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Garcia-Recio S, Hinoue T, Wheeler GL, Kelly BJ, Garrido-Castro AC, Pascual T, De Cubas AA, Xia Y, Felsheim BM, McClure MB, Rajkovic A, Karaesmen E, Smith MA, Fan C, Ericsson PIG, Sanders ME, Creighton CJ, Bowen J, Leraas K, Burns RT, Coppens S, Wheless A, Rezk S, Garrett AL, Parker JS, Foy KK, Shen H, Park BH, Krop I, Anders C, Gastier-Foster J, Rimawi MF, Nanda R, Lin NU, Isaacs C, Marcom PK, Storniolo AM, Couch FJ, Chandran U, Davis M, Silverstein J, Ropelewski A, Liu MC, Hilsenbeck SG, Norton L, Richardson AL, Symmans WF, Wolff AC, Davidson NE, Carey LA, Lee AV, Balko JM, Hoadley KA, Laird PW, Mardis ER, King TA, Perou CM. Multiomics in primary and metastatic breast tumors from the AURORA US network finds microenvironment and epigenetic drivers of metastasis. Nat Cancer 2023; 4:128-147. [PMID: 36585450 PMCID: PMC9886551 DOI: 10.1038/s43018-022-00491-x] [Citation(s) in RCA: 17] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/05/2022] [Accepted: 11/11/2022] [Indexed: 12/31/2022]
Abstract
The AURORA US Metastasis Project was established with the goal to identify molecular features associated with metastasis. We assayed 55 females with metastatic breast cancer (51 primary cancers and 102 metastases) by RNA sequencing, tumor/germline DNA exome and low-pass whole-genome sequencing and global DNA methylation microarrays. Expression subtype changes were observed in ~30% of samples and were coincident with DNA clonality shifts, especially involving HER2. Downregulation of estrogen receptor (ER)-mediated cell-cell adhesion genes through DNA methylation mechanisms was observed in metastases. Microenvironment differences varied according to tumor subtype; the ER+/luminal subtype had lower fibroblast and endothelial content, while triple-negative breast cancer/basal metastases showed a decrease in B and T cells. In 17% of metastases, DNA hypermethylation and/or focal deletions were identified near HLA-A and were associated with reduced expression and lower immune cell infiltrates, especially in brain and liver metastases. These findings could have implications for treating individuals with metastatic breast cancer with immune- and HER2-targeting therapies.
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Affiliation(s)
| | | | | | | | | | - Tomas Pascual
- University of North Carolina, Chapel Hill, NC, USA
- SOLTI Cancer Research Group, Barcelona, Spain
| | - Aguirre A De Cubas
- Vanderbilt University Medical Center, Nashville, TN, USA
- Medical University of South Carolina, Charleston, SC, USA
| | - Youli Xia
- University of North Carolina, Chapel Hill, NC, USA
- Boehringer Ingelheim, Ridgefield, CT, USA
| | | | - Marni B McClure
- University of North Carolina, Chapel Hill, NC, USA
- Johns Hopkins University, Baltimore, MD, USA
| | | | | | | | - Cheng Fan
- University of North Carolina, Chapel Hill, NC, USA
| | | | | | | | - Jay Bowen
- Nationwide Children's Hospital, Columbus, OH, USA
| | | | - Robyn T Burns
- Translational Breast Cancer Research Consortium, Baltimore, USA
| | - Sara Coppens
- Nationwide Children's Hospital, Columbus, OH, USA
| | - Amy Wheless
- University of North Carolina, Chapel Hill, NC, USA
| | - Salma Rezk
- University of North Carolina, Chapel Hill, NC, USA
| | | | | | | | - Hui Shen
- Van Andel Institute, Grand Rapids, MI, USA
| | - Ben H Park
- Vanderbilt University Medical Center, Nashville, TN, USA
| | - Ian Krop
- Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | | | | | | | | | - Nancy U Lin
- Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | | | | | | | | | - Uma Chandran
- UPMC Hillman Cancer Center, University of Pittsburgh, Pittsburgh, PA, USA
| | - Michael Davis
- UPMC Hillman Cancer Center, University of Pittsburgh, Pittsburgh, PA, USA
| | | | - Alexander Ropelewski
- Pittsburgh Supercomputing Center, Carnegie Mellon University, Pittsburgh, PA, USA
| | | | | | - Larry Norton
- Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | | | | | | | - Nancy E Davidson
- Fred Hutchinson Cancer Research Center, University of Washington, Seattle, WA, USA
| | - Lisa A Carey
- University of North Carolina, Chapel Hill, NC, USA
| | - Adrian V Lee
- UPMC Hillman Cancer Center, University of Pittsburgh, Pittsburgh, PA, USA
| | - Justin M Balko
- Vanderbilt University Medical Center, Nashville, TN, USA
| | | | | | | | - Tari A King
- Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
- Division of Breast Surgery, Brigham and Women's Hospital, Boston, MA, USA
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Zhou W, Hinoue T, Barnes B, Mitchell O, Iqbal W, Lee SM, Foy KK, Lee KH, Moyer EJ, VanderArk A, Koeman JM, Ding W, Kalkat M, Spix NJ, Eagleson B, Pospisilik JA, Szabó PE, Bartolomei MS, Vander Schaaf NA, Kang L, Wiseman AK, Jones PA, Krawczyk CM, Adams M, Porecha R, Chen BH, Shen H, Laird PW. DNA methylation dynamics and dysregulation delineated by high-throughput profiling in the mouse. Cell Genom 2022; 2:100144. [PMID: 35873672 PMCID: PMC9306256 DOI: 10.1016/j.xgen.2022.100144] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/08/2021] [Revised: 03/20/2022] [Accepted: 05/20/2022] [Indexed: 05/21/2023]
Abstract
We have developed a mouse DNA methylation array that contains 296,070 probes representing the diversity of mouse DNA methylation biology. We present a mouse methylation atlas as a rich reference resource of 1,239 DNA samples encompassing distinct tissues, strains, ages, sexes, and pathologies. We describe applications for comparative epigenomics, genomic imprinting, epigenetic inhibitors, patient-derived xenograft assessment, backcross tracing, and epigenetic clocks. We dissect DNA methylation processes associated with differentiation, aging, and tumorigenesis. Notably, we find that tissue-specific methylation signatures localize to binding sites for transcription factors controlling the corresponding tissue development. Age-associated hypermethylation is enriched at regions of Polycomb repression, while hypomethylation is enhanced at regions bound by cohesin complex members. Apc Min/+ polyp-associated hypermethylation affects enhancers regulating intestinal differentiation, while hypomethylation targets AP-1 binding sites. This Infinium Mouse Methylation BeadChip (version MM285) is widely accessible to the research community and will accelerate high-sample-throughput studies in this important model organism.
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Affiliation(s)
- Wanding Zhou
- Center for Computational and Genomic Medicine, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
- Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
- Corresponding author
| | - Toshinori Hinoue
- Department of Epigenetics, Van Andel Institute, Grand Rapids, MI 49503, USA
| | - Bret Barnes
- Illumina, Inc., Bioinformatics and Instrument Software Department, San Diego, CA 92122, USA
| | - Owen Mitchell
- Department of Epigenetics, Van Andel Institute, Grand Rapids, MI 49503, USA
| | - Waleed Iqbal
- Center for Computational and Genomic Medicine, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Sol Moe Lee
- Center for Computational and Genomic Medicine, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Kelly K. Foy
- Department of Epigenetics, Van Andel Institute, Grand Rapids, MI 49503, USA
| | - Kwang-Ho Lee
- Department of Epigenetics, Van Andel Institute, Grand Rapids, MI 49503, USA
| | - Ethan J. Moyer
- Center for Computational and Genomic Medicine, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Alexandra VanderArk
- Department of Metabolism and Nutritional Programming, Van Andel Institute, Grand Rapids, MI 49503, USA
| | - Julie M. Koeman
- Genomics Core, Van Andel Institute, Grand Rapids, MI 49503, USA
| | - Wubin Ding
- Center for Computational and Genomic Medicine, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Manpreet Kalkat
- Department of Epigenetics, Van Andel Institute, Grand Rapids, MI 49503, USA
| | - Nathan J. Spix
- Department of Epigenetics, Van Andel Institute, Grand Rapids, MI 49503, USA
| | - Bryn Eagleson
- Vivarium and Transgenics Core, Van Andel Institute, Grand Rapids, MI 49503, USA
| | | | - Piroska E. Szabó
- Department of Epigenetics, Van Andel Institute, Grand Rapids, MI 49503, USA
| | - Marisa S. Bartolomei
- Department of Cell and Developmental Biology, Epigenetics Institute, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA
| | | | - Liang Kang
- Department of Epigenetics, Van Andel Institute, Grand Rapids, MI 49503, USA
| | - Ashley K. Wiseman
- Department of Epigenetics, Van Andel Institute, Grand Rapids, MI 49503, USA
| | - Peter A. Jones
- Department of Epigenetics, Van Andel Institute, Grand Rapids, MI 49503, USA
| | - Connie M. Krawczyk
