastatic gene expression. CONCLUSION This paper highlights the potential of sEVs in monitoring ovarian cancer progression and metastatic development. We identified a 7-gene panel in sEVs derived from plasma, serum, and ascites that overlapped with an established metastatic ovarian carcinoma signature. We found the 7-gene panel to be differentially expressed with tumor development and metastatic spread in a mouse model of ovarian cancer. The most notable finding was a significant change in the ascites-derived sEV gene signature that overlapped with that of the plasma-derived sEV signature at varying stages of disease progression. While there were quantifiable changes in genes from the 7-gene panel in serum-derived sEVs from ovarian cancer patients, we were unable to establish a definitive signature due to low sample number. Taken together our findings show that differential expression of metastatic genes derived from circulating sEVs present a minimally invasive screening tool for ovarian cancer detection and longitudinal monitoring of molecular changes associated with progression and metastatic spread.
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Affiliation(s)
- Amber Gonda
- Department of Biomedical Engineering, Rutgers University, Piscataway, NJ, United States
| | - Nanxia Zhao
- Department of Chemical and Biochemical Engineering, Rutgers University, Piscataway, NJ, United States
| | - Jay V. Shah
- Department of Biomedical Engineering, Rutgers University, Piscataway, NJ, United States
| | - Jake N. Siebert
- Department of Biomedical Engineering, Rutgers University, Piscataway, NJ, United States
- Rutgers-Robert Wood Johnson Medical School, Rutgers University, New Brunswick, NJ, United States
| | - Srujanesh Gunda
- School of Environmental and Biological Sciences, Rutgers University, New Brunswick, NJ, United States
| | - Berk Inan
- School of Environmental and Biological Sciences, Rutgers University, New Brunswick, NJ, United States
| | - Mijung Kwon
- Rutgers Cancer Institute of New Jersey, Rutgers University, New Brunswick, NJ, United States
| | - Steven K. Libutti
- Rutgers Cancer Institute of New Jersey, Rutgers University, New Brunswick, NJ, United States
| | - Prabhas V. Moghe
- Department of Biomedical Engineering, Rutgers University, Piscataway, NJ, United States
- Department of Chemical and Biochemical Engineering, Rutgers University, Piscataway, NJ, United States
| | - Nicola L. Francis
- Department of Biomedical Engineering, Rutgers University, Piscataway, NJ, United States
| | - Vidya Ganapathy
- Department of Biomedical Engineering, Rutgers University, Piscataway, NJ, United States
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15
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NGS Analysis of Liquid Biopsy (LB) and Formalin-Fixed Paraffin-Embedded (FFPE) Melanoma Samples Using Oncomine™ Pan-Cancer Cell-Free Assay. Genes (Basel) 2021; 12:genes12071080. [PMID: 34356096 PMCID: PMC8303399 DOI: 10.3390/genes12071080] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2021] [Revised: 07/14/2021] [Accepted: 07/15/2021] [Indexed: 12/12/2022] Open
Abstract
Next-generation sequencing (NGS) in liquid biopsies may contribute to the diagnosis, monitoring, and personalized therapy of cancer through the real-time detection of a tumor’s genetic profile. There are a few NGS platforms offering high-sensitivity sequencing of cell-free DNA (cfDNA) samples. The aim of this study was to evaluate the Ion AmpliSeq HD Technology for targeted sequencing of tumor and liquid biopsy samples from patients with fourth-stage melanoma. Sequencing of 30 samples (FFPE tumor and liquid biopsy) derived from 14 patients using the Oncomine™ Pan-Cancer Cell-Free Assay was performed. The analysis revealed high concordance between the qPCR and NGS results of the BRAF mutation in FFPE samples (91%), as well as between the FFPE and liquid biopsy samples (91%). The plasma-tumor concordance of the non-BRAF mutations was 28%. A total of 17 pathogenic variants in 14 genes (from 52-gene panel), including TP53, CTNNB1, CCND1, MET, MAP2K1, and GNAS, were identified, with the CTNNB1S45F variant being the most frequent. A positive correlation between the LDH level and cfDNA concentration as well as negative correlation between the LDH level and time to progression was confirmed in a 22-patient cohort. The analysis showed both the potential and limitations of liquid biopsy genetic profiling using HD technology and the Ion Torrent platform.
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Li S, Li X. Analysis of EGFR, KRAS, and PIK3CA gene mutation rates and clinical distribution in patients with different types of lung cancer. World J Surg Oncol 2021; 19:197. [PMID: 34217313 PMCID: PMC8254946 DOI: 10.1186/s12957-021-02315-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2020] [Accepted: 06/22/2021] [Indexed: 01/10/2023] Open
Abstract
Background To analyze and evaluate EGFR, KRAS, and PIK3CA gene mutation rates and clinical distribution in patients with different types of lung cancer Method A total of 221 lung cancer patients treated in our hospital between January 2016 and June 2019 were enrolled. Tissue and whole blood samples were collected and analyzed to determine the mutation status of EGFR, KRAS, and PIK3CA genes. The gene exon mutation rates were determined. Relevant clinical data, such as age, gender, tumor sample type, treatment method, pathologic type, and lung cancer stage were recorded and statistically analyzed. Results The EGFR gene mutation rates in exons E18-E21 were 2.3%, 17.6%, 3.6%, and 20.4%, respectively. E18, E19, and E20 mutations were commonly detected in adenosquamous carcinoma, and E21 mutations were commonly detected in adenocarcinoma. Mutations in exons E18-E21 were frequently detected in patients with lung cancer stages IA, IB, IIA, or IIB, respectively. The KRAS gene mutation rate in lung cancer patients in exon E2 was higher in whole blood and tissue samples than other exon mutations, while the KRAS gene mutation rate in exons E2 and E3 was significantly higher in patients with lung cancer stages IIB and IA, respectively. PIK3CA gene mutations in exons E9 and E20 occurred in patients < 60 years of age. Exon E9-positive mutations were more common in men or patients with squamous cell carcinoma, while exon E20-positive mutations were more common in females. Conclusion The EGFR, KRAS, and PIK3CA gene exon mutation rates differ and were shown to be correlated with different clinical indicators, which have significance in clinical treatment.
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Affiliation(s)
- Shuo Li
- Department of Thoracic Surgery, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, 710061, Shaanxi Province, China
| | - Xinju Li
- Department of Thoracic Surgery, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, 710061, Shaanxi Province, China.
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Kato R, Hayashi H, Sakai K, Suzuki S, Haratani K, Takahama T, Tanizaki J, Nonagase Y, Tanaka K, Yoshida T, Takeda M, Yonesaka K, Kaneda H, Nishio K, Nakagawa K. CAPP-seq analysis of circulating tumor DNA from patients with EGFR T790M-positive lung cancer after osimertinib. Int J Clin Oncol 2021; 26:1628-1639. [PMID: 34117553 DOI: 10.1007/s10147-021-01947-3] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2021] [Accepted: 05/25/2021] [Indexed: 01/16/2023]
Abstract
BACKGROUND We here applied cancer personalized profiling by deep sequencing (CAPP-seq) to analysis of circulating tumor DNA (ctDNA) to identify resistance mechanisms in osimertinib-treated patients with EGFR T790M-positive non-small cell lung cancer (NSCLC). METHODS The study included patients with EGFR activating mutation-positive advanced NSCLC who were positive for T790M in tumor tissue or plasma after previous treatment with an EGFR tyrosine kinase inhibitor, who received osimertinib at Kindai University Hospital between August 2014 and September 2017, and for whom plasma collected after progression on osimertinib was available. Clinical data were extracted from medical records. Patients with innate resistance to osimertinib were defined as those whose best response was progressive disease or stable disease for < 6 months, whereas patients with a complete or partial response or stable disease for > 6 months were considered as having acquired resistance. RESULTS We performed CAPP-seq for 20 patients at progression on osimertinib. Distinct patterns of genomic alterations were apparent in patients with innate versus acquired resistance. Mutations in PIK3CA, KRAS, or BRAF and copy number gain for EGFR, ERBB2, or MET were more common in patients with innate resistance than in those with acquired resistance. In addition, one patient who underwent a repeat biopsy was found to harbor the C797S mutation of EGFR after disease progression during osimertinib rechallenge, with this mutation not having been detected at the time of initial progression on osimertinib. CONCLUSIONS CAPP-seq analysis of ctDNA was able to identify potentially targetable genetic alterations in patients with osimertinib resistance.
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Affiliation(s)
- Ryoji Kato
- Department of Medical Oncology, Kindai University Faculty of Medicine, 377-2 Ohno-higashi, Osaka-Sayama, Osaka, 589-8511, Japan
| | - Hidetoshi Hayashi
- Department of Medical Oncology, Kindai University Faculty of Medicine, 377-2 Ohno-higashi, Osaka-Sayama, Osaka, 589-8511, Japan.
| | - Kazuko Sakai
- Department of Genome Biology, Kindai University Faculty of Medicine, 377-2 Ohno-higashi, Osaka-Sayama, Osaka, 589-8511, Japan
| | - Shinichiro Suzuki
- Department of Medical Oncology, Kindai University Faculty of Medicine, 377-2 Ohno-higashi, Osaka-Sayama, Osaka, 589-8511, Japan
| | - Koji Haratani
- Department of Medical Oncology, Kindai University Faculty of Medicine, 377-2 Ohno-higashi, Osaka-Sayama, Osaka, 589-8511, Japan
| | - Takayuki Takahama
- Department of Medical Oncology, Kindai University Faculty of Medicine, 377-2 Ohno-higashi, Osaka-Sayama, Osaka, 589-8511, Japan
- Department of Medical Oncology, Kindai University Nara Hospital, 1248-1 Otoda-cho, Ikoma, Nara, 630-0293, Japan
| | - Junko Tanizaki
- Department of Medical Oncology, Kindai University Faculty of Medicine, 377-2 Ohno-higashi, Osaka-Sayama, Osaka, 589-8511, Japan
- Department of Medical Oncology, Kishiwada City Hospital, 1001 Gakuhara-cho, Kishiwada-shi, Osaka, 596-8501, Japan
| | - Yoshikane Nonagase
- Department of Medical Oncology, Kindai University Faculty of Medicine, 377-2 Ohno-higashi, Osaka-Sayama, Osaka, 589-8511, Japan
- Department of Medical Oncology, Kishiwada City Hospital, 1001 Gakuhara-cho, Kishiwada-shi, Osaka, 596-8501, Japan
| | - Kaoru Tanaka
- Department of Medical Oncology, Kindai University Faculty of Medicine, 377-2 Ohno-higashi, Osaka-Sayama, Osaka, 589-8511, Japan
| | - Takeshi Yoshida
- Department of Medical Oncology, Kindai University Faculty of Medicine, 377-2 Ohno-higashi, Osaka-Sayama, Osaka, 589-8511, Japan
| | - Masayuki Takeda
- Department of Medical Oncology, Kindai University Faculty of Medicine, 377-2 Ohno-higashi, Osaka-Sayama, Osaka, 589-8511, Japan
| | - Kimio Yonesaka
- Department of Medical Oncology, Kindai University Faculty of Medicine, 377-2 Ohno-higashi, Osaka-Sayama, Osaka, 589-8511, Japan
| | - Hiroyasu Kaneda
- Department of Medical Oncology, Kindai University Faculty of Medicine, 377-2 Ohno-higashi, Osaka-Sayama, Osaka, 589-8511, Japan
- Department of Clinical Oncology, Graduate School of Medicine, Osaka City University, 1-4-3 Asahi-machi, Abeno-ku, Osaka City, Osaka, 545-8585, Japan
| | - Kazuto Nishio
- Department of Genome Biology, Kindai University Faculty of Medicine, 377-2 Ohno-higashi, Osaka-Sayama, Osaka, 589-8511, Japan
| | - Kazuhiko Nakagawa
- Department of Medical Oncology, Kindai University Faculty of Medicine, 377-2 Ohno-higashi, Osaka-Sayama, Osaka, 589-8511, Japan
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Pasini L, Notarangelo M, Vagheggini A, Burgio MA, Crinò L, Chiadini E, Prochowski AI, Delmonte A, Ulivi P, D'Agostino VG. Unveiling mutational dynamics in non-small cell lung cancer patients by quantitative EGFR profiling in vesicular RNA. Mol Oncol 2021; 15:2423-2438. [PMID: 33942501 PMCID: PMC8410558 DOI: 10.1002/1878-0261.12976] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2021] [Revised: 04/08/2021] [Accepted: 04/30/2021] [Indexed: 12/15/2022] Open
Abstract
The mutational status of the epidermal growth factor receptor (EGFR) guides the stratification of non‐small cell lung cancer (NSCLC) patients for treatment with tyrosine kinase inhibitors (TKIs). A liquid biopsy test on cell‐free DNA is recommended as a clinical decision‐supporting tool, although it has limited sensitivity. Here, we comparatively investigated the extracellular vesicle (EV)‐RNA as an independent source for multidimensional and longitudinal EGFR profiling in a cohort of 27 NSCLC patients. We introduced and validated a new rapid, highly specific EV‐RNA test with wild‐type (WT) and mutant‐sensitive probes (E746‐A750del, L858R, and T790M). We included a cohort of 20 NSCLC patients with EGFR WT tumor tissues and systematically performed molecular EV‐RNA and circulating tumor DNA analyses with clinical data statistics and biophysical profiles of EVs. At the single‐patient level, we detected variegated tumor heterogeneity dynamics supported by combinations of driver EGFR mutations. EV‐RNA‐based mutation analysis showed an unprecedented sensitivity of over 90%. The resistance‐associated mutation T790M frequently pre‐existed at baseline with a gained EV‐transcript copy number at progression, while the general mutational burden was mostly decreasing during the intermediate follow‐up. The biophysical profile of EVs and the quantitative assessment of T790M revealed an association with tumor size determined by the sum of the longest diameters in target lesions. Vesicular RNA provides a validated tool suitable for use in clinical practice to investigate the dynamics of common driver EGFR mutations in NSCLC patients receiving TKIs.
