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Biskup E, Lopacinska-Jørgensen J, Vestergaard LK, Høgdall E. Validating reference-based algorithms to determine cell-type heterogeneity in ovarian cancer DNA methylation studies. Sci Rep 2024; 14:11048. [PMID: 38745057 PMCID: PMC11094148 DOI: 10.1038/s41598-024-61857-y] [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: 02/16/2024] [Accepted: 05/10/2024] [Indexed: 05/16/2024] Open
Abstract
Information about cell composition in tissue samples is crucial for biomarker discovery and prognosis. Specifically, cancer tissue samples present challenges in deconvolution studies due to mutations and genetic rearrangements. Here, we optimized a robust, DNA methylation-based protocol, to be used for deconvolution of ovarian cancer samples. We compared several state-of-the-art methods (HEpiDISH, MethylCIBERSORT and ARIC) and validated the proposed protocol in an in-silico mixture and in an external dataset containing samples from ovarian cancer patients and controls. The deconvolution protocol we eventually implemented is based on MethylCIBERSORT. Comparing deconvolution methods, we paid close attention to the role of a reference panel. We postulate that a possibly high number of samples (in our case: 247) should be used when building a reference panel to ensure robustness and to compensate for biological and technical variation between samples. Subsequently, we tested the performance of the validated protocol in our own study cohort, consisting of 72 patients with malignant and benign ovarian disease as well as in five external cohorts. In conclusion, we refined and validated a reference-based algorithm to determine cell type composition of ovarian cancer tissue samples to be used in cancer biology studies in larger cohorts.
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Affiliation(s)
- Edyta Biskup
- Department of Pathology, Copenhagen University Hospital, Herlev, Denmark.
| | | | | | - Estrid Høgdall
- Department of Pathology, Copenhagen University Hospital, Herlev, Denmark
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2
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Beddows I, Fan H, Heinze K, Johnson BK, Leonova A, Senz J, Djirackor S, Cho KR, Pearce CL, Huntsman DG, Anglesio MS, Shen H. Cell State of Origin Impacts Development of Distinct Endometriosis-Related Ovarian Carcinoma Histotypes. Cancer Res 2024; 84:26-38. [PMID: 37874327 PMCID: PMC10758692 DOI: 10.1158/0008-5472.can-23-1362] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2023] [Revised: 09/01/2023] [Accepted: 10/20/2023] [Indexed: 10/25/2023]
Abstract
Clear cell ovarian carcinoma (CCOC) and endometrioid ovarian carcinoma (ENOC) are ovarian carcinoma histotypes, which are both thought to arise from ectopic endometrial (or endometrial-like) cells through an endometriosis intermediate. How the same cell type of origin gives rise to two morphologically and biologically different histotypes has been perplexing, particularly given that recurrent genetic mutations are common to both and present in nonmalignant precursors. We used RNA transcription analysis to show that the expression profiles of CCOC and ENOC resemble those of normal endometrium at secretory and proliferative phases of the menstrual cycle, respectively. DNA methylation at the promoter of the estrogen receptor (ER) gene (ESR1) was enriched in CCOC, which could potentially lock the cells in the secretory state. Compared with normal secretory-type endometrium, CCOC was further defined by increased expression of cysteine and glutathione synthesis pathway genes and downregulation of the iron antiporter, suggesting iron addiction and highlighting ferroptosis as a potential therapeutic target. Overall, these findings suggest that while CCOC and ENOC arise from the same cell type, these histotypes likely originate from different cell states. This "cell state of origin" model may help to explain the presence of histologic and molecular cancer subtypes arising in other organs. SIGNIFICANCE Two cancer histotypes diverge from a common cell of origin epigenetically locked in different cell states, highlighting the importance of considering cell state to better understand the cell of origin of cancer.
