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Maguluri G, Grimble J, Caron A, Zhu G, Krishnamurthy S, McWatters A, Beamer G, Lee SY, Iftimia N. Core Needle Biopsy Guidance Based on Tissue Morphology Assessment with AI-OCT Imaging. Diagnostics (Basel) 2023; 13:2276. [PMID: 37443670 DOI: 10.3390/diagnostics13132276] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2023] [Revised: 06/26/2023] [Accepted: 07/03/2023] [Indexed: 07/15/2023] Open
Abstract
This paper presents a combined optical imaging/artificial intelligence (OI/AI) technique for the real-time analysis of tissue morphology at the tip of the biopsy needle, prior to collecting a biopsy specimen. This is an important clinical problem as up to 40% of collected biopsy cores provide low diagnostic value due to high adipose or necrotic content. Micron-scale-resolution optical coherence tomography (OCT) images can be collected with a minimally invasive needle probe and automatically analyzed using a computer neural network (CNN)-based AI software. The results can be conveyed to the clinician in real time and used to select the biopsy location more adequately. This technology was evaluated on a rabbit model of cancer. OCT images were collected with a hand-held custom-made OCT probe. Annotated OCT images were used as ground truth for AI algorithm training. The overall performance of the AI model was very close to that of the humans performing the same classification tasks. Specifically, tissue segmentation was excellent (~99% accuracy) and provided segmentation that closely mimicked the ground truth provided by the human annotations, while over 84% correlation accuracy was obtained for tumor and non-tumor classification.
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Affiliation(s)
| | | | | | - Ge Zhu
- Physical Sciences Inc., Andover, MA 01810, USA
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2
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Marotta V, Cennamo M, La Civita E, Vitale M, Terracciano D. Cell-Free DNA Analysis within the Challenges of Thyroid Cancer Management. Cancers (Basel) 2022; 14:cancers14215370. [PMID: 36358788 PMCID: PMC9654679 DOI: 10.3390/cancers14215370] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2022] [Revised: 10/26/2022] [Accepted: 10/28/2022] [Indexed: 11/06/2022] Open
Abstract
Simple Summary Liquid biopsy is a minimally invasive method that emerged as a new promising tool for improving diagnosis, risk stratification, follow-up, and treatment of cancer patients. To date, the majority of the research in the area of liquid biopsy has focused on plasma-based cell-free DNA as a potential surrogate for tumor DNA obtained from a tissue biopsy. In the last decades, breakthrough advancements have been performed in the knowledge of thyroid cancer genetics, and the role of molecular characterization in clinical decision-making is continuously rising, from diagnosis completion to the personalization of treatment approach. Hence, it is expectable for cell-free DNA to be applicable in thyroid cancer management. This review aims to investigate the cell-free DNA utility for thyroid cancer patients’ care. Abstract Thyroid cancer is the most frequent endocrine malignancy with an increasing incidence trend during the past forty years and a concomitant rise in cancer-related mortality. The circulating cell-free DNA (cfDNA) analysis is a patient’s friendly and repeatable procedure allowing to obtain surrogate information about the genetics and epigenetics of the tumor. The aim of the present review was to address the suitability of cfDNA testing in different forms of thyroid cancer, and the potential clinical applications, as referred to the clinical weaknesses. Despite being limited by the absence of standardization and by reproducibility and validity issues, cfDNA assessment has great potential for the improvement of thyroid cancer management. cfDNA may support the pre-surgical definition of thyroid nodules by complementing invasive thyroid fine needle aspiration cytology. In addition, it may empower risk stratification and could be used as a biomarker for monitoring the post-surgical disease status, both during active surveillance and in the case of anti-tumor treatment.
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Affiliation(s)
- Vincenzo Marotta
- UOC Clinica Endocrinologica e Diabetologica, AOU San Giovanni di Dio e Ruggi d’Aragona, 84131 Salerno, Italy
- Correspondence: ; Tel.: +39-333-852-1005
| | - Michele Cennamo
- Department of Translational Medical Sciences, University of Naples “Federico II”, 80138 Naples, Italy
| | - Evelina La Civita
- Department of Translational Medical Sciences, University of Naples “Federico II”, 80138 Naples, Italy
| | - Mario Vitale
- Dipartimento di Medicina, Chirurgia e Odontoiatria, Università di Salerno, 84081 Baronissi, Italy
| | - Daniela Terracciano
- Department of Translational Medical Sciences, University of Naples “Federico II”, 80138 Naples, Italy
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3
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Shah UJ, Alsulimani A, Ahmad F, Mathkor DM, Alsaieedi A, Harakeh S, Nasiruddin M, Haque S. Bioplatforms in liquid biopsy: advances in the techniques for isolation, characterization and clinical applications. Biotechnol Genet Eng Rev 2022; 38:339-383. [PMID: 35968863 DOI: 10.1080/02648725.2022.2108994] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Tissue biopsy analysis has conventionally been the gold standard for cancer prognosis, diagnosis and prediction of responses/resistances to treatments. The existing biopsy procedures used in clinical practice are, however, invasive, painful and often associated with pitfalls like poor recovery of tumor cells and infeasibility for repetition in single patients. To circumvent these limitations, alternative non-invasive, rapid and economical, yet sturdy, consistent and dependable, biopsy techniques are required. Liquid biopsy is an emerging technology that fulfills these criteria and potentially much more in terms of subject-specific real-time monitoring of cancer progression, determination of tumor heterogeneity and treatment responses, and specific identification of the type and stages of cancers. The present review first briefly revisits the state-of-the-art technique of liquid biopsy and then proceeds to address in detail, the advances in the potential clinical applications of four major biological agencies present in liquid biopsy samples (circulating tumor DNA (ctDNA), circulating tumor cells (CTCs), exosomes and tumor-educated platelets (TEPs)). Finally, the authors conclude with the limitations that need to be addressed in order for liquid biopsy to effectively replace the conventional invasive biopsy methods in the clinical settings.
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Affiliation(s)
- Ushma Jaykamal Shah
- MedGenome Labs Ltd, Kailash Cancer Hospital and Research Center, Vadodara, India
| | - Ahmad Alsulimani
- Medical Laboratory Technology Department, College of Applied Medical Sciences, Jazan University, Jazan, Saudi Arabia
| | - Faraz Ahmad
- Department of Biotechnology, School of Bio Sciences and Technology (SBST), Vellore Institute of Technology, Vellore, India
| | - Darin Mansor Mathkor
- Research and Scientific Studies Unit, College of Nursing and Allied Health Sciences, Jazan University, Jazan, Saudi Arabia
| | - Ahdab Alsaieedi
- Department of Medical Laboratory Sciences, Faculty of Applied Medical Sciences, King Abdulaziz University, Jeddah, Saudi Arabia.,Vaccines and Immunotherapy Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Steve Harakeh
- King Fahd Medical Research Center, and Yousef Abdullatif Jameel Chair of Prophetic Medicine Application, Faculty of Medicine, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Mohammad Nasiruddin
- MedGenome Labs Ltd, Narayana Health City, Bangalore, India.,Genomics Lab, Orbito Asia Diagnostics, Coimbatore, India
| | - Shafiul Haque
- Research and Scientific Studies Unit, College of Nursing and Allied Health Sciences, Jazan University, Jazan, Saudi Arabia
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4
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Lawrence EM, Lubner MG, Pickhardt PJ, Hartung MP. Ultrasound-guided biopsy of challenging abdominopelvic targets. ABDOMINAL RADIOLOGY (NEW YORK) 2022; 47:2567-2583. [PMID: 34322727 DOI: 10.1007/s00261-021-03223-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/01/2021] [Revised: 07/16/2021] [Accepted: 07/19/2021] [Indexed: 01/18/2023]
Abstract
Percutaneous ultrasound-guided biopsies have become the standard of practice for tissue diagnosis in the abdomen and pelvis for many sites including liver, kidney, abdominal wall, and peripheral nodal stations. Additional targets may appear difficult or impossible to safely biopsy by ultrasound due to interposed bowel loops/vasculature, deep positioning, association with the bowel, or concern for poor visibility; however, by optimizing technique, it is often possible to safely and efficiently use real-time ultrasound guidance for sampling targets that normally would be considered only appropriate for CT guided or surgical/endoscopic biopsy.
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Affiliation(s)
- Edward M Lawrence
- Department of Radiology, University of Wisconsin School of Medicine and Public Health, E3/311 Clinical Science Center, 600 Highland Avenue, Madison, WI, 53792, USA
| | - Meghan G Lubner
- Department of Radiology, University of Wisconsin School of Medicine and Public Health, E3/311 Clinical Science Center, 600 Highland Avenue, Madison, WI, 53792, USA
| | - Perry J Pickhardt
- Department of Radiology, University of Wisconsin School of Medicine and Public Health, E3/311 Clinical Science Center, 600 Highland Avenue, Madison, WI, 53792, USA
| | - Michael P Hartung
- Department of Radiology, University of Wisconsin School of Medicine and Public Health, E3/311 Clinical Science Center, 600 Highland Avenue, Madison, WI, 53792, USA.
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5
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Poh J, Ngeow KC, Pek M, Tan KH, Lim JS, Chen H, Ong CK, Lim JQ, Lim ST, Lim CM, Goh BC, Choudhury Y. Analytical and clinical validation of an amplicon-based next generation sequencing assay for ultrasensitive detection of circulating tumor DNA. PLoS One 2022; 17:e0267389. [PMID: 35486650 PMCID: PMC9053827 DOI: 10.1371/journal.pone.0267389] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2021] [Accepted: 04/07/2022] [Indexed: 11/19/2022] Open
Abstract
Next-generation sequencing of circulating tumor DNA presents a promising approach to cancer diagnostics, complementing conventional tissue-based diagnostic testing by enabling minimally invasive serial testing and broad genomic coverage through a simple blood draw to maximize therapeutic benefit to patients. LiquidHALLMARK® is an amplicon-based next-generation sequencing assay developed for the genomic profiling of plasma-derived cell-free DNA (cfDNA). The comprehensive 80-gene panel profiles point mutations, insertions/deletions, copy number alterations, and gene fusions, and further detects oncogenic viruses (Epstein-Barr virus (EBV) and hepatitis B virus (HBV)) and microsatellite instability (MSI). Here, the analytical and clinical validation of the assay is reported. Analytical validation using reference genetic materials demonstrated a sensitivity of 99.38% for point mutations and 95.83% for insertions/deletions at 0.1% variant allele frequency (VAF), and a sensitivity of 91.67% for gene fusions at 0.5% VAF. In non-cancer samples, a high specificity (≥99.9999% per-base) was observed. The limit of detection for copy number alterations, EBV, HBV, and MSI were also empirically determined. Orthogonal comparison of epidermal growth factor receptor (EGFR) variant calls made by LiquidHALLMARK and a reference allele-specific polymerase chain reaction (AS-PCR) method for 355 lung cancer specimens revealed an overall concordance of 93.80%, while external validation with cobas® EGFR Mutation Test v2 for 50 lung cancer specimens demonstrated an overall concordance of 84.00%, with a 100% concordance rate for EGFR variants above 0.4% VAF. Clinical application of LiquidHALLMARK in 1,592 consecutive patients demonstrated a high detection rate (74.8% circulating tumor DNA (ctDNA)-positive in cancer samples) and broad actionability (50.0% of cancer samples harboring alterations with biological evidence for actionability). Among ctDNA-positive lung cancers, 72.5% harbored at least one biomarker with a guideline-approved drug indication. These results establish the high sensitivity, specificity, accuracy, and precision of the LiquidHALLMARK assay and supports its clinical application for blood-based genomic testing.
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Affiliation(s)
- Jonathan Poh
- Lucence Diagnostics Pte Ltd, Singapore, Singapore
| | | | - Michelle Pek
- Lucence Health Inc, Palo Alto, California, United States of America
| | - Kian-Hin Tan
- Lucence Health Inc, Palo Alto, California, United States of America
| | | | - Hao Chen
- Lucence Diagnostics Pte Ltd, Singapore, Singapore
| | | | - Jing Quan Lim
- National Cancer Centre Singapore, Singapore, Singapore
| | - Soon Thye Lim
- National Cancer Centre Singapore, Singapore, Singapore
| | - Chwee Ming Lim
- Department of Otolaryngology-Head and Neck Surgery, Singapore General Hospital, Duke-NUS Medical School, Singapore, Singapore
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6
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Handke NA, Koch DC, Muschler E, Thomas D, Luetkens JA, Attenberger UI, Kuetting D, Pieper CC, Wilhelm K. Bleeding management in computed tomography-guided liver biopsies by biopsy tract plugging with gelatin sponge slurry. Sci Rep 2021; 11:24506. [PMID: 34969958 PMCID: PMC8718535 DOI: 10.1038/s41598-021-04155-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2021] [Accepted: 12/13/2021] [Indexed: 01/12/2023] Open
Abstract
To evaluate the safety and impact of biopsy tract plugging with gelatin sponge slurry in percutaneous liver biopsy. 300 consecutive patients (158 females, 142 males; median age, 63 years) who underwent computed tomography-guided core biopsy of the liver in coaxial technique (16/18 Gauge) with and without biopsy tract plugging were retrospectively reviewed (January 2013 to May 2018). Complications were rated according to the common criteria for adverse events (NCI-CTCAE). The study cohort was dichotomized into a plugged (71%; n = 214) and an unplugged (29%; n = 86) biopsy tract group. Biopsy tract plugging with gelatin sponge slurry was technically successful in all cases. Major bleeding events were only observed in the unplugged group (0.7%; n = 2), whereas minor bleedings (4.3%) were observed in both groups (plugged, 3.6%, n = 11; unplugged, 0.7%, n = 2). Analysis of biopsies and adverse events showed a significant association between number of needle-passes and overall (P = 0.038; odds ratio: 1.395) as well as minor bleeding events (P = 0.020; odds ratio: 1.501). No complications associated with gelatin sponge slurry were observed. Biopsy tract plugging with gelatin sponge slurry is a technically easy and safe procedure that can prevent major bleeding events following liver biopsy.
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Affiliation(s)
- Nikolaus A Handke
- Department of Radiology, Johanniter-Hospital Bonn, Bonn, Germany.
- Department of Radiology, University Hospital Bonn, Bonn, Germany.
| | - Dennis C Koch
- Department of Radiology, Johanniter-Hospital Bonn, Bonn, Germany
| | - Eugen Muschler
- Department of Radiology, Johanniter-Hospital Bonn, Bonn, Germany
| | - Daniel Thomas
- Department of Radiology, University Hospital Bonn, Bonn, Germany
| | | | | | - Daniel Kuetting
- Department of Radiology, University Hospital Bonn, Bonn, Germany
| | - Claus C Pieper
- Department of Radiology, University Hospital Bonn, Bonn, Germany
| | - Kai Wilhelm
- Department of Radiology, Johanniter-Hospital Bonn, Bonn, Germany
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7
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Ferndale L, Moodley M, Chen WC, Wadee R, Wright CA, Parker MI, Willem P, Mathew CG. Processing and Analysis of Tissue Samples from Esophageal Cancer Patients in an African Setting. Biopreserv Biobank 2021; 20:185-194. [PMID: 34388042 DOI: 10.1089/bio.2021.0030] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Although infectious diseases continue to present a major health care problem in Africa, the incidence of cancer is increasing rapidly on the African continent and this merits an increased investment in cancer research in low to medium resource settings. Esophageal squamous cell carcinoma (ESCC) has a high incidence in Eastern and Southern Africa, with late clinical presentation and a very poor prognosis. There is limited research on the molecular pathology of this cancer in Africa, partly as a result of a lack of infrastructure for biobanking and sample processing in many African countries. The aim of this study was to establish a practical and robust workflow to collect, store, and process esophageal cancer samples such that both the tissue architecture and quality of the samples would be preserved and suitable for future genomic research. We developed a workflow that allows storage of fresh biopsy tissue in sterile Eppendorf tubes containing RNAlater, an efficient RNAse inhibitor. We collected 142 ESCC biopsy samples and showed that storage in RNAlater for up to 18 months did not alter tissue morphology, thus allowing histologic assessment by experienced pathologists and determination of tumor content in each biopsied sample. DNA and RNA extracted from tissue samples was assessed for purity, molecular size, and yield. The quantity and quality of nucleic acids obtained were suitable for genomic applications, and whole-exome sequencing of DNA from tumor tissues produced sequence data with a high proportion of both usable reads and correct base calling. We conclude that this workflow may be applicable to a wide range of malignancies for future genomic research in low-resource settings.
