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Saha D, Animireddy S, Bartholomew B. The SWI/SNF ATP-dependent chromatin remodeling complex in cell lineage priming and early development. Biochem Soc Trans 2024; 52:603-616. [PMID: 38572912 PMCID: PMC11088921 DOI: 10.1042/bst20230416] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2023] [Revised: 03/22/2024] [Accepted: 03/26/2024] [Indexed: 04/05/2024]
Abstract
ATP dependent chromatin remodelers have pivotal roles in transcription, DNA replication and repair, and maintaining genome integrity. SWI/SNF remodelers were first discovered in yeast genetic screens for factors involved in mating type switching or for using alternative energy sources therefore termed SWI/SNF complex (short for SWItch/Sucrose NonFermentable). The SWI/SNF complexes utilize energy from ATP hydrolysis to disrupt histone-DNA interactions and shift, eject, or reposition nucleosomes making the underlying DNA more accessible to specific transcription factors and other regulatory proteins. In development, SWI/SNF orchestrates the precise activation and repression of genes at different stages, safe guards the formation of specific cell lineages and tissues. Dysregulation of SWI/SNF have been implicated in diseases such as cancer, where they can drive uncontrolled cell proliferation and tumor metastasis. Additionally, SWI/SNF defects are associated with neurodevelopmental disorders, leading to disruption of neural development and function. This review offers insights into recent developments regarding the roles of the SWI/SNF complex in pluripotency and cell lineage primining and the approaches that have helped delineate its importance. Understanding these molecular mechanisms is crucial for unraveling the intricate processes governing embryonic stem cell biology and developmental transitions and may potentially apply to human diseases linked to mutations in the SWI/SNF complex.
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Affiliation(s)
- Dhurjhoti Saha
- Department of Epigenetics and Molecular Carcinogenesis, Center for Cancer Epigenetics, University of Texas MD Anderson Cancer Center, Houston, TX 77054, U.S.A
| | - Srinivas Animireddy
- Department of Epigenetics and Molecular Carcinogenesis, Center for Cancer Epigenetics, University of Texas MD Anderson Cancer Center, Houston, TX 77054, U.S.A
| | - Blaine Bartholomew
- Department of Epigenetics and Molecular Carcinogenesis, Center for Cancer Epigenetics, University of Texas MD Anderson Cancer Center, Houston, TX 77054, U.S.A
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2
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Contreras-Jurado C, Montero-Pedrazuela A, Pérez RF, Alemany S, Fraga MF, Aranda A. The thyroid hormone enhances mouse embryonic fibroblasts reprogramming to pluripotent stem cells: role of the nuclear receptor corepressor 1. Front Endocrinol (Lausanne) 2023; 14:1235614. [PMID: 38107517 PMCID: PMC10722291 DOI: 10.3389/fendo.2023.1235614] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/27/2023] [Accepted: 10/23/2023] [Indexed: 12/19/2023] Open
Abstract
Introduction Pluripotent stem cells can be generated from somatic cells by the Yamanaka factors Oct4, Sox2, Klf4 and c-Myc. Methods Mouse embryonic fibroblasts (MEFs) were transduced with the Yamanaka factors and generation of induced pluripotent stem cells (iPSCs) was assessed by formation of alkaline phosphatase positive colonies, pluripotency gene expression and embryod bodies formation. Results The thyroid hormone triiodothyronine (T3) enhances MEFs reprogramming. T3-induced iPSCs resemble embryonic stem cells in terms of the expression profile and DNA methylation pattern of pluripotency genes, and of their potential for embryod body formation and differentiation into the three major germ layers. T3 induces reprogramming even though it increases expression of the cyclin kinase inhibitors p21 and p27, which are known to oppose acquisition of pluripotency. The actions of T3 on reprogramming are mainly mediated by the thyroid hormone receptor beta and T3 can enhance iPSC generation in the absence of c-Myc. The hormone cannot replace Oct4 on reprogramming, but in the presence of T3 is possible to obtain iPSCs, although with low efficiency, without exogenous Klf4. Furthermore, depletion of the corepressor NCoR (or Nuclear Receptor Corepressor 1) reduces MEFs reprogramming in the absence of the hormone and strongly decreases iPSC generation by T3 and also by 9cis-retinoic acid, a well-known inducer of reprogramming. NCoR depletion also markedly antagonizes induction of pluripotency gene expression by both ligands. Conclusions Inclusion of T3 on reprogramming strategies has a potential use in enhancing the generation of functional iPSCs for studies of cell plasticity, disease and regenerative medicine.