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Affiliation(s)
- Ian Beddows
- Department of Epigenetics, Van Andel Institute, Grand Rapids, Michigan
| | - Huihui Fan
- Department of Epigenetics, Van Andel Institute, Grand Rapids, Michigan
| | - Karolin Heinze
- Department of Obstetrics and Gynaecology, Faculty of Medicine, University of British Columbia, Vancouver, British Columbia, Canada
| | | | - Anna Leonova
- Department of Obstetrics and Gynaecology, Faculty of Medicine, University of British Columbia, Vancouver, British Columbia, Canada
| | - Janine Senz
- Department of Obstetrics and Gynaecology, Faculty of Medicine, University of British Columbia, Vancouver, British Columbia, Canada
| | | | - Kathleen R. Cho
- Department of Pathology, University of Michigan Medical School, Ann Arbor, Michigan
| | - Celeste Leigh Pearce
- Department of Epidemiology, University of Michigan School of Public Health, Ann Arbor, Michigan
| | - David G. Huntsman
- Department of Obstetrics and Gynaecology, Faculty of Medicine, University of British Columbia, Vancouver, British Columbia, Canada
- Department of Pathology & Laboratory Medicine, Faculty of Medicine, University of British Columbia, Vancouver, British Columbia, Canada
| | - Michael S. Anglesio
- Department of Obstetrics and Gynaecology, Faculty of Medicine, University of British Columbia, Vancouver, British Columbia, Canada
| | - Hui Shen
- Department of Epigenetics, Van Andel Institute, Grand Rapids, Michigan
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3
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Wang C, Block MS, Cunningham JM, Sherman ME, McCauley BM, Armasu SM, Vierkant RA, Traficante N, Talhouk A, Ramus SJ, Pejovic N, Köbel M, Jorgensen BD, Garsed DW, Fereday S, Doherty JA, Ariyaratne D, Anglesio MS, Widschwendter M, Pejovic T, Bosquet JG, Bowtell DD, Winham SJ, Goode EL. Methylation Signature Implicated in Immuno-Suppressive Activities in Tubo-Ovarian High-Grade Serous Carcinoma. Cancer Epidemiol Biomarkers Prev 2023; 32:542-549. [PMID: 36790339 PMCID: PMC10073286 DOI: 10.1158/1055-9965.epi-22-0941] [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: 08/31/2022] [Revised: 11/07/2022] [Accepted: 01/23/2023] [Indexed: 02/16/2023] Open
Abstract
BACKGROUND Better understanding of prognostic factors in tubo-ovarian high-grade serous carcinoma (HGSC) is critical, as diagnosis confers an aggressive disease course. Variation in tumor DNA methylation shows promise predicting outcome, yet prior studies were largely platform-specific and unable to evaluate multiple molecular features. METHODS We analyzed genome-wide DNA methylation in 1,040 frozen HGSC, including 325 previously reported upon, seeking a multi-platform quantitative methylation signature that we evaluated in relation to clinical features, tumor characteristics, time to recurrence/death, extent of CD8+ tumor-infiltrating lymphocytes (TIL), gene expression molecular subtypes, and gene expression of the ATP-binding cassette transporter TAP1. RESULTS Methylation signature was associated with shorter time to recurrence, independent of clinical factors (N = 715 new set, hazard ratio (HR), 1.65; 95% confidence interval (CI), 1.10-2.46; P = 0.015; N = 325 published set HR, 2.87; 95% CI, 2.17-3.81; P = 2.2 × 10-13) and remained prognostic after adjustment for gene expression molecular subtype and TAP1 expression (N = 599; HR, 2.22; 95% CI, 1.66-2.95; P = 4.1 × 10-8). Methylation signature was inversely related to CD8+ TIL levels (P = 2.4 × 10-7) and TAP1 expression (P = 0.0011) and was associated with gene expression molecular subtype (P = 5.9 × 10-4) in covariate-adjusted analysis. CONCLUSIONS Multi-center analysis identified a novel quantitative tumor methylation signature of HGSC applicable to numerous commercially available platforms indicative of shorter time to recurrence/death, adjusting for other factors. Along with immune cell composition analysis, these results suggest a role for DNA methylation in the immunosuppressive microenvironment. IMPACT This work aids in identification of targetable epigenome processes and stratification of patients for whom tailored treatment may be most beneficial.
