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De Wilde J, Van Paemel R, De Koker A, Roelandt S, Van de Velde S, Callewaert N, Van Dorpe J, Creytens D, De Wilde B, De Preter K. A Fast, Affordable, and Minimally Invasive Diagnostic Test for Cancer of Unknown Primary Using DNA Methylation Profiling. J Transl Med 2024; 104:102091. [PMID: 38830578 DOI: 10.1016/j.labinv.2024.102091] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2023] [Revised: 05/16/2024] [Accepted: 05/25/2024] [Indexed: 06/05/2024] Open
Abstract
Currently, we cannot provide a conclusive diagnosis for 3% to 5% of people who are confronted with cancer. These patients have cancer of unknown primary (CUP), ie, a metastasized cancer for which the tissue of origin cannot be determined. Studies have shown that the DNA methylation profile is a unique "fingerprint" that can be used to classify tumors. Here we used cell-free reduced representation bisulfite sequencing (cfRRBS), a technique that allows us to identify the methylation profile starting from minimal amounts of highly fragmented DNA, for CUP diagnosis on formalin-fixed paraffin-embedded (FFPE) tissue and liquid biopsies. We collected 80 primary tumor FFPE samples covering 16 tumor entities together with 15 healthy plasma samples to use as a custom cfRRBS reference data set. Entity-specific methylation regions are defined for each entity to build a classifier based on nonnegative least squares deconvolution. This classification framework was tested on 30 FFPE, 19 plasma, and 40 pleural and peritoneal effusion samples of both known metastatic tumors and clinical CUPs for which pathological investigation finally resulted in a cancer diagnosis. Using this framework, 27 of 30 FFPE (all CUPs) and 16 of 19 plasma samples (10/13 CUPs) obtained an accurate diagnosis, with a minimal DNA input of 400 pg. Diagnosis of the 40 pleural and peritoneal effusion samples is possible in 9 of 27 samples with negative/inconclusive cytology (6/13 CUPs), showing that cell-free DNA (cfDNA) methylation profiling could complement routine cytologic analysis. However, a low "cfDNA - high-molecular weight DNA ratio" has a considerable impact on the prediction accuracy. Moreover, the accuracy improves significantly if the predicted tumor percentage is >7%. This proof-of-concept study shows the feasibility of using DNA methylation profiling on FFPE and liquid biopsy samples such as blood, ascites, and pleural effusions in a fast and affordable way. Our novel RRBS-based technique requires minimal DNA input, can be performed in <1 week, and is highly adaptable to specific diagnostic problems as we only use 5 FFPE references per tumor entity. We believe that cfRRBS methylation profiling could be a valuable addition to the pathologist's toolbox in the diagnosis of CUPs.
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Affiliation(s)
- Jilke De Wilde
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium; Department of Pathology, Ghent University Hospital, Ghent, Belgium; Cancer Research Institute Ghent (CRIG), Ghent, Belgium
| | - Ruben Van Paemel
- Cancer Research Institute Ghent (CRIG), Ghent, Belgium; Department of Internal Medicine and Pediatrics, Ghent University, Ghent, Belgium
| | - Andries De Koker
- Cancer Research Institute Ghent (CRIG), Ghent, Belgium; Center for Medical Biotechnology, VIB-UGent, Ghent, Belgium; Department of Biochemistry and Microbiology, Ghent University, Belgium
| | - Sofie Roelandt
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium; Cancer Research Institute Ghent (CRIG), Ghent, Belgium; Center for Medical Biotechnology, VIB-UGent, Ghent, Belgium
| | - Sofie Van de Velde
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium; Cancer Research Institute Ghent (CRIG), Ghent, Belgium; Center for Medical Biotechnology, VIB-UGent, Ghent, Belgium
| | - Nico Callewaert
- Cancer Research Institute Ghent (CRIG), Ghent, Belgium; Center for Medical Biotechnology, VIB-UGent, Ghent, Belgium; Department of Biochemistry and Microbiology, Ghent University, Belgium
| | - Jo Van Dorpe
- Department of Pathology, Ghent University Hospital, Ghent, Belgium; Cancer Research Institute Ghent (CRIG), Ghent, Belgium
| | - David Creytens
- Department of Pathology, Ghent University Hospital, Ghent, Belgium; Cancer Research Institute Ghent (CRIG), Ghent, Belgium
| | - Bram De Wilde
- Cancer Research Institute Ghent (CRIG), Ghent, Belgium; Department of Internal Medicine and Pediatrics, Ghent University, Ghent, Belgium
| | - Katleen De Preter
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium; Cancer Research Institute Ghent (CRIG), Ghent, Belgium; Center for Medical Biotechnology, VIB-UGent, Ghent, Belgium.