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Affiliation(s)
- Constanza Contreras-Jurado
- Instituto de Investigaciones Biomédicas Sols-Morreale (IIBM), Consejo Superior de Investigaciones Científicas (CSIC)-Universidad Autónoma de Madrid (UAM), Madrid, Spain
- Departamento de Bioquímica, Facultad de Medicina, Universidad Alfonso X El Sabio, Madrid, Spain
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Instituto de Salud Carlos III, Madrid, Spain
| | - Ana Montero-Pedrazuela
- Instituto de Investigaciones Biomédicas Sols-Morreale (IIBM), Consejo Superior de Investigaciones Científicas (CSIC)-Universidad Autónoma de Madrid (UAM), Madrid, Spain
| | - Raúl F. Pérez
- Cancer Epigenetics and Nanomedicine Laboratory, Centro de Investigación en Nanomateriales y Nanotecnología (CINN), CSIC-UNIOVI-Principado de Asturias, Oviedo, Spain
- Health Research Institute of Asturias (ISPA), Oviedo, Spain
- Institute of Oncology of Asturias (IUOPA), University of Oviedo, Oviedo, Spain
- Department of Organisms and Systems Biology (BOS), University of Oviedo, Oviedo, Spain
- CIBER of Rare Diseases (CIBERER), Oviedo, Spain
| | - Susana Alemany
- Instituto de Investigaciones Biomédicas Sols-Morreale (IIBM), Consejo Superior de Investigaciones Científicas (CSIC)-Universidad Autónoma de Madrid (UAM), Madrid, Spain
| | - Mario F. Fraga
- Cancer Epigenetics and Nanomedicine Laboratory, Centro de Investigación en Nanomateriales y Nanotecnología (CINN), CSIC-UNIOVI-Principado de Asturias, Oviedo, Spain
- Health Research Institute of Asturias (ISPA), Oviedo, Spain
- Institute of Oncology of Asturias (IUOPA), University of Oviedo, Oviedo, Spain
- Department of Organisms and Systems Biology (BOS), University of Oviedo, Oviedo, Spain
- CIBER of Rare Diseases (CIBERER), Oviedo, Spain
| | - Ana Aranda
- Instituto de Investigaciones Biomédicas Sols-Morreale (IIBM), Consejo Superior de Investigaciones Científicas (CSIC)-Universidad Autónoma de Madrid (UAM), Madrid, Spain
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Instituto de Salud Carlos III, Madrid, Spain
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3
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Gong Z, Shu Z, Zhou Y, Chen Y, Zhu H. KLF2 regulates stemness of human mesenchymal stem cells by targeting FGFR3. Biotech Histochem 2023; 98:447-455. [PMID: 37381732 DOI: 10.1080/10520295.2023.2225225] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/30/2023] Open
Abstract
Mesenchymal stem cells (MSCs) are an attractive source of pluripotent cells for regenerative therapy; however, maintaining stemness and self-renewal of MSCs during expansion ex vivo is challenging. For future clinical applications, it is essential to define the roles and signaling pathways that regulate the fate of MSCs. Based on our earlier finding that Krüppel-like factor 2 (KLF2) participates in maintaining stemness in MSCs, we examined further the role of this factor in intrinsic signaling pathways. Using a chromatin immunoprecipitation (ChIP)-sequence assay, we found that the FGFR3 gene is a KLF2 binding site. Knockdown of FGFR3 significantly decreased the levels of key pluripotency factors, enhanced the expression of differentiation-related genes and down-regulated colony formation of human bone marrow MSCs (hBMSCs). Using alizarin red S and oil red O staining, we found that knockdown of FGFR3 inhibited the osteogenic and adipogenic ability of MSCs under conditions of differentiation. The ChIP-qPCR assay confirmed that KLF2 interacts with the promoter regions of FGFR3. Our findings suggest that KLF2 promotes hBMSC stemness by direct regulation of FGFR. Our findings may contribute to enhanced MSC stemness by genetic modification of stemness-related genes.
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Affiliation(s)
- Zhiyuan Gong
- Department of Oral and Maxillofacial Surgery, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
- Key Laboratory of Oral Biomedical Research of Zhejiang Province, Zhejiang University School of Stomatology, Hangzhou, China
| | - Zhanhao Shu
- Department of Oral and Maxillofacial Surgery, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
- Key Laboratory of Oral Biomedical Research of Zhejiang Province, Zhejiang University School of Stomatology, Hangzhou, China
| | - Ying Zhou
- Key Laboratory of Oral Biomedical Research of Zhejiang Province, Zhejiang University School of Stomatology, Hangzhou, China
- Stomatology Hospital, School of Stomatology, Zhejiang University School of Medicine, Hangzhou, China
| | - Yin Chen
- Department of Oral and Maxillofacial Surgery, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
- Key Laboratory of Oral Biomedical Research of Zhejiang Province, Zhejiang University School of Stomatology, Hangzhou, China
| | - Huiyong Zhu
- Department of Oral and Maxillofacial Surgery, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
- Key Laboratory of Oral Biomedical Research of Zhejiang Province, Zhejiang University School of Stomatology, Hangzhou, China
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4
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Varisli L, Dancik GM, Tolan V, Vlahopoulos S. Critical Roles of SRC-3 in the Development and Progression of Breast Cancer, Rendering It a Prospective Clinical Target. Cancers (Basel) 2023; 15:5242. [PMID: 37958417 PMCID: PMC10648290 DOI: 10.3390/cancers15215242] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2023] [Revised: 10/27/2023] [Accepted: 10/30/2023] [Indexed: 11/15/2023] Open
Abstract
Breast cancer (BCa) is the most frequently diagnosed malignant tumor in women and is also one of the leading causes of cancer-related death. Most breast tumors are hormone-dependent and estrogen signaling plays a critical role in promoting the survival and malignant behaviors of these cells. Estrogen signaling involves ligand-activated cytoplasmic estrogen receptors that translocate to the nucleus with various co-regulators, such as steroid receptor co-activator (SRC) family members, and bind to the promoters of target genes and regulate their expression. SRC-3 is a member of this family that interacts with, and enhances, the transcriptional activity of the ligand activated estrogen receptor. Although SRC-3 has important roles in normal homeostasis and developmental processes, it has been shown to be amplified and overexpressed in breast cancer and to promote malignancy. The malignancy-promoting potential of SRC-3 is diverse and involves both promoting malignant behavior of tumor cells and creating a tumor microenvironment that has an immunosuppressive phenotype. SRC-3 also inhibits the recruitment of tumor-infiltrating lymphocytes with effector function and promotes stemness. Furthermore, SRC-3 is also involved in the development of resistance to hormone therapy and immunotherapy during breast cancer treatment. The versatility of SRC-3 in promoting breast cancer malignancy in this way makes it a good target, and methodical targeting of SRC-3 probably will be important for the success of breast cancer treatment.