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Affiliation(s)
- Luigi Pasini
- Bioscience Laboratory, IRCCS Istituto Romagnolo per lo Studio dei Tumori (IRST) "Dino Amadori", Meldola, Italy
| | - Michela Notarangelo
- Laboratory of Biotechnology and Nanomedicine, Department of Cellular, Computational and Integrative Biology (CIBIO), University of Trento, Italy
| | - Alessandro Vagheggini
- Unit of Biostatistics, IRCCS Istituto Romagnolo per lo Studio dei Tumori (IRST) "Dino Amadori", Meldola, Italy
| | - Marco Angelo Burgio
- Medical Oncology Unit, IRCCS Istituto Romagnolo per lo Studio dei Tumori (IRST) "Dino Amadori", Meldola, Italy
| | - Lucio Crinò
- Medical Oncology Unit, IRCCS Istituto Romagnolo per lo Studio dei Tumori (IRST) "Dino Amadori", Meldola, Italy
| | - Elisa Chiadini
- Bioscience Laboratory, IRCCS Istituto Romagnolo per lo Studio dei Tumori (IRST) "Dino Amadori", Meldola, Italy
| | - Andrea Iamurri Prochowski
- Radiology Unit, IRCCS Istituto Romagnolo per lo Studio dei Tumori (IRST) "Dino Amadori", Meldola, Italy
| | - Angelo Delmonte
- Medical Oncology Unit, IRCCS Istituto Romagnolo per lo Studio dei Tumori (IRST) "Dino Amadori", Meldola, Italy
| | - Paola Ulivi
- Bioscience Laboratory, IRCCS Istituto Romagnolo per lo Studio dei Tumori (IRST) "Dino Amadori", Meldola, Italy
| | - Vito Giuseppe D'Agostino
- Laboratory of Biotechnology and Nanomedicine, Department of Cellular, Computational and Integrative Biology (CIBIO), University of Trento, Italy
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19
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Mokánszki A, Bádon ES, Mónus A, Tóth L, Bittner N, Méhes G. Cell-free DNA From Pleural Effusion Samples: Is It Right for Molecular Testing in Lung Adenocarcinoma? Pathol Oncol Res 2021; 27:613071. [PMID: 34257581 PMCID: PMC8262152 DOI: 10.3389/pore.2021.613071] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/01/2020] [Accepted: 02/19/2021] [Indexed: 12/03/2022]
Abstract
Pathogenic molecular features gained specific significance in therapeutic decisions in lung carcinoma in the past decade. Initial and follow up genetic testing requres appropriate amounts and quality of tumor derived DNA, but tumor sampling, especially for disease monitoring is generally limited. Further to the peripheral blood (PB), samples from pleural fluid, accumulating in diverse lung processes might serve as an alternative source for cell-free DNA (cfDNA) for genetic profiling. In our study, cfDNA isolated from the pleural effusion and from the PB, and genomic DNA (gDNA) obtained from tissue/cellular samples were analyzed and compared from altogether 65 patients with pulmonary disease, including 36 lung adenocarcinomas. The quantity of effusion cfDNA yield appeared to be significantly higher compared to that from simultaneously collected PB plasma (23.2 vs. 4.8 ng/μl, p < 0.05). Gene mutations could be safely demonstrated from the effusion cfDNA fraction obtained from adenocarcinoma patients, 3/36 EGFR, 9/36 KRAS and 1/36 BRAF gene variants were detected. In this series, 9/13 samples showed an effusion+/plasma-mutational status, while only 1/13 samples presented with the opposite findings (effusion-/plasma+). gDNA analysis from sediment cell blocks from the identical effusion sample was surprisingly ineffective for lung adenocarcinoma profiling due to the low DNA yield. In conclusion, the cell free supernatant of pleural effusions appears to concentrate cancer derived cfDNA and seems to be particularly suitable for serial genotyping of pulmonary adenocarcinoma.
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Affiliation(s)
- Attila Mokánszki
- Department of Pathology, Faculty of Medicine, University of Debrecen, Debrecen, Hungary
| | - Emese Sarolta Bádon
- Department of Pathology, Faculty of Medicine, University of Debrecen, Debrecen, Hungary
| | - Anikó Mónus
- Department of Pathology, Faculty of Medicine, University of Debrecen, Debrecen, Hungary
| | - László Tóth
- Department of Pathology, Faculty of Medicine, University of Debrecen, Debrecen, Hungary
| | - Nóra Bittner
- Department of Pulmonology, Faculty of Medicine, University of Debrecen, Debrecen, Hungary
| | - Gábor Méhes
- Department of Pathology, Faculty of Medicine, University of Debrecen, Debrecen, Hungary
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20
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Rodríguez J, Avila J, Rolfo C, Ruíz-Patiño A, Russo A, Ricaurte L, Ordóñez-Reyes C, Arrieta O, Zatarain-Barrón ZL, Recondo G, Cardona AF. When Tissue is an Issue the Liquid Biopsy is Nonissue: A Review. Oncol Ther 2021; 9:89-110. [PMID: 33689160 PMCID: PMC8140006 DOI: 10.1007/s40487-021-00144-6] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2020] [Accepted: 02/11/2021] [Indexed: 02/07/2023] Open
Abstract
Precision medicine has impacted the field of medical oncology by introducing personalized therapies, improving all measurable outcomes. This field, in turn, has expanded to obtaining and analyzing a vast and ever-increasing amount of genomic information. One technique currently applied is the liquid biopsy, which consists of detecting and isolating DNA and exosomes in cancer patients. Newly developed techniques have made it possible to use the liquid biopsy in a wide range of settings. However, challenges regarding the validation of its clinical utility exist because of a lack of standardization across different techniques and tumor types, confounder genomic information, lack of appropriate clinical trial designs, and a non-measured, and therefore not estimated, economic impact on population health. Nowadays, liquid biopsy is not routinely used, but ongoing research is increasing its popularity, and a new era in oncology is developing. Therefore, it is essential to have an in-depth understanding of the liquid biopsy technique. In this review, we summarize the leading techniques and liquid biopsy applications in cancer.
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Affiliation(s)
- July Rodríguez
- Foundation for Clinical and Applied Cancer Research (FICMAC), Bogota, Colombia
- Molecular Oncology and Biology Systems Research Group (Fox-G/ONCOLGroup), Universidad El Bosque, Bogota, Colombia
| | - Jenny Avila
- Foundation for Clinical and Applied Cancer Research (FICMAC), Bogota, Colombia
- Molecular Oncology and Biology Systems Research Group (Fox-G/ONCOLGroup), Universidad El Bosque, Bogota, Colombia
| | - Christian Rolfo
- Marlene and Stewart Greenebaum Comprehensive Cancer Center, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Alejandro Ruíz-Patiño
- Foundation for Clinical and Applied Cancer Research (FICMAC), Bogota, Colombia
- Molecular Oncology and Biology Systems Research Group (Fox-G/ONCOLGroup), Universidad El Bosque, Bogota, Colombia
| | - Alessandro Russo
- Medical Oncology Unit A.O. Papardo and Department of Human Pathology, University of Messina, Messina, Italy
| | - Luisa Ricaurte
- Foundation for Clinical and Applied Cancer Research (FICMAC), Bogota, Colombia
- Pathology Department, Mayo Clinic, Rochester, MN, USA
| | | | - Oscar Arrieta
- Thoracic Oncology Unit, Instituto Nacional de Cancerología (INCan), Mexico City, Mexico
| | | | - Gonzalo Recondo
- Thoracic Oncology Section, Centro de Educación Médica e Investigaciones Clínicas (CEMIC), Buenos Aires, Argentina
| | - Andrés F Cardona
- Foundation for Clinical and Applied Cancer Research (FICMAC), Bogota, Colombia.
- Molecular Oncology and Biology Systems Research Group (Fox-G/ONCOLGroup), Universidad El Bosque, Bogota, Colombia.
- Clinical and Traslational Oncology Group, Clinica del Country, Bogota, Colombia.
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21
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Martins I, Ribeiro IP, Jorge J, Gonçalves AC, Sarmento-Ribeiro AB, Melo JB, Carreira IM. Liquid Biopsies: Applications for Cancer Diagnosis and Monitoring. Genes (Basel) 2021; 12:349. [PMID: 33673461 PMCID: PMC7997281 DOI: 10.3390/genes12030349] [Citation(s) in RCA: 72] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2021] [Revised: 02/22/2021] [Accepted: 02/24/2021] [Indexed: 02/06/2023] Open
Abstract
The minimally-or non-invasive detection of circulating tumor-derived components in biofluids, such as blood, liquid biopsy is a revolutionary approach with significant potential for the management of cancer. Genomic and transcriptomic alterations can be accurately detected through liquid biopsies, which provide a more comprehensive characterization of the heterogeneous tumor profile than tissue biopsies alone. Liquid biopsies could assist diagnosis, prognosis, and treatment selection, and hold great potential to complement current surveilling strategies to monitor disease evolution and treatment response in real-time. In particular, these are able to detect minimal residual disease, to predict progression, and to identify mechanisms of resistance, allowing to re-orient treatment strategies in a timelier manner. In this review we gathered current knowledge regarding the role and potential of liquid biopsies for the diagnosis and follow-up of cancer patients. The presented findings emphasize the strengths of liquid biopsies, revealing their chance of improving the diagnosis and monitoring of several tumor types in the near future. However, despite growing evidence supporting their value as a management tool in oncology, some limitations still need to be overcome for their implementation in the routine clinical setting.
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Affiliation(s)
- Ivana Martins
- Cytogenetics and Genomics Laboratory, Faculty of Medicine University of Coimbra, Institute of Cellular and Molecular Biology, University of Coimbra, 3004-531 Coimbra, Portugal; (I.M.); (I.P.R.); (J.B.M.)
| | - Ilda Patrícia Ribeiro
- Cytogenetics and Genomics Laboratory, Faculty of Medicine University of Coimbra, Institute of Cellular and Molecular Biology, University of Coimbra, 3004-531 Coimbra, Portugal; (I.M.); (I.P.R.); (J.B.M.)