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Affiliation(s)
- Chen Wang
- Department of Quantitative Health Sciences, Division of Computational Biology, Mayo Clinic, Rochester, MN, USA
| | | | - Julie M. Cunningham
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
| | - Mark E. Sherman
- Department of Quantitative Health Sciences, Mayo Clinic, Jacksonville, FL, USA
| | - Bryan M. McCauley
- Department of Quantitative Health Sciences, Division of Clinical Trials and Biostatistics, Mayo Clinic, Rochester, MN, USA
| | - Sebastian M. Armasu
- Department of Quantitative Health Sciences, Division of Clinical Trials and Biostatistics, Mayo Clinic, Rochester, MN, USA
| | - Robert A. Vierkant
- Department of Quantitative Health Sciences, Division of Computational Biology, Mayo Clinic, Rochester, MN, USA
| | - Nadia Traficante
- Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
- Sir Peter MacCallum Department of Oncology, The University of Melbourne, Parkville, Victoria, Australia
| | - Australian Ovarian Cancer Study Group
- Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
- Centre for Cancer Research, The Westmead Institute for Medical Research and Department of Gynaecological Oncology, Westmead Hospital, The University of Sydney, Sydney, New South Wales, Australia
| | - Aline Talhouk
- British Columbia’s Ovarian Cancer Research (OVCARE) Program, BC Cancer, Vancouver General Hospital, and University of British Columbia, Vancouver, BC, Canada
- Department of Obstetrics and Gynecology, University of British Columbia, Vancouver, BC, Canada
| | - Susan J. Ramus
- School of Clinical Medicine, Faculty of Medicine, University of NSW Sydney, Sydney, New South Wales, Australia
- Adult Cancer Program, Lowy Cancer Research Centre, University of NSW Sydney, Sydney, New South Wales, Australia
| | | | - Martin Köbel
- Department of Pathology and Laboratory Medicine, University of Calgary, Calgary, AB, Canada
| | - Brooke D. Jorgensen
- Department of Quantitative Health Sciences, Division of Epidemiology, Mayo Clinic, Rochester, MN, USA
| | - Dale W. Garsed
- Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
- Sir Peter MacCallum Department of Oncology, The University of Melbourne, Parkville, Victoria, Australia
| | - Sian Fereday
- Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
- Sir Peter MacCallum Department of Oncology, The University of Melbourne, Parkville, Victoria, Australia
| | - Jennifer A. Doherty
- Huntsman Cancer Institute, Department of Population Health Sciences, University of Utah, Salt Lake City, UT, USA
| | | | - Michael S. Anglesio
- British Columbia’s Ovarian Cancer Research (OVCARE) Program, BC Cancer, Vancouver General Hospital, and University of British Columbia, Vancouver, BC, Canada
- Department of Obstetrics and Gynecology, University of British Columbia, Vancouver, BC, Canada
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC, Canada
| | - Martin Widschwendter
- European Translational Oncology Prevention and Screening (EUTOPS) Institute, Universität Innsbruck, Hall in Tirol, Austria
| | - Tanja Pejovic
- Department of Obstetrics and Gynecology, Oregon Health & Science University, Portland, OR, USA
- Knight Cancer Institute, Oregon Health & Science University, Portland, OR, USA
| | - Jesus Gonzalez Bosquet
- Department of Obstetrics and Gynecologic, Division of Gynecologic Oncology, University of Iowa, Iowa City, IA, USA
| | - David D. Bowtell
- Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
- Sir Peter MacCallum Department of Oncology, The University of Melbourne, Parkville, Victoria, Australia
| | - Stacey J. Winham
- Department of Quantitative Health Sciences, Division of Computational Biology, Mayo Clinic, Rochester, MN, USA
| | - Ellen L. Goode
- Department of Quantitative Health Sciences, Division of Epidemiology, Mayo Clinic, Rochester, MN, USA
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4
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Bartlett TE. Comodularity and detection of co-communities. Phys Rev E 2021; 104:054309. [PMID: 34942704 DOI: 10.1103/physreve.104.054309] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2021] [Accepted: 11/08/2021] [Indexed: 11/07/2022]
Abstract
This paper introduces the notion of comodularity, to cocluster observations of bipartite networks into co-communities. The task of coclustering is to group together nodes of one type with nodes of another type, according to the interactions that are the most similar. The measure of comodularity is introduced to assess the strength of co-communities, as well as to arrange the representation of nodes and clusters for visualization, and to define an objective function for optimization. We demonstrate the usefulness of our proposed methodology on simulated data, and with examples from genomics and consumer-product reviews.
