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Janiszewska M, Tabassum DP, Castaño Z, Cristea S, Yamamoto KN, Kingston NL, Murphy KC, Shu S, Harper NW, Del Alcazar CG, Alečković M, Ekram MB, Cohen O, Kwak M, Qin Y, Laszewski T, Luoma A, Marusyk A, Wucherpfennig KW, Wagle N, Fan R, Michor F, McAllister SS, Polyak K. Author Correction: Subclonal cooperation drives metastasis by modulating local and systemic immune microenvironments. Nat Cell Biol 2024; 26:841. [PMID: 38443568 DOI: 10.1038/s41556-024-01385-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/07/2024]
Affiliation(s)
- Michalina Janiszewska
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
- Department of Molecular Medicine, The Scripps Research Institute, Jupiter, FL, USA
| | - Doris P Tabassum
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Research Square, Durham, NC, USA
| | - Zafira Castaño
- Department of Medicine, Harvard Medical School, Boston, MA, USA
- Hematology Division, Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA
| | - Simona Cristea
- Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Biostatistics, Harvard T. H. Chan School of Public Health, Boston, MA, USA
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, USA
| | - Kimiyo N Yamamoto
- Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Biostatistics, Harvard T. H. Chan School of Public Health, Boston, MA, USA
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, USA
| | - Natalie L Kingston
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Katherine C Murphy
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Shaokun Shu
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - Nicholas W Harper
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Carlos Gil Del Alcazar
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - Maša Alečković
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - Muhammad B Ekram
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
- WuXi NextCODE, Cambridge, MA, USA
| | - Ofir Cohen
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- The Eli and Edythe L. Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Minsuk Kwak
- Department of Biomedical Engineering, Yale School of Medicine, New Haven, CT, USA
- Yale Comprehensive Cancer Center, New Haven, CT, USA
| | - Yuanbo Qin
- Department of Medicine, Harvard Medical School, Boston, MA, USA
- Hematology Division, Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA
- EdiGene, Cambridge, MA, USA
| | - Tyler Laszewski
- Hematology Division, Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA
| | - Adrienne Luoma
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, and Department of Microbiology and Immunobiology, Harvard Medical School, Boston, MA, USA
| | - Andriy Marusyk
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
- Department of Cancer Imaging and Metabolism, Moffitt Cancer Center, Tampa, FL, USA
| | - Kai W Wucherpfennig
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, and Department of Microbiology and Immunobiology, Harvard Medical School, Boston, MA, USA
| | - Nikhil Wagle
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA
- The Eli and Edythe L. Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Rong Fan
- Department of Biomedical Engineering, Yale School of Medicine, New Haven, CT, USA
- Yale Comprehensive Cancer Center, New Haven, CT, USA
| | - Franziska Michor
- Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Biostatistics, Harvard T. H. Chan School of Public Health, Boston, MA, USA
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, USA
- The Eli and Edythe L. Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Center for Cancer Evolution, Dana-Farber Cancer Institute, Boston, MA, USA
- Ludwig Center at Harvard, Boston, MA, USA
| | - Sandra S McAllister
- Department of Medicine, Harvard Medical School, Boston, MA, USA
- Hematology Division, Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA
- The Eli and Edythe L. Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Harvard Stem Cell Institute, Cambridge, MA, USA
| | - Kornelia Polyak
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA.
- Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA.
- Department of Medicine, Harvard Medical School, Boston, MA, USA.
- The Eli and Edythe L. Broad Institute of Harvard and MIT, Cambridge, MA, USA.
- Center for Cancer Evolution, Dana-Farber Cancer Institute, Boston, MA, USA.
- Ludwig Center at Harvard, Boston, MA, USA.
- Harvard Stem Cell Institute, Cambridge, MA, USA.
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Jovanović B, Temko D, Stevens LE, Seehawer M, Fassl A, Murphy K, Anand J, Garza K, Gulvady A, Qiu X, Harper NW, Daniels VW, Xiao-Yun H, Ge JY, Alečković M, Pyrdol J, Hinohara K, Egri SB, Papanastasiou M, Vadhi R, Font-Tello A, Witwicki R, Peluffo G, Trinh A, Shu S, Diciaccio B, Ekram MB, Subedee A, Herbert ZT, Wucherpfennig KW, Letai AG, Jaffe JD, Sicinski P, Brown M, Dillon D, Long HW, Michor F, Polyak K. Heterogeneity and transcriptional drivers of triple-negative breast cancer. Cell Rep 2023; 42:113564. [PMID: 38100350 PMCID: PMC10842760 DOI: 10.1016/j.celrep.2023.113564] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2023] [Revised: 10/05/2023] [Accepted: 11/22/2023] [Indexed: 12/17/2023] Open
Abstract
Triple-negative breast cancer (TNBC) is a heterogeneous disease with limited treatment options. To characterize TNBC heterogeneity, we defined transcriptional, epigenetic, and metabolic subtypes and subtype-driving super-enhancers and transcription factors by combining functional and molecular profiling with computational analyses. Single-cell RNA sequencing revealed relative homogeneity of the major transcriptional subtypes (luminal, basal, and mesenchymal) within samples. We found that mesenchymal TNBCs share features with mesenchymal neuroblastoma and rhabdoid tumors and that the PRRX1 transcription factor is a key driver of these tumors. PRRX1 is sufficient for inducing mesenchymal features in basal but not in luminal TNBC cells via reprogramming super-enhancer landscapes, but it is not required for mesenchymal state maintenance or for cellular viability. Our comprehensive, large-scale, multiplatform, multiomics study of both experimental and clinical TNBC is an important resource for the scientific and clinical research communities and opens venues for future investigation.
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Affiliation(s)
- Bojana Jovanović
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Medicine, Brigham and Women's Hospital, Boston, MA 02115, USA; Department of Medicine, Harvard Medical School, Boston, MA 02115, USA
| | - Daniel Temko
- Department of Data Science, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA; Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA
| | - Laura E Stevens
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Medicine, Brigham and Women's Hospital, Boston, MA 02115, USA; Department of Medicine, Harvard Medical School, Boston, MA 02115, USA
| | - Marco Seehawer
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Medicine, Brigham and Women's Hospital, Boston, MA 02115, USA; Department of Medicine, Harvard Medical School, Boston, MA 02115, USA
| | - Anne Fassl
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Katherine Murphy
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Jayati Anand
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Kodie Garza
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Anushree Gulvady
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Medicine, Brigham and Women's Hospital, Boston, MA 02115, USA; Department of Medicine, Harvard Medical School, Boston, MA 02115, USA
| | - Xintao Qiu
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Nicholas W Harper
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Veerle W Daniels
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Huang Xiao-Yun
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Jennifer Y Ge
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Data Science, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Harvard-MIT Division of Health Sciences and Technology, Harvard Medical School, Boston, MA 02115, USA
| | - Maša Alečković
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Medicine, Brigham and Women's Hospital, Boston, MA 02115, USA; Department of Medicine, Harvard Medical School, Boston, MA 02115, USA
| | - Jason Pyrdol
- Departments of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Departments of Microbiology and Immunobiology, Harvard Medical School, Boston, MA 02115, USA
| | - Kunihiko Hinohara
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Medicine, Brigham and Women's Hospital, Boston, MA 02115, USA; Department of Medicine, Harvard Medical School, Boston, MA 02115, USA
| | - Shawn B Egri
- The Eli and Edythe L. Broad Institute, Cambridge, MA 02142, USA
| | | | - Raga Vadhi
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Alba Font-Tello
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Robert Witwicki
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Medicine, Brigham and Women's Hospital, Boston, MA 02115, USA; Department of Medicine, Harvard Medical School, Boston, MA 02115, USA
| | - Guillermo Peluffo
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Medicine, Brigham and Women's Hospital, Boston, MA 02115, USA; Department of Medicine, Harvard Medical School, Boston, MA 02115, USA
| | - Anne Trinh
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Medicine, Brigham and Women's Hospital, Boston, MA 02115, USA; Department of Medicine, Harvard Medical School, Boston, MA 02115, USA
| | - Shaokun Shu
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Medicine, Brigham and Women's Hospital, Boston, MA 02115, USA; Department of Medicine, Harvard Medical School, Boston, MA 02115, USA
| | - Benedetto Diciaccio
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Muhammad B Ekram
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Medicine, Brigham and Women's Hospital, Boston, MA 02115, USA; Department of Medicine, Harvard Medical School, Boston, MA 02115, USA
| | - Ashim Subedee
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Zachary T Herbert
- Department of Molecular Biology Core Facility, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Kai W Wucherpfennig
- Departments of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Departments of Microbiology and Immunobiology, Harvard Medical School, Boston, MA 02115, USA
| | - Anthony G Letai
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Medicine, Brigham and Women's Hospital, Boston, MA 02115, USA; Department of Medicine, Harvard Medical School, Boston, MA 02115, USA
| | - Jacob D Jaffe
- The Eli and Edythe L. Broad Institute, Cambridge, MA 02142, USA
| | - Piotr Sicinski
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Myles Brown
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Medicine, Brigham and Women's Hospital, Boston, MA 02115, USA; Department of Medicine, Harvard Medical School, Boston, MA 02115, USA; Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Ludwig Center at Harvard, Harvard Medical School, Boston, MA 02115, USA
| | - Deborah Dillon
- Department of Pathology, Brigham and Women's Hospital, Boston, MA 02115, USA
| | - Henry W Long
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Franziska Michor
- Department of Data Science, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA; Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA; The Eli and Edythe L. Broad Institute, Cambridge, MA 02142, USA; Ludwig Center at Harvard, Harvard Medical School, Boston, MA 02115, USA; Center for Cancer Evolution, Dana-Farber Cancer Institute, Boston, MA 02215, USA.
| | - Kornelia Polyak
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Medicine, Brigham and Women's Hospital, Boston, MA 02115, USA; Department of Medicine, Harvard Medical School, Boston, MA 02115, USA; Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA 02215, USA; The Eli and Edythe L. Broad Institute, Cambridge, MA 02142, USA; Ludwig Center at Harvard, Harvard Medical School, Boston, MA 02115, USA; Center for Cancer Evolution, Dana-Farber Cancer Institute, Boston, MA 02215, USA.
