1
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Mehta S, Bernt M, Chambers M, Fahrner M, Föll MC, Gruening B, Horro C, Johnson JE, Loux V, Rajczewski AT, Schilling O, Vandenbrouck Y, Gustafsson OJR, Thang WCM, Hyde C, Price G, Jagtap PD, Griffin TJ. A Galaxy of informatics resources for MS-based proteomics. Expert Rev Proteomics 2023; 20:251-266. [PMID: 37787106 DOI: 10.1080/14789450.2023.2265062] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2023] [Accepted: 09/06/2023] [Indexed: 10/04/2023]
Abstract
INTRODUCTION Continuous advances in mass spectrometry (MS) technologies have enabled deeper and more reproducible proteome characterization and a better understanding of biological systems when integrated with other 'omics data. Bioinformatic resources meeting the analysis requirements of increasingly complex MS-based proteomic data and associated multi-omic data are critically needed. These requirements included availability of software that would span diverse types of analyses, scalability for large-scale, compute-intensive applications, and mechanisms to ease adoption of the software. AREAS COVERED The Galaxy ecosystem meets these requirements by offering a multitude of open-source tools for MS-based proteomics analyses and applications, all in an adaptable, scalable, and accessible computing environment. A thriving global community maintains these software and associated training resources to empower researcher-driven analyses. EXPERT OPINION The community-supported Galaxy ecosystem remains a crucial contributor to basic biological and clinical studies using MS-based proteomics. In addition to the current status of Galaxy-based resources, we describe ongoing developments for meeting emerging challenges in MS-based proteomic informatics. We hope this review will catalyze increased use of Galaxy by researchers employing MS-based proteomics and inspire software developers to join the community and implement new tools, workflows, and associated training content that will add further value to this already rich ecosystem.
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Affiliation(s)
- Subina Mehta
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, MN, USA
| | - Matthias Bernt
- Helmholtz Centre for Environmental Research - UFZ, Department Computational Biology, Leipzig, Germany
| | | | - Matthias Fahrner
- Institute for Surgical Pathology, Medical Center - University of Freiburg, Freiburg, Germany
- German Cancer Consortium (DKTK) and German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Melanie Christine Föll
- Institute for Surgical Pathology, Medical Center - University of Freiburg, Freiburg, Germany
- German Cancer Consortium (DKTK) and German Cancer Research Center (DKFZ), Heidelberg, Germany
- Khoury College of Computer Sciences, Northeastern University, Boston, MA, USA
| | - Bjoern Gruening
- Bioinformatics Group, Department of Computer Science, Albert-Ludwigs-University Freiburg, Freiburg, Germany
| | - Carlos Horro
- Proteomics Unit, Department of Biomedicine, University of Bergen, Bergen, Norway
- Computational Biology Unit, Department of Informatics, University of Bergen, Bergen, Norway
| | - James E Johnson
- Minnesota Supercomputing Institute, University of Minnesota, Minneapolis, MN, USA
| | - Valentin Loux
- Université Paris-Saclay, INRAE, MaIAGE, Jouy-en-Josas, France
- Université Paris-Saclay, INRAE, BioinfOmics, MIGALE bioinformatics facility, Jouy-en-Josas, France
| | - Andrew T Rajczewski
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, MN, USA
| | - Oliver Schilling
- Institute for Surgical Pathology, Medical Center - University of Freiburg, Freiburg, Germany
- German Cancer Consortium (DKTK) and German Cancer Research Center (DKFZ), Heidelberg, Germany
| | | | | | - W C Mike Thang
- Queensland Cyber Infrastructure Foundation (QCIF), Australia
- Institute of Molecular Bioscience, University of Queensland, St Lucia, Australia
| | - Cameron Hyde
- Queensland Cyber Infrastructure Foundation (QCIF), Australia
- Sippy Downs, University of the Sunshine Coast, Australia
| | - Gareth Price
- Queensland Cyber Infrastructure Foundation (QCIF), Australia
- Institute of Molecular Bioscience, University of Queensland, St Lucia, Australia
| | - Pratik D Jagtap
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, MN, USA
| | - Timothy J Griffin
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, MN, USA
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2
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Optimized cutting laser trajectory for laser capture microdissection. Biologia (Bratisl) 2019. [DOI: 10.2478/s11756-019-00234-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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3
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Pawlikowska P, Faugeroux V, Oulhen M, Aberlenc A, Tayoun T, Pailler E, Farace F. Circulating tumor cells (CTCs) for the noninvasive monitoring and personalization of non-small cell lung cancer (NSCLC) therapies. J Thorac Dis 2019; 11:S45-S56. [PMID: 30775027 DOI: 10.21037/jtd.2018.12.80] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Growing evidences for tumor heterogeneity confirm that single-tumor biopsies frequently fail to reveal the widespread mutagenic profile of tumor. Repeated biopsies are in most cases unfeasible, especially in advanced cancers. We describe here how circulating tumor cells (CTCs) isolated from minimally invasive blood sample might inform us about intratumor heterogeneity, tumor evolution and treatment resistance. We also discuss the advances of CTCs research, most notably in molecularly selected non-small cell lung cancer (NSCLC) patients, highlighting challenges and opportunities related to personalized therapy.
