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Li Y, Wu J, Feng Y, Wang D, Tao H, Wen J, Jiang F, Qian P, Liu Y. Kinetics of plasma cell-free DNA as a prospective biomarker to predict the prognosis and radiotherapy effect of esophageal cancer. Cancer Radiother 2024; 28:242-250. [PMID: 38876937 DOI: 10.1016/j.canrad.2023.11.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2023] [Revised: 11/03/2023] [Accepted: 11/09/2023] [Indexed: 06/16/2024]
Abstract
PURPOSE The lack of reliable biomarkers for the prognosis and radiotherapy efficacy in esophageal cancer (EC) necessitates further research. The aim of our study was to investigate the predictive utility of plasma cell-free DNA (cfDNA) kinetics in patients with EC. MATERIALS AND METHODS We retrospectively analyzed the clinical data and cfDNA levels (pre-radiotherapy [pre-RT] and post-radiotherapy [post-RT]) and the cfDNA kinetics (cfDNA ratio: post-RT cfDNA/pre-RT cfDNA) of 88 patients. We employed Kaplan-Meier curves to examine the relationship between cfDNA and overall survival (OS) as well as progression-free survival (PFS). Univariate and multivariate Cox regression analyses were executed to ascertain the independent risk factors in EC. RESULTS The pre-RT cfDNA levels were positively correlated with clinical stage (P=0.001). The pre-RT cfDNA levels (cutoff value=16.915ng/mL), but not the post-RT cfDNA levels, were linked to a diminished OS (P<0.001) and PFS (P=0.0137). CfDNA kinetics (cutoff value=0.883) were positively associated with OS (P=0.0326) and PFS (P=0.0020). Notably, we identified independent risk factors for OS in EC treated with RT, including cfDNA ratio (high/low) (HR=0.447 [0.221-0.914] P=0.025), ECOG (0/1/2) (HR=0.501 [0.285-0.880] p=0.016), and histological type (esophagal squamous cell carcinoma [ESCC]/non-ESCC) (HR=3.973 [1.074-14.692] P=0.039). CONCLUSION Plasma cfDNA kinetics is associated with prognosis and radiotherapy effect in EC undergoing RT, suggesting potential clinical application of a cheap and simple blood-based test.
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Affiliation(s)
- Y Li
- Department of Radiation Oncology, Nanjing Medical University Affiliated Cancer Hospital & Jiangsu Cancer Hospital & Jiangsu Institute of Cancer Research, 21009 Nanjing, China
| | - J Wu
- Department of Radiation Oncology, Nanjing Medical University Affiliated Cancer Hospital & Jiangsu Cancer Hospital & Jiangsu Institute of Cancer Research, 21009 Nanjing, China
| | - Y Feng
- Department of Thoracic Surgery, Nanjing Medical University Affiliated Cancer Hospital & Jiangsu Cancer Hospital & Jiangsu Institute of Cancer Research, 21009 Nanjing, China
| | - D Wang
- Department of Radiation Oncology, Nanjing Medical University Affiliated Cancer Hospital & Jiangsu Cancer Hospital & Jiangsu Institute of Cancer Research, 21009 Nanjing, China
| | - H Tao
- Department of Radiation Oncology, Nanjing Medical University Affiliated Cancer Hospital & Jiangsu Cancer Hospital & Jiangsu Institute of Cancer Research, 21009 Nanjing, China
| | - J Wen
- Department of Radiation Oncology, Nanjing Medical University Affiliated Cancer Hospital & Jiangsu Cancer Hospital & Jiangsu Institute of Cancer Research, 21009 Nanjing, China
| | - F Jiang
- Department of Thoracic Surgery, Nanjing Medical University Affiliated Cancer Hospital & Jiangsu Cancer Hospital & Jiangsu Institute of Cancer Research, 21009 Nanjing, China
| | - P Qian
- Department of Radiation Oncology, Nanjing Medical University Affiliated Cancer Hospital & Jiangsu Cancer Hospital & Jiangsu Institute of Cancer Research, 21009 Nanjing, China.
| | - Y Liu
- Department of Radiation Oncology, Nanjing Medical University Affiliated Cancer Hospital & Jiangsu Cancer Hospital & Jiangsu Institute of Cancer Research, 21009 Nanjing, China.
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2
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Keup C, Kimmig R, Kasimir-Bauer S. The Diversity of Liquid Biopsies and Their Potential in Breast Cancer Management. Cancers (Basel) 2023; 15:5463. [PMID: 38001722 PMCID: PMC10670968 DOI: 10.3390/cancers15225463] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2023] [Revised: 11/10/2023] [Accepted: 11/14/2023] [Indexed: 11/26/2023] Open
Abstract
Analyzing blood as a so-called liquid biopsy in breast cancer (BC) patients has the potential to adapt therapy management. Circulating tumor cells (CTCs), extracellular vesicles (EVs), cell-free DNA (cfDNA) and other blood components mirror the tumoral heterogeneity and could support a range of clinical decisions. Multi-cancer early detection tests utilizing blood are advancing but are not part of any clinical routine yet. Liquid biopsy analysis in the course of neoadjuvant therapy has potential for therapy (de)escalation.Minimal residual disease detection via serial cfDNA analysis is currently on its way. The prognostic value of blood analytes in early and metastatic BC is undisputable, but the value of these prognostic biomarkers for clinical management is controversial. An interventional trial confirmed a significant outcome benefit when therapy was changed in case of newly emerging cfDNA mutations under treatment and thus showed the clinical utility of cfDNA analysis for therapy monitoring. The analysis of PIK3CA or ESR1 variants in plasma of metastatic BC patients to prescribe targeted therapy with alpesilib or elacestrant has already arrived in clinical practice with FDA-approved tests available and is recommended by ASCO. The translation of more liquid biopsy applications into clinical practice is still pending due to a lack of knowledge of the analytes' biology, lack of standards and difficulties in proving clinical utility.
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Affiliation(s)
- Corinna Keup
- Department of Gynecology and Obstetrics, University Hospital of Essen, 45147 Essen, Germany
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3
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Karimi F, Azadbakht O, Veisi A, Sabaghan M, Owjfard M, Kharazinejad E, Dinarvand N. Liquid biopsy in ovarian cancer: advantages and limitations for prognosis and diagnosis. Med Oncol 2023; 40:265. [PMID: 37561363 DOI: 10.1007/s12032-023-02128-0] [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: 04/13/2023] [Accepted: 07/17/2023] [Indexed: 08/11/2023]
Abstract
Ovarian cancer (OC) is a highly fatal gynecologic malignancy, often diagnosed at an advanced stage which presents significant challenges for disease management. The clinical application of conventional tissue biopsy methods and serological biomarkers has limitations for the diagnosis and prognosis of OC patients. Liquid biopsy is a novel sampling method that involves analyzing distinctive tumor elements secreted into the peripheral blood. Growing evidence suggests that liquid biopsy methods such as circulating tumor cells, cell-free RNA, circulating tumor DNA, exosomes, and tumor-educated platelets may improve early prognosis and diagnosis of OC, leading to enhanced therapeutic management of the disease. This study reviewed the evidence demonstrating the utility of liquid biopsy components in OC prognosis and diagnosis, and evaluated the current advantages and limitations of these methods. Additionally, the existing obstacles and crucial topics for future studies utilizing liquid biopsy in OC patients were discussed.