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3
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Janiszewska M, Tabassum DP, Castaño Z, Cristea S, Yamamoto KN, Kingston NL, Murphy KC, Shu S, Harper NW, Del Alcazar CG, Alečković M, Ekram MB, Cohen O, Kwak M, Qin Y, Laszewski T, Luoma A, Marusyk A, Wucherpfennig KW, Wagle N, Fan R, Michor F, McAllister SS, Polyak K. Subclonal cooperation drives metastasis by modulating local and systemic immune microenvironments. Nat Cell Biol 2019; 21:879-888. [PMID: 31263265 PMCID: PMC6609451 DOI: 10.1038/s41556-019-0346-x] [Citation(s) in RCA: 92] [Impact Index Per Article: 18.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2018] [Accepted: 05/22/2019] [Indexed: 12/22/2022]
Abstract
Most human tumours are heterogeneous, composed of cellular clones with different properties present at variable frequencies. Highly heterogeneous tumours have poor clinical outcomes, yet the underlying mechanism remains poorly understood. Here, we show that minor subclones of breast cancer cells expressing IL11 and FIGF (VEGFD) cooperate to promote metastatic progression and generate polyclonal metastases composed of driver and neutral subclones. Expression profiling of the epithelial and stromal compartments of monoclonal and polyclonal primary and metastatic lesions revealed that this cooperation is indirect, mediated through the local and systemic microenvironments. We identified neutrophils as a leukocyte population stimulated by the IL11-expressing minor subclone and showed that the depletion of neutrophils prevents metastatic outgrowth. Single-cell RNA-seq of CD45+ cell populations from primary tumours, blood and lungs demonstrated that IL11 acts on bone-marrow-derived mesenchymal stromal cells, which induce pro-tumorigenic and pro-metastatic neutrophils. Our results indicate key roles for non-cell-autonomous drivers and minor subclones in metastasis.
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Affiliation(s)
- Michalina Janiszewska
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
- Department of Molecular Medicine, The Scripps Research Institute, Jupiter, FL, USA
| | - Doris P Tabassum
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Research Square, Durham, NC, USA
| | - Zafira Castaño
- Department of Medicine, Harvard Medical School, Boston, MA, USA
- Hematology Division, Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA
| | - Simona Cristea
- Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Biostatistics, Harvard T. H. Chan School of Public Health, Boston, MA, USA
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, USA
| | - Kimiyo N Yamamoto
- Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Biostatistics, Harvard T. H. Chan School of Public Health, Boston, MA, USA
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, USA
| | - Natalie L Kingston
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Katherine C Murphy
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Shaokun Shu
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - Nicholas W Harper
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Carlos Gil Del Alcazar
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - Maša Alečković
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - Muhammad B Ekram
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
- WuXi NextCODE, Cambridge, MA, USA
| | - Ofir Cohen
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- The Eli and Edythe L. Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Minsuk Kwak
- Department of Biomedical Engineering, Yale School of Medicine, New Haven, CT, USA
- Yale Comprehensive Cancer Center, New Haven, CT, USA
| | - Yuanbo Qin
- Department of Medicine, Harvard Medical School, Boston, MA, USA
- Hematology Division, Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA
- EdiGene, Cambridge, MA, USA
| | - Tyler Laszewski
- Hematology Division, Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA
| | - Adrienne Luoma
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, and Department of Microbiology and Immunobiology, Harvard Medical School, Boston, MA, USA
| | - Andriy Marusyk
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
- Department of Cancer Imaging and Metabolism, Moffitt Cancer Center, Tampa, FL, USA
| | - Kai W Wucherpfennig
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, and Department of Microbiology and Immunobiology, Harvard Medical School, Boston, MA, USA
| | - Nikhil Wagle
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA
- The Eli and Edythe L. Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Rong Fan
- Department of Biomedical Engineering, Yale School of Medicine, New Haven, CT, USA
- Yale Comprehensive Cancer Center, New Haven, CT, USA
| | - Franziska Michor
- Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Biostatistics, Harvard T. H. Chan School of Public Health, Boston, MA, USA
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, USA
- The Eli and Edythe L. Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Center for Cancer Evolution, Dana-Farber Cancer Institute, Boston, MA, USA
- Ludwig Center at Harvard, Boston, MA, USA
| | - Sandra S McAllister
- Department of Medicine, Harvard Medical School, Boston, MA, USA
- Hematology Division, Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA
- The Eli and Edythe L. Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Harvard Stem Cell Institute, Cambridge, MA, USA
| | - Kornelia Polyak
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA.
- Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA.
- Department of Medicine, Harvard Medical School, Boston, MA, USA.
- The Eli and Edythe L. Broad Institute of Harvard and MIT, Cambridge, MA, USA.
- Center for Cancer Evolution, Dana-Farber Cancer Institute, Boston, MA, USA.
- Ludwig Center at Harvard, Boston, MA, USA.
- Harvard Stem Cell Institute, Cambridge, MA, USA.
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4
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Ding L, Shunkwiler LB, Harper NW, Zhao Y, Hinohara K, Huh SJ, Ekram MB, Guz J, Kern MJ, Awgulewitsch A, Shull JD, Smits BMG, Polyak K. Deletion of Cdkn1b in ACI rats leads to increased proliferation and pregnancy-associated changes in the mammary gland due to perturbed systemic endocrine environment. PLoS Genet 2019; 15:e1008002. [PMID: 30893315 PMCID: PMC6443185 DOI: 10.1371/journal.pgen.1008002] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2018] [Revised: 04/01/2019] [Accepted: 02/02/2019] [Indexed: 12/16/2022] Open
Abstract
Mammary epithelial progenitors are the normal cell-of-origin of breast cancer. We previously defined a population of p27+ quiescent hormone-responsive progenitor cells in the normal human breast whose frequency associates with breast cancer risk. Here, we describe that deletion of the Cdkn1b gene encoding the p27 cyclin-dependent kinase inhibitor in the estrogen-induced mammary tumor-susceptible ACI rat strain leads to a decrease in the relative frequencies of Cd49b+ mammary luminal epithelial progenitors and pregnancy-related differentiation. We show by comprehensive gene expression profiling of purified progenitor and differentiated mammary epithelial cell populations that p27 deletion has the most pronounced effects on luminal progenitors. Cdkn1b-/- females have decreased fertility, but rats that are able to get pregnant had normal litter size and were able to nurse their pups implying that loss of p27 in ACI rats does not completely abrogate ovarian function and lactation. Reciprocal mammary gland transplantation experiments indicate that the p27-loss-induced changes in mammary epithelial cells are not only caused by alterations in their intrinsic properties, but are likely due to altered hormonal signaling triggered by the perturbed systemic endocrine environment observed in Cdkn1b-/- females. We also observed a decrease in the frequency of mammary epithelial cells positive for progesterone receptor (Pr) and FoxA1, known direct transcriptional targets of the estrogen receptor (Erα), and an increase in phospho-Stat5 positive cells commonly induced by prolactin (Prl). Characterization of genome-wide Pr chromatin binding revealed distinct binding patterns in mammary epithelial cells of Cdkn1b+/+ and Cdkn1b-/- females and enrichment in genes with known roles in Notch, ErbB, leptin, and Erα signaling and regulation of G1-S transition. Our data support a role for p27 in regulating the pool size of hormone-responsive luminal progenitors that could impact breast cancer risk. The frequency and proliferation of tissue-specific stem and progenitor cells is associated with the risk of malignancy. Thus, regulators of the pool size and proliferation of progenitor cells determine cancer risk. p27 is a key regulator of cellular proliferation and is required for the terminal differentiation of a number of cell types. Here we show that genetic deletion of Cdkn1b in ACI rats susceptible to estrogen-induced mammary tumors decreases the relative fraction of Cd49b+ luminal progenitors identifying p27 as a key regulator of the proliferation and pool size of these cells. Progesterone, acting via the progesterone receptor (Pr), is an important regulator of mammary epithelial cell proliferation and differentiation. Based on ChIP-seq we found that Pr targets different sets of genes in Cdkn1b+/+ and Cdkn1b-/- mammary epithelium and that this is associated with differences in proliferation and differentiation states. Thus, p27 regulates breast cancer risk and tumor development via regulating the pool size and hormonal-responsiveness of luminal progenitors.