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Affiliation(s)
- Patrycja Pawlikowska
- INSERM, U981 "Identification of Molecular Predictors and new Targets for Cancer Treatment", Villejuif, France.,Gustave Roussy, Université Paris-Saclay, "Circulating Tumor Cells" Translational Platform, Villejuif, France
| | - Vincent Faugeroux
- INSERM, U981 "Identification of Molecular Predictors and new Targets for Cancer Treatment", Villejuif, France.,Gustave Roussy, Université Paris-Saclay, "Circulating Tumor Cells" Translational Platform, Villejuif, France
| | - Marianne Oulhen
- Gustave Roussy, Université Paris-Saclay, "Circulating Tumor Cells" Translational Platform, Villejuif, France
| | - Agathe Aberlenc
- Gustave Roussy, Université Paris-Saclay, "Circulating Tumor Cells" Translational Platform, Villejuif, France
| | - Tala Tayoun
- INSERM, U981 "Identification of Molecular Predictors and new Targets for Cancer Treatment", Villejuif, France.,Gustave Roussy, Université Paris-Saclay, "Circulating Tumor Cells" Translational Platform, Villejuif, France
| | - Emma Pailler
- INSERM, U981 "Identification of Molecular Predictors and new Targets for Cancer Treatment", Villejuif, France.,Gustave Roussy, Université Paris-Saclay, "Circulating Tumor Cells" Translational Platform, Villejuif, France
| | - Françoise Farace
- INSERM, U981 "Identification of Molecular Predictors and new Targets for Cancer Treatment", Villejuif, France.,Gustave Roussy, Université Paris-Saclay, "Circulating Tumor Cells" Translational Platform, Villejuif, France
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4
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Murray C, Miwa H, Dhar M, Park DE, Pao E, Martinez J, Kaanumale S, Loghin E, Graf J, Rhaddassi K, Kwok WW, Hafler D, Puleo C, Di Carlo D. Unsupervised capture and profiling of rare immune cells using multi-directional magnetic ratcheting. LAB ON A CHIP 2018; 18:2396-2409. [PMID: 30039125 PMCID: PMC6095198 DOI: 10.1039/c8lc00518d] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
Immunotherapies (IT) require induction, expansion, and maintenance of specific changes to a patient's immune cell repertoire which yield a therapeutic benefit. Recently, mechanistic understanding of these changes at the cellular level has revealed that IT results in complex phenotypic transitions in target cells, and that therapeutic effectiveness may be predicted by monitoring these transitions during therapy. However, monitoring will require unique tools that enable capture, manipulation, and profiling of rare immune cell populations. In this study, we introduce a method of automated and unsupervised separation and processing of rare immune cells, using high-force and multidimensional magnetic ratcheting (MR). We demonstrate capture of target immune cells using samples with up to 1 : 10 000 target cell to background cell ratios from input volumes as small as 25 microliters (i.e. a low volume and low cell frequency sample sparing assay interface). Cell capture is shown to achieve up to 90% capture efficiency and purity, and captured cell analysis is shown using both on-chip culture/activity assays and off-chip ejection and nucleic acid analysis. These results demonstrate that multi-directional magnetic ratcheting offers a unique separation system for dealing with blood cell samples that contain either rare cells or significantly small volumes, and the "sample sparing" capability leads to an expanded spectrum of parameters that can be measured. These tools will be paramount to advancing techniques for immune monitoring under conditions in which both the sample volume and number of antigen-specific target cells are often exceedingly small, including during IT and treatment of allergy, asthma, autoimmunity, immunodeficiency, cell based therapy, transplantation, and infection.
