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Link KE, Schnurman Z, Liu C, Kwon YJF, Jiang LY, Nasir-Moin M, Neifert S, Alzate JD, Bernstein K, Qu T, Chen V, Yang E, Golfinos JG, Orringer D, Kondziolka D, Oermann EK. Longitudinal deep neural networks for assessing metastatic brain cancer on a large open benchmark. Nat Commun 2024; 15:8170. [PMID: 39289405 PMCID: PMC11408643 DOI: 10.1038/s41467-024-52414-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2023] [Accepted: 09/06/2024] [Indexed: 09/19/2024] Open
Abstract
The detection and tracking of metastatic cancer over the lifetime of a patient remains a major challenge in clinical trials and real-world care. Advances in deep learning combined with massive datasets may enable the development of tools that can address this challenge. We present NYUMets-Brain, the world's largest, longitudinal, real-world dataset of cancer consisting of the imaging, clinical follow-up, and medical management of 1,429 patients. Using this dataset we developed Segmentation-Through-Time, a deep neural network which explicitly utilizes the longitudinal structure of the data and obtained state-of-the-art results at small (<10 mm3) metastases detection and segmentation. We also demonstrate that the monthly rate of change of brain metastases over time are strongly predictive of overall survival (HR 1.27, 95%CI 1.18-1.38). We are releasing the dataset, codebase, and model weights for other cancer researchers to build upon these results and to serve as a public benchmark.
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Affiliation(s)
- Katherine E Link
- Department of Neurosurgery, NYU Langone Health, New York, NY, USA
- NVIDIA, Santa Clara, CA, USA
| | - Zane Schnurman
- Department of Neurosurgery, NYU Langone Health, New York, NY, USA
| | - Chris Liu
- Department of Neurosurgery, NYU Langone Health, New York, NY, USA
- Electrical and Computer Engineering, NYU Tandon School of Engineering, New York, NY, USA
| | | | - Lavender Yao Jiang
- Department of Neurosurgery, NYU Langone Health, New York, NY, USA
- Center for Data Science, New York University, New York, NY, USA
| | | | - Sean Neifert
- Department of Neurosurgery, NYU Langone Health, New York, NY, USA
| | | | | | - Tanxia Qu
- Department of Radiation Oncology, NYU Langone Health, New York, NY, USA
| | | | - Eunice Yang
- Columbia University Vagelos College of Surgeons and Physicians, New York, NY, USA
| | - John G Golfinos
- Department of Neurosurgery, NYU Langone Health, New York, NY, USA
| | - Daniel Orringer
- Department of Neurosurgery, NYU Langone Health, New York, NY, USA
| | | | - Eric Karl Oermann
- Department of Neurosurgery, NYU Langone Health, New York, NY, USA.
- Department of Radiology, NYU Langone Health, New York, NY, USA.
- Center for Data Science, New York University, New York, NY, USA.
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2
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Resnick K, Shah A, Mason J, Kuhn P, Nieva J, Shishido SN. Circulation of rare events in the liquid biopsy for early detection of lung mass lesions. Thorac Cancer 2024. [PMID: 39233479 DOI: 10.1111/1759-7714.15429] [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: 05/14/2024] [Revised: 07/30/2024] [Accepted: 08/05/2024] [Indexed: 09/06/2024] Open
Abstract
BACKGROUND Lung cancer screening with low-dose computed tomography (CT) scans (LDCT) has reduced mortality for patients with high-risk smoking histories, but it has significant limitations: LDCT screening implementation remains low, high rates of false-positive scans, and current guidelines exclude those without smoking histories. We sought to explore the utility of liquid biopsy (LBx) in early cancer screening and diagnosis of lung cancer. METHODS Using the high-definition single-cell assay workflow, we analyzed 99 peripheral blood samples from three cohorts: normal donors (NDs) with no known pathology (n = 50), screening CT patients (n = 25) with Lung-RADS score of 1-2, and biopsy (BX) patients (n = 24) with abnormal CT scans requiring tissue biopsy. RESULTS For CT and BX patients, demographic information was roughly equivalent; however, average pack-years smoked differed. A total of 14 (58%) BX patients were diagnosed with primary lung cancer (BX+). The comparison of the rare event enumerations among the cohorts revealed a greater incidence of total events, rare cells, and oncosomes, as well as specific cellular phenotypes in the CT and BX cohorts compared with the ND cohort. LBx analytes were also significantly elevated in the BX compared with the CT samples, but there was no difference between BX+ and BX- samples. CONCLUSIONS The data support the utility of the LBx in distinguishing patients with an alveolar lesion from those without, providing a potential avenue for prescreening before LDCT.
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Affiliation(s)
- Karen Resnick
- Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, California, USA
| | - Anya Shah
- Convergent Science Institute for Cancer, Michelson Center, University of Southern California, Los Angeles, California, USA
| | - Jeremy Mason
- Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, California, USA
- Convergent Science Institute for Cancer, Michelson Center, University of Southern California, Los Angeles, California, USA
- Institute of Urology, Catherine & Joseph Aresty Department of Urology, Keck School of Medicine, University of Southern California, Los Angeles, California, USA
| | - Peter Kuhn
- Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, California, USA
- Convergent Science Institute for Cancer, Michelson Center, University of Southern California, Los Angeles, California, USA
- Institute of Urology, Catherine & Joseph Aresty Department of Urology, Keck School of Medicine, University of Southern California, Los Angeles, California, USA
- Department of Biomedical Engineering, Viterbi School of Engineering, University of Southern California, Los Angeles, California, USA
- Department of Aerospace and Mechanical Engineering, Viterbi School of Engineering, University of Southern California, Los Angeles, California, USA
- Department of Biological Sciences, Dornsife College of Letters, Arts, and Sciences, University of Southern California, Los Angeles, California, USA
| | - Jorge Nieva
- Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, California, USA
| | - Stephanie N Shishido
- Convergent Science Institute for Cancer, Michelson Center, University of Southern California, Los Angeles, California, USA
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3
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Smit DJ, Schneegans S, Pantel K. Clinical applications of circulating tumor cells in patients with solid tumors. Clin Exp Metastasis 2024; 41:403-411. [PMID: 38281256 PMCID: PMC11374849 DOI: 10.1007/s10585-024-10267-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2023] [Accepted: 01/11/2024] [Indexed: 01/30/2024]
Abstract
The concept of liquid biopsy analysis has been established more than a decade ago. Since the establishment of the term, tremendous advances have been achieved and plenty of methods as well as analytes have been investigated in basic research as well in clinical trials. Liquid biopsy refers to a body fluid-based biopsy that is minimal-invasive, and most importantly, allows dense monitoring of tumor responses by sequential blood sampling. Blood is the most important analyte for liquid biopsy analyses, providing an easily accessible source for a plethora of cells, cell-derived products, free nucleic acids, proteins as well as vesicles. More than 12,000 publications are listed in PubMed as of today including the term liquid biopsy. In this manuscript, we critically review the current implications of liquid biopsy, with special focus on circulating tumor cells, and describe the hurdles that need to be addressed before liquid biopsy can be implemented in clinical standard of care guidelines.
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Affiliation(s)
- Daniel J Smit
- Institute of Tumor Biology, University Medical Center Hamburg-Eppendorf, Martinistraße 52, 20246, Hamburg, Germany
- Fleur Hiege Center for Skin Cancer Research, Institute of Tumor Biology, University Medical Center Hamburg-Eppendorf, Martinistraße 52, 20246, Hamburg, Germany
| | - Svenja Schneegans
- Institute of Tumor Biology, University Medical Center Hamburg-Eppendorf, Martinistraße 52, 20246, Hamburg, Germany
| | - Klaus Pantel
- Institute of Tumor Biology, University Medical Center Hamburg-Eppendorf, Martinistraße 52, 20246, Hamburg, Germany.
- Fleur Hiege Center for Skin Cancer Research, Institute of Tumor Biology, University Medical Center Hamburg-Eppendorf, Martinistraße 52, 20246, Hamburg, Germany.
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4
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Nicolò E, Gianni C, Pontolillo L, Serafini MS, Munoz-Arcos LS, Andreopoulou E, Curigliano G, Reduzzi C, Cristofanilli M. Circulating tumor cells et al.: towards a comprehensive liquid biopsy approach in breast cancer. TRANSLATIONAL BREAST CANCER RESEARCH : A JOURNAL FOCUSING ON TRANSLATIONAL RESEARCH IN BREAST CANCER 2024; 5:10. [PMID: 38751670 PMCID: PMC11093063 DOI: 10.21037/tbcr-23-55] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/12/2023] [Accepted: 03/21/2024] [Indexed: 05/18/2024]
Abstract
Liquid biopsy has emerged as a crucial tool in managing breast cancer (BC) patients, offering a minimally invasive approach to detect circulating tumor biomarkers. Until recently, the majority of the studies in BC focused on evaluating a single liquid biopsy analyte, primarily circulating tumor DNA and circulating tumor cells (CTCs). Despite the proven prognostic and predictive value of CTCs, their low abundance when detected using enrichment methods, especially in the early stages, poses a significant challenge. It is becoming evident that combining diverse circulating biomarkers, each representing different facets of tumor biology, has the potential to enhance the management of patients with BC. This article emphasizes the importance of considering these biomarkers as complementary/synergistic rather than competitive, recognizing their ability to contribute to a comprehensive disease profile. The review provides an overview of the clinical significance of simultaneously analyzing CTCs and other biomarkers, including cell-free circulating DNA, extracellular vesicles, non-canonical CTCs, cell-free RNAs, and non-malignant cells. Such a comprehensive liquid biopsy approach holds promise not only in BC but also in other cancer types, offering opportunities for early detection, prognostication, and therapy monitoring. However, addressing associated challenges, such as refining detection methods and establishing standardized protocols, is crucial for realizing the full potential of liquid biopsy in transforming our understanding and approach to BC. As the field evolves, collaborative efforts will be instrumental in unlocking the revolutionary impact of liquid biopsy in BC research and management.
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Affiliation(s)
- Eleonora Nicolò
- Department of Medicine, Division of Hematology-Oncology, Weill Cornell Medicine, New York, NY, USA
- Department of Oncology and Hematology-Oncology, University of Milan, Milan, Italy
- Division of Early Drug Development, European Institute of Oncology IRCCS, Milan, Italy
| | - Caterina Gianni
- Department of Medicine, Division of Hematology-Oncology, Weill Cornell Medicine, New York, NY, USA
- Department of Medical Oncology, IRCCS Istituto Romagnolo per lo Studio dei Tumori (IRST) “Dino Amadori”, Meldola, Italy
| | - Letizia Pontolillo
- Department of Medicine, Division of Hematology-Oncology, Weill Cornell Medicine, New York, NY, USA
- Medical Oncology Department, Catholic University of Sacred Heart, Fondazione Policlinico Universitario Agostino Gemelli IRCCS, Rome, Italy
| | - Mara Serena Serafini
- Department of Medicine, Division of Hematology-Oncology, Weill Cornell Medicine, New York, NY, USA
| | - Laura Sofia Munoz-Arcos
- Department of Medicine, Division of Hematology-Oncology, Weill Cornell Medicine, New York, NY, USA
| | - Eleni Andreopoulou
- Department of Medicine, Division of Hematology-Oncology, Weill Cornell Medicine, New York, NY, USA
| | - Giuseppe Curigliano
- Department of Oncology and Hematology-Oncology, University of Milan, Milan, Italy
- Division of Early Drug Development, European Institute of Oncology IRCCS, Milan, Italy
| | - Carolina Reduzzi
- Department of Medicine, Division of Hematology-Oncology, Weill Cornell Medicine, New York, NY, USA
| | - Massimo Cristofanilli
- Department of Medicine, Division of Hematology-Oncology, Weill Cornell Medicine, New York, NY, USA
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Keup C, Kimmig R, Kasimir-Bauer S. The Diversity of Liquid Biopsies and Their Potential in Breast Cancer Management. Cancers (Basel) 2023; 15:5463. [PMID: 38001722 PMCID: PMC10670968 DOI: 10.3390/cancers15225463] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2023] [Revised: 11/10/2023] [Accepted: 11/14/2023] [Indexed: 11/26/2023] Open
Abstract
Analyzing blood as a so-called liquid biopsy in breast cancer (BC) patients has the potential to adapt therapy management. Circulating tumor cells (CTCs), extracellular vesicles (EVs), cell-free DNA (cfDNA) and other blood components mirror the tumoral heterogeneity and could support a range of clinical decisions. Multi-cancer early detection tests utilizing blood are advancing but are not part of any clinical routine yet. Liquid biopsy analysis in the course of neoadjuvant therapy has potential for therapy (de)escalation.Minimal residual disease detection via serial cfDNA analysis is currently on its way. The prognostic value of blood analytes in early and metastatic BC is undisputable, but the value of these prognostic biomarkers for clinical management is controversial. An interventional trial confirmed a significant outcome benefit when therapy was changed in case of newly emerging cfDNA mutations under treatment and thus showed the clinical utility of cfDNA analysis for therapy monitoring. The analysis of PIK3CA or ESR1 variants in plasma of metastatic BC patients to prescribe targeted therapy with alpesilib or elacestrant has already arrived in clinical practice with FDA-approved tests available and is recommended by ASCO. The translation of more liquid biopsy applications into clinical practice is still pending due to a lack of knowledge of the analytes' biology, lack of standards and difficulties in proving clinical utility.
