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Alonso A, Yuwono NL, Houshdaran S, Abbott J, Rodgers R, Ford CE, Warton K. Comparison of total and endometrial circulating cell-free DNA in women with and without endometriosis. Reprod Biomed Online 2021; 44:495-503. [PMID: 35031240 DOI: 10.1016/j.rbmo.2021.11.006] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2021] [Revised: 10/25/2021] [Accepted: 11/08/2021] [Indexed: 11/26/2022]
Abstract
RESEARCH QUESTION Do women with laparoscopically confirmed endometriosis have higher plasma concentrations of circulating cell-free DNA (cirDNA) than those without endometriosis? DESIGN Prospective study of women aged 18-45 years undergoing benign gynaecological laparoscopy at two tertiary hospitals. Venous blood was collected immediately before surgery, and women were allocated to the endometriosis or control groups based on surgical findings. Total plasma cirDNA and cirDNA integrity were measured by quantitative polymerase chain reaction (qPCR) targeting short (115 bases) and long (247 bases) ALU segments. Endometrial-derived cirDNA was measured by qPCR of bisulfite-treated cirDNA using primers selective for a FAM101A sequence uniquely unmethylated in endometrial tissue. Five cirDNA parameters were compared between the control and endometriosis cohorts: total cirDNA concentration, long-stranded cirDNA concentration, integrity ratio, endometrial cirDNA concentration and endometrial cirDNA proportion. RESULTS Twenty-eight endometriosis and 15 control samples were included. Women with and without endometriosis had cirDNA concentrations of 2.24 ± 0.89 ng/ml and 2.56 ± 0.92 ng/ml, respectively. Analysis by phenotype of endometriosis revealed a significantly higher endometrial cirDNA concentration in women with superficial disease (n = 10) compared with deep endometriosis (n = 18) (mean difference 0.14 ng/ml; 95% CI 0.15 to 0.26; P = 0.025), but not with controls. CONCLUSIONS No significant differences were found in any of the cirDNA parameters between women with and without endometriosis. The low statistical power and heterogenous pelvic pathology in the control group render it difficult to determine whether the negative results reflect a true lack of increase in cirDNA in endometriosis.
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Affiliation(s)
- Anais Alonso
- Gynaecological Research and Clinical Evaluation (GRACE) Unit, Royal Hospital for Women, Sydney NSW, Australia; School of Women's and Children's Health, Faculty of Medicine and Health, University of New South Wales, Sydney NSW, Australia
| | - Nicole Laurencia Yuwono
- Gynaecological Cancer Research Group, Adult Cancer Program, School of Women's and Children's Health, Faculty of Medicine and Health, University of New South Wales, Sydney NSW, Australia
| | - Sahar Houshdaran
- Center for Reproductive Sciences, Department of Obstetrics, Gynecology and Reproductive Sciences, University of California, San Francisco, USA
| | - Jason Abbott
- Gynaecological Research and Clinical Evaluation (GRACE) Unit, Royal Hospital for Women, Sydney NSW, Australia; School of Women's and Children's Health, Faculty of Medicine and Health, University of New South Wales, Sydney NSW, Australia
| | - Rachael Rodgers
- Center for Reproductive Sciences, Department of Obstetrics, Gynecology and Reproductive Sciences, University of California, San Francisco, USA; Department of Gynaecology and Reproductive Medicine, Royal Hospital for Women, Sydney NSW, Australia
| | - Caroline Elizabeth Ford
- Gynaecological Cancer Research Group, Adult Cancer Program, School of Women's and Children's Health, Faculty of Medicine and Health, University of New South Wales, Sydney NSW, Australia
| | - Kristina Warton
- Gynaecological Cancer Research Group, Adult Cancer Program, School of Women's and Children's Health, Faculty of Medicine and Health, University of New South Wales, Sydney NSW, Australia.