- Center of Investigation on Environment Genetics and Oncobiology (CIMAGO), Faculty of Medicine University of Coimbra, Coimbra Institute for Clinical and Biomedical Research (iCBR), University of Coimbra, 3004-531 Coimbra, Portugal; (J.J.); (A.C.G.); (A.B.S.-R.)
- Center for Innovative Biomedicine and Biotechnology (CIBB), University of Coimbra, 3004-531 Coimbra, Portugal
- Clinical Academic Center of Coimbra (CACC), 3004-531 Coimbra, Portugal
| | - Joana Jorge
- Center of Investigation on Environment Genetics and Oncobiology (CIMAGO), Faculty of Medicine University of Coimbra, Coimbra Institute for Clinical and Biomedical Research (iCBR), University of Coimbra, 3004-531 Coimbra, Portugal; (J.J.); (A.C.G.); (A.B.S.-R.)
- Center for Innovative Biomedicine and Biotechnology (CIBB), University of Coimbra, 3004-531 Coimbra, Portugal
- Clinical Academic Center of Coimbra (CACC), 3004-531 Coimbra, Portugal
- Laboratory of Oncobiology and Haematology and University Clinic of Haematology, Faculty of Medicine, University of Coimbra, 3004-531 Coimbra, Portugal
| | - Ana Cristina Gonçalves
- Center of Investigation on Environment Genetics and Oncobiology (CIMAGO), Faculty of Medicine University of Coimbra, Coimbra Institute for Clinical and Biomedical Research (iCBR), University of Coimbra, 3004-531 Coimbra, Portugal; (J.J.); (A.C.G.); (A.B.S.-R.)
- Center for Innovative Biomedicine and Biotechnology (CIBB), University of Coimbra, 3004-531 Coimbra, Portugal
- Clinical Academic Center of Coimbra (CACC), 3004-531 Coimbra, Portugal
- Laboratory of Oncobiology and Haematology and University Clinic of Haematology, Faculty of Medicine, University of Coimbra, 3004-531 Coimbra, Portugal
| | - Ana Bela Sarmento-Ribeiro
- Center of Investigation on Environment Genetics and Oncobiology (CIMAGO), Faculty of Medicine University of Coimbra, Coimbra Institute for Clinical and Biomedical Research (iCBR), University of Coimbra, 3004-531 Coimbra, Portugal; (J.J.); (A.C.G.); (A.B.S.-R.)
- Center for Innovative Biomedicine and Biotechnology (CIBB), University of Coimbra, 3004-531 Coimbra, Portugal
- Clinical Academic Center of Coimbra (CACC), 3004-531 Coimbra, Portugal
- Laboratory of Oncobiology and Haematology and University Clinic of Haematology, Faculty of Medicine, University of Coimbra, 3004-531 Coimbra, Portugal
- Clinical Haematology Department, Coimbra University Hospital Centre (CHUC), 3004-531 Coimbra, Portugal
| | - Joana Barbosa Melo
- Cytogenetics and Genomics Laboratory, Faculty of Medicine University of Coimbra, Institute of Cellular and Molecular Biology, University of Coimbra, 3004-531 Coimbra, Portugal; (I.M.); (I.P.R.); (J.B.M.)
- Center of Investigation on Environment Genetics and Oncobiology (CIMAGO), Faculty of Medicine University of Coimbra, Coimbra Institute for Clinical and Biomedical Research (iCBR), University of Coimbra, 3004-531 Coimbra, Portugal; (J.J.); (A.C.G.); (A.B.S.-R.)
- Center for Innovative Biomedicine and Biotechnology (CIBB), University of Coimbra, 3004-531 Coimbra, Portugal
- Clinical Academic Center of Coimbra (CACC), 3004-531 Coimbra, Portugal
| | - Isabel Marques Carreira
- Cytogenetics and Genomics Laboratory, Faculty of Medicine University of Coimbra, Institute of Cellular and Molecular Biology, University of Coimbra, 3004-531 Coimbra, Portugal; (I.M.); (I.P.R.); (J.B.M.)
- Center of Investigation on Environment Genetics and Oncobiology (CIMAGO), Faculty of Medicine University of Coimbra, Coimbra Institute for Clinical and Biomedical Research (iCBR), University of Coimbra, 3004-531 Coimbra, Portugal; (J.J.); (A.C.G.); (A.B.S.-R.)
- Center for Innovative Biomedicine and Biotechnology (CIBB), University of Coimbra, 3004-531 Coimbra, Portugal
- Clinical Academic Center of Coimbra (CACC), 3004-531 Coimbra, Portugal
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22
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Giménez-Capitán A, Bracht J, García JJ, Jordana-Ariza N, García B, Garzón M, Mayo-de-Las-Casas C, Viteri-Ramirez S, Martinez-Bueno A, Aguilar A, Sullivan IG, Johnson E, Huang CY, Gerlach JL, Warren S, Beechem JM, Teixidó C, Rosell R, Reguart N, Molina-Vila MA. Multiplex Detection of Clinically Relevant Mutations in Liquid Biopsies of Cancer Patients Using a Hybridization-Based Platform. Clin Chem 2021; 67:554-563. [PMID: 33439966 DOI: 10.1093/clinchem/hvaa248] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2020] [Accepted: 09/30/2020] [Indexed: 12/22/2022]
Abstract
BACKGROUND With the advent of precision oncology, liquid biopsies are quickly gaining acceptance in the clinical setting. However, in some cases, the amount of DNA isolated is insufficient for Next-Generation Sequencing (NGS) analysis. The nCounter platform could be an alternative, but it has never been explored for detection of clinically relevant alterations in fluids. METHODS Circulating-free DNA (cfDNA) was purified from blood, cerebrospinal fluid, and ascites of patients with cancer and analyzed with the nCounter 3 D Single Nucleotide Variant (SNV) Solid Tumor Panel, which allows for detection of 97 driver mutations in 24 genes. RESULTS Validation experiments revealed that the nCounter SNV panel could detect mutations at allelic fractions of 0.02-2% in samples with ≥5 pg mutant DNA/µL. In a retrospective analysis of 70 cfDNAs from patients with cancer, the panel successfully detected EGFR, KRAS, BRAF, PIK3CA, and NRAS mutations when compared with previous genotyping in the same liquid biopsies and paired tumor tissues [Cohen kappa of 0.96 (CI = 0.92-1.00) and 0.90 (CI = 0.74-1.00), respectively]. In a prospective study including 91 liquid biopsies from patients with different malignancies, 90 yielded valid results with the SNV panel and mutations in EGFR, KRAS, BRAF, PIK3CA, TP53, NFE2L2, CTNNB1, ALK, FBXW7, and PTEN were found. Finally, serial liquid biopsies from a patient with NSCLC revealed that the semiquantitative results of the mutation analysis by the SNV panel correlated with the evolution of the disease. CONCLUSIONS The nCounter platform requires less DNA than NGS and can be employed for routine mutation testing in liquid biopsies of patients with cancer.
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Affiliation(s)
- Ana Giménez-Capitán
- Pangaea Oncology, Laboratory of Oncology, Quirón Dexeus University Hospital, Barcelona, Spain
| | - Jillian Bracht
- Pangaea Oncology, Laboratory of Oncology, Quirón Dexeus University Hospital, Barcelona, Spain.,Universitat Autónoma de Barcelona, Barcelona, Spain
| | - Juan José García
- Dr Rosell Oncology Institute, Quirón Dexeus University Hospital, Barcelona, Spain
| | - Núria Jordana-Ariza
- Pangaea Oncology, Laboratory of Oncology, Quirón Dexeus University Hospital, Barcelona, Spain
| | - Beatriz García
- Pangaea Oncology, Laboratory of Oncology, Quirón Dexeus University Hospital, Barcelona, Spain
| | - Mónica Garzón
- Pangaea Oncology, Laboratory of Oncology, Quirón Dexeus University Hospital, Barcelona, Spain
| | - Clara Mayo-de-Las-Casas
- Pangaea Oncology, Laboratory of Oncology, Quirón Dexeus University Hospital, Barcelona, Spain
| | | | | | - Andrés Aguilar
- Dr Rosell Oncology Institute, Quirón Dexeus University Hospital, Barcelona, Spain
| | | | | | | | | | | | | | - Cristina Teixidó
- Department of Pathology, Thoracic Oncology Unit, Hospital Clínic, Barcelona, Spain.,Translational Genomics and Targeted Therapeutics in Solid Tumors, Institut d'Investigacions Biomèdiques August Pi i Sunyer, Barcelona, Spain
| | - Rafael Rosell
- Dr Rosell Oncology Institute, Quirón Dexeus University Hospital, Barcelona, Spain.,Cancer Biology and Precision Medicine Program, Catalán Institute of Oncology, Germans Trias i Pujol Health Sciences Institute and Hospital, Badalona, Barcelona, Spain
| | - Noemí Reguart
- Translational Genomics and Targeted Therapeutics in Solid Tumors, Institut d'Investigacions Biomèdiques August Pi i Sunyer, Barcelona, Spain.,Medical Oncology, Thoracic Oncology Unit, Hospital Clínic, Barcelona, Spain
| | - Miguel A Molina-Vila
- Pangaea Oncology, Laboratory of Oncology, Quirón Dexeus University Hospital, Barcelona, Spain
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23
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Danesi R, Fogli S, Indraccolo S, Del Re M, Dei Tos AP, Leoncini L, Antonuzzo L, Bonanno L, Guarneri V, Pierini A, Amunni G, Conte P. Druggable targets meet oncogenic drivers: opportunities and limitations of target-based classification of tumors and the role of Molecular Tumor Boards. ESMO Open 2021; 6:100040. [PMID: 33540286 PMCID: PMC7859305 DOI: 10.1016/j.esmoop.2020.100040] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2020] [Revised: 11/15/2020] [Accepted: 12/16/2020] [Indexed: 02/06/2023] Open
Abstract
The therapeutic landscape of cancer is changing rapidly due to the growing number of approved drugs capable of targeting specific genetic alterations. This aspect, together with the development of noninvasive methods for the assessment of somatic mutations in the peripheral blood of patients, generated a growing interest toward a new tumor-agnostic classification system based on ‘predictive’ biomarkers. The current review article discusses this emerging alternative approach to the classification of cancer and its implications for the selection of treatments. It is suggested that different types of cancers sharing the same molecular profiles could benefit from the same targeted drugs. Although recent clinical trials have demonstrated that this approach cannot be generalized, there are also specific examples that demonstrate the clinical utility of this alternative vision. In this rapidly evolving scenario, a multidisciplinary approach managed by institutional Molecular Tumor Boards is fundamental to interpret the biological and clinical relevance of genetic alterations and the complexity of their relationship with treatment response. The identification of oncogenic drivers offers the opportunity to develop target-specific drugs. The inhibition of crucial pathways realizes the principle of druggable target to exploit cancer vulnerability. The approval of new anticancer agents based on target-based concept represents a paradigm shift in cancer therapy. However, only few drugs have been approved so far on an agnostic basis and the concept of biomarker cannot be generalized. Tumor Molecular Boards will have an increasing role in the identification of new therapeutic options in selected patients.
