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MicroRNAs: A Link between Mammary Gland Development and Breast Cancer. Int J Mol Sci 2022; 23:ijms232415978. [PMID: 36555616 PMCID: PMC9786715 DOI: 10.3390/ijms232415978] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Revised: 12/13/2022] [Accepted: 12/13/2022] [Indexed: 12/23/2022] Open
Abstract
Breast cancer is among the most common cancers in women, second to skin cancer. Mammary gland development can influence breast cancer development in later life. Processes such as proliferation, invasion, and migration during mammary gland development can often mirror processes found in breast cancer. MicroRNAs (miRNAs), small, non-coding RNAs, can repress post-transcriptional RNA expression and can regulate up to 80% of all genes. Expression of miRNAs play a key role in mammary gland development, and aberrant expression can initiate or promote breast cancer. Here, we review the role of miRNAs in mammary development and breast cancer, and potential parallel roles. A total of 32 miRNAs were found to be expressed in both mammary gland development and breast cancer. These miRNAs are involved in proliferation, metastasis, invasion, and apoptosis in both processes. Some miRNAs were found to have contradictory roles, possibly due to their ability to target many genes at once. Investigation of miRNAs and their role in mammary gland development may inform about their role in breast cancer. In particular, by studying miRNA in development, mechanisms and potential targets for breast cancer treatment may be elucidated.
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2
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In silico identification of variations in microRNAs with a potential impact on dairy traits using whole ruminant genome SNP datasets. Sci Rep 2021; 11:19580. [PMID: 34599210 PMCID: PMC8486775 DOI: 10.1038/s41598-021-98639-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2021] [Accepted: 09/03/2021] [Indexed: 11/09/2022] Open
Abstract
MicroRNAs are small noncoding RNAs that have important roles in the lactation process and milk biosynthesis. Some polymorphisms have been studied in various livestock species from the perspective of pathology or production traits. To target variants that could be the causal variants of dairy traits, genetic variants of microRNAs expressed in the mammary gland or present in milk and localized in dairy quantitative trait loci (QTLs) were investigated in bovine, caprine, and ovine species. In this study, a total of 59,124 (out of 28 millions), 13,427 (out of 87 millions), and 4761 (out of 38 millions) genetic variants in microRNAs expressed in the mammary gland or present in milk were identified in bovine, caprine, and ovine species, respectively. A total of 4679 of these detected bovine genetic variants are located in dairy QTLs. In caprine species, 127 genetic variants are localized in dairy QTLs. In ovine species, no genetic variant was identified in dairy QTLs. This study leads to the detection of microRNA genetic variants of interest in the context of dairy production, taking advantage of whole genome data to identify microRNA genetic variants expressed in the mammary gland and localized in dairy QTLs.
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3
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Slepicka PF, Somasundara AVH, Dos Santos CO. The molecular basis of mammary gland development and epithelial differentiation. Semin Cell Dev Biol 2021; 114:93-112. [PMID: 33082117 PMCID: PMC8052380 DOI: 10.1016/j.semcdb.2020.09.014] [Citation(s) in RCA: 48] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2020] [Revised: 09/28/2020] [Accepted: 09/30/2020] [Indexed: 02/07/2023]
Abstract
Our understanding of the molecular events underpinning the development of mammalian organ systems has been increasing rapidly in recent years. With the advent of new and improved next-generation sequencing methods, we are now able to dig deeper than ever before into the genomic and epigenomic events that play critical roles in determining the fates of stem and progenitor cells during the development of an embryo into an adult. In this review, we detail and discuss the genes and pathways that are involved in mammary gland development, from embryogenesis, through maturation into an adult gland, to the role of pregnancy signals in directing the terminal maturation of the mammary gland into a milk producing organ that can nurture the offspring. We also provide an overview of the latest research in the single-cell genomics of mammary gland development, which may help us to understand the lineage commitment of mammary stem cells (MaSCs) into luminal or basal epithelial cells that constitute the mammary gland. Finally, we summarize the use of 3D organoid cultures as a model system to study the molecular events during mammary gland development. Our increased investigation of the molecular requirements for normal mammary gland development will advance the discovery of targets to predict breast cancer risk and the development of new breast cancer therapies.
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Affiliation(s)
- Priscila Ferreira Slepicka
- Stem Cell Transplantation and Regenerative Medicine, Department of Pediatrics, Stanford University School of Medicine, Palo Alto, CA 94305, USA
| | | | - Camila O Dos Santos
- Cold Spring Harbor Laboratory, 1 Bungtown Road, Cold Spring Harbor, NY 11724, USA.
