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Gram SB, Alosi D, Bagger FO, Østrup O, von Buchwald C, Friborg J, Wessel I, Vogelius IR, Rohrberg K, Rasmussen JH. Clinical implication of genetic intratumor heterogeneity for targeted therapy in head and neck cancer. Acta Oncol 2023; 62:1831-1839. [PMID: 37902999 DOI: 10.1080/0284186x.2023.2272293] [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: 07/24/2023] [Accepted: 10/15/2023] [Indexed: 11/01/2023]
Abstract
BACKGROUND Genomic profiling is increasingly used both in therapeutic decision-making and as inclusion criteria for trials testing targeted therapies. However, the mutational landscape may vary across different areas of a tumor and intratumor heterogeneity will challenge treatments or clinical decisions based on single tumor biopsies. The purpose of this study was to assess the clinical relevance of genetic intratumor heterogeneity in head and neck squamous cell carcinomas (HNSCC) using the ESMO Scale for Clinical Actionability of Molecular Targets (ESCAT). MATERIALS AND METHODS This prospective study included 33 whole tumor specimens from 28 patients with primary or recurrent HNSCC referred for surgery. Three tumor blocks were selected from central, semi-peripheral, and peripheral positions, mimicking biopsies in three different locations. Genetic analysis of somatic copy number alterations (SCNAs) was performed on the three biopsies using Oncoscan, focusing on 45 preselected HNSCC genes of interest. Clinical relevance was assessed using the ESCAT score to investigate whether and how treatment decisions would change based on the three biopsies from the same tumor. RESULTS The SCNAs identified among 45 preselected genes within the three tumor biopsies derived from the same tumor revealed distinct variations. The detected discrepancies could potentially influence treatment approaches or clinical decisions in 36% of the patients if only one tumor biopsy was used. Recurrent tumors exhibited significantly higher variation in SCNAs than primary tumors (p = .024). No significant correlation between tumor size and heterogeneity (p = .7) was observed. CONCLUSION In 36% of patients diagnosed with HNSCC, clinically significant intratumor heterogeneity was observed which may have implications for patient management. This finding substantiates the need for future studies that specifically investigate the clinical implications associated with intratumor heterogeneity.
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Affiliation(s)
- Signe Buhl Gram
- Department of Otorhinolaryngology, Head and Neck Surgery and Audiology, Copenhagen University Hospital - Rigshospitalet, Copenhagen, Denmark
| | - Daniela Alosi
- Center for Genomic Medicine, Copenhagen University Hospital - Rigshospitalet, Copenhagen, Denmark
| | - Frederik Otzen Bagger
- Center for Genomic Medicine, Copenhagen University Hospital - Rigshospitalet, Copenhagen, Denmark
| | - Olga Østrup
- Center for Genomic Medicine, Copenhagen University Hospital - Rigshospitalet, Copenhagen, Denmark
| | - Christian von Buchwald
- Department of Otorhinolaryngology, Head and Neck Surgery and Audiology, Copenhagen University Hospital - Rigshospitalet, Copenhagen, Denmark
| | - Jeppe Friborg
- Department of Oncology, Section of Radiotherapy, Copenhagen University Hospital - Rigshospitalet, Copenhagen, Denmark
| | - Irene Wessel
- Department of Otorhinolaryngology, Head and Neck Surgery and Audiology, Copenhagen University Hospital - Rigshospitalet, Copenhagen, Denmark
| | - Ivan Richter Vogelius
- Department of Oncology, Section of Radiotherapy, Copenhagen University Hospital - Rigshospitalet, Copenhagen, Denmark
| | - Kristoffer Rohrberg
- Department of Oncology, Copenhagen University Hospital - Rigshospitalet, Copenhagen, Denmark
| | - Jacob Høygaard Rasmussen
- Department of Otorhinolaryngology, Head and Neck Surgery and Audiology, Copenhagen University Hospital - Rigshospitalet, Copenhagen, Denmark
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Osei-Bordom DC, Sachdeva G, Christou N. Liquid Biopsy as a Prognostic and Theranostic Tool for the Management of Pancreatic Ductal Adenocarcinoma. Front Med (Lausanne) 2022; 8:788869. [PMID: 35096878 PMCID: PMC8795626 DOI: 10.3389/fmed.2021.788869] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2021] [Accepted: 12/02/2021] [Indexed: 12/24/2022] Open
Abstract
Pancreatic ductal adenocarcinomas (PDAC) represent one of the deadliest cancers worldwide. Survival is still low due to diagnosis at an advanced stage and resistance to treatment. Herein, we review the main types of liquid biopsy able to help in both prognosis and adaptation of treatments.