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Affiliation(s)
- R Danesi
- Clinical Pharmacology and Pharmacogenetics Unit, Department of Clinical and Experimental Medicine, University of Pisa, Pisa, Italy
| | - S Fogli
- Clinical Pharmacology and Pharmacogenetics Unit, Department of Clinical and Experimental Medicine, University of Pisa, Pisa, Italy
| | - S Indraccolo
- Molecular Oncology Unit, Veneto Institute of Oncology IOV - IRCCS, Padua, Italy
| | - M Del Re
- Clinical Pharmacology and Pharmacogenetics Unit, Department of Clinical and Experimental Medicine, University of Pisa, Pisa, Italy
| | - A P Dei Tos
- Department of Medicine, School of Medicine, University of Padua, Padua, Italy
| | - L Leoncini
- Department of Medical Biotechnology, Anatomic Pathology Division, University of Siena, Siena, Italy
| | - L Antonuzzo
- Medical Oncology Unit, Careggi University Hospital, Florence, Italy
| | - L Bonanno
- Medical Oncology 2, Veneto Institute of Oncology IOV - IRCCS, Padua, Italy
| | - V Guarneri
- Medical Oncology 2, Veneto Institute of Oncology IOV - IRCCS, Padua, Italy; Department of Surgery, Oncology and Gastroenterology, University of Padua, Padua, Italy
| | - A Pierini
- Integrated Access, Roche, Monza, Italy
| | - G Amunni
- Institute for the Study, Prevention and Oncology Network (ISPRO), Florence, Italy.
| | - P Conte
- Medical Oncology 2, Veneto Institute of Oncology IOV - IRCCS, Padua, Italy; Department of Surgery, Oncology and Gastroenterology, University of Padua, Padua, Italy
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24
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Ma S, Shi M, Chen X, Wang Y, Yang Z, Lizaso A, Li M, Li H, Zhang L, Mao X, Xu X, Song Y. The prognostic value of longitudinal circulating tumor DNA profiling during osimertinib treatment. Transl Lung Cancer Res 2021; 10:326-339. [PMID: 33569316 PMCID: PMC7867761 DOI: 10.21037/tlcr-20-371] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Background Serial profiling of circulating tumor DNA (ctDNA) could reflect dynamic molecular changes in response to treatment and potentially predict impending disease progression (PD). Herein, we investigated the molecular factors and dynamic changes in ctDNA that can serve as predictors of survival outcomes of patients with epidermal growth factor receptor (EGFR)-mutated advanced non-small cell lung cancer (NSCLC) who received osimertinib therapy after progression from prior EGFR inhibitor regimen. Methods Capture-based targeted sequencing was performed on the baseline and longitudinal plasma samples collected from 72 and 57 patients, respectively, using a 168-gene panel. Results Analysis revealed that inferior overall survival (OS) was correlated with various baseline molecular features including high allelic fraction (AF) of EGFR sensitizing mutations (P=0.045), high maximum AF (maxAF, P=0.060), or harboring concurrent genomic alterations such as copy number amplification (CNA) in EGFR (P=0.026) or in other genes (P=0.026), and genes involved in the cell cycle (P=0.004) or TP53 signaling pathway (P=0.032). Moreover, ctDNA clearance at first follow-up after 6 weeks of osimertinib therapy was correlated with significantly longer progression-free survival (PFS) (P=0.022) and OS (P=0.009). Molecular PD, reflected by the emergence of new mutation or increased AF of existing mutations, was detected at an average lead time of 2.5 months prior to radiological PD. Patients with molecular PD were more likely to harbor CNA (P=0.035) and TP53 mutations (P=0.023). Conclusions Molecular factors derived from serial ctDNA profiling can serve as predictive and prognostic markers, which could allow early detection of PD, preceding imaging modalities by 2.5 months.
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Affiliation(s)
- Shenglin Ma
- Department of Thoracic Oncology, Key Laboratory of Clinical Cancer Pharmacology and Toxicology Research of Zhejiang Province, Affiliated Hangzhou First People's Hospital, Zhejiang University School of Medicine, Zhejiang University Cancer Center, Hangzhou, China
| | - Meiqi Shi
- Department of Medical Oncology, Affiliated Cancer Hospital of Nanjing Medical University, Jiangsu Cancer Hospital and Jiangsu Institute of Cancer Research, Nanjing, China
| | - Xueqin Chen
- Department of Thoracic Oncology, Key Laboratory of Clinical Cancer Pharmacology and Toxicology Research of Zhejiang Province, Affiliated Hangzhou First People's Hospital, Zhejiang University School of Medicine, Zhejiang University Cancer Center, Hangzhou, China
| | - Yong Wang
- Department of Medical Oncology, Anhui Provincial Hospital, Hefei, China
| | - Zhenhua Yang
- Department of Respiratory Medicine, Nanjing Hospital Affiliated to Nanjing Medical University, Nanjing, China
| | | | - Min Li
- Burning Rock Biotech, Guangzhou, China
| | - Haiyan Li
- Burning Rock Biotech, Guangzhou, China
| | - Lu Zhang
- Burning Rock Biotech, Guangzhou, China
| | - Xinru Mao
- Burning Rock Biotech, Guangzhou, China
| | - Xingxiang Xu
- Department of Respiratory Medicine, North Jiangsu General Hospital, Yangzhou, China
| | - Yong Song
- Department of Respiratory Medicine, Jinling Hospital, Nanjing University School of Medicine, Nanjing, China
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25
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Chromosomal Junction Detection from Whole-Genome Sequencing on Formalin-Fixed, Paraffin-Embedded Tumors. J Mol Diagn 2020; 23:375-388. [PMID: 33387698 DOI: 10.1016/j.jmoldx.2020.12.006] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2020] [Revised: 11/20/2020] [Accepted: 12/14/2020] [Indexed: 11/22/2022] Open
Abstract
DNA junctions (DNAJs) frequently impact clinically relevant genes in tumors and are important for diagnostic and therapeutic purposes. Although routinely screened through fluorescence in situ hybridization assays, such testing only allows the interrogation of single-gene regions or known fusion partners. Comprehensive assessment of DNAJs present across the entire genome can only be determined from whole-genome sequencing. Structural variance analysis from whole-genome paired-end sequencing data is, however, frequently restricted to copy number changes without DNAJ detection. Through optimized whole-genome sequencing and specialized bioinformatics algorithms, complete structural variance analysis is reported, including DNAJs, from formalin-fixed DNA. Selective library assembly from larger fragments (>500 bp) and economical sequencing depths (300 to 400 million reads) provide representative genomic coverage profiles and increased allelic coverage to levels compatible with DNAJ calling (40× to 60×). Although consistently fragmented, more recently formalin-fixed, specimens (<2 years' storage) revealed consistent populations of larger DNA fragments. Optimized bioinformatics efficiently detected >90% of DNAJs in two prostate tumors (approximately 60% tumor) previously analyzed by mate-pair sequencing on fresh frozen tissue, with evidence of at least one spanning-read in 99% of DNAJs. Rigorous masking with data from unrelated formalin-fixed tissue progressively eliminated many false-positive DNAJs, without loss of true positives, resulting in low numbers of false-positive passing current filters. This methodology enables more comprehensive clinical genomics testing on formalin-fixed clinical specimens.
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26
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Kumar A, Rocke JPJ, Kumar BN. Evolving treatments in high-risk neuroblastoma. Expert Opin Orphan Drugs 2020. [DOI: 10.1080/21678707.2020.1865918] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Affiliation(s)
- Abhinav Kumar
- Division of Medicine, University College London Medical School, London, UK
| | - John P J Rocke
- ENT Department, Royal Albert Edward Infirmary, Wigan, UK
| | - B Nirmal Kumar
- ENT Department, Wrightington, Wigan & Leigh Teaching NHS, Wigan, UK
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27
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Liao H, Huang W, Pei W, Li H. Detection of ESR1 Mutations Based on Liquid Biopsy in Estrogen Receptor-Positive Metastatic Breast Cancer: Clinical Impacts and Prospects. Front Oncol 2020; 10:587671. [PMID: 33384956 PMCID: PMC7770162 DOI: 10.3389/fonc.2020.587671] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2020] [Accepted: 11/17/2020] [Indexed: 12/19/2022] Open
Abstract
Endocrine therapy is the main treatment option for estrogen receptor-positive (ER+) breast cancer (BC). Compared with other clinical subtypes, ER+ BC patients usually have a more favorable prognosis. However, almost all ER+ BCpatients develop endocrine resistance and disease progression eventually. A large number of studies based on liquid biopsy suggest that ESR1 mutations may play a key role in this process. For patients with ER+ metastatic BC (MBC), ESR1 is an important prognostic factor and may associate with the resistance to endocrine therapy, like aromatase inhibitors. The advances of sequencing technologies allow us to conduct longitudinal monitoring of disease and unveil the clinical implications of each ESR1 sub-clone in ER+ MBC. Moreover, since the ESR1-related endocrine resistance has not been fully addressed by existing agents, more potent cornerstone drugs should be developed as soon as possible. Herein, we reviewed the recent progress of detecting ESR1 mutations based on liquid biopsy and different sequencing technologies in ER+ MBC and discussed its clinical impacts and prospects.
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Affiliation(s)
- Hao Liao
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Department of Breast Oncology, Peking University Cancer Hospital and Institute, Beijing, China
| | - Wenfa Huang
- Department of Hematology-Oncology, International Cancer Center, Shenzhen University General Hospital, Shenzhen University Health Science Center, Shenzhen, China
| | - Wendi Pei
- Center for Reproductive Medicine, Department of Obstetrics and Gynecology, Beijing Key Laboratory of Reproductive Endocrinology and Assisted Reproductive Technology and Key Laboratory of Assisted Reproduction, Ministry of Education, Peking University Third Hospital, Beijing, China
| | - Huiping Li
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Department of Breast Oncology, Peking University Cancer Hospital and Institute, Beijing, China
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Dagogo-Jack I, Ritterhouse LL. The role of plasma genotyping in ALK- and ROS1-rearranged lung cancer. Transl Lung Cancer Res 2020; 9:2557-2570. [PMID: 33489818 PMCID: PMC7815348 DOI: 10.21037/tlcr-2019-cnsclc-09] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2020] [Accepted: 09/11/2020] [Indexed: 01/04/2023]
Abstract
Several subsets of non-small cell lung cancer (NSCLC) are defined by the presence of oncogenic rearrangements that result in constitutive activation of a chimeric fusion protein. In NSCLCs that harbor ALK or ROS1 rearrangements, aberrant signaling from these fusion proteins can be overcome by potent and selective tyrosine kinase inhibitors (TKIs). These targeted therapies can induce durable responses and significantly improve prognostic outcomes. Historically, analysis of tissue biopsies was the primary approach to identifying key activating rearrangements. In recent years, non-invasive genotyping of tumor-derived nucleic acids in the circulation has gained ground as a strategy for determining the genetic composition of NSCLCs at diagnosis and throughout the disease course based on prospective and retrospective studies validating the utility of plasma analysis in heterogeneous populations of patients with metastatic NSCLC. Notably, these practice-changing studies predominantly included patients with NSCLCs with oncogenic mutations. Compared to other types of molecular alterations such as mutations and insertions/deletions, oncogenic rearrangements are more complex as they incorporate a variety of fusion partners and diverse breakpoints. Because of this structural complexity, detecting oncogenic rearrangements with plasma assays is more challenging than identifying disease-defining point mutations. In this review, we discuss technical aspects of plasma genotyping strategies and summarize findings from studies exploring plasma genotyping (including ctDNA analysis and profiling of nucleic acids contained in other plasma components) in two rearrangement-driven NSCLC subsets (ALK-rearranged and ROS1-rearranged).