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Affiliation(s)
- Lokman Varisli
- Department of Molecular Biology and Genetics, Science Faculty, Dicle University, Diyarbakir 21280, Turkey;
| | - Garrett M. Dancik
- Department of Computer Science, Eastern Connecticut State University, Willimantic, CT 06226, USA;
| | - Veysel Tolan
- Department of Molecular Biology and Genetics, Science Faculty, Dicle University, Diyarbakir 21280, Turkey;
| | - Spiros Vlahopoulos
- First Department of Pediatrics, National and Kapodistrian University of Athens, Thivon & Levadeias 8, Goudi, 11527 Athens, Greece
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Knudsen TE, Hamilton WB, Proks M, Lykkegaard M, Linneberg-Agerholm M, Nielsen AV, Perera M, Malzard LL, Trusina A, Brickman JM. A bipartite function of ESRRB can integrate signaling over time to balance self-renewal and differentiation. Cell Syst 2023; 14:788-805.e8. [PMID: 37633265 DOI: 10.1016/j.cels.2023.07.008] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2022] [Revised: 03/22/2023] [Accepted: 07/28/2023] [Indexed: 08/28/2023]
Abstract
Cooperative DNA binding of transcription factors (TFs) integrates the cellular context to support cell specification during development. Naive mouse embryonic stem cells are derived from early development and can sustain their pluripotent identity indefinitely. Here, we ask whether TFs associated with pluripotency evolved to directly support this state or if the state emerges from their combinatorial action. NANOG and ESRRB are key pluripotency factors that co-bind DNA. We find that when both factors are expressed, ESRRB supports pluripotency. However, when NANOG is absent, ESRRB supports a bistable culture of cells with an embryo-like primitive endoderm identity ancillary to pluripotency. The stoichiometry between NANOG and ESRRB allows quantitative titration of this differentiation, and in silico modeling of bipartite ESRRB activity suggests it safeguards plasticity in differentiation. Thus, the concerted activity of cooperative TFs can transform their effect to sustain intermediate cell identities and allow ex vivo expansion of immortal stem cells. A record of this paper's transparent peer review process is included in the supplemental information.
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Affiliation(s)
- Teresa E Knudsen
- The Novo Nordisk Foundation Center for Stem Cell Medicine (reNEW), University of Copenhagen, Copenhagen, Denmark
| | - William B Hamilton
- The Novo Nordisk Foundation Center for Stem Cell Medicine (reNEW), University of Copenhagen, Copenhagen, Denmark.
| | - Martin Proks
- The Novo Nordisk Foundation Center for Stem Cell Medicine (reNEW), University of Copenhagen, Copenhagen, Denmark
| | - Maria Lykkegaard
- The Novo Nordisk Foundation Center for Stem Cell Medicine (reNEW), University of Copenhagen, Copenhagen, Denmark
| | - Madeleine Linneberg-Agerholm
- The Novo Nordisk Foundation Center for Stem Cell Medicine (reNEW), University of Copenhagen, Copenhagen, Denmark
| | | | - Marta Perera
- The Novo Nordisk Foundation Center for Stem Cell Medicine (reNEW), University of Copenhagen, Copenhagen, Denmark
| | | | - Ala Trusina
- Niels Bohr Institute, University of Copenhagen, Copenhagen, Denmark
| | - Joshua M Brickman
- The Novo Nordisk Foundation Center for Stem Cell Medicine (reNEW), University of Copenhagen, Copenhagen, Denmark.
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Nakadai T, Shimada M, Ito K, Cevher MA, Chu CS, Kumegawa K, Maruyama R, Malik S, Roeder RG. Two target gene activation pathways for orphan ERR nuclear receptors. Cell Res 2023; 33:165-183. [PMID: 36646760 PMCID: PMC9892517 DOI: 10.1038/s41422-022-00774-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2021] [Accepted: 12/02/2022] [Indexed: 01/18/2023] Open
Abstract
Estrogen-related receptors (ERRα/β/γ) are orphan nuclear receptors that function in energy-demanding physiological processes, as well as in development and stem cell maintenance, but mechanisms underlying target gene activation by ERRs are largely unknown. Here, reconstituted biochemical assays that manifest ERR-dependent transcription have revealed two complementary mechanisms. On DNA templates, ERRs activate transcription with just the normal complement of general initiation factors through an interaction of the ERR DNA-binding domain with the p52 subunit of initiation factor TFIIH. On chromatin templates, activation by ERRs is dependent on AF2 domain interactions with the cell-specific coactivator PGC-1α, which in turn recruits the ubiquitous p300 and MED1/Mediator coactivators. This role of PGC-1α may also be fulfilled by other AF2-interacting coactivators like NCOA3, which is shown to recruit Mediator selectively to ERRβ and ERRγ. Importantly, combined genetic and RNA-seq analyses establish that both the TFIIH and the AF2 interaction-dependent pathways are essential for ERRβ/γ-selective gene expression and pluripotency maintenance in embryonic stem cells in which NCOA3 is a critical coactivator.
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Affiliation(s)
- Tomoyoshi Nakadai
- Laboratory of Biochemistry and Molecular Biology, The Rockefeller University, New York, NY, USA
- Project for Cancer Epigenomics, Cancer Institute, Japanese Foundation for Cancer Research, Tokyo, Japan
| | - Miho Shimada
- Laboratory of Biochemistry and Molecular Biology, The Rockefeller University, New York, NY, USA
- Department of Molecular Biology, Yokohama City University Graduate School of Medical Science, Yokohama, Japan
| | - Keiichi Ito
- Laboratory of Biochemistry and Molecular Biology, The Rockefeller University, New York, NY, USA
| | - Murat Alper Cevher
- Laboratory of Biochemistry and Molecular Biology, The Rockefeller University, New York, NY, USA
- Department of Molecular Biology and Genetics, Bilkent University, Ankara, Turkey
| | - Chi-Shuen Chu
- Laboratory of Biochemistry and Molecular Biology, The Rockefeller University, New York, NY, USA
| | - Kohei Kumegawa
- Cancer Cell Diversity Project, NEXT-Ganken Program, Japanese Foundation for Cancer Research, Tokyo, Japan
| | - Reo Maruyama
- Project for Cancer Epigenomics, Cancer Institute, Japanese Foundation for Cancer Research, Tokyo, Japan
| | - Sohail Malik
- Laboratory of Biochemistry and Molecular Biology, The Rockefeller University, New York, NY, USA
| | - Robert G Roeder
- Laboratory of Biochemistry and Molecular Biology, The Rockefeller University, New York, NY, USA.