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2
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Trevisi E, Sessa C, Colombo I. Clinical relevance of circulating tumor DNA in ovarian cancer: current issues and future opportunities. EXPLORATION OF TARGETED ANTI-TUMOR THERAPY 2024; 5:627-640. [PMID: 38966171 PMCID: PMC11220313 DOI: 10.37349/etat.2024.00239] [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: 02/18/2024] [Accepted: 03/13/2024] [Indexed: 07/06/2024] Open
Abstract
Ovarian cancer (OC) is the most lethal gynecologic malignancy worldwide. Due to the lack of effective screening and early detection strategies, many patients with OC are diagnosed with advanced disease, where treatment is rarely curative. Moreover, OC is characterized by high intratumor heterogeneity, which represents a major barrier to the development of effective treatments. Conventional tumor biopsy and blood-based biomarkers, such as cancer antigen 125 (CA125), have different limitations. Liquid biopsy has recently emerged as an attractive and promising area of investigation in oncology, due to its minimally invasive, safe, comprehensive, and real-time dynamic nature. Preliminary evidence suggests a potential role of liquid biopsy to refine OC management, by improving screening, early diagnosis, assessment of response to treatment, detection, and profiling of drug resistance. The current knowledge and the potential clinical value of liquid biopsy in OC is discussed in this review to provide an overview of the clinical settings in which its use might support and improve diagnosis and treatment.
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Affiliation(s)
- Elena Trevisi
- Oncology Institute of Southern Switzerland (IOSI), Ente Ospedaliero Cantonale (EOC), 6500 Bellinzona, Switzerland
| | - Cristiana Sessa
- Oncology Institute of Southern Switzerland (IOSI), Ente Ospedaliero Cantonale (EOC), 6500 Bellinzona, Switzerland
| | - Ilaria Colombo
- Oncology Institute of Southern Switzerland (IOSI), Ente Ospedaliero Cantonale (EOC), 6500 Bellinzona, Switzerland
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Werner B, Sjoquist KM, Espinoza D, Yip S, Chang G, Cummins MM, Mileshkin L, Ananda S, Shannon C, Friedlander M, Warton K, Ford CE. Cell-free DNA in plasma and ascites as a biomarker of bevacizumab response- a translational research sub-study of the REZOLVE (ANZGOG-1101) clinical trial. Transl Oncol 2024; 43:101914. [PMID: 38417292 DOI: 10.1016/j.tranon.2024.101914] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2023] [Revised: 11/30/2023] [Accepted: 02/13/2024] [Indexed: 03/01/2024] Open
Abstract
OBJECTIVE To investigate cell-free DNA (cfDNA) in plasma and ascites and its association with clinical outcomes (paracentesis-free interval, overall survival) and CA125 level in participants with advanced ovarian cancer, treated with palliative intraperitoneal bevacizumab to delay re-accumulation of ascites. METHODS cfDNA was extracted from 0.3 to 1 mL samples from 20/24 participants of the REZOLVE trial. Standard and methylation-specific PCRs were performed to measure 3 biomarkers: total cfDNA (Alu), tumour-derived cfDNA (ctDNA, methylated IFFO1 promoter) and endothelium-derived cfDNA (ec-cfDNA, unmethylated CDH5 promoter). Values were correlated to clinical outcomes. RESULTS cfDNA was detected in all samples, with higher yield in ascites (mean 669 ng/mL) than plasma (mean 75 ng/mL, p < 0.0001). Ascites had a higher ctDNA proportion than plasma (74 % vs. 20 %, p < 0.0001) and plasma had a higher ec-cfDNA proportion than ascites (24 % vs. 16 %, p < 0.002). High ctDNA proportion (>75 %) in ascites was associated with a significantly shorter paracentesis-free interval (median interval 47.5 versus 84 days, hazard ratio (HR) 2.21, 95 % confidence interval (CI) 0.85 to 5.73, p = 0.039) and ctDNA presence in plasma was unfavourable for survival (median survival 56 versus 242 days, HR 3.21, 95 % CI 1.15 to 9.00, p = 0.008). A significant positive correlation was observed between ctDNA proportion in plasma and CA125 level (p = 0.012). No significant difference in total cfDNA, ctDNA nor ec-cfDNA was observed between participants who were responders versus non-responders. CONCLUSION Sufficient cfDNA was detected in both plasma and ascites to study three biomarkers. These samples can provide useful information and should be considered in the design of future ovarian cancer trials.
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Affiliation(s)
- Bonnita Werner
- Gynaecological Cancer Research Group, School of Clinical Medicine, Faculty of Medicine and Health, University of New South Wales, Sydney, Australia
| | - Katrin M Sjoquist
- National Health and Medical Research Council Clinical Trials Centre, University of Sydney, Sydney, Australia
| | - David Espinoza
- National Health and Medical Research Council Clinical Trials Centre, University of Sydney, Sydney, Australia
| | - Sonia Yip
- National Health and Medical Research Council Clinical Trials Centre, University of Sydney, Sydney, Australia
| | - Garry Chang
- National Health and Medical Research Council Clinical Trials Centre, University of Sydney, Sydney, Australia
| | - Michelle M Cummins
- National Health and Medical Research Council Clinical Trials Centre, University of Sydney, Sydney, Australia
| | | | - Sumitra Ananda
- Peter MacCallum Cancer Centre, Melbourne, Australia; Western Health, Furlong Road, St Albans, Australia; Epworth Freemasons Hospital, East Melbourne, Australia; Department of Medicine, Western Health, University of Melbourne, Melbourne, Australia
| | | | - Michael Friedlander
- Prince of Wales Hospital, Sydney, Australia; School of Clinical Medicine, Faculty of Medicine and Health, University of New South Wales, Sydney, Australia
| | - Kristina Warton
- Gynaecological Cancer Research Group, School of Clinical Medicine, Faculty of Medicine and Health, University of New South Wales, Sydney, Australia
| | - Caroline E Ford
- Gynaecological Cancer Research Group, School of Clinical Medicine, Faculty of Medicine and Health, University of New South Wales, Sydney, Australia.