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Affiliation(s)
- Corinna Keup
- Department of Gynecology and Obstetrics, University Hospital of Essen, 45147 Essen, Germany
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Qi E, Courcoubetis G, Liljegren E, Herrera E, Nguyen N, Nadri M, Ghandehari S, Kazemian E, Reckamp KL, Merin NM, Merchant A, Mason J, Figueiredo JC, Shishido SN, Kuhn P. Investigation of liquid biopsy analytes in peripheral blood of individuals after SARS-CoV-2 infection. EBioMedicine 2023; 90:104519. [PMID: 36921564 PMCID: PMC10008671 DOI: 10.1016/j.ebiom.2023.104519] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2022] [Revised: 02/21/2023] [Accepted: 02/23/2023] [Indexed: 03/14/2023] Open
Abstract
BACKGROUND Post-acute COVID-19 syndrome (PACS) is linked to severe organ damage. The identification and stratification of at-risk SARS-CoV-2 infected individuals is vital to providing appropriate care. This exploratory study looks for a potential liquid biopsy signal for PACS using both manual and machine learning approaches. METHODS Using a high definition single cell assay (HDSCA) workflow for liquid biopsy, we analysed 100 Post-COVID patients and 19 pre-pandemic normal donor (ND) controls. Within our patient cohort, 73 had received at least 1 dose of vaccination prior to SARS-CoV-2 infection. We stratified the COVID patients into 25 asymptomatic, 22 symptomatic COVID-19 but not suspected for PACS and 53 PACS suspected. All COVID-19 patients investigated in this study were diagnosed between April 2020 and January 2022 with a median 243 days (range 16-669) from diagnosis to their blood draw. We did a histopathological examination of rare events in the peripheral blood and used a machine learning model to evaluate predictors of PACS. FINDINGS The manual classification found rare cellular and acellular events consistent with features of endothelial cells and platelet structures in the PACS-suspected cohort. The three categories encompassing the hypothesised events were observed at a significantly higher incidence in the PACS-suspected cohort compared to the ND (p-value < 0.05). The machine learning classifier performed well when separating the NDs from Post-COVID with an accuracy of 90.1%, but poorly when separating the patients suspected and not suspected of PACS with an accuracy of 58.7%. INTERPRETATION Both the manual and the machine learning model found differences in the Post-COVID cohort and the NDs, suggesting the existence of a liquid biopsy signal after active SARS-CoV-2 infection. More research is needed to stratify PACS and its subsyndromes. FUNDING This work was funded in whole or in part by Fulgent Genetics, Kathy and Richard Leventhal and Vassiliadis Research Fund. This work was also supported by the National Cancer InstituteU54CA260591.
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Affiliation(s)
- Elizabeth Qi
- Convergent Science Institute in Cancer, Michelson Center for Convergent Bioscience, Dornsife College of Letters, Arts and Sciences, University of Southern California, Los Angeles, CA 90089, USA
| | - George Courcoubetis
- Convergent Science Institute in Cancer, Michelson Center for Convergent Bioscience, Dornsife College of Letters, Arts and Sciences, University of Southern California, Los Angeles, CA 90089, USA
| | - Emmett Liljegren
- Convergent Science Institute in Cancer, Michelson Center for Convergent Bioscience, Dornsife College of Letters, Arts and Sciences, University of Southern California, Los Angeles, CA 90089, USA
| | - Ergueen Herrera
- Department of Medicine, Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, 8700 Beverly Blvd Suite AC1072, Los Angeles, CA 90048, USA
| | - Nathalie Nguyen
- Division of Medical Oncology, Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Maimoona Nadri
- Division of Medical Oncology, Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Sara Ghandehari
- Cedars-Sinai Medical Center, Pulmonary Rehabilitation in the Women's Guild Lung Institute, Los Angeles, CA 90048, USA
| | - Elham Kazemian
- Department of Medicine, Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, 8700 Beverly Blvd Suite AC1072, Los Angeles, CA 90048, USA
| | - Karen L Reckamp
- Department of Medicine, Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, 8700 Beverly Blvd Suite AC1072, Los Angeles, CA 90048, USA
| | - Noah M Merin
- Division of Hematology and Cellular Therapy, Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Akil Merchant
- Division of Hematology and Cellular Therapy, Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Jeremy Mason
- Convergent Science Institute in Cancer, Michelson Center for Convergent Bioscience, Dornsife College of Letters, Arts and Sciences, University of Southern California, Los Angeles, CA 90089, USA; Catherine & Joseph Aresty Department of Urology, Institute of Urology, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA; Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA
| | - Jane C Figueiredo
- Department of Medicine, Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, 8700 Beverly Blvd Suite AC1072, Los Angeles, CA 90048, USA
| | - Stephanie N Shishido
- Convergent Science Institute in Cancer, Michelson Center for Convergent Bioscience, Dornsife College of Letters, Arts and Sciences, University of Southern California, Los Angeles, CA 90089, USA
| | - Peter Kuhn
- Convergent Science Institute in Cancer, Michelson Center for Convergent Bioscience, Dornsife College of Letters, Arts and Sciences, University of Southern California, Los Angeles, CA 90089, USA; Catherine & Joseph Aresty Department of Urology, Institute of Urology, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA; Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA; Department of Biomedical Engineering, Viterbi School of Engineering, University of Southern California, Los Angeles, CA 90089, USA; Department of Aerospace and Mechanical Engineering, Viterbi School of Engineering, University of Southern California, Los Angeles, CA 90089, USA; Department of Biological Sciences, Dornsife College of Letters, Arts, and Sciences, University of Southern California, Los Angeles, CA 90089, USA.
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7
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Casasent AK, Almekinders MM, Mulder C, Bhattacharjee P, Collyar D, Thompson AM, Jonkers J, Lips EH, van Rheenen J, Hwang ES, Nik-Zainal S, Navin NE, Wesseling J. Learning to distinguish progressive and non-progressive ductal carcinoma in situ. Nat Rev Cancer 2022; 22:663-678. [PMID: 36261705 DOI: 10.1038/s41568-022-00512-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 09/07/2022] [Indexed: 02/07/2023]
Abstract
Ductal carcinoma in situ (DCIS) is a non-invasive breast neoplasia that accounts for 25% of all screen-detected breast cancers diagnosed annually. Neoplastic cells in DCIS are confined to the ductal system of the breast, although they can escape and progress to invasive breast cancer in a subset of patients. A key concern of DCIS is overtreatment, as most patients screened for DCIS and in whom DCIS is diagnosed will not go on to exhibit symptoms or die of breast cancer, even if left untreated. However, differentiating low-risk, indolent DCIS from potentially progressive DCIS remains challenging. In this Review, we summarize our current knowledge of DCIS and explore open questions about the basic biology of DCIS, including those regarding how genomic events in neoplastic cells and the surrounding microenvironment contribute to the progression of DCIS to invasive breast cancer. Further, we discuss what information will be needed to prevent overtreatment of indolent DCIS lesions without compromising adequate treatment for high-risk patients.
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Affiliation(s)
- Anna K Casasent
- Department of Genetics, MD Anderson Cancer Center, Houston, TX, USA
| | | | - Charlotta Mulder
- Division of Molecular Pathology, Netherlands Cancer Institute, Amsterdam, Netherlands
| | | | | | | | - Jos Jonkers
- Division of Molecular Pathology, Netherlands Cancer Institute, Amsterdam, Netherlands
| | - Esther H Lips
- Division of Molecular Pathology, Netherlands Cancer Institute, Amsterdam, Netherlands
| | - Jacco van Rheenen
- Division of Molecular Pathology, Netherlands Cancer Institute, Amsterdam, Netherlands
| | | | - Serena Nik-Zainal
- Department of Medical Genetics, University of Cambridge, Cambridge, UK
| | - Nicholas E Navin
- Department of Genetics, MD Anderson Cancer Center, Houston, TX, USA
- Department of Bioinformatics, MD Anderson Cancer Center, Houston, TX, USA
| | - Jelle Wesseling
- Division of Molecular Pathology, Netherlands Cancer Institute, Amsterdam, Netherlands.
- Department of Pathology, Leiden University Medical Center, Leiden, Netherlands.
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8
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Ndacayisaba LJ, Rappard KE, Shishido SN, Setayesh SM, Tang G, Lin P, Matsumoto N, Hsu CJ, Nevarez R, Velasco CR, Naghdloo A, Yang E, Kelly K, Hicks J, Mason J, Orlowski RZ, Manasanch EE, Kuhn P. Characterization of BCMA Expression in Circulating Rare Single Cells of Patients with Plasma Cell Neoplasms. Int J Mol Sci 2022; 23:13427. [PMID: 36362214 PMCID: PMC9658574 DOI: 10.3390/ijms232113427] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2022] [Revised: 10/21/2022] [Accepted: 10/30/2022] [Indexed: 11/06/2022] Open
Abstract
B-cell maturation antigen (BCMA), a key regulator of B-cell proliferation and survival, is highly expressed in almost all cases of plasma cell neoplasms and B-lymphoproliferative malignancies. BCMA is a robust biomarker of plasma cells and a therapeutic target with substantial clinical significance. However, the expression of BCMA in circulating tumor cells of patients with hematological malignancies has not been validated for the detection of circulating plasma and B cells. The application of BCMA as a biomarker in single-cell detection and profiling of circulating tumor cells in patients' blood could enable early disease profiling and therapy response monitoring. Here, we report the development and validation of a slide-based immunofluorescence assay (i.e., CD138, BCMA, CD45, DAPI) for enrichment-free detection, quantification, and morphogenomic characterization of BCMA-expressing cells in patients (N = 9) with plasma cell neoplasms. Varying morphological subtypes of circulating BCMA-expressing cells were detected across the CD138(+/-) and CD45(+/-) compartments, representing candidate clonotypic post-germinal center B cells, plasmablasts, and both normal and malignant plasma cells. Genomic analysis by single-cell sequencing and correlation to clinical FISH cytogenetics provides validation, with data showing that patients across the different neoplastic states carry both normal and altered BCMA-expressing cells. Furthermore, altered cells harbor cytogenetic events detected by clinical FISH. The reported enrichment-free liquid biopsy approach has potential applications as a single-cell methodology for the early detection of BCMA+ B-lymphoid malignancies and in monitoring therapy response for patients undergoing anti-BCMA treatments.
