1
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Grisanti S, Sonntag SR, Tura SA. [Circulating tumor cells in uveal melanoma : "The needle in the haystack"]. DIE OPHTHALMOLOGIE 2024; 121:954-962. [PMID: 39580374 DOI: 10.1007/s00347-024-02136-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/01/2024] [Revised: 10/22/2024] [Accepted: 10/22/2024] [Indexed: 11/25/2024]
Abstract
BACKGROUND A fundamental prerequisite for the development of clinically manifested metastases in uveal melanoma (UM) is the hematogenous dissemination of melanoma cells, which circulate in the systemic circulation, deposit in organs and can subsequently colonize the organs. MATERIAL AND METHODS This article presents a review of the literature on the detection of circulating tumor cells (CTC) from UM and their relevance for the clinical and pathophysiological aspects of the malignancy. RESULTS Since the first description of CTC in UM patients 20 years ago, only 20 articles have been published on the detection of intact CTCs in UM. Besides demonstrating the presence of CTCs in the systemic circulation, these articles give insights into the pathophysiology and chronology of CTC dissemination, the diagnostics and risk stratification of UM. CONCLUSION The detection of CTC in UM has proved to be beneficial in many ways. The early time of cell dissemination and also the associated factors should lead to a rethinking in the clinical routine in the context of the fatal danger of metastases.
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Affiliation(s)
- Salvatore Grisanti
- Klinik für Augenheilkunde, Universität zu Lübeck, Universitätsklinikum Schleswig-Holstein, Ratzeburger Allee 160, 23562, Lübeck, Deutschland.
| | - S R Sonntag
- Klinik für Augenheilkunde, Universität zu Lübeck, Universitätsklinikum Schleswig-Holstein, Ratzeburger Allee 160, 23562, Lübeck, Deutschland
| | - S A Tura
- Klinik für Augenheilkunde, Universität zu Lübeck, Universitätsklinikum Schleswig-Holstein, Ratzeburger Allee 160, 23562, Lübeck, Deutschland
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2
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Lewis F, Beirne J, Henderson B, Norris L, Cadoo K, Kelly T, Martin C, Hurley S, Kanjuga M, O'Driscoll L, Gately K, Oner E, Saini VM, Brooks D, Selemidis S, Kamran W, Haughey N, Maguire P, O'Gorman C, Saadeh FA, Ward MP, O'Leary JJ, O'Toole SA. Unravelling the biological and clinical challenges of circulating tumour cells in epithelial ovarian carcinoma. Cancer Lett 2024; 605:217279. [PMID: 39341451 DOI: 10.1016/j.canlet.2024.217279] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2024] [Revised: 09/22/2024] [Accepted: 09/24/2024] [Indexed: 10/01/2024]
Abstract
Epithelial ovarian carcinoma (EOC) is the eighth most common cancer in women and the leading cause of gynaecological cancer death, predominantly due to the absence of effective screening tools, advanced stage at diagnosis, and high rates of recurrence. Circulating tumour cells (CTCs), a rare subset of tumour cells that disseminate from a tumour and migrate into the circulation, play a pivotal role in the metastatic cascade, and therefore hold promise as biomarkers for disease monitoring and prognostication. Exploring CTCs from liquid biopsies is an appealing approach for research and clinical practice, given it is minimally invasive, facilitates serial sampling and enables the capture of the entire spectrum of cancer cells circulating in the blood. The prognostic utility of CTC enumeration has been FDA-approved for clinical use in metastatic breast, prostate, and colorectal cancers. However, the unique biology of EOC, discussed herein, compounds the detection and characterisation complexities already inherent in CTC research, consequently hindering progress towards clinical applications. The aim of this review is to provide an overview of both the biological and clinical challenges encountered in harnessing the power of CTCs in EOC.
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Affiliation(s)
- Faye Lewis
- Department of Histopathology, School of Medicine, Trinity College Dublin, Dublin, Ireland; Department of Obstetrics and Gynaecology, School of Medicine, Trinity College Dublin, Dublin, Ireland; Trinity St. James's Cancer Institute, Trinity College Dublin, Dublin, Ireland
| | - James Beirne
- Blackrock Health Hermitage Clinic, Old Lucan Road, Dublin, Ireland
| | - Brian Henderson
- Department of Histopathology, School of Medicine, Trinity College Dublin, Dublin, Ireland; Department of Obstetrics and Gynaecology, School of Medicine, Trinity College Dublin, Dublin, Ireland; Trinity St. James's Cancer Institute, Trinity College Dublin, Dublin, Ireland
| | - Lucy Norris
- Department of Obstetrics and Gynaecology, School of Medicine, Trinity College Dublin, Dublin, Ireland; Trinity St. James's Cancer Institute, Trinity College Dublin, Dublin, Ireland
| | - Karen Cadoo
- Trinity St. James's Cancer Institute, Trinity College Dublin, Dublin, Ireland; The Haematology, Oncology and Palliative Care (HOPe) Directorate, St James's Hospital, Dublin, Ireland
| | - Tanya Kelly
- Department of Histopathology, School of Medicine, Trinity College Dublin, Dublin, Ireland; Department of Obstetrics and Gynaecology, School of Medicine, Trinity College Dublin, Dublin, Ireland; Trinity St. James's Cancer Institute, Trinity College Dublin, Dublin, Ireland
| | - Cara Martin
- Department of Histopathology, School of Medicine, Trinity College Dublin, Dublin, Ireland; Trinity St. James's Cancer Institute, Trinity College Dublin, Dublin, Ireland
| | - Sinéad Hurley
- Department of Histopathology, School of Medicine, Trinity College Dublin, Dublin, Ireland; Trinity St. James's Cancer Institute, Trinity College Dublin, Dublin, Ireland; Department of Clinical Medicine, School of Medicine, Trinity College Dublin, Ireland; Thoracic Oncology Research Group, Trinity Translational Medicine Institute, St James's Hospital, Dublin, Ireland
| | - Marika Kanjuga
- Department of Histopathology, School of Medicine, Trinity College Dublin, Dublin, Ireland; Department of Obstetrics and Gynaecology, School of Medicine, Trinity College Dublin, Dublin, Ireland; Trinity St. James's Cancer Institute, Trinity College Dublin, Dublin, Ireland
| | - Lorraine O'Driscoll
- Trinity St. James's Cancer Institute, Trinity College Dublin, Dublin, Ireland; School of Pharmacy and Pharmaceutical Sciences, Trinity College Dublin, Ireland; Trinity Biomedical Sciences Institute, Trinity College Dublin, Ireland
| | - Kathy Gately
- Trinity St. James's Cancer Institute, Trinity College Dublin, Dublin, Ireland; Department of Clinical Medicine, School of Medicine, Trinity College Dublin, Ireland; Thoracic Oncology Research Group, Trinity Translational Medicine Institute, St James's Hospital, Dublin, Ireland
| | - Ezgi Oner
- Trinity St. James's Cancer Institute, Trinity College Dublin, Dublin, Ireland; Department of Clinical Medicine, School of Medicine, Trinity College Dublin, Ireland; Thoracic Oncology Research Group, Trinity Translational Medicine Institute, St James's Hospital, Dublin, Ireland
| | - Volga M Saini
- Trinity St. James's Cancer Institute, Trinity College Dublin, Dublin, Ireland; Department of Clinical Medicine, School of Medicine, Trinity College Dublin, Ireland; Thoracic Oncology Research Group, Trinity Translational Medicine Institute, St James's Hospital, Dublin, Ireland
| | - Doug Brooks
- Cancer Research Institute, University of South Australia, 5001, Adelaide, Australia
| | - Stavros Selemidis
- School of Health and Biomedical Sciences, RMIT University, Victoria, 3083, Bundoora, Australia
| | - Waseem Kamran
- Department of Obstetrics and Gynaecology, School of Medicine, Trinity College Dublin, Dublin, Ireland; Trinity St. James's Cancer Institute, Trinity College Dublin, Dublin, Ireland; Division of Gynaecological Oncology, St James's Hospital, Dublin, Ireland
| | - Niamh Haughey
- Department of Obstetrics and Gynaecology, School of Medicine, Trinity College Dublin, Dublin, Ireland; Trinity St. James's Cancer Institute, Trinity College Dublin, Dublin, Ireland; Division of Gynaecological Oncology, St James's Hospital, Dublin, Ireland
| | - Patrick Maguire
- Department of Obstetrics and Gynaecology, School of Medicine, Trinity College Dublin, Dublin, Ireland; Trinity St. James's Cancer Institute, Trinity College Dublin, Dublin, Ireland; Division of Gynaecological Oncology, St James's Hospital, Dublin, Ireland
| | - Catherine O'Gorman
- Department of Obstetrics and Gynaecology, School of Medicine, Trinity College Dublin, Dublin, Ireland; Trinity St. James's Cancer Institute, Trinity College Dublin, Dublin, Ireland; Division of Gynaecological Oncology, St James's Hospital, Dublin, Ireland
| | - Feras Abu Saadeh
- Department of Obstetrics and Gynaecology, School of Medicine, Trinity College Dublin, Dublin, Ireland; Trinity St. James's Cancer Institute, Trinity College Dublin, Dublin, Ireland; Division of Gynaecological Oncology, St James's Hospital, Dublin, Ireland
| | - Mark P Ward
- Department of Histopathology, School of Medicine, Trinity College Dublin, Dublin, Ireland; Department of Obstetrics and Gynaecology, School of Medicine, Trinity College Dublin, Dublin, Ireland; Trinity St. James's Cancer Institute, Trinity College Dublin, Dublin, Ireland.
| | - John J O'Leary
- Department of Histopathology, School of Medicine, Trinity College Dublin, Dublin, Ireland; Trinity St. James's Cancer Institute, Trinity College Dublin, Dublin, Ireland.
| | - Sharon A O'Toole
- Department of Histopathology, School of Medicine, Trinity College Dublin, Dublin, Ireland; Department of Obstetrics and Gynaecology, School of Medicine, Trinity College Dublin, Dublin, Ireland; Trinity St. James's Cancer Institute, Trinity College Dublin, Dublin, Ireland.
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3
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Shishido SN, Marvit A, Pham D, Luo T, Xu L, Mason J, Priceman SJ, Portnow J, Kuhn P. Multi-Omic Characterization of Single Cells and Cell-Free Components Detected in the Cerebrospinal Fluid of Patients with Leptomeningeal Disease. Cancers (Basel) 2024; 16:3746. [PMID: 39594700 PMCID: PMC11592257 DOI: 10.3390/cancers16223746] [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: 09/12/2024] [Revised: 10/29/2024] [Accepted: 10/31/2024] [Indexed: 11/28/2024] Open
Abstract
BACKGROUND/OBJECTIVES Up to 30% of patients with breast cancers will develop brain or leptomeningeal metastases, and this risk is especially high with HER2-positive cancers. For patients with central nervous system metastases, cerebrospinal fluid (CSF) liquid biopsies are a promising opportunity to monitor disease, inform treatment, and predict prognosis. This pilot study investigated CSF liquid biopsy analytes from three patients diagnosed with central nervous system metastases based on imaging but not confirmed via clinical cytology. METHODS The detection of cellular analytes with the non-enrichment high-definition single-cell assay (HDSCA3.0) workflow was compared between the CSF and matched peripheral blood (PB) samples. RESULTS Circulating tumor cells (CTCs) were detected in the CSF but not the PB and were subsequently molecularly characterized using single-cell genomics and targeted multiplexed proteomics to reveal a clonal population of phenotypically heterogeneous cells. There was a lack of concordance in the copy number alteration profiles between CTCs and cell-free DNA (cfDNA) in the CSF. Extracellular vesicle surface marker analysis in CSF revealed a prominent signal among tetraspanins (CD9/CD63/CD81), with CD81 exhibiting the highest signal across all patients. CONCLUSIONS The data presented suggest that CSF could be a useful tool for diagnosing and assessing disease severity.
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Affiliation(s)
- Stephanie N. Shishido
- Convergent Science Institute for Cancer, Michelson Center, University of Southern California, Los Angeles, CA 90089, USA (D.P.); (T.L.); (J.M.)
| | - Amelia Marvit
- Convergent Science Institute for Cancer, Michelson Center, University of Southern California, Los Angeles, CA 90089, USA (D.P.); (T.L.); (J.M.)
| | - Doanna Pham
- Convergent Science Institute for Cancer, Michelson Center, University of Southern California, Los Angeles, CA 90089, USA (D.P.); (T.L.); (J.M.)
| | - Theresa Luo
- Convergent Science Institute for Cancer, Michelson Center, University of Southern California, Los Angeles, CA 90089, USA (D.P.); (T.L.); (J.M.)
| | - Liya Xu
- The Vision Center at Children’s Hospital Los Angeles, Los Angeles, CA 90027, USA;
- USC Roski Eye Institute, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA
| | - Jeremy Mason
- Convergent Science Institute for Cancer, Michelson Center, University of Southern California, Los Angeles, CA 90089, USA (D.P.); (T.L.); (J.M.)