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4
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Zebic DS, Tjokrowidjaja A, Francis KE, Friedlander M, Gebski V, Lortholary A, Joly F, Hasenburg A, Mirza M, Denison U, Cecere SC, Ferrero A, Pujade-Lauraine E, Lee CK. Discordance between GCIG CA-125 progression and RECIST progression in the CALYPSO trial of patients with platinum-sensitive recurrent ovarian cancer. Br J Cancer 2024; 130:425-433. [PMID: 38097739 PMCID: PMC10844635 DOI: 10.1038/s41416-023-02528-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2023] [Revised: 11/10/2023] [Accepted: 11/27/2023] [Indexed: 02/07/2024] Open
Abstract
BACKGROUND CA-125 alone is widely used to diagnose progressive disease (PD) in platinum-sensitive recurrent ovarian cancer (PSROC) on chemotherapy. However, there are increasing concerns regarding its accuracy. We assessed concordance between progression defined by CA-125 and RECIST using data from the CALYPSO trial. METHODS We computed concordance rates for PD by CA-125 and RECIST to determine the positive (PPV) and negative predictive values (NPV). RESULTS Of 769 (79%) evaluable participants, 387 had CA-125 PD, where only 276 had concordant RECIST PD (PPV 71%, 95% CI 67-76%). For 382 without CA-125 PD, 255 had RECIST PD but 127 did not (NPV 33%, 95% CI 29-38). There were significant differences in NPV according to baseline CA-125 (≤100 vs >100: 42% vs 25%, P < 0.001); non-measurable vs measurable disease (51% vs 26%, P < 0.001); and platinum-free-interval (>12 vs 6-12 months: 41% vs 14%, P < 0.001). We observed falling CA-125 levels in 78% of patients with RECIST PD and CA-125 non-PD. CONCLUSION Approximately 2 in 3 women with PSROC have RECIST PD but not CA-125 PD by GCIG criteria. Monitoring CA-125 levels alone is not reliable for detecting PD. Further research is required to investigate the survival impact of local therapy in radiological detected early asymptomatic PD.
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Affiliation(s)
- Danka Sinikovic Zebic
- National Health and Medical Research Council Clinical Trials Centre, The University of Sydney, Sydney, NSW, 2050, Australia.
- Department of Medical Oncology, St George Hospital, Kogarah, NSW, 2217, Australia.
| | - Angelina Tjokrowidjaja
- National Health and Medical Research Council Clinical Trials Centre, The University of Sydney, Sydney, NSW, 2050, Australia
- Department of Medical Oncology, St George Hospital, Kogarah, NSW, 2217, Australia
| | - Katherine Elizabeth Francis
- National Health and Medical Research Council Clinical Trials Centre, The University of Sydney, Sydney, NSW, 2050, Australia
- Department of Medical Oncology, South East Regional Hospital, Bega, NSW, 2550, Australia
| | - Michael Friedlander
- Department of Medical Oncology, Prince of Wales Hospital, Randwick, NSW, 2031, Australia
| | - Val Gebski
- National Health and Medical Research Council Clinical Trials Centre, The University of Sydney, Sydney, NSW, 2050, Australia
| | | | - Florence Joly
- Centre François Baclesse, Caen and GINECO, Caen, France
| | - Annette Hasenburg
- Department of Gynecology and Obstetrics, University Medical Center, Mainz and AGO, Mainz, Germany
| | - Mansoor Mirza
- Rigshospitalet-Copenhagen University Hospital, Copenhagen and NSGO, Copenhagen, Denmark
| | - Ursula Denison
- Institute for gynaecological oncology und senology - Karl Landsteiner, Vienna and AGO Austria, Vienna, Austria
| | - Sabrina Chiara Cecere
- Oncologia Clinica Sperimentale Uro-Ginecologica, Istituto Nazionale Tumori - IRCCS- Fondazione G.Pascale, Napoli and MITO Italia, Napoli, Italy
| | - Annamaria Ferrero
- Academic Division Gynaecology, Mauriziano Hospital, University of Torino, and MaNGO, Torino, Italy
| | | | - Chee Khoon Lee
- National Health and Medical Research Council Clinical Trials Centre, The University of Sydney, Sydney, NSW, 2050, Australia
- Department of Medical Oncology, St George Hospital, Kogarah, NSW, 2217, Australia
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5
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Gressel GM, Frey MK, Norquist B, Senter L, Blank SV, Urban RR. Germline and somatic testing for ovarian Cancer: An SGO clinical practice statement. Gynecol Oncol 2024; 181:170-178. [PMID: 38215513 DOI: 10.1016/j.ygyno.2023.12.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2023] [Revised: 12/09/2023] [Accepted: 12/13/2023] [Indexed: 01/14/2024]
Abstract
Germline and somatic genetic testing have become critical components of care for people with ovarian cancer. The identification of germline and somatic pathogenic variants as well as homologous recombination deficiency can contribute to the prediction of treatment response, prognostic outcome, and suitability for targeted agents (e.g. poly (ADP-ribose) polymerase (PARP) inhibitors). Furthermore, identifying germline pathogenic variants can prompt cascade genetic testing for at-risk relatives. Despite the clinical benefits and consensus recommendations from several organizations calling for universal genetic testing in ovarian cancer, only about one third of patients complete germline or somatic genetic testing. The members of the Society of Gynecologic Oncology (SGO) Clinical Practice Committee have composed this statement to provide an overview of germline and somatic genetic testing for patients with epithelial ovarian cancer, focusing on available testing modalities and options for care delivery.