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Affiliation(s)
- Ibiayi Dagogo-Jack
- Department of Medicine and Cancer Center, Massachusetts General Hospital, Boston, MA, USA
- Harvard Medical School, Massachusetts General Hospital, Boston, MA, USA
| | - Lauren L. Ritterhouse
- Harvard Medical School, Massachusetts General Hospital, Boston, MA, USA
- Department of Pathology, Massachusetts General Hospital, Boston, MA, USA
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29
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Navarro S, Cuatrecasas M, Hernández-Losa J, Landolfi S, Musulén E, Ramón Y Cajal S, García-Carbonero R, García-Foncillas J, Pérez-Segura P, Salazar R, Vera R, García-Alfonso P. [Update of the recommendations for the determination of biomarkers in colorectal carcinoma. National Consensus of the Spanish Society of Medical Oncology and the Spanish Society of Pathology]. REVISTA ESPAÑOLA DE PATOLOGÍA : PUBLICACIÓN OFICIAL DE LA SOCIEDAD ESPAÑOLA DE ANATOMÍA PATOLÓGICA Y DE LA SOCIEDAD ESPAÑOLA DE CITOLOGÍA 2020; 54:41-54. [PMID: 33455693 DOI: 10.1016/j.patol.2020.07.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/04/2020] [Revised: 07/02/2020] [Accepted: 07/26/2020] [Indexed: 11/25/2022]
Abstract
This update of the consensus of the Spanish Society of Medical Oncology (Sociedad Española de Oncología Médica - SEOM) and the Spanish Society of Pathology (Sociedad Española de Anatomía Patológica - SEAP), reviews the advances in the analysis of biomarkers in advanced colorectal cancer (CRC) as well as susceptibility markers of hereditary CRC and molecular biomarkers of localized CRC. Recently published information on the essential determination of KRAS, NRAS and BRAF mutations and the possible benefits of determining the amplification of human epidermal growth factor receptor 2 (HER2), the expression of proteins in the DNA repair pathway and the study of NTRK fusions are also evaluated. From a pathological point of view, the importance of analysing the tumour budding and poorly differentiated clusters and its prognostic value in CRC is reviewed, as well as the impact of molecular lymph node analysis on lymph node staging in CRC. The incorporation of pan-genomic technologies, such as next-generation sequencing (NGS) and liquid biopsy in the clinical management of patients with CRC is also outlined. All these aspects are developed in this guide which, like the previous one, will be revised when necessary in the future.
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Affiliation(s)
- Samuel Navarro
- Departamento de Patología, Universidad de Valencia, Hospital Clínico Universitario de Valencia, CIBERONC, Valencia, España.
| | | | - Javier Hernández-Losa
- Departamento de Patología, Hospital Universitario Vall d'Hebron, CIBERONC, Barcelona, España
| | - Stefania Landolfi
- Departamento de Patología, Hospital Universitario Vall d'Hebron, CIBERONC, Barcelona, España
| | - Eva Musulén
- Departamento de Patología, Hospital Universitari General de Catalunya, Grupo Quirónsalud, Sant Cugat del Vallès, España; Grupo de Epigenética del Cáncer, Institut de Recerca contra la Leucèmia Josep Carreras, Badalona, España
| | - Santiago Ramón Y Cajal
- Departamento de Patología, Hospital Universitario Vall d'Hebron, CIBERONC, Barcelona, España
| | - Rocío García-Carbonero
- Departamento de Oncología Médica, Hospital Universitario 12 de Octubre, Instituto de Investigación Sanitaria Hospital 12 de Octubre (imas12), UCM, CNIO, CIBERONC, Madrid, España
| | - Jesús García-Foncillas
- Departamento de Oncología, Hospital Universitario Fundación Jiménez Díaz, Universidad Autónoma de Madrid, Madrid, España
| | - Pedro Pérez-Segura
- Departamento de Oncología Médica, Hospital Clínico Universitario San Carlos, CIBERONC, Madrid, España
| | - Ramón Salazar
- Departamento de Oncología Médica, ICO ĹHospitalet, Oncobell Program (IDIBELL), CIBERONC, Hospitalet de Llobregat, España
| | - Ruth Vera
- Departamento de Oncología Médica, Complejo Hospitalario de Navarra, Navarrabiomed, IDISNA, Pamplona, España
| | - Pilar García-Alfonso
- Departamento de Oncología Médica, Hospital General Universitario Gregorio Marañón, Madrid, España
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30
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Internò V, Tucci M, Pezzicoli G, Silvestris F, Porta C, Mannavola F. Liquid Biopsy as a Tool Exploring in Real-Time Both Genomic Perturbation and Resistance to EGFR Antagonists in Colorectal Cancer. Front Oncol 2020; 10:581130. [PMID: 33102237 PMCID: PMC7546030 DOI: 10.3389/fonc.2020.581130] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2020] [Accepted: 09/07/2020] [Indexed: 12/13/2022] Open
Abstract
The treatment of metastatic colorectal cancer (mCRC) has improved since the introduction of the epithelial growth factor receptor (EGFR) inhibitors as cetuximab and panitumumab. However, only patients with peculiar genomic profiles benefit from these targeting therapies. In fact, the molecular integrity of RAS genes is a predominant factor conditioning both primary and acquired resistance in non-responders although additional molecular derangements induced by selective anti-EGFR pressure may concur to the failure of those disease treatment, liquid biopsy (LB) appears as a surrogate of tissue biopsy, provides the genomic information to reveal tumor resistance to anti-EGFR agents, the detection of minimal residual disease before adjuvant therapies, and the discovery of tumor molecular status suitable for rechallenging treatments with EGFR antagonists. LB investigates circulating tumor cells (CTCs), cell-free tumor DNA (ctDNA), and tumor-derived exosomes. In mCRC, ctDNA analysis has been demonstrated as a useful method in the mutational tracking of defined genes as well as on tumor burden and detection of molecular alterations driving the resistance to anti-EGFR targeting treatments. However, despite their efficiency in molecular diagnosis and prognostic evaluation of mCRC, the affordability of these procedures is prevalently restricted to research centers, and the lack of consensus validation prevents their translation to clinical practice. Here, we revisit the major mechanisms responsible for resistance to EGFR blockade and review the different methods of LB potentially useful for treatment options in mCRC.
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Affiliation(s)
- Valeria Internò
- Department of Biomedical Sciences and Clinical Oncology, University of Bari Aldo Moro, Bari, Italy
| | - Marco Tucci
- Department of Biomedical Sciences and Clinical Oncology, University of Bari Aldo Moro, Bari, Italy.,National Cancer Research Centre, Istituto Tumori Bari "Giovanni Paolo II", Bari, Italy
| | - Gaetano Pezzicoli
- Department of Biomedical Sciences and Clinical Oncology, University of Bari Aldo Moro, Bari, Italy
| | - Franco Silvestris
- Department of Biomedical Sciences and Clinical Oncology, University of Bari Aldo Moro, Bari, Italy
| | - Camillo Porta
- Department of Biomedical Sciences and Clinical Oncology, University of Bari Aldo Moro, Bari, Italy
| | - Francesco Mannavola
- Department of Biomedical Sciences and Clinical Oncology, University of Bari Aldo Moro, Bari, Italy
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31
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Ravaioli S, Limarzi F, Tumedei MM, Palleschi M, Maltoni R, Bravaccini S. Are we ready to use TMB in breast cancer clinical practice? Cancer Immunol Immunother 2020; 69:1943-1945. [PMID: 32725361 DOI: 10.1007/s00262-020-02682-w] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2020] [Accepted: 07/22/2020] [Indexed: 12/13/2022]
Abstract
We discussed the potentialities of tumor mutation burden (TMB) as a predictive marker for immunotherapy in breast cancer, also highlighting the limits that have hindered its introduction in the clinical practice. Although some studies have demonstrated the possibility to select patients more responsive to immune-checkpoint inhibitors by evaluating TMB, some issues emerged regarding the complexity of the methodologies for its determination, the costs of the analysis, and the necessity to improve the TMB determination with that of neoantigen identification.
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Affiliation(s)
- Sara Ravaioli
- Istituto Scientifico Romagnolo per lo Studio e la Cura dei Tumori (IRST) IRCCS, Via P. Maroncelli 40, 47014, Meldola, FC, Italy
| | - Francesco Limarzi
- Istituto Scientifico Romagnolo per lo Studio e la Cura dei Tumori (IRST) IRCCS, Via P. Maroncelli 40, 47014, Meldola, FC, Italy
| | - Maria Maddalena Tumedei
- Istituto Scientifico Romagnolo per lo Studio e la Cura dei Tumori (IRST) IRCCS, Via P. Maroncelli 40, 47014, Meldola, FC, Italy
| | - Michela Palleschi
- Istituto Scientifico Romagnolo per lo Studio e la Cura dei Tumori (IRST) IRCCS, Via P. Maroncelli 40, 47014, Meldola, FC, Italy
| | - Roberta Maltoni
- Istituto Scientifico Romagnolo per lo Studio e la Cura dei Tumori (IRST) IRCCS, Via P. Maroncelli 40, 47014, Meldola, FC, Italy
| | - Sara Bravaccini
- Istituto Scientifico Romagnolo per lo Studio e la Cura dei Tumori (IRST) IRCCS, Via P. Maroncelli 40, 47014, Meldola, FC, Italy.
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32
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Limited Practical Utility of Liquid Biopsy in the Treated Patients with Advanced Breast Cancer. Diagnostics (Basel) 2020; 10:diagnostics10080523. [PMID: 32731384 PMCID: PMC7460238 DOI: 10.3390/diagnostics10080523] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2020] [Accepted: 07/24/2020] [Indexed: 12/16/2022] Open
Abstract
Recently, liquid biopsy has emerged as a tool to monitor oncologic disease progression and the effects of treatment. In this study we aimed to determine the clinical utility of liquid biopsy relative to conventional oncological post-treatment surveillance. Plasma cell-free (cf) DNA was collected from six healthy women and 37 patients with breast cancer (18 and 19 with stage III and IV tumors, respectively). CfDNA was assessed using the Oncomine Pan-Cancer Cell-Free Assay. In cfDNA samples from patients with BC, 1112 variants were identified, with only a few recurrent or hotspot mutations within specific regions of cancer genes. Of 65 potentially pathogenic variants detected in tumors, only 19 were also discovered in at least one blood sample. The allele frequencies of detected variants (VAFs) were <1% in cfDNA from all controls and patients with stage III BC, and 24/85 (28.2%) variants had VAFs > 1% in only 8 of 25 (32%) patients with stage IV BC. Copy number variations (CNVs) spanning CDK4, MET, FGFR1, FGFR2, ERBB2, MYC, and CCND3 were found in 1 of 12 (8%) and 8 of 25 (32%) patients with stage III and IV tumors, respectively. In healthy controls and patients without BC progression after treatment, VAFs were <1%, while in patients with metastatic disease and/or more advanced genomic alterations, VAFs > 1% and/or CNV were detected in approximately 30%. Therefore, most patients with stage IV BC could not be distinguished from those with stage III disease following therapy, based on liquid biopsy results.
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33
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Belli C, Anand S, Gainor JF, Penault-Llorca F, Subbiah V, Drilon A, Andrè F, Curigliano G. Progresses Toward Precision Medicine in RET-altered Solid Tumors. Clin Cancer Res 2020; 26:6102-6111. [PMID: 32665298 DOI: 10.1158/1078-0432.ccr-20-1587] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2020] [Revised: 06/08/2020] [Accepted: 07/10/2020] [Indexed: 11/16/2022]
Abstract
RET (rearranged during transfection) gene encodes a receptor tyrosine kinase essential for many physiologic functions, but RET aberrations are involved in many pathologies. While RET loss-of-function mutations are associated with congenital disorders like Hirschsprung disease and CAKUT, RET gain-of-function mutations and rearrangements are critical drivers of tumor growth and proliferation in many different cancers. RET-altered (RET+ ) tumors have been hitherto targeted with multikinase inhibitors (MKI) having anti-RET activities, but they inhibit other kinase targets more potently and show limited clinical activities. The lack of target specificity and consequently increased side effects, responsible for dose reduction and drug discontinuation, are critical limitations of MKIs in the clinics. New selective RET inhibitors, selpercatinib and pralsetinib, are showing promising activities, improved response rates, and more favorable toxicity profiles in early clinical trials. This review critically discusses the oncogenic activation of RET and its role in different kinds of tumors, clinical features of RET+ tumors, clinically actionable genetic RET alterations and their diagnosis, and the available data and results of nonselective and selective targeting of RET.