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Affiliation(s)
- Farzaneh Karimi
- Department of Physiology, Behbahan Faculty of Medical Sciences, Behbahan, Iran.
| | - Omid Azadbakht
- Department of Radiology Technology, Behbahan Faculty of Medical Sciences, Behbahan, Iran
| | - Ali Veisi
- Department of Physiology, Behbahan Faculty of Medical Sciences, Behbahan, Iran
| | - Mohammad Sabaghan
- Department of Parasitology, Behbahan Faculty of Medical Sciences, Behbahan, Iran
| | - Maryam Owjfard
- Clinical Neurology Research Center, Shiraz University of Medical Sciences, Shiraz, Iran
- Shiraz University of Applied Science and Technology (UAST), Shiraz, Iran
| | | | - Negar Dinarvand
- Hyperlipidemia Research Center, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
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4
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Jongbloed EM, Jansen MPHM, de Weerd V, Helmijr JA, Beaufort CM, Reinders MJT, van Marion R, van IJcken WFJ, Sonke GS, Konings IR, Jager A, Martens JWM, Wilting SM, Makrodimitris S. Machine learning-based somatic variant calling in cell-free DNA of metastatic breast cancer patients using large NGS panels. Sci Rep 2023; 13:10424. [PMID: 37369746 DOI: 10.1038/s41598-023-37409-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2023] [Accepted: 06/21/2023] [Indexed: 06/29/2023] Open
Abstract
Next generation sequencing of cell-free DNA (cfDNA) is a promising method for treatment monitoring and therapy selection in metastatic breast cancer (MBC). However, distinguishing tumor-specific variants from sequencing artefacts and germline variation with low false discovery rate is challenging when using large targeted sequencing panels covering many tumor suppressor genes. To address this, we built a machine learning model to remove false positive variant calls and augmented it with additional filters to ensure selection of tumor-derived variants. We used cfDNA of 70 MBC patients profiled with both the small targeted Oncomine breast panel (Thermofisher) and the much larger Qiaseq Human Breast Cancer Panel (Qiagen). The model was trained on the panels' common regions using Oncomine hotspot mutations as ground truth. Applied to Qiaseq data, it achieved 35% sensitivity and 36% precision, outperforming basic filtering. For 20 patients we used germline DNA to filter for somatic variants and obtained 245 variants in total, while our model found seven variants, of which six were also detected using the germline strategy. In ten tumor-free individuals, our method detected in total one (potentially germline) variant, in contrast to 521 variants detected without our model. These results indicate that our model largely detects somatic variants.
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Affiliation(s)
- Elisabeth M Jongbloed
- Department of Medical Oncology, Erasmus MC Cancer Institute, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Maurice P H M Jansen
- Department of Medical Oncology, Erasmus MC Cancer Institute, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Vanja de Weerd
- Department of Medical Oncology, Erasmus MC Cancer Institute, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Jean A Helmijr
- Department of Medical Oncology, Erasmus MC Cancer Institute, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Corine M Beaufort
- Department of Medical Oncology, Erasmus MC Cancer Institute, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Marcel J T Reinders
- Delft Bioinformatics Lab, Delft University of Technology, Delft, The Netherlands
| | - Ronald van Marion
- Department of Pathology, Erasmus MC Cancer Institute, Rotterdam, The Netherlands
| | - Wilfred F J van IJcken
- Erasmus Center for Biomics, Erasmus University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Gabe S Sonke
- Department of Medical Oncology, Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Inge R Konings
- Department of Medical Oncology, Amsterdam UMC, location Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - Agnes Jager
- Department of Medical Oncology, Erasmus MC Cancer Institute, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - John W M Martens
- Department of Medical Oncology, Erasmus MC Cancer Institute, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Saskia M Wilting
- Department of Medical Oncology, Erasmus MC Cancer Institute, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Stavros Makrodimitris
- Department of Medical Oncology, Erasmus MC Cancer Institute, Erasmus University Medical Center, Rotterdam, The Netherlands.
- Delft Bioinformatics Lab, Delft University of Technology, Delft, The Netherlands.
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Jiang H, Ouyang Q, Yin Y, Tong Z, Shen K, Yuan Z, Geng C, Liu Y, Song G, Ran R, Li W, Qu Q, Wang M, Meng L, Tong Y, Li H. Proxalutamide in patients with AR-positive metastatic breast cancer: Results from an open-label multicentre phase Ib study and biomarker analysis. Eur J Cancer 2022; 176:1-12. [PMID: 36182805 DOI: 10.1016/j.ejca.2022.08.025] [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: 06/08/2022] [Revised: 08/20/2022] [Accepted: 08/24/2022] [Indexed: 12/15/2022]
Abstract
AIM Proxalutamide is a novel second-generation non-steroidal androgen receptor (AR) antagonist. This study aimed to evaluate the preliminary efficacy and safety of proxalutamide in patients with AR-positive metastatic breast cancer (AR+ mBC). METHODS In this open-label, dose-expansion, multicentre phase Ib trial, patients with AR+ mBC (immunohistochemistry [IHC] ≥1%) received proxalutamide orally once daily. Two proxalutamide dose cohorts (cohort A: 200 mg; cohort B: 300 mg) were sequentially investigated. Primary endpoints were disease control rate (DCR) at 8 and 16 weeks and recommended phase II dose (RP2D). RESULTS Forty-five patients with three median lines (range, 1-13) prior systemic therapy were enrolled (cohort A, n = 30; cohort B, n = 15). Among 39 evaluable patients, DCR at 8 and 16 weeks was 25.6% (95% confidence interval [CI], 11.9-39.4%), with 26.9% in cohort A and 23.1% in cohort B. No patient achieved partial response or complete response. Proxalutamide 200 mg/day was determined as RP2D. The 6-month progression-free survival (PFS) rate was 19.6% (95% CI, 10.2-37.5%). In the triple-negative subgroup, DCR at 8 weeks was 38.5%, with median PFS of 9.1 months (95% CI, 7.8-NA) in those who achieved response at 8 weeks (n = 5). Most common grade 3/4 adverse events were aspartate aminotransferase increase (8.9%) and γ-glutamyltransferase increase (8.9%). By biomarker analysis, patients with moderate AR expression of IHC (26%-75%), PIK3CA pathogenic mutations, or <60 ng/ml cell-free DNA yield showed longer PFS. CONCLUSION Proxalutamide showed promising anti-tumour activity with good tolerability in patients with heavily pretreated AR+ mBC, supporting further investigation. TRIAL REGISTRATION This clinical study was prospectively registered at chinadrugtrials.org.cn (Identifier: CTR20170757) and clinical trials.gov (Identifier: NCT04103853).