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Affiliation(s)
- Lucien Ferndale
- Department of Surgery, Grey's Hospital, Pietermaritzburg, South Africa.,Department of Surgery, College of Health Sciences, School of Clinical Medicine, University of KwaZulu-Natal, Durban, South Africa
| | - Mishalan Moodley
- Department of Molecular Medicine and Haematology, School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg and the National Health Laboratory Service, Johannesburg, South Africa
| | - Wenlong C Chen
- National Cancer Registry, National Health Laboratory Service, Johannesburg, South Africa.,Sydney Brenner Institute for Molecular Bioscience, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Reubina Wadee
- Department of Anatomical Pathology, School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg and the National Health Laboratory Service, Johannesburg, South Africa
| | - Colleen A Wright
- Department of Anatomical Pathology, School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg and the National Health Laboratory Service, Johannesburg, South Africa.,Lancet Laboratories, Johannesburg, South Africa
| | - Mohamed Iqbal Parker
- Division of Medical Biochemistry and Institute of Infectious Disease and Molecular Medicine, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
| | - Pascale Willem
- Department of Molecular Medicine and Haematology, School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg and the National Health Laboratory Service, Johannesburg, South Africa
| | - Christopher G Mathew
- Sydney Brenner Institute for Molecular Bioscience, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa.,Division of Human Genetics, National Health Laboratory Service, and School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
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8
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Limaye S. Synchronized Tissue Acquisition Techniques for Novel Biomarker Discovery: Are You Ready to Waltz? JOURNAL OF IMMUNOTHERAPY AND PRECISION ONCOLOGY 2021; 4:168-169. [PMID: 35663103 PMCID: PMC9138434 DOI: 10.36401/jipo-21-x3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/17/2021] [Accepted: 05/18/2021] [Indexed: 05/01/2023]
Affiliation(s)
- Sewanti Limaye
- Department of Medical Oncology, Kokilaben Dhirubhai Ambani Hospital, Mumbai, India
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9
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Annaratone L, De Palma G, Bonizzi G, Sapino A, Botti G, Berrino E, Mannelli C, Arcella P, Di Martino S, Steffan A, Daidone MG, Canzonieri V, Parodi B, Paradiso AV, Barberis M, Marchiò C. Basic principles of biobanking: from biological samples to precision medicine for patients. Virchows Arch 2021; 479:233-246. [PMID: 34255145 PMCID: PMC8275637 DOI: 10.1007/s00428-021-03151-0] [Citation(s) in RCA: 55] [Impact Index Per Article: 18.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2021] [Revised: 06/24/2021] [Accepted: 06/30/2021] [Indexed: 12/15/2022]
Abstract
The term "biobanking" is often misapplied to any collection of human biological materials (biospecimens) regardless of requirements related to ethical and legal issues or the standardization of different processes involved in tissue collection. A proper definition of biobanks is large collections of biospecimens linked to relevant personal and health information (health records, family history, lifestyle, genetic information) that are held predominantly for use in health and medical research. In addition, the International Organization for Standardization, in illustrating the requirements for biobanking (ISO 20387:2018), stresses the concept of biobanks being legal entities driving the process of acquisition and storage together with some or all of the activities related to collection, preparation, preservation, testing, analysing and distributing defined biological material as well as related information and data. In this review article, we aim to discuss the basic principles of biobanking, spanning from definitions to classification systems, standardization processes and documents, sustainability and ethical and legal requirements. We also deal with emerging specimens that are currently being generated and shaping the so-called next-generation biobanking, and we provide pragmatic examples of cancer-associated biobanking by discussing the process behind the construction of a biobank and the infrastructures supporting the implementation of biobanking in scientific research.
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Affiliation(s)
- Laura Annaratone
- Candiolo Cancer Institute, FPO-IRCCS, Candiolo, Italy.,Department of Medical Sciences, University of Turin, Turin, Italy
| | - Giuseppe De Palma
- Institutional BioBank, Experimental Oncology and Biobank Management Unit, IRCCS Istituto Tumori "Giovanni Paolo II", Bari, Italy
| | - Giuseppina Bonizzi
- Unit of Histopathology and Molecular Diagnostics, Division of Pathology and Laboratory Medicine, IEO, European Institute of Oncology, IRCCS, Milan, Italy
| | - Anna Sapino
- Candiolo Cancer Institute, FPO-IRCCS, Candiolo, Italy.,Department of Medical Sciences, University of Turin, Turin, Italy
| | - Gerardo Botti
- Istituto Nazionale Tumori, Fondazione G. Pascale, IRCCS, Naples, Italy
| | - Enrico Berrino
- Candiolo Cancer Institute, FPO-IRCCS, Candiolo, Italy.,Department of Medical Sciences, University of Turin, Turin, Italy
| | | | - Pamela Arcella
- Department of Oncology, University of Turin, Turin, Italy
| | - Simona Di Martino
- Department of Pathology, IRCCS Regina Elena National Cancer Institute, Rome, Italy
| | - Agostino Steffan
- Immunopathology and Cancer Biomarkers, IRCCS CRO Aviano-National Cancer Institute, Aviano, Italy
| | | | - Vincenzo Canzonieri
- Department of Medical, Surgical and Health Sciences, University of Trieste, Trieste, Italy.,Pathology Unit, IRCCS CRO Aviano-National Cancer Institute, Aviano, Italy
| | | | - Angelo Virgilio Paradiso
- Institutional BioBank, Experimental Oncology and Biobank Management Unit, IRCCS Istituto Tumori "Giovanni Paolo II", Bari, Italy
| | - Massimo Barberis
- Unit of Histopathology and Molecular Diagnostics, Division of Pathology and Laboratory Medicine, IEO, European Institute of Oncology, IRCCS, Milan, Italy
| | - Caterina Marchiò
- Candiolo Cancer Institute, FPO-IRCCS, Candiolo, Italy. .,Department of Medical Sciences, University of Turin, Turin, Italy.
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10
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Labib M, Kelley SO. Circulating tumor cell profiling for precision oncology. Mol Oncol 2021; 15:1622-1646. [PMID: 33448107 PMCID: PMC8169448 DOI: 10.1002/1878-0261.12901] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2020] [Revised: 12/19/2020] [Accepted: 01/11/2021] [Indexed: 02/06/2023] Open
Abstract
Analysis of circulating tumor cells (CTCs) collected from patient's blood offers a broad range of opportunities in the field of precision oncology. With new advances in profiling technology, it is now possible to demonstrate an association between the molecular profiles of CTCs and tumor response to therapy. In this Review, we discuss mechanisms of tumor resistance to therapy and their link to phenotypic and genotypic properties of CTCs. We summarize key technologies used to isolate and analyze CTCs and discuss recent clinical studies that examined CTCs for genomic and proteomic predictors of responsiveness to therapy. We also point out current limitations that still hamper the implementation of CTCs into clinical practice. We finally reflect on how these shortcomings can be addressed with the likely contribution of multiparametric approaches and advanced data analytics.
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Affiliation(s)
- Mahmoud Labib
- Department of Pharmaceutical SciencesUniversity of TorontoCanada
| | - Shana O. Kelley
- Department of Pharmaceutical SciencesUniversity of TorontoCanada
- Institute for Biomaterials and Biomedical EngineeringUniversity of TorontoCanada
- Department of BiochemistryUniversity of TorontoCanada
- Department of ChemistryUniversity of TorontoCanada
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11
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Abstract
BACKGROUND Systems biology is a rapidly advancing field of science that allows us to look into disease mechanisms, patient diagnosis and stratification, and drug development in a completely new light. It is based on the utilization of unbiased computational systems free of the traditional experimental approaches based on personal choices of what is important and what select experiments should be performed to obtain the expected results. METHODS Systems biology can be applied to inflammatory bowel disease (IBD) by learning basic concepts of omes and omics and how omics-derived "big data" can be integrated to discover the biological networks underlying highly complex diseases like IBD. Once these biological networks (interactomes) are identified, then the molecules controlling the disease network can be singled out and specific blockers developed. RESULTS The field of systems biology in IBD is just emerging, and there is still limited information on how to best utilize its power to advance our understanding of Crohn disease and ulcerative colitis to develop novel therapeutic strategies. Few centers have embraced systems biology in IBD, but the creation of international consortia and large biobanks will make biosamples available to basic and clinical IBD investigators for further research studies. CONCLUSIONS The implementation of systems biology is indispensable and unavoidable, and the patient and medical communities will both benefit immensely from what it will offer in the near future.
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Affiliation(s)
- Claudio Fiocchi
- Department of Inflammation & Immunity, Lerner Research Institute, Cleveland Clinic, Cleveland, Ohio, USA.,Department of Gastroenterology, Hepatology and Nutrition, Digestive Disease and Surgery Institute, Cleveland Clinic, Cleveland, Ohio, USA
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12
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Gambaro K, Marques M, McNamara S, Couetoux du Tertre M, Diaz Z, Hoffert C, Srivastava A, Hébert S, Samson B, Lespérance B, Ko Y, Dalfen R, St‐Hilaire E, Sideris L, Couture F, Burkes R, Harb M, Camlioglu E, Gologan A, Pelsser V, Constantin A, Greenwood CM, Tejpar S, Kavan P, Kleinman CL, Batist G. Copy number and transcriptome alterations associated with metastatic lesion response to treatment in colorectal cancer. Clin Transl Med 2021; 11:e401. [PMID: 33931971 PMCID: PMC8087915 DOI: 10.1002/ctm2.401] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2020] [Revised: 04/09/2021] [Accepted: 04/12/2021] [Indexed: 12/16/2022] Open
Abstract
BACKGROUND Therapeutic resistance is the main cause of death in metastatic colorectal cancer. To investigate genomic plasticity, most specifically of metastatic lesions, associated with response to first-line systemic therapy, we collected longitudinal liver metastatic samples and characterized the copy number aberration (CNA) landscape and its effect on the transcriptome. METHODS Liver metastatic biopsies were collected prior to treatment (pre, n = 97) and when clinical imaging demonstrated therapeutic resistance (post, n = 43). CNAs were inferred from whole exome sequencing and were correlated with both the status of the lesion and overall patient progression-free survival (PFS). We used RNA sequencing data from the same sample set to validate aberrations as well as independent datasets to prioritize candidate genes. RESULTS We identified a significantly increased frequency gain of a unique CN, in liver metastatic lesions after first-line treatment, on chr18p11.32 harboring 10 genes, including TYMS, which has not been reported in primary tumors (GISTIC method and test of equal proportions, FDR-adjusted p = 0.0023). CNA lesion profiles exhibiting different treatment responses were compared and we detected focal genomic divergences in post-treatment resistant lesions but not in responder lesions (two-tailed Fisher's Exact test, unadjusted p ≤ 0.005). The importance of examining metastatic lesions is highlighted by the fact that 15 out of 18 independently validated CNA regions found to be associated with PFS in this study were only identified in the metastatic lesions and not in the primary tumors. CONCLUSION This investigation of genomic-phenotype associations in a large colorectal cancer liver metastases cohort identified novel molecular features associated with treatment response, supporting the clinical importance of collecting metastatic samples in a defined clinical setting.
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Affiliation(s)
- Karen Gambaro
- Canadian National Centres of Excellence—Exactis Innovation5450 Cote‐des‐NeigesMontrealQuebecH3T 1Y6Canada
- McGill University‐Segal Cancer Centre, Jewish General Hospital3755 Côte Ste‐CatherineMontrealQuebecH3T 1E2Canada
| | - Maud Marques
- Canadian National Centres of Excellence—Exactis Innovation5450 Cote‐des‐NeigesMontrealQuebecH3T 1Y6Canada
- McGill University‐Segal Cancer Centre, Jewish General Hospital3755 Côte Ste‐CatherineMontrealQuebecH3T 1E2Canada
| | - Suzan McNamara
- Canadian National Centres of Excellence—Exactis Innovation5450 Cote‐des‐NeigesMontrealQuebecH3T 1Y6Canada
| | | | - Zuanel Diaz
- Canadian National Centres of Excellence—Exactis Innovation5450 Cote‐des‐NeigesMontrealQuebecH3T 1Y6Canada
| | - Cyrla Hoffert
- Canadian National Centres of Excellence—Exactis Innovation5450 Cote‐des‐NeigesMontrealQuebecH3T 1Y6Canada
- McGill University‐Segal Cancer Centre, Jewish General Hospital3755 Côte Ste‐CatherineMontrealQuebecH3T 1E2Canada
| | - Archana Srivastava
- Canadian National Centres of Excellence—Exactis Innovation5450 Cote‐des‐NeigesMontrealQuebecH3T 1Y6Canada
- McGill University‐Segal Cancer Centre, Jewish General Hospital3755 Côte Ste‐CatherineMontrealQuebecH3T 1E2Canada
| | - Steven Hébert
- McGill University‐Segal Cancer Centre, Jewish General Hospital3755 Côte Ste‐CatherineMontrealQuebecH3T 1E2Canada
| | - Benoit Samson
- Charles LeMoyne Hospital3120 Taschereau Blvd.Greenfield ParkQuebecJ4V 2H1Canada
| | | | - Yoo‐Joung Ko
- Sunnybrook Health Science Centre2075 Bayview Ave.TorontoOntarioM4N 3M5Canada
| | - Richard Dalfen
- St. Mary's Hospital3830 LacombeMontrealQuebecH3T 1M5Canada
| | - Eve St‐Hilaire
- Georges Dumont Hospital220 Avenue UniversiteMonctonNew BrunswickE1C 2Z3Canada
| | - Lucas Sideris
- Hôpital Maisonneuve Rosemont5415 Assumption BlvdMontrealQuebecH1T 2M4Canada
| | - Felix Couture
- Hôtel‐Dieu de Quebec11 Cote du PalaisMontrealQuebecG1R 2J6Canada
| | - Ronald Burkes
- Mount Sinai Hospital600 University AvenueTorontoOntarioM5G 1X5Canada
| | - Mohammed Harb
- Moncton Hospital135 Macbeath AveMonctonNew BrunswickE1C 6Z8Canada
| | - Errol Camlioglu
- McGill University‐Segal Cancer Centre, Jewish General Hospital3755 Côte Ste‐CatherineMontrealQuebecH3T 1E2Canada
| | - Adrian Gologan
- McGill University‐Segal Cancer Centre, Jewish General Hospital3755 Côte Ste‐CatherineMontrealQuebecH3T 1E2Canada
| | - Vincent Pelsser
- McGill University‐Segal Cancer Centre, Jewish General Hospital3755 Côte Ste‐CatherineMontrealQuebecH3T 1E2Canada
| | - André Constantin
- McGill University‐Segal Cancer Centre, Jewish General Hospital3755 Côte Ste‐CatherineMontrealQuebecH3T 1E2Canada
| | - Celia M.T. Greenwood
- McGill University‐Segal Cancer Centre, Jewish General Hospital3755 Côte Ste‐CatherineMontrealQuebecH3T 1E2Canada
- Gerald Bronfman Department of OncologyMcGill University3755 Côte Ste‐CatherineMontrealQuebecH3T 1E2Canada
- Department of Epidemiology, Biostatistics and Occupational HealthMcGill University3755 Côte Ste‐CatherineMontrealQuebecH3T 1E2Canada
| | - Sabine Tejpar
- Digestive Oncology UnitKatholieke Universiteit LeuvenOude Markt 13Leuven3000Belgium
| | - Petr Kavan
- McGill University‐Segal Cancer Centre, Jewish General Hospital3755 Côte Ste‐CatherineMontrealQuebecH3T 1E2Canada
| | - Claudia L. Kleinman
- McGill University‐Segal Cancer Centre, Jewish General Hospital3755 Côte Ste‐CatherineMontrealQuebecH3T 1E2Canada
- Department of Human GeneticsLady Davis Research Institute, McGill University3755 Côte Ste‐CatherineMontrealQuebecH3T 1E2Canada
| | - Gerald Batist
- McGill University‐Segal Cancer Centre, Jewish General Hospital3755 Côte Ste‐CatherineMontrealQuebecH3T 1E2Canada
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Early, On-Treatment Levels and Dynamic Changes of Genomic Instability in Circulating Tumor DNA Predict Response to Treatment and Outcome in Metastatic Breast Cancer Patients. Cancers (Basel) 2021; 13:cancers13061331. [PMID: 33809567 PMCID: PMC7999382 DOI: 10.3390/cancers13061331] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2021] [Revised: 03/11/2021] [Accepted: 03/13/2021] [Indexed: 12/14/2022] Open
Abstract
Simple Summary Liquid biopsies offer the opportunity to monitor cancer progression and the response to treatment with a simple blood test. However, most of the technologies available analyze specific molecular alterations or require tumor tissue for analysis, which is very difficult to obtain in metastatic patients. In this study, we made use of a novel method that allows to measure the overall molecular tumor changes in a blood sample without the need for tissue or to look for specific molecular alterations. We demonstrated the ability of this method to very early monitor the treatment clinical response and progression in a cohort of metastatic breast cancer patients. Abstract Background: Circulating tumor DNA (ctDNA) offers high sensitivity and specificity in metastatic cancer. However, many ctDNA assays rely on specific mutations in recurrent genes or require the sequencing of tumor tissue, difficult to do in a metastatic disease. The purpose of this study was to define the predictive and prognostic values of the whole-genome sequencing (WGS) of ctDNA in metastatic breast cancer (MBC). Methods: Plasma from 25 patients with MBC were taken at the baseline, prior to treatment (T0), one week (T1) and two weeks (T2) after treatment initiation and subjected to low-pass WGS. DNA copy number changes were used to calculate a Genomic Instability Number (GIN). A minimum predefined GIN value of 170 indicated detectable ctDNA. GIN values were correlated with the treatment response at three and six months by Response Evaluation Criteria in Solid Tumours assessed by imaging (RECIST) criteria and with overall survival (OS). Results: GIN values were detectable (>170) in 64% of patients at the baseline and were significantly prognostic (41 vs. 18 months OS for nondetectable vs. detectable GIN). Detectable GIN values at T1 and T2 were significantly associated with poor OS. Declines in GIN at T1 and T2 of > 50% compared to the baseline were associated with three-month response and, in the case of T1, with OS. On the other hand, a rise in GIN at T2 was associated with a poor response at three months. Conclusions: Very early measurements using WGS of cell-free DNA (cfDNA) from the plasma of MBC patients provided a tumor biopsy-free approach to ctDNA measurement that was both predictive of the early tumor response at three months and prognostic.