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Affiliation(s)
- Coleman Murray
- Dept. of Bioengineering; University of California, Los Angeles, CA, USA
| | - Hiromi Miwa
- Dept. of Bioengineering; University of California, Los Angeles, CA, USA
| | - Manjima Dhar
- Dept. of Bioengineering; University of California, Los Angeles, CA, USA
| | - Da Eun Park
- Dept. of Bioengineering; University of California, Los Angeles, CA, USA
| | - Edward Pao
- Dept. of Bioengineering; University of California, Los Angeles, CA, USA
| | | | | | | | - John Graf
- GE Global Research Centre, Niskayuna, NY, USA
| | | | - William W Kwok
- Benaroya Research Institute, Virginia Mason, Seattle, WA, USA
| | - David Hafler
- Dept. of Neurology, Yale University, New Haven, CT, USA
| | - Chris Puleo
- GE Global Research Centre, Niskayuna, NY, USA
| | - Dino Di Carlo
- Dept. of Bioengineering; University of California, Los Angeles, CA, USA
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5
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Negishi R, Takai K, Tanaka T, Matsunaga T, Yoshino T. High-Throughput Manipulation of Circulating Tumor Cells Using a Multiple Single-Cell Encapsulation System with a Digital Micromirror Device. Anal Chem 2018; 90:9734-9741. [DOI: 10.1021/acs.analchem.8b00896] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Affiliation(s)
- Ryo Negishi
- Division of Biotechnology and Life science, Institute of Engineering, Tokyo University of Agriculture and Technology, 2-24-16, Naka-cho, Koganei, Tokyo, 184-8588, Japan
| | - Kaori Takai
- Division of Biotechnology and Life science, Institute of Engineering, Tokyo University of Agriculture and Technology, 2-24-16, Naka-cho, Koganei, Tokyo, 184-8588, Japan
| | - Tsuyoshi Tanaka
- Division of Biotechnology and Life science, Institute of Engineering, Tokyo University of Agriculture and Technology, 2-24-16, Naka-cho, Koganei, Tokyo, 184-8588, Japan
| | - Tadashi Matsunaga
- Division of Biotechnology and Life science, Institute of Engineering, Tokyo University of Agriculture and Technology, 2-24-16, Naka-cho, Koganei, Tokyo, 184-8588, Japan
| | - Tomoko Yoshino
- Division of Biotechnology and Life science, Institute of Engineering, Tokyo University of Agriculture and Technology, 2-24-16, Naka-cho, Koganei, Tokyo, 184-8588, Japan
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6
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Mansilla C, Soria E, Ramírez N. The identification and isolation of CTCs: A biological Rubik's cube. Crit Rev Oncol Hematol 2018; 126:129-134. [PMID: 29759554 DOI: 10.1016/j.critrevonc.2018.03.027] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2017] [Revised: 02/22/2018] [Accepted: 03/29/2018] [Indexed: 12/17/2022] Open
Abstract
Liquid biopsy represents an alternative to conventional biopsies for the evaluation of tumors mainly due to its easy sampling. One of the main applications is the enumeration of Circulating Tumor Cells (CTCs) to evaluate tumor progression or response to treatment. The analysis of the functional characteristics of CTCs could give us much more information about their role in order to establish a more personalized treatment for the patients. The major issue that has to be solved is the isolation of the CTC population. Multiple protocols have been developed, however none of them has demonstrated to be the definitive one. In fact, a combination of these techniques has often been performed in order to obtain a purer and viable population of CTCs. In this review we have summarized for the first time the different combinatorial approaches used in the last years to optimize the isolation of CTCs and their limitations.
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Affiliation(s)
- Cristina Mansilla
- Oncohematology Research Group, Navarrabiomed, Complejo Hospitalario de Navarra, Universidad Pública de Navarra, Instituto de Investigación Sanitaria de Navarra (IdiSNA), Irunlarrea 3, 31008 Pamplona, Spain
| | - Elena Soria
- Oncohematology Research Group, Navarrabiomed, Complejo Hospitalario de Navarra, Universidad Pública de Navarra, Instituto de Investigación Sanitaria de Navarra (IdiSNA), Irunlarrea 3, 31008 Pamplona, Spain
| | - Natalia Ramírez
- Oncohematology Research Group, Navarrabiomed, Complejo Hospitalario de Navarra, Universidad Pública de Navarra, Instituto de Investigación Sanitaria de Navarra (IdiSNA), Irunlarrea 3, 31008 Pamplona, Spain.