- Institute of Urology, Catherine & Joseph Aresty Department of Urology, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA
| | - Saul J. Priceman
- Department of Hematology and Hematopoietic Cell Transplantation, City of Hope, 1500 East Duarte Road, Duarte, CA 91010, USA;
- Department of Medicine, KSOM/NCCC Center for Cancer Cellular Immunotherapy, Keck School of Medicine of USC, Los Angeles, CA 90033, USA
| | - Jana Portnow
- Department of Medical Oncology & Therapeutics Research, City of Hope, 1500 East Duarte Road, Duarte, CA 91010, USA;
| | - Peter Kuhn
- Convergent Science Institute for Cancer, Michelson Center, University of Southern California, Los Angeles, CA 90089, USA (D.P.); (T.L.); (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 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
- Department of Biomedical Engineering, Viterbi School of Engineering, University of Southern California, Los Angeles, CA 90089, USA
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4
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Shishido SN, Suresh D, Courcoubetis G, Ye B, Lin E, Mason J, Park K, Lewis M, Wang R, Lo SK, Kuhn P, Pandol S. Determining the efficacy of ExThera Seraph100 blood filtration in patients diagnosed with pancreatic cancer through the liquid biopsy. BJC REPORTS 2024; 2:47. [PMID: 39516545 PMCID: PMC11524105 DOI: 10.1038/s44276-024-00069-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/13/2024] [Revised: 05/22/2024] [Accepted: 06/02/2024] [Indexed: 11/16/2024]
Abstract
BACKGROUND Cancer becomes lethal as it spreads from the primary site to the rest of the body. Circulating tumor cells (CTCs) are biomarkers of disease progression and have been associated with decreased overall survival. Blood filtration is a novel concept for removing CTCs from circulation to improve patient prognosis. METHODS This study utilizes liquid biopsy to assess the efficacy of ExThera Medical's Seraph® 100 Microbind® Affinity Blood Filter on the blood of patients with pancreatic ductal adenocarcinoma (PDAC) using the third generation high-definition single cell assay workflow. Blood samples from treatment-naïve PDAC patients were collected and analyzed to characterize the CTCs and other rare cells present before and after filtration. RESULTS Examination of 6 paired portal vein blood (PoVB) samples demonstrated a statistically significant decrease in total rare cells, total cytokeratin (CK)+ cells, and CTCs across all patients due to filtration. Furthermore, analysis of 2 paired peripheral blood (PB) samples showed a decrease in total rare cells, total CK+ cells, and specific phenotypes of rare cells after filtration. DISCUSSION These preliminary results demonstrate initial proof of concept that this filtration device can remove CTCs from circulation and may therefore be useful as a therapy or adjunct in PDAC patient care.
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Affiliation(s)
- Stephanie N Shishido
- Convergent Science Institute for Cancer, Michelson Center, University of Southern California, Los Angeles, CA, 90089, USA
| | - Divya Suresh
- Convergent Science Institute for Cancer, Michelson Center, University of Southern California, Los Angeles, CA, 90089, USA
| | - George Courcoubetis
- Convergent Science Institute for Cancer, Michelson Center, University of Southern California, Los Angeles, CA, 90089, USA
| | - Brandon Ye
- Convergent Science Institute for Cancer, Michelson Center, University of Southern California, Los Angeles, CA, 90089, USA
| | - Emmeline Lin
- Convergent Science Institute for Cancer, Michelson Center, University of Southern California, Los Angeles, CA, 90089, USA
| | - Jeremy Mason
- Convergent Science Institute for Cancer, Michelson Center, University of Southern California, Los Angeles, CA, 90089, USA
- 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
| | - Ken Park
- Pancreatic and Biliary Diseases Program, Cedars Sinai Medical Center, Los Angeles, CA, 90048, USA
| | - Michael Lewis
- Departments of Medicine and Pathology, Cedars Sinai Medical Center, Los Angeles, CA, 90048, USA
- Department of Pathology, VA Greater Los Angeles Medical Center, Los Angeles, CA, 90073, USA
- Center for Cancer Research and Development, Clark Atlanta University, Atlanta, GA, 30314, USA
| | - Ruoxiang Wang
- Pancreatic and Biliary Diseases Program, Cedars Sinai Medical Center, Los Angeles, CA, 90048, USA
| | - Simon K Lo
- Pancreatic and Biliary Diseases Program, Cedars Sinai Medical Center, Los Angeles, CA, 90048, USA
| | - Peter Kuhn
- Convergent Science Institute for Cancer, Michelson Center, University of Southern California, Los Angeles, CA, 90089, USA.
- 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.
| | - Stephen Pandol
- Pancreatic and Biliary Diseases Program, Cedars Sinai Medical Center, Los Angeles, CA, 90048, USA
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5
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Beigi YZ, Lanjanian H, Fayazi R, Salimi M, Hoseyni BHM, Noroozizadeh MH, Masoudi-Nejad A. Heterogeneity and molecular landscape of melanoma: implications for targeted therapy. MOLECULAR BIOMEDICINE 2024; 5:17. [PMID: 38724687 PMCID: PMC11082128 DOI: 10.1186/s43556-024-00182-2] [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: 11/19/2023] [Accepted: 04/08/2024] [Indexed: 05/12/2024] Open
Abstract
Uveal cancer (UM) offers a complex molecular landscape characterized by substantial heterogeneity, both on the genetic and epigenetic levels. This heterogeneity plays a critical position in shaping the behavior and response to therapy for this uncommon ocular malignancy. Targeted treatments with gene-specific therapeutic molecules may prove useful in overcoming radiation resistance, however, the diverse molecular makeups of UM call for a patient-specific approach in therapy procedures. We need to understand the intricate molecular landscape of UM to develop targeted treatments customized to each patient's specific genetic mutations. One of the promising approaches is using liquid biopsies, such as circulating tumor cells (CTCs) and circulating tumor DNA (ctDNA), for detecting and monitoring the disease at the early stages. These non-invasive methods can help us identify the most effective treatment strategies for each patient. Single-cellular is a brand-new analysis platform that gives treasured insights into diagnosis, prognosis, and remedy. The incorporation of this data with known clinical and genomics information will give a better understanding of the complicated molecular mechanisms that UM diseases exploit. In this review, we focused on the heterogeneity and molecular panorama of UM, and to achieve this goal, the authors conducted an exhaustive literature evaluation spanning 1998 to 2023, using keywords like "uveal melanoma, "heterogeneity". "Targeted therapies"," "CTCs," and "single-cellular analysis".
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Affiliation(s)
- Yasaman Zohrab Beigi
- Laboratory of System Biology and Bioinformatics (LBB), Institute of Biochemistry and Biophysics, University of Tehran, Tehran, Iran
| | - Hossein Lanjanian
- Software Engineering Department, Engineering Faculty, Istanbul Topkapi University, Istanbul, Turkey
| | - Reyhane Fayazi
- Laboratory of System Biology and Bioinformatics (LBB), Institute of Biochemistry and Biophysics, University of Tehran, Tehran, Iran
| | - Mahdieh Salimi
- Department of Medical Genetics, Institute of Medical Biotechnology, National Institute of Genetic Engineering and Biotechnology (NIGEB), Tehran, Iran
| | - Behnaz Haji Molla Hoseyni
- Laboratory of System Biology and Bioinformatics (LBB), Institute of Biochemistry and Biophysics, University of Tehran, Tehran, Iran
| | | | - Ali Masoudi-Nejad
- Laboratory of System Biology and Bioinformatics (LBB), Institute of Biochemistry and Biophysics, University of Tehran, Tehran, Iran.
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Hassanzadeh-Barforoushi A, Tukova A, Nadalini A, Inglis DW, Chang-Hao Tsao S, Wang Y. Microfluidic-SERS Technologies for CTC: A Perspective on Clinical Translation. ACS APPLIED MATERIALS & INTERFACES 2024. [PMID: 38652011 DOI: 10.1021/acsami.4c01158] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/25/2024]
Abstract
Enumeration and phenotypic profiling of circulating tumor cells (CTCs) provide critical information for clinical diagnosis and treatment monitoring in cancer. To achieve this goal, an integrated system is needed to efficiently isolate CTCs from patient samples and sensitively evaluate their phenotypes. Such integration would comprise a high-throughput single-cell processing unit for the isolation and manipulation of CTCs and a sensitive and multiplexed quantitation unit to detect clinically relevant signals from these cells. Surface-enhanced Raman scattering (SERS) has been used as an analytical method for molecular profiling and in vitro cancer diagnosis. More recently, its multiplexing capability and power to create distinct molecular signatures against their targets have garnered attention. Here, we share our insights into the combined power of microfluidics and SERS in realizing CTC isolation, enumeration, and detection from a clinical translation perspective. We highlight the key operational factors in CTC microfluidic processing and SERS detection from patient samples. We further discuss microfluidic-SERS integration and its clinical utility as a paradigm shift in clinical CTC-based cancer diagnosis and prognostication. Finally, we summarize the challenges and attempt to look forward to what lies ahead of us in potentially translating the technique into real clinical applications.
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Affiliation(s)
- Amin Hassanzadeh-Barforoushi
- School of Natural Sciences, Faculty of Science and Engineering, Macquarie University, Sydney, New South Wales 2109, Australia
| | - Anastasiia Tukova
- School of Natural Sciences, Faculty of Science and Engineering, Macquarie University, Sydney, New South Wales 2109, Australia
| | - Audrey Nadalini
- School of Natural Sciences, Faculty of Science and Engineering, Macquarie University, Sydney, New South Wales 2109, Australia
| | - David W Inglis
- School of Engineering, Faculty of Science and Engineering, Macquarie University, Sydney, New South Wales 2109, Australia
| | - Simon Chang-Hao Tsao
- School of Natural Sciences, Faculty of Science and Engineering, Macquarie University, Sydney, New South Wales 2109, Australia
- Department of Surgery, Austin Health, University of Melbourne, Heidelberg, Victoria 3084, Australia
| | - Yuling Wang
- School of Natural Sciences, Faculty of Science and Engineering, Macquarie University, Sydney, New South Wales 2109, Australia
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7
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Shishido SN, Hart O, Jeong S, Moriarty A, Heeke D, Rossi J, Bot A, Kuhn P. Liquid biopsy approach to monitor the efficacy and response to CAR-T cell therapy. J Immunother Cancer 2024; 12:e007329. [PMID: 38350684 PMCID: PMC10862257 DOI: 10.1136/jitc-2023-007329] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/25/2024] [Indexed: 02/15/2024] Open
Abstract
BACKGROUND Chimeric antigen receptor (CAR)-T cells are approved for use in the treatment of hematological malignancies. Axicabtagene ciloleucel (YESCARTA) and brexucabtagene autoleucel (TECARTUS) genetically modified autologous T cells expressing an anti-CD19 scFv based on the FMC63 clone have shown impressive response rates for the treatment of CD19+B cell malignancies, but there remain challenges in monitoring long-term persistence as well as the functional characterization of low-level persisting CAR-T cells in patients. Furthermore, due to CD19-negative driven relapse, having the capability to monitor patients with simultaneous detection of the B cell malignancy and persisting CAR-T cells in patient peripheral blood is important for ensuring timely treatment optionality and understanding relapse. METHODS This study demonstrates the development and technical validation of a comprehensive liquid biopsy, high-definition single cell assay (HDSCA)-HemeCAR for (1) KTE-X19 CAR-T cell identification and analysis and (2) simultaneously monitoring the CD19-epitope landscape on neoplastic B cells in cryopreserved or fresh peripheral blood. Proprietary anti-CD19 CAR reagents, healthy donor transduced CAR-T cells, and patient samples consisting of malignant B cell fractions from manufacturing were used for assay development. RESULTS The CAR-T assay showed an approximate limit of detection at 1 cell in 3 million with a sensitivity of 91%. Genomic analysis was additionally used to confirm the presence of the CAR transgene. This study additionally reports the successful completion of two B cell assays with multiple CD19 variants (FMC63 and LE-CD19) and a unique fourth channel biomarker (CD20 or CD22). In patient samples, we observed that CD19 isoforms were highly heterogeneous both intrapatient and interpatient. CONCLUSIONS With the simultaneous detection of the CAR-T cells and the B cell malignancy in patient peripheral blood, the HDSCA-HemeCAR workflow may be considered for risk monitoring and patient management.
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Affiliation(s)
- Stephanie N Shishido
- Convergent Science Institute in Cancer, Michelson Center for Convergent Bioscience, University of Southern California, Los Angeles, California, USA
| | - Olivia Hart
- Convergent Science Institute in Cancer, Michelson Center for Convergent Bioscience, University of Southern California, Los Angeles, California, USA
| | - Sujin Jeong
- Convergent Science Institute in Cancer, Michelson Center for Convergent Bioscience, University of Southern California, Los Angeles, California, USA
| | - Aidan Moriarty
- Convergent Science Institute in Cancer, Michelson Center for Convergent Bioscience, University of Southern California, Los Angeles, California, USA
| | - Darren Heeke
- Kite A Gilead Company, Santa Monica, California, USA
| | - John Rossi
- Kite A Gilead Company, Santa Monica, California, USA
| | - Adrian Bot
- Kite A Gilead Company, Santa Monica, California, USA
| | - Peter Kuhn
- Convergent Science Institute in Cancer, Michelson Center for Convergent Bioscience, University of Southern California, Los Angeles, California, USA
- Department of Biological Sciences Sciences, Dornsife College of Letters, Arts, and Sciences, 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
- Institute of Urology, Catherine & Joseph Aresty Department of Urology, Keck School of Medicine, University of Southern California, Los Angeles, California, USA
- Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, California, USA
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8
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Batool SM, Hsia T, Beecroft A, Lewis B, Ekanayake E, Rosenfeld Y, Escobedo AK, Gamblin AS, Rawal S, Cote RJ, Watson M, Wong DTW, Patel AA, Skog J, Papadopoulos N, Bettegowda C, Castro CM, Lee H, Srivastava S, Carter BS, Balaj L. Extrinsic and intrinsic preanalytical variables affecting liquid biopsy in cancer. Cell Rep Med 2023; 4:101196. [PMID: 37725979 PMCID: PMC10591035 DOI: 10.1016/j.xcrm.2023.101196] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2022] [Revised: 12/01/2022] [Accepted: 08/22/2023] [Indexed: 09/21/2023]
Abstract
Liquid biopsy, through isolation and analysis of disease-specific analytes, has evolved as a promising tool for safe and minimally invasive diagnosis and monitoring of tumors. It also has tremendous utility as a companion diagnostic allowing detection of biomarkers in a range of cancers (lung, breast, colon, ovarian, brain). However, clinical implementation and validation remains a challenge. Among other stages of development, preanalytical variables are critical in influencing the downstream cellular and molecular analysis of different analytes. Although considerable progress has been made to address these challenges, a comprehensive assessment of the impact on diagnostic parameters and consensus on standardized and optimized protocols is still lacking. Here, we summarize and critically evaluate key variables in the preanalytical stage, including study population selection, choice of biofluid, sample handling and collection, processing, and storage. There is an unmet need to develop and implement comprehensive preanalytical guidelines on the optimal practices and methodologies.
