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Terrón-Bautista J, Martínez-Sánchez MDM, López-Hernández L, Vadusevan AA, García-Domínguez M, Williams RS, Aguilera A, Millán-Zambrano G, Cortés-Ledesma F. Topological regulation of the estrogen transcriptional response by ZATT-mediated inhibition of TOP2B activity. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.22.576640. [PMID: 38328138 PMCID: PMC10849543 DOI: 10.1101/2024.01.22.576640] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/09/2024]
Abstract
Human type-II topoisomerases, TOP2A and TOP2B, remove transcription associated DNA supercoiling, thereby affecting gene-expression programs, and have recently been associated with 3D genome architecture. Here, we study the regulatory roles of TOP2 paralogs in response to estrogen, which triggers an acute transcriptional induction that involves rewiring of genome organization. We find that, whereas TOP2A facilitates transcription, as expected for a topoisomerase, TOP2B limits the estrogen response. Consistent with this, TOP2B activity is locally downregulated upon estrogen treatment to favor the establishment and stabilization of regulatory chromatin contacts, likely through an accumulation of DNA supercoiling. We show that estrogen-mediated inhibition of TOP2B requires estrogen receptor α (ERα), a non-catalytic function of TOP2A, and the action of the atypical SUMO-ligase ZATT. This mechanism of topological transcriptional-control, which may be shared by additional gene-expression circuits, highlights the relevance of DNA topoisomerases as central actors of genome dynamics.
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Affiliation(s)
- José Terrón-Bautista
- Centro Andaluz de Biología Molecular y Medicina Regenerativa-CABIMER, Universidad de Sevilla-CSIC-Universidad Pablo de Olavide, Sevilla, Spain
- Topology and DNA Breaks Group, Spanish National Cancer Centre (CNIO), Madrid 28029, Spain
| | | | - Laura López-Hernández
- Centro Andaluz de Biología Molecular y Medicina Regenerativa-CABIMER, Universidad de Sevilla-CSIC-Universidad Pablo de Olavide, Sevilla, Spain
- Departamento de Genética, Universidad de Sevilla, Spain
| | - Ananda Ayyappan Vadusevan
- Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, US Department of Health and Human Services, Research Triangle Park, NC 27709, USA
| | - Mario García-Domínguez
- Centro Andaluz de Biología Molecular y Medicina Regenerativa-CABIMER, Universidad de Sevilla-CSIC-Universidad Pablo de Olavide, Sevilla, Spain
| | - R. Scott Williams
- Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, US Department of Health and Human Services, Research Triangle Park, NC 27709, USA
| | - Andrés Aguilera
- Centro Andaluz de Biología Molecular y Medicina Regenerativa-CABIMER, Universidad de Sevilla-CSIC-Universidad Pablo de Olavide, Sevilla, Spain
- Departamento de Genética, Universidad de Sevilla, Spain
| | - Gonzalo Millán-Zambrano
- Centro Andaluz de Biología Molecular y Medicina Regenerativa-CABIMER, Universidad de Sevilla-CSIC-Universidad Pablo de Olavide, Sevilla, Spain
- Departamento de Genética, Universidad de Sevilla, Spain
| | - Felipe Cortés-Ledesma
- Centro Andaluz de Biología Molecular y Medicina Regenerativa-CABIMER, Universidad de Sevilla-CSIC-Universidad Pablo de Olavide, Sevilla, Spain
- Topology and DNA Breaks Group, Spanish National Cancer Centre (CNIO), Madrid 28029, Spain
- Lead contact
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Abstract
The human genome is organized into multiple structural layers, ranging from chromosome territories to progressively smaller substructures, such as topologically associating domains (TADs) and chromatin loops. These substructures, collectively referred to as long-range chromatin interactions (LRIs), have a significant role in regulating gene expression. TADs are regions of the genome that harbour groups of genes and regulatory elements that frequently interact with each other and are insulated from other regions, thereby preventing widespread uncontrolled DNA contacts. Chromatin loops formed within TADs through enhancer and promoter interactions are elastic, allowing transcriptional heterogeneity and stochasticity. Over the past decade, it has become evident that the 3D genome structure, also referred to as the chromatin architecture, is central to many transcriptional cellular decisions. In this Review, we delve into the intricate relationship between steroid receptors and LRIs, discussing how steroid receptors interact with and modulate these chromatin interactions. Genetic alterations in the many processes involved in organizing the nuclear architecture are often associated with the development of hormone-dependent cancers. A better understanding of the interplay between architectural proteins and hormone regulatory networks can ultimately be exploited to develop improved approaches for cancer treatment.
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Affiliation(s)
- Theophilus T Tettey
- Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, NIH, Bethesda, MD, USA
| | - Lorenzo Rinaldi
- Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, NIH, Bethesda, MD, USA
| | - Gordon L Hager
- Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, NIH, Bethesda, MD, USA.
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3
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Lee JJK, Jung YL, Cheong TC, Espejo Valle-Inclan J, Chu C, Gulhan DC, Ljungström V, Jin H, Viswanadham VV, Watson EV, Cortés-Ciriano I, Elledge SJ, Chiarle R, Pellman D, Park PJ. ERα-associated translocations underlie oncogene amplifications in breast cancer. Nature 2023; 618:1024-1032. [PMID: 37198482 PMCID: PMC10307628 DOI: 10.1038/s41586-023-06057-w] [Citation(s) in RCA: 23] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2021] [Accepted: 04/05/2023] [Indexed: 05/19/2023]
Abstract
Focal copy-number amplification is an oncogenic event. Although recent studies have revealed the complex structure1-3 and the evolutionary trajectories4 of oncogene amplicons, their origin remains poorly understood. Here we show that focal amplifications in breast cancer frequently derive from a mechanism-which we term translocation-bridge amplification-involving inter-chromosomal translocations that lead to dicentric chromosome bridge formation and breakage. In 780 breast cancer genomes, we observe that focal amplifications are frequently connected to each other by inter-chromosomal translocations at their boundaries. Subsequent analysis indicates the following model: the oncogene neighbourhood is translocated in G1 creating a dicentric chromosome, the dicentric chromosome is replicated, and as dicentric sister chromosomes segregate during mitosis, a chromosome bridge is formed and then broken, with fragments often being circularized in extrachromosomal DNAs. This model explains the amplifications of key oncogenes, including ERBB2 and CCND1. Recurrent amplification boundaries and rearrangement hotspots correlate with oestrogen receptor binding in breast cancer cells. Experimentally, oestrogen treatment induces DNA double-strand breaks in the oestrogen receptor target regions that are repaired by translocations, suggesting a role of oestrogen in generating the initial translocations. A pan-cancer analysis reveals tissue-specific biases in mechanisms initiating focal amplifications, with the breakage-fusion-bridge cycle prevalent in some and the translocation-bridge amplification in others, probably owing to the different timing of DNA break repair. Our results identify a common mode of oncogene amplification and propose oestrogen as its mechanistic origin in breast cancer.
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Affiliation(s)
- Jake June-Koo Lee
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA.
- Ludwig Center at Harvard, Harvard Medical School, Boston, MA, USA.
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
| | - Youngsook Lucy Jung
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
- Division of Genetics and Genomics, Boston Children's Hospital, Boston, MA, USA
| | - Taek-Chin Cheong
- Department of Pathology, Boston Children's Hospital and Harvard Medical School, Boston, MA, USA
| | | | - Chong Chu
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
| | - Doga C Gulhan
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
- Ludwig Center at Harvard, Harvard Medical School, Boston, MA, USA
| | - Viktor Ljungström
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
| | - Hu Jin
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
| | | | - Emma V Watson
- Department of Genetics, Harvard Medical School, Boston, MA, USA
- Department of Systems Biology, University of Massachusetts Chan Medical School, Worcester, MA, USA
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA
| | - Isidro Cortés-Ciriano
- European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, UK
| | - Stephen J Elledge
- Ludwig Center at Harvard, Harvard Medical School, Boston, MA, USA
- Department of Genetics, Harvard Medical School, Boston, MA, USA
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA
- Howard Hughes Medical Institute, Chevy Chase, MD, USA
| | - Roberto Chiarle
- Department of Pathology, Boston Children's Hospital and Harvard Medical School, Boston, MA, USA
- Department of Molecular Biotechnology and Health Sciences, University of Torino, Torino, Italy
| | - David Pellman
- Ludwig Center at Harvard, Harvard Medical School, Boston, MA, USA
- Howard Hughes Medical Institute, Chevy Chase, MD, USA
- Department of Cell Biology, Harvard Medical School, Boston, MA, USA
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Peter J Park
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA.
- Ludwig Center at Harvard, Harvard Medical School, Boston, MA, USA.
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4
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Kusi M, Zand M, Lin LL, Chen M, Lopez A, Lin CL, Wang CM, Lucio ND, Kirma NB, Ruan J, Huang THM, Mitsuya K. 2-Hydroxyglutarate destabilizes chromatin regulatory landscape and lineage fidelity to promote cellular heterogeneity. Cell Rep 2022; 38:110220. [PMID: 35021081 PMCID: PMC8811753 DOI: 10.1016/j.celrep.2021.110220] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2021] [Revised: 09/23/2021] [Accepted: 12/15/2021] [Indexed: 02/07/2023] Open
Abstract
The epigenome delineates lineage-specific transcriptional programs and restricts cell plasticity to prevent non-physiological cell fate transitions. Although cell diversification fosters tumor evolution and therapy resistance, upstream mechanisms that regulate the stability and plasticity of the cancer epigenome remain elusive. Here we show that 2-hydroxyglutarate (2HG) not only suppresses DNA repair but also mediates the high-plasticity chromatin landscape. A combination of single-cell epigenomics and multi-omics approaches demonstrates that 2HG disarranges otherwise well-preserved stable nucleosome positioning and promotes cell-to-cell variability. 2HG induces loss of motif accessibility to the luminal-defining transcriptional factors FOXA1, FOXP1, and GATA3 and a shift from luminal to basal-like gene expression. Breast tumors with high 2HG exhibit enhanced heterogeneity with undifferentiated epigenomic signatures linked to adverse prognosis. Further, ascorbate-2-phosphate (A2P) eradicates heterogeneity and impairs growth of high 2HG-producing breast cancer cells. These findings suggest 2HG as a key determinant of cancer plasticity and provide a rational strategy to counteract tumor cell evolution. Kusi et al. show that the oncometabolite 2-hydroxyglutarate (2HG) initiates cell-level epigenome fluctuations in the chromatin regulatory landscape, accompanied by loss of lineage fidelity. Breast tumors with high 2HG accumulation exhibit enhanced cellular heterogeneity with undifferentiated stem-like epigenomic signatures. The findings suggest metabolic derangement as a molecular origin of breast cancer heterogeneity.
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Affiliation(s)
- Meena Kusi
- Department of Molecular Medicine, University of Texas Health Science Center at San Antonio, 7703 Floyd Curl Drive, San Antonio, TX 78229, USA
| | - Maryam Zand
- Department of Computer Science, University of Texas at San Antonio, San Antonio, TX 78249, USA
| | - Li-Ling Lin
- Department of Molecular Medicine, University of Texas Health Science Center at San Antonio, 7703 Floyd Curl Drive, San Antonio, TX 78229, USA
| | - Meizhen Chen
- Department of Molecular Medicine, University of Texas Health Science Center at San Antonio, 7703 Floyd Curl Drive, San Antonio, TX 78229, USA
| | - Anthony Lopez
- Department of Molecular Medicine, University of Texas Health Science Center at San Antonio, 7703 Floyd Curl Drive, San Antonio, TX 78229, USA
| | - Chun-Lin Lin
- Department of Molecular Medicine, University of Texas Health Science Center at San Antonio, 7703 Floyd Curl Drive, San Antonio, TX 78229, USA
| | - Chiou-Miin Wang
- Department of Molecular Medicine, University of Texas Health Science Center at San Antonio, 7703 Floyd Curl Drive, San Antonio, TX 78229, USA
| | - Nicholas D Lucio
- Department of Molecular Medicine, University of Texas Health Science Center at San Antonio, 7703 Floyd Curl Drive, San Antonio, TX 78229, USA
| | - Nameer B Kirma
- Department of Molecular Medicine, University of Texas Health Science Center at San Antonio, 7703 Floyd Curl Drive, San Antonio, TX 78229, USA
| | - Jianhua Ruan
- Department of Computer Science, University of Texas at San Antonio, San Antonio, TX 78249, USA
| | - Tim H-M Huang
- Department of Molecular Medicine, University of Texas Health Science Center at San Antonio, 7703 Floyd Curl Drive, San Antonio, TX 78229, USA.
| | - Kohzoh Mitsuya
- Department of Molecular Medicine, University of Texas Health Science Center at San Antonio, 7703 Floyd Curl Drive, San Antonio, TX 78229, USA.
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Farcas AM, Nagarajan S, Cosulich S, Carroll JS. Genome-Wide Estrogen Receptor Activity in Breast Cancer. Endocrinology 2021; 162:bqaa224. [PMID: 33284960 PMCID: PMC7787425 DOI: 10.1210/endocr/bqaa224] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Indexed: 12/13/2022]
Abstract
The largest subtype of breast cancer is characterized by the expression and activity of the estrogen receptor alpha (ERalpha/ER). Although several effective therapies have significantly improved survival, the adaptability of cancer cells means that patients frequently stop responding or develop resistance to endocrine treatment. ER does not function in isolation and multiple associating factors have been reported to play a role in regulating the estrogen-driven transcriptional program. This review focuses on the dynamic interplay between some of these factors which co-occupy ER-bound regulatory elements, their contribution to estrogen signaling, and their possible therapeutic applications. Furthermore, the review illustrates how some ER association partners can influence and reprogram the genomic distribution of the estrogen receptor. As this dynamic ER activity enables cancer cell adaptability and impacts the clinical outcome, defining how this plasticity is determined is fundamental to our understanding of the mechanisms of disease progression.
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Affiliation(s)
- Anca M Farcas
- Bioscience, Oncology R&D, AstraZeneca, Cambridge, UK
- CRUK Cambridge Institute, University of Cambridge, Cambridge, UK
| | - Sankari Nagarajan
- CRUK Cambridge Institute, University of Cambridge, Cambridge, UK
- Division of Molecular and Cellular Function, School of Biological Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester, UK
| | | | - Jason S Carroll
- CRUK Cambridge Institute, University of Cambridge, Cambridge, UK
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Xu Y, Zhu Y, Yue Y, Pu S, Wu J, Lv Y, Du D. Tamoxifen attenuates reactive astrocyte-induced brain metastasis and drug resistance through the IL-6/STAT3 signaling pathway. Acta Biochim Biophys Sin (Shanghai) 2020; 52:1299-1305. [PMID: 33355355 DOI: 10.1093/abbs/gmaa127] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2020] [Indexed: 12/21/2022] Open
Abstract
Brain metastasis affects approximately 20%-30% of patients with triple-negative breast cancers (TNBCs). Even small metastatic lesions in the brain can trigger severe neurological impairments and result in extremely short survival time. Recently, active astrocytes were reported to be associated with brain metastases. However, how activated astrocytes regulate the behaviors of disseminated breast cancer cells in the brain remains unknown. In this study, human primary astrocytes were stimulated with IL-1β to form active astrocytes to study the cross-talk between stromal cells (astrocytes) and TNBC cells in brain metastases. Our results showed that active astrocytes significantly increase the malignancy of TNBC cells and prevent them from undergoing apoptosis caused by doxorubicin. We also found that the high level of IL-6 secreted by activated astrocytes was responsible for the drug resistance of breast cancer, which could be abolished by treatment of astrocytes with tamoxifen (TAM). The blockage of active astrocyte-derived IL-6 by a neutralizing antibody resulted in the attenuation of drug resistance, consequently enhancing the sensitivity of breast cancer cells to doxorubicin. Furthermore, the possible involved TAM-modulated drug resistance mechanism may be associated with a decrease in IL-6 expression in astrocytes and the downregulation of MAPK and JAK2/STAT3 signaling in cancer cells. Our data suggested that TAMs might reduce drug resistance through the IL-6/JAK2/STAT3 signaling pathway, providing a possible therapy to treat brain metastasis in TNBCs, as estrogen receptor inhibitors (TAMs, etc.) can cross the blood-brain barrier.
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Affiliation(s)
- Yongming Xu
- Department of Pain Management, Shanghai Sixth People’s Hospital, Shanghai Jiao Tong University, Shanghai 200233, China
| | - Yanrong Zhu
- Department of Clinical Laboratory, Liaocheng People’s Hospital, Liaocheng 252000, China
| | - Yong Yue
- Department of Anesthesiology, Zhejiang Putuo Hospital, Zhoushan 316100, China
| | - Shaofeng Pu
- Department of Pain Management, Shanghai Sixth People’s Hospital, Shanghai Jiao Tong University, Shanghai 200233, China
| | - Junzhen Wu
- Department of Pain Management, Shanghai Sixth People’s Hospital, Shanghai Jiao Tong University, Shanghai 200233, China
| | - Yingying Lv
- Department of Pain Management, Shanghai Sixth People’s Hospital, Shanghai Jiao Tong University, Shanghai 200233, China
| | - Dongping Du
- Department of Pain Management, Shanghai Sixth People’s Hospital, Shanghai Jiao Tong University, Shanghai 200233, China
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Sun G, Wang C, Wang S, Sun H, Zeng K, Zou R, Lin L, Liu W, Sun N, Song H, Liu W, Zhou T, Jin F, Shan Z, Zhao Y. An H3K4me3 reader, BAP18 as an adaptor of COMPASS-like core subunits co-activates ERα action and associates with the sensitivity of antiestrogen in breast cancer. Nucleic Acids Res 2020; 48:10768-10784. [PMID: 32986841 PMCID: PMC7641737 DOI: 10.1093/nar/gkaa787] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2020] [Revised: 08/19/2020] [Accepted: 09/10/2020] [Indexed: 12/18/2022] Open
Abstract
Estrogen receptor alpha (ERα) signaling pathway is essential for ERα-positive breast cancer progression and endocrine therapy resistance. Bromodomain PHD Finger Transcription Factor (BPTF) associated protein of 18kDa (BAP18) has been recognized as a crucial H3K4me3 reader. However, the whole genomic occupation of BAP18 and its biological function in breast cancer is still elusive. Here, we found that higher expression of BAP18 in ERα-positive breast cancer is positively correlated with poor prognosis. ChIP-seq analysis further demonstrated that the half estrogen response elements (EREs) and the CCCTC binding factor (CTCF) binding sites are the significant enrichment sites found in estrogen-induced BAP18 binding sites. Also, we provide the evidence to demonstrate that BAP18 as a novel co-activator of ERα is required for the recruitment of COMPASS-like core subunits to the cis-regulatory element of ERα target genes in breast cancer cells. BAP18 is recruited to the promoter regions of estrogen-induced genes, accompanied with the enrichment of the lysine 4-trimethylated histone H3 tail (H3K4me3) in the presence of E2. Furthermore, BAP18 promotes cell growth and associates the sensitivity of antiestrogen in ERα-positive breast cancer. Our data suggest that BAP18 facilitates the association between ERα and COMPASS-like core subunits, which might be an essential epigenetic therapeutic target for breast cancer.