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7
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Loss of skeletal muscle estrogen-related receptors leads to severe exercise intolerance. Mol Metab 2023; 68:101670. [PMID: 36642217 PMCID: PMC9938320 DOI: 10.1016/j.molmet.2023.101670] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/06/2022] [Revised: 01/02/2023] [Accepted: 01/09/2023] [Indexed: 01/15/2023] Open
Abstract
OBJECTIVE Skeletal muscle oxidative capacity is central to physical activity, exercise capacity and whole-body metabolism. The three estrogen-related receptors (ERRs) are regulators of oxidative metabolism in many cell types, yet their roles in skeletal muscle remain unclear. The main aim of this study was to compare the relative contributions of ERRs to oxidative capacity in glycolytic and oxidative muscle, and to determine defects associated with loss of skeletal muscle ERR function. METHODS We assessed ERR expression, generated mice lacking one or two ERRs specifically in skeletal muscle and compared the effects of ERR loss on the transcriptomes of EDL (predominantly glycolytic) and soleus (oxidative) muscles. We also determined the consequences of the loss of ERRs for exercise capacity and energy metabolism in mice with the most severe loss of ERR activity. RESULTS ERRs were induced in human skeletal muscle in response to an exercise bout. Mice lacking both ERRα and ERRγ (ERRα/γ dmKO) had the broadest and most dramatic disruption in skeletal muscle gene expression. The most affected pathway was "mitochondrial function", in particular Oxphos and TCA cycle genes, and transcriptional defects were more pronounced in the glycolytic EDL than the oxidative soleus. Mice lacking ERRβ and ERRγ, the two isoforms expressed highly in oxidative muscles, also exhibited defects in lipid and branch chain amino acid metabolism genes, specifically in the soleus. The pronounced disruption of oxidative metabolism in ERRα/γ dmKO mice led to pale muscles, decreased oxidative capacity, histochemical patterns reminiscent of minicore myopathies, and severe exercise intolerance, with the dmKO mice unable to switch to lipid utilization upon running. ERRα/γ dmKO mice showed no defects in whole-body glucose and energy homeostasis. CONCLUSIONS Our findings define gene expression programs in skeletal muscle that depend on different combinations of ERRs, and establish a central role for ERRs in skeletal muscle oxidative metabolism and exercise capacity. Our data reveal a high degree of functional redundancy among muscle ERR isoforms for the protection of oxidative capacity, and show that ERR isoform-specific phenotypes are driven in part, but not exclusively, by their relative levels in different muscles.
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8
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Ozyurt R, Ozpolat B. Molecular Mechanisms of Anti-Estrogen Therapy Resistance and Novel Targeted Therapies. Cancers (Basel) 2022; 14:5206. [PMID: 36358625 PMCID: PMC9655708 DOI: 10.3390/cancers14215206] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2022] [Revised: 10/05/2022] [Accepted: 10/20/2022] [Indexed: 07/29/2023] Open
Abstract
Breast cancer (BC) is the most commonly diagnosed cancer in women, constituting one-third of all cancers in women, and it is the second leading cause of cancer-related deaths in the United States. Anti-estrogen therapies, such as selective estrogen receptor modulators, significantly improve survival in estrogen receptor-positive (ER+) BC patients, which represents about 70% of cases. However, about 60% of patients inevitably experience intrinsic or acquired resistance to anti-estrogen therapies, representing a major clinical problem that leads to relapse, metastasis, and patient deaths. The resistance mechanisms involve mutations of the direct targets of anti-estrogen therapies, compensatory survival pathways, as well as alterations in the expression of non-coding RNAs (e.g., microRNA) that regulate the activity of survival and signaling pathways. Although cyclin-dependent kinase 4/6 and phosphatidylinositol 3-kinase (PI3K)/AKT/mammalian target of rapamycin (mTOR) inhibitors have significantly improved survival, the efficacy of these therapies alone and in combination with anti-estrogen therapy for advanced ER+ BC, are not curative in advanced and metastatic disease. Therefore, understanding the molecular mechanisms causing treatment resistance is critical for developing highly effective therapies and improving patient survival. This review focuses on the key mechanisms that contribute to anti-estrogen therapy resistance and potential new treatment strategies alone and in combination with anti-estrogen drugs to improve the survival of BC patients.
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Affiliation(s)
- Rumeysa Ozyurt
- Department of Experimental Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
- Houston Methodist Research Institute, Department of Nanomedicine, 6670 Bertner Ave, Houston, TX 77030, USA
| | - Bulent Ozpolat
- Department of Experimental Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
- Houston Methodist Research Institute, Department of Nanomedicine, 6670 Bertner Ave, Houston, TX 77030, USA
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Prediction of Regulatory SNPs in Putative Minor Genes of the Neuro-Cardiovascular Variant in Fabry Reveals Insights into Autophagy/Apoptosis and Fibrosis. BIOLOGY 2022; 11:biology11091287. [PMID: 36138766 PMCID: PMC9495465 DOI: 10.3390/biology11091287] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/11/2022] [Revised: 07/30/2022] [Accepted: 08/03/2022] [Indexed: 11/17/2022]
Abstract
Even though a mutation in monogenic diseases leads to a “classic” manifestation, many disorders exhibit great clinical variability that could be due to modifying genes also called minor genes. Fabry disease (FD) is an X-linked inborn error resulting from the deficient or absent activity of alpha-galactosidase A (α-GAL) enzyme, that leads to deposits of globotriaosylceramide. With our proprietary software SNPclinic v.1.0, we analyzed 110 single nucleotide polymorphisms (SNPs) in the proximal promoter of 14 genes that could modify the FD phenotype FD. We found seven regulatory-SNP (rSNPs) in three genes (IL10, TGFB1 and EDN1) in five cell lines relevant to FD (Cardiac myocytes and fibroblasts, Astrocytes-cerebellar, endothelial cells and T helper cells 1-TH1). Each SNP was confirmed as a true rSNP in public eQTL databases, and additional software suggested the prediction of variants. The two proposed rSNPs in IL10, could explain components for the regulation of active B cells that influence the fibrosis process. The three predicted rSNPs in TGFB1, could act in apoptosis-autophagy regulation. The two putative rSNPs in EDN1, putatively regulate chronic inflammation. The seven rSNPs described here could act to modulate Fabry’s clinical phenotype so we propose that IL10, TGFB1 and EDN1 be considered minor genes in FD.
