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Carrasco R, Ingelmo-Torres M, Oriola J, Roldán FL, Rodríguez-Carunchio L, Herranz S, Mellado B, Alcaraz A, Izquierdo L, Mengual L. Assessment of aggressive bladder cancer mutations in plasma cell-free DNA. Front Oncol 2023; 13:1270962. [PMID: 38098507 PMCID: PMC10720633 DOI: 10.3389/fonc.2023.1270962] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2023] [Accepted: 11/13/2023] [Indexed: 12/17/2023] Open
Abstract
Background and aims The spatial and temporal genetic heterogeneity of bladder cancer (BC) makes challenging to find specific drivers of metastatic disease, thus preventing to determine those BC patients at high risk of tumor progression. Our aim was to identify DNA mutations providing aggressive behavior to bladder tumors and analyze them in patients' cell-free DNA (cfDNA) during their follow-up after radical cystectomy (RC) in order to monitor tumor evolution. Methods Six BC patients who underwent RC and presented disease progression during their follow-up were included. Next-generation sequencing was used to determine somatic mutations in several primary tumor and metastatic specimens from each patient. Shared DNA mutations between primary bladder tumor and metastatic sites were identified in cfDNA samples through droplet digital PCR. Results Besides BC genetic heterogeneity, specific mutations in at least one of these genes -TERT, ATM, RB1, and FGFR3- were found in primary tumors and their metastases in all patients. These mutations were also identified in the patients' cfDNA at different follow-up time points. Additionally, the dynamic changes of these mutations in cfDNA allowed us to determine tumor evolution in response to treatment. Conclusion The analysis of BC mutations associated with poor prognosis in plasma cfDNA could be a valuable tool to monitor tumor evolution, thus improving the clinical management of BC patients.
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Affiliation(s)
- Raquel Carrasco
- Laboratori i Servei d’Urologia, Hospital Clínic de Barcelona, Barcelona, Spain
- Genètica i tumors urològics, Fundació de Recerca Clínic Barcelona-Institut d’Investigacions Biomèdiques August Pi i Sunyer (FRCB-IDIBAPS), Barcelona, Spain
- Departament de Biomedicina, Facultat de Medicina i Ciències de la Salut, Universitat de Barcelona (UB), Barcelona, Spain
| | - Mercedes Ingelmo-Torres
- Laboratori i Servei d’Urologia, Hospital Clínic de Barcelona, Barcelona, Spain
- Genètica i tumors urològics, Fundació de Recerca Clínic Barcelona-Institut d’Investigacions Biomèdiques August Pi i Sunyer (FRCB-IDIBAPS), Barcelona, Spain
| | - Josep Oriola
- Departament de Biomedicina, Facultat de Medicina i Ciències de la Salut, Universitat de Barcelona (UB), Barcelona, Spain
| | - Fiorella L. Roldán
- Laboratori i Servei d’Urologia, Hospital Clínic de Barcelona, Barcelona, Spain
- Genètica i tumors urològics, Fundació de Recerca Clínic Barcelona-Institut d’Investigacions Biomèdiques August Pi i Sunyer (FRCB-IDIBAPS), Barcelona, Spain
| | | | - Sandra Herranz
- Laboratori i Servei d’Urologia, Hospital Clínic de Barcelona, Barcelona, Spain
| | - Begoña Mellado
- Servei d’Oncologia Mèdica, Hospital Clínic de Barcelona, Barcelona, Spain
| | - Antonio Alcaraz
- Laboratori i Servei d’Urologia, Hospital Clínic de Barcelona, Barcelona, Spain
- Genètica i tumors urològics, Fundació de Recerca Clínic Barcelona-Institut d’Investigacions Biomèdiques August Pi i Sunyer (FRCB-IDIBAPS), Barcelona, Spain
| | - Laura Izquierdo
- Laboratori i Servei d’Urologia, Hospital Clínic de Barcelona, Barcelona, Spain
- Genètica i tumors urològics, Fundació de Recerca Clínic Barcelona-Institut d’Investigacions Biomèdiques August Pi i Sunyer (FRCB-IDIBAPS), Barcelona, Spain
| | - Lourdes Mengual
- Laboratori i Servei d’Urologia, Hospital Clínic de Barcelona, Barcelona, Spain
- Genètica i tumors urològics, Fundació de Recerca Clínic Barcelona-Institut d’Investigacions Biomèdiques August Pi i Sunyer (FRCB-IDIBAPS), Barcelona, Spain
- Departament de Biomedicina, Facultat de Medicina i Ciències de la Salut, Universitat de Barcelona (UB), Barcelona, Spain
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Carrasco R, Ingelmo-Torres M, Trullas R, Roldán FL, Rodríguez-Carunchio L, Juez L, Sureda J, Alcaraz A, Mengual L, Izquierdo L. Tumor-Agnostic Circulating Tumor DNA Testing for Monitoring Muscle-Invasive Bladder Cancer. Int J Mol Sci 2023; 24:16578. [PMID: 38068899 PMCID: PMC10706140 DOI: 10.3390/ijms242316578] [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: 11/05/2023] [Revised: 11/17/2023] [Accepted: 11/19/2023] [Indexed: 12/18/2023] Open
Abstract
Circulating tumor DNA (ctDNA) has recently emerged as a real-time prognostic and predictive biomarker for monitoring cancer patients. Here, we aimed to ascertain whether tumor-agnostic ctDNA testing would be a feasible strategy to monitor disease progression and therapeutic response in muscle-invasive bladder cancer (MIBC) patients after radical cystectomy (RC). Forty-two MIBC patients who underwent RC were prospectively included. Blood samples from these patients were collected at different follow-up time points. Two specific mutations (TERT c.1-124C>T and ATM c.1236-2A>T) were analyzed in the patients' plasma samples by droplet digital PCR to determine their ctDNA status. During a median follow-up of 21 months, 24% of patients progressed in a median of six months. ctDNA status was identified as a prognostic biomarker of tumor progression before RC and 4 and 12 months later (HR 6.774, HR 3.673, and HR 30.865, respectively; p < 0.05). Lastly, dynamic changes in ctDNA status between baseline and four months later were significantly associated with patient outcomes (p = 0.045). In conclusion, longitudinal ctDNA analysis using a tumor-agnostic approach is a potential tool for monitoring MIBC patients after RC. The implementation of this testing in a clinical setting could improve disease management and patients' outcomes.
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Affiliation(s)
- Raquel Carrasco
- Laboratori i Servei d’Urologia, Hospital Clinic de Barcelona, 08036 Barcelona, Spain; (R.C.); (M.I.-T.); (F.L.R.); (L.J.); (J.S.); (A.A.); (L.I.)
- Genètica i Tumors Urològics, Fundació de Recerca Clinic Barcelona-Institut d’Investigacions Biomèdiques August Pi i Sunyer (FRCB-IDIBAPS), 08036 Barcelona, Spain
- Departament de Biomedicina, Facultat de Medicina i Ciències de la Salut, Universitat de Barcelona (UB), 08036 Barcelona, Spain
| | - Mercedes Ingelmo-Torres
- Laboratori i Servei d’Urologia, Hospital Clinic de Barcelona, 08036 Barcelona, Spain; (R.C.); (M.I.-T.); (F.L.R.); (L.J.); (J.S.); (A.A.); (L.I.)
- Genètica i Tumors Urològics, Fundació de Recerca Clinic Barcelona-Institut d’Investigacions Biomèdiques August Pi i Sunyer (FRCB-IDIBAPS), 08036 Barcelona, Spain
| | - Ramón Trullas
- Unitat de Neurobiologia, Institut d’Investigacions Biomèdiques de Barcelona (IIBB/CSIC/IDIBAPS), 08036 Barcelona, Spain;
| | - Fiorella L. Roldán
- Laboratori i Servei d’Urologia, Hospital Clinic de Barcelona, 08036 Barcelona, Spain; (R.C.); (M.I.-T.); (F.L.R.); (L.J.); (J.S.); (A.A.); (L.I.)
- Genètica i Tumors Urològics, Fundació de Recerca Clinic Barcelona-Institut d’Investigacions Biomèdiques August Pi i Sunyer (FRCB-IDIBAPS), 08036 Barcelona, Spain
| | | | - Lourdes Juez
- Laboratori i Servei d’Urologia, Hospital Clinic de Barcelona, 08036 Barcelona, Spain; (R.C.); (M.I.-T.); (F.L.R.); (L.J.); (J.S.); (A.A.); (L.I.)
| | - Joan Sureda
- Laboratori i Servei d’Urologia, Hospital Clinic de Barcelona, 08036 Barcelona, Spain; (R.C.); (M.I.-T.); (F.L.R.); (L.J.); (J.S.); (A.A.); (L.I.)
| | - Antonio Alcaraz
- Laboratori i Servei d’Urologia, Hospital Clinic de Barcelona, 08036 Barcelona, Spain; (R.C.); (M.I.-T.); (F.L.R.); (L.J.); (J.S.); (A.A.); (L.I.)
- Genètica i Tumors Urològics, Fundació de Recerca Clinic Barcelona-Institut d’Investigacions Biomèdiques August Pi i Sunyer (FRCB-IDIBAPS), 08036 Barcelona, Spain
| | - Lourdes Mengual
- Laboratori i Servei d’Urologia, Hospital Clinic de Barcelona, 08036 Barcelona, Spain; (R.C.); (M.I.-T.); (F.L.R.); (L.J.); (J.S.); (A.A.); (L.I.)
- Genètica i Tumors Urològics, Fundació de Recerca Clinic Barcelona-Institut d’Investigacions Biomèdiques August Pi i Sunyer (FRCB-IDIBAPS), 08036 Barcelona, Spain
- Departament de Biomedicina, Facultat de Medicina i Ciències de la Salut, Universitat de Barcelona (UB), 08036 Barcelona, Spain
| | - Laura Izquierdo
- Laboratori i Servei d’Urologia, Hospital Clinic de Barcelona, 08036 Barcelona, Spain; (R.C.); (M.I.-T.); (F.L.R.); (L.J.); (J.S.); (A.A.); (L.I.)
