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Xu J, Gao H, Guan X, Meng J, Ding S, Long Q, Yi W. Circulating tumor DNA: from discovery to clinical application in breast cancer. Front Immunol 2024; 15:1355887. [PMID: 38745646 PMCID: PMC11091288 DOI: 10.3389/fimmu.2024.1355887] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2023] [Accepted: 04/16/2024] [Indexed: 05/16/2024] Open
Abstract
Breast cancer (BC) stands out as the cancer with the highest incidence of morbidity and mortality among women worldwide, and its incidence rate is currently trending upwards. Improving the efficiency of breast cancer diagnosis and treatment is crucial, as it can effectively reduce the disease burden. Circulating tumor DNA (ctDNA) originates from the release of tumor cells and plays a pivotal role in the occurrence, development, and metastasis of breast cancer. In recent years, the widespread application of high-throughput analytical technology has made ctDNA a promising biomarker for early cancer detection, monitoring minimal residual disease, early recurrence monitoring, and predicting treatment outcomes. ctDNA-based approaches can effectively compensate for the shortcomings of traditional screening and monitoring methods, which fail to provide real-time information and prospective guidance for breast cancer diagnosis and treatment. This review summarizes the applications of ctDNA in various aspects of breast cancer, including screening, diagnosis, prognosis, treatment, and follow-up. It highlights the current research status in this field and emphasizes the potential for future large-scale clinical applications of ctDNA-based approaches.
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Affiliation(s)
- Jiachi Xu
- Department of General Surgery, The Second Xiangya Hospital, Central South University, Changsha, Hunan, China
- Clinical Research Center For Breast Disease In Hunan Province, Changsha, China
| | - Hongyu Gao
- Department of General Surgery, The Second Xiangya Hospital, Central South University, Changsha, Hunan, China
- Clinical Research Center For Breast Disease In Hunan Province, Changsha, China
| | - Xinyu Guan
- Department of General Surgery, The Second Xiangya Hospital, Central South University, Changsha, Hunan, China
- Clinical Research Center For Breast Disease In Hunan Province, Changsha, China
| | - Jiahao Meng
- Department of General Surgery, The Second Xiangya Hospital, Central South University, Changsha, Hunan, China
- Clinical Research Center For Breast Disease In Hunan Province, Changsha, China
| | - Shirong Ding
- Department of Oncology, The Second Xiangya Hospital of Central South University, Changsha, Hunan, China
| | - Qian Long
- Department of General Surgery, The Second Xiangya Hospital, Central South University, Changsha, Hunan, China
- Clinical Research Center For Breast Disease In Hunan Province, Changsha, China
| | - Wenjun Yi
- Department of General Surgery, The Second Xiangya Hospital, Central South University, Changsha, Hunan, China
- Clinical Research Center For Breast Disease In Hunan Province, Changsha, China
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Bar Y, Keenan JC, Niemierko A, Medford AJ, Isakoff SJ, Ellisen LW, Bardia A, Vidula N. Genomic spectrum of actionable alterations in serial cell free DNA (cfDNA) analysis of patients with metastatic breast cancer. NPJ Breast Cancer 2024; 10:27. [PMID: 38605020 PMCID: PMC11009384 DOI: 10.1038/s41523-024-00633-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2023] [Accepted: 03/25/2024] [Indexed: 04/13/2024] Open
Abstract
We aimed to study the incidence and genomic spectrum of actionable alterations (AA) detected in serial cfDNA collections from patients with metastatic breast cancer (MBC). Patients with MBC who underwent plasma-based cfDNA testing (Guardant360®) between 2015 and 2021 at an academic institution were included. For patients with serial draws, new pathogenic alterations in each draw were classified as actionable alterations (AA) if they met ESCAT I or II criteria of the ESMO Scale for Clinical Actionability of Molecular Targets (ESCAT). A total of 344 patients with hormone receptor-positive (HR+)/HER2-negative (HER2-) MBC, 95 patients with triple-negative (TN) MBC and 42 patients with HER2-positive (HER2 + ) MBC had a baseline (BL) cfDNA draw. Of these, 139 HR+/HER2-, 33 TN and 13 HER2+ patients underwent subsequent cfDNA draws. In the HR+/HER2- cohort, the proportion of patients with new AA decreased from 63% at BL to 27-33% in the 2nd-4th draws (p < 0.0001). While some of the new AA in subsequent draws from patients with HR+/HER2- MBC were new actionable variants in the same genes that were known to be altered in previous draws, 10-24% of patients had new AA in previously unaltered genes. The incidence of new AA also decreased with subsequent draws in the TN and HER2+ cohorts (TN: 25% to 0-9%, HER2 + : 38% to 14-15%). While the incidence of new AA in serial cfDNA decreased with subsequent draws across all MBC subtypes, new alterations with a potential impact on treatment selection continued to emerge, particularly for patients with HR+/HER2- MBC.
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Affiliation(s)
- Yael Bar
- Massachusetts General Hospital Cancer Center, Boston, MA, USA.
- Tel Aviv Sourasky Medical Center and The Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel.
| | | | | | - Arielle J Medford
- Massachusetts General Hospital Cancer Center, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
| | - Steven J Isakoff
- Massachusetts General Hospital Cancer Center, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
| | - Leif W Ellisen
- Massachusetts General Hospital Cancer Center, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
| | - Aditya Bardia
- Massachusetts General Hospital Cancer Center, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
| | - Neelima Vidula
- Massachusetts General Hospital Cancer Center, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
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Kim YJ, Rho WY, Park SM, Jun BH. Optical nanomaterial-based detection of biomarkers in liquid biopsy. J Hematol Oncol 2024; 17:10. [PMID: 38486294 PMCID: PMC10938695 DOI: 10.1186/s13045-024-01531-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2023] [Accepted: 03/02/2024] [Indexed: 03/18/2024] Open
Abstract
Liquid biopsy, which is a minimally invasive procedure as an alternative to tissue biopsy, has been introduced as a new diagnostic/prognostic measure. By screening disease-related markers from the blood or other biofluids, it promises early diagnosis, timely prognostication, and effective treatment of the diseases. However, there will be a long way until its realization due to its conceptual and practical challenges. The biomarkers detected by liquid biopsy, such as circulating tumor cell (CTC) and circulating tumor DNA (ctDNA), are extraordinarily rare and often obscured by an abundance of normal cellular components, necessitating ultra-sensitive and accurate detection methods for the advancement of liquid biopsy techniques. Optical biosensors based on nanomaterials open an important opportunity in liquid biopsy because of their enhanced sensing performance with simple and practical properties. In this review article, we summarized recent innovations in optical nanomaterials to demonstrate the sensitive detection of protein, peptide, ctDNA, miRNA, exosome, and CTCs. Each study prepares the optical nanomaterials with a tailored design to enhance the sensing performance and to meet the requirements of each biomarker. The unique optical characteristics of metallic nanoparticles (NPs), quantum dots, upconversion NPs, silica NPs, polymeric NPs, and carbon nanomaterials are exploited for sensitive detection mechanisms. These recent advances in liquid biopsy using optical nanomaterials give us an opportunity to overcome challenging issues and provide a resource for understanding the unknown characteristics of the biomarkers as well as the mechanism of the disease.
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Affiliation(s)
- Young Jun Kim
- Department of Bioscience and Biotechnology, Konkuk University, Seoul, 05029, Republic of Korea
| | - Won-Yeop Rho
- School of International Engineering and Science, Jeonbuk National University, Chonju, 54896, Republic of Korea
| | - Seung-Min Park
- School of Chemistry, Chemical Engineering and Biotechnology, Nanyang Technological University, Singapore, 637459, Singapore.
| | - Bong-Hyun Jun
- Department of Bioscience and Biotechnology, Konkuk University, Seoul, 05029, Republic of Korea.
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Mavrogenis AF, Altsitzioglou P, Tsukamoto S, Errani C. Biopsy Techniques for Musculoskeletal Tumors: Basic Principles and Specialized Techniques. Curr Oncol 2024; 31:900-917. [PMID: 38392061 PMCID: PMC10888002 DOI: 10.3390/curroncol31020067] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2024] [Revised: 02/01/2024] [Accepted: 02/02/2024] [Indexed: 02/24/2024] Open
Abstract
Biopsy is a pivotal component in the diagnostic process of bone and soft tissue tumors. The objective is to obtain adequate tissue without compromising local tumor dissemination and the patient's survival. This review explores contemporary principles and practices in musculoskeletal biopsies, emphasizing the critical role of diagnostic accuracy while also delving into the evolving landscape of liquid biopsies as a promising alternative in the field. A thorough literature search was done in PubMed and Google Scholar as well as in physical books in libraries to summarize the available biopsy techniques for musculoskeletal tumors, discuss the available methods, risk factors, and complications, and to emphasize the challenges related to biopsies in oncology. Research articles that studied the basic principles and specialized techniques of biopsy techniques in tumor patients were deemed eligible. Their advantages and disadvantages, technical and pathophysiological mechanisms, and possible risks and complications were reviewed, summarized, and discussed. An inadequately executed biopsy may hinder diagnosis and subsequently impact treatment outcomes. All lesions should be approached with a presumption of malignancy until proven otherwise. Liquid biopsies have emerged as a potent non-invasive tool for analyzing tumor phenotype, progression, and drug resistance and guiding treatment decisions in bone sarcomas and metastases. Despite advancements, several barriers remain in biopsies, including challenges related to costs, scalability, reproducibility, and isolation methods. It is paramount that orthopedic oncologists work together with radiologists and pathologists to enhance diagnosis, patient outcomes, and healthcare costs.
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Affiliation(s)
- Andreas F. Mavrogenis
- First Department of Orthopaedics, School of Medicine, National and Kapodistrian University of Athens, 1 Rimini, 157 72 Athens, Greece;
| | - Pavlos Altsitzioglou
- First Department of Orthopaedics, School of Medicine, National and Kapodistrian University of Athens, 1 Rimini, 157 72 Athens, Greece;
| | - Shinji Tsukamoto
- Department of Orthopaedic Surgery, Nara Medical University, 840 Shijo-cho, Kashihara 634-8521, Japan;
| | - Costantino Errani
- Department of Orthopaedic Oncology, IRCCS Istituto Ortopedico Rizzoli, Via Pupilli 1, 40136 Bologna, Italy;
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Smit DJ, Schneegans S, Pantel K. Clinical applications of circulating tumor cells in patients with solid tumors. Clin Exp Metastasis 2024:10.1007/s10585-024-10267-5. [PMID: 38281256 DOI: 10.1007/s10585-024-10267-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2023] [Accepted: 01/11/2024] [Indexed: 01/30/2024]
Abstract
The concept of liquid biopsy analysis has been established more than a decade ago. Since the establishment of the term, tremendous advances have been achieved and plenty of methods as well as analytes have been investigated in basic research as well in clinical trials. Liquid biopsy refers to a body fluid-based biopsy that is minimal-invasive, and most importantly, allows dense monitoring of tumor responses by sequential blood sampling. Blood is the most important analyte for liquid biopsy analyses, providing an easily accessible source for a plethora of cells, cell-derived products, free nucleic acids, proteins as well as vesicles. More than 12,000 publications are listed in PubMed as of today including the term liquid biopsy. In this manuscript, we critically review the current implications of liquid biopsy, with special focus on circulating tumor cells, and describe the hurdles that need to be addressed before liquid biopsy can be implemented in clinical standard of care guidelines.
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Affiliation(s)
- Daniel J Smit
- Institute of Tumor Biology, University Medical Center Hamburg-Eppendorf, Martinistraße 52, 20246, Hamburg, Germany
- Fleur Hiege Center for Skin Cancer Research, Institute of Tumor Biology, University Medical Center Hamburg-Eppendorf, Martinistraße 52, 20246, Hamburg, Germany
| | - Svenja Schneegans
- Institute of Tumor Biology, University Medical Center Hamburg-Eppendorf, Martinistraße 52, 20246, Hamburg, Germany
| | - Klaus Pantel
- Institute of Tumor Biology, University Medical Center Hamburg-Eppendorf, Martinistraße 52, 20246, Hamburg, Germany.
- Fleur Hiege Center for Skin Cancer Research, Institute of Tumor Biology, University Medical Center Hamburg-Eppendorf, Martinistraße 52, 20246, Hamburg, Germany.
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Wishart G, Templeman A, Hendry F, Miller K, Pailhes-Jimenez AS. Molecular Profiling of Circulating Tumour Cells and Circulating Tumour DNA: Complementary Insights from a Single Blood Sample Utilising the Parsortix ® System. Curr Issues Mol Biol 2024; 46:773-787. [PMID: 38248352 PMCID: PMC10814787 DOI: 10.3390/cimb46010050] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2023] [Revised: 01/12/2024] [Accepted: 01/15/2024] [Indexed: 01/23/2024] Open
Abstract
The study of molecular drivers of cancer is an area of rapid growth and has led to the development of targeted treatments, significantly improving patient outcomes in many cancer types. The identification of actionable mutations informing targeted treatment strategies are now considered essential to the management of cancer. Traditionally, this information has been obtained through biomarker assessment of a tissue biopsy which is costly and can be associated with clinical complications and adverse events. In the last decade, blood-based liquid biopsy has emerged as a minimally invasive, fast, and cost-effective alternative, which is better suited to the requirement for longitudinal monitoring. Liquid biopsies allow for the concurrent study of multiple analytes, such as circulating tumour cells (CTCs) and circulating tumour DNA (ctDNA), from a single blood sample. Although ctDNA assays are commercially more advanced, there is an increasing awareness of the clinical significance of the transcriptome and proteome which can be analysed using CTCs. Herein, we review the literature in which the microfluidic, label-free Parsortix® system is utilised for CTC capture, harvest and analysis, alongside the analysis of ctDNA from a single blood sample. This detailed summary of the literature demonstrates how these two analytes can provide complementary disease information.
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Affiliation(s)
- Gabrielle Wishart
- ANGLE plc, Guildford GU2 7QB, UK; (A.T.); (F.H.); (K.M.); (A.-S.P.-J.)
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Yang T, Li W, Huang T, Zhou J. Genetic Testing Enhances the Precision Diagnosis and Treatment of Breast Cancer. Int J Mol Sci 2023; 24:16607. [PMID: 38068930 PMCID: PMC10706486 DOI: 10.3390/ijms242316607] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2023] [Revised: 11/14/2023] [Accepted: 11/20/2023] [Indexed: 12/18/2023] Open
Abstract
The contemporary comprehension of breast cancer has progressed to the molecular level. As a heterogeneous malignancy, conventional pathological diagnosis and histological classification could no longer meet the needs of precisely managing breast cancer. Genetic testing based on gene expression profiles and gene mutations has emerged and substantially contributed to the precise diagnosis and treatment of breast cancer. Multigene assays (MGAs) are explored for early-stage breast cancer patients, aiding the selection of adjuvant therapy and predicting prognosis. For metastatic breast cancer patients, testing specific genes indicates potentially effective antitumor agents. In this review, genetic testing in early-stage and metastatic breast cancer is summarized, as well as the advantages and challenges of genetic testing in breast cancer.
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Affiliation(s)
| | | | - Tao Huang
- Department of Breast and Thyroid Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, China (W.L.)
| | - Jun Zhou
- Department of Breast and Thyroid Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, China (W.L.)
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Trivedi R, Bhat KP. Liquid biopsy: creating opportunities in brain space. Br J Cancer 2023; 129:1727-1746. [PMID: 37752289 PMCID: PMC10667495 DOI: 10.1038/s41416-023-02446-0] [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: 05/24/2023] [Revised: 09/10/2023] [Accepted: 09/15/2023] [Indexed: 09/28/2023] Open
Abstract
In recent years, liquid biopsy has emerged as an alternative method to diagnose and monitor tumors. Compared to classical tissue biopsy procedures, liquid biopsy facilitates the repetitive collection of diverse cellular and acellular analytes from various biofluids in a non/minimally invasive manner. This strategy is of greater significance for high-grade brain malignancies such as glioblastoma as the quantity and accessibility of tumors are limited, and there are collateral risks of compromised life quality coupled with surgical interventions. Currently, blood and cerebrospinal fluid (CSF) are the most common biofluids used to collect circulating cells and biomolecules of tumor origin. These liquid biopsy analytes have created opportunities for real-time investigations of distinct genetic, epigenetic, transcriptomics, proteomics, and metabolomics alterations associated with brain tumors. This review describes different classes of liquid biopsy biomarkers present in the biofluids of brain tumor patients. Moreover, an overview of the liquid biopsy applications, challenges, recent technological advances, and clinical trials in the brain have also been provided.
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Affiliation(s)
- Rakesh Trivedi
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.
| | - Krishna P Bhat
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
- Department of Neurosurgery, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
- The University of Texas MD Anderson Cancer Center UTHealth Graduate School of Biomedical Sciences, Houston, TX, USA
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Chen TWW, Hsiao W, Dai MS, Lin CH, Chang DY, Chen IC, Wang MY, Chang SH, Huang SM, Cheng AL, Wu KW, Tan KT, Lu YS. Plasma cell-free tumor DNA, PIK3CA and TP53 mutations predicted inferior endocrine-based treatment outcome in endocrine receptor-positive metastatic breast cancer. Breast Cancer Res Treat 2023; 201:377-385. [PMID: 37344660 PMCID: PMC10460702 DOI: 10.1007/s10549-023-06967-3] [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: 01/18/2023] [Accepted: 05/03/2023] [Indexed: 06/23/2023]
Abstract
PURPOSE How to factor both tumor burden and oncogenic genomic mutations as variables to predict the outcome of endocrine-based therapy (ET) in ER-positive/HER2-negative metastatic breast cancer patients (MBC) remains to be explored. METHOD Blood samples prospectively collected from 163 ER-positive/HER2-negative female MBC patients, before ET, were used for cell-free tumor DNA (cfDNA) analysis. cfDNA was subjected to next-generation sequencing (NGS) to interrogate oncogenic PIK3CA hotspot and TP53 DNA-binding domain (DBD) mutations, including single nucleotide variants (SNVs) or small insertions and deletions (InDels). The variant calling threshold was set at 0.5%. Progression-free survival (PFS) was measured from the start of the ET treatment to the time of disease progression of the same treatment regimen. RESULTS Overall, the median PFS was 8.3 months (95% CI 5.7-11.1 months). The median cfDNA was 38.5 ng (range 4.4-1935 ng). The proportion of patients with PIK3CA and TP53 alterations were 25.1 and 15.3%, respectively. Patients with high total cfDNA (HR 1.74, p = 0.003), PIK3CA mutation (HR 1.74, p = 0.007), and TP53 mutation (HR 1.64, p = 0.047) in liquid biopsy conferred worse outcome after ET. Even for patients with low tumor burden, the detrimental effect of PIK3CA or TP53 mutation remained significant (p < 0.001). For patients with either PIK3CA (p < 0.001) or TP53 mutation (p = 0.004), there was significant positive correlation between allele frequency (AF) and total cfDNA. CONCLUSION After adjustment of cfDNA level, PIK3CA and TP53 mutations observed in liquid biopsy exerted detrimental effects on the outcome of ET-based regimens. The AF of PIK3CA or TP53 may be a surrogate marker for PFS.
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Affiliation(s)
- Tom Wei-Wu Chen
- Department of Oncology, National Taiwan University Hospital, Taipei, Taiwan
- Graduate Institute of Oncology, National Taiwan University College of Medicine, Taipei, Taiwan
- Department of Medical Oncology, National Taiwan University Cancer Center, Taipei, Taiwan
| | - Wen Hsiao
- ACT Genomics Co., Ltd, Taipei, Taiwan
| | - Ming-Shen Dai
- Division of Hematology and Oncology, Department of Medicine, Tri-Service General Hospital, Taipei, Taiwan
| | - Ching-Hung Lin
- Department of Oncology, National Taiwan University Hospital, Taipei, Taiwan
- Department of Medical Oncology, National Taiwan University Cancer Center, Taipei, Taiwan
| | - Dwan-Ying Chang
- Department of Oncology, National Taiwan University Hospital, Taipei, Taiwan
- Department of Medical Oncology, National Taiwan University Cancer Center, Taipei, Taiwan
| | - I-Chun Chen
- Department of Oncology, National Taiwan University Hospital, Taipei, Taiwan
- Graduate Institute of Oncology, National Taiwan University College of Medicine, Taipei, Taiwan
- Department of Medical Oncology, National Taiwan University Cancer Center, Taipei, Taiwan
| | - Ming-Yang Wang
- Department of Surgery, National Taiwan University Cancer Center, Taipei, Taiwan
| | - Shu-Han Chang
- Department of Oncology, National Taiwan University Hospital, Taipei, Taiwan
| | - Shu-Min Huang
- Department of Oncology, National Taiwan University Hospital, Taipei, Taiwan
| | - Ann-Lii Cheng
- Department of Oncology, National Taiwan University Hospital, Taipei, Taiwan
- Department of Medical Oncology, National Taiwan University Cancer Center, Taipei, Taiwan
| | - Ko-Wen Wu
- ACT Genomics Co., Ltd, Taipei, Taiwan
| | | | - Yen-Shen Lu
- Department of Oncology, National Taiwan University Hospital, Taipei, Taiwan.