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Peavey J, Parmar VM, Malek G. Nuclear Receptor Atlases of Choroidal Tissues Reveal Candidate Receptors Associated with Age-Related Macular Degeneration. Cells 2022; 11:2386. [PMID: 35954227 PMCID: PMC9367936 DOI: 10.3390/cells11152386] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2022] [Revised: 07/06/2022] [Accepted: 07/28/2022] [Indexed: 01/27/2023] Open
Abstract
The choroid is a vulnerable tissue site in the eye, impacted in several blinding diseases including age related macular degeneration (AMD), which is the leading cause of central vision loss in the aging population. Choroidal thinning and choriocapillary dropout are features of the early form of AMD, and endothelial dysfunction and vascular changes are primary characteristics of the neovascular clinical sub-type of AMD. Given the importance, the choroidal endothelium and outer vasculature play in supporting visual function, a better understanding of baseline choroidal signaling pathways engaged in tissue and cellular homeostasis is needed. Nuclear receptors are a large family of transcription factors responsible for maintaining various cellular processes during development, aging and disease. Herein we developed a comprehensive nuclear receptor atlas of human choroidal endothelial cells and freshly isolated choroidal tissue by examining the expression levels of all members of this transcription family using quantitative real time PCR. Given the close relationship between the choroid and retinal pigment epithelium (RPE), this data was cross-referenced with the expression profile of nuclear receptors in human RPE cells, to discover potential overlap versus cell-specific nuclear receptor expression. Finally, to identify candidate receptors that may participate in the pathobiology of AMD, we cataloged nuclear receptor expression in a murine model of wet AMD, from which we discovered a subset of nuclear receptors differentially regulated following neovascularization. Overall, these databases serve as useful resources establishing the influence of nuclear receptor signaling pathways on the outer vascular tissue of the eye, while providing a list of receptors, for more focused investigations in the future, to determine their suitability as potential therapeutic targets for diseases, in which the choroid is affected.
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Affiliation(s)
- Jeremy Peavey
- Duke Eye Center, Department of Ophthalmology, Duke University School of Medicine, Durham, NC 27710, USA; (J.P.); (V.M.P.)
| | - Vipul M. Parmar
- Duke Eye Center, Department of Ophthalmology, Duke University School of Medicine, Durham, NC 27710, USA; (J.P.); (V.M.P.)
| | - Goldis Malek
- Duke Eye Center, Department of Ophthalmology, Duke University School of Medicine, Durham, NC 27710, USA; (J.P.); (V.M.P.)
- Department of Pathology, Duke University School of Medicine, Durham, NC 27710, USA
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Herchcovici Levy S, Feldman Cohen S, Arnon L, Lahav S, Awawdy M, Alajem A, Bavli D, Sun X, Buganim Y, Ram O. Esrrb is a cell-cycle-dependent associated factor balancing pluripotency and XEN differentiation. Stem Cell Reports 2022; 17:1334-1350. [PMID: 35594859 PMCID: PMC9214067 DOI: 10.1016/j.stemcr.2022.04.016] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2022] [Revised: 04/25/2022] [Accepted: 04/25/2022] [Indexed: 01/02/2023] Open
Abstract
Cell cycle and differentiation decisions are linked; however, the underlying principles that drive these decisions are unclear. Here, we combined cell-cycle reporter system and single-cell RNA sequencing (scRNA-seq) profiling to study the transcriptomes of embryonic stem cells (ESCs) in the context of cell-cycle states and differentiation. By applying retinoic acid, to G1 and G2/M ESCs, we show that, while both populations can differentiate toward epiblast stem cells (EpiSCs), only G2/M ESCs could differentiate into extraembryonic endoderm cells. We identified Esrrb, a pluripotency factor that is upregulated during G2/M, as a driver of extraembryonic endoderm stem cell (XEN) differentiation. Furthermore, enhancer chromatin states based on wild-type (WT) and ESRRB knockout (KO) ESCs show association of ESRRB with XEN poised enhancers. G1 cells overexpressing Esrrb allow ESCs to produce XENs, while ESRRB-KO ESCs lost their potential to differentiate into XEN. Overall, this study reveals a vital link between Esrrb and cell-cycle states during the exit from pluripotency.
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Affiliation(s)
- Sapir Herchcovici Levy
- Department of Biological Chemistry, Alexander Silberman Institute of Life Sciences, The Hebrew University, Jerusalem 91904, Israel
| | - Sharon Feldman Cohen
- Department of Biological Chemistry, Alexander Silberman Institute of Life Sciences, The Hebrew University, Jerusalem 91904, Israel
| | - Lee Arnon
- Department of Biological Chemistry, Alexander Silberman Institute of Life Sciences, The Hebrew University, Jerusalem 91904, Israel
| | - Shlomtzion Lahav
- Department of Biological Chemistry, Alexander Silberman Institute of Life Sciences, The Hebrew University, Jerusalem 91904, Israel
| | - Muhammad Awawdy
- Department of Biological Chemistry, Alexander Silberman Institute of Life Sciences, The Hebrew University, Jerusalem 91904, Israel
| | - Adi Alajem
- Department of Biological Chemistry, Alexander Silberman Institute of Life Sciences, The Hebrew University, Jerusalem 91904, Israel
| | - Danny Bavli
- Department of Biological Chemistry, Alexander Silberman Institute of Life Sciences, The Hebrew University, Jerusalem 91904, Israel
| | - Xue Sun
- Department of Biological Chemistry, Alexander Silberman Institute of Life Sciences, The Hebrew University, Jerusalem 91904, Israel
| | - Yosef Buganim
- Department of Developmental Biology and Cancer Research, Institute for Medical Research Israel-Canada, The Hebrew University, Hadassah Medical School, Jerusalem 91120, Israel
| | - Oren Ram
- Department of Biological Chemistry, Alexander Silberman Institute of Life Sciences, The Hebrew University, Jerusalem 91904, Israel.