- Genètica i Tumors Urològics, Fundació de Recerca Clinic Barcelona-Institut d’Investigacions Biomèdiques August Pi i Sunyer (FRCB-IDIBAPS), 08036 Barcelona, Spain
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Boutin M, Topham JT, Feilotter H, Kennecke HF, Couture F, Harb M, Kavan P, Berry S, Lim HJ, Goffin JR, Ahmad C, Lott A, Renouf DJ, Jonker DJ, Tu D, O’Callaghan CJ, Chen EX, Loree JM. Optimizing the number of variants tracked to follow disease burden with circulating tumor DNA assays in metastatic colorectal cancer. Ther Adv Med Oncol 2023; 15:17588359231183682. [PMID: 37389190 PMCID: PMC10302520 DOI: 10.1177/17588359231183682] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2023] [Accepted: 05/31/2023] [Indexed: 07/01/2023] Open
Abstract
Background The number of somatic mutations detectable in circulating tumor DNA (ctDNA) is highly heterogeneous in metastatic colorectal cancer (mCRC). The optimal number of mutations required to assess disease kinetics is relevant and remains poorly understood. Objectives To determine whether increasing panel breadth (the number of tracked variants in a ctDNA assay) would alter the sensitivity in detecting ctDNA in patients with mCRC. Design We used archival tissue sequencing to perform an in silico assessment of the optimal number of tracked mutations to detect and monitor disease kinetics in mCRC using sequencing data from the Canadian Cancer Trials Group CO.26 trial. Methods For each patient, 1, 2, 4, 8, 12, or 16 of the most clonal (highest variant allele frequency) somatic variants were selected from archival tissue-based whole-exome sequencing and assessed for the proportion of variants detected in matched ctDNA at baseline, week 8, and progression timepoints. Results Data from 110 patients were analyzed. Genes most frequently encountered among the top four highest VAF variants in archival tissue were TP53 (51.9% of patients), APC (43.3%), KRAS (42.3%), and SMAD4 (9.6%). While the frequency of detecting at least one tracked variant increased when expanding beyond variant pool sizes of 1 and 2 in baseline (p = 0.0030) and progression (p = 0.0030) ctDNA samples, we observed no significant benefit to increases in variant pool size past four variants in any of the ctDNA timepoints (p < 0.05). Conclusion While increasing panel breadth beyond two tracked variants improved variant re-detection in ctDNA samples from patients with treatment refractory mCRC, increases beyond four tracked variants yielded no significant improvement in variant re-detection.
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Affiliation(s)
- Mélina Boutin
- Division of Medical Oncology, BC Cancer, Vancouver, BC, Canada Centre Intégré de Cancérologie de la Montérégie, Université de Sherbrooke, QC, Canada
| | | | - Harriet Feilotter
- Canadian Cancer Trials Group, Queen’s University, Kingston, ON, Canada
| | | | | | | | | | - Scott Berry
- Department of Oncology, Queen’s University, Kingston, ON, Canada
| | - Howard J. Lim
- Division of Medical Oncology, BC Cancer, Vancouver, BC, Canada
| | | | | | | | - Daniel J. Renouf
- Division of Medical Oncology, BC Cancer, Vancouver, BC, Canada Pancreas Center BC, Vancouver, BC, Canada
| | - Derek J. Jonker
- The Ottawa Hospital, University of Ottawa, Ottawa, ON, Canada
| | - Dongsheng Tu
- Canadian Cancer Trials Group, Queen’s University, Kingston, ON, Canada
| | | | - Eric X. Chen
- Princess Margaret Cancer Centre, Toronto, ON, Canada
| | - Jonathan M. Loree
- Division of Medical Oncology, BC Cancer, 600 West 10th Avenue, Vancouver, BC V5Z 4E6, Canada
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Enzymatic Methods for Mutation Detection in Cancer Samples and Liquid Biopsies. Int J Mol Sci 2023; 24:ijms24020923. [PMID: 36674433 PMCID: PMC9865676 DOI: 10.3390/ijms24020923] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2022] [Revised: 12/28/2022] [Accepted: 12/29/2022] [Indexed: 01/06/2023] Open
Abstract
Low-level tumor somatic DNA mutations in tissue and liquid biopsies obtained from cancer patients can have profound implications for development of metastasis, prognosis, choice of treatment, follow-up, or early cancer detection. Unless detected, such low-frequency DNA alterations can misinform patient management decisions or become missed opportunities for personalized medicine. Next-generation sequencing technologies and digital-PCR can resolve low-level mutations but require access to specialized instrumentation, time, and resources. Enzymatic-based approaches to detection of low-level mutations provide a simple, straightforward, and affordable alternative to enrich and detect such alterations and is broadly available to low-resource laboratory settings. This review summarizes the traditional uses of enzymatic mutation detection and describes the latest exciting developments, potential, and applications with specific reference to the field of liquid biopsy in cancer.
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Callesen LB, Hamfjord J, Boysen AK, Pallisgaard N, Guren TK, Kure EH, Spindler KLG. Circulating tumour DNA and its clinical utility in predicting treatment response or survival in patients with metastatic colorectal cancer: a systematic review and meta-analysis. Br J Cancer 2022; 127:500-513. [PMID: 35440666 PMCID: PMC9345951 DOI: 10.1038/s41416-022-01816-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2021] [Revised: 03/29/2022] [Accepted: 03/31/2022] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND We investigate the current knowledge on circulating tumour DNA (ctDNA) and its clinical utility in predicting outcomes in patients with metastatic colorectal cancer (mCRC). METHODS PubMed, Embase, Cochrane Database of Systematic Reviews and Cochrane Central Register of Controlled Trials were searched. Last search 16/12/2020. We included studies on patients with mCRC reporting the predictive or prognostic value of ctDNA. We performed separate random-effects meta-analyses to investigate if baseline ctDNA and early changes in ctDNA levels during treatment were associated with survival. The risk of bias was assessed according to the Quality in Prognosis Studies tool. RESULTS Seventy-one studies were included with 6930 patients. Twenty-four studies were included in meta-analyses. High baseline ctDNA level was associated with short progression-free survival (PFS) (HR = 2.2; 95% CI 1.8-2.8; n = 509) and overall survival (OS) (HR = 2.4; 95% CI 1.9-3.1; n = 1336). A small or no early decrease in ctDNA levels during treatment was associated with short PFS (HR = 3.0; 95% CI 2.2-4.2; n = 479) and OS (HR = 2.8; 95% CI 2.1-3.9; n = 583). Results on clonal evolution and lead-time were inconsistent. A majority of included studies (n = 50/71) had high risk of bias in at least one domain. CONCLUSIONS Plasma ctDNA is a strong prognostic biomarker in mCRC. However, true clinical utility is lacking.
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Affiliation(s)
- Louise B Callesen
- Department of Experimental Clinical Oncology, Aarhus University Hospital, Aarhus, Denmark.
- Institute of Clinical Medicine, Aarhus University, Aarhus, Denmark.
| | - Julian Hamfjord
- Department of Oncology, Oslo University Hospital, Oslo, Norway
- Department of Cancer Genetics, Institute for Cancer Research, Oslo University Hospital, Oslo, Norway
- Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo, Norway
| | - Anders K Boysen
- Department of Experimental Clinical Oncology, Aarhus University Hospital, Aarhus, Denmark
| | - Niels Pallisgaard
- Department of Pathology, Zealand University Hospital, Roskilde, Denmark
| | - Tormod K Guren
- Department of Oncology, Oslo University Hospital, Oslo, Norway
| | - Elin H Kure
- Department of Cancer Genetics, Institute for Cancer Research, Oslo University Hospital, Oslo, Norway
- Department of Natural Sciences and Environmental Health, Faculty of Technology, Natural Sciences and Maritime Sciences, University of South-Eastern Norway, Campus Bø, Bø, Norway
| | - Karen-Lise G Spindler
- Department of Experimental Clinical Oncology, Aarhus University Hospital, Aarhus, Denmark
- Institute of Clinical Medicine, Aarhus University, Aarhus, Denmark
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Pre-PCR Mutation-Enrichment Methods for Liquid Biopsy Applications. Cancers (Basel) 2022; 14:cancers14133143. [PMID: 35804916 PMCID: PMC9264780 DOI: 10.3390/cancers14133143] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2022] [Revised: 06/20/2022] [Accepted: 06/23/2022] [Indexed: 01/25/2023] Open
Abstract
Liquid biopsy is having a remarkable impact on healthcare- and disease-management in the context of personalized medicine. Circulating free DNA (cfDNA) is one of the most instructive liquid-biopsy-based biomarkers and harbors valuable information for diagnostic, predictive, and prognostic purposes. When it comes to cancer, circulating DNA from the tumor (ctDNA) has a wide range of applications, from early cancer detection to the early detection of relapse or drug resistance, and the tracking of the dynamic genomic make-up of tumor cells. However, the detection of ctDNA remains technically challenging, due, in part, to the low frequency of ctDNA among excessive circulating cfDNA originating from normal tissues. During the past three decades, mutation-enrichment methods have emerged to boost sensitivity and enable facile detection of low-level mutations. Although most developed techniques apply mutation enrichment during or following initial PCR, there are a few techniques that allow mutation selection prior to PCR, which provides advantages. Pre-PCR enrichment techniques can be directly applied to genomic DNA and diminish the influence of PCR errors that can take place during amplification. Moreover, they have the capability for high multiplexity and can be followed by established mutation detection and enrichment technologies without changes to their established procedures. The first approaches for pre-PCR enrichment were developed by employing restriction endonucleases directly on genomic DNA in the early 1990s. However, newly developed pre-PCR enrichment methods provide higher sensitivity and versatility. This review describes the available pre-PCR enrichment methods and focuses on the most recently developed techniques (NaME-PrO, UVME, and DEASH/MAESTRO), emphasizing their applications in liquid biopsies.
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Nuclease-Assisted, Multiplexed Minor-Allele Enrichment: Application in Liquid Biopsy of Cancer. METHODS IN MOLECULAR BIOLOGY (CLIFTON, N.J.) 2022; 2394:433-451. [PMID: 35094339 DOI: 10.1007/978-1-0716-1811-0_22] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
The use of next-generation sequencing (NGS) to profile genomic variation of individual cancer species is revolutionizing the practice of clinical oncology. In liquid biopsy of cancer, sequencing of circulating-free DNA (cfDNA) is gradually applied to all stages of cancer diagnosis and treatment, serving as complement or replacement of tissue biopsies. However, analysis of cfDNA obtained from blood draws still faces technical obstacles due in part to an excess of wild-type DNA originating from normal tissues and hematopoietic cells. The resulting low-level mutation abundance often falls below routine NGS detection sensitivity and limits reliable mutation identification that meets clinical sensitivity and specificity standards. Despite sample preparation advances that reduce sequencing error rates via use of unique molecular identifiers (molecular barcodes) and error-suppression algorithms, excessive amounts of sequencing are still required to detect mutations at allelic frequency levels below 1%. This requirement reduces throughput and increases cost.In this chapter, we describe a sensitive multiplex mutation detection method that enriches mutation-containing DNA during sample preparation, prior to sequencing, thereby increasing signal-to-noise ratios and providing low-level mutation detection without excessive sequencing depth. We couple targeted next-generation sequencing with wild-type DNA removal using Nuclease-assisted Minor-allele Enrichment using Probe Overlap, NaME-PrO, a recently developed method to eliminate wild-type sequences from multiple targets simultaneously. A step by step guide to library preparation and data analysis are provided as well as some precautions during the sample handling.