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Affiliation(s)
| | - Tiffaney Hsia
- Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Alexandra Beecroft
- Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Brian Lewis
- Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Emil Ekanayake
- Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Yulia Rosenfeld
- Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Ana K Escobedo
- Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Austin S Gamblin
- Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Siddarth Rawal
- Washington University School of Medicine, St. Louis, MO, USA; Circulogix Inc., St. Louis, MO, USA
| | - Richard J Cote
- Washington University School of Medicine, St. Louis, MO, USA; Circulogix Inc., St. Louis, MO, USA
| | - Mark Watson
- Washington University School of Medicine, St. Louis, MO, USA
| | - David T W Wong
- University of California Los Angeles, Los Angeles, CA, USA
| | | | - Johan Skog
- Exosome Diagnostics, Waltham, MA 02451, USA
| | | | | | - Cesar M Castro
- Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Hakho Lee
- Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Sudhir Srivastava
- Cancer Biomarkers Research Group, Division of Cancer Prevention, National Cancer Institute, Bethesda, MD, USA
| | - Bob S Carter
- Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Leonora Balaj
- Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA.
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9
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Setayesh SM, Ndacayisaba LJ, Rappard KE, Hennes V, Rueda LYM, Tang G, Lin P, Orlowski RZ, Symer DE, Manasanch EE, Shishido SN, Kuhn P. Targeted single-cell proteomic analysis identifies new liquid biopsy biomarkers associated with multiple myeloma. NPJ Precis Oncol 2023; 7:95. [PMID: 37723227 PMCID: PMC10507120 DOI: 10.1038/s41698-023-00446-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2023] [Accepted: 09/05/2023] [Indexed: 09/20/2023] Open
Abstract
Multiple myeloma (MM) is accompanied by alterations to the normal plasma cell (PC) proteome, leading to changes to the tumor microenvironment and disease progression. There is a great need for understanding the consequences that lead to MM progression and for the discovery of new biomarkers that can aid clinical diagnostics and serve as targets for therapeutics. This study demonstrates the applicability of utilizing the single-cell high-definition liquid biopsy assay (HDSCA) and imaging mass cytometry to characterize the proteomic profile of myeloma. In our study, we analyzed ~87,000 cells from seven patient samples (bone marrow and peripheral blood) across the myeloma disease spectrum and utilized our multiplexed panel to characterize the expression of clinical markers for PC classification, additional potential therapeutic targets, and the tumor microenvironment cells. Our analysis showed BCMA, ICAM3 (CD50), CD221, and CS1 (SLAMF7) as the most abundantly expressed markers on PCs across all myeloma stages, with BCMA, ICAM3, and CD221 having significantly higher expression levels on disease versus precursor PCs. Additionally, we identify significantly elevated levels of expression for CD74, MUM1, CD229, CD44, IGLL5, Cyclin D1, UBA52, and CD317 on PCs from overt disease conditions compared to those from precursor states.
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Affiliation(s)
- Sonia M Setayesh
- Convergent Science Institute in Cancer, Michelson Center for Convergent Bioscience, University of Southern California, Los Angeles, CA, 90089, USA
| | - Libere J Ndacayisaba
- Convergent Science Institute in Cancer, Michelson Center for Convergent Bioscience, University of Southern California, Los Angeles, CA, 90089, USA
| | - Kate E Rappard
- Convergent Science Institute in Cancer, Michelson Center for Convergent Bioscience, University of Southern California, Los Angeles, CA, 90089, USA
| | - Valerie Hennes
- Convergent Science Institute in Cancer, Michelson Center for Convergent Bioscience, University of Southern California, Los Angeles, CA, 90089, USA
| | - Luz Yurany Moreno Rueda
- Department of Lymphoma and Myeloma, Division of Cancer Medicine, University of Texas MD Anderson Cancer Center, Houston, TX, 77030, 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
| | - Robert Z Orlowski
- Department of Lymphoma and Myeloma, Division of Cancer Medicine, University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - David E Symer
- Department of Lymphoma and Myeloma, Division of Cancer Medicine, University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Elisabet E Manasanch
- Department of Lymphoma and Myeloma, Division of Cancer Medicine, University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Stephanie N Shishido
- Convergent Science Institute in Cancer, Michelson Center for Convergent Bioscience, University of Southern California, Los Angeles, CA, 90089, USA.
| | - Peter Kuhn
- Convergent Science Institute in Cancer, Michelson Center for Convergent Bioscience, 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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10
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Welter L, Zheng S, Setayesh SM, Morikado M, Agrawal A, Nevarez R, Naghdloo A, Pore M, Higa N, Kolatkar A, Thiele JA, Sharma P, Moore HCF, Richer JK, Elias A, Pienta KJ, Zurita AJ, Gross ME, Shishido SN, Hicks J, Velasco CR, Kuhn P. Cell State and Cell Type: Deconvoluting Circulating Tumor Cell Populations in Liquid Biopsies by Multi-Omics. Cancers (Basel) 2023; 15:3949. [PMID: 37568766 PMCID: PMC10417732 DOI: 10.3390/cancers15153949] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2023] [Revised: 07/14/2023] [Accepted: 07/21/2023] [Indexed: 08/13/2023] Open
Abstract
Bi-directional crosstalk between the tumor and the tumor microenvironment (TME) has been shown to increase the rate of tumor evolution and to play a key role in neoplastic progression, therapeutic resistance, and a patient's overall survival. Here, we set out to use a comprehensive liquid-biopsy analysis to study cancer and specific TME cells in circulation and their association with disease status. Cytokeratin+, CD45- circulating rare cells (CRCs) from nine breast and four prostate cancer patients were characterized through morphometrics, single-cell copy number analysis, and targeted multiplexed proteomics to delineate cancer cell lineage from other rare cells originating in the TME. We show that we can detect epithelial circulating tumor cells (EPI.CTC), CTCs undergoing epithelial-to-mesenchymal transition (EMT.CTC) and circulating endothelial cells (CECs) using a universal rare event detection platform (HDSCA). Longitudinal analysis of an index patient finds that CTCs are present at the time of disease progression, while CECs are predominately present at the time of stable disease. In a small cohort of prostate and breast cancer patients, we find high inter-patient and temporal intra-patient variability in the expression of tissue specific markers such as ER, HER2, AR, PSA and PSMA and EpCAM. Our study stresses the importance of the multi-omic characterization of circulating rare cells in patients with breast and prostate carcinomas, specifically highlighting overlapping and cell type defining proteo-genomic characteristics of CTCs and CECs.
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Affiliation(s)
- Lisa Welter
- Convergent Science Institute in Cancer, Michelson Center for Convergent Bioscience, University of Southern California, Los Angeles, CA 90089, USA; (L.W.); (S.Z.); (S.M.S.); (M.M.); (A.A.); (R.N.); (A.N.); (M.P.); (N.H.); (A.K.); (J.-A.T.); (S.N.S.); (C.R.V.)
- Department of Biological Sciences, Dornsife College of Letters, Arts, and Sciences, University of Southern California, Los Angeles, CA 90089, USA
| | - Serena Zheng
- Convergent Science Institute in Cancer, Michelson Center for Convergent Bioscience, University of Southern California, Los Angeles, CA 90089, USA; (L.W.); (S.Z.); (S.M.S.); (M.M.); (A.A.); (R.N.); (A.N.); (M.P.); (N.H.); (A.K.); (J.-A.T.); (S.N.S.); (C.R.V.)
| | - Sonia Maryam Setayesh
- Convergent Science Institute in Cancer, Michelson Center for Convergent Bioscience, University of Southern California, Los Angeles, CA 90089, USA; (L.W.); (S.Z.); (S.M.S.); (M.M.); (A.A.); (R.N.); (A.N.); (M.P.); (N.H.); (A.K.); (J.-A.T.); (S.N.S.); (C.R.V.)
- Department of Biological Sciences, Dornsife College of Letters, Arts, and Sciences, University of Southern California, Los Angeles, CA 90089, USA
| | - Michael Morikado
- Convergent Science Institute in Cancer, Michelson Center for Convergent Bioscience, University of Southern California, Los Angeles, CA 90089, USA; (L.W.); (S.Z.); (S.M.S.); (M.M.); (A.A.); (R.N.); (A.N.); (M.P.); (N.H.); (A.K.); (J.-A.T.); (S.N.S.); (C.R.V.)
| | - Arushi Agrawal
- Convergent Science Institute in Cancer, Michelson Center for Convergent Bioscience, University of Southern California, Los Angeles, CA 90089, USA; (L.W.); (S.Z.); (S.M.S.); (M.M.); (A.A.); (R.N.); (A.N.); (M.P.); (N.H.); (A.K.); (J.-A.T.); (S.N.S.); (C.R.V.)
| | - Rafael Nevarez
- Convergent Science Institute in Cancer, Michelson Center for Convergent Bioscience, University of Southern California, Los Angeles, CA 90089, USA; (L.W.); (S.Z.); (S.M.S.); (M.M.); (A.A.); (R.N.); (A.N.); (M.P.); (N.H.); (A.K.); (J.-A.T.); (S.N.S.); (C.R.V.)
| | - Amin Naghdloo
- Convergent Science Institute in Cancer, Michelson Center for Convergent Bioscience, University of Southern California, Los Angeles, CA 90089, USA; (L.W.); (S.Z.); (S.M.S.); (M.M.); (A.A.); (R.N.); (A.N.); (M.P.); (N.H.); (A.K.); (J.-A.T.); (S.N.S.); (C.R.V.)
- Department of Aerospace and Mechanical Engineering, Viterbi School of Engineering, University of Southern California, Los Angeles, CA 90089, USA
| | - Milind Pore
- Convergent Science Institute in Cancer, Michelson Center for Convergent Bioscience, University of Southern California, Los Angeles, CA 90089, USA; (L.W.); (S.Z.); (S.M.S.); (M.M.); (A.A.); (R.N.); (A.N.); (M.P.); (N.H.); (A.K.); (J.-A.T.); (S.N.S.); (C.R.V.)
| | - Nikki Higa
- Convergent Science Institute in Cancer, Michelson Center for Convergent Bioscience, University of Southern California, Los Angeles, CA 90089, USA; (L.W.); (S.Z.); (S.M.S.); (M.M.); (A.A.); (R.N.); (A.N.); (M.P.); (N.H.); (A.K.); (J.-A.T.); (S.N.S.); (C.R.V.)
- Department of Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA
| | - Anand Kolatkar
- Convergent Science Institute in Cancer, Michelson Center for Convergent Bioscience, University of Southern California, Los Angeles, CA 90089, USA; (L.W.); (S.Z.); (S.M.S.); (M.M.); (A.A.); (R.N.); (A.N.); (M.P.); (N.H.); (A.K.); (J.-A.T.); (S.N.S.); (C.R.V.)
| | - Jana-Aletta Thiele
- Convergent Science Institute in Cancer, Michelson Center for Convergent Bioscience, University of Southern California, Los Angeles, CA 90089, USA; (L.W.); (S.Z.); (S.M.S.); (M.M.); (A.A.); (R.N.); (A.N.); (M.P.); (N.H.); (A.K.); (J.-A.T.); (S.N.S.); (C.R.V.)
| | - Priyanka Sharma
- University of Kansas Medical Center, Westwood, KS 66205, USA;
| | - Halle C. F. Moore
- Cleveland Clinic Taussig Cancer Institute, Cleveland, OH 44195, USA;
| | - Jennifer K. Richer
- University of Colorado Cancer Center, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA; (J.K.R.); (A.E.)
| | - Anthony Elias
- University of Colorado Cancer Center, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA; (J.K.R.); (A.E.)
| | - Kenneth J. Pienta
- The Cancer Ecology Center, Brady Urological Institute, Johns Hopkins School of Medicine, Baltimore, MD 21287, USA;
| | - Amado J. Zurita
- Department of Genitourinary Medical Oncology, MD Anderson, Houston, TX 77230, USA;
| | - Mitchell E. Gross
- Lawrence J. Ellison Institute for Transformative Medicine, Los Angeles, CA 90064, USA;
- Department of Biomedical Engineering, Viterbi School of Engineering, 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; (L.W.); (S.Z.); (S.M.S.); (M.M.); (A.A.); (R.N.); (A.N.); (M.P.); (N.H.); (A.K.); (J.-A.T.); (S.N.S.); (C.R.V.)
| | - James Hicks
- Convergent Science Institute in Cancer, Michelson Center for Convergent Bioscience, University of Southern California, Los Angeles, CA 90089, USA; (L.W.); (S.Z.); (S.M.S.); (M.M.); (A.A.); (R.N.); (A.N.); (M.P.); (N.H.); (A.K.); (J.-A.T.); (S.N.S.); (C.R.V.)