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14
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Pavan A, Bragadin AB, Calvetti L, Ferro A, Zulato E, Attili I, Nardo G, Dal Maso A, Frega S, Menin AG, Fassan M, Calabrese F, Pasello G, Guarneri V, Aprile G, Conte P, Rosell R, Indraccolo S, Bonanno L. Role of next generation sequencing-based liquid biopsy in advanced non-small cell lung cancer patients treated with immune checkpoint inhibitors: impact of STK11, KRAS and TP53 mutations and co-mutations on outcome. Transl Lung Cancer Res 2021; 10:202-220. [PMID: 33569305 PMCID: PMC7867770 DOI: 10.21037/tlcr-20-674] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
BACKGROUND Characterization of tumor-related genetic alterations is promising for the screening of new predictive markers in non-small cell lung cancer (NSCLC). Aim of the study was to evaluate prognostic and predictive role of most frequent tumor-associated genetic alterations detected in plasma before starting immune checkpoint inhibitors (ICIs). METHODS Between January 2017 and October 2019, advanced NSCLC patients were prospectively screened with plasma next-generation sequencing (NGS) while included in two trials: VISION (NCT02864992), using Guardant360® test, and MAGIC (Monitoring Advanced NSCLC through plasma Genotyping during Immunotherapy: Clinical feasibility and application), using Myriapod NGS-IL 56G Assay. A control group of patients not receiving ICIs was analyzed. RESULTS A total of 103 patients receiving ICIs were analyzed: median overall survival (OS) was 20.8 (95% CI: 16.7-24.9) months and median immune-related progression free disease (irPFS) 4.2 (95% CI: 2.3-6.1) months. TP53 mutations in plasma negatively affected OS both in patients treated with ICIs and in control group (P=0.001 and P=0.009), indicating a prognostic role. STK11 mutated patients (n=9) showed a trend for worse OS only if treated with ICIs. The presence of KRAS/STK11 co-mutation and KRAS/STK11/TP53 co-mutation affected OS only in patients treated with ICIs (HR =10.936, 95% CI: 2.337-51.164, P=0.002; HR =17.609, 95% CI: 3.777-82.089, P<0.001, respectively), indicating a predictive role. CONCLUSIONS Plasma genotyping demonstrated prognostic value of TP53 mutations and predictive value of KRAS/STK11 and KRAS/STK11/TP53 co-mutations.
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Affiliation(s)
- Alberto Pavan
- Medical Oncology 2, Istituto Oncologico Veneto IOV - IRCCS, Padova, Italy
| | - Andrea Boscolo Bragadin
- Department of Surgery, Oncology and Gastroenterology, Università degli Studi di Padova, Padova, Italy
| | - Lorenzo Calvetti
- Department of Oncology, San Bortolo General Hospital, ULSS8 Berica - East District, Vicenza, Italy
| | - Alessandra Ferro
- Medical Oncology 2, Istituto Oncologico Veneto IOV - IRCCS, Padova, Italy;,Department of Surgery, Oncology and Gastroenterology, Università degli Studi di Padova, Padova, Italy
| | - Elisabetta Zulato
- Immunology and Molecular Oncology Unit, Istituto Oncologico Veneto IOV - IRCCS, Padova, Italy
| | - Ilaria Attili
- Medical Oncology 2, Istituto Oncologico Veneto IOV - IRCCS, Padova, Italy;,Department of Surgery, Oncology and Gastroenterology, Università degli Studi di Padova, Padova, Italy
| | - Giorgia Nardo
- Immunology and Molecular Oncology Unit, Istituto Oncologico Veneto IOV - IRCCS, Padova, Italy
| | - Alessandro Dal Maso
- Medical Oncology 2, Istituto Oncologico Veneto IOV - IRCCS, Padova, Italy;,Department of Surgery, Oncology and Gastroenterology, Università degli Studi di Padova, Padova, Italy
| | - Stefano Frega
- Medical Oncology 2, Istituto Oncologico Veneto IOV - IRCCS, Padova, Italy
| | - Andrea Giovanni Menin
- Department of Pathology, San Bortolo General Hospital, ULSS8 Berica - East District, Vicenza, Italy
| | - Matteo Fassan
- Department of Medicine, Surgical Pathology and Cytopathology Unit, Università degli Studi di Padova, Padova, Italy
| | - Fiorella Calabrese
- Department of Cardiac, Thoracic, Vascular Sciences and Public Health, Università degli Studi di Padova, Padova, Italy
| | - Giulia Pasello
- Medical Oncology 2, Istituto Oncologico Veneto IOV - IRCCS, Padova, Italy
| | - Valentina Guarneri
- Medical Oncology 2, Istituto Oncologico Veneto IOV - IRCCS, Padova, Italy;,Department of Surgery, Oncology and Gastroenterology, Università degli Studi di Padova, Padova, Italy
| | - Giuseppe Aprile
- Department of Oncology, San Bortolo General Hospital, ULSS8 Berica - East District, Vicenza, Italy
| | - PierFranco Conte
- Medical Oncology 2, Istituto Oncologico Veneto IOV - IRCCS, Padova, Italy;,Department of Surgery, Oncology and Gastroenterology, Università degli Studi di Padova, Padova, Italy
| | - Rafael Rosell
- Cancer Biology and Precision Medicine Program, Catalan Institute of Oncology, Germans Trias I Pujol Health Sciences Institute and Hospital Badalona, Barcelona, Spain
| | - Stefano Indraccolo
- Immunology and Molecular Oncology Unit, Istituto Oncologico Veneto IOV - IRCCS, Padova, Italy
| | - Laura Bonanno
- Medical Oncology 2, Istituto Oncologico Veneto IOV - IRCCS, Padova, Italy
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15
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Jensen PSH, Johansen M, Bak LK, Jensen LJ, Kjær C. Yield and Integrity of RNA from Brain Samples are Largely Unaffected by Pre-analytical Procedures. Neurochem Res 2020; 46:447-454. [PMID: 33249516 DOI: 10.1007/s11064-020-03183-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2020] [Revised: 11/13/2020] [Accepted: 11/17/2020] [Indexed: 11/28/2022]
Abstract
Gene expression studies are reported to be influenced by pre-analytical factors that can compromise RNA yield and integrity, which in turn may confound the experimental findings. Here we investigate the impact of four pre-analytical factors on brain-derived RNA: time-before-collection, tissue specimen size, tissue collection method, and RNA isolation method. We report no significant differences in RNA yield or integrity between 20 mg and 60 mg tissue samples collected in either liquid nitrogen or the RNAlater stabilizing solution. Isolation of RNA employing the TRIzol reagent resulted in a higher yield compared to isolation via the QIAcube kit while the latter resulted in RNA of slightly better integrity. Keeping brain tissue samples at room temperature for up to 160 min prior to collection and isolation of RNA resulted in no significant difference in yield or integrity. Our findings have significant practical and financial consequences for clinical genomic departments and other laboratory settings performing large-scale routine RNA expression analysis of brain samples.
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Affiliation(s)
- Pernille Søs Hovgaard Jensen
- Department of Technology, Faculty of Health and Technology, University College Copenhagen, 2200, Copenhagen, Denmark
| | - Maja Johansen
- Department of Technology, Faculty of Health and Technology, University College Copenhagen, 2200, Copenhagen, Denmark
| | - Lasse K Bak
- Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, 2100, Copenhagen, Denmark
| | - Lars Juhl Jensen
- Disease Systems Biology Program, Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, 2200, Copenhagen, Denmark
| | - Christina Kjær
- Department of Technology, Faculty of Health and Technology, University College Copenhagen, 2200, Copenhagen, Denmark. .,Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, 2100, Copenhagen, Denmark.
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16
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The value of interventional radiology in clinical trial teams: experience from the BATTLE lung cancer trials. Clin Radiol 2020; 76:155.e25-155.e34. [PMID: 33268083 DOI: 10.1016/j.crad.2020.09.024] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2020] [Accepted: 09/30/2020] [Indexed: 11/22/2022]
Abstract
AIM To report on the multidisciplinary approach, focusing specifically on the role of the interventional radiologist (IR), used to support the Biomarker-integrated Approaches of Targeted Therapy for Lung Cancer Elimination (BATTLE) and BATTLE-2 trials. MATERIALS AND METHODS Patients who underwent percutaneous image-guided biopsy for the BATTLE and BATTLE-2 trials were reviewed. A radiology-based, three-point, lesion-scoring system was developed and used by two IRs. Lesions were given a score of 3 (most likely to yield sufficient material for biomarker analysis) if they met the following criteria: size >2 cm, solid mass, demonstrated imaging evidence of viability, and were technically easy to sample. Lesions not meeting all four criteria were scored 2 with the missing criteria noted as negative factors. Lesions considered to have risks that outweighed potential benefits receive a score of 1 and were not biopsied. Univariate and multivariate analyses were performed to evaluate the score's ability to predict successful yield for biomarker adequacy. RESULTS A total of 555 biopsies were performed. The overall yield for analysis of the required biomarkers was 86.1% (478/555), and 84% (268/319) and 88.9% (210/236) for BATTLE and BATTLE-2, respectively (p=0.09). Lesions receiving a score of 3 were adequate for biomarker analysis in 89% of cases. Lesions receiving a score of 2 with more than two negative factors were adequate for molecular analysis in 69.2% (IR1, p=0.03) and 74% (IR2, p=0.04) of cases. The two IRs scored 78.4% of the lesions the same indicating moderate agreement (kappa=0.55; 95% confidence interval [CI]: 0.48, 0.61). CONCLUSIONS IRs add value to clinical trial teams by optimising lesions selected for biopsy and biomarker analysis.
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17
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O'Shea A, Tam AL, Kilcoyne A, Flaherty KT, Lee SI. Image-guided biopsy in the age of personalised medicine: strategies for success and safety. Clin Radiol 2020; 76:154.e1-154.e9. [PMID: 32896425 DOI: 10.1016/j.crad.2020.08.010] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2020] [Accepted: 08/04/2020] [Indexed: 12/28/2022]
Abstract
Oncology has progressed into an era of personalised medicine, whereby the therapeutic regimen is tailored to the molecular profile of the patient's cancer. Determining personalised therapeutic options is achieved by using tumour genomics and proteomics to identify the specific molecular targets against which candidate drugs can interact. Several dozen targeted drugs, many for multiple cancer types are already widely in clinical use. Molecular profiling of tumours is contingent on high-quality biopsy specimens and the most common method of tissue sampling is image-guided biopsy. Thus, for radiologists performing these biopsies, the paradigm has now shifted away from obtaining specimens simply for histopathological diagnosis to acquiring larger amounts of viable tumour cells for DNA, RNA, or protein analysis. These developments have highlighted the central role now played by radiologists in the delivery of personalised cancer care. This review describes the principles of molecular profiling assays and biopsy techniques for optimising yield, and describes a scoring system to assist in patient selection for percutaneous biopsy.
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Affiliation(s)
- A O'Shea
- Department of Radiology, Division of Abdominal Imaging, Massachusetts General Hospital, Boston, MA, 02114, USA.
| | - A L Tam
- Department of Interventional Radiology, Division of Diagnostic Imaging, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - A Kilcoyne
- Department of Radiology, Division of Abdominal Imaging, Massachusetts General Hospital, Boston, MA, 02114, USA
| | - K T Flaherty
- Department of Medicine, Division of Oncology, Massachusetts General Hospital, Boston, MA, 02114, USA
| | - S I Lee
- Department of Radiology, Division of Abdominal Imaging, Massachusetts General Hospital, Boston, MA, 02114, USA
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18
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Ko J, Oh J, Ahmed MS, Carlson JCT, Weissleder R. Ultra-fast cycling for multiplexed cellular fluorescence imaging. ANGEWANDTE CHEMIE (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2020; 132:6906-6913. [PMID: 34366494 PMCID: PMC8340598 DOI: 10.1002/ange.201915153] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/28/2019] [Indexed: 11/11/2022]
Abstract
Rapid analysis of single and scant cell populations is essential in modern diagnostics, yet existing methods are often limited and slow. Here we describe an ultra-fast, highly efficient cycling method for the analysis of single cells based on unique linkers for tetrazine (Tz) / trans-cyclooctene (TCO) mediated quenching. Surprisingly, the quenching reaction rates were more than 3 orders of magnitude faster (t1/2 < 1 sec) than predicted. This allowed multi-cycle staining and immune cell profiling within an hour, leveraging the accelerated kinetics to open new diagnostic possibilities for rapid cellular analyses.
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Affiliation(s)
- Jina Ko
- Center for Systems Biology, Massachusetts General Hospital Research Institute, Boston, MA 02114
| | - Juhyun Oh
- Center for Systems Biology, Massachusetts General Hospital Research Institute, Boston, MA 02114
| | - Maaz S. Ahmed
- Center for Systems Biology, Massachusetts General Hospital Research Institute, Boston, MA 02114
| | - Jonathan C. T. Carlson
- Center for Systems Biology, Massachusetts General Hospital Research Institute, Boston, MA 02114
- Cancer Center, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114
| | - Ralph Weissleder
- Center for Systems Biology, Massachusetts General Hospital Research Institute, Boston, MA 02114
- Department of Systems Biology, Harvard Medical School, Boston, MA 02115
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19
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Cescon DW, Bratman SV, Chan SM, Siu LL. Circulating tumor DNA and liquid biopsy in oncology. ACTA ACUST UNITED AC 2020; 1:276-290. [DOI: 10.1038/s43018-020-0043-5] [Citation(s) in RCA: 164] [Impact Index Per Article: 41.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2019] [Accepted: 02/18/2020] [Indexed: 02/07/2023]
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20
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Ko J, Oh J, Ahmed MS, Carlson JCT, Weissleder R. Ultra-fast Cycling for Multiplexed Cellular Fluorescence Imaging. Angew Chem Int Ed Engl 2020; 59:6839-6846. [PMID: 32004403 DOI: 10.1002/anie.201915153] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2019] [Revised: 01/08/2020] [Indexed: 12/26/2022]
Abstract
Rapid analysis of single and scant cell populations is essential in modern diagnostics, yet existing methods are often limited and slow. Herein, we describe an ultra-fast, highly efficient cycling method for the analysis of single cells based on unique linkers for tetrazine (Tz)/trans-cyclooctene (TCO)-mediated quenching. Surprisingly, the quenching reaction rates were more than 3 orders of magnitude faster (t1/2 <1 s) than predicted. This allowed multi-cycle staining and immune cell profiling within an hour, leveraging the accelerated kinetics to open new diagnostic possibilities for rapid cellular analyses.