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Affiliation(s)
- Hanfang Jiang
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Department of Breast Oncology, Peking University Cancer Hospital & Institute, Beijing, China
| | - Quchang Ouyang
- Department of Breast Oncology, Hunan Cancer Hospital, Changsha, Hunan, China
| | - Yongmei Yin
- Department of Breast Oncology, Jiangsu Province Hospital, Nanjing, Jiangsu, China
| | - Zhongshen Tong
- Department of Breast Oncology, Tianjin Medical University Cancer Institute and Hospital, Tianjin, China
| | - Kunwei Shen
- Department of Breast Oncology, Ruijin Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - Zhongyu Yuan
- Department of Breast Oncology, Sun-Yat-sen University Cancer Center, Guangzhou, Guangdong, China
| | - Cuizhi Geng
- Department of Breast Centre, The Fourth Hospital of Hebei Medical University, Shijiazhuang, Hebei, China
| | - Yaxin Liu
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Department of Breast Oncology, Peking University Cancer Hospital & Institute, Beijing, China
| | - Guohong Song
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Department of Breast Oncology, Peking University Cancer Hospital & Institute, Beijing, China
| | - Ran Ran
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Department of Breast Oncology, Peking University Cancer Hospital & Institute, Beijing, China
| | - Wei Li
- Department of Breast Oncology, Jiangsu Province Hospital, Nanjing, Jiangsu, China
| | - Qing Qu
- Department of Breast Oncology, Ruijin Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - Meiyu Wang
- Suzhou Kintor Pharmaceuticals, Inc., Suzhou, Jiangsu, China
| | - Luping Meng
- Suzhou Kintor Pharmaceuticals, Inc., Suzhou, Jiangsu, China
| | - Youzhi Tong
- Suzhou Kintor Pharmaceuticals, Inc., Suzhou, Jiangsu, China.
| | - Huiping Li
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Department of Breast Oncology, Peking University Cancer Hospital & Institute, Beijing, China.
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Keup C, Kimmig R, Kasimir-Bauer S. Combinatorial Power of cfDNA, CTCs and EVs in Oncology. Diagnostics (Basel) 2022; 12:870. [PMID: 35453918 PMCID: PMC9031112 DOI: 10.3390/diagnostics12040870] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2022] [Revised: 03/18/2022] [Accepted: 03/28/2022] [Indexed: 01/01/2023] Open
Abstract
Liquid biopsy is a promising technique for clinical management of oncological patients. The diversity of analytes circulating in the blood useable for liquid biopsy testing is enormous. Circulating tumor cells (CTCs), cell-free DNA (cfDNA) and extracellular vesicles (EVs), as well as blood cells and other soluble components in the plasma, were shown as liquid biopsy analytes. A few studies directly comparing two liquid biopsy analytes showed a benefit of one analyte over the other, while most authors concluded the benefit of the additional analyte. Only three years ago, the first studies to examine the value of a characterization of more than two liquid biopsy analytes from the same sample were conducted. We attempt to reflect on the recent development of multimodal liquid biopsy testing in this review. Although the analytes and clinical purposes of the published multimodal studies differed significantly, the additive value of the analytes was concluded in almost all projects. Thus, the blood components, as liquid biopsy reservoirs, are complementary rather than competitive, and orthogonal data sets were even shown to harbor synergistic effects. The unmistakable potential of multimodal liquid biopsy testing, however, is dampened by its clinical utility, which is yet to be proven, the lack of methodical standardization and insufficiently mature reimbursement, logistics and data handling.
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Affiliation(s)
- Corinna Keup
- Department of Gynecology and Obstetrics, University Hospital of Essen, Hufelandstr. 55, 45122 Essen, Germany
| | - Rainer Kimmig
- Department of Gynecology and Obstetrics, University Hospital of Essen, Hufelandstr. 55, 45122 Essen, Germany
| | - Sabine Kasimir-Bauer
- Department of Gynecology and Obstetrics, University Hospital of Essen, Hufelandstr. 55, 45122 Essen, Germany
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Lieb V, Abdulrahman A, Weigelt K, Hauch S, Gombert M, Guzman J, Bellut L, Goebell PJ, Stöhr R, Hartmann A, Wullich B, Taubert H, Wach S. Cell-Free DNA Variant Sequencing Using Plasma and AR-V7 Testing of Circulating Tumor Cells in Prostate Cancer Patients. Cells 2021; 10:cells10113223. [PMID: 34831445 PMCID: PMC8620951 DOI: 10.3390/cells10113223] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2021] [Revised: 11/10/2021] [Accepted: 11/16/2021] [Indexed: 11/16/2022] Open
Abstract
Prostate cancer (PCa) is the second most common malignant cancer and is a major cause of morbidity and mortality among men worldwide. There is still an urgent need for biomarkers applicable for diagnosis, prognosis, therapy prediction, or therapy monitoring in PCa. Liquid biopsies, including cell-free DNA (cfDNA) and circulating tumor cells (CTCs), are a valuable source for studying such biomarkers and are minimally invasive. In our study, we investigated the cfDNA of 34 progressive PCa patients, via targeted sequencing, for sequence variants and for the occurrence of CTCs, with a focus on androgen receptor splice variant 7 (AR-V7)-positive CTCs. The cfDNA content was associated with overall survival (OS; p = 0.014), disease-specific survival (DSS; p = 0.004), and time to treatment change (TTC; p = 0.001). Moreover, when considering all sequence variants grouped by their functional impact and allele frequency, a significant association with TTC (p = 0.017) was observed. When investigating only pathogenic or likely pathogenic gene variants, variants of the BRCA1 gene (p = 0.029) and the AR ligand-binding domain (p = 0.050) were associated with a shorter TTC. Likewise, the presence of CTCs was associated with a shorter TTC (p = 0.031). The presence of AR-V7-positive CTCs was associated with TTC (p < 0.001) in Kaplan–Meier analysis. Interestingly, all patients with AR-V7-positive CTCs also carried TP53 point mutations. Altogether, analysis of cfDNA and CTCs can provide complementary information that may support temporal and targeted treatment decisions and may elucidate the optimal choice within the variety of therapy options for advanced PCa patients.
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Affiliation(s)
- Verena Lieb
- Department of Urology and Pediatric Urology, Universitätsklinikum Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg, 91054 Erlangen, Germany; (V.L.); (A.A.); (K.W.); (J.G.); (L.B.); (P.J.G.); (B.W.); (S.W.)
- Comprehensive Cancer Center Erlangen-EMN (CCC ER-EMN), 91054 Erlangen, Germany; (R.S.); (A.H.)
| | - Amer Abdulrahman
- Department of Urology and Pediatric Urology, Universitätsklinikum Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg, 91054 Erlangen, Germany; (V.L.); (A.A.); (K.W.); (J.G.); (L.B.); (P.J.G.); (B.W.); (S.W.)
- Comprehensive Cancer Center Erlangen-EMN (CCC ER-EMN), 91054 Erlangen, Germany; (R.S.); (A.H.)
| | - Katrin Weigelt
- Department of Urology and Pediatric Urology, Universitätsklinikum Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg, 91054 Erlangen, Germany; (V.L.); (A.A.); (K.W.); (J.G.); (L.B.); (P.J.G.); (B.W.); (S.W.)
- Comprehensive Cancer Center Erlangen-EMN (CCC ER-EMN), 91054 Erlangen, Germany; (R.S.); (A.H.)
| | | | | | - Juan Guzman
- Department of Urology and Pediatric Urology, Universitätsklinikum Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg, 91054 Erlangen, Germany; (V.L.); (A.A.); (K.W.); (J.G.); (L.B.); (P.J.G.); (B.W.); (S.W.)
- Comprehensive Cancer Center Erlangen-EMN (CCC ER-EMN), 91054 Erlangen, Germany; (R.S.); (A.H.)
| | - Laura Bellut
- Department of Urology and Pediatric Urology, Universitätsklinikum Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg, 91054 Erlangen, Germany; (V.L.); (A.A.); (K.W.); (J.G.); (L.B.); (P.J.G.); (B.W.); (S.W.)