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Muraoka M, Maekawa S, Katoh R, Komiyama Y, Nakakuki N, Takada H, Matsuda S, Suzuki Y, Sato M, Tatsumi A, Miura M, Amemiya F, Shindo H, Takano S, Fukasawa M, Yamauchi K, Yamaguchi T, Nakayama Y, Inoue T, Enomoto N. Usefulness of Cell-Free Human Telomerase Reverse Transcriptase Mutant DNA Quantification in Blood for Predicting Hepatocellular Carcinoma Treatment Efficacy. Hepatol Commun 2021; 5:1927-1938. [PMID: 34558819 PMCID: PMC8557313 DOI: 10.1002/hep4.1762] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/28/2021] [Revised: 04/28/2021] [Accepted: 05/16/2021] [Indexed: 12/26/2022] Open
Abstract
Although the usefulness of liquid biopsy as a biomarker in the treatment of hepatocellular carcinoma (HCC) has been suggested, its usefulness in transcatheter arterial chemoembolization (TACE) or tyrosine kinase inhibitor (TKI) therapies has not been reported in detail. In this study, we investigated the clinical value of a cell-free (cf)DNA quantification system targeting the human telomerase reverse transcriptase (hTERT) promoter mutation in advanced HCC treatment. Plasma from 67 patients with advanced HCC, treated with TACE and TKI, was used for extraction of cfDNA. We defined cfDNA with the hTERT promoter C228T mutation as circulating mutant DNA (mutant DNA) and without the mutation as circulating wild-type DNA (wild-type DNA). We analyzed the changes in mutant and wild-type DNA levels during HCC treatment and examined the relationship between changes in the cfDNA level and the clinical course. Mutant DNA was detected in 73.1% (49/67) of the patients during HCC treatment. In univariate analysis, factors associated with detection of mutant DNA before treatment were the intrahepatic maximum tumor diameter (P = 0.015) and protein induced by vitamin K absence (PIVKAII) (P = 0.006). The degree of mutant DNA change after TACE was significantly correlated with tumor volume (P < 0.001), reflecting the treated tumor volume. Responders with peak cfDNA levels within 1 week of TKI initiation had significantly better progression-free survival than nonresponders (P = 0.004). Conclusion: Changes in blood hTERT promoter mutant DNA levels during TACE or TKI treatment indirectly reflect the amount of HCCs and are useful for predicting long-term treatment responses.
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Affiliation(s)
- Masaru Muraoka
- First Department of Internal MedicineFaculty of MedicineUniversity of YamanashiChuoJapan
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Sensitive detection of microsatellite instability in tissues and liquid biopsies: Recent developments and updates. Comput Struct Biotechnol J 2021; 19:4931-4940. [PMID: 34527197 PMCID: PMC8433064 DOI: 10.1016/j.csbj.2021.08.037] [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: 02/28/2021] [Revised: 08/23/2021] [Accepted: 08/24/2021] [Indexed: 12/16/2022] Open
Abstract
Microsatellite instability (MSI), a phenotype displayed as deletions/insertions of repetitive genomic sequences, has drawn great attention due to its application in cancer including diagnosis, prognosis and immunotherapy response prediction. Several methods have been developed for the detection of MSI, facilitating the MSI classification of cancer patients. In view of recent interest in minimally-invasive detection of MSI via liquid biopsy samples, which requires methods with high sensitivity to identify small fractions of altered DNA in the presence of large amount of wild type copies, sensitive MSI detection approaches are emerging. Here we review the available MSI detection methods and their detection limits and focus on recently developed next-generation-sequencing based approaches and bioinformatics algorithms available for MSI analysis in various cancer types.
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Clinical Applications of Minimal Residual Disease Assessments by Tumor-Informed and Tumor-Uninformed Circulating Tumor DNA in Colorectal Cancer. Cancers (Basel) 2021; 13:cancers13184547. [PMID: 34572774 PMCID: PMC8471730 DOI: 10.3390/cancers13184547] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2021] [Revised: 09/08/2021] [Accepted: 09/08/2021] [Indexed: 12/20/2022] Open
Abstract
Simple Summary Circulating tumor DNA, or ctDNA, are fragments of tumor DNA that can be detected in the blood of patients with colorectal cancer. Measuring ctDNA levels in the blood has shown the potential to provide important information that can be helpful in the clinical care of patients with colorectal cancer. For example, in patients with colon cancer that has been removed by surgery, measuring ctDNA in the blood can predict the likelihood of cancer recurrence, while in those with metastatic colorectal cancer, measuring ctDNA can inform the clinician whether chemotherapy is effective at earlier timepoints than currently available tests. In this review, we discuss the results from ongoing studies describing the utility of ctDNA measurements across all stages of colorectal cancer. We also discuss the various clinical scenarios that ctDNA may have the most immediate impact in colorectal cancer management. Abstract Emerging data suggest that circulating tumor DNA (ctDNA) can detect colorectal cancer (CRC)-specific signals across both non-metastatic and metastatic settings. With the development of multiple platforms, including tumor-informed and tumor-agnostic ctDNA assays and demonstration of their provocative analytic performance to detect minimal residual disease, there are now ongoing, phase III randomized clinical trials to evaluate their role in the management paradigm of CRC. In this review, we highlight landmark studies that have formed the basis for ongoing studies on the clinically applicability of plasma ctDNA assays in resected, stage I–III CRC and metastatic CRC. We discuss clinical settings by which ctDNA may have the most immediate impact in routine clinical practice. These include the potential for ctDNA to (1) guide surveillance and intensification or de-intensification strategies of adjuvant therapy in resected, stage I–III CRC, (2) predict treatment response to neoadjuvant therapy in locally advanced rectal cancer inclusive of total neoadjuvant therapy (TNT), and (3) predict response to systemic and surgical therapies in metastatic disease. We end by considering clinical variables that can influence our ability to reliably interpret ctDNA dynamics in the clinic.
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Pastor B, André T, Henriques J, Trouilloud I, Tournigand C, Jary M, Mazard T, Louvet C, Azan S, Bauer A, Roch B, Sanchez C, Vernerey D, Thierry AR, Adenis A. Monitoring levels of circulating cell-free DNA in patients with metastatic colorectal cancer as a potential biomarker of responses to regorafenib treatment. Mol Oncol 2021; 15:2401-2411. [PMID: 33934494 PMCID: PMC8410523 DOI: 10.1002/1878-0261.12972] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2020] [Revised: 03/09/2021] [Accepted: 04/20/2021] [Indexed: 12/25/2022] Open
Abstract
Circulating cell‐free DNA (cfDNA) contains circulating tumor DNA (ctDNA), which can be obtained from serial liquid biopsies to enable tumor genome analysis throughout the course of treatment. We investigated cfDNA and mutant ctDNA as potential biomarkers to predict the best outcomes of regorafenib‐treated metastatic colorectal cancer (mCRC) patients. We analyzed longitudinally collected plasma cfDNA of 43 mCRC patients prospectively enrolled in the phase II TEXCAN trial by IntPlex qPCR. Qualitative (KRAS, NRAS, BRAFV600E mutations) and quantitative (total cfDNA concentration, mutant ctDNA concentration, mutant ctDNA fraction) parameters were correlated with overall survival (OS) and progression‐free survival (PFS). When examined as classes or continuous variables, the concentrations of total cfDNA, mutant ctDNA, and, partly, mutant ctDNA fraction prior to regorafenib treatment correlated with OS. Patients with baseline cfDNA > 26 ng·mL−1 had shorter OS than those with cfDNA value below this threshold (4.0 vs 6.9 months; log‐rank P = 0.0366). Patients with baseline mutant ctDNA > 2 ng·mL−1 had shorter OS than those with mutant ctDNA below this threshold (log‐rank P = 0.0154). We show that pretreatment cfDNA and mutant ctDNA levels may identify mCRC patients that may benefit from regorafenib treatment.
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Affiliation(s)
- Brice Pastor
- Institut de Recherche en Cancérologie de Montpellier (IRCM), INSERM, Université de Montpellier, Montpellier Cancer Institute (ICM), France
| | - Thierry André
- Department of Medical Oncology, Saint-Antoine University Hospital, Sorbonne University, Paris, France.,Oncology Multidisciplinary Research Group (GERCOR), Paris, France
| | - Julie Henriques
- Methodology and Quality of Life Unit in Oncology, Besançon University Hospital, France
| | - Isabelle Trouilloud
- Department of Medical Oncology, Saint-Antoine University Hospital, Sorbonne University, Paris, France.,Oncology Multidisciplinary Research Group (GERCOR), Paris, France
| | - Christophe Tournigand
- Oncology Multidisciplinary Research Group (GERCOR), Paris, France.,Medical Oncology Service, Henri Mondor Hospital, AP-HP, Université Paris Est Créteil Créteil, France
| | - Marine Jary
- Oncology Multidisciplinary Research Group (GERCOR), Paris, France.,INSERM, Etablissement Français du Sang Bourgogne Franche-Comté, UMR1098, Interactions Hôte-Greffon-Tumeur/Ingénierie Cellulaire et Génique, Bourgogne Franche-Comté University, Besançon, France.,Department of Medical Oncology, Besançon University Hospital, France
| | - Thibault Mazard
- Institut de Recherche en Cancérologie de Montpellier (IRCM), INSERM, Université de Montpellier, Montpellier Cancer Institute (ICM), France.,Department of Medical Oncology, Montpellier Cancer Institute (ICM), France
| | - Christophe Louvet
- Oncology Multidisciplinary Research Group (GERCOR), Paris, France.,Department of Medical Oncology, Institut Monsouris, Paris, France
| | - Simon Azan
- Institut de Recherche en Cancérologie de Montpellier (IRCM), INSERM, Université de Montpellier, Montpellier Cancer Institute (ICM), France
| | - Audrey Bauer
- Institut de Recherche en Cancérologie de Montpellier (IRCM), INSERM, Université de Montpellier, Montpellier Cancer Institute (ICM), France
| | - Benoit Roch
- Institut de Recherche en Cancérologie de Montpellier (IRCM), INSERM, Université de Montpellier, Montpellier Cancer Institute (ICM), France.,Department of Thoracic Oncology, Montpellier University Hospital, Université de Montpellier, France
| | - Cynthia Sanchez
- Institut de Recherche en Cancérologie de Montpellier (IRCM), INSERM, Université de Montpellier, Montpellier Cancer Institute (ICM), France
| | - Dewi Vernerey
- Oncology Multidisciplinary Research Group (GERCOR), Paris, France.,Methodology and Quality of Life Unit in Oncology, Besançon University Hospital, France
| | - Alain R Thierry
- Institut de Recherche en Cancérologie de Montpellier (IRCM), INSERM, Université de Montpellier, Montpellier Cancer Institute (ICM), France.,Department of Medical Oncology, Montpellier Cancer Institute (ICM), France
| | - Antoine Adenis
- Institut de Recherche en Cancérologie de Montpellier (IRCM), INSERM, Université de Montpellier, Montpellier Cancer Institute (ICM), France.,Department of Medical Oncology, Montpellier Cancer Institute (ICM), France
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12
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Martínez-Sáez O, Pascual T, Brasó-Maristany F, Chic N, González-Farré B, Sanfeliu E, Rodríguez A, Martínez D, Galván P, Rodríguez AB, Schettini F, Conte B, Vidal M, Adamo B, Martínez A, Muñoz M, Moreno R, Villagrasa P, Salvador F, Ciruelos EM, Faull I, Odegaard JI, Prat A. Circulating tumor DNA dynamics in advanced breast cancer treated with CDK4/6 inhibition and endocrine therapy. NPJ Breast Cancer 2021; 7:8. [PMID: 33536433 PMCID: PMC7859394 DOI: 10.1038/s41523-021-00218-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2020] [Accepted: 01/07/2021] [Indexed: 12/24/2022] Open
Abstract
Circulating tumor DNA (ctDNA) levels may predict response to anticancer drugs, including CDK4/6 inhibitors and endocrine therapy combinations (CDK4/6i+ET); however, critical questions remain unanswered such as which assay or statistical method to use. Here, we obtained paired plasma samples at baseline and week 4 in 45 consecutive patients with advanced breast cancer treated with CDK4/6i+ET. ctDNA was detected in 96% of cases using the 74-gene Guardant360 assay. A variant allele fraction ratio (VAFR) was calculated for each of the 79 detected mutations between both timepoints. Mean of all VAFRs (mVAFR) was computed for each patient. In our dataset, mVAFR was significantly associated with progression-free survival (PFS). Baseline VAF, on-treatment VAF or absolute changes in VAF were not associated with PFS, nor were CA-15.3 levels at baseline, week 4 or the CA-15.3 ratio. These findings demonstrate that ctDNA dynamics using a standardized multi-gene panel and a unique methodological approach predicts treatment outcome. Clinical trials in patients with an unfavorable ctDNA response are needed.