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Affiliation(s)
- Jina Ko
- Center for Systems Biology, Massachusetts General Hospital Research Institute, Boston, MA, 02114, USA
| | - Juhyun Oh
- Center for Systems Biology, Massachusetts General Hospital Research Institute, Boston, MA, 02114, USA
| | - Maaz S Ahmed
- Center for Systems Biology, Massachusetts General Hospital Research Institute, Boston, MA, 02114, USA
| | - Jonathan C T Carlson
- Center for Systems Biology, Massachusetts General Hospital Research Institute, Boston, MA, 02114, USA.,Cancer Center, Massachusetts General Hospital and Harvard Medical School, Boston, MA, 02114, USA
| | - Ralph Weissleder
- Center for Systems Biology, Massachusetts General Hospital Research Institute, Boston, MA, 02114, USA.,Department of Systems Biology, Harvard Medical School, Boston, MA, 02115, USA
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21
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Krishnamurthy S, Sabir S, Ban K, Wu Y, Sheth R, Tam A, Meric-Bernstam F, Shaw K, Mills G, Bassett R, Hamilton S, Hicks M, Gupta S. Comparison of Real-Time Fluorescence Confocal Digital Microscopy With Hematoxylin-Eosin-Stained Sections of Core-Needle Biopsy Specimens. JAMA Netw Open 2020; 3:e200476. [PMID: 32134465 PMCID: PMC7059022 DOI: 10.1001/jamanetworkopen.2020.0476] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
IMPORTANCE Strategies to procure high-quality core-needle biopsy (CNB) specimens are critical for making basic tissue diagnoses and for ancillary testing. OBJECTIVES To investigate acquisition of fluorescence confocal microscopy (FCM) images of interventional radiology (IR)-guided CNB in real time in the radiology suite and to compare the accuracy of FCM diagnoses with those of hematoxylin-eosin (H&E)-stained CNB sections. DESIGN, SETTING, AND PARTICIPANTS In this diagnostic study, FCM imaging of IR-guided CNBs was performed in the radiology suite at a major cancer center for patients with an imaging abnormality from August 1, 2016, to April 30, 2019. The time taken to acquire FCM images and the quality of FCM images based on percentage of interpretable tissue with optimal resolution was recorded. The FCM images were read by 2 pathologists and categorized as nondiagnostic, benign/atypical, or suspicious/malignant; these diagnoses were compared with those made using H&E-stained tissue sections. Cases with discrepant diagnosis were reassessed by the pathologists together for a consensus diagnosis. Data were analyzed from June 3 to July 19, 2019. INTERVENTIONS Each IR-guided CNB was stained with 0.6mM acridine orange, subjected to FCM imaging, and then processed to generate H&E-stained sections. MAIN OUTCOMES AND MEASURES Mean time taken for acquisition of FCM images, quality of FCM images based on interpretable percentage of the image, and accuracy of diagnostic categorization based on FCM images compared with H&E-stained sections. RESULTS A total of 105 patients (57 male [54.3%]; mean [SD] age, 63 [13] years) underwent IR-guided CNBs in a mean (SD) of 7 (2) minutes each. The FCM images showed at least 20% of the tissue with optimal quality in 101 CNB specimens (96.2%). The FCM images were accurately interpreted by the 2 pathologists in 100 of 105 cases (95.2%) (2 false-positive and 3 false-negative) and 90 of 105 cases (85.7%) (6 false-positive and 9 false-negative). A reassessment of 14 discordant diagnoses resulted in consensus diagnoses that were accurate in 101 of 105 cases (96.2%) (1 false-positive and 3 false-negative). CONCLUSIONS AND RELEVANCE The ease of acquisition of FCM images of acceptable quality and the high accuracy of the diagnoses suggest that FCM may be useful for rapid evaluation of IR-guided CNBs. This approach warrants further investigation.
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Affiliation(s)
- Savitri Krishnamurthy
- Division of Pathology and Laboratory Medicine, The University of Texas MD Anderson Cancer Center, Houston
| | - Sharjeel Sabir
- Department of Radiology, Scripps Mercy Hospital, San Diego, California
| | - Kechen Ban
- Division of Pathology and Laboratory Medicine, The University of Texas MD Anderson Cancer Center, Houston
| | - Yun Wu
- Division of Pathology and Laboratory Medicine, The University of Texas MD Anderson Cancer Center, Houston
| | - Rahul Sheth
- Department of Interventional Radiology, The University of Texas MD Anderson Cancer Center, Houston
| | - Alda Tam
- Department of Interventional Radiology, The University of Texas MD Anderson Cancer Center, Houston
| | - Funda Meric-Bernstam
- Department of Investigational Cancer Therapeutics, The University of Texas MD Anderson Cancer Center, Houston
- Sheikh Khalifa Bin Zayed Al Nahyan Institute for Personalized Cancer Therapy, The University of Texas MD Anderson Cancer Center, Houston
| | - Kenna Shaw
- Sheikh Khalifa Bin Zayed Al Nahyan Institute for Personalized Cancer Therapy, The University of Texas MD Anderson Cancer Center, Houston
| | - Gordon Mills
- Oregon Health and Science University Knight Cancer Institute, Portland
| | - Roland Bassett
- Department of Biostatistics, The University of Texas MD Anderson Cancer Center, Houston
| | - Stanley Hamilton
- Division of Pathology and Laboratory Medicine, The University of Texas MD Anderson Cancer Center, Houston
| | - Marshall Hicks
- Department of Interventional Radiology, The University of Texas MD Anderson Cancer Center, Houston
| | - Sanjay Gupta
- Department of Interventional Radiology, The University of Texas MD Anderson Cancer Center, Houston
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22
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Proteogenomics of Colorectal Cancer Liver Metastases: Complementing Precision Oncology with Phenotypic Data. Cancers (Basel) 2019; 11:cancers11121907. [PMID: 31805664 PMCID: PMC6966481 DOI: 10.3390/cancers11121907] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2019] [Revised: 11/22/2019] [Accepted: 11/26/2019] [Indexed: 12/17/2022] Open
Abstract
Hotspot testing for activating KRAS mutations is used in precision oncology to select colorectal cancer (CRC) patients who are eligible for anti-EGFR treatment. However, even for KRASwildtype tumors anti-EGFR response rates are <30%, while mutated-KRAS does not entirely rule out response, indicating the need for improved patient stratification. We performed proteogenomic phenotyping of KRASwildtype and KRASG12V CRC liver metastases (mCRC). Among >9000 proteins we detected considerable expression changes including numerous proteins involved in progression and resistance in CRC. We identified peptides representing a number of predicted somatic mutations, including KRASG12V. For eight of these, we developed a multiplexed parallel reaction monitoring (PRM) mass spectrometry assay to precisely quantify the mutated and canonical protein variants. This allowed phenotyping of eight mCRC tumors and six paired healthy tissues, by determining mutation rates on the protein level. Total KRAS expression varied between tumors (0.47–1.01 fmol/µg total protein) and healthy tissues (0.13–0.64 fmol/µg). In KRASG12V-mCRC, G12V-mutation levels were 42–100%, while one patient had only 10% KRASG12V but 90% KRASwildtype. This might represent a missed therapeutic opportunity: based on hotspot sequencing, the patient was excluded from anti-EGFR treatment and instead received chemotherapy, while PRM-based tumor-phenotyping indicates the patient might have benefitted from anti-EGFR therapy.
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23
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Thiemeyer H, Taher L, Schille JT, Harder L, Hungerbuehler SO, Mischke R, Hewicker-Trautwein M, Kiełbowicz Z, Brenig B, Schütz E, Beck J, Murua Escobar H, Nolte I. Suitability of ultrasound-guided fine-needle aspiration biopsy for transcriptome sequencing of the canine prostate. Sci Rep 2019; 9:13216. [PMID: 31519932 PMCID: PMC6744464 DOI: 10.1038/s41598-019-49271-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2018] [Accepted: 08/15/2019] [Indexed: 02/06/2023] Open
Abstract
Ultrasound-guided fine-needle aspiration (US-FNA) biopsy is a widely used minimally invasive sampling procedure for cytological diagnosis. This study investigates the feasibility of using US-FNA samples for both cytological diagnosis and whole transcriptome RNA-sequencing analysis (RNA-Seq), with the ultimate aim of improving canine prostate cancer management. The feasibility of the US-FNA procedure was evaluated intra vitam on 43 dogs. Additionally, aspirates from 31 euthanised dogs were collected for standardising the procedure. Each aspirate was separated into two subsamples: for cytology and RNA extraction. Additional prostate tissue samples served as control for RNA quantity and quality evaluation, and differential expression analysis. The US-FNA sampling procedure was feasible in 95% of dogs. RNA isolation of US-FNA samples was successfully performed using phenol-chloroform extraction. The extracted RNA of 56% of a subset of US-FNA samples met the quality requirements for RNA-Seq. Expression analysis revealed that only 153 genes were exclusively differentially expressed between non-malignant US-FNAs and tissues. Moreover, only 36 differentially expressed genes were associated with the US-FNA sampling technique and unrelated to the diagnosis. Furthermore, the gene expression profiles clearly distinguished between non-malignant and malignant samples. This proves US-FNA to be useful for molecular profiling.
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Affiliation(s)
- H Thiemeyer
- Small Animal Clinic, University of Veterinary Medicine Hannover, Foundation, Hannover, Germany
- Department of Haematology/Oncology/Palliative Care, Rostock University Medical Centre, Rostock, Germany
| | - L Taher
- Division of Bioinformatics, Department of Biology, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
| | - J T Schille
- Small Animal Clinic, University of Veterinary Medicine Hannover, Foundation, Hannover, Germany
- Department of Haematology/Oncology/Palliative Care, Rostock University Medical Centre, Rostock, Germany
| | - L Harder
- Small Animal Clinic, University of Veterinary Medicine Hannover, Foundation, Hannover, Germany
| | - S O Hungerbuehler
- Small Animal Clinic, University of Veterinary Medicine Hannover, Foundation, Hannover, Germany
| | - R Mischke
- Small Animal Clinic, University of Veterinary Medicine Hannover, Foundation, Hannover, Germany
| | - M Hewicker-Trautwein
- Institute of Pathology, University of Veterinary Medicine Hannover, Foundation, Hannover, Germany
| | - Z Kiełbowicz
- Department and Clinic of Veterinary Surgery, Faculty of Veterinary Medicine, Wroclaw University of Environmental and Life Sciences, Wrocław, Poland
| | - B Brenig
- University of Göttingen, Institute of Veterinary Medicine, Göttingen, Germany
| | - E Schütz
- Chronix Biomedical, Göttingen, Germany
| | - J Beck
- Chronix Biomedical, Göttingen, Germany
| | - H Murua Escobar
- Small Animal Clinic, University of Veterinary Medicine Hannover, Foundation, Hannover, Germany
- Department of Haematology/Oncology/Palliative Care, Rostock University Medical Centre, Rostock, Germany
| | - I Nolte
- Small Animal Clinic, University of Veterinary Medicine Hannover, Foundation, Hannover, Germany.
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24
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Bavi P, Siva M, Abi-Saab T, Chadwick D, Dhani N, Butany J, Joshua AM, Roehrl MH. Developing a pan-cancer research autopsy programme. J Clin Pathol 2019; 72:689-695. [PMID: 31262953 PMCID: PMC6817699 DOI: 10.1136/jclinpath-2019-205874] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2019] [Revised: 05/31/2019] [Accepted: 06/07/2019] [Indexed: 12/29/2022]
Abstract
Aims Rapid procurement of a wide variety of metastatic and primary cancers and normal tissues after death through rapid autopsy opens largely unexplored avenues in cancer research. We describe a high-volume rapid research autopsy programme at a large academic medical centre. Methods Advanced-stage cancer patients, most commonly inpatients in palliative care facilities, were approached to participate in a cancer research autopsy programme with the goal of acquiring multidimensionally annotated tissue for cancer research. On death of an enrolled patient, a predetermined notification plan was enacted, with the medical oncologist/clinical research coordinator informing a team of pathologists, researchers and allied staff. Quality assurance metrics were measured. Thereafter, tissues were annotated in a tissue bioinformatics database and linked to electronic patient records. All banked tissues were reviewed for tumour integrity, including DNA and RNA quality. Results Over 100 rapid research autopsies from diverse cancer sites were performed, and specimens were procured and annotated with detailed clinical information, including treatment and response. Tissues were successfully enabling studies of tumour immunology, xenografts, genomics and proteomics. Conclusions Large-scale rapid procurement and biobanking of cancer tissues from a rapid autopsy programme is feasible. Multidisciplinary integration between health and administrative staff from medical oncology, palliative care, pathology and biospecimen sciences is critical for the success of this challenging endeavour.
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Affiliation(s)
- Prashant Bavi
- Department of Pathology, University Health Network, Toronto, Ontario, Canada
| | - Madura Siva
- Department of Pathology, University Health Network, Toronto, Ontario, Canada
| | - Tarek Abi-Saab
- Department of Pathology, University Health Network, Toronto, Ontario, Canada
| | - Dianne Chadwick
- Department of Pathology, University Health Network, Toronto, Ontario, Canada
| | - Neesha Dhani
- Department of Medical Oncology, Princess Margaret Cancer Centre, Toronto, Ontario, Canada
| | - Jagdish Butany
- Department of Pathology, University Health Network, Toronto, Ontario, Canada
| | - Anthony M Joshua
- Department of Medical Oncology, Princess Margaret Cancer Centre, Toronto, Ontario, Canada .,Kinghorn Cancer Centre, St. Vincent's Hospital, Sydney, New South Wales, Australia.,Garvan Institute of Medical Research, Sydney, New South Wales, Australia
| | - Michael H Roehrl
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York, USA .,Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York, USA.,Weill Cornell Medicine, New York, New York, USA.,Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada
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25
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Cherukuri AR, Lubner MG, Zea R, Hinshaw JL, Lubner SJ, Matkowskyj KA, Foltz ML, Pickhardt PJ. Tissue sampling in the era of precision medicine: comparison of percutaneous biopsies performed for clinical trials or tumor genomics versus routine clinical care. Abdom Radiol (NY) 2019; 44:2074-2080. [PMID: 30032384 DOI: 10.1007/s00261-018-1702-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
PURPOSE The purpose of the study was to determine if patients undergoing percutaneous biopsy for genetic profiling are undergoing more biopsies (procedures, passes per procedure), or experiencing more procedure-related complications. METHODS 60 patients undergoing biopsy procedures for genetic profiling were retrospectively compared with 60 consecutive control patients undergoing routine biopsies. Procedural details and related complications were collected. Results were analyzed using t-tests and logistic regression. RESULTS Biopsied organs included mainly lung (n = 31), liver (n = 50), and lymph nodes (n = 18). The average number of core biopsy passes was 3.45 in the study group and 2.18 in the control group (0.73, 1.81; p = 0.0001). The average study patient underwent 1.44 biopsy procedures by radiology from 2016 to 2017, whereas the average control patient underwent 1.08 (0.1657, 0.5010, p = 0.0002). Results were similar when looking at the subset of patients undergoing liver biopsies. In our cohort of 120 patients total, only 6 complications were noted. There were 4 complications in the control patients and 2 complications in the study patients, all of which were pneumothoraces in patients undergoing lung biopsy; only 2 of these required treatment. The odds ratio for a complication occurring from an increase in one core biopsy is 1.07 (0.601, 1.573; p = 0.775), suggesting no significant relationship among the number of biopsies taken and the probability of complication in this cohort. CONCLUSIONS Patients being biopsied for genetic profiling or clinical study enrollment are undergoing more biopsy procedures and more biopsy passes per procedure, but are not experiencing a detectable increased rate of complications in this small cohort, single-center study.
