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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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Seo J, Kumar M, Mason J, Blackhall F, Matsumoto N, Dive C, Hicks J, Kuhn P, Shishido SN. Plasticity of circulating tumor cells in small cell lung cancer. Sci Rep 2023; 13:11775. [PMID: 37479829 PMCID: PMC10362013 DOI: 10.1038/s41598-023-38881-5] [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: 03/15/2023] [Accepted: 07/17/2023] [Indexed: 07/23/2023] Open
Abstract
Small cell lung cancer (SCLC) is an aggressive neuroendocrine tumor with low five-year survival rates. Recently described molecular phenotypes of SCLC exhibit differential vulnerabilities heralding potential for stratified treatment. Whilst tumor biopsy in SCLC is challenging, circulating tumor cells in the liquid biopsy are prevalent and can be repeatedly sampled accommodating the dynamic plasticity of SCLC phenotypes. The aim of this study was to characterize the heterogeneity of rare circulating cells with confirmed tumor origin and to explore a liquid biopsy approach for future clinical trials of targeted therapies. This study applied the 3rd generation of a previously validated direct imaging platform to 14 chemo-naive SCLC patients and 10 non-cancerous normal donor (ND) samples. Phenotypic heterogeneity of circulating rare cells in SCLC was observed and a patient-level classification model was established to stratify SCLC patients from non-cancerous donors. Eight rare cell groups, with combinations of epithelial, endothelial, and mesenchymal biomarker expression patterns, were phenotypically characterized. The single-cell genomic analysis confirmed the cancer cell plasticity in every rare cell group harboring clonal genomic alterations. This study shows rare cell heterogeneity and confirms cellular plasticity in SCLC providing a valuable resource for better opportunities to discover novel therapeutic targets in SCLC.
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Affiliation(s)
- Jiyoun Seo
- Convergent Science Institute in Cancer, Michelson Center for Convergent Bioscience, University of Southern California, Los Angeles, CA, 90089, USA
| | - Mihir Kumar
- Convergent Science Institute in Cancer, Michelson Center for Convergent Bioscience, 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
- Institute of Urology, Catherine & Joseph Aresty Department of Urology, Keck School of Medicine, University of Southern California, Los Angeles, CA, 90033, USA
- Keck School of Medicine, Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, CA, 90033, USA
| | - Fiona Blackhall
- Department of Medical Oncology, The Christie NHS Foundation Trust, Manchester, UK
| | - Nicholas Matsumoto
- Convergent Science Institute in Cancer, Michelson Center for Convergent Bioscience, University of Southern California, Los Angeles, CA, 90089, USA
| | - Caroline Dive
- Cancer Research UK Lung Cancer Centre of Excellence, University of Manchester and University College London, Manchester, UK
- CRUK Manchester Institute Cancer Biomarker Centre, University of Manchester, Manchester, UK
| | - James Hicks
- Convergent Science Institute in Cancer, Michelson Center for Convergent Bioscience, University of Southern California, Los Angeles, CA, 90089, USA
- Department of Biological Sciences, Dornsife College of Letters, Arts, and Sciences, University of Southern California, Los Angeles, CA, 90089, USA
| | - Peter Kuhn
- Convergent Science Institute in Cancer, Michelson Center for Convergent Bioscience, 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.
- Keck School of Medicine, Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, CA, 90033, USA.
- Department of Biological Sciences, Dornsife College of Letters, Arts, and Sciences, University of Southern California, Los Angeles, CA, 90089, USA.
- Department of Aerospace and Mechanical Engineering, Viterbi School of Engineering, University of Southern California, Los Angeles, CA, 90089, USA.
- 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.
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3
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Cerón R, Martínez A, Ramos C, De la Cruz A, García A, Mendoza I, Palmeros G, Montaño Figueroa EH, Navarrete J, Jiménez-Morales S, Martinez-Murillo C, Olarte I. Overexpression of BCL2, BCL6, VEGFR1 and TWIST1 in Circulating Tumor Cells Derived from Patients with DLBCL Decreases Event-Free Survival. Onco Targets Ther 2022; 15:1583-1595. [PMID: 36606244 PMCID: PMC9809418 DOI: 10.2147/ott.s386562] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2022] [Accepted: 12/08/2022] [Indexed: 12/31/2022] Open
Abstract
Purpose Diffuse large B-cell lymphoma (DLBCL) is a heterogeneous malignant lymphoid neoplasm and is the most common subtype of non-Hodgkin lymphoma in adults. More than half of patients with DLBCL can achieve remission with standard R-CHOP regimes; however, approximately 30-40% of patients are still failing this standard therapy, which remains as an important cause of progression and mortality of this disease. It is necessary to have diagnostic and monitoring tools that allow us to improve the accuracy of prognosis in these patients. Circulating tumor cells (CTCs) identification through molecular biomarkers is one of the novel strategies that have been used in other types of cancer, and we aim to use this tool to analyze the potential role in DLBCL. Patients and Methods We analyzed 138 blood samples of patients with DLBCL, of which CTCs were isolated by density gradient for subsequent detection and quantitation of molecular biomarkers using RT-qPCR with TaqMan probes. Survival analysis was performed using Kaplan-Meier curves. Results We found overexpression of ABCB1, αSMA, BCL2, BCL6 and VEGFR1 genes, as well as the presence of CK19, EpCAM, KI67, MAGE-A4, SNAIL and TWIST1 genes. CK19 and EpCAM expression were associated with a minor OS (85.7% vs 98.1%, p = 0.002). The overexpression of BCL2, BCL6, VEGFR1 and TWIST1 was related to a minor EFS (p = 0.001). Conclusion This study showed that in liquid biopsies analyzed, the presence of CTCs can be confirmed through molecular biomarkers, and it has an impact on OS and EFs, making this detection useful in the follow-up and prognosis of patients with DLBCL.
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Affiliation(s)
- Rafael Cerón
- Posgrado en Ciencias Biológicas, Biomedicina, UNAM, CDMX, México,Department of Molecular Biology, Hematology Service, Hospital General de México, “Dr. Eduardo Liceaga”, Mexico City, Mexico
| | - Adolfo Martínez
- Department of Molecular Biology, Hematology Service, Hospital General de México, “Dr. Eduardo Liceaga”, Mexico City, Mexico
| | - Christian Ramos
- Department of Medical Hematology, Hospital General de México, “Dr. Eduardo Liceaga”, Mexico City, Mexico
| | - Adrián De la Cruz
- Department of Molecular Biology, Hematology Service, Hospital General de México, “Dr. Eduardo Liceaga”, Mexico City, Mexico
| | - Anel García
- Department of Molecular Biology, Hematology Service, Hospital General de México, “Dr. Eduardo Liceaga”, Mexico City, Mexico
| | - Iveth Mendoza
- Department of Molecular Biology, Hematology Service, Hospital General de México, “Dr. Eduardo Liceaga”, Mexico City, Mexico
| | - Goujon Palmeros
- Department of Molecular Biology, Hematology Service, Hospital General de México, “Dr. Eduardo Liceaga”, Mexico City, Mexico
| | | | - Juan Navarrete
- Department of Hematopathology, Hospital General de México, “Dr. Eduardo Liceaga”, Mexico City, Mexico
| | - Silvia Jiménez-Morales
- Laboratory of Cancer Genomics, National Institute of Genomic Medicine, Mexico City, Mexico
| | - Carlos Martinez-Murillo
- Department of Medical Hematology, Hospital General de México, “Dr. Eduardo Liceaga”, Mexico City, Mexico
| | - Irma Olarte
- Department of Molecular Biology, Hematology Service, Hospital General de México, “Dr. Eduardo Liceaga”, Mexico City, Mexico,Correspondence: Irma Olarte, Dr. Balmis 148, Col. Doctores, Alc. Cuauhtémoc, Mexico City, ZC. 06726, Mexico, Tel +525527892000 Ext. 1609, Email
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Characterization of BCMA Expression in Circulating Rare Single Cells of Patients with Plasma Cell Neoplasms. Int J Mol Sci 2022; 23:ijms232113427. [PMID: 36362214 PMCID: PMC9658574 DOI: 10.3390/ijms232113427] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2022] [Revised: 10/21/2022] [Accepted: 10/30/2022] [Indexed: 11/06/2022] Open
Abstract
B-cell maturation antigen (BCMA), a key regulator of B-cell proliferation and survival, is highly expressed in almost all cases of plasma cell neoplasms and B-lymphoproliferative malignancies. BCMA is a robust biomarker of plasma cells and a therapeutic target with substantial clinical significance. However, the expression of BCMA in circulating tumor cells of patients with hematological malignancies has not been validated for the detection of circulating plasma and B cells. The application of BCMA as a biomarker in single-cell detection and profiling of circulating tumor cells in patients' blood could enable early disease profiling and therapy response monitoring. Here, we report the development and validation of a slide-based immunofluorescence assay (i.e., CD138, BCMA, CD45, DAPI) for enrichment-free detection, quantification, and morphogenomic characterization of BCMA-expressing cells in patients (N = 9) with plasma cell neoplasms. Varying morphological subtypes of circulating BCMA-expressing cells were detected across the CD138(+/-) and CD45(+/-) compartments, representing candidate clonotypic post-germinal center B cells, plasmablasts, and both normal and malignant plasma cells. Genomic analysis by single-cell sequencing and correlation to clinical FISH cytogenetics provides validation, with data showing that patients across the different neoplastic states carry both normal and altered BCMA-expressing cells. Furthermore, altered cells harbor cytogenetic events detected by clinical FISH. The reported enrichment-free liquid biopsy approach has potential applications as a single-cell methodology for the early detection of BCMA+ B-lymphoid malignancies and in monitoring therapy response for patients undergoing anti-BCMA treatments.