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Affiliation(s)
- Thomas E Bartlett
- Department of Statistical Science, University College London, London WC1E 7HB, United Kingdom
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5
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Bartlett TE, Jia P, Chandna S, Roy S. Inference of tissue relative proportions of the breast epithelial cell types luminal progenitor, basal, and luminal mature. Sci Rep 2021; 11:23702. [PMID: 34880407 PMCID: PMC8655091 DOI: 10.1038/s41598-021-03161-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2021] [Accepted: 11/26/2021] [Indexed: 12/15/2022] Open
Abstract
Single-cell analysis has revolutionised genomic science in recent years. However, due to cost and other practical considerations, single-cell analyses are impossible for studies based on medium or large patient cohorts. For example, a single-cell analysis usually costs thousands of euros for one tissue sample from one volunteer, meaning that typical studies using single-cell analyses are based on very few individuals. While single-cell genomic data can be used to examine the phenotype of individual cells, cell-type deconvolution methods are required to track the quantities of these cells in bulk-tissue genomic data. Hormone receptor negative breast cancers are highly aggressive, and are thought to originate from a subtype of epithelial cells called the luminal progenitor. In this paper, we show how to quantify the number of luminal progenitor cells as well as other epithelial subtypes in breast tissue samples using DNA and RNA based measurements. We find elevated levels of cells which resemble these hormone receptor negative luminal progenitor cells in breast tumour biopsies of hormone receptor negative cancers, as well as in healthy breast tissue samples from BRCA1 (FANCS) mutation carriers. We also find that breast tumours from carriers of heterozygous mutations in non-BRCA Fanconi Anaemia pathway genes are much more likely to be hormone receptor negative. These findings have implications for understanding hormone receptor negative breast cancers, and for breast cancer screening in carriers of heterozygous mutations of Fanconi Anaemia pathway genes.
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Affiliation(s)
- Thomas E Bartlett
- Department of Statistical Science, University College London, London, UK.
| | - Peiwen Jia
- Department of Statistical Science, University College London, London, UK
| | - Swati Chandna
- Department of Economics, Mathematics and Statistics, Birkbeck University of London, London, UK
| | - Sandipan Roy
- Department of Mathematical Sciences, University of Bath, Bath, UK
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6
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Assessing ZNF154 methylation in patient plasma as a multicancer marker in liquid biopsies from colon, liver, ovarian and pancreatic cancer patients. Sci Rep 2021; 11:221. [PMID: 33420235 PMCID: PMC7794477 DOI: 10.1038/s41598-020-80345-7] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2020] [Accepted: 12/08/2020] [Indexed: 12/21/2022] Open
Abstract
One epigenetic hallmark of many cancer types is differential DNA methylation occurring at multiple loci compared to normal tissue. Detection and assessment of the methylation state at a specific locus could be an effective cancer diagnostic. We assessed the effectiveness of hypermethylation at the CpG island of ZNF154, a previously reported multi-cancer specific signature for use in a blood-based cancer detection assay. To predict its effectiveness, we compared methylation levels of 3698 primary tumors encompassing 11 solid cancers, 724 controls, 2711 peripheral blood cell samples, and 350 noncancer disease tissues from publicly available methylation array datasets. We performed a single-molecule high-resolution DNA melt analysis on 71 plasma samples from cancer patients and 20 noncancer individuals to assess ZNF154 methylation as a candidate diagnostic metric in liquid biopsy and compared results to KRAS mutation frequency in the case of pancreatic carcinoma. We documented ZNF154 hypermethylation in early stage tumors, which did not increase in most noncancer disease or with respect to age or sex in peripheral blood cells, suggesting it is a promising target in liquid biopsy. ZNF154 cfDNA methylation discriminated cases from healthy donor plasma samples in minimal plasma volumes and outperformed KRAS mutation frequency in pancreatic cancer.