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7
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Riethdorf S, O'Flaherty L, Hille C, Pantel K. Clinical applications of the CellSearch platform in cancer patients. Adv Drug Deliv Rev 2018; 125:102-121. [PMID: 29355669 DOI: 10.1016/j.addr.2018.01.011] [Citation(s) in RCA: 159] [Impact Index Per Article: 26.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2017] [Revised: 01/12/2018] [Accepted: 01/15/2018] [Indexed: 12/29/2022]
Abstract
The CellSearch® system (CS) enables standardized enrichment and enumeration of circulating tumor cells (CTCs) that are repeatedly assessable via non-invasive "liquid biopsy". While the association of CTCs with poor clinical outcome for cancer patients has clearly been demonstrated in numerous clinical studies, utilizing CTCs for the identification of therapeutic targets, stratification of patients for targeted therapies and uncovering mechanisms of resistance is still under investigation. Here, we comprehensively review the current benefits and drawbacks of clinical CTC analyses for patients with metastatic and non-metastatic tumors. Furthermore, the review focuses on approaches beyond CTC enumeration that aim to uncover therapeutically relevant antigens, genomic aberrations, transcriptional profiles and epigenetic alterations of CTCs at a single cell level. This characterization of CTCs may shed light on the heterogeneity and genomic landscapes of malignant tumors, an understanding of which is highly important for the development of new therapeutic strategies.
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8
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Xin X, Jiang X, Lichtler A, Kronenberg M, Rowe D, Pachter JS. Laser-Capture Microdissection and RNA Extraction from Perfusion-Fixed Cartilage and Bone Tissue from Mice Implanted with Human iPSC-Derived MSCs in a Calvarial Defect Model. Methods Mol Biol 2018; 1723:385-396. [PMID: 29344873 DOI: 10.1007/978-1-4939-7558-7_22] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Laser-capture microdissection (LCM) coupled to downstream RNA analysis poses unique difficulties for the evaluation of mineralized tissues. A rapid protocol was thus developed to enable sufficient integrity of bone and cartilage tissue for reliable sectioning, while minimizing RNA loss associated with prolonged decalcification and purification steps. Specifically, the protocol involves pump-assisted, cardiac perfusion-fixation with paraformaldehyde, and moderate digestion of LCM-acquired tissue with proteinase K followed by DNase treatment and separation of RNA using magnetic beads. Reverse transcription and cDNA synthesis are performed immediately after RNA purification, without need for further protein removal.
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Affiliation(s)
- Xiaonan Xin
- Center for Regenerative Medicine and Skeletal Development, School of Dental Medicine, UConn Health, Farmington, CT, USA.,Department of Reconstructive Sciences, School of Dental Medicine, UConn Health, Farmington, CT, USA
| | - Xi Jiang
- Center for Regenerative Medicine and Skeletal Development, School of Dental Medicine, UConn Health, Farmington, CT, USA.,Department of Reconstructive Sciences, School of Dental Medicine, UConn Health, Farmington, CT, USA
| | - Alexander Lichtler
- Center for Regenerative Medicine and Skeletal Development, School of Dental Medicine, UConn Health, Farmington, CT, USA.,Department of Reconstructive Sciences, School of Dental Medicine, UConn Health, Farmington, CT, USA
| | - Mark Kronenberg
- Center for Regenerative Medicine and Skeletal Development, School of Dental Medicine, UConn Health, Farmington, CT, USA.,Department of Reconstructive Sciences, School of Dental Medicine, UConn Health, Farmington, CT, USA
| | - David Rowe
- Center for Regenerative Medicine and Skeletal Development, School of Dental Medicine, UConn Health, Farmington, CT, USA.,Department of Reconstructive Sciences, School of Dental Medicine, UConn Health, Farmington, CT, USA
| | - Joel S Pachter
- Department of Cell Biology, Director Laser Capture Microdissection Core Facility, School of Medicine, UConn Health, Farmington, CT, USA.
