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Nguyen TH, Doan NNT, Tran TH, Huynh LAK, Doan PL, Nguyen THH, Nguyen VTC, Nguyen GTH, Nguyen HN, Giang H, Tran LS, Phan MD. Tissue of origin detection for cancer tumor using low-depth cfDNA samples through combination of tumor-specific methylation atlas and genome-wide methylation density in graph convolutional neural networks. J Transl Med 2024; 22:618. [PMID: 38961476 PMCID: PMC11223394 DOI: 10.1186/s12967-024-05416-z] [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: 01/03/2024] [Accepted: 06/19/2024] [Indexed: 07/05/2024] Open
Abstract
BACKGROUND Cell free DNA (cfDNA)-based assays hold great potential in detecting early cancer signals yet determining the tissue-of-origin (TOO) for cancer signals remains a challenging task. Here, we investigated the contribution of a methylation atlas to TOO detection in low depth cfDNA samples. METHODS We constructed a tumor-specific methylation atlas (TSMA) using whole-genome bisulfite sequencing (WGBS) data from five types of tumor tissues (breast, colorectal, gastric, liver and lung cancer) and paired white blood cells (WBC). TSMA was used with a non-negative least square matrix factorization (NNLS) deconvolution algorithm to identify the abundance of tumor tissue types in a WGBS sample. We showed that TSMA worked well with tumor tissue but struggled with cfDNA samples due to the overwhelming amount of WBC-derived DNA. To construct a model for TOO, we adopted the multi-modal strategy and used as inputs the combination of deconvolution scores from TSMA with other features of cfDNA. RESULTS Our final model comprised of a graph convolutional neural network using deconvolution scores and genome-wide methylation density features, which achieved an accuracy of 69% in a held-out validation dataset of 239 low-depth cfDNA samples. CONCLUSIONS In conclusion, we have demonstrated that our TSMA in combination with other cfDNA features can improve TOO detection in low-depth cfDNA samples.
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Affiliation(s)
| | | | - Trung Hieu Tran
- Medical Genetics Institute, Gene Solutions, Ho Chi Minh, Vietnam
| | - Le Anh Khoa Huynh
- Medical Genetics Institute, Gene Solutions, Ho Chi Minh, Vietnam
- Department of Biostatistics, School of Medicine, Virginia Commonwealth University, Richmond, USA
| | - Phuoc Loc Doan
- Medical Genetics Institute, Gene Solutions, Ho Chi Minh, Vietnam
| | | | | | | | | | - Hoa Giang
- Medical Genetics Institute, Gene Solutions, Ho Chi Minh, Vietnam
| | - Le Son Tran
- Medical Genetics Institute, Gene Solutions, Ho Chi Minh, Vietnam
| | - Minh Duy Phan
- Medical Genetics Institute, Gene Solutions, Ho Chi Minh, Vietnam.
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2
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Buckley DN, Tew BY, Gooden C, Salhia B. A comprehensive analysis of minimally differentially methylated regions common to pediatric and adult solid tumors. NPJ Precis Oncol 2024; 8:125. [PMID: 38824198 PMCID: PMC11144230 DOI: 10.1038/s41698-024-00590-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2023] [Accepted: 04/14/2024] [Indexed: 06/03/2024] Open
Abstract
Cancer is the second most common cause of death in children aged 1-14 years in the United States, with 11,000 new cases and 1200 deaths annually. Pediatric cancers typically have lower mutational burden compared to adult-onset cancers, however, the epigenomes in pediatric cancer are highly altered, with widespread DNA methylation changes. The rarity of pediatric cancers poses a significant challenge to developing cancer-type specific biomarkers for diagnosis, prognosis, or treatment monitoring. In the current study, we explored the potential of a DNA methylation profile common across various pediatric cancers. To do this, we conducted whole genome bisulfite sequencing (WGBS) on 31 recurrent pediatric tumor tissues, 13 normal tissues, and 20 plasma cell-free (cf)DNA samples, representing 11 different pediatric cancer types. We defined minimal focal regions that were differentially methylated across samples in the multiple cancer types which we termed minimally differentially methylated regions (mDMRs). These methylation changes were also observed in 506 pediatric and 5691 adult cancer samples accessed from publicly available databases, and in 44 pediatric cancer samples we analyzed using a targeted hybridization probe capture assay. Finally, we found that these methylation changes were detectable in cfDNA and could serve as potential cfDNA methylation biomarkers for early detection or minimal residual disease.
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Affiliation(s)
- David N Buckley
- Department of Translational Genomics, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Ben Yi Tew
- Department of Translational Genomics, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Chris Gooden
- Department of Translational Genomics, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Bodour Salhia
- Department of Translational Genomics, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA.
- Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, CA, USA.