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Affiliation(s)
- G M Gressel
- Corewell Health Cancer Center, Division of Gynecologic Oncology, Michigan State University- College of Human Medicine, United States.
| | - M K Frey
- Weill Cornell Medicine, Division of Gynecologic Oncology, United States
| | - B Norquist
- University of Washington School of Medicine, Division of Gynecologic Oncology, United States
| | - L Senter
- The Ohio State University, Comprehensive Cancer Center,United States
| | - S V Blank
- Icahn School of Medicine at Mount Sinai, United States
| | - R R Urban
- University of Washington School of Medicine, Division of Gynecologic Oncology, United States
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6
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Gao Y, Zhou N, Liu J. Ovarian Cancer Diagnosis and Prognosis Based on Cell-Free DNA Methylation. Cancer Control 2024; 31:10732748241255548. [PMID: 38764160 PMCID: PMC11104031 DOI: 10.1177/10732748241255548] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2024] [Revised: 04/12/2024] [Accepted: 04/30/2024] [Indexed: 05/21/2024] Open
Abstract
Background: Ovarian cancer stands as the deadliest malignant tumor within the female reproductive tract. As a result of the absence of effective diagnostic and monitoring markers, 75% of ovarian cancer cases are diagnosed at a late stage, leading to a mere 50% survival rate within five years. The advancement of molecular biology is essential for accurate diagnosis and treatment of ovarian cancer. Methods: A review of several randomized clinical trials, focusing on the ovarian cancer, was undertaken. The advancement of molecular biology and diagnostic methods related to accurate diagnosis and treatment of ovarian cancer were examined. Results: Liquid biopsy is an innovative method of detecting malignant tumors that has gained increasing attention over the past few years. Cell-free DNA assay-based liquid biopsies show potential in delineating tumor status heterogeneity and tracking tumor recurrence. DNA methylation influences a multitude of biological functions and diseases, especially during the initial phases of cancer. The cell-free DNA methylation profiling system has emerged as a sensitive and non-invasive technique for identifying and detecting the biological origins of cancer. It holds promise as a biomarker, enabling early screening, recurrence monitoring, and prognostic evaluation of cancer. Conclusions: This review evaluates recent advancements and challenges associated with cell-free DNA methylation analysis for the diagnosis, prognosis monitoring, and assessment of therapeutic responses in the management of ovarian cancers, aiming to offer guidance for precise diagnosis and treatment of this disease.