- Department of Medical Oncology, National Taiwan University Cancer Center, Taipei, Taiwan.
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Welter L, Zheng S, Setayesh SM, Morikado M, Agrawal A, Nevarez R, Naghdloo A, Pore M, Higa N, Kolatkar A, Thiele JA, Sharma P, Moore HCF, Richer JK, Elias A, Pienta KJ, Zurita AJ, Gross ME, Shishido SN, Hicks J, Velasco CR, Kuhn P. Cell State and Cell Type: Deconvoluting Circulating Tumor Cell Populations in Liquid Biopsies by Multi-Omics. Cancers (Basel) 2023; 15:3949. [PMID: 37568766 PMCID: PMC10417732 DOI: 10.3390/cancers15153949] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2023] [Revised: 07/14/2023] [Accepted: 07/21/2023] [Indexed: 08/13/2023] Open
Abstract
Bi-directional crosstalk between the tumor and the tumor microenvironment (TME) has been shown to increase the rate of tumor evolution and to play a key role in neoplastic progression, therapeutic resistance, and a patient's overall survival. Here, we set out to use a comprehensive liquid-biopsy analysis to study cancer and specific TME cells in circulation and their association with disease status. Cytokeratin+, CD45- circulating rare cells (CRCs) from nine breast and four prostate cancer patients were characterized through morphometrics, single-cell copy number analysis, and targeted multiplexed proteomics to delineate cancer cell lineage from other rare cells originating in the TME. We show that we can detect epithelial circulating tumor cells (EPI.CTC), CTCs undergoing epithelial-to-mesenchymal transition (EMT.CTC) and circulating endothelial cells (CECs) using a universal rare event detection platform (HDSCA). Longitudinal analysis of an index patient finds that CTCs are present at the time of disease progression, while CECs are predominately present at the time of stable disease. In a small cohort of prostate and breast cancer patients, we find high inter-patient and temporal intra-patient variability in the expression of tissue specific markers such as ER, HER2, AR, PSA and PSMA and EpCAM. Our study stresses the importance of the multi-omic characterization of circulating rare cells in patients with breast and prostate carcinomas, specifically highlighting overlapping and cell type defining proteo-genomic characteristics of CTCs and CECs.
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Affiliation(s)
- Lisa Welter
- Convergent Science Institute in Cancer, Michelson Center for Convergent Bioscience, University of Southern California, Los Angeles, CA 90089, USA; (L.W.); (S.Z.); (S.M.S.); (M.M.); (A.A.); (R.N.); (A.N.); (M.P.); (N.H.); (A.K.); (J.-A.T.); (S.N.S.); (C.R.V.)
- Department of Biological Sciences, Dornsife College of Letters, Arts, and Sciences, University of Southern California, Los Angeles, CA 90089, USA
| | - Serena Zheng
- Convergent Science Institute in Cancer, Michelson Center for Convergent Bioscience, University of Southern California, Los Angeles, CA 90089, USA; (L.W.); (S.Z.); (S.M.S.); (M.M.); (A.A.); (R.N.); (A.N.); (M.P.); (N.H.); (A.K.); (J.-A.T.); (S.N.S.); (C.R.V.)
| | - Sonia Maryam Setayesh
- Convergent Science Institute in Cancer, Michelson Center for Convergent Bioscience, University of Southern California, Los Angeles, CA 90089, USA; (L.W.); (S.Z.); (S.M.S.); (M.M.); (A.A.); (R.N.); (A.N.); (M.P.); (N.H.); (A.K.); (J.-A.T.); (S.N.S.); (C.R.V.)
- Department of Biological Sciences, Dornsife College of Letters, Arts, and Sciences, University of Southern California, Los Angeles, CA 90089, USA
| | - Michael Morikado
- Convergent Science Institute in Cancer, Michelson Center for Convergent Bioscience, University of Southern California, Los Angeles, CA 90089, USA; (L.W.); (S.Z.); (S.M.S.); (M.M.); (A.A.); (R.N.); (A.N.); (M.P.); (N.H.); (A.K.); (J.-A.T.); (S.N.S.); (C.R.V.)
| | - Arushi Agrawal
- Convergent Science Institute in Cancer, Michelson Center for Convergent Bioscience, University of Southern California, Los Angeles, CA 90089, USA; (L.W.); (S.Z.); (S.M.S.); (M.M.); (A.A.); (R.N.); (A.N.); (M.P.); (N.H.); (A.K.); (J.-A.T.); (S.N.S.); (C.R.V.)
| | - Rafael Nevarez
- Convergent Science Institute in Cancer, Michelson Center for Convergent Bioscience, University of Southern California, Los Angeles, CA 90089, USA; (L.W.); (S.Z.); (S.M.S.); (M.M.); (A.A.); (R.N.); (A.N.); (M.P.); (N.H.); (A.K.); (J.-A.T.); (S.N.S.); (C.R.V.)
| | - Amin Naghdloo
- Convergent Science Institute in Cancer, Michelson Center for Convergent Bioscience, University of Southern California, Los Angeles, CA 90089, USA; (L.W.); (S.Z.); (S.M.S.); (M.M.); (A.A.); (R.N.); (A.N.); (M.P.); (N.H.); (A.K.); (J.-A.T.); (S.N.S.); (C.R.V.)
- Department of Aerospace and Mechanical Engineering, Viterbi School of Engineering, University of Southern California, Los Angeles, CA 90089, USA
| | - Milind Pore
- Convergent Science Institute in Cancer, Michelson Center for Convergent Bioscience, University of Southern California, Los Angeles, CA 90089, USA; (L.W.); (S.Z.); (S.M.S.); (M.M.); (A.A.); (R.N.); (A.N.); (M.P.); (N.H.); (A.K.); (J.-A.T.); (S.N.S.); (C.R.V.)
| | - Nikki Higa
- Convergent Science Institute in Cancer, Michelson Center for Convergent Bioscience, University of Southern California, Los Angeles, CA 90089, USA; (L.W.); (S.Z.); (S.M.S.); (M.M.); (A.A.); (R.N.); (A.N.); (M.P.); (N.H.); (A.K.); (J.-A.T.); (S.N.S.); (C.R.V.)
- Department of Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA
| | - Anand Kolatkar
- Convergent Science Institute in Cancer, Michelson Center for Convergent Bioscience, University of Southern California, Los Angeles, CA 90089, USA; (L.W.); (S.Z.); (S.M.S.); (M.M.); (A.A.); (R.N.); (A.N.); (M.P.); (N.H.); (A.K.); (J.-A.T.); (S.N.S.); (C.R.V.)
| | - Jana-Aletta Thiele
- Convergent Science Institute in Cancer, Michelson Center for Convergent Bioscience, University of Southern California, Los Angeles, CA 90089, USA; (L.W.); (S.Z.); (S.M.S.); (M.M.); (A.A.); (R.N.); (A.N.); (M.P.); (N.H.); (A.K.); (J.-A.T.); (S.N.S.); (C.R.V.)
| | - Priyanka Sharma
- University of Kansas Medical Center, Westwood, KS 66205, USA;
| | - Halle C. F. Moore
- Cleveland Clinic Taussig Cancer Institute, Cleveland, OH 44195, USA;
| | - Jennifer K. Richer
- University of Colorado Cancer Center, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA; (J.K.R.); (A.E.)
| | - Anthony Elias
- University of Colorado Cancer Center, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA; (J.K.R.); (A.E.)
| | - Kenneth J. Pienta
- The Cancer Ecology Center, Brady Urological Institute, Johns Hopkins School of Medicine, Baltimore, MD 21287, USA;
| | - Amado J. Zurita
- Department of Genitourinary Medical Oncology, MD Anderson, Houston, TX 77230, USA;
| | - Mitchell E. Gross
- Lawrence J. Ellison Institute for Transformative Medicine, Los Angeles, CA 90064, USA;
- Department of Biomedical Engineering, Viterbi School of Engineering, University of Southern California, Los Angeles, CA 90089, USA
| | - Stephanie N. Shishido
- Convergent Science Institute in Cancer, Michelson Center for Convergent Bioscience, University of Southern California, Los Angeles, CA 90089, USA; (L.W.); (S.Z.); (S.M.S.); (M.M.); (A.A.); (R.N.); (A.N.); (M.P.); (N.H.); (A.K.); (J.-A.T.); (S.N.S.); (C.R.V.)
| | - James Hicks
- Convergent Science Institute in Cancer, Michelson Center for Convergent Bioscience, University of Southern California, Los Angeles, CA 90089, USA; (L.W.); (S.Z.); (S.M.S.); (M.M.); (A.A.); (R.N.); (A.N.); (M.P.); (N.H.); (A.K.); (J.-A.T.); (S.N.S.); (C.R.V.)
- Department of Biological Sciences, Dornsife College of Letters, Arts, and Sciences, University of Southern California, Los Angeles, CA 90089, USA
| | - Carmen Ruiz Velasco
- Convergent Science Institute in Cancer, Michelson Center for Convergent Bioscience, University of Southern California, Los Angeles, CA 90089, USA; (L.W.); (S.Z.); (S.M.S.); (M.M.); (A.A.); (R.N.); (A.N.); (M.P.); (N.H.); (A.K.); (J.-A.T.); (S.N.S.); (C.R.V.)
| | - Peter Kuhn
- Convergent Science Institute in Cancer, Michelson Center for Convergent Bioscience, University of Southern California, Los Angeles, CA 90089, USA; (L.W.); (S.Z.); (S.M.S.); (M.M.); (A.A.); (R.N.); (A.N.); (M.P.); (N.H.); (A.K.); (J.-A.T.); (S.N.S.); (C.R.V.)
- Department of Biological Sciences, Dornsife College of Letters, Arts, and Sciences, University of Southern California, Los Angeles, CA 90089, USA
- Department of Aerospace and Mechanical Engineering, Viterbi School of Engineering, University of Southern California, Los Angeles, CA 90089, USA
- Department of Biomedical Engineering, Viterbi School of Engineering, University of Southern California, Los Angeles, CA 90089, USA
- Catherine & Joseph Aresty Department of Urology, Institute of Urology, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA
- Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA
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11
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Mangum R, Reuther J, Baksi KS, Gandhi I, Zabriskie RC, Recinos A, Raesz-Martinez R, Lin FY, Potter SL, Sher AC, Kralik SF, Mohila CA, Chintagumpala MM, Muzny D, Hu J, Gibbs RA, Fisher KE, Bernini JC, Gill J, Griffin TC, Tomlinson GE, Vallance KL, Plon SE, Roy A, Parsons DW. Circulating tumor DNA sequencing of pediatric solid and brain tumor patients: An institutional feasibility study. Pediatr Hematol Oncol 2023; 40:719-738. [PMID: 37366551 PMCID: PMC10592361 DOI: 10.1080/08880018.2023.2228837] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/29/2023] [Revised: 05/15/2023] [Accepted: 06/01/2023] [Indexed: 06/28/2023]
Abstract
The potential of circulating tumor DNA (ctDNA) analysis to serve as a real-time "liquid biopsy" for children with central nervous system (CNS) and non-CNS solid tumors remains to be fully elucidated. We conducted a study to investigate the feasibility and potential clinical utility of ctDNA sequencing in pediatric patients enrolled on an institutional clinical genomics trial. A total of 240 patients had tumor DNA profiling performed during the study period. Plasma samples were collected at study enrollment from 217 patients and then longitudinally from a subset of patients. Successful cell-free DNA extraction and quantification occurred in 216 of 217 (99.5%) of these initial samples. Twenty-four patients were identified whose tumors harbored 30 unique variants that were potentially detectable on a commercially-available ctDNA panel. Twenty of these 30 mutations (67%) were successfully detected by next-generation sequencing in the ctDNA from at least one plasma sample. The rate of ctDNA mutation detection was higher in patients with non-CNS solid tumors (7/9, 78%) compared to those with CNS tumors (9/15, 60%). A higher ctDNA mutation detection rate was also observed in patients with metastatic disease (9/10, 90%) compared to non-metastatic disease (7/14, 50%), although tumor-specific variants were detected in a few patients in the absence of radiographic evidence of disease. This study illustrates the feasibility of incorporating longitudinal ctDNA analysis into the management of relapsed or refractory patients with childhood CNS or non-CNS solid tumors.
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Affiliation(s)
- Ross Mangum
- Center for Cancer and Blood Disorders, Phoenix Children’s Hospital, Phoenix, Arizona
| | - Jacquelyn Reuther
- Department of Pathology & Immunology, Baylor College of Medicine, Houston, Texas
| | - Koel Sen Baksi
- Texas Children’s Cancer Center, Department of Pediatrics, Baylor College of Medicine, Houston, Texas
| | - Ilavarasi Gandhi
- Department of Pathology & Immunology, Baylor College of Medicine, Houston, Texas
| | - Ryan C. Zabriskie
- Texas Children’s Cancer Center, Department of Pediatrics, Baylor College of Medicine, Houston, Texas
| | - Alva Recinos
- Texas Children’s Cancer Center, Department of Pediatrics, Baylor College of Medicine, Houston, Texas
| | - Robin Raesz-Martinez
- Texas Children’s Cancer Center, Department of Pediatrics, Baylor College of Medicine, Houston, Texas
| | - Frank Y. Lin
- Texas Children’s Cancer Center, Department of Pediatrics, Baylor College of Medicine, Houston, Texas
- The Dan L. Duncan Cancer Center, Baylor College of Medicine, Houston, Texas
| | - Samara L. Potter
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Nationwide Children’s Hospital, Columbus, Ohio
- Department of Pediatrics, The Ohio State University, Columbus, Ohio
| | - Andrew C. Sher
- Department of Radiology, Texas Children’s Hospital, Houston, Texas
| | | | - Carrie A. Mohila
- Department of Pathology & Immunology, Baylor College of Medicine, Houston, Texas
- Department of Pathology, Texas Children’s Hospital, Houston, Texas
| | - Murali M. Chintagumpala
- Texas Children’s Cancer Center, Department of Pediatrics, Baylor College of Medicine, Houston, Texas
- The Dan L. Duncan Cancer Center, Baylor College of Medicine, Houston, Texas
| | - Donna Muzny
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
- The Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas
| | - Jianhong Hu
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
- The Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas
| | - Richard A Gibbs
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
- The Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas
| | - Kevin E. Fisher
- Department of Pathology & Immunology, Baylor College of Medicine, Houston, Texas
- The Dan L. Duncan Cancer Center, Baylor College of Medicine, Houston, Texas
- Department of Pathology, Texas Children’s Hospital, Houston, Texas
| | - Juan Carlos Bernini
- Texas Children’s Cancer Center, Department of Pediatrics, Baylor College of Medicine, Houston, Texas
| | - Jonathan Gill
- Division of Pediatrics, University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Timothy C. Griffin
- Department of Hematology Oncology, The Children’s Hospital of San Antonio, Baylor College of Medicine, San Antonio, Texas
| | - Gail E Tomlinson
- Greehey Children’s Cancer Research Institute, UT Health San Antonio, San Antonio, Texas
| | - Kelly L. Vallance
- Hematology and Oncology, Cook Children’s Medical Center, Fort Worth, Texas
| | - Sharon E. Plon
- Texas Children’s Cancer Center, Department of Pediatrics, Baylor College of Medicine, Houston, Texas
- The Dan L. Duncan Cancer Center, Baylor College of Medicine, Houston, Texas
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
- The Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas
| | - Angshumoy Roy
- Department of Pathology & Immunology, Baylor College of Medicine, Houston, Texas
- Texas Children’s Cancer Center, Department of Pediatrics, Baylor College of Medicine, Houston, Texas
- The Dan L. Duncan Cancer Center, Baylor College of Medicine, Houston, Texas
- Department of Pathology, Texas Children’s Hospital, Houston, Texas
| | - D. Williams Parsons
- Texas Children’s Cancer Center, Department of Pediatrics, Baylor College of Medicine, Houston, Texas
- The Dan L. Duncan Cancer Center, Baylor College of Medicine, Houston, Texas
- Department of Pathology, Texas Children’s Hospital, Houston, Texas
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
- The Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas
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12
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Wei Y, Yang W, Huang Q, Chen Y, Zeng K, Chen J, Chen J. Clinical significance of circulating tumor cell (CTC)-specific microRNA (miRNA) in breast cancer. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2023; 177:229-234. [PMID: 36574883 DOI: 10.1016/j.pbiomolbio.2022.12.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/17/2022] [Revised: 10/05/2022] [Accepted: 12/22/2022] [Indexed: 12/25/2022]
Abstract
As a noninvasive method, circulating tumor cell (CTC) provides ideal liquid biopsy specimens for early cancer screening and diagnosis. CTCs detection in breast cancer is correlated with patient prognosis such as disease-free survival (DFS) and overall survival (OS). Besides, accumulating evidence supported that CTCs count may be indicator for chemotherapy response as well. The functional roles of microRNA (miRNA) in breast cancer have been well-recognized for the last few years. Due to its stability in circulation, numerous studies have proven that circulating miRNA may serve as promising diagnostic and prognostic biomarkers in breast cancer. The potential ability of miRNAs in disease screening, staging or even molecular subtype classification makes them valuable tools for early breast cancer patients. It would be of great significance to characterize the miRNA expression profile in CTCs, which could provide reliable biological information originated from tumor. However, some issues need to be addressed before the utility of CTC-specific miRNAs in clinical setting. Taken together, we believe that CTC-specific miRNA detection will be trend for early breast cancer screening, diagnosis and treatment monitor in near future.
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Affiliation(s)
- Yanghui Wei
- Department of Surgery, The Eighth Affiliated Hospital, Sun Yat-Sen University, Hong Kong, China.
| | - Weiqin Yang
- School of Biomedical Sciences, The Chinese, University of Hong Kong, Hong Kong, China.
| | - Qingnan Huang
- Department of Surgery, The Eighth Affiliated Hospital, Sun Yat-Sen University, Hong Kong, China.
| | - Yong Chen
- Department of Surgery, The Eighth Affiliated Hospital, Sun Yat-Sen University, Hong Kong, China.
| | - Kai Zeng
- Department of Surgery, The Eighth Affiliated Hospital, Sun Yat-Sen University, Hong Kong, China.
| | - Juan Chen
- Department of Medicine & Rehabilitation, Tung Wah Eastern Hospital, Hong Kong, China.
| | - Jiawei Chen
- Department of Surgery, The Eighth Affiliated Hospital, Sun Yat-Sen University, Hong Kong, China.
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Geus PF, Hehnen F, Krakowski S, Lücke K, Hoon DSB, Frost N, Kertzscher U, Wendt G. Verification of a Novel Minimally Invasive Device for the Isolation of Rare Circulating Tumor Cells (CTC) in Cancer Patients’ Blood. Cancers (Basel) 2022; 14:cancers14194753. [PMID: 36230675 PMCID: PMC9562020 DOI: 10.3390/cancers14194753] [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: 09/16/2022] [Accepted: 09/23/2022] [Indexed: 11/16/2022] Open
Abstract
Simple Summary Detection of circulating tumor cells (CTCs) in blood can be used to diagnose cancer or monitor treatment response for various cancers. However, these cells are rare in the bloodstream in the early stages of cancers, and it, therefore, remains a technical challenge to isolate them. To overcome the limitations of a blood draw, we introduce a minimally invasive device, called the BMProbe™, for the isolation of CTCs directly from the bloodstream. Thereby a large volume of blood is screened. This study first shows how the geometry of the in vivo BMProbe™ causes improved cell deposition conditions. We then performed a verification of the in vivo device using blood samples from lung cancer patients. The results indicate the functionality of the BMProbe™ to isolate CTCs in blood samples. The future step is to use the BMProbe™ in various types of cancer patients to detect CTCs. Abstract Circulating tumor cells (CTCs) exist in low quantities in the bloodstream in the early stages of cancers. It, therefore, remains a technical challenge to isolate them in large enough quantities for a precise diagnosis and downstream analysis. We introduce the BMProbe™, a minimally invasive device that isolates CTCs during a 30-minute incubation in the median cubital vein. The optimized geometry of the device creates flow conditions for improved cell deposition. The CTCs are isolated using antibodies that are bound to the surface of the BMProbe™. In this study, flow experiments using cell culture cells were conducted. They indicate a 31 times greater cell binding efficiency of the BMProbe™ compared to a flat geometry. Further, the functionality of isolating CTCs from patient blood was verified in a small ex vivo study that compared the cell count from seven non-small-cell lung carcinoma (NSCLC) patients compared to nine healthy controls with 10 mL blood samples. The median cell count was 1 in NSCLC patients and 0 in healthy controls. In conclusion, the BMProbe™ is a promising method to isolate CTCs in large quantities directly from the venous bloodstream without removing blood from a patient. The future step is to verify the functionality in vivo.