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Affiliation(s)
- Lina Ding
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts, United States of America
- Department of Medicine, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Lauren B. Shunkwiler
- Department of Pathology and Laboratory Medicine, Medical University of South Carolina, Charleston, South Carolina, United States of America
| | - Nicholas W. Harper
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts, United States of America
| | - Yang Zhao
- Department of Pathology and Laboratory Medicine, Medical University of South Carolina, Charleston, South Carolina, United States of America
| | - Kunihiko Hinohara
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts, United States of America
- Department of Medicine, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Sung Jin Huh
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts, United States of America
- Department of Medicine, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Muhammad B. Ekram
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts, United States of America
- Department of Medicine, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Jan Guz
- Department of Regenerative Medicine and Cell Biology, Transgenic and Gene Function Core, Medical University of South Carolina, Charleston, South Carolina, United States of America
| | - Michael J. Kern
- Department of Regenerative Medicine and Cell Biology, Transgenic and Gene Function Core, Medical University of South Carolina, Charleston, South Carolina, United States of America
| | - Alexander Awgulewitsch
- Department of Medicine, Transgenic and Gene Function Core, Medical University of South Carolina, Charleston, South Carolina, United States of America
| | - James D. Shull
- Department of Oncology, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Bart M. G. Smits
- Department of Pathology and Laboratory Medicine, Medical University of South Carolina, Charleston, South Carolina, United States of America
- * E-mail: (BMGS); (KP)
| | - Kornelia Polyak
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts, United States of America
- Department of Medicine, Harvard Medical School, Boston, Massachusetts, United States of America
- * E-mail: (BMGS); (KP)
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Bakshi A, Ekram MB, Kim J. High-Throughput Targeted Repeat Element Bisulfite Sequencing (HT-TREBS). Methods Mol Biol 2019; 1908:219-228. [PMID: 30649731 DOI: 10.1007/978-1-4939-9004-7_15] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
High-throughput targeted repeat element bisulfite sequencing (HT-TREBS) is designed to assay the methylation level of individual retrotransposon loci of a targeted family, in a locus-specific manner, and on a genome-wide scale. Briefly, genomic DNA is sheared and ligated to Ion Torrent A adaptors (with methylated cytosines), followed by bisulfite-conversion, and amplification with primers designed to bind the targeted retrotransposon. Since the primers carry the Ion Torrent P1 adaptor as a 5'-extension, the amplified library is ready to be size-selected and sequenced on a next-generation sequencing platform. Once sequenced, each retrotransposon is mapped to a particular genomic locus, which is achieved through ensuring at least a 10-bp overlap with flanking unique sequence, followed by the calculation of methylation levels of the mapped retrotransposon using a BiQ Analyzer HT. A complete protocol for library construction as well as the bioinformatics for HT-TREBS is described in this chapter.
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Affiliation(s)
- Arundhati Bakshi
- Department of Biological Sciences, Louisiana State University, Baton Rouge, LA, USA
| | - Muhammad B Ekram
- Department of Biological Sciences, Louisiana State University, Baton Rouge, LA, USA
| | - Joomyeong Kim
- Department of Biological Sciences, Louisiana State University, Baton Rouge, LA, USA.
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6
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Alcazar CRGD, Huh S, Ekram MB, Trinh A, Liu LL, Beca F, Xiaoyuan Z, Kwak M, Bergholtz H, Su Y, Ding L, Ding L, Russnes HG, Richardson AL, Babski K, Kim EMH, McDonnell CH, Wagner J, Rowberry R, Freeman G, Dillon D, Sorlie T, Coussens LM, Garber JE, Fan R, Bobolis K, Jeong J, Park SY, Michor F, Polyak K. Abstract A15: Immune-related changes in breast cancer tumor evolution. Cancer Immunol Res 2018. [DOI: 10.1158/2326-6074.tumimm17-a15] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Immunotherapy is a highly promising therapeutic option in metastatic disease albeit only in a subset of patients possibly due to heterogeneity in the mechanisms by which tumors escape immune surveillance. Immune cells shape tumor evolution directly (e.g., anti-tumor immune response) and indirectly (e.g., changing the microenvironment) by selecting for cancer cells with certain properties. We hypothesized that the in situ (DCIS) to invasive ductal carcinoma (IDC) transition is a critical tumor progression step for immune escape in breast cancer that defines subsequent tumor evolution. In DCIS, cancer cells are physically separated from the stroma by the basement membrane and myoepithelial cell layer, and tumor-infiltrating leukocytes are rarely detected in direct contact with cancer cells. In contrast, in IDC, cancer cells and leukocytes are intermingled, thus, only cancer cells that can survive in this environment will play a role in disease progression. To dissect mechanisms of immune escape in breast cancer, we first analyzed the composition of leukocytes in normal breast tissues, DCIS, and IDC by polychromatic FACS. We found that DCIS and IDC contained significantly higher numbers of leukocytes, compared to normal breast, whereas in normal tissues more leukocytes were in the stromal than in the epithelial fraction. We also observed significant differences in the relative frequencies of several CD45+ cell types including increased neutrophils and decreased CD8+/CD4+ T cell ratios in tumors compared to normal stroma. Next, we analyzed the gene expression profiles of CD45+CD3+ T cells and found gene set enrichment of cytotoxic cells in DCIS including CD8+ T cells and NKT cells when compared to IDC. Conversely, we found enrichment for gene sets corresponding to regulatory T cells in IDC when compared to DCIS. Overall this suggested that DCIS had a more activated immune environment and IDC a more suppressed immune environment. We further explored this result by immunofluorescence (IF) and found fewer activated GZMB+CD8+ T cells in IDC than in DCIS, including a set of matched DCIS and locally recurrent IDC tissues. We also found that the TCR clonotype was more diverse in DCIS than in normal breast and IDCs. Interestingly we detected a few relatively frequent clones that were shared among different DCIS, one of which was previously shown to recognize a protein from the Epstein-Bar virus. To elucidate mechanisms of immune evasion in IDC, we performed IF analysis of immune checkpoint proteins PD-L1 and TIGIT and found significant differences between DCIS and IDC. TIGIT-expressing T cells were more slightly frequent in DCIS than in IDC. PD-L1 expression was higher in the epithelial cancer cells in triple negative IDC compared to DCIS, and amplification of CD274 (encoding PD-L1) was only detected in triple negative IDCs. Given the close proximity of ERBB2 (encoding HER2) to a cluster of genes encoding several chemokines, we analyzed the HER2+ samples from the TCGA. We found that co-amplification of 17q12 chemokine cluster (CC) with ERBB2 was enriched in HER+ER+ luminal-like tumors but not in the HER2+ER breast tumors. We also found higher expression of both T cell activation and inhibition-related genes in tumors that lack CC gain. Also by assessing tumor samples by multicolor FISH and IF, we determined that there is an inverse correlation between CC amplification and activation of CD8+ T cells. Overall our results show co-evolution of cancer cells and the immune microenvironment during tumor progression.
Citation Format: Carlos R. Gil del Alcazar, SungJin Huh, Muhammad B. Ekram, Anne Trinh, Lin L. Liu, Francisco Beca, Zi Xiaoyuan, Misuk Kwak, Helga Bergholtz, Ying Su, Lina Ding, Lina Ding, Hege G. Russnes, Andrea L. Richardson, Kirsten Babski, Elizabeth Min Hui Kim, Charles H. McDonnell, III, Jon Wagner, Ron Rowberry, Gordon Freeman, Deborah Dillon, Therese Sorlie, Lisa M. Coussens, Judy E. Garber, Rong Fan, Kristie Bobolis, Joon Jeong, So Yeon Park, Franziska Michor, Kornelia Polyak. Immune-related changes in breast cancer tumor evolution [abstract]. In: Proceedings of the AACR Special Conference on Tumor Immunology and Immunotherapy; 2017 Oct 1-4; Boston, MA. Philadelphia (PA): AACR; Cancer Immunol Res 2018;6(9 Suppl):Abstract nr A15.