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7
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Miller BF, Pisanic Ii TR, Margolin G, Petrykowska HM, Athamanolap P, Goncearenco A, Osei-Tutu A, Annunziata CM, Wang TH, Elnitski L. Leveraging locus-specific epigenetic heterogeneity to improve the performance of blood-based DNA methylation biomarkers. Clin Epigenetics 2020; 12:154. [PMID: 33081832 PMCID: PMC7574234 DOI: 10.1186/s13148-020-00939-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2019] [Accepted: 09/21/2020] [Indexed: 12/20/2022] Open
Abstract
BACKGROUND Variation in intercellular methylation patterns can complicate the use of methylation biomarkers for clinical diagnostic applications such as blood-based cancer testing. Here, we describe development and validation of a methylation density binary classification method called EpiClass (available for download at https://github.com/Elnitskilab/EpiClass ) that can be used to predict and optimize the performance of methylation biomarkers, particularly in challenging, heterogeneous samples such as liquid biopsies. This approach is based upon leveraging statistical differences in single-molecule sample methylation density distributions to identify ideal thresholds for sample classification. RESULTS We developed and tested the classifier using reduced representation bisulfite sequencing (RRBS) data derived from ovarian carcinoma tissue DNA and controls. We used these data to perform in silico simulations using methylation density profiles from individual epiallelic copies of ZNF154, a genomic locus known to be recurrently methylated in numerous cancer types. From these profiles, we predicted the performance of the classifier in liquid biopsies for the detection of epithelial ovarian carcinomas (EOC). In silico analysis indicated that EpiClass could be leveraged to better identify cancer-positive liquid biopsy samples by implementing precise thresholds with respect to methylation density profiles derived from circulating cell-free DNA (cfDNA) analysis. These predictions were confirmed experimentally using DREAMing to perform digital methylation density analysis on a cohort of low volume (1-ml) plasma samples obtained from 26 EOC-positive and 41 cancer-free women. EpiClass performance was then validated in an independent cohort of 24 plasma specimens, derived from a longitudinal study of 8 EOC-positive women, and 12 plasma specimens derived from 12 healthy women, respectively, attaining a sensitivity/specificity of 91.7%/100.0%. Direct comparison of CA-125 measurements with EpiClass demonstrated that EpiClass was able to better identify EOC-positive women than standard CA-125 assessment. Finally, we used independent whole genome bisulfite sequencing (WGBS) datasets to demonstrate that EpiClass can also identify other cancer types as well or better than alternative methylation-based classifiers. CONCLUSIONS Our results indicate that assessment of intramolecular methylation density distributions calculated from cfDNA facilitates the use of methylation biomarkers for diagnostic applications. Furthermore, we demonstrated that EpiClass analysis of ZNF154 methylation was able to outperform CA-125 in the detection of etiologically diverse ovarian carcinomas, indicating broad utility of ZNF154 for use as a biomarker of ovarian cancer.
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Affiliation(s)
- Brendan F Miller
- Translational Functional Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Thomas R Pisanic Ii
- Institute for NanoBioTechnology, Johns Hopkins University, Baltimore, MD, 21218, USA.
| | - Gennady Margolin
- Translational Functional Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Hanna M Petrykowska
- Translational Functional Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Pornpat Athamanolap
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD, 21218, USA
| | - Alexander Goncearenco
- Translational Functional Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Akosua Osei-Tutu
- Women's Malignancy Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Christina M Annunziata
- Women's Malignancy Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Tza-Huei Wang
- Institute for NanoBioTechnology, Johns Hopkins University, Baltimore, MD, 21218, USA
- Department of Mechanical Engineering, Johns Hopkins University, Baltimore, MD, 21218, USA
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD, 21218, USA
| | - Laura Elnitski
- Translational Functional Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, 20892, USA.
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8
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Teschendorff AE. Avoiding common pitfalls in machine learning omic data science. NATURE MATERIALS 2019; 18:422-427. [PMID: 30478452 DOI: 10.1038/s41563-018-0241-z] [Citation(s) in RCA: 54] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Affiliation(s)
- Andrew E Teschendorff
- Statistical Cancer Genomics, UCL Cancer Institute and Department of Woman's Cancer, University College London, London, UK.
- CAS Key Lab of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai Institute of Nutrition and Health, Shanghai Institute for Biological Sciences, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China.