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Affiliation(s)
- Libere J. Ndacayisaba
- Convergent Science Institute in Cancer, Michelson Center for Convergent Bioscience, University of Southern California, Los Angeles, CA 90089, USA
- Programs in Biomedical and Biological Sciences, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA
| | - Kate E. Rappard
- Convergent Science Institute in Cancer, Michelson Center for Convergent Bioscience, University of Southern California, Los Angeles, CA 90089, USA
| | - Stephanie N. Shishido
- Convergent Science Institute in Cancer, Michelson Center for Convergent Bioscience, University of Southern California, Los Angeles, CA 90089, USA
| | - Sonia M. Setayesh
- Convergent Science Institute in Cancer, Michelson Center for Convergent Bioscience, University of Southern California, Los Angeles, CA 90089, USA
- Department of Biological Sciences, Dornsife College of Letters, Arts, and Sciences, University of Southern California, Los Angeles, CA 90089, USA
| | - Guilin Tang
- Department of Hematopathology, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Pei Lin
- Department of Hematopathology, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Nicholas Matsumoto
- Convergent Science Institute in Cancer, Michelson Center for Convergent Bioscience, University of Southern California, Los Angeles, CA 90089, USA
| | - Ching-Ju Hsu
- Convergent Science Institute in Cancer, Michelson Center for Convergent Bioscience, University of Southern California, Los Angeles, CA 90089, USA
| | - Rafael Nevarez
- Convergent Science Institute in Cancer, Michelson Center for Convergent Bioscience, University of Southern California, Los Angeles, CA 90089, USA
| | - Carmen Ruiz Velasco
- Convergent Science Institute in Cancer, Michelson Center for Convergent Bioscience, University of Southern California, Los Angeles, CA 90089, USA
| | - Amin Naghdloo
- Convergent Science Institute in Cancer, Michelson Center for Convergent Bioscience, University of Southern California, Los Angeles, CA 90089, USA
- Department of Aerospace and Mechanical Engineering, Viterbi School of Engineering, University of Southern California, Los Angeles, CA 90089, USA
| | - Eric Yang
- Convergent Science Institute in Cancer, Michelson Center for Convergent Bioscience, University of Southern California, Los Angeles, CA 90089, USA
- Department of Biological Sciences, Dornsife College of Letters, Arts, and Sciences, University of Southern California, Los Angeles, CA 90089, USA
| | - Kevin Kelly
- Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA
| | - James Hicks
- Convergent Science Institute in Cancer, Michelson Center for Convergent Bioscience, University of Southern California, Los Angeles, CA 90089, USA
- Department of Biological Sciences, Dornsife College of Letters, Arts, and Sciences, University of Southern California, Los Angeles, CA 90089, USA
| | - Jeremy Mason
- Convergent Science Institute in Cancer, Michelson Center for Convergent Bioscience, University of Southern California, Los Angeles, CA 90089, USA
- Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA
- Catherine & Joseph Aresty Department of Urology, Institute of Urology, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA
| | - Robert Z. Orlowski
- Department of Lymphoma/Myeloma, Division of Cancer Medicine, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Elisabet E. Manasanch
- Department of Lymphoma/Myeloma, Division of Cancer Medicine, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Peter Kuhn
- Convergent Science Institute in Cancer, Michelson Center for Convergent Bioscience, University of Southern California, Los Angeles, CA 90089, USA
- Department of Biological Sciences, Dornsife College of Letters, Arts, and Sciences, University of Southern California, Los Angeles, CA 90089, USA
- Department of Aerospace and Mechanical Engineering, Viterbi School of Engineering, University of Southern California, Los Angeles, CA 90089, USA
- Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA
- Catherine & Joseph Aresty Department of Urology, Institute of Urology, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA
- Department of Biomedical Engineering, Viterbi School of Engineering, University of Southern California, Los Angeles, CA 90089, USA
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Defining A Liquid Biopsy Profile of Circulating Tumor Cells and Oncosomes in Metastatic Colorectal Cancer for Clinical Utility. Cancers (Basel) 2022; 14:cancers14194891. [PMID: 36230811 PMCID: PMC9563925 DOI: 10.3390/cancers14194891] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2022] [Accepted: 09/30/2022] [Indexed: 11/23/2022] Open
Abstract
Simple Summary Metastatic colorectal cancer (mCRC) is typified by its tumor heterogeneity and changing disease states, suggesting that personalized medicine approaches could be vital to improving clinical practice. As a minimally invasive approach, the liquid biopsy has the potential to be a powerful longitudinal prognostic tool. We investigated mCRC patients’ peripheral blood samples using an enrichment-free single-cell approach to capture the broader rare-event population beyond the conventionally detected epithelial-derived circulating tumor cell (CTC). Our analysis reveals a heterogenous profile of CTCs and oncosomes not commonly found in normal donor samples. We identified select rare cell types based on their distinct immunofluorescence expression and morphology across multiple assays. Lastly, we highlight correlations between enumerations of the blood-based analytes and progression-free survival. This study clinically validates an unbiased rare-event approach in the liquid biopsy, motivating future studies to further investigate these analytes for their prognostic potential. Abstract Metastatic colorectal cancer (mCRC) is characterized by its extensive disease heterogeneity, suggesting that individualized analysis could be vital to improving patient outcomes. As a minimally invasive approach, the liquid biopsy has the potential to longitudinally monitor heterogeneous analytes. Current platforms primarily utilize enrichment-based approaches for epithelial-derived circulating tumor cells (CTC), but this subtype is infrequent in the peripheral blood (PB) of mCRC patients, leading to the liquid biopsy’s relative disuse in this cancer type. In this study, we evaluated 18 PB samples from 10 mCRC patients using the unbiased high-definition single-cell assay (HDSCA). We first employed a rare-event (Landscape) immunofluorescence (IF) protocol, which captured a heterogenous CTC and oncosome population, the likes of which was not observed across 50 normal donor (ND) samples. Subsequent analysis was conducted using a colorectal-targeted IF protocol to assess the frequency of CDX2-expressing CTCs and oncosomes. A multi-assay clustering analysis isolated morphologically distinct subtypes across the two IF stains, demonstrating the value of applying an unbiased single-cell approach to multiple assays in tandem. Rare-event enumerations at a single timepoint and the variation of these events over time correlated with progression-free survival. This study supports the clinical utility of an unbiased approach to interrogating the liquid biopsy in mCRC, representing the heterogeneity within the CTC classification and warranting the further molecular characterization of the rare-event analytes with clinical promise.
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Multianalyte liquid biopsy to aid the diagnostic workup of breast cancer. NPJ Breast Cancer 2022; 8:112. [PMID: 36167819 PMCID: PMC9515081 DOI: 10.1038/s41523-022-00480-4] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2021] [Accepted: 09/16/2022] [Indexed: 11/19/2022] Open
Abstract
Breast cancer (BC) affects 1 in every 8 women in the United States and is currently the most prevalent cancer worldwide. Precise staging at diagnosis and prognosis are essential components for the clinical management of BC patients. In this study, we set out to evaluate the feasibility of the high-definition single cell (HDSCA) liquid biopsy (LBx) platform to stratify late-stage BC, early-stage BC, and normal donors using peripheral blood samples. Utilizing 5 biomarkers, we identified rare circulating events with epithelial, mesenchymal, endothelial and hematological origin. We detected a higher level of CTCs in late-stage patients, compared to the early-stage and normal donors. Additionally, we observed more tumor-associated large extracellular vesicles (LEVs) in the early-stage, compared to late-stage and the normal donor groups. Overall, we were able to detect reproducible patterns in the enumeration of rare cells and LEVs of cancer vs. normal donors and early-stage vs. late-stage BC with high accuracy, allowing for robust stratification. Our findings illustrate the feasibility of the LBx assay to provide robust detection of rare circulating events in peripheral blood draws and to stratify late-stage BC, early-stage BC, and normal donor samples.
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Liquid Biopsy Landscape in Patients with Primary Upper Tract Urothelial Carcinoma. Cancers (Basel) 2022; 14:cancers14123007. [PMID: 35740671 PMCID: PMC9221424 DOI: 10.3390/cancers14123007] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2022] [Revised: 06/07/2022] [Accepted: 06/10/2022] [Indexed: 01/27/2023] Open
Abstract
Urothelial carcinomas (UCs) are a broad and heterogeneous group of malignancies, with the prevalence of upper tract urothelial carcinoma (UTUC) being rare, accounting for only 5-10% of total malignancies. There is a need for additional toolsets to assist the current clinical paradigm of care for patients with UTUC. As a non-invasive tool for the discovery of cancer-related biomarkers, the liquid biopsy has the potential to represent the complex process of tumorigenesis and metastasis. Herein, we show the efficacy of the liquid biopsy as a source of biomarkers for detecting UTUC. Using the third-generation high-definition single-cell assay (HDSCA3.0) workflow, we investigate liquid biopsy samples collected from patients with UTUC and normal donors (NDs) to provide critical information regarding the molecular and morphological characteristics of circulating rare events. We document several important findings from the liquid biopsy analysis of patients diagnosed with UTUC prior to surgery: (1) Large extracellular vesicles (LEVs) and circulating tumor cells (CTCs) are detectable in the peripheral blood. (2) The rare-event profile is highly heterogeneous. (3) Clinical data elements correlate with liquid biopsy analytes. Overall, this study provides evidence for the efficacy of the liquid biopsy in understanding the biology of UTUC with the future intent of informing clinical decision making, ultimately improving patient outcomes.
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Ndacayisaba LJ, Rappard KE, Shishido SN, Ruiz Velasco C, Matsumoto N, Navarez R, Tang G, Lin P, Setayesh SM, Naghdloo A, Hsu CJ, Maney C, Symer D, Bethel K, Kelly K, Merchant A, Orlowski R, Hicks J, Mason J, Manasanch EE, Kuhn P. Enrichment-Free Single-Cell Detection and Morphogenomic Profiling of Myeloma Patient Samples to Delineate Circulating Rare Plasma Cell Clones. Curr Oncol 2022; 29:2954-2972. [PMID: 35621632 PMCID: PMC9139906 DOI: 10.3390/curroncol29050242] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2022] [Revised: 04/07/2022] [Accepted: 04/18/2022] [Indexed: 01/27/2023] Open
Abstract
Multiple myeloma is an incurable malignancy that initiates from a bone marrow resident clonal plasma cell and acquires successive mutational changes and genomic alterations, eventually resulting in tumor burden accumulation and end-organ damage. It has been recently recognized that myeloma secondary genomic events result in extensive sub-clonal heterogeneity both in localized bone marrow areas and circulating peripheral blood plasma cells. Rare genomic subclones, including myeloma initiating cells, could be the drivers of disease progression and recurrence. Additionally, evaluation of rare myeloma cells in blood for disease monitoring has numerous advantages over invasive bone marrow biopsies. To this end, an unbiased method for detecting rare cells and delineating their genomic makeup enables disease detection and monitoring in conditions with low abundant cancer cells. In this study, we applied an enrichment-free four-plex (CD138, CD56, CD45, DAPI) immunofluorescence assay and single-cell DNA sequencing for morphogenomic characterization of plasma cells to detect and delineate common and rare plasma cells and discriminate between normal and malignant plasma cells in paired blood and bone marrow aspirates from five patients with newly diagnosed myeloma (N = 4) and monoclonal gammopathy of undetermined significance (n = 1). Morphological analysis confirms CD138+CD56+ cells in the peripheral blood carry genomic alterations that are clonally identical to those in the bone marrow. A subset of altered CD138+CD56- cells are also found in the peripheral blood consistent with the known variability in CD56 expression as a marker of plasma cell malignancy. Bone marrow tumor clinical cytogenetics is highly correlated with the single-cell copy number alterations of the liquid biopsy rare cells. A subset of rare cells harbors genetic alterations not detected by standard clinical diagnostic methods of random localized bone marrow biopsies. This enrichment-free morphogenomic approach detects and characterizes rare cell populations derived from the liquid biopsies that are consistent with clinical diagnosis and have the potential to extend our understanding of subclonality at the single-cell level in this disease. Assay validation in larger patient cohorts has the potential to offer liquid biopsy for disease monitoring with similar or improved disease detection as traditional blind bone marrow biopsies.
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Affiliation(s)
- Libere J. Ndacayisaba
- Convergent Science Institute in Cancer, Michelson Center for Convergent Bioscience, University of Southern California, Los Angeles, CA 90089, USA; (L.J.N.); (K.E.R.); (S.N.S.); (C.R.V.); (N.M.); (R.N.); (S.M.S.); (A.N.); (C.-J.H.); (C.M.); (J.H.); (J.M.)
- Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA;
| | - Kate E. Rappard
- Convergent Science Institute in Cancer, Michelson Center for Convergent Bioscience, University of Southern California, Los Angeles, CA 90089, USA; (L.J.N.); (K.E.R.); (S.N.S.); (C.R.V.); (N.M.); (R.N.); (S.M.S.); (A.N.); (C.-J.H.); (C.M.); (J.H.); (J.M.)
| | - Stephanie N. Shishido
- Convergent Science Institute in Cancer, Michelson Center for Convergent Bioscience, University of Southern California, Los Angeles, CA 90089, USA; (L.J.N.); (K.E.R.); (S.N.S.); (C.R.V.); (N.M.); (R.N.); (S.M.S.); (A.N.); (C.-J.H.); (C.M.); (J.H.); (J.M.)
| | - Carmen Ruiz Velasco
- Convergent Science Institute in Cancer, Michelson Center for Convergent Bioscience, University of Southern California, Los Angeles, CA 90089, USA; (L.J.N.); (K.E.R.); (S.N.S.); (C.R.V.); (N.M.); (R.N.); (S.M.S.); (A.N.); (C.-J.H.); (C.M.); (J.H.); (J.M.)
| | - Nicholas Matsumoto
- Convergent Science Institute in Cancer, Michelson Center for Convergent Bioscience, University of Southern California, Los Angeles, CA 90089, USA; (L.J.N.); (K.E.R.); (S.N.S.); (C.R.V.); (N.M.); (R.N.); (S.M.S.); (A.N.); (C.-J.H.); (C.M.); (J.H.); (J.M.)
| | - Rafael Navarez
- Convergent Science Institute in Cancer, Michelson Center for Convergent Bioscience, University of Southern California, Los Angeles, CA 90089, USA; (L.J.N.); (K.E.R.); (S.N.S.); (C.R.V.); (N.M.); (R.N.); (S.M.S.); (A.N.); (C.-J.H.); (C.M.); (J.H.); (J.M.)
| | - Guilin Tang
- Department of Hematopathology, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA; (G.T.); (P.L.)
| | - Pei Lin
- Department of Hematopathology, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA; (G.T.); (P.L.)
| | - Sonia M. Setayesh
- Convergent Science Institute in Cancer, Michelson Center for Convergent Bioscience, University of Southern California, Los Angeles, CA 90089, USA; (L.J.N.); (K.E.R.); (S.N.S.); (C.R.V.); (N.M.); (R.N.); (S.M.S.); (A.N.); (C.-J.H.); (C.M.); (J.H.); (J.M.)
| | - Amin Naghdloo
- Convergent Science Institute in Cancer, Michelson Center for Convergent Bioscience, University of Southern California, Los Angeles, CA 90089, USA; (L.J.N.); (K.E.R.); (S.N.S.); (C.R.V.); (N.M.); (R.N.); (S.M.S.); (A.N.); (C.-J.H.); (C.M.); (J.H.); (J.M.)
| | - Ching-Ju Hsu
- Convergent Science Institute in Cancer, Michelson Center for Convergent Bioscience, University of Southern California, Los Angeles, CA 90089, USA; (L.J.N.); (K.E.R.); (S.N.S.); (C.R.V.); (N.M.); (R.N.); (S.M.S.); (A.N.); (C.-J.H.); (C.M.); (J.H.); (J.M.)
| | - Carlisle Maney
- Convergent Science Institute in Cancer, Michelson Center for Convergent Bioscience, University of Southern California, Los Angeles, CA 90089, USA; (L.J.N.); (K.E.R.); (S.N.S.); (C.R.V.); (N.M.); (R.N.); (S.M.S.); (A.N.); (C.-J.H.); (C.M.); (J.H.); (J.M.)
| | - David Symer
- Department of Lymphoma/Myeloma, Division of Cancer Medicine, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA; (D.S.); (R.O.); (E.E.M.)
| | - Kelly Bethel
- Department of Pathology, Scripps Clinic Medical Group, La Jolla, CA 92037, USA;
| | - Kevin Kelly
- Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA;
| | - Akil Merchant
- Department of Medicine, Cedars Sinai Medical Center, Los Angeles, CA 90048, USA;
| | - Robert Orlowski
- Department of Lymphoma/Myeloma, Division of Cancer Medicine, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA; (D.S.); (R.O.); (E.E.M.)
| | - James Hicks
- Convergent Science Institute in Cancer, Michelson Center for Convergent Bioscience, University of Southern California, Los Angeles, CA 90089, USA; (L.J.N.); (K.E.R.); (S.N.S.); (C.R.V.); (N.M.); (R.N.); (S.M.S.); (A.N.); (C.-J.H.); (C.M.); (J.H.); (J.M.)
- Department of Pathology, Scripps Clinic Medical Group, La Jolla, CA 92037, USA;
| | - Jeremy Mason
- Convergent Science Institute in Cancer, Michelson Center for Convergent Bioscience, University of Southern California, Los Angeles, CA 90089, USA; (L.J.N.); (K.E.R.); (S.N.S.); (C.R.V.); (N.M.); (R.N.); (S.M.S.); (A.N.); (C.-J.H.); (C.M.); (J.H.); (J.M.)
- Institute of Urology, Catherine & Joseph Aresty Department of Urology, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA
- Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA
| | - Elisabeth E. Manasanch
- Department of Lymphoma/Myeloma, Division of Cancer Medicine, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA; (D.S.); (R.O.); (E.E.M.)
| | - Peter Kuhn
- Convergent Science Institute in Cancer, Michelson Center for Convergent Bioscience, University of Southern California, Los Angeles, CA 90089, USA; (L.J.N.); (K.E.R.); (S.N.S.); (C.R.V.); (N.M.); (R.N.); (S.M.S.); (A.N.); (C.-J.H.); (C.M.); (J.H.); (J.M.)
- Institute of Urology, Catherine & Joseph Aresty Department of Urology, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA
- Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA
- Department of Biomedical Engineering, Viterbi School of Engineering, University of Southern California, Los Angeles, CA 90089, USA
- Department of Aerospace and Mechanical Engineering, Viterbi School of Engineering, University of Southern California, Los Angeles, CA 90089, USA
- Department of Biological Sciences, Dornsife College of Letters, Arts, and Sciences, University of Southern California, Los Angeles, CA 90089, USA
- Correspondence: ; Tel.: +1-213-821-3980
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Keup C, Kimmig R, Kasimir-Bauer S. Combinatorial Power of cfDNA, CTCs and EVs in Oncology. Diagnostics (Basel) 2022; 12:870. [PMID: 35453918 PMCID: PMC9031112 DOI: 10.3390/diagnostics12040870] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2022] [Revised: 03/18/2022] [Accepted: 03/28/2022] [Indexed: 01/01/2023] Open
Abstract
Liquid biopsy is a promising technique for clinical management of oncological patients. The diversity of analytes circulating in the blood useable for liquid biopsy testing is enormous. Circulating tumor cells (CTCs), cell-free DNA (cfDNA) and extracellular vesicles (EVs), as well as blood cells and other soluble components in the plasma, were shown as liquid biopsy analytes. A few studies directly comparing two liquid biopsy analytes showed a benefit of one analyte over the other, while most authors concluded the benefit of the additional analyte. Only three years ago, the first studies to examine the value of a characterization of more than two liquid biopsy analytes from the same sample were conducted. We attempt to reflect on the recent development of multimodal liquid biopsy testing in this review. Although the analytes and clinical purposes of the published multimodal studies differed significantly, the additive value of the analytes was concluded in almost all projects. Thus, the blood components, as liquid biopsy reservoirs, are complementary rather than competitive, and orthogonal data sets were even shown to harbor synergistic effects. The unmistakable potential of multimodal liquid biopsy testing, however, is dampened by its clinical utility, which is yet to be proven, the lack of methodical standardization and insufficiently mature reimbursement, logistics and data handling.
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Affiliation(s)
- Corinna Keup
- Department of Gynecology and Obstetrics, University Hospital of Essen, Hufelandstr. 55, 45122 Essen, Germany
| | - Rainer Kimmig
- Department of Gynecology and Obstetrics, University Hospital of Essen, Hufelandstr. 55, 45122 Essen, Germany
| | - Sabine Kasimir-Bauer
- Department of Gynecology and Obstetrics, University Hospital of Essen, Hufelandstr. 55, 45122 Essen, Germany
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Circulating Cell-Free DNA Reflects the Clonal Evolution of Breast Cancer Tumors. Cancers (Basel) 2022; 14:cancers14051332. [PMID: 35267640 PMCID: PMC8909912 DOI: 10.3390/cancers14051332] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2022] [Revised: 02/28/2022] [Accepted: 03/01/2022] [Indexed: 02/08/2023] Open
Abstract
Simple Summary Liquid biopsy of cell-free DNA (cfDNA) is proposed as potential method for the early detection of breast cancer (BC) metastases and following the clonal evolution of BC. Though the use of liquid biopsy is widely discussed, only few studies have demonstrated such usage so far. The aim of this study was to evaluate how accurately cfDNA resembles the genetic profile of tumor DNA and how liquid biopsy reflects the clonal evolution of 18 Eastern-Finnish BC cases with locoregional or distant metastases. Although notable discordance between the sequenced cfDNA and tumor DNA was observed, our results show that liquid biopsy reflects the heterogeneity and clonal evolution of BC and may help to identify potential driver variants and therapeutic targets that are not detected with the sequencing of tumor DNA. This information may be used to detect metastatic BC earlier and to support decision-making in clinical practice. Abstract Liquid biopsy of cell-free DNA (cfDNA) is proposed as a potential method for the early detection of breast cancer (BC) metastases and following the clonal evolution of BC. Though the use of liquid biopsy is a widely discussed topic in the field, only a few studies have demonstrated such usage so far. We sequenced the DNA of matched primary tumor and metastatic sites together with the matched cfDNA samples from 18 Eastern Finnish BC patients and investigated how well cfDNA reflected the clonal evolution of BC interpreted from tumor DNA. On average, liquid biopsy detected 56.2 ± 7.2% of the somatic variants that were present either in the matched primary tumor or metastatic sites. Despite the high discordance observed between matched samples, liquid biopsy was found to reflect the clonal evolution of BC and identify novel driver variants and therapeutic targets absent from the tumor DNA. Tumor-specific somatic variants were detected in cfDNA at the time of diagnosis and 8.4 ± 2.4 months prior to detection of locoregional recurrence or distant metastases. Our results demonstrate that the sequencing of cfDNA may be used for the early detection of locoregional and distant BC metastases. Observed discordance between tumor DNA sequencing and liquid biopsy supports the parallel sequencing of cfDNA and tumor DNA to yield the most comprehensive overview for the genetic landscape of BC.
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Shishido SN, Masson R, Xu L, Welter L, Prabakar RK, D' Souza A, Spicer D, Kang I, Jayachandran P, Hicks J, Lu J, Kuhn P. Disease characterization in liquid biopsy from HER2-mutated, non-amplified metastatic breast cancer patients treated with neratinib. NPJ Breast Cancer 2022; 8:22. [PMID: 35181666 PMCID: PMC8857263 DOI: 10.1038/s41523-022-00390-5] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2021] [Accepted: 01/14/2022] [Indexed: 12/18/2022] Open
Abstract
Metastatic breast cancer (mBC) patients have a high risk of progression and face poor prognosis overall, with about one third (34%) surviving five years or more. In rare instances (2-4% of cases) patients with mBC have ERBB2 (HER2) activating mutations but are ERBB2 non-amplified. Neratinib is a potent, irreversible inhibitor that binds HER2 and inhibits downstream signaling. We used the previously validated high-definition single cell assay (HDSCA) workflow to investigate the clinical significance of the liquid biopsy in ERBB2 mutant, non-amplified, post-menopausal mBC patients starting neratinib and fulvestrant combination therapy. Characterization with a comprehensive liquid biopsy methodology (HDSCA) included genomic analysis of both the cell-free DNA (cfDNA) and single circulating tumor cells (CTCs) to monitor tumor evolution and identify potential mutational variants unique to the patient's clinical response. A limited series of five sequentially enrolled patients presented here were from the MutHER ( https://www.clinicaltrials.gov , NCT01670877) or SUMMIT ( https://www.clinicaltrials.gov , NCT01953926) trials. Patients had an average of 5.4 lines of therapy before enrollment, variable hormone receptor status, and ERBB2 mutations at diagnosis and during treatment. CTC enumeration alone was not sufficient to predict clinical response. Treatment pressure was shown to lead to an observable change in CTC morphology and genomic instability (GI), suggesting these parameters may inform prognosis. Single cell copy number alteration (CNA) analysis indicated that the persistence or development of a clonal population of CTCs during treatment was associated with a worse response. Hierarchical clustering analysis of the single cells across all patients and timepoints identified distinct aberrant regions shared among patients, comprised of 26 genes that are similarly affected and may be related to drug resistance. Additionally, the genomic analysis of the cfDNA, identified new mutations in ERBB2, PIK3CA, and TP53 that arose likely due to treatment pressure in a patient with poor response, further providing insights on the dynamics of the cancer genome over the course of therapy. The data presented in this small cohort study demonstrates the feasibility of real-time molecular profiling of the cellular and acellular fractions of the liquid biopsy using the HDSCA methodology. Additional studies are necessary to determine the potential use of morphometric and genomic analysis as a prognostic tool to advance personalized oncology.