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Affiliation(s)
- Ge Sun
- Department of Cell Biology, Key Laboratory of Cell Biology, Ministry of Public Health, and Key Laboratory of Medical Cell Biology, Ministry of Education, School of Life Sciences, China Medical University, Shenyang City 110122, Liaoning Province, China
| | - Chunyu Wang
- Department of Cell Biology, Key Laboratory of Cell Biology, Ministry of Public Health, and Key Laboratory of Medical Cell Biology, Ministry of Education, School of Life Sciences, China Medical University, Shenyang City 110122, Liaoning Province, China
| | - Shengli Wang
- Department of Cell Biology, Key Laboratory of Cell Biology, Ministry of Public Health, and Key Laboratory of Medical Cell Biology, Ministry of Education, School of Life Sciences, China Medical University, Shenyang City 110122, Liaoning Province, China
| | - Hongmiao Sun
- Department of Cell Biology, Key Laboratory of Cell Biology, Ministry of Public Health, and Key Laboratory of Medical Cell Biology, Ministry of Education, School of Life Sciences, China Medical University, Shenyang City 110122, Liaoning Province, China
| | - Kai Zeng
- Department of Cell Biology, Key Laboratory of Cell Biology, Ministry of Public Health, and Key Laboratory of Medical Cell Biology, Ministry of Education, School of Life Sciences, China Medical University, Shenyang City 110122, Liaoning Province, China
| | - Renlong Zou
- Department of Cell Biology, Key Laboratory of Cell Biology, Ministry of Public Health, and Key Laboratory of Medical Cell Biology, Ministry of Education, School of Life Sciences, China Medical University, Shenyang City 110122, Liaoning Province, China
| | - Lin Lin
- Department of Cell Biology, Key Laboratory of Cell Biology, Ministry of Public Health, and Key Laboratory of Medical Cell Biology, Ministry of Education, School of Life Sciences, China Medical University, Shenyang City 110122, Liaoning Province, China
| | - Wei Liu
- Department of Cell Biology, Key Laboratory of Cell Biology, Ministry of Public Health, and Key Laboratory of Medical Cell Biology, Ministry of Education, School of Life Sciences, China Medical University, Shenyang City 110122, Liaoning Province, China
| | - Ning Sun
- Department of Cell Biology, Key Laboratory of Cell Biology, Ministry of Public Health, and Key Laboratory of Medical Cell Biology, Ministry of Education, School of Life Sciences, China Medical University, Shenyang City 110122, Liaoning Province, China
| | - Huijuan Song
- Department of Cell Biology, Key Laboratory of Cell Biology, Ministry of Public Health, and Key Laboratory of Medical Cell Biology, Ministry of Education, School of Life Sciences, China Medical University, Shenyang City 110122, Liaoning Province, China
| | - Wensu Liu
- Department of Cell Biology, Key Laboratory of Cell Biology, Ministry of Public Health, and Key Laboratory of Medical Cell Biology, Ministry of Education, School of Life Sciences, China Medical University, Shenyang City 110122, Liaoning Province, China
| | - Tingting Zhou
- Department of Cell Biology, Key Laboratory of Cell Biology, Ministry of Public Health, and Key Laboratory of Medical Cell Biology, Ministry of Education, School of Life Sciences, China Medical University, Shenyang City 110122, Liaoning Province, China
| | - Feng Jin
- Department of Breast Surgery, the First Affiliated Hospital of China Medical University, Shenyang City 110001, Liaoning Province, China
| | - Zhongyan Shan
- Department of Endocrinology and Metabolism, Institute of Endocrinology, The First Affiliated Hospital of China Medical University, ShenyangCity110001, Liaoning Province, China
| | - Yue Zhao
- Department of Cell Biology, Key Laboratory of Cell Biology, Ministry of Public Health, and Key Laboratory of Medical Cell Biology, Ministry of Education, School of Life Sciences, China Medical University, Shenyang City 110122, Liaoning Province, China.,Department of Endocrinology and Metabolism, Institute of Endocrinology, The First Affiliated Hospital of China Medical University, ShenyangCity110001, Liaoning Province, China
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8
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The 3D genomic landscape of differential response to EGFR/HER2 inhibition in endocrine-resistant breast cancer cells. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2020; 1863:194631. [PMID: 32956836 DOI: 10.1016/j.bbagrm.2020.194631] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/14/2020] [Revised: 08/10/2020] [Accepted: 09/14/2020] [Indexed: 11/23/2022]
Abstract
BACKGROUND Recent studies suggested that crosstalk between ERα and EGFR/HER2 pathways plays a critical role in mediating endocrine therapy resistance. Several inhibitors targeting EGFR/HER2 signaling, including FDA-approved lapatinib and gefitinib as well as a novel dual tyrosine kinase inhibitor (TKI) sapitinib, showed greater therapeutic efficacies. However, how 3D chromatin landscape responds to the inhibition of EGFR/HER2 pathway remains to be elucidated. METHODS In this study, we conducted in situ Hi-C and RNA-seq in two ERα+ breast cancer cell systems, 1) parental MCF7 cells and its associated tamoxifen-resistant MCF7TR cells; and 2) parental T47D cells and its associated tamoxifen-resistant T47DTR cells, before and after the treatment of sapitinib. RESULTS We identified differential responses in topologically associated domains (TADs), looping genes and expressed genes. Interestingly, we found that many differential TADs and looping genes are reversible after sapitinib treatment, indicating that EGFR/HER2 signaling may play a role in reshaping and rewiring the high order genome organization. We further examined and recapitulated the reversible looping genes in 3D spheroids of breast cancer cells, demonstrating that 3D cell culture spheroid of breast cancer cells could be a potential preclinical breast cancer model for studying 3D chromatin regulation. CONCLUSIONS Our study has provided significant insights into our understanding of 3D genomic landscape changes in response to EGFR/HER2 Inhibition in endocrine-resistant breast cancer cells. Our data provides a rich resource for further evaluating chromatin structural responses to EGFR/HER2 targeted therapies in endocrine-resistant breast cancer cells. Our analyses suggest that these alterations of chromatin structures and transcriptional programs may provide new avenues for intervention or designing of patient selection for targeted endocrine treatment.
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9
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Zhou Y, Cheng X, Yang Y, Li T, Li J, Huang THM, Wang J, Lin S, Jin VX. Modeling and analysis of Hi-C data by HiSIF identifies characteristic promoter-distal loops. Genome Med 2020; 12:69. [PMID: 32787954 PMCID: PMC7425017 DOI: 10.1186/s13073-020-00769-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2020] [Accepted: 07/28/2020] [Indexed: 01/04/2023] Open
Abstract
Current computational methods on Hi-C analysis focused on identifying Mb-size domains often failed to unveil the underlying functional and mechanistic relationship of chromatin structure and gene regulation. We developed a novel computational method HiSIF to identify genome-wide interacting loci. We illustrated HiSIF outperformed other tools for identifying chromatin loops. We applied it to Hi-C data in breast cancer cells and identified 21 genes with gained loops showing worse relapse-free survival in endocrine-treated patients, suggesting the genes with enhanced loops can be used for prognostic signatures for measuring the outcome of the endocrine treatment. HiSIF is available at https://github.com/yufanzhouonline/HiSIF .
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Affiliation(s)
- Yufan Zhou
- Department of Molecular Medicine, University of Texas Health San Antonio, San Antonio, TX, 78229, USA
| | - Xiaolong Cheng
- Department of Molecular Medicine, University of Texas Health San Antonio, San Antonio, TX, 78229, USA
| | - Yini Yang
- Department of Molecular Medicine, University of Texas Health San Antonio, San Antonio, TX, 78229, USA
| | - Tian Li
- Department of Molecular Medicine, University of Texas Health San Antonio, San Antonio, TX, 78229, USA
| | - Jingwei Li
- Department of Molecular Medicine, University of Texas Health San Antonio, San Antonio, TX, 78229, USA
| | - Tim H-M Huang
- Department of Molecular Medicine, University of Texas Health San Antonio, San Antonio, TX, 78229, USA
| | - Junbai Wang
- Department of Pathology, Oslo University Hospital - Norwegian Radium Hospital, Montebello, 0310, Oslo, Norway
| | - Shili Lin
- Department of Statistics, The Ohio State University, Columbus, OH, 43210, USA
| | - Victor X Jin
- Department of Molecular Medicine, University of Texas Health San Antonio, San Antonio, TX, 78229, USA.
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10
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Abstract
Tamoxifen is beneficial in treating estrogen receptor–positive breast cancer, but resistance to this treatment eventually ensues. A method to identify mechanisms of tamoxifen resistance identified the histone deacetylase ZIP, leading to the finding that increased expression of the tyrosine kinase JAK2 is one important factor. As a result of this discovery, it may be possible to use an inhibitor of JAK2 to block the aberrant activation of STAT3 caused by ZIP deficiency to help overcome or prevent tamoxifen resistance. Tamoxifen, a widely used modulator of the estrogen receptor (ER), targets ER-positive breast cancer preferentially. We used a powerful validation-based insertion mutagenesis method to find that expression of a dominant-negative, truncated form of the histone deacetylase ZIP led to resistance to tamoxifen. Consistently, increased expression of full-length ZIP gives the opposite phenotype, inhibiting the expression of genes whose products mediate resistance. An important example is JAK2. By binding to two specific sequences in the promoter, ZIP suppresses JAK2 expression. Increased expression and activation of JAK2 when ZIP is inhibited lead to increased STAT3 phosphorylation and increased resistance to tamoxifen, both in cell culture experiments and in a mouse xenograft model. Furthermore, data from human tumors are consistent with the conclusion that decreased expression of ZIP leads to resistance to tamoxifen in ER-positive breast cancer.
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11
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Lin CL, Tan X, Chen M, Kusi M, Hung CN, Chou CW, Hsu YT, Wang CM, Kirma N, Chen CL, Lin CH, Lathrop KI, Elledge R, Kaklamani VG, Mitsuya K, Huang THM. ERα-related chromothripsis enhances concordant gene transcription on chromosome 17q11.1-q24.1 in luminal breast cancer. BMC Med Genomics 2020; 13:69. [PMID: 32408897 PMCID: PMC7222439 DOI: 10.1186/s12920-020-0729-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2019] [Accepted: 04/30/2020] [Indexed: 12/22/2022] Open
Abstract
BACKGROUND Chromothripsis is an event of genomic instability leading to complex chromosomal alterations in cancer. Frequent long-range chromatin interactions between transcription factors (TFs) and targets may promote extensive translocations and copy-number alterations in proximal contact regions through inappropriate DNA stitching. Although studies have proposed models to explain the initiation of chromothripsis, few discussed how TFs influence this process for tumor progression. METHODS This study focused on genomic alterations in amplification associated regions within chromosome 17. Inter-/intra-chromosomal rearrangements were analyzed using whole genome sequencing data of breast tumors in the Cancer Genome Atlas (TCGA) cohort. Common ERα binding sites were defined based on MCF-7, T47D, and MDA-MB-134 breast cancer cell lines using univariate K-means clustering methods. Nanopore sequencing technology was applied to validate frequent rearrangements detected between ATC loci on 17q23 and an ERα hub on 20q13. The efficacy of pharmacological inhibition of a potentially druggable target gene on 17q23 was evaluated using breast cancer cell lines and patient-derived circulating breast tumor cells. RESULTS There are five adjoining regions from 17q11.1 to 17q24.1 being hotspots of chromothripsis. Inter-/intra-chromosomal rearrangements of these regions occurred more frequently in ERα-positive tumors than in ERα-negative tumors. In addition, the locations of the rearrangements were often mapped within or close to dense ERα binding sites localized on these five 17q regions or other chromosomes. This chromothriptic event was linked to concordant upregulation of 96 loci that predominantly regulate cell-cycle machineries in advanced luminal tumors. Genome-editing analysis confirmed that an ERα hub localized on 20q13 coordinately regulates a subset of these loci localized on 17q23 through long-range chromosome interactions. One of these loci, Tousled Like Kinase 2 (TLK2) known to participate in DNA damage checkpoint control, is an actionable target using phenothiazine antipsychotics (PTZs). The antiproliferative effect of PTZs was prominent in high TLK2-expressing cells, compared to low expressing cells. CONCLUSION This study demonstrates a new approach for identifying tumorigenic drivers from genomic regions highly susceptible to ERα-related chromothripsis. We found a group of luminal breast tumors displaying 17q-related chromothripsis for which antipsychotics can be repurposed as treatment adjuncts.
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Affiliation(s)
- Chun-Lin Lin
- Department of Molecular Medicine, University of Texas Health Science Center at San Antonio, 7703 Floyd Curl Drive, San Antonio, TX, 78229, USA
| | - Xi Tan
- Department of Molecular Medicine, University of Texas Health Science Center at San Antonio, 7703 Floyd Curl Drive, San Antonio, TX, 78229, USA
| | - Meizhen Chen
- Department of Molecular Medicine, University of Texas Health Science Center at San Antonio, 7703 Floyd Curl Drive, San Antonio, TX, 78229, USA
| | - Meena Kusi
- Department of Molecular Medicine, University of Texas Health Science Center at San Antonio, 7703 Floyd Curl Drive, San Antonio, TX, 78229, USA
| | - Chia-Nung Hung
- Department of Molecular Medicine, University of Texas Health Science Center at San Antonio, 7703 Floyd Curl Drive, San Antonio, TX, 78229, USA
| | - Chih-Wei Chou
- Department of Molecular Medicine, University of Texas Health Science Center at San Antonio, 7703 Floyd Curl Drive, San Antonio, TX, 78229, USA
| | - Ya-Ting Hsu
- Department of Molecular Medicine, University of Texas Health Science Center at San Antonio, 7703 Floyd Curl Drive, San Antonio, TX, 78229, USA
| | - Chiou-Miin Wang
- Department of Molecular Medicine, University of Texas Health Science Center at San Antonio, 7703 Floyd Curl Drive, San Antonio, TX, 78229, USA
| | - Nameer Kirma
- Department of Molecular Medicine, University of Texas Health Science Center at San Antonio, 7703 Floyd Curl Drive, San Antonio, TX, 78229, USA
| | - Chun-Liang Chen
- Department of Molecular Medicine, University of Texas Health Science Center at San Antonio, 7703 Floyd Curl Drive, San Antonio, TX, 78229, USA
| | - Ching-Hung Lin
- Department of Oncology, National Taiwan University Hospital, Taipei, Taiwan
- Department of Internal Medicine, National Taiwan University Hospital, Taipei, Taiwan
| | - Kate I Lathrop
- Department of Medicine, Mays Cancer Center, University of Texas Health Science Center at San Antonio, San Antonio, TX, USA
| | - Richard Elledge
- Department of Medicine, Mays Cancer Center, University of Texas Health Science Center at San Antonio, San Antonio, TX, USA
| | - Virginia G Kaklamani
- Department of Medicine, Mays Cancer Center, University of Texas Health Science Center at San Antonio, San Antonio, TX, USA
| | - Kohzoh Mitsuya
- Department of Molecular Medicine, University of Texas Health Science Center at San Antonio, 7703 Floyd Curl Drive, San Antonio, TX, 78229, USA.
| | - Tim H-M Huang
- Department of Molecular Medicine, University of Texas Health Science Center at San Antonio, 7703 Floyd Curl Drive, San Antonio, TX, 78229, USA.
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12
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Zhou Y, Gerrard DL, Wang J, Li T, Yang Y, Fritz AJ, Rajendran M, Fu X, Stein G, Schiff R, Lin S, Frietze S, Jin VX. Temporal dynamic reorganization of 3D chromatin architecture in hormone-induced breast cancer and endocrine resistance. Nat Commun 2019; 10:1522. [PMID: 30944316 PMCID: PMC6447566 DOI: 10.1038/s41467-019-09320-9] [Citation(s) in RCA: 43] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2017] [Accepted: 02/27/2019] [Indexed: 01/01/2023] Open
Abstract
Recent studies have demonstrated that chromatin architecture is linked to the progression of cancers. However, the roles of 3D structure and its dynamics in hormone-dependent breast cancer and endocrine resistance are largely unknown. Here we report the dynamics of 3D chromatin structure across a time course of estradiol (E2) stimulation in human estrogen receptor α (ERα)-positive breast cancer cells. We identified subsets of temporally highly dynamic compartments predominantly associated with active open chromatin and found that these highly dynamic compartments showed higher alteration in tamoxifen-resistant breast cancer cells. Remarkably, these compartments are characterized by active chromatin states, and enhanced ERα binding but decreased transcription factor CCCTC-binding factor (CTCF) binding. We finally identified a set of ERα-bound promoter-enhancer looping genes enclosed within altered domains that are enriched with cancer invasion, aggressiveness or metabolism signaling pathways. This large-scale analysis expands our understanding of high-order temporal chromatin reorganization underlying hormone-dependent breast cancer.
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Affiliation(s)
- Yufan Zhou
- Department of Molecular Medicine, University of Texas Health San Antonio, San Antonio, TX, 78229, USA
| | - Diana L Gerrard
- MLRS Department, University of Vermont, Burlington, VT, 05405, USA
| | - Junbai Wang
- Department of Pathology, Oslo University Hospital-Norwegian Radium Hospital, 0310, Montebello, Oslo, Norway
| | - Tian Li
- Department of Molecular Medicine, University of Texas Health San Antonio, San Antonio, TX, 78229, USA
| | - Yini Yang
- Department of Molecular Medicine, University of Texas Health San Antonio, San Antonio, TX, 78229, USA
| | - Andrew J Fritz
- Department of Biochemistry, University of Vermont, Burlington, VT, 05405, USA
| | - Mahitha Rajendran
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX, 77030, USA.,Department of Medicine, Baylor College of Medicine, Houston, TX, 77030, USA.,Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, TX, 77030, USA.,Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Xiaoyong Fu
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX, 77030, USA.,Department of Medicine, Baylor College of Medicine, Houston, TX, 77030, USA.,Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, TX, 77030, USA.,Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Gary Stein
- Department of Surgery, University of Vermont Larner College of Medicine, 89 Beaumont Avenue, Given C401, Burlington, Vermont, 05405, USA
| | - Rachel Schiff
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX, 77030, USA.,Department of Medicine, Baylor College of Medicine, Houston, TX, 77030, USA.,Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, TX, 77030, USA.,Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Shili Lin
- Department of Statistics, The Ohio State University, Columbus, OH, 43210, USA
| | - Seth Frietze
- MLRS Department, University of Vermont, Burlington, VT, 05405, USA.
| | - Victor X Jin
- Department of Molecular Medicine, University of Texas Health San Antonio, San Antonio, TX, 78229, USA.