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9
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Beije N, Sieuwerts AM, Kraan J, Van NM, Onstenk W, Vitale SR, van der Vlugt-Daane M, Dirix LY, Brouwer A, Hamberg P, de Jongh FE, Jager A, Seynaeve CM, Jansen MPHM, Foekens JA, Martens JWM, Sleijfer S. Estrogen receptor mutations and splice variants determined in liquid biopsies from metastatic breast cancer patients. Mol Oncol 2017; 12:48-57. [PMID: 29063679 PMCID: PMC5748489 DOI: 10.1002/1878-0261.12147] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2017] [Revised: 09/24/2017] [Accepted: 10/07/2017] [Indexed: 01/09/2023] Open
Abstract
Mutations and splice variants in the estrogen receptor (ER) gene, ESR1, may yield endocrine resistance in metastatic breast cancer (MBC) patients. These putative endocrine resistance markers are likely to emerge during treatment, and therefore, its detection in liquid biopsies, such as circulating tumor cells (CTCs) and cell‐free DNA (cfDNA), is of great interest. This research aimed to determine whether ESR1 mutations and splice variants occur more frequently in CTCs of MBC patients progressing on endocrine treatment. In addition, the presence of ESR1 mutations was evaluated in matched cfDNA and compared to CTCs. CellSearch‐enriched CTC fractions (≥5/7.5 mL) of two MBC cohorts were evaluated, namely (a) patients starting first‐line endocrine therapy (n = 43, baseline cohort) and (b) patients progressing on any line of endocrine therapy (n = 40, progressing cohort). ESR1 hotspot mutations (D538G and Y537S/N/C) were evaluated in CTC‐enriched DNA using digital PCR and compared with matched cfDNA (n = 18 baseline cohort; n = 26 progressing cohort). Expression of ESR1 full‐length and 4 of its splice variants (∆5, ∆7, 36 kDa, and 46 kDa) was evaluated in CTC‐enriched mRNA. It was observed that in the CTCs, the ESR1 mutations were not enriched in the progressing cohort (8%), when compared with the baseline cohort (5%) (P = 0.66). In the cfDNA, however, ESR1 mutations were more prevalent in the progressing cohort (42%) than in the baseline cohort (11%) (P = 0.04). Three of the same mutations were observed in both CTCs and cfDNA, 1 mutation in CTCs only, and 11 in cfDNA only. Only the ∆5 ESR1 splice variant was CTC‐specific expressed, but was not enriched in the progressing cohort. In conclusion, sensitivity for detecting ESR1 mutations in CTC‐enriched fractions was lower than for cfDNA. ESR1 mutations detected in cfDNA, rarely present at the start of first‐line endocrine therapy, were enriched at progression, strongly suggesting a role in conferring endocrine resistance in MBC.
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Affiliation(s)
- Nick Beije
- Erasmus MC Cancer Institute, Department of Medical Oncology and Cancer Genomics Netherlands, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Anieta M Sieuwerts
- Erasmus MC Cancer Institute, Department of Medical Oncology and Cancer Genomics Netherlands, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Jaco Kraan
- Erasmus MC Cancer Institute, Department of Medical Oncology and Cancer Genomics Netherlands, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Ngoc M Van
- Erasmus MC Cancer Institute, Department of Medical Oncology and Cancer Genomics Netherlands, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Wendy Onstenk
- Erasmus MC Cancer Institute, Department of Medical Oncology and Cancer Genomics Netherlands, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Silvia R Vitale
- Erasmus MC Cancer Institute, Department of Medical Oncology and Cancer Genomics Netherlands, Erasmus University Medical Center, Rotterdam, The Netherlands.,Department of Clinical and Molecular Medicine, University of Catania, Italy
| | - Michelle van der Vlugt-Daane
- Erasmus MC Cancer Institute, Department of Medical Oncology and Cancer Genomics Netherlands, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Luc Y Dirix