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Affiliation(s)
- Olga Martínez-Sáez
- SOLTI Cancer Research Group, Barcelona, Spain.,Department of Medical Oncology, Hospital Clinic of Barcelona, Barcelona, Spain.,Translational Genomics and Targeted Therapies in Solid Tumors, August Pi i Sunyer Biomedical Research Institute (IDIBAPS), Barcelona, Spain
| | - Tomás Pascual
- SOLTI Cancer Research Group, Barcelona, Spain.,Department of Medical Oncology, Hospital Clinic of Barcelona, Barcelona, Spain.,Translational Genomics and Targeted Therapies in Solid Tumors, August Pi i Sunyer Biomedical Research Institute (IDIBAPS), Barcelona, Spain.,Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Fara Brasó-Maristany
- SOLTI Cancer Research Group, Barcelona, Spain.,Department of Medical Oncology, Hospital Clinic of Barcelona, Barcelona, Spain.,Translational Genomics and Targeted Therapies in Solid Tumors, August Pi i Sunyer Biomedical Research Institute (IDIBAPS), Barcelona, Spain
| | - Nuria Chic
- SOLTI Cancer Research Group, Barcelona, Spain.,Department of Medical Oncology, Hospital Clinic of Barcelona, Barcelona, Spain.,Translational Genomics and Targeted Therapies in Solid Tumors, August Pi i Sunyer Biomedical Research Institute (IDIBAPS), Barcelona, Spain
| | - Blanca González-Farré
- SOLTI Cancer Research Group, Barcelona, Spain.,Translational Genomics and Targeted Therapies in Solid Tumors, August Pi i Sunyer Biomedical Research Institute (IDIBAPS), Barcelona, Spain.,Department of Pathology, Hospital Clinic of Barcelona, Barcelona, Spain
| | - Esther Sanfeliu
- SOLTI Cancer Research Group, Barcelona, Spain.,Translational Genomics and Targeted Therapies in Solid Tumors, August Pi i Sunyer Biomedical Research Institute (IDIBAPS), Barcelona, Spain.,Department of Pathology, Hospital Clinic of Barcelona, Barcelona, Spain
| | - Adela Rodríguez
- Department of Medical Oncology, Hospital Clinic of Barcelona, Barcelona, Spain
| | - Débora Martínez
- SOLTI Cancer Research Group, Barcelona, Spain.,Department of Medical Oncology, Hospital Clinic of Barcelona, Barcelona, Spain.,Translational Genomics and Targeted Therapies in Solid Tumors, August Pi i Sunyer Biomedical Research Institute (IDIBAPS), Barcelona, Spain
| | - Patricia Galván
- SOLTI Cancer Research Group, Barcelona, Spain.,Department of Medical Oncology, Hospital Clinic of Barcelona, Barcelona, Spain.,Translational Genomics and Targeted Therapies in Solid Tumors, August Pi i Sunyer Biomedical Research Institute (IDIBAPS), Barcelona, Spain
| | - Anna Belén Rodríguez
- SOLTI Cancer Research Group, Barcelona, Spain.,Department of Medical Oncology, Hospital Clinic of Barcelona, Barcelona, Spain.,Translational Genomics and Targeted Therapies in Solid Tumors, August Pi i Sunyer Biomedical Research Institute (IDIBAPS), Barcelona, Spain
| | - Francesco Schettini
- SOLTI Cancer Research Group, Barcelona, Spain.,Translational Genomics and Targeted Therapies in Solid Tumors, August Pi i Sunyer Biomedical Research Institute (IDIBAPS), Barcelona, Spain.,Department of Clinical Medicine and Surgery, University of Naples Federico II, Naples, Italy
| | - Benedetta Conte
- SOLTI Cancer Research Group, Barcelona, Spain.,Translational Genomics and Targeted Therapies in Solid Tumors, August Pi i Sunyer Biomedical Research Institute (IDIBAPS), Barcelona, Spain.,Department of Medical Oncology U.O. Oncologia Medica 2, IRCCS Ospedale Policlinico San Martino, Genova, Italy
| | - Maria Vidal
- SOLTI Cancer Research Group, Barcelona, Spain.,Department of Medical Oncology, Hospital Clinic of Barcelona, Barcelona, Spain.,Translational Genomics and Targeted Therapies in Solid Tumors, August Pi i Sunyer Biomedical Research Institute (IDIBAPS), Barcelona, Spain
| | - Barbara Adamo
- SOLTI Cancer Research Group, Barcelona, Spain.,Department of Medical Oncology, Hospital Clinic of Barcelona, Barcelona, Spain.,Translational Genomics and Targeted Therapies in Solid Tumors, August Pi i Sunyer Biomedical Research Institute (IDIBAPS), Barcelona, Spain
| | - Antoni Martínez
- Department of Pathology, Hospital Clinic of Barcelona, Barcelona, Spain
| | - Montserrat Muñoz
- SOLTI Cancer Research Group, Barcelona, Spain.,Department of Medical Oncology, Hospital Clinic of Barcelona, Barcelona, Spain.,Translational Genomics and Targeted Therapies in Solid Tumors, August Pi i Sunyer Biomedical Research Institute (IDIBAPS), Barcelona, Spain
| | - Reinaldo Moreno
- SOLTI Cancer Research Group, Barcelona, Spain.,Department of Medical Oncology, Hospital Clinic of Barcelona, Barcelona, Spain.,Translational Genomics and Targeted Therapies in Solid Tumors, August Pi i Sunyer Biomedical Research Institute (IDIBAPS), Barcelona, Spain
| | | | | | - Eva M Ciruelos
- SOLTI Cancer Research Group, Barcelona, Spain.,Department of Medical Oncology, Hospital Universitario 12 de Octubre, Madrid, Spain
| | - Iris Faull
- Guardant Health, Inc., Redwood City, CA, USA
| | | | - Aleix Prat
- SOLTI Cancer Research Group, Barcelona, Spain. .,Department of Medical Oncology, Hospital Clinic of Barcelona, Barcelona, Spain. .,Translational Genomics and Targeted Therapies in Solid Tumors, August Pi i Sunyer Biomedical Research Institute (IDIBAPS), Barcelona, Spain. .,Department of Medicine, University of Barcelona, Barcelona, Spain.
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13
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Morris VK, Strickler JH. Use of Circulating Cell-Free DNA to Guide Precision Medicine in Patients with Colorectal Cancer. Annu Rev Med 2021; 72:399-413. [PMID: 33502901 DOI: 10.1146/annurev-med-070119-120448] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Patient-specific biomarkers form the foundation of precision medicine strategies. To realize the promise of precision medicine in patients with colorectal cancer (CRC), access to cost-effective, convenient, and safe assays is critical. Improvements in diagnostic technology have enabled ultrasensitive and specific assays to identify cell-free DNA (cfDNA) from a routine blood draw. Clinicians are already employing these minimally invasive assays to identify drivers of therapeutic resistance and measure genomic heterogeneity, particularly when tumor tissue is difficult to access or serial sampling is necessary. As cfDNA diagnostic technology continues to improve, more innovative applications are anticipated. In this review, we focus on four clinical applications for cfDNA analysis in the management of CRC: detecting minimal residual disease, monitoring treatment response in the metastatic setting, identifying drivers of treatment sensitivity and resistance, and guiding therapeutic strategies to overcome resistance.
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Affiliation(s)
- Van K Morris
- Department of Gastrointestinal Medical Oncology, University of Texas MD Anderson Cancer Center, Houston, Texas 77030, USA
| | - John H Strickler
- Division of Medical Oncology, Duke University Medical Center, Durham, North Carolina 27710, USA;
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14
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Jones RP, Pugh SA, Graham J, Primrose JN, Barriuso J. Circulating tumour DNA as a biomarker in resectable and irresectable stage IV colorectal cancer; a systematic review and meta-analysis. Eur J Cancer 2021; 144:368-381. [PMID: 33422803 DOI: 10.1016/j.ejca.2020.11.025] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2020] [Revised: 11/01/2020] [Accepted: 11/15/2020] [Indexed: 12/17/2022]
Abstract
BACKGROUND For patients with metastatic colorectal cancer, stratification for treatment (surgery or chemotherapy) is often based on crude clinicopathological characteristics like tumour size and number of lesions. Circulating tumour DNA (ctDNA) acts as a potential biomarker of disease trajectory and biology, allowing better stratification. This study aims to systematically review ctDNA in stage IV colorectal cancer to assess its potential role as a prospective biomarker to guide management decisions. METHODS A literature search was performed to identify studies where the measurement of ctDNA in stage IV colorectal cancer was correlated with a clinical outcome (radiological response, secondary resection rate, PFS, DFS or OS). RESULTS Twenty-eight studies were included, reporting on 2823 patients. Circulating tumour DNA was detectable in between 80% and 90% of patients prior to treatment. Meta-analysis identified a strong correlation between detectable ctDNA after treatment (surgery or chemotherapy) and overall survival (HR 2.2, 95% CI 1.79-2.69, p < 0.00001), as well as progression-free survival (HR 3.15, 95% CI 2.10-4.73, p < 0.00001). ctDNA consistently offered an early marker of long-term prognosis in irresectable disease, with changes after one cycle of systemic therapy demonstrating prognostic value. In resectable disease treated with curative intent, detection of ctDNA offered a lead time over radiological recurrence of 10 months. CONCLUSION Circulating tumour DNA is detectable in the majority of resectable and irresectable patients. The presence of ctDNA is clearly associated with shorter overall survival, with changes in ctDNA an early biomarker of adverse disease behaviour. Prospective trials are essential to test its clinical efficacy.