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Affiliation(s)
| | | | | | - Anne Trinh
- 1Dana-Farber Cancer Institute, Boston, MA,
| | - Lin L. Liu
- 1Dana-Farber Cancer Institute, Boston, MA,
| | | | | | | | | | - Ying Su
- 1Dana-Farber Cancer Institute, Boston, MA,
| | - Lina Ding
- 1Dana-Farber Cancer Institute, Boston, MA,
| | - Lina Ding
- 1Dana-Farber Cancer Institute, Boston, MA,
| | | | | | | | | | | | - Jon Wagner
- 4Sutter Roseville Medical Center, Roseville, CA,
| | - Ron Rowberry
- 4Sutter Roseville Medical Center, Roseville, CA,
| | | | | | | | | | | | - Rong Fan
- 2Yale University, New Haven, CT,
| | | | - Joon Jeong
- 7Yonsei University Medical College, Seoul, Korea, Republic of,
| | - So Yeon Park
- 8Seoul National University College of Medicine, Seongnam, Korea, Republic of
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7
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Alcazar CRGD, Huh S, Ekram MB, Trinh A, Liu LL, Beca F, Xiaoyuan Z, Kwak M, Bergholtz H, Su Y, Ding L, Russnes HG, Richardson AL, Babski K, Kim EMH, McDonnell CH, Wagner J, Rowberry R, Freeman GJ, Dillon D, Sorlie T, Coussens LM, Garber JE, Fan R, Bobolis K, Allred DC, Jeong J, Park SY, Michor F, Polyak K. Abstract A21: Characterization of the immune environment in the in situ to invasive breast carcinoma transition. Mol Cancer Res 2018. [DOI: 10.1158/1557-3125.advbc17-a21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Reactivation of immune responses against cancer cells—immunotherapy—is one of the few cancer therapies that can successfully eliminate even metastatic disease in a relatively nontoxic manner. However, its success has been limited to a subset of patients. For example, in breast cancer only ~20% of triple-negative breast cancer (TNBC) patients benefit from anti-PDL1 therapy. One reason for this limited success can be that different tumors evade the immune system via different mechanisms, which suggests that they may respond to different types of immunotherapies. Epithelial cancer cells in ductal carcinoma in situ (DCIS) are physically separated from the tumor-infiltrating leukocytes by the myoepithelial cell layer and the basement membrane, whereas in invasive ductal carcinoma (IDC), the epithelial cancer cells are intermingled with leukocytes. Therefore, we hypothesize that the DCIS to IDC transition is a key step in tumor progression as cancer cells are under different selection pressures, and only those that can evade the immune system can continue tumor progression, hence shaping subsequent tumor evolution. To dissect the role of leukocytes in the DCIS to IDC transition, we began by analyzing the composition and molecular profiles of leukocytes, with special emphasis on T cells, in normal breast tissues, DCIS, and IDC. We found that the relative frequency of leukocytes increases during tumor progression but the CD8/CD4 T cell ratio decreases. In addition, the gene expression profile of CD45+CD3+ T cells is different in DCIS compared to those isolated from normal breast tissue and IDCs. We found that gene set signatures corresponding to CD8+ T cells and NKT cells were enriched over regulatory T-cell signatures in DCIS compared to IDC. This result suggested that DCIS had a more activated immune environment compared to IDC. We further examined T-cell activation by immunofluorescence (IF) analysis and found a higher percentage of activated GZMB+CD8+ T cells in DCIS compared to IDC including a set of matched DCIS and locally recurrent IDC. We also found that the TCR clonotype was more diverse in DCIS than in IDCs. Interestingly, we detected a few relatively frequent clones that were shared among different DCIS patients, one of which was previously shown to recognize a protein from the Epstein-Bar virus. In order to dissect mechanisms of immune evasion in IDC, we analyzed immune checkpoint genes and proteins by FISH and IF. We found that TIGIT+ T cells were slightly more frequent in DCIS than in IDC. In triple-negative IDC, there was high expression of PD-L1 in epithelial cells and in 3/10 cases amplification of CD274 (encoding PD-L1), whereas DCIS had lower expression of PD-L1 and no amplification of CD274. To further elucidate mechanisms of immune evasion, we explored the significance of a cluster of genes encoding several chemokines that are located in close proximity of ERBB2 (encoding HER2). When analyzing the HER2+ samples from the TCGA, we found that coamplification of the 17q12 chemokine cluster (CC) with ERBB2 was enriched in HER2+ER+ luminal-like tumors, whereas there was either no gain or loss of the cluster in the HER2+ER breast tumors. Interestingly, we found higher expression of both T-cell activation and exhaustion-related genes in tumors that lack CC gain. Moreover, when assessing a cohort of HER2+ samples by multicolor FISH and IF, we found an inverse correlation between CC amplification and activation of CD8+ T cells. There was no correlation between CC amplification and recruitment of macrophages or myeloid-derived suppressor cells. Overall our results show coevolution of cancer cells and the immune microenvironment during tumor progression.
Citation Format: Carlos R. Gil del Alcazar, SungJin Huh, Muhammad B. Ekram, Anne Trinh, Lin L. Liu, Francisco Beca, Zi Xiaoyuan, Misuk Kwak, Helga Bergholtz, Ying Su, Lina Ding, Hege G. Russnes, Andrea L. Richardson, Kirsten Babski, Elizabeth Min Hui Kim, Charles H. McDonnell, III, Jon Wagner, Ron Rowberry, Gordon J. Freeman, Deborah Dillon, Therese Sorlie, Lisa M. Coussens, Judy E. Garber, Rong Fan, Kristie Bobolis, D. Craig Allred, Joon Jeong, So Yeon Park, Franziska Michor, Kornelia Polyak. Characterization of the immune environment in the in situ to invasive breast carcinoma transition [abstract]. In: Proceedings of the AACR Special Conference: Advances in Breast Cancer Research; 2017 Oct 7-10; Hollywood, CA. Philadelphia (PA): AACR; Mol Cancer Res 2018;16(8_Suppl):Abstract nr A21.
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Affiliation(s)
| | | | | | - Anne Trinh
- 1Dana-Farber Cancer Institute, Boston, MA,
| | - Lin L. Liu
- 1Dana-Farber Cancer Institute, Boston, MA,
| | | | | | | | | | - Ying Su
- 1Dana-Farber Cancer Institute, Boston, MA,
| | - Lina Ding
- 1Dana-Farber Cancer Institute, Boston, MA,
| | | | | | | | | | | | - Jon Wagner
- 4Sutter Roseville Medical Center, Roseville, CA,
| | - Ron Rowberry
- 4Sutter Roseville Medical Center, Roseville, CA,
| | | | | | | | | | | | - Rong Fan
- 2Yale University, New Haven, CT,
| | | | | | - Joon Jeong
- 8Yonsei University Medical College, Seoul, Korea, Republic of,
| | - So Yeon Park
- 9Seoul National University College of Medicine, Seongnam, Korea, Republic of
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8
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Janiszewska M, Tabassum DP, Marusyk A, Ekram MB, Castaño Z, Kingston NL, Qin Y, Laszewski T, Kwak M, Nakamura K, Fan R, Michor F, McAllister SS, Polyak K. Abstract PR02: Minor clones can drive polyclonal metastasis by affecting immune microenvironment. Mol Cancer Res 2018. [DOI: 10.1158/1557-3125.advbc17-pr02] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Most breast tumors display a high degree of intratumor heterogeneity, with many distinct subpopulations of cancer cells present. Elevated diversity within a tumor increases the chance for cellular adaptation, as individual clones may react differently to changes in the tumor microenvironment. Thus, treatment of heterogeneous tumors my lead to selection of a resistant clone, its expansion, and tumor progression. However, the fitness of cancer cells depends not only on their intrinsic properties, but could also be affected through interactions between different subpopulations. These interactions could be the reason for maintenance of minor clones along the major population. Therefore, intratumor heterogeneity may have functional relevance in tumor progression and colonization of metastatic sites.
To emulate clonal interactions, we used the previously developed polyclonal breast cancer model of MDA-MB-468 cell line expressing soluble factors, IL-11 and FIGF. The IL-11 and FIGF clones, when present as minor population, support the growth of other clones in vivo. Moreover, polyclonal tumors with minor driving clone population are highly metastatic. Thus, we hypothesized that clonal interactions could not only drive tumor growth, but could also play an important role in metastasis.
We have found that polyclonal tumors lead to polyclonal metastases, composed of mixture of neutral and driver clones. To investigate the mechanisms of clonal interactions driving polyclonal metastasis, we performed RNA profiling of subpopulations and stroma from polyclonal tumors. Our results suggest that this cooperation is indirect and that driver clones promote metastasis by altering the tumor microenvironment. We have also found that minor driver clones affect the immune cells within primary tumor, circulating blood, and metastatic site. These systemic changes significantly influence the metastatic progression. We are currently testing whether a treatment targeting this indirect clonal interaction mechanism could prevent polyclonal metastatic spread.
Our study shows that the interaction between minor clones and other cancer cells could drive tumor growth and metastasis. Moreover, our results suggest that clonal cooperation in metastatic progression may be indirect and involve modulation of immune microenvironment of the primary tumor and distant organs.
This abstract is also being presented as Poster B03.
Citation Format: Michalina Janiszewska, Doris P. Tabassum, Andriy Marusyk, Muhammad B. Ekram, Zafira Castaño, Natalie L. Kingston, Yuanbo Qin, Tyler Laszewski, Minsuk Kwak, Kimiyo Nakamura, Rong Fan, Franziska Michor, Sandra S. McAllister, Kornelia Polyak. Minor clones can drive polyclonal metastasis by affecting immune microenvironment [abstract]. In: Proceedings of the AACR Special Conference: Advances in Breast Cancer Research; 2017 Oct 7-10; Hollywood, CA. Philadelphia (PA): AACR; Mol Cancer Res 2018;16(8_Suppl):Abstract nr PR02.