- Translational Cancer Research Unit, Department of Medical Oncology, Oncology Center GZA Hospital Sint Augustinus, Antwerp, Belgium
| | - Anja Brouwer
- Translational Cancer Research Unit, Department of Medical Oncology, Oncology Center GZA Hospital Sint Augustinus, Antwerp, Belgium
| | - Paul Hamberg
- Department of Internal Medicine, Franciscus Gasthuis, Rotterdam, The Netherlands
| | - Felix E de Jongh
- Department of Internal Medicine, Ikazia Hospital, Rotterdam, The Netherlands
| | - Agnes Jager
- Erasmus MC Cancer Institute, Department of Medical Oncology and Cancer Genomics Netherlands, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Caroline M Seynaeve
- Erasmus MC Cancer Institute, Department of Medical Oncology and Cancer Genomics Netherlands, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Maurice P H M Jansen
- Erasmus MC Cancer Institute, Department of Medical Oncology and Cancer Genomics Netherlands, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - John A Foekens
- Erasmus MC Cancer Institute, Department of Medical Oncology and Cancer Genomics Netherlands, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - John W M Martens
- Erasmus MC Cancer Institute, Department of Medical Oncology and Cancer Genomics Netherlands, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Stefan Sleijfer
- Erasmus MC Cancer Institute, Department of Medical Oncology and Cancer Genomics Netherlands, Erasmus University Medical Center, Rotterdam, The Netherlands
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10
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Beije N, Sieuwerts AM, Kraan J, Van NM, Onstenk W, Vitale SR, van der Vlugt-Daane M, Dirix LY, Brouwer A, Hamberg P, de Jongh FE, Jager A, Seynaeve CM, Jansen MPHM, Foekens JA, Martens JWM, Sleijfer S. Estrogen receptor mutations and splice variants determined in liquid biopsies from metastatic breast cancer patients. Mol Oncol 2017. [PMID: 29063679 DOI: 10.1002/1878‐0261.12147] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Mutations and splice variants in the estrogen receptor (ER) gene, ESR1, may yield endocrine resistance in metastatic breast cancer (MBC) patients. These putative endocrine resistance markers are likely to emerge during treatment, and therefore, its detection in liquid biopsies, such as circulating tumor cells (CTCs) and cell-free DNA (cfDNA), is of great interest. This research aimed to determine whether ESR1 mutations and splice variants occur more frequently in CTCs of MBC patients progressing on endocrine treatment. In addition, the presence of ESR1 mutations was evaluated in matched cfDNA and compared to CTCs. CellSearch-enriched CTC fractions (≥5/7.5 mL) of two MBC cohorts were evaluated, namely (a) patients starting first-line endocrine therapy (n = 43, baseline cohort) and (b) patients progressing on any line of endocrine therapy (n = 40, progressing cohort). ESR1 hotspot mutations (D538G and Y537S/N/C) were evaluated in CTC-enriched DNA using digital PCR and compared with matched cfDNA (n = 18 baseline cohort; n = 26 progressing cohort). Expression of ESR1 full-length and 4 of its splice variants (∆5, ∆7, 36 kDa, and 46 kDa) was evaluated in CTC-enriched mRNA. It was observed that in the CTCs, the ESR1 mutations were not enriched in the progressing cohort (8%), when compared with the baseline cohort (5%) (P = 0.66). In the cfDNA, however, ESR1 mutations were more prevalent in the progressing cohort (42%) than in the baseline cohort (11%) (P = 0.04). Three of the same mutations were observed in both CTCs and cfDNA, 1 mutation in CTCs only, and 11 in cfDNA only. Only the ∆5 ESR1 splice variant was CTC-specific expressed, but was not enriched in the progressing cohort. In conclusion, sensitivity for detecting ESR1 mutations in CTC-enriched fractions was lower than for cfDNA. ESR1 mutations detected in cfDNA, rarely present at the start of first-line endocrine therapy, were enriched at progression, strongly suggesting a role in conferring endocrine resistance in MBC.