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Affiliation(s)
- Carmen Belli
- Division of Early Drug Development for Innovative Therapies, European Institute of Oncology IRCCS, Milan, Italy
| | - Santosh Anand
- Department of Genetic Medicine and Development (GEDEV), Faculty of Medicine, University of Geneva Medical School, Geneva, Switzerland.,Department of Informatics, Systems and Communications (DISCo), University of Milano-Bicocca, Milan, Italy
| | | | - Frederique Penault-Llorca
- Department of Biopathology, Centre Jean Perrin and University Clermont Auvergne/INSERM U1240, Clermont-Ferrand, France
| | - Vivek Subbiah
- The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Alexander Drilon
- Division of Solid Tumor Oncology, Department of Medicine, Memorial Sloan Kettering Cancer Center, Weill Cornell Medical College, New York, New York.,Department of Medicine, Memorial Sloan Kettering Cancer Center, Weill Cornell Medical College, New York, New York
| | | | - Giuseppe Curigliano
- Division of Early Drug Development for Innovative Therapies, European Institute of Oncology IRCCS, Milan, Italy. .,Department of Oncology and Hemato-Oncology, University of Milan, Milan, Italy
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34
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Origin of circulating free DNA in patients with lung cancer. PLoS One 2020; 15:e0235611. [PMID: 32634139 PMCID: PMC7340299 DOI: 10.1371/journal.pone.0235611] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2020] [Accepted: 06/19/2020] [Indexed: 12/15/2022] Open
Abstract
Liquid biopsy has become widely applied in clinical medicine along with the progress in innovative technologies, such as next generation sequencing, but the origin of circulating tumor DNA (ctDNA) has not yet been precisely established. We reported bimodal peaks of long fragment circulating free DNA (cfDNA) of 5 kb and short fragment cfDNA of 170 bp in patients with advanced lung cancer, and both contained ctDNA. In this paper, we demonstrate that the total amount of cfDNA is higher when patients with lung cancer have extrathoracic metastases, and the amount of long fragment cfDNA is significantly higher in those patients. To investigate the origin of long fragment cfDNA, conditioned media isolated from lung cancer cell lines was fractionated. Long fragment cfDNA was found concomitant with extracellular vesicles (EVs), but short fragment cfDNA was not observed in any fractions. However, in peripheral blood from a metastatic animal model both fragments were detected even with those same lung cancer cell lines. In human plasma samples, long fragment cfDNA was observed in the same fraction as that from conditioned media, and short fragment cfDNA existed in the supernatant after centrifugation at 100,000g. Concentration of ctDNA in the supernatant was two times higher than that in plasma isolated by the conventional procedure. Long fragment cfDNA associated with tumor progression might therefore be released into peripheral blood, and it is possible that the long fragment cfDNA escapes degradation by co-existing with EVs. Examination of the biological characteristics of long fragment cfDNA is a logical subject of further investigation.
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35
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Tao Z, Li T, Feng Z, Liu C, Shao Y, Zhu M, Gong C, Wang B, Cao J, Wang L, Du Y, Lizaso A, Li B, Zhang J, Hu X. Characterizations of Cancer Gene Mutations in Chinese Metastatic Breast Cancer Patients. Front Oncol 2020; 10:1023. [PMID: 32695676 PMCID: PMC7338574 DOI: 10.3389/fonc.2020.01023] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2019] [Accepted: 05/22/2020] [Indexed: 12/20/2022] Open
Abstract
Background: Breast cancer (BC) is a type of disease with high heterogeneity. Molecular profiling, by revealing the intrinsic nature of its various subtypes, has extensively improved the therapeutic management of BC patients. However, the genomic mutation landscape of Chinese metastatic BC has not been fully explored. Methods: Matched plasma and mononuclear cells from 290 Chinese women with metastatic BC were sequenced using either of the two commercially-available panels consisting of 520 cancer-related and 108 BC-related genes. Both panels cover the same critical regions of 91 genes. The circulating tumor DNA mutation profile from our cohort was then compared with publicly-available metastatic BC datasets from Memorial Sloan Kettering Cancer Center (MSKCC) and Pan-cancer analysis of whole genomes (PCAWG). Results: A total of 1,201 mutations spanning 91 genes were detected from 234 patients, resulting in a mutation detection rate of 80.7%. TP53 (64.1%) was the gene with highest mutation frequency, followed by PIK3CA (31%), PTEN (11%), and RB1 (10%). Copy number amplifications (CNAs) in MYC (14.1%), FGFR1 (13.3%), CCND1 (6.6%), FGF3 (6.6%), FGF4 (6.2%) and FGF19 (6.2%) were also detected from our cohort. TP53 mutations were significantly more frequent among triple negative BC (TNBC), HR-/HER2+, and HR+/HER2+ BC, while less common in HR+/HER2- (P < 0.01). Meanwhile, PIK3CA mutations were significantly more frequent among HR+/HER2+, HR+/HER2-, and HR-/HER2+ BC, while less common in TNBC (P < 0.01). Pathogenic or likely pathogenic BRCA1/2 germline mutations were detected in 5.9% of the cohort and 4.4% in TNBC subgroup. Maximum allelic fraction (maxAF) of TP53, RB1, and PIK3CA mutations were associated with multiple organ metastasis. Patients with PIK3CA, PTEN, and RB1 mutation were more likely to have liver metastasis (P < 0.02). Compared with MSKCC and PCAWG dataset, Chinese patients had observably difference in genetic variation rates in different molecular subtypes (TNBC: TP53 73.0 vs. 91.5%, P < 0.001; PIK3CA 21.2 vs. 13.2%, P = 0.061; HR+/HER2-: FGFR1 3.3 vs. 0.7%, P = 0.035; TP 53 46.2 vs. 27.7%, P < 0.001; RB1 6.6 vs. 2.7%, P = 0.046; CDKN2A 7.7 vs. 1.0%, P < 0.001; PIK3CA 30.8 vs. 44.2%, P = 0.012; CDH1 1.1 vs. 18.2%, P < 0.001; GATA3 7.7 vs. 17.2%, P = 0.02). Conclusions: A distinct gene mutation profile was elucidated in Chinese women with metastatic BC, justifying further research. Liquid biopsy provides a quick, real-time, and minimally invasive tool for future clinical trial and routine practice.
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Affiliation(s)
- Zhonghua Tao
- Department of Medical Oncology, Fudan University Shanghai Cancer Center, Shanghai, China.,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Ting Li
- Department of Medical Oncology, Fudan University Shanghai Cancer Center, Shanghai, China.,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Zhe Feng
- Department of Medical Oncology, Fudan University Shanghai Cancer Center, Shanghai, China.,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Chang Liu
- Department of Medical Oncology, Fudan University Shanghai Cancer Center, Shanghai, China.,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Yilin Shao
- Department of Medical Oncology, Fudan University Shanghai Cancer Center, Shanghai, China.,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Mingyu Zhu
- Department of Medical Oncology, Fudan University Shanghai Cancer Center, Shanghai, China.,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Chengcheng Gong
- Department of Medical Oncology, Fudan University Shanghai Cancer Center, Shanghai, China.,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Biyun Wang
- Department of Medical Oncology, Fudan University Shanghai Cancer Center, Shanghai, China.,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Jun Cao
- Department of Medical Oncology, Fudan University Shanghai Cancer Center, Shanghai, China.,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Leipin Wang
- Department of Medical Oncology, Fudan University Shanghai Cancer Center, Shanghai, China.,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Yiqun Du
- Department of Medical Oncology, Fudan University Shanghai Cancer Center, Shanghai, China.,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | | | - Bing Li
- Burning Rock Biotech, Guangzhou, China
| | - Jian Zhang
- Department of Medical Oncology, Fudan University Shanghai Cancer Center, Shanghai, China.,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Xichun Hu
- Department of Medical Oncology, Fudan University Shanghai Cancer Center, Shanghai, China.,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
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36
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Wadowska K, Bil-Lula I, Trembecki Ł, Śliwińska-Mossoń M. Genetic Markers in Lung Cancer Diagnosis: A Review. Int J Mol Sci 2020; 21:E4569. [PMID: 32604993 PMCID: PMC7369725 DOI: 10.3390/ijms21134569] [Citation(s) in RCA: 103] [Impact Index Per Article: 25.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2020] [Revised: 06/19/2020] [Accepted: 06/25/2020] [Indexed: 12/14/2022] Open
Abstract
Lung cancer is the most often diagnosed cancer in the world and the most frequent cause of cancer death. The prognosis for lung cancer is relatively poor and 75% of patients are diagnosed at its advanced stage. The currently used diagnostic tools are not sensitive enough and do not enable diagnosis at the early stage of the disease. Therefore, searching for new methods of early and accurate diagnosis of lung cancer is crucial for its effective treatment. Lung cancer is the result of multistage carcinogenesis with gradually increasing genetic and epigenetic changes. Screening for the characteristic genetic markers could enable the diagnosis of lung cancer at its early stage. The aim of this review was the summarization of both the preclinical and clinical approaches in the genetic diagnostics of lung cancer. The advancement of molecular strategies and analytic platforms makes it possible to analyze the genome changes leading to cancer development-i.e., the potential biomarkers of lung cancer. In the reviewed studies, the diagnostic values of microsatellite changes, DNA hypermethylation, and p53 and KRAS gene mutations, as well as microRNAs expression, have been analyzed as potential genetic markers. It seems that microRNAs and their expression profiles have the greatest diagnostic potential value in lung cancer diagnosis, but their quantification requires standardization.
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Affiliation(s)
- Katarzyna Wadowska
- Department of Medical Laboratory Diagnostics, Division of Clinical Chemistry and Laboratory Haematology, Wroclaw Medical University, 50-556 Wroclaw, Poland; (K.W.); (I.B.-L.)
| | - Iwona Bil-Lula
- Department of Medical Laboratory Diagnostics, Division of Clinical Chemistry and Laboratory Haematology, Wroclaw Medical University, 50-556 Wroclaw, Poland; (K.W.); (I.B.-L.)
| | - Łukasz Trembecki
- Department of Radiation Oncology, Lower Silesian Oncology Center, 53-413 Wroclaw, Poland;
- Department of Oncology, Faculty of Medicine, Wroclaw Medical University, 53-413 Wroclaw, Poland
| | - Mariola Śliwińska-Mossoń
- Department of Medical Laboratory Diagnostics, Division of Clinical Chemistry and Laboratory Haematology, Wroclaw Medical University, 50-556 Wroclaw, Poland; (K.W.); (I.B.-L.)
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37
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Weber S, Spiegl B, Perakis SO, Ulz CM, Abuja PM, Kashofer K, van der Leest P, Azpurua MA, Tamminga M, Brudzewsky D, Rothwell DG, Mohan S, Sartori A, Lampignano R, Konigshofer Y, Sprenger-Haussels M, Wikman H, Bergheim IR, Kloten V, Schuuring E, Speicher MR, Heitzer E. Technical Evaluation of Commercial Mutation Analysis Platforms and Reference Materials for Liquid Biopsy Profiling. Cancers (Basel) 2020; 12:E1588. [PMID: 32560092 PMCID: PMC7352370 DOI: 10.3390/cancers12061588] [Citation(s) in RCA: 45] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2020] [Revised: 05/15/2020] [Accepted: 06/11/2020] [Indexed: 02/06/2023] Open
Abstract
Molecular profiling from liquid biopsy, in particular cell-free DNA (cfDNA), represents an attractive alternative to tissue biopsies for the detection of actionable targets and tumor monitoring. In addition to PCR-based assays, Next Generation Sequencing (NGS)-based cfDNA assays are now commercially available and are being increasingly adopted in clinical practice. However, the validity of these products as well as the clinical utility of cfDNA in the management of patients with cancer has yet to be proven. Within framework of the Innovative Medicines Initiative (IMI) program CANCER-ID we evaluated the use of commercially available reference materials designed for ctDNA testing and cfDNA derived from Diagnostic Leukaphereses (DLA) for inter- and intra-assay as well as intra- and inter-laboratory comparisons. In three experimental setups, a broad range of assays including ddPCR, MassARRAY and various NGS-based assays were tested. We demonstrate that both reference materials with predetermined VAFs and DLA samples are extremely useful for the performance assessment of mutation analysis platforms. Moreover, our data indicate a substantial variability of NGS assays with respect to sensitivity and specificity highlighting the importance of extensive validation of the test performance before offering these tests in clinical routine practice.