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Affiliation(s)
- Paul Friedrich Geus
- Biofluid Mechanics Laboratory, Institute of Computer-assisted Cardiovascular Medicine, Charité-Universitätsmedizin Berlin, 13353 Berlin, Germany
- Correspondence:
| | - Felix Hehnen
- Biofluid Mechanics Laboratory, Institute of Computer-assisted Cardiovascular Medicine, Charité-Universitätsmedizin Berlin, 13353 Berlin, Germany
| | - Sophia Krakowski
- Biofluid Mechanics Laboratory, Institute of Computer-assisted Cardiovascular Medicine, Charité-Universitätsmedizin Berlin, 13353 Berlin, Germany
| | - Klaus Lücke
- Invicol GmbH, Müllerstraße 178, 13353 Berlin, Germany
- HaimaChek Inc., 2200 Santa Monica Blvd, Santa Monica, CA 90404, USA
| | - Dave S. B. Hoon
- HaimaChek Inc., 2200 Santa Monica Blvd, Santa Monica, CA 90404, USA
- Department of Translational Molecular Medicine, Saint John’s Cancer Institute (SJCI), Providence Saint John’s Health Center (SJHC), Santa Monica, CA 90404, USA
| | - Nikolaj Frost
- Department of Infectious Diseases and Respiratory Medicine, Charité-Universitätsmedizin Berlin, 13353 Berlin, Germany
| | - Ulrich Kertzscher
- Biofluid Mechanics Laboratory, Institute of Computer-assisted Cardiovascular Medicine, Charité-Universitätsmedizin Berlin, 13353 Berlin, Germany
| | - Gabi Wendt
- Invicol GmbH, Müllerstraße 178, 13353 Berlin, Germany
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14
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Hassan S, Shehzad A, Khan SA, Miran W, Khan S, Lee YS. Diagnostic and Therapeutic Potential of Circulating-Free DNA and Cell-Free RNA in Cancer Management. Biomedicines 2022; 10:biomedicines10082047. [PMID: 36009594 PMCID: PMC9405989 DOI: 10.3390/biomedicines10082047] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2022] [Revised: 07/27/2022] [Accepted: 07/31/2022] [Indexed: 11/20/2022] Open
Abstract
Over time, molecular biology and genomics techniques have been developed to speed up the early diagnosis and clinical management of cancer. These therapies are often most effective when administered to the subset of malignancies harboring the target identified by molecular testing. Important advances in applying molecular testing involve circulating-free DNA (cfDNA)- and cell-free RNA (cfRNA)-based liquid biopsies for the diagnosis, prognosis, prediction, and treatment of cancer. Both cfDNA and cfRNA are sensitive and specific biomarkers for cancer detection, which have been clinically proven through multiple randomized and prospective trials. These help in cancer management based on the noninvasive evaluation of size, quantity, and point mutations, as well as copy number alterations at the tumor site. Moreover, personalized detection of ctDNA helps in adjuvant therapeutics and predicts the chances of recurrence of cancer and resistance to cancer therapy. Despite the controversial diagnostic values of cfDNA and cfRNA, many clinical trials have been completed, and the Food and Drug Administration has approved many multigene assays to detect genetic alterations in the cfDNA of cancer patients. In this review, we underpin the recent advances in the physiological roles of cfDNA and cfRNA, as well as their roles in cancer detection by highlighting recent clinical trials and their roles as prognostic and predictive markers in cancer management.
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Affiliation(s)
- Sadia Hassan
- Department of Biomedical Engineering and Sciences, School of Mechanical and Manufacturing Engineering (SMME), National University of Sciences and Technology (NUST), Islamabad 44000, Pakistan
| | - Adeeb Shehzad
- Department of Biomedical Engineering and Sciences, School of Mechanical and Manufacturing Engineering (SMME), National University of Sciences and Technology (NUST), Islamabad 44000, Pakistan
- Correspondence: (A.S.); (Y.-S.L.)
| | - Shahid Ali Khan
- Department of Chemistry, School of Natural Sciences (SNS), National University of Sciences and Technology (NUST), Islamabad 44000, Pakistan
| | - Waheed Miran
- Department of Chemical Engineering, School of Chemical and Materials Engineering National University of Sciences and Technology (NUST), Islamabad 44000, Pakistan
| | - Salman Khan
- Department of pharmacy, Quaid-i-Azam University, Islamabad 44000, Pakistan
| | - Young-Sup Lee
- School of Life Sciences, College of Natural Sciences, Kyungpook National University, Daegu 41566, Korea
- Correspondence: (A.S.); (Y.-S.L.)
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15
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Detection of circulating tumor cells: opportunities and challenges. Biomark Res 2022; 10:58. [PMID: 35962400 PMCID: PMC9375360 DOI: 10.1186/s40364-022-00403-2] [Citation(s) in RCA: 25] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2022] [Accepted: 07/26/2022] [Indexed: 11/25/2022] Open
Abstract
Circulating tumor cells (CTCs) are cells that shed from a primary tumor and travel through the bloodstream. Studying the functional and molecular characteristics of CTCs may provide in-depth knowledge regarding highly lethal tumor diseases. Researchers are working to design devices and develop analytical methods that can capture and detect CTCs in whole blood from cancer patients with improved sensitivity and specificity. Techniques using whole blood samples utilize physical prosperity, immunoaffinity or a combination of the above methods and positive and negative enrichment during separation. Further analysis of CTCs is helpful in cancer monitoring, efficacy evaluation and designing of targeted cancer treatment methods. Although many advances have been achieved in the detection and molecular characterization of CTCs, several challenges still exist that limit the current use of this burgeoning diagnostic approach. In this review, a brief summary of the biological characterization of CTCs is presented. We focus on the current existing CTC detection methods and the potential clinical implications and challenges of CTCs. We also put forward our own views regarding the future development direction of CTCs.
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16
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Liao H, Zhang J, Zheng T, Liu X, Zhong J, Shao B, Dong X, Wang X, Du P, King BL, Jia S, Yu J, Li H. Identification of mutation patterns and circulating tumour DNA-derived prognostic markers in advanced breast cancer patients. J Transl Med 2022; 20:211. [PMID: 35562750 PMCID: PMC9101837 DOI: 10.1186/s12967-022-03421-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Accepted: 05/02/2022] [Indexed: 12/14/2022] Open
Abstract
BACKGROUND The correlations between circulating tumour DNA (ctDNA)-derived genomic markers and treatment response and survival outcome in Chinese patients with advanced breast cancer (ABC) have not been extensively characterized. METHODS Blood samples from 141 ABC patients who underwent first-line standard treatment in Peking University Cancer Hospital were collected. A next-generation sequencing based liquid biopsy assay (PredicineCARE) was used to detect somatic mutations and copy number variations (CNVs) in ctDNA. A subset of matched blood samples and tumour tissue biopsies were compared to evaluate the concordance. RESULTS Overall, TP53 (44.0%) and PIK3CA (28.4%) were the top two altered genes. Frequent CNVs included amplifications of ERBB2 (24.8%) and FGFR1 (8.5%) and deletions of CDKN2A (3.5%). PIK3CA/TP53 and FGFR1/2/3 variants were associated with drug resistance in hormone receptor-positive (HR +) and human epidermal growth factor receptor 2-positive (HER2 +) patients. The comparison of genomic variants across matched tumour tissue and ctDNA samples revealed a moderate to high concordance that was gene dependent. Triple-negative breast cancer (TNBC) patients harbouring TP53 or PIK3CA alterations had a shorter overall survival than those without corresponding mutations (P = 0.03 and 0.008). A high ctDNA fraction was correlated with a shorter progression-free survival (PFS) (P = 0.005) in TNBC patients. High blood-based tumor mutation burden (bTMB) was associated with a shorter PFS for HER2 + and TNBC patients (P = 0.009 and 0.05). Moreover, disease monitoring revealed several acquired genomic variants such as ESR1 mutations, CDKN2A deletions, and FGFR1 amplifications. CONCLUSIONS This study revealed the molecular profiles of Chinese patients with ABC and the clinical validity of ctDNA-derived markers, including the ctDNA fraction and bTMB, for predicting treatment response, prognosis, and disease progression. TRIAL REGISTRATION ClinicalTrials.gov ID: NCT03792529. Registered January 3rd 2019, https://clinicaltrials.gov/ct2/show/NCT03792529 .
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Affiliation(s)
- Hao Liao
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Department of Breast Oncology, Peking University Cancer Hospital & Institute, 52 Fucheng Rd, Beijing, 100142, China
| | - Jiayang Zhang
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Department of Breast Oncology, Peking University Cancer Hospital & Institute, 52 Fucheng Rd, Beijing, 100142, China
| | - Tiantian Zheng
- Huidu Shanghai Medical Sciences Ltd, Shanghai, 201499, China
| | - Xiaoran Liu
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Department of Breast Oncology, Peking University Cancer Hospital & Institute, 52 Fucheng Rd, Beijing, 100142, China
| | - Jianxin Zhong
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Department of Breast Oncology, Peking University Cancer Hospital & Institute, 52 Fucheng Rd, Beijing, 100142, China
| | - Bin Shao
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Department of Breast Oncology, Peking University Cancer Hospital & Institute, 52 Fucheng Rd, Beijing, 100142, China
| | - Xiaoxi Dong
- Huidu Shanghai Medical Sciences Ltd, Shanghai, 201499, China
| | - Xiaohong Wang
- Huidu Shanghai Medical Sciences Ltd, Shanghai, 201499, China
| | - Pan Du
- Huidu Shanghai Medical Sciences Ltd, Shanghai, 201499, China
| | - Bonnie L King
- Huidu Shanghai Medical Sciences Ltd, Shanghai, 201499, China
| | - Shidong Jia
- Huidu Shanghai Medical Sciences Ltd, Shanghai, 201499, China
| | - Jianjun Yu
- Huidu Shanghai Medical Sciences Ltd, Shanghai, 201499, China
| | - Huiping Li
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Department of Breast Oncology, Peking University Cancer Hospital & Institute, 52 Fucheng Rd, Beijing, 100142, China.
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17
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Bera A, Russ E, Karaian J, Landa A, Radhakrishnan S, Subramanian M, Hueman M, Pollard HB, Hu H, Shriver CD, Srivastava M. Circulating Cell-free DNA in Serum as a Marker for the Early Detection of Tumor Recurrence in Breast Cancer Patients. CANCER DIAGNOSIS & PROGNOSIS 2022; 2:285-292. [PMID: 35530653 PMCID: PMC9066529 DOI: 10.21873/cdp.10106] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/04/2022] [Accepted: 03/28/2022] [Indexed: 06/14/2023]
Abstract
BACKGROUND/AIM Circulating cell-free DNA (cfDNA) isolated from serum by noninvasive procedures can serve as a potential biomarker for the early detection of many cancers. The aim of this study was to implement a simple, yet effective quantitative method for measuring the cfDNA in serum and to investigate the relationship between cfDNA and the occurrence of recurrence in breast cancer (BrCa) patients. PATIENTS AND METHODS A total of 240 cases were selected, which comprised different subtypes of BrCa patients and control individuals. We selected 20 serum samples from patients which showed recurrence after 4-7 years of disease-free survival. SYBR green was used as a reporter molecule to estimate the amount of cfDNA in these serum samples. RESULTS A global Wilcoxon analysis was performed to compare the cfDNA abundance between non-recurrent and recurrent patients. The amount of cfDNA was higher in recurrent patients (recurrent vs. non-recurrent ratio=1.3; p=0.03; AUC=0.76) compared to non-recurrent patients. The data between normal/healthy controls and non-recurrent patients indicated no significant differences (n=20 in each group, healthy to non-recurrent ratio=1.03; p=0.20; AUC=0.61). CONCLUSION We implemented a straightforward one-step technique to measure the amount of cfDNA in serum, which can translate into a clinical diagnostic tool in the near future. The high levels of cfDNA in the serum of recurrent BrCa patients compared to non-recurrent BrCa patients indicates a possible uncovered role for circulating genetic information, which either contributes to the cancer recurrence phenomenon or at the very least, serves as an identifier for the potential of recurrence.
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Affiliation(s)
- Alakesh Bera
- Department of Anatomy, Physiology and Genetics, Uniformed Services University of the Health Sciences, Bethesda, MD, U.S.A
| | - Eric Russ
- Department of Anatomy, Physiology and Genetics, Uniformed Services University of the Health Sciences, Bethesda, MD, U.S.A
| | - John Karaian
- Department of Anatomy, Physiology and Genetics, Uniformed Services University of the Health Sciences, Bethesda, MD, U.S.A
| | - Adam Landa
- Department of Anatomy, Physiology and Genetics, Uniformed Services University of the Health Sciences, Bethesda, MD, U.S.A
| | - Surya Radhakrishnan
- Department of Anatomy, Physiology and Genetics, Uniformed Services University of the Health Sciences, Bethesda, MD, U.S.A
| | - Madhan Subramanian
- Department of Anatomy, Physiology and Genetics, Uniformed Services University of the Health Sciences, Bethesda, MD, U.S.A
| | - Matthew Hueman
- Murtha Cancer Center, Uniformed Services University/Walter Reed National Military Medical Center, Bethesda, MD, U.S.A
| | - Harvey B Pollard
- Department of Anatomy, Physiology and Genetics, Uniformed Services University of the Health Sciences, Bethesda, MD, U.S.A
| | - Hai Hu
- Chan Soon-Shiong Institute of Molecular Medicine, Windber, PA, U.S.A
| | - Craig D Shriver
- Murtha Cancer Center, Uniformed Services University/Walter Reed National Military Medical Center, Bethesda, MD, U.S.A
| | - Meera Srivastava
- Department of Anatomy, Physiology and Genetics, Uniformed Services University of the Health Sciences, Bethesda, MD, U.S.A
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Wu HJ, Chu PY. Current and Developing Liquid Biopsy Techniques for Breast Cancer. Cancers (Basel) 2022; 14:2052. [PMID: 35565189 PMCID: PMC9105073 DOI: 10.3390/cancers14092052] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2022] [Revised: 04/13/2022] [Accepted: 04/15/2022] [Indexed: 12/12/2022] Open
Abstract
Breast cancer is the most commonly diagnosed cancer and leading cause of cancer mortality among woman worldwide. The techniques of diagnosis, prognosis, and therapy monitoring of breast cancer are critical. Current diagnostic techniques are mammography and tissue biopsy; however, they have limitations. With the development of novel techniques, such as personalized medicine and genetic profiling, liquid biopsy is emerging as the less invasive tool for diagnosing and monitoring breast cancer. Liquid biopsy is performed by sampling biofluids and extracting tumor components, such as circulating tumor cells (CTCs), circulating tumor DNA (ctDNA), cell-free mRNA (cfRNA) and microRNA (miRNA), proteins, and extracellular vehicles (EVs). In this review, we summarize and focus on the recent discoveries of tumor components and biomarkers applied in liquid biopsy and novel development of detection techniques, such as surface-enhanced Raman spectroscopy (SERS) and microfluidic devices.
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Affiliation(s)
- Hsing-Ju Wu
- Research Assistant Center, Show Chwan Memorial Hospital, Changhua 500, Taiwan;
- Department of Medical Research, Chang Bing Show Chwan Memorial Hospital, Lukang Town, Changhua 505, Taiwan
- Department of Biology, National Changhua University of Education, Changhua 500, Taiwan
| | - Pei-Yi Chu
- Department of Post-Baccalaureate Medicine, College of Medicine, National Chung Hsing University, Taichung 402, Taiwan
- Department of Pathology, Show Chwan Memorial Hospital, Changhua 500, Taiwan
- School of Medicine, College of Medicine, Fu Jen Catholic University, New Taipei City 242, Taiwan
- Department of Health Food, Chung Chou University of Science and Technology, Changhua 510, Taiwan
- National Institute of Cancer Research, National Health Research Institutes, Tainan 704, Taiwan
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19
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The potential of liquid biopsy in the management of cancer patients. Semin Cancer Biol 2022; 84:69-79. [DOI: 10.1016/j.semcancer.2022.03.013] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2021] [Revised: 03/06/2022] [Accepted: 03/17/2022] [Indexed: 02/07/2023]
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20
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Tombolan L, Rossi E, Binatti A, Zin A, Manicone M, Facchinetti A, Lucchetta S, Carmen Affinita M, Bonvini P, Bortoluzzi S, Zamarchi R, Bisogno G. Clinical significance of circulating tumor cells and cell-free DNA in pediatric rhabdomyosarcoma. Mol Oncol 2022; 16:2071-2085. [PMID: 35212153 PMCID: PMC9120897 DOI: 10.1002/1878-0261.13197] [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: 10/14/2021] [Revised: 01/19/2022] [Accepted: 02/21/2022] [Indexed: 11/10/2022] Open
Abstract
Liquid biopsy analysis represents a powerful and noninvasive tool to uncover biomarkers for disseminated disease assessment and longitudinal monitoring of patients. Herein, we explored the value of circulating and disseminated tumor cells (CTC and DTC, respectively) and cell‐free DNA (cfDNA) in pediatric rhabdomyosarcoma (RMS). Peripheral blood and bone marrow samples were analyzed to detect and enumerate CTC and DTC, respectively. We used the epithelial cellular adhesion molecule (EpCAM)‐based CellSearch platform coupled with an automatic device to collect both EpCAM‐positive and EpCAM‐low/negative CTCs. The standard assay was implemented, including the mesenchymal marker desmin. For selected cases, we molecularly profiled primary tumors and liquid biopsy biomarkers using whole‐exome sequencing and droplet digital PCR, respectively. RMS patients with metastatic disease had a significantly higher number of CTCs compared to those with localized disease, whereas DTCs were detected independently of disease presentation. The use of the desmin marker remarkably increased the identification of CTCs and DTCs in RMS samples. Of note, CTC clusters were detected in RMS patients with disseminated disease. Further, cfDNA and CTC molecular features closely reflected the molecular makeup of primary tumors and informed of disease course.
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Affiliation(s)
- Lucia Tombolan
- Institute of Pediatric Research, Fondazione Città della Speranza, Padova, Italy.,Department of Woman's and Children's Health, Hematology and Oncology Unit, University of Padova, Padova, Italy
| | - Elisabetta Rossi
- Department of Surgery, Oncology and Gastroenterology, Oncology Section, University of Padova, Padova, Italy.,Veneto Institute of Oncology IOV - IRCCS, Padua, Italy
| | - Andrea Binatti
- Department of Molecular Medicine, University of Padova, Padova, Italy
| | - Angelica Zin
- Institute of Pediatric Research, Fondazione Città della Speranza, Padova, Italy
| | | | - Antonella Facchinetti
- Department of Surgery, Oncology and Gastroenterology, Oncology Section, University of Padova, Padova, Italy.,Veneto Institute of Oncology IOV - IRCCS, Padua, Italy
| | - Silvia Lucchetta
- Department of Woman's and Children's Health, Hematology and Oncology Unit, University of Padova, Padova, Italy
| | - Maria Carmen Affinita
- Department of Woman's and Children's Health, Hematology and Oncology Unit, University of Padova, Padova, Italy
| | - Paolo Bonvini
- Institute of Pediatric Research, Fondazione Città della Speranza, Padova, Italy
| | | | - Rita Zamarchi
- Veneto Institute of Oncology IOV - IRCCS, Padua, Italy
| | - Gianni Bisogno
- Department of Woman's and Children's Health, Hematology and Oncology Unit, University of Padova, Padova, Italy
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21
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Abstract
Alterations in DNAs could not reveal what happened in proteins. The accumulated alterations of DNAs would change the manifestation of proteins. Therefore, as is the case in cancer liquid biopsies, deep proteome profiling will likely provide invaluable and clinically relevant information in real-time throughout all stages of cancer progression. However, due to the great complexity of proteomes in liquid biopsy samples and the limitations of proteomic technologies compared to high-plex sequencing technologies, proteomic discoveries have yet lagged behind their counterpart, genomic technologies. Therefore, novel protein technologies are in urgent demand to fulfill the goals set out for biomarker discovery in cancer liquid biopsies.Notably, conventional and innovative technologies are being rapidly developed for proteomic analysis in cancer liquid biopsies. These advances have greatly facilitated early detection, diagnosis, prognosis, and monitoring of cancer evolution, adapted or adopted in response to therapeutic interventions. In this paper, we review the high-plex proteomics technologies that are capable of measuring at least hundreds of proteins simultaneously from liquid biopsy samples, ranging from traditional technologies based on mass spectrometry (MS) and antibody/antigen arrays to innovative technologies based on aptamer, proximity extension assay (PEA), and reverse phase protein arrays (RPPA).