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4
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Ivanova E, Le Guillou S, Hue-Beauvais C, Le Provost F. Epigenetics: New Insights into Mammary Gland Biology. Genes (Basel) 2021; 12:genes12020231. [PMID: 33562534 PMCID: PMC7914701 DOI: 10.3390/genes12020231] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2020] [Revised: 01/23/2021] [Accepted: 01/28/2021] [Indexed: 12/14/2022] Open
Abstract
The mammary gland undergoes important anatomical and physiological changes from embryogenesis through puberty, pregnancy, lactation and involution. These steps are under the control of a complex network of molecular factors, in which epigenetic mechanisms play a role that is increasingly well described. Recently, studies investigating epigenetic modifications and their impacts on gene expression in the mammary gland have been performed at different physiological stages and in different mammary cell types. This has led to the establishment of a role for epigenetic marks in milk component biosynthesis. This review aims to summarize the available knowledge regarding the involvement of the four main molecular mechanisms in epigenetics: DNA methylation, histone modifications, polycomb protein activity and non-coding RNA functions.
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5
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Dissecting miRNA facilitated physiology and function in human breast cancer for therapeutic intervention. Semin Cancer Biol 2020; 72:46-64. [PMID: 32497683 DOI: 10.1016/j.semcancer.2020.05.017] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2020] [Revised: 05/17/2020] [Accepted: 05/27/2020] [Indexed: 12/12/2022]
Abstract
MicroRNAs (miRNAs) are key epigenomic regulators of biological processes in animals and plants. These small non coding RNAs form a complex networks that regulate cellular function and development. MiRNAs prevent translation by either inactivation or inducing degradation of mRNA, a major concern in post-transcriptional gene regulation. Aberrant regulation of gene expression by miRNAs is frequently observed in cancer. Overexpression of various 'oncomiRs' and silencing of tumor suppressor miRNAs are associated with various types of human cancers, although overall downregulation of miRNA expression is reported as a hallmark of cancer. Modulations of the total pool of cellular miRNA by alteration in genetic and epigenetic factors associated with the biogenesis of miRNA machinery. It also depends on the availability of cellular miRNAs from its store in the organelles which affect tumor development and cancer progression. Here, we have dissected the roles and pathways of various miRNAs during normal cellular and molecular functions as well as during breast cancer progression. Recent research works and prevailing views implicate that there are two major types of miRNAs; (i) intracellular miRNAs and (ii) extracellular miRNAs. Concept, that the functions of intracellular miRNAs are driven by cellular organelles in mammalian cells. Extracellular miRNAs function in cell-cell communication in extracellular spaces and distance cells through circulation. A detailed understanding of organelle driven miRNA function and the precise role of extracellular miRNAs, pre- and post-therapeutic implications of miRNAs in this scenario would open several avenues for further understanding of miRNA function and can be better exploited for the treatment of breast cancers.
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6
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Patel Y, Soni M, Awgulewitsch A, Kern MJ, Liu S, Shah N, Singh UP, Chen H. Overexpression of miR-489 derails mammary hierarchy structure and inhibits HER2/neu-induced tumorigenesis. Oncogene 2019; 38:445-453. [PMID: 30104710 PMCID: PMC6338493 DOI: 10.1038/s41388-018-0439-1] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [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: 05/30/2018] [Accepted: 06/29/2018] [Indexed: 01/23/2023]
Abstract
Although it has been demonstrated that transformed progenitor cell population can contribute to tumor initiation, factors contributing to this malignant transformation are poorly known. Using in vitro and xenograft-based models, previous studies demonstrated that miR-489 acts as a tumor suppressor miRNA by targeting various oncogenic pathways. It has been demonstrated that miR-489 directly targets HER2 and inhibits the HER2 signaling pathway; however, its role in mammary gland development and HER2-induced tumor initiation hasn't been studied. To dissect the role of miR-489, we sorted different populations of mammary epithelial cells and determined that miR-489 was highly expressed in mammary stem cells. MMTV-miR-489 mice that overexpressed miR-489 in mammary epithelial cells were developed and these mice exhibited an inhibition of mammary gland development in early ages with a specific impact on highly proliferative cells. Double transgenic MMTV-Her2-miR489 mice were then generated to observe how miR-489 overexpression affects HER2-induced tumorigenesis. miR-489 overexpression delayed HER2-induced tumor initiation significantly. Moreover, miR-489 overexpression inhibited tumor growth and lung metastasis. miR-489 overexpression reduced mammary progenitor cell population significantly in preneoplastic mammary glands of MMTV-Her2 mice which showed a putative transformed population in HER2-induced tumorigenesis. The miR-489 overexpression reduced CD49fhiCD61hi populations in tumors that have stem-like properties, and miR-489 overexpression altered the HER2 signaling pathway in mammary tumors. Altogether, these data indicate that the inhibition of HER2-induced tumorigenesis by miR-489 overexpression was due to altering progenitor cell populations while decreasing tumor growth and metastasis via influencing tumor promoting genes DEK and SHP2.