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13
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Fritz AJ, Gillis NE, Gerrard DL, Rodriguez PD, Hong D, Rose JT, Ghule PN, Bolf EL, Gordon JA, Tye CE, Boyd JR, Tracy KM, Nickerson JA, van Wijnen AJ, Imbalzano AN, Heath JL, Frietze SE, Zaidi SK, Carr FE, Lian JB, Stein JL, Stein GS. Higher order genomic organization and epigenetic control maintain cellular identity and prevent breast cancer. Genes Chromosomes Cancer 2019; 58:484-499. [PMID: 30873710 DOI: 10.1002/gcc.22731] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2018] [Revised: 01/07/2019] [Accepted: 01/07/2019] [Indexed: 12/24/2022] Open
Abstract
Cells establish and sustain structural and functional integrity of the genome to support cellular identity and prevent malignant transformation. In this review, we present a strategic overview of epigenetic regulatory mechanisms including histone modifications and higher order chromatin organization (HCO) that are perturbed in breast cancer onset and progression. Implications for dysfunctions that occur in hormone regulation, cell cycle control, and mitotic bookmarking in breast cancer are considered, with an emphasis on epithelial-to-mesenchymal transition and cancer stem cell activities. The architectural organization of regulatory machinery is addressed within the contexts of translating cancer-compromised genomic organization to advances in breast cancer risk assessment, diagnosis, prognosis, and identification of novel therapeutic targets with high specificity and minimal off target effects.
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Affiliation(s)
- A J Fritz
- Department of Biochemistry, Larner College of Medicine, University of Vermont, Burlington, Vermont.,University of Vermont Cancer Center, Burlington, Vermont
| | - N E Gillis
- University of Vermont Cancer Center, Burlington, Vermont.,Department of Pharmacology, Larner college of Medicine, University of Vermont, Burlington, Vermont
| | - D L Gerrard
- Cellular Molecular Biomedical Sciences Program, University of Vermont, Burlington, Vermont.,Department of Biomedical and Health Sciences, University of Vermont, Burlington, Vermont
| | - P D Rodriguez
- Cellular Molecular Biomedical Sciences Program, University of Vermont, Burlington, Vermont.,Department of Biomedical and Health Sciences, University of Vermont, Burlington, Vermont
| | - D Hong
- Department of Medical Oncology, Dana Farber Cancer Institute, Boston, Massachusetts
| | - J T Rose
- Department of Biochemistry, Larner College of Medicine, University of Vermont, Burlington, Vermont.,University of Vermont Cancer Center, Burlington, Vermont
| | - P N Ghule
- Department of Biochemistry, Larner College of Medicine, University of Vermont, Burlington, Vermont.,University of Vermont Cancer Center, Burlington, Vermont
| | - E L Bolf
- University of Vermont Cancer Center, Burlington, Vermont.,Department of Pharmacology, Larner college of Medicine, University of Vermont, Burlington, Vermont
| | - J A Gordon
- Department of Biochemistry, Larner College of Medicine, University of Vermont, Burlington, Vermont.,University of Vermont Cancer Center, Burlington, Vermont
| | - C E Tye
- Department of Biochemistry, Larner College of Medicine, University of Vermont, Burlington, Vermont.,University of Vermont Cancer Center, Burlington, Vermont
| | - J R Boyd
- Department of Biochemistry, Larner College of Medicine, University of Vermont, Burlington, Vermont.,University of Vermont Cancer Center, Burlington, Vermont
| | - K M Tracy
- Department of Biochemistry, Larner College of Medicine, University of Vermont, Burlington, Vermont.,University of Vermont Cancer Center, Burlington, Vermont
| | - J A Nickerson
- Division of Genes and Development of the Department of Pediatrics, University of Massachusetts Medical School, Worcester, Massachusetts
| | - A J van Wijnen
- Orthopedic Surgery and Biochemistry and Molecular Biology, Mayo Clinic Minnesota, Rochester, Minnesota
| | - A N Imbalzano
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, Massachusetts
| | - J L Heath
- Department of Biochemistry, Larner College of Medicine, University of Vermont, Burlington, Vermont.,University of Vermont Cancer Center, Burlington, Vermont.,Department of Pediatrics, Larner College of Medicine, University of Vermont, Burlington, Vermont
| | - S E Frietze
- Cellular Molecular Biomedical Sciences Program, University of Vermont, Burlington, Vermont.,Department of Biomedical and Health Sciences, University of Vermont, Burlington, Vermont
| | - S K Zaidi
- Department of Biochemistry, Larner College of Medicine, University of Vermont, Burlington, Vermont.,University of Vermont Cancer Center, Burlington, Vermont
| | - F E Carr
- Department of Biochemistry, Larner College of Medicine, University of Vermont, Burlington, Vermont.,University of Vermont Cancer Center, Burlington, Vermont.,Department of Pharmacology, Larner college of Medicine, University of Vermont, Burlington, Vermont
| | - J B Lian
- Department of Biochemistry, Larner College of Medicine, University of Vermont, Burlington, Vermont.,University of Vermont Cancer Center, Burlington, Vermont
| | - J L Stein
- Department of Biochemistry, Larner College of Medicine, University of Vermont, Burlington, Vermont.,University of Vermont Cancer Center, Burlington, Vermont
| | - G S Stein
- Department of Biochemistry, Larner College of Medicine, University of Vermont, Burlington, Vermont.,University of Vermont Cancer Center, Burlington, Vermont
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14
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Liu B, Huang G, Zhu H, Ma Z, Tian X, Yin L, Gao X, He X. Analysis of gene co‑expression network reveals prognostic significance of CNFN in patients with head and neck cancer. Oncol Rep 2019; 41:2168-2180. [PMID: 30816522 PMCID: PMC6412593 DOI: 10.3892/or.2019.7019] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2018] [Accepted: 02/07/2019] [Indexed: 01/20/2023] Open
Abstract
In patients with head and neck cancer (HNC), lymph node (N) metastases are associated with cancer aggressiveness and poor prognosis. Identifying meaningful gene modules and representative biomarkers relevant to the N stage helps predict prognosis and reveal mechanisms underlying tumor progression. The present study used a step-wise approach for weighted gene co-expression network analysis (WGCNA). Dataset GSE65858 was subjected to WGCNA. RNA sequencing data of HNC downloaded from the Cancer Genome Atlas (TCGA) and dataset GSE39366 were utilized to validate the results. Following data preprocessing, 4,295 genes were screened, and blue and black modules associated with the N stage of HNC were identified. A total of 16 genes [keratinocyte differentiation associated protein, suprabasin, cornifelin (CNFN), small proline rich protein 1B, desmoglein 1 (DSG1), chromosome 10 open reading frame 99, keratin 16 pseudogene 3, gap junction protein β2, dermokine, LY6/PLAUR domain containing 3, transmembrane protein 79, phospholipase A2 group IVE, transglutaminase 5, potassium two pore domain channel subfamily K member 6, involucrin, kallikrein related peptidase 8] that had a negative association with the N-stage in the blue module, and two genes (structural maintenance of chromosomes 4 and mutS homolog 6) that had a positive association in the black module, were identified to be candidate hub genes. Following further validation in TCGA and dataset GSE65858, it was identified that CNFN and DSG1 were associated with the clinical stage of HNC. Survival analysis of CNFN and DSG1 was subsequently performed. Patients with increased expression of CNFN displayed better survival probability in dataset GSE65858 and TCGA. Therefore, CNFN was selected as the hub gene for further verification in the Gene Expression Profiling Interactive Analysis database. Finally, functional enrichment and gene set enrichment analyses were performed using datasets GSE65858 and GSE39366. Three gene sets, namely ‘P53 pathway’, ‘estrogen response early’ and ‘estrogen response late’, were enriched in the two datasets. In conclusion, CNFN, identified via the WGCNA algorithm, may contribute to the prediction of lymph node metastases and prognosis, probably by regulating the pathways associated with P53, and the early and late estrogen response.
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Affiliation(s)
- Baoling Liu
- Department of Physiology, School of Basic Medical Sciences, Nanjing Medical University, Nanjing, Jiangsu 211166, P.R. China
| | - Guanhong Huang
- Department of Radiotherapy, No. 2 People's Hospital of Lianyungang, Lianyungang, Jiangsu 222000, P.R. China
| | - Hongming Zhu
- Department of Radiotherapy, Jiangsu Cancer Hospital, Jiangsu Institute of Cancer Research, Nanjing Medical University Affiliated Cancer Hospital, Nanjing, Jiangsu 210000, P.R. China
| | - Zhaoming Ma
- Department of Radiotherapy, No. 2 People's Hospital of Lianyungang, Lianyungang, Jiangsu 222000, P.R. China
| | - Xiaokang Tian
- Department of Radiotherapy, Jiangsu Cancer Hospital, Jiangsu Institute of Cancer Research, Nanjing Medical University Affiliated Cancer Hospital, Nanjing, Jiangsu 210000, P.R. China
| | - Li Yin
- Department of Radiotherapy, Jiangsu Cancer Hospital, Jiangsu Institute of Cancer Research, Nanjing Medical University Affiliated Cancer Hospital, Nanjing, Jiangsu 210000, P.R. China
| | - Xingya Gao
- Department of Physiology, School of Basic Medical Sciences, Nanjing Medical University, Nanjing, Jiangsu 211166, P.R. China
| | - Xia He
- Department of Radiotherapy, Jiangsu Cancer Hospital, Jiangsu Institute of Cancer Research, Nanjing Medical University Affiliated Cancer Hospital, Nanjing, Jiangsu 210000, P.R. China
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15
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Li Y, He Y, Liang Z, Wang Y, Chen F, Djekidel MN, Li G, Zhang X, Xiang S, Wang Z, Gao J, Zhang MQ, Chen Y. Alterations of specific chromatin conformation affect ATRA-induced leukemia cell differentiation. Cell Death Dis 2018; 9:200. [PMID: 29422670 PMCID: PMC5833835 DOI: 10.1038/s41419-017-0173-6] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2017] [Revised: 10/10/2017] [Accepted: 11/20/2017] [Indexed: 12/31/2022]
Abstract
Chromatin conformation plays a key role in regulating gene expression and controlling cell differentiation. However, the whole-genome chromatin conformation changes that occur during leukemia cell differentiation are poorly understood. Here, we characterized the changes in chromatin conformation, histone states, chromatin accessibility, and gene expression using an all-trans retinoic acid (ATRA)-induced HL-60 cell differentiation model. The results showed that the boundaries of topological associated domains (TADs) were stable during differentiation; however, the chromatin conformations within several specific TADs were obviously changed. By combining H3K4me3, H3K27ac, and Hi-C signals, we annotated the differential gene-regulatory chromatin interactions upon ATRA induction. The gains and losses of the gene-regulatory chromatin interactions are significantly correlated with gene expression and chromatin accessibility. Finally, we found that the loss of GATA2 expression and DNA binding are crucial for the differentiation process, and changes in the chromatin structure around the GATA2 regulate its expression upon ATRA induction. This study provided both statistical insights and experimental details regarding the relationship between chromatin conformation changes and transcription regulation during leukemia cell differentiation, and the results suggested that the chromatin conformation is a new type of potential drug target for cancer therapy.
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Affiliation(s)
- Yanjian Li
- MOE Key Laboratory of Bioinformatics, Bioinformatics Division and Center for Synthetic & Systems Biology, TNLIST, School of Medicine, Tsinghua University, Beijing, 100084, China
| | - Yi He
- School of Pharmaceutical Sciences, Tsinghua University, Beijing, 100084, China
| | - Zhengyu Liang
- MOE Key Laboratory of Bioinformatics, Bioinformatics Division and Center for Synthetic & Systems Biology, TNLIST, School of Medicine, Tsinghua University, Beijing, 100084, China
| | - Yang Wang
- MOE Key Laboratory of Bioinformatics, Bioinformatics Division and Center for Synthetic & Systems Biology, TNLIST, Department of Automation, Tsinghua University, Beijing, 100084, China
| | - Fengling Chen
- MOE Key Laboratory of Bioinformatics, Bioinformatics Division and Center for Synthetic & Systems Biology, TNLIST, Department of Automation, Tsinghua University, Beijing, 100084, China
| | - Mohamed Nadhir Djekidel
- MOE Key Laboratory of Bioinformatics, Bioinformatics Division and Center for Synthetic & Systems Biology, TNLIST, Department of Automation, Tsinghua University, Beijing, 100084, China
| | - Guipeng Li
- MOE Key Laboratory of Bioinformatics, Bioinformatics Division and Center for Synthetic & Systems Biology, TNLIST, Department of Automation, Tsinghua University, Beijing, 100084, China
| | - Xu Zhang
- MOE Key Laboratory of Bioinformatics, Bioinformatics Division and Center for Synthetic & Systems Biology, TNLIST, Department of Automation, Tsinghua University, Beijing, 100084, China
| | - Shuqin Xiang
- MOE Key Laboratory of Bioinformatics, Bioinformatics Division and Center for Synthetic & Systems Biology, TNLIST, School of Medicine, Tsinghua University, Beijing, 100084, China
| | - Zejun Wang
- MOE Key Laboratory of Bioinformatics, Bioinformatics Division and Center for Synthetic & Systems Biology, TNLIST, Department of Automation, Tsinghua University, Beijing, 100084, China
| | - Juntao Gao
- MOE Key Laboratory of Bioinformatics, Bioinformatics Division and Center for Synthetic & Systems Biology, TNLIST, Department of Automation, Tsinghua University, Beijing, 100084, China
| | - Michael Q Zhang
- MOE Key Laboratory of Bioinformatics, Bioinformatics Division and Center for Synthetic & Systems Biology, TNLIST, School of Medicine, Tsinghua University, Beijing, 100084, China. .,MOE Key Laboratory of Bioinformatics, Bioinformatics Division and Center for Synthetic & Systems Biology, TNLIST, Department of Automation, Tsinghua University, Beijing, 100084, China. .,Department of Biological Sciences, Center for Systems Biology, The University of Texas, Dallas 800 West Campbell Road, RL11, Richardson, TX, 75080-3021, USA.
| | - Yang Chen
- MOE Key Laboratory of Bioinformatics, Bioinformatics Division and Center for Synthetic & Systems Biology, TNLIST, School of Medicine, Tsinghua University, Beijing, 100084, China. .,MOE Key Laboratory of Bioinformatics, Bioinformatics Division and Center for Synthetic & Systems Biology, TNLIST, Department of Automation, Tsinghua University, Beijing, 100084, China.
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16
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Yang J, Harris AL, Davidoff AM. Hypoxia and Hormone-Mediated Pathways Converge at the Histone Demethylase KDM4B in Cancer. Int J Mol Sci 2018; 19:E240. [PMID: 29342868 PMCID: PMC5796188 DOI: 10.3390/ijms19010240] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2017] [Revised: 01/08/2018] [Accepted: 01/09/2018] [Indexed: 02/07/2023] Open
Abstract
Hormones play an important role in pathophysiology. The hormone receptors, such as estrogen receptor alpha and androgen receptor in breast cancer and prostate cancer, are critical to cancer cell proliferation and tumor growth. In this review we focused on the cross-talk between hormone and hypoxia pathways, particularly in breast cancer. We delineated a novel signaling pathway from estrogen receptor to hypoxia-inducible factor 1, and discussed the role of this pathway in endocrine therapy resistance. Further, we discussed the estrogen and hypoxia pathways converging at histone demethylase KDM4B, an important epigenetic modifier in cancer.
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Affiliation(s)
- Jun Yang
- Department of Surgery, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105, USA.
| | - Adrian L Harris
- Molecular Oncology Laboratories, Department of Oncology, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford OX3 9DS, UK.
| | - Andrew M Davidoff
- Department of Surgery, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105, USA.
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17
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Jiang CF, Li DM, Shi ZM, Wang L, Liu MM, Ge X, Liu X, Qian YC, Wen YY, Zhen LL, Lin J, Liu LZ, Jiang BH. Estrogen regulates miRNA expression: implication of estrogen receptor and miR-124/AKT2 in tumor growth and angiogenesis. Oncotarget 2018; 7:36940-36955. [PMID: 27175587 PMCID: PMC5095050 DOI: 10.18632/oncotarget.9230] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2015] [Accepted: 04/16/2016] [Indexed: 12/21/2022] Open
Abstract
It is currently known that estrogen plays an important role in breast cancer (BC) development, but the underlying molecular mechanism remains to be elucidated. Accumulating evidence has revealed important roles of microRNAs in various kinds of human cancers, including BC. In this study, we found that among the microRNAs regulated by estrogen, miR-124 was the most prominent downregulated miRNA. miR-124 was downregulated by estradiol (E2) treatment in estrogen receptor (ER) positive BC cells, miR-124 overexpression suppressed cell proliferation, migration and invasion in BC cells; while the suppression of miR-124 using Anti-miR-124 inhibitor had opposite cellular functions. Under the E2 treatment, miR-124 had stronger effect to inhibit cellular functions in MCF7 cells than that in MDA-MB-231 cells. In addition, we identified that ERα, but not ERβ, was required for E2-induced miR-124 downregulation. Furthermore, AKT2, a known oncogene, was a novel direct target of miR-124. AKT2 expression levels were inversely correlated with miR-124 expression levels in human breast cancer specimens. AKT2 was overexpressed in BC specimens, and its expression levels were much higher in ERα positive cancer tissues than those ERα negative cancer tissues. Consistent with miR-124 suppression, E2 treatment increased AKT2 expression levels in MCF7 cells via ERα. Finally, overexpression of miR-124 in MCF7 cells significantly suppressed tumor growth and angiogenesis by targeting AKT2. Our results provide a mechanistic insight into a functional role of new ERα/miR-124/AKT2 signaling pathway in BC development. miR-124 and AKT2 may be used as biomarkers for ERα positive BC and therapeutic effect in the future.