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22
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Sant M, Bernat-Peguera A, Felip E, Margelí M. Role of ctDNA in Breast Cancer. Cancers (Basel) 2022; 14:310. [PMID: 35053474 PMCID: PMC8773730 DOI: 10.3390/cancers14020310] [Citation(s) in RCA: 29] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2021] [Revised: 01/01/2022] [Accepted: 01/06/2022] [Indexed: 12/16/2022] Open
Abstract
Breast cancer is currently classified by immunohistochemistry. However, technological advances in the detection of circulating tumor DNA (ctDNA) have made new options available for diagnosis, classification, biological knowledge, and treatment selection. Breast cancer is a heterogeneous disease and ctDNA can accurately reflect this heterogeneity, allowing us to detect, monitor, and understand the evolution of the disease. Breast cancer patients have higher levels of circulating DNA than healthy subjects, and ctDNA can be used for different objectives at different timepoints of the disease, ranging from screening and early detection to monitoring for resistance mutations in advanced disease. In early breast cancer, ctDNA clearance has been associated with higher rates of complete pathological response after neoadjuvant treatment and with fewer recurrences after radical treatments. In metastatic disease, ctDNA can help select the optimal sequencing of treatments. In the future, thanks to new bioinformatics tools, the use of ctDNA in breast cancer will become more frequent, enhancing our knowledge of the biology of tumors. Moreover, deep learning algorithms may also be able to predict breast cancer evolution or treatment sensitivity. In the coming years, continued research and the improvement of liquid biopsy techniques will be key to the implementation of ctDNA analysis in routine clinical practice.
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Affiliation(s)
- Marta Sant
- Medical Oncology Department, Catalan Institute of Oncology-Badalona, Hospital Germans Trias i Pujol (HGTiP), 08916 Badalona, Spain
| | - Adrià Bernat-Peguera
- Badalona Applied Research Group in Oncology (B-ARGO), Institut d’Investigació en Ciències de la Salut Germans Trias i Pujol (IGTP), Universitat Autònoma de Barcelona, 08916 Badalona, Spain
| | - Eudald Felip
- Medical Oncology Department, Catalan Institute of Oncology-Badalona, Hospital Germans Trias i Pujol (HGTiP), 08916 Badalona, Spain
- Badalona Applied Research Group in Oncology (B-ARGO), Institut d’Investigació en Ciències de la Salut Germans Trias i Pujol (IGTP), Universitat Autònoma de Barcelona, 08916 Badalona, Spain
| | - Mireia Margelí
- Medical Oncology Department, Catalan Institute of Oncology-Badalona, Hospital Germans Trias i Pujol (HGTiP), 08916 Badalona, Spain
- Badalona Applied Research Group in Oncology (B-ARGO), Institut d’Investigació en Ciències de la Salut Germans Trias i Pujol (IGTP), Universitat Autònoma de Barcelona, 08916 Badalona, Spain
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23
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Fitzpatrick A, Iravani M, Mills A, Childs L, Alaguthurai T, Clifford A, Garcia-Murillas I, Van Laere S, Dirix L, Harries M, Okines A, Turner NC, Haider S, Tutt ANJ, Isacke CM. Assessing CSF ctDNA to improve diagnostic accuracy and therapeutic monitoring in breast cancer leptomeningeal metastasis. Clin Cancer Res 2021; 28:1180-1191. [PMID: 34921020 DOI: 10.1158/1078-0432.ccr-21-3017] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2021] [Revised: 10/23/2021] [Accepted: 12/14/2021] [Indexed: 11/16/2022]
Abstract
PURPOSE Cerebrospinal fluid (CSF) cytology is the gold standard diagnostic test for breast cancer leptomeningeal metastasis (BCLM), but has impaired sensitivity, often necessitating repeated lumbar puncture to confirm or refute diagnosis. Further, there is no quantitative response tool to assess response or progression during BCLM treatment. EXPERIMENTAL DESIGN Facing the challenge of working with small volume samples and the lack of common recurrent mutations in breast cancers, cell-free DNA was extracted from CSF and plasma of patients undergoing investigation for BCLM (n=30). ctDNA fraction was assessed by ultra-low pass whole genome sequencing (ulpWGS), which does not require prior tumor sequencing. RESULTS In this proof-of-concept study ctDNA was detected (fraction {greater than or equal to}0.10) in CSF of all 24 BCLM+ patients (median ctDNA fraction 0.57), regardless of negative cytology or borderline MRI imaging, whereas CSF ctDNA was not detected in the 6 BCLM- patients (median ctDNA fraction 0.03, P<0.0001). Plasma ctDNA was only detected in patients with extracranial disease progression or who had previously received whole brain radiotherapy. ctDNA fraction was highly concordant with mutant allele fraction measured by tumor mutation-specific ddPCR assays (r=0.852, P<0.0001). During intrathecal treatment, serial monitoring (n=12 patients) showed that suppression of CSF ctDNA fraction was associated with longer BCLM survival (P=0.034) and rising ctDNA fraction was detectable up to 12 weeks before clinical progression. CONCLUSION Measuring ctDNA fraction by ulpWGS is a quantitative marker demonstrating potential for timely and accurate BCLM diagnosis and therapy response monitoring, with the ultimate aim to improve management of this poor prognosis patient group.
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Affiliation(s)
- Amanda Fitzpatrick
- Breast Cancer Now Toby Robins Research Centre, Institute of Cancer Research
| | - Marjan Iravani
- The Breast Cancer Now Toby Robins Research Centre, Institute of Cancer Research
| | - Adam Mills
- The Breast Cancer Now Toby Robins Research Centre, Institute of Cancer Research
| | - Lucy Childs
- Department of Clinical Radiology, Guy's and St Thomas' NHS Foundation Trust
| | | | - Angela Clifford
- Breast Cancer Now Research Unit, Guy's Hospital, King's College London
| | - Isaac Garcia-Murillas
- Breast Cancer Now Research Centre, Institute of Cancer Research and The Royal Marsden Hospital
| | - Steven Van Laere
- Translational Cancer Research Unit, Oncology Center, General Hospital Sint-Augustinus
| | - Luc Dirix
- Translational Cancer Research Unit, Oncology Center, AZ Sint-Augustinus
| | - Mark Harries
- Clinical Oncology, Guy's and St Thomas' NHS Foundation Trust
| | | | - Nicholas C Turner
- Breast Unit, The Royal Marsden NHS Foundation Trust, and Breast Cancer Now Research Centre, The Institute of Cancer Research
| | - Syed Haider
- The Breast Cancer Now Research Centre, Institute of Cancer Research
| | - Andrew N J Tutt
- Division of Breast Cancer Research, Institute of Cancer Research London
| | - Clare M Isacke
- The Breast Cancer Now Toby Robins Research Centre, Institute of Cancer Research
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24
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Kim N, Kim SM, Lee BJ, Choi BI, Yoon HS, Kang SH, Kim SH, Joo MK, Park JJ, Kim C. Detection of Microsatellite Instability in Colorectal Cancer Patients With a Plasma-Based Real-Time PCR Analysis. Front Pharmacol 2021; 12:758830. [PMID: 34955830 PMCID: PMC8694627 DOI: 10.3389/fphar.2021.758830] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2021] [Accepted: 11/19/2021] [Indexed: 11/13/2022] Open
Abstract
A microsatellite instability (MSI) test is crucial for screening for HNPCC (Hereditary nonpolyposis colorectal cancer; Lynch syndrome) and optimization of colorectal cancer (CRC) treatment. Mismatch repair (MMR) deficiency is a predictor for good response of immune checkpoint inhibitors in various malignancies. In this study, we evaluated the results of a newly developed plasma-based real-time PCR kit for the detection of MSI in CRC patients. We assessed a peptide nucleotide acid (PNA) probe-mediated real-time PCR test (U-TOP MSI Detection Kit Plus) that determines MSI status by using amplicon melting analysis of five markers (NR21, NR24, NR27, BAT25, and BAT26) from plasma. Eighty-four CRC patients (46 dMMR and 38 pMMR) with colorectal cancer were analyzed. The concordance rate of MSI status assessment between the plasma kit and IHC was 63.0% in dMMR patients (29/46), but in the pMMR evaluation, a 100% (38/38) concordance rate was observed. In the evaluation of the performance of a custom tissue U-TOP MSI Detection Kit and plasma kit in 28 patients, sensitivity, specificity, PPV (positive predictive value) and NPV (negative predictive value) of plasma kit were 68.4, 100, 100, and 44.4%, respectively, with the tissue U-TOP MSI Detection Kit. Our results demonstrate the feasibility of a non-invasive and rapid plasma-based real-time PCR kit (U-TOP MSI Detection Kit Plus) for the detection of MSI in colorectal cancer.
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Affiliation(s)
- Namjoo Kim
- Department of Gastroenterology, Korea University Guro Hospital, Seoul, South Korea
| | - Sung Min Kim
- Department of Gastroenterology, Korea University Guro Hospital, Seoul, South Korea
| | - Beom Jae Lee
- Department of Gastroenterology, Korea University Guro Hospital, Seoul, South Korea
- *Correspondence: Beom Jae Lee,
| | - Byung il Choi
- Department of Gastroenterology, Korea University Guro Hospital, Seoul, South Korea
| | - Hee Sook Yoon
- Department of Gastroenterology, Korea University Guro Hospital, Seoul, South Korea
| | - Sang Hee Kang
- Department of Surgery, Korea University Guro Hospital, Seoul, South Korea
| | - Seung Han Kim
- Department of Gastroenterology, Korea University Guro Hospital, Seoul, South Korea
| | - Moon Kyung Joo
- Department of Gastroenterology, Korea University Guro Hospital, Seoul, South Korea
| | - Jong-Jae Park
- Department of Gastroenterology, Korea University Guro Hospital, Seoul, South Korea
| | - Chungyeul Kim
- Department of Pathology, College of Medicine, Korea University, Seoul, South Korea
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25
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Nista EC, Schepis T, Candelli M, Giuli L, Pignataro G, Franceschi F, Gasbarrini A, Ojetti V. Humoral Predictors of Malignancy in IPMN: A Review of the Literature. Int J Mol Sci 2021; 22:ijms222312839. [PMID: 34884643 PMCID: PMC8657857 DOI: 10.3390/ijms222312839] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2021] [Revised: 11/21/2021] [Accepted: 11/23/2021] [Indexed: 02/05/2023] Open
Abstract
Pancreatic cystic lesions are increasingly detected in cross-sectional imaging. Intraductal papillary mucinous neoplasm (IPMN) is a mucin-producing subtype of the pancreatic cyst lesions arising from the pancreatic duct system. IPMN is a potential precursor of pancreatic cancer. The transformation of IPMN in pancreatic cancer is progressive and requires the occurrence of low-grade dysplasia, high-grade dysplasia, and ultimately invasive cancer. Jaundice, enhancing mural nodule >5 mm, main pancreatic duct diameter >10 mm, and positive cytology for high-grade dysplasia are considered high-risk stigmata of malignancy. While increased levels of carbohydrate antigen 19-9 (CA 19-9) (>37 U/mL), main pancreatic duct diameter 5-9.9 mm, cyst diameter >40 mm, enhancing mural nodules <5 mm, IPMN-induced acute pancreatitis, new onset of diabetes, cyst grow-rate >5 mm/year are considered worrisome features of malignancy. However, cross-sectional imaging is often inadequate in the prediction of high-grade dysplasia and invasive cancer. Several studies evaluated the role of humoral and intra-cystic biomarkers in the prediction of malignancy in IPMN. Carcinoembryonic antigen (CEA), CA 19-9, intra-cystic CEA, intra-cystic glucose, and cystic fluid cytology are widely used in clinical practice to distinguish between mucinous and non-mucinous cysts and to predict the presence of invasive cancer. Other biomarkers such as cystic fluid DNA sequencing, microRNA (mi-RNA), circulating microvesicles, and liquid biopsy are the new options for the mini-invasive diagnosis of degenerated IPMN. The aim of this study is to review the literature to assess the role of humoral and intracystic biomarkers in the prediction of advanced IPMN with high-grade dysplasia or invasive carcinoma.
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Affiliation(s)
- Enrico C. Nista
- Department of Internal Medicine, Università Cattolica Sacro Cuore, Fondazione Policlinico Universitario A. Gemelli IRCCS, 00168 Rome, Italy; (E.C.N.); (T.S.); (L.G.); (A.G.)
| | - Tommaso Schepis
- Department of Internal Medicine, Università Cattolica Sacro Cuore, Fondazione Policlinico Universitario A. Gemelli IRCCS, 00168 Rome, Italy; (E.C.N.); (T.S.); (L.G.); (A.G.)
| | - Marcello Candelli
- Department of Emergency Medicine, Fondazione Policlinico Universitario, Università Cattolica del Sacro Cuore, 00168 Rome, Italy; (M.C.); (G.P.); (F.F.)
| | - Lucia Giuli
- Department of Internal Medicine, Università Cattolica Sacro Cuore, Fondazione Policlinico Universitario A. Gemelli IRCCS, 00168 Rome, Italy; (E.C.N.); (T.S.); (L.G.); (A.G.)
| | - Giulia Pignataro
- Department of Emergency Medicine, Fondazione Policlinico Universitario, Università Cattolica del Sacro Cuore, 00168 Rome, Italy; (M.C.); (G.P.); (F.F.)
| | - Francesco Franceschi
- Department of Emergency Medicine, Fondazione Policlinico Universitario, Università Cattolica del Sacro Cuore, 00168 Rome, Italy; (M.C.); (G.P.); (F.F.)
| | - Antonio Gasbarrini
- Department of Internal Medicine, Università Cattolica Sacro Cuore, Fondazione Policlinico Universitario A. Gemelli IRCCS, 00168 Rome, Italy; (E.C.N.); (T.S.); (L.G.); (A.G.)
| | - Veronica Ojetti
- Department of Emergency Medicine, Fondazione Policlinico Universitario, Università Cattolica del Sacro Cuore, 00168 Rome, Italy; (M.C.); (G.P.); (F.F.)
- Correspondence: ; Tel.: +39-063-0153-188
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26
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Lin D, Shen L, Luo M, Zhang K, Li J, Yang Q, Zhu F, Zhou D, Zheng S, Chen Y, Zhou J. Circulating tumor cells: biology and clinical significance. Signal Transduct Target Ther 2021; 6:404. [PMID: 34803167 PMCID: PMC8606574 DOI: 10.1038/s41392-021-00817-8] [Citation(s) in RCA: 255] [Impact Index Per Article: 85.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2021] [Revised: 10/06/2021] [Accepted: 10/27/2021] [Indexed: 02/07/2023] Open
Abstract
Circulating tumor cells (CTCs) are tumor cells that have sloughed off the primary tumor and extravasate into and circulate in the blood. Understanding of the metastatic cascade of CTCs has tremendous potential for the identification of targets against cancer metastasis. Detecting these very rare CTCs among the massive blood cells is challenging. However, emerging technologies for CTCs detection have profoundly contributed to deepening investigation into the biology of CTCs and have facilitated their clinical application. Current technologies for the detection of CTCs are summarized herein, together with their advantages and disadvantages. The detection of CTCs is usually dependent on molecular markers, with the epithelial cell adhesion molecule being the most widely used, although molecular markers vary between different types of cancer. Properties associated with epithelial-to-mesenchymal transition and stemness have been identified in CTCs, indicating their increased metastatic capacity. Only a small proportion of CTCs can survive and eventually initiate metastases, suggesting that an interaction and modulation between CTCs and the hostile blood microenvironment is essential for CTC metastasis. Single-cell sequencing of CTCs has been extensively investigated, and has enabled researchers to reveal the genome and transcriptome of CTCs. Herein, we also review the clinical applications of CTCs, especially for monitoring response to cancer treatment and in evaluating prognosis. Hence, CTCs have and will continue to contribute to providing significant insights into metastatic processes and will open new avenues for useful clinical applications.
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Affiliation(s)
- Danfeng Lin
- Department of Breast Surgery, the Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
- Cancer Institute (Key Laboratory of Cancer Prevention and Intervention, China National Ministry of Education), the Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
- Department of Breast Surgery, the First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
| | - Lesang Shen
- Department of Breast Surgery, the Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Meng Luo
- Department of Breast Surgery, the Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
- Cancer Institute (Key Laboratory of Cancer Prevention and Intervention, China National Ministry of Education), the Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Kun Zhang
- Department of Breast Surgery, the Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Jinfan Li
- Department of Pathology, the Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Qi Yang
- Department of Pathology, the Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Fangfang Zhu
- Department of Breast Surgery, the Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Dan Zhou
- Department of Surgery, Traditional Chinese Medical Hospital of Zhuji, Shaoxing, China
| | - Shu Zheng
- Department of Breast Surgery, the Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
- Cancer Institute (Key Laboratory of Cancer Prevention and Intervention, China National Ministry of Education), the Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Yiding Chen
- Department of Breast Surgery, the Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China.
- Cancer Institute (Key Laboratory of Cancer Prevention and Intervention, China National Ministry of Education), the Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China.
| | - Jiaojiao Zhou
- Department of Breast Surgery, the Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China.
- Cancer Institute (Key Laboratory of Cancer Prevention and Intervention, China National Ministry of Education), the Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China.
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27
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Li C, Feng X, Yang S, Xu H, Yin X, Yu Y. Capture, Detection, and Simultaneous Identification of Rare Circulating Tumor Cells Based on a Rhodamine 6G-Loaded Metal-Organic Framework. ACS APPLIED MATERIALS & INTERFACES 2021; 13:52406-52416. [PMID: 34709779 DOI: 10.1021/acsami.1c15838] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Circulating tumor cells (CTCs) play a key role in the development of tumor metastasis. It will be a big step forward for CTC application as a reliable clinical liquid biopsy marker to be able to identify the captured CTCs while achieving a high capture efficiency within one analytical system. Herein, in this work, a stimuli-responsive and rhodamine 6G (Rho 6G)-entrapped fluorescent metal-organic framework (MOF) probe, named MOF-Rho 6G-DNA, was designed to capture, detect, and subsequently identify CTCs from blood samples of cancer patients. The probe was fabricated by modifying the epithelial cell adhesion molecule (EpCAM) hairpin DNA aptamer with Rho 6G enclosed and an Arm-DNA-attached UiO-66-NH2 MOF by sequence complementation. CTCs could be captured by the EpCAM hairpin DNA on the probe; as a result, Rho 6G loaded in the probe was released, and the number of CTCs was positively related to the concentration of released Rho 6G. An excellent correlation of fluorescence intensities with CTC numbers was obtained from 2 to 500 cells/mL. More importantly, the MOF-Rho 6G-DNA probe simultaneously realized rapid identification of the captured cells within 30 min by only relying on the residue Rho 6G in the MOF cavity. The captured target cells can be conveniently released from the probe using the complementary DNA sequence. These performance features of the probe were further verified by blood samples from patients of various types of tumor.
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Affiliation(s)
- Chenglin Li
- Jiangsu Key Laboratory of New Drug Research and Clinical Pharmacy, Xuzhou Medical University, Jiangsu 221004, Xuzhou, China
| | - Xingqing Feng
- Jiangsu Key Laboratory of New Drug Research and Clinical Pharmacy, Xuzhou Medical University, Jiangsu 221004, Xuzhou, China
| | - Shenhao Yang
- Jiangsu Key Laboratory of New Drug Research and Clinical Pharmacy, Xuzhou Medical University, Jiangsu 221004, Xuzhou, China
| | - Hao Xu
- Jiangsu Key Laboratory of New Drug Research and Clinical Pharmacy, Xuzhou Medical University, Jiangsu 221004, Xuzhou, China
| | - Xiaoxing Yin
- Jiangsu Key Laboratory of New Drug Research and Clinical Pharmacy, Xuzhou Medical University, Jiangsu 221004, Xuzhou, China
| | - Yanyan Yu
- Jiangsu Key Laboratory of New Drug Research and Clinical Pharmacy, Xuzhou Medical University, Jiangsu 221004, Xuzhou, China
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28
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Lian S, Yang L, Feng Q, Wang P, Wang Y, Li Z. Folate-Receptor Positive Circulating Tumor Cell Is a Potential Diagnostic Marker of Prostate Cancer. Front Oncol 2021; 11:708214. [PMID: 34692484 PMCID: PMC8531518 DOI: 10.3389/fonc.2021.708214] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2021] [Accepted: 09/17/2021] [Indexed: 11/30/2022] Open
Abstract
Folate-receptor positive circulating tumor cells (FR+CTCs) shows an important role in the diagnosis and dynamic monitoring for many solid tumors; however, the application of FR+CTCs in prostate cancer remains unclear. We explored the potential application of FR+CTCs in this retrospective study. The levels of FR+CTCs were detected in 30 prostate cancer patients and 7 bladder cancer patients in Peking University Cancer Hospital from August 2017 to August 2021. Clinical and pathology data were collected. One-way ANOVA was used to compare the difference in FR+CTCs levels in patients with prostate cancer, bladder cancer, and benign disease. The area under the receiver operating curve (AUROC) was used to compare the accuracy of FR+CTCs and tPSA in the diagnosis of prostate cancer. We found that levels of FR+CTCs were significantly higher in cancer patients (both prostate and bladder cancer) than in patients with benign urinary disease (p < 0.001). Besides, FR+CTCs level was consistently high in the prostate cancer patients with different tPSA levels (p < 0.001), and it was significantly higher in the patients with f/tPSA levels <0.16 than in those patients with f/tPSA levels >0.16 (12.20 ± 1.31 vs. 8.73 ± 0.92 FU/3 ml, p = 0.043). The diagnosis efficiency of FR+CTCs is better than the tPSA in prostate cancer patients with tPSA <10 ng/ml (0.871 vs. 0.857). In the prostate cancer patients with tPSA <10 ng/ml and f/tPSA <0.16, a combination of FR+CTCs and tPSA (AUROC, 0.934) further increased the diagnosis efficiency of each of these biomarkers alone (FR+CTCs, 0.912; tPSA, 0.857). Therefore, FR+CTCs could serve as an early diagnosis marker in the prostate cancer patients with uncertain tPSA levels.