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MESH Headings
- Animals
- Antigens, CD/analysis
- Cell Differentiation
- Cell Transformation, Neoplastic/genetics
- DNA-Binding Proteins/genetics
- DNA-Binding Proteins/metabolism
- Epithelial Cells/metabolism
- Female
- Gene Expression Regulation, Neoplastic
- Lung Neoplasms/secondary
- Mammary Glands, Animal/cytology
- Mammary Glands, Animal/growth & development
- Mammary Glands, Animal/metabolism
- Mammary Neoplasms, Experimental/genetics
- Mammary Neoplasms, Experimental/metabolism
- Mammary Neoplasms, Experimental/pathology
- Mammary Tumor Virus, Mouse/genetics
- Mice
- Mice, Transgenic
- MicroRNAs/biosynthesis
- MicroRNAs/genetics
- MicroRNAs/physiology
- Neoplastic Stem Cells/cytology
- Neoplastic Stem Cells/metabolism
- Oncogene Proteins/genetics
- Oncogene Proteins/metabolism
- Poly-ADP-Ribose Binding Proteins/genetics
- Poly-ADP-Ribose Binding Proteins/metabolism
- Pregnancy
- Protein Tyrosine Phosphatase, Non-Receptor Type 11/genetics
- Protein Tyrosine Phosphatase, Non-Receptor Type 11/metabolism
- RNA, Neoplasm/biosynthesis
- RNA, Neoplasm/genetics
- RNA, Neoplasm/physiology
- Receptor, ErbB-2/genetics
- Receptor, ErbB-2/physiology
- Recombinant Fusion Proteins/biosynthesis
- Recombinant Fusion Proteins/metabolism
- Stem Cells/metabolism
- Tumor Stem Cell Assay
- Up-Regulation
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Affiliation(s)
- Y Patel
- Department of Biological Science, University of South Carolina, Columbia, SC, 29208, USA
- Center for Colon Cancer Research, University of South Carolina, Columbia, SC, 29208, USA
| | - M Soni
- Department of Biological Science, University of South Carolina, Columbia, SC, 29208, USA
- Center for Colon Cancer Research, University of South Carolina, Columbia, SC, 29208, USA
| | - A Awgulewitsch
- Department of Medicine and Department of Regenerative Medicine and Cell Biology, Transgenic and Genome Editing Core, Medical University of South Carolina (MUSC), Charleston, SC, 29425, USA
| | - M J Kern
- Department of Regenerative Medicine and Cell Biology, Director, Gene Function Core, Medical University of South Carolina, Charleston, SC, 29425, USA
| | - S Liu
- Department of Biological Science, University of South Carolina, Columbia, SC, 29208, USA
- Center for Colon Cancer Research, University of South Carolina, Columbia, SC, 29208, USA
| | - N Shah
- Department of Biological Science, University of South Carolina, Columbia, SC, 29208, USA
- Center for Colon Cancer Research, University of South Carolina, Columbia, SC, 29208, USA
| | - U P Singh
- Department of Pathology, Microbiology and Immunology, School of Medicine, University of South Carolina, Columbia, SC, 29208, USA
| | - H Chen
- Department of Biological Science, University of South Carolina, Columbia, SC, 29208, USA.
- Center for Colon Cancer Research, University of South Carolina, Columbia, SC, 29208, USA.
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7
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Abstract
MicroRNAs (miRNAs) are ∼22 nt RNAs that direct posttranscriptional repression of mRNA targets in diverse eukaryotic lineages. In humans and other mammals, these small RNAs help sculpt the expression of most mRNAs. This article reviews advances in our understanding of the defining features of metazoan miRNAs and their biogenesis, genomics, and evolution. It then reviews how metazoan miRNAs are regulated, how they recognize and cause repression of their targets, and the biological functions of this repression, with a compilation of knockout phenotypes that shows that important biological functions have been identified for most of the broadly conserved miRNAs of mammals.
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Affiliation(s)
- David P Bartel
- Howard Hughes Medical Institute and Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA; Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.