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3
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Rendek T, Pos O, Duranova T, Saade R, Budis J, Repiska V, Szemes T. Current Challenges of Methylation-Based Liquid Biopsies in Cancer Diagnostics. Cancers (Basel) 2024; 16:2001. [PMID: 38893121 PMCID: PMC11171112 DOI: 10.3390/cancers16112001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2024] [Revised: 05/13/2024] [Accepted: 05/16/2024] [Indexed: 06/21/2024] Open
Abstract
In current clinical practice, effective cancer testing and screening paradigms are limited to specific types of cancer, exhibiting varying efficiency, acceptance, and adherence. Cell-free DNA (cfDNA) methylation profiling holds promise in providing information about the presence of malignity regardless of its type and location while leveraging blood-based liquid biopsies as a method to obtain analytical samples. However, technical difficulties, costs and challenges resulting from biological variations, tumor heterogeneity, and exogenous factors persist. This method exploits the mechanisms behind cfDNA release but faces issues like fragmentation, low concentrations, and high background noise. This review explores cfDNA methylation's origins, means of detection, and profiling for cancer diagnostics. The critical evaluation of currently available multi-cancer early detection methods (MCEDs) as well as tests targeting single genes, emphasizing their potential and limits to refine strategies for early cancer detection, are explained. The current methodology limitations, workflows, comparisons of clinically approved liquid biopsy-based methylation tests for cancer, their utilization in companion diagnostics as well as the biological limitations of the epigenetics approach are discussed, aiming to help healthcare providers as well as researchers to orient themselves in this increasingly complex and evolving field of diagnostics.
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Affiliation(s)
- Tomas Rendek
- Institute of Medical Biology, Genetics and Clinical Genetics, Faculty of Medicine, Comenius University, 811 08 Bratislava, Slovakia;
| | - Ondrej Pos
- Geneton Ltd., 841 04 Bratislava, Slovakia; (O.P.); (J.B.); (T.S.)
- Comenius University Science Park, 841 04 Bratislava, Slovakia;
| | | | - Rami Saade
- 2nd Department of Gynaecology and Obstetrics, Faculty of Medicine, Comenius University, 811 08 Bratislava, Slovakia;
| | - Jaroslav Budis
- Geneton Ltd., 841 04 Bratislava, Slovakia; (O.P.); (J.B.); (T.S.)
- Comenius University Science Park, 841 04 Bratislava, Slovakia;
| | - Vanda Repiska
- Institute of Medical Biology, Genetics and Clinical Genetics, Faculty of Medicine, Comenius University, 811 08 Bratislava, Slovakia;
| | - Tomas Szemes
- Geneton Ltd., 841 04 Bratislava, Slovakia; (O.P.); (J.B.); (T.S.)
- Comenius University Science Park, 841 04 Bratislava, Slovakia;
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Lagarde CB, Kavalakatt J, Benz MC, Hawes ML, Arbogast CA, Cullen NM, McConnell EC, Rinderle C, Hebert KL, Khosla M, Belgodere JA, Hoang VT, Collins-Burow BM, Bunnell BA, Burow ME, Alahari SK. Obesity-associated epigenetic alterations and the obesity-breast cancer axis. Oncogene 2024; 43:763-775. [PMID: 38310162 DOI: 10.1038/s41388-024-02954-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2023] [Revised: 01/18/2024] [Accepted: 01/22/2024] [Indexed: 02/05/2024]
Abstract
Both breast cancer and obesity can regulate epigenetic changes or be regulated by epigenetic changes. Due to the well-established link between obesity and an increased risk of developing breast cancer, understanding how obesity-mediated epigenetic changes affect breast cancer pathogenesis is critical. Researchers have described how obesity and breast cancer modulate the epigenome individually and synergistically. In this review, the epigenetic alterations that occur in obesity, including DNA methylation, histone, and chromatin modification, accelerated epigenetic age, carcinogenesis, metastasis, and tumor microenvironment modulation, are discussed. Delineating the relationship between obesity and epigenetic regulation is vital to furthering our understanding of breast cancer pathogenesis.