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9
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Pisanic TR, Cope LM, Lin SF, Yen TT, Athamanolap P, Asaka R, Nakayama K, Fader AN, Wang TH, Shih IM, Wang TL. Methylomic Analysis of Ovarian Cancers Identifies Tumor-Specific Alterations Readily Detectable in Early Precursor Lesions. Clin Cancer Res 2018; 24:6536-6547. [PMID: 30108103 DOI: 10.1158/1078-0432.ccr-18-1199] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2018] [Revised: 07/12/2018] [Accepted: 08/09/2018] [Indexed: 12/22/2022]
Abstract
PURPOSE High-grade serous ovarian carcinoma (HGSOC) typically remains undiagnosed until advanced stages when peritoneal dissemination has already occurred. Here, we sought to identify HGSOC-specific alterations in DNA methylation and assess their potential to provide sensitive and specific detection of HGSOC at its earliest stages. EXPERIMENTAL DESIGN MethylationEPIC genome-wide methylation analysis was performed on a discovery cohort comprising 23 HGSOC, 37 non-HGSOC malignant, and 36 histologically unremarkable gynecologic tissue samples. The resulting data were processed using selective bioinformatic criteria to identify regions of high-confidence HGSOC-specific differential methylation. Quantitative methylation-specific real-time PCR (qMSP) assays were then developed for 8 of the top-performing regions and analytically validated in a cohort of 90 tissue samples. Lastly, qMSP assays were used to assess and compare methylation in 30 laser-capture microdissected (LCM) fallopian tube epithelia samples obtained from cancer-free and serous tubal intraepithelial carcinoma (STIC) positive women. RESULTS Bioinformatic selection identified 91 regions of robust, HGSOC-specific hypermethylation, 23 of which exhibited an area under the receiver-operator curve (AUC) value ≥ 0.9 in the discovery cohort. Seven of 8 top-performing regions demonstrated AUC values between 0.838 and 0.968 when analytically validated by qMSP in a 90-patient cohort. A panel of the 3 top-performing genes (c17orf64, IRX2, and TUBB6) was able to perfectly discriminate HGSOC (AUC 1.0). Hypermethylation within these loci was found exclusively in LCM fallopian tube epithelia from women with STIC lesions, but not in cancer-free fallopian tubes. CONCLUSIONS A panel of methylation biomarkers can be used to accurately identify HGSOC, even at precursor stages of the disease.
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Affiliation(s)
- Thomas R Pisanic
- Johns Hopkins Institute for NanoBioTechnology, Johns Hopkins University, Baltimore, Maryland.
| | - Leslie M Cope
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland.,Departments of Oncology and Biostatistics, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Shiou-Fu Lin
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland.,Departments of Gynecology and Obstetrics and Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Ting-Tai Yen
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland.,Departments of Gynecology and Obstetrics and Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Pornpat Athamanolap
- Department of Biomedical Engineering, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Ryoichi Asaka
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland.,Departments of Gynecology and Obstetrics and Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Kentaro Nakayama
- Department of Obstetrics and Gynecology, Shimane University School of Medicine, Izumo, Japan
| | - Amanda N Fader
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland.,Departments of Gynecology and Obstetrics and Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Tza-Huei Wang
- Johns Hopkins Institute for NanoBioTechnology, Johns Hopkins University, Baltimore, Maryland.,Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland.,Department of Biomedical Engineering, Johns Hopkins University School of Medicine, Baltimore, Maryland.,Department of Mechanical Engineering, Johns Hopkins University, Baltimore, Maryland
| | - Ie-Ming Shih
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland.,Departments of Gynecology and Obstetrics and Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Tian-Li Wang
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland. .,Departments of Gynecology and Obstetrics and Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland
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10
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Affiliation(s)
- Andrew P Feinberg
- From the Department of Medicine, Johns Hopkins University School of Medicine, the Department of Biomedical Engineering, Whiting School of Engineering, and the Department of Mental Health, Johns Hopkins Bloomberg School of Public Health - all in Baltimore
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11