- Department of Biological Sciences, Dornsife College of Letters, Arts, and Sciences, 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; (L.W.); (S.Z.); (S.M.S.); (M.M.); (A.A.); (R.N.); (A.N.); (M.P.); (N.H.); (A.K.); (J.-A.T.); (S.N.S.); (C.R.V.)
| | - Peter Kuhn
- Convergent Science Institute in Cancer, Michelson Center for Convergent Bioscience, University of Southern California, Los Angeles, CA 90089, USA; (L.W.); (S.Z.); (S.M.S.); (M.M.); (A.A.); (R.N.); (A.N.); (M.P.); (N.H.); (A.K.); (J.-A.T.); (S.N.S.); (C.R.V.)
- 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
- Department of Biomedical Engineering, Viterbi School of Engineering, 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
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11
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Orrapin S, Thongkumkoon P, Udomruk S, Moonmuang S, Sutthitthasakul S, Yongpitakwattana P, Pruksakorn D, Chaiyawat P. Deciphering the Biology of Circulating Tumor Cells through Single-Cell RNA Sequencing: Implications for Precision Medicine in Cancer. Int J Mol Sci 2023; 24:12337. [PMID: 37569711 PMCID: PMC10418766 DOI: 10.3390/ijms241512337] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2023] [Revised: 07/25/2023] [Accepted: 07/27/2023] [Indexed: 08/13/2023] Open
Abstract
Circulating tumor cells (CTCs) hold unique biological characteristics that directly involve them in hematogenous dissemination. Studying CTCs systematically is technically challenging due to their extreme rarity and heterogeneity and the lack of specific markers to specify metastasis-initiating CTCs. With cutting-edge technology, single-cell RNA sequencing (scRNA-seq) provides insights into the biology of metastatic processes driven by CTCs. Transcriptomics analysis of single CTCs can decipher tumor heterogeneity and phenotypic plasticity for exploring promising novel therapeutic targets. The integrated approach provides a perspective on the mechanisms underlying tumor development and interrogates CTCs interactions with other blood cell types, particularly those of the immune system. This review aims to comprehensively describe the current study on CTC transcriptomic analysis through scRNA-seq technology. We emphasize the workflow for scRNA-seq analysis of CTCs, including enrichment, single cell isolation, and bioinformatic tools applied for this purpose. Furthermore, we elucidated the translational knowledge from the transcriptomic profile of individual CTCs and the biology of cancer metastasis for developing effective therapeutics through targeting key pathways in CTCs.
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Affiliation(s)
- Santhasiri Orrapin
- Center of Multidisciplinary Technology for Advanced Medicine (CMUTEAM), Faculty of Medicine, Chiang Mai University, Muang, Chiang Mai 50200, Thailand; (S.O.); (P.T.); (S.U.); (S.M.); (S.S.); (P.Y.); (D.P.)
| | - Patcharawadee Thongkumkoon
- Center of Multidisciplinary Technology for Advanced Medicine (CMUTEAM), Faculty of Medicine, Chiang Mai University, Muang, Chiang Mai 50200, Thailand; (S.O.); (P.T.); (S.U.); (S.M.); (S.S.); (P.Y.); (D.P.)
| | - Sasimol Udomruk
- Center of Multidisciplinary Technology for Advanced Medicine (CMUTEAM), Faculty of Medicine, Chiang Mai University, Muang, Chiang Mai 50200, Thailand; (S.O.); (P.T.); (S.U.); (S.M.); (S.S.); (P.Y.); (D.P.)
- Musculoskeletal Science and Translational Research (MSTR) Center, Faculty of Medicine, Chiang Mai University, Muang, Chiang Mai 50200, Thailand
| | - Sutpirat Moonmuang
- Center of Multidisciplinary Technology for Advanced Medicine (CMUTEAM), Faculty of Medicine, Chiang Mai University, Muang, Chiang Mai 50200, Thailand; (S.O.); (P.T.); (S.U.); (S.M.); (S.S.); (P.Y.); (D.P.)
| | - Songphon Sutthitthasakul
- Center of Multidisciplinary Technology for Advanced Medicine (CMUTEAM), Faculty of Medicine, Chiang Mai University, Muang, Chiang Mai 50200, Thailand; (S.O.); (P.T.); (S.U.); (S.M.); (S.S.); (P.Y.); (D.P.)
| | - Petlada Yongpitakwattana
- Center of Multidisciplinary Technology for Advanced Medicine (CMUTEAM), Faculty of Medicine, Chiang Mai University, Muang, Chiang Mai 50200, Thailand; (S.O.); (P.T.); (S.U.); (S.M.); (S.S.); (P.Y.); (D.P.)
| | - Dumnoensun Pruksakorn
- Center of Multidisciplinary Technology for Advanced Medicine (CMUTEAM), Faculty of Medicine, Chiang Mai University, Muang, Chiang Mai 50200, Thailand; (S.O.); (P.T.); (S.U.); (S.M.); (S.S.); (P.Y.); (D.P.)
- Musculoskeletal Science and Translational Research (MSTR) Center, Faculty of Medicine, Chiang Mai University, Muang, Chiang Mai 50200, Thailand
- Department of Orthopedics, Faculty of Medicine, Chiang Mai University, Muang, Chiang Mai 50200, Thailand
| | - Parunya Chaiyawat
- Center of Multidisciplinary Technology for Advanced Medicine (CMUTEAM), Faculty of Medicine, Chiang Mai University, Muang, Chiang Mai 50200, Thailand; (S.O.); (P.T.); (S.U.); (S.M.); (S.S.); (P.Y.); (D.P.)
- Musculoskeletal Science and Translational Research (MSTR) Center, Faculty of Medicine, Chiang Mai University, Muang, Chiang Mai 50200, Thailand
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12
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Chowdhury T, Cressiot B, Parisi C, Smolyakov G, Thiébot B, Trichet L, Fernandes FM, Pelta J, Manivet P. Circulating Tumor Cells in Cancer Diagnostics and Prognostics by Single-Molecule and Single-Cell Characterization. ACS Sens 2023; 8:406-426. [PMID: 36696289 DOI: 10.1021/acssensors.2c02308] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
Circulating tumor cells (CTCs) represent an interesting source of biomarkers for diagnosis, prognosis, and the prediction of cancer recurrence, yet while they are extensively studied in oncobiology research, their diagnostic utility has not yet been demonstrated and validated. Their scarcity in human biological fluids impedes the identification of dangerous CTC subpopulations that may promote metastatic dissemination. In this Perspective, we discuss promising techniques that could be used for the identification of these metastatic cells. We first describe methods for isolating patient-derived CTCs and then the use of 3D biomimetic matrixes in their amplification and analysis, followed by methods for further CTC analyses at the single-cell and single-molecule levels. Finally, we discuss how the elucidation of mechanical and morphological properties using techniques such as atomic force microscopy and molecular biomarker identification using nanopore-based detection could be combined in the future to provide patients and their healthcare providers with a more accurate diagnosis.
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Affiliation(s)
- Tafsir Chowdhury
- Centre de Ressources Biologiques Biobank Lariboisière (BB-0033-00064), DMU BioGem, AP-HP, 75010 Paris, France
| | | | - Cleo Parisi
- Centre de Ressources Biologiques Biobank Lariboisière (BB-0033-00064), DMU BioGem, AP-HP, 75010 Paris, France.,Sorbonne Université, UMR 7574, Laboratoire de Chimie de la Matière Condensée de Paris, 75005 Paris, France
| | - Georges Smolyakov
- Centre de Ressources Biologiques Biobank Lariboisière (BB-0033-00064), DMU BioGem, AP-HP, 75010 Paris, France
| | | | - Léa Trichet
- Sorbonne Université, UMR 7574, Laboratoire de Chimie de la Matière Condensée de Paris, 75005 Paris, France
| | - Francisco M Fernandes
- Sorbonne Université, UMR 7574, Laboratoire de Chimie de la Matière Condensée de Paris, 75005 Paris, France
| | - Juan Pelta
- CY Cergy Paris Université, CNRS, LAMBE, 95000 Cergy, France.,Université Paris-Saclay, Université d'Evry, CNRS, LAMBE, 91190 Evry, France
| | - Philippe Manivet
- Centre de Ressources Biologiques Biobank Lariboisière (BB-0033-00064), DMU BioGem, AP-HP, 75010 Paris, France.,Université Paris Cité, Inserm, NeuroDiderot, F-75019 Paris, France
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13
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Obermayr E, Koppensteiner N, Heinzl N, Schuster E, Holzer B, Fabikan H, Weinlinger C, Illini O, Hochmair MJ, Zeillinger R. Effect of short-term storage of blood samples on gene expression in lung cancer patients. Clin Chem Lab Med 2023; 61:294-301. [PMID: 36395488 DOI: 10.1515/cclm-2022-0738] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Accepted: 11/07/2022] [Indexed: 11/18/2022]
Abstract
OBJECTIVES The stability of gene transcripts associated with the presence of circulating tumor cells (CTCs) has been predominantly studied in cultured cancer cell lines added to blood samples under artificial conditions. In the present study the effect of storage on CTC-related transcripts was assessed in blood samples taken from patients with non-small lung cancer (n=58). METHODS The blood samples were split in two equal parts to compare the gene expression with and without storage for 24 h at ambient temperature without preservative added. After enrichment using the microfluidic Parsortix® technology, the expression levels of selected genes were assessed using quantitative PCR following a gene-specific pre-amplification. The prognostic relevance of each gene in fresh and stored blood samples was evaluated using the R-package Survminer. RESULTS Some genes were either not affected (TWIST1, CDH5, CK19) or upregulated upon storage (NANOG, MET, UCHL1) but still associated with poor prognosis. In contrast, ERBB3, PTHLH, EpCAM, and TERT were no longer associated with the overall survival of the patients. CONCLUSIONS The study demonstrates the surprising stability of CTC-related transcripts, which makes overnight shipping of native blood samples possible. Careful verification is required when using model systems - such as normal blood spiked with tumor cells - or other CTC-related markers, as individual transcripts may respond differently to storage.
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Affiliation(s)
- Eva Obermayr
- Department of Obstetrics and Gynecology, Molecular Oncology Group, Comprehensive Cancer Center, Medical University of Vienna, Vienna, Austria
| | - Nina Koppensteiner
- Department of Obstetrics and Gynecology, Molecular Oncology Group, Comprehensive Cancer Center, Medical University of Vienna, Vienna, Austria
| | - Nicole Heinzl
- Department of Obstetrics and Gynecology, Molecular Oncology Group, Comprehensive Cancer Center, Medical University of Vienna, Vienna, Austria
| | - Eva Schuster
- Department of Obstetrics and Gynecology, Molecular Oncology Group, Comprehensive Cancer Center, Medical University of Vienna, Vienna, Austria
| | - Barbara Holzer
- Department of Obstetrics and Gynecology, Molecular Oncology Group, Comprehensive Cancer Center, Medical University of Vienna, Vienna, Austria
| | - Hannah Fabikan
- Karl Landsteiner Institute of Lung Research and Pulmonary Oncology, Klinik Floridsdorf, Vienna, Austria
| | - Christoph Weinlinger
- Karl Landsteiner Institute of Lung Research and Pulmonary Oncology, Klinik Floridsdorf, Vienna, Austria
| | - Oliver Illini
- Karl Landsteiner Institute of Lung Research and Pulmonary Oncology, Klinik Floridsdorf, Vienna, Austria
- Department of Respiratory and Critical Care Medicine, Klinik Floridsdorf, Vienna Healthcare Group, Vienna, Austria
| | - Maximilian J Hochmair
- Karl Landsteiner Institute of Lung Research and Pulmonary Oncology, Klinik Floridsdorf, Vienna, Austria
- Department of Respiratory and Critical Care Medicine, Klinik Floridsdorf, Vienna Healthcare Group, Vienna, Austria
| | - Robert Zeillinger
- Department of Obstetrics and Gynecology, Molecular Oncology Group, Comprehensive Cancer Center, Medical University of Vienna, Vienna, Austria
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14
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Aktar S, Baghaie H, Islam F, Gopalan V, Lam AKY. Current Status of Circulating Tumor Cells in Head and Neck Squamous Cell Carcinoma: A Review. Otolaryngol Head Neck Surg 2023; 168:988-1005. [PMID: 36939466 DOI: 10.1002/ohn.186] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2022] [Revised: 09/28/2022] [Accepted: 10/09/2022] [Indexed: 01/20/2023]
Abstract
OBJECTIVE Circulating tumor cells (CTCs) are found in the blood of patients with cancer, including head and neck squamous cell carcinomas (HNSCCs). The aim is to review the most up-to-date status of CTCs for applications in patients with HNSCC. DATA SOURCES English articles in PubMed. REVIEW METHODS All the studies on CTCs in HNSCCs in the literature were reviewed. CONCLUSIONS There is emerging information on the diagnostic and prognostic value of CTCs in HNSCCs. Evidence also highlights the advantages of various downstream analysis approaches over circulating tumor DNA (ctDNA), such as single-CTC analysis, ex vivo, and in vivo expansion of CTCs. Multiple phenotypic surface markers (cytokeratins, EpCAM, vimentin, etc.), used for CTCs characterization using different immunoassays, could predict disease progression as well as patients' response to treatment efficacy. Immune checkpoint inhibitors' status in CTCs could also provide better insight into treatment. Clonal expansion of CTCs and single-cell analysis of CTCs are the most emerging fields nowadays which may offer an understanding of the mechanism of tumor evolution as well as therapeutic efficacy. Although several clinical trials are ongoing, limitations still exist in the detection and characterization of CTCs. Due to the lack of a gold standard protocol, the sensitivity and specificity of CTC enumeration methods vary. IMPLICATIONS FOR PRACTICE Prospective clinical trials are still needed before CTCs can be employed as diagnostic and prognostic markers in the clinical management of patients with HNSCC.