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Affiliation(s)
- Stephanie N Shishido
- Convergent Science Institute in Cancer (CSI-Cancer), Michelson Center for Convergent Bioscience, University of Southern California,1002 Childs Way, MCB 220, Los Angeles, CA, 90089, USA
| | - Rahul Masson
- Convergent Science Institute in Cancer (CSI-Cancer), Michelson Center for Convergent Bioscience, University of Southern California,1002 Childs Way, MCB 220, Los Angeles, CA, 90089, USA
| | - Liya Xu
- Convergent Science Institute in Cancer (CSI-Cancer), Michelson Center for Convergent Bioscience, University of Southern California,1002 Childs Way, MCB 220, Los Angeles, CA, 90089, USA
| | - Lisa Welter
- Convergent Science Institute in Cancer (CSI-Cancer), Michelson Center for Convergent Bioscience, University of Southern California,1002 Childs Way, MCB 220, Los Angeles, CA, 90089, USA
| | - Rishvanth Kaliappan Prabakar
- Convergent Science Institute in Cancer (CSI-Cancer), Michelson Center for Convergent Bioscience, University of Southern California,1002 Childs Way, MCB 220, Los Angeles, CA, 90089, USA
| | - Anishka D' Souza
- USC Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, 1441 Eastlake Ave, NTT-3440, Los Angeles, CA, 90033, USA
| | - Darcy Spicer
- USC Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, 1441 Eastlake Ave, NTT-3440, Los Angeles, CA, 90033, USA
| | - Irene Kang
- USC Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, 1441 Eastlake Ave, NTT-3440, Los Angeles, CA, 90033, USA
| | - Priya Jayachandran
- USC Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, 1441 Eastlake Ave, NTT-3440, Los Angeles, CA, 90033, USA
| | - James Hicks
- Convergent Science Institute in Cancer (CSI-Cancer), Michelson Center for Convergent Bioscience, University of Southern California,1002 Childs Way, MCB 220, Los Angeles, CA, 90089, USA
| | - Janice Lu
- USC Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, 1441 Eastlake Ave, NTT-3440, Los Angeles, CA, 90033, USA
| | - Peter Kuhn
- Convergent Science Institute in Cancer (CSI-Cancer), Michelson Center for Convergent Bioscience, University of Southern California,1002 Childs Way, MCB 220, Los Angeles, CA, 90089, USA.
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Moore HCF, Barlow WE, Somlo G, Gralow JR, Schott AF, Hayes DF, Kuhn P, Hicks JB, Welter L, Dy PA, Yeon CH, Conlin AK, Balcueva E, Lew DL, Tripathy D, Pusztai L, Hortobagyi GN. A Randomized Trial of Fulvestrant, Everolimus, and Anastrozole for the Front-line Treatment of Patients with Advanced Hormone Receptor-positive Breast Cancer, SWOG S1222. Clin Cancer Res 2022; 28:611-617. [PMID: 34844978 PMCID: PMC9782801 DOI: 10.1158/1078-0432.ccr-21-3131] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2021] [Revised: 10/26/2021] [Accepted: 11/22/2021] [Indexed: 12/27/2022]
Abstract
PURPOSE Metastatic hormone receptor (HR)-positive, HER2-negative breast cancer is an important cause of cancer mortality. Endocrine treatment with or without additional targeted therapies has been the mainstay of treatment. This trial was designed to evaluate the combination of fulvestrant plus everolimus versus fulvestrant, everolimus, and anastrozole compared with fulvestrant alone in the first-line treatment of advanced HR-positive, HER2-negative breast cancer. PATIENTS AND METHODS This randomized placebo-controlled trial included postmenopausal women with HR-positive, HER2-negative advanced breast cancer who had received no prior systemic therapy for metastatic disease. Participants were randomized to one of three treatment arms and the primary outcome was progression-free survival (PFS), comparing combinations of fulvestrant and everolimus with or without anastrozole with fulvestrant alone. Circulating tumor cells (CTC), as measured with two different methods, and circulating tumor DNA (ctDNA) were evaluated serially prior to treatment and the beginning of the second cycle of therapy. RESULTS Due in part to changes in clinical practice, the study was closed after accruing only 37 participants. There was no evidence that everolimus-containing combination treatment improved PFS or overall survival relative to fulvestrant alone. When modeled continuously, an association was observed of baseline CTC and ctDNA with poorer survival. CONCLUSIONS Although power of the study was limited, the findings were unable to support the routine use of everolimus combination endocrine therapy in the first-line treatment of advanced hormone-sensitive breast cancer. Prognostic impact of baseline ctDNA and copy-number variations in CTC was demonstrated.
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Affiliation(s)
| | | | | | - Julie R. Gralow
- University of Washington School of Medicine/Seattle Cancer Care Alliance, Seattle, WA
| | - Anne F. Schott
- University of Michigan Rogel Cancer Center, Ann Arbor, MI
| | | | - Peter Kuhn
- University of Southern California, Los Angeles, CA
| | | | - Lisa Welter
- University of Southern California, Los Angeles, CA
| | - Philip A. Dy
- Crossroads Cancer Center (Cancer Care Specialists of Illinois), Heartland NCORP
| | | | | | | | - Danika L. Lew
- SWOG Statistics and Data Management Center, Seattle, WA
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Kolenčík D, Narayan S, Thiele JA, McKinley D, Gerdtsson AS, Welter L, Hošek P, Ostašov P, Vyčítal O, Brůha J, Fiala O, Šorejs O, Liška V, Pitule P, Kuhn P, Shishido SN. Circulating Tumor Cell Kinetics and Morphology from the Liquid Biopsy Predict Disease Progression in Patients with Metastatic Colorectal Cancer Following Resection. Cancers (Basel) 2022; 14:642. [PMID: 35158910 PMCID: PMC8833610 DOI: 10.3390/cancers14030642] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2021] [Revised: 01/05/2022] [Accepted: 01/11/2022] [Indexed: 02/04/2023] Open
Abstract
The liquid biopsy has the potential to improve current clinical practice in oncology by providing real-time personalized information about a patient's disease status and response to treatment. In this study, we evaluated 161 peripheral blood (PB) samples that were collected around surgical resection from 47 metastatic colorectal cancer (mCRC) patients using the High-Definition Single Cell Assay (HDSCA) workflow. In conjunction with the standard circulating tumor cell (CTC) enumeration, cellular morphology and kinetics between time-points of collection were considered in the survival analysis. CTCs, CTC-Apoptotic, and CTC clusters were found to indicate poor survival with an increase in cell count from pre-resection to post-resection. This study demonstrates that CTC subcategorization based on morphological differences leads to nuanced results between the subtypes, emphasizing the heterogeneity within the CTC classification. Furthermore, we show that factoring in the time-point of each blood collection is critical, both for its static enumeration and for the change in cell populations between draws. By integrating morphology and time-based analysis alongside standard CTC enumeration, liquid biopsy platforms can provide greater insight into the pathophysiology of mCRC by highlighting the complexity of the disease across a patient's treatment.
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Affiliation(s)
- Drahomír Kolenčík
- Biomedical Center, Faculty of Medicine in Pilsen, Charles University, 32300 Pilsen, Czech Republic; (D.K.); (J.-A.T.); (P.H.); (P.O.); (O.V.); (J.B.); (O.F.); (O.Š.); (V.L.); (P.P.)
| | - Sachin Narayan
- Convergent Science Institute in Cancer, Michelson Center for Convergent Bioscience, Dornsife College of Letters, Arts and Sciences, University of Southern California, Los Angeles, CA 90089, USA; (S.N.); (D.M.); (A.S.G.); (L.W.); (S.N.S.)
| | - Jana-Aletta Thiele
- Biomedical Center, Faculty of Medicine in Pilsen, Charles University, 32300 Pilsen, Czech Republic; (D.K.); (J.-A.T.); (P.H.); (P.O.); (O.V.); (J.B.); (O.F.); (O.Š.); (V.L.); (P.P.)
| | - Dillon McKinley
- Convergent Science Institute in Cancer, Michelson Center for Convergent Bioscience, Dornsife College of Letters, Arts and Sciences, University of Southern California, Los Angeles, CA 90089, USA; (S.N.); (D.M.); (A.S.G.); (L.W.); (S.N.S.)
| | - Anna Sandström Gerdtsson
- Convergent Science Institute in Cancer, Michelson Center for Convergent Bioscience, Dornsife College of Letters, Arts and Sciences, University of Southern California, Los Angeles, CA 90089, USA; (S.N.); (D.M.); (A.S.G.); (L.W.); (S.N.S.)
| | - Lisa Welter
- Convergent Science Institute in Cancer, Michelson Center for Convergent Bioscience, Dornsife College of Letters, Arts and Sciences, University of Southern California, Los Angeles, CA 90089, USA; (S.N.); (D.M.); (A.S.G.); (L.W.); (S.N.S.)
| | - Petr Hošek
- Biomedical Center, Faculty of Medicine in Pilsen, Charles University, 32300 Pilsen, Czech Republic; (D.K.); (J.-A.T.); (P.H.); (P.O.); (O.V.); (J.B.); (O.F.); (O.Š.); (V.L.); (P.P.)
| | - Pavel Ostašov
- Biomedical Center, Faculty of Medicine in Pilsen, Charles University, 32300 Pilsen, Czech Republic; (D.K.); (J.-A.T.); (P.H.); (P.O.); (O.V.); (J.B.); (O.F.); (O.Š.); (V.L.); (P.P.)
| | - Ondřej Vyčítal
- Biomedical Center, Faculty of Medicine in Pilsen, Charles University, 32300 Pilsen, Czech Republic; (D.K.); (J.-A.T.); (P.H.); (P.O.); (O.V.); (J.B.); (O.F.); (O.Š.); (V.L.); (P.P.)
- Department of Surgery, Faculty of Medicine and University Hospital in Pilsen, Charles University, 32300 Pilsen, Czech Republic
| | - Jan Brůha
- Biomedical Center, Faculty of Medicine in Pilsen, Charles University, 32300 Pilsen, Czech Republic; (D.K.); (J.-A.T.); (P.H.); (P.O.); (O.V.); (J.B.); (O.F.); (O.Š.); (V.L.); (P.P.)
- Department of Surgery, Faculty of Medicine and University Hospital in Pilsen, Charles University, 32300 Pilsen, Czech Republic
| | - Ondřej Fiala
- Biomedical Center, Faculty of Medicine in Pilsen, Charles University, 32300 Pilsen, Czech Republic; (D.K.); (J.-A.T.); (P.H.); (P.O.); (O.V.); (J.B.); (O.F.); (O.Š.); (V.L.); (P.P.)
- Department of Oncology and Radiotherapeutics, Faculty of Medicine and University Hospital in Pilsen, Charles University, 32300 Pilsen, Czech Republic
| | - Ondřej Šorejs
- Biomedical Center, Faculty of Medicine in Pilsen, Charles University, 32300 Pilsen, Czech Republic; (D.K.); (J.-A.T.); (P.H.); (P.O.); (O.V.); (J.B.); (O.F.); (O.Š.); (V.L.); (P.P.)