- Comprehensive Cancer Center Erlangen-EMN (CCC ER-EMN), 91054 Erlangen, Germany; (R.S.); (A.H.)
| | - Peter J. Goebell
- Department of Urology and Pediatric Urology, Universitätsklinikum Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg, 91054 Erlangen, Germany; (V.L.); (A.A.); (K.W.); (J.G.); (L.B.); (P.J.G.); (B.W.); (S.W.)
- Comprehensive Cancer Center Erlangen-EMN (CCC ER-EMN), 91054 Erlangen, Germany; (R.S.); (A.H.)
| | - Robert Stöhr
- Comprehensive Cancer Center Erlangen-EMN (CCC ER-EMN), 91054 Erlangen, Germany; (R.S.); (A.H.)
- Institute of Pathology, University Hospital Erlangen, FAU Erlangen-Nürnberg, 91054 Erlangen, Germany
| | - Arndt Hartmann
- Comprehensive Cancer Center Erlangen-EMN (CCC ER-EMN), 91054 Erlangen, Germany; (R.S.); (A.H.)
- Institute of Pathology, University Hospital Erlangen, FAU Erlangen-Nürnberg, 91054 Erlangen, Germany
| | - Bernd Wullich
- Department of Urology and Pediatric Urology, Universitätsklinikum Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg, 91054 Erlangen, Germany; (V.L.); (A.A.); (K.W.); (J.G.); (L.B.); (P.J.G.); (B.W.); (S.W.)
- Comprehensive Cancer Center Erlangen-EMN (CCC ER-EMN), 91054 Erlangen, Germany; (R.S.); (A.H.)
| | - Helge Taubert
- Department of Urology and Pediatric Urology, Universitätsklinikum Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg, 91054 Erlangen, Germany; (V.L.); (A.A.); (K.W.); (J.G.); (L.B.); (P.J.G.); (B.W.); (S.W.)
- Comprehensive Cancer Center Erlangen-EMN (CCC ER-EMN), 91054 Erlangen, Germany; (R.S.); (A.H.)
- Correspondence: ; Tel.: +49-93138523373
| | - Sven Wach
- Department of Urology and Pediatric Urology, Universitätsklinikum Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg, 91054 Erlangen, Germany; (V.L.); (A.A.); (K.W.); (J.G.); (L.B.); (P.J.G.); (B.W.); (S.W.)
- Comprehensive Cancer Center Erlangen-EMN (CCC ER-EMN), 91054 Erlangen, Germany; (R.S.); (A.H.)
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Li LS, Guo XY, Sun K. Recent advances in blood-based and artificial intelligence-enhanced approaches for gastrointestinal cancer diagnosis. World J Gastroenterol 2021; 27:5666-5681. [PMID: 34629793 PMCID: PMC8473600 DOI: 10.3748/wjg.v27.i34.5666] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/27/2021] [Revised: 05/14/2021] [Accepted: 08/03/2021] [Indexed: 02/06/2023] Open
Abstract
Gastrointestinal (GI) cancers are among the most common cancer types and leading causes of cancer-related deaths worldwide. There is a tremendous clinical need for effective early diagnosis for better healthcare of GI cancer patients. In this article, we provide a short overview of the recent advances in GI cancer diagnosis. In the first part, we discuss the applications of blood-based biomarkers, such as plasma circulating cell-free DNA, circulating tumor cells, extracellular vesicles, and circulating cell-free RNA, for cancer liquid biopsies. In the second part, we review the current trends of artificial intelligence (AI) for pathology image and tissue biopsy analysis for GI cancer, as well as deep learning-based approaches for purity assessment of tissue biopsies. We further provide our opinions on the future directions in blood-based and AI-enhanced approaches for GI cancer diagnosis, and we think that these fields will have more intensive integrations with clinical needs in the near future.
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Affiliation(s)
- Li-Shi Li
- School of Chemical Biology and Biotechnology, Shenzhen Graduate School, Peking University, Shenzhen 518055, Guangdong Province, China
- Institute of Cancer Research, Shenzhen Bay Laboratory, Shenzhen 518132, Guangdong Province, China
| | - Xiang-Yu Guo
- Institute of Cancer Research, Shenzhen Bay Laboratory, Shenzhen 518132, Guangdong Province, China
| | - Kun Sun
- Institute of Cancer Research, Shenzhen Bay Laboratory, Shenzhen 518132, Guangdong Province, China
- BGI-Shenzhen, Shenzhen 518083, Guangdong Province, China
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9
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Underhill HR. Leveraging the Fragment Length of Circulating Tumour DNA to Improve Molecular Profiling of Solid Tumour Malignancies with Next-Generation Sequencing: A Pathway to Advanced Non-invasive Diagnostics in Precision Oncology? Mol Diagn Ther 2021; 25:389-408. [PMID: 34018157 PMCID: PMC8249304 DOI: 10.1007/s40291-021-00534-6] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/29/2021] [Indexed: 12/20/2022]
Abstract
Circulating cell-free DNA (ccfDNA) has emerged as a promising diagnostic tool in oncology. Identification of tumour-derived ccfDNA (i.e. circulating tumour DNA [ctDNA]) provides non-invasive access to a malignancy’s molecular landscape to diagnose, inform therapeutic strategies, and monitor treatment efficacy. Current applications of ccfDNA to detect somatic mutations, however, have been largely constrained to tumour-informed searches and identification of common mutations because of the interaction between ctDNA signal and next-generation sequencing (NGS) noise. Specifically, the low allele frequency of ctDNA associated with non-metastatic and early-stage lesions may be indistinguishable from artifacts that accrue during sample preparation and NGS. Thus, using ccfDNA to achieve non-invasive and personalized molecular profiling to optimize individual patient care is a highly sought goal that remains limited in clinical practice. There is growing evidence, however, that further advances in the field of ccfDNA diagnostics may be achieved by improving detection of somatic mutations through leveraging the inherently shorter fragment lengths of ctDNA compared to non-neoplastic ccfDNA. Here, the origins and rationale for seeking to improve the mutation-based detection of ctDNA by using ccfDNA size profiling are reviewed. Subsequently, in vitro and in silico methods to enrich for a target ccfDNA fragment length are detailed to identify current practices and provide perspective into the potential of using ccfDNA size profiling to impact clinical applications in oncology.
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Affiliation(s)
- Hunter R Underhill
- Division of Medical Genetics, Department of Pediatrics, University of Utah, 295 Chipeta Way, Salt Lake City, UT, 84108, USA. .,Department of Radiology, University of Utah, Salt Lake City, UT, USA. .,Huntsman Cancer Institute, University of Utah, Salt Lake City, UT, USA.