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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: 0] [Impact Index Per Article: 0] [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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Khan T, Becker TM, Po JW, Chua W, Ma Y. Single-Circulating Tumor Cell Whole Genome Amplification to Unravel Cancer Heterogeneity and Actionable Biomarkers. Int J Mol Sci 2022; 23:ijms23158386. [PMID: 35955517 PMCID: PMC9369222 DOI: 10.3390/ijms23158386] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2022] [Revised: 07/25/2022] [Accepted: 07/27/2022] [Indexed: 12/04/2022] Open
Abstract
The field of single-cell analysis has advanced rapidly in the last decade and is providing new insights into the characterization of intercellular genetic heterogeneity and complexity, especially in human cancer. In this regard, analyzing single circulating tumor cells (CTCs) is becoming particularly attractive due to the easy access to CTCs from simple blood samples called “liquid biopsies”. Analysis of multiple single CTCs has the potential to allow the identification and characterization of cancer heterogeneity to guide best therapy and predict therapeutic response. However, single-CTC analysis is restricted by the low amounts of DNA in a single cell genome. Whole genome amplification (WGA) techniques have emerged as a key step, enabling single-cell downstream molecular analysis. Here, we provide an overview of recent advances in WGA and their applications in the genetic analysis of single CTCs, along with prospective views towards clinical applications. First, we focus on the technical challenges of isolating and recovering single CTCs and then explore different WGA methodologies and recent developments which have been utilized to amplify single cell genomes for further downstream analysis. Lastly, we list a portfolio of CTC studies which employ WGA and single-cell analysis for genetic heterogeneity and biomarker detection.
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Affiliation(s)
- Tanzila Khan
- School of Medicine, Western Sydney University, Campbelltown, NSW 2560, Australia; (T.K.); (T.M.B.); (W.C.)
- Medical Oncology, Ingham Institute of Applied Medical Research, Liverpool, NSW 2170, Australia
- Centre of Circulating Tumor Cells Diagnostics & Research, Ingham Institute of Applied Medical Research, Liverpool, NSW 2170, Australia;
| | - Therese M. Becker
- School of Medicine, Western Sydney University, Campbelltown, NSW 2560, Australia; (T.K.); (T.M.B.); (W.C.)
- Medical Oncology, Ingham Institute of Applied Medical Research, Liverpool, NSW 2170, Australia
- Centre of Circulating Tumor Cells Diagnostics & Research, Ingham Institute of Applied Medical Research, Liverpool, NSW 2170, Australia;
- South West Sydney Clinical School, University of New South Wales, Liverpool, NSW 2170, Australia
| | - Joseph W. Po
- Centre of Circulating Tumor Cells Diagnostics & Research, Ingham Institute of Applied Medical Research, Liverpool, NSW 2170, Australia;
- Surgical Innovations Unit, Westmead Hospital, Westmead, NSW 2145, Australia
| | - Wei Chua
- School of Medicine, Western Sydney University, Campbelltown, NSW 2560, Australia; (T.K.); (T.M.B.); (W.C.)
- Medical Oncology, Liverpool Hospital, Liverpool, NSW 2170, Australia
| | - Yafeng Ma
- School of Medicine, Western Sydney University, Campbelltown, NSW 2560, Australia; (T.K.); (T.M.B.); (W.C.)
- Medical Oncology, Ingham Institute of Applied Medical Research, Liverpool, NSW 2170, Australia
- Centre of Circulating Tumor Cells Diagnostics & Research, Ingham Institute of Applied Medical Research, Liverpool, NSW 2170, Australia;
- South West Sydney Clinical School, University of New South Wales, Liverpool, NSW 2170, Australia
- Correspondence:
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Liquid Biopsy Landscape in Patients with Primary Upper Tract Urothelial Carcinoma. Cancers (Basel) 2022; 14:cancers14123007. [PMID: 35740671 PMCID: PMC9221424 DOI: 10.3390/cancers14123007] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2022] [Revised: 06/07/2022] [Accepted: 06/10/2022] [Indexed: 01/27/2023] Open
Abstract
Urothelial carcinomas (UCs) are a broad and heterogeneous group of malignancies, with the prevalence of upper tract urothelial carcinoma (UTUC) being rare, accounting for only 5-10% of total malignancies. There is a need for additional toolsets to assist the current clinical paradigm of care for patients with UTUC. As a non-invasive tool for the discovery of cancer-related biomarkers, the liquid biopsy has the potential to represent the complex process of tumorigenesis and metastasis. Herein, we show the efficacy of the liquid biopsy as a source of biomarkers for detecting UTUC. Using the third-generation high-definition single-cell assay (HDSCA3.0) workflow, we investigate liquid biopsy samples collected from patients with UTUC and normal donors (NDs) to provide critical information regarding the molecular and morphological characteristics of circulating rare events. We document several important findings from the liquid biopsy analysis of patients diagnosed with UTUC prior to surgery: (1) Large extracellular vesicles (LEVs) and circulating tumor cells (CTCs) are detectable in the peripheral blood. (2) The rare-event profile is highly heterogeneous. (3) Clinical data elements correlate with liquid biopsy analytes. Overall, this study provides evidence for the efficacy of the liquid biopsy in understanding the biology of UTUC with the future intent of informing clinical decision making, ultimately improving patient outcomes.
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Ndacayisaba LJ, Rappard KE, Shishido SN, Ruiz Velasco C, Matsumoto N, Navarez R, Tang G, Lin P, Setayesh SM, Naghdloo A, Hsu CJ, Maney C, Symer D, Bethel K, Kelly K, Merchant A, Orlowski R, Hicks J, Mason J, Manasanch EE, Kuhn P. Enrichment-Free Single-Cell Detection and Morphogenomic Profiling of Myeloma Patient Samples to Delineate Circulating Rare Plasma Cell Clones. Curr Oncol 2022; 29:2954-2972. [PMID: 35621632 PMCID: PMC9139906 DOI: 10.3390/curroncol29050242] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2022] [Revised: 04/07/2022] [Accepted: 04/18/2022] [Indexed: 01/27/2023] Open
Abstract
Multiple myeloma is an incurable malignancy that initiates from a bone marrow resident clonal plasma cell and acquires successive mutational changes and genomic alterations, eventually resulting in tumor burden accumulation and end-organ damage. It has been recently recognized that myeloma secondary genomic events result in extensive sub-clonal heterogeneity both in localized bone marrow areas and circulating peripheral blood plasma cells. Rare genomic subclones, including myeloma initiating cells, could be the drivers of disease progression and recurrence. Additionally, evaluation of rare myeloma cells in blood for disease monitoring has numerous advantages over invasive bone marrow biopsies. To this end, an unbiased method for detecting rare cells and delineating their genomic makeup enables disease detection and monitoring in conditions with low abundant cancer cells. In this study, we applied an enrichment-free four-plex (CD138, CD56, CD45, DAPI) immunofluorescence assay and single-cell DNA sequencing for morphogenomic characterization of plasma cells to detect and delineate common and rare plasma cells and discriminate between normal and malignant plasma cells in paired blood and bone marrow aspirates from five patients with newly diagnosed myeloma (N = 4) and monoclonal gammopathy of undetermined significance (n = 1). Morphological analysis confirms CD138+CD56+ cells in the peripheral blood carry genomic alterations that are clonally identical to those in the bone marrow. A subset of altered CD138+CD56- cells are also found in the peripheral blood consistent with the known variability in CD56 expression as a marker of plasma cell malignancy. Bone marrow tumor clinical cytogenetics is highly correlated with the single-cell copy number alterations of the liquid biopsy rare cells. A subset of rare cells harbors genetic alterations not detected by standard clinical diagnostic methods of random localized bone marrow biopsies. This enrichment-free morphogenomic approach detects and characterizes rare cell populations derived from the liquid biopsies that are consistent with clinical diagnosis and have the potential to extend our understanding of subclonality at the single-cell level in this disease. Assay validation in larger patient cohorts has the potential to offer liquid biopsy for disease monitoring with similar or improved disease detection as traditional blind bone marrow biopsies.