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Affiliation(s)
- Yajuan Gao
- Department of Gynecology and Obstetrics, Hangzhou Women’s Hospital (Hangzhou Maternity and Child Health Care Hospital), Hangzhou, China
| | - Nanyang Zhou
- Department of Traditional Chinese Medicine, Hangzhou Women’s Hospital (Hangzhou Maternity and Child Health Care Hospital), Hangzhou, China
| | - Jie Liu
- Department of Gynecology and Obstetrics, Hangzhou Women’s Hospital (Hangzhou Maternity and Child Health Care Hospital), Hangzhou, China
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7
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Roussel-Simonin C, Blanc-Durand F, Tang R, Vasseur D, Le Formal A, Chardin L, Yaniz E, Gouy S, Maulard A, Scherier S, Sanson C, Lacroix L, Cotteret S, Mauny L, Zaccarini F, Rouleau E, Leary A. Homologous recombination deficiency (HRD) testing on cell-free tumor DNA from peritoneal fluid. Mol Cancer 2023; 22:178. [PMID: 37932736 PMCID: PMC10626673 DOI: 10.1186/s12943-023-01864-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2023] [Accepted: 09/19/2023] [Indexed: 11/08/2023] Open
Abstract
BACKGROUND Knowing the homologous recombination deficiency (HRD) status in advanced epithelial ovarian cancer (EOC) is vital for patient management. HRD is determined by BRCA1/BRCA2 pathogenic variants or genomic instability. However, tumor DNA analysis is inconclusive in 15-19% of cases. Peritoneal fluid, available in > 95% of advanced EOC cases, could serve as an alternative source of cell-free tumor DNA (cftDNA) for HRD testing. Limited data show the feasibility of cancer panel gene testing on ascites cfDNA but no study, to date, has investigated HRD testing. METHODS We collected ascites/peritoneal washings from 53 EOC patients (19 from retrospective cohort and 34 from prospective cohort) and performed a Cancer Gene Panel (CGP) using NGS for TP53/HR genes and shallow Whole Genome Sequencing (sWGS) for genomic instability on cfDNA. RESULTS cfDNA was detectable in 49 out of 53 patients (92.5%), including those with limited peritoneal fluid. Median cfDNA was 3700 ng/ml, with a turnaround time of 21 days. TP53 pathogenic variants were detected in 86% (42/49) of patients, all with HGSOC. BRCA1 and BRCA2 pathogenic variants were found in 14% (7/49) and 10% (5/49) of cases, respectively. Peritoneal cftDNA showed high sensitivity (97%), specificity (83%), and concordance (95%) with tumor-based TP53 variant detection. NGS CGP on cftDNA identified BRCA2 pathogenic variants in one case where tumor-based testing failed. sWGS on cftDNA provided informative results even when tumor-based genomic instability testing failed. CONCLUSION Profiling cftDNA from peritoneal fluid is feasible, providing a significant amount of tumor DNA. This fast and reliable approach enables HRD testing, including BRCA1/2 mutations and genomic instability assessment. HRD testing on cfDNA from peritoneal fluid should be offered to all primary laparoscopy patients.
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Affiliation(s)
- Cyril Roussel-Simonin
- Drug Development Department (DITEP), Gustave-Roussy Cancer Campus, Villejuif. Sorbonne Université, Paris, France.
| | - Felix Blanc-Durand
- Departement of Medecine, Gustave-Roussy Cancer Campus, INSERM U981, Université Paris-Saclay, Villejuif, France
- Université Paris-Saclay, Gustave-Roussy Cancer Campus, Inserm U981, Villejuif, France
| | - Roseline Tang
- Cancer Genetics Laboratory, Medical Biology and Pathology Department, Gustave-Roussy Cancer Campus, Villejuif, France
| | - Damien Vasseur
- Cancer Genetics Laboratory, Medical Biology and Pathology Department, Gustave-Roussy Cancer Campus, Villejuif, France
| | - Audrey Le Formal
- Université Paris-Saclay, Gustave-Roussy Cancer Campus, Inserm U981, Villejuif, France
| | - Laure Chardin
- Université Paris-Saclay, Gustave-Roussy Cancer Campus, Inserm U981, Villejuif, France
| | - Elisa Yaniz
- Université Paris-Saclay, Gustave-Roussy Cancer Campus, Inserm U981, Villejuif, France
| | - Sébastien Gouy
- Department of Pathology and Medical Biology, Gustave-Roussy Cancer Campus, Villejuif, France
| | - Amandine Maulard
- Department of Pathology and Medical Biology, Gustave-Roussy Cancer Campus, Villejuif, France
| | - Stéphanie Scherier
- Department of Pathology and Medical Biology, Gustave-Roussy Cancer Campus, Villejuif, France
| | - Claire Sanson
- Department of Pathology and Medical Biology, Gustave-Roussy Cancer Campus, Villejuif, France
| | - Ludovic Lacroix
- Department of Gynecologic Surgery, Gustave-Roussy Cancer Campus, Villejuif, France
| | - Sophie Cotteret
- Cancer Genetics Laboratory, Medical Biology and Pathology Department, Gustave-Roussy Cancer Campus, Villejuif, France
| | - Lea Mauny
- Department of Pathology and Medical Biology, Gustave-Roussy Cancer Campus, Villejuif, France
| | - François Zaccarini
- Department of Pathology and Medical Biology, Gustave-Roussy Cancer Campus, Villejuif, France
| | - Etienne Rouleau
- Université Paris-Saclay, Gustave-Roussy Cancer Campus, Inserm U981, Villejuif, France
- Cancer Genetics Laboratory, Medical Biology and Pathology Department, Gustave-Roussy Cancer Campus, Villejuif, France
| | - Alexandra Leary
- Departement of Medecine, Gustave-Roussy Cancer Campus, INSERM U981, Université Paris-Saclay, Villejuif, France
- Université Paris-Saclay, Gustave-Roussy Cancer Campus, Inserm U981, Villejuif, France
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8
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Allan Z, Witts S, Tie J, Tebbutt N, Clemons NJ, Liu DS. The prognostic impact of peritoneal tumour DNA in gastrointestinal and gynaecological malignancies: a systematic review. Br J Cancer 2023; 129:1717-1726. [PMID: 37700064 PMCID: PMC10667497 DOI: 10.1038/s41416-023-02424-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2023] [Revised: 08/23/2023] [Accepted: 08/31/2023] [Indexed: 09/14/2023] Open
Abstract
Peritoneal metastases from various abdominal cancer types are common and carry poor prognosis. The presence of peritoneal disease upstages cancer diagnosis and alters disease trajectory and treatment pathway in many cancer types. Therefore, accurate and timely detection of peritoneal disease is crucial. The current practice of diagnostic laparoscopy and peritoneal lavage cytology (PLC) in detecting peritoneal disease has variable sensitivity. The significant proportion of peritoneal recurrence seen during follow-up in patients where initial PLC was negative indicates the ongoing need for a better diagnostic tool for detecting clinically occult peritoneal disease, especially peritoneal micro-metastases. Advancement in liquid biopsy has allowed the development and use of peritoneal tumour DNA (ptDNA) as a cancer-specific biomarker within the peritoneum, and the presence of ptDNA may be a surrogate marker for early peritoneal metastases. A growing body of literature on ptDNA in different cancer types portends promising results. Here, we conduct a systematic review to evaluate the prognostic impact of ptDNA in various cancer types and discuss its potential future clinical applications, with a focus on gastrointestinal and gynaecological malignancies.