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Affiliation(s)
| | | | | | | | - Zafira Castaño
- 3Brigham & Women’s Hospital, Harvard Medical School, Boston, MA,
| | | | - Yuanbo Qin
- 3Brigham & Women’s Hospital, Harvard Medical School, Boston, MA,
| | - Tyler Laszewski
- 3Brigham & Women’s Hospital, Harvard Medical School, Boston, MA,
| | - Minsuk Kwak
- 4Yale Comprehensive Cancer Center, Yale School of Medicine, New Haven, CT,
| | - Kimiyo Nakamura
- 5Dana-Farber Cancer Institute, Harvard School of Public Health, Boston, MA
| | - Rong Fan
- 4Yale Comprehensive Cancer Center, Yale School of Medicine, New Haven, CT,
| | - Franziska Michor
- 5Dana-Farber Cancer Institute, Harvard School of Public Health, Boston, MA
| | | | - Kornelia Polyak
- 1Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA,
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9
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Liang Y, Ahmed M, Guo H, Soares F, Hua JT, Gao S, Lu C, Poon C, Han W, Langstein J, Ekram MB, Li B, Davicioni E, Takhar M, Erho N, Karnes RJ, Chadwick D, van der Kwast T, Boutros PC, Arrowsmith CH, Feng FY, Joshua AM, Zoubeidi A, Cai C, He HH. LSD1-Mediated Epigenetic Reprogramming Drives CENPE Expression and Prostate Cancer Progression. Cancer Res 2017; 77:5479-5490. [PMID: 28916652 DOI: 10.1158/0008-5472.can-17-0496] [Citation(s) in RCA: 59] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2017] [Revised: 06/28/2017] [Accepted: 08/17/2017] [Indexed: 12/31/2022]
Abstract
Androgen receptor (AR) signaling is a key driver of prostate cancer, and androgen-deprivation therapy (ADT) is a standard treatment for patients with advanced and metastatic disease. However, patients receiving ADT eventually develop incurable castration-resistant prostate cancer (CRPC). Here, we report that the chromatin modifier LSD1, an important regulator of AR transcriptional activity, undergoes epigenetic reprogramming in CRPC. LSD1 reprogramming in this setting activated a subset of cell-cycle genes, including CENPE, a centromere binding protein and mitotic kinesin. CENPE was regulated by the co-binding of LSD1 and AR to its promoter, which was associated with loss of RB1 in CRPC. Notably, genetic deletion or pharmacological inhibition of CENPE significantly decreases tumor growth. Our findings show how LSD1-mediated epigenetic reprogramming drives CRPC, and they offer a mechanistic rationale for its therapeutic targeting in this disease. Cancer Res; 77(20); 5479-90. ©2017 AACR.
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Affiliation(s)
- Yi Liang
- Princess Margaret Cancer Centre/University Health Network, Toronto, Ontario, Canada
| | - Musaddeque Ahmed
- Princess Margaret Cancer Centre/University Health Network, Toronto, Ontario, Canada
| | - Haiyang Guo
- Princess Margaret Cancer Centre/University Health Network, Toronto, Ontario, Canada
| | - Fraser Soares
- Princess Margaret Cancer Centre/University Health Network, Toronto, Ontario, Canada
| | - Junjie T Hua
- Princess Margaret Cancer Centre/University Health Network, Toronto, Ontario, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
| | - Shuai Gao
- Center for Personalized Cancer Therapy, University of Massachusetts Boston, Boston, Massachusetts
| | - Catherine Lu
- Princess Margaret Cancer Centre/University Health Network, Toronto, Ontario, Canada
| | - Christine Poon
- Princess Margaret Cancer Centre/University Health Network, Toronto, Ontario, Canada
| | - Wanting Han
- Center for Personalized Cancer Therapy, University of Massachusetts Boston, Boston, Massachusetts
| | - Jens Langstein
- Princess Margaret Cancer Centre/University Health Network, Toronto, Ontario, Canada
- German Cancer Research Center, DKFZ, Heidelberg, Germany
| | - Muhammad B Ekram
- Department of Medical Oncology, The Center for Functional Cancer Epigenetics, Dana Farber Cancer Institute, Boston, Massachusetts
- Department of Medicine, Brigham and Women's Hospital, Boston, Massachusetts
- Department of Medicine, Harvard Medical School, Boston, Massachusetts
| | - Brian Li
- Princess Margaret Cancer Centre/University Health Network, Toronto, Ontario, Canada
| | - Elai Davicioni
- Research & Development, GenomeDx Biosciences Inc., Vancouver BC, Canada
| | - Mandeep Takhar
- Research & Development, GenomeDx Biosciences Inc., Vancouver BC, Canada
| | - Nicholas Erho
- Research & Development, GenomeDx Biosciences Inc., Vancouver BC, Canada
| | | | - Dianne Chadwick
- UHN Program in BioSpecimen Sciences, Department of Pathology, University Health Network, Toronto, Ontario, Canada
| | - Theodorus van der Kwast
- Department of Pathology and Laboratory Medicine, Toronto General Hospital/University Health Network, Toronto, Canada
| | - Paul C Boutros
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
- Informatics and Biocomputing Program, Ontario Institute for Cancer Research, Toronto, Ontario, Canada
- Department of Pharmacology and Toxicology, University of Toronto, Toronto, Ontario, Canada
| | - Cheryl H Arrowsmith
- Princess Margaret Cancer Centre/University Health Network, Toronto, Ontario, Canada
- Structural Genomics Consortium, University of Toronto, Toronto, Ontario, Canada
| | - Felix Y Feng
- Department of Radiation Oncology, University of California at San Francisco, San Francisco, California
- Department of Urology, University of California at San Francisco, San Francisco, California
- Department of Medicine, University of California at San Francisco, San Francisco, California
- Helen Diller Family Comprehensive Cancer Center, University of California at San Francisco, San Francisco, California
| | - Anthony M Joshua
- Princess Margaret Cancer Centre/University Health Network, Toronto, Ontario, Canada
- Kinghorn Cancer Centre, St Vincent's Hospital, Sydney, Australia
| | - Amina Zoubeidi
- Vancouver Prostate Centre, Vancouver, British Columbia, Canada
| | - Changmeng Cai
- Center for Personalized Cancer Therapy, University of Massachusetts Boston, Boston, Massachusetts
| | - Housheng H He
- Princess Margaret Cancer Centre/University Health Network, Toronto, Ontario, Canada.
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
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Gil Del Alcazar CR, Huh SJ, Ekram MB, Trinh A, Liu LL, Beca F, Zi X, Kwak M, Bergholtz H, Su Y, Ding L, Russnes HG, Richardson AL, Babski K, Min Hui Kim E, McDonnell CH, Wagner J, Rowberry R, Freeman GJ, Dillon D, Sorlie T, Coussens LM, Garber JE, Fan R, Bobolis K, Allred DC, Jeong J, Park SY, Michor F, Polyak K. Immune Escape in Breast Cancer During In Situ to Invasive Carcinoma Transition. Cancer Discov 2017; 7:1098-1115. [PMID: 28652380 PMCID: PMC5628128 DOI: 10.1158/2159-8290.cd-17-0222] [Citation(s) in RCA: 158] [Impact Index Per Article: 22.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2017] [Revised: 05/22/2017] [Accepted: 06/21/2017] [Indexed: 11/16/2022]
Abstract
To investigate immune escape during breast tumor progression, we analyzed the composition of leukocytes in normal breast tissues, ductal carcinoma in situ (DCIS), and invasive ductal carcinomas (IDC). We found significant tissue and tumor subtype-specific differences in multiple cell types including T cells and neutrophils. Gene expression profiling of CD45+CD3+ T cells demonstrated a decrease in CD8+ signatures in IDCs. Immunofluorescence analysis showed fewer activated GZMB+CD8+ T cells in IDC than in DCIS, including in matched DCIS and recurrent IDC. T-cell receptor clonotype diversity was significantly higher in DCIS than in IDCs. Immune checkpoint protein TIGIT-expressing T cells were more frequent in DCIS, whereas high PD-L1 expression and amplification of CD274 (encoding PD-L1) was only detected in triple-negative IDCs. Coamplification of a 17q12 chemokine cluster with ERBB2 subdivided HER2+ breast tumors into immunologically and clinically distinct subtypes. Our results show coevolution of cancer cells and the immune microenvironment during tumor progression.Significance: The design of effective cancer immunotherapies requires the understanding of mechanisms underlying immune escape during tumor progression. Here we demonstrate a switch to a less active tumor immune environment during the in situ to invasive breast carcinoma transition, and identify immune regulators and genomic alterations that shape tumor evolution. Cancer Discov; 7(10); 1098-115. ©2017 AACR.See related commentary by Speiser and Verdeil, p. 1062This article is highlighted in the In This Issue feature, p. 1047.