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Affiliation(s)
- Robert P Jones
- School of Cancer Studies, Institute of Translational Medicine, University of Liverpool, Liverpool, UK; Department of Hepatobiliary Surgery, Liverpool University Teaching Hospitals NHS Foundation Trust, Liverpool, UK.
| | | | - Janet Graham
- Beatson West of Scotland Cancer Centre, Glasgow, UK; University of Glasgow, UK
| | | | - Jorge Barriuso
- Division of Cancer Sciences, Faculty of Biology, Medicine and Health, University of Manchester, UK; Department of Medical Oncology, The Christie NHS Foundation Trust, Manchester, UK
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15
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Clinical Utility of Plasma KRAS, NRAS and BRAF Mutational Analysis with Real Time PCR in Metastatic Colorectal Cancer Patients-The Importance of Tissue/Plasma Discordant Cases. J Clin Med 2020; 10:jcm10010087. [PMID: 33383664 PMCID: PMC7794782 DOI: 10.3390/jcm10010087] [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: 11/26/2020] [Revised: 12/22/2020] [Accepted: 12/25/2020] [Indexed: 02/05/2023] Open
Abstract
BACKGROUND Tumor tissue (T) mutational analysis represents the standard for metastatic colorectal cancer (mCRC); however, circulating tumor DNA (ctDNA) detected by liquid biopsy in plasma (PL) can better represent tumor heterogeneity. METHODS mCRC patients undergoing standard first-line chemotherapy with known T-KRAS/NRAS/BRAF status were enrolled in the present prospective study. PL mutations were assessed within 2 weeks before chemotherapy start with real time PCR and correlated with T status and Progression free survival (PFS). Clinical and biochemical variables including also total number of tumor lesions (TNL) and the sum of maximum diameter (SMD) of all lesions were assessed as potential predictors of T/PL discordance. RESULTS Among 45 enrolled patients, all BRAF mutations were concordant between T and PL and there were 20% of patients RAS discordant: 9% wild type in T and mutated in PL and 11% mutated in T and wild type in PL. T mutations were significantly associated to median PFS (mPFS of 4.5, 8.3 and 22.9 months for T-BRAF mutated, T-RAS mutated, and T-wild type patients, respectively, p for trend 0.00014). PL mutations further refined prognosis: RAS wild type in T and mutated in PL had significantly shorter PFS than concordant RAS wild type in T and PL: mPFS 9.6 vs. 23.3 months, respectively, p = 0.02. Patients RAS mutated in T and wild type in PL had longer PFS than concordant RAS mutated in T and PL: 24.4 vs. 7.8 months, respectively, p = 0.008. At a multivariate cox regression analysis for PFS, PL mutations were independent prognostic factor superior to T analysis (HR 0.13, p = 0.0008). At multivariate logistic regression analysis TNL and SMD were significant predictors of discordant cases. CONCLUSIONS PL mutational analysis allows a better prognostication than T analysis alone and could help in mCRC treatment management.
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16
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Dasari A, Morris VK, Allegra CJ, Atreya C, Benson AB, Boland P, Chung K, Copur MS, Corcoran RB, Deming DA, Dwyer A, Diehn M, Eng C, George TJ, Gollub MJ, Goodwin RA, Hamilton SR, Hechtman JF, Hochster H, Hong TS, Innocenti F, Iqbal A, Jacobs SA, Kennecke HF, Lee JJ, Lieu CH, Lenz HJ, Lindwasser OW, Montagut C, Odisio B, Ou FS, Porter L, Raghav K, Schrag D, Scott AJ, Shi Q, Strickler JH, Venook A, Yaeger R, Yothers G, You YN, Zell JA, Kopetz S. ctDNA applications and integration in colorectal cancer: an NCI Colon and Rectal-Anal Task Forces whitepaper. Nat Rev Clin Oncol 2020; 17:757-770. [PMID: 32632268 PMCID: PMC7790747 DOI: 10.1038/s41571-020-0392-0] [Citation(s) in RCA: 188] [Impact Index Per Article: 47.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/12/2020] [Indexed: 02/07/2023]
Abstract
An increasing number of studies are describing potential uses of circulating tumour DNA (ctDNA) in the care of patients with colorectal cancer. Owing to this rapidly developing area of research, the Colon and Rectal-Anal Task Forces of the United States National Cancer Institute convened a panel of multidisciplinary experts to summarize current data on the utility of ctDNA in the management of colorectal cancer and to provide guidance in promoting the efficient development and integration of this technology into clinical care. The panel focused on four key areas in which ctDNA has the potential to change clinical practice, including the detection of minimal residual disease, the management of patients with rectal cancer, monitoring responses to therapy, and tracking clonal dynamics in response to targeted therapies and other systemic treatments. The panel also provides general guidelines with relevance for ctDNA-related research efforts, irrespective of indication.
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Affiliation(s)
- Arvind Dasari
- Department of Gastrointestinal Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.
| | - Van K Morris
- Department of Gastrointestinal Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | | | - Chloe Atreya
- University of California at San Francisco Comprehensive Cancer Center, San Francisco, CA, USA
| | - Al B Benson
- Division of Hematology/Oncology, Northwestern University, Chicago, IL, USA
| | - Patrick Boland
- Department of Medicine, Roswell Park Cancer Center, Buffalo, NY, USA
| | - Ki Chung
- Division of Hematology & Oncology, Medical University of South Carolina, Charleston, SC, USA
| | - Mehmet S Copur
- CHI Health St Francis Cancer Treatment Center, Grand Island, NE, USA
| | - Ryan B Corcoran
- Department of Medical Oncology, Massachusetts General Hospital Cancer Center, Boston, MA, USA
| | - Dustin A Deming
- Division of Hematology, Medical Oncology and Palliative Care, Department of Medicine, University of Wisconsin-Madison, Madison, WI, USA
| | - Andrea Dwyer
- University of Colorado Cancer Center, Aurora, CO, USA
| | - Maximilian Diehn
- Department of Radiation Oncology, Stanford University, Stanford, CA, USA
| | - Cathy Eng
- Department of Gastrointestinal Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Thomas J George
- Department of Medicine, University of Florida Health Cancer Center, Gainesville, FL, USA
| | - Marc J Gollub
- Department of Radiology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | | | - Stanley R Hamilton
- Department of Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Jaclyn F Hechtman
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Howard Hochster
- Rutgers Cancer Institute of New Jersey, New Brunswick, NJ, USA
| | - Theodore S Hong
- Department of Radiation Oncology, Massachusetts General Hospital Cancer Center, Boston, MD, USA
| | - Federico Innocenti
- Center for Pharmacogenomics and Individualized Therapy, University of North Carolina, Chapel Hill, NC, USA
| | - Atif Iqbal
- Section of Colorectal Surgery, Division of Surgery, Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX, USA
| | - Samuel A Jacobs
- National Adjuvant Surgical and Bowel Project Foundation/NRG Oncology, Pittsburgh, PA, USA
| | - Hagen F Kennecke
- Department of Oncology, Virginia Mason Cancer Institute, Seattle, WA, USA
| | - James J Lee
- Division of Hematology-Oncology, Department of Medicine, University of Pittsburgh Medical Center, Hillman Cancer Center, Pittsburgh, PA, USA
| | - Christopher H Lieu
- Division of Medical Oncology, University of Colorado Cancer Center, Aurora, CO, USA
| | - Heinz-Josef Lenz
- Department of Preventive Medicine, University of Southern California/Norris Comprehensive Cancer Center, Los Angeles, CA, USA
| | - O Wolf Lindwasser
- Coordinating Center for Clinical Trials, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Clara Montagut
- Hospital del Mar-Institut Hospital del Mar d'Investigacions Mèdiques, Universitat Pompeu Fabra, Barcelona, Spain
| | - Bruno Odisio
- Department of Interventional Radiology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Fang-Shu Ou
- Division of Biomedical Statistics and Informatics, Mayo Clinic, Rochester, MN, USA
| | - Laura Porter
- Patient Advocate, NCI Colon Task Force, Boston, MA, USA
| | - Kanwal Raghav
- Department of Gastrointestinal Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Deborah Schrag
- Division of Population Sciences, Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Aaron J Scott
- Division of Hematology and Oncology, Banner University of Arizona Cancer Center, Tucson, AZ, USA
| | - Qian Shi
- Division of Biomedical Statistics and Informatics, Mayo Clinic, Rochester, MN, USA
| | - John H Strickler
- Division of Medical Oncology, Department of Medicine, Duke University Medical Center, Durham, NC, USA
| | - Alan Venook
- University of California at San Francisco Comprehensive Cancer Center, San Francisco, CA, USA
| | - Rona Yaeger
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Greg Yothers
- Department of Biostatistics, University of Pittsburgh, Pittsburgh, PA, USA
| | - Y Nancy You
- Department of Surgical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Jason A Zell
- Department of Epidemiology, Chao Family Comprehensive Cancer Center, University of California, Irvine, CA, USA
- Division of Hematology/Oncology, Department of Medicine, University of California, Irvine, CA, USA
| | - Scott Kopetz
- Department of Gastrointestinal Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
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17
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Lueong SS, Herbst A, Liffers ST, Bielefeld N, Horn PA, Tannapfel A, Reinacher-Schick A, Hinke A, Hegewisch-Becker S, Kolligs FT, Siveke JT. Serial Circulating Tumor DNA Mutational Status in Patients with KRAS-Mutant Metastatic Colorectal Cancer from the Phase 3 AIO KRK0207 Trial. Clin Chem 2020; 66:1510-1520. [PMID: 33257977 DOI: 10.1093/clinchem/hvaa223] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2019] [Accepted: 08/28/2020] [Indexed: 12/31/2022]
Abstract
BACKGROUND We assessed the usefulness of circulating tumor DNA (ctDNA) pre- or post-treatment initiation for outcome prediction and treatment monitoring in metastatic colorectal cancer (mCRC). METHODS Droplet digital PCR was used to measure absolute mutant V-Ki-ras2 Kirsten rat sarcoma viral oncogene ((mut)KRAS) ctDNA concentrations in 214 healthy controls (plasma and sera) and in 151 tissue-based mutKRAS positive patients with mCRC from the prospective multicenter phase 3 trial AIO KRK0207. Serial mutKRAS ctDNA was analyzed prior to and 2-3 weeks after first-line chemotherapy initiation with fluoropyrimidine, oxaliplatin, and bevacizumab in patients with mCRC and correlated with clinical parameters. RESULTS mut KRAS ctDNA was detected in 74.8% (113/151) of patients at baseline and in 59.6% (90/151) at follow-up. mutKRAS ctDNA at baseline and follow-up was associated with poor overall survival (OS) (hazard ratio [HR] =1.88, 95% confidence interval [CI] 1.20-2.95; HR = 2.15, 95% CI 1.47-3.15) and progression-free survival (PFS) (HR = 2.53, 95% CI 1.44-4.46; HR = 1.90, 95% CI 1.23-2.95), respectively. mutKRAS ctDNA clearance at follow-up conferred better disease control (P = 0.0075), better OS (log-rank P = 0.0018), and PFS (log-rank P = 0.0018). Measurable positive mutKRAS ctDNA at follow-up was the strongest and most significant independent prognostic factor on OS in multivariable analysis (HR = 2.31, 95% CI 1.40-3.25). CONCLUSIONS Serial analysis of circulating mutKRAS concentrations in mCRC has prognostic value. Post treatment mutKRAS concentrations 2 weeks after treatment initiation were associated with therapeutic response in multivariable analysis and may be an early response predictor in patients receiving first-line combination chemotherapy. CLINICALTRIALSGOV IDENTIFIER NCT00973609.