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Affiliation(s)
- Zexi Allan
- Division of Cancer Research, Peter MacCallum Cancer Centre, 305 Grattan Street, Parkville, VIC, 3000, Australia.
- Sir Peter MacCallum Department of Oncology, University of Melbourne, Grattan Street, Parkville, VIC, 3000, Australia.
| | - Sasha Witts
- Division of Cancer Research, Peter MacCallum Cancer Centre, 305 Grattan Street, Parkville, VIC, 3000, Australia
| | - Jeanne Tie
- Sir Peter MacCallum Department of Oncology, University of Melbourne, Grattan Street, Parkville, VIC, 3000, Australia
- Department of Medical Oncology, Peter MacCallum Cancer Centre, 305 Grattan Street, Parkville, VIC, 3000, Australia
- The Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, VIC, 3052, Australia
| | - Niall Tebbutt
- Department of Surgery, University of Melbourne, Grattan Street, Parkville, VIC, 3000, Australia
- Department of Medical Oncology, Austin Health, 145 Studley Road, Heidelberg, VIC, 3084, Australia
| | - Nicholas J Clemons
- Division of Cancer Research, Peter MacCallum Cancer Centre, 305 Grattan Street, Parkville, VIC, 3000, Australia
- Sir Peter MacCallum Department of Oncology, University of Melbourne, Grattan Street, Parkville, VIC, 3000, Australia
| | - David S Liu
- Sir Peter MacCallum Department of Oncology, University of Melbourne, Grattan Street, Parkville, VIC, 3000, Australia
- Division of Cancer Surgery, Peter MacCallum Cancer Centre, 305 Grattan Street, Parkville, VIC, 3000, Australia
- Upper Gastrointestinal Surgery Unit, Division of Surgery, Anaesthesia, and Procedural Medicine, Austin Health, 145 Studley Road, Heidelberg, VIC, 3084, Australia
- General and Gastrointestinal Surgery Research and Trials Group, The University of Melbourne Department of Surgery, Austin Health, 145 Studley Road, Heidelberg, VIC, 3084, Australia
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9
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Zhang Y, Qiu JG, Jia XY, Ke Y, Zhang MK, Stieg D, Liu WJ, Liu LZ, Wang L, Jiang BH. METTL3-mediated N6-methyladenosine modification and HDAC5/YY1 promote IFFO1 downregulation in tumor development and chemo-resistance. Cancer Lett 2023; 553:215971. [PMID: 36257380 DOI: 10.1016/j.canlet.2022.215971] [Citation(s) in RCA: 15] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2022] [Revised: 09/28/2022] [Accepted: 10/12/2022] [Indexed: 11/16/2022]
Abstract
Ovarian cancer (OC) is a malignant tumor that seriously threatens women's health. Due to the difficulty of early diagnosis, most patients exhibit advanced disease or peritoneal metastasis at diagnosis. We discovered that IFFO1 is a novel tumor suppressor, but its role in tumorigenesis, development and chemoresistance is unknown. In this study, IFFO1 levels were downregulated across cancers, leading to the acceleration of tumor development, metastasis and/or cisplatin resistance. Overexpression of IFFO1 inhibited the translocation of β-catenin to the nucleus and decreased tumor metastasis and cisplatin resistance. Furthermore, we demonstrated that IFFO1 was regulated at both the transcriptional and posttranscriptional levels. At the transcriptional level, the recruitment of HDAC5 inhibited IFFO1 expression, which is mediated by the transcription factor YY1, and the METTL3/YTHDF2 axis regulated the mRNA stability of IFFO1 in an m6A-dependent manner. Mice injected with IFFO1-overexpressing cells had lower ascites volumes and tumor weights throughout the peritoneal cavity than those injected with parental cells expressing the vector control. In conclusion, we demonstrated that IFFO1 is a novel tumor suppressor that inhibits tumor metastasis and reverses drug resistance in ovarian cancer. IFFO1 was downregulated at both the transcriptional level and posttranscriptional level by histone deacetylase and RNA methylation, respectively, and the IFFO1 signaling pathway was identified as a potential therapeutic target for cancer.