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Affiliation(s)
- Sharmin Aktar
- Cancer Molecular Pathology, School of Medicine and Dentistry, Menzies Health Institute Queensland, Griffith University, Gold Coast, Australia.,Department of Biochemistry and Molecular Biology, Mawlana Bhashani Science and Technology University, Tangail, Bangladesh
| | - Hooman Baghaie
- School of Dentistry, University of Queensland, Herston, Australia
| | - Farhadul Islam
- Department of Biochemistry and Molecular Biology, University of Rajshahi, Rajshahi, Bangladesh
| | - Vinod Gopalan
- Cancer Molecular Pathology, School of Medicine and Dentistry, Menzies Health Institute Queensland, Griffith University, Gold Coast, Australia
| | - Alfred King-Yin Lam
- Cancer Molecular Pathology, School of Medicine and Dentistry, Menzies Health Institute Queensland, Griffith University, Gold Coast, Australia.,Pathology Queensland, Gold Coast University Hospital, Southport, Australia
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15
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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: 8] [Impact Index Per Article: 2.7] [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: 13] [Impact Index Per Article: 4.3] [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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17
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Beasley AB, Chen FK, Isaacs TW, Gray ES. Future perspectives of uveal melanoma blood based biomarkers. Br J Cancer 2022; 126:1511-1528. [PMID: 35190695 PMCID: PMC9130512 DOI: 10.1038/s41416-022-01723-8] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2021] [Revised: 01/15/2022] [Accepted: 01/27/2022] [Indexed: 01/06/2023] Open
Abstract
Uveal melanoma (UM) is the most common primary intraocular malignancy affecting adults. Despite successful local treatment of the primary tumour, metastatic disease develops in up to 50% of patients. Metastatic UM carries a particularly poor prognosis, with no effective therapeutic option available to date. Genetic studies of UM have demonstrated that cytogenetic features, including gene expression, somatic copy number alterations and specific gene mutations can allow more accurate assessment of metastatic risk. Pre-emptive therapies to avert metastasis are being tested in clinical trials in patients with high-risk UM. However, current prognostic methods require an intraocular tumour biopsy, which is a highly invasive procedure carrying a risk of vision-threatening complications and is limited by sampling variability. Recently, a new diagnostic concept known as "liquid biopsy" has emerged, heralding a substantial potential for minimally invasive genetic characterisation of tumours. Here, we examine the current evidence supporting the potential of blood circulating tumour cells (CTCs), circulating tumour DNA (ctDNA), microRNA (miRNA) and exosomes as biomarkers for UM. In particular, we discuss the potential of these biomarkers to aid clinical decision making throughout the management of UM patients.
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Affiliation(s)
- Aaron B Beasley
- School of Medical and Health Sciences, Edith Cowan University, Joondalup, WA, Australia
- Centre for Precision Health, Edith Cowan University, Joondalup, WA, Australia
| | - Fred K Chen
- Centre for Ophthalmology and Visual Sciences (incorporating Lions Eye Institute), The University of Western Australia, Nedlands, WA, Australia
- Department of Ophthalmology, Royal Perth Hospital, Perth, WA, Australia
- Department of Ophthalmology, Perth Children's Hospital, Perth, WA, Australia
| | - Timothy W Isaacs
- Centre for Ophthalmology and Visual Sciences (incorporating Lions Eye Institute), The University of Western Australia, Nedlands, WA, Australia
- Department of Ophthalmology, Royal Perth Hospital, Perth, WA, Australia
- Perth Retina, West Leederville, WA, Australia
| | - Elin S Gray
- School of Medical and Health Sciences, Edith Cowan University, Joondalup, WA, Australia.
- Centre for Precision Health, Edith Cowan University, Joondalup, WA, Australia.
- Centre for Ophthalmology and Visual Sciences (incorporating Lions Eye Institute), The University of Western Australia, Nedlands, WA, Australia.
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18
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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: 0.7] [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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19
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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: 15] [Impact Index Per Article: 5.0] [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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20
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Shishido SN, Sayeed S, Courcoubetis G, Djaladat H, Miranda G, Pienta KJ, Nieva J, Hansel DE, Desai M, Gill IS, Kuhn P, Mason J. Characterization of Cellular and Acellular Analytes from Pre-Cystectomy Liquid Biopsies in Patients Newly Diagnosed with Primary Bladder Cancer. Cancers (Basel) 2022; 14:758. [PMID: 35159025 PMCID: PMC8833768 DOI: 10.3390/cancers14030758] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2021] [Revised: 01/14/2022] [Accepted: 01/21/2022] [Indexed: 02/04/2023] Open
Abstract
Urinary bladder cancer (BCa) is the 10th most frequent cancer in the world, most commonly found among the elderly population, and becomes highly lethal once cells have spread from the primary tumor to surrounding tissues and distant organs. Cystectomy, alone or with other treatments, is used to treat most BCa patients, as it offers the best chance of cure. However, even with curative intent, 29% of patients experience relapse of the cancer, 50% of which occur within the first year of surgery. This study aims to use the liquid biopsy to noninvasively detect disease and discover prognostic markers for disease progression. Using the third generation high-definition single cell assay (HDSCA3.0), 50 bladder cancer patient samples and 50 normal donor (ND) samples were analyzed for circulating rare events in the peripheral blood (PB), including circulating tumor cells (CTCs) and large extracellular vesicles (LEVs). Here, we show that (i) CTCs and LEVs are detected in the PB of BCa patients prior to cystectomy, (ii) there is a high heterogeneity of CTCs, and (iii) liquid biopsy analytes correlate with clinical data elements. We observed a significant difference in the incidence of rare cells and LEVs between BCa and ND samples (median of 74.61 cells/mL and 30.91 LEVs/mL vs. 34.46 cells/mL and 3.34 LEVs/mL, respectively). Furthermore, using classification models for the liquid biopsy data, we achieved a sensitivity of 78% and specificity of 92% for the identification of BCa patient samples. Taken together, these data support the clinical utility of the liquid biopsy in detecting BCa, as well as the potential for predicting cancer recurrence and survival post-cystectomy to better inform treatment decisions in BCa care.
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Affiliation(s)
- Stephanie N. Shishido
- Convergent Science Institute in Cancer, Michelson Center for Convergent Bioscience, University of Southern California, Los Angeles, CA 90089, USA; (S.N.S.); (S.S.); (G.C.)
| | - Salmaan Sayeed
- Convergent Science Institute in Cancer, Michelson Center for Convergent Bioscience, University of Southern California, Los Angeles, CA 90089, USA; (S.N.S.); (S.S.); (G.C.)
| | - George Courcoubetis
- Convergent Science Institute in Cancer, Michelson Center for Convergent Bioscience, University of Southern California, Los Angeles, CA 90089, USA; (S.N.S.); (S.S.); (G.C.)
| | - Hooman Djaladat
- Catherine & Joseph Aresty Department of Urology, Institute of Urology, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA; (H.D.); (G.M.); (M.D.); (I.S.G.)
| | - Gus Miranda
- Catherine & Joseph Aresty Department of Urology, Institute of Urology, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA; (H.D.); (G.M.); (M.D.); (I.S.G.)
| | - Kenneth J. Pienta
- The James Buchanan Brady Urological Institute, Johns Hopkins University School of Medicine, Baltimore, MD 21231, USA;
| | - Jorge Nieva
- Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA;
| | - Donna E. Hansel
- Department of Pathology, School of Medicine, University of California San Diego, La Jolla, CA 92093, USA;
| | - Mihir Desai
- Catherine & Joseph Aresty Department of Urology, Institute of Urology, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA; (H.D.); (G.M.); (M.D.); (I.S.G.)
| | - Inderbir S. Gill
- Catherine & Joseph Aresty Department of Urology, Institute of Urology, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA; (H.D.); (G.M.); (M.D.); (I.S.G.)
- Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA;
| | - Peter Kuhn
- Convergent Science Institute in Cancer, Michelson Center for Convergent Bioscience, University of Southern California, Los Angeles, CA 90089, USA; (S.N.S.); (S.S.); (G.C.)
- Catherine & Joseph Aresty Department of Urology, Institute of Urology, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA; (H.D.); (G.M.); (M.D.); (I.S.G.)
- 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
| | - Jeremy Mason
- Convergent Science Institute in Cancer, Michelson Center for Convergent Bioscience, University of Southern California, Los Angeles, CA 90089, USA; (S.N.S.); (S.S.); (G.C.)
- Catherine & Joseph Aresty Department of Urology, Institute of Urology, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA; (H.D.); (G.M.); (M.D.); (I.S.G.)
- Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA;
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21
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Exploring the Clinical Utility of Pancreatic Cancer Circulating Tumor Cells. Int J Mol Sci 2022; 23:ijms23031671. [PMID: 35163592 PMCID: PMC8836025 DOI: 10.3390/ijms23031671] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2021] [Revised: 01/27/2022] [Accepted: 01/28/2022] [Indexed: 01/27/2023] Open
Abstract
Pancreatic ductal adenocarcinoma (PDAC) is the most frequent pancreatic cancer type, characterized by a dismal prognosis due to late diagnosis, frequent metastases, and limited therapeutic response to standard chemotherapy. Circulating tumor cells (CTCs) are a rare subset of tumor cells found in the blood of cancer patients. CTCs has the potential utility for screening, early and definitive diagnosis, prognostic and predictive assessment, and offers the potential for personalized management. However, a gold-standard CTC detection and enrichment method remains elusive, hindering comprehensive comparisons between studies. In this review, we summarize data regarding the utility of CTCs at different stages of PDAC from early to metastatic disease and discuss the molecular profiling and culture of CTCs. The characterization of CTCs brings us closer to defining the specific CTC subpopulation responsible for metastasis with the potential to uncover new therapies and more effective management options for PDAC.
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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: 1.0] [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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Payne K, Brooks JM, Taylor GS, Batis N, Noyvert B, Pan Y, Nankivell P, Mehanna H. Immediate Sample Fixation Increases Circulating Tumour Cell (CTC) Capture and Preserves Phenotype in Head and Neck Squamous Cell Carcinoma: Towards a Standardised Approach to Microfluidic CTC Biomarker Discovery. Cancers (Basel) 2021; 13:cancers13215519. [PMID: 34771681 PMCID: PMC8583049 DOI: 10.3390/cancers13215519] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2021] [Revised: 10/08/2021] [Accepted: 10/13/2021] [Indexed: 12/25/2022] Open
Abstract
Simple Summary Circulating tumour cells (CTCs) have shown potential to act as markers of disease and prognosis in head and neck squamous cell carcinoma (HNSCC). However, there are a number of methods and devices reported to isolate and characterise CTCs. Translating CTC markers to clinical practice, for patient benefit, requires a reliable, reproducible and standardised approach. We report the benefit of the Parsortix microfluidic CTC enrichment platform in HNSCC. We demonstrate consistent cell capture rates between 10 and 100 cells/mL of whole blood. Analysis of gene expression with unfixed cells before and after Parsortix enrichment demonstrated a cell stress response and downregulation of key genes. We highlight the benefit of using a fixative blood collection tube (Transfix) to increase cell capture rate and preserve the CTC marker expression profile. Such evidence is crucial when designing sample processing protocols for large cohort multi-centre clinical trials investigating CTCs in any cancer type. Abstract Introduction: Research demonstrates strong evidence that circulating tumour cells (CTCs) can provide diagnostic and/or prognostic biomarkers in head and neck squamous cell carcinoma (HNSCC) and a potential tool for therapeutic stratification. However, the question still remains as to the optimum method of CTC enrichment and how this can be translated into clinical practice. We aimed to evaluate the Parsortix microfluidic device for CTC enrichment and characterisation in HNSCC, seeking to optimise a sample collection and processing protocol that preserves CTC integrity and phenotype. Method: Spiking experiments of the FaDu and SCC040 HNSCC cell lines were used to determine the Parsortix capture rate of rare “CTC-like” cells. Capture rates of cancer cells spiked into EDTA blood collections tubes (BCTs) were compared to the Transfix fixative BCT and Cytodelics whole blood freezing protocol. The Lexogen Quantseq library preparation was used to profile gene expression of unfixed cells before and after microfluidic enrichment and enriched cell line spiked Transfix blood samples. An antibody panel was optimised to enable immunofluorescence microscopy CTC detection in HNSCC patient Transfix blood samples, using epithelial (EpCAM) and mesenchymal (N-cadherin) CTC markers. Results: Across a spiked cell concentration range of 9–129 cells/mL, Parsortix demonstrated a mean cell capture rate of 53.5% for unfixed cells, with no significant relationship between spiked cell concentration and capture rate. Samples preserved in Transfix BCTs demonstrated significantly increased capture rates at 0 h (time to processing) compared to EDTA BCTs (65.3% vs. 51.0%). Capture rates in Transfix BCTs were maintained at 24 h and 72 h timepoints, but dropped significantly in EDTA BCTs. Gene expression profiling revealed that microfluidic enrichment of unfixed cell lines caused downregulation of RNA processing/binding gene pathways and upregulation of genes involved in cell injury, apoptosis and oxidative stress. RNA was successfully extracted and sequenced from Transfix preserved cells enriched using Parsortix, demonstrating epithelial specific transcripts from spiked cells. In a proof-of-concept cohort of four patients with advanced HNSCC, CTCs were successfully identified and visualised with epithelial and epithelial-mesenchymal phenotypes. Conclusion: We have optimised a protocol for detection of CTCs in HNSCC with the Parsortix microfluidic device, using Transfix BCTs. We report a significant benefit, both in terms of cell capture rates and preserving cell phenotype, for using a fixative BCT- particularly if samples are stored before processing. In the design of large cohort multi-site clinical trials, such data are of paramount importance.