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Werner B, Yuwono N, Duggan J, Liu D, David C, Srirangan S, Provan P, DeFazio A, Arora V, Farrell R, Lee YC, Warton K, Ford C. Cell-free DNA is abundant in ascites and represents a liquid biopsy of ovarian cancer. Gynecol Oncol 2021; 162:720-727. [PMID: 34454680 DOI: 10.1016/j.ygyno.2021.06.028] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2021] [Revised: 06/15/2021] [Accepted: 06/27/2021] [Indexed: 02/09/2023]
Abstract
OBJECTIVE Malignant ascites is a common clinical feature of ovarian cancer and represents a readily accessible sample of tumour cells and tumour DNA. This study aimed to characterise the cell-free DNA (cfDNA) in ascites in terms of its size profile, stability and cell-free tumour DNA (cftDNA) content. METHODS Cell spheroids, loose cells and cell-free fluid was collected from ascites from 18 patients with ovarian cancer. cfDNA was isolated and assessed for size by electrophoresis, concentration by fluorometry,cftDNA content by methylation specific qPCR of HOXA9 and IFFO1 promoter regions and by targeted sequencing. Stability was assessed after ascites fluid was stored at 4 °C for 24 and 72 h before fractionating. RESULTS The concentration of cfDNA in ascites ranged from 6.6 to 300 ng/mL. cfDNA size distribution resembled blood plasma-derived cfDNA, with major peaks corresponding to mono- and di-nucleosome DNA fragments. High molecular weight cfDNA was observed in 7 of 18 patients and appeared to be associated with extracellular vesicles. IFFO1 and HOXA9 methylation was proportionately higher in cfDNA than spheroid- and loose-cell fractions and was not observed in healthy primary cells. Variant allele frequency was highest in cfDNA compared to single cells and spheroids from ascites. Though cancer cell numbers in ascites declined to near zero in recurrent ascites from one patient undertaking chemotherapy, cftDNA could still be sampled. cfDNA size, concentration and tumour content was stable over 72 h. CONCLUSION cfDNA in ovarian cancer ascites demonstrates inter-patient variability, yet is consistently a rich source of cftDNA, which is a stable substrate. This supports the wider clinical use of ascites in the molecular analysis of ovarian cancer.
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Affiliation(s)
- Bonnita Werner
- Gynaecological Cancer Research Group, School of Women's and Children's Health, Faculty of Medicine and Health, University of New South Wales, Australia
| | - Nicole Yuwono
- Gynaecological Cancer Research Group, School of Women's and Children's Health, Faculty of Medicine and Health, University of New South Wales, Australia
| | - Jennifer Duggan
- Gynaecological Oncology Department, Royal Hospital for Women, Sydney, Australia
| | - Dongli Liu
- Gynaecological Cancer Research Group, School of Women's and Children's Health, Faculty of Medicine and Health, University of New South Wales, Australia
| | - Catherine David
- Gynaecological Oncology Department, Royal Hospital for Women, Sydney, Australia
| | - Sivatharsny Srirangan
- Centre for Cancer Research, The Westmead Institute for Medical Research, Sydney, Australia
| | - Pamela Provan
- Centre for Cancer Research, The Westmead Institute for Medical Research, Sydney, Australia; Faculty of Medicine and Health, The University of Sydney, Sydney, Australia
| | | | - Anna DeFazio
- Centre for Cancer Research, The Westmead Institute for Medical Research, Sydney, Australia; Faculty of Medicine and Health, The University of Sydney, Sydney, Australia; Department of Gynaecological Oncology, Westmead Hospital, Sydney, Australia
| | - Vivek Arora
- Gynaecological Oncology Department, Royal Hospital for Women, Sydney, Australia; Prince of Wales Private Hospital, Sydney, Australia; School of Women's and Children's Health, Faculty of Medicine and Health, University of New South Wales, Australia
| | | | - Yeh Chen Lee
- Gynaecological Oncology Department, Royal Hospital for Women, Sydney, Australia; Faculty of Medicine and Health, University of New South Wales, Australia
| | - Kristina Warton
- Gynaecological Cancer Research Group, School of Women's and Children's Health, Faculty of Medicine and Health, University of New South Wales, Australia
| | - Caroline Ford
- Gynaecological Cancer Research Group, School of Women's and Children's Health, Faculty of Medicine and Health, University of New South Wales, Australia.
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