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Affiliation(s)
- Libere J. Ndacayisaba
- Convergent Science Institute in Cancer, Michelson Center for Convergent Bioscience, University of Southern California, Los Angeles, CA 90089, USA; (L.J.N.); (K.E.R.); (S.N.S.); (C.R.V.); (N.M.); (R.N.); (S.M.S.); (A.N.); (C.-J.H.); (C.M.); (J.H.); (J.M.)
- Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA;
| | - Kate E. Rappard
- Convergent Science Institute in Cancer, Michelson Center for Convergent Bioscience, University of Southern California, Los Angeles, CA 90089, USA; (L.J.N.); (K.E.R.); (S.N.S.); (C.R.V.); (N.M.); (R.N.); (S.M.S.); (A.N.); (C.-J.H.); (C.M.); (J.H.); (J.M.)
| | - Stephanie N. Shishido
- Convergent Science Institute in Cancer, Michelson Center for Convergent Bioscience, University of Southern California, Los Angeles, CA 90089, USA; (L.J.N.); (K.E.R.); (S.N.S.); (C.R.V.); (N.M.); (R.N.); (S.M.S.); (A.N.); (C.-J.H.); (C.M.); (J.H.); (J.M.)
| | - Carmen Ruiz Velasco
- Convergent Science Institute in Cancer, Michelson Center for Convergent Bioscience, University of Southern California, Los Angeles, CA 90089, USA; (L.J.N.); (K.E.R.); (S.N.S.); (C.R.V.); (N.M.); (R.N.); (S.M.S.); (A.N.); (C.-J.H.); (C.M.); (J.H.); (J.M.)
| | - Nicholas Matsumoto
- Convergent Science Institute in Cancer, Michelson Center for Convergent Bioscience, University of Southern California, Los Angeles, CA 90089, USA; (L.J.N.); (K.E.R.); (S.N.S.); (C.R.V.); (N.M.); (R.N.); (S.M.S.); (A.N.); (C.-J.H.); (C.M.); (J.H.); (J.M.)
| | - Rafael Navarez
- Convergent Science Institute in Cancer, Michelson Center for Convergent Bioscience, University of Southern California, Los Angeles, CA 90089, USA; (L.J.N.); (K.E.R.); (S.N.S.); (C.R.V.); (N.M.); (R.N.); (S.M.S.); (A.N.); (C.-J.H.); (C.M.); (J.H.); (J.M.)
| | - Guilin Tang
- Department of Hematopathology, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA; (G.T.); (P.L.)
| | - Pei Lin
- Department of Hematopathology, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA; (G.T.); (P.L.)
| | - Sonia M. Setayesh
- Convergent Science Institute in Cancer, Michelson Center for Convergent Bioscience, University of Southern California, Los Angeles, CA 90089, USA; (L.J.N.); (K.E.R.); (S.N.S.); (C.R.V.); (N.M.); (R.N.); (S.M.S.); (A.N.); (C.-J.H.); (C.M.); (J.H.); (J.M.)
| | - Amin Naghdloo
- Convergent Science Institute in Cancer, Michelson Center for Convergent Bioscience, University of Southern California, Los Angeles, CA 90089, USA; (L.J.N.); (K.E.R.); (S.N.S.); (C.R.V.); (N.M.); (R.N.); (S.M.S.); (A.N.); (C.-J.H.); (C.M.); (J.H.); (J.M.)
| | - Ching-Ju Hsu
- Convergent Science Institute in Cancer, Michelson Center for Convergent Bioscience, University of Southern California, Los Angeles, CA 90089, USA; (L.J.N.); (K.E.R.); (S.N.S.); (C.R.V.); (N.M.); (R.N.); (S.M.S.); (A.N.); (C.-J.H.); (C.M.); (J.H.); (J.M.)
| | - Carlisle Maney
- Convergent Science Institute in Cancer, Michelson Center for Convergent Bioscience, University of Southern California, Los Angeles, CA 90089, USA; (L.J.N.); (K.E.R.); (S.N.S.); (C.R.V.); (N.M.); (R.N.); (S.M.S.); (A.N.); (C.-J.H.); (C.M.); (J.H.); (J.M.)
| | - David Symer
- Department of Lymphoma/Myeloma, Division of Cancer Medicine, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA; (D.S.); (R.O.); (E.E.M.)
| | - Kelly Bethel
- Department of Pathology, Scripps Clinic Medical Group, La Jolla, CA 92037, USA;
| | - Kevin Kelly
- Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA;
| | - Akil Merchant
- Department of Medicine, Cedars Sinai Medical Center, Los Angeles, CA 90048, USA;
| | - Robert Orlowski
- Department of Lymphoma/Myeloma, Division of Cancer Medicine, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA; (D.S.); (R.O.); (E.E.M.)
| | - James Hicks
- Convergent Science Institute in Cancer, Michelson Center for Convergent Bioscience, University of Southern California, Los Angeles, CA 90089, USA; (L.J.N.); (K.E.R.); (S.N.S.); (C.R.V.); (N.M.); (R.N.); (S.M.S.); (A.N.); (C.-J.H.); (C.M.); (J.H.); (J.M.)
- Department of Pathology, Scripps Clinic Medical Group, La Jolla, CA 92037, USA;
| | - Jeremy Mason
- Convergent Science Institute in Cancer, Michelson Center for Convergent Bioscience, University of Southern California, Los Angeles, CA 90089, USA; (L.J.N.); (K.E.R.); (S.N.S.); (C.R.V.); (N.M.); (R.N.); (S.M.S.); (A.N.); (C.-J.H.); (C.M.); (J.H.); (J.M.)
- Institute of Urology, Catherine & Joseph Aresty Department of Urology, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA
- Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA
| | - Elisabeth E. Manasanch
- Department of Lymphoma/Myeloma, Division of Cancer Medicine, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA; (D.S.); (R.O.); (E.E.M.)
| | - Peter Kuhn
- Convergent Science Institute in Cancer, Michelson Center for Convergent Bioscience, University of Southern California, Los Angeles, CA 90089, USA; (L.J.N.); (K.E.R.); (S.N.S.); (C.R.V.); (N.M.); (R.N.); (S.M.S.); (A.N.); (C.-J.H.); (C.M.); (J.H.); (J.M.)
- Institute of Urology, Catherine & Joseph Aresty Department of Urology, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA
- Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA
- Department of Biomedical Engineering, Viterbi School of Engineering, University of Southern California, Los Angeles, CA 90089, USA
- Department of Aerospace and Mechanical Engineering, Viterbi School of Engineering, University of Southern California, Los Angeles, CA 90089, USA
- Department of Biological Sciences, Dornsife College of Letters, Arts, and Sciences, University of Southern California, Los Angeles, CA 90089, USA
- Correspondence: ; Tel.: +1-213-821-3980
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9
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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:cancers14030758. [PMID: 35159025 PMCID: PMC8833768 DOI: 10.3390/cancers14030758] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [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
- Correspondence: (P.K.); (J.M.); Tel.: +1-213-821-3980 (P.K.)
| | - 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;
- Correspondence: (P.K.); (J.M.); Tel.: +1-213-821-3980 (P.K.)