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8
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Yang X, Wang H, Jiao B. Mammary gland stem cells and their application in breast cancer. Oncotarget 2018; 8:10675-10691. [PMID: 27793013 PMCID: PMC5354691 DOI: 10.18632/oncotarget.12893] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2016] [Accepted: 10/14/2016] [Indexed: 12/30/2022] Open
Abstract
The mammary gland is an organ comprising two primary lineages, specifically the inner luminal and the outer myoepithelial cell layers. Mammary gland stem cells (MaSCs) are highly dynamic and self-renewing, and can give rise to these mammary gland lineages. The lineages are responsible for gland generation during puberty as well as expansion during pregnancy. In recent years, researchers have focused on understanding how MaSCs are regulated during mammary gland development and transformation of breast cancer. Here, we summarize the identification of MaSCs, and how they are regulated by the signaling transduction pathways, mammary gland microenvironment, and non-coding RNAs (ncRNAs). Moreover, we debate the evidence for their serving as the origin of breast cancer, and discuss the therapeutic perspectives of targeting breast cancer stem cells (BCSCs). In conclusion, a better understanding of the key regulators of MaSCs is crucial for the clinical treatment of breast cancer.
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Affiliation(s)
- Xing Yang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Hui Wang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, China
| | - Baowei Jiao
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, China
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9
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Facultative CTCF sites moderate mammary super-enhancer activity and regulate juxtaposed gene in non-mammary cells. Nat Commun 2017; 8:16069. [PMID: 28714474 PMCID: PMC5520053 DOI: 10.1038/ncomms16069] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2016] [Accepted: 05/25/2017] [Indexed: 01/06/2023] Open
Abstract
Precise spatiotemporal gene regulation is paramount for the establishment and maintenance of cell-specific programmes. Although there is evidence that chromatin neighbourhoods, formed by the zinc-finger protein CTCF, can sequester enhancers and their target genes, there is limited in vivo evidence for CTCF demarcating super-enhancers and preventing cross talk between distinct regulatory elements. Here, we address these questions in the Wap locus with its mammary-specific super-enhancer separated by CTCF sites from widely expressed genes. Mutational analysis demonstrates that the Wap super-enhancer controls Ramp3, despite three separating CTCF sites. Their deletion in mice results in elevated expression of Ramp3 in mammary tissue through augmented promoter–enhancer interactions. Deletion of the distal CTCF-binding site results in loss of Ramp3 expression in non-mammary tissues. This suggests that CTCF sites are porous borders, allowing a super-enhancer to activate a secondary target. Likewise, CTCF sites shield a widely expressed gene from suppressive influences of a silent locus. Chromatin neighbourhoods, formed by CTCF, have been proposed to isolate enhancers and their target genes from other regulatory elements. Here, the authors provide evidence that while CTCF binding does regulates mammary-specific super-enhancers, CTCF sites are relatively porous borders.
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10
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Histone Demethylase KDM6A Controls the Mammary Luminal Lineage through Enzyme-Independent Mechanisms. Mol Cell Biol 2016; 36:2108-20. [PMID: 27215382 DOI: 10.1128/mcb.00089-16] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2016] [Accepted: 05/08/2016] [Indexed: 02/06/2023] Open
Abstract
Establishment of the mammary luminal cell lineage is controlled primarily by hormones and through specific transcription factors (TFs). Previous studies have linked histone methyltransferases to the differentiation of mammary epithelium, thus opening the possibility of biological significance of counteracting demethylases. We have now demonstrated an essential role for the H3K27me3 demethylase KDM6A in generating a balanced alveolar compartment. Deletion of Kdm6a in the mammary luminal cell lineage led to a paucity of luminal cells and an excessive expansion of basal cells, both in vivo and in vitro The inability to form structurally normal ducts and alveoli during pregnancy resulted in lactation failure. Mutant luminal cells did not exhibit their distinctive transcription factor pattern and displayed basal characteristics. The genomic H3K27me3 landscape was unaltered in mutant tissue, and support for a demethylase-independent mechanism came from mice expressing a catalytically inactive KDM6A. Mammary tissue developed normally in these mice. Chromatin immunoprecipitation sequencing (ChIP-seq) experiments demonstrated KDM6A binding to putative enhancers enriched for key mammary TFs and H3K27ac. This study demonstrated for the first time that the mammary luminal lineage relies on KDM6A to ensure a transcription program leading to differentiated alveoli. Failure to fully implement this program results in structurally and functionally impaired mammary tissue.