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Affiliation(s)
- Cheng-Fei Jiang
- State Key Laboratory of Reproductive Medicine, Department of Pathology, Nanjing Medical University, Nanjing, China
| | - Dong-Mei Li
- State Key Laboratory of Reproductive Medicine, Department of Pathology, Nanjing Medical University, Nanjing, China
| | - Zhu-Mei Shi
- State Key Laboratory of Reproductive Medicine, Department of Pathology, Nanjing Medical University, Nanjing, China.,Department of Neurosurgery, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Lin Wang
- State Key Laboratory of Reproductive Medicine, Department of Pathology, Nanjing Medical University, Nanjing, China
| | - Min-Min Liu
- Huai'an First People's Hospital, Nanjing Medical University, Huai'an, China
| | - Xin Ge
- State Key Laboratory of Reproductive Medicine, Department of Pathology, Nanjing Medical University, Nanjing, China
| | - Xue Liu
- State Key Laboratory of Reproductive Medicine, Department of Pathology, Nanjing Medical University, Nanjing, China
| | - Ying-Chen Qian
- State Key Laboratory of Reproductive Medicine, Department of Pathology, Nanjing Medical University, Nanjing, China
| | - Yi-Yang Wen
- State Key Laboratory of Reproductive Medicine, Department of Pathology, Nanjing Medical University, Nanjing, China
| | - Lin-Lin Zhen
- Huai'an First People's Hospital, Nanjing Medical University, Huai'an, China
| | - Jie Lin
- Faculty of Software, Fujian Normal University, Fuzhou, China
| | - Ling-Zhi Liu
- Department of Pathology, Anatomy and Cell Biology, Thomas Jefferson University, Philadelphia, PA, USA
| | - Bing-Hua Jiang
- State Key Laboratory of Reproductive Medicine, Department of Pathology, Nanjing Medical University, Nanjing, China.,Department of Pathology, Anatomy and Cell Biology, Thomas Jefferson University, Philadelphia, PA, USA
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18
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Yang H, Jaeger M, Walker A, Wei D, Leiker K, Weitao T. Break Breast Cancer Addiction by CRISPR/Cas9 Genome Editing. J Cancer 2018; 9:219-231. [PMID: 29344267 PMCID: PMC5771328 DOI: 10.7150/jca.22554] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2017] [Accepted: 09/25/2017] [Indexed: 12/14/2022] Open
Abstract
Breast cancer is the leading diagnosed cancer for women globally. Evolution of breast cancer in tumorigenesis, metastasis and treatment resistance appears to be driven by the aberrant gene expression and protein degradation encoded by the cancer genomes. The uncontrolled cancer growth relies on these cellular events, thus constituting the cancerous programs and rendering the addiction towards them. These programs are likely the potential anticancer biomarkers for Personalized Medicine of breast cancer. This review intends to delineate the impact of the CRSPR/Cas-mediated genome editing in identification and validation of these anticancer biomarkers. It reviews the progress in three aspects of CRISPR/Cas9-mediated editing of the breast cancer genomes: Somatic genome editing, transcription and protein degradation addictions.
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Affiliation(s)
- Haitao Yang
- Laboratory for Cancer Genome Editing, Zhuhai Lifecode Medical Technologies. Inc. Department of Prenatal Diagnosis, Huizhou 2nd Hospital for Children and Women, #101 University Road, Tangjiawan, Zhuhai, 518900, Guangdong, China
| | - MariaLynn Jaeger
- College of Science and Mathematics, Southwest Baptist University, 1600 University Avenue, Bolivar, Missouri 65613, USA
| | - Averi Walker
- College of Science and Mathematics, Southwest Baptist University, 1600 University Avenue, Bolivar, Missouri 65613, USA
| | - Daniel Wei
- University of Texas at Dallas, 800 W Campbell Rd, Richardson, TX 75080, USA
| | - Katie Leiker
- College of Science and Mathematics, Southwest Baptist University, 1600 University Avenue, Bolivar, Missouri 65613, USA
| | - Tao Weitao
- College of Science and Mathematics, Southwest Baptist University, 1600 University Avenue, Bolivar, Missouri 65613, USA
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19
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Song SH, Kim TY. CTCF, Cohesin, and Chromatin in Human Cancer. Genomics Inform 2017; 15:114-122. [PMID: 29307136 PMCID: PMC5769866 DOI: 10.5808/gi.2017.15.4.114] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2017] [Accepted: 11/29/2017] [Indexed: 12/20/2022] Open
Abstract
It is becoming increasingly clear that eukaryotic genomes are subjected to higher-order chromatin organization by the CCCTC-binding factor/cohesin complex. Their dynamic interactions in three dimensions within the nucleus regulate gene transcription by changing the chromatin architecture. Such spatial genomic organization is functionally important for the spatial disposition of chromosomes to control cell fate during development and differentiation. Thus, the dysregulation of proper long-range chromatin interactions may influence the development of tumorigenesis and cancer progression.
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Affiliation(s)
- Sang-Hyun Song
- Cancer Genomics Research Laboratory, Cancer Research Institute, Seoul National University, Seoul 03080, Korea
| | - Tae-You Kim
- Cancer Genomics Research Laboratory, Cancer Research Institute, Seoul National University, Seoul 03080, Korea.,Department of Molecular Medicine and Biopharmaceutical Sciences, Graduate School of Convergence Science and Technology, Seoul National University, Seoul 03080, Korea.,Department of Internal Medicine, Seoul National University Hospital, Seoul 03080, Korea
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20
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Tang B, Cheng X, Xi Y, Chen Z, Zhou Y, Jin VX. Advances in Genomic Profiling and Analysis of 3D Chromatin Structure and Interaction. Genes (Basel) 2017; 8:E223. [PMID: 28885554 PMCID: PMC5615356 DOI: 10.3390/genes8090223] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2017] [Revised: 08/25/2017] [Accepted: 09/04/2017] [Indexed: 02/08/2023] Open
Abstract
Recent sequence-based profiling technologies such as high-throughput sequencing to detect fragment nucleotide sequence (Hi-C) and chromatin interaction analysis by paired-end tag sequencing (ChIA-PET) have revolutionized the field of three-dimensional (3D) chromatin architecture. It is now recognized that human genome functions as folded 3D chromatin units and looping paradigm is the basic principle of gene regulation. To better interpret the 3D data dramatically accumulating in past five years and to gain deep biological insights, huge efforts have been made in developing novel quantitative analysis methods. However, the full understanding of genome regulation requires thorough knowledge in both genomic technologies and their related data analyses. We summarize the recent advances in genomic technologies in identifying the 3D chromatin structure and interaction, and illustrate the quantitative analysis methods to infer functional domains and chromatin interactions, and further elucidate the emerging single-cell Hi-C technique and its computational analysis, and finally discuss the future directions such as advances of 3D chromatin techniques in diseases.
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Affiliation(s)
- Binhua Tang
- Epigenetics & Function Group, School of the Internet of Things, Hohai University, Changzhou Campus, Changzhou 213022, Jiangsu, China.
- School of Public Health, Shanghai Jiao Tong University, Shanghai 200025, China.
| | - Xiaolong Cheng
- Department of Molecular Medicine, University of Texas Health Science Center, San Antonio, TX 78229, USA.
| | - Yunlong Xi
- Epigenetics & Function Group, School of the Internet of Things, Hohai University, Changzhou Campus, Changzhou 213022, Jiangsu, China.
| | - Zixin Chen
- Epigenetics & Function Group, School of the Internet of Things, Hohai University, Changzhou Campus, Changzhou 213022, Jiangsu, China.
| | - Yufan Zhou
- Department of Molecular Medicine, University of Texas Health Science Center, San Antonio, TX 78229, USA.
| | - Victor X Jin
- Department of Molecular Medicine, University of Texas Health Science Center, San Antonio, TX 78229, USA.
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21
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Liu D, Ho MF, Schaid DJ, Scherer SE, Kalari K, Liu M, Biernacka J, Yee V, Evans J, Carlson E, Goetz MP, Kubo M, Wickerham DL, Wang L, Ingle JN, Weinshilboum RM. Breast cancer chemoprevention pharmacogenomics: Deep sequencing and functional genomics of the ZNF423 and CTSO genes. NPJ Breast Cancer 2017; 3:30. [PMID: 28856246 PMCID: PMC5566425 DOI: 10.1038/s41523-017-0036-4] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2016] [Revised: 07/01/2017] [Accepted: 07/12/2017] [Indexed: 12/14/2022] Open
Abstract
Our previous GWAS using samples from the NSABP P-1 and P-2 selective estrogen receptor modulator (SERM) breast cancer prevention trials identified SNPs in ZNF423 and near CTSO that were associated with breast cancer risk during SERM chemoprevention. We have now performed Next Generation DNA sequencing to identify additional SNPs that might contribute to breast cancer risk and to extend our observation that SNPs located hundreds of bp from estrogen response elements (EREs) can alter estrogen receptor alpha (ERα) binding in a SERM-dependent fashion. Our study utilized a nested case-control cohort selected from patients enrolled in the original GWAS, with 199 cases who developed breast cancer during SERM therapy and 201 matched controls who did not. We resequenced approximately 500 kb across both ZNF423 and CTSO, followed by functional genomic studies. We identified 4079 SNPs across ZNF423 and 3876 across CTSO, with 9 SNPs in ZNF423 and 12 in CTSO with p < 1E-02 that were within 500 bp of an ERE motif. The rs746157 (p = 8.44E-04) and rs12918288 SNPs (p = 3.43E-03) in intron 5 of ZNF423, were in linkage equilibrium and were associated with alterations in ER-binding to an ERE motif distant from these SNPs. We also studied all nonsynonymous SNPs in both genes and observed that one nsSNP in ZNF423 displayed decreased protein expression. In conclusion, we identified additional functional SNPs in ZNF423 that were associated with SNP and SERM-dependent alternations in ER binding and transcriptional regulation for an ERE at a distance from the SNPs, thus providing novel insight into mechanisms of SERM effect.
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Affiliation(s)
- Duan Liu
- Division of Clinical Pharmacology, Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, MN USA
| | - Ming-Fen Ho
- Division of Clinical Pharmacology, Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, MN USA
| | - Daniel J Schaid
- Division of Biomedical Statistics and Informatics, Department of Health Sciences Research, Mayo Clinic, Rochester, MN USA
| | - Steven E Scherer
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX USA
| | - Krishna Kalari
- Division of Biomedical Statistics and Informatics, Department of Health Sciences Research, Mayo Clinic, Rochester, MN USA
| | - Mohan Liu
- Division of Clinical Pharmacology, Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, MN USA
| | - Joanna Biernacka
- Division of Biomedical Statistics and Informatics, Department of Health Sciences Research, Mayo Clinic, Rochester, MN USA
| | - Vivien Yee
- Department of Biochemistry, Case Western Reserve University, Cleveland, OH USA
| | - Jared Evans
- Division of Biomedical Statistics and Informatics, Department of Health Sciences Research, Mayo Clinic, Rochester, MN USA
| | - Erin Carlson
- Division of Biomedical Statistics and Informatics, Department of Health Sciences Research, Mayo Clinic, Rochester, MN USA
| | - Matthew P Goetz
- Division of Medical Oncology, Mayo Clinic, Rochester, MN USA
| | - Michiaki Kubo
- RIKEN Center for Integrative Medical Science, Yokohama, Japan
| | - D Lawrence Wickerham
- Section of Cancer Genetics and Prevention, Allegheny General Hospital and the National Surgical Adjuvant Breast and Bowel Project (NSABP), Pittsburgh, PA USA
| | - Liewei Wang
- Division of Clinical Pharmacology, Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, MN USA
| | - James N Ingle
- Division of Medical Oncology, Mayo Clinic, Rochester, MN USA
| | - Richard M Weinshilboum
- Division of Clinical Pharmacology, Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, MN USA
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22
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Reprimo, a Potential p53-Dependent Tumor Suppressor Gene, Is Frequently Hypermethylated in Estrogen Receptor α-Positive Breast Cancer. Int J Mol Sci 2017; 18:ijms18081525. [PMID: 28809778 PMCID: PMC5577992 DOI: 10.3390/ijms18081525] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2017] [Revised: 07/01/2017] [Accepted: 07/05/2017] [Indexed: 01/31/2023] Open
Abstract
Aberrant DNA methylation is a hallmark of many cancers. Currently, there are four intrinsic molecular subtypes in breast cancer (BC): Luminal A, B, Her2-positive, and triple negative (TNBC). Recently, The Cancer Genome Atlas (TCGA) project has revealed that Luminal subtypes have higher levels of genome-wide methylation that may be a result of Estrogen/Estrogen receptor α (E2/ERα) signaling pathway activation. In this study, we analyze promoter CpG-island (CGIs) of the Reprimo (RPRM) gene in breast cancers (n = 77), cell lines (n = 38), and normal breast tissue (n = 10) using a MBDCap-seq database. Then, a validation cohort (n = 26) was used to confirm the results found in the MBDCap-seq platform. A differential methylation pattern was found between BC and cell lines compared to normal breast tissue. In BC, a higher DNA methylation was observed in tissues that were ERα-positive than in ERα-negative ones; more precisely, subtypes Luminal A compared to TNBC. Also, significant reverse correlation was observed between DNA methylation and RPRM mRNA expression in BC. Our data suggest that ERα expression in BC may affect the DNA methylation of CGIs in the RPRM gene. This approach suggests that DNA methylation status in CGIs of some tumor suppressor genes could be driven by E2 availability, subsequently inducing the activation of the ERα pathway.
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23
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Arnal JF, Lenfant F, Metivier R, Flouriot G, Henrion D, Adlanmerini M, Fontaine C, Gourdy P, Chambon P, Katzenellenbogen B, Katzenellenbogen J. Membrane and Nuclear Estrogen Receptor Alpha Actions: From Tissue Specificity to Medical Implications. Physiol Rev 2017; 97:1045-1087. [DOI: 10.1152/physrev.00024.2016] [Citation(s) in RCA: 213] [Impact Index Per Article: 30.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2016] [Revised: 12/19/2016] [Accepted: 01/18/2017] [Indexed: 12/22/2022] Open
Abstract
Estrogen receptor alpha (ERα) has been recognized now for several decades as playing a key role in reproduction and exerting functions in numerous nonreproductive tissues. In this review, we attempt to summarize the in vitro studies that are the basis of our current understanding of the mechanisms of action of ERα as a nuclear receptor and the key roles played by its two activation functions (AFs) in its transcriptional activities. We then depict the consequences of the selective inactivation of these AFs in mouse models, focusing on the prominent roles played by ERα in the reproductive tract and in the vascular system. Evidence has accumulated over the two last decades that ERα is also associated with the plasma membrane and activates non-nuclear signaling from this site. These rapid/nongenomic/membrane-initiated steroid signals (MISS) have been characterized in a variety of cell lines, and in particular in endothelial cells. The development of selective pharmacological tools that specifically activate MISS and the generation of mice expressing an ERα protein impeded for membrane localization have begun to unravel the physiological role of MISS in vivo. Finally, we discuss novel perspectives for the design of tissue-selective ER modulators based on the integration of the physiological and pathophysiological roles of MISS actions of estrogens.
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Affiliation(s)
- Jean-Francois Arnal
- I2MC, Institut National de la Santé et de la Recherche Médicale (INSERM) U 1048, Université de Toulouse 3 and CHU de Toulouse, Toulouse, France; Equipe SP@RTE UMR 6290 CNRS, Institut de Genétique et Développement de Rennes, Université de Rennes 1, Campus de Beaulieu, Rennes, France; Université de Rennes 1, Institut de Recherche en Santé, Environnement et Travail (Irest–INSERM UMR 1085), Equipe TREC, Rennes, France; Unité Mixte de Recherche 6214, Centre National de la Recherche Scientifique, Angers,
| | - Françoise Lenfant
- I2MC, Institut National de la Santé et de la Recherche Médicale (INSERM) U 1048, Université de Toulouse 3 and CHU de Toulouse, Toulouse, France; Equipe SP@RTE UMR 6290 CNRS, Institut de Genétique et Développement de Rennes, Université de Rennes 1, Campus de Beaulieu, Rennes, France; Université de Rennes 1, Institut de Recherche en Santé, Environnement et Travail (Irest–INSERM UMR 1085), Equipe TREC, Rennes, France; Unité Mixte de Recherche 6214, Centre National de la Recherche Scientifique, Angers,
| | - Raphaël Metivier
- I2MC, Institut National de la Santé et de la Recherche Médicale (INSERM) U 1048, Université de Toulouse 3 and CHU de Toulouse, Toulouse, France; Equipe SP@RTE UMR 6290 CNRS, Institut de Genétique et Développement de Rennes, Université de Rennes 1, Campus de Beaulieu, Rennes, France; Université de Rennes 1, Institut de Recherche en Santé, Environnement et Travail (Irest–INSERM UMR 1085), Equipe TREC, Rennes, France; Unité Mixte de Recherche 6214, Centre National de la Recherche Scientifique, Angers,
| | - Gilles Flouriot
- I2MC, Institut National de la Santé et de la Recherche Médicale (INSERM) U 1048, Université de Toulouse 3 and CHU de Toulouse, Toulouse, France; Equipe SP@RTE UMR 6290 CNRS, Institut de Genétique et Développement de Rennes, Université de Rennes 1, Campus de Beaulieu, Rennes, France; Université de Rennes 1, Institut de Recherche en Santé, Environnement et Travail (Irest–INSERM UMR 1085), Equipe TREC, Rennes, France; Unité Mixte de Recherche 6214, Centre National de la Recherche Scientifique, Angers,
| | - Daniel Henrion
- I2MC, Institut National de la Santé et de la Recherche Médicale (INSERM) U 1048, Université de Toulouse 3 and CHU de Toulouse, Toulouse, France; Equipe SP@RTE UMR 6290 CNRS, Institut de Genétique et Développement de Rennes, Université de Rennes 1, Campus de Beaulieu, Rennes, France; Université de Rennes 1, Institut de Recherche en Santé, Environnement et Travail (Irest–INSERM UMR 1085), Equipe TREC, Rennes, France; Unité Mixte de Recherche 6214, Centre National de la Recherche Scientifique, Angers,
| | - Marine Adlanmerini
- I2MC, Institut National de la Santé et de la Recherche Médicale (INSERM) U 1048, Université de Toulouse 3 and CHU de Toulouse, Toulouse, France; Equipe SP@RTE UMR 6290 CNRS, Institut de Genétique et Développement de Rennes, Université de Rennes 1, Campus de Beaulieu, Rennes, France; Université de Rennes 1, Institut de Recherche en Santé, Environnement et Travail (Irest–INSERM UMR 1085), Equipe TREC, Rennes, France; Unité Mixte de Recherche 6214, Centre National de la Recherche Scientifique, Angers,
| | - Coralie Fontaine
- I2MC, Institut National de la Santé et de la Recherche Médicale (INSERM) U 1048, Université de Toulouse 3 and CHU de Toulouse, Toulouse, France; Equipe SP@RTE UMR 6290 CNRS, Institut de Genétique et Développement de Rennes, Université de Rennes 1, Campus de Beaulieu, Rennes, France; Université de Rennes 1, Institut de Recherche en Santé, Environnement et Travail (Irest–INSERM UMR 1085), Equipe TREC, Rennes, France; Unité Mixte de Recherche 6214, Centre National de la Recherche Scientifique, Angers,
| | - Pierre Gourdy
- I2MC, Institut National de la Santé et de la Recherche Médicale (INSERM) U 1048, Université de Toulouse 3 and CHU de Toulouse, Toulouse, France; Equipe SP@RTE UMR 6290 CNRS, Institut de Genétique et Développement de Rennes, Université de Rennes 1, Campus de Beaulieu, Rennes, France; Université de Rennes 1, Institut de Recherche en Santé, Environnement et Travail (Irest–INSERM UMR 1085), Equipe TREC, Rennes, France; Unité Mixte de Recherche 6214, Centre National de la Recherche Scientifique, Angers,
| | - Pierre Chambon
- I2MC, Institut National de la Santé et de la Recherche Médicale (INSERM) U 1048, Université de Toulouse 3 and CHU de Toulouse, Toulouse, France; Equipe SP@RTE UMR 6290 CNRS, Institut de Genétique et Développement de Rennes, Université de Rennes 1, Campus de Beaulieu, Rennes, France; Université de Rennes 1, Institut de Recherche en Santé, Environnement et Travail (Irest–INSERM UMR 1085), Equipe TREC, Rennes, France; Unité Mixte de Recherche 6214, Centre National de la Recherche Scientifique, Angers,
| | - Benita Katzenellenbogen
- I2MC, Institut National de la Santé et de la Recherche Médicale (INSERM) U 1048, Université de Toulouse 3 and CHU de Toulouse, Toulouse, France; Equipe SP@RTE UMR 6290 CNRS, Institut de Genétique et Développement de Rennes, Université de Rennes 1, Campus de Beaulieu, Rennes, France; Université de Rennes 1, Institut de Recherche en Santé, Environnement et Travail (Irest–INSERM UMR 1085), Equipe TREC, Rennes, France; Unité Mixte de Recherche 6214, Centre National de la Recherche Scientifique, Angers,
| | - John Katzenellenbogen
- I2MC, Institut National de la Santé et de la Recherche Médicale (INSERM) U 1048, Université de Toulouse 3 and CHU de Toulouse, Toulouse, France; Equipe SP@RTE UMR 6290 CNRS, Institut de Genétique et Développement de Rennes, Université de Rennes 1, Campus de Beaulieu, Rennes, France; Université de Rennes 1, Institut de Recherche en Santé, Environnement et Travail (Irest–INSERM UMR 1085), Equipe TREC, Rennes, France; Unité Mixte de Recherche 6214, Centre National de la Recherche Scientifique, Angers,
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24
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Detecting Susceptibility to Breast Cancer with SNP-SNP Interaction Using BPSOHS and Emotional Neural Networks. BIOMED RESEARCH INTERNATIONAL 2017; 2016:5164347. [PMID: 27294121 PMCID: PMC4879248 DOI: 10.1155/2016/5164347] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/23/2016] [Revised: 04/18/2016] [Accepted: 04/20/2016] [Indexed: 02/08/2023]
Abstract
Studies for the association between diseases and informative single nucleotide polymorphisms (SNPs) have received great attention. However, most of them just use the whole set of useful SNPs and fail to consider the SNP-SNP interactions, while these interactions have already been proven in biology experiments. In this paper, we use a binary particle swarm optimization with hierarchical structure (BPSOHS) algorithm to improve the effective of PSO for the identification of the SNP-SNP interactions. Furthermore, in order to use these SNP interactions in the susceptibility analysis, we propose an emotional neural network (ENN) to treat SNP interactions as emotional tendency. Different from the normal architecture, just as the emotional brain, this architecture provides a specific path to treat the emotional value, by which the SNP interactions can be considered more quickly and directly. The ENN helps us use the prior knowledge about the SNP interactions and other influence factors together. Finally, the experimental results prove that the proposed BPSOHS_ENN algorithm can detect the informative SNP-SNP interaction and predict the breast cancer risk with a much higher accuracy than existing methods.