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10
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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:cancers14030642. [PMID: 35158910 PMCID: PMC8833610 DOI: 10.3390/cancers14030642] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [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
Simple Summary As a minimally invasive procedure, the liquid biopsy enables the longitudinal evaluation of a patient’s disease and response to treatment. Current clinical practice stratifies patient status based on a uniform threshold for circulating tumor cell (CTC) positivity, overlooking various cell subtypes and timepoints of sample collection. In a disease known for its tumor heterogeneity, we investigated colorectal cancer patients’ peripheral blood samples to determine whether the prevalence of morphologically distinct CTC subtypes and time-points of sample collection correlate with clinical disease hallmarks and survival data. Our results highlight nuances between the CTC subtypes’ clinical and survival significance. Furthermore, we found that time-point-conscious cell enumeration is critical, both for determining CTC positivity and the change in cell populations over time. To improve its clinical utility moving forward, we suggest that liquid biopsy analysis integrates morphology and time-based analysis alongside standard CTC enumeration at various stages of a patient’s treatment. 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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11
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Campbell NR, Rao A, Hunter MV, Sznurkowska MK, Briker L, Zhang M, Baron M, Heilmann S, Deforet M, Kenny C, Ferretti LP, Huang TH, Perlee S, Garg M, Nsengimana J, Saini M, Montal E, Tagore M, Newton-Bishop J, Middleton MR, Corrie P, Adams DJ, Rabbie R, Aceto N, Levesque MP, Cornell RA, Yanai I, Xavier JB, White RM. Cooperation between melanoma cell states promotes metastasis through heterotypic cluster formation. Dev Cell 2021; 56:2808-2825.e10. [PMID: 34529939 DOI: 10.1016/j.devcel.2021.08.018] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2020] [Revised: 07/07/2021] [Accepted: 08/20/2021] [Indexed: 02/08/2023]
Abstract
Melanomas can have multiple coexisting cell states, including proliferative (PRO) versus invasive (INV) subpopulations that represent a "go or grow" trade-off; however, how these populations interact is poorly understood. Using a combination of zebrafish modeling and analysis of patient samples, we show that INV and PRO cells form spatially structured heterotypic clusters and cooperate in the seeding of metastasis, maintaining cell state heterogeneity. INV cells adhere tightly to each other and form clusters with a rim of PRO cells. Intravital imaging demonstrated cooperation in which INV cells facilitate dissemination of less metastatic PRO cells. We identified the TFAP2 neural crest transcription factor as a master regulator of clustering and PRO/INV states. Isolation of clusters from patients with metastatic melanoma revealed a subset with heterotypic PRO-INV clusters. Our data suggest a framework for the co-existence of these two divergent cell populations, in which heterotypic clusters promote metastasis via cell-cell cooperation.
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Affiliation(s)
- Nathaniel R Campbell
- Weill Cornell/Rockefeller Memorial Sloan Kettering Tri-Institutional MD-PhD Program, New York, NY 10065, USA; Computational and Systems Biology, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA; Cancer Biology and Genetics, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Anjali Rao
- Institute for Computational Medicine, NYU Grossman School of Medicine, New York, NY 10016, USA
| | - Miranda V Hunter
- Cancer Biology and Genetics, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Magdalena K Sznurkowska
- Department of Biology, Institute of Molecular Health Sciences, Swiss Federal Institute of Technology (ETH) Zurich, 8093 Zurich, Switzerland
| | - Luzia Briker
- Department of Dermatology, University of Zürich Hospital, University of Zürich, Zurich, Switzerland
| | - Maomao Zhang
- Cancer Biology and Genetics, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Maayan Baron
- Institute for Computational Medicine, NYU Grossman School of Medicine, New York, NY 10016, USA
| | - Silja Heilmann
- Computational and Systems Biology, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Maxime Deforet
- Computational and Systems Biology, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Colin Kenny
- Department of Anatomy and Cell Biology, University of Iowa, Iowa City, IA 52242, USA
| | - Lorenza P Ferretti
- Department of Dermatology, University of Zürich Hospital, University of Zürich, Zurich, Switzerland; Department of Molecular Mechanisms of Disease, University of Zürich, Zurich, Switzerland
| | - Ting-Hsiang Huang
- Cancer Biology and Genetics, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Sarah Perlee
- Cancer Biology and Genetics, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Manik Garg
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Hinxton, Cambridgeshire, UK
| | - Jérémie Nsengimana
- Leeds Institute of Medical Research at St. James's, University of Leeds School of Medicine, Leeds, UK
| | - Massimo Saini
- Department of Biology, Institute of Molecular Health Sciences, Swiss Federal Institute of Technology (ETH) Zurich, 8093 Zurich, Switzerland
| | - Emily Montal
- Cancer Biology and Genetics, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Mohita Tagore
- Cancer Biology and Genetics, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Julia Newton-Bishop
- Leeds Institute of Medical Research at St. James's, University of Leeds School of Medicine, Leeds, UK
| | - Mark R Middleton
- Oxford NIHR Biomedical Research Centre and Department of Oncology, University of Oxford, Oxford, UK
| | - Pippa Corrie
- Cambridge Cancer Centre, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
| | - David J Adams
- Experimental Cancer Genetics, the Wellcome Sanger Institute, Hinxton, Cambridgeshire, UK
| | - Roy Rabbie
- Cambridge Cancer Centre, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK; Experimental Cancer Genetics, the Wellcome Sanger Institute, Hinxton, Cambridgeshire, UK
| | - Nicola Aceto
- Department of Biology, Institute of Molecular Health Sciences, Swiss Federal Institute of Technology (ETH) Zurich, 8093 Zurich, Switzerland
| | - Mitchell P Levesque
- Department of Dermatology, University of Zürich Hospital, University of Zürich, Zurich, Switzerland
| | - Robert A Cornell
- Department of Anatomy and Cell Biology, University of Iowa, Iowa City, IA 52242, USA
| | - Itai Yanai
- Institute for Computational Medicine, NYU Grossman School of Medicine, New York, NY 10016, USA
| | - Joao B Xavier
- Computational and Systems Biology, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA.
| | - Richard M White
- Cancer Biology and Genetics, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA.
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12
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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: 17] [Impact Index Per Article: 5.7] [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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13
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Ramani NS, Aung PP, Gu J, Sfamenos S, Sdringola-Maranga C, Nagarajan P, Tetzlaff MT, Curry JL, Ivan D, Diab A, Prieto VG, Hwu WJ, Torres-Cabala CA. TERT amplification but not activation of canonical Wnt/β-catenin pathway is involved in acral lentiginous melanoma progression to metastasis. Mod Pathol 2020; 33:2067-2074. [PMID: 32404956 DOI: 10.1038/s41379-020-0565-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2020] [Revised: 04/24/2020] [Accepted: 04/28/2020] [Indexed: 01/10/2023]
Abstract
Acral lentiginous melanoma (ALM) is a rare tumor that occurs on non-sun exposed skin areas of the hands and feet. Reports suggest that ALM exhibits poor prognosis, although mechanisms driving this remain poorly understood. Alterations in TERT and the Wnt/β-catenin (Wnt) pathway have been suggested to correlate with prognosis of ALM. Thus, immunohistochemical expression of β-catenin and LEF1 along with TERT amplification by FISH was investigated in 34 primary ALMs, 20 metastatic ALMs, 10 primary non-ALMs, and 15 acral nevi. Foot/toe was the most common primary tumor location (85%) for ALM. TERT amplification was detected in 6 of 28 (21.4%) primary ALM, 2 of 8 (25%) primary non-ALM, and 8 of 18 (44.4%) metastatic ALM, the latter showing significantly higher frequency compared with primary melanomas (P = 0.043). Most metastatic ALMs positive for TERT amplification lacked BRAF V600E (87.5%). Cytoplasmic and nonnuclear expression of β-catenin was variably detected in all cases. Metastatic ALM revealed lower expression of β-catenin compared with primary ALM (P = 0.017). No differences in LEF1 expression were detected among the groups; however, acral nevi showed decreased labeling with dermal descent, in contrast to melanoma. No molecular-genetic alteration correlated with prognosis. TERT amplification by FISH is a frequent finding in primary ALM and appears to increase in metastatic tumors, suggesting a role in tumor progression to metastasis. Although TERT amplification has been reported to be infrequent in primary non-ALM, it showed comparable frequency with ALM in our series. Our immunohistochemical findings are not fully supportive of activation of either canonical or noncanonical Wnt cascades in ALM. TERT amplification by FISH and LEF1 immunohistochemistry may help in the differential diagnosis between primary ALM and acral nevus. TERT amplification appears to be a promising target for therapy in patients with metastatic ALM.