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Affiliation(s)
- Daniel C Osei-Bordom
- Department of General Surgery, Queen Elizabeth Hospital, University Hospitals Birmingham, Birmingham, United Kingdom
- Institute of Immunology and Immunotherapy, University of Birmingham, Birmingham, United Kingdom
- National Institute for Health Research (NIHR) Birmingham Biomedical Research Centre, Centre for Liver and Gastroenterology Research, University of Birmingham, Birmingham, United Kingdom
| | - Gagandeep Sachdeva
- Institute of Immunology and Immunotherapy, University of Birmingham, Birmingham, United Kingdom
| | - Niki Christou
- Department of General Surgery, Queen Elizabeth Hospital, University Hospitals Birmingham, Birmingham, United Kingdom
- Department of General Surgery, University Hospital of Limoges, Limoges, France
- EA3842 CAPTuR Laboratory "Cell Activation Control, Tumor Progression and Therapeutic Resistance", Faculty of Medicine, Limoges, France
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3
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Liu Z, Filip I, Gomez K, Engelbrecht D, Meer S, Lalloo PN, Patel P, Perner Y, Zhao J, Wang J, Pasqualucci L, Rabadan R, Willem P. Genomic Characterization of HIV-Associated Plasmablastic Lymphoma Identifies Pervasive Mutations in the JAK–STAT Pathway. Blood Cancer Discov 2020; 1:112-125. [PMID: 33225311 PMCID: PMC7679070 DOI: 10.1158/2643-3230.bcd-20-0051] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Plasmablastic lymphoma (PBL) is an aggressive B-cell non-Hodgkin lymphoma associated with immunodeficiency in the context of Human Immunodeficiency Virus (HIV) infection or iatrogenic immunosuppression. While a rare disease in general, the incidence is dramatically increased in regions of the world with high HIV prevalence. The molecular pathogenesis of this disease is poorly characterized. Here, we defined the genomic features of PBL in a cohort of 110 patients from South Africa (15 by whole exome sequencing and 95 by deep targeted sequencing). We identified recurrent mutations in genes of the JAK-STAT signaling pathway, including STAT3 (42%), JAK1 (14%) and SOCS1 (10%), leading to its constitutive activation. Moreover, 24% of cases harbored gain-of-function mutations in RAS family members (NRAS and KRAS). Comparative analysis with other B-cell malignancies uncovered PBL-specific somatic mutations and transcriptional programs. We also found recurrent copy number gains encompassing the CD44 gene (37%), which encodes for a cell surface receptor involved in lymphocyte activation and homing, and was found expressed at high levels in all tested cases, independent of genetic alterations. These findings have implications for the understanding of the pathogenesis of this disease and the development of personalized medicine approaches.
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Affiliation(s)
- Zhaoqi Liu
- Program for Mathematical Genomics, Columbia University, New York, New York
- Departments of Systems Biology and Biomedical Informatics, Columbia University, New York, New York
| | - Ioan Filip
- Program for Mathematical Genomics, Columbia University, New York, New York
- Departments of Systems Biology and Biomedical Informatics, Columbia University, New York, New York
| | - Karen Gomez
- Program for Mathematical Genomics, Columbia University, New York, New York
- Departments of Systems Biology and Biomedical Informatics, Columbia University, New York, New York
| | - Dewaldt Engelbrecht
- Department of Haematology and Molecular Medicine, National Health Laboratory Service, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Shabnum Meer
- Department of Oral Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Pooja N Lalloo
- Department of Haematology and Molecular Medicine, National Health Laboratory Service, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Pareen Patel
- Department of Haematology and Molecular Medicine, National Health Laboratory Service, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Yvonne Perner
- Department of Anatomical Pathology, National Health Laboratory Service, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Junfei Zhao
- Program for Mathematical Genomics, Columbia University, New York, New York
- Departments of Systems Biology and Biomedical Informatics, Columbia University, New York, New York
| | - Jiguang Wang
- Division of Life Science, Department of Chemical and Biological Engineering, Center for Systems Biology and Human Health and State Key Laboratory of Molecular Neuroscience, The Hong Kong University of Science and Technology, Hong Kong SAR, China
| | - Laura Pasqualucci
- Institute for Cancer Genetics.
- Herbert Irving Comprehensive Cancer Center, Columbia University, New York, New York
- Department of Pathology and Cell Biology, Herbert Irving Comprehensive Cancer Center, Columbia University, New York, New York
| | - Raul Rabadan
- Program for Mathematical Genomics, Columbia University, New York, New York.
- Departments of Systems Biology and Biomedical Informatics, Columbia University, New York, New York
| | - Pascale Willem
- Department of Haematology and Molecular Medicine, National Health Laboratory Service, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa.