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Affiliation(s)
- Anjuli R Cherukuri
- Departments of Radiology, University of Wisconsin School of Medicine and Public Health, E3/311 Clinical Sciences Center, 600 Highland Ave, Madison, WI, 53792, USA
| | - Meghan G Lubner
- Departments of Radiology, University of Wisconsin School of Medicine and Public Health, E3/311 Clinical Sciences Center, 600 Highland Ave, Madison, WI, 53792, USA.
| | - Ryan Zea
- Biostatistics, University of Wisconsin School of Medicine and Public Health, E3/311 Clinical Sciences Center, 600 Highland Ave, Madison, WI, 53792, USA
| | - J Louis Hinshaw
- Departments of Radiology, University of Wisconsin School of Medicine and Public Health, E3/311 Clinical Sciences Center, 600 Highland Ave, Madison, WI, 53792, USA
| | - Sam J Lubner
- Internal Medicine - Division of Human Oncology, University of Wisconsin School of Medicine and Public Health, E3/311 Clinical Sciences Center, 600 Highland Ave, Madison, WI, 53792, USA
| | - Kristina A Matkowskyj
- Pathology and Lab Medicine, University of Wisconsin School of Medicine and Public Health, E3/311 Clinical Sciences Center, 600 Highland Ave, Madison, WI, 53792, USA
| | - Marcia L Foltz
- Departments of Radiology, University of Wisconsin School of Medicine and Public Health, E3/311 Clinical Sciences Center, 600 Highland Ave, Madison, WI, 53792, USA
| | - Perry J Pickhardt
- Departments of Radiology, University of Wisconsin School of Medicine and Public Health, E3/311 Clinical Sciences Center, 600 Highland Ave, Madison, WI, 53792, USA
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Pritzker KPH, Nieminen HJ. Needle Biopsy Adequacy in the Era of Precision Medicine and Value-Based Health Care. Arch Pathol Lab Med 2019; 143:1399-1415. [PMID: 31100015 DOI: 10.5858/arpa.2018-0463-ra] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
CONTEXT.— Needle biopsy of diseased tissue is an essential diagnostic tool that is becoming even more important as precision medicine develops. However, the capability of this modality to efficiently provide samples adequate for diagnostic and prognostic analysis remains quite limited relative to current diagnostic needs. For physicians and patients, inadequate biopsy frequently leads to diagnostic delay, procedure duplication, or insufficient information about tumor biology leading to delay in treatment; for health systems, this results in substantial incremental costs and inefficient use of scarce specialized diagnostic resources. OBJECTIVE.— To review current needle biopsy technology, devices, and practice with a perspective to identify current limitations and opportunities for improvement in the context of advancing precision medicine. DATA SOURCES.— PubMed searches of fine-needle aspiration and core needle biopsy devices and similar technologies were made generally, by tissue site, and by adequacy as well as by health economics of these technologies. CONCLUSIONS.— Needle biopsy adequacy can be improved by recognizing the importance of this diagnostic tool by promoting common criteria for needle biopsy adequacy; by optimizing needle biopsy procedural technique, technologies, clinical practice, professional education, and quality assurance; and by bundling biopsy procedure costs with downstream diagnostic modalities to provide better accountability and incentives to improve the diagnostic process.
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Affiliation(s)
- Kenneth P H Pritzker
- From the Departments of Laboratory Medicine and Pathobiology, and Surgery, University of Toronto, Toronto, Ontario, Canada (Dr Pritzker); and the Department of Neuroscience and Biomedical Engineering, Aalto University School of Science, Espoo, Finland (Dr Nieminen)
| | - Heikki J Nieminen
- From the Departments of Laboratory Medicine and Pathobiology, and Surgery, University of Toronto, Toronto, Ontario, Canada (Dr Pritzker); and the Department of Neuroscience and Biomedical Engineering, Aalto University School of Science, Espoo, Finland (Dr Nieminen)
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27
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Salivary Exosomes as Nanocarriers for Cancer Biomarker Delivery. MATERIALS 2019; 12:ma12040654. [PMID: 30795593 PMCID: PMC6416587 DOI: 10.3390/ma12040654] [Citation(s) in RCA: 52] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/01/2019] [Revised: 02/16/2019] [Accepted: 02/18/2019] [Indexed: 01/01/2023]
Abstract
Human saliva is an ideal body fluid for developing non-invasive diagnostics. Saliva contains naturally-occurring nanoparticles with unique structural and biochemical characteristics. The salivary exosome, a nanoscale extracellular vesicle, has been identified as a highly informative nanovesicle with clinically-relevant information. Salivary exosomes have brought forth a pathway and mechanism by which cancer-derived biomarkers can be shuttled through the systemic circulation into the oral cavity. Despite such clinical potential, routine and reliable analyses of exosomes remain challenging due to their small sizes. Characterization of individual exosome nanostructures provides critical data for understanding their pathophysiological condition and diagnostic potential. In this review, we summarize a current array of discovered salivary biomarkers and nanostructural properties of salivary exosomes associated with specific cancers. In addition, we describe a novel electrochemical sensing technology, EFIRM (electric field-induced release and measurement), that advances saliva liquid biopsy, covering the current landscape of point-of-care saliva testing.
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28
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Wang L, Yang Y, Liu Y, Ning L, Xiang Y, Li G. Bridging exosome and liposome through zirconium–phosphate coordination chemistry: a new method for exosome detection. Chem Commun (Camb) 2019; 55:2708-2711. [DOI: 10.1039/c9cc00220k] [Citation(s) in RCA: 48] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
An exosomes–zirconium–liposomes sandwich structure is proposed to detect exosomes by using zirconium–phosphate coordination chemistry with lower cost, no modified label, and simplicity.
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Affiliation(s)
- Lei Wang
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences
- Nanjing University
- Nanjing
- P. R. China
| | - Yucai Yang
- Department of Oncology, the Second Affiliated Hospital of Anhui Medical University
- Hefei
- P. R. China
| | - Yunfei Liu
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences
- Nanjing University
- Nanjing
- P. R. China
| | - Limin Ning
- College of Medicine and Life Sciences, Nanjing University of Chinese Medicine
- Nanjing
- P. R. China
| | - Yang Xiang
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences
- Nanjing University
- Nanjing
- P. R. China
| | - Genxi Li
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences
- Nanjing University
- Nanjing
- P. R. China
- Center for Molecular Recognition and Biosensing
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Dagher G, Lavitrano ML, Hofman P. [Next generation biobanking: the challenge of data]. Med Sci (Paris) 2018; 34:849-851. [PMID: 30451660 DOI: 10.1051/medsci/2018203] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Human biological samples are key resources in unravelling physiopathological factors underlying diseases and influencing their outcome. By making use of these resources, genomics, proteomics and molecular imaging techniques have achieved unprecedented progress in the past decade. The development of genomics platforms, molecular imaging as well as bioinformatics allowed a significant development of the biomarkers field thus realizing significant advances towards personalized medicine. The exponential increase of data, their complexity, the necessity of their integration for analysis require the development of appropriate infrastructures. These latter should integrate experts from different fields as well as an optimal organisation of biobanks including novel access and exchange rules for biological material and data.
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Affiliation(s)
- Georges Dagher
- Biobanques, Inserm US013, Hôpital de la Salpêtrière, 47, boulevard de l'Hôpital, 75651 Paris, France
| | | | - Paul Hofman
- Université Côte d'Azur, BB-0033-00025, Campus Valrose, 28, avenue de Valrose, 06108 Nice, France
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30
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Ferry-Galow KV, Datta V, Makhlouf HR, Wright J, Wood BJ, Levy E, Pisano ED, Tam AL, Lee SI, Mahmood U, Rubinstein LV, Doroshow JH, Chen AP. What Can Be Done to Improve Research Biopsy Quality in Oncology Clinical Trials? J Oncol Pract 2018; 14:JOP1800092. [PMID: 30285529 PMCID: PMC6237512 DOI: 10.1200/jop.18.00092] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
PURPOSE: Research biopsy specimens collected in clinical trials often present requirements beyond those of tumor biopsy specimens collected for diagnostic purposes. Research biopsies underpin hypothesis-driven drug development, pharmacodynamic assessment of molecularly targeted anticancer agents, and, increasingly, genomic assessment for precision medicine; insufficient biopsy specimen quality or quantity therefore compromises the scientific value of a study and the resources devoted to it, as well as each patient's contribution to and potential benefit from a clinical trial. METHODS: To improve research biopsy specimen quality, we consulted with other translational oncology teams and reviewed current best practices. RESULTS: Among the recommendations were improving communication between oncologists and interventional radiologists, providing feedback on specimen sufficiency, increasing academic recognition and financial support for the time investment required by radiologists to collect and preserve research biopsy specimens, and improving real-time assessment of tissue quality. CONCLUSION: Implementing these recommendations at the National Cancer Institute's Developmental Therapeutics Clinic has demonstrably improved the quality of biopsy specimens collected; more widespread dissemination of these recommendations beyond large clinical cancer centers is possible and will be of value to the community in improving clinical research and, ultimately, patient care.
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Affiliation(s)
- Katherine V. Ferry-Galow
- Frederick National Laboratory for Cancer Research, Frederick; National Cancer Institute, Bethesda MD; Beth Israel Deaconess Medical Center; Harvard Medical School; Massachusetts General Hospital, Boston, MA; American College of Radiology, Reston, VA; and University of Texas MD Anderson Cancer Center, Houston, TX
| | - Vivekananda Datta
- Frederick National Laboratory for Cancer Research, Frederick; National Cancer Institute, Bethesda MD; Beth Israel Deaconess Medical Center; Harvard Medical School; Massachusetts General Hospital, Boston, MA; American College of Radiology, Reston, VA; and University of Texas MD Anderson Cancer Center, Houston, TX
| | - Hala R. Makhlouf
- Frederick National Laboratory for Cancer Research, Frederick; National Cancer Institute, Bethesda MD; Beth Israel Deaconess Medical Center; Harvard Medical School; Massachusetts General Hospital, Boston, MA; American College of Radiology, Reston, VA; and University of Texas MD Anderson Cancer Center, Houston, TX
| | - John Wright
- Frederick National Laboratory for Cancer Research, Frederick; National Cancer Institute, Bethesda MD; Beth Israel Deaconess Medical Center; Harvard Medical School; Massachusetts General Hospital, Boston, MA; American College of Radiology, Reston, VA; and University of Texas MD Anderson Cancer Center, Houston, TX
| | - Bradford J. Wood
- Frederick National Laboratory for Cancer Research, Frederick; National Cancer Institute, Bethesda MD; Beth Israel Deaconess Medical Center; Harvard Medical School; Massachusetts General Hospital, Boston, MA; American College of Radiology, Reston, VA; and University of Texas MD Anderson Cancer Center, Houston, TX
| | - Elliot Levy
- Frederick National Laboratory for Cancer Research, Frederick; National Cancer Institute, Bethesda MD; Beth Israel Deaconess Medical Center; Harvard Medical School; Massachusetts General Hospital, Boston, MA; American College of Radiology, Reston, VA; and University of Texas MD Anderson Cancer Center, Houston, TX
| | - Etta D. Pisano
- Frederick National Laboratory for Cancer Research, Frederick; National Cancer Institute, Bethesda MD; Beth Israel Deaconess Medical Center; Harvard Medical School; Massachusetts General Hospital, Boston, MA; American College of Radiology, Reston, VA; and University of Texas MD Anderson Cancer Center, Houston, TX
| | - Alda L. Tam
- Frederick National Laboratory for Cancer Research, Frederick; National Cancer Institute, Bethesda MD; Beth Israel Deaconess Medical Center; Harvard Medical School; Massachusetts General Hospital, Boston, MA; American College of Radiology, Reston, VA; and University of Texas MD Anderson Cancer Center, Houston, TX
| | - Susanna I. Lee
- Frederick National Laboratory for Cancer Research, Frederick; National Cancer Institute, Bethesda MD; Beth Israel Deaconess Medical Center; Harvard Medical School; Massachusetts General Hospital, Boston, MA; American College of Radiology, Reston, VA; and University of Texas MD Anderson Cancer Center, Houston, TX
| | - Umar Mahmood
- Frederick National Laboratory for Cancer Research, Frederick; National Cancer Institute, Bethesda MD; Beth Israel Deaconess Medical Center; Harvard Medical School; Massachusetts General Hospital, Boston, MA; American College of Radiology, Reston, VA; and University of Texas MD Anderson Cancer Center, Houston, TX
| | - Lawrence V. Rubinstein
- Frederick National Laboratory for Cancer Research, Frederick; National Cancer Institute, Bethesda MD; Beth Israel Deaconess Medical Center; Harvard Medical School; Massachusetts General Hospital, Boston, MA; American College of Radiology, Reston, VA; and University of Texas MD Anderson Cancer Center, Houston, TX
| | - James H. Doroshow
- Frederick National Laboratory for Cancer Research, Frederick; National Cancer Institute, Bethesda MD; Beth Israel Deaconess Medical Center; Harvard Medical School; Massachusetts General Hospital, Boston, MA; American College of Radiology, Reston, VA; and University of Texas MD Anderson Cancer Center, Houston, TX
| | - Alice P. Chen
- Frederick National Laboratory for Cancer Research, Frederick; National Cancer Institute, Bethesda MD; Beth Israel Deaconess Medical Center; Harvard Medical School; Massachusetts General Hospital, Boston, MA; American College of Radiology, Reston, VA; and University of Texas MD Anderson Cancer Center, Houston, TX
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Ruíz-Godoy LM, Baez-Revueltas FB, de Lourdes Suarez-Roa M, Maldonado-Martínez H, Enriquez-Carcamo V, Colín-González AL, Meneses-García A. A pharmacoeconomic analysis of the collection and preservation of samples in the biobank of the "Instituto Nacional de Cancerología" in Mexico City. Cell Tissue Bank 2018; 19:569-580. [PMID: 30155658 DOI: 10.1007/s10561-018-9706-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2016] [Accepted: 06/20/2018] [Indexed: 10/28/2022]
Abstract
In this work we estimated the budgetary impact of the samples produced by the biobank of the "Instituto Nacional de Cancerología" (BT-INCan) to set a recuperation fee from the perspective of the Health Ministry of Mexico. The study is an observational retrospective review of the direct medical costs (DMCs) of the processes involved in cryopreservation of the samples collected, on a per sample basis, including materials, laboratory tests, personnel, and administrative costs. Materials and labor costs were determined by information collected from the BT-INCan. DMCs were provided depending on the type of sample: plasma, tissue and biopsy; they were calculated according to the process required to preserve them. Sensitivity analysis was performed using bootstrap. Recuperation costs ranged from 130 to 155 USD. Costs were considered on a 5-year time frame for the maintenance per sample, which is the average time that a sample is kept in the BT-INCan. The cost analysis is perceived as an approximation to the most adequate recuperation fee per sample needed to guarantee the correct development of the BT-INCan. This work provides a basis and valuable information about costs, to enable several health institutions to strategically plan and manage a biobank or even motivate to establish their own biobank.
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Affiliation(s)
- Luz María Ruíz-Godoy
- Banco de Tumores, Instituto Nacional de Cancerología, S.S.A., 14080, Mexico City, Mexico
| | | | | | | | | | | | - Abelardo Meneses-García
- Dirección General, Instituto Nacional de Cancerología, S.S.A. San Fernando 22 Col. Sección XVI, Tlalpan, C.P. 14080, Mexico City, Mexico.
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Washetine K, Heeke S, Bonnetaud C, Kara-Borni M, Ilié M, Lassalle S, Butori C, Long-Mira E, Marquette CH, Cohen C, Mouroux J, Selva E, Tanga V, Bence C, Félix JM, Gazoppi L, Skhiri T, Gormally E, Boucher P, Clément B, Dagher G, Hofman V, Hofman P. Establishing a Dedicated Lung Cancer Biobank at the University Center Hospital of Nice (France). Why and How? Cancers (Basel) 2018; 10:cancers10070220. [PMID: 29966305 PMCID: PMC6070810 DOI: 10.3390/cancers10070220] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2018] [Revised: 06/20/2018] [Accepted: 06/28/2018] [Indexed: 12/11/2022] Open
Abstract
Lung cancer is the major cause of death from cancer in the world and its incidence is increasing in women. Despite the progress made in developing immunotherapies and therapies targeting genomic alterations, improvement in the survival rate of advanced stages or metastatic patients remains low. Thus, urgent development of effective therapeutic molecules is needed. The discovery of novel therapeutic targets and their validation requires high quality biological material and associated clinical data. With this aim, we established a biobank dedicated to lung cancers. We describe here our strategy and the indicators used and, through an overall assessment, present the strengths, weaknesses, opportunities and associated risks of this biobank.