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Affiliation(s)
- Karl Payne
- Institute of Head and Neck Studies and Education, Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham B15 2TT, UK; (J.M.B.); (N.B.); (P.N.); (H.M.)
- Correspondence:
| | - Jill M. Brooks
- Institute of Head and Neck Studies and Education, Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham B15 2TT, UK; (J.M.B.); (N.B.); (P.N.); (H.M.)
| | - Graham S. Taylor
- Institute of Immunology and Immunotherapy, University of Birmingham, Birmingham B15 2TT, UK;
| | - Nikolaos Batis
- Institute of Head and Neck Studies and Education, Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham B15 2TT, UK; (J.M.B.); (N.B.); (P.N.); (H.M.)
| | - Boris Noyvert
- Cancer Research UK Birmingham Centre, University of Birmingham, Birmingham B15 2TT, UK; (B.N.); (Y.P.)
- Centre for Computational Biology, University of Birmingham, Birmingham B15 2TT, UK
| | - Yi Pan
- Cancer Research UK Birmingham Centre, University of Birmingham, Birmingham B15 2TT, UK; (B.N.); (Y.P.)
- Centre for Computational Biology, University of Birmingham, Birmingham B15 2TT, UK
| | - Paul Nankivell
- Institute of Head and Neck Studies and Education, Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham B15 2TT, UK; (J.M.B.); (N.B.); (P.N.); (H.M.)
| | - Hisham Mehanna
- Institute of Head and Neck Studies and Education, Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham B15 2TT, UK; (J.M.B.); (N.B.); (P.N.); (H.M.)
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Grossman RL, Dry JR, Hanlon SE, Johann DJ, Kolatkar A, Lee JSH, Meyer C, Salvatore L, Wells W, Leiman L. BloodPAC Data Commons for Liquid Biopsy Data. JCO Clin Cancer Inform 2021; 5:479-486. [PMID: 33929890 PMCID: PMC8140805 DOI: 10.1200/cci.20.00179] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2020] [Revised: 02/16/2021] [Accepted: 03/16/2021] [Indexed: 01/22/2023] Open
Abstract
PURPOSE The Blood Profiling Atlas in Cancer (BloodPAC) Data Commons (BPDC) is being developed and is operated by the public-private BloodPAC Consortium to support the liquid biopsy community. It is an interoperable data commons with the ultimate aim of serving as a recognized source of valid scientific evidence for liquid biopsy assays for industry, academia, and standards and regulatory stakeholders. METHODS The BPDC is implemented using the open source Gen3 data commons platform (https://gen3.org). In particular, the BPDC Data Exploration Portal, BPDC Data Submission Portal, the BPDC Workspace Hub, and the BloodPAC application programming interface (API) were all automatically generated from the BloodPAC Data Model using the Gen3 data commons platform. BPDC uses Gen3's implementation of the data commons framework services so that it can interoperate through secure, compliant APIs with other data commons using data commons framework service, such as National Cancer Institute's Cancer Research Data Commons. RESULTS The BPDC contains 57 studies and projects spanning more than 4,100 cases. This amounts to 5,700 aliquots (blood plasma, serum, or a contrived sample) that have been subjected to a liquid biopsy assay, quantified, and then contributed by members of the BloodPAC Consortium. In all, there are more than 31,000 files in the commons as of December 2020. We describe the BPDC, the data it manages, the process that the BloodPAC Consortium used to develop it, and some of the applications that have been developed using its API. CONCLUSION The BPDC has been the data platform used by BloodPAC during the past 4 years to manage the data for the consortium and to provide workspaces for its working groups.
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Affiliation(s)
- Robert L. Grossman
- Center for Translational Data Science, University of Chicago, Chicago, IL
- Open Commons Consortium, Chicago, IL
| | | | | | | | - Anand Kolatkar
- Convergent Science Institute in Cancer, Michelson Center for Convergent Bioscience, University of Southern California, Los Angeles, CA
| | - Jerry S. H. Lee
- Lawrence J. Ellison Institute for Transformative Medicine, University of Southern California, Los Angeles, CA
| | - Christopher Meyer
- Center for Translational Data Science, University of Chicago, Chicago, IL
| | | | - Walt Wells
- Center for Translational Data Science, University of Chicago, Chicago, IL
- Progressive Insurance, Cleveland, OH
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Large Extracellular Vesicle Characterization and Association with Circulating Tumor Cells in Metastatic Castrate Resistant Prostate Cancer. Cancers (Basel) 2021; 13:cancers13051056. [PMID: 33801459 PMCID: PMC7958848 DOI: 10.3390/cancers13051056] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2021] [Revised: 02/16/2021] [Accepted: 02/24/2021] [Indexed: 01/08/2023] Open
Abstract
Liquid biopsies hold potential as minimally invasive sources of tumor biomarkers for diagnosis, prognosis, therapy prediction or disease monitoring. We present an approach for parallel single-object identification of circulating tumor cells (CTCs) and tumor-derived large extracellular vesicles (LEVs) based on automated high-resolution immunofluorescence followed by downstream multiplexed protein profiling. Identification of LEVs >6 µm in size and CTC enumeration was highly correlated, with LEVs being 1.9 times as frequent as CTCs, and additional LEVs were identified in 73% of CTC-negative liquid biopsy samples from metastatic castrate resistant prostate cancer. Imaging mass cytometry (IMC) revealed that 49% of cytokeratin (CK)-positive LEVs and CTCs were EpCAM-negative, while frequently carrying prostate cancer tumor markers including AR, PSA, and PSMA. HSPD1 was shown to be a specific biomarker for tumor derived circulating cells and LEVs. CTCs and LEVs could be discriminated based on size, morphology, DNA load and protein score but not by protein signatures. Protein profiles were overall heterogeneous, and clusters could be identified across object classes. Parallel analysis of CTCs and LEVs confers increased sensitivity for liquid biopsies and expanded specificity with downstream characterization. Combined, it raises the possibility of a more comprehensive assessment of the disease state for precise diagnosis and monitoring.
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26
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Kahana-Edwin S, Cain LE, Karpelowsky J. Roadmap to Liquid Biopsy Biobanking from Pediatric Cancers-Challenges and Opportunities. Biopreserv Biobank 2021; 19:124-129. [PMID: 33493007 DOI: 10.1089/bio.2020.0117] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Liquid biopsy is rapidly gaining traction for potentially revolutionizing cancer diagnosis and treatment through blood-based utilization of shed biomolecules. This approach can provide a global picture of the cancer in real time, at multiple time points, and with minimal invasiveness. In this review, we familiarize cancer biobanks with the principles used for liquid biopsy work and highlight unique aspects of applying liquid biopsy approaches to pediatric cancers to enable high-quality and efficient translational research.
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Affiliation(s)
- Smadar Kahana-Edwin
- Children's Cancer Research Unit, Kids Research, The Children's Hospital at Westmead, Westmead, Australia
| | - Lucy E Cain
- Children's Cancer Research Unit, Kids Research, The Children's Hospital at Westmead, Westmead, Australia
| | - Jonathan Karpelowsky
- Children's Cancer Research Unit, Kids Research, The Children's Hospital at Westmead, Westmead, Australia
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27
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Fundamentals of liquid biopsies in metastatic prostate cancer: from characterization to stratification. Curr Opin Oncol 2020; 32:527-534. [PMID: 32675591 DOI: 10.1097/cco.0000000000000655] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
PURPOSE OF REVIEW In this review, we provide an overview of the recent developments and prospects on the applications of blood-based liquid biopsies, including circulating tumor DNA and circulating tumor cells, in metastatic prostate cancer. RECENT FINDINGS Guidelines and consensus statements have been formulated to standardize preanalytical conditions that affect liquid biopsy analysis. Currently, there are four FDA approved assays for the analysis of liquid biopsies and many quantitative and qualitative assays are being developed. Comprehensive analyses of cell-free tumor DNA (ctDNA) and circulating tumor cells (CTCs) demonstrate that they adequately reflect the genomic makeup of the tumor and may thus complement or even replace tumor biopsies. The assessment of genomic aberrations in ctDNA can potentially predict therapy response and detect mechanisms of resistance. CTC count is not only a strong prognosticator in metastatic prostate cancer but can also measure therapy response. SUMMARY Liquid biopsies may provide a temporal snapshot of the biologic variables that affect tumor growth and progression in metastatic prostate cancer. Liquid biopsies could inform on prognostic, predictive, and response measures. However, prospective clinical trials need to be performed to provide definitive validation of the clinical value of the most advanced assays.
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Welter L, Xu L, McKinley D, Dago AE, Prabakar RK, Restrepo-Vassalli S, Xu K, Rodriguez-Lee M, Kolatkar A, Nevarez R, Ruiz C, Nieva J, Kuhn P, Hicks J. Treatment response and tumor evolution: lessons from an extended series of multianalyte liquid biopsies in a metastatic breast cancer patient. Cold Spring Harb Mol Case Stud 2020; 6:mcs.a005819. [PMID: 33203646 PMCID: PMC7784493 DOI: 10.1101/mcs.a005819] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2020] [Accepted: 11/15/2020] [Indexed: 12/17/2022] Open
Abstract
Currently, clinical characterization of metastatic breast cancer is based on tissue samples taken at time of diagnosis. However, tissue biopsies are invasive and tumors are continuously evolving, which indicates the need for minimally invasive longitudinal assessment of the tumor. Blood-based liquid biopsies provide minimal invasive means for serial sampling over the course of treatment and the opportunity to adjust therapies based on molecular markers. Here, we aim to identify cellular changes that occur in breast cancer over the lifespan of an affected patient through single-cell proteomic and genomic analysis of longitudinally sampled solid and liquid biopsies. Three solid and 17 liquid biopsies from peripheral blood of an ER+/HER2− metastatic breast cancer patient collected over 4 years and eight treatment regimens were analyzed for morphology, protein expression, copy-number alterations, and single-nucleotide variations. Analysis of 563 single morphometrically similar circulating tumor cells (CTCs) and 13 cell-free DNA (cfDNA) samples along with biopsies of the primary and metastatic tumor revealed progressive genomic evolution away from the primary tumor profiles, along with changes in ER expression and the appearance of resistance mutations. Both the abundance and the genomic alterations of CTCs and cfDNA were highly correlated and consistent with genomic alterations in the tissue samples. We demonstrate that genomic evolution and acquisition of drug resistance can be detected in real time and at single-cell resolution through liquid biopsy analytes and highlight the utility of liquid biopsies to guide treatment decisions.
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Affiliation(s)
- Lisa Welter
- Convergent Science Institute in Cancer, Michelson Center for Convergent Bioscience, University of Southern California, Los Angeles, California 90089, USA
| | - Liya Xu
- Convergent Science Institute in Cancer, Michelson Center for Convergent Bioscience, University of Southern California, Los Angeles, California 90089, USA
| | - Dillon McKinley
- Convergent Science Institute in Cancer, Michelson Center for Convergent Bioscience, University of Southern California, Los Angeles, California 90089, USA
| | - Angel E Dago
- The Scripps Research Institute, La Jolla, California 92037, USA
| | - Rishvanth K Prabakar
- Convergent Science Institute in Cancer, Michelson Center for Convergent Bioscience, University of Southern California, Los Angeles, California 90089, USA
| | - Sara Restrepo-Vassalli
- Convergent Science Institute in Cancer, Michelson Center for Convergent Bioscience, University of Southern California, Los Angeles, California 90089, USA
| | - Kevin Xu
- Convergent Science Institute in Cancer, Michelson Center for Convergent Bioscience, University of Southern California, Los Angeles, California 90089, USA
| | - Mariam Rodriguez-Lee
- Convergent Science Institute in Cancer, Michelson Center for Convergent Bioscience, University of Southern California, Los Angeles, California 90089, USA
| | - Anand Kolatkar
- Convergent Science Institute in Cancer, Michelson Center for Convergent Bioscience, University of Southern California, Los Angeles, California 90089, USA
| | - Rafael Nevarez
- Convergent Science Institute in Cancer, Michelson Center for Convergent Bioscience, University of Southern California, Los Angeles, California 90089, USA
| | - Carmen Ruiz
- Convergent Science Institute in Cancer, Michelson Center for Convergent Bioscience, University of Southern California, Los Angeles, California 90089, USA
| | - Jorge Nieva
- Keck School of Medicine, University of Southern California, Los Angeles, California 90033, USA
| | - Peter Kuhn
- Convergent Science Institute in Cancer, Michelson Center for Convergent Bioscience, University of Southern California, Los Angeles, California 90089, USA.,Keck School of Medicine, University of Southern California, Los Angeles, California 90033, USA.,Viterbi School of Engineering, University of Southern California, Los Angeles, California 90089, USA
| | - James Hicks
- Convergent Science Institute in Cancer, Michelson Center for Convergent Bioscience, University of Southern California, Los Angeles, California 90089, USA
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Assessment of Pre-Analytical Sample Handling Conditions for Comprehensive Liquid Biopsy Analysis. J Mol Diagn 2020; 22:1070-1086. [PMID: 32497717 DOI: 10.1016/j.jmoldx.2020.05.006] [Citation(s) in RCA: 47] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2019] [Revised: 05/05/2020] [Accepted: 05/19/2020] [Indexed: 12/25/2022] Open
Abstract
Liquid biopsies as a minimally invasive approach have the potential to revolutionize molecular diagnostics. Yet, although protocols for sample handling and the isolation of circulating tumor DNA (ctDNA) are numerous, comprehensive guidelines for diagnostics and research considering all aspects of real-life multicenter clinical studies are currently not available. These include limitations in sample volume, transport, and blood collection tubes. We tested the impact of commonly used (EDTA and heparin) and specialized blood collection tubes and storage conditions on the yield and purity of cell-free DNA for the application in down-stream analysis. Moreover, we evaluated the feasibility of a combined workflow for ctDNA and tumor cell genomic testing and parallel flow cytometric analysis of leukocytes. For genomic analyses, EDTA tubes showed good results if stored for a maximum of 4 hours at room temperature or for up to 24 hours when stored at 4°C. Spike-in experiments revealed that EDTA tubes in combination with density gradient centrifugation allowed the parallel isolation of ctDNA, leukocytes, and low amounts of tumor cells (0.1%) and their immunophenotyping by flow cytometry and down-stream genomic analysis by whole genome sequencing. In conclusion, adhering to time and temperature limits allows the use of routine EDTA blood samples for liquid biopsy analyses. We further provide a workflow enabling the parallel analysis of cell-free and cellular features for disease monitoring and for clonal evolution studies.