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25
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Colacino JA. 3D human tissue culture: modeling environmental effects on the stem cell epigenome. Epigenomics 2016; 8:1453-1457. [DOI: 10.2217/epi-2016-0107] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Affiliation(s)
- Justin A Colacino
- Department of Environmental Health Sciences, University of Michigan School of Public Health, Ann Arbor, MI, USA
- Department of Nutritional Sciences, University of Michigan School of Public Health, Ann Arbor, MI, USA
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26
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Alayev A, Salamon RS, Manna S, Schwartz NS, Berman AY, Holz MK. Estrogen induces RAD51C expression and localization to sites of DNA damage. Cell Cycle 2016; 15:3230-3239. [PMID: 27753535 DOI: 10.1080/15384101.2016.1241927] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Homologous recombination (HR) is a conserved process that maintains genome stability and cell survival by repairing DNA double-strand breaks (DSBs). The RAD51-related family of proteins is involved in repair of DSBs; consequently, deregulation of RAD51 causes chromosomal rearrangements and stimulates tumorigenesis. RAD51C has been identified as a potential tumor suppressor and a breast and ovarian cancer susceptibility gene. Recent studies have also implicated estrogen as a DNA-damaging agent that causes DSBs. We found that in ERα-positive breast cancer cells, estrogen transcriptionally regulates RAD51C expression in ERα-dependent mechanism. Moreover, estrogen induces RAD51C assembly into nuclear foci at DSBs, which is a precursor to RAD51 complex recruitment to the nucleus. Additionally, disruption of ERα signaling by either anti-estrogens or siRNA prevented estrogen induced upregulation of RAD51C. We have also found an association of a worse clinical outcome between RAD51C expression and ERα status of tumors. These findings provide insight into the mechanism of genomic instability in ERα-positive breast cancer and suggest that individuals with mutations in RAD51C that are exposed to estrogen would be more susceptible to accumulation of DNA damage, leading to cancer progression.
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Affiliation(s)
- Anya Alayev
- a Department of Biology , Yeshiva University , New York , NY , USA
| | - Rachel S Salamon
- a Department of Biology , Yeshiva University , New York , NY , USA
| | - Subrata Manna
- a Department of Biology , Yeshiva University , New York , NY , USA
| | - Naomi S Schwartz
- a Department of Biology , Yeshiva University , New York , NY , USA
| | - Adi Y Berman
- a Department of Biology , Yeshiva University , New York , NY , USA
| | - Marina K Holz
- a Department of Biology , Yeshiva University , New York , NY , USA.,b Department of Molecular Pharmacology and the Albert Einstein Cancer Center , Albert Einstein College of Medicine , Bronx , NY , USA
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27
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Abstract
Enhancer elements function as the logic gates of the genetic regulatory circuitry. One of their most important functions is the integration of extracellular signals with intracellular cell fate information to generate cell type-specific transcriptional responses. Mutations occurring in cancer often misregulate enhancers that normally control the signal-dependent expression of growth-related genes. This misregulation can result from trans-acting mechanisms, such as activation of the transcription factors or epigenetic regulators that control enhancer activity, or can be caused in cis by direct mutations that alter the activity of the enhancer or its target gene specificity. These processes can generate tumour type-specific super-enhancers and establish a 'locked' gene regulatory state that drives the uncontrolled proliferation of cancer cells. Here, we review the role of enhancers in cancer, and their potential as therapeutic targets.
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Affiliation(s)
- Inderpreet Sur
- Division of Functional Genomics and Systems Biology, Department of Medical Biochemistry and Biophysics, and Department of Biosciences and Nutrition, Karolinska Institutet, Stockholm SE-171 77, Sweden
| | - Jussi Taipale
- Division of Functional Genomics and Systems Biology, Department of Medical Biochemistry and Biophysics, and Department of Biosciences and Nutrition, Karolinska Institutet, Stockholm SE-171 77, Sweden
- Genome-Scale Biology Program, University of Helsinki, Biomedicum, PO Box 63, Helsinki 00014, Finland
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28
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Mishra A, La Perle K, Kwiatkowski S, Sullivan LA, Sams GH, Johns J, Curphey DP, Wen J, McConnell K, Qi J, Wong H, Russo G, Zhang J, Marcucci G, Bradner JE, Porcu P, Caligiuri MA. Mechanism, Consequences, and Therapeutic Targeting of Abnormal IL15 Signaling in Cutaneous T-cell Lymphoma. Cancer Discov 2016; 6:986-1005. [PMID: 27422033 DOI: 10.1158/2159-8290.cd-15-1297] [Citation(s) in RCA: 72] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2015] [Accepted: 07/11/2016] [Indexed: 12/12/2022]
Abstract
UNLABELLED Cutaneous T-cell lymphoma (CTCL) is the most common type of primary cutaneous lymphoma. Here, we report that patients with CTCL show increased IL15 in a clinical stage-dependent manner. Mechanistically, we show that ZEB1 is a transcriptional repressor of IL15 in T cells and that hypermethylation of the ZEB1 binding region within the IL15 promoter, as seen in patients with CTCL, prevents ZEB1 binding and causes increased transcription of IL15 Using a transgenic mouse model of IL15, we provide evidence that overexpression of IL15 induces a spontaneous CTCL that mimics the human neoplasm. Excessive autocrine production of IL15 in T cells inhibits an HDAC1-mediated negative autoregulatory loop, resulting in the upregulation of HDAC1 and HDAC6 and transcriptional induction of the onco-miR-21. Interruption of IL15 downstream signaling with isotype-specific HDAC inhibitors halts (HDAC1) or significantly delays (HDAC6) the progression of CTCL in vivo and provides preclinical evidence supporting a hierarchical model of oncogenic signaling in CTCL. SIGNIFICANCE To date, CTCL pathogenesis remains unknown, and there are no curative therapies. Our findings not only demonstrate a critical role for IL15-mediated inflammation in cutaneous T-cell lymphomagenesis, but also uncover a new oncogenic regulatory loop in CTCL involving IL15, HDAC1, HDAC6, and miR-21 that shows differential sensitivity to isotype-specific HDAC inhibitors. Cancer Discov; 6(9); 986-1005. ©2016 AACR.This article is highlighted in the In This Issue feature, p. 932.
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Affiliation(s)
- Anjali Mishra
- Division of Dermatology, Department of Internal Medicine, The Ohio State University, Columbus, Ohio. Comprehensive Cancer Center, James Cancer Hospital and Solove Research Institute, The Ohio State University, Columbus, Ohio.
| | - Krista La Perle
- Comprehensive Cancer Center, James Cancer Hospital and Solove Research Institute, The Ohio State University, Columbus, Ohio. Department of Veterinary Biosciences, College of Veterinary Medicine, The Ohio State University, Columbus, Ohio
| | - Sonya Kwiatkowski
- Comprehensive Cancer Center, James Cancer Hospital and Solove Research Institute, The Ohio State University, Columbus, Ohio
| | - Laura A Sullivan
- Comprehensive Cancer Center, James Cancer Hospital and Solove Research Institute, The Ohio State University, Columbus, Ohio
| | - Gregory H Sams
- Comprehensive Cancer Center, James Cancer Hospital and Solove Research Institute, The Ohio State University, Columbus, Ohio
| | - Jessica Johns
- Comprehensive Cancer Center, James Cancer Hospital and Solove Research Institute, The Ohio State University, Columbus, Ohio
| | - Douglas P Curphey
- Comprehensive Cancer Center, James Cancer Hospital and Solove Research Institute, The Ohio State University, Columbus, Ohio
| | - Jing Wen
- Comprehensive Cancer Center, James Cancer Hospital and Solove Research Institute, The Ohio State University, Columbus, Ohio
| | - Kathleen McConnell
- Comprehensive Cancer Center, James Cancer Hospital and Solove Research Institute, The Ohio State University, Columbus, Ohio
| | - Jun Qi
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts
| | - Henry Wong
- Division of Dermatology, Department of Internal Medicine, The Ohio State University, Columbus, Ohio. Comprehensive Cancer Center, James Cancer Hospital and Solove Research Institute, The Ohio State University, Columbus, Ohio
| | - Giandomenico Russo
- Istituto Dermopatico dell'Immacolata-Istituto di Ricovero e Cura a Carattere Scientifico, Rome, Italy
| | - Jianying Zhang
- Centers for Biostatistics, The Ohio State University, Columbus, Ohio
| | - Guido Marcucci
- Division of Hematopoietic Stem Cell and Leukemia Research, Beckman Research Institute, Norbert Gehr and Family Leukemia Center, City of Hope Medical Center, Duarte, California
| | - James E Bradner
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts
| | - Pierluigi Porcu
- Comprehensive Cancer Center, James Cancer Hospital and Solove Research Institute, The Ohio State University, Columbus, Ohio. Division of Hematology, Department of Internal Medicine, The Ohio State University, Columbus, Ohio.
| | - Michael A Caligiuri
- Comprehensive Cancer Center, James Cancer Hospital and Solove Research Institute, The Ohio State University, Columbus, Ohio. Division of Hematology, Department of Internal Medicine, The Ohio State University, Columbus, Ohio.
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Ho MF, Bongartz T, Liu M, Kalari KR, Goss PE, Shepherd LE, Goetz MP, Kubo M, Ingle JN, Wang L, Weinshilboum RM. Estrogen, SNP-Dependent Chemokine Expression and Selective Estrogen Receptor Modulator Regulation. Mol Endocrinol 2016; 30:382-98. [PMID: 26866883 DOI: 10.1210/me.2015-1267] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Abstract
We previously reported, on the basis of a genome-wide association study for aromatase inhibitor-induced musculoskeletal symptoms, that single-nucleotide polymorphisms (SNPs) near the T-cell leukemia/lymphoma 1A (TCL1A) gene were associated with aromatase inhibitor-induced musculoskeletal pain and with estradiol (E2)-induced TCL1A expression. Furthermore, variation in TCL1A expression influenced the downstream expression of proinflammatory cytokines and cytokine receptors. Specifically, the top hit genome-wide association study SNP, rs11849538, created a functional estrogen response element (ERE) that displayed estrogen receptor (ER) binding and increased E2 induction of TCL1A expression only for the variant SNP genotype. In the present study, we pursued mechanisms underlying the E2-SNP-dependent regulation of TCL1A expression and, in parallel, our subsequent observations that SNPs at a distance from EREs can regulate ERα binding and that ER antagonists can reverse phenotypes associated with those SNPs. Specifically, we performed a series of functional genomic studies using a large panel of lymphoblastoid cell lines with dense genomic data that demonstrated that TCL1A SNPs at a distance from EREs can modulate ERα binding and expression of TCL1A as well as the expression of downstream immune mediators. Furthermore, 4-hydroxytamoxifen or fulvestrant could reverse these SNP-genotype effects. Similar results were found for SNPs in the IL17A cytokine and CCR6 chemokine receptor genes. These observations greatly expand our previous results and support the existence of a novel molecular mechanism that contributes to the complex interplay between estrogens and immune systems. They also raise the possibility of the pharmacological manipulation of the expression of proinflammatory cytokines and chemokines in a SNP genotype-dependent fashion.