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Affiliation(s)
- Shenyi Lian
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Department of Pathology, Peking University Cancer Hospital & Institute, Beijing, China
| | - Lujing Yang
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Department of Pathology, Peking University Cancer Hospital & Institute, Beijing, China
| | - Qin Feng
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Department of Pathology, Peking University Cancer Hospital & Institute, Beijing, China
| | - Ping Wang
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Department of Pathology, Peking University Cancer Hospital & Institute, Beijing, China
| | - Yue Wang
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Department of Pathology, Peking University Cancer Hospital & Institute, Beijing, China
| | - Zhongwu Li
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Department of Pathology, Peking University Cancer Hospital & Institute, Beijing, China
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29
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Duque G, Manterola C, Otzen T, Arias C, Galindo B, Mora M, Guerrero E, García N. Clinical utility of liquid biopsy in breast cancer: A systematic review. Clin Genet 2021; 101:285-295. [PMID: 34687555 DOI: 10.1111/cge.14077] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2021] [Revised: 10/14/2021] [Accepted: 10/15/2021] [Indexed: 12/18/2022]
Abstract
Advancements in genetic sequencing techniques along with the identification of specific mutations and structural changes in multiple cancer genes, make it possible to identify circulating tumor cells and cell free nucleic acids as blood-based biomarkers, serving as a liquid biopsy (LB) with great utility for the diagnosis, treatment and follow-up of patients with neoplasms. This systematic review focuses on the clinical utility of LB in patients with breast cancer (BC). Articles published between 1990 and 2021 were included. Databases searched: Trip Database, WoS, EMBASE, PubMed, SCOPUS, and Clinical Keys. Variables studied: Publication year, country, number of cases, primary study design, LB detection methods, genes found, overall survival, disease-free survival, stage, response to treatment, clinical utility, BC molecular type, systemic treatment and methodological quality of primary studies. Of 2619 articles, 74 were retained representing 12 658 patients, mainly cohort studies (66.2%), the majority were from China (15%) and Japan (12.2%). All primary studies described clinical stage and type of systemic treatment used. Most used biomarker detection method: DNA (52.7%) and type of analysis: quantification of total cfDNA (35.1%). PIK3CA mutation was most frequent (62.9%). Evidence suggests clinically useful applications of BC. Though heterogeneous, publications suggest that LB will constitute part of the standard diagnostic-therapeutic process of BC.
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Affiliation(s)
- Galo Duque
- PhD Program in Medical Sciences, Universidad de La Frontera, Temuco, Chile.,Faculty of Medicine, Universidad del Azuay, Cuenca, Ecuador
| | - Carlos Manterola
- PhD Program in Medical Sciences, Universidad de La Frontera, Temuco, Chile.,Center of Excellence in Morphological and Surgical Studies (CEMyQ), Universidad de La Frontera, Temuco, Chile
| | - Tamara Otzen
- PhD Program in Medical Sciences, Universidad de La Frontera, Temuco, Chile.,Center of Excellence in Morphological and Surgical Studies (CEMyQ), Universidad de La Frontera, Temuco, Chile
| | - Cristina Arias
- Faculty of Medicine, Universidad del Azuay, Cuenca, Ecuador
| | - Bryan Galindo
- Faculty of Medicine, Universidad del Azuay, Cuenca, Ecuador
| | - Miriann Mora
- PhD Program in Medical Sciences, Universidad de La Frontera, Temuco, Chile.,Faculty of Medicine, Universidad del Azuay, Cuenca, Ecuador
| | - Enmanuel Guerrero
- PhD Program in Medical Sciences, Universidad de La Frontera, Temuco, Chile.,Solca Cancer Institute, Sociedad de Lucha Contra el Cáncer, Cuenca, Ecuador
| | - Nayeli García
- PhD Program in Medical Sciences, Universidad de La Frontera, Temuco, Chile
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30
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Bortolini Silveira A, Bidard FC, Tanguy ML, Girard E, Trédan O, Dubot C, Jacot W, Goncalves A, Debled M, Levy C, Ferrero JM, Jouannaud C, Rios M, Mouret-Reynier MA, Dalenc F, Hego C, Rampanou A, Albaud B, Baulande S, Berger F, Lemonnier J, Renault S, Desmoulins I, Proudhon C, Pierga JY. Multimodal liquid biopsy for early monitoring and outcome prediction of chemotherapy in metastatic breast cancer. NPJ Breast Cancer 2021; 7:115. [PMID: 34504096 PMCID: PMC8429692 DOI: 10.1038/s41523-021-00319-4] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2021] [Accepted: 07/28/2021] [Indexed: 12/12/2022] Open
Abstract
Circulating tumor cells (CTCs) and circulating tumor DNA (ctDNA) are two cancer-derived blood biomarkers that inform on patient prognosis and treatment efficacy in breast cancer. We prospectively evaluated the clinical validity of quantifying both CTCs (CellSearch) and ctDNA (targeted next-generation sequencing). Their combined value as prognostic and early monitoring markers was assessed in 198 HER2-negative metastatic breast cancer patients. All patients were included in the prospective multicenter UCBG study COMET (NCT01745757) and treated by first-line chemotherapy with weekly paclitaxel and bevacizumab. Blood samples were obtained at baseline and before the second cycle of chemotherapy. At baseline, CTCs and ctDNA were respectively detected in 72 and 74% of patients and were moderately correlated (Kendall’s τ = 0.3). Only 26 (13%) patients had neither detectable ctDNA nor CTCs. Variants were most frequently observed in TP53 and PIK3CA genes. KMT2C/MLL3 variants detected in ctDNA were significantly associated with a lower CTC count, while the opposite trend was seen with GATA3 alterations. Both CTC and ctDNA levels at baseline and after four weeks of treatment were correlated with survival. For progression-free and overall survival, the best multivariate prognostic model included tumor subtype (triple negative vs other), grade (grade 3 vs other), ctDNA variant allele frequency (VAF) at baseline (per 10% increase), and CTC count at four weeks (≥5CTC/7.5 mL). Overall, this study demonstrates that CTCs and ctDNA have nonoverlapping detection profiles and complementary prognostic values in metastatic breast cancer patients. A comprehensive liquid-biopsy approach may involve simultaneous detection of ctDNA and CTCs.
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Affiliation(s)
| | - François-Clément Bidard
- Circulating Tumor Biomarkers laboratory, INSERM CIC BT-1428, Institut Curie, Paris, France.,Department of Medical Oncology, Institut Curie, Paris and Saint Cloud, Paris, France.,UVSQ, Université Paris-Saclay, Paris, France
| | | | - Elodie Girard
- INSERM U900, Institut Curie, Mines ParisTech, PSL Research University, Paris, France
| | - Olivier Trédan
- Department of Medical Oncology, Centre Léon Bérard, Lyon, France
| | - Coraline Dubot
- Department of Medical Oncology, Institut Curie, Paris and Saint Cloud, Paris, France
| | - William Jacot
- Department of Medical Oncology, Institut du Cancer de Montpellier, Montpellier University, IRCM INSERM, Montpellier, France
| | - Anthony Goncalves
- Department of Medical Oncology, Aix-Marseille Univ, INSERM U1068, CNRS UMR7258, Institut Paoli-Calmettes, CRCM, Marseille, France
| | - Marc Debled
- Department of Medical Oncology, Institut Bergonié, Bordeaux, France
| | - Christelle Levy
- Department of Medical Oncology, Centre François Baclesse, Caen, France
| | - Jean-Marc Ferrero
- Department of Medical Oncology, Centre Antoine Lacassagne, Nice, France
| | | | - Maria Rios
- Department of Medical Oncology, Institut de Cancérologie de Lorraine, Vandoeuvre-Lès-Nancy, France
| | | | - Florence Dalenc
- Department of Medical Oncology, Institut Claudius Regaud, IUCT-Oncopole, Toulouse, France
| | - Caroline Hego
- Circulating Tumor Biomarkers laboratory, INSERM CIC BT-1428, Institut Curie, Paris, France
| | - Aurore Rampanou
- Circulating Tumor Biomarkers laboratory, INSERM CIC BT-1428, Institut Curie, Paris, France
| | - Benoit Albaud
- ICGex Next-Generation Sequencing Platform, Institut Curie, Paris, France
| | - Sylvain Baulande
- ICGex Next-Generation Sequencing Platform, Institut Curie, Paris, France
| | | | | | - Shufang Renault
- Circulating Tumor Biomarkers laboratory, INSERM CIC BT-1428, Institut Curie, Paris, France
| | - Isabelle Desmoulins
- Department of Medical Oncology, Centre Georges-François Leclerc, Dijon, France
| | - Charlotte Proudhon
- Circulating Tumor Biomarkers laboratory, INSERM CIC BT-1428, Institut Curie, Paris, France.,INSERM U934 CNRS UMR3215, Paris, France
| | - Jean-Yves Pierga
- Circulating Tumor Biomarkers laboratory, INSERM CIC BT-1428, Institut Curie, Paris, France. .,Department of Medical Oncology, Institut Curie, Paris and Saint Cloud, Paris, France. .,Université de Paris, Paris, France.
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31
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Tay TKY, Tan PH. Liquid Biopsy in Breast Cancer: A Focused Review. Arch Pathol Lab Med 2021; 145:678-686. [PMID: 32045277 DOI: 10.5858/arpa.2019-0559-ra] [Citation(s) in RCA: 52] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/11/2019] [Indexed: 01/27/2023]
Abstract
CONTEXT.— The role of liquid biopsy in cancer management has been gaining increased prominence in the past decade, with well-defined clinical applications now being established in lung cancer. Recently, the US Food and Drug Administration also approved the Therascreen PIK3CA RGQ polymerase chain reaction assay as a companion diagnostic assay to detect PIK3CA mutations in breast cancer for both tissue and liquid biopsies, bringing the role of liquid biopsy in breast cancer management to the fore. Its utility in other aspects of breast cancer, however, is yet to be clearly defined. OBJECTIVE.— To review the studies that looked at liquid biopsies in breast cancer and examine their potential for clinical application in the areas of early diagnosis, prognostication, monitoring disease response, detecting minimal residual disease, and predicting risk of progression or relapse. We focus mainly on circulating tumor cells and circulating tumor DNA. DATA SOURCES.— Peer-reviewed articles in PubMed. CONCLUSIONS.— Liquid biopsies in breast cancers have yielded promising results, especially in the areas of monitoring treatment response and predicting disease progression or relapse. With further study, and hopefully coupled with continued improvements in technologies that isolate tumor-derived materials, liquid biopsies may go on to play a greater role in the breast cancer clinic.
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Affiliation(s)
- Timothy Kwang Yong Tay
- From the Department of Anatomical Pathology (Tay, Tan), Singapore General Hospital, Singapore
| | - Puay Hoon Tan
- From the Department of Anatomical Pathology (Tay, Tan), Singapore General Hospital, Singapore.,The Division of Pathology (Tan), Singapore General Hospital, Singapore
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32
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Liu L, Chen X, Petinrin OO, Zhang W, Rahaman S, Tang ZR, Wong KC. Machine Learning Protocols in Early Cancer Detection Based on Liquid Biopsy: A Survey. Life (Basel) 2021; 11:638. [PMID: 34209249 PMCID: PMC8308091 DOI: 10.3390/life11070638] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2021] [Revised: 06/23/2021] [Accepted: 06/24/2021] [Indexed: 12/24/2022] Open
Abstract
With the advances of liquid biopsy technology, there is increasing evidence that body fluid such as blood, urine, and saliva could harbor the potential biomarkers associated with tumor origin. Traditional correlation analysis methods are no longer sufficient to capture the high-resolution complex relationships between biomarkers and cancer subtype heterogeneity. To address the challenge, researchers proposed machine learning techniques with liquid biopsy data to explore the essence of tumor origin together. In this survey, we review the machine learning protocols and provide corresponding code demos for the approaches mentioned. We discuss algorithmic principles and frameworks extensively developed to reveal cancer mechanisms and consider the future prospects in biomarker exploration and cancer diagnostics.
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Affiliation(s)
- Linjing Liu
- Department of Computer Science, City University of Hong Kong, Hong Kong, China; (L.L.); (X.C.); (O.O.P.); (W.Z.); (S.R.); (Z.-R.T.)
| | - Xingjian Chen
- Department of Computer Science, City University of Hong Kong, Hong Kong, China; (L.L.); (X.C.); (O.O.P.); (W.Z.); (S.R.); (Z.-R.T.)
| | - Olutomilayo Olayemi Petinrin
- Department of Computer Science, City University of Hong Kong, Hong Kong, China; (L.L.); (X.C.); (O.O.P.); (W.Z.); (S.R.); (Z.-R.T.)
| | - Weitong Zhang
- Department of Computer Science, City University of Hong Kong, Hong Kong, China; (L.L.); (X.C.); (O.O.P.); (W.Z.); (S.R.); (Z.-R.T.)
| | - Saifur Rahaman
- Department of Computer Science, City University of Hong Kong, Hong Kong, China; (L.L.); (X.C.); (O.O.P.); (W.Z.); (S.R.); (Z.-R.T.)
| | - Zhi-Ri Tang
- Department of Computer Science, City University of Hong Kong, Hong Kong, China; (L.L.); (X.C.); (O.O.P.); (W.Z.); (S.R.); (Z.-R.T.)
| | - Ka-Chun Wong
- Department of Computer Science, City University of Hong Kong, Hong Kong, China; (L.L.); (X.C.); (O.O.P.); (W.Z.); (S.R.); (Z.-R.T.)
- Hong Kong Institute for Data Science, City University of Hong Kong, Hong Kong, China
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33
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Asperger H, Cieslik JP, Alberter B, Köstler C, Polzer B, Müller V, Pantel K, Riethdorf S, Koch A, Hartkopf A, Wiesmüller L, Janni W, Schochter F, Franken A, Niederacher D, Fehm T, Neubauer H. ViBiBa: Virtual BioBanking for the DETECT multicenter trial program - decentralized storage and processing. Transl Oncol 2021; 14:101132. [PMID: 34051621 PMCID: PMC8176360 DOI: 10.1016/j.tranon.2021.101132] [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: 04/26/2021] [Accepted: 05/19/2021] [Indexed: 12/05/2022] Open
Abstract
ViBiBa is an open-source sample banking tool. ViBiBa was purpose built for liquid biopsy specimen. ViBiBa allows for decentralized storage while promoting collaboration. ViBiBa's plugin support requires no change in existing data structures. ViBiBa empowers translational research projects and cohort formation.
Background Liquid Biopsy (LB) in the form of e.g., circulating tumor cells (CTCs) is a promising non-invasive approach to support current therapeutic cancer management. However, the proof of clinical utility of CTCs in informing therapeutic decision-making for e.g., breast cancer in clinical trials and associated translational research projects is facing the issues of low CTC positivity rates and low CTC numbers – even in the metastasized situation. To compensate for this dilemma, clinical CTC trials are designed as large multicenter endeavors with decentralized sample collection, processing and storage of products, making data management highly important to enable high-quality translational CTC research. Aim In the DETECT clinical CTC trials we aimed at developing a custom-made, browser-based virtual database to harmonize and organize both decentralized processing and storage of LB specimens and to enable the collection of clinically meaningful LB sample. Methods ViBiBa processes data from various sources, harmonizes the data and creates an easily searchable multilayered database. Results An open-source virtual bio-banking web-application termed ViBiBa was created, which automatically processes data from multiple non-standardized sources. These data are automatically checked and merged into one centralized databank and are providing the opportunity to extract clinically relevant patient cohorts and CTC sample collections. Summary ViBiBa, which is a highly flexible tool that allows for decentralized sample storage of liquid biopsy specimens, facilitates a solution which promotes collaboration in a user-friendly, federalist and highly structured way. The source code is available under the MIT license from https://vibiba.com or https://github.com/asperciesl/ViBiBa
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Affiliation(s)
- H Asperger
- Department of Obstetrics and Gynecology, University Hospital Duesseldorf, Moorenstraße 5, Düsseldorf, Germany
| | - J-P Cieslik
- Department of Obstetrics and Gynecology, University Hospital Duesseldorf, Moorenstraße 5, Düsseldorf, Germany
| | - B Alberter
- Division of Personalized Tumor Therapy, Fraunhofer ITEM, Germany, Am Biopark 9, Regensburg, Germany
| | - C Köstler
- Division of Personalized Tumor Therapy, Fraunhofer ITEM, Germany, Am Biopark 9, Regensburg, Germany
| | - B Polzer
- Division of Personalized Tumor Therapy, Fraunhofer ITEM, Germany, Am Biopark 9, Regensburg, Germany
| | - V Müller
- Department of Obstetrics and Gynecology, University Hospital Hamburg-Eppendorf, Germany, Martinistraße 52, Hamburg, Germany
| | - K Pantel
- Department of Tumor Biology, University Hospital Hamburg-Eppendorf, Germany, Martinistraße 52, Hamburg, Germany
| | - S Riethdorf
- Department of Tumor Biology, University Hospital Hamburg-Eppendorf, Germany, Martinistraße 52, Hamburg, Germany
| | - A Koch
- Department of Obstetrics and Gynecology, University of Tübingen, Germany, Calwerstraße 7, Tübingen, Germany
| | - A Hartkopf
- Department of Obstetrics and Gynecology, University of Tübingen, Germany, Calwerstraße 7, Tübingen, Germany
| | - L Wiesmüller
- Department of Obstetrics and Gynecology, University Hospital Ulm, Germany, Albert-Einstein-Allee 23, Ulm, Germany
| | - W Janni
- Department of Obstetrics and Gynecology, University Hospital Ulm, Germany, Albert-Einstein-Allee 23, Ulm, Germany
| | - F Schochter
- Department of Obstetrics and Gynecology, University Hospital Ulm, Germany, Albert-Einstein-Allee 23, Ulm, Germany
| | - A Franken
- Department of Obstetrics and Gynecology, University Hospital Duesseldorf, Moorenstraße 5, Düsseldorf, Germany
| | - D Niederacher
- Department of Obstetrics and Gynecology, University Hospital Duesseldorf, Moorenstraße 5, Düsseldorf, Germany
| | - T Fehm
- Department of Obstetrics and Gynecology, University Hospital Duesseldorf, Moorenstraße 5, Düsseldorf, Germany
| | - H Neubauer
- Department of Obstetrics and Gynecology, University Hospital Duesseldorf, Moorenstraße 5, Düsseldorf, Germany.
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34
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Zhu A, Yuan P, Hu N, Li M, Wang W, Wang X, Yue J, Wang J, Luo Y, Ma F, Zhang P, Li Q, Xu B, Cao S, Lippi G, Naito Y, Osman MA, Marta GN, Franceschini G, Orlandi A. Phase II study of apatinib in combination with oral vinorelbine in heavily pretreated HER2-negative metastatic breast cancer and clinical implications of monitoring ctDNA. Cancer Biol Med 2021; 18:j.issn.2095-3941.2020.0418. [PMID: 34037346 PMCID: PMC8330536 DOI: 10.20892/j.issn.2095-3941.2020.0418] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2020] [Accepted: 11/11/2020] [Indexed: 12/14/2022] Open
Abstract
OBJECTIVE Apatinib is an oral TKI targeting VEGFR-2. Single-agent apatinib treatment has been shown to produce an objective response in patients with pretreated mBC. Oral vinorelbine also holds promise as a treatment of choice in patients with mBC. This study aimed to investigate the efficacy and safety of the oral vinorelbine-apatinib combination in patients with pretreated mBC. In addition, we detected gene variants in ctDNA to explore the therapeutic implications. METHODS This study enrolled patients with HER2-negative mBC who were pretreated with anthracycline/taxanes. Patients were treated with apatinib at 500 mg/425 mg daily plus oral vinorelbine 60 mg/m2 on days 1, 8, and 15 of every cycle (3 weeks). The primary endpoint was PFS. The secondary endpoints were ORR, CBR, OS, and safety. Patients eligible for ctDNA detection were evaluated before and during treatment. RESULTS Forty patients were enrolled. The median PFS was 5.2 months (95% CI, 3.4-7.0 months), and the median OS was 17.4 months (95% CI, 8.0-27.0 months). The ORR was 17.1% (6/35), and the CBR was 45.7% (16/35). The most common AEs included gastrointestinal reaction, myelosuppression, and hypertension. In 20 patients, ctDNA was detected at baseline and during treatment. A significant difference was found in PFS for undetected vs. detected baseline ctDNA (13.9 months vs. 3.6 months, P = 0.018). CONCLUSIONS All-oral therapy with apatinib plus vinorelbine displayed objective efficacy in patients with heavily pretreated HER2-negative mBC, with acceptable and manageable toxicity profiles. Patients with no gene variant detected and lower variant allele frequencies in ctDNA at baseline showed longer PFS.