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12
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Huang Y, Duan X, Wang Z, Sun Y, Guan Q, Kang L, Zhang Q, Fang L, Li J, Wong J. An acetylation-enhanced interaction between transcription factor Sox2 and the steroid receptor coactivators facilitates Sox2 transcriptional activity and function. J Biol Chem 2021; 297:101389. [PMID: 34762910 PMCID: PMC8668987 DOI: 10.1016/j.jbc.2021.101389] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2021] [Revised: 10/25/2021] [Accepted: 10/26/2021] [Indexed: 12/02/2022] Open
Abstract
SRY-box 2 (Sox2) is a transcription factor with critical roles in maintaining embryonic stem (ES) cell and adult stem cell functions and in tumorigenesis. However, how Sox2 exerts its transcriptional function remains unclear. Here, we used an in vitro protein–protein interaction assay to discover transcriptional regulators for ES cell core transcription factors (Oct4, Sox2, Klf4, and c-Myc) and identified members of the steroid receptor coactivators (SRCs) as Sox2-specific interacting proteins. The SRC family coactivators have broad roles in transcriptional regulation, but it is unknown whether they also serve as Sox2 coactivators. We demonstrated that these proteins facilitate Sox2 transcriptional activity and act synergistically with p300. Furthermore, we uncovered an acetylation-enhanced interaction between Sox2 and SRC-2/3, but not SRC-1, demonstrating it is Sox2 acetylation that promotes the interaction. We identified putative Sox2 acetylation sites required for acetylation-enhanced interaction between Sox2 and SRC-3 and demonstrated that acetylation on these sites contributes to Sox2 transcriptional activity and recruitment of SRC-3. We showed that activation domains 1 and 2 of SRC-3 both display a preferential binding to acetylated Sox2. Finally, functional analyses in mouse ES cells demonstrated that knockdown of SRC-2/3 but not SRC-1 in mouse ES cells significantly downregulates the transcriptional activities of various Sox2 target genes and impairs ES cell stemness. Taken together, we identify specific SRC family proteins as novel Sox2 coactivators and uncover the role of Sox2 acetylation in promoting coactivator recruitment and Sox2 transcriptional function.
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Affiliation(s)
- Yuanyong Huang
- Shanghai Key Laboratory of Regulatory Biology, Fengxian District Central Hospital-ECNU Joint Center of Translational Medicine, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai, China
| | - Xiaoya Duan
- Shanghai Key Laboratory of Regulatory Biology, Fengxian District Central Hospital-ECNU Joint Center of Translational Medicine, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai, China
| | - Zhen Wang
- Shanghai Key Laboratory of Regulatory Biology, Fengxian District Central Hospital-ECNU Joint Center of Translational Medicine, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai, China
| | - Yimei Sun
- Shanghai Key Laboratory of Regulatory Biology, Fengxian District Central Hospital-ECNU Joint Center of Translational Medicine, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai, China
| | - Qingqing Guan
- Shanghai Key Laboratory of Regulatory Biology, Fengxian District Central Hospital-ECNU Joint Center of Translational Medicine, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai, China
| | - Li Kang
- Shanghai Key Laboratory of Regulatory Biology, Fengxian District Central Hospital-ECNU Joint Center of Translational Medicine, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai, China
| | - Qiao Zhang
- Shanghai Key Laboratory of Regulatory Biology, Fengxian District Central Hospital-ECNU Joint Center of Translational Medicine, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai, China
| | - Lan Fang
- Shanghai Key Laboratory of Regulatory Biology, Fengxian District Central Hospital-ECNU Joint Center of Translational Medicine, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai, China
| | - Jiwen Li
- Shanghai Key Laboratory of Regulatory Biology, Fengxian District Central Hospital-ECNU Joint Center of Translational Medicine, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai, China
| | - Jiemin Wong
- Shanghai Key Laboratory of Regulatory Biology, Fengxian District Central Hospital-ECNU Joint Center of Translational Medicine, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai, China; Joint Center for Translational Medicine, Fengxian District Central Hospital, Shanghai, China.
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13
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Festuccia N, Owens N, Chervova A, Dubois A, Navarro P. The combined action of Esrrb and Nr5a2 is essential for murine naïve pluripotency. Development 2021; 148:271840. [PMID: 34397088 PMCID: PMC8451941 DOI: 10.1242/dev.199604] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2021] [Accepted: 08/04/2021] [Indexed: 12/16/2022]
Abstract
The maintenance of pluripotency in mouse embryonic stem cells (ESCs) is governed by the action of an interconnected network of transcription factors. Among them, only Oct4 and Sox2 have been shown to be strictly required for the self-renewal of ESCs and pluripotency, particularly in culture conditions in which differentiation cues are chemically inhibited. Here, we report that the conjunct activity of two orphan nuclear receptors, Esrrb and Nr5a2, parallels the importance of that of Oct4 and Sox2 in naïve mouse ESCs. By occupying a large common set of regulatory elements, these two factors control the binding of Oct4, Sox2 and Nanog to DNA. Consequently, in their absence the pluripotency network collapses and the transcriptome is substantially deregulated, leading to the differentiation of ESCs. Altogether, this work identifies orphan nuclear receptors, previously thought to be performing supportive functions, as a set of core regulators of naïve pluripotency. Summary: Esrrb and Nr5a2, two orphan nuclear receptors, are identified as essential regulators of pluripotency in mouse embryonic stem cells.