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Affiliation(s)
- Ming-Fen Ho
- Division of Clinical Pharmacology (M.-F.H., M.L., L.W., R.M.W.), Department of Molecular Pharmacology and Experimental Therapeutics, Division of Rheumatology (M.-F.H., T.B.), Department of Medicine, Division of Biomedical Statistics and Informatics (K.R.K.), Department of Health Sciences Research, and Division of Medical Oncology (M.P.G., J.N.I.), Department of Oncology, Mayo Clinic, Rochester, Minnesota 55905; Division of Hematology/Oncology (P.E.G.), Department of Medicine, Massachusetts General Hospital Cancer Center, Harvard University, Boston, Massachusetts 02114; National Cancer Institute of Canada Clinical Trials Group (L.E.S.), Kingston, Ontario, Canada K7L 3N6; and RIKEN Center for Integrative Medical Science (M.K.), Yokohama 230-0045, Japan
| | - Tim Bongartz
- Division of Clinical Pharmacology (M.-F.H., M.L., L.W., R.M.W.), Department of Molecular Pharmacology and Experimental Therapeutics, Division of Rheumatology (M.-F.H., T.B.), Department of Medicine, Division of Biomedical Statistics and Informatics (K.R.K.), Department of Health Sciences Research, and Division of Medical Oncology (M.P.G., J.N.I.), Department of Oncology, Mayo Clinic, Rochester, Minnesota 55905; Division of Hematology/Oncology (P.E.G.), Department of Medicine, Massachusetts General Hospital Cancer Center, Harvard University, Boston, Massachusetts 02114; National Cancer Institute of Canada Clinical Trials Group (L.E.S.), Kingston, Ontario, Canada K7L 3N6; and RIKEN Center for Integrative Medical Science (M.K.), Yokohama 230-0045, Japan
| | - Mohan Liu
- Division of Clinical Pharmacology (M.-F.H., M.L., L.W., R.M.W.), Department of Molecular Pharmacology and Experimental Therapeutics, Division of Rheumatology (M.-F.H., T.B.), Department of Medicine, Division of Biomedical Statistics and Informatics (K.R.K.), Department of Health Sciences Research, and Division of Medical Oncology (M.P.G., J.N.I.), Department of Oncology, Mayo Clinic, Rochester, Minnesota 55905; Division of Hematology/Oncology (P.E.G.), Department of Medicine, Massachusetts General Hospital Cancer Center, Harvard University, Boston, Massachusetts 02114; National Cancer Institute of Canada Clinical Trials Group (L.E.S.), Kingston, Ontario, Canada K7L 3N6; and RIKEN Center for Integrative Medical Science (M.K.), Yokohama 230-0045, Japan
| | - Krishna R Kalari
- Division of Clinical Pharmacology (M.-F.H., M.L., L.W., R.M.W.), Department of Molecular Pharmacology and Experimental Therapeutics, Division of Rheumatology (M.-F.H., T.B.), Department of Medicine, Division of Biomedical Statistics and Informatics (K.R.K.), Department of Health Sciences Research, and Division of Medical Oncology (M.P.G., J.N.I.), Department of Oncology, Mayo Clinic, Rochester, Minnesota 55905; Division of Hematology/Oncology (P.E.G.), Department of Medicine, Massachusetts General Hospital Cancer Center, Harvard University, Boston, Massachusetts 02114; National Cancer Institute of Canada Clinical Trials Group (L.E.S.), Kingston, Ontario, Canada K7L 3N6; and RIKEN Center for Integrative Medical Science (M.K.), Yokohama 230-0045, Japan
| | - Paul E Goss
- Division of Clinical Pharmacology (M.-F.H., M.L., L.W., R.M.W.), Department of Molecular Pharmacology and Experimental Therapeutics, Division of Rheumatology (M.-F.H., T.B.), Department of Medicine, Division of Biomedical Statistics and Informatics (K.R.K.), Department of Health Sciences Research, and Division of Medical Oncology (M.P.G., J.N.I.), Department of Oncology, Mayo Clinic, Rochester, Minnesota 55905; Division of Hematology/Oncology (P.E.G.), Department of Medicine, Massachusetts General Hospital Cancer Center, Harvard University, Boston, Massachusetts 02114; National Cancer Institute of Canada Clinical Trials Group (L.E.S.), Kingston, Ontario, Canada K7L 3N6; and RIKEN Center for Integrative Medical Science (M.K.), Yokohama 230-0045, Japan
| | - Lois E Shepherd
- Division of Clinical Pharmacology (M.-F.H., M.L., L.W., R.M.W.), Department of Molecular Pharmacology and Experimental Therapeutics, Division of Rheumatology (M.-F.H., T.B.), Department of Medicine, Division of Biomedical Statistics and Informatics (K.R.K.), Department of Health Sciences Research, and Division of Medical Oncology (M.P.G., J.N.I.), Department of Oncology, Mayo Clinic, Rochester, Minnesota 55905; Division of Hematology/Oncology (P.E.G.), Department of Medicine, Massachusetts General Hospital Cancer Center, Harvard University, Boston, Massachusetts 02114; National Cancer Institute of Canada Clinical Trials Group (L.E.S.), Kingston, Ontario, Canada K7L 3N6; and RIKEN Center for Integrative Medical Science (M.K.), Yokohama 230-0045, Japan
| | - Matthew P Goetz
- Division of Clinical Pharmacology (M.-F.H., M.L., L.W., R.M.W.), Department of Molecular Pharmacology and Experimental Therapeutics, Division of Rheumatology (M.-F.H., T.B.), Department of Medicine, Division of Biomedical Statistics and Informatics (K.R.K.), Department of Health Sciences Research, and Division of Medical Oncology (M.P.G., J.N.I.), Department of Oncology, Mayo Clinic, Rochester, Minnesota 55905; Division of Hematology/Oncology (P.E.G.), Department of Medicine, Massachusetts General Hospital Cancer Center, Harvard University, Boston, Massachusetts 02114; National Cancer Institute of Canada Clinical Trials Group (L.E.S.), Kingston, Ontario, Canada K7L 3N6; and RIKEN Center for Integrative Medical Science (M.K.), Yokohama 230-0045, Japan
| | - Michiaki Kubo
- Division of Clinical Pharmacology (M.-F.H., M.L., L.W., R.M.W.), Department of Molecular Pharmacology and Experimental Therapeutics, Division of Rheumatology (M.-F.H., T.B.), Department of Medicine, Division of Biomedical Statistics and Informatics (K.R.K.), Department of Health Sciences Research, and Division of Medical Oncology (M.P.G., J.N.I.), Department of Oncology, Mayo Clinic, Rochester, Minnesota 55905; Division of Hematology/Oncology (P.E.G.), Department of Medicine, Massachusetts General Hospital Cancer Center, Harvard University, Boston, Massachusetts 02114; National Cancer Institute of Canada Clinical Trials Group (L.E.S.), Kingston, Ontario, Canada K7L 3N6; and RIKEN Center for Integrative Medical Science (M.K.), Yokohama 230-0045, Japan
| | - James N Ingle
- Division of Clinical Pharmacology (M.-F.H., M.L., L.W., R.M.W.), Department of Molecular Pharmacology and Experimental Therapeutics, Division of Rheumatology (M.-F.H., T.B.), Department of Medicine, Division of Biomedical Statistics and Informatics (K.R.K.), Department of Health Sciences Research, and Division of Medical Oncology (M.P.G., J.N.I.), Department of Oncology, Mayo Clinic, Rochester, Minnesota 55905; Division of Hematology/Oncology (P.E.G.), Department of Medicine, Massachusetts General Hospital Cancer Center, Harvard University, Boston, Massachusetts 02114; National Cancer Institute of Canada Clinical Trials Group (L.E.S.), Kingston, Ontario, Canada K7L 3N6; and RIKEN Center for Integrative Medical Science (M.K.), Yokohama 230-0045, Japan
| | - Liewei Wang
- Division of Clinical Pharmacology (M.-F.H., M.L., L.W., R.M.W.), Department of Molecular Pharmacology and Experimental Therapeutics, Division of Rheumatology (M.-F.H., T.B.), Department of Medicine, Division of Biomedical Statistics and Informatics (K.R.K.), Department of Health Sciences Research, and Division of Medical Oncology (M.P.G., J.N.I.), Department of Oncology, Mayo Clinic, Rochester, Minnesota 55905; Division of Hematology/Oncology (P.E.G.), Department of Medicine, Massachusetts General Hospital Cancer Center, Harvard University, Boston, Massachusetts 02114; National Cancer Institute of Canada Clinical Trials Group (L.E.S.), Kingston, Ontario, Canada K7L 3N6; and RIKEN Center for Integrative Medical Science (M.K.), Yokohama 230-0045, Japan
| | - Richard M Weinshilboum
- Division of Clinical Pharmacology (M.-F.H., M.L., L.W., R.M.W.), Department of Molecular Pharmacology and Experimental Therapeutics, Division of Rheumatology (M.-F.H., T.B.), Department of Medicine, Division of Biomedical Statistics and Informatics (K.R.K.), Department of Health Sciences Research, and Division of Medical Oncology (M.P.G., J.N.I.), Department of Oncology, Mayo Clinic, Rochester, Minnesota 55905; Division of Hematology/Oncology (P.E.G.), Department of Medicine, Massachusetts General Hospital Cancer Center, Harvard University, Boston, Massachusetts 02114; National Cancer Institute of Canada Clinical Trials Group (L.E.S.), Kingston, Ontario, Canada K7L 3N6; and RIKEN Center for Integrative Medical Science (M.K.), Yokohama 230-0045, Japan
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Zhang X, He X, Liu C, Liu J, Hu Q, Pan T, Duan X, Liu B, Zhang Y, Chen J, Ma X, Zhang X, Luo H, Zhang H. IL-4 Inhibits the Biogenesis of an Epigenetically Suppressive PIWI-Interacting RNA To Upregulate CD1a Molecules on Monocytes/Dendritic Cells. THE JOURNAL OF IMMUNOLOGY 2016; 196:1591-603. [PMID: 26755820 DOI: 10.4049/jimmunol.1500805] [Citation(s) in RCA: 75] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/10/2015] [Accepted: 11/09/2015] [Indexed: 12/22/2022]
Abstract
The discovery of PIWI-interacting RNAs (piRNAs) revealed the complexity of the RNA world. Although piRNAs were first deemed to be germline specific, substantial evidence shows their various roles in somatic cells; however, their function in highly differentiated immune cells remains elusive. In this study, by initially screening with a small RNA deep-sequencing analysis, we found that a piRNA, tRNA-Glu-derived piRNA [td-piR(Glu)], was expressed much more abundantly in human monocytes than in dendritic cells. By regulating the polymerase III activity, IL-4 potently decreased the biogenesis of tRNA-Glu and, subsequently, td-piR(Glu). Further, we revealed that the td-piR(Glu)/PIWIL4 complex recruited SETDB1, SUV39H1, and heterochromatin protein 1β to the CD1A promoter region and facilitated H3K9 methylation. As a result, the transcription of CD1A was significantly inhibited. Collectively, we demonstrated that a piRNA acted as the signal molecule for a cytokine to regulate the expression of an important membrane protein for lipid Ag presentation.
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Affiliation(s)
- Xue Zhang
- Institute of Human Virology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong 510080, China; Key Laboratory of Tropical Disease Control of Ministry of Education, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong 510080, China; and Guangdong Engineering Research Center for Antimicrobial Agent and Immunotechnology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong 510080, China
| | - Xin He
- Institute of Human Virology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong 510080, China; Key Laboratory of Tropical Disease Control of Ministry of Education, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong 510080, China; and Guangdong Engineering Research Center for Antimicrobial Agent and Immunotechnology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong 510080, China
| | - Chao Liu
- Institute of Human Virology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong 510080, China; Key Laboratory of Tropical Disease Control of Ministry of Education, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong 510080, China; and Guangdong Engineering Research Center for Antimicrobial Agent and Immunotechnology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong 510080, China
| | - Jun Liu
- Institute of Human Virology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong 510080, China; Key Laboratory of Tropical Disease Control of Ministry of Education, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong 510080, China; and Guangdong Engineering Research Center for Antimicrobial Agent and Immunotechnology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong 510080, China
| | - Qifei Hu
- Institute of Human Virology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong 510080, China; Key Laboratory of Tropical Disease Control of Ministry of Education, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong 510080, China; and Guangdong Engineering Research Center for Antimicrobial Agent and Immunotechnology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong 510080, China
| | - Ting Pan
- Institute of Human Virology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong 510080, China; Key Laboratory of Tropical Disease Control of Ministry of Education, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong 510080, China; and Guangdong Engineering Research Center for Antimicrobial Agent and Immunotechnology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong 510080, China
| | - Xiaobing Duan
- Institute of Human Virology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong 510080, China; Key Laboratory of Tropical Disease Control of Ministry of Education, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong 510080, China; and Guangdong Engineering Research Center for Antimicrobial Agent and Immunotechnology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong 510080, China
| | - Bingfeng Liu
- Institute of Human Virology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong 510080, China; Key Laboratory of Tropical Disease Control of Ministry of Education, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong 510080, China; and Guangdong Engineering Research Center for Antimicrobial Agent and Immunotechnology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong 510080, China
| | - Yiwen Zhang
- Institute of Human Virology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong 510080, China; Key Laboratory of Tropical Disease Control of Ministry of Education, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong 510080, China; and Guangdong Engineering Research Center for Antimicrobial Agent and Immunotechnology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong 510080, China
| | - Jingliang Chen
- Institute of Human Virology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong 510080, China; Key Laboratory of Tropical Disease Control of Ministry of Education, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong 510080, China; and Guangdong Engineering Research Center for Antimicrobial Agent and Immunotechnology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong 510080, China
| | - Xingru Ma
- Institute of Human Virology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong 510080, China; Key Laboratory of Tropical Disease Control of Ministry of Education, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong 510080, China; and Guangdong Engineering Research Center for Antimicrobial Agent and Immunotechnology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong 510080, China
| | - Xu Zhang
- Institute of Human Virology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong 510080, China; Key Laboratory of Tropical Disease Control of Ministry of Education, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong 510080, China; and Guangdong Engineering Research Center for Antimicrobial Agent and Immunotechnology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong 510080, China
| | - Haihua Luo
- Institute of Human Virology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong 510080, China; Key Laboratory of Tropical Disease Control of Ministry of Education, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong 510080, China; and Guangdong Engineering Research Center for Antimicrobial Agent and Immunotechnology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong 510080, China
| | - Hui Zhang
- Institute of Human Virology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong 510080, China; Key Laboratory of Tropical Disease Control of Ministry of Education, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong 510080, China; and Guangdong Engineering Research Center for Antimicrobial Agent and Immunotechnology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong 510080, China
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31
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Zhao Y, Li Z. Interplay of estrogen receptors and FOXA factors in the liver cancer. Mol Cell Endocrinol 2015; 418 Pt 3:334-9. [PMID: 25661537 PMCID: PMC4524798 DOI: 10.1016/j.mce.2015.01.043] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/02/2014] [Revised: 01/29/2015] [Accepted: 01/30/2015] [Indexed: 12/15/2022]
Abstract
Liver cancer is the fifth most common cancer in human with male dominance. Sexual dimorphism of liver cancer is conserved from rodents to humans, which was firstly found in mice in late 1930s and female mice were resistant to liver cancer. Sex hormones were found to affect the incidence of liver cancer in rodents. Estrogen receptor alpha (ERα)-mediated estrogen signaling or androgen receptor-mediated androgen signaling prevents or promotes the growth of rodent liver tumors, respectively. Forkhead box protein A (Foxa) factors, Foxa1 and Foxa2, also known as pioneer transcription factors in liver specification, are essential for both estrogen and androgen signaling by acting as central regulators of sexual dimorphism in liver cancer. This review mainly focuses on the interplay between ERα and FOXA factors in liver cancer, and summarizes recent breakthrough studies in elucidating the mechanisms of sexual dimorphism in liver cancer.
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Affiliation(s)
- Yongbing Zhao
- Department of Cancer Biology, Mayo Clinic, 4500 San Pablo Road, Jacksonville, FL 32224, USA
| | - Zhaoyu Li
- Department of Cancer Biology, Mayo Clinic, 4500 San Pablo Road, Jacksonville, FL 32224, USA.
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32
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Yang J, AlTahan A, Jones DT, Buffa FM, Bridges E, Interiano RB, Qu C, Vogt N, Li JL, Baban D, Ragoussis J, Nicholson R, Davidoff AM, Harris AL. Estrogen receptor-α directly regulates the hypoxia-inducible factor 1 pathway associated with antiestrogen response in breast cancer. Proc Natl Acad Sci U S A 2015; 112:15172-7. [PMID: 26598706 PMCID: PMC4679044 DOI: 10.1073/pnas.1422015112] [Citation(s) in RCA: 103] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A majority of breast cancers are driven by estrogen via estrogen receptor-α (ERα). Our previous studies indicate that hypoxia-inducible factor 1α (HIF-1α) cooperates with ERα in breast cancer cells. However, whether ERα is implicated in the direct regulation of HIF-1α and the role of HIF-1α in endocrine therapy response are unknown. In this study we found that a subpopulation of HIF-1α targets, many of them bearing both hypoxia response elements and estrogen response elements, are regulated by ERα in normoxia and hypoxia. Interestingly, the HIF-1α gene itself also bears an estrogen response element, and its expression is directly regulated by ERα. Clinical data revealed that expression of the HIF-1α gene or a hypoxia metagene signature is associated with a poor outcome to endocrine treatment in ERα(+) breast cancer. HIF-1α was able to confer endocrine therapy resistance to ERα(+) breast cancer cells. Our findings define, for the first time to our knowledge, a direct regulatory pathway between ERα and HIF-1α, which might modulate hormone response in treatment.
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Affiliation(s)
- Jun Yang
- Growth Factor Group, Cancer Research UK, Molecular Oncology Laboratories, Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Headington, Oxford OX3 9DS, United Kingdom; Department of Surgery, St. Jude Children's Research Hospital, Memphis, TN 38105;
| | - Alaa AlTahan
- Department of Surgery, St. Jude Children's Research Hospital, Memphis, TN 38105
| | - Dylan T Jones
- Growth Factor Group, Cancer Research UK, Molecular Oncology Laboratories, Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Headington, Oxford OX3 9DS, United Kingdom
| | - Francesca M Buffa
- Growth Factor Group, Cancer Research UK, Molecular Oncology Laboratories, Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Headington, Oxford OX3 9DS, United Kingdom
| | - Esther Bridges
- Growth Factor Group, Cancer Research UK, Molecular Oncology Laboratories, Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Headington, Oxford OX3 9DS, United Kingdom
| | - Rodrigo B Interiano
- Department of Surgery, St. Jude Children's Research Hospital, Memphis, TN 38105
| | - Chunxu Qu
- Department of Bioinformatics, St. Jude Children's Research Hospital, Memphis, TN 38105
| | - Nathan Vogt
- Department of Surgery, St. Jude Children's Research Hospital, Memphis, TN 38105
| | - Ji-Liang Li
- Growth Factor Group, Cancer Research UK, Molecular Oncology Laboratories, Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Headington, Oxford OX3 9DS, United Kingdom
| | - Dilair Baban
- Genomics Group, Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, United Kingdom
| | - Jiannis Ragoussis
- Genomics Group, Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, United Kingdom
| | - Robert Nicholson
- Tenovus Centre for Cancer Research, Welsh School of Pharmacy, Cardiff University, Cardiff CF10 3NB, United Kingdom
| | - Andrew M Davidoff
- Department of Surgery, St. Jude Children's Research Hospital, Memphis, TN 38105
| | - Adrian L Harris
- Growth Factor Group, Cancer Research UK, Molecular Oncology Laboratories, Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Headington, Oxford OX3 9DS, United Kingdom
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Barutcu AR, Lajoie BR, McCord RP, Tye CE, Hong D, Messier TL, Browne G, van Wijnen AJ, Lian JB, Stein JL, Dekker J, Imbalzano AN, Stein GS. Chromatin interaction analysis reveals changes in small chromosome and telomere clustering between epithelial and breast cancer cells. Genome Biol 2015; 16:214. [PMID: 26415882 PMCID: PMC4587679 DOI: 10.1186/s13059-015-0768-0] [Citation(s) in RCA: 146] [Impact Index Per Article: 16.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2015] [Accepted: 09/03/2015] [Indexed: 12/17/2022] Open
Abstract
Background Higher-order chromatin structure is often perturbed in cancer and other pathological states. Although several genetic and epigenetic differences have been charted between normal and breast cancer tissues, changes in higher-order chromatin organization during tumorigenesis have not been fully explored. To probe the differences in higher-order chromatin structure between mammary epithelial and breast cancer cells, we performed Hi-C analysis on MCF-10A mammary epithelial and MCF-7 breast cancer cell lines. Results Our studies reveal that the small, gene-rich chromosomes chr16 through chr22 in the MCF-7 breast cancer genome display decreased interaction frequency with each other compared to the inter-chromosomal interaction frequency in the MCF-10A epithelial cells. Interestingly, this finding is associated with a higher occurrence of open compartments on chr16–22 in MCF-7 cells. Pathway analysis of the MCF-7 up-regulated genes located in altered compartment regions on chr16–22 reveals pathways related to repression of WNT signaling. There are also differences in intra-chromosomal interactions between the cell lines; telomeric and sub-telomeric regions in the MCF-10A cells display more frequent interactions than are observed in the MCF-7 cells. Conclusions We show evidence of an intricate relationship between chromosomal organization and gene expression between epithelial and breast cancer cells. Importantly, this work provides a genome-wide view of higher-order chromatin dynamics and a resource for studying higher-order chromatin interactions in two cell lines commonly used to study the progression of breast cancer. Electronic supplementary material The online version of this article (doi:10.1186/s13059-015-0768-0) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- A Rasim Barutcu
- Department of Cell and Developmental Biology, University of Massachusetts Medical School, 55 Lake Avenue North, Worcester, MA, 01655, USA
| | - Bryan R Lajoie
- Program in Systems Biology, University of Massachusetts Medical School, 55 Lake Avenue North, Worcester, MA, 01655, USA
| | - Rachel P McCord
- Program in Systems Biology, University of Massachusetts Medical School, 55 Lake Avenue North, Worcester, MA, 01655, USA
| | - Coralee E Tye
- Department of Biochemistry and University of Vermont Cancer Center, University of Vermont College of Medicine, 89 Beaumont Avenue, Burlington, VT, 05405, USA
| | - Deli Hong
- Department of Cell and Developmental Biology, University of Massachusetts Medical School, 55 Lake Avenue North, Worcester, MA, 01655, USA.,Department of Biochemistry and University of Vermont Cancer Center, University of Vermont College of Medicine, 89 Beaumont Avenue, Burlington, VT, 05405, USA
| | - Terri L Messier
- Department of Biochemistry and University of Vermont Cancer Center, University of Vermont College of Medicine, 89 Beaumont Avenue, Burlington, VT, 05405, USA
| | - Gillian Browne
- Department of Biochemistry and University of Vermont Cancer Center, University of Vermont College of Medicine, 89 Beaumont Avenue, Burlington, VT, 05405, USA
| | - Andre J van Wijnen
- Department of Biochemistry & Molecular Biology, Mayo Clinic, 200 First Street SW, Rochester, MN, 55905, USA
| | - Jane B Lian
- Department of Biochemistry and University of Vermont Cancer Center, University of Vermont College of Medicine, 89 Beaumont Avenue, Burlington, VT, 05405, USA
| | - Janet L Stein
- Department of Biochemistry and University of Vermont Cancer Center, University of Vermont College of Medicine, 89 Beaumont Avenue, Burlington, VT, 05405, USA
| | - Job Dekker
- Program in Systems Biology, University of Massachusetts Medical School, 55 Lake Avenue North, Worcester, MA, 01655, USA.,Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, 55 Lake Avenue North, Worcester, MA, 01655, USA
| | - Anthony N Imbalzano
- Department of Cell and Developmental Biology, University of Massachusetts Medical School, 55 Lake Avenue North, Worcester, MA, 01655, USA
| | - Gary S Stein
- Department of Biochemistry and University of Vermont Cancer Center, University of Vermont College of Medicine, 89 Beaumont Avenue, Burlington, VT, 05405, USA.