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Affiliation(s)
- Nisha S Ramani
- Department of Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Phyu P Aung
- Department of Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Jun Gu
- Cytogenetics Training Laboratory, School of Health Professions, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Steven Sfamenos
- Cytogenetics Training Laboratory, School of Health Professions, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Chiara Sdringola-Maranga
- Cytogenetics Training Laboratory, School of Health Professions, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Priyardhisini Nagarajan
- Department of Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Michael T Tetzlaff
- Department of Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
- Department of Molecular Translational Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Jonathan L Curry
- Department of Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
- Department of Dermatology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Doina Ivan
- Department of Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Adi Diab
- Department of Melanoma Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Victor G Prieto
- Department of Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
- Department of Dermatology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Wen-Jen Hwu
- Department of Melanoma Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Carlos A Torres-Cabala
- Department of Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.
- Department of Dermatology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.
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14
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Ahrens TD, Bang-Christensen SR, Jørgensen AM, Løppke C, Spliid CB, Sand NT, Clausen TM, Salanti A, Agerbæk MØ. The Role of Proteoglycans in Cancer Metastasis and Circulating Tumor Cell Analysis. Front Cell Dev Biol 2020; 8:749. [PMID: 32984308 PMCID: PMC7479181 DOI: 10.3389/fcell.2020.00749] [Citation(s) in RCA: 40] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2020] [Accepted: 07/17/2020] [Indexed: 12/14/2022] Open
Abstract
Circulating tumor cells (CTCs) are accessible by liquid biopsies via an easy blood draw. They represent not only the primary tumor site, but also potential metastatic lesions, and could thus be an attractive supplement for cancer diagnostics. However, the analysis of rare CTCs in billions of normal blood cells is still technically challenging and novel specific CTC markers are needed. The formation of metastasis is a complex process supported by numerous molecular alterations, and thus novel CTC markers might be found by focusing on this process. One example of this is specific changes in the cancer cell glycocalyx, which is a network on the cell surface composed of carbohydrate structures. Proteoglycans are important glycocalyx components and consist of a protein core and covalently attached long glycosaminoglycan chains. A few CTC assays have already utilized proteoglycans for both enrichment and analysis of CTCs. Nonetheless, the biological function of proteoglycans on clinical CTCs has not been studied in detail so far. Therefore, the present review describes proteoglycan functions during the metastatic cascade to highlight their importance to CTCs. We also outline current approaches for CTC assays based on targeting proteoglycans by their protein cores or their glycosaminoglycan chains. Lastly, we briefly discuss important technical aspects, which should be considered for studying proteoglycans.
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Affiliation(s)
- Theresa D Ahrens
- Centre for Medical Parasitology at Department of Immunology and Microbiology, Faculty of Health and Medical Sciences, University of Copenhagen and Department of Infectious Diseases, Copenhagen University Hospital, Copenhagen, Denmark
| | - Sara R Bang-Christensen
- Centre for Medical Parasitology at Department of Immunology and Microbiology, Faculty of Health and Medical Sciences, University of Copenhagen and Department of Infectious Diseases, Copenhagen University Hospital, Copenhagen, Denmark
- VarCT Diagnostics, Copenhagen, Denmark
| | | | - Caroline Løppke
- Centre for Medical Parasitology at Department of Immunology and Microbiology, Faculty of Health and Medical Sciences, University of Copenhagen and Department of Infectious Diseases, Copenhagen University Hospital, Copenhagen, Denmark
| | - Charlotte B Spliid
- Centre for Medical Parasitology at Department of Immunology and Microbiology, Faculty of Health and Medical Sciences, University of Copenhagen and Department of Infectious Diseases, Copenhagen University Hospital, Copenhagen, Denmark
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA, United States
| | - Nicolai T Sand
- Centre for Medical Parasitology at Department of Immunology and Microbiology, Faculty of Health and Medical Sciences, University of Copenhagen and Department of Infectious Diseases, Copenhagen University Hospital, Copenhagen, Denmark
| | - Thomas M Clausen
- Centre for Medical Parasitology at Department of Immunology and Microbiology, Faculty of Health and Medical Sciences, University of Copenhagen and Department of Infectious Diseases, Copenhagen University Hospital, Copenhagen, Denmark
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA, United States
| | - Ali Salanti
- Centre for Medical Parasitology at Department of Immunology and Microbiology, Faculty of Health and Medical Sciences, University of Copenhagen and Department of Infectious Diseases, Copenhagen University Hospital, Copenhagen, Denmark
| | - Mette Ø Agerbæk
- Centre for Medical Parasitology at Department of Immunology and Microbiology, Faculty of Health and Medical Sciences, University of Copenhagen and Department of Infectious Diseases, Copenhagen University Hospital, Copenhagen, Denmark
- VarCT Diagnostics, Copenhagen, Denmark
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15
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Chondroitin sulfate proteoglycan 4 enhanced melanoma motility and growth requires a cysteine in the core protein transmembrane domain. Melanoma Res 2020; 29:365-375. [PMID: 31140988 DOI: 10.1097/cmr.0000000000000574] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
Chondroitin sulfate proteoglycan 4 (CSPG4) is a cell surface proteoglycan that enhances malignant potential in melanoma and several other tumor types. CSPG4 functions as a transmembrane scaffold in melanoma cells to activate oncogenic signaling pathways such as focal adhesion kinase (FAK) and extracellular signal regulated kinases 1,2, that control motility, invasion and anchorage independent growth. Here, we demonstrate that CSPG4 promotes directional motility and anchorage independent growth of melanoma cells by organizing and positioning a signaling complex containing activated FAK to lipid rafts within the plasma membrane of migrating cells. This FAK-containing signal transduction platform, which consists of syntenin-1, active Src and caveolin-1 requires the cytoplasmic domain of CSPG4 for assembly. Enhanced directional motility promoted by this complex also requires a CSPG4 transmembrane cysteine residue C2230. Substituting C2230 with alanine (CSPG4) still permits assembly of the signaling complex, however Src remains in an inactive state. CSPG4 also fails to promote anchorage independent growth and activation of extracellular signal regulated kinases 1,2. Therapies that target the transmembrane domain of CSPG4 could be a novel strategy for limiting progression by disrupting its function as a compartmentalized motogenic and growth-promoting oncogenic signaling node.
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16
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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: 5.0] [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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17
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A Novel Antibody-Drug Conjugate (ADC) Delivering a DNA Mono-Alkylating Payload to Chondroitin Sulfate Proteoglycan (CSPG4)-Expressing Melanoma. Cancers (Basel) 2020; 12:cancers12041029. [PMID: 32331483 PMCID: PMC7226475 DOI: 10.3390/cancers12041029] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2020] [Revised: 04/13/2020] [Accepted: 04/18/2020] [Indexed: 12/18/2022] Open
Abstract
Despite emerging targeted and immunotherapy treatments, no monoclonal antibodies or antibody-drug conjugates (ADCs) directly targeting tumor cells are currently approved for melanoma therapy. The tumor-associated antigen chondroitin sulphate proteoglycan 4 (CSPG4), a neural crest glycoprotein over-expressed on 70% of melanomas, contributes to proliferative signaling pathways, but despite highly tumor-selective expression it has not yet been targeted using ADCs. We developed a novel ADC comprising an anti-CSPG4 antibody linked to a DNA minor groove-binding agent belonging to the novel pyrridinobenzodiazepine (PDD) class. Unlike conventional DNA-interactive pyrrolobenzodiazepine (PBD) dimer payloads that cross-link DNA, PDD-based payloads are mono-alkylating agents but have similar efficacy and substantially enhanced tolerability profiles compared to PBD-based cross-linkers. We investigated the anti-tumor activity and safety of the anti-CSPG4-(PDD) ADC in vitro and in human melanoma xenografts. Anti-CSPG4-(PDD) inhibited CSPG4-expressing melanoma cell growth and colony formation and triggered apoptosis in vitro at low nanomolar to picomolar concentrations without off-target Fab-mediated or Fc-mediated toxicity. Anti-CSPG4-(PDD) restricted xenograft growth in vivo at 2 mg/kg doses. One 5 mg/kg injection triggered tumor regression in the absence of overt toxic effects or of acquired residual tumor cell resistance. This anti-CSPG4-(PDD) can deliver a highly cytotoxic DNA mono-alkylating payload to CSPG4-expressing tumors at doses tolerated in vivo.