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Affiliation(s)
- Kevin Washetine
- Hospital-Integrated Biobank (BB-0033-00025), Université Côte d'Azur, CHU de Nice, 06001 Nice CEDEX 1, France.
- Laboratory of Clinical and Experimental Pathology, Université Côte d'Azur, CHU de Nice, University Hospital Federation OncoAge, 06001 Nice CEDEX 1, France.
| | - Simon Heeke
- Team 4, Institute of Research on Cancer and Aging of Nice (IRCAN), Inserm U1081, CNRS UMR7284, Université Côte d'Azur, CHU de Nice, 06107 Nice CEDEX 2, France.
| | - Christelle Bonnetaud
- Hospital-Integrated Biobank (BB-0033-00025), Université Côte d'Azur, CHU de Nice, 06001 Nice CEDEX 1, France.
| | - Mehdi Kara-Borni
- Hospital-Integrated Biobank (BB-0033-00025), Université Côte d'Azur, CHU de Nice, 06001 Nice CEDEX 1, France.
| | - Marius Ilié
- Hospital-Integrated Biobank (BB-0033-00025), Université Côte d'Azur, CHU de Nice, 06001 Nice CEDEX 1, France.
- Laboratory of Clinical and Experimental Pathology, Université Côte d'Azur, CHU de Nice, University Hospital Federation OncoAge, 06001 Nice CEDEX 1, France.
- Team 4, Institute of Research on Cancer and Aging of Nice (IRCAN), Inserm U1081, CNRS UMR7284, Université Côte d'Azur, CHU de Nice, 06107 Nice CEDEX 2, France.
- FHU OncoAge, University of Nice Sophia Antipolis, 06001 Nice CEDEX 1, France.
| | - Sandra Lassalle
- Laboratory of Clinical and Experimental Pathology, Université Côte d'Azur, CHU de Nice, University Hospital Federation OncoAge, 06001 Nice CEDEX 1, France.
- Team 4, Institute of Research on Cancer and Aging of Nice (IRCAN), Inserm U1081, CNRS UMR7284, Université Côte d'Azur, CHU de Nice, 06107 Nice CEDEX 2, France.
- FHU OncoAge, University of Nice Sophia Antipolis, 06001 Nice CEDEX 1, France.
| | - Catherine Butori
- Laboratory of Clinical and Experimental Pathology, Université Côte d'Azur, CHU de Nice, University Hospital Federation OncoAge, 06001 Nice CEDEX 1, France.
- FHU OncoAge, University of Nice Sophia Antipolis, 06001 Nice CEDEX 1, France.
| | - Elodie Long-Mira
- Laboratory of Clinical and Experimental Pathology, Université Côte d'Azur, CHU de Nice, University Hospital Federation OncoAge, 06001 Nice CEDEX 1, France.
- Team 4, Institute of Research on Cancer and Aging of Nice (IRCAN), Inserm U1081, CNRS UMR7284, Université Côte d'Azur, CHU de Nice, 06107 Nice CEDEX 2, France.
- FHU OncoAge, University of Nice Sophia Antipolis, 06001 Nice CEDEX 1, France.
| | - Charles Hugo Marquette
- Team 4, Institute of Research on Cancer and Aging of Nice (IRCAN), Inserm U1081, CNRS UMR7284, Université Côte d'Azur, CHU de Nice, 06107 Nice CEDEX 2, France.
- FHU OncoAge, University of Nice Sophia Antipolis, 06001 Nice CEDEX 1, France.
- Department of Pulmonary Medicine and Oncology, Université Côte d'Azur, CHU de Nice, University Hospital Federation OncoAge, 06001 Nice CEDEX 1, France.
| | - Charlotte Cohen
- FHU OncoAge, University of Nice Sophia Antipolis, 06001 Nice CEDEX 1, France.
- Department of Thoracic Surgery, Université Côte d'Azur, CHU de Nice, University Hospital Federation OncoAge, 06001 Nice CEDEX 1, France.
| | - Jérôme Mouroux
- Team 4, Institute of Research on Cancer and Aging of Nice (IRCAN), Inserm U1081, CNRS UMR7284, Université Côte d'Azur, CHU de Nice, 06107 Nice CEDEX 2, France.
- FHU OncoAge, University of Nice Sophia Antipolis, 06001 Nice CEDEX 1, France.
- Department of Thoracic Surgery, Université Côte d'Azur, CHU de Nice, University Hospital Federation OncoAge, 06001 Nice CEDEX 1, France.
| | - Eric Selva
- Hospital-Integrated Biobank (BB-0033-00025), Université Côte d'Azur, CHU de Nice, 06001 Nice CEDEX 1, France.
| | - Virginie Tanga
- Hospital-Integrated Biobank (BB-0033-00025), Université Côte d'Azur, CHU de Nice, 06001 Nice CEDEX 1, France.
| | - Coraline Bence
- Laboratory of Clinical and Experimental Pathology, Université Côte d'Azur, CHU de Nice, University Hospital Federation OncoAge, 06001 Nice CEDEX 1, France.
| | - Jean-Marc Félix
- Hospital-Integrated Biobank (BB-0033-00025), Université Côte d'Azur, CHU de Nice, 06001 Nice CEDEX 1, France.
| | - Loic Gazoppi
- Hospital-Integrated Biobank (BB-0033-00025), Université Côte d'Azur, CHU de Nice, 06001 Nice CEDEX 1, France.
| | - Taycir Skhiri
- FHU OncoAge, University of Nice Sophia Antipolis, 06001 Nice CEDEX 1, France.
| | | | - Pascal Boucher
- French National Cancer Institut, 92513 Boulogne Billancourt CEDEX, France.
| | - Bruno Clément
- INSERM, INRA, University of Rennes, NuMeCan, CRB Santé, CHU Rennes, 35042 Rennes, France.
| | | | - Véronique Hofman
- Hospital-Integrated Biobank (BB-0033-00025), Université Côte d'Azur, CHU de Nice, 06001 Nice CEDEX 1, France.
- Laboratory of Clinical and Experimental Pathology, Université Côte d'Azur, CHU de Nice, University Hospital Federation OncoAge, 06001 Nice CEDEX 1, France.
- Team 4, Institute of Research on Cancer and Aging of Nice (IRCAN), Inserm U1081, CNRS UMR7284, Université Côte d'Azur, CHU de Nice, 06107 Nice CEDEX 2, France.
- FHU OncoAge, University of Nice Sophia Antipolis, 06001 Nice CEDEX 1, France.
| | - Paul Hofman
- Hospital-Integrated Biobank (BB-0033-00025), Université Côte d'Azur, CHU de Nice, 06001 Nice CEDEX 1, France.
- Laboratory of Clinical and Experimental Pathology, Université Côte d'Azur, CHU de Nice, University Hospital Federation OncoAge, 06001 Nice CEDEX 1, France.
- Team 4, Institute of Research on Cancer and Aging of Nice (IRCAN), Inserm U1081, CNRS UMR7284, Université Côte d'Azur, CHU de Nice, 06107 Nice CEDEX 2, France.
- FHU OncoAge, University of Nice Sophia Antipolis, 06001 Nice CEDEX 1, France.
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Rieber N, Bohnert R, Ziehm U, Jansen G. Reliability of algorithmic somatic copy number alteration detection from targeted capture data. Bioinformatics 2018; 33:2791-2798. [PMID: 28472276 PMCID: PMC5870863 DOI: 10.1093/bioinformatics/btx284] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2016] [Accepted: 05/03/2017] [Indexed: 01/11/2023] Open
Abstract
Motivation Whole exome and gene panel sequencing are increasingly used for oncological diagnostics. To investigate the accuracy of SCNA detection algorithms on simulated and clinical tumor samples, the precision and sensitivity of four SCNA callers were measured using 50 simulated whole exome and 50 simulated targeted gene panel datasets, and using 119 TCGA tumor samples for which SNP array data were available. Results On synthetic exome and panel data, VarScan2 mostly called false positives, whereas Control-FREEC was precise (>90% correct calls) at the cost of low sensitivity (<40% detected). ONCOCNV was slightly less precise on gene panel data, with similarly low sensitivity. This could be explained by low sensitivity for amplifications and high precision for deletions. Surprisingly, these results were not strongly affected by moderate tumor impurities; only contaminations with more than 60% non-cancerous cells resulted in strongly declining precision and sensitivity. On the 119 clinical samples, both Control-FREEC and CNVkit called 71.8% and 94%, respectively, of the SCNAs found by the SNP arrays, but with a considerable amount of false positives (precision 29% and 4.9%). Discussion Whole exome and targeted gene panel methods by design limit the precision of SCNA callers, making them prone to false positives. SCNA calls cannot easily be integrated in clinical pipelines that use data from targeted capture-based sequencing. If used at all, they need to be cross-validated using orthogonal methods. Availability and implementation Scripts are provided as supplementary information. Supplementary information Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Nora Rieber
- Molecular Health GmbH, Kurfürsten-Anlage 21, 69115 Heidelberg, Germany
| | - Regina Bohnert
- Molecular Health GmbH, Kurfürsten-Anlage 21, 69115 Heidelberg, Germany
| | - Ulrike Ziehm
- Molecular Health GmbH, Kurfürsten-Anlage 21, 69115 Heidelberg, Germany
| | - Gunther Jansen
- Molecular Health GmbH, Kurfürsten-Anlage 21, 69115 Heidelberg, Germany
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Janssens JP, Schuster K, Voss A. Preventive, predictive, and personalized medicine for effective and affordable cancer care. EPMA J 2018; 9:113-123. [PMID: 29896312 PMCID: PMC5972138 DOI: 10.1007/s13167-018-0130-1] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2018] [Accepted: 02/14/2018] [Indexed: 10/17/2022]
Abstract
Preventive, predictive, and personalized medicine (PPPM) has created a wealth of new opportunities but added also new complexities and challenges. The European Cancer Prevention Organization already embraced unanimously molecular biology for primary and secondary prevention. The rapidly exploding genomic language and complexity of methods face oncologists with exponentially growing knowledge they need to assess and apply. Tissue specimen quality becomes one major concern. Some new innovative medicines cost beyond any reasonable threshold of financial support from patients, health care providers, and governments and risk sustainability for the health care system. In this review, we evaluate the path for genomic guidance to become the standard for diagnostics in cancer care and formulate potential solutions to simplify its implementation. Basically, introduction of molecular biology to guide therapeutic decisions can be facilitated through supporting the oncologist, the pathologist, the molecular laboratory, and the interventionist. Oncologists need to know the exact indication, utility, and limitations of each genomic service. Minimal requirements on the label must be addressed by the service provider. The interventionist is there to bring the most optimal tissue sample to pathology where the tissue is expanded to a variety of appropriate liquid-based samples. The large body of results then should be translated into meaningful clinical guidance for the individual patient. Surveillance, with the appropriate application of health economic indicators, can make this system long lasting. For governments and health care providers, optimal cancer care must result in a cost-effective, resource-sustainable, and patient-focused outcome.
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Affiliation(s)
- Jaak Ph. Janssens
- The European Cancer Prevention Organization, Klein Hilststraat 5, 3500 Hasselt, Belgium
| | - Klaus Schuster
- Caris Life Sciences, St. Jakobsstrasse 199, 4052 Basel, Switzerland
| | - Andreas Voss
- Caris Life Sciences, St. Jakobsstrasse 199, 4052 Basel, Switzerland
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Park J, Im H, Hong S, Castro CM, Weissleder R, Lee H. Analyses of Intravesicular Exosomal Proteins Using a Nano-Plasmonic System. ACS PHOTONICS 2018; 5:487-494. [PMID: 29805987 PMCID: PMC5966285 DOI: 10.1021/acsphotonics.7b00992] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
Extracellular vesicles (EVs), including exosomes, are nanoscale membrane particles shed from cells and contain cellular proteins whose makeup could inform cancer diagnosis and treatment. Most analyses have focused on surface proteins while analysis of intravesicular proteins has been more challenging. Herein, we report an EV screening assay for both intravesicular and transmembrane proteins using a nanoplasmonic sensor. Termed iNPS (intravesicular nanoplasmonic system), this platform used nanohole-based surface plasmon resonance (SPR) for molecular detection. Specifically, we i) established a unified assay protocol to detect intravesicular as well as transmembrane proteins; and ii) engineered plasmonic substrates to enhance detection sensitivity. The resulting iNPS enabled sensitive (0.5 μL sample per marker) and high-throughput (a 10 × 10 array) detection for EV proteins. When applied to monitor EVs from drug-treated cancer cells, the iNPS assay revealed drug-dependent unique EV protein signatures. We envision that iNPS could be a powerful tool for comprehensive molecular screening of EVs.
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Affiliation(s)
- Jongmin Park
- Center for Systems Biology, Massachusetts General Hospital, 185 Cambridge St, CPZN 5206, Boston, MA 02114
- Department of Radiology, Massachusetts General Hospital, Boston, MA 02114
| | - Hyungsoon Im
- Center for Systems Biology, Massachusetts General Hospital, 185 Cambridge St, CPZN 5206, Boston, MA 02114
- Department of Radiology, Massachusetts General Hospital, Boston, MA 02114
| | - Seonki Hong
- Center for Systems Biology, Massachusetts General Hospital, 185 Cambridge St, CPZN 5206, Boston, MA 02114
| | - Cesar M. Castro
- Center for Systems Biology, Massachusetts General Hospital, 185 Cambridge St, CPZN 5206, Boston, MA 02114
- Massachusetts General Hospital Cancer Center, Boston, MA 02114
| | - Ralph Weissleder
- Center for Systems Biology, Massachusetts General Hospital, 185 Cambridge St, CPZN 5206, Boston, MA 02114
- Department of Systems Biology, Harvard Medical School, Boston, MA 02115
| | - Hakho Lee
- Center for Systems Biology, Massachusetts General Hospital, 185 Cambridge St, CPZN 5206, Boston, MA 02114
- Department of Radiology, Massachusetts General Hospital, Boston, MA 02114
- Corresponding author: H. Lee, PhD, Center for Systems Biology, Massachusetts General Hospital, 185 Cambridge St, CPZN 5206, Boston, MA, 02114, 617-726-8226,
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Characteristics of percutaneous core biopsies adequate for next generation genomic sequencing. PLoS One 2017; 12:e0189651. [PMID: 29281680 PMCID: PMC5744968 DOI: 10.1371/journal.pone.0189651] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2017] [Accepted: 11/28/2017] [Indexed: 12/18/2022] Open
Abstract
Purpose Determine the characteristics of percutaneous core biopsies that are adequate for a next generation sequencing (NGS) genomic panel. Materials and methods All patients undergoing percutaneous core biopsies in interventional radiology (IR) with samples evaluated for a 46-gene NGS panel during 1-year were included in this retrospective study. Patient and procedure variables were collected. An imaging-based likelihood of adequacy score incorporating targeting and sampling factors was assigned to each biopsied lesion. Univariate and multivariate logistic regression was performed. Results 153 patients were included (58.2% female, average age 59.5 years). The most common malignancy was lung cancer (40.5%), most common biopsied site was lung (36%), and average size of biopsied lesions was 3.8 cm (+/- 2.7). Adequacy for NGS was 69.9%. Univariate analysis showed higher likelihood of adequacy score (p = 0.004), primary malignancy type (p = 0.03), and absence of prior systemic therapy (p = 0.018) were associated with adequacy for NGS. Multivariate analysis showed higher adequacy for lesions with likelihood of adequacy scored 3 (high) versus lesions scored 1 (low) (OR, 7.82; p = 0.002). Melanoma lesions had higher adequacy for NGS versus breast cancer lesions (OR 9.5; p = 0.01). Absence of prior systemic therapy (OR, 6.1; p = 0.02) and systemic therapy </ = 3 months (OR 3.24; p = 0.01) compared to systemic therapy >3 months before biopsy yielded greater adequacy for NGS. Lesions <3 cm had greater adequacy for NGS than larger lesions (OR 2.72, p = 0.02). Conclusion As targeted therapy becomes standard for more cancers, percutaneous biopsy specimens adequate for NGS genomic testing will be needed. An imaging-based likelihood of adequacy score assigned by IR physicians and other pre-procedure variables can help predict the likelihood of biopsy adequacy for NGS.