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30
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Kolenčík D, Shishido SN, Pitule P, Mason J, Hicks J, Kuhn P. Liquid Biopsy in Colorectal Carcinoma: Clinical Applications and Challenges. Cancers (Basel) 2020; 12:E1376. [PMID: 32471160 PMCID: PMC7352156 DOI: 10.3390/cancers12061376] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2020] [Revised: 05/16/2020] [Accepted: 05/25/2020] [Indexed: 12/24/2022] Open
Abstract
Colorectal carcinoma (CRC) is characterized by wide intratumor heterogeneity with general genomic instability and there is a need for improved diagnostic, prognostic, and therapeutic tools. The liquid biopsy provides a noninvasive route of sample collection for analysis of circulating tumor cells (CTCs) and genomic material, including cell-free DNA (cfDNA), as a complementary biopsy to the solid tumor tissue. The solid biopsy is critical for molecular characterization and diagnosis at the time of collection. The liquid biopsy has the advantage of longitudinal molecular characterization of the disease, which is crucial for precision medicine and patient-oriented treatment. In this review, we provide an overview of CRC and the different methodologies for the detection of CTCs and cfDNA, followed by a discussion on the potential clinical utility of the liquid biopsy in CRC patient care, and lastly, current challenges in the field.
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Affiliation(s)
- Drahomír Kolenčík
- Biomedical Centre, Faculty of Medicine in Pilsen, Charles University, 32300 Pilsen, Czech Republic; (D.K.); (P.P.)
| | - 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.S.); (J.M.); (J.H.)
| | - Pavel Pitule
- Biomedical Centre, Faculty of Medicine in Pilsen, Charles University, 32300 Pilsen, Czech Republic; (D.K.); (P.P.)
| | - 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; (S.N.S.); (J.M.); (J.H.)
- USC Institute of Urology, Catherine & Joseph Aresty Department of Urology, 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, Dornsife College of Letters, Arts and Sciences, University of Southern California, Los Angeles, CA 90089, USA; (S.N.S.); (J.M.); (J.H.)
| | - 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.S.); (J.M.); (J.H.)
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31
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Shishido SN, Welter L, Rodriguez-Lee M, Kolatkar A, Xu L, Ruiz C, Gerdtsson AS, Restrepo-Vassalli S, Carlsson A, Larsen J, Greenspan EJ, Hwang ES, Waitman KR, Nieva J, Bethel K, Hicks J, Kuhn P. Preanalytical Variables for the Genomic Assessment of the Cellular and Acellular Fractions of the Liquid Biopsy in a Cohort of Breast Cancer Patients. J Mol Diagn 2020; 22:319-337. [PMID: 31978562 PMCID: PMC7103765 DOI: 10.1016/j.jmoldx.2019.11.006] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2019] [Revised: 08/19/2019] [Accepted: 11/18/2019] [Indexed: 01/02/2023] Open
Abstract
Liquid biopsy allows assessment of multiple analytes, providing temporal information with potential for improving understanding of cancer evolution and clinical management of patients. Although liquid biopsies are intensely investigated for prediction and response monitoring, preanalytic variables are of primary concern for clinical implementation, including categories of collection method and sample storage. Herein, an integrated high-density single-cell assay workflow for morphometric and genomic analysis of the liquid biopsy is used to characterize the effects of preanalytical variation and reproducibility of data from a breast cancer cohort. Following prior work quantifying performance of commonly used blood collection tubes, this study completes the analysis of four time points to assay (24, 48, 72, and 96 hours), demonstrating precision up to 48 hours after collection for assay sensitivity, highly reproducible rare cell enumeration, morphometric characterization, and high efficiency and capacity for single-cell genomic analysis. For the cell-free analysis, both freezing and use of fresh plasma produced similar quality and quantity of cell-free DNA for sequencing. The genomic analysis (copy number variation and single-nucleotide variation) described herein is broadly applicable to liquid biopsy platforms capable of isolating cell-free and cell-based DNA. Morphometric parameters and genomic signatures of individual circulating tumor cells were evaluated in relation to patient clinical response, providing preliminary evidence of clinical validity as a potential biomarker aiding clinical diagnostics or monitoring progression.
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Affiliation(s)
- Stephanie N Shishido
- Department of Biological Sciences, Michelson Center for Convergent Bioscience, University of Southern California, Los Angeles, California
| | - Lisa Welter
- Department of Biological Sciences, Michelson Center for Convergent Bioscience, University of Southern California, Los Angeles, California
| | - Mariam Rodriguez-Lee
- Department of Biological Sciences, Michelson Center for Convergent Bioscience, University of Southern California, Los Angeles, California
| | - Anand Kolatkar
- Department of Biological Sciences, Michelson Center for Convergent Bioscience, University of Southern California, Los Angeles, California
| | - Liya Xu
- Department of Biological Sciences, Michelson Center for Convergent Bioscience, University of Southern California, Los Angeles, California
| | - Carmen Ruiz
- Department of Biological Sciences, Michelson Center for Convergent Bioscience, University of Southern California, Los Angeles, California
| | - Anna S Gerdtsson
- Department of Biological Sciences, Michelson Center for Convergent Bioscience, University of Southern California, Los Angeles, California
| | - Sara Restrepo-Vassalli
- Department of Biological Sciences, Michelson Center for Convergent Bioscience, University of Southern California, Los Angeles, California
| | - Anders Carlsson
- Department of Biological Sciences, Michelson Center for Convergent Bioscience, University of Southern California, Los Angeles, California
| | - Joe Larsen
- Department of Biological Sciences, Michelson Center for Convergent Bioscience, University of Southern California, Los Angeles, California
| | - Emily J Greenspan
- Center for Strategic Scientific Initiatives, National Cancer Institute, Bethesda, Maryland
| | - E Shelley Hwang
- Department of Surgery, Duke University Hospital, Durham, North Carolina
| | | | - Jorge Nieva
- Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, California
| | - Kelly Bethel
- Department of Pathology, Scripps Clinic Medical Group, La Jolla, California
| | - James Hicks
- Department of Biological Sciences, Michelson Center for Convergent Bioscience, University of Southern California, Los Angeles, California
| | - Peter Kuhn
- Department of Biological Sciences, Michelson Center for Convergent Bioscience, University of Southern California, Los Angeles, California.
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32
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Keomanee-Dizon K, Shishido SN, Kuhn P. Circulating Tumor Cells: High-Throughput Imaging of CTCs and Bioinformatic Analysis. Recent Results Cancer Res 2020; 215:89-104. [PMID: 31605225 PMCID: PMC7679175 DOI: 10.1007/978-3-030-26439-0_5] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Circulating tumor cells (CTCs) represent novel biomarkers, since they are obtainable through a simple and noninvasive blood draw or liquid biopsy. Here, we review the high-definition single-cell analysis (HD-SCA) workflow, which brings together modern methods of immunofluorescence with more sophisticated image processing to rapidly and accurately detect rare tumor cells among the milieu of platelets, erythrocytes, and leukocytes in the peripheral blood. In particular, we discuss progress in methods to measure CTC morphology and subcellular protein expression, and we highlight some initial applications that lead to fundamental new insights about the hematogenous phase of cancer, as well as its performance in early-stage diagnosis and treatment monitoring. We end with an outlook on how to further probe CTCs and the unique advantages of the HD-SCA workflow for improving the precision of cancer care.
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Affiliation(s)
- Kevin Keomanee-Dizon
- Convergent Science Institute in Cancer, Michelson Center for Convergent Bioscience, Dornsife College of Letters, Arts and Sciences, University of Southern California, 1002 W. Childs Way, Los Angeles, 90089-3502, CA, United States
- Viterbi School of Engineering, University of Southern California, 1002 W. Childs Way, Los Angeles, CA, 90089, United States
| | - Stephanie N Shishido
- Convergent Science Institute in Cancer, Michelson Center for Convergent Bioscience, Dornsife College of Letters, Arts and Sciences, University of Southern California, 1002 W. Childs Way, Los Angeles, 90089-3502, CA, United States
| | - Peter Kuhn
- Convergent Science Institute in Cancer, Michelson Center for Convergent Bioscience, Dornsife College of Letters, Arts and Sciences, University of Southern California, 1002 W. Childs Way, Los Angeles, 90089-3502, CA, United States.
- Viterbi School of Engineering, University of Southern California, 1002 W. Childs Way, Los Angeles, CA, 90089, United States.
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Gerdtsson AS, Thiele JA, Shishido SN, Zheng S, Schaffer R, Bethel K, Curley S, Lenz HJ, Hanna DL, Nieva J, Kolatkar A, Ruiz C, Rodriguez-Lee M, Oakley III GJ, Lee JS, Hicks J, Kuhn P. Single cell correlation analysis of liquid and solid biopsies in metastatic colorectal cancer. Oncotarget 2019; 10:7016-7030. [PMID: 31903162 PMCID: PMC6925029 DOI: 10.18632/oncotarget.27271] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2019] [Accepted: 09/24/2019] [Indexed: 01/13/2023] Open
Abstract
As cancer care is transitioning to personalized therapies with necessary complementary or companion biomarkers there is significant interest in determining to what extent non-invasive liquid biopsies reflect the gold standard solid biopsy. We have established an approach for measuring patient-specific circulating and solid cell concordance by introducing tumor touch preparations to the High-Definition Single Cell Analysis workflow for high-resolution cytomorphometric characterization of metastatic colorectal cancer (mCRC). Subgroups of cells based on size, shape and protein expression were identified in both liquid and solid biopsies, which overall displayed high inter- and intra- patient pleomorphism at the single-cell level of analysis. Concordance of liquid and solid biopsies was patient-dependent and between 0.1-0.9. Morphometric variables displayed particularly high correlation, suggesting that circulating cells do not represent distinct subpopulations from the solid tumor. This was further substantiated by significant decrease in concentration of circulating cells after mCRC resection. Combined with the association of circulating cells with tumor burden and necrosis of hepatic lesions, our overall findings demonstrate that liquid biopsy cells can be informative biomarkers in the mCRC setting. Patient-specific level of concordance can readily be measured to establish the utility of circulating cells as biomarkers and define biosignatures for liquid biopsy assays.
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Affiliation(s)
- Anna S. Gerdtsson
- USC Michelson Center for Convergent Bioscience, University of Southern California, Los Angeles, CA, USA
| | - Jana-Aletta Thiele
- Biomedical Center, Faculty of Medicine in Pilsen, Charles University, Pilsen, Czech Republic
| | - Stephanie N. Shishido
- USC Michelson Center for Convergent Bioscience, University of Southern California, Los Angeles, CA, USA
| | - Serena Zheng
- USC Michelson Center for Convergent Bioscience, University of Southern California, Los Angeles, CA, USA
| | | | - Kelly Bethel
- Scripps MDAnderson Cancer Center, La Jolla, CA, USA
| | - Steven Curley
- Division of Surgical Oncology, Baylor College of Medicine, Houston, TX, USA
| | - Heinz-Josef Lenz
- Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Diana L. Hanna
- Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Jorge Nieva
- Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Anand Kolatkar
- USC Michelson Center for Convergent Bioscience, University of Southern California, Los Angeles, CA, USA
| | - Carmen Ruiz
- USC Michelson Center for Convergent Bioscience, University of Southern California, Los Angeles, CA, USA
| | - Mariam Rodriguez-Lee
- USC Michelson Center for Convergent Bioscience, University of Southern California, Los Angeles, CA, USA
| | - Gerard J. Oakley III
- Diagnostic and Experimental Pathology, Eli Lilly and Company, Lilly Corporate Center, Indianapolis, IN, USA
| | - Jerry S.H. Lee
- Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - James Hicks
- USC Michelson Center for Convergent Bioscience, University of Southern California, Los Angeles, CA, USA
| | - Peter Kuhn
- USC Michelson Center for Convergent Bioscience, University of Southern California, Los Angeles, CA, USA
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Salvianti F, Gelmini S, Costanza F, Mancini I, Sonnati G, Simi L, Pazzagli M, Pinzani P. The pre-analytical phase of the liquid biopsy. N Biotechnol 2019; 55:19-29. [PMID: 31580920 DOI: 10.1016/j.nbt.2019.09.006] [Citation(s) in RCA: 48] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2019] [Revised: 09/11/2019] [Accepted: 09/26/2019] [Indexed: 02/07/2023]
Abstract
The term 'liquid biopsy', introduced in 2013 in reference to the analysis of circulating tumour cells (CTCs) in cancer patients, was extended to cell-free nucleic acids (cfNAs) circulating in blood and other body fluids. CTCs and cfNAs are now considered diagnostic and prognostic markers, used as surrogate materials for the molecular characterisation of solid tumours, in particular for research on tumour-specific or actionable somatic mutations. Molecular characterisation of cfNAs and CTCs (especially at the single cell level) is technically challenging, requiring highly sensitive and specific methods and/or multi-step processes. The analysis of the liquid biopsy relies on a plethora of methods whose standardisation cannot be accomplished without disclosing criticisms related to the pre-analytical phase. Thus, pre-analytical factors potentially influencing downstream cellular and molecular analyses must be considered in order to translate the liquid biopsy approach into clinical practice. The present review summarises the most recent reports in this field, discussing the main pre-analytical aspects related to CTCs, cfNAs and exosomes in blood samples for liquid biopsy analysis. A short discussion on non-blood liquid biopsy samples is also included.