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11
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Sandhu GK, Milevskiy MJG, Wilson W, Shewan AM, Brown MA. Non-coding RNAs in Mammary Gland Development and Disease. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2016; 886:121-153. [PMID: 26659490 DOI: 10.1007/978-94-017-7417-8_7] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Non-coding RNAs (ncRNAs) are untranslated RNA molecules that function to regulate the expression of numerous genes and associated biochemical pathways and cellular functions. NcRNAs include small interfering RNAs (siRNAs), microRNAs (miRNAs), PIWI-interacting RNAs (piRNAs), small nucleolar RNAs (snoRNAs) and long non-coding RNAs (lncRNAs). They participate in the regulation of all developmental processes and are frequently aberrantly expressed or functionally defective in disease. This Chapter will focus on the role of ncRNAs, in particular miRNAs and lncRNAs, in mammary gland development and disease.
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Affiliation(s)
- Gurveen K Sandhu
- School of Chemistry and Molecular Biosciences, The University of Queensland, St Lucia, Australia
| | - Michael J G Milevskiy
- School of Chemistry and Molecular Biosciences, The University of Queensland, St Lucia, Australia
| | - Wesley Wilson
- School of Chemistry and Molecular Biosciences, The University of Queensland, St Lucia, Australia
| | - Annette M Shewan
- School of Chemistry and Molecular Biosciences, The University of Queensland, St Lucia, Australia
| | - Melissa A Brown
- School of Chemistry and Molecular Biosciences, The University of Queensland, St Lucia, Australia.
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12
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Haetscher N, Feuermann Y, Wingert S, Rehage M, Thalheimer FB, Weiser C, Bohnenberger H, Jung K, Schroeder T, Serve H, Oellerich T, Hennighausen L, Rieger MA. STAT5-regulated microRNA-193b controls haematopoietic stem and progenitor cell expansion by modulating cytokine receptor signalling. Nat Commun 2015; 6:8928. [PMID: 26603207 PMCID: PMC4674773 DOI: 10.1038/ncomms9928] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2015] [Accepted: 10/16/2015] [Indexed: 02/06/2023] Open
Abstract
Haematopoietic stem cells (HSCs) require the right composition of microRNAs (miR) for proper life-long balanced blood regeneration. Here we show a regulatory circuit that prevents excessive HSC self-renewal by upregulation of miR-193b upon self-renewal promoting thrombopoietin (TPO)-MPL-STAT5 signalling. In turn, miR-193b restricts cytokine signalling, by targeting the receptor tyrosine kinase c-KIT. We generated a miR-193b knockout mouse model to unravel the physiological function of miR-193b in haematopoiesis. MiR-193b−/− mice show a selective gradual enrichment of functional HSCs, which are fully competent in multilineage blood reconstitution upon transplantation. The absence of miR-193b causes an accelerated expansion of HSCs, without altering cell cycle or survival, but by decelerating differentiation. Conversely, ectopic miR-193b expression restricts long-term repopulating HSC expansion and blood reconstitution. MiR-193b-deficient haematopoietic stem and progenitor cells exhibit increased basal and cytokine-induced STAT5 and AKT signalling. This STAT5-induced microRNA provides a negative feedback for excessive signalling to restrict uncontrolled HSC expansion. MicroRNAs regulate haematopoietic stem cell (HSC) development to ensure the correct generation of blood cells. Haetscher et al. show in mice that miR-193b controls the life-long self-renewal ability of HSCs via AKT and STAT5 pathways, with loss of miR-193b accelerating HSC expansion and reducing differentiation.