- Department of Metabolism and Nutritional Programming, Van Andel Institute, Grand Rapids, MI 49503, USA
| | - Marie Adams
- Genomics Core, Van Andel Institute, Grand Rapids, MI 49503, USA
| | - Rishi Porecha
- Illumina, Inc., Bioinformatics and Instrument Software Department, San Diego, CA 92122, USA
| | | | - Hui Shen
- Department of Epigenetics, Van Andel Institute, Grand Rapids, MI 49503, USA
- Corresponding author
| | - Peter W. Laird
- Department of Epigenetics, Van Andel Institute, Grand Rapids, MI 49503, USA
- Corresponding author
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Morrison J, Koeman JM, Johnson BK, Foy KK, Beddows I, Zhou W, Chesla DW, Rossell LL, Siegwald EJ, Adams M, Shen H. Evaluation of whole-genome DNA methylation sequencing library preparation protocols. Epigenetics Chromatin 2021; 14:28. [PMID: 34147133 PMCID: PMC8214260 DOI: 10.1186/s13072-021-00401-y] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2021] [Accepted: 05/27/2021] [Indexed: 12/18/2022] Open
Abstract
Background With rapidly dropping sequencing cost, the popularity of whole-genome DNA methylation sequencing has been on the rise. Multiple library preparation protocols currently exist. We have performed 22 whole-genome DNA methylation sequencing experiments on snap frozen human samples, and extensively benchmarked common library preparation protocols for whole-genome DNA methylation sequencing, including three traditional bisulfite-based protocols and a new enzyme-based protocol. In addition, different input DNA quantities were compared for two kits compatible with a reduced starting quantity. In addition, we also present bioinformatic analysis pipelines for sequencing data from each of these library types. Results An assortment of metrics were collected for each kit, including raw read statistics, library quality and uniformity metrics, cytosine retention, and CpG beta value consistency between technical replicates. Overall, the NEBNext Enzymatic Methyl-seq and Swift Accel-NGS Methyl-Seq kits performed quantitatively better than the other two protocols. In addition, the NEB and Swift kits performed well at low-input amounts, validating their utility in applications where DNA is the limiting factor. Results The NEBNext Enzymatic Methyl-seq kit appeared to be the best option for whole-genome DNA methylation sequencing of high-quality DNA, closely followed by the Swift kit, which potentially works better for degraded samples. Further, a general bioinformatic pipeline is applicable across the four protocols, with the exception of extra trimming needed for the Swift Biosciences’s Accel-NGS Methyl-Seq protocol to remove the Adaptase sequence. Supplementary Information The online version contains supplementary material available at 10.1186/s13072-021-00401-y.
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Affiliation(s)
- Jacob Morrison
- Department of Epigenetics, Van Andel Research Institute, 333 Bostwick Avenue NE, Grand Rapids, MI, 49503, USA
| | - Julie M Koeman
- Genomics Core, Van Andel Research Institute, 333 Bostwick Avenue NE, Grand Rapids, MI, 49503, USA
| | - Benjamin K Johnson
- Department of Epigenetics, Van Andel Research Institute, 333 Bostwick Avenue NE, Grand Rapids, MI, 49503, USA
| | - Kelly K Foy
- Department of Epigenetics, Van Andel Research Institute, 333 Bostwick Avenue NE, Grand Rapids, MI, 49503, USA
| | - Ian Beddows
- Department of Epigenetics, Van Andel Research Institute, 333 Bostwick Avenue NE, Grand Rapids, MI, 49503, USA
| | - Wanding Zhou
- Center for Computational and Genomic Medicine, The Children's Hospital of Philadelphia, 3501 Civic Center Boulevard, Philadelphia, PA, 19104, USA.,Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - David W Chesla
- Spectrum Health Office of Research and Education, Spectrum Health System, 15 Michigan Street NE, Grand Rapids, MI, 49503, USA
| | - Larissa L Rossell
- Spectrum Health Office of Research and Education, Spectrum Health System, 15 Michigan Street NE, Grand Rapids, MI, 49503, USA
| | - Emily J Siegwald
- Spectrum Health Office of Research and Education, Spectrum Health System, 15 Michigan Street NE, Grand Rapids, MI, 49503, USA
| | - Marie Adams
- Genomics Core, Van Andel Research Institute, 333 Bostwick Avenue NE, Grand Rapids, MI, 49503, USA.
| | - Hui Shen
- Department of Epigenetics, Van Andel Research Institute, 333 Bostwick Avenue NE, Grand Rapids, MI, 49503, USA.