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MESH Headings
- B7-H1 Antigen/genetics
- Biomarkers, Tumor/genetics
- Breast Neoplasms/genetics
- Breast Neoplasms/immunology
- CD3 Complex/genetics
- Carcinoma, Ductal, Breast/genetics
- Carcinoma, Ductal, Breast/immunology
- Carcinoma, Intraductal, Noninfiltrating/genetics
- Carcinoma, Intraductal, Noninfiltrating/immunology
- Disease Progression
- Female
- Gene Expression Profiling/methods
- Gene Expression Regulation, Neoplastic
- Humans
- Leukocyte Common Antigens/genetics
- Receptor, ErbB-2/genetics
- T-Lymphocytes/immunology
- Tumor Microenvironment
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Affiliation(s)
- Carlos R Gil Del Alcazar
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
- Department of Medicine, Brigham and Women's Hospital, Boston, Massachusetts
- Department of Medicine, Harvard Medical School, Boston, Massachusetts
| | - Sung Jin Huh
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
- Department of Medicine, Brigham and Women's Hospital, Boston, Massachusetts
- Department of Medicine, Harvard Medical School, Boston, Massachusetts
| | - Muhammad B Ekram
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
- Department of Medicine, Brigham and Women's Hospital, Boston, Massachusetts
- Department of Medicine, Harvard Medical School, Boston, Massachusetts
| | - Anne Trinh
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
- Department of Medicine, Brigham and Women's Hospital, Boston, Massachusetts
- Department of Medicine, Harvard Medical School, Boston, Massachusetts
| | - Lin L Liu
- Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Boston, Massachusetts
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, Massachusetts
| | - Francisco Beca
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
- Department of Medicine, Brigham and Women's Hospital, Boston, Massachusetts
- Department of Medicine, Harvard Medical School, Boston, Massachusetts
| | - Xiaoyuan Zi
- Department of Biomedical Engineering, Yale University, New Haven, Connecticut
- Second Military Medical University, Shanghai, P.R. China
| | - Minsuk Kwak
- Department of Biomedical Engineering, Yale University, New Haven, Connecticut
| | - Helga Bergholtz
- Department of Cancer Genetics, Institute for Cancer Research, Oslo University Hospital, Oslo, Norway
| | - Ying Su
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
- Department of Medicine, Brigham and Women's Hospital, Boston, Massachusetts
- Department of Medicine, Harvard Medical School, Boston, Massachusetts
| | - Lina Ding
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
- Department of Medicine, Brigham and Women's Hospital, Boston, Massachusetts
- Department of Medicine, Harvard Medical School, Boston, Massachusetts
| | - Hege G Russnes
- Department of Cancer Genetics, Institute for Cancer Research, Oslo University Hospital, Oslo, Norway
| | - Andrea L Richardson
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, Massachusetts
- Department of Pathology, Brigham and Women's Hospital, Boston, Massachusetts
- Department of Pathology, Harvard Medical School, Boston, Massachusetts
| | | | | | | | - Jon Wagner
- Sutter Roseville Medical Center, Roseville, California
| | - Ron Rowberry
- Sutter Roseville Medical Center, Roseville, California
| | - Gordon J Freeman
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
- Department of Medicine, Harvard Medical School, Boston, Massachusetts
| | - Deborah Dillon
- Department of Pathology, Brigham and Women's Hospital, Boston, Massachusetts
- Department of Pathology, Harvard Medical School, Boston, Massachusetts
| | - Therese Sorlie
- Department of Cancer Genetics, Institute for Cancer Research, Oslo University Hospital, Oslo, Norway
| | - Lisa M Coussens
- Department of Cell, Developmental & Cancer Biology, Knight Cancer Institute, Oregon Health and Science University, Portland, Oregon
| | - Judy E Garber
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
- Department of Medicine, Brigham and Women's Hospital, Boston, Massachusetts
- Department of Medicine, Harvard Medical School, Boston, Massachusetts
| | - Rong Fan
- Department of Biomedical Engineering, Yale University, New Haven, Connecticut
| | | | - D Craig Allred
- Department of Pathology, Washington University School of Medicine, St. Louis, Missouri
| | - Joon Jeong
- Department of Surgery, Gangnam Severance Hospital, Yonsei University Medical College, Seoul, Korea
| | - So Yeon Park
- Department of Pathology, Seoul National University Bundang Hospital, Seoul National University College of Medicine, Seongnam, Korea
| | - Franziska Michor
- Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Boston, Massachusetts
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, Massachusetts
| | - Kornelia Polyak
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts.
- Department of Medicine, Brigham and Women's Hospital, Boston, Massachusetts
- Department of Medicine, Harvard Medical School, Boston, Massachusetts
- The Broad Institute, Cambridge, Massachusetts
- Harvard Stem Cell Institute, Cambridge, Massachusetts
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11
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Shu S, Lin CY, He HH, Witwicki RM, Tabassum DP, Roberts JM, Janiszewska M, Huh SJ, Liang Y, Ryan J, Doherty E, Mohammed H, Guo H, Stover DG, Ekram MB, Brown J, D'Santos C, Krop IE, Dillon D, McKeown M, Ott C, Qi J, Ni M, Rao PK, Duarte M, Wu SY, Chiang CM, Anders L, Young RA, Winer E, Letai A, Barry WT, Carroll JS, Long H, Brown M, Liu XS, Meyer CA, Bradner JE, Polyak K. Response and resistance to BET bromodomain inhibitors in triple-negative breast cancer. Nature 2016; 529:413-417. [PMID: 26735014 PMCID: PMC4854653 DOI: 10.1038/nature16508] [Citation(s) in RCA: 444] [Impact Index Per Article: 55.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2014] [Accepted: 12/03/2015] [Indexed: 12/15/2022]
Abstract
Triple-negative breast cancer (TNBC) is a heterogeneous and clinically aggressive disease for which there is no targeted therapy. BET bromodomain inhibitors, which have shown efficacy in several models of cancer, have not been evaluated in TNBC. These inhibitors displace BET bromodomain proteins such as BRD4 from chromatin by competing with their acetyl-lysine recognition modules, leading to inhibition of oncogenic transcriptional programs. Here we report the preferential sensitivity of TNBCs to BET bromodomain inhibition in vitro and in vivo, establishing a rationale for clinical investigation and further motivation to understand mechanisms of resistance. In paired cell lines selected for acquired resistance to BET inhibition from previously sensitive TNBCs, we failed to identify gatekeeper mutations, new driver events or drug pump activation. BET-resistant TNBC cells remain dependent on wild-type BRD4, which supports transcription and cell proliferation in a bromodomain-independent manner. Proteomic studies of resistant TNBC identify strong association with MED1 and hyper-phosphorylation of BRD4 attributable to decreased activity of PP2A, identified here as a principal BRD4 serine phosphatase. Together, these studies provide a rationale for BET inhibition in TNBC and present mechanism-based combination strategies to anticipate clinical drug resistance.
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MESH Headings
- Animals
- Azepines/pharmacology
- Azepines/therapeutic use
- Binding, Competitive/drug effects
- Casein Kinase II/metabolism
- Cell Cycle Proteins
- Cell Line, Tumor
- Cell Proliferation/drug effects
- Cell Proliferation/genetics
- Chromatin/genetics
- Chromatin/metabolism
- Drug Resistance, Neoplasm/drug effects
- Drug Resistance, Neoplasm/genetics
- Epigenesis, Genetic/drug effects
- Epigenesis, Genetic/genetics
- Female
- Gene Expression Regulation, Neoplastic/drug effects
- Genome, Human/drug effects
- Genome, Human/genetics
- Humans
- Mediator Complex Subunit 1/metabolism
- Mice
- Nuclear Proteins/antagonists & inhibitors
- Nuclear Proteins/deficiency
- Nuclear Proteins/genetics
- Nuclear Proteins/metabolism
- Phosphorylation/drug effects
- Phosphoserine/metabolism
- Protein Binding/drug effects
- Protein Phosphatase 2/metabolism
- Protein Structure, Tertiary/drug effects
- Proteomics
- Transcription Factors/antagonists & inhibitors
- Transcription Factors/deficiency
- Transcription Factors/genetics
- Transcription Factors/metabolism
- Transcription, Genetic/drug effects
- Triazoles/pharmacology
- Triazoles/therapeutic use
- Triple Negative Breast Neoplasms/drug therapy
- Triple Negative Breast Neoplasms/genetics
- Triple Negative Breast Neoplasms/metabolism
- Triple Negative Breast Neoplasms/pathology
- Xenograft Model Antitumor Assays
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Affiliation(s)
- Shaokun Shu
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
- Department of Medicine, Brigham and Women's Hospital, and Department of Medicine, Harvard Medical School, Boston, Massachusetts, USA
| | - Charles Y Lin
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
- Department of Medicine, Brigham and Women's Hospital, and Department of Medicine, Harvard Medical School, Boston, Massachusetts, USA
| | - Housheng Hansen He
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
- Department of Medicine, Brigham and Women's Hospital, and Department of Medicine, Harvard Medical School, Boston, Massachusetts, USA
- Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, and Department of Biostatistics, Harvard School of Public Health, Boston, Massachusetts USA
- Princess Margaret Cancer Center/University Health Network, Toronto, Ontario, M5G1L7, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario, M5G2M9, Canada
| | - Robert M Witwicki
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
- Department of Medicine, Brigham and Women's Hospital, and Department of Medicine, Harvard Medical School, Boston, Massachusetts, USA
| | - Doris P Tabassum
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
| | - Justin M Roberts
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
| | - Michalina Janiszewska
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
- Department of Medicine, Brigham and Women's Hospital, and Department of Medicine, Harvard Medical School, Boston, Massachusetts, USA
| | - Sung Jin Huh
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
- Department of Medicine, Brigham and Women's Hospital, and Department of Medicine, Harvard Medical School, Boston, Massachusetts, USA
| | - Yi Liang
- Princess Margaret Cancer Center/University Health Network, Toronto, Ontario, M5G1L7, Canada
| | - Jeremy Ryan
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
- Department of Medicine, Brigham and Women's Hospital, and Department of Medicine, Harvard Medical School, Boston, Massachusetts, USA
| | - Ernest Doherty
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
- Harvard University, Cambridge, Massachusetts, USA
| | - Hisham Mohammed
- Cancer Research UK, Cambridge Institute, University of Cambridge, UK, CB2 0RE