- Department of Oncology and Radiotherapeutics, Faculty of Medicine and University Hospital in Pilsen, Charles University, 32300 Pilsen, Czech Republic
| | - Václav Liška
- Biomedical Center, Faculty of Medicine in Pilsen, Charles University, 32300 Pilsen, Czech Republic; (D.K.); (J.-A.T.); (P.H.); (P.O.); (O.V.); (J.B.); (O.F.); (O.Š.); (V.L.); (P.P.)
- Department of Surgery, Faculty of Medicine and University Hospital in Pilsen, Charles University, 32300 Pilsen, Czech Republic
| | - Pavel Pitule
- Biomedical Center, Faculty of Medicine in Pilsen, Charles University, 32300 Pilsen, Czech Republic; (D.K.); (J.-A.T.); (P.H.); (P.O.); (O.V.); (J.B.); (O.F.); (O.Š.); (V.L.); (P.P.)
| | - Peter Kuhn
- Convergent Science Institute in Cancer, Michelson Center for Convergent Bioscience, Dornsife College of Letters, Arts and Sciences, University of Southern California, Los Angeles, CA 90089, USA; (S.N.); (D.M.); (A.S.G.); (L.W.); (S.N.S.)
| | - Stephanie N. Shishido
- Convergent Science Institute in Cancer, Michelson Center for Convergent Bioscience, Dornsife College of Letters, Arts and Sciences, University of Southern California, Los Angeles, CA 90089, USA; (S.N.); (D.M.); (A.S.G.); (L.W.); (S.N.S.)
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Rehm HL, Page AJ, Smith L, Adams JB, Alterovitz G, Babb LJ, Barkley MP, Baudis M, Beauvais MJ, Beck T, Beckmann JS, Beltran S, Bernick D, Bernier A, Bonfield JK, Boughtwood TF, Bourque G, Bowers SR, Brookes AJ, Brudno M, Brush MH, Bujold D, Burdett T, Buske OJ, Cabili MN, Cameron DL, Carroll RJ, Casas-Silva E, Chakravarty D, Chaudhari BP, Chen SH, Cherry JM, Chung J, Cline M, Clissold HL, Cook-Deegan RM, Courtot M, Cunningham F, Cupak M, Davies RM, Denisko D, Doerr MJ, Dolman LI, Dove ES, Dursi LJ, Dyke SO, Eddy JA, Eilbeck K, Ellrott KP, Fairley S, Fakhro KA, Firth HV, Fitzsimons MS, Fiume M, Flicek P, Fore IM, Freeberg MA, Freimuth RR, Fromont LA, Fuerth J, Gaff CL, Gan W, Ghanaim EM, Glazer D, Green RC, Griffith M, Griffith OL, Grossman RL, Groza T, Guidry Auvil JM, Guigó R, Gupta D, Haendel MA, Hamosh A, Hansen DP, Hart RK, Hartley DM, Haussler D, Hendricks-Sturrup RM, Ho CW, Hobb AE, Hoffman MM, Hofmann OM, Holub P, Hsu JS, Hubaux JP, Hunt SE, Husami A, Jacobsen JO, Jamuar SS, Janes EL, Jeanson F, Jené A, Johns AL, Joly Y, Jones SJ, Kanitz A, Kato K, Keane TM, Kekesi-Lafrance K, Kelleher J, Kerry G, Khor SS, Knoppers BM, Konopko MA, Kosaki K, Kuba M, Lawson J, Leinonen R, Li S, Lin MF, Linden M, Liu X, Liyanage IU, Lopez J, Lucassen AM, Lukowski M, Mann AL, Marshall J, Mattioni M, Metke-Jimenez A, Middleton A, Milne RJ, Molnár-Gábor F, Mulder N, Munoz-Torres MC, Nag R, Nakagawa H, Nasir J, Navarro A, Nelson TH, Niewielska A, Nisselle A, Niu J, Nyrönen TH, O’Connor BD, Oesterle S, Ogishima S, Ota Wang V, Paglione LA, Palumbo E, Parkinson HE, Philippakis AA, Pizarro AD, Prlic A, Rambla J, Rendon A, Rider RA, Robinson PN, Rodarmer KW, Rodriguez LL, Rubin AF, Rueda M, Rushton GA, Ryan RS, Saunders GI, Schuilenburg H, Schwede T, Scollen S, Senf A, Sheffield NC, Skantharajah N, Smith AV, Sofia HJ, Spalding D, Spurdle AB, Stark Z, Stein LD, Suematsu M, Tan P, Tedds JA, Thomson AA, Thorogood A, Tickle TL, Tokunaga K, Törnroos J, Torrents D, Upchurch S, Valencia A, Guimera RV, Vamathevan J, Varma S, Vears DF, Viner C, Voisin C, Wagner AH, Wallace SE, Walsh BP, Williams MS, Winkler EC, Wold BJ, Wood GM, Woolley JP, Yamasaki C, Yates AD, Yung CK, Zass LJ, Zaytseva K, Zhang J, Goodhand P, North K, Birney E. GA4GH: International policies and standards for data sharing across genomic research and healthcare. CELL GENOMICS 2021; 1:100029. [PMID: 35072136 PMCID: PMC8774288 DOI: 10.1016/j.xgen.2021.100029] [Citation(s) in RCA: 88] [Impact Index Per Article: 29.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
The Global Alliance for Genomics and Health (GA4GH) aims to accelerate biomedical advances by enabling the responsible sharing of clinical and genomic data through both harmonized data aggregation and federated approaches. The decreasing cost of genomic sequencing (along with other genome-wide molecular assays) and increasing evidence of its clinical utility will soon drive the generation of sequence data from tens of millions of humans, with increasing levels of diversity. In this perspective, we present the GA4GH strategies for addressing the major challenges of this data revolution. We describe the GA4GH organization, which is fueled by the development efforts of eight Work Streams and informed by the needs of 24 Driver Projects and other key stakeholders. We present the GA4GH suite of secure, interoperable technical standards and policy frameworks and review the current status of standards, their relevance to key domains of research and clinical care, and future plans of GA4GH. Broad international participation in building, adopting, and deploying GA4GH standards and frameworks will catalyze an unprecedented effort in data sharing that will be critical to advancing genomic medicine and ensuring that all populations can access its benefits.
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Affiliation(s)
- Heidi L. Rehm
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Massachusetts General Hospital, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
| | - Angela J.H. Page
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Global Alliance for Genomics and Health, Toronto, ON, Canada
| | - Lindsay Smith
- Global Alliance for Genomics and Health, Toronto, ON, Canada
- Ontario Institute for Cancer Research, Toronto, ON, Canada
| | - Jeremy B. Adams
- Global Alliance for Genomics and Health, Toronto, ON, Canada
- Ontario Institute for Cancer Research, Toronto, ON, Canada
| | - Gil Alterovitz
- Brigham and Women’s Hospital, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
| | | | | | - Michael Baudis
- University of Zurich, Zurich, Switzerland
- SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Michael J.S. Beauvais
- Global Alliance for Genomics and Health, Toronto, ON, Canada
- McGill University, Montreal, QC, Canada
| | - Tim Beck
- University of Leicester, Leicester, UK
| | | | - Sergi Beltran
- CNAG-CRG, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
- Universitat de Barcelona, Barcelona, Spain
| | - David Bernick
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | | | | | - Tiffany F. Boughtwood
- Australian Genomics, Parkville, VIC, Australia
- Murdoch Children’s Research Institute, Parkville, VIC, Australia
| | - Guillaume Bourque
- McGill University, Montreal, QC, Canada
- Canadian Center for Computational Genomics, Montreal, QC, Canada
| | | | | | - Michael Brudno
- Canadian Center for Computational Genomics, Montreal, QC, Canada
- University of Toronto, Toronto, ON, Canada
- University Health Network, Toronto, ON, Canada
- Vector Institute, Toronto, ON, Canada
- Canadian Distributed Infrastructure for Genomics (CanDIG), Toronto, ON, Canada
| | | | - David Bujold
- McGill University, Montreal, QC, Canada
- Canadian Center for Computational Genomics, Montreal, QC, Canada
- Canadian Distributed Infrastructure for Genomics (CanDIG), Toronto, ON, Canada
| | - Tony Burdett
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Hinxton, UK
| | | | | | - Daniel L. Cameron
- Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia
- University of Melbourne, Melbourne, VIC, Australia
| | | | | | | | - Bimal P. Chaudhari
- Nationwide Children’s Hospital, Columbus, OH, USA
- The Ohio State University, Columbus, OH, USA
| | - Shu Hui Chen
- National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, USA
| | | | - Justina Chung
- Global Alliance for Genomics and Health, Toronto, ON, Canada
- Ontario Institute for Cancer Research, Toronto, ON, Canada
| | - Melissa Cline
- UC Santa Cruz Genomics Institute, Santa Cruz, CA, USA
| | | | | | - Mélanie Courtot
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Hinxton, UK
| | - Fiona Cunningham
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Hinxton, UK
| | | | | | | | | | | | | | - L. Jonathan Dursi
- University Health Network, Toronto, ON, Canada
- Canadian Distributed Infrastructure for Genomics (CanDIG), Toronto, ON, Canada
| | | | | | | | | | - Susan Fairley
- Global Alliance for Genomics and Health, Toronto, ON, Canada
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Hinxton, UK
| | - Khalid A. Fakhro
- Sidra Medicine, Doha, Qatar
- Weill Cornell Medicine - Qatar, Doha, Qatar
| | - Helen V. Firth
- Wellcome Sanger Institute, Hinxton, UK
- Addenbrooke’s Hospital, Cambridge, UK
| | | | | | - Paul Flicek
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Hinxton, UK
| | - Ian M. Fore
- National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Mallory A. Freeberg
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Hinxton, UK
| | | | - Lauren A. Fromont
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | | | - Clara L. Gaff
- Australian Genomics, Parkville, VIC, Australia
- Murdoch Children’s Research Institute, Parkville, VIC, Australia
- Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia
- University of Melbourne, Melbourne, VIC, Australia
| | - Weiniu Gan
- National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, USA
| | - Elena M. Ghanaim
- National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - David Glazer
- Verily Life Sciences, South San Francisco, CA, USA
| | - Robert C. Green
- Brigham and Women’s Hospital, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
| | - Malachi Griffith
- Washington University School of Medicine in St. Louis, St. Louis, MO, USA
| | - Obi L. Griffith
- Washington University School of Medicine in St. Louis, St. Louis, MO, USA
| | | | | | | | - Roderic Guigó
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Dipayan Gupta
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Hinxton, UK
| | | | - Ada Hamosh
- Johns Hopkins University, Baltimore, MD, USA
| | - David P. Hansen
- Australian Genomics, Parkville, VIC, Australia
- The Australian e-Health Research Centre, CSIRO, Herston, QLD, Australia
| | - Reece K. Hart
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Invitae, San Francisco, CA, USA
- MyOme, Inc, San Bruno, CA, USA
| | | | - David Haussler
- UC Santa Cruz Genomics Institute, Santa Cruz, CA, USA
- Howard Hughes Medical Institute, University of California, Santa Cruz, CA, USA
| | | | | | | | - Michael M. Hoffman
- University of Toronto, Toronto, ON, Canada
- University Health Network, Toronto, ON, Canada
- Vector Institute, Toronto, ON, Canada
| | - Oliver M. Hofmann
- University of Toronto, Toronto, ON, Canada
- University of Melbourne, Melbourne, VIC, Australia
| | - Petr Holub
- BBMRI-ERIC, Graz, Austria
- Masaryk University, Brno, Czech Republic
| | | | | | - Sarah E. Hunt
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Hinxton, UK
| | - Ammar Husami
- Cincinnati Children’s Hospital Medical Center, Cincinnati, OH, USA
| | | | - Saumya S. Jamuar
- SingHealth Duke-NUS Genomic Medicine Centre, Singapore, Republic of Singapore
- SingHealth Duke-NUS Institute of Precision Medicine, Singapore, Republic of Singapore
| | - Elizabeth L. Janes
- Global Alliance for Genomics and Health, Toronto, ON, Canada
- University of Waterloo, Waterloo, ON, Canada
| | | | - Aina Jené
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Amber L. Johns
- Garvan Institute of Medical Research, Darlinghurst, NSW, Australia
| | - Yann Joly
- McGill University, Montreal, QC, Canada
| | - Steven J.M. Jones
- Canada’s Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, BC, Canada
| | - Alexander Kanitz
- SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland
- University of Basel, Basel, Switzerland
| | | | - Thomas M. Keane
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Hinxton, UK
- University of Nottingham, Nottingham, UK
| | - Kristina Kekesi-Lafrance
- Global Alliance for Genomics and Health, Toronto, ON, Canada
- McGill University, Montreal, QC, Canada
| | | | - Giselle Kerry
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Hinxton, UK
| | - Seik-Soon Khor
- National Center for Global Health and Medicine Hospital, Tokyo, Japan
- University of Tokyo, Tokyo, Japan
| | | | | | | | | | | | - Rasko Leinonen
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Hinxton, UK
| | - Stephanie Li
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Global Alliance for Genomics and Health, Toronto, ON, Canada
| | | | - Mikael Linden
- CSC–IT Center for Science, Espoo, Finland