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Ahlborn LB, Rohrberg KS, Gabrielaite M, Tuxen IV, Yde CW, Spanggaard I, Santoni-Rugiu E, Nielsen FC, Lassen U, Mau-Sorensen M, Østrup O. Application of cell-free DNA for genomic tumor profiling: a feasibility study. Oncotarget 2019; 10:1388-1398. [PMID: 30858924 PMCID: PMC6402712 DOI: 10.18632/oncotarget.26642] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2014] [Accepted: 01/17/2019] [Indexed: 12/19/2022] Open
Abstract
PURPOSE Access to genomic tumor material is required to select patients for targeted therapies. However, tissue biopsies are not always feasible and therefore circulating cell-free DNA (cfDNA) has emerged as an alternative. Here we investigate the utility of cfDNA for genomic tumor profiling in the phase I setting. STUDY DESIGN Peripheral blood was collected from patients with advanced solid cancers eligible for phase I treatment. Patients failing the initial tissue biopsy due to inaccessible lesions or insufficient tumor cellularity (<10%) were included in the study. Genomic profiling of cfDNA including whole exome sequencing (WES) and somatic copy number alterations (SCNAs) analysis (OncoScan). RESULTS Plasma cfDNA was pro- and retrospectively profiled from 24 and 20 patients, respectively. The median turnaround time was 29 days (N= 24, range 13-87 days) compared to tissue re-analyses of median 60 days (N= 6, range 29-98). Selected cancer-associated alterations (SCAAs) were identified in 70% (31/44) of patients, predominantly by WES due to the low sensitivity of OncoScan on cfDNA. Primarily, inaccessible cases of prostate and lung cancers could benefit from cfDNA profiling. In contrast, breast cancer patients showed a low level of tumor-specific cfDNA which might be due to cancer type and/or active treatment at the time of plasma collection. CONCLUSION Plasma cfDNA profiling using WES is feasible within a clinically relevant timeframe and represents an alternative to invasive tissue biopsies to identify possible treatment targets. Especially, difficult-to-biopsy cancers can benefit from cfDNA profiling, but tumor tissue remains the gold standard for molecular analyses.
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Affiliation(s)
- Lise B. Ahlborn
- The Phase I Unit, Department of Oncology, Rigshospitalet, Copenhagen University, Copenhagen, Denmark
- Center for Genomic Medicine, Rigshospitalet, Copenhagen University, Copenhagen, Denmark
| | - Kristoffer S. Rohrberg
- The Phase I Unit, Department of Oncology, Rigshospitalet, Copenhagen University, Copenhagen, Denmark
| | - Migle Gabrielaite
- Center for Genomic Medicine, Rigshospitalet, Copenhagen University, Copenhagen, Denmark
| | - Ida V. Tuxen
- The Phase I Unit, Department of Oncology, Rigshospitalet, Copenhagen University, Copenhagen, Denmark
| | - Christina W. Yde
- Center for Genomic Medicine, Rigshospitalet, Copenhagen University, Copenhagen, Denmark
| | - Iben Spanggaard
- The Phase I Unit, Department of Oncology, Rigshospitalet, Copenhagen University, Copenhagen, Denmark
| | - Eric Santoni-Rugiu
- Department of Pathology, Rigshospitalet, Copenhagen University, Copenhagen, Denmark
| | - Finn C. Nielsen
- Center for Genomic Medicine, Rigshospitalet, Copenhagen University, Copenhagen, Denmark
| | - Ulrik Lassen
- The Phase I Unit, Department of Oncology, Rigshospitalet, Copenhagen University, Copenhagen, Denmark
| | - Morten Mau-Sorensen
- The Phase I Unit, Department of Oncology, Rigshospitalet, Copenhagen University, Copenhagen, Denmark
| | - Olga Østrup
- Center for Genomic Medicine, Rigshospitalet, Copenhagen University, Copenhagen, Denmark
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Franczak C, Filhine-Tresarrieu P, Gilson P, Merlin JL, Au L, Harlé A. Technical considerations for circulating tumor DNA detection in oncology. Expert Rev Mol Diagn 2019; 19:121-135. [DOI: 10.1080/14737159.2019.1568873] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Claire Franczak
- Service de Biopathologie, Institut de Cancérologie de Lorraine, Vandoeuvre les Nancy, France
| | | | - Pauline Gilson
- Service de Biopathologie, Institut de Cancérologie de Lorraine, Université de Lorraine, CNRS UMR 7039 CRAN, Nancy, France
| | - Jean-Louis Merlin
- Service de Biopathologie, Institut de Cancérologie de Lorraine, Université de Lorraine, CNRS UMR 7039 CRAN, Nancy, France
| | - Lewis Au
- Skin and Renal Units, The Royal Marsden NHS Foundation Trust, London, UK
| | - Alexandre Harlé
- Service de Biopathologie, Institut de Cancérologie de Lorraine, Université de Lorraine, CNRS UMR 7039 CRAN, Nancy, France