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Affiliation(s)
- Nicola Festuccia
- Regulatory Dynamics and Cell Identity, MRC London Institute of Medical Sciences (LMS), Faculty of Medicine, Imperial College London, Du Cane Road, London W12 0NN, UK.,Epigenomics, Proliferation, and the Identity of Cells, Department of Developmental and Stem Cell Biology, Institut Pasteur, CNRS UMR3738, 75015 Paris, France
| | - Nick Owens
- Institute of Biomedical and Clinical Science, University of Exeter Medical School, Exeter EX2 5DW, UK
| | - Almira Chervova
- Epigenomics, Proliferation, and the Identity of Cells, Department of Developmental and Stem Cell Biology, Institut Pasteur, CNRS UMR3738, 75015 Paris, France
| | - Agnès Dubois
- Epigenomics, Proliferation, and the Identity of Cells, Department of Developmental and Stem Cell Biology, Institut Pasteur, CNRS UMR3738, 75015 Paris, France
| | - Pablo Navarro
- Epigenomics, Proliferation, and the Identity of Cells, Department of Developmental and Stem Cell Biology, Institut Pasteur, CNRS UMR3738, 75015 Paris, France
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14
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Mullany LK, Lonard DM, O’Malley BW. Wound Healing-related Functions of the p160 Steroid Receptor Coactivator Family. Endocrinology 2021; 162:6042238. [PMID: 33340403 PMCID: PMC7814297 DOI: 10.1210/endocr/bqaa232] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/03/2020] [Indexed: 12/24/2022]
Abstract
Multicellular organisms have evolved sophisticated mechanisms to recover and maintain original tissue functions following injury. Injury responses require a robust transcriptomic response associated with cellular reprogramming involving complex gene expression programs critical for effective tissue repair following injury. Steroid receptor coactivators (SRCs) are master transcriptional regulators of cell-cell signaling that is integral for embryogenesis, reproduction, normal physiological function, and tissue repair following injury. Effective therapeutic approaches for facilitating improved tissue regeneration and repair will likely involve temporal and combinatorial manipulation of cell-intrinsic and cell-extrinsic factors. Pleiotropic actions of SRCs that are critical for wound healing range from immune regulation and angiogenesis to maintenance of metabolic regulation in diverse organ systems. Recent evidence derived from studies of model organisms during different developmental stages indicates the importance of the interplay of immune cells and stromal cells to wound healing. With SRCs being the master regulators of cell-cell signaling integral to physiologic changes necessary for wound repair, it is becoming clear that therapeutic targeting of SRCs provides a unique opportunity for drug development in wound healing. This review will provide an overview of wound healing-related functions of SRCs with a special focus on cellular and molecular interactions important for limiting tissue damage after injury. Finally, we review recent findings showing stimulation of SRCs following cardiac injury with the SRC small molecule stimulator MCB-613 can promote cardiac protection and inhibit pathologic remodeling after myocardial infarction.
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Affiliation(s)
- Lisa K Mullany
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX, USA
| | - David M Lonard
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX, USA
| | - Bert W O’Malley
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX, USA
- Correspondence: Bert W. O’Malley, MD, Department of Molecular and Cellular Biology, Baylor College of Medicine, One Baylor Plaza, Houston TX 77030, USA.
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15
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Shahsavari A, Weeratunga P, Ovchinnikov DA, Whitworth DJ. Pluripotency and immunomodulatory signatures of canine induced pluripotent stem cell-derived mesenchymal stromal cells are similar to harvested mesenchymal stromal cells. Sci Rep 2021; 11:3486. [PMID: 33568729 PMCID: PMC7875972 DOI: 10.1038/s41598-021-82856-3] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2020] [Accepted: 01/25/2021] [Indexed: 01/30/2023] Open
Abstract
With a view towards harnessing the therapeutic potential of canine mesenchymal stromal cells (cMSCs) as modulators of inflammation and the immune response, and to avoid the issues of the variable quality and quantity of harvested cMSCs, we examined the immunomodulatory properties of cMSCs derived from canine induced pluripotent stem cells (ciMSCs), and compared them to cMSCs harvested from adipose tissue (cAT-MSC) and bone marrow (cBM-MSC). A combination of deep sequencing and quantitative RT-PCR of the ciMSC transcriptome confirmed that ciMSCs express more genes in common with cBM-MSCs and cAT-MSCs than with the ciPSCs from which they were derived. Both ciMSCs and harvested cMSCs express a range of pluripotency factors in common with the ciPSCs including NANOG, POU5F1 (OCT-4), SOX-2, KLF-4, LIN-28A, MYC, LIF, LIFR, and TERT. However, ESRRB and PRDM-14, both factors associated with naïve, rather than primed, pluripotency were expressed only in the ciPSCs. CXCR-4, which is essential for the homing of MSCs to sites of inflammation, is also detectable in ciMSCs, cAT- and cBM-MSCs, but not ciPSCs. ciMSCs constitutively express the immunomodulatory factors iNOS, GAL-9, TGF-β1, PTGER-2α and VEGF, and the pro-inflammatory mediators COX-2, IL-1β and IL-8. When stimulated with the canine pro-inflammatory cytokines tumor necrosis factor-α (cTNF-α), interferon-γ (cIFN-γ), or a combination of both, ciMSCs upregulated their expression of IDO, iNOS, GAL-9, HGF, TGF-β1, PTGER-2α, VEGF, COX-2, IL-1β and IL-8. When co-cultured with mitogen-stimulated lymphocytes, ciMSCs downregulated their expression of iNOS, HGF, TGF-β1 and PTGER-2α, while increasing their expression of COX-2, IDO and IL-1β. Taken together, these findings suggest that ciMSCs possess similar immunomodulatory capabilities as harvested cMSCs and support further investigation into their potential use for the management of canine immune-mediated and inflammatory disorders.
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Affiliation(s)
- Arash Shahsavari
- grid.1003.20000 0000 9320 7537School of Veterinary Science, University of Queensland, Gatton, QLD 4343 Australia
| | - Prasanna Weeratunga
- grid.1003.20000 0000 9320 7537School of Veterinary Science, University of Queensland, Gatton, QLD 4343 Australia
| | - Dmitry A. Ovchinnikov
- grid.1003.20000 0000 9320 7537Australian Institute for Bioengineering and Nanotechnology, University of Queensland, St Lucia, QLD 4067 Australia
| | - Deanne J. Whitworth
- grid.1003.20000 0000 9320 7537School of Veterinary Science, University of Queensland, Gatton, QLD 4343 Australia ,grid.1003.20000 0000 9320 7537Australian Institute for Bioengineering and Nanotechnology, University of Queensland, St Lucia, QLD 4067 Australia
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16
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A steroid receptor coactivator stimulator (MCB-613) attenuates adverse remodeling after myocardial infarction. Proc Natl Acad Sci U S A 2020; 117:31353-31364. [PMID: 33229578 PMCID: PMC7733826 DOI: 10.1073/pnas.2011614117] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
We are at an exciting era of identification of the cell and molecular processes necessary for tissue remodeling and repair. Unlike current systemic therapeutics, our studies reveal pharmacologic stimulation of SRCs modulates macrophage and fibrotic reparative cell responses to promote more effective repair and lasting beneficial remodeling after myocardial infarction. Progressive remodeling of the heart, resulting in cardiomyocyte (CM) loss and increased inflammation, fibrosis, and a progressive decrease in cardiac function, are hallmarks of myocardial infarction (MI)-induced heart failure. We show that MCB-613, a potent small molecule stimulator of steroid receptor coactivators (SRCs) attenuates pathological remodeling post-MI. MCB-613 decreases infarct size, apoptosis, hypertrophy, and fibrosis while maintaining significant cardiac function. MCB-613, when given within hours post MI, induces lasting protection from adverse remodeling concomitant with: 1) inhibition of macrophage inflammatory signaling and interleukin 1 (IL-1) signaling, which attenuates the acute inflammatory response, 2) attenuation of fibroblast differentiation, and 3) promotion of Tsc22d3-expressing macrophages—all of which may limit inflammatory damage. SRC stimulation with MCB-613 (and derivatives) is a potential therapeutic approach for inhibiting cardiac dysfunction after MI.