- ELIXIR Finland, Espoo, Finland
| | | | - Isuru Udara Liyanage
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Hinxton, UK
| | | | | | | | - Alice L. Mann
- Global Alliance for Genomics and Health, Toronto, ON, Canada
- Wellcome Sanger Institute, Hinxton, UK
| | | | | | | | - Anna Middleton
- Wellcome Connecting Science, Hinxton, UK
- University of Cambridge, Cambridge, UK
| | - Richard J. Milne
- Wellcome Connecting Science, Hinxton, UK
- University of Cambridge, Cambridge, UK
| | | | - Nicola Mulder
- H3ABioNet, Computational Biology Division, IDM, Faculty of Health Sciences, Cape Town, South Africa
| | | | - Rishi Nag
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Hinxton, UK
| | - Hidewaki Nakagawa
- Japan Agency for Medical Research & Development (AMED), Tokyo, Japan
- RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | | | - Arcadi Navarro
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain
- Institute of Evolutionary Biology (UPF-CSIC), Universitat Pompeu Fabra (UPF), Barcelona, Spain
- Institució Catalana de Recerca i Estudis Avançats, Barcelona, Spain
- Barcelonaβeta Brain Research Center (BBRC), Pasqual Maragall Foundation, Barcelona, Spain
| | | | - Ania Niewielska
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Hinxton, UK
| | - Amy Nisselle
- Murdoch Children’s Research Institute, Parkville, VIC, Australia
- University of Melbourne, Melbourne, VIC, Australia
- Human Genetics Society of Australasia Education, Ethics & Social Issues Committee, Alexandria, NSW, Australia
| | - Jeffrey Niu
- University Health Network, Toronto, ON, Canada
| | - Tommi H. Nyrönen
- CSC–IT Center for Science, Espoo, Finland
- ELIXIR Finland, Espoo, Finland
| | | | - Sabine Oesterle
- SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | | | - Vivian Ota Wang
- National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | | | - Emilio Palumbo
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Helen E. Parkinson
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Hinxton, UK
| | | | | | | | - Jordi Rambla
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | | | - Renee A. Rider
- National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Peter N. Robinson
- The Jackson Laboratory, Farmington, CT, USA
- University of Connecticut, Farmington, CT, USA
| | - Kurt W. Rodarmer
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA
| | | | - Alan F. Rubin
- Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia
- University of Melbourne, Melbourne, VIC, Australia
| | - Manuel Rueda
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | | | | | | | - Helen Schuilenburg
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Hinxton, UK
| | - Torsten Schwede
- SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland
- University of Basel, Basel, Switzerland
| | | | | | | | - Neerjah Skantharajah
- Global Alliance for Genomics and Health, Toronto, ON, Canada
- Ontario Institute for Cancer Research, Toronto, ON, Canada
| | | | - Heidi J. Sofia
- National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Dylan Spalding
- CSC–IT Center for Science, Espoo, Finland
- ELIXIR Finland, Espoo, Finland
| | | | - Zornitza Stark
- Australian Genomics, Parkville, VIC, Australia
- Murdoch Children’s Research Institute, Parkville, VIC, Australia
- University of Melbourne, Melbourne, VIC, Australia
| | - Lincoln D. Stein
- Ontario Institute for Cancer Research, Toronto, ON, Canada
- University of Toronto, Toronto, ON, Canada
| | | | - Patrick Tan
- SingHealth Duke-NUS Genomic Medicine Centre, Singapore, Republic of Singapore
- Precision Health Research Singapore, Singapore, Republic of Singapore
- Genome Institute of Singapore, Singapore, Republic of Singapore
| | | | - Alastair A. Thomson
- National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, USA
| | - Adrian Thorogood
- McGill University, Montreal, QC, Canada
- University of Luxembourg, Esch-sur-Alzette, Luxembourg
| | | | - Katsushi Tokunaga
- University of Tokyo, Tokyo, Japan
- National Center for Global Health and Medicine, Tokyo, Japan
| | - Juha Törnroos
- CSC–IT Center for Science, Espoo, Finland
- ELIXIR Finland, Espoo, Finland
| | - David Torrents
- Institució Catalana de Recerca i Estudis Avançats, Barcelona, Spain
- Barcelona Supercomputing Center, Barcelona, Spain
| | - Sean Upchurch
- California Institute of Technology, Pasadena, CA, USA
| | - Alfonso Valencia
- Institució Catalana de Recerca i Estudis Avançats, Barcelona, Spain
- Barcelona Supercomputing Center, Barcelona, Spain
| | | | - Jessica Vamathevan
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Hinxton, UK
| | - Susheel Varma
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Hinxton, UK
- Health Data Research UK, London, UK
| | - Danya F. Vears
- Murdoch Children’s Research Institute, Parkville, VIC, Australia
- University of Melbourne, Melbourne, VIC, Australia
- Human Genetics Society of Australasia Education, Ethics & Social Issues Committee, Alexandria, NSW, Australia
- Melbourne Law School, University of Melbourne, Parkville, VIC, Australia
| | - Coby Viner
- University of Toronto, Toronto, ON, Canada
- University Health Network, Toronto, ON, Canada
| | | | - Alex H. Wagner
- Nationwide Children’s Hospital, Columbus, OH, USA
- The Ohio State University, Columbus, OH, USA
| | | | | | | | - Eva C. Winkler
- Section of Translational Medical Ethics, University Hospital Heidelberg, Heidelberg, Germany
| | | | | | | | | | - Andrew D. Yates
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Hinxton, UK
| | - Christina K. Yung
- Ontario Institute for Cancer Research, Toronto, ON, Canada
- Indoc Research, Toronto, ON, Canada
| | - Lyndon J. Zass
- H3ABioNet, Computational Biology Division, IDM, Faculty of Health Sciences, Cape Town, South Africa
| | - Ksenia Zaytseva
- McGill University, Montreal, QC, Canada
- Canadian Centre for Computational Genomics, Montreal, QC, Canada
| | - Junjun Zhang
- Ontario Institute for Cancer Research, Toronto, ON, Canada
| | - Peter Goodhand
- Global Alliance for Genomics and Health, Toronto, ON, Canada
- Ontario Institute for Cancer Research, Toronto, ON, Canada
| | - Kathryn North
- Murdoch Children’s Research Institute, Parkville, VIC, Australia
- University of Toronto, Toronto, ON, Canada
- University of Melbourne, Melbourne, VIC, Australia
| | - Ewan Birney
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Hinxton, UK
- European Molecular Biology Laboratory, Heidelberg, Germany
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19
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Chai S, Matsumoto N, Storgard R, Peng CC, Aparicio A, Ormseth B, Rappard K, Cunningham K, Kolatkar A, Nevarez R, Tu KH, Hsu CJ, Malihi P, Corn P, Zurita A, Hicks J, Kuhn P, Ruiz-Velasco C. Platelet-Coated Circulating Tumor Cells Are a Predictive Biomarker in Patients with Metastatic Castrate-Resistant Prostate Cancer. Mol Cancer Res 2021; 19:2036-2045. [PMID: 34462330 DOI: 10.1158/1541-7786.mcr-21-0383] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2021] [Revised: 07/27/2021] [Accepted: 08/23/2021] [Indexed: 11/16/2022]
Abstract
Metastatic castration-resistant prostate cancer (mCRPC) includes a subset of patients with particularly unfavorable prognosis characterized by combined defects in at least two of three tumor suppressor genes: PTEN, RB1, and TP53 as aggressive variant prostate cancer molecular signature (AVPC-MS). We aimed to identify circulating tumor cells (CTC) signatures that could inform treatment decisions of patients with mCRPC with cabazitaxel-carboplatin combination therapy versus cabazitaxel alone. Liquid biopsy samples were collected prospectively from 79 patients for retrospective analysis. CTCs were detected, classified, enumerated through a computational pipeline followed by manual curation, and subjected to single-cell genome-wide copy-number profiling for AVPC-MS detection. On the basis of immunofluorescence intensities, detected rare cells were classified into 8 rare-cell groups. Further morphologic characterization categorized CTC subtypes from 4 cytokeratin-positive rare-cell groups, utilizing presence of mesenchymal features and platelet attachment. Of 79 cases, 77 (97.5%) had CTCs, 24 (30.4%) were positive for platelet-coated CTCs (pc.CTCs) and 25 (38.5%) of 65 sequenced patients exhibited AVPC-MS in CTCs. Survival analysis indicated that the presence of pc.CTCs identified the subset of patients who were AVPC-MS-positive with the worst prognosis and minimal benefit from combination therapy. In AVPC-MS-negative patients, its presence showed significant survival improvement from combination therapy. Our findings suggest the presence of pc.CTCs as a predictive biomarker to further stratify AVPC subsets with the worst prognosis and the most significant benefit of additional platinum therapy. IMPLICATIONS: HDSCA3.0 can be performed with rare cell detection, categorization, and genomic characterization for pc.CTC identification and AVPC-MS detection as a potential predictive biomarker of mCRPC.
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Affiliation(s)
- Shoujie Chai
- Convergent Science Institute in Cancer, Michelson Center for Convergent Bioscience, University of Southern California, Los Angeles, California.,Molecular and Computational Biology, Department of Biological Sciences, University of Southern California, Los Angeles, California
| | - Nicholas Matsumoto
- Convergent Science Institute in Cancer, Michelson Center for Convergent Bioscience, University of Southern California, Los Angeles, California
| | - Ryan Storgard
- Convergent Science Institute in Cancer, Michelson Center for Convergent Bioscience, University of Southern California, Los Angeles, California
| | - Chen-Ching Peng
- Convergent Science Institute in Cancer, Michelson Center for Convergent Bioscience, University of Southern California, Los Angeles, California
| | - Ana Aparicio
- Department of Genitourinary Medical Oncology, University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Benjamin Ormseth
- Convergent Science Institute in Cancer, Michelson Center for Convergent Bioscience, University of Southern California, Los Angeles, California
| | - Kate Rappard
- Convergent Science Institute in Cancer, Michelson Center for Convergent Bioscience, University of Southern California, Los Angeles, California
| | - Katherine Cunningham
- Convergent Science Institute in Cancer, Michelson Center for Convergent Bioscience, University of Southern California, Los Angeles, California
| | - Anand Kolatkar
- Convergent Science Institute in Cancer, Michelson Center for Convergent Bioscience, University of Southern California, Los Angeles, California
| | - Rafael Nevarez
- Convergent Science Institute in Cancer, Michelson Center for Convergent Bioscience, University of Southern California, Los Angeles, California
| | - Kai-Han Tu
- Convergent Science Institute in Cancer, Michelson Center for Convergent Bioscience, University of Southern California, Los Angeles, California
| | - Ching-Ju Hsu
- Convergent Science Institute in Cancer, Michelson Center for Convergent Bioscience, University of Southern California, Los Angeles, California
| | - Paymaneh Malihi
- Convergent Science Institute in Cancer, Michelson Center for Convergent Bioscience, University of Southern California, Los Angeles, California.,Molecular and Computational Biology, Department of Biological Sciences, University of Southern California, Los Angeles, California
| | - Paul Corn
- Department of Genitourinary Medical Oncology, University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Amado Zurita
- Department of Genitourinary Medical Oncology, University of Texas MD Anderson Cancer Center, Houston, Texas
| | - James Hicks
- Convergent Science Institute in Cancer, Michelson Center for Convergent Bioscience, University of Southern California, Los Angeles, California.,Molecular and Computational Biology, Department of Biological Sciences, University of Southern California, Los Angeles, California
| | - Peter Kuhn
- Convergent Science Institute in Cancer, Michelson Center for Convergent Bioscience, University of Southern California, Los Angeles, California. .,Molecular and Computational Biology, Department of Biological Sciences, University of Southern California, Los Angeles, California
| | - Carmen Ruiz-Velasco
- Convergent Science Institute in Cancer, Michelson Center for Convergent Bioscience, University of Southern California, Los Angeles, California.