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Affiliation(s)
- Smiths S Lueong
- Institute for Developmental Cancer Therapeutics, West German Cancer Center, University Medicine Essen, Essen, Germany.,Division of Solid Tumor Translational Oncology, German Cancer Consortium (DKTK, Partner Site Essen) and German Cancer Research Center, DKFZ, Heidelberg, Germany
| | - Andreas Herbst
- Institute of Laboratory Medicine, University of Munich, Munich, Germany.,German Cancer Consortium (DKTK, Partner Site Munich) and German Cancer Research Center, DKFZ, Heidelberg, Germany
| | - Sven-Thorsten Liffers
- Institute for Developmental Cancer Therapeutics, West German Cancer Center, University Medicine Essen, Essen, Germany.,Division of Solid Tumor Translational Oncology, German Cancer Consortium (DKTK, Partner Site Essen) and German Cancer Research Center, DKFZ, Heidelberg, Germany
| | - Nicola Bielefeld
- Institute for Developmental Cancer Therapeutics, West German Cancer Center, University Medicine Essen, Essen, Germany.,Division of Solid Tumor Translational Oncology, German Cancer Consortium (DKTK, Partner Site Essen) and German Cancer Research Center, DKFZ, Heidelberg, Germany
| | - Peter A Horn
- Division of Solid Tumor Translational Oncology, German Cancer Consortium (DKTK, Partner Site Essen) and German Cancer Research Center, DKFZ, Heidelberg, Germany.,Institute for Transfusion Medicine, University Hospital Essen, Essen, Germany
| | | | - Anke Reinacher-Schick
- Department of Hematology, Oncology and Palliative Care, St. Josef-Hospital, Ruhr-University Bochum
| | - Axel Hinke
- CCRC: Cancer Clinical Research Consulting, Düsseldorf, Germany
| | | | - Frank T Kolligs
- German Cancer Consortium (DKTK, Partner Site Munich) and German Cancer Research Center, DKFZ, Heidelberg, Germany.,Department of Medicine, Division of- Gastroenterology, Hepatology & Infectiology, Helios Clinic Berlin-Buch, Berlin, Germany.,Department of Medicine II, University of Munich, Munich, Germany
| | - Jens T Siveke
- Institute for Developmental Cancer Therapeutics, West German Cancer Center, University Medicine Essen, Essen, Germany.,Division of Solid Tumor Translational Oncology, German Cancer Consortium (DKTK, Partner Site Essen) and German Cancer Research Center, DKFZ, Heidelberg, Germany
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18
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Unseld M, Belic J, Pierer K, Zhou Q, Moser T, Bauer R, Piringer G, Gerger A, Siebenhüner A, Speicher M, Heitzer E, Prager GW. A higher ctDNA fraction decreases survival in regorafenib-treated metastatic colorectal cancer patients. Results from the regorafenib's liquid biopsy translational biomarker phase II pilot study. Int J Cancer 2020; 148:1452-1461. [PMID: 32949150 PMCID: PMC7894541 DOI: 10.1002/ijc.33303] [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: 06/12/2020] [Revised: 08/24/2020] [Accepted: 08/25/2020] [Indexed: 12/25/2022]
Abstract
The predictive effect of circulating tumor DNA (ctDNA) in colorectal cancer (CRC) treatment is still highly discussed. The primary objective of our study was to investigate a possible prognostic/predictive value of ctDNA under regorafenib treatment. This prospective multicenter translational biomarker phase II pilot study enrolled 30 metastatic CRC patients (67% men, 33% women) treated with regorafenib. ctDNA was assessed in plasma before treatment start and at defined time points during administration. Measurement of tumor fraction as well as mutation and copy number analysis of CRC driver genes were performed by next-generation sequencing approaches. Multivariate analyses for survival and treatment efficacy were adjusted to age, gender and Eastern Cooperative Oncology Group. Disease control rate was 30%. Median tumor fraction at baseline was 18.5% (0-49.9). Mutations in CRC driver genes or genes involved in angiogenesis were identified in 25 patients (83.3%). KRAS mutations were detected in 13 of 14 KRAS-positive tumors; in three patients without KRAS mutation in the respective tumors, acquired mutations as a consequence of prior anti-EGFR treatment were detected. In a subset of patients, novel occurring mutations or focal amplifications were detected. A tumor fraction of 5% and higher at baseline was significantly associated with a decreased OS (P = .022; hazard ratio 3.110 (95% confidence interval: 1.2-8.2). ctDNA is detectable in a high proportion of mCRC patients. Higher ctDNA levels are associated with survival among regorafenib treatment. Moreover, our data highlight the benefit of a combined evaluation of mutations and somatic copy number alterations in advanced cancer patients.
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Affiliation(s)
- Matthias Unseld
- Department of Medicine I, Division of Palliative Medicine, Medical University of Vienna, Vienna, Austria
| | - Jelena Belic
- Institute of Human Genetics, Diagnostic and Research Center for Molecular BioMedicine, Medical University of Graz, Graz, Austria
| | - Kerstin Pierer
- Institute of Human Genetics, Diagnostic and Research Center for Molecular BioMedicine, Medical University of Graz, Graz, Austria.,Christian Doppler Laboratory for Liquid Biopsies for Early Detection of Cancer, Graz, Austria
| | - Qing Zhou
- Institute of Human Genetics, Diagnostic and Research Center for Molecular BioMedicine, Medical University of Graz, Graz, Austria
| | - Tina Moser
- Institute of Human Genetics, Diagnostic and Research Center for Molecular BioMedicine, Medical University of Graz, Graz, Austria
| | - Raimund Bauer
- Center for Pathobiochemistry and Genetics, Institute of Medical Chemistry, Medical University of Vienna, Vienna, Austria
| | | | - Armin Gerger
- Department of Internal Medicine, Division of Oncology, Medical University of Graz, Austria
| | | | - Michael Speicher
- Institute of Human Genetics, Diagnostic and Research Center for Molecular BioMedicine, Medical University of Graz, Graz, Austria
| | - Ellen Heitzer
- Institute of Human Genetics, Diagnostic and Research Center for Molecular BioMedicine, Medical University of Graz, Graz, Austria.,Christian Doppler Laboratory for Liquid Biopsies for Early Detection of Cancer, Graz, Austria
| | - Gerald W Prager
- Department of Medicine I, Division of Oncology, Medical University of Vienna, Vienna, Austria
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19
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Calandri M, Siravegna G, Yevich SM, Stranieri G, Gazzera C, Kopetz S, Fonio P, Gupta S, Bardelli A, Veltri A, Odisio BC. Liquid biopsy, a paradigm shift in oncology: what interventional radiologists should know. Eur Radiol 2020; 30:4496-4503. [PMID: 32193642 DOI: 10.1007/s00330-020-06700-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2019] [Revised: 01/21/2020] [Accepted: 01/31/2020] [Indexed: 02/08/2023]
Abstract
The acquisition of adequate tumor sample is required to verify primary tumor type and specific biomarkers and to assess response to therapy. Historically, invasive surgical procedures were the standard methods to acquire tumor samples until advancements in imaging and minimally invasive equipment facilitated the paradigm shift image-guided biopsy. Image-guided biopsy has improved sampling yield and minimized risk to the patient; however, there are still limitations, such as its invasive nature and its consequent limitations to longitudinal tumor monitoring. The next paradigm shift in sampling technique will need to address these issues to provide a more reliable and less invasive technique. Recently, liquid biopsy (LB) has emerged as a non-invasive alternative to tissue sampling. This technique relies on direct sampling of blood or other bodily fluids in contact with the tumor in order to collect circulating tumor DNA (ctDNA), circulating tumor cells (CTCs), and circulating RNAs-in particular microRNA (miRNAs). Clinical applications of LB involve different steps of cancer patient management including screening, detection of disease recurrence, and evaluation of acquired resistance. With any paradigm shift, old techniques are often relegated to a secondary option. Although image-guided biopsies may appear as a passive spectator on the rapid advancement of LB, the two techniques may well be codependent. Interventional radiology may be integral to directly sample the liquid surrounding or draining from the tumor. In addition, LB may help to correctly select the patients for image-guided loco-regional treatments, to determine its treatment endpoint, and to early detect recurrence. KEY POINTS: • Liquid biopsy is a novel technology with potential high impact in the management of patients undergoing image-guided procedures. • Interventional radiology procedures may increase liquid biopsy sensitivity through direct fluid sampling. • Liquid biopsy techniques may provide a venue for improving patients' selection and enhance outcomes of interventional loco-regional therapies performed by interventional radiologists.
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Affiliation(s)
- Marco Calandri
- Radiology Unit, A.O.U. San Luigi Gonzaga - Orbassano (To), Orbassano, TO, Italy.,Department of Oncology, University of Torino, Turin, Italy
| | - Giulia Siravegna
- Candiolo Cancer Institute-FPO, IRCCS, Candiolo (To), Candiolo, TO, Italy.,Cancer Center, Massachusetts General Hospital, Harvard Medical School, Boston, USA
| | - Steven M Yevich
- Department of Interventional Radiology, MD Anderson Cancer Center, The University of Texas, Houston, TX, USA
| | - Giuseppe Stranieri
- Radiology Unit, A.O.U. San Luigi Gonzaga - Orbassano (To), Orbassano, TO, Italy
| | - Carlo Gazzera
- Radiology Institute, Città della Salute e della Scienza - Torino Department of Surgical Sciences, University of Turin, Turin, Italy
| | - Scott Kopetz
- Department of Gastrointestinal Medical Oncology, MD Anderson Cancer Center, The University of Texas, Houston, TX, USA
| | - Paolo Fonio
- Radiology Institute, Città della Salute e della Scienza - Torino Department of Surgical Sciences, University of Turin, Turin, Italy
| | - Sanjay Gupta
- Department of Interventional Radiology, MD Anderson Cancer Center, The University of Texas, Houston, TX, USA
| | - Alberto Bardelli
- Department of Oncology, University of Torino, Turin, Italy.,Candiolo Cancer Institute-FPO, IRCCS, Candiolo (To), Candiolo, TO, Italy
| | - Andrea Veltri
- Radiology Unit, A.O.U. San Luigi Gonzaga - Orbassano (To), Orbassano, TO, Italy.,Department of Oncology, University of Torino, Turin, Italy
| | - Bruno C Odisio
- Department of Interventional Radiology, MD Anderson Cancer Center, The University of Texas, Houston, TX, USA.