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Affiliation(s)
- Courtney B Lagarde
- Department of Medicine, Section of Hematology and Oncology, Tulane University School of Medicine, New Orleans, LA, 70112, USA
| | - Joachim Kavalakatt
- Department of Microbiology, Immunology and Genetics, University of North Texas Health Science Center, Fort Worth, TX, 76107, USA
| | - Megan C Benz
- Department of Medicine, Section of Hematology and Oncology, Tulane University School of Medicine, New Orleans, LA, 70112, USA
| | - Mackenzie L Hawes
- Department of Medicine, Section of Hematology and Oncology, Tulane University School of Medicine, New Orleans, LA, 70112, USA
| | - Carter A Arbogast
- Department of Medicine, Section of Hematology and Oncology, Tulane University School of Medicine, New Orleans, LA, 70112, USA
| | - Nicole M Cullen
- Department of Medicine, Section of Hematology and Oncology, Tulane University School of Medicine, New Orleans, LA, 70112, USA
| | - Emily C McConnell
- Department of Medicine, Section of Hematology and Oncology, Tulane University School of Medicine, New Orleans, LA, 70112, USA
| | - Caroline Rinderle
- Department of Microbiology, Immunology and Genetics, University of North Texas Health Science Center, Fort Worth, TX, 76107, USA
| | - Katherine L Hebert
- Department of Medicine, Section of Hematology and Oncology, Tulane University School of Medicine, New Orleans, LA, 70112, USA
| | - Maninder Khosla
- Department of Biochemistry and Molecular Biology, LSU Health Science Center School of Medicine, New Orleans, LA, 70112, USA
| | - Jorge A Belgodere
- Department of Medicine, Section of Hematology and Oncology, Tulane University School of Medicine, New Orleans, LA, 70112, USA
- Department of Biological and Agricultural Engineering, Louisiana State University and Agricultural Center, Baton Rouge, LA, 70803, USA
| | - Van T Hoang
- Department of Medicine, Section of Hematology and Oncology, Tulane University School of Medicine, New Orleans, LA, 70112, USA
| | - Bridgette M Collins-Burow
- Department of Medicine, Section of Hematology and Oncology, Tulane University School of Medicine, New Orleans, LA, 70112, USA
| | - Bruce A Bunnell
- Department of Microbiology, Immunology and Genetics, University of North Texas Health Science Center, Fort Worth, TX, 76107, USA
| | - Matthew E Burow
- Department of Medicine, Section of Hematology and Oncology, Tulane University School of Medicine, New Orleans, LA, 70112, USA.
| | - Suresh K Alahari
- Department of Biochemistry and Molecular Biology, LSU Health Science Center School of Medicine, New Orleans, LA, 70112, USA.
- Stanley S. Scott Cancer Center, LSU Health Science Center School of Medicine, New Orleans, LA, 70112, USA.
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Zavarykina TM, Lomskova PK, Pronina IV, Khokhlova SV, Stenina MB, Sukhikh GT. Circulating Tumor DNA Is a Variant of Liquid Biopsy with Predictive and Prognostic Clinical Value in Breast Cancer Patients. Int J Mol Sci 2023; 24:17073. [PMID: 38069396 PMCID: PMC10706922 DOI: 10.3390/ijms242317073] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2023] [Revised: 11/24/2023] [Accepted: 11/27/2023] [Indexed: 12/18/2023] Open
Abstract
This paper introduces the reader to the field of liquid biopsies and cell-free nucleic acids, focusing on circulating tumor DNA (ctDNA) in breast cancer (BC). BC is the most common type of cancer in women, and progress with regard to treatment has been made in recent years. Despite this, there remain a number of unresolved issues in the treatment of BC; in particular, early detection and diagnosis, reliable markers of response to treatment and for the prediction of recurrence and metastasis, especially for unfavorable subtypes, are needed. It is also important to identify biomarkers for the assessment of drug resistance and for disease monitoring. Our work is devoted to ctDNA, which may be such a marker. Here, we describe its main characteristics and potential applications in clinical oncology. This review considers the results of studies devoted to the analysis of the prognostic and predictive roles of various methods for the determination of ctDNA in BC patients. Currently known epigenetic changes in ctDNA with clinical significance are reviewed. The possibility of using ctDNA as a predictive and prognostic marker for monitoring BC and predicting the recurrence and metastasis of cancer is also discussed, which may become an important part of a precision approach to the treatment of BC.
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Affiliation(s)
- Tatiana M. Zavarykina
- N.M. Emanuel Institute of Biochemical Physics of the Russian Academy of Sciences, Moscow 119334, Russia;
- “B.I. Kulakov National Medical Research Center of Obstetrics, Gynecology, and Perinatology of Ministry of Health of the Russian Federation, Moscow 117997, Russia; (S.V.K.); (G.T.S.)
| | - Polina K. Lomskova
- N.M. Emanuel Institute of Biochemical Physics of the Russian Academy of Sciences, Moscow 119334, Russia;
| | - Irina V. Pronina
- Institute of General Pathology and Pathophysiology, Moscow 125315, Russia;
| | - Svetlana V. Khokhlova
- “B.I. Kulakov National Medical Research Center of Obstetrics, Gynecology, and Perinatology of Ministry of Health of the Russian Federation, Moscow 117997, Russia; (S.V.K.); (G.T.S.)
| | - Marina B. Stenina
- “N.N. Blokhin National Medical Research Center of Oncology of Ministry of Health of the Russian Federation, Moscow 115522, Russia;
| | - Gennady T. Sukhikh
- “B.I. Kulakov National Medical Research Center of Obstetrics, Gynecology, and Perinatology of Ministry of Health of the Russian Federation, Moscow 117997, Russia; (S.V.K.); (G.T.S.)