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Abstract
Transcription factors (TFs) are commonly deregulated in the pathogenesis of human cancer and are a major class of cancer cell dependencies. Consequently, targeting of TFs can be highly effective in treating particular malignancies, as highlighted by the clinical efficacy of agents that target nuclear hormone receptors. In this review we discuss recent advances in our understanding of TFs as drug targets in oncology, with an emphasis on the emerging chemical approaches to modulate TF function. The remarkable diversity and potency of TFs as drivers of cell transformation justifies a continued pursuit of TFs as therapeutic targets for drug discovery.
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Affiliation(s)
- Anand S. Bhagwat
- Cold Spring Harbor Laboratory, 1 Bungtown Road, Cold Spring Harbor, NY 11724, USA
| | - Christopher R. Vakoc
- Cold Spring Harbor Laboratory, 1 Bungtown Road, Cold Spring Harbor, NY 11724, USA
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35
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Hsu PY, Hsu HK, Hsiao TH, Ye Z, Wang E, Profit AL, Jatoi I, Chen Y, Kirma NB, Jin VX, Sharp ZD, Huang THM. Spatiotemporal control of estrogen-responsive transcription in ERα-positive breast cancer cells. Oncogene 2015; 35:2379-89. [PMID: 26300005 PMCID: PMC4865474 DOI: 10.1038/onc.2015.298] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2015] [Revised: 06/20/2015] [Accepted: 07/05/2015] [Indexed: 12/29/2022]
Abstract
Recruitment of transcription machinery to target promoters for aberrant gene expression has been well studied, but underlying control directed by distant-acting enhancers remains unclear in cancer development. Our previous study demonstrated that distant estrogen response elements (DEREs) located on chromosome 20q13 are frequently amplified and translocated to other chromosomes in ERα-positive breast cancer cells. In this study, we used three-dimensional interphase fluorescence in situ hybridization to decipher spatiotemporal gathering of multiple DEREs in the nucleus. Upon estrogen stimulation, scattered 20q13 DEREs were mobilized to form regulatory depots for synchronized gene expression of target loci. A chromosome conformation capture assay coupled with chromatin immunoprecipitation further uncovered that ERα-bound regulatory depots are tethered to heterochromatin protein 1 (HP1) for coordinated chromatin movement and histone modifications of target loci, resulting in transcription repression. Neutralizing HP1 function dysregulated the formation of DERE-involved regulatory depots and transcription inactivation of candidate tumor-suppressor genes. Deletion of amplified DEREs using the CRISPR/Cas9 genomic-editing system profoundly altered transcriptional profiles of proliferation-associated signaling networks, resulting in reduction of cancer cell growth. These findings reveal a formerly uncharacterized feature wherein multiple copies of the amplicon congregate as transcriptional units in the nucleus for synchronous regulation of function-related loci in tumorigenesis. Disruption of their assembly can be a new strategy for treating breast cancers and other malignancies.
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Affiliation(s)
- P-Y Hsu
- Department of Molecular Medicine, Institute of Biotechnology, The University of Texas Health Science Center at San Antonio, San Antonio, TX, USA
| | - H-K Hsu
- Department of Molecular Medicine, Institute of Biotechnology, The University of Texas Health Science Center at San Antonio, San Antonio, TX, USA
| | - T-H Hsiao
- Greehey Children's Cancer Research Institute, The University of Texas Health Science Center at San Antonio, San Antonio, TX, USA.,Cancer Therapy and Research Center, The University of Texas Health Science Center at San Antonio, San Antonio, TX, USA.,Department of Medical Research, Taichung Veterans General Hospital, Taichung City, Taiwan
| | - Z Ye
- Department of Molecular Medicine, Institute of Biotechnology, The University of Texas Health Science Center at San Antonio, San Antonio, TX, USA
| | - E Wang
- Department of Cellular and Structural Biology, The University of Texas Health Science Center at San Antonio, San Antonio, TX, USA
| | - A L Profit
- Cancer Therapy and Research Center, The University of Texas Health Science Center at San Antonio, San Antonio, TX, USA.,Department of Pathology, The University of Texas Health Science Center at San Antonio, San Antonio, TX, USA
| | - I Jatoi
- Cancer Therapy and Research Center, The University of Texas Health Science Center at San Antonio, San Antonio, TX, USA.,Department of Surgery, The University of Texas Health Science Center at San Antonio, San Antonio TX, USA
| | - Y Chen
- Greehey Children's Cancer Research Institute, The University of Texas Health Science Center at San Antonio, San Antonio, TX, USA.,Cancer Therapy and Research Center, The University of Texas Health Science Center at San Antonio, San Antonio, TX, USA.,Department of Epidemiology and Biostatistics, The University of Texas Health Science Center at San Antonio, San Antonio, TX, USA
| | - N B Kirma
- Department of Molecular Medicine, Institute of Biotechnology, The University of Texas Health Science Center at San Antonio, San Antonio, TX, USA
| | - V X Jin
- Department of Molecular Medicine, Institute of Biotechnology, The University of Texas Health Science Center at San Antonio, San Antonio, TX, USA.,Department of Epidemiology and Biostatistics, The University of Texas Health Science Center at San Antonio, San Antonio, TX, USA
| | - Z D Sharp
- Department of Molecular Medicine, Institute of Biotechnology, The University of Texas Health Science Center at San Antonio, San Antonio, TX, USA.,Cancer Therapy and Research Center, The University of Texas Health Science Center at San Antonio, San Antonio, TX, USA
| | - T H-M Huang
- Department of Molecular Medicine, Institute of Biotechnology, The University of Texas Health Science Center at San Antonio, San Antonio, TX, USA.,Cancer Therapy and Research Center, The University of Texas Health Science Center at San Antonio, San Antonio, TX, USA
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Jin K, Park S, Teo WW, Korangath P, Cho SS, Yoshida T, Győrffy B, Goswami CP, Nakshatri H, Cruz LA, Zhou W, Ji H, Su Y, Ekram M, Wu Z, Zhu T, Polyak K, Sukumar S. HOXB7 Is an ERα Cofactor in the Activation of HER2 and Multiple ER Target Genes Leading to Endocrine Resistance. Cancer Discov 2015; 5:944-59. [PMID: 26180042 DOI: 10.1158/2159-8290.cd-15-0090] [Citation(s) in RCA: 64] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2015] [Accepted: 07/01/2015] [Indexed: 11/16/2022]
Abstract
UNLABELLED Why breast cancers become resistant to tamoxifen despite continued expression of the estrogen receptor-α (ERα) and what factors are responsible for high HER2 expression in these tumors remains an enigma. HOXB7 chromatin immunoprecipitation analysis followed by validation showed that HOXB7 physically interacts with ERα, and that the HOXB7-ERα complex enhances transcription of many ERα target genes, including HER2. Investigating strategies for controlling HOXB7, our studies revealed that MYC, stabilized via phosphorylation mediated by EGFR-HER2 signaling, inhibits transcription of miR-196a, a HOXB7 repressor. This leads to increased expression of HOXB7, ER target genes, and HER2. Repressing MYC using small-molecule inhibitors reverses these events and causes regression of breast cancer xenografts. The MYC-HOXB7-HER2 signaling pathway is eminently targetable in endocrine-resistant breast cancer. SIGNIFICANCE HOXB7 acts as an ERα cofactor regulating a myriad of ER target genes, including HER2, in tamoxifen-resistant breast cancer. HOXB7 expression is controlled by MYC via transcriptional regulation of the HOXB7 repressor miR-196a; consequently, antagonists of MYC cause reversal of selective ER modulator resistance both in vitro and in vivo.
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Affiliation(s)
- Kideok Jin
- Breast Cancer Program, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Sunju Park
- Breast Cancer Program, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Wei Wen Teo
- Breast Cancer Program, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Preethi Korangath
- Breast Cancer Program, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Sean Soonweng Cho
- Breast Cancer Program, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Takahiro Yoshida
- Breast Cancer Program, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Balázs Győrffy
- MTA TTK Lendület Cancer Biomarker Research Group and 2nd Department of Pediatrics, Semmelweis University, Budapest, Hungary
| | - Chirayu Pankaj Goswami
- Center for Computational Biology and Bioinformatics, Indiana University, Bloomington, Indiana
| | - Harikrishna Nakshatri
- Center for Computational Biology and Bioinformatics, Indiana University, Bloomington, Indiana
| | - Leigh-Ann Cruz
- Breast Cancer Program, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Weiqiang Zhou
- Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland
| | - Hongkai Ji
- Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland
| | - Ying Su
- Dana-Farber Cancer Institute, Boston, Massachusetts
| | | | - Zhengsheng Wu
- Hefei National Laboratory for Physical Sciences at Microscale and School of Life Sciences, University of Science and Technology of China, Hefei, Anhui, People's Republic of China
| | - Tao Zhu
- Hefei National Laboratory for Physical Sciences at Microscale and School of Life Sciences, University of Science and Technology of China, Hefei, Anhui, People's Republic of China
| | | | - Saraswati Sukumar
- Breast Cancer Program, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland.
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Deregulation of the EGFR/PI3K/PTEN/Akt/mTORC1 pathway in breast cancer: possibilities for therapeutic intervention. Oncotarget 2015; 5:4603-50. [PMID: 25051360 PMCID: PMC4148087 DOI: 10.18632/oncotarget.2209] [Citation(s) in RCA: 179] [Impact Index Per Article: 19.9] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Abstract
The EGFR/PI3K/PTEN/Akt/mTORC1/GSK-3 pathway plays prominent roles in malignant transformation, prevention of apoptosis, drug resistance and metastasis. The expression of this pathway is frequently altered in breast cancer due to mutations at or aberrant expression of: HER2, ERalpha, BRCA1, BRCA2, EGFR1, PIK3CA, PTEN, TP53, RB as well as other oncogenes and tumor suppressor genes. In some breast cancer cases, mutations at certain components of this pathway (e.g., PIK3CA) are associated with a better prognosis than breast cancers lacking these mutations. The expression of this pathway and upstream HER2 has been associated with breast cancer initiating cells (CICs) and in some cases resistance to treatment. The anti-diabetes drug metformin can suppress the growth of breast CICs and herceptin-resistant HER2+ cells. This review will discuss the importance of the EGFR/PI3K/PTEN/Akt/mTORC1/GSK-3 pathway primarily in breast cancer but will also include relevant examples from other cancer types. The targeting of this pathway will be discussed as well as clinical trials with novel small molecule inhibitors. The targeting of the hormone receptor, HER2 and EGFR1 in breast cancer will be reviewed in association with suppression of the EGFR/PI3K/PTEN/Akt/mTORC1/GSK-3 pathway.
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Jadhav RR, Ye Z, Huang RL, Liu J, Hsu PY, Huang YW, Rangel LB, Lai HC, Roa JC, Kirma NB, Huang THM, Jin VX. Genome-wide DNA methylation analysis reveals estrogen-mediated epigenetic repression of metallothionein-1 gene cluster in breast cancer. Clin Epigenetics 2015; 7:13. [PMID: 25763113 PMCID: PMC4355986 DOI: 10.1186/s13148-015-0045-9] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2014] [Accepted: 01/13/2015] [Indexed: 12/23/2022] Open
Abstract
Background Recent genome-wide analysis has shown that DNA methylation spans long stretches of chromosome regions consisting of clusters of contiguous CpG islands or gene families. Hypermethylation of various gene clusters has been reported in many types of cancer. In this study, we conducted methyl-binding domain capture (MBDCap) sequencing (MBD-seq) analysis on a breast cancer cohort consisting of 77 patients and 10 normal controls, as well as a panel of 38 breast cancer cell lines. Results Bioinformatics analysis determined seven gene clusters with a significant difference in overall survival (OS) and further revealed a distinct feature that the conservation of a large gene cluster (approximately 70 kb) metallothionein-1 (MT1) among 45 species is much lower than the average of all RefSeq genes. Furthermore, we found that DNA methylation is an important epigenetic regulator contributing to gene repression of MT1 gene cluster in both ERα positive (ERα+) and ERα negative (ERα−) breast tumors. In silico analysis revealed much lower gene expression of this cluster in The Cancer Genome Atlas (TCGA) cohort for ERα + tumors. To further investigate the role of estrogen, we conducted 17β-estradiol (E2) and demethylating agent 5-aza-2′-deoxycytidine (DAC) treatment in various breast cancer cell types. Cell proliferation and invasion assays suggested MT1F and MT1M may play an anti-oncogenic role in breast cancer. Conclusions Our data suggests that DNA methylation in large contiguous gene clusters can be potential prognostic markers of breast cancer. Further investigation of these clusters revealed that estrogen mediates epigenetic repression of MT1 cluster in ERα + breast cancer cell lines. In all, our studies identify thousands of breast tumor hypermethylated regions for the first time, in particular, discovering seven large contiguous hypermethylated gene clusters. Electronic supplementary material The online version of this article (doi:10.1186/s13148-015-0045-9) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Rohit R Jadhav
- Department of Molecular Medicine/Institute of Biotechnology, University of Texas Health Science Center at San Antonio, STRF, Room 225, 7703 Floyd Curl Drive, San Antonio, 78229 TX USA
| | - Zhenqing Ye
- Department of Molecular Medicine/Institute of Biotechnology, University of Texas Health Science Center at San Antonio, STRF, Room 225, 7703 Floyd Curl Drive, San Antonio, 78229 TX USA
| | - Rui-Lan Huang
- Department of Obstetrics and Gynecology, Taipei Medical University Shuang Ho Hospital, New Taipei City, 23561 Taiwan
| | - Joseph Liu
- Department of Molecular Medicine/Institute of Biotechnology, University of Texas Health Science Center at San Antonio, STRF, Room 225, 7703 Floyd Curl Drive, San Antonio, 78229 TX USA
| | - Pei-Yin Hsu
- Department of Molecular Medicine/Institute of Biotechnology, University of Texas Health Science Center at San Antonio, STRF, Room 225, 7703 Floyd Curl Drive, San Antonio, 78229 TX USA
| | - Yi-Wen Huang
- Department of Obstetrics and Gynecology, Medical College of Wisconsin, 9200 West Wisconsin Avenue, Froedtert Medical College Lab Building (FMCLB) 258, Milwaukee, 53226 WI USA
| | - Leticia B Rangel
- Department of Molecular Medicine/Institute of Biotechnology, University of Texas Health Science Center at San Antonio, STRF, Room 225, 7703 Floyd Curl Drive, San Antonio, 78229 TX USA ; Department of Pharmaceutical Sciences, Biotechnology Program/RENORBIO, Health Sciences Center, Universidade Federal do Espirito Santo, Av. Marechal Campos, 1468, Maruipe, 29040-090 Vitoria ES Brazil ; Programa Ciencias Sem Fronteiras, CNPq, Brasilia, Brazil
| | - Hung-Cheng Lai
- Department of Obstetrics and Gynecology, Taipei Medical University Shuang Ho Hospital, New Taipei City, 23561 Taiwan ; School of Medicine, Taipei Medical University, No. 250, Wu-Hsing Street, Taipei, 110 Taiwan ; Graduate Institute of Life Sciences, Department and Graduate Institute of Biochemistry, Tri-Service General Hospital, National Defense Medical Center, Taipei, Taiwan
| | - Juan Carlos Roa
- Departamento de Pathologı'a, Universidad de la Frontera, Claro Solar 115, Temuco, Chile
| | - Nameer B Kirma
- Department of Molecular Medicine/Institute of Biotechnology, University of Texas Health Science Center at San Antonio, STRF, Room 225, 7703 Floyd Curl Drive, San Antonio, 78229 TX USA ; Cancer Therapy and Research Center, University of Texas Health Science Center, 7703 Floyd Curl Drive, San Antonio, 78229 TX USA ; Department of Epidemiology and Biostatistics, University of Texas Health Science Center, 7703 Floyd Curl Drive, San Antonio, 78229 TX USA
| | - Tim Hui-Ming Huang
- Department of Molecular Medicine/Institute of Biotechnology, University of Texas Health Science Center at San Antonio, STRF, Room 225, 7703 Floyd Curl Drive, San Antonio, 78229 TX USA ; Cancer Therapy and Research Center, University of Texas Health Science Center, 7703 Floyd Curl Drive, San Antonio, 78229 TX USA ; Department of Epidemiology and Biostatistics, University of Texas Health Science Center, 7703 Floyd Curl Drive, San Antonio, 78229 TX USA
| | - Victor X Jin
- Department of Molecular Medicine/Institute of Biotechnology, University of Texas Health Science Center at San Antonio, STRF, Room 225, 7703 Floyd Curl Drive, San Antonio, 78229 TX USA ; Cancer Therapy and Research Center, University of Texas Health Science Center, 7703 Floyd Curl Drive, San Antonio, 78229 TX USA ; Department of Epidemiology and Biostatistics, University of Texas Health Science Center, 7703 Floyd Curl Drive, San Antonio, 78229 TX USA
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39
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Potapenko IO, Lüders T, Russnes HG, Helland Å, Sørlie T, Kristensen VN, Nord S, Lingjærde OC, Børresen-Dale AL, Haakensen VD. Glycan-related gene expression signatures in breast cancer subtypes; relation to survival. Mol Oncol 2015; 9:861-76. [PMID: 25655580 DOI: 10.1016/j.molonc.2014.12.013] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2014] [Accepted: 12/27/2014] [Indexed: 01/23/2023] Open
Abstract
Alterations in glycan structures are early signs of malignancy and have recently been proposed to be in part a driving force behind malignant transformation. Here, we explore whether differences in expression of genes related to the process of glycosylation exist between breast carcinoma subtypes - and look for their association to clinical parameters. Five expression datasets of 454 invasive breast carcinomas, 31 ductal carcinomas in situ (DCIS), and 79 non-malignant breast tissue samples were analysed. Results were validated in 1960 breast carcinomas. 419 genes encoding glycosylation-related proteins were selected. The DCIS samples appeared expression-wise similar to carcinomas, showing altered gene expression related to glycosaminoglycans (GAGs) and N-glycans when compared to non-malignant samples. In-situ lesions with different aggressiveness potentials demonstrated changes in glycosaminoglycan sulfation and adhesion proteins. Subtype-specific expression patterns revealed down-regulation of genes encoding glycan-binding proteins in the luminal A and B subtypes. Clustering basal-like samples using a consensus list of genes differentially expressed across discovery datasets produced two clusters with significantly differing prognosis in the validation dataset. Finally, our analyses suggest that glycolipids may play an important role in carcinogenesis of breast tumors - as demonstrated by association of B3GNT5 and UGCG genes to patient survival. In conclusion, most glycan-specific changes occur early in the carcinogenic process. We have identified glycan-related alterations specific to breast cancer subtypes including a prognostic signature for two basal-like subgroups. Future research in this area may potentially lead to markers for better prognostication and treatment stratification of breast cancer patients.