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Agrawal L, Engel KB, Greytak SR, Moore HM. Understanding preanalytical variables and their effects on clinical biomarkers of oncology and immunotherapy. Semin Cancer Biol 2017; 52:26-38. [PMID: 29258857 DOI: 10.1016/j.semcancer.2017.12.008] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2017] [Revised: 12/07/2017] [Accepted: 12/13/2017] [Indexed: 12/20/2022]
Abstract
Identifying a suitable course of immunotherapy treatment for a given patient as well as monitoring treatment response is heavily reliant on biomarkers detected and quantified in blood and tissue biospecimens. Suboptimal or variable biospecimen collection, processing, and storage practices have the potential to alter clinically relevant biomarkers, including those used in cancer immunotherapy. In the present review, we summarize effects reported for immunologically relevant biomarkers and highlight preanalytical factors associated with specific analytical platforms and assays used to predict and gauge immunotherapy response. Given that many of the effects introduced by preanalytical variability are gene-, transcript-, and protein-specific, biospecimen practices should be standardized and validated for each biomarker and assay to ensure accurate results and facilitate clinical implementation of newly identified immunotherapy approaches.
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Affiliation(s)
- Lokesh Agrawal
- Biorepositories and Biospecimen Research Branch (BBRB), Cancer Diagnosis Program, Division of Cancer Treatment and Diagnosis, National Cancer Institute, 9609 Medical Center Drive, Bethesda, Maryland, USA
| | | | | | - Helen M Moore
- Biorepositories and Biospecimen Research Branch (BBRB), Cancer Diagnosis Program, Division of Cancer Treatment and Diagnosis, National Cancer Institute, 9609 Medical Center Drive, Bethesda, Maryland, USA.
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Faiella E, Frauenfelder G, Santucci D, Luppi G, Schena E, Beomonte Zobel B, Grasso RF. Percutaneous low-dose CT-guided lung biopsy with an augmented reality navigation system: validation of the technique on 496 suspected lesions. Clin Imaging 2017; 49:101-105. [PMID: 29207301 DOI: 10.1016/j.clinimag.2017.11.013] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2017] [Revised: 11/20/2017] [Accepted: 11/28/2017] [Indexed: 11/26/2022]
Abstract
PURPOSE To validate a CT-navigation system during percutaneous lung biopsy (PLB). METHODS Four hundred-ninety-six patients underwent low-dose CT-guided PLB. Lesion diameter (LD), procedural time (PT), histologic validity, lesion distance from pleural surface (DPS), needle distance travelled during procedure (DTP), complications and radiation exposure were recorded. RESULTS Hysto-patological diagnosis was obtained in 96.2% cases. Mean PT, DPS, DTP, LD were respectively 29.5min, 12.4mm, 17.9mm, 20.7mm. In cases of major complications (4.6%), higher values of DTP were measured. CONCLUSIONS CT-navigation system allowed a good success in terms of diagnosis in small lesions and when a long DTP is required.
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Affiliation(s)
- Eliodoro Faiella
- Department of Diagnostic and Interventional Radiology, Università Campus Bio-Medico di Roma, Via Alvaro del Portillo, 200, 00128 Roma, Italy.
| | - Giulia Frauenfelder
- Department of Diagnostic and Interventional Radiology, Università Campus Bio-Medico di Roma, Via Alvaro del Portillo, 200, 00128 Roma, Italy.
| | - Domiziana Santucci
- Department of Diagnostic and Interventional Radiology, Università Campus Bio-Medico di Roma, Via Alvaro del Portillo, 200, 00128 Roma, Italy.
| | - Giacomo Luppi
- Department of Diagnostic and Interventional Radiology, Università Campus Bio-Medico di Roma, Via Alvaro del Portillo, 200, 00128 Roma, Italy.
| | - Emiliano Schena
- Department of Measurement and Biomedical Instrumentation, Università Campus Bio-Medico di Roma, Via Alvaro del Portillo, 21, 00128 Roma, Italy.
| | - Bruno Beomonte Zobel
- Department of Diagnostic and Interventional Radiology, Università Campus Bio-Medico di Roma, Via Alvaro del Portillo, 200, 00128 Roma, Italy.
| | - Rosario Francesco Grasso
- Department of Diagnostic and Interventional Radiology, Università Campus Bio-Medico di Roma, Via Alvaro del Portillo, 200, 00128 Roma, Italy.
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Park J, Lin HY, Assaker JP, Jeong S, Huang CH, Kurdi A, Lee K, Fraser K, Min C, Eskandari S, Routray S, Tannous B, Abdi R, Riella L, Chandraker A, Castro CM, Weissleder R, Lee H, Azzi JR. Integrated Kidney Exosome Analysis for the Detection of Kidney Transplant Rejection. ACS NANO 2017; 11:11041-11046. [PMID: 29053921 PMCID: PMC6237084 DOI: 10.1021/acsnano.7b05083] [Citation(s) in RCA: 86] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Kidney transplant patients require life-long surveillance to detect allograft rejection. Repeated biopsy, albeit the clinical gold standard, is an invasive procedure with the risk of complications and comparatively high cost. Conversely, serum creatinine or urinary proteins are noninvasive alternatives but are late markers with low specificity. We report a urine-based platform to detect kidney transplant rejection. Termed iKEA (integrated kidney exosome analysis), the approach detects extracellular vesicles (EVs) released by immune cells into urine; we reasoned that T cells, attacking kidney allografts, would shed EVs, which in turn can be used as a surrogate marker for inflammation. We optimized iKEA to detect T-cell-derived EVs and implemented a portable sensing system. When applied to clinical urine samples, iKEA revealed high level of CD3-positive EVs in kidney rejection patients and achieved high detection accuracy (91.1%). Fast, noninvasive, and cost-effective, iKEA could offer new opportunities in managing transplant recipients, perhaps even in a home setting.
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Affiliation(s)
- Jongmin Park
- Center for Systems Biology, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts 02114, United States
- Department of Radiology, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts 02114, United States
| | - Hsing-Ying Lin
- Center for Systems Biology, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts 02114, United States
- Department of Radiology, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts 02114, United States
| | - Jean Pierre Assaker
- Transplantation Research Center, Renal Division, Brigham and Women’s Hospital, Harvard Medical School, Boston, Massachusetts 02115, United States
| | - Sangmoo Jeong
- Center for Systems Biology, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts 02114, United States
- Department of Radiology, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts 02114, United States
| | - Chen-Han Huang
- Center for Systems Biology, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts 02114, United States
- Department of Radiology, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts 02114, United States
| | - Ahmed Kurdi
- Transplantation Research Center, Renal Division, Brigham and Women’s Hospital, Harvard Medical School, Boston, Massachusetts 02115, United States
| | - Kyungheon Lee
- Center for Systems Biology, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts 02114, United States
- Department of Radiology, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts 02114, United States
| | - Kyle Fraser
- Center for Systems Biology, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts 02114, United States
- Department of Radiology, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts 02114, United States
| | - Changwook Min
- Center for Systems Biology, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts 02114, United States
- Department of Radiology, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts 02114, United States
| | - Siawosh Eskandari
- Transplantation Research Center, Renal Division, Brigham and Women’s Hospital, Harvard Medical School, Boston, Massachusetts 02115, United States
| | - Sujit Routray
- Transplantation Research Center, Renal Division, Brigham and Women’s Hospital, Harvard Medical School, Boston, Massachusetts 02115, United States
| | - Bakhos Tannous
- Experimental Therapeutics and Molecular Imaging Laboratory and Department of Neurology, Neuro-Oncology Division, Massachusetts General Hospital, Boston, Massachusetts 02129, United States
| | - Reza Abdi
- Transplantation Research Center, Renal Division, Brigham and Women’s Hospital, Harvard Medical School, Boston, Massachusetts 02115, United States
| | - Leonardo Riella
- Transplantation Research Center, Renal Division, Brigham and Women’s Hospital, Harvard Medical School, Boston, Massachusetts 02115, United States
| | - Anil Chandraker
- Transplantation Research Center, Renal Division, Brigham and Women’s Hospital, Harvard Medical School, Boston, Massachusetts 02115, United States
| | - Cesar M. Castro
- Center for Systems Biology, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts 02114, United States
- Department of Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts 02114, United States
| | - Ralph Weissleder
- Center for Systems Biology, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts 02114, United States
- Department of Systems Biology, Harvard Medical School, Boston, Massachusetts 02115, United States
| | - Hakho Lee
- Center for Systems Biology, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts 02114, United States
- Department of Radiology, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts 02114, United States
| | - Jamil R. Azzi
- Transplantation Research Center, Renal Division, Brigham and Women’s Hospital, Harvard Medical School, Boston, Massachusetts 02115, United States
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The identification of challenges in tissue collection for biomarker studies: the Q-CROC-03 neoadjuvant breast cancer translational trial experience. Mod Pathol 2017; 30:1567-1576. [PMID: 28752846 DOI: 10.1038/modpathol.2017.82] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2017] [Revised: 05/23/2017] [Accepted: 05/25/2017] [Indexed: 12/29/2022]
Abstract
One of the major challenges in biomarker development is the collection of tumor tissue of adequate quality for analysis. A prospective clinical trial was initiated to collect tissues from triple negative breast cancers prior to and after neoadjuvant chemotherapy in order to study the mechanisms of chemoresistance. Sixty patients had pre-chemotherapy biopsies performed by either a surgeon or a radiologist, while those with residual tumor after chemotherapy had research-only biopsies and/or surgical samples collected in liquid nitrogen, RNA-later and formalin. We examined each core for tumor cellularity, stromal content, and necrosis after which, RNA and DNA extraction was performed. We found that biopsies collected with ultrasound guidance were more likely to contain tumor than those collected by the surgeon. Patient reluctance to undergo research-only biopsies after chemotherapy was not a problem. Pre-chemotherapy tumor biopsies frequently did not contain any tumor cells (15%) or did not have ≥50% tumor content (63%). Indeed, 50% of patients had at least 2 pre-chemotherapy core biopsies with <50% tumor content. After chemotherapy, 30% of biopsy or surgical samples in patients with incomplete response did not contain any tumor. Finally, RNA-later not only made histopathological assessment of tumor content difficult, but yielded less DNA than fresh snap frozen samples. We recommend that high-quality tissue procurement can be best accomplished if at least three image-guided core biopsies be obtained per sample, each of these cores be examined for tumor cellularity and that at least some of them be freshly snap frozen in liquid nitrogen.
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Bohnert R, Vivas S, Jansen G. Comprehensive benchmarking of SNV callers for highly admixed tumor data. PLoS One 2017; 12:e0186175. [PMID: 29020110 PMCID: PMC5636151 DOI: 10.1371/journal.pone.0186175] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2017] [Accepted: 09/26/2017] [Indexed: 12/30/2022] Open
Abstract
Precision medicine attempts to individualize cancer therapy by matching tumor-specific genetic changes with effective targeted therapies. A crucial first step in this process is the reliable identification of cancer-relevant variants, which is considerably complicated by the impurity and heterogeneity of clinical tumor samples. We compared the impact of admixture of non-cancerous cells and low somatic allele frequencies on the sensitivity and precision of 19 state-of-the-art SNV callers. We studied both whole exome and targeted gene panel data and up to 13 distinct parameter configurations for each tool. We found vast differences among callers. Based on our comprehensive analyses we recommend joint tumor-normal calling with MuTect, EBCall or Strelka for whole exome somatic variant calling, and HaplotypeCaller or FreeBayes for whole exome germline calling. For targeted gene panel data on a single tumor sample, LoFreqStar performed best. We further found that tumor impurity and admixture had a negative impact on precision, and in particular, sensitivity in whole exome experiments. At admixture levels of 60% to 90% sometimes seen in pathological biopsies, sensitivity dropped significantly, even when variants were originally present in the tumor at 100% allele frequency. Sensitivity to low-frequency SNVs improved with targeted panel data, but whole exome data allowed more efficient identification of germline variants. Effective somatic variant calling requires high-quality pathological samples with minimal admixture, a consciously selected sequencing strategy, and the appropriate variant calling tool with settings optimized for the chosen type of data.
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Im H, Lee K, Weissleder R, Lee H, Castro CM. Novel nanosensing technologies for exosome detection and profiling. LAB ON A CHIP 2017; 17:2892-2898. [PMID: 28745363 PMCID: PMC5572557 DOI: 10.1039/c7lc00247e] [Citation(s) in RCA: 56] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
Exosomes have recently emerged as highly promising cancer biomarkers because they are abundant in biofluids, carry proteins and RNA reflecting their originating cells and are stable over weeks. Beyond abundance and stability, detailed exosome analyses could be clinically useful for diagnosing and profiling cancers. Despite their clinical potential, simple, reliable and sensitive approaches for rapidly quantifying exosomes and their molecular information has been challenging. Therefore, there is a clear need to develop next-generation sensing technologies for exosome detection and analysis. In this critical review, we will describe three nanotechnology sensing platforms developed for analysis of exosomal proteins and RNAs directly from clinical specimens and discuss future development to facilitate their translation into routine clinical use.
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Affiliation(s)
- Hyungsoon Im
- Center for Systems Biology, Massachusetts General Hospital, Boston, MA 02114
- Department of Radiology, Massachusetts General Hospital, Boston, MA 02114
| | - Kyungheon Lee
- Center for Systems Biology, Massachusetts General Hospital, Boston, MA 02114
| | - Ralph Weissleder
- Center for Systems Biology, Massachusetts General Hospital, Boston, MA 02114
- Department of Radiology, Massachusetts General Hospital, Boston, MA 02114
- Department of Systems Biology, Harvard Medical School, Boston, MA 02115
| | - Hakho Lee
- Center for Systems Biology, Massachusetts General Hospital, Boston, MA 02114
- Department of Radiology, Massachusetts General Hospital, Boston, MA 02114
| | - Cesar M. Castro
- Center for Systems Biology, Massachusetts General Hospital, Boston, MA 02114
- Massachusetts General Hospital Cancer Center, Boston, MA 02114
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Rebonato A, Maiettini D, Andolfi M, Fischer MJ, Vannucci J, Metro G, Basile A, Rossi M, Duranti M. CT-Guided Percutaneous Trans-scapular Lung Biopsy in the Diagnosis of Peripheral Pulmonary Lesion Nodules of the Superior Lobes Using Large Needles. Cardiovasc Intervent Radiol 2017; 41:284-290. [DOI: 10.1007/s00270-017-1768-0] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/18/2017] [Accepted: 08/09/2017] [Indexed: 12/19/2022]
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Abstract
Recent advances in the molecular characterization of cancers have triggered interest in developing a new taxonomy of disease in oncology with the goal of using the molecular profile of a patient's tumor to predict response to treatment. Image-guided needle biopsy is central to this "precision medicine" effort. In this review, we first discuss the current role of biopsy in relation to clinical examples of molecular medicine. We then outline important bottlenecks to the advancement of precision medicine and highlight the potential role of image-guided biopsy to address these challenges.