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Lee KH, Shin TJ, Kim WH, Cho JY. Methylation of LINE-1 in cell-free DNA serves as a liquid biopsy biomarker for human breast cancers and dog mammary tumors. Sci Rep 2019; 9:175. [PMID: 30655558 PMCID: PMC6336845 DOI: 10.1038/s41598-018-36470-5] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2018] [Accepted: 11/21/2018] [Indexed: 12/15/2022] Open
Abstract
Breast cancer (BC) is one of the most common cancers in both women and female dogs. Methylation changes of LINE-1 have been reported in human cancers. The aim of this study was to determine the hypomethylation of canine LINE-1 in liquid biopsies for canine mammary tumors (CMT) and to assess its diagnostic performance in human plasma. BC associated LINE-1 methylation was measured by methylation sensitive (HpaII) and insensitive (MspI) restriction enzyme digestion followed by real-time PCR using the cfDNA isolated from 300 µl of plasma. The relative level of methylated canine LINE-1 was less than 0.4 in the benign and malignant CMTs (0.29 ± 0.061 and 0.39 ± 0.066, respectively) when it was 0.92 ± 0.067 in the healthy controls. The area under the ROC curve (AUC) was significantly high in both benign and malignant tumors (0.97 and 0.93). Furthermore, this approach was also successfully implemented in a set of 26 human BCs with 10 healthy controls (AUC = 0.78). Altogether, our data suggest that the comparative approach using a dog model might be helpful to rapidly develop a new diagnostic biomarker and that the methylation of LINE-1 in cfDNA may be a good target as a diagnostic marker of both human BC and CMT.
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Affiliation(s)
- Kang-Hoon Lee
- Department of Biochemistry, BK21 Plus and Research Institute for Veterinary Science, School of Veterinary Medicine, Seoul National University, Seoul, South Korea
| | - Tae-Jin Shin
- Department of Biochemistry, BK21 Plus and Research Institute for Veterinary Science, School of Veterinary Medicine, Seoul National University, Seoul, South Korea
| | - Wan-Hee Kim
- Department of Veterinary Clinical Sciences, College of Veterinary Medicine and Research Institute for Veterinary Science, Seoul National University, Seoul, Republic of Korea
| | - Je-Yoel Cho
- Department of Biochemistry, BK21 Plus and Research Institute for Veterinary Science, School of Veterinary Medicine, Seoul National University, Seoul, South Korea.
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Arneth B. Update on the types and usage of liquid biopsies in the clinical setting: a systematic review. BMC Cancer 2018; 18:527. [PMID: 29728089 PMCID: PMC5935950 DOI: 10.1186/s12885-018-4433-3] [Citation(s) in RCA: 63] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2017] [Accepted: 04/25/2018] [Indexed: 12/23/2022] Open
Abstract
Background This systematic review aimed to gather evidence from research on the current state of liquid biopsy in medical practice, specifically focusing on mutation detection and monitoring. Methods A systematic search was performed via Medline. Results The results of this investigation indicate that liquid biopsy plays a critical role in the detection and management of tumors. This technique gives healthcare providers the ability to gather critical and reliable information that may potentially shape the diagnosis, treatment, and prognosis of a variety of cancers in the near future. This study further reveals that liquid biopsy has several potential shortcomings that may limit its application and use in the healthcare setting. Nevertheless, liquid biopsy remains a valuable tool that is gradually becoming a part of routine healthcare practice in oncology departments and hospitals worldwide. Conclusions The evidence described herein reveals the potential relevance of liquid biopsy as an important prognostic, diagnostic, and theranostic tool. This non-invasive procedure enables healthcare practitioners to detect and monitor genomic alterations and will likely replace tumor tissue biopsy as the standard method for detecting and monitoring mutations in the future. The information obtained herein can enable physicians to make informed decisions regarding current treatment options; however, liquid biopsy has not yet been incorporated into routine clinical diagnostics for cancer patients.
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Affiliation(s)
- Borros Arneth
- Institute of Laboratory Medicine and Pathobiochemistry, Molecular Diagnostics, University Hospital of the Universities of Giessen and Marburg UKGM, Justus Liebig University Giessen, Feulgenstr. 12, 35392, Giessen, Germany.
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