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Affiliation(s)
- Anjie Zhu
- Department of Medical Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100021, China
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Department of Breast Oncology, Peking University Cancer Hospital & Institute, Beijing 100142, China
| | - Peng Yuan
- Department of VIP Medical Services, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100021, China
| | - Nanlin Hu
- Department of Medical Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100021, China
| | - Mingzhou Li
- Department of Medical Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100021, China
| | - Wenmiao Wang
- Department of Pathology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100021, China
| | - Xue Wang
- Department of VIP Medical Services, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100021, China
| | - Jian Yue
- Department of VIP Medical Services, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100021, China
| | - Jiayu Wang
- Department of Medical Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100021, China
| | - Yang Luo
- Department of Medical Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100021, China
| | - Fei Ma
- Department of Medical Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100021, China
| | - Pin Zhang
- Department of Medical Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100021, China
| | - Qing Li
- Department of Medical Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100021, China
| | - Binghe Xu
- Department of Medical Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100021, China
| | - Shanbo Cao
- AcornMed Biotechnology Co., Ltd., Beijing 101102, China
| | - Giuseppe Lippi
- Section of Clinical Biochemistry, University Hospital of Verona, Verona 37100, Italy
| | - Yoichi Naito
- Department of Breast and Medical Oncology, National Cancer Center Hospital East, Kashiwa 277-8577, Japan
| | - Mohammed A. Osman
- Clinical Oncology, General Organization for Teaching Hospitals, Cairo 11435, Egypt
| | - Gustavo N. Marta
- Department of Radiation Oncology, Hospital Sírio-Libanês, Sao Paulo 01308-050, Brazil
| | - Gianluca Franceschini
- Multidisciplinary Breast Center, Fondazione Policlinico Universitario A. Gemelli IRCCS, Università Cattolica del Sacro Cuore, Rome 00176, Italy
| | - Armando Orlandi
- Unit of Medical Oncology, Fondazione Policlinico Universitario A. Gemelli IRCCS, Roma 00176, Italy
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35
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Keup C, Suryaprakash V, Hauch S, Storbeck M, Hahn P, Sprenger-Haussels M, Kolberg HC, Tewes M, Hoffmann O, Kimmig R, Kasimir-Bauer S. Integrative statistical analyses of multiple liquid biopsy analytes in metastatic breast cancer. Genome Med 2021; 13:85. [PMID: 34001236 PMCID: PMC8130163 DOI: 10.1186/s13073-021-00902-1] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2020] [Accepted: 04/30/2021] [Indexed: 02/08/2023] Open
Abstract
Background Single liquid biopsy analytes (LBAs) have been utilized for therapy selection in metastatic breast cancer (MBC). We performed integrative statistical analyses to examine the clinical relevance of using multiple LBAs: matched circulating tumor cell (CTC) mRNA, CTC genomic DNA (gDNA), extracellular vesicle (EV) mRNA, and cell-free DNA (cfDNA). Methods Blood was drawn from 26 hormone receptor-positive, HER2-negative MBC patients. CTC mRNA and EV mRNA were analyzed using a multi-marker qPCR. Plasma from CTC-depleted blood was utilized for cfDNA isolation. gDNA from CTCs was isolated from mRNA-depleted CTC lysates. CTC gDNA and cfDNA were analyzed by targeted sequencing. Hierarchical clustering was performed within each analyte, and its results were combined into a score termed Evaluation of multiple Liquid biopsy analytes In Metastatic breast cancer patients All from one blood sample (ELIMA.score), which calculates the contribution of each analyte to the overall survival prediction. Singular value decomposition (SVD), mutual information calculation, k-means clustering, and graph-theoretic analysis were conducted to elucidate the dependence between individual analytes. Results A combination of two/three/four LBAs increased the prevalence of patients with actionable signals. Aggregating the results of hierarchical clustering of individual LBAs into the ELIMA.score resulted in a highly significant correlation with overall survival, thereby bolstering evidence for the additive value of using multiple LBAs. Computation of mutual information indicated that none of the LBAs is independent of the others, but the ability of a single LBA to describe the others is rather limited—only CTC gDNA could partially describe the other three LBAs. SVD revealed that the strongest singular vectors originate from all four LBAs, but a majority originated from CTC gDNA. After k-means clustering of patients based on parameters of all four LBAs, the graph-theoretic analysis revealed CTC ERBB2 variants only in patients belonging to one particular cluster. Conclusions The additional benefits of using all four LBAs were objectively demonstrated in this pilot study, which also indicated a relative dominance of CTC gDNA over the other LBAs. Consequently, a multi-parametric liquid biopsy approach deconvolutes the genomic and transcriptomic complexity and should be considered in clinical practice. Supplementary Information The online version contains supplementary material available at 10.1186/s13073-021-00902-1.
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Affiliation(s)
- Corinna Keup
- Department of Gynecology and Obstetrics, University Hospital of Essen, Hufelandstr. 55, 45122, Essen, Germany.
| | | | | | | | | | | | - Hans-Christian Kolberg
- Department of Gynecology and Obstetrics, Marienhospital Bottrop, 46236, Bottrop, Germany
| | - Mitra Tewes
- Department of Medical Oncology, University Hospital of Essen, 45122, Essen, Germany
| | - Oliver Hoffmann
- Department of Gynecology and Obstetrics, University Hospital of Essen, Hufelandstr. 55, 45122, Essen, Germany
| | - Rainer Kimmig
- Department of Gynecology and Obstetrics, University Hospital of Essen, Hufelandstr. 55, 45122, Essen, Germany
| | - Sabine Kasimir-Bauer
- Department of Gynecology and Obstetrics, University Hospital of Essen, Hufelandstr. 55, 45122, Essen, Germany
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Bai H, Yu J, Jia S, Liu X, Liang X, Li H. Prognostic Value of the TP53 Mutation Location in Metastatic Breast Cancer as Detected by Next-Generation Sequencing. Cancer Manag Res 2021; 13:3303-3316. [PMID: 33889023 PMCID: PMC8057094 DOI: 10.2147/cmar.s298729] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2020] [Accepted: 03/19/2021] [Indexed: 11/23/2022] Open
Abstract
Purpose The status of TP53 mutations was measured in cell-free DNA from patients with metastatic breast cancer (MBC) to investigate disease characteristics and the prognostic role of different locations of the TP53 mutation site. Patients and Methods Blood samples were taken from a total of 187 patients diagnosed with MBC who were treated at the Department of Breast Oncology, Peking University Cancer Hospital between January 2013 and March 2020. Next-generation sequencing was used to investigate the TP53 mutation spectra of circulating free DNA in these blood samples. Results Among the 187 MBC patients, TP53-mutated patients had a significantly shorter median disease-free survival (DFS) and overall survival (OS) compared with TP53 wild-type patients (P=0.001 and P=0.006, respectively). Additionally, in hormone receptor positive/HER2 negative (HR+/HER2-) and triple negative (TNBC) cohorts, TP53-mutated patients had a significantly shorter median DFS than TP53 wild-type patients (P=0.038 and P=0.023, respectively). The 79 patients with TP53 mutations carried 87 somatic TP53 mutations, of which most (77.0%) mapped to the DNA-binding domain (DBD) of the protein encoded by TP53 exons 5–8. In patients with TP53 mutations, those occurring in the non-DBD had a significantly shorter median DFS and OS than TP53 wild type (P<0.001 and P=0.001, respectively). Additionally, patients with non-missense mutations in the DBD had a significantly shorter median DFS and OS than TP53 wild-type patients (P=0.001 and P<0.001, respectively). TP53-mutated patients had a significantly shorter DFS than TP53 wild-type patients in the adjuvant endocrine therapy sensitive group (P=0.008), but differences in the endocrine therapy resistant group were not significant. Conclusion TP53-mutated MBC patients had a significantly worse outcome than TP53 wild-type patients especially those in HR+/HER2– and TNBC cohorts. Of TP53-mutated patients, those with non-missense mutations in the DBD had worse breast cancer-related survival. TP53 mutations were also associated with endocrine resistance.
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Affiliation(s)
- Han Bai
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Department of Breast Oncology, Peking University Cancer Hospital and Institute, Beijing, 100142, People's Republic of China
| | - Jianjun Yu
- Huidu Shanghai Medical Sciences, Shanghai, 201499, People's Republic of China
| | - Shidong Jia
- Huidu Shanghai Medical Sciences, Shanghai, 201499, People's Republic of China
| | - Xiaoran Liu
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Department of Breast Oncology, Peking University Cancer Hospital and Institute, Beijing, 100142, People's Republic of China
| | - Xu Liang
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Department of Breast Oncology, Peking University Cancer Hospital and Institute, Beijing, 100142, People's Republic of China
| | - Huiping Li
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Department of Breast Oncology, Peking University Cancer Hospital and Institute, Beijing, 100142, People's Republic of China
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Magbanua MJM, Li W, Wolf DM, Yau C, Hirst GL, Swigart LB, Newitt DC, Gibbs J, Delson AL, Kalashnikova E, Aleshin A, Zimmermann B, Chien AJ, Tripathy D, Esserman L, Hylton N, van 't Veer L. Circulating tumor DNA and magnetic resonance imaging to predict neoadjuvant chemotherapy response and recurrence risk. NPJ Breast Cancer 2021; 7:32. [PMID: 33767190 PMCID: PMC7994408 DOI: 10.1038/s41523-021-00239-3] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2020] [Accepted: 03/02/2021] [Indexed: 12/13/2022] Open
Abstract
We investigated whether serial measurements of circulating tumor DNA (ctDNA) and functional tumor volume (FTV) by magnetic resonance imaging (MRI) can be combined to improve prediction of pathologic complete response (pCR) and estimation of recurrence risk in early breast cancer patients treated with neoadjuvant chemotherapy (NAC). We examined correlations between ctDNA and FTV, evaluated the additive value of ctDNA to FTV-based predictors of pCR using area under the curve (AUC) analysis, and analyzed the impact of FTV and ctDNA on distant recurrence-free survival (DRFS) using Cox regressions. The levels of ctDNA (mean tumor molecules/mL plasma) were significantly correlated with FTV at all time points (p < 0.05). Median FTV in ctDNA-positive patients was significantly higher compared to those who were ctDNA-negative (p < 0.05). FTV and ctDNA trajectories in individual patients showed a general decrease during NAC. Exploratory analysis showed that adding ctDNA information early during treatment to FTV-based predictors resulted in numerical but not statistically significant improvements in performance for pCR prediction (e.g., AUC 0.59 vs. 0.69, p = 0.25). In contrast, ctDNA-positivity after NAC provided significant additive value to FTV in identifying patients with increased risk of metastatic recurrence and death (p = 0.004). In this pilot study, we demonstrate that ctDNA and FTV were correlated measures of tumor burden. Our preliminary findings based on a limited cohort suggest that ctDNA at surgery improves FTV as a predictor of metastatic recurrence and death. Validation in larger studies is warranted.
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Affiliation(s)
- Mark Jesus M Magbanua
- Department of Laboratory Medicine, University of California San Francisco, San Francisco, CA, USA.
| | - Wen Li
- Department of Radiology and Biomedical Imaging, University of California San Francisco, San Francisco, CA, USA.
| | - Denise M Wolf
- Department of Laboratory Medicine, University of California San Francisco, San Francisco, CA, USA
| | - Christina Yau
- Department of Surgery, University of California San Francisco, San Francisco, CA, USA
| | - Gillian L Hirst
- Department of Surgery, University of California San Francisco, San Francisco, CA, USA
| | - Lamorna Brown Swigart
- Department of Laboratory Medicine, University of California San Francisco, San Francisco, CA, USA
| | - David C Newitt
- Department of Radiology and Biomedical Imaging, University of California San Francisco, San Francisco, CA, USA
| | - Jessica Gibbs
- Department of Radiology and Biomedical Imaging, University of California San Francisco, San Francisco, CA, USA
| | - Amy L Delson
- Breast Science Advocacy Core, University of California San Francisco, San Francisco, CA, USA
| | | | | | | | - A Jo Chien
- Division of Hematology Oncology, University of California San Francisco, San Francisco, CA, USA
| | - Debu Tripathy
- Department of Breast Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Laura Esserman
- Department of Surgery, University of California San Francisco, San Francisco, CA, USA
| | - Nola Hylton
- Department of Radiology and Biomedical Imaging, University of California San Francisco, San Francisco, CA, USA.
| | - Laura van 't Veer
- Department of Laboratory Medicine, University of California San Francisco, San Francisco, CA, USA.
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Hu N, Si Y, Yue J, Sun T, Wang X, Jia Z, Gao S, Li Q, Shao Y, Wang J, Luo Y, Ma F, Xu B, Yuan P. Anlotinib has good efficacy and low toxicity: a phase II study of anlotinib in pre-treated HER-2 negative metastatic breast cancer. Cancer Biol Med 2021; 18:j.issn.2095-3941.2020.0463. [PMID: 33710812 PMCID: PMC8330540 DOI: 10.20892/j.issn.2095-3941.2020.0463] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2020] [Accepted: 10/15/2020] [Indexed: 12/25/2022] Open
Abstract
OBJECTIVE Anlotinib is a novel tyrosine kinase inhibitor blocking angiogenesis. This study was performed to assess the efficacy and safety of anlotinib in patients with metastatic breast cancer. METHODS Patients with HER2-negative breast cancer, who were pre-treated with anthracycline or taxanes in a neoadjuvant, adjuvant, or metastatic setting, and had treatment failure after at least one prior chemotherapy regimen in the metastatic setting were enrolled. Anlotinib was administered at 12 mg daily for 14 days in a 21-day cycle until disease progression or unacceptable toxicity occurred. Simultaneously, 5-10 mL of venous blood was collected to perform circulating tumor DNA (ctDNA) testing every 2 treatment cycles. The primary endpoint was the objective response rate (ORR). Secondary endpoints included the disease control rate (DCR), progression-free survival (PFS), overall survival, safety, and biomarkers. RESULTS Twenty-six eligible patients were enrolled, with a median age of 56 (30-75) years. The median follow-up time was 10.5 months. The ORR was 15.4%, the DCR was 80.8%, and the median PFS was 5.22 months (95% confidence interval 2.86-6.24). Fourteen (53.8%) patients survived for more than 10 months. The changes in the detectable ctDNA variant allele frequency were consistent with the tumor response. The most common treatment-related adverse events were hypertension (57.7%), thyroidstimulating hormone elevation (34.6%), and hand-foot syndrome (23.1%). CONCLUSIONS Anlotinib showed objective efficacy with tolerable toxicity in heavily pre-treated, metastatic HER2-negative breast cancer. The dynamic changes in the ctDNA variant allele fraction may be predictive of the tumor response.
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Affiliation(s)
- Nanlin Hu
- Department of Medical Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100021, China
| | - Yiran Si
- Department of Medical Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100021, China
| | - Jian Yue
- Department of VIP Medical Services, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100021, China
| | - Tingting Sun
- Nanjing Geneseeq Technology Inc., Nanjing 210032, China
| | - Xue Wang
- Department of VIP Medical Services, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100021, China
| | - Zhuqing Jia
- Cancer Hospital of Huanxing Chaoyang District Beijing, Beijing 100021, China
| | - Songlin Gao
- Department of Medical Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100021, China
| | - Qiao Li
- Department of Medical Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100021, China
| | - Yang Shao
- Nanjing Geneseeq Technology Inc., Nanjing 210032, China
| | - Jiayu Wang
- Department of Medical Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100021, China
| | - Yang Luo
- Department of Medical Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100021, China
| | - Fei Ma
- Department of Medical Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100021, China
| | - Binghe Xu
- Department of Medical Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100021, China
| | - Peng Yuan
- Department of VIP Medical Services, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100021, China
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Nakai M, Yamada T, Sekiya K, Sato A, Hankyo M, Kuriyama S, Takahashi G, Kurita T, Yanagihara K, Yoshida H, Ohashi R, Takei H. PIK3CA mutation detected by liquid biopsy in patients with metastatic breast cancer. J NIPPON MED SCH 2021; 89:66-71. [PMID: 33692304 DOI: 10.1272/jnms.jnms.2022_89-107] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
BACKGROUND PIK3CA is associated with tumor progression, and the prevalence of its mutation is high in breast cancer. Liquid biopsy offers convenient, non-invasive, and real-time insight into genetic alternation. In this study, we attempted to detect PIK3CA mutations in breast cancer patients through liquid biopsy. METHODS We recruited patients with histologically confirmed breast cancer with distant metastases between April 2020 and September 2020. Circulating DNA was extracted from plasma (ctDNA) and exosomes (exoDNA). PIK3CA mutations (exons 9 and 20) were analyzed by droplet digital PCR. RESULTS Of a total of 52 patients recruited, 16 had PIK3CA mutations in their tumor tissue or blood, which comprised 9 with exon 9 mutations (E542K and E545K) and 8 with exon 20 mutations (H1047L and H1047R). In 8 (15%) of the 52 patients, PIK3CA mutations were detected by liquid biopsies using ctDNA in 5 (9%), exoDNA in 6 (11%), and both ctDNA and exoDNA in 3 (6%). Of the 8 patients with PIK3CA mutations detected by liquid biopsies, 3 had no PIK3CA mutations in the primary tumors. CONCLUSIONS PIK3CA mutations can be detected using liquid biopsy even in patients with no PIK3CA mutations in their primary tumors; thus, combination analysis using tissue and liquid biopsies can provide clinically useful information for patients with breast cancer.
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Affiliation(s)
- Maki Nakai
- Department of Breast Surgery and Oncology, Nippon Medical School
| | - Takeshi Yamada
- Department of Gastrointestinal and Hepato-Biliary-Pancreatic Surgery, Nippon Medical School
| | - Kenta Sekiya
- Department of Breast Surgery and Oncology, Nippon Medical School
| | - Ai Sato
- Department of Breast Surgery and Oncology, Nippon Medical School
| | - Meishi Hankyo
- Department of Breast Surgery and Oncology, Nippon Medical School
| | - Sho Kuriyama
- Department of Gastrointestinal and Hepato-Biliary-Pancreatic Surgery, Nippon Medical School
| | - Goro Takahashi
- Department of Gastrointestinal and Hepato-Biliary-Pancreatic Surgery, Nippon Medical School
| | - Tomoko Kurita
- Department of Breast Surgery and Oncology, Nippon Medical School
| | - Keiko Yanagihara
- Department of Surgery, Nippon Medical School Tamanagayama Hospital
| | - Hiroshi Yoshida
- Department of Gastrointestinal and Hepato-Biliary-Pancreatic Surgery, Nippon Medical School
| | - Ryuji Ohashi
- Department of Integrated Diagnostic Pathology, Nippon Medical School
| | - Hiroyuki Takei
- Department of Breast Surgery and Oncology, Nippon Medical School
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Huang C, Lin X, He J, Liu N. Enrichment and detection method for the prognostic value of circulating tumor cells in ovarian cancer: A meta-analysis. Gynecol Oncol 2021; 161:613-620. [PMID: 33674144 DOI: 10.1016/j.ygyno.2021.02.024] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2020] [Accepted: 02/17/2021] [Indexed: 02/07/2023]
Abstract
OBJECTIVES Recent studies have revealed that circulating tumor cells (CTCs) might predict bad prognosis, but the results were conflicting. Sampling time, treatment, enrichment method and detection method also varied. We aimed to evaluate whether patients with CTCs in peripheral blood have bad survival outcomes with consideration of the above four aspects. METHODS Relevant studies were searched on Pubmed, Embase and the Cochrane Library. Studies of CTCs involving survival data available were identified for a systematic review and meta-analysis. HRs and 95% CIs for PFS and OS were extracted directly or from the Kaplan-Meier survival curves by the Engauge Digitizer v4.1. Subgroup analyses were performed to evaluate the effect of sampling time, treatment, enrichment method and detection method. RESULTS Two clinical trials and thirteen retrospective studies with a total of 1285 patients were included. CTCs significantly correlated with OS (HR = 1.77, 95%CI:1.42-2.21, p < 0.00001 and PFS (HR = 1.53, 95%CI:1.26-1.86, p < 0.0001). Subgroup analyses showed that CTCs were significant associated with OS in the "Pre-therapy" subgroup (HR = 1.79, 95%CI:1.43-2.24, p < 0.00001), the "Surgery" group (HR = 1.82, 95%CI:1.42-2.33, p < 0.00001), and the "RT-PCR"subgroup (HR = 2.29, 95%CI:1.53-3.42, p < 0.0001). While for enrichment method, CTCs significantly correlated with OS in the"Physical method" subgroup (HR = 1.94, 95%CI:1.21-3.09, p = 0.006) and the "Immunological method" subgroup (HR = 1.84, 95%CI:1.37-2.48, p < 0.0001). CONCLUSIONS The presence of CTCs prior to the treatment indicated worse OS and PFS and CTCs might be predictive biomarker for ovarian cancer patients . CTCs detected using RT-PCR seem to be associated with poorer OS and PFS in patients with ovarian cancer.