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20
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Matsuoka T, Yashiro M. Precision medicine for gastrointestinal cancer: Recent progress and future perspective. World J Gastrointest Oncol 2020; 12:1-20. [PMID: 31966910 PMCID: PMC6960076 DOI: 10.4251/wjgo.v12.i1.1] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/14/2019] [Revised: 10/12/2019] [Accepted: 11/04/2019] [Indexed: 02/05/2023] Open
Abstract
Gastrointestinal (GI) cancer has a high tumor incidence and mortality rate worldwide. Despite significant improvements in radiotherapy, chemotherapy, and targeted therapy for GI cancer over the last decade, GI cancer is characterized by high recurrence rates and a dismal prognosis. There is an urgent need for new diagnostic and therapeutic approaches. Recent technological advances and the accumulation of clinical data are moving toward the use of precision medicine in GI cancer. Here we review the application and status of precision medicine in GI cancer. Analyses of liquid biopsy specimens provide comprehensive real-time data of the tumor-associated changes in an individual GI cancer patient with malignancy. With the introduction of gene panels including next-generation sequencing, it has become possible to identify a variety of mutations and genetic biomarkers in GI cancer. Although the genomic aberration of GI cancer is apparently less actionable compared to other solid tumors, novel informative analyses derived from comprehensive gene profiling may lead to the discovery of precise molecular targeted drugs. These progressions will make it feasible to incorporate clinical, genome-based, and phenotype-based diagnostic and therapeutic approaches and apply them to individual GI cancer patients for precision medicine.
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Affiliation(s)
- Tasuku Matsuoka
- Department of Gastroenterological Surgery, Osaka City University Graduate School of Medicine, Osaka 5458585, Japan
| | - Masakazu Yashiro
- Department of Gastroenterological Surgery, Osaka City University Graduate School of Medicine, Osaka 5458585, Japan
- Oncology Institute of Geriatrics and Medical Science, Osaka City University Graduate School of Medicine, Osaka 5458585, Japan
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21
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Arai H, Battaglin F, Wang J, Lo JH, Soni S, Zhang W, Lenz HJ. Molecular insight of regorafenib treatment for colorectal cancer. Cancer Treat Rev 2019; 81:101912. [PMID: 31715423 PMCID: PMC7491975 DOI: 10.1016/j.ctrv.2019.101912] [Citation(s) in RCA: 87] [Impact Index Per Article: 17.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2019] [Revised: 10/22/2019] [Accepted: 10/23/2019] [Indexed: 12/22/2022]
Abstract
Regorafenib is a multi-targeting kinase inhibitor approved for the treatment of metastatic colorectal cancer patients in refractory to standard chemotherapy. Similarly to sorafenib, this agent was originally developed as a RAF1 inhibitor. However, the kinase inhibitory profile is distinct from sorafenib. A broad-spectrum of kinase inhibition induces wide-range drug sensitivity, irrespective of mutation status of major oncogenes. This agent's main therapeutic effects are anti-angiogenesis and the remodeling of tumor microenvironment through several mechanisms of action. The dual blockade of VEGF receptors and TIE2 can lead to both additive anti-angiogenesis effects and the suggestive unique regulation of vessel stability. Additionally, it inhibits molecular escape pathways to VEGF inhibition (e.g., FGF, PIGF, and PDGF signaling), enabling its continuous antiangiogenic effect even in tumors resistant to VEGF inhibitors. Furthermore, regorafenib has the important effect of enhancing anti-tumor immunity via macrophage modulation. Based on this concept, clinical trials have been recently launched for the development of a combination strategy with immune checkpoint inhibitors. Contrary to regorafenib induced clinical benefits and advances in the novel strategy, currently no predictive biomarkers have been identified. In the present review, we revisit and summarize regorafenib's unique mechanisms of action. The review could highlight molecular insights and provide some perspective for the search of predictive biomarkers used in metastatic colorectal cancer patients treated with regorafenib.
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Affiliation(s)
- Hiroyuki Arai
- Division of Medical Oncology, Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, 1441 Eastlate Avenue, Los Angeles, CA 90033, United States
| | - Francesca Battaglin
- Division of Medical Oncology, Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, 1441 Eastlate Avenue, Los Angeles, CA 90033, United States.
| | - Jingyuan Wang
- Division of Medical Oncology, Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, 1441 Eastlate Avenue, Los Angeles, CA 90033, United States.
| | - Jae Ho Lo
- Division of Medical Oncology, Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, 1441 Eastlate Avenue, Los Angeles, CA 90033, United States.
| | - Shivani Soni
- Division of Medical Oncology, Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, 1441 Eastlate Avenue, Los Angeles, CA 90033, United States
| | - Wu Zhang
- Division of Medical Oncology, Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, 1441 Eastlate Avenue, Los Angeles, CA 90033, United States.
| | - Heinz-Josef Lenz
- Division of Medical Oncology, Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, 1441 Eastlate Avenue, Los Angeles, CA 90033, United States.
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22
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Reece M, Saluja H, Hollington P, Karapetis CS, Vatandoust S, Young GP, Symonds EL. The Use of Circulating Tumor DNA to Monitor and Predict Response to Treatment in Colorectal Cancer. Front Genet 2019; 10:1118. [PMID: 31824558 PMCID: PMC6881479 DOI: 10.3389/fgene.2019.01118] [Citation(s) in RCA: 44] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2019] [Accepted: 10/16/2019] [Indexed: 12/20/2022] Open
Abstract
Background: Colorectal cancer is one of the most common cancers worldwide and has a high mortality rate following disease recurrence. Treatment efficacy is maximized by providing tailored cancer treatment, ideally involving surgical resection and personalized neoadjuvant and adjuvant therapies, including chemotherapy, radiotherapy and increasingly, targeted therapy. Early detection of recurrence or disease progression results in more treatable disease and is essential to improving survival outcomes. Recent advances in the understanding of tumor genetics have resulted in the discovery of circulating tumor DNA (ctDNA). A growing body of evidence supports the use of these sensitive biomarkers in detecting residual disease and diagnosing recurrence as well as enabling targeted and tumor-specific adjuvant therapies. Methods: A literature search in Pubmed was performed to identify all original articles preceding April 2019 that utilize ctDNA for the purpose of monitoring response to colorectal cancer treatment. Results: Ninety-two clinical studies were included. These studies demonstrate that ctDNA is a reliable measure of tumor burden. Studies show the utility of ctDNA in assessing the adequacy of surgical tumor clearance and changes in ctDNA levels reflect response to systemic treatments. ctDNA can be used in the selection of targeted treatments. The reappearance or increase in ctDNA, as well as the emergence of new mutations, correlates with disease recurrence, progression, and resistance to therapy, with ctDNA measurement allowing more sensitive monitoring than currently used clinical tools. Conclusions: ctDNA shows enormous promise as a sensitive biomarker for monitoring response to many treatment modalities and for targeting therapy. Thus, it is emerging as a new way for guiding treatment decisions-initiating, altering, and ceasing treatments, or prompting investigation into the potential for residual disease. However, many potentially useful ctDNA markers are available and more work is needed to determine which are best suited for specific purposes and for improving specific outcomes.
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Affiliation(s)
- Mifanwy Reece
- Colorectal Surgery, Division of Surgery & Perioperative Medicine, Flinders Medical Centre, Bedford Park, SA, Australia
| | - Hariti Saluja
- Department of Medicine, College of Medicine and Public Health, Flinders University, Bedford Park, SA, Australia.,Flinders Centre for Innovation in Cancer, College of Medicine and Public Health, Flinders University, Bedford Park, SA, Australia
| | - Paul Hollington
- Colorectal Surgery, Division of Surgery & Perioperative Medicine, Flinders Medical Centre, Bedford Park, SA, Australia
| | - Christos S Karapetis
- Flinders Centre for Innovation in Cancer, College of Medicine and Public Health, Flinders University, Bedford Park, SA, Australia.,Department of Medical Oncology, Flinders Medical Centre, Bedford Park, SA, Australia
| | - Sina Vatandoust
- Department of Medical Oncology, Flinders Medical Centre, Bedford Park, SA, Australia
| | - Graeme P Young
- Flinders Centre for Innovation in Cancer, College of Medicine and Public Health, Flinders University, Bedford Park, SA, Australia
| | - Erin L Symonds
- Flinders Centre for Innovation in Cancer, College of Medicine and Public Health, Flinders University, Bedford Park, SA, Australia.,Bowel Health Service, Flinders Medical Centre, Bedford Park, SA, Australia
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23
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Next-generation sequencing in liquid biopsy: cancer screening and early detection. Hum Genomics 2019; 13:34. [PMID: 31370908 PMCID: PMC6669976 DOI: 10.1186/s40246-019-0220-8] [Citation(s) in RCA: 248] [Impact Index Per Article: 49.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2019] [Accepted: 07/19/2019] [Indexed: 12/19/2022] Open
Abstract
In recent years, the rapid development of next-generation sequencing (NGS) technologies has led to a significant reduction in sequencing cost with improved accuracy. In the area of liquid biopsy, NGS has been applied to sequence circulating tumor DNA (ctDNA). Since ctDNA is the DNA fragments released by tumor cells, it can provide a molecular profile of cancer. Liquid biopsy can be applied to all stages of cancer diagnosis and treatment, allowing non-invasive and real-time monitoring of disease development. The most promising aspects of liquid biopsy in cancer applications are cancer screening and early diagnosis because they can lead to better survival results and less disease burden. Although many ctDNA sequencing methods have enough sensitivity to detect extremely low levels of mutation frequency at the early stage of cancer, how to effectively implement them in population screening settings remains challenging. This paper focuses on the application of liquid biopsy in the early screening and diagnosis of cancer, introduces NGS-related methods, reviews recent progress, summarizes challenges, and discusses future research directions.