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10
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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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11
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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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12
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Gašperšič J, Videtič Paska A. Potential of modern circulating cell-free DNA diagnostic tools for detection of specific tumour cells in clinical practice. Biochem Med (Zagreb) 2020; 30:030504. [PMID: 32774122 PMCID: PMC7394254 DOI: 10.11613/bm.2020.030504] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2020] [Accepted: 06/20/2020] [Indexed: 12/11/2022] Open
Abstract
Personalized medicine is a developing field of medicine that has gained in importance in recent decades. New diagnostic tests based on the analysis of circulating cell-free DNA (cfDNA) were developed as a tool of diagnosing different cancer types. By detecting the subpopulation of mutated DNA from cancer cells, it is possible to detect the presence of a specific tumour in early stages of the disease. Mutation analysis is performed by quantitative polymerase chain reaction (qPCR) or the next generation sequencing (NGS), however, cfDNA protocols need to be modified carefully in preanalytical, analytical, and postanalytical stages. To further improve treatment of cancer the Food and Drug Administration approved more than 20 companion diagnostic tests that combine cancer drugs with highly efficient genetic diagnostic tools. Tools detect mutations in the DNA originating from cancer cells directly through the subpopulation of cfDNA, the circular tumour DNA (ctDNA) analysis or with visualization of cells through intracellular DNA probes. A large number of ctDNA tests in clinical studies demonstrate the importance of new findings in the field of cancer diagnosis. We describe the innovations in personalized medicine: techniques for detecting ctDNA and genomic DNA (gDNA) mutations approved Food and Drug Administration companion genetic diagnostics, candidate genes for assembling the cancer NGS panels, and a brief mention of the multitude of cfDNA currently in clinical trials. Additionally, an overview of the development steps of the diagnostic tools will refresh and expand the knowledge of clinics and geneticists for research opportunities beyond the development phases.
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Affiliation(s)
- Jernej Gašperšič
- Medical Centre for Molecular Biology, Institute of Biochemistry, Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia
| | - Alja Videtič Paska
- Medical Centre for Molecular Biology, Institute of Biochemistry, Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia
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13
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Liu HE, Vuppalapaty M, Wilkerson C, Renier C, Chiu M, Lemaire C, Che J, Matsumoto M, Carroll J, Crouse S, Hanft VR, Jeffrey SS, Di Carlo D, Garon EB, Goldman J, Sollier E. Detection of EGFR Mutations in cfDNA and CTCs, and Comparison to Tumor Tissue in Non-Small-Cell-Lung-Cancer (NSCLC) Patients. Front Oncol 2020; 10:572895. [PMID: 33117705 PMCID: PMC7578230 DOI: 10.3389/fonc.2020.572895] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2020] [Accepted: 09/02/2020] [Indexed: 12/17/2022] Open
Abstract
Lung cancer is the leading cause of cancer-related mortality worldwide. Epidermal growth factor receptor (EGFR) tyrosine kinase inhibitor (TKI) therapies, based on the evaluation of EGFR mutations, have shown dramatic clinical benefits. EGFR mutation assays are mainly performed on tumor biopsies, which carry risks, are not always successful and give results relevant to the timepoint of the assay. To detect secondary EGFR mutations, which cause resistance to 1st and 2nd generation TKIs and lead to the administration of a 3rd generation drug, effective and non-invasive monitoring of EGFR mutation status is needed. Liquid biopsy analytes, such as circulating tumor cells (CTCs) and circulating tumor DNA (cfDNA), allow such monitoring over the course of the therapy. The aim of this study was to develop and optimize a workflow for the evaluation of cfDNA and CTCs in NSCLC patients all from one blood sample. Using Vortex technology and EntroGen ctEGFR assay, EGFR mutations were identified at 0.5 ng of DNA (∼83 cells), with a sensitivity ranging from 0.1 to 2.0% for a total DNA varying from 25 ng (∼4 CTCs among 4000 white blood cells, WBCs) to 1 ng (∼4 CTCs among 200 WBCs). The processing of plasma-depleted-blood provided comparable capture recovery as whole blood, confirming the possibility of a multimodality liquid biopsy analysis (cfDNA and CTC DNA) from a single tube of blood. Different anticoagulants were evaluated and compared in terms of respective performance. Blood samples from 24 NSCLC patients and 6 age-matched healthy donors were analyzed with this combined workflow to minimize blood volume needed and sample-to-sample bias, and the EGFR mutation profile detected from CTCs and cfDNA was compared to matched tumor tissues. Despite the limited size of the patient cohort, results from this non-invasive EGFR mutation analysis are encouraging and this combined workflow represents a valuable means for informing therapy selection and for monitoring treatment of patients with NSCLC.
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Affiliation(s)
- Haiyan E Liu
- Vortex Biosciences, Inc., Pleasanton, CA, United States
| | | | | | | | - Michael Chiu
- Vortex Biosciences, Inc., Pleasanton, CA, United States
| | | | - James Che
- Vortex Biosciences, Inc., Pleasanton, CA, United States
| | - Melissa Matsumoto
- Department of Bioengineering, University of California, Los Angeles, Los Angeles, CA, United States
| | - James Carroll
- Department of Medicine, David Geffen School of Medicine at UCLA, Los Angeles, CA, United States
| | - Steve Crouse
- Vortex Biosciences, Inc., Pleasanton, CA, United States
| | - Violet R Hanft
- Department of Surgery, Stanford University School of Medicine, Stanford, CA, United States
| | - Stefanie S Jeffrey
- Department of Surgery, Stanford University School of Medicine, Stanford, CA, United States
| | - Dino Di Carlo
- Department of Bioengineering, University of California, Los Angeles, Los Angeles, CA, United States.,California NanoSystems Institute, Los Angeles, CA, United States.,UCLA Jonsson Comprehensive Cancer Center, Los Angeles, CA, United States
| | - Edward B Garon
- Department of Medicine, David Geffen School of Medicine at UCLA, Los Angeles, CA, United States.,UCLA Jonsson Comprehensive Cancer Center, Los Angeles, CA, United States
| | - Jonathan Goldman
- Department of Medicine, David Geffen School of Medicine at UCLA, Los Angeles, CA, United States.,UCLA Jonsson Comprehensive Cancer Center, Los Angeles, CA, United States
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14
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Keup C, Kimmig R, Kasimir-Bauer S. Liquid Biopsies to Evaluate Immunogenicity of Gynecological/Breast Tumors: On the Way to Blood-Based Biomarkers for Immunotherapies. Breast Care (Basel) 2020; 15:470-480. [PMID: 33223990 PMCID: PMC7650128 DOI: 10.1159/000510509] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2020] [Accepted: 07/28/2020] [Indexed: 12/19/2022] Open
Abstract
BACKGROUND Despite the assumption of breast cancer (BC) as a cold, non-immunogenic tumor, immune checkpoint inhibitor (ICI) therapy is favorable for a subgroup of patients. Immunohistochemical assessment of the programmed cell death ligand 1 (PD-L1) is the only approved companion diagnostic for anti-PD-L1 therapy in metastatic triple-negative BC; however, challenges regarding the standardization of PD-L1 scoring in tumor tissue still remain. Consequently, to select patients most likely to respond to ICI, blood-based biomarkers are urgently needed. SUMMARY AND KEY MESSAGES Liquid biopsy, comprising circulating immune cells, circulating tumor cells and extracellular vesicles, as well as their surface proteins, is of high potential, and these analytes were already shown to be molecular correlates or regulators of the evasion from antitumoral immune reaction. Liquid biopsy, also enabling the evaluation of tumor mutational burden (TMB), microsatellite instability, and the T-cell receptor repertoire, allows serial sampling for monitoring purposes and reflects intra-tumoral heterogeneity which qualifies as marker for immunogenicity. Only a very few studies have already elucidated the potential of these analytes as biomarkers under ICI therapy. Nonetheless, the topic is of growing interest and has high relevance for the future. However, for clinical implementation, these multifarious analytes first need to pass robust standardization and validation procedures.