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18
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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: 14] [Impact Index Per Article: 3.5] [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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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: 1.3] [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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20
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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: 2.0] [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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21
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Abstract
Circulating tumor cells (CTCs) are rare cells that can be found in the peripheral blood of cancer patients. They have been demonstrated to be useful prognostic markers in many cancer types. Within the last decade various methods have been developed to detect rare cells within a liquid biopsy from a cancer patient. These methods have revealed the phenotypic diversity of CTCs and how they can represent the complement of cells that are found in a tumor. Single-cell proteogenomics has emerged as an all-encompassing next-generation technological approach for CTC research. This allows for the deconstruction of cellular heterogeneity, dynamics of metastatic initiation and progression, and response or resistance to therapeutics in the clinical settings. We take advantage of this opportunity to investigate CTC heterogeneity and understand their full potential in precision medicine.The high-definition single-cell analysis (HD-SCA) workflow combines detection of the entire population of CTCs and rare cancer related cells with single-cell genomic analysis and may therefore provide insight into their subpopulations based on molecular as well as morphological data. In this chapter we describe in detail the protocols from isolation of a candidate cell from a microscopy slide, through whole-genome amplification and library preparation, to CNV analysis of identified cells from the HD-SCA workflow. This process may also be applicable to any platform starting with a standard microscopy slide or isolated cell of interest.
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Affiliation(s)
- Jana- A Thiele
- Biomedical Center, Faculty of Medicine in Pilsen, Charles University, Pilsen, Czech Republic
| | - Pavel Pitule
- Biomedical Center, Faculty of Medicine in Pilsen, Charles University, Pilsen, Czech Republic
| | - James Hicks
- USC Michelson Center for Convergent Biosciences, CSI-Cancer, Department of Biological Sciences, Dornsife College of Letters, Arts and Sciences, University of Southern California, Los Angeles, CA, USA
| | - Peter Kuhn
- USC Michelson Center for Convergent Biosciences, CSI-Cancer, Department of Biological Sciences, Dornsife College of Letters, Arts and Sciences, University of Southern California, Los Angeles, CA, USA.
- Department of Biomedical Engineering and Aerospace and Mechanical Engineering, Viterbi School of Engineering, University of Southern California, Los Angeles, CA, USA.
- Department of Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA.
- Department of Urology, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA.
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22
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Abstract
Cellular heterogeneity within and across tumors has been a major obstacle in understanding and treating cancer, and the complex heterogeneity is masked if bulk tumor tissues are used for analysis. The advent of rapidly developing single-cell sequencing technologies, which include methods related to single-cell genome, epigenome, transcriptome, and multi-omics sequencing, have been applied to cancer research and led to exciting new findings in the fields of cancer evolution, metastasis, resistance to therapy, and tumor microenvironment. In this review, we discuss recent advances and limitations of these new technologies and their potential applications in cancer studies.
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Affiliation(s)
- Xianwen Ren
- Beijing Advanced Innovation Centre for Genomics, Peking-Tsinghua Centre for Life Sciences, Biomedical Pioneering Innovation Center (BIOPIC), School of Life Sciences, Peking University, Beijing, 100871, China.
| | - Boxi Kang
- Beijing Advanced Innovation Centre for Genomics, Peking-Tsinghua Centre for Life Sciences, Biomedical Pioneering Innovation Center (BIOPIC), School of Life Sciences, Peking University, Beijing, 100871, China
| | - Zemin Zhang
- Beijing Advanced Innovation Centre for Genomics, Peking-Tsinghua Centre for Life Sciences, Biomedical Pioneering Innovation Center (BIOPIC), School of Life Sciences, Peking University, Beijing, 100871, China.
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23
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Analyzing Circulating Tumor Cells One at a Time. Trends Cell Biol 2018; 28:764-775. [PMID: 29891227 DOI: 10.1016/j.tcb.2018.05.004] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2018] [Revised: 05/12/2018] [Accepted: 05/16/2018] [Indexed: 11/20/2022]
Abstract
Whole-genome sequencing has made a significant impact on cancer research, but traditional bulk methods fail to detect information from rare cells. Recently developed single-cell sequencing methods have provided new insights and unprecedented details about cancer progression and diversity. These advancements also enable the investigation of rare cells, such as circulating tumor cells (CTCs) derived from cancer patients. In this review, we outline various single-cell sequencing techniques that can elucidate the molecular properties of CTCs. In addition, we explain the drawbacks that need to be overcome for each method.
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24
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Marsavela G, Aya-Bonilla CA, Warkiani ME, Gray ES, Ziman M. Melanoma circulating tumor cells: Benefits and challenges required for clinical application. Cancer Lett 2018; 424:1-8. [PMID: 29548820 DOI: 10.1016/j.canlet.2018.03.013] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2017] [Revised: 02/01/2018] [Accepted: 03/09/2018] [Indexed: 02/07/2023]
Abstract
The implementation of novel therapeutic interventions has improved the survival rates of melanoma patients with metastatic disease. Nonetheless, only 33% of treated cases exhibit long term responses. Circulating tumor cell (CTC) measurements are currently of clinical value in breast, prostate and colorectal cancers. However, the clinical utility of melanoma CTCs (MelCTCs) is still unclear due to challenges that appear intrinsic to MelCTCs (i.e. rarity, heterogeneity) and a lack of standardization in their isolation, across research laboratories. Here, we review the latest developments, pinpoint the challenges in MelCTC isolation and address their potential role in melanoma management.
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Affiliation(s)
- G Marsavela
- School of Medical and Health Sciences, Edith Cowan University, Joondalup, Australia
| | - C A Aya-Bonilla
- School of Medical and Health Sciences, Edith Cowan University, Joondalup, Australia.
| | - M E Warkiani
- School of Medical and Health Sciences, Edith Cowan University, Joondalup, Australia; School of Biomedical Engineering, University of Technology Sydney, Sydney, Australia; Institute of Molecular Medicine, Sechenov First Moscow State University, Moscow, Russia
| | - E S Gray
- School of Medical and Health Sciences, Edith Cowan University, Joondalup, Australia
| | - M Ziman
- School of Medical and Health Sciences, Edith Cowan University, Joondalup, Australia; School of Pathology and Laboratory Medicine, University of Western Australia, Crawley, Australia
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25
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Integrating Analysis of Cellular Heterogeneity in High-Content Dose-Response Studies. Methods Mol Biol 2018. [PMID: 29476461 DOI: 10.1007/978-1-4939-7680-5_2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
Abstract
Heterogeneity is a complex property of cellular systems and therefore presents challenges to the reliable identification and characterization. Large-scale biology projects may span many months, requiring a systematic approach to quality control to track reproducibility and correct for instrumental variation and assay drift that could mask biological heterogeneity and preclude comparisons of heterogeneity between runs or even between plates. However, presently there is no standard approach to the tracking and analysis of heterogeneity. Previously, we demonstrated the use of the Kolmogorov-Smirnov statistic as a metric for monitoring the reproducibility of heterogeneity in a screen and described the use of three heterogeneity indices as a means to characterize, filter, and browse cellular heterogeneity in big data sets (Gough et al., Methods 96:12-26, 2016). In this chapter, we present a detailed method for integrating the analysis of cellular heterogeneity in assay development, validation, screening, and post screen. Importantly, we provide a detailed method for quality control, to normalize cellular data, track heterogeneity over time, and analyze heterogeneity in big data sets, along with software tools to assist in that process. The example screen for this method is from an HCS project, but the approach applies equally to other experimental methods that measure populations of cells.
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26
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Dietrich P, Kuphal S, Spruss T, Hellerbrand C, Bosserhoff AK. Wild-type KRAS is a novel therapeutic target for melanoma contributing to primary and acquired resistance to BRAF inhibition. Oncogene 2018; 37:897-911. [PMID: 29059159 DOI: 10.1038/onc.2017.391] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2017] [Revised: 08/08/2017] [Accepted: 09/07/2017] [Indexed: 12/14/2022]
Abstract
Malignant melanoma reveals rapidly increasing incidence and mortality rates worldwide. By now, BRAF inhibition is the standard therapy for advanced melanoma in patients carrying BRAF mutations. However, only approximately 50% of melanoma patients harbor therapeutically attackable BRAF mutations, and overall survival after treatment with BRAF inhibitors is modest. KRAS (Kirsten Rat sarcoma) proteins are acting upstream of BRAF and have a major role in human cancer. Recent approaches awaken the hope to use KRAS inhibition (KRASi) as a clinical tool. In this study, we identified wild-type KRAS as a novel therapeutic target in melanoma. KRASi functions synergistically with BRAF inhibition to reduce melanoma proliferation and to induce apoptosis independently of BRAF mutational status. Moreover, acquired resistance to BRAF inhibitors in melanoma is dependent on dynamic regulation of KRAS expression with subsequent AKT and extracellular-signal regulated kinase activation and can be overcome by KRASi. This suggests KRASi as novel approach in melanoma-alone or in combination with other therapeutic regimes.