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Affiliation(s)
- Ye Zhang
- Academy of Medical Science, School of Basic Medical Science, The Affiliated Cancer Hospital of Zhengzhou University & Henan Cancer Hospital, Zhengzhou University, Zhengzhou, 450008, China
| | - Jian-Ge Qiu
- Academy of Medical Science, School of Basic Medical Science, The Affiliated Cancer Hospital of Zhengzhou University & Henan Cancer Hospital, Zhengzhou University, Zhengzhou, 450008, China
| | - Xiao-Yu Jia
- Academy of Medical Science, School of Basic Medical Science, The Affiliated Cancer Hospital of Zhengzhou University & Henan Cancer Hospital, Zhengzhou University, Zhengzhou, 450008, China
| | - Yu Ke
- School of Pharmaceutical Sciences, Zhengzhou University, Zhengzhou, 450001, China
| | - Ming-Kun Zhang
- School of Pharmaceutical Sciences, Zhengzhou University, Zhengzhou, 450001, China
| | - David Stieg
- Department of Medical Oncology, Sidney Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, PA, 19107, USA
| | - Wen-Jing Liu
- Academy of Medical Science, School of Basic Medical Science, The Affiliated Cancer Hospital of Zhengzhou University & Henan Cancer Hospital, Zhengzhou University, Zhengzhou, 450008, China; Department of Pathology, Anatomy & Cell Biology, Sidney Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, PA, 19107, USA
| | - Ling-Zhi Liu
- Department of Medical Oncology, Sidney Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, PA, 19107, USA
| | - Lin Wang
- Academy of Medical Science, School of Basic Medical Science, The Affiliated Cancer Hospital of Zhengzhou University & Henan Cancer Hospital, Zhengzhou University, Zhengzhou, 450008, China.
| | - Bing-Hua Jiang
- Academy of Medical Science, School of Basic Medical Science, The Affiliated Cancer Hospital of Zhengzhou University & Henan Cancer Hospital, Zhengzhou University, Zhengzhou, 450008, China.
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10
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Keup C, Kimmig R, Kasimir-Bauer S. Combinatorial Power of cfDNA, CTCs and EVs in Oncology. Diagnostics (Basel) 2022; 12:870. [PMID: 35453918 PMCID: PMC9031112 DOI: 10.3390/diagnostics12040870] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2022] [Revised: 03/18/2022] [Accepted: 03/28/2022] [Indexed: 01/01/2023] Open
Abstract
Liquid biopsy is a promising technique for clinical management of oncological patients. The diversity of analytes circulating in the blood useable for liquid biopsy testing is enormous. Circulating tumor cells (CTCs), cell-free DNA (cfDNA) and extracellular vesicles (EVs), as well as blood cells and other soluble components in the plasma, were shown as liquid biopsy analytes. A few studies directly comparing two liquid biopsy analytes showed a benefit of one analyte over the other, while most authors concluded the benefit of the additional analyte. Only three years ago, the first studies to examine the value of a characterization of more than two liquid biopsy analytes from the same sample were conducted. We attempt to reflect on the recent development of multimodal liquid biopsy testing in this review. Although the analytes and clinical purposes of the published multimodal studies differed significantly, the additive value of the analytes was concluded in almost all projects. Thus, the blood components, as liquid biopsy reservoirs, are complementary rather than competitive, and orthogonal data sets were even shown to harbor synergistic effects. The unmistakable potential of multimodal liquid biopsy testing, however, is dampened by its clinical utility, which is yet to be proven, the lack of methodical standardization and insufficiently mature reimbursement, logistics and data handling.
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Affiliation(s)
- Corinna Keup
- Department of Gynecology and Obstetrics, University Hospital of Essen, Hufelandstr. 55, 45122 Essen, Germany
| | - Rainer Kimmig
- Department of Gynecology and Obstetrics, University Hospital of Essen, Hufelandstr. 55, 45122 Essen, Germany
| | - Sabine Kasimir-Bauer
- Department of Gynecology and Obstetrics, University Hospital of Essen, Hufelandstr. 55, 45122 Essen, Germany
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11
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Faaborg L, Andersen RF, Waldstrøm M, Henriksen JR, Adimi P, Jakobsen A, Steffensen KD. Prognostic Impact of Circulating Methylated Homeobox A9 DNA in Patients Undergoing Treatment for Recurrent Ovarian Cancer. Cancers (Basel) 2022; 14:1766. [PMID: 35406538 PMCID: PMC8997085 DOI: 10.3390/cancers14071766] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2022] [Revised: 03/27/2022] [Accepted: 03/28/2022] [Indexed: 01/23/2023] Open
Abstract
Methylated Homeobox A9 circulating tumor DNA (meth-HOXA9) has been suggested as a blood-based biomarker in epithelial ovarian cancer (EOC), although its prognostic significance remains unproven. The aim of the present study was to investigate the prognostic impact of meth-HOXA9 in patients with recurrent EOC. DNA was purified from 4 mL plasma and, following bilsulfite conversion, meth-HOXA9 was analyzed using a methylation-specific droplet digital PCR. Detection of meth-HOXA9 was reported as a percentage of total DNA and as a binary variable (detectable and undetectable). Meth-HOXA9 status and its dynamics during palliative treatment were correlated with overall survival (OS) as the primary endpoint. At baseline, meth-HOXA9 was detected in 65.9% (83/126) of the patients. The median OS was 8.9 and 17.9 months in patients with detectable and undetectable meth-HOXA9 at baseline (hazard ratio: 2.04, p = 0.002), which remained significant in the multivariate analysis. Median OS in patients with an increase in meth-HOXA9 after one treatment cycle was 5.3 months compared to 33 months in patients with undetectable meth-HOXA9 (p < 0.001). Meth-HOXA9 was significantly related to poor survival and may serve as a prognostic marker in patients with recurrent EOC. The longitudinal monitoring of meth-HOXA9 is clinically feasible with the perspective of aiding clinical decision making.