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Affiliation(s)
- Sabrina Weber
- Institute of Human Genetics, Diagnostic & Research Center for Molecular BioMedicine, Medical University of Graz, 8010 Graz, Austria; (S.W.); (B.S.); (S.O.P.); (M.R.S.)
- Christian Doppler Laboratory for Liquid Biopsies for Early Detection of Cancer, Medical University of Graz, 8010 Graz, Austria;
| | - Benjamin Spiegl
- Institute of Human Genetics, Diagnostic & Research Center for Molecular BioMedicine, Medical University of Graz, 8010 Graz, Austria; (S.W.); (B.S.); (S.O.P.); (M.R.S.)
| | - Samantha O. Perakis
- Institute of Human Genetics, Diagnostic & Research Center for Molecular BioMedicine, Medical University of Graz, 8010 Graz, Austria; (S.W.); (B.S.); (S.O.P.); (M.R.S.)
| | - Christine M. Ulz
- Institute of Pathology, Diagnostic & Research Center for Molecular BioMedicine, Medical University of Graz, 8010 Graz, Austria; (C.M.U.); (K.K.); (P.v.d.L.)
| | - Peter M. Abuja
- Christian Doppler Laboratory for Liquid Biopsies for Early Detection of Cancer, Medical University of Graz, 8010 Graz, Austria;
- Institute of Pathology, Diagnostic & Research Center for Molecular BioMedicine, Medical University of Graz, 8010 Graz, Austria; (C.M.U.); (K.K.); (P.v.d.L.)
| | - Karl Kashofer
- Institute of Pathology, Diagnostic & Research Center for Molecular BioMedicine, Medical University of Graz, 8010 Graz, Austria; (C.M.U.); (K.K.); (P.v.d.L.)
| | - Paul van der Leest
- Institute of Pathology, Diagnostic & Research Center for Molecular BioMedicine, Medical University of Graz, 8010 Graz, Austria; (C.M.U.); (K.K.); (P.v.d.L.)
| | - Maria Aguirre Azpurua
- University of Groningen, University Medical Center of Groningen, 9713 GZ Groningen, The Netherlands; (M.A.A.); (M.T.); (E.S.)
| | - Menno Tamminga
- University of Groningen, University Medical Center of Groningen, 9713 GZ Groningen, The Netherlands; (M.A.A.); (M.T.); (E.S.)
| | - Dan Brudzewsky
- LGC SeraCare Life Sciences, Milford, MA 01757, USA; (D.B.); (Y.K.)
| | - Dominic G. Rothwell
- Cancer Research UK MI, University of Manchester, Manchester SK10 4TG, UK; (D.G.R.); (S.M.)
| | - Sumitra Mohan
- Cancer Research UK MI, University of Manchester, Manchester SK10 4TG, UK; (D.G.R.); (S.M.)
| | | | - Rita Lampignano
- Bayer AG, Biomarker Research, 42113 Wuppertal, Germany; (R.L.); (V.K.)
| | - Yves Konigshofer
- LGC SeraCare Life Sciences, Milford, MA 01757, USA; (D.B.); (Y.K.)
| | | | - Harriet Wikman
- University Medical Center Hamburg-Eppendorf, 20251 Hamburg, Germany;
| | - Inger R. Bergheim
- Department of Cancer Genetics, Institute of Cancer Research, Oslo University Hospital, N-0310 Oslo, Norway;
| | - Vera Kloten
- Bayer AG, Biomarker Research, 42113 Wuppertal, Germany; (R.L.); (V.K.)
| | - Ed Schuuring
- University of Groningen, University Medical Center of Groningen, 9713 GZ Groningen, The Netherlands; (M.A.A.); (M.T.); (E.S.)
| | - Michael R. Speicher
- Institute of Human Genetics, Diagnostic & Research Center for Molecular BioMedicine, Medical University of Graz, 8010 Graz, Austria; (S.W.); (B.S.); (S.O.P.); (M.R.S.)
| | - Ellen Heitzer
- Institute of Human Genetics, Diagnostic & Research Center for Molecular BioMedicine, Medical University of Graz, 8010 Graz, Austria; (S.W.); (B.S.); (S.O.P.); (M.R.S.)
- Christian Doppler Laboratory for Liquid Biopsies for Early Detection of Cancer, Medical University of Graz, 8010 Graz, Austria;
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García-Alfonso P, García-Carbonero R, García-Foncillas J, Pérez-Segura P, Salazar R, Vera R, Ramón Y Cajal S, Hernández-Losa J, Landolfi S, Musulén E, Cuatrecasas M, Navarro S. Update of the recommendations for the determination of biomarkers in colorectal carcinoma: National Consensus of the Spanish Society of Medical Oncology and the Spanish Society of Pathology. Clin Transl Oncol 2020; 22:1976-1991. [PMID: 32418154 PMCID: PMC7505870 DOI: 10.1007/s12094-020-02357-z] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2019] [Accepted: 04/28/2020] [Indexed: 12/16/2022]
Abstract
In this update of the consensus of the Spanish Society of Medical Oncology (Sociedad Española de Oncología Médica—SEOM) and the Spanish Society of Pathology (Sociedad Española de Anatomía Patológica—SEAP), advances in the analysis of biomarkers in advanced colorectal cancer (CRC) as well as susceptibility markers of hereditary CRC and molecular biomarkers of localized CRC are reviewed. Recently published information on the essential determination of KRAS, NRAS and BRAF mutations and the convenience of determining the amplification of human epidermal growth factor receptor 2 (HER2), the expression of proteins in the DNA repair pathway and the study of NTRK fusions are also evaluated. From the pathological point of view, the importance of analysing the tumour budding and poorly differentiated clusters, and its prognostic value in CRC is reviewed, as well as the impact of molecular lymph node analysis on lymph node staging in CRC. The incorporation of pan-genomic technologies, such as next-generation sequencing (NGS) and liquid biopsy in the clinical management of patients with CRC is also outlined. All these aspects are developed in this guide, which, like the previous one, will remain open to any necessary revision in the future.
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Affiliation(s)
- P García-Alfonso
- Departament of Medical Oncology, Hospital General Universitario Gregorio Marañón, Madrid, Spain.
| | - R García-Carbonero
- Departament of Medical Oncology, Hospital Universitario 12 de Octubre, Instituto de Investigación Sanitaria Hospital 12 de Octubre (imas12), UCM, CNIO, CIBERONC, Madrid, Spain
| | - J García-Foncillas
- Departament of Medical Oncology, Hospital Universitario Fundación Jiménez Díaz, Universidad Autónoma de Madrid, Madrid, Spain
| | - P Pérez-Segura
- Departament of Medical Oncology, Hospital Clínico Universitario San Carlos, CIBERONC, Madrid, Spain
| | - R Salazar
- Departament of Medical Oncology, ICO L'Hospitalet, Oncobell Program (IDIBELL), CIBERONC, Hospitalet de Llobregat, Spain
| | - R Vera
- Departament of Medical Oncology, Complejo Hospitalario de Navarra; Navarrabiomed, IDISNA, Pamplona, Spain
| | - S Ramón Y Cajal
- Department of Pathology, Hospital Universitario Vall D'Hebron, CIBERONC, Barcelona, Spain
| | - J Hernández-Losa
- Department of Pathology, Hospital Universitario Vall D'Hebron, CIBERONC, Barcelona, Spain
| | - S Landolfi
- Department of Pathology, Hospital Universitario Vall D'Hebron, CIBERONC, Barcelona, Spain
| | - E Musulén
- Department of Pathology, Hospital Universitari General de Catalunya, Grupo Quirónsalud, Sant Cugat del Vallès, Spain.,Cancer Epigenetics Group, Institut de Recerca Contra La Leucèmia Josep Carreras, Badalona, Spain
| | - M Cuatrecasas
- Department of Pathology, Hospital Clinic, CIBERehd, Barcelona, Spain
| | - S Navarro
- Department of Pathology, University of Valencia, Hospital Clínico Universitario de Valencia, CIBERONC, Valencia, Spain
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Nguyen B, Meehan K, Pereira MR, Mirzai B, Lim SH, Leslie C, Clark M, Sader C, Friedland P, Lindsay A, Tang C, Millward M, Gray ES, Lim AM. A comparative study of extracellular vesicle-associated and cell-free DNA and RNA for HPV detection in oropharyngeal squamous cell carcinoma. Sci Rep 2020; 10:6083. [PMID: 32269293 PMCID: PMC7142128 DOI: 10.1038/s41598-020-63180-8] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2019] [Accepted: 03/04/2020] [Indexed: 12/16/2022] Open
Abstract
Purpose: This study compares the detection sensitivity of two separate liquid biopsy sources, cell-free (cf) DNA/RNA and extracellular vesicle (EV)-associated DNA/RNA (EV-DNA/RNA), to identify circulating Human Papilloma Virus (HPV) DNA/RNA in plasma obtained from patients with oropharyngeal squamous cell carcinoma (OPCSCC). We also report on the longitudinal changes observed in HPV-DNA levels in response to treatment. Experimental design: A prospective study was conducted that included 22 patients with locally advanced disease and six patients with metastatic OPCSCC. Twenty-three patients had HPV-related OPCSCC defined by p16 immunohistochemistry. Levels of circulating HPV-DNA and HPV-RNA from plasma-derived cf-DNA/RNA and EV-DNA/RNA were quantified using digital droplet PCR. Results: Circulating HPV-DNA was detected with higher sensitivity in cf-DNA compared to EV-DNA at 91% vs. 42% (p = <0.001). Similarly, circulating tumoral HPV-RNA was detected at a higher sensitivity in cf-RNA compared to EV-RNA, at 83% vs. 50% (p = 0.0019). In the locally advanced cohort, 100% (n = 16) of HPV-OPCSCC patients demonstrated a reduction in circulating HPV-DNA levels in cf-DNA following curative treatment, with 81% of patients demonstrating complete clearance to undetectable levels. However, in metastatic HPV-OPCSCC patients (n = 4), HPV-DNA levels did not correlate with treatment response. Conclusion: Our study demonstrates that although HPV-DNA/RNA can be detected in EV associated DNA/RNA, cf-DNA/RNA is the more sensitive liquid biopsy medium. As circulating HPV-DNA levels were found to only correlate with treatment response in the locally advanced but not metastatic setting in our small cohort of patients, the use of HPV-DNA as a dynamic biomarker to monitor treatment response requires further evaluation.