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Affiliation(s)
| | | | - Sabine Kasimir-Bauer
- Department of Gynecology and Obstetrics, University Hospital Essen, Essen, Germany
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15
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A Multi-Analyte Approach for Improved Sensitivity of Liquid Biopsies in Prostate Cancer. Cancers (Basel) 2020; 12:cancers12082247. [PMID: 32796730 PMCID: PMC7465186 DOI: 10.3390/cancers12082247] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2020] [Revised: 08/07/2020] [Accepted: 08/09/2020] [Indexed: 01/04/2023] Open
Abstract
Novel androgen receptor (AR) signaling inhibitors have improved the treatment of castration-resistant prostate cancer (CRPC). Nonetheless, the effect of these drugs is often time-limited and eventually most patients become resistant due to various AR alterations. Although liquid biopsy approaches are powerful tools for early detection of such therapy resistances, most assays investigate only a single resistance mechanism. In combination with the typically low abundance of circulating biomarkers, liquid biopsy assays are therefore informative only in a subset of patients. In this pilot study, we aimed to increase overall sensitivity for tumor-related information by combining three liquid biopsy approaches into a multi-analyte approach. In a cohort of 19 CRPC patients, we (1) enumerated and characterized circulating tumor cells (CTCs) by mRNA-based in situ padlock probe analysis, (2) used RT-qPCR to detect cancer-associated transcripts (e.g., AR and AR-splice variant 7) in lysed whole blood, and (3) conducted shallow whole-genome plasma sequencing to detect AR amplification. Although 44–53% of patient samples were informative for each assay, a combination of all three approaches led to improved diagnostic sensitivity, providing tumor-related information in 89% of patients. Additionally, distinct resistance mechanisms co-occurred in two patients, further reinforcing the implementation of multi-analyte liquid biopsy approaches.
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16
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Habli Z, AlChamaa W, Saab R, Kadara H, Khraiche ML. Circulating Tumor Cell Detection Technologies and Clinical Utility: Challenges and Opportunities. Cancers (Basel) 2020; 12:cancers12071930. [PMID: 32708837 PMCID: PMC7409125 DOI: 10.3390/cancers12071930] [Citation(s) in RCA: 101] [Impact Index Per Article: 25.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2020] [Revised: 06/03/2020] [Accepted: 06/17/2020] [Indexed: 12/16/2022] Open
Abstract
The potential clinical utility of circulating tumor cells (CTCs) in the diagnosis and management of cancer has drawn a lot of attention in the past 10 years. CTCs disseminate from tumors into the bloodstream and are believed to carry vital information about tumor onset, progression, and metastasis. In addition, CTCs reflect different biological aspects of the primary tumor they originate from, mainly in their genetic and protein expression. Moreover, emerging evidence indicates that CTC liquid biopsies can be extended beyond prognostication to pharmacodynamic and predictive biomarkers in cancer patient management. A key challenge in harnessing the clinical potential and utility of CTCs is enumerating and isolating these rare heterogeneous cells from a blood sample while allowing downstream CTC analysis. That being said, there have been serious doubts regarding the potential value of CTCs as clinical biomarkers for cancer due to the low number of promising outcomes in the published results. This review aims to present an overview of the current preclinical CTC detection technologies and the advantages and limitations of each sensing platform, while surveying and analyzing the published evidence of the clinical utility of CTCs.
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Affiliation(s)
- Zeina Habli
- Neural Engineering and Nanobiosensors Group, Biomedical Engineering Program, Maroun Semaan Faculty of Engineering and Architecture, American University of Beirut, Beirut 1107 2020, Lebanon; (Z.H.); (W.A.)
| | - Walid AlChamaa
- Neural Engineering and Nanobiosensors Group, Biomedical Engineering Program, Maroun Semaan Faculty of Engineering and Architecture, American University of Beirut, Beirut 1107 2020, Lebanon; (Z.H.); (W.A.)
| | - Raya Saab
- Department of Pediatric and Adolescent Medicine, American University of Beirut Medical Center, Beirut 1107 2020, Lebanon;
- Department of Anatomy, Cell Biology and Physiological Sciences, American University of Beirut, Beirut 1107 2020, Lebanon
| | - Humam Kadara
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, 77030 TX, USA;
| | - Massoud L. Khraiche
- Neural Engineering and Nanobiosensors Group, Biomedical Engineering Program, Maroun Semaan Faculty of Engineering and Architecture, American University of Beirut, Beirut 1107 2020, Lebanon; (Z.H.); (W.A.)
- Correspondence:
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17
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Maltoni R, Palleschi M, Ravaioli S, Tumedei MM, Rocca A, Melegari E, Altini M, Puccetti M, Manunta S, Bravaccini S. Cell-Free DNA Variant Sequencing Using CTC-Depleted Blood for Comprehensive Liquid Biopsy Testing in Metastatic Breast Cancer. Cell Transplant 2020; 29:963689720925057. [PMID: 32584148 PMCID: PMC7586254 DOI: 10.1177/0963689720925057] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Keup and colleagues provide liquid biopsy preliminary results by sequencing variants in circulating tumor cells (CTCs) and cell-free deoxyribonucleic acid (cfDNA) “all from one tube” format, in order to use the same blood sample under the same isolation conditions of both analytes to reach an unbiased comparability and consistency. We appreciated the attempt of the authors to improve technical procedures in liquid biopsy research area, but we wanted to raise several issues related to cfDNA detection, reporting our research experience. This is a feasibility study as the authors analyzed only one sample from a small case series at an advanced line of treatment. In the clinical practice to monitor the disease and predict the treatment response, the analysis should be done at multiple time points. We have previously demonstrated that the quantity and the integrity of the cfDNA are not useful to determine the evolution of early breast cancer (bc), maybe due to the fact that cfDNA is not strictly related to cancer but also to an inflammatory status. Given that a high content of cfDNA could reflect inflammatory processes, we decided to investigate the role of stimulator of interferon gene (STING), an important regulator of cancer cell growth and senescence, in bc tissue in relation to cfDNA. STING biomarker analyzed by immunohistochemistry on tumor tissue could reflect a circulating inflammatory status and needs to be further investigated, not only on CTCs but also on cfDNA. One of the major issues of cfDNA is to decide what to analyze on it, in terms of type of cells and genetic alterations. Considering that multiple tests could be done to study gene copy number alterations, mutations, and variant fusions, the proper molecular test should be chosen, on the basis of the clinical need, starting from the treatment choice to disease monitoring.