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Affiliation(s)
- P Dietrich
- Institute of Biochemistry, Emil-Fischer-Zentrum, Friedrich-Alexander-University Erlangen-Nuremberg, Erlangen, Germany
| | - S Kuphal
- Institute of Biochemistry, Emil-Fischer-Zentrum, Friedrich-Alexander-University Erlangen-Nuremberg, Erlangen, Germany
| | - T Spruss
- Institute of Pharmacy, University of Regensburg, Regensburg, Germany
| | - C Hellerbrand
- Institute of Biochemistry, Emil-Fischer-Zentrum, Friedrich-Alexander-University Erlangen-Nuremberg, Erlangen, Germany
- Comprehensive Cancer Center (CCC) Erlangen-EMN, Erlangen, Germany
| | - A K Bosserhoff
- Institute of Biochemistry, Emil-Fischer-Zentrum, Friedrich-Alexander-University Erlangen-Nuremberg, Erlangen, Germany
- Comprehensive Cancer Center (CCC) Erlangen-EMN, Erlangen, Germany
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27
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Thiele JA, Bethel K, Králíčková M, Kuhn P. Circulating Tumor Cells: Fluid Surrogates of Solid Tumors. ANNUAL REVIEW OF PATHOLOGY-MECHANISMS OF DISEASE 2017; 12:419-447. [PMID: 28135562 DOI: 10.1146/annurev-pathol-052016-100256] [Citation(s) in RCA: 72] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Evaluation of circulating tumor cells (CTCs) has demonstrated clinical validity as a prognostic tool based on enumeration, but since the introduction of this tool to the clinic in 2004, further clinical utility and widespread adoption have been limited. However, immense efforts have been undertaken to further the understanding of the mechanisms behind the biology and kinetics of these rare cells, and progress continues toward better applicability in the clinic. This review describes recent advances within the field, with a particular focus on understanding the biological significance of CTCs, and summarizes emerging methods for identifying, isolating, and interrogating the cells that may provide technical advantages allowing for the discovery of more specific clinical applications. Included is an atlas of high-definition images of CTCs from various cancer types, including uncommon CTCs captured only by broadly inclusive nonenrichment techniques.
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Affiliation(s)
- J-A Thiele
- Biomedical Center, Faculty of Medicine in Pilsen, Charles University in Prague, 323 00 Pilsen, Czech Republic
| | - K Bethel
- Scripps Clinic Medical Group, Scripps Clinic, La Jolla, California 92121
| | - M Králíčková
- Department of Histology and Embryology, Faculty of Medicine in Pilsen, Charles University in Prague, 301 00 Pilsen, Czech Republic
| | - P Kuhn
- Bridge Institute, Dornsife College of Letters, Arts and Sciences, University of Southern California, Los Angeles, California 90089; .,Department of Biomedical Engineering, Viterbi School of Engineering, University of Southern California, Los Angeles, California 90089
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28
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Su DW, Nieva J. Biophysical technologies for understanding circulating tumor cell biology and metastasis. Transl Lung Cancer Res 2017; 6:473-485. [PMID: 28904890 DOI: 10.21037/tlcr.2017.05.08] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
An understanding of cancer evolution in lung cancer with its associated resistance to therapy can only be achieved with repeated sampling and analysis of the cancer. Given the high risks and costs associated with repeat physical biopsy, alternative technologies must be applied. Several modalities exist for analysis and re-analysis of cancer biology. Among them are the CellSearch platform, the CTC chip, and the high-definition CTC platform. While the former is primarily able to provide prognosticating information in the form of CTC enumeration, the latter two have the advantage of serving as a platform to study tumor biology. Techniques for analysis of single cell genomics, as well as protein expression on a single cell basis provide scientists with the capacity to understand cancer cell populations as a collection of individual cells, rather than as an average of all cells. A multimodal combination of circulating tumor DNAs (ctDNAs), CTCs, proteomics, and CTC-derived xenografts (CDXs) to create computational models useful in diagnosis, prognostication, and predictiveness to treatment is likely the future of tailoring individualized cancer care.
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Affiliation(s)
- Derrick W Su
- Norris Cancer Center, University of Southern California, Los Angeles, USA
| | - Jorge Nieva
- Norris Cancer Center, University of Southern California, Los Angeles, USA
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29
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Gough A, Stern AM, Maier J, Lezon T, Shun TY, Chennubhotla C, Schurdak ME, Haney SA, Taylor DL. Biologically Relevant Heterogeneity: Metrics and Practical Insights. SLAS DISCOVERY 2017; 22:213-237. [PMID: 28231035 DOI: 10.1177/2472555216682725] [Citation(s) in RCA: 45] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Heterogeneity is a fundamental property of biological systems at all scales that must be addressed in a wide range of biomedical applications, including basic biomedical research, drug discovery, diagnostics, and the implementation of precision medicine. There are a number of published approaches to characterizing heterogeneity in cells in vitro and in tissue sections. However, there are no generally accepted approaches for the detection and quantitation of heterogeneity that can be applied in a relatively high-throughput workflow. This review and perspective emphasizes the experimental methods that capture multiplexed cell-level data, as well as the need for standard metrics of the spatial, temporal, and population components of heterogeneity. A recommendation is made for the adoption of a set of three heterogeneity indices that can be implemented in any high-throughput workflow to optimize the decision-making process. In addition, a pairwise mutual information method is suggested as an approach to characterizing the spatial features of heterogeneity, especially in tissue-based imaging. Furthermore, metrics for temporal heterogeneity are in the early stages of development. Example studies indicate that the analysis of functional phenotypic heterogeneity can be exploited to guide decisions in the interpretation of biomedical experiments, drug discovery, diagnostics, and the design of optimal therapeutic strategies for individual patients.
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Affiliation(s)
- Albert Gough
- 1 Department of Computational and Systems Biology, University of Pittsburgh, Pittsburgh, PA, USA.,2 University of Pittsburgh Drug Discovery Institute, Pittsburgh, PA, USA
| | - Andrew M Stern
- 1 Department of Computational and Systems Biology, University of Pittsburgh, Pittsburgh, PA, USA.,2 University of Pittsburgh Drug Discovery Institute, Pittsburgh, PA, USA
| | - John Maier
- 3 Department of Family Medicine, University of Pittsburgh, Pittsburgh, PA, USA
| | - Timothy Lezon
- 1 Department of Computational and Systems Biology, University of Pittsburgh, Pittsburgh, PA, USA.,2 University of Pittsburgh Drug Discovery Institute, Pittsburgh, PA, USA
| | - Tong-Ying Shun
- 2 University of Pittsburgh Drug Discovery Institute, Pittsburgh, PA, USA
| | - Chakra Chennubhotla
- 1 Department of Computational and Systems Biology, University of Pittsburgh, Pittsburgh, PA, USA.,2 University of Pittsburgh Drug Discovery Institute, Pittsburgh, PA, USA
| | - Mark E Schurdak
- 1 Department of Computational and Systems Biology, University of Pittsburgh, Pittsburgh, PA, USA.,2 University of Pittsburgh Drug Discovery Institute, Pittsburgh, PA, USA.,4 University of Pittsburgh Cancer Institute, Pittsburgh, PA, USA
| | - Steven A Haney
- 5 Eli Lilly and Company, Lilly Corporate Center, Indianapolis, IN, USA
| | - D Lansing Taylor
- 1 Department of Computational and Systems Biology, University of Pittsburgh, Pittsburgh, PA, USA.,2 University of Pittsburgh Drug Discovery Institute, Pittsburgh, PA, USA.,4 University of Pittsburgh Cancer Institute, Pittsburgh, PA, USA
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Wang J, Bettegowda C. Applications of DNA-Based Liquid Biopsy for Central Nervous System Neoplasms. J Mol Diagn 2016; 19:24-34. [PMID: 27863260 DOI: 10.1016/j.jmoldx.2016.08.007] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2016] [Revised: 08/04/2016] [Accepted: 08/12/2016] [Indexed: 12/18/2022] Open
Abstract
The management of central nervous system malignancies remains reliant on histopathological analysis and neuroimaging, despite their complex genetic profile. The intratumoral heterogeneity displayed by these tumors necessitates a more sophisticated method of tumor analysis and monitoring, with the ability to assess tumors over space and time. Circulating biomarkers, including circulating tumor cells, circulating tumor DNA, and extracellular vesicles, hold promise as a type of real-time liquid biopsy able to provide dynamic information not only regarding tumor burden to monitor disease progression and treatment response, but also regarding genetic profile to enable changes in management to match a constantly evolving tumor. In numerous cancer types, including glioma, they have demonstrated their clinical utility as a minimally invasive means for diagnosis, prognostication, and prediction. In addition, they can be used in the laboratory to probe mechanisms of acquired drug resistance and tumor invasion and dissemination.