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Affiliation(s)
- Nadine Haetscher
- LOEWE Center for Cell and Gene Therapy and Department of Medicine, Hematology/Oncology, Goethe University Frankfurt, Theodor-Stern-Kai 7, Frankfurt 60590, Germany.,Georg-Speyer-Haus, Paul-Ehrlich-Street 42-44, Frankfurt 60596, Germany
| | - Yonatan Feuermann
- LOEWE Center for Cell and Gene Therapy and Department of Medicine, Hematology/Oncology, Goethe University Frankfurt, Theodor-Stern-Kai 7, Frankfurt 60590, Germany.,Laboratory of Genetics and Physiology, NIDDK, National Institutes of Health, 9000 Rockville Pike, Bethesda, Maryland 20892, USA
| | - Susanne Wingert
- LOEWE Center for Cell and Gene Therapy and Department of Medicine, Hematology/Oncology, Goethe University Frankfurt, Theodor-Stern-Kai 7, Frankfurt 60590, Germany.,Georg-Speyer-Haus, Paul-Ehrlich-Street 42-44, Frankfurt 60596, Germany
| | - Maike Rehage
- LOEWE Center for Cell and Gene Therapy and Department of Medicine, Hematology/Oncology, Goethe University Frankfurt, Theodor-Stern-Kai 7, Frankfurt 60590, Germany.,Georg-Speyer-Haus, Paul-Ehrlich-Street 42-44, Frankfurt 60596, Germany
| | - Frederic B Thalheimer
- LOEWE Center for Cell and Gene Therapy and Department of Medicine, Hematology/Oncology, Goethe University Frankfurt, Theodor-Stern-Kai 7, Frankfurt 60590, Germany.,Georg-Speyer-Haus, Paul-Ehrlich-Street 42-44, Frankfurt 60596, Germany
| | - Christian Weiser
- Georg-Speyer-Haus, Paul-Ehrlich-Street 42-44, Frankfurt 60596, Germany
| | - Hanibal Bohnenberger
- Department of Pathology, University Medical Center Göttingen, Robert-Koch-Street 40, Goettingen 37075, Germany
| | - Klaus Jung
- Department of Medical Statistics, University Medical Center Göttingen, Humboldtallee 32, Goettingen 37073, Germany
| | - Timm Schroeder
- Department of Biosystems Science and Engineering, ETH Zurich, Mattenstrasse 26, Basel 4058, Switzerland
| | - Hubert Serve
- LOEWE Center for Cell and Gene Therapy and Department of Medicine, Hematology/Oncology, Goethe University Frankfurt, Theodor-Stern-Kai 7, Frankfurt 60590, Germany.,German Cancer Consortium (DKTK), Heidelberg, Germany.,German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, Heidelberg 69120, Germany
| | - Thomas Oellerich
- LOEWE Center for Cell and Gene Therapy and Department of Medicine, Hematology/Oncology, Goethe University Frankfurt, Theodor-Stern-Kai 7, Frankfurt 60590, Germany.,German Cancer Consortium (DKTK), Heidelberg, Germany.,German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, Heidelberg 69120, Germany
| | - Lothar Hennighausen
- Laboratory of Genetics and Physiology, NIDDK, National Institutes of Health, 9000 Rockville Pike, Bethesda, Maryland 20892, USA
| | - Michael A Rieger
- LOEWE Center for Cell and Gene Therapy and Department of Medicine, Hematology/Oncology, Goethe University Frankfurt, Theodor-Stern-Kai 7, Frankfurt 60590, Germany.,Georg-Speyer-Haus, Paul-Ehrlich-Street 42-44, Frankfurt 60596, Germany.,German Cancer Consortium (DKTK), Heidelberg, Germany.,German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, Heidelberg 69120, Germany
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13
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Food Deprivation Affects the miRNome in the Lactating Goat Mammary Gland. PLoS One 2015; 10:e0140111. [PMID: 26473604 PMCID: PMC4608672 DOI: 10.1371/journal.pone.0140111] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2015] [Accepted: 09/22/2015] [Indexed: 11/19/2022] Open
Abstract
Background Nutrition affects milk composition thus influencing its nutritional properties. Nutrition also modifies the expression of mammary genes, whose regulation is not fully understood. MicroRNAs (miRNA) are small non coding RNA which are important post-transcriptional regulators of gene expression by targeting messenger RNAs. Our goal was to characterize miRNA whose expression is regulated by nutrition in the lactating goat mammary gland, which may provide clues to deciphering regulations of the biosynthesis and secretion of milk components. Methodology/principal findings Using high-throughput sequencing technology, miRNomes of the lactating mammary gland were established from lactating goats fed ad libitum or deprived of food for 48h affecting milk production and composition. High throughput miRNA sequencing revealed 30 miRNA with an expression potentially modulated by food deprivation; 16 were down-regulated and 14 were up-regulated. Diana-microT predictive tools suggested a potential role for several nutriregulated miRNA in lipid metabolism. Among the putative targets, 19 were previously identified as differently expressed genes (DEG). The functions of these 19 DEG revealed, notably, their involvement in tissue remodelling. Conclusion/significance In conclusion, this study offers the first evidence of nutriregulated miRNA in the ruminant mammary gland. Characterization of these 30 miRNA could contribute to a clearer understanding of gene regulation in the mammary gland in response to nutrition.