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Affiliation(s)
- Francesca Salvianti
- Clinical Biochemistry and Clinical Molecular Biology Unit, Department of Experimental and Clinical Biomedical Sciences "Mario Serio", University of Florence, Viale Pieraccini,6, 50139 Florence, Italy
| | - Stefania Gelmini
- Clinical Biochemistry and Clinical Molecular Biology Unit, Department of Experimental and Clinical Biomedical Sciences "Mario Serio", University of Florence, Viale Pieraccini,6, 50139 Florence, Italy.
| | - Filomena Costanza
- Clinical Biochemistry and Clinical Molecular Biology Unit, Department of Experimental and Clinical Biomedical Sciences "Mario Serio", University of Florence, Viale Pieraccini,6, 50139 Florence, Italy
| | - Irene Mancini
- Clinical Biochemistry and Clinical Molecular Biology Unit, Department of Experimental and Clinical Biomedical Sciences "Mario Serio", University of Florence, Viale Pieraccini,6, 50139 Florence, Italy
| | - Gemma Sonnati
- Clinical Biochemistry and Clinical Molecular Biology Unit, Department of Experimental and Clinical Biomedical Sciences "Mario Serio", University of Florence, Viale Pieraccini,6, 50139 Florence, Italy
| | - Lisa Simi
- Molecular and Clinical Biochemistry Laboratory, Careggi University Hospital, Viale Pieraccini,6, 50139 Florence, Italy
| | - Mario Pazzagli
- Clinical Biochemistry and Clinical Molecular Biology Unit, Department of Experimental and Clinical Biomedical Sciences "Mario Serio", University of Florence, Viale Pieraccini,6, 50139 Florence, Italy
| | - Pamela Pinzani
- Clinical Biochemistry and Clinical Molecular Biology Unit, Department of Experimental and Clinical Biomedical Sciences "Mario Serio", University of Florence, Viale Pieraccini,6, 50139 Florence, Italy
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35
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Snow A, Chen D, Lang JE. The current status of the clinical utility of liquid biopsies in cancer. Expert Rev Mol Diagn 2019; 19:1031-1041. [PMID: 31482746 DOI: 10.1080/14737159.2019.1664290] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Introduction: Liquid biopsies have attracted considerable attention as potential diagnostic, prognostic, predictive, and screening assays in oncology. The term liquid biopsies include circulating tumor cells (CTCs) and circulating tumor DNA (ctDNA) in the blood. While many liquid biopsy technologies are under active investigation, relatively few liquid biopsy assays have been proven to serve as a diagnostic surrogate for biopsies of metastatic disease as predictive biomarkers to guide the selection of therapy in the clinic. Areas covered: The objective of this review is to highlight the status of liquid biopsies in solid tumors in the oncology literature with attention to proven utility as diagnostic surrogates for macrometastases. Expert opinion: Carefully designed clinical-translational studies are needed to establish the diagnostic accuracy and clinical utility of liquid biopsy biomarkers in oncology. Investigators must fully consider relevant pre-analytical variables, assay sensitivity, bioinformatics considerations as well as the clinical utility of rare event profiling in the context of the normal blood background. Future liquid biopsy research should address the concern that not all DNA mutations are expressed and should provide the means to discover potential therapeutic targets in metastatic patients via a minimally invasive blood draw.
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Affiliation(s)
- Anson Snow
- Department of Surgery, University of Southern California Norris Comprehensive Cancer Center , Los Angeles , CA , USA
| | - Denaly Chen
- Department of Medicine, University of Southern California Norris Comprehensive Cancer Center , Los Angeles , CA , USA
| | - Julie E Lang
- Department of Surgery, University of Southern California Norris Comprehensive Cancer Center , Los Angeles , CA , USA
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Shishido SN, Carlsson A, Nieva J, Bethel K, Hicks JB, Bazhenova L, Kuhn P. Circulating tumor cells as a response monitor in stage IV non-small cell lung cancer. J Transl Med 2019; 17:294. [PMID: 31462312 PMCID: PMC6714097 DOI: 10.1186/s12967-019-2035-8] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2019] [Accepted: 08/18/2019] [Indexed: 12/22/2022] Open
Abstract
BACKGROUND Monitoring circulating tumor cells (CTC) has been shown to be prognostic in most solid malignancies. There is no CTC assay in clinical use for lung cancer therapy monitoring due to inconclusive clinical utility data. Limited data has been published outside of the standard CTC enumerations, regarding clinical significance of phenotypic heterogeneity of CTCs in late stage NSCLC and its ability to correlate with treatment outcomes. METHODS In 81 patients with stage IV NSCLC, multiple timepoints for CTC analysis were collected after initiation of treatment across 139 lines of therapy using single cell high definition diagnostic pathology imaging of all nucleated cells from 362 peripheral blood samples as a liquid biopsy. RESULTS We analyzed the subset of 25 patients with complete time series data, totaling 117 blood samples, to determine the significance of HD-CTC kinetics during the initiation of treatment. These kinetics follow three distinct patterns: an increase in HD-CTCs with therapy (mean + 118.40 HD-CTCs/mL), unchanged HD-CTCs numbers (stable; mean 0.54 HD-CTCs/mL), and a decrease in HD-CTCs numbers (mean - 81.40 HD-CTCs/mL). Patients with an increasing CTC count during the first 3 months post initiation of new treatment had a better PFS and OS compared to the other groups. There was weak correlation between the absolute number of HD-CTCs at a single time point of therapy and patient outcomes (OS p value = 0.0754). In the whole cohort of 81 patients, HD-CTCs were detected in 51 (63%) patients at initiation of therapy with a median of 2.20 (range 0-509.20) and a mean of 26.21 HD-CTCs/mL (± 15.64). CONCLUSIONS CTCs are identifiable in most patients with stage IV NSCLC. While absolute HD-CTC counts do not correlate with prognosis, the changes in CTC counts were predictive of survival in patients with metastatic lung cancer receiving chemotherapy. The level and dynamics of CTCs indicate very different biological and pharmacological phenomena at different stages of disease and timepoints of treatment, highlighting the complex role of CTCs in cancer research and clinical management.
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Affiliation(s)
- Stephanie N. Shishido
- Michelson Center for Convergent Bioscience, Dornsife College of Letters, Arts and Sciences, University of Southern California, 1002 W Childs Way, MCB351, MC:3502, Los Angeles, CA 90089-3502 USA
| | - Anders Carlsson
- Michelson Center for Convergent Bioscience, Dornsife College of Letters, Arts and Sciences, University of Southern California, 1002 W Childs Way, MCB351, MC:3502, Los Angeles, CA 90089-3502 USA
| | - Jorge Nieva
- University of Southern California, 1441 Eastlake Avenue, Suite 3440, Los Angeles, CA 90033 USA
| | - Kelly Bethel
- Scripps Clinic, Department of Pathology, 10666 North Torrey Pines Road, MC211C, La Jolla, CA 92037 USA
| | - James B. Hicks
- Michelson Center for Convergent Bioscience, Dornsife College of Letters, Arts and Sciences, University of Southern California, 1002 W Childs Way, MCB351, MC:3502, Los Angeles, CA 90089-3502 USA
| | - Lyudmila Bazhenova
- Moores Cancer Center, University of California San Diego, 3855 Health Sciences Dr, La Jolla, CA 92093 USA
| | - Peter Kuhn
- Michelson Center for Convergent Bioscience, Dornsife College of Letters, Arts and Sciences, University of Southern California, 1002 W Childs Way, MCB351, MC:3502, Los Angeles, CA 90089-3502 USA
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37
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Lianidou E, Pantel K. Liquid biopsies. Genes Chromosomes Cancer 2019; 58:219-232. [PMID: 30382599 DOI: 10.1002/gcc.22695] [Citation(s) in RCA: 101] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2018] [Revised: 08/28/2018] [Accepted: 10/01/2018] [Indexed: 02/06/2023] Open
Abstract
Liquid biopsy is based on minimally invasive blood tests and has a high potential to significantly change the therapeutic strategy in cancer patients, providing an extremely powerful and reliable noninvasive clinical tool for the individual molecular profiling of patients in real time. Liquid biopsy approaches include the analysis of circulating tumor cells (CTCs), circulating tumor DNA (ctDNA), circulating miRNAs, and tumor-derived extracellular vesicles (EVs) that are shed from primary tumors and their metastatic sites into peripheral blood. The major advantage of liquid biopsy analysis is that it is minimally invasive, and can be serially repeated, thus allowing extracting information from the tumor in real time. Moreover, the identification of predictive biomarkers in peripheral blood that can monitor response to therapy in real time holds a very strong potential for novel approaches in the therapeutic management of cancer patients. In this review, we summarize recent knowledge on CTCs and ctDNA and discuss future trends in the field.
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Affiliation(s)
- Evi Lianidou
- Analysis of Circulating Tumor Cells Laboratory, Department of Chemistry, University of Athens, Athens, Greece
| | - Klaus Pantel
- Department of Tumor Biology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
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Abstract
Circulating tumor cells (CTCs) have long been assumed to be the substrate of cancer metastasis. However, only in recent years have we begun to leverage the potential of CTCs found in minimally invasive peripheral blood specimens to improve care for cancer patients. Currently, CTC enumeration is an accepted prognostic indicator for breast, prostate, and colorectal cancer; however, CTC enumeration remains largely a research tool. More recently, the focus has shifted to CTC characterization and isolation which holds great promise for predictive testing. This review summarizes the relevant clinical, biological, and technical background necessary for pathologists and cytopathologists to appreciate the potential of CTC techniques. A summary of relevant systematic reviews of CTCs for specific cancers is then presented, as well as potential applications to precision medicine. Finally, we suggest future applications of CTC technologies that can be easily incorporated in the pathology laboratory, with the recommendation that pathologists and particularly cytopathologists apply these technologies to small specimens in the era of "doing more with less."
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Zavridou M, Mastoraki S, Strati A, Tzanikou E, Chimonidou M, Lianidou E. Evaluation of Preanalytical Conditions and Implementation of Quality Control Steps for Reliable Gene Expression and DNA Methylation Analyses in Liquid Biopsies. Clin Chem 2018; 64:1522-1533. [DOI: 10.1373/clinchem.2018.292318] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2018] [Accepted: 06/28/2018] [Indexed: 01/09/2023]
Abstract
Abstract
BACKGROUND
Liquid biopsy provides important information for the prognosis and treatment of cancer patients. In this study, we evaluated the effects of preanalytical conditions on gene expression and DNA methylation analyses in liquid biopsies.
METHODS
We tested the stability of circulating tumor cell (CTC) messenger RNA by spiking MCF-7 cells in healthy donor peripheral blood (PB) drawn into 6 collection-tube types with various storage conditions. CTCs were enriched based on epithelial cell adhesion molecule positivity, and RNA was isolated followed by cDNA synthesis. Gene expression was quantified using RT-quantitative PCR for CK19 and B2M. We evaluated the stability of DNA methylation in plasma under different storage conditions by spiking DNA isolated from MCF-7 cells in healthy donor plasma. Two commercially available sodium bisulfite (SB)-conversion kits were compared, in combination with whole genome amplification (WGA), to evaluate the stability of SB-converted DNA. SB-converted DNA samples were analyzed by real-time methylation-specific PCR (MSP) for ACTB, SOX17, and BRMS1. Quality control was assessed using Levey–Jennings graphs.
RESULTS
RNA-based analysis in CTCs is severely impeded by the preservatives used in many PB collection tubes (except for EDTA), as well as by time to analysis. Plasma and SB-converted DNA samples are stable and can be used safely for MSP when kept at −80 °C. Downstream WGA of SB-converted DNA compensated for the limited amount of available sample in liquid biopsies.
CONCLUSIONS
Standardization of preanalytical conditions and implementation of quality control steps is extremely important for reliable liquid biopsy analysis, and a prerequisite for routine applications in the clinic.
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Affiliation(s)
- Martha Zavridou
- Analysis of Circulating Tumor Cells, Lab of Analytical Chemistry, Department of Chemistry, University of Athens, Athens, Greece
| | - Sofia Mastoraki
- Analysis of Circulating Tumor Cells, Lab of Analytical Chemistry, Department of Chemistry, University of Athens, Athens, Greece
| | - Areti Strati
- Analysis of Circulating Tumor Cells, Lab of Analytical Chemistry, Department of Chemistry, University of Athens, Athens, Greece
| | - Eleni Tzanikou
- Analysis of Circulating Tumor Cells, Lab of Analytical Chemistry, Department of Chemistry, University of Athens, Athens, Greece
| | - Maria Chimonidou
- Analysis of Circulating Tumor Cells, Lab of Analytical Chemistry, Department of Chemistry, University of Athens, Athens, Greece
| | - Evi Lianidou
- Analysis of Circulating Tumor Cells, Lab of Analytical Chemistry, Department of Chemistry, University of Athens, Athens, Greece
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