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24
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Amatu A, Schirripa M, Tosi F, Lonardi S, Bencardino K, Bonazzina E, Palmeri L, Patanè DA, Pizzutilo EG, Mussolin B, Bergamo F, Alberti G, Intini R, Procaccio L, Arese M, Marsoni S, Nichelatti M, Zagonel V, Siena S, Bardelli A, Loupakis F, Di Nicolantonio F, Sartore-Bianchi A, Barault L. High Circulating Methylated DNA Is a Negative Predictive and Prognostic Marker in Metastatic Colorectal Cancer Patients Treated With Regorafenib. Front Oncol 2019; 9:622. [PMID: 31355139 PMCID: PMC6640154 DOI: 10.3389/fonc.2019.00622] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2018] [Accepted: 06/24/2019] [Indexed: 12/12/2022] Open
Abstract
Background: Regorafenib improves progression free survival (PFS) in a subset of metastatic colorectal cancer (mCRC) patients, although no biomarkers of efficacy are available. Circulating methylated DNA (cmDNA) assessed by a five-gene panel was previously associated with outcome in chemotherapy treated mCRC patients. We hypothesized that cmDNA could be used to identify cases most likely to benefit from regorafenib (i.e., patients with PFS longer than 4 months). Methods: Plasma samples from mCRC patients were collected prior to (baseline samples N = 60) and/or during regorafenib treatment (N = 62) for the assessment of cmDNA and total amount of cell free DNA (cfDNA). Results: In almost all patients, treatment with regorafenib increased the total cfDNA, but decreased cmDNA warranting the normalization of cmDNA to the total amount of circulating DNA (i.e., cmDNA/ml). We report that cmDNA/ml dynamics reflects clinical response with an increase in cmDNA/ml associated with higher risk of progression (HR for progression = 1.78 [95%CI: 1.01-3.13], p = 0.028). Taken individually, high baseline cmDNA/ml (above median) was associated with worst prognosis (HR for death = 3.471 [95%CI: 1.83-6.57], p < 0.0001) and also predicted shorter PFS (<16 weeks with PPV 86%). In addition, high cmDNA/ml values during regorafenib treatment predicted with higher accuracy shorter PFS (<16 weeks with a PPV of 96%), therefore associated with increased risk of progression (HR for progression = 2.985; [95%CI: 1.63-5.46; p < 0.0001). Conclusions: Our data highlight the predictive and prognostic value of cmDNA/ml in mCRC patients treated with regorafenib.
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Affiliation(s)
- Alessio Amatu
- Niguarda Cancer Center, Grande Ospedale Metropolitano Niguarda, Milan, Italy
| | - Marta Schirripa
- Medical Oncology 1, Veneto Institute of Oncology, IRCCS, Padua, Italy
| | - Federica Tosi
- Niguarda Cancer Center, Grande Ospedale Metropolitano Niguarda, Milan, Italy
| | - Sara Lonardi
- Medical Oncology 1, Veneto Institute of Oncology, IRCCS, Padua, Italy
| | - Katia Bencardino
- Niguarda Cancer Center, Grande Ospedale Metropolitano Niguarda, Milan, Italy
| | - Erica Bonazzina
- Niguarda Cancer Center, Grande Ospedale Metropolitano Niguarda, Milan, Italy
| | - Laura Palmeri
- Niguarda Cancer Center, Grande Ospedale Metropolitano Niguarda, Milan, Italy
| | | | | | | | - Francesca Bergamo
- Medical Oncology 1, Veneto Institute of Oncology, IRCCS, Padua, Italy
| | - Giulia Alberti
- Medical Oncology 1, Veneto Institute of Oncology, IRCCS, Padua, Italy.,Department of Surgery, Oncology and Gastroenterology, University of Padua, Padua, Italy
| | - Rossana Intini
- Medical Oncology 1, Veneto Institute of Oncology, IRCCS, Padua, Italy
| | - Letizia Procaccio
- Medical Oncology 1, Veneto Institute of Oncology, IRCCS, Padua, Italy.,Department of Surgery, Oncology and Gastroenterology, University of Padua, Padua, Italy
| | - Marco Arese
- Candiolo Cancer Institute, FPO-IRCCS, Candiolo, Italy.,Department of Oncology, University of Turin, Candiolo, Italy
| | - Silvia Marsoni
- Niguarda Cancer Center, Grande Ospedale Metropolitano Niguarda, Milan, Italy.,Department of Precision Oncology, FIRC Institute of Molecular Oncology (IFOM), Milan, Italy
| | - Michele Nichelatti
- Niguarda Cancer Center, Grande Ospedale Metropolitano Niguarda, Milan, Italy
| | - Vittorina Zagonel
- Medical Oncology 1, Veneto Institute of Oncology, IRCCS, Padua, Italy
| | - Salvatore Siena
- Niguarda Cancer Center, Grande Ospedale Metropolitano Niguarda, Milan, Italy.,Dipartimento di Oncologia ed Emato-Oncologia, Università degli Studi di Milano, Milan, Italy
| | - Alberto Bardelli
- Candiolo Cancer Institute, FPO-IRCCS, Candiolo, Italy.,Department of Oncology, University of Turin, Candiolo, Italy
| | - Fotios Loupakis
- Medical Oncology 1, Veneto Institute of Oncology, IRCCS, Padua, Italy
| | - Federica Di Nicolantonio
- Candiolo Cancer Institute, FPO-IRCCS, Candiolo, Italy.,Department of Oncology, University of Turin, Candiolo, Italy
| | - Andrea Sartore-Bianchi
- Niguarda Cancer Center, Grande Ospedale Metropolitano Niguarda, Milan, Italy.,Dipartimento di Oncologia ed Emato-Oncologia, Università degli Studi di Milano, Milan, Italy
| | - Ludovic Barault
- Candiolo Cancer Institute, FPO-IRCCS, Candiolo, Italy.,Department of Oncology, University of Turin, Candiolo, Italy
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25
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Cervena K, Vodicka P, Vymetalkova V. Diagnostic and prognostic impact of cell-free DNA in human cancers: Systematic review. MUTATION RESEARCH-REVIEWS IN MUTATION RESEARCH 2019; 781:100-129. [DOI: 10.1016/j.mrrev.2019.05.002] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/15/2019] [Revised: 05/03/2019] [Accepted: 05/07/2019] [Indexed: 02/06/2023]
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26
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McCoach CE, Bivona TG. Engineering Multidimensional Evolutionary Forces to Combat Cancer. Cancer Discov 2019; 9:587-604. [PMID: 30992280 PMCID: PMC6497542 DOI: 10.1158/2159-8290.cd-18-1196] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2018] [Revised: 12/28/2018] [Accepted: 01/29/2019] [Indexed: 02/07/2023]
Abstract
With advances in technology and bioinformatics, we are now positioned to view and manage cancer through an evolutionary lens. This perspective is critical as our appreciation for the role of tumor heterogeneity, tumor immune compartment, and tumor microenvironment on cancer pathogenesis and evolution grows. Here, we explore recent knowledge on the evolutionary basis of cancer pathogenesis and progression, viewing tumors as multilineage, multicomponent organisms whose growth is regulated by subcomponent fitness relationships. We propose reconsidering some current tenets of the cancer management paradigm in order to take better advantage of crucial fitness relationships to improve outcomes of patients with cancer. SIGNIFICANCE: Tumor and tumor immune compartment and microenvironment heterogeneity, and their evolution, are critical disease features that affect treatment response. The impact and interplay of these components during treatment are viable targets to improve clinical response. In this article, we consider how tumor cells, the tumor immune compartment and microenvironment, and epigenetic factors interact and also evolve during treatment. We evaluate the convergence of these factors and suggest innovative treatment concepts that leverage evolutionary relationships to limit tumor growth and drug resistance.
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Affiliation(s)
- Caroline E McCoach
- Department of Medicine, University of California, San Francisco, California.
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, California
| | - Trever G Bivona
- Department of Medicine, University of California, San Francisco, California.
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, California
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, California
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27
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Circulating tumor DNA applications in monitoring the treatment of metastatic colorectal cancer patients. GASTROENTEROLOGY AND HEPATOLOGY FROM BED TO BENCH 2019. [PMCID: PMC7009314] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Colorectal cancer is the third most common cancer worldwide. New cancer treatment strategies such as monoclonal antibodies against growth factor and angiogenesis receptors have improved the overall survival (OS) and progression-free survival (PFS) in metastatic colorectal cancer (mCRC) patients. However, acquired resistance could happen after these therapies. Circulating tumor DNA (ctDNA) is the DNA fraction derived from tumor cells which could be applied as a non-invasive method for detecting tumor mutations before, during, and after therapies. Here, we reviewed most of the studies examining ctDNA as treatment monitoring in mCRC patients who receive different target therapies. Also, we compared ctDNA with other existing cancer-treatment monitoring methods.
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28
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Vymetalkova V, Cervena K, Bartu L, Vodicka P. Circulating Cell-Free DNA and Colorectal Cancer: A Systematic Review. Int J Mol Sci 2018; 19:ijms19113356. [PMID: 30373199 PMCID: PMC6274807 DOI: 10.3390/ijms19113356] [Citation(s) in RCA: 70] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2018] [Revised: 10/22/2018] [Accepted: 10/24/2018] [Indexed: 02/06/2023] Open
Abstract
There is a strong demand for the identification of new biomarkers in colorectal cancer (CRC) diagnosis. Among all liquid biopsy analysts, cell-free circulating DNA (cfDNA) is probably the most promising tool with respect to the identification of minimal residual diseases, assessment of treatment response and prognosis, and identification of resistance mechanisms. Circulating cell-free tumor DNA (ctDNA) maintains the same genomic signatures that are present in the matching tumor tissue allowing for the quantitative and qualitative evaluation of mutation burdens in body fluids. Thus, ctDNA-based research represents a non-invasive method for cancer detection. Among the numerous possible applications, the diagnostic, predictive, and/or prognostic utility of ctDNA in CRC has attracted intense research during the last few years. In the present review, we will describe the different aspects related to cfDNA research and evidence from studies supporting its potential use in CRC diagnoses and the improvement of therapy efficacy. We believe that ctDNA-based research should be considered as key towards the introduction of personalized medicine and patient benefits.
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Affiliation(s)
- Veronika Vymetalkova
- Institute of Experimental Medicine of the Czech Academy of Sciences, Videnska 1083, 142 00 Prague, Czech Republic.
- Institute of Biology and Medical Genetics, 1st Medical Faculty, Charles University, Albertov 4, 128 00 Prague, Czech Republic.
- Biomedical Centre, Faculty of Medicine in Pilsen, Charles University in Prague, 323 00 Pilsen, Czech Republic.
| | - Klara Cervena
- Institute of Experimental Medicine of the Czech Academy of Sciences, Videnska 1083, 142 00 Prague, Czech Republic.
- Institute of Biology and Medical Genetics, 1st Medical Faculty, Charles University, Albertov 4, 128 00 Prague, Czech Republic.
| | - Linda Bartu
- Institute of Experimental Medicine of the Czech Academy of Sciences, Videnska 1083, 142 00 Prague, Czech Republic.
- Institute of Biology and Medical Genetics, 1st Medical Faculty, Charles University, Albertov 4, 128 00 Prague, Czech Republic.
| | - Pavel Vodicka
- Institute of Experimental Medicine of the Czech Academy of Sciences, Videnska 1083, 142 00 Prague, Czech Republic.
- Institute of Biology and Medical Genetics, 1st Medical Faculty, Charles University, Albertov 4, 128 00 Prague, Czech Republic.
- Biomedical Centre, Faculty of Medicine in Pilsen, Charles University in Prague, 323 00 Pilsen, Czech Republic.
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