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14
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Yoo KH, Oh S, Kang K, Hensel T, Robinson GW, Hennighausen L. Loss of EZH2 results in precocious mammary gland development and activation of STAT5-dependent genes. Nucleic Acids Res 2015; 43:8774-89. [PMID: 26250110 PMCID: PMC4605299 DOI: 10.1093/nar/gkv776] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2014] [Accepted: 07/21/2015] [Indexed: 01/08/2023] Open
Abstract
Establishment and differentiation of mammary alveoli during pregnancy are controlled by prolactin through the transcription factors STAT5A and STAT5B (STAT5), which also regulate temporal activation of mammary signature genes. This study addressed the question whether the methyltransferase and transcriptional co-activator EZH2 controls the differentiation clock of mammary epithelium. Ablation of Ezh2 from mammary stem cells resulted in precocious differentiation of alveolar epithelium during pregnancy and the activation of mammary-specific STAT5 target genes. This coincided with enhanced occupancy of these loci by STAT5, EZH1 and RNA Pol II. Limited activation of differentiation-specific genes was observed in mammary epithelium lacking both EZH2 and STAT5, suggesting a modulating but not mandatory role for STAT5. Loss of EZH2 did not result in overt changes in genome-wide and gene-specific H3K27me3 profiles, suggesting compensation through enhanced EZH1 recruitment. Differentiated mammary epithelia did not form in the combined absence of EZH1 and EZH2. Transplantation experiments failed to demonstrate a role for EZH2 in the activity of mammary stem and progenitor cells. In summary, while EZH1 and EZH2 serve redundant functions in the establishment of H3K27me3 marks and the formation of mammary alveoli, the presence of EZH2 is required to control progressive differentiation of milk secreting epithelium during pregnancy.
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Affiliation(s)
- Kyung Hyun Yoo
- Laboratory of Genetics and Physiology, National Institutes of Diabetes, Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Sumin Oh
- Laboratory of Genetics and Physiology, National Institutes of Diabetes, Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA Department of Nanobiomedical Science and BK21 PLUS NBM Global Research Center for Regenerative Medicine, Dankook University, Cheonan, Chungnam 330-714, Republic of Korea
| | - Keunsoo Kang
- Laboratory of Genetics and Physiology, National Institutes of Diabetes, Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA Department of Microbiology, Dankook University, Cheonan, Chungnam 330-714, Republic of Korea
| | - Tim Hensel
- Laboratory of Genetics and Physiology, National Institutes of Diabetes, Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Gertraud W Robinson
- Laboratory of Genetics and Physiology, National Institutes of Diabetes, Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Lothar Hennighausen
- Laboratory of Genetics and Physiology, National Institutes of Diabetes, Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA
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Pal B, Chen Y, Bert A, Hu Y, Sheridan JM, Beck T, Shi W, Satterley K, Jamieson P, Goodall GJ, Lindeman GJ, Smyth GK, Visvader JE. Integration of microRNA signatures of distinct mammary epithelial cell types with their gene expression and epigenetic portraits. Breast Cancer Res 2015; 17:85. [PMID: 26080807 PMCID: PMC4497411 DOI: 10.1186/s13058-015-0585-0] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2015] [Accepted: 05/13/2015] [Indexed: 12/21/2022] Open
Abstract
INTRODUCTION MicroRNAs (miRNAs) have been implicated in governing lineage specification and differentiation in multiple organs; however, little is known about their specific roles in mammopoiesis. We have determined the global miRNA expression profiles of functionally distinct epithelial subpopulations in mouse and human mammary tissue, and compared these to their cognate transcriptomes and epigenomes. Finally, the human miRNA signatures were used to interrogate the different subtypes of breast cancer, with a view to determining miRNA networks deregulated during oncogenesis. METHODS RNA from sorted mouse and human mammary cell subpopulations was subjected to miRNA expression analysis using the TaqMan MicroRNA Array. Differentially expressed (DE) miRNAs were correlated with gene expression and histone methylation profiles. Analysis of miRNA signatures of the intrinsic subtypes of breast cancer in The Cancer Genome Atlas (TCGA) database versus those of normal human epithelial subpopulations was performed. RESULTS Unique miRNA signatures characterized each subset (mammary stem cell (MaSC)/basal, luminal progenitor, mature luminal, stromal), with a high degree of conservation across species. Comparison of miRNA and transcriptome profiles for the epithelial subtypes revealed an inverse relationship and pinpointed key developmental genes. Interestingly, expression of the primate-specific miRNA cluster (19q13.4) was found to be restricted to the MaSC/basal subset. Comparative analysis of miRNA signatures with H3 lysine modification maps of the different epithelial subsets revealed a tight correlation between active or repressive marks for the top DE miRNAs, including derepression of miRNAs in Ezh2-deficient cellular subsets. Interrogation of TCGA-identified miRNA profiles with the miRNA signatures of different human subsets revealed specific relationships. CONCLUSIONS The derivation of global miRNA expression profiles for the different mammary subpopulations provides a comprehensive resource for understanding the interplay between miRNA networks and target gene expression. These data have highlighted lineage-specific miRNAs and potential miRNA-mRNA networks, some of which are disrupted in neoplasia. Furthermore, our findings suggest that key developmental miRNAs are regulated by global changes in histone modification, thus linking the mammary epigenome with genome-wide changes in the expression of genes and miRNAs. Comparative miRNA signature analyses between normal breast epithelial cells and breast tumors confirmed an important linkage between luminal progenitor cells and basal-like tumors.