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Affiliation(s)
- Chengying Huang
- Department of Obstetrics and Gynecology, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Xiaoli Lin
- Department of Obstetrics and Gynecology, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Jinmei He
- Department of Obstetrics and Gynecology, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Nan Liu
- Department of Obstetrics and Gynecology, Nanfang Hospital, Southern Medical University, Guangzhou, China.
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Zhao L, Wu X, Li T, Luo J, Dong D. ctcRbase: the gene expression database of circulating tumor cells and microemboli. DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION 2021; 2020:5819651. [PMID: 32294193 DOI: 10.1093/database/baaa020] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/21/2019] [Revised: 02/16/2020] [Accepted: 02/17/2020] [Indexed: 01/04/2023]
Abstract
Circulating tumor cells/microemboli (CTCs/CTMs) are malignant cells that depart from cancerous lesions and shed into the bloodstream. Analysis of CTCs can allow the investigation of tumor cell biomarker expression from a non-invasive liquid biopsy. To date, high-throughput technologies have become a powerful tool to provide a genome-wide view of transcriptomic changes associated with CTCs/CTMs. These data provided us much information to understand the tumor heterogeneity, and the underlying molecular mechanism of tumor metastases. Unfortunately, these data have been deposited into various repositories, and a uniform resource for the cancer metastasis is still unavailable. To this end, we integrated previously published transcriptome datasets of CTCs/CTMs and constructed a web-accessible database. The first release of ctcRbase contains 526 CTCs/CTM samples across seven cancer types. The expression of 14 631 mRNAs and 3642 long non-coding RNAs of CTCs/CTMs were included. Experimental validations from the published literature are also included. Since CTCs/CTMs are considered to be precursors of metastases, ctcRbase also collected the expression data of primary tumors and metastases, which allows user to discover a unique 'circulating tumor cell gene signature' that is distinct from primary tumor and metastases. An easy-to-use database was constructed to query and browse CTCs/CTMs genes. ctcRbase can be freely accessible at http://www.origin-gene.cn/database/ctcRbase/.
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Affiliation(s)
- Lei Zhao
- Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences, School of Life Sciences, East China Normal University, No.500 Dongchuan Road, Shanghai, 200241 China
| | - Xiaohong Wu
- Department of General Surgery, the Affiliated Yixing Hospital of Jiangsu University, No. 75 Zhenguan Road, Yixing, Jiangsu 214200, China
| | - Tong Li
- Thyroid and breast surgery, the Fourth Hospital of Jinan City, No. 50 Shifan Road, Jinan, Shandong 250021, China
| | - Jian Luo
- Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences, School of Life Sciences, East China Normal University, No.500 Dongchuan Road, Shanghai, 200241 China
| | - Dong Dong
- Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences, School of Life Sciences, East China Normal University, No.500 Dongchuan Road, Shanghai, 200241 China.,Cancer Institute, Xuzhou Medical University, No. 84 West huaihai Road, Xuzhou, Jiangsu 221006, China.,Center of Clinical Oncology, Affiliated Hospital of Xuzhou Medical University, No.315 West huaihai Road, Xuzhou, Jiangsu 221006, China
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ESR1 NAPA Assay: Development and Analytical Validation of a Highly Sensitive and Specific Blood-Based Assay for the Detection of ESR1 Mutations in Liquid Biopsies. Cancers (Basel) 2021; 13:cancers13030556. [PMID: 33535614 PMCID: PMC7867152 DOI: 10.3390/cancers13030556] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2020] [Revised: 01/15/2021] [Accepted: 01/26/2021] [Indexed: 01/04/2023] Open
Abstract
Simple Summary A considerable number of estrogen-receptor–positive (ER+) breast cancer patients develop resistance to endocrine treatment. One of the most important resistance mechanisms is the presence of ESR1 mutations. In the present study, we developed and analytically validated a novel, highly sensitive and specific nuclease-assisted minor-allele enrichment with probe-overlap (NaME-PrO)-assisted Amplification refractory mutation system (ARMS) (NAPA) assay for the detection of four ESR1 mutations (Y537S, Y537C, Y537N and D538G). The assay was further applied in 13 ER+ breast cancer (BrCa) primary tumour tissues (FFPEs), 13 non-cancerous breast tissues (mammoplasties), and 32 pairs of liquid biopsy samples [circulating tumour cells (CTCs) and paired plasma circulating tumour DNA (ctDNA)] obtained at different time points from 8 ER+ metastatic breast cancer patients. In the plasma ctDNA, the ESR1 mutations were not identified at the baseline, whereas the D538G mutation was detected during the follow-up period at five consecutive time points in one patient. In the CTCs, only the Y537C mutation was detected in one patient sample at the baseline. A direct comparison of the ESR1 NAPA assay with the drop-off ddPCR using 32 identical plasma ctDNA samples gave a concordance of 90.6%. We present a low-cost, highly specific, sensitive and robust assay for blood-based ESR1 profiling. Abstract A considerable number of estrogen receptor-positive breast cancer (ER+ BrCa) patients develop resistance to endocrine treatment. One of the most important resistance mechanisms is the presence of ESR1 mutations. We developed and analytically validated a highly sensitive and specific NaME-PrO-assisted ARMS (NAPA) assay for the detection of four ESR1 mutations (Y537S, Y537C, Y537N and D538G) in circulating tumour cells (CTCs) and paired plasma circulating tumour DNA (ctDNA) in patients with ER+ BrCa. The analytical specificity, analytical sensitivity and reproducibility of the assay were validated using synthetic oligos standards. We further applied the developed ESR1 NAPA assay in 13 ER+ BrCa primary tumour tissues, 13 non-cancerous breast tissues (mammoplasties) and 64 liquid biopsy samples: 32 EpCAM-positive cell fractions and 32 paired plasma ctDNA samples obtained at different time points from 8 ER+ metastatic breast cancer patients, during a 5-year follow-up period. Peripheral blood from 11 healthy donors (HD) was used as a control. The developed assay is highly sensitive (a detection of mutation-allelic-frequency (MAF) of 0.5% for D538G and 0.1% for Y537S, Y537C, Y537N), and highly specific (0/13 mammoplasties and 0/11 HD for all mutations). In the plasma ctDNA, ESR1 mutations were not identified at the baseline, whereas the D538G mutation was detected in five sequential ctDNA samples during the follow-up period in the same patient. In the EpCAM-isolated cell fractions, only the Y537C mutation was detected in one patient sample at the baseline. A direct comparison of the ESR1 NAPA assay with the drop-off ddPCR using 32 identical plasma ctDNA samples gave a concordance of 90.6%. We present a low cost, highly specific, sensitive and robust assay for blood-based ESR1 profiling. The clinical performance of the ESR1 NAPA assay will be prospectively evaluated in a large number of well-characterized patient cohorts.
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Keup C, Suryaprakash V, Storbeck M, Hoffmann O, Kimmig R, Kasimir-Bauer S. Longitudinal Multi-Parametric Liquid Biopsy Approach Identifies Unique Features of Circulating Tumor Cell, Extracellular Vesicle, and Cell-Free DNA Characterization for Disease Monitoring in Metastatic Breast Cancer Patients. Cells 2021; 10:212. [PMID: 33494385 PMCID: PMC7912374 DOI: 10.3390/cells10020212] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2020] [Revised: 01/08/2021] [Accepted: 01/18/2021] [Indexed: 02/07/2023] Open
Abstract
Dynamics of mRNA from circulating tumor cells (CTCs), mRNA from extracellular vesicles (EVs), and cell-free DNA (cfDNA) were assessed to examine the relevance of a longitudinal multi-parametric liquid biopsy strategy. Eighteen milliliters of blood was drawn from 27 hormone receptor-positive and human epidermal growth factor receptor 2 (HER2)-negative metastatic breast cancer (MBC) patients at disease progression and at two subsequent radiologic staging time points. CTC mRNA and EV mRNA were analyzed using multi-marker qPCR, and cfDNA was analyzed using targeted next-generation sequencing (NGS). The presence of ERBB2 or ERBB3 overexpression signals in CTCs significantly correlated with disease progression (87% specificity, 36% sensitivity, p-value = 0.023), and the presence of either ERBB3 signals in CTCs or EVs or cfDNA variants in ERBB3 also showed a significant association with progressive MBC. Fluctuations during treatment were detected in the EV fraction with the appearance of hitherto undetected ERCC1 signals correlating with progressive disease (97% specificity, 18% sensitivity, p-value = 0.030). Allele frequency development of ESR1 and PIK3CA variants detected at subsequent staging time points could be used as a predictor for therapy success and, importantly, might help guide therapy decisions. The three analytes, each with their own unique features for disease monitoring, were shown to be complementary, underlining the usefulness of the longitudinal multi-parametric liquid biopsy approach.
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Affiliation(s)
- Corinna Keup
- Department of Gynecology and Obstetrics, University Hospital of Essen, 45122 Essen, Germany; (O.H.); (R.K.); (S.K.-B.)
| | | | | | - Oliver Hoffmann
- Department of Gynecology and Obstetrics, University Hospital of Essen, 45122 Essen, Germany; (O.H.); (R.K.); (S.K.-B.)
| | - Rainer Kimmig
- Department of Gynecology and Obstetrics, University Hospital of Essen, 45122 Essen, Germany; (O.H.); (R.K.); (S.K.-B.)
| | - Sabine Kasimir-Bauer
- Department of Gynecology and Obstetrics, University Hospital of Essen, 45122 Essen, Germany; (O.H.); (R.K.); (S.K.-B.)
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Welter L, Xu L, McKinley D, Dago AE, Prabakar RK, Restrepo-Vassalli S, Xu K, Rodriguez-Lee M, Kolatkar A, Nevarez R, Ruiz C, Nieva J, Kuhn P, Hicks J. Treatment response and tumor evolution: lessons from an extended series of multianalyte liquid biopsies in a metastatic breast cancer patient. Cold Spring Harb Mol Case Stud 2020; 6:mcs.a005819. [PMID: 33203646 PMCID: PMC7784493 DOI: 10.1101/mcs.a005819] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2020] [Accepted: 11/15/2020] [Indexed: 12/17/2022] Open
Abstract
Currently, clinical characterization of metastatic breast cancer is based on tissue samples taken at time of diagnosis. However, tissue biopsies are invasive and tumors are continuously evolving, which indicates the need for minimally invasive longitudinal assessment of the tumor. Blood-based liquid biopsies provide minimal invasive means for serial sampling over the course of treatment and the opportunity to adjust therapies based on molecular markers. Here, we aim to identify cellular changes that occur in breast cancer over the lifespan of an affected patient through single-cell proteomic and genomic analysis of longitudinally sampled solid and liquid biopsies. Three solid and 17 liquid biopsies from peripheral blood of an ER+/HER2− metastatic breast cancer patient collected over 4 years and eight treatment regimens were analyzed for morphology, protein expression, copy-number alterations, and single-nucleotide variations. Analysis of 563 single morphometrically similar circulating tumor cells (CTCs) and 13 cell-free DNA (cfDNA) samples along with biopsies of the primary and metastatic tumor revealed progressive genomic evolution away from the primary tumor profiles, along with changes in ER expression and the appearance of resistance mutations. Both the abundance and the genomic alterations of CTCs and cfDNA were highly correlated and consistent with genomic alterations in the tissue samples. We demonstrate that genomic evolution and acquisition of drug resistance can be detected in real time and at single-cell resolution through liquid biopsy analytes and highlight the utility of liquid biopsies to guide treatment decisions.
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Affiliation(s)
- Lisa Welter
- Convergent Science Institute in Cancer, Michelson Center for Convergent Bioscience, University of Southern California, Los Angeles, California 90089, USA
| | - Liya Xu
- Convergent Science Institute in Cancer, Michelson Center for Convergent Bioscience, University of Southern California, Los Angeles, California 90089, USA
| | - Dillon McKinley
- Convergent Science Institute in Cancer, Michelson Center for Convergent Bioscience, University of Southern California, Los Angeles, California 90089, USA
| | - Angel E Dago
- The Scripps Research Institute, La Jolla, California 92037, USA
| | - Rishvanth K Prabakar
- Convergent Science Institute in Cancer, Michelson Center for Convergent Bioscience, University of Southern California, Los Angeles, California 90089, USA
| | - Sara Restrepo-Vassalli
- Convergent Science Institute in Cancer, Michelson Center for Convergent Bioscience, University of Southern California, Los Angeles, California 90089, USA
| | - Kevin Xu
- Convergent Science Institute in Cancer, Michelson Center for Convergent Bioscience, University of Southern California, Los Angeles, California 90089, USA
| | - Mariam Rodriguez-Lee
- Convergent Science Institute in Cancer, Michelson Center for Convergent Bioscience, University of Southern California, Los Angeles, California 90089, USA
| | - Anand Kolatkar
- Convergent Science Institute in Cancer, Michelson Center for Convergent Bioscience, University of Southern California, Los Angeles, California 90089, USA
| | - Rafael Nevarez
- Convergent Science Institute in Cancer, Michelson Center for Convergent Bioscience, University of Southern California, Los Angeles, California 90089, USA
| | - Carmen Ruiz
- Convergent Science Institute in Cancer, Michelson Center for Convergent Bioscience, University of Southern California, Los Angeles, California 90089, USA
| | - Jorge Nieva
- Keck School of Medicine, University of Southern California, Los Angeles, California 90033, USA
| | - Peter Kuhn
- Convergent Science Institute in Cancer, Michelson Center for Convergent Bioscience, University of Southern California, Los Angeles, California 90089, USA.,Keck School of Medicine, University of Southern California, Los Angeles, California 90033, USA.,Viterbi School of Engineering, University of Southern California, Los Angeles, California 90089, USA
| | - James Hicks
- Convergent Science Institute in Cancer, Michelson Center for Convergent Bioscience, University of Southern California, Los Angeles, California 90089, USA
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45
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Jacob S, Davis AA, Gerratana L, Velimirovic M, Shah AN, Wehbe F, Katam N, Zhang Q, Flaum L, Siziopikou KP, Platanias LC, Gradishar WJ, Behdad A, Bardia A, Cristofanilli M. The Use of Serial Circulating Tumor DNA to Detect Resistance Alterations in Progressive Metastatic Breast Cancer. Clin Cancer Res 2020; 27:1361-1370. [PMID: 33323406 DOI: 10.1158/1078-0432.ccr-20-1566] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2020] [Revised: 10/18/2020] [Accepted: 12/11/2020] [Indexed: 11/16/2022]
Abstract
PURPOSE Circulating tumor DNA (ctDNA) is a promising tool for noninvasive longitudinal monitoring of genomic alterations. We analyzed serial ctDNA to characterize genomic evolution in progressive metastatic breast cancer. EXPERIMENTAL DESIGN This was a retrospective cohort between 2015 and 2019 obtained under an Institutional Review Board-approved protocol at Northwestern University (Chicago, IL). ctDNA samples were analyzed with Guardant360 next-generation sequencing (NGS) assay. A total of 86 patients had at least two serial ctDNA collections with the second drawn at first post-NGS progression (PN1) by imaging and clinical assessment. A total of 27 participants had ctDNA drawn at second post-NGS clinical progression (PN2). We analyzed alterations, mutant allele frequency (MAF), number of alterations (NOA), and sites of disease on imaging in close proximity to ctDNA evaluation. Matched pairs' variations in MAF, NOA, and alterations at progression were tested through Wilcoxon test. We identified an independent control cohort at Massachusetts General Hospital (Boston, MA) of 63 patients with serial ctDNA sampling and no evidence of progression. RESULTS We identified 44 hormone receptor-positive, 20 HER2+, and 22 triple-negative breast cancer cases. The significant alterations observed between baseline and PN1 were TP53 (P < 0.0075), PIK3CA (P < 0.0126), AR (P < 0.0126), FGFR1 (P < 0.0455), and ESR1 (P < 0.0143). Paired analyses revealed increased MAF and NOA from baseline to PN1 (P = 0.0026, and P < 0.0001, respectively). When compared with controls without progression, patients with ctDNA collection at times of progression were associated with increased MAF and NOA (P = 0.0042 and P < 0.0001, respectively). CONCLUSIONS Serial ctDNA testing identified resistance alterations and increased NOA and MAF were associated with disease progression. Prospective longitudinal ctDNA evaluation could potentially monitor tumor genomic evolution.
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Affiliation(s)
- Saya Jacob
- Division of Hematology and Oncology, Department of Medicine, Northwestern University Feinberg School of Medicine, Chicago, Illinois
| | - Andrew A Davis
- Division of Hematology and Oncology, Department of Medicine, Northwestern University Feinberg School of Medicine, Chicago, Illinois.,Robert H. Lurie Comprehensive Cancer Center of Northwestern University, Chicago, Illinois.,Division of Hematology and Oncology, Department of Medicine, Washington University in St. Louis, St. Louis, Missouri
| | - Lorenzo Gerratana
- Division of Hematology and Oncology, Department of Medicine, Northwestern University Feinberg School of Medicine, Chicago, Illinois.,Robert H. Lurie Comprehensive Cancer Center of Northwestern University, Chicago, Illinois.,Department of Medicine, University of Udine, Udine, Italy
| | | | - Ami N Shah
- Division of Hematology and Oncology, Department of Medicine, Northwestern University Feinberg School of Medicine, Chicago, Illinois.,Robert H. Lurie Comprehensive Cancer Center of Northwestern University, Chicago, Illinois
| | - Firas Wehbe
- Robert H. Lurie Comprehensive Cancer Center of Northwestern University, Chicago, Illinois
| | - Neelima Katam
- Robert H. Lurie Comprehensive Cancer Center of Northwestern University, Chicago, Illinois
| | - Qiang Zhang
- Division of Hematology and Oncology, Department of Medicine, Northwestern University Feinberg School of Medicine, Chicago, Illinois.,Robert H. Lurie Comprehensive Cancer Center of Northwestern University, Chicago, Illinois
| | - Lisa Flaum
- Division of Hematology and Oncology, Department of Medicine, Northwestern University Feinberg School of Medicine, Chicago, Illinois.,Robert H. Lurie Comprehensive Cancer Center of Northwestern University, Chicago, Illinois
| | - Kalliopi P Siziopikou
- Robert H. Lurie Comprehensive Cancer Center of Northwestern University, Chicago, Illinois.,Department of Pathology, Northwestern University, Chicago, Illinois
| | - Leonidas C Platanias
- Division of Hematology and Oncology, Department of Medicine, Northwestern University Feinberg School of Medicine, Chicago, Illinois.,Robert H. Lurie Comprehensive Cancer Center of Northwestern University, Chicago, Illinois
| | - William J Gradishar
- Division of Hematology and Oncology, Department of Medicine, Northwestern University Feinberg School of Medicine, Chicago, Illinois.,Robert H. Lurie Comprehensive Cancer Center of Northwestern University, Chicago, Illinois
| | - Amir Behdad
- Division of Hematology and Oncology, Department of Medicine, Northwestern University Feinberg School of Medicine, Chicago, Illinois.,Robert H. Lurie Comprehensive Cancer Center of Northwestern University, Chicago, Illinois.,Department of Pathology, Northwestern University, Chicago, Illinois
| | - Aditya Bardia
- Massachusetts General Hospital, Boston, Massachusetts
| | - Massimo Cristofanilli
- Division of Hematology and Oncology, Department of Medicine, Northwestern University Feinberg School of Medicine, Chicago, Illinois. .,Robert H. Lurie Comprehensive Cancer Center of Northwestern University, Chicago, Illinois
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46
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Rungkamoltip P, Temisak S, Piboonprai K, Japrung D, Thangsunan P, Chanpanitkitchot S, Chaowawanit W, Chandeying N, Tangjitgamol S, Iempridee T. Rapid and ultrasensitive detection of circulating human papillomavirus E7 cell-free DNA as a cervical cancer biomarker. Exp Biol Med (Maywood) 2020; 246:654-666. [PMID: 33307803 DOI: 10.1177/1535370220978899] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Abstract
Circulating cell-free DNA (cfDNA) has attracted attention as a non-invasive biomarker for diagnosing and monitoring various cancers. Given that human papillomavirus (HPV) DNA integration and overexpression of E6/E7 oncogenes are pivotal events for carcinogenesis, we sought to determine if HPV E7 cfDNA could serve as a specific biomarker for cervical cancer detection. We applied droplet digital PCR (ddPCR) to quantify HPV16/18 E7 cfDNA from the serum of patients with cervical cancer, cervical intraepithelial neoplasia, and controls. HPV16/18 E7 cfDNA was highly specific for cervical cancer, displaying 30.77% sensitivity, 100% specificity, and an area under the curve of 0.65. Furthermore, we developed a sensitive isothermal detection of HPV16/18 E7 and the PIK3CA WT reference gene based on recombinase polymerase amplification combined with a lateral flow strip (RPA-LF). The assay took less than 30 min and the detection limit was 5-10 copies. RPA-LF exhibited 100% sensitivity and 88.24% specificity towards HPV16/18 E7 cfDNA in clinical samples. The agreement between RPA-LF and ddPCR was 83.33% (κ = 0.67) for HPV16 E7 and 100% (κ = 1.0) for HPV18 E7, indicating a good correlation between both tests. Therefore, we conclude that HPV E7 cfDNA represents a potential tumor marker with excellent specificity and moderate sensitivity for minimally invasive cervical cancer monitoring. Moreover, the RPA-LF assay provides an affordable, rapid, and ultrasensitive tool for detecting HPV cfDNA in resource-limited settings.