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Fan H, Atiya HI, Wang Y, Pisanic TR, Wang TH, Shih IM, Foy KK, Frisbie L, Buckanovich RJ, Chomiak AA, Tiedemann RL, Rothbart SB, Chandler C, Shen H, Coffman LG. Epigenomic Reprogramming toward Mesenchymal-Epithelial Transition in Ovarian-Cancer-Associated Mesenchymal Stem Cells Drives Metastasis. Cell Rep 2020; 33:108473. [PMID: 33296650 PMCID: PMC7747301 DOI: 10.1016/j.celrep.2020.108473] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2019] [Revised: 08/26/2020] [Accepted: 11/11/2020] [Indexed: 12/12/2022] Open
Abstract
A role for cancer cell epithelial-to-mesenchymal transition (EMT) in cancer is well established. Here, we show that, in addition to cancer cell EMT, ovarian cancer cell metastasis relies on an epigenomic mesenchymal-to-epithelial transition (MET) in host mesenchymal stem cells (MSCs). These reprogrammed MSCs, termed carcinoma-associated MSCs (CA-MSCs), acquire pro-tumorigenic functions and directly bind cancer cells to serve as a metastatic driver/chaperone. Cancer cells induce this epigenomic MET characterized by enhancer-enriched DNA hypermethylation, altered chromatin accessibility, and differential histone modifications. This phenomenon appears clinically relevant, as CA-MSC MET is highly correlated with patient survival. Mechanistically, mirroring MET observed in development, MET in CA-MSCs is mediated by WT1 and EZH2. Importantly, EZH2 inhibitors, which are clinically available, significantly inhibited CA-MSC-mediated metastasis in mouse models of ovarian cancer.
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Affiliation(s)
- Huihui Fan
- Center for Epigenetics, Van Andel Research Institute, Grand Rapids, MI, USA
| | - Huda I Atiya
- Division of Hematology/Oncology, Department of Medicine, Hillman Cancer Center, University of Pittsburgh, Pittsburgh, PA, USA
| | - Yeh Wang
- Department of Gynecology and Obstetrics, Department of Oncology, and Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Thomas R Pisanic
- Johns Hopkins Institute for NanoBiotechnology, Johns Hopkins University, Baltimore, MD, USA
| | - Tza-Huei Wang
- Johns Hopkins Institute for NanoBiotechnology, Johns Hopkins University, Baltimore, MD, USA
| | - Ie-Ming Shih
- Department of Gynecology and Obstetrics, Department of Oncology, and Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Kelly K Foy
- Center for Epigenetics, Van Andel Research Institute, Grand Rapids, MI, USA
| | - Leonard Frisbie
- Division of Hematology/Oncology, Department of Medicine, Hillman Cancer Center, University of Pittsburgh, Pittsburgh, PA, USA
| | - Ronald J Buckanovich
- Division of Hematology/Oncology, Department of Medicine, Hillman Cancer Center, University of Pittsburgh, Pittsburgh, PA, USA; Division of Gynecologic Oncology, Department of Obstetrics, Gynecology, and Reproductive Sciences, Magee Women's Research Institute, University of Pittsburgh, Pittsburgh, PA, USA
| | - Alison A Chomiak
- Center for Epigenetics, Van Andel Research Institute, Grand Rapids, MI, USA
| | | | - Scott B Rothbart
- Center for Epigenetics, Van Andel Research Institute, Grand Rapids, MI, USA
| | - Chelsea Chandler
- Division of Gynecologic Oncology, Department of Obstetrics, Gynecology, and Reproductive Sciences, Magee Women's Research Institute, University of Pittsburgh, Pittsburgh, PA, USA
| | - Hui Shen
- Center for Epigenetics, Van Andel Research Institute, Grand Rapids, MI, USA.
| | - Lan G Coffman
- Division of Hematology/Oncology, Department of Medicine, Hillman Cancer Center, University of Pittsburgh, Pittsburgh, PA, USA; Division of Gynecologic Oncology, Department of Obstetrics, Gynecology, and Reproductive Sciences, Magee Women's Research Institute, University of Pittsburgh, Pittsburgh, PA, USA.
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