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Widschwendter M, Zikan M, Wahl B, Lempiäinen H, Paprotka T, Evans I, Jones A, Ghazali S, Reisel D, Eichner J, Rujan T, Yang Z, Teschendorff AE, Ryan A, Cibula D, Menon U, Wittenberger T. The potential of circulating tumor DNA methylation analysis for the early detection and management of ovarian cancer. Genome Med 2017; 9:116. [PMID: 29268796 PMCID: PMC5740748 DOI: 10.1186/s13073-017-0500-7] [Citation(s) in RCA: 104] [Impact Index Per Article: 14.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2017] [Accepted: 11/24/2017] [Indexed: 02/07/2023] Open
Abstract
Background Despite a myriad of attempts in the last three decades to diagnose ovarian cancer (OC) earlier, this clinical aim still remains a significant challenge. Aberrant methylation patterns of linked CpGs analyzed in DNA fragments shed by cancers into the bloodstream (i.e. cell-free DNA) can provide highly specific signals indicating cancer presence. Methods We analyzed 699 cancerous and non-cancerous tissues using a methylation array or reduced representation bisulfite sequencing to discover the most specific OC methylation patterns. A three-DNA-methylation-serum-marker panel was developed using targeted ultra-high coverage bisulfite sequencing in 151 women and validated in 250 women with various conditions, particularly in those associated with high CA125 levels (endometriosis and other benign pelvic masses), serial samples from 25 patients undergoing neoadjuvant chemotherapy, and a nested case control study of 172 UKCTOCS control arm participants which included serum samples up to two years before OC diagnosis. Results The cell-free DNA amount and average fragment size in the serum samples was up to ten times higher than average published values (based on samples that were immediately processed) due to leakage of DNA from white blood cells owing to delayed time to serum separation. Despite this, the marker panel discriminated high grade serous OC patients from healthy women or patients with a benign pelvic mass with specificity/sensitivity of 90.7% (95% confidence interval [CI] = 84.3–94.8%) and 41.4% (95% CI = 24.1–60.9%), respectively. Levels of all three markers plummeted after exposure to chemotherapy and correctly identified 78% and 86% responders and non-responders (Fisher’s exact test, p = 0.04), respectively, which was superior to a CA125 cut-off of 35 IU/mL (20% and 75%). 57.9% (95% CI 34.0–78.9%) of women who developed OC within two years of sample collection were identified with a specificity of 88.1% (95% CI = 77.3–94.3%). Sensitivity and specificity improved further when specifically analyzing CA125 negative samples only (63.6% and 87.5%, respectively). Conclusions Our data suggest that DNA methylation patterns in cell-free DNA have the potential to detect a proportion of OCs up to two years in advance of diagnosis and may potentially guide personalized treatment. The prospective use of novel collection vials, which stabilize blood cells and reduce background DNA contamination in serum/plasma samples, will facilitate clinical implementation of liquid biopsy analyses. Electronic supplementary material The online version of this article (doi:10.1186/s13073-017-0500-7) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Martin Widschwendter
- Department of Women's Cancer, UCL Elizabeth Garrett Anderson Institute for Women's Health, University College London, Medical School Building, Room 340, 74 Huntley Street, London, WC1E 6AU, UK.
| | - Michal Zikan
- Gynaecologic Oncology Center, Department of Obstetrics & Gynaecology, First Faculty of Medicine & General University Hospital, Charles University, Prague, Czech Republic
| | - Benjamin Wahl
- GATC Biotech AG, Jakob-Stadler-Platz 7, 78467, Konstanz, Germany
| | | | - Tobias Paprotka
- GATC Biotech AG, Jakob-Stadler-Platz 7, 78467, Konstanz, Germany
| | - Iona Evans
- Department of Women's Cancer, UCL Elizabeth Garrett Anderson Institute for Women's Health, University College London, Medical School Building, Room 340, 74 Huntley Street, London, WC1E 6AU, UK
| | - Allison Jones
- Department of Women's Cancer, UCL Elizabeth Garrett Anderson Institute for Women's Health, University College London, Medical School Building, Room 340, 74 Huntley Street, London, WC1E 6AU, UK
| | - Shohreh Ghazali
- Department of Women's Cancer, UCL Elizabeth Garrett Anderson Institute for Women's Health, University College London, Medical School Building, Room 340, 74 Huntley Street, London, WC1E 6AU, UK
| | - Daniel Reisel
- Department of Women's Cancer, UCL Elizabeth Garrett Anderson Institute for Women's Health, University College London, Medical School Building, Room 340, 74 Huntley Street, London, WC1E 6AU, UK
| | | | - Tamas Rujan
- Genedata AG, Margarethenstrasse 38, 4053, Basel, Switzerland
| | - Zhen Yang
- CAS Max-Planck Partner Institute for Computational Biology, Shanghai Institute of Biological Sciences, 320 Yue Yang Road, Shanghai, 200031, China
| | - Andrew E Teschendorff