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20
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Keup C, Suryaprakash V, Hauch S, Storbeck M, Hahn P, Sprenger-Haussels M, Kolberg HC, Tewes M, Hoffmann O, Kimmig R, Kasimir-Bauer S. Integrative statistical analyses of multiple liquid biopsy analytes in metastatic breast cancer. Genome Med 2021; 13:85. [PMID: 34001236 PMCID: PMC8130163 DOI: 10.1186/s13073-021-00902-1] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2020] [Accepted: 04/30/2021] [Indexed: 02/08/2023] Open
Abstract
Background Single liquid biopsy analytes (LBAs) have been utilized for therapy selection in metastatic breast cancer (MBC). We performed integrative statistical analyses to examine the clinical relevance of using multiple LBAs: matched circulating tumor cell (CTC) mRNA, CTC genomic DNA (gDNA), extracellular vesicle (EV) mRNA, and cell-free DNA (cfDNA). Methods Blood was drawn from 26 hormone receptor-positive, HER2-negative MBC patients. CTC mRNA and EV mRNA were analyzed using a multi-marker qPCR. Plasma from CTC-depleted blood was utilized for cfDNA isolation. gDNA from CTCs was isolated from mRNA-depleted CTC lysates. CTC gDNA and cfDNA were analyzed by targeted sequencing. Hierarchical clustering was performed within each analyte, and its results were combined into a score termed Evaluation of multiple Liquid biopsy analytes In Metastatic breast cancer patients All from one blood sample (ELIMA.score), which calculates the contribution of each analyte to the overall survival prediction. Singular value decomposition (SVD), mutual information calculation, k-means clustering, and graph-theoretic analysis were conducted to elucidate the dependence between individual analytes. Results A combination of two/three/four LBAs increased the prevalence of patients with actionable signals. Aggregating the results of hierarchical clustering of individual LBAs into the ELIMA.score resulted in a highly significant correlation with overall survival, thereby bolstering evidence for the additive value of using multiple LBAs. Computation of mutual information indicated that none of the LBAs is independent of the others, but the ability of a single LBA to describe the others is rather limited—only CTC gDNA could partially describe the other three LBAs. SVD revealed that the strongest singular vectors originate from all four LBAs, but a majority originated from CTC gDNA. After k-means clustering of patients based on parameters of all four LBAs, the graph-theoretic analysis revealed CTC ERBB2 variants only in patients belonging to one particular cluster. Conclusions The additional benefits of using all four LBAs were objectively demonstrated in this pilot study, which also indicated a relative dominance of CTC gDNA over the other LBAs. Consequently, a multi-parametric liquid biopsy approach deconvolutes the genomic and transcriptomic complexity and should be considered in clinical practice. Supplementary Information The online version contains supplementary material available at 10.1186/s13073-021-00902-1.
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Affiliation(s)
- Corinna Keup
- Department of Gynecology and Obstetrics, University Hospital of Essen, Hufelandstr. 55, 45122, Essen, Germany.
| | | | | | | | | | | | - Hans-Christian Kolberg
- Department of Gynecology and Obstetrics, Marienhospital Bottrop, 46236, Bottrop, Germany
| | - Mitra Tewes
- Department of Medical Oncology, University Hospital of Essen, 45122, Essen, Germany
| | - Oliver Hoffmann
- Department of Gynecology and Obstetrics, University Hospital of Essen, Hufelandstr. 55, 45122, Essen, Germany
| | - Rainer Kimmig
- Department of Gynecology and Obstetrics, University Hospital of Essen, Hufelandstr. 55, 45122, Essen, Germany
| | - Sabine Kasimir-Bauer
- Department of Gynecology and Obstetrics, University Hospital of Essen, Hufelandstr. 55, 45122, Essen, Germany
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21
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Koval AP, Blagodatskikh KA, Kushlinskii NE, Shcherbo DS. The Detection of Cancer Epigenetic Traces in Cell-Free DNA. Front Oncol 2021; 11:662094. [PMID: 33996585 PMCID: PMC8118693 DOI: 10.3389/fonc.2021.662094] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2021] [Accepted: 04/12/2021] [Indexed: 12/23/2022] Open
Abstract
Nucleic acid fragments found in blood circulation originate mostly from dying cells and carry signs pointing to specific features of the parental cell types. Deciphering these clues may be transformative for numerous research and clinical applications but strongly depends on the development and implementation of robust analytical methods. Remarkable progress has been achieved in the reliable detection of sequence alterations in cell-free DNA while decoding epigenetic information from methylation and fragmentation patterns requires more sophisticated approaches. This review discusses the currently available strategies for detecting and analyzing the epigenetic marks in the liquid biopsies.
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Affiliation(s)
- Anastasia P Koval
- Institute of Translational Medicine, Pirogov Russian National Research Medical University, Moscow, Russia
| | - Konstantin A Blagodatskikh
- Institute of Translational Medicine, Pirogov Russian National Research Medical University, Moscow, Russia
| | - Nikolay E Kushlinskii
- Laboratory of Clinical Biochemistry, N.N. Blokhin Cancer Research Medical Center of Oncology, Moscow, Russia
| | - Dmitry S Shcherbo
- Institute of Translational Medicine, Pirogov Russian National Research Medical University, Moscow, Russia
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22
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Spiliotaki M, Kallergi G, Nikolaou C, Xenidis N, Politaki E, Apostolaki S, Georgoulia N, Koinis F, Tsoukalas N, Hatzidaki D, Kotsakis A, Georgoulias V. Dynamic changes of CTCs in patients with metastatic HR(+)/HER2(-) breast cancer receiving salvage treatment with everolimus/exemestane. Cancer Chemother Pharmacol 2021; 87:277-287. [PMID: 33515073 DOI: 10.1007/s00280-020-04227-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2020] [Accepted: 12/29/2020] [Indexed: 01/23/2023]
Abstract
PURPOSE Detection of CTCs represents a poor prognostic factor in patients with early and metastatic breast cancer (mBC) and treatment with everolimus-exemestane (E/E) is an established effective treatment in hormone receptor-positive/HER2-negative mBC patients. The effect of E/E on CTCs in mBC patients was prospectively investigated. METHODS CTCs from 50 pre-treated patients with mBC receiving E/E were analyzed using the CellSearch (CS) platform and triple immunofluorescence (IF) staining for cytokeratin, M30 and Ki67 expression to assess their proliferative and apoptotic status. RESULTS CTCs (by CS) were detected in 64% of patients before treatment and E/E administration resulted in their decreased prevalence [(n = 18; 36%, p = 0.004) and (n = 7; 19.4%, p = 0.019) post-1st and post-3rd treatment cycle, respectively] whereas it was significantly increased at disease progression (PD: 61%) compared to post-1st and post-3rd cycle (p = 0.049 and p = 0.021, respectively). Ki67-positive CTCs were detected in 60%, 60%, 17% and 50% of patients before treatment, post-1st, post-3rd cycle and at PD, respectively, while the opposite was observed for M30-positive CTCs (0% at baseline, 10% after the 1st cycle, 50% after the 3rd cycle and 0% at PD). The detection of even ≥ 1 CTC/5 ml after one cycle was associated with decreased PFS (3.3 vs 9.0 months, p = 0.025) whereas the detection of even ≥ 2 CTCs at PD was associated with decreased OS (32.4 vs 19.5 months; p = 0.009). CONCLUSIONS The combination of E/E resulted in early elimination of proliferating CTCs in mBC patients and this effect was associated with a favorable clinical outcome.
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Affiliation(s)
- Maria Spiliotaki
- Laboratory of Tumor Cell Biology, School of Medicine, University of Crete, Crete, Greece
| | - Galatea Kallergi
- Department of Biochemistry, University of Crete Medical School, Heraklion, Crete, Greece
| | - Christos Nikolaou
- Laboratory of Tumor Cell Biology, School of Medicine, University of Crete, Crete, Greece
| | - Nikolaos Xenidis
- Hellenic Oncology Research Group (HORG), 55 Lombardou str, 11474, Athens, Greece.,Department of Medical Oncology, Medical School, Democritus University of Thrace, Xanthi, Greece
| | - Eleni Politaki
- Laboratory of Tumor Cell Biology, School of Medicine, University of Crete, Crete, Greece
| | - Stella Apostolaki
- Laboratory of Tumor Cell Biology, School of Medicine, University of Crete, Crete, Greece
| | - Nefeli Georgoulia
- Hellenic Oncology Research Group (HORG), 55 Lombardou str, 11474, Athens, Greece
| | - Filippos Koinis
- Laboratory of Tumor Cell Biology, School of Medicine, University of Crete, Crete, Greece.,Hellenic Oncology Research Group (HORG), 55 Lombardou str, 11474, Athens, Greece.,Department of Medical Oncology, Faculty of Medicine, School of Health Sciences, University Hospital of Larissa & Laboratory of Oncology, University of Thessaly Mezourlo, Larissa, Thessaly, Greece
| | - Nikolaos Tsoukalas
- Hellenic Oncology Research Group (HORG), 55 Lombardou str, 11474, Athens, Greece.,Medical Oncology Unit, NIMITS Hospital, Athens, Greece
| | - Dora Hatzidaki
- Laboratory of Tumor Cell Biology, School of Medicine, University of Crete, Crete, Greece.,Hellenic Oncology Research Group (HORG), 55 Lombardou str, 11474, Athens, Greece
| | - Athanasios Kotsakis
- Laboratory of Tumor Cell Biology, School of Medicine, University of Crete, Crete, Greece.,Hellenic Oncology Research Group (HORG), 55 Lombardou str, 11474, Athens, Greece.,Department of Medical Oncology, Faculty of Medicine, School of Health Sciences, University Hospital of Larissa & Laboratory of Oncology, University of Thessaly Mezourlo, Larissa, Thessaly, Greece
| | - Vassilis Georgoulias
- Laboratory of Tumor Cell Biology, School of Medicine, University of Crete, Crete, Greece. .,Hellenic Oncology Research Group (HORG), 55 Lombardou str, 11474, Athens, Greece.
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23
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Cooperation and Interplay between EGFR Signalling and Extracellular Vesicle Biogenesis in Cancer. Cells 2020; 9:cells9122639. [PMID: 33302515 PMCID: PMC7764760 DOI: 10.3390/cells9122639] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2020] [Revised: 11/30/2020] [Accepted: 12/02/2020] [Indexed: 12/13/2022] Open
Abstract
Epidermal growth factor receptor (EGFR) takes centre stage in carcinogenesis throughout its entire cellular trafficking odyssey. When loaded in extracellular vesicles (EVs), EGFR is one of the key proteins involved in the transfer of information between parental cancer and bystander cells in the tumour microenvironment. To hijack EVs, EGFR needs to play multiple signalling roles in the life cycle of EVs. The receptor is involved in the biogenesis of specific EV subpopulations, it signals as an active cargo, and it can influence the uptake of EVs by recipient cells. EGFR regulates its own inclusion in EVs through feedback loops during disease progression and in response to challenges such as hypoxia, epithelial-to-mesenchymal transition and drugs. Here, we highlight how the spatiotemporal rules that regulate EGFR intracellular function intersect with and influence different EV biogenesis pathways and discuss key regulatory features and interactions of this interplay. We also elaborate on outstanding questions relating to EGFR-driven EV biogenesis and available methods to explore them. This mechanistic understanding will be key to unravelling the functional consequences of direct anti-EGFR targeted and indirect EGFR-impacting cancer therapies on the secretion of pro-tumoural EVs and on their effects on drug resistance and microenvironment subversion.
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