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Affiliation(s)
- Phetploy Rungkamoltip
- National Nanotechnology Center (NANOTEC), National Science and Technology Development Agency, Pathum Thani 12120, Thailand
| | - Sasithon Temisak
- Chemical Metrology and Biometry Department, National Institute of Metrology (NIMT), Pathum Thani 12120, Thailand
| | - Kitiya Piboonprai
- National Nanotechnology Center (NANOTEC), National Science and Technology Development Agency, Pathum Thani 12120, Thailand.,Laboratory of Host Defense, The World Premier International Research Center Initiative (WPI) Immunology Frontier Research Center (IFReC), Osaka University, Osaka 565-0871, Japan
| | - Deanpen Japrung
- National Nanotechnology Center (NANOTEC), National Science and Technology Development Agency, Pathum Thani 12120, Thailand
| | - Pattanapong Thangsunan
- Chemical Metrology and Biometry Department, National Institute of Metrology (NIMT), Pathum Thani 12120, Thailand
| | - Saranya Chanpanitkitchot
- Department of Obstetrics and Gynecology, Rajavithi Hospital, College of Medicine, Rangsit University, Bangkok 10400, Thailand
| | - Woraphot Chaowawanit
- Department of Obstetrics and Gynecology, Faculty of Medicine Vajira Hospital, Navamindhadhiraj University, Bangkok 10300, Thailand
| | - Nutthaporn Chandeying
- Department of Obstetrics and Gynecology, Faculty of Medicine Vajira Hospital, Navamindhadhiraj University, Bangkok 10300, Thailand
| | - Siriwan Tangjitgamol
- Department of Obstetrics and Gynecology, Faculty of Medicine Vajira Hospital, Navamindhadhiraj University, Bangkok 10300, Thailand.,Obstetrics and Gynecology Section, MedPark Hospital, Bangkok 10110, Thailand
| | - Tawin Iempridee
- National Nanotechnology Center (NANOTEC), National Science and Technology Development Agency, Pathum Thani 12120, Thailand
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47
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Garrido-Navas MC, García-Díaz A, Molina-Vallejo MP, González-Martínez C, Alcaide Lucena M, Cañas-García I, Bayarri C, Delgado JR, González E, Lorente JA, Serrano MJ. The Polemic Diagnostic Role of TP53 Mutations in Liquid Biopsies from Breast, Colon and Lung Cancers. Cancers (Basel) 2020; 12:E3343. [PMID: 33198130 PMCID: PMC7696715 DOI: 10.3390/cancers12113343] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2020] [Revised: 11/02/2020] [Accepted: 11/10/2020] [Indexed: 12/15/2022] Open
Abstract
Being minimally invasive and thus allowing repeated measures over time, liquid biopsies are taking over traditional solid biopsies in certain circumstances such as those for unreachable tumors, very early stages or treatment monitoring. However, regarding TP53 mutation status analysis, liquid biopsies have not yet substituted tissue samples, mainly due to the lack of concordance between the two types of biopsies. This needs to be examined in a study-dependent manner, taking into account the particular type of liquid biopsy analyzed, that is, circulating tumor cells (CTCs) or cell-free DNA (cfDNA), its involvement in the tumor biology and evolution and, finally, the technology used to analyze each biopsy type. Here, we review the main studies analyzing TP53 mutations in either CTCs or cfDNA in the three more prevalent solid tumors: breast, colon and lung cancers. We evaluate the correlation for mutation status between liquid biopsies and tumor tissue, suggesting possible sources of discrepancies, as well as evaluating the clinical utility of using liquid biopsies for the analysis of TP53 mutation status and the future actions that need to be undertaken to make liquid biopsy analysis a reality for the evaluation of TP53 mutations.
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Affiliation(s)
- M. Carmen Garrido-Navas
- GENYO Centre for Genomics and Oncological Research, formed by Pfizer, the University of Granada and the Andalusian Regional Government, PTS Granada, Liquid Biopsy and Cancer Interception Group, Av. de la Ilustración, 114, 18016 Granada, Spain; (A.G.-D.); (M.P.M.-V.); (C.G.-M.); (M.A.L.); (I.C.-G.); (C.B.); (J.A.L.)
- Universidad Internacional de la Rioja, Avenida de la Paz, 137, 26006 Logroño, Spain
| | - Abel García-Díaz
- GENYO Centre for Genomics and Oncological Research, formed by Pfizer, the University of Granada and the Andalusian Regional Government, PTS Granada, Liquid Biopsy and Cancer Interception Group, Av. de la Ilustración, 114, 18016 Granada, Spain; (A.G.-D.); (M.P.M.-V.); (C.G.-M.); (M.A.L.); (I.C.-G.); (C.B.); (J.A.L.)
- Departamento de Medicina, Facultad de Medicina, Universidad de Granada, 18016 Granada, Spain
| | - Maria Pilar Molina-Vallejo
- GENYO Centre for Genomics and Oncological Research, formed by Pfizer, the University of Granada and the Andalusian Regional Government, PTS Granada, Liquid Biopsy and Cancer Interception Group, Av. de la Ilustración, 114, 18016 Granada, Spain; (A.G.-D.); (M.P.M.-V.); (C.G.-M.); (M.A.L.); (I.C.-G.); (C.B.); (J.A.L.)
| | - Coral González-Martínez
- GENYO Centre for Genomics and Oncological Research, formed by Pfizer, the University of Granada and the Andalusian Regional Government, PTS Granada, Liquid Biopsy and Cancer Interception Group, Av. de la Ilustración, 114, 18016 Granada, Spain; (A.G.-D.); (M.P.M.-V.); (C.G.-M.); (M.A.L.); (I.C.-G.); (C.B.); (J.A.L.)
| | - Miriam Alcaide Lucena
- GENYO Centre for Genomics and Oncological Research, formed by Pfizer, the University of Granada and the Andalusian Regional Government, PTS Granada, Liquid Biopsy and Cancer Interception Group, Av. de la Ilustración, 114, 18016 Granada, Spain; (A.G.-D.); (M.P.M.-V.); (C.G.-M.); (M.A.L.); (I.C.-G.); (C.B.); (J.A.L.)
- Servicio de Cirugía General y del Aparato Digestivo, Hospital Clínico San Cecilio, 18016 Granada, Spain
| | - Inés Cañas-García
- GENYO Centre for Genomics and Oncological Research, formed by Pfizer, the University of Granada and the Andalusian Regional Government, PTS Granada, Liquid Biopsy and Cancer Interception Group, Av. de la Ilustración, 114, 18016 Granada, Spain; (A.G.-D.); (M.P.M.-V.); (C.G.-M.); (M.A.L.); (I.C.-G.); (C.B.); (J.A.L.)
- Servicio de Cirugía General y del Aparato Digestivo, Hospital Clínico San Cecilio, 18016 Granada, Spain
| | - Clara Bayarri
- GENYO Centre for Genomics and Oncological Research, formed by Pfizer, the University of Granada and the Andalusian Regional Government, PTS Granada, Liquid Biopsy and Cancer Interception Group, Av. de la Ilustración, 114, 18016 Granada, Spain; (A.G.-D.); (M.P.M.-V.); (C.G.-M.); (M.A.L.); (I.C.-G.); (C.B.); (J.A.L.)
- Department of Thoracic Surgery, Virgen de las Nieves University Hospital, Av. de las Fuerzas Armadas, 2, 18014 Granada, Spain
| | - Juan Ramón Delgado
- Bio-Health Research Institute (Instituto de Investigación Biosanitaria ibs. GRANADA), Complejo Hospitalario Universitario Granada (CHUG), University of Granada, 18012 Granada, Spain; (J.R.D.); (E.G.)
| | - Encarna González
- Bio-Health Research Institute (Instituto de Investigación Biosanitaria ibs. GRANADA), Complejo Hospitalario Universitario Granada (CHUG), University of Granada, 18012 Granada, Spain; (J.R.D.); (E.G.)
| | - Jose Antonio Lorente
- GENYO Centre for Genomics and Oncological Research, formed by Pfizer, the University of Granada and the Andalusian Regional Government, PTS Granada, Liquid Biopsy and Cancer Interception Group, Av. de la Ilustración, 114, 18016 Granada, Spain; (A.G.-D.); (M.P.M.-V.); (C.G.-M.); (M.A.L.); (I.C.-G.); (C.B.); (J.A.L.)
- Laboratory of Genetic Identification, Department of Legal Medicine, University of Granada, Av. de la Investigación, 11, 18071 Granada, Spain
| | - M. Jose Serrano
- GENYO Centre for Genomics and Oncological Research, formed by Pfizer, the University of Granada and the Andalusian Regional Government, PTS Granada, Liquid Biopsy and Cancer Interception Group, Av. de la Ilustración, 114, 18016 Granada, Spain; (A.G.-D.); (M.P.M.-V.); (C.G.-M.); (M.A.L.); (I.C.-G.); (C.B.); (J.A.L.)
- Bio-Health Research Institute (Instituto de Investigación Biosanitaria ibs. GRANADA), Complejo Hospitalario Universitario Granada (CHUG), University of Granada, 18012 Granada, Spain; (J.R.D.); (E.G.)
- Department of Pathological Anatomy, Faculty of Medicine, Campus de Ciencias de la Salud, University of Granada, 18016 Granada, Spain
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48
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Gerratana L, Basile D, Franzoni A, Allegri L, Viotto D, Corvaja C, Bortot L, Bertoli E, Buriolla S, Targato G, Da Ros L, Russo S, Bonotto M, Belletti B, Baldassarre G, Damante G, Puglisi F. Plasma-Based Longitudinal Evaluation of ESR1 Epigenetic Status in Hormone Receptor-Positive HER2-Negative Metastatic Breast Cancer. Front Oncol 2020; 10:550185. [PMID: 33072577 PMCID: PMC7531252 DOI: 10.3389/fonc.2020.550185] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2020] [Accepted: 08/20/2020] [Indexed: 12/30/2022] Open
Abstract
Background Endocrine therapy (ET) is the mainstay of treatment for hormone receptor-positive human epidermal growth factor receptor 2 (HER2)-negative metastatic breast cancer; however, adaptive mechanisms emerge in about 25–30% of cases through alterations in the estrogen receptor ligand-binding domain, with a consequent ligand-independent estrogen receptor activity. Epigenetic-mediated events are less known and potentially involved in alternative mechanisms of resistance. The aim of this study was to test the feasibility of estrogen receptor 1 (ESR1) epigenetic characterization through liquid biopsy and to show its potential longitudinal application for an early ET sensitivity assessment. Methods A cohort of 49 women with hormone receptor-positive HER2-negative MBC was prospectively enrolled and characterized through circulating tumor DNA using methylation-specific droplet digital PCR (MS-ddPCR) before treatment start (BL) and after 3 months concomitantly with computed tomography (CT) scan restaging (EV1). ESR1 epigenetic status was defined by assessing the methylation of its main promoters (promA and promB). The most established cell-free tumor DNA (ctDNA) factors associated with ET resistance [ESR1 and phosphatidylinositol-4,5-bisphosphate 3-kinase, catalytic subunit alpha (PIK3CA) mutations] were assessed through next-generation sequencing. Associations were tested through Mann–Whitney U test, matched pairs variations through Wilcoxon signed rank test, and survival was analyzed by log-rank test. Results The ET backbone was mainly based on aromatase inhibitors (AIs) (70.83%) in association with CDK4/6 inhibitors (93.75%). Significantly lower promA levels at baseline were observed in patients with liver metastases (P = 0.0212) and in patients with ESR1 mutations (P = 0.0091). No significant impact on PFS was observed for promA (P = 0.3777) and promB (P = 0.7455) dichotomized at the median while a ≥2-fold increase in promB or in either promA or promB at EV1 resulted in a significantly worse prognosis (respectively P = 0.0189, P = 0.0294). A significant increase at EV1 was observed for promB among patients with PIK3CA mutation (P = 0.0173). A trend was observed for promB in ESR1 wild-type patients and for promA in the ESR1 mutant subgroup. Conclusion The study proofed the concept of an epigenetic characterization strategy based on ctDNA and is capable of being integrated in the current clinical workflow to give useful insights on treatment sensitivity.
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Affiliation(s)
- Lorenzo Gerratana
- Department of Medicine (DAME), University of Udine, Udine, Italy.,Department of Medical Oncology, Centro di Riferimento Oncologico di Aviano (CRO), IRCCS, Aviano, Italy
| | - Debora Basile
- Department of Medicine (DAME), University of Udine, Udine, Italy.,Department of Medical Oncology, Centro di Riferimento Oncologico di Aviano (CRO), IRCCS, Aviano, Italy
| | | | - Lorenzo Allegri
- Department of Medicine (DAME), University of Udine, Udine, Italy
| | - Davide Viotto
- Unit of Molecular Oncology, Centro di Riferimento Oncologico di Aviano (CRO), IRCCS, Aviano, Italy
| | - Carla Corvaja
- Department of Medicine (DAME), University of Udine, Udine, Italy.,Department of Medical Oncology, Centro di Riferimento Oncologico di Aviano (CRO), IRCCS, Aviano, Italy
| | - Lucia Bortot
- Department of Medicine (DAME), University of Udine, Udine, Italy.,Department of Medical Oncology, Centro di Riferimento Oncologico di Aviano (CRO), IRCCS, Aviano, Italy
| | - Elisa Bertoli
- Department of Medicine (DAME), University of Udine, Udine, Italy.,Department of Oncology, ASUFC University Hospital, Udine, Italy
| | - Silvia Buriolla
- Department of Medicine (DAME), University of Udine, Udine, Italy.,Department of Medical Oncology, Centro di Riferimento Oncologico di Aviano (CRO), IRCCS, Aviano, Italy
| | - Giada Targato
- Department of Medicine (DAME), University of Udine, Udine, Italy.,Department of Oncology, ASUFC University Hospital, Udine, Italy
| | - Lucia Da Ros
- Department of Medical Oncology, Centro di Riferimento Oncologico di Aviano (CRO), IRCCS, Aviano, Italy
| | - Stefania Russo
- Department of Oncology, ASUFC University Hospital, Udine, Italy
| | - Marta Bonotto
- Department of Oncology, ASUFC University Hospital, Udine, Italy
| | - Barbara Belletti
- Unit of Molecular Oncology, Centro di Riferimento Oncologico di Aviano (CRO), IRCCS, Aviano, Italy
| | - Gustavo Baldassarre
- Unit of Molecular Oncology, Centro di Riferimento Oncologico di Aviano (CRO), IRCCS, Aviano, Italy
| | - Giuseppe Damante
- Institute of Human Genetics, ASUFC University Hospital, Udine, Italy
| | - Fabio Puglisi
- Department of Medicine (DAME), University of Udine, Udine, Italy.,Department of Medical Oncology, Centro di Riferimento Oncologico di Aviano (CRO), IRCCS, Aviano, Italy
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Chen Y, Li X, Liu G, Chen S, Xu M, Song L, Wang Y. ctDNA Concentration, MIKI67 Mutations and Hyper-Progressive Disease Related Gene Mutations Are Prognostic Markers for Camrelizumab and Apatinib Combined Multiline Treatment in Advanced NSCLC. Front Oncol 2020; 10:1706. [PMID: 33014846 PMCID: PMC7509428 DOI: 10.3389/fonc.2020.01706] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2020] [Accepted: 07/30/2020] [Indexed: 12/22/2022] Open
Abstract
Immunotherapy by immune checkpoint inhibitors (ICIs) has showed outstanding efficacy in the treatment of advanced non-small cell lung cancer (NSCLC). The combination of immunotherapy with anti-angiogenic therapy exhibited enhanced efficacy in multiline treatment. However, the potential biomarkers for predicting and monitoring the therapeutic response of the combined therapy remain undefined. In this study, we performed a pilot study by prospectively recruiting 22 advanced NSCLC patients who failed to previous lines of chemotherapy, chemoradiotherapy, TKI therapy, surgery, or any combination of the therapies, and investigated the prognostic factors for patients who received anti-PD-1 (Camrelizumab) and anti-angiogenic (Apatinib) combined therapy. The objective response rate (ORR) assessed by an independent radiology review was 22.7%, and the median progression-free survival (PFS) was 5.25 months. We found that high concentration of circulating-free DNA (cfDNA) (HR = 27.75, P = 0.003), MIKI67 mutation (HR = 114.11, P = 0.009) and gene variations related to hyper-progressive disease (HPD) (HR = 36.85, P = 0.004) were independent risk factors and exhibited significant correlation with PFS. Circulating tumor DNA (ctDNA) mutational status was also a predicting indicator for PFS. In contrast, the blood tumor mutational burden (bTMB) could not stratify the clinical benefit in this combined therapy (HR = 0.81, P = 0.137). Furthermore, we found that the variant allele fraction (VAF) of mutations in ctDNA was sensitive indicators of therapeutic response and therefore can be used to monitor the tumor relief or progression. In conclusion, cfDNA concentration, MIKI67 mutations and HPD-related mutations were independent risk factors and PFS predictors for multiline combined anti-angiogenic/ICI combined therapy. ctDNA may be a novel monitoring biomarker for therapeutic response and predicting biomarker for prognosis in future combined therapy involving PD-1 blockade.
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Affiliation(s)
- Yao Chen
- Department of Oncology, First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, China
| | | | | | | | | | - Lele Song
- HaploX Biotechnology, Shenzhen, China.,Department of Radiotherapy, The Eighth Medical Center of the Chinese PLA General Hospital, Beijing, China
| | - Yina Wang
- Department of Oncology, First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, China
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Rizzo A, Ricci AD, Tavolari S, Brandi G. Circulating Tumor DNA in Biliary Tract Cancer: Current Evidence and Future Perspectives. Cancer Genomics Proteomics 2020; 17:441-452. [PMID: 32859625 PMCID: PMC7472453 DOI: 10.21873/cgp.20203] [Citation(s) in RCA: 74] [Impact Index Per Article: 18.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2020] [Revised: 05/19/2020] [Accepted: 05/29/2020] [Indexed: 02/06/2023] Open
Abstract
Peripheral blood of cancer patients "physiologically" presents cells and cellular components deriving from primary or metastatic sites, including circulating tumor cells (CTCs), circulating free DNA (cfDNA) and exosomes containing proteins, lipids and nucleic acids. The term circulating tumor DNA (ctDNA) indicates the part of cfDNA which derives from primary tumors and/or metastatic sites, carrying tumor-specific genetic or epigenetic alterations. Analysis of ctDNA has enormous potential applications in all stages of cancer management, including earlier diagnosis of cancer, identification of driver alterations, monitoring of treatment response and detection of resistance mechanisms. Thus, ctDNA has the potential to profoundly change current clinical practice, by moving from tissue to peripheral blood as a source of information. Herein, we review current literature regarding the potential role for ctDNA in biliary tract cancer (BTC) patients, with a particular focus on state-of-the-art techniques and future perspectives of this highly aggressive disease.
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Affiliation(s)
- Alessandro Rizzo
- Department of Experimental, Diagnostic and Specialty Medicine, S. Orsola-Malpighi University Hospital, Bologna, Italy
| | - Angela Dalia Ricci
- Department of Experimental, Diagnostic and Specialty Medicine, S. Orsola-Malpighi University Hospital, Bologna, Italy
| | - Simona Tavolari
- Department of Experimental, Diagnostic and Specialty Medicine, S. Orsola-Malpighi University Hospital, Bologna, Italy
| | - Giovanni Brandi
- Department of Experimental, Diagnostic and Specialty Medicine, S. Orsola-Malpighi University Hospital, Bologna, Italy
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