- Department of Women's Cancer, UCL Elizabeth Garrett Anderson Institute for Women's Health, University College London, Medical School Building, Room 340, 74 Huntley Street, London, WC1E 6AU, UK.,CAS Max-Planck Partner Institute for Computational Biology, Shanghai Institute of Biological Sciences, 320 Yue Yang Road, Shanghai, 200031, China
| | - Andy Ryan
- Department of Women's Cancer, UCL Elizabeth Garrett Anderson Institute for Women's Health, University College London, Medical School Building, Room 340, 74 Huntley Street, London, WC1E 6AU, UK
| | - David Cibula
- Gynaecologic Oncology Center, Department of Obstetrics & Gynaecology, First Faculty of Medicine & General University Hospital, Charles University, Prague, Czech Republic
| | - Usha Menon
- Department of Women's Cancer, UCL Elizabeth Garrett Anderson Institute for Women's Health, University College London, Medical School Building, Room 340, 74 Huntley Street, London, WC1E 6AU, UK
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Ozer B, Sezerman U. An integrative study on the impact of highly differentially methylated genes on expression and cancer etiology. PLoS One 2017; 12:e0171694. [PMID: 28178311 PMCID: PMC5298317 DOI: 10.1371/journal.pone.0171694] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2016] [Accepted: 01/24/2017] [Indexed: 12/13/2022] Open
Abstract
DNA methylation is an important epigenetic phenomenon that plays a key role in the regulation of expression. Most of the studies on the topic of methylation's role in cancer mechanisms include analyses based on differential methylation, with the integration of expression information as supporting evidence. In the present study, we sought to identify methylation-driven patterns by also integrating protein-protein interaction information. We performed integrative analyses of DNA methylation, expression, SNP and copy number data on paired samples from six different cancer types. As a result, we found that genes that show a methylation change larger than 32.2% may influence cancer-related genes via fewer interaction steps and with much higher percentages compared with genes showing a methylation change less than 32.2%. Additionally, we investigated whether there were shared cancer mechanisms among different cancer types. Specifically, five cancer types shared a change in AGTR1 and IGF1 genes, which implies that there may be similar underlying disease mechanisms among these cancers. Additionally, when the focus was placed on distinctly altered genes within each cancer type, we identified various cancer-specific genes that are also supported in the literature and may play crucial roles as therapeutic targets. Overall, our novel graph-based approach for identifying methylation-driven patterns will improve our understanding of the effects of methylation on cancer progression and lead to improved knowledge of cancer etiology.
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Affiliation(s)
- Bugra Ozer
- Biological Sciences and Bioengineering Program, Faculty of Engineering and Natural Sciences, Sabanci University, Istanbul, Turkey
- * E-mail:
| | - Ugur Sezerman
- Department of Biostatistics and Medical Informatics, Acibadem University, Istanbul, Turkey
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Epigenetic reprogramming of fallopian tube fimbriae in BRCA mutation carriers defines early ovarian cancer evolution. Nat Commun 2016; 7:11620. [PMID: 27216078 PMCID: PMC4890182 DOI: 10.1038/ncomms11620] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2015] [Accepted: 04/14/2016] [Indexed: 02/06/2023] Open
Abstract
The exact timing and contribution of epigenetic reprogramming to carcinogenesis are unclear. Women harbouring BRCA1/2 mutations demonstrate a 30–40-fold increased risk of high-grade serous extra-uterine Müllerian cancers (HGSEMC), otherwise referred to as ‘ovarian carcinomas', which frequently develop from fimbrial cells but not from the proximal portion of the fallopian tube. Here we compare the DNA methylome of the fimbrial and proximal ends of the fallopian tube in BRCA1/2 mutation carriers and non-carriers. We show that the number of CpGs displaying significant differences in methylation levels between fimbrial and proximal fallopian tube segments are threefold higher in BRCA mutation carriers than in controls, correlating with overexpression of activation-induced deaminase in their fimbrial epithelium. The differentially methylated CpGs accurately discriminate HGSEMCs from non-serous subtypes. Epigenetic reprogramming is an early pre-malignant event integral to BRCA1/2 mutation-driven carcinogenesis. Our findings may provide a basis for cancer-preventative strategies. Women with germline variants in BRCA genes are predisposed to ovarian cancer. In this study, the authors demonstrate that fimbrial tissue from the ovary, the site of ovarian cancer, in BRCA mutant carriers contains marked DNA methylation changes compared with the proximal region of the ovary.
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