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Affiliation(s)
- Nick Beije
- Erasmus MC Cancer Institute, Department of Medical Oncology and Cancer Genomics Netherlands, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Anieta M Sieuwerts
- Erasmus MC Cancer Institute, Department of Medical Oncology and Cancer Genomics Netherlands, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Jaco Kraan
- Erasmus MC Cancer Institute, Department of Medical Oncology and Cancer Genomics Netherlands, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Ngoc M Van
- Erasmus MC Cancer Institute, Department of Medical Oncology and Cancer Genomics Netherlands, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Wendy Onstenk
- Erasmus MC Cancer Institute, Department of Medical Oncology and Cancer Genomics Netherlands, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Silvia R Vitale
- Erasmus MC Cancer Institute, Department of Medical Oncology and Cancer Genomics Netherlands, Erasmus University Medical Center, Rotterdam, The Netherlands.,Department of Clinical and Molecular Medicine, University of Catania, Italy
| | - Michelle van der Vlugt-Daane
- Erasmus MC Cancer Institute, Department of Medical Oncology and Cancer Genomics Netherlands, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Luc Y Dirix
- Translational Cancer Research Unit, Department of Medical Oncology, Oncology Center GZA Hospital Sint Augustinus, Antwerp, Belgium
| | - Anja Brouwer
- Translational Cancer Research Unit, Department of Medical Oncology, Oncology Center GZA Hospital Sint Augustinus, Antwerp, Belgium
| | - Paul Hamberg
- Department of Internal Medicine, Franciscus Gasthuis, Rotterdam, The Netherlands
| | - Felix E de Jongh
- Department of Internal Medicine, Ikazia Hospital, Rotterdam, The Netherlands
| | - Agnes Jager
- Erasmus MC Cancer Institute, Department of Medical Oncology and Cancer Genomics Netherlands, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Caroline M Seynaeve
- Erasmus MC Cancer Institute, Department of Medical Oncology and Cancer Genomics Netherlands, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Maurice P H M Jansen
- Erasmus MC Cancer Institute, Department of Medical Oncology and Cancer Genomics Netherlands, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - John A Foekens
- Erasmus MC Cancer Institute, Department of Medical Oncology and Cancer Genomics Netherlands, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - John W M Martens
- Erasmus MC Cancer Institute, Department of Medical Oncology and Cancer Genomics Netherlands, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Stefan Sleijfer
- Erasmus MC Cancer Institute, Department of Medical Oncology and Cancer Genomics Netherlands, Erasmus University Medical Center, Rotterdam, The Netherlands
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11
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Tan CRC, Zhou L, El-Deiry WS. Circulating Tumor Cells Versus Circulating Tumor DNA in Colorectal Cancer: Pros and Cons. CURRENT COLORECTAL CANCER REPORTS 2016; 12:151-161. [PMID: 27516729 DOI: 10.1007/s11888-016-0320-y] [Citation(s) in RCA: 49] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Circulating tumor cells (CTCs) and circulating tumor DNA (ctDNA) are emerging noninvasive multifunctional biomarkers in liquid biopsy allowing for early diagnosis, accurate prognosis, therapeutic target selection, spatiotemporal monitoring of metastasis, as well as monitoring response and resistance to treatment. CTCs and ctDNA are released from different tumor types at different stages and contribute complementary information for clinical decision. Although big strides have been taken in technology development for detection, isolation and characterization of CTCs and sensitive and specific detection of ctDNA, CTC-, and ctDNA-based liquid biopsies may not be widely adopted for routine cancer patient care until the suitability, accuracy, and reliability of these tests are validated and more standardized protocols are corroborated in large, independent, prospectively designed trials. This review covers CTC- and ctDNA-related technologies and their application in colorectal cancer. The promise of CTC-and ctDNA-based liquid biopsies is envisioned.
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Affiliation(s)
- Carlyn Rose C Tan
- Department of Hematology/Oncology and Molecular Therapeutics Program, Fox Chase Cancer Center, Philadelphia, PA 19111, USA
| | - Lanlan Zhou
- Department of Hematology/Oncology and Molecular Therapeutics Program, Fox Chase Cancer Center, Philadelphia, PA 19111, USA
| | - Wafik S El-Deiry
- Department of Hematology/Oncology and Molecular Therapeutics Program, Fox Chase Cancer Center, Philadelphia, PA 19111, USA
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Lianidou ES. Gene expression profiling and DNA methylation analyses of CTCs. Mol Oncol 2016; 10:431-42. [PMID: 26880168 DOI: 10.1016/j.molonc.2016.01.011] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2015] [Revised: 01/19/2016] [Accepted: 01/25/2016] [Indexed: 01/26/2023] Open
Abstract
A variety of molecular assays have been developed for CTCs detection and molecular characterization. Molecular assays are based on the nucleic acid analysis in CTCs and are based on total RNA isolation and subsequent mRNA quantification of specific genes, or isolation of genomic DNA that can be for DNA methylation studies and mutation analysis. This review is mainly focused on gene expression and methylation studies in CTCs in various types of cancer.
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Affiliation(s)
- Evi S Lianidou
- Analysis of Circulating Tumor Cells Lab, Lab of Analytical Chemistry, Department of Chemistry, University of Athens, 15771, Greece.
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