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Affiliation(s)
- Ivan O Potapenko
- Department of Genetics, Institute for Cancer Research, Oslo University Hospital Radiumhospitalet, Norway; K.G. Jebsen Center for Breast Cancer Research, Institute for Clinical Medicine, Faculty of Medicine, University of Oslo, Norway
| | - Torben Lüders
- Department of Clinical Epidemiology and Molecular Biology (Epi-Gen), Akershus University Hospital, Institute for Clinical Medicine, Faculty of Medicine, University of Oslo, Norway
| | - Hege G Russnes
- Department of Genetics, Institute for Cancer Research, Oslo University Hospital Radiumhospitalet, Norway; K.G. Jebsen Center for Breast Cancer Research, Institute for Clinical Medicine, Faculty of Medicine, University of Oslo, Norway
| | - Åslaug Helland
- Department of Genetics, Institute for Cancer Research, Oslo University Hospital Radiumhospitalet, Norway; K.G. Jebsen Center for Breast Cancer Research, Institute for Clinical Medicine, Faculty of Medicine, University of Oslo, Norway; Department of Oncology, Oslo University Hospital Radiumhospitalet, Norway
| | - Therese Sørlie
- Department of Genetics, Institute for Cancer Research, Oslo University Hospital Radiumhospitalet, Norway; K.G. Jebsen Center for Breast Cancer Research, Institute for Clinical Medicine, Faculty of Medicine, University of Oslo, Norway
| | - Vessela N Kristensen
- Department of Genetics, Institute for Cancer Research, Oslo University Hospital Radiumhospitalet, Norway; K.G. Jebsen Center for Breast Cancer Research, Institute for Clinical Medicine, Faculty of Medicine, University of Oslo, Norway; Department of Clinical Epidemiology and Molecular Biology (Epi-Gen), Akershus University Hospital, Institute for Clinical Medicine, Faculty of Medicine, University of Oslo, Norway
| | - Silje Nord
- Department of Genetics, Institute for Cancer Research, Oslo University Hospital Radiumhospitalet, Norway; K.G. Jebsen Center for Breast Cancer Research, Institute for Clinical Medicine, Faculty of Medicine, University of Oslo, Norway
| | - Ole C Lingjærde
- Institute for Informatics, Faculty of Natural Sciences and Mathematics, University of Oslo, Norway
| | - Anne-Lise Børresen-Dale
- Department of Genetics, Institute for Cancer Research, Oslo University Hospital Radiumhospitalet, Norway; K.G. Jebsen Center for Breast Cancer Research, Institute for Clinical Medicine, Faculty of Medicine, University of Oslo, Norway
| | - Vilde D Haakensen
- Department of Genetics, Institute for Cancer Research, Oslo University Hospital Radiumhospitalet, Norway; K.G. Jebsen Center for Breast Cancer Research, Institute for Clinical Medicine, Faculty of Medicine, University of Oslo, Norway.
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40
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Mourad R, Hsu PY, Juan L, Shen C, Koneru P, Lin H, Liu Y, Nephew K, Huang TH, Li L. Estrogen induces global reorganization of chromatin structure in human breast cancer cells. PLoS One 2014; 9:e113354. [PMID: 25470140 PMCID: PMC4255042 DOI: 10.1371/journal.pone.0113354] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2014] [Accepted: 10/22/2014] [Indexed: 12/21/2022] Open
Abstract
In the cell nucleus, each chromosome is confined to a chromosome territory. This spatial organization of chromosomes plays a crucial role in gene regulation and genome stability. An additional level of organization has been discovered at the chromosome scale: the spatial segregation into open and closed chromatins to form two genome-wide compartments. Although considerable progress has been made in our knowledge of chromatin organization, a fundamental issue remains the understanding of its dynamics, especially in cancer. To address this issue, we performed genome-wide mapping of chromatin interactions (Hi-C) over the time after estrogen stimulation of breast cancer cells. To biologically interpret these interactions, we integrated with estrogen receptor (ERα) binding events, gene expression and epigenetic marks. We show that gene-rich chromosomes as well as areas of open and highly transcribed chromatins are rearranged to greater spatial proximity, thus enabling genes to share transcriptional machinery and regulatory elements. At a smaller scale, differentially interacting loci are enriched for cancer proliferation and estrogen-related genes. Moreover, these loci are correlated with higher ERα binding events and gene expression. Taken together these results reveal the role of a hormone - estrogen - on genome organization, and its effect on gene regulation in cancer.
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Affiliation(s)
- Raphaël Mourad
- Department of Medical and Molecular Genetics, Center for Computational Biology and Bioinformatics, Indiana School of Medicine, Indiana University, Indianapolis, IN, 46202, United States of America
| | - Pei-Yin Hsu
- Departments of Molecular Medicine/Institute of Biotechnology, University of Texas Health Science Center, San Antonio, TX, 78245, United States of America
| | - Liran Juan
- Department of Medical and Molecular Genetics, Center for Computational Biology and Bioinformatics, Indiana School of Medicine, Indiana University, Indianapolis, IN, 46202, United States of America
| | - Changyu Shen
- Department of Biostatistics, Center for Computational Biology and Bioinformatics, Indiana School of Medicine, Indiana University, Indianapolis, IN, 46202, United States of America
| | - Prasad Koneru
- Department of Medical and Molecular Genetics, Center for Computational Biology and Bioinformatics, Indiana School of Medicine, Indiana University, Indianapolis, IN, 46202, United States of America
| | - Hai Lin
- Department of Medical and Molecular Genetics, Center for Computational Biology and Bioinformatics, Indiana School of Medicine, Indiana University, Indianapolis, IN, 46202, United States of America
| | - Yunlong Liu
- Department of Medical and Molecular Genetics, Center for Computational Biology and Bioinformatics, Indiana School of Medicine, Indiana University, Indianapolis, IN, 46202, United States of America
| | - Kenneth Nephew
- Laboratory of Ovarian Cancer Epigenomics, Indiana University, Bloomington, IN, 47405, United States of America
| | - Tim H. Huang
- Departments of Molecular Medicine/Institute of Biotechnology, University of Texas Health Science Center, San Antonio, TX, 78245, United States of America
| | - Lang Li
- Department of Medical and Molecular Genetics, Center for Computational Biology and Bioinformatics, Indiana School of Medicine, Indiana University, Indianapolis, IN, 46202, United States of America
- * E-mail:
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Li SC, Tachiki LML, Kabeer MH, Dethlefs BA, Anthony MJ, Loudon WG. Cancer genomic research at the crossroads: realizing the changing genetic landscape as intratumoral spatial and temporal heterogeneity becomes a confounding factor. Cancer Cell Int 2014; 14:115. [PMID: 25411563 PMCID: PMC4236490 DOI: 10.1186/s12935-014-0115-7] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2014] [Accepted: 10/24/2014] [Indexed: 02/06/2023] Open
Abstract
The US National Cancer Institute (NCI) and the National Human Genome Research Institute (NHGRI) created the Cancer Genome Atlas (TCGA) Project in 2006. The TCGA’s goal was to sequence the genomes of 10,000 tumors to identify common genetic changes among different types of tumors for developing genetic-based treatments. TCGA offered great potential for cancer patients, but in reality has little impact on clinical applications. Recent reports place the past TCGA approach of testing a small tumor mass at a single time-point at a crossroads. This crossroads presents us with the conundrum of whether we should sequence more tumors or obtain multiple biopsies from each individual tumor at different time points. Sequencing more tumors with the past TCGA approach of single time-point sampling can neither capture the heterogeneity between different parts of the same tumor nor catch the heterogeneity that occurs as a function of time, error rates, and random drift. Obtaining multiple biopsies from each individual tumor presents multiple logistical and financial challenges. Here, we review current literature and rethink the utility and application of the TCGA approach. We discuss that the TCGA-led catalogue may provide insights into studying the functional significance of oncogenic genes in reference to non-cancer genetic background. Different methods to enhance identifying cancer targets, such as single cell technology, real time imaging of cancer cells with a biological global positioning system, and cross-referencing big data sets, are offered as ways to address sampling discrepancies in the face of tumor heterogeneity. We predict that TCGA landmarks may prove far more useful for cancer prevention than for cancer diagnosis and treatment when considering the effect of non-cancer genes and the normal genetic background on tumor microenvironment. Cancer prevention can be better realized once we understand how therapy affects the genetic makeup of cancer over time in a clinical setting. This may help create novel therapies for gene mutations that arise during a tumor’s evolution from the selection pressure of treatment.
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Affiliation(s)
- Shengwen Calvin Li
- CHOC Children's Hospital Research Institute, University of California Irvine, 1201 West La Veta Ave, Orange, CA 92868 USA ; Department of Neurology, University of California Irvine School of Medicine, Irvine, CA 92697-4292 USA ; Department of Biological Science, California State University, Fullerton, CA 92834 USA
| | - Lisa May Ling Tachiki
- CHOC Children's Hospital Research Institute, University of California Irvine, 1201 West La Veta Ave, Orange, CA 92868 USA ; University of California Irvine School of Medicine, Irvine, CA 92697 USA
| | - Mustafa H Kabeer
- CHOC Children's Hospital Research Institute, University of California Irvine, 1201 West La Veta Ave, Orange, CA 92868 USA ; Department of Pediatric Surgery, CHOC Children's Hospital, 1201 West La Veta Ave, Orange, CA 92868 USA ; Department of Surgery, University of California Irvine School of Medicine, 333 City Blvd. West, Suite 700, Orange, CA 92868 USA
| | - Brent A Dethlefs
- CHOC Children's Hospital Research Institute, University of California Irvine, 1201 West La Veta Ave, Orange, CA 92868 USA
| | | | - William G Loudon
- CHOC Children's Hospital Research Institute, University of California Irvine, 1201 West La Veta Ave, Orange, CA 92868 USA ; Department of Neurological Surgery, Saint Joseph Hospital, Orange, CA 92868 USA ; Department of Neurological Surgery, University of California Irvine School of Medicine, Orange, CA 92862 USA ; Department of Biological Science, California State University, Fullerton, CA 92834 USA
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42
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McCubrey JA, Davis NM, Abrams SL, Montalto G, Cervello M, Libra M, Nicoletti F, D'Assoro AB, Cocco L, Martelli AM, Steelman LS. Targeting breast cancer initiating cells: advances in breast cancer research and therapy. Adv Biol Regul 2014; 56:81-107. [PMID: 24913694 DOI: 10.1016/j.jbior.2014.05.003] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2014] [Accepted: 05/06/2014] [Indexed: 06/03/2023]
Abstract
Over the past 10 years there have been significant advances in our understanding of breast cancer and the important roles that breast cancer initiating cells (CICs) play in the development and resistance of breast cancer. Breast CICs endowed with self-renewing and tumor-initiating capacities are believed to be responsible for the relapses which often occur after various breast cancer therapies. In this review, we will summarize some of the key developments in breast CICs which will include discussion of some of the key genes implicated: estrogen receptor (ER), HER2, BRCA1, TP53, PIK3CA, RB, P16INK1 and various miRs as well some drugs which are showing promise in targeting CICs. In addition, the concept of combined therapies will be discussed. Basic and clinical research is resulting in novel approaches to improve breast cancer therapy by targeting the breast CICs.
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Affiliation(s)
- James A McCubrey
- Department of Microbiology and Immunology, Brody School of Medicine at East Carolina University, Brody Building 5N98C, Greenville, NC 27858, USA.
| | - Nicole M Davis
- Department of Microbiology and Immunology, Brody School of Medicine at East Carolina University, Brody Building 5N98C, Greenville, NC 27858, USA
| | - Stephen L Abrams
- Department of Microbiology and Immunology, Brody School of Medicine at East Carolina University, Brody Building 5N98C, Greenville, NC 27858, USA
| | - Giuseppe Montalto
- Biomedical Department of Internal Medicine and Specialties, University of Palermo, Palermo, Italy; Consiglio Nazionale delle Ricerche, Istituto di Biomedicina e Immunologia Molecolare "Alberto Monroy", Palermo, Italy
| | - Melchiorre Cervello
- Consiglio Nazionale delle Ricerche, Istituto di Biomedicina e Immunologia Molecolare "Alberto Monroy", Palermo, Italy
| | - Massimo Libra
- Department of Bio-Medical Sciences, University of Catania, Catania, Italy
| | | | - Antonino B D'Assoro
- Department of Medical Oncology, Mayo Clinic Cancer Center, Rochester, MN, USA
| | - Lucio Cocco
- Dipartimento di Scienze Biomediche e Neuromotorie, Università di Bologna, Bologna, Italy
| | - Alberto M Martelli
- Dipartimento di Scienze Biomediche e Neuromotorie, Università di Bologna, Bologna, Italy
| | - Linda S Steelman
- Department of Microbiology and Immunology, Brody School of Medicine at East Carolina University, Brody Building 5N98C, Greenville, NC 27858, USA
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Sikora MJ, Cooper KL, Bahreini A, Luthra S, Wang G, Chandran UR, Davidson NE, Dabbs DJ, Welm AL, Oesterreich S. Invasive lobular carcinoma cell lines are characterized by unique estrogen-mediated gene expression patterns and altered tamoxifen response. Cancer Res 2014; 74:1463-74. [PMID: 24425047 PMCID: PMC3955299 DOI: 10.1158/0008-5472.can-13-2779] [Citation(s) in RCA: 96] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Invasive lobular carcinoma (ILC) is a histologic subtype of breast cancer that is frequently associated with favorable outcomes, as approximately 90% of ILC express the estrogen receptor (ER). However, recent retrospective analyses suggest that patients with ILC receiving adjuvant endocrine therapy may not benefit as much as patients with invasive ductal carcinoma. On the basis of these observations, we characterized ER function and endocrine response in ILC models. The ER-positive ILC cell lines MDA MB 134VI (MM134) and SUM44PE were used to examine the ER-regulated transcriptome via gene expression microarray analyses and ER ChIP-Seq, and to examine response to endocrine therapy. In parallel, estrogen response was assessed in vivo in the patient-derived ILC xenograft HCI-013. We identified 915 genes that were uniquely E2 regulated in ILC cell lines versus other breast cancer cell lines, and a subset of these genes were also E2 regulated in vivo in HCI-013. MM134 cells were de novo tamoxifen resistant and were induced to grow by 4-hydroxytamoxifen, as well as other antiestrogens, as partial agonists. Growth was accompanied by agonist activity of tamoxifen on ER-mediated gene expression. Though tamoxifen induced cell growth, MM134 cells required fibroblast growth factor receptor (FGFR)-1 signaling to maintain viability and were sensitive to combined endocrine therapy and FGFR1 inhibition. Our observation that ER drives a unique program of gene expression in ILC cells correlates with the ability of tamoxifen to induce growth in these cells. Targeting growth factors using FGFR1 inhibitors may block survival pathways required by ILC and reverse tamoxifen resistance.
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MESH Headings
- Antineoplastic Agents, Hormonal/pharmacology
- Breast Neoplasms/drug therapy
- Breast Neoplasms/genetics
- Breast Neoplasms/metabolism
- Carcinoma, Lobular/drug therapy
- Carcinoma, Lobular/genetics
- Carcinoma, Lobular/metabolism
- Cell Line, Tumor
- Estrogens/genetics
- Estrogens/metabolism
- Female
- Gene Expression/drug effects
- Gene Expression/genetics
- Humans
- MCF-7 Cells
- Middle Aged
- Receptor, Fibroblast Growth Factor, Type 1/genetics
- Receptor, Fibroblast Growth Factor, Type 1/metabolism
- Receptors, Estrogen/genetics
- Receptors, Estrogen/metabolism
- Signal Transduction/drug effects
- Signal Transduction/genetics
- Tamoxifen/pharmacology
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Affiliation(s)
- Matthew J. Sikora
- Women’s Cancer Research Center, Univ. of Pittsburgh
- Dept. of Pharmacology and Chemical Biology, Univ. of Pittsburgh
| | | | | | - Soumya Luthra
- Dept. of Biomedical Informatics, Univ. of Pittsburgh
| | - Guoying Wang
- Dept. of Oncological Sciences, Huntsman Cancer Institute, Univ. of Utah
| | | | - Nancy E. Davidson
- Women’s Cancer Research Center, Univ. of Pittsburgh
- Dept. of Pharmacology and Chemical Biology, Univ. of Pittsburgh
| | - David J. Dabbs
- Dept. of Pathology, Magee-Womens Hospital, Univ. of Pittsburgh Medical Center
| | - Alana L. Welm
- Dept. of Oncological Sciences, Huntsman Cancer Institute, Univ. of Utah
| | - Steffi Oesterreich
- Women’s Cancer Research Center, Univ. of Pittsburgh
- Dept. of Pharmacology and Chemical Biology, Univ. of Pittsburgh
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The RON receptor tyrosine kinase promotes metastasis by triggering MBD4-dependent DNA methylation reprogramming. Cell Rep 2014; 6:141-54. [PMID: 24388747 PMCID: PMC5312658 DOI: 10.1016/j.celrep.2013.12.010] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2013] [Revised: 10/25/2013] [Accepted: 12/04/2013] [Indexed: 12/14/2022] Open
Abstract
Metastasis is the major cause of death in cancer patients, yet the genetic and epigenetic programs that drive metastasis are poorly understood. Here, we report an epigenetic reprogramming pathway that is required for breast cancer metastasis. Concerted differential DNA methylation is initiated by the activation of the RON receptor tyrosine kinase by its ligand, macrophage stimulating protein (MSP). Through PI3K signaling, RON/MSP promotes expression of the G:T mismatch-specific thymine glycosylase MBD4. RON/MSP and MBD4-dependent aberrant DNA methylation results in the misregulation of a specific set of genes. Knockdown of MBD4 reverses methylation at these specific loci and blocks metastasis. We also show that the MBD4 glycosylase catalytic residue is required for RON/MSP-driven metastasis. Analysis of human breast cancers revealed that this epigenetic program is significantly associated with poor clinical outcome. Furthermore, inhibition of Ron kinase activity with a pharmacological agent blocks metastasis of patient-derived breast tumor grafts in vivo.
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Rangel LBA, Huang THM. Estrogen response in luminal breast cancer. Oncotarget 2013; 4:1548-9. [PMID: 24077736 PMCID: PMC3858541 DOI: 10.18632/oncotarget.1354] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Affiliation(s)
- Leticia B A Rangel
- University of Texas Health Science Center at San Antonio, TX, USA and Universidade Federal do Espirito Santo, ES, Brazil/CNPq (Ciencias sem Fronteiras)
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Cancer mutation has a long reach. Nature 2013. [DOI: 10.1038/500505c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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