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Affiliation(s)
- Louise Faaborg
- Department of Oncology, Lillebaelt Hospital, University Hospital of Southern Denmark, Beriderbakken 4, 7100 Vejle, Denmark; (P.A.); (A.J.); (K.D.S.)
- Department of Regional Health Research, University of Southern Denmark, J.B. Winsløws Vej 19, 5000 Odense C, Denmark
| | - Rikke Fredslund Andersen
- Department of Clinical Biochemistry and Immunology, Lillebaelt Hospital, University Hospital of Southern Denmark, Beriderbakken 4, 7100 Vejle, Denmark;
| | - Marianne Waldstrøm
- Department of Pathology, Lillebaelt Hospital, University Hospital of Southern Denmark, Beriderbakken 4, 7100 Vejle, Denmark;
| | - Jon Røikjær Henriksen
- Department of Oncology, Odense University Hospital, J.B. Winsløws Vej 4, 5000 Odense C, Denmark;
| | - Parvin Adimi
- Department of Oncology, Lillebaelt Hospital, University Hospital of Southern Denmark, Beriderbakken 4, 7100 Vejle, Denmark; (P.A.); (A.J.); (K.D.S.)
| | - Anders Jakobsen
- Department of Oncology, Lillebaelt Hospital, University Hospital of Southern Denmark, Beriderbakken 4, 7100 Vejle, Denmark; (P.A.); (A.J.); (K.D.S.)
- Department of Regional Health Research, University of Southern Denmark, J.B. Winsløws Vej 19, 5000 Odense C, Denmark
| | - Karina Dahl Steffensen
- Department of Oncology, Lillebaelt Hospital, University Hospital of Southern Denmark, Beriderbakken 4, 7100 Vejle, Denmark; (P.A.); (A.J.); (K.D.S.)
- Department of Regional Health Research, University of Southern Denmark, J.B. Winsløws Vej 19, 5000 Odense C, Denmark
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12
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Transcending Blood—Opportunities for Alternate Liquid Biopsies in Oncology. Cancers (Basel) 2022; 14:cancers14051309. [PMID: 35267615 PMCID: PMC8909855 DOI: 10.3390/cancers14051309] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2022] [Revised: 02/28/2022] [Accepted: 03/01/2022] [Indexed: 12/24/2022] Open
Abstract
Simple Summary Cell-free DNA—DNA that has been expelled from cells and can be isolated from blood plasma and other body fluids—is a useful tool in medicine, with applications as a biomarker in diagnosis, prognosis, disease profiling, and treatment selection. In oncology, the ease of access to the tumour genome is a major advantage of cell-free DNA, but while this has led to significant research in blood, other body fluids have not received equal attention. This review article summarises the current research into cell-free DNA in non-blood body fluids, highlighting its values and limitations, and suggesting the direction of future studies. We conclude that cell-free DNA from non-blood body fluids may provide additional information to supplement traditional biopsies, allowing informative and improved patient care across many cancer types. Abstract Cell-free DNA (cfDNA) is a useful molecular biomarker in oncology research and treatment, but while research into its properties in blood has flourished, there remains much to be discovered about cfDNA in other body fluids. The cfDNA from saliva, sputum, cerebrospinal fluid, urine, faeces, pleural effusions, and ascites has unique advantages over blood, and has potential as an alternative ‘liquid biopsy’ template. This review summarises the state of current knowledge and identifies the gaps in our understanding of non-blood liquid biopsies; where their advantages lie, where caution is needed, where they might fit clinically, and where research should focus in order to accelerate clinical implementation. An emphasis is placed on ascites and pleural effusions, being pathological fluids directly associated with cancer. We conclude that non-blood fluids are viable sources of cfDNA in situations where solid tissue biopsies are inaccessible, or only accessible from dated archived specimens. In addition, we show that due to the abundance of cfDNA in non-blood fluids, they can outperform blood in many circumstances. We demonstrate multiple instances in which DNA from various sources can provide additional information, and thus we advocate for analysing non-blood sources as a complement to blood and/or tissue. Further research into these fluids will highlight opportunities to improve patient outcomes across cancer types.
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