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Affiliation(s)
- Joanna Wang
- Department of Internal Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Chetan Bettegowda
- Department of Neurosurgery, Johns Hopkins University School of Medicine, Baltimore, Maryland.
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Ignatiadis M, Lee M, Jeffrey SS. Circulating Tumor Cells and Circulating Tumor DNA: Challenges and Opportunities on the Path to Clinical Utility. Clin Cancer Res 2016; 21:4786-800. [PMID: 26527805 DOI: 10.1158/1078-0432.ccr-14-1190] [Citation(s) in RCA: 258] [Impact Index Per Article: 32.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Recent technological advances have enabled the detection and detailed characterization of circulating tumor cells (CTC) and circulating tumor DNA (ctDNA) in blood samples from patients with cancer. Often referred to as a "liquid biopsy," CTCs and ctDNA are expected to provide real-time monitoring of tumor evolution and therapeutic efficacy, with the potential for improved cancer diagnosis and treatment. In this review, we focus on these opportunities as well as the challenges that should be addressed so that these tools may eventually be implemented into routine clinical care.
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Affiliation(s)
- Michail Ignatiadis
- Department of Medical Oncology and Breast Cancer Translational Research Laboratory J. C. Heuson, Institut Jules Bordet, Université Libre de Bruxelles, Brussels, Belgium
| | - Mark Lee
- Google[x] Life Sciences, Google, Inc, Mountain View, California
| | - Stefanie S Jeffrey
- Department of Surgery, Stanford University School of Medicine, Stanford, California.
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Abstract
Single-cell sequencing (SCS) is a powerful new tool for investigating evolution and diversity in cancer and understanding the role of rare cells in tumor progression. These methods have begun to unravel key questions in cancer biology that have been difficult to address with bulk tumor measurements. Over the past five years, there has been extraordinary progress in technological developments and research applications, but these efforts represent only the tip of the iceberg. In the coming years, SCS will greatly improve our understanding of invasion, metastasis, and therapy resistance during cancer progression. These tools will also have direct translational applications in the clinic, in areas such as early detection, noninvasive monitoring, and guiding targeted therapy. In this perspective, I discuss the progress that has been made and the myriad of unexplored applications that still lie ahead in cancer research and medicine.
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Affiliation(s)
- Nicholas E Navin
- Department of Genetics, University of Texas, MD Anderson Cancer Center, Houston, Texas 77030, USA; Department of Bioinformatics and Computational Biology, University of Texas, MD Anderson Cancer Center, Houston, Texas 77030, USA; Graduate Program in Genes and Development, Graduate School of Biomedical Sciences, University of Texas Health Science Center at Houston, Houston, Texas 77030, USA
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Xu MJ, Dorsey JF, Amaravadi R, Karakousis G, Simone CB, Xu X, Xu W, Carpenter EL, Schuchter L, Kao GD. Circulating Tumor Cells, DNA, and mRNA: Potential for Clinical Utility in Patients With Melanoma. Oncologist 2015; 21:84-94. [PMID: 26614709 DOI: 10.1634/theoncologist.2015-0207] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2015] [Accepted: 10/08/2015] [Indexed: 12/25/2022] Open
Abstract
UNLABELLED : Circulating tumor cells (CTCs), circulating tumor DNA (ctDNA), and messenger RNA (mRNA), collectively termed circulating tumor products (CTPs), represent areas of immense interest from scientists' and clinicians' perspectives. In melanoma, CTP analysis may have clinical utility in many areas, from screening and diagnosis to clinical decision-making aids, as surveillance biomarkers or sources of real-time genetic or molecular characterization. In addition, CTP analysis can be useful in the discovery of new biomarkers, patterns of treatment resistance, and mechanisms of metastasis development. Here, we compare and contrast CTCs, ctDNA, and mRNA, review the extent of translational evidence to date, and discuss how future studies involving both scientists and clinicians can help to further develop this tool for the benefit of melanoma patients. IMPLICATIONS FOR PRACTICE Scientific advancement has enabled the rapid development of tools to analyze circulating tumor cells, tumor DNA, and messenger RNA, collectively termed circulating tumor products (CTPs). A variety of techniques have emerged to detect and characterize melanoma CTPs; however, only a fraction has been applied to human subjects. This review summarizes the available human data that investigate clinical utility of CTP in cancer screening, melanoma diagnosis, prognosis, prediction, and genetic or molecular characterization. It provides a rationale for how CTPs may be useful for future research and discusses how clinicians can be involved in developing this exciting new technology.
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Affiliation(s)
- Melody J Xu
- Department of Radiation Oncology, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Jay F Dorsey
- Department of Radiation Oncology, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Ravi Amaravadi
- Division of Hematology and Oncology, Department of Medicine, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Giorgos Karakousis
- Division of Surgical Oncology, Department of Surgery, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Charles B Simone
- Department of Radiation Oncology, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Xiaowei Xu
- Department of Pathology, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Wei Xu
- Abramson Cancer Center, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Erica L Carpenter
- Division of Hematology and Oncology, Department of Medicine, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Lynn Schuchter
- Division of Hematology and Oncology, Department of Medicine, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Gary D Kao
- Department of Radiation Oncology, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania, USA
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Zhang Z, Ramnath N, Nagrath S. Current Status of CTCs as Liquid Biopsy in Lung Cancer and Future Directions. Front Oncol 2015; 5:209. [PMID: 26484313 PMCID: PMC4588111 DOI: 10.3389/fonc.2015.00209] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2015] [Accepted: 09/08/2015] [Indexed: 12/16/2022] Open
Abstract
Circulating tumor cells (CTCs) have garnered a lot of attention in the past few decades. Isolation of these rare cells from the billions of blood cells has been a challenge until recent times. With the advent of new sensitive technologies that permit live cell isolation and downstream genomic analysis, the existing paradigm of CTC research has evolved to explore clinical utility of these cells. CTCs have been identified as prognostic and pharmacodynamic biomarkers in many solid tumors, including lung cancer. As a means of liquid biopsy, CTCs could play a major role in the development of personalized medicine and targeted therapies. This review discusses the state of various isolation strategies, cell separation techniques and key studies that illustrate the application of liquid biopsy to lung cancer.
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Affiliation(s)
- Zhuo Zhang
- Department of Chemical Engineering, University of Michigan , Ann Arbor, MI , USA
| | - Nithya Ramnath
- Department of Internal Medicine, University of Michigan , Ann Arbor, MI , USA ; Veterans Administration Ann Arbor Healthcare System , Ann Arbor, MI , USA
| | - Sunitha Nagrath
- Department of Chemical Engineering, University of Michigan , Ann Arbor, MI , USA ; Translational Oncology Program, University of Michigan , Ann Arbor, MI , USA
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Huang L, Ma F, Chapman A, Lu S, Xie XS. Single-Cell Whole-Genome Amplification and Sequencing: Methodology and Applications. Annu Rev Genomics Hum Genet 2015; 16:79-102. [PMID: 26077818 DOI: 10.1146/annurev-genom-090413-025352] [Citation(s) in RCA: 261] [Impact Index Per Article: 29.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
We present a survey of single-cell whole-genome amplification (WGA) methods, including degenerate oligonucleotide-primed polymerase chain reaction (DOP-PCR), multiple displacement amplification (MDA), and multiple annealing and looping-based amplification cycles (MALBAC). The key parameters to characterize the performance of these methods are defined, including genome coverage, uniformity, reproducibility, unmappable rates, chimera rates, allele dropout rates, false positive rates for calling single-nucleotide variations, and ability to call copy-number variations. Using these parameters, we compare five commercial WGA kits by performing deep sequencing of multiple single cells. We also discuss several major applications of single-cell genomics, including studies of whole-genome de novo mutation rates, the early evolution of cancer genomes, circulating tumor cells (CTCs), meiotic recombination of germ cells, preimplantation genetic diagnosis (PGD), and preimplantation genomic screening (PGS) for in vitro-fertilized embryos.
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Affiliation(s)
- Lei Huang
- Biodynamic Optical Imaging Center (BIOPIC), School of Life Sciences, Peking University, Beijing 100871, China
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