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Affiliation(s)
- Roberta Maltoni
- Istituto Scientifico Romagnolo per Lo Studio e la Cura dei Tumori (IRST) IRCCS, Meldola, Italy
| | - Michela Palleschi
- Istituto Scientifico Romagnolo per Lo Studio e la Cura dei Tumori (IRST) IRCCS, Meldola, Italy
| | - Sara Ravaioli
- Istituto Scientifico Romagnolo per Lo Studio e la Cura dei Tumori (IRST) IRCCS, Meldola, Italy
| | - Maria Maddalena Tumedei
- Istituto Scientifico Romagnolo per Lo Studio e la Cura dei Tumori (IRST) IRCCS, Meldola, Italy
| | - Andrea Rocca
- Istituto Scientifico Romagnolo per Lo Studio e la Cura dei Tumori (IRST) IRCCS, Meldola, Italy
| | - Elisabetta Melegari
- Istituto Scientifico Romagnolo per Lo Studio e la Cura dei Tumori (IRST) IRCCS, Meldola, Italy
| | - Mattia Altini
- Istituto Scientifico Romagnolo per Lo Studio e la Cura dei Tumori (IRST) IRCCS, Meldola, Italy
| | | | - Silvia Manunta
- Istituto Scientifico Romagnolo per Lo Studio e la Cura dei Tumori (IRST) IRCCS, Meldola, Italy
| | - Sara Bravaccini
- Istituto Scientifico Romagnolo per Lo Studio e la Cura dei Tumori (IRST) IRCCS, Meldola, Italy
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Multimodal Targeted Deep Sequencing of Circulating Tumor Cells and Matched Cell-Free DNA Provides a More Comprehensive Tool to Identify Therapeutic Targets in Metastatic Breast Cancer Patients. Cancers (Basel) 2020; 12:cancers12051084. [PMID: 32349306 PMCID: PMC7281124 DOI: 10.3390/cancers12051084] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2020] [Revised: 04/17/2020] [Accepted: 04/22/2020] [Indexed: 12/14/2022] Open
Abstract
Cell-free DNA (cfDNA) and circulating tumor cells (CTCs) exhibit great potential for therapy management in oncology. We aimed to establish a multimodal liquid biopsy strategy that is usable with minimized blood volume to deconvolute the genomic complexity of metastatic breast cancer. CTCs were isolated from 10ml blood of 18 hormone receptor-positive and human epidermal growth factor receptor 2-negative (HER2-) metastatic breast cancer patients. cfDNA was isolated from plasma generated after CTC depletion and targeted sequencing analyses were conducted. PIK3CA and ESR1 variants were less common in CTC gDNA, while ERBB2 variants were only detected in CTC gDNA. A total of 62% of all cfDNA variants were recovered in the matched CTC gDNA, while 72% of all variants were unique in either cfDNA (14 variants) or CTC gDNA (104 variants). The percentage of patients with no detectable cfDNA variants or CTC gDNA variants was 17%/11%, but a combined analysis identified variants in 94% of all patients. In univariate and multivariate regression models, ESR1 variants in cfDNA and CTC gDNA correlated significantly with survival. We suggest a coordinated analysis of both fractions in order to provide a comprehensive genomic footprint that may contribute to identifying the most suitable therapy for each individual.
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19
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Treatment Strategies and Survival Outcomes in Breast Cancer. Cancers (Basel) 2020; 12:cancers12030735. [PMID: 32244985 PMCID: PMC7140050 DOI: 10.3390/cancers12030735] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2020] [Accepted: 03/19/2020] [Indexed: 12/19/2022] Open
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20
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Thanh Huong P, Gurshaney S, Thanh Binh N, Gia Pham A, Hoang Nguyen H, Thanh Nguyen X, Pham-The H, Tran PT, Truong Vu K, Xuan Duong N, Pelucchi C, La Vecchia C, Boffetta P, Nguyen HD, Luu HN. Emerging Role of Circulating Tumor Cells in Gastric Cancer. Cancers (Basel) 2020; 12:E695. [PMID: 32183503 PMCID: PMC7140068 DOI: 10.3390/cancers12030695] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2020] [Revised: 03/11/2020] [Accepted: 03/13/2020] [Indexed: 02/07/2023] Open
Abstract
With over 1 million incidence cases and more than 780,000 deaths in 2018, gastric cancer (GC) was ranked as the 5th most common cancer and the 3rd leading cause of cancer deaths worldwide. Though several biomarkers, including carcinoembryonic antigen (CEA), cancer antigen 19-9 (CA19-9), and cancer antigen 72-4 (CA72-4), have been identified, their diagnostic accuracies were modest. Circulating tumor cells (CTCs), cells derived from tumors and present in body fluids, have recently emerged as promising biomarkers, diagnostically and prognostically, of cancers, including GC. In this review, we present the landscape of CTCs from migration, to the presence in circulation, biologic properties, and morphologic heterogeneities. We evaluated clinical implications of CTCs in GC patients, including diagnosis, prognosis, and therapeutic management, as well as their application in immunotherapy. On the one hand, major challenges in using CTCs in GC were analyzed, from the differences of cut-off values of CTC positivity, to techniques used for sampling, storage conditions, and CTC molecular markers, as well as the unavailability of relevant enrichment and detection techniques. On the other hand, we discussed future perspectives of using CTCs in GC management and research, including the use of circulating tumor microembolies; of CTC checkpoint blockade in immunotherapy; and of organoid models. Despite the fact that there are remaining challenges in techniques, CTCs have potential as novel biomarkers and/or a non-invasive method for diagnostics, prognostics, and treatment monitoring of GC, particularly in the era of precision medicine.
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Affiliation(s)
- Phung Thanh Huong
- Department of Biochemistry, Hanoi University of Pharmacy, Hanoi 10000, Vietnam;
| | - Sanjeev Gurshaney
- Cancer Division, Burnett School of Biomedical Science, College of Medicine, University of Central Florida, Orlando, FL 32827, USA;
| | - Nguyen Thanh Binh
- Department of Pharmaceutical Management and Economics, Hanoi University of Pharmacy, Hanoi 10000, Vietnam;
| | - Anh Gia Pham
- Department of Surgical Oncology, Viet-Duc University Hospital, Hanoi 10000, Vietnam; (A.G.P.); (H.H.N.); (X.T.N.)
| | - Huy Hoang Nguyen
- Department of Surgical Oncology, Viet-Duc University Hospital, Hanoi 10000, Vietnam; (A.G.P.); (H.H.N.); (X.T.N.)
| | - Xuan Thanh Nguyen
- Department of Surgical Oncology, Viet-Duc University Hospital, Hanoi 10000, Vietnam; (A.G.P.); (H.H.N.); (X.T.N.)
| | - Hai Pham-The
- Department of Pharmaceutical Chemistry, Hanoi University of Pharmacy, Hanoi 10000, Vietnam; (H.P.-T.); (P.-T.T.)
| | - Phuong-Thao Tran
- Department of Pharmaceutical Chemistry, Hanoi University of Pharmacy, Hanoi 10000, Vietnam; (H.P.-T.); (P.-T.T.)
| | - Khanh Truong Vu
- Department of Gastroenterology, Bach Mai Hospital, Hanoi 10000, Vietnam;
| | | | - Claudio Pelucchi
- Department of Clinical, Sciences and Community Health, University of Milan, 20133 Milan, Italy; (C.P.); (C.L.V.)
| | - Carlo La Vecchia
- Department of Clinical, Sciences and Community Health, University of Milan, 20133 Milan, Italy; (C.P.); (C.L.V.)