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Hallermayr A, Keßler T, Steinke-Lange V, Heitzer E, Holinski-Feder E, Speicher M. The utility of liquid biopsy in clinical genetic diagnosis of cancer and monogenic mosaic disorders. MED GENET-BERLIN 2023; 35:275-284. [PMID: 38835734 PMCID: PMC11006364 DOI: 10.1515/medgen-2023-2066] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/06/2024]
Abstract
Liquid biopsy for minimally invasive diagnosis and monitoring of cancer patients is progressing toward routine clinical practice. With the implementation of highly sensitive next-generation sequencing (NGS) based assays for the analysis of cfDNA, however, consideration of the utility of liquid biopsy for clinical genetic testing is critical. While the focus of liquid biopsy for cancer diagnosis is the detection of circulating tumor DNA (ctDNA) as a fraction of total cell-free DNA (cfDNA), cfDNA analysis reveals both somatic mosaic tumor and germline variants and clonal hematopoiesis. Here we outline advantages and limitations of mosaic and germline variant detection as well as the impact of clonal hematopoiesis on liquid biopsy in cancer diagnosis. We also evaluate the potential of cfDNA analysis for the molecular diagnosis of monogenic mosaic disorders.
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Affiliation(s)
| | - Thomas Keßler
- MGZ - Medizinisch Genetisches Zentrum München Germany
| | | | - Ellen Heitzer
- Medical University of Graz Institute of Human Genetics, Diagnostic and Research Center for Molecular Biomedicine (Austria) Graz Austria
| | | | - Michael Speicher
- Medical University of Graz Institute of Human Genetics, Diagnostic and Research Center for Molecular Biomedicine (Austria), Neue Stiftingtalstraße 2 Graz Austria
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7
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Nguyen VTC, Nguyen TH, Doan NNT, Pham TMQ, Nguyen GTH, Nguyen TD, Tran TTT, Vo DL, Phan TH, Jasmine TX, Nguyen VC, Nguyen HT, Nguyen TV, Nguyen THH, Huynh LAK, Tran TH, Dang QT, Doan TN, Tran AM, Nguyen VH, Nguyen VTA, Ho LMQ, Tran QD, Pham TTT, Ho TD, Nguyen BT, Nguyen TNV, Nguyen TD, Phu DTB, Phan BHH, Vo TL, Nai THT, Tran TT, Truong MH, Tran NC, Le TK, Tran THT, Duong ML, Bach HPT, Kim VV, Pham TA, Tran DH, Le TNA, Pham TVN, Le MT, Vo DH, Tran TMT, Nguyen MN, Van TTV, Nguyen AN, Tran TT, Tran VU, Le MP, Do TT, Phan TV, Nguyen HDL, Nguyen DS, Cao VT, Do TTT, Truong DK, Tang HS, Giang H, Nguyen HN, Phan MD, Tran LS. Multimodal analysis of methylomics and fragmentomics in plasma cell-free DNA for multi-cancer early detection and localization. eLife 2023; 12:RP89083. [PMID: 37819044 PMCID: PMC10567114 DOI: 10.7554/elife.89083] [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] [Indexed: 10/13/2023] Open
Abstract
Despite their promise, circulating tumor DNA (ctDNA)-based assays for multi-cancer early detection face challenges in test performance, due mostly to the limited abundance of ctDNA and its inherent variability. To address these challenges, published assays to date demanded a very high-depth sequencing, resulting in an elevated price of test. Herein, we developed a multimodal assay called SPOT-MAS (screening for the presence of tumor by methylation and size) to simultaneously profile methylomics, fragmentomics, copy number, and end motifs in a single workflow using targeted and shallow genome-wide sequencing (~0.55×) of cell-free DNA. We applied SPOT-MAS to 738 non-metastatic patients with breast, colorectal, gastric, lung, and liver cancer, and 1550 healthy controls. We then employed machine learning to extract multiple cancer and tissue-specific signatures for detecting and locating cancer. SPOT-MAS successfully detected the five cancer types with a sensitivity of 72.4% at 97.0% specificity. The sensitivities for detecting early-stage cancers were 73.9% and 62.3% for stages I and II, respectively, increasing to 88.3% for non-metastatic stage IIIA. For tumor-of-origin, our assay achieved an accuracy of 0.7. Our study demonstrates comparable performance to other ctDNA-based assays while requiring significantly lower sequencing depth, making it economically feasible for population-wide screening.
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