| | - Hao Guo
- Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, and Department of Biostatistics, Harvard School of Public Health, Boston, Massachusetts USA
| | - Daniel G Stover
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
- Department of Medicine, Brigham and Women's Hospital, and Department of Medicine, Harvard Medical School, Boston, Massachusetts, USA
| | - Muhammad B Ekram
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
- Department of Medicine, Brigham and Women's Hospital, and Department of Medicine, Harvard Medical School, Boston, Massachusetts, USA
| | - Jonathan Brown
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
- Department of Medicine, Brigham and Women's Hospital, and Department of Medicine, Harvard Medical School, Boston, Massachusetts, USA
| | - Clive D'Santos
- Cancer Research UK, Cambridge Institute, University of Cambridge, UK, CB2 0RE
| | - Ian E Krop
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
- Department of Medicine, Brigham and Women's Hospital, and Department of Medicine, Harvard Medical School, Boston, Massachusetts, USA
| | - Deborah Dillon
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
- Department of Pathology, Brigham and Women's Hospital, and Department of Pathology, Harvard Medical School, Boston, Massachusetts, USA
| | - Michael McKeown
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
- Department of Medicine, Brigham and Women's Hospital, and Department of Medicine, Harvard Medical School, Boston, Massachusetts, USA
| | - Christopher Ott
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
- Department of Medicine, Brigham and Women's Hospital, and Department of Medicine, Harvard Medical School, Boston, Massachusetts, USA
| | - Jun Qi
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
- Department of Medicine, Brigham and Women's Hospital, and Department of Medicine, Harvard Medical School, Boston, Massachusetts, USA
| | - Min Ni
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
- Department of Medicine, Brigham and Women's Hospital, and Department of Medicine, Harvard Medical School, Boston, Massachusetts, USA
| | - Prakash K Rao
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
| | - Melissa Duarte
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
| | - Shwu-Yuan Wu
- Simmons Comprehensive Cancer Center, Departments of Biochemistry and Pharmacology, University of Texas Southwestern Medical Center, Dallas, Texas, USA
| | - Cheng-Ming Chiang
- Simmons Comprehensive Cancer Center, Departments of Biochemistry and Pharmacology, University of Texas Southwestern Medical Center, Dallas, Texas, USA
| | - Lars Anders
- Whitehead Institute for Biomedical Research, Cambridge, Massachusetts, USA
| | - Richard A Young
- Whitehead Institute for Biomedical Research, Cambridge, Massachusetts, USA
| | - Eric Winer
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
- Department of Medicine, Brigham and Women's Hospital, and Department of Medicine, Harvard Medical School, Boston, Massachusetts, USA
| | - Antony Letai
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
- Department of Medicine, Brigham and Women's Hospital, and Department of Medicine, Harvard Medical School, Boston, Massachusetts, USA
| | - William T Barry
- Department of Medicine, Brigham and Women's Hospital, and Department of Medicine, Harvard Medical School, Boston, Massachusetts, USA
- Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, and Department of Biostatistics, Harvard School of Public Health, Boston, Massachusetts USA
| | - Jason S Carroll
- Cancer Research UK, Cambridge Institute, University of Cambridge, UK, CB2 0RE
| | - Henry Long
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
| | - Myles Brown
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
- Department of Medicine, Brigham and Women's Hospital, and Department of Medicine, Harvard Medical School, Boston, Massachusetts, USA
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
| | - X Shirley Liu
- Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, and Department of Biostatistics, Harvard School of Public Health, Boston, Massachusetts USA
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
- Broad Institute, Cambridge, Massachusetts, USA
| | - Clifford A Meyer
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
- Department of Medicine, Brigham and Women's Hospital, and Department of Medicine, Harvard Medical School, Boston, Massachusetts, USA
- Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, and Department of Biostatistics, Harvard School of Public Health, Boston, Massachusetts USA
| | - James E Bradner
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
- Department of Medicine, Brigham and Women's Hospital, and Department of Medicine, Harvard Medical School, Boston, Massachusetts, USA
- Broad Institute, Cambridge, Massachusetts, USA
| | - Kornelia Polyak
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
- Department of Medicine, Brigham and Women's Hospital, and Department of Medicine, Harvard Medical School, Boston, Massachusetts, USA
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
- Broad Institute, Cambridge, Massachusetts, USA
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12
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Kim H, Ekram MB, Bakshi A, Kim J. AEBP2 as a transcriptional activator and its role in cell migration. Genomics 2014; 105:108-15. [PMID: 25451679 DOI: 10.1016/j.ygeno.2014.11.007] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [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: 07/15/2014] [Revised: 10/31/2014] [Accepted: 11/16/2014] [Indexed: 10/24/2022]
Abstract
Aebp2 encodes an evolutionarily conserved zinc finger protein that has not been well studied so far, yet recent studies indicated that this gene is closely associated with the Polycomb Repressive Complex 2 (PRC2). Thus, the current study characterized the basic aspects of this gene, including alternative promoters and protein isoforms. According to the results, Aebp2 is controlled through three alternative promoters, deriving three different transcripts encoding the embryonic (32 kDa) and somatic (52 kDa) forms. Chromatin Immuno-Precipitation (ChIP) experiments revealed that AEBP2 binds to its own promoter as well as the promoters of Jarid2 and Snai2. While the embryonic form acts as a transcriptional repressor for Snai2, the somatic form functions as a transcriptional activator for Jarid2, Aebp2 and Snai2. Cell migration assays also demonstrated that the Aebp2 somatic form has an enhancing activity in cell migration. This is consistent with the functional association of Aebp2 with migratory neural crest cells. These results suggest that the two protein isoforms of AEBP2 may have opposite functions for the PcG target genes, and may play significant roles in cell migration during development.
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Affiliation(s)
- Hana Kim
- Department of Biological Sciences, Louisiana State University, Baton Rouge, LA 70803, USA
| | - Muhammad B Ekram
- Department of Biological Sciences, Louisiana State University, Baton Rouge, LA 70803, USA
| | - Arundhati Bakshi
- Department of Biological Sciences, Louisiana State University, Baton Rouge, LA 70803, USA
| | - Joomyeong Kim
- Department of Biological Sciences, Louisiana State University, Baton Rouge, LA 70803, USA.
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13
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Ekram MB, Kim J. High-throughput targeted repeat element bisulfite sequencing (HT-TREBS): genome-wide DNA methylation analysis of IAP LTR retrotransposon. PLoS One 2014; 9:e101683. [PMID: 25003790 PMCID: PMC4086960 DOI: 10.1371/journal.pone.0101683] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2013] [Accepted: 06/10/2014] [Indexed: 01/23/2023] Open
Abstract
In vertebrates, DNA methylation-mediated repression of retrotransposons is essential for the maintenance of genomic integrity. In the current study, we developed a technique termed HT-TREBS (High-Throughput Targeted Repeat Element Bisulfite Sequencing). This technique is designed to measure the DNA methylation levels of individual loci of any repeat families with next-generation sequencing approaches. To test the feasibility of HT-TREBS, we analyzed the DNA methylation levels of the IAP LTR family using a set of 12 different genomic DNA isolated from the brain, liver and kidney of 4 one-week-old littermates of the mouse strain C57BL/6N. This technique has successfully generated the CpG methylation data of 5,233 loci common in all the samples, representing more than 80% of the individual loci of the five targeted subtypes of the IAP LTR family. According to the results, approximately 5% of the IAP LTR loci have less than 80% CpG methylation levels with no genomic position preference. Further analyses of the IAP LTR loci also revealed the presence of extensive DNA methylation variations between different tissues and individuals. Overall, these data demonstrate the efficiency and robustness of the new technique, HT-TREBS, and also provide new insights regarding the genome-wide DNA methylation patterns of the IAP LTR repeat elements.
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Affiliation(s)
- Muhammad B. Ekram
- Department of Biological Sciences, Louisiana State University, Baton Rouge, Louisiana, United States of America
| | - Joomyeong Kim
- Department of Biological Sciences, Louisiana State University, Baton Rouge, Louisiana, United States of America
- * E-mail:
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14
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Yamamoto S, Wu Z, Russnes HG, Takagi S, Peluffo G, Vaske C, Zhao X, Moen Vollan HK, Maruyama R, Ekram MB, Sun H, Kim JH, Carver K, Zucca M, Feng J, Almendro V, Bessarabova M, Rueda OM, Nikolsky Y, Caldas C, Liu XS, Polyak K. JARID1B is a luminal lineage-driving oncogene in breast cancer. Cancer Cell 2014; 25:762-77. [PMID: 24937458 PMCID: PMC4079039 DOI: 10.1016/j.ccr.2014.04.024] [Citation(s) in RCA: 140] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/21/2013] [Revised: 02/12/2014] [Accepted: 04/24/2014] [Indexed: 12/17/2022]
Abstract
Recurrent mutations in histone-modifying enzymes imply key roles in tumorigenesis, yet their functional relevance is largely unknown. Here, we show that JARID1B, encoding a histone H3 lysine 4 (H3K4) demethylase, is frequently amplified and overexpressed in luminal breast tumors and a somatic mutation in a basal-like breast cancer results in the gain of unique chromatin binding and luminal expression and splicing patterns. Downregulation of JARID1B in luminal cells induces basal genes expression and growth arrest, which is rescued by TGFβ pathway inhibitors. Integrated JARID1B chromatin binding, H3K4 methylation, and expression profiles suggest a key function for JARID1B in luminal cell-specific expression programs. High luminal JARID1B activity is associated with poor outcome in patients with hormone receptor-positive breast tumors.