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Affiliation(s)
- Bella Nguyen
- Department of Medical Oncology, Sir Charles Gairdner Hospital, Perth, Western Australia, Australia.,School of Biomedical Sciences, University of Western Australia, Perth, Western Australia, Australia
| | - Katie Meehan
- School of Biomedical Sciences, University of Western Australia, Perth, Western Australia, Australia.,Chinese University of Hong Kong, Shatin, Hong Kong
| | - Michelle R Pereira
- School of Medical and Health Sciences, Edith Cowan University, Joondalup, Western Australia, Australia
| | - Bob Mirzai
- School of Biomedical Sciences, University of Western Australia, Perth, Western Australia, Australia.,Department of Anatomical Pathology, PathWest, QEII Medical Centre, Perth, Western Australia, Australia
| | - Si Hong Lim
- Genomics Western Australia, Telethon Kids Institute, Western Australia, Perth, Australia
| | - Connull Leslie
- School of Pathology and Laboratory Medicine, The University of Western Australia, Perth, Western Australia, Australia.,Department of Anatomical Pathology, PathWest, QEII Medical Centre, Perth, Western Australia, Australia
| | - Michael Clark
- School of Medical and Health Sciences, Edith Cowan University, Joondalup, Western Australia, Australia
| | - Chady Sader
- Department of Otolaryngology, Head and Neck Surgery, Sir Charles Gairdner Hospital, Perth, Western Australia, Australia.,Department of Otolaryngology, Head and Neck Surgery, St John of God Murdoch Hospital, Perth, Western Australia, Australia
| | - Peter Friedland
- Department of Otolaryngology, Head and Neck Surgery, Sir Charles Gairdner Hospital, Perth, Western Australia, Australia.,Faculty of Medical and Health Sciences, University of Western Australia, Perth, Western Australia, Australia.,School of Medicine, University of Notre Dame, Fremantle, Western Australia, Australia
| | - Andrew Lindsay
- Department of Otolaryngology, Head and Neck Surgery, Hollywood Private Hospital, Perth, Western Australia, Australia
| | - Colin Tang
- School of Medical and Health Sciences, Edith Cowan University, Joondalup, Western Australia, Australia.,Department of Radiation Oncology, Sir Charles Gairdner Hospital, Perth, Western Australia, Australia
| | - Michael Millward
- Department of Medical Oncology, Sir Charles Gairdner Hospital, Perth, Western Australia, Australia.,School of Medicine, The University of Western Australia, Perth, Western Australia, Australia
| | - Elin S Gray
- School of Medical and Health Sciences, Edith Cowan University, Joondalup, Western Australia, Australia
| | - Annette M Lim
- Department of Medical Oncology, Sir Charles Gairdner Hospital, Perth, Western Australia, Australia. .,Department of Medical Oncology, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia. .,Sir Peter MacCallum Department of Oncology, The University of Melbourne, Melbourne, Victoria, Australia.
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Baldacchino S, Grech G. Somatic copy number aberrations in metastatic patients: The promise of liquid biopsies. Semin Cancer Biol 2019; 60:302-310. [PMID: 31891778 DOI: 10.1016/j.semcancer.2019.12.014] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2019] [Revised: 11/20/2019] [Accepted: 12/03/2019] [Indexed: 01/14/2023]
Abstract
Cancer metastasis is the leading cause of cancer-related mortality. The metastatic process involves measurable cellular changes that confer migratory potential, proliferative advantage and the ability to colonise a distinct microenvironment. Accumulation of aberrations and clonal evolution add complexity to patient management and the assessment of the therapeutic sensitivity profile of malignancies. Liquid biopsy presents a repeatable and minimally invasive assessment tool to detect early metastasis, characterise tumour phenotype and detect minimal residual disease. The promise of liquid biopsies is to inform patient management and therapeutic decisions in a timely manner. Clinical translation requires robust methodologies with high sensitivity and tumour specificity. This can be achieved through technological advances but also through novel biologically informed approaches that harness existing knowledge on tumorigenesis. Here we present a review of copy number variations as potential biomarkers for early detection of metastatic potential and outline a biomarker validation process in the context of liquid biopsies.
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Affiliation(s)
- Shawn Baldacchino
- Applied Biotech Ltd, Cambridge, UK; Department of Pathology, Faculty of Medicine & Surgery, University of Malta, Malta.
| | - Godfrey Grech
- Department of Pathology, Faculty of Medicine & Surgery, University of Malta, Malta
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Antoniotti C, Pietrantonio F, Corallo S, De Braud F, Falcone A, Cremolini C. Circulating Tumor DNA Analysis in Colorectal Cancer: From Dream to Reality. JCO Precis Oncol 2019; 3:1-14. [DOI: 10.1200/po.18.00397] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Affiliation(s)
- Carlotta Antoniotti
- Unit of Medical Oncology 2, Azienda Ospedaliera-Universitaria Pisana, Pisa, Italy
- Department of Translational Research and New Technologies in Medicine, University of Pisa, Pisa, Italy
| | - Filippo Pietrantonio
- Medical Oncology Department, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
- Department of Oncology and Hemato-oncology, University of Milan, Milan, Italy
| | - Salvatore Corallo
- Medical Oncology Department, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | - Filippo De Braud
- Medical Oncology Department, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
- Department of Oncology and Hemato-oncology, University of Milan, Milan, Italy
| | - Alfredo Falcone
- Unit of Medical Oncology 2, Azienda Ospedaliera-Universitaria Pisana, Pisa, Italy
- Department of Translational Research and New Technologies in Medicine, University of Pisa, Pisa, Italy
| | - Chiara Cremolini
- Unit of Medical Oncology 2, Azienda Ospedaliera-Universitaria Pisana, Pisa, Italy
- Department of Translational Research and New Technologies in Medicine, University of Pisa, Pisa, Italy
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42
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Zhu VW, Klempner SJ, Ou SHI. Receptor Tyrosine Kinase Fusions as an Actionable Resistance Mechanism to EGFR TKIs in EGFR-Mutant Non-Small-Cell Lung Cancer. Trends Cancer 2019; 5:677-692. [DOI: 10.1016/j.trecan.2019.09.008] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2019] [Revised: 09/14/2019] [Accepted: 09/26/2019] [Indexed: 02/06/2023]
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43
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Temilola DO, Wium M, Coulidiati TH, Adeola HA, Carbone GM, Catapano CV, Zerbini LF. The Prospect and Challenges to the Flow of Liquid Biopsy in Africa. Cells 2019; 8:E862. [PMID: 31404988 PMCID: PMC6721679 DOI: 10.3390/cells8080862] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2019] [Revised: 07/30/2019] [Accepted: 08/03/2019] [Indexed: 12/24/2022] Open
Abstract
Liquid biopsy technologies have the potential to transform cancer patient management as it offers non-invasive diagnosis and real-time monitoring of disease progression and treatment responses. The use of liquid biopsy for non-invasive cancer diagnosis can have pivotal importance for the African continent where access to medical infrastructures is limited, as it eliminates the need for surgical biopsies. To apply liquid biopsy technologies in the African setting, the influence of environmental and population genetic factors must be known. In this review, we discuss the use of circulating tumor cells, cell-free nucleic acids, extracellular vesicles, protein, and other biomolecules in liquid biopsy technology for cancer management with special focus on African studies. We discussed the prospect, barriers, and other aspects that pose challenges to the use of liquid biopsy in the African continent.
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Affiliation(s)
- Dada Oluwaseyi Temilola
- International Centre for Genetic Engineering and Biotechnology (ICGEB), Cape Town 7925, South Africa
- Integrative Biomedical Sciences Division, Faculty of Health Sciences, University of Cape Town, Cape Town 7925, South Africa
| | - Martha Wium
- International Centre for Genetic Engineering and Biotechnology (ICGEB), Cape Town 7925, South Africa
| | - Tangbadioa Herve Coulidiati
- International Centre for Genetic Engineering and Biotechnology (ICGEB), Cape Town 7925, South Africa
- Training and Research unit in Sciences and Technology, University Norbert Zongo, P.O. Box 376, Koudougou 376, Burkina Faso
| | - Henry Ademola Adeola
- Division of Dermatology, Department of Medicine, Faculty of Health Sciences and Groote Schuur Hospital, University of Cape Town, Cape Town 7925, South Africa
| | - Giuseppina Maria Carbone
- Institute of Oncology Research, Università della Svizzera Italiana, Via Vincenzo Vela 6, CH-6500 Bellinzona, Switzerland
| | - Carlo Vittorio Catapano
- Institute of Oncology Research, Università della Svizzera Italiana, Via Vincenzo Vela 6, CH-6500 Bellinzona, Switzerland
| | - Luiz Fernando Zerbini
- International Centre for Genetic Engineering and Biotechnology (ICGEB), Cape Town 7925, South Africa.
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Sinha S, Brown H, Tabak J, Fang Z, Tertre MCD, McNamara S, Gambaro K, Batist G, Buell JF. Multiplexed real-time polymerase chain reaction cell-free DNA assay as a potential method to monitor stage IV colorectal cancer. Surgery 2019; 166:534-539. [PMID: 31378479 DOI: 10.1016/j.surg.2019.06.004] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2019] [Revised: 04/11/2019] [Accepted: 06/03/2019] [Indexed: 12/25/2022]
Abstract
BACKGROUND Liquid biopsy is a new area in cancer diagnostics that measures cell-free DNA in plasma from tumor that may serve as a monitoring tool in colorectal cancer patients. METHODS Multiplexed real-time polymerase chain reaction based on multicopy retro-transposable elements (targeting 80 base pair and 265 base pair sequences and an internal-positive-control) was used to evaluate the ability of cell-free DNA concentration and DNA Integrity Index to discriminate cancer from healthy patients. A cohort of 40 healthy controls and 39 stage IV colorectal patient's plasma were interrogated. The potency of each biomarker was measured by using receiver operating characteristic curves and derived area under the curve measures. RESULTS Significant differences in cell-free DNA concentration and DNA integrity index were observed between controls and stage IV patients with a limit of detection <0.1 pg/μL. Investigation of the ability of both biomarker candidates to differentiate cancer from healthy patients showed an area under the curve of 0.9891 and 0.9859 for 80 base pair and 265 amplicons respectively and 0.8603 for DNA integrity index-265/80. CONCLUSIONS After establishing differences in cell-free DNA levels between healthy and treated and untreated stage IV patients, the multiplexed real-time polymerase chain reaction measurements of retro-transposable elements in cancer patient plasma potentially possess the ability to monitor therapy responsiveness in near real time.
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Affiliation(s)
| | | | | | - Zhide Fang
- Louisiana State University, New Orleans, LA
| | | | - Susan McNamara
- Jewish General Hospital, Montreal, Quebec; Exactis Innovations, Montreal, Quebec
| | - Karen Gambaro
- Jewish General Hospital, Montreal, Quebec; Exactis Innovations, Montreal, Quebec
| | - Gerald Batist
- Jewish General Hospital, Montreal, Quebec; Exactis Innovations, Montreal, Quebec
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45
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Moreno JG, Gomella LG. Evolution of the Liquid Biopsy in Metastatic Prostate Cancer. Urology 2019; 132:1-9. [PMID: 31207303 DOI: 10.1016/j.urology.2019.06.006] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2019] [Revised: 06/05/2019] [Accepted: 06/07/2019] [Indexed: 12/11/2022]
Abstract
We reviewed the literature for the biologic, prognostic, and predictive significance of circulating prostate cancer tumor cells (CTCs), and circulating tumor DNA in the blood of metastatic castration resistant prostate cancer patients. CTCs demonstrate robust prognostic value independent of PSA in predicting overall survival. The CTC androgen receptor variant receptor 7 phenotype predicts resistance to androgen receptor synthesis inhibitors and sensitivity to taxane based chemotherapy in metastatic castration resistant prostate cancer patients who are candidates for second line therapy. Research is rapidly pivoting toward circulating tumor DNA analysis because the approach is sensitive, prognostic, cost effective, and it can elucidate mechanisms of systemic therapy.
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Affiliation(s)
- Jose G Moreno
- Department of Urology, Sidney Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, PA; MidLantic Urology, LLC, Pottstown, PA
| | - Leonard G Gomella
- Department of Urology, Sidney Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, PA.
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46
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Liquid biopsy: a new diagnostic, predictive and prognostic window in cancers of unknown primary. Eur J Cancer 2018; 105:28-32. [PMID: 30388661 DOI: 10.1016/j.ejca.2018.09.035] [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] [Received: 09/20/2018] [Accepted: 09/26/2018] [Indexed: 01/07/2023]
Abstract
Cancer of unknown primary (CUP) is a heterogeneous group of metastatic cancers characterised by early dissemination of metastases in the absence of any identifiable primary site. Most patients with CUP have poor prognosis with the traditional diagnostic and treatment modalities. Recognising the putative primary tumour is hypothesised to ameliorate the prognosis of patients with CUP by guiding treatment decisions. The active efforts in molecular oncology have shown that gene expression profiling is able to identify the primary tumour site and to determine targetable mutations. In this regard, liquid biopsy opens a new diagnostic, predictive and prognostic window in CUP that may lead to substantial improvement in the management of patients with CUP.
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