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Affiliation(s)
- Etay Ziv
- Interventional Radiology Service, Department of Radiology, Memorial Sloan-Kettering Cancer Center, New York, NY 10065
| | - Jeremy C. Durack
- Interventional Radiology Service, Department of Radiology, Memorial Sloan-Kettering Cancer Center, New York, NY 10065
| | - Stephen B. Solomon
- Interventional Radiology Service, Department of Radiology, Memorial Sloan-Kettering Cancer Center, New York, NY 10065
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Avanzini S, Faticato MG, Crocoli A, Virgone C, Viglio C, Severi E, Fagnani AM, Cecchetto G, Riccipetitoni G, Noccioli B, Leva E, Sementa AR, Mattioli G, Inserra A. Comparative retrospective study on the modalities of biopsying peripheral neuroblastic tumors: a report from the Italian Pediatric Surgical Oncology Group (GICOP). Pediatr Blood Cancer 2017; 64. [PMID: 27762097 DOI: 10.1002/pbc.26284] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/29/2016] [Revised: 09/06/2016] [Accepted: 09/08/2016] [Indexed: 12/14/2022]
Abstract
BACKGROUND Peripheral neuroblastic tumors are the most common extracranial solid neoplasms in children. Early and adequate tissue sampling may speed up the diagnostic process and ensure a prompt start of optimal treatment whenever needed. Different biopsy techniques have been described. The purpose of this multi-center study is to evaluate the accuracy and safety of the various examined techniques and to determine whether a preferential procedure exists. METHODS All children who underwent a biopsy, from January 2010 to December 2014, as a result of being diagnosed with a peripheral neuroblastic tumor, were retrospectively reviewed. Data collected included patients' demographics, clinical presentation, intraoperative technical details, postoperative parameters, complications, and histology reports. The Mann-Whitney U and Fisher's exact tests were used for statistical analysis. RESULTS The cohort included 100 patients, 32 of whom underwent an incisional biopsy (performed through open or minimally invasive access) (Group A), and the remaining 68 underwent multiple needle-core biopsies (either imaging-guided or laparoscopy/thoracoscopy-assisted) (Group B). Comparing the two groups revealed that Group A patients had a higher rate of complications, a greater need for postoperative analgesia, and required red blood cell transfusion more often. Overall adequacy rate was 94%, without significant differences between the two groups (100% vs. 91.2% for Group A and Group B, respectively, P = 0.0933). CONCLUSIONS Both incision and needle-core biopsying methods provided sub-optimal to optimal sampling adequacy rates in children affected by peripheral neuroblastic tumors. However, the former method was associated with a higher risk of both intraoperative and postoperative complications compared with the latter.
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Affiliation(s)
| | - Maria Grazia Faticato
- Department of Pediatric Surgery, IRCCS G. Gaslini, Genoa, Italy.,Department of Neuroscience, Rehabilitation, Ophtalmology, Gynecology, and Maternal-Infantile sciences (DINOGMI), University of Genoa, Genoa, Italy
| | - Alessandro Crocoli
- Department of General and Thoracic Surgery, Bambino Gesù Children Hospital-Research Institute, Rome, Italy
| | - Calogero Virgone
- Department of Pediatric Surgery, Padova University Hospital, Padova, Italy
| | - Camilla Viglio
- Department of Pediatric Surgery, Buzzi Hospital, Milan, Italy
| | - Elisa Severi
- Department of Pediatric Surgery, Meyer Children Hospital, Florence, Italy
| | - Anna Maria Fagnani
- Department of Pediatric Surgery, Foundation IRCCS Ca' Granda, Ospedale Maggiore Policlinico, Milan, Italy
| | - Giovanni Cecchetto
- Department of Pediatric Surgery, Padova University Hospital, Padova, Italy
| | | | - Bruno Noccioli
- Department of Pediatric Surgery, Meyer Children Hospital, Florence, Italy
| | - Ernesto Leva
- Department of Pediatric Surgery, Foundation IRCCS Ca' Granda, Ospedale Maggiore Policlinico, Milan, Italy
| | | | - Girolamo Mattioli
- Department of Pediatric Surgery, IRCCS G. Gaslini, Genoa, Italy.,Department of Neuroscience, Rehabilitation, Ophtalmology, Gynecology, and Maternal-Infantile sciences (DINOGMI), University of Genoa, Genoa, Italy
| | - Alessandro Inserra
- Department of General and Thoracic Surgery, Bambino Gesù Children Hospital-Research Institute, Rome, Italy
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Shen Y, Tong M, Liang Q, Guo Y, Sun HQ, Zheng W, Ao L, Guo Z, She F. Epigenomics alternations and dynamic transcriptional changes in responses to 5-fluorouracil stimulation reveal mechanisms of acquired drug resistance of colorectal cancer cells. THE PHARMACOGENOMICS JOURNAL 2017; 18:23-28. [PMID: 28045128 PMCID: PMC5817391 DOI: 10.1038/tpj.2016.91] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/20/2016] [Revised: 11/06/2016] [Accepted: 11/14/2016] [Indexed: 12/19/2022]
Abstract
A drug-induced resistant cancer cell is different from its parent cell in transcriptional response to drug treatment. The distinct transcriptional response pattern of a drug-induced resistant cancer cell to drug treatment might be introduced by acquired DNA methylation aberration in the cell exposing to sustained drug stimulation. In this study, we performed both transcriptional and DNA methylation profiles of the HCT-8 wild-type cells (HCT-8/WT) for human colorectal cancer (CRC) and the 5-fluorouracil (5-FU)-induced resistant cells (HCT-8/5-FU) after treatment with 5-FU for 0, 24 and 48 h. Integrated analysis of transcriptional and DNA methylation profiles showed that genes with promoter hypermethylation and concordant expression silencing in the HCT-8/5-FU cells are mainly involved in pathways of pyrimidine metabolism and drug metabolism-cytochrome P450. Transcriptional analysis confirmed that genes with transcriptional differences between a drug-induced resistant cell and its parent cell after drug treatment for a certain time, rather than their primary transcriptional differences, are more likely to be involved in drug resistance. Specifically, transcriptional differences between the drug-induced resistant cells and parental cells after drug treatment for 24 h were significantly consistent with the differentially expressed genes (termed as CRG5-FU) between the tissues of nonresponders and responders of CRCs to 5-FU-based therapy and the consistence increased after drug treatment for 48 h (binomial test, P-value=1.88E−06). This study reveals a major epigenetic mechanism inducing the HCT-8/WT cells to acquire resistance to 5-FU and suggests an appropriate time interval (24–48 h) of 5-FU exposure for identifying clinically relevant drug resistance signatures from drug-induced resistant cell models.
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Affiliation(s)
- Y Shen
- Department of Bioinformatics, Key Laboratory of Ministry of Education for Gastrointestinal Cancer, Fujian Medical University, Fuzhou, China
| | - M Tong
- Department of Bioinformatics, Key Laboratory of Ministry of Education for Gastrointestinal Cancer, Fujian Medical University, Fuzhou, China
| | - Q Liang
- Department of Bioinformatics, Key Laboratory of Ministry of Education for Gastrointestinal Cancer, Fujian Medical University, Fuzhou, China
| | - Y Guo
- Department of Preventive Medicine, School of Basic Medicine Sciences, Gannan Medical University, Ganzhou, China
| | - H Q Sun
- Department of Bioinformatics, Key Laboratory of Ministry of Education for Gastrointestinal Cancer, Fujian Medical University, Fuzhou, China
| | - W Zheng
- Department of Bioinformatics, Key Laboratory of Ministry of Education for Gastrointestinal Cancer, Fujian Medical University, Fuzhou, China
| | - L Ao
- Department of Bioinformatics, Key Laboratory of Ministry of Education for Gastrointestinal Cancer, Fujian Medical University, Fuzhou, China
| | - Z Guo
- Department of Bioinformatics, Key Laboratory of Ministry of Education for Gastrointestinal Cancer, Fujian Medical University, Fuzhou, China
| | - F She
- Department of Bioinformatics, Key Laboratory of Ministry of Education for Gastrointestinal Cancer, Fujian Medical University, Fuzhou, China
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47
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Sheffield BS, Tessier-Cloutier B, Li-Chang H, Shen Y, Pleasance E, Kasaian K, Li Y, Jones SJM, Lim HJ, Renouf DJ, Huntsman DG, Yip S, Laskin J, Marra M, Schaeffer DF. Personalized oncogenomics in the management of gastrointestinal carcinomas-early experiences from a pilot study. ACTA ACUST UNITED AC 2016; 23:e571-e575. [PMID: 28050146 DOI: 10.3747/co.23.3165] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
BACKGROUND Gastrointestinal carcinomas are genomically complex cancers that are lethal in the metastatic setting. Whole-genome and transcriptome sequencing allow for the simultaneous characterization of multiple oncogenic pathways. METHODS We report 3 cases of metastatic gastrointestinal carcinoma in patients enrolled in the Personalized Onco-Genomics program at the BC Cancer Agency. Real-time genomic profiling was combined with clinical expertise to diagnose a carcinoma of unknown primary, to explore treatment response to bevacizumab in a colorectal cancer, and to characterize an appendiceal adenocarcinoma. RESULTS In the first case, genomic profiling revealed an IDH1 somatic mutation, supporting the diagnosis of cholangiocarcinoma in a malignancy of unknown origin, and further guided therapy by identifying epidermal growth factor receptor amplification. In the second case, a BRAF V600E mutation and wild-type KRAS profile justified the use of targeted therapies to treat a colonic adenocarcinoma. The third case was an appendiceal adenocarcinoma defined by a p53 inactivation; Ras/raf/mek, Akt/mtor, Wnt, and notch pathway activation; and overexpression of ret, erbb2 (her2), erbb3, met, and cell cycle regulators. SUMMARY We show that whole-genome and transcriptome sequencing can be achieved within clinically effective timelines, yielding clinically useful and actionable information.
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Affiliation(s)
- B S Sheffield
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC
| | - B Tessier-Cloutier
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC
| | - H Li-Chang
- Royal Victoria Regional Health Centre, Department of Pathology and Laboratory Medicine, Barrie, ON
| | - Y Shen
- Canada's Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver, BC
| | - E Pleasance
- Canada's Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver, BC
| | - K Kasaian
- Canada's Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver, BC
| | - Y Li
- Canada's Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver, BC
| | - S J M Jones
- Canada's Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver, BC
| | - H J Lim
- Division of Medical Oncology, BC Cancer Agency, Vancouver, BC
| | - D J Renouf
- Division of Medical Oncology, BC Cancer Agency, Vancouver, BC
| | - D G Huntsman
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC
| | - S Yip
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC
| | - J Laskin
- Division of Medical Oncology, BC Cancer Agency, Vancouver, BC
| | - M Marra
- Canada's Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver, BC.; Department of Medical Genetics, University of British Columbia, Vancouver, BC
| | - D F Schaeffer
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC
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Identifying clinically relevant drug resistance genes in drug-induced resistant cancer cell lines and post-chemotherapy tissues. Oncotarget 2016; 6:41216-27. [PMID: 26515599 PMCID: PMC4747401 DOI: 10.18632/oncotarget.5649] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2015] [Accepted: 09/12/2015] [Indexed: 12/13/2022] Open
Abstract
Until recently, few molecular signatures of drug resistance identified in drug-induced resistant cancer cell models can be translated into clinical practice. Here, we defined differentially expressed genes (DEGs) between pre-chemotherapy colorectal cancer (CRC) tissue samples of non-responders and responders for 5-fluorouracil and oxaliplatin-based therapy as clinically relevant drug resistance genes (CRG5-FU/L-OHP). Taking CRG5-FU/L-OHP as reference, we evaluated the clinical relevance of several types of genes derived from HCT116 CRC cells with resistance to 5-fluorouracil and oxaliplatin, respectively. The results revealed that DEGs between parental and resistant cells, when both were treated with the corresponding drug for a certain time, were significantly consistent with the CRG5-FU/L-OHP as well as the DEGs between the post-chemotherapy CRC specimens of responders and non-responders. This study suggests a novel strategy to extract clinically relevant drug resistance genes from both drug-induced resistant cell models and post-chemotherapy cancer tissue specimens.
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Abi-Jaoudeh N, Fisher T, Jacobus J, Skopec M, Radaelli A, Van Der Bom IM, Wesley R, Wood BJ. Prospective Randomized Trial for Image-Guided Biopsy Using Cone-Beam CT Navigation Compared with Conventional CT. J Vasc Interv Radiol 2016; 27:1342-1349. [PMID: 27461586 PMCID: PMC7869923 DOI: 10.1016/j.jvir.2016.05.034] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2016] [Revised: 05/23/2016] [Accepted: 05/24/2016] [Indexed: 11/19/2022] Open
Abstract
PURPOSE To compare cone-beam computed tomography (CT) navigation vs conventional CT image guidance during biopsies. MATERIALS AND METHODS Patients scheduled for image-guided biopsies were prospectively and randomly assigned to conventional CT guidance vs cone-beam CT navigation. Radiation dose, accuracy of final needle position, rate of histopathologic diagnosis, and number of needle repositions to reach the target (defined as pullback to adjust position) were compared. RESULTS A total of 58 patients (mean age, 57 y; 62.1% men) were randomized: 29 patients underwent 33 biopsies with CT guidance and 29 patients with 33 lesions underwent biopsy with cone-beam CT navigation. The average body mass index (BMI) was similar between groups, at 28.8 kg/m(2) ± 6.55 (P = .18). There was no difference between groups in terms of patient and lesion characteristics (eg, size, depth). The average lesion size was 29.1 ± 12.7mm for CT group vs 32.1mm ±16.8mm for cone-beam CT group (P < 0.59). Location of lesions was equally divided between the 2 groups, 20 lung lesions, 18 renal lesions and 20 other abdominal lesions. Mean number of needle repositions in the cone-beam CT group was 0.3 ± 0.5, compared with 1.9 ± 2.3 with conventional CT (P < .001). The average skin entry dose was 29% lower with cone-beam CT than with conventional CT (P < .04 accounting for BMI). The average estimated effective dose for the planning scan from phantom data was 49% lower with cone-beam CT vs conventional CT (P = .018). Accuracy, defined as the difference between planned and final needle positions, was 4.9 mm ± 4.1 for the cone-beam CT group, compared with 12.2 mm ± 8.1 for conventional CT (P < .001). Histopathologic diagnosis rates were similar between groups, at 90.9% for conventional CT and 93.9% for cone-beam CT (P = .67). CONCLUSIONS Cone-beam CT navigation for biopsies improved targeting accuracy with fewer needle repositions, lower skin entry dose, and lower effective dose for planning scan, and a comparable histopathologic diagnosis rate.
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Affiliation(s)
- Nadine Abi-Jaoudeh
- Department of Radiology and Imaging Sciences, National Institutes of Health, Bethesda, Maryland.
| | - Teresa Fisher
- Division of Radiation Safety, Office of Research Services, National Institutes of Health, Bethesda, Maryland
| | - John Jacobus
- Division of Radiation Safety, Office of Research Services, National Institutes of Health, Bethesda, Maryland
| | - Marlene Skopec
- Department of Radiology and Imaging Sciences, National Institutes of Health, Bethesda, Maryland
| | | | | | - Robert Wesley
- Office of the Deputy Director for the Clinical Center, National Institutes of Health, Bethesda, Maryland
| | - Bradford J Wood
- Department of Radiology and Imaging Sciences, National Institutes of Health, Bethesda, Maryland
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50
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Iriana S, Ahmed S, Gong J, Annamalai AA, Tuli R, Hendifar AE. Targeting mTOR in Pancreatic Ductal Adenocarcinoma. Front Oncol 2016; 6:99. [PMID: 27200288 PMCID: PMC4843105 DOI: 10.3389/fonc.2016.00099] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2016] [Accepted: 04/11/2016] [Indexed: 12/31/2022] Open
Abstract
Treatment options for advanced pancreatic ductal adenocarcinoma (PDAC) are limited; however, new therapies targeting specific tumor-related molecular characteristics may help certain patient cohorts. Emerging preclinical data have shown that inhibition of mammalian target of rapamycin (mTOR) in specific KRAS-dependent PDAC subtypes leads to inhibition of tumorigenesis in vitro and in vivo. Early phase II studies of mono-mTOR inhibition have not shown promise. However, studies have shown that combined inhibition of multiple steps along the mTOR signaling pathway may lead to sustained responses by targeting mechanisms of tumor resistance. Coordinated inhibition of mTOR along with specific KRAS-dependent mutations in molecularly defined PDAC subpopulations may offer a viable alternative for treatment in the future.
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Affiliation(s)
- Sentia Iriana
- Department of Medicine, Cedars-Sinai Medical Center , Los Angeles, CA , USA
| | - Shahzad Ahmed
- Department of Medicine, Cedars-Sinai Medical Center , Los Angeles, CA , USA
| | - Jun Gong
- Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, CA, USA; Department of Medical Oncology, City of Hope National Medical Center, Duarte, CA, USA
| | | | - Richard Tuli
- Department of Radiation Oncology, Cedars-Sinai Medical Center , Los Angeles, CA , USA
| | - Andrew Eugene Hendifar
- Department of Medicine, Division of Medical Oncology, Cedars-Sinai Medical Center , Los Angeles, CA , USA
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