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Affiliation(s)
- Shoji Yamamoto
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Medicine, Brigham and Women's Hospital, Boston, MA 02115, USA; Department of Medicine, Harvard Medical School, Boston, MA 02115, USA
| | - Zhenhua Wu
- Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Harvard School of Public Health, Boston, MA 02115, USA
| | - Hege G Russnes
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Medicine, Brigham and Women's Hospital, Boston, MA 02115, USA; Department of Medicine, Harvard Medical School, Boston, MA 02115, USA; Oslo University Hospital, Radiumhospitalet, Oslo 0310, Norway
| | - Shinji Takagi
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Medicine, Brigham and Women's Hospital, Boston, MA 02115, USA; Department of Medicine, Harvard Medical School, Boston, MA 02115, USA
| | - Guillermo Peluffo
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Medicine, Brigham and Women's Hospital, Boston, MA 02115, USA; Department of Medicine, Harvard Medical School, Boston, MA 02115, USA
| | | | - Xi Zhao
- Stanford Center for Cancer Systems Biology, Department of Radiology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | | | - Reo Maruyama
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Medicine, Brigham and Women's Hospital, Boston, MA 02115, USA; Department of Medicine, Harvard Medical School, Boston, MA 02115, USA; School of Medicine, Sapporo Medical University, Sapporo 060-8556, Japan
| | - Muhammad B Ekram
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Medicine, Brigham and Women's Hospital, Boston, MA 02115, USA; Department of Medicine, Harvard Medical School, Boston, MA 02115, USA
| | - Hanfei Sun
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Bioinformatics, School of Life Science and Technology, Tongji University, Shanghai 200092, China
| | - Jee Hyun Kim
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Medicine, Brigham and Women's Hospital, Boston, MA 02115, USA; Department of Medicine, Harvard Medical School, Boston, MA 02115, USA; Department of Internal Medicine, Seoul National University College of Medicine, Seoul 110-799, Korea
| | - Kristopher Carver
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Medicine, Brigham and Women's Hospital, Boston, MA 02115, USA; Department of Medicine, Harvard Medical School, Boston, MA 02115, USA
| | - Mattia Zucca
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA 02215, USA; San Raffaele University, 20132 Milan, Italy
| | - Jianxing Feng
- Department of Bioinformatics, School of Life Science and Technology, Tongji University, Shanghai 200092, China
| | - Vanessa Almendro
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Medicine, Brigham and Women's Hospital, Boston, MA 02115, USA; Department of Medicine, Harvard Medical School, Boston, MA 02115, USA
| | | | - Oscar M Rueda
- Cancer Research UK, Cambridge Institute, University of Cambridge, Cambridge CB2 0RE, UK
| | - Yuri Nikolsky
- Thomson Reuters Healthcare & Science, Encinitas, CA 92024, USA
| | - Carlos Caldas
- Cancer Research UK, Cambridge Institute, University of Cambridge, Cambridge CB2 0RE, UK
| | - X Shirley Liu
- Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Harvard School of Public Health, Boston, MA 02115, USA; Broad Institute, Cambridge, MA 02141, USA
| | - Kornelia Polyak
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Medicine, Brigham and Women's Hospital, Boston, MA 02115, USA; Department of Medicine, Harvard Medical School, Boston, MA 02115, USA; Broad Institute, Cambridge, MA 02141, USA; Harvard Stem Cell Institute, Cambridge, MA 02138, USA.
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15
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Thiaville MM, Huang JM, Kim H, Ekram MB, Roh TY, Kim J. DNA-binding motif and target genes of the imprinted transcription factor PEG3. Gene 2012; 512:314-20. [PMID: 23078764 DOI: 10.1016/j.gene.2012.10.005] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2012] [Accepted: 10/07/2012] [Indexed: 01/06/2023]
Abstract
The Peg3 gene is expressed only from the paternally inherited allele located on proximal mouse chromosome 7. The PEG3 protein encoded by this imprinted gene is predicted to bind DNA based on its multiple zinc finger motifs and nuclear localization. In the current study, we demonstrated PEG3's DNA-binding ability by characterizing its binding motif and target genes. We successfully identified target regions bound by PEG3 from mouse brain extracts using chromatin immunoprecipitation analysis. PEG3 was demonstrated to bind these candidate regions through the consensus DNA-binding motif AGTnnCnnnTGGCT. In vitro promoter assays established that PEG3 controls the expression of a given gene through this motif. Consistent with these observations, the transcriptional levels of a subset of the target genes are also affected in a mutant mouse model with reduced levels of PEG3 protein. Overall, these results confirm PEG3 as a DNA-binding protein controlling specific target genes that are involved in distinct cellular functions.
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Affiliation(s)
- Michelle M Thiaville
- Department of Biological Sciences, Louisiana State University, Baton Rouge, LA 70803, USA
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16
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Abstract
Transcription of retrotransposons is usually repressed by DNA methylation, but a few elements, such as intracisternal A-particles (IAPs) associated with the Agouti and Axin-fused loci, partially escape this repression mechanism. The levels of this repression are also variable among individuals with an identical genome sequence, generating epigenetically different states of loci or 'epialleles.' In the current study, we tested the existence of additional retrotransposon-derived epialleles in the mouse genome. Using a series of bioinformatic approaches, 143 candidate epialleles were first identified from the mouse genome based on their promoter activity and association with active histone modification marks. Detailed analyses suggest that a subset of these elements showed variable levels of DNA methylation among the individual mice of an isogenic background, revealing their stochastic nature (metastability) of DNA methylation. The analyses also identified two opposite patterns of DNA methylation during development, progressive gaining vs. losing, confirming the dynamic nature of their DNA methylation patterns. qRT-PCR analyses demonstrated that the expression levels of these elements are indeed variable among the individual mice, suggesting functional consequences on their associated endogenous genes. Overall, these data confirm the presence of a number of new retrotransposon-derived epialleles with suggestions of the presence of more, and further identify retrotransposons as a major source of epigenetic variations in the mammalian genome.
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Affiliation(s)
- Muhammad B Ekram
- Department of Biological Sciences, Louisiana State University, Baton Rouge, LA, USA
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17
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Kim J, Ekram MB, Kim H, Faisal M, Frey WD, Huang JM, Tran K, Kim MM, Yu S. Imprinting control region (ICR) of the Peg3 domain. Hum Mol Genet 2012; 21:2677-87. [PMID: 22394678 DOI: 10.1093/hmg/dds092] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The imprinting and transcription of the 500 kb genomic region surrounding the mouse Peg3 is predicted to be regulated by the Peg3-differentially methylated region (DMR). In the current study, this prediction was tested using a mutant mouse line lacking this potential imprinting control region (ICR). At the organismal level, paternal and maternal transmission of this knockout (KO) allele caused either reduced or increased growth rates in the mouse, respectively. In terms of the imprinting control, the paternal transmission of the KO allele resulted in bi-allelic expression of the normally maternally expressed Zim2, whereas the maternal transmission switched the transcriptionally dominant allele for Zfp264 (paternal to maternal). However, the allele-specific DNA methylation patterns of the DMRs of Peg3, Zim2 and Zim3 were not affected in the mice that inherited the KO allele either paternally or maternally. In terms of the transcriptional control, the paternal transmission caused a dramatic down-regulation in Peg3 expression, but overall up-regulation in the other nearby imprinted genes. Taken together, deletion of the Peg3-DMR caused global changes in the imprinting and transcription of the Peg3 domain, confirming that the Peg3-DMR is an ICR for this imprinted domain.
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Affiliation(s)
- Joomyeong Kim
- Department of Biological Sciences, Louisiana State University, Baton Rouge, LA 70803, USA.
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18
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Abstract
Aebp2 is a potential targeting protein for the mammalian Polycomb Repression Complex 2 (PRC2). We generated a mutant mouse line disrupting the transcription of Aebp2 to investigate its in vivo roles. Aebp2-mutant homozygotes were embryonic lethal while heterozygotes survived to adulthood with fertility. In developing mouse embryos, Aebp2 is expressed mainly within cells of neural crest origin. In addition, many heterozygotes display a set of phenotypes, enlarged colon and hypopigmentation, similar to those observed in human patients with Hirschsprung's disease and Waardenburg syndrome. These phenotypes are usually caused by the absence of the neural crest-derived ganglia in hindguts and melanocytes. ChIP analyses demonstrated that the majority of the genes involved in the migration and development process of neural crest cells are downstream target genes of AEBP2 and PRC2. Furthermore, expression analyses confirmed that some of these genes are indeed affected in the Aebp2 heterozygotes. Taken together, these results suggest that Aebp2 may regulate the migration and development of the neural crest cells through the PRC2-mediated epigenetic mechanism.
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Affiliation(s)
- Hana Kim
- Department of Biological Sciences, Louisiana State University, Baton Rouge, Louisiana, United States of America
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19
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Abstract
Zfp42/Rex1 (reduced expression gene 1) is a well-known stem-cell marker that has been duplicated from YY1 in the eutherian lineage. In the current study, we characterized the in vivo roles of Rex1 using a mutant mouse line disrupting its transcription. In contrast to the ubiquitous expression of YY1, Rex1 is expressed only during spermatogenesis and early embryogenesis and also in a very limited area of the placenta. Yet, the gene dosage of Rex1 is very critical for the survival of the late-stage embryos and neonates. This delayed phenotypic consequence suggests potential roles for Rex1 in establishing and maintaining unknown epigenetic modifications. Consistently, Rex1-null blastocysts display hypermethylation in the differentially methylated regions (DMRs) of Peg3 and Gnas imprinted domains, which are known to contain YY1 binding sites. Further analyses confirmed in vivo binding of Rex1 only to the unmethylated allele of these two regions. Thus, Rex1 may function as a protector for these DMRs against DNA methylation. Overall, the functional connection of Rex1 to genomic imprinting represents another case where newly made genes have co-evolved with lineage-specific phenomena.
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Affiliation(s)
- Jeong Do Kim
- Department of Biological Sciences, Louisiana State University, Baton Rouge, LA 70803, USA
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