| | - Paolo Boffetta
- Icahn School of Medicine at Mount Sinai, Tisch Cancer Institute, Division of Hematology and Medical Oncology, New York, NY 10029, USA;
| | - Hung D. Nguyen
- Cancer Division, Burnett School of Biomedical Science, College of Medicine, University of Central Florida, Orlando, FL 32827, USA;
| | - Hung N. Luu
- Department of Epidemiology, University of Pittsburg Graduate School of Public Health, Pittsburg, PA 15261, USA
- Division of Cancer Control and Population Sciences, UPMC Hillman Cancer Center, University of Pittsburgh Medical Center, Pittsburgh, PA 15232, USA
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21
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Zheng J, Ye X, Liu Y, Zhao Y, He M, Xiao H. The combination of CTCs and CEA can help guide the management of patients with SPNs suspected of being lung cancer. BMC Cancer 2020; 20:106. [PMID: 32041568 PMCID: PMC7011271 DOI: 10.1186/s12885-020-6524-1] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2019] [Accepted: 01/08/2020] [Indexed: 12/15/2022] Open
Abstract
Objective Solitary pulmonary nodules (SPNs) is a common radiographic finding and require further evaluation because of the possibility of lung cancer. This study aimed to determine the sensitivity and specificity of circulating tumour cells (CTCs) as a marker for the diagnosis of SPNs and the integration of CTCs, carcinoembryonic antigen (CEA) and imaging findings to improve the sensitivity and specificity of diagnosis in patients with SPNs suspected of being lung cancer. Method For the serum biomarker assay, the concentration of CEA was measured by an automated electrochemiluminescence analyzer. CTCs were collected from 6 ml of blood by the SE i-FISH method, which detects the gene copy number in eight chromosomes and the tumour-associated antigen CK18. Results With a threshold of 6 CTC units, the method showed a sensitivity of 67.1% and a specificity of 56.5% in the diagnosis of NSCLC, especially in the upper lobe, in which the diagnostic strength was the highest (P < 0.01). CTCs, CEA and nodule type had the highest diagnostic efficacy (area under the curve, 0.827; 95% confidence interval, 0.752–0.901) in patients with SPNs being suspected lung cancer. Combining CTCs (cut-off value 12 units) with CEA (1.78 ng/ml), the method showed a sensitivity of 77.8% and a specificity of 90% in the diagnosis of NSCLC, especially in the upper lobe, subsolid nodules and nodules ≥8 mm. Conclusions Our results demonstrated that CTCs are feasible diagnostic biomarkers in patients with SPNs, especially in the upper lobe. Furthermore, CTCs combined with CEA showed higher diagnostic efficacy in the upper lobe, subsolid nodules and nodules ≥8 mm.
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Affiliation(s)
- Jian Zheng
- Department of Thoracic Surgery, Shanghai General Hospital, Shanghai Jiaotong University, Shanghai, China
| | - Xiong Ye
- College of Clinical Medicine, Shanghai University of Medicine & Health Science, Shanghai, China
| | - Yanan Liu
- Department of Clinical Laboratory, Shanghai Children's Hospital, Shanghai Jiaotong University, Shanghai, China
| | - Yuxia Zhao
- College of Clinical Medicine, Shanghai University of Medicine & Health Science, Shanghai, China
| | - Mudan He
- Department of Respiratory and Critical Care Medicine, Shanghai First Hospital of Baoshan Branch, Shanghai, China
| | - Hui Xiao
- Department of Respiratory and Critical Care Medicine, Shanghai General Hospital, Shanghai Jiaotong University, 85Wujin Road, Shanghai, 200080, China.
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22
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Keup C, Benyaa K, Hauch S, Sprenger-Haussels M, Tewes M, Mach P, Bittner AK, Kimmig R, Hahn P, Kasimir-Bauer S. Targeted deep sequencing revealed variants in cell-free DNA of hormone receptor-positive metastatic breast cancer patients. Cell Mol Life Sci 2020; 77:497-509. [PMID: 31254045 PMCID: PMC7010653 DOI: 10.1007/s00018-019-03189-z] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2019] [Revised: 06/07/2019] [Accepted: 06/11/2019] [Indexed: 02/06/2023]
Abstract
Cell-free DNA (cfDNA) is described to mirror intratumoral heterogeneity and gives insight about clonal evolution for improved therapeutic decisions. We sequenced cfDNA of a hormone receptor-positive, HER2-negative metastatic breast cancer (MBC) cohort with a high coverage to examine the prevalence and relevance of any detected variant. cfDNA of 44 MBC patients was isolated, followed by library construction using a customized targeted DNA panel with integrated unique molecular indices analyzing AKT1, AR, BRCA1, BRCA2, EGFR, ERCC4, ERBB2, ERBB3, ESR1, FGFR1, KRAS, MUC16, PIK3CA, PIK3R1, PTEN, PTGFR, and TGFB1. CfDNA was sequenced on the NextSeq® 550 platform (Illumina) and variants were analyzed with Ingenuity Variant Analysis (QIAGEN). We evaluated cfDNA variants in 40 of the 44 hormone receptor-positive and HER2-negative patients with a high mean coverage of 22,000×, resulting in MUC16, BRCA2, ERBB3, and AR variant calling in > 90% of the patients. 47% of all AR variants were pathogenic and at least one pathogenic or likely pathogenic variant was detected in each patient. A specific BRCA1 variant and > 3.5 pathogenic variants significantly associated with a reduced survival after diagnosis of metastasis. Longitudinal monitoring revealed an increase of pathogenic and likely pathogenic PIK3CA and ESR1 variant allele frequency under everolimus and exemestane, 8 months before proof of therapy failure by visual staging in one exemplary case. The identification of new variants with high prevalence, prognostic value, and dynamics under treatment by deep sequencing of cfDNA might empower sensitive monitoring and personalized therapeutic decisions.
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Affiliation(s)
- Corinna Keup
- Department of Gynecology and Obstetrics, University Hospital of Essen, Essen, Germany.
| | | | | | | | - Mitra Tewes
- Department of Medical Oncology, University Hospital of Essen, Essen, Germany
| | - Pawel Mach
- Department of Gynecology and Obstetrics, University Hospital of Essen, Essen, Germany
| | - Ann-Kathrin Bittner
- Department of Gynecology and Obstetrics, University Hospital of Essen, Essen, Germany
| | - Rainer Kimmig
- Department of Gynecology and Obstetrics, University Hospital of Essen, Essen, Germany
| | | | - Sabine Kasimir-Bauer
- Department of Gynecology and Obstetrics, University Hospital of Essen, Essen, Germany
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23
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Wang J, Xu B. Targeted therapeutic options and future perspectives for HER2-positive breast cancer. Signal Transduct Target Ther 2019; 4:34. [PMID: 31637013 PMCID: PMC6799843 DOI: 10.1038/s41392-019-0069-2] [Citation(s) in RCA: 200] [Impact Index Per Article: 40.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2019] [Revised: 08/22/2019] [Accepted: 08/22/2019] [Indexed: 12/12/2022] Open
Abstract
Over the past 2 decades, there has been an extraordinary progress in the regimens developed for the treatment of human epidermal growth factor receptor 2 (HER2)-positive breast cancer. Trastuzumab, pertuzumab, lapatinib, and ado-trastuzumab emtansine (T-DM1) are commonly recommended anti-HER2 target agents by the U.S. Food and Drug Administration. This review summarizes the most significant and updated research on clinical scenarios related to HER2-positive breast cancer management in order to revise the guidelines of everyday clinical practices. In this article, we present the data on anti-HER2 clinical research of neoadjuvant, adjuvant, and metastatic studies from the past 2 decades. We also highlight some of the promising strategies that should be critically considered. Lastly, this review lists some of the ongoing clinical trials, findings of which may soon be available.
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Affiliation(s)
- Jiani 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, No. 17, Panjiayuannanli, Chaoyang District, 100021 Beijing, 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, No. 17, Panjiayuannanli, Chaoyang District, 100021 Beijing, China
- State Key Laboratory of Molecular Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, No. 17, Panjiayuannanli, Chaoyang District, 100021 Beijing, China
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