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Affiliation(s)
- Bhupinder Pal
- ACRF Stem Cells and Cancer Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, 3052, Australia. .,Department of Medical Biology, The University of Melbourne, Parkville, VIC, 3010, Australia.
| | - Yunshun Chen
- Department of Medical Biology, The University of Melbourne, Parkville, VIC, 3010, Australia. .,Bioinformatics Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, 3052, Australia.
| | - Andrew Bert
- Centre for Cancer Biology, SA Pathology and University of South Australia, Adelaide, SA, 5000, Australia.
| | - Yifang Hu
- Bioinformatics Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, 3052, Australia.
| | - Julie M Sheridan
- ACRF Stem Cells and Cancer Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, 3052, Australia. .,Department of Medical Biology, The University of Melbourne, Parkville, VIC, 3010, Australia.
| | - Tamara Beck
- ACRF Stem Cells and Cancer Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, 3052, Australia. .,Department of Medical Biology, The University of Melbourne, Parkville, VIC, 3010, Australia.
| | - Wei Shi
- Bioinformatics Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, 3052, Australia. .,Department of Computing and Information Systems, The University of Melbourne, Parkville, VIC, 3010, Australia.
| | - Keith Satterley
- Bioinformatics Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, 3052, Australia.
| | - Paul Jamieson
- ACRF Stem Cells and Cancer Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, 3052, Australia. .,Department of Medical Biology, The University of Melbourne, Parkville, VIC, 3010, Australia.
| | - Gregory J Goodall
- Centre for Cancer Biology, SA Pathology and University of South Australia, Adelaide, SA, 5000, Australia. .,School of Medicine and School of Molecular and Biomedical Science, University of Adelaide, Adelaide, SA, 5005, Australia.
| | - Geoffrey J Lindeman
- ACRF Stem Cells and Cancer Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, 3052, Australia. .,Department of Medicine, The University of Melbourne, Parkville, VIC, 3010, Australia. .,Department of Medical Oncology, The Royal Melbourne Hospital, Parkville, VIC, 3010, Australia.
| | - Gordon K Smyth
- Bioinformatics Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, 3052, Australia. .,Department of Mathematics and Statistics, The University of Melbourne, Parkville, VIC, 3010, Australia.
| | - Jane E Visvader
- ACRF Stem Cells and Cancer Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, 3052, Australia. .,Department of Medical Biology, The University of Melbourne, Parkville, VIC, 3010, Australia.
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Sackmann-Sala L, Guidotti JE, Goffin V. Minireview: prolactin regulation of adult stem cells. Mol Endocrinol 2015; 29:667-81. [PMID: 25793405 DOI: 10.1210/me.2015-1022] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Adult stem/progenitor cells are found in many tissues, where their primary role is to maintain homeostasis. Recent studies have evaluated the regulation of adult stem/progenitor cells by prolactin in various target tissues or cell types, including the mammary gland, the prostate, the brain, the bone marrow, the hair follicle, and colon cancer cells. Depending on the tissue, prolactin can either maintain stem cell quiescence or, in contrast, promote stem/progenitor cell expansion and push their progeny towards differentiation. In many instances, whether these effects are direct or involve paracrine regulators remains debated. This minireview aims to overview the current knowledge in the field.
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Affiliation(s)
- Lucila Sackmann-Sala
- Institut Necker Enfants Malades, Inserm Unité1151, Centre National de la Recherche Scientifique, Unité Mixte de Recherche 8253, Team Prolactin/Growth Hormone Pathophysiology, Faculty of Medicine, University Paris Descartes, Sorbonne Paris Cité, 75014 Paris, France
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Frey KG, Bishop-Lilly KA. Next-Generation Sequencing for Pathogen Detection and Identification. METHODS IN MICROBIOLOGY 2015. [DOI: 10.1016/bs.mim.2015.06.004] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
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