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17
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Gallagher KM, Roderick JE, Tan SH, Tan TK, Murphy L, Yu J, Li R, O'Connor KW, Zhu J, Green MR, Sanda T, Kelliher MA. ESRRB regulates glucocorticoid gene expression in mice and patients with acute lymphoblastic leukemia. Blood Adv 2020; 4:3154-3168. [PMID: 32658986 PMCID: PMC7362368 DOI: 10.1182/bloodadvances.2020001555] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2020] [Accepted: 05/21/2020] [Indexed: 12/20/2022] Open
Abstract
Synthetic glucocorticoids (GCs), such as dexamethasone and prednisone, remain key components of therapy for patients with lymphoid malignancies. For pediatric patients with acute lymphoblastic leukemia (ALL), response to GCs remains the most reliable prognostic indicator; failure to respond to GC correlates with poor event-free survival. To uncover GC resistance mechanisms, we performed a genome-wide, survival-based short hairpin RNA screen and identified the orphan nuclear receptor estrogen-related receptor-β (ESRRB) as a critical transcription factor that cooperates with the GC receptor (GR) to mediate the GC gene expression signature in mouse and human ALL cells. Esrrb knockdown interfered with the expression of genes that were induced and repressed by GR and resulted in GC resistance in vitro and in vivo. Dexamethasone treatment stimulated ESRRB binding to estrogen-related receptor elements (ERREs) in canonical GC-regulated genes, and H3K27Ac Hi-chromatin immunoprecipitation revealed increased interactions between GR- and ERRE-containing regulatory regions in dexamethasone-treated human T-ALL cells. Furthermore, ESRRB agonists enhanced GC target gene expression and synergized with dexamethasone to induce leukemic cell death, indicating that ESRRB agonists may overcome GC resistance in ALL, and potentially, in other lymphoid malignancies.
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Affiliation(s)
- Kayleigh M Gallagher
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Medical School, Worcester, MA; and
| | - Justine E Roderick
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Medical School, Worcester, MA; and
| | - Shi Hao Tan
- Cancer Science Institute of Singapore, Center of Translational Medicine, Singapore
| | - Tze King Tan
- Cancer Science Institute of Singapore, Center of Translational Medicine, Singapore
| | - Leonard Murphy
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Medical School, Worcester, MA; and
| | - Jun Yu
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Medical School, Worcester, MA; and
| | - Rui Li
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Medical School, Worcester, MA; and
| | - Kevin W O'Connor
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Medical School, Worcester, MA; and
| | - Julie Zhu
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Medical School, Worcester, MA; and
| | - Michael R Green
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Medical School, Worcester, MA; and
| | - Takaomi Sanda
- Cancer Science Institute of Singapore, Center of Translational Medicine, Singapore
| | - Michelle A Kelliher
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Medical School, Worcester, MA; and
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18
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Jing R, Guo X, Yang Y, Chen W, Kang J, Zhu S. Long noncoding RNA Q associates with Sox2 and is involved in the maintenance of pluripotency in mouse embryonic stem cells. Stem Cells 2020; 38:834-848. [PMID: 32277787 DOI: 10.1002/stem.3180] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2020] [Revised: 03/11/2020] [Accepted: 03/17/2020] [Indexed: 11/11/2022]
Abstract
Large intergenic noncoding RNAs (lincRNAs) in ESCs may play an important role in the maintenance of pluripotency. The identification of stem cell-specific lincRNAs and their interacting partners will deepen our understanding of the maintenance of stem cell pluripotency. We identified a lincRNA, LincQ, which is specifically expressed in ESCs and is regulated by core pluripotent transcription factors. It was rapidly downregulated during the differentiation process. Knockdown of LincQ in ESCs led to differentiation, downregulation of pluripotency-related genes, and upregulation of differentiation-related genes. We found that exon 1 of LincQ can specifically bind to Sox2. The Soxp region in Sox2, rather than the high mobility group domain, is responsible for LincQ binding. Importantly, the interaction between LincQ and Sox2 is required for the maintenance of pluripotency in ESCs and the transcription of pluripotency genes. Esrrb and Tfcp2l1 are key downstream targets of LincQ and Sox2, since overexpression of Esrrb and Tfcp2l1 can restore the loss of ESC pluripotency that is induced by LincQ depletion. In summary, we found that LincQ specifically interacts with Sox2 and contributes to the maintenance of pluripotency, highlighting the critical role of lincRNA in the pluripotency regulatory network.
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Affiliation(s)
- Ruiqi Jing
- Clinical and Translational Research Center of Shanghai First Maternity and Infant Hospital, Shanghai Key Laboratory of Signaling and Disease Research, Collaborative Innovation Center for Brain Science, School of Life Sciences and Technology, Tongji University, Shanghai, People's Republic of China.,Institute of Biophysics, Chinese Academy of Sciences, Beijing, People's Republic of China.,College of Life Sciences, University of Chinese Academy of Sciences, Beijing, People's Republic of China
| | - Xudong Guo
- Clinical and Translational Research Center of Shanghai First Maternity and Infant Hospital, Shanghai Key Laboratory of Signaling and Disease Research, Collaborative Innovation Center for Brain Science, School of Life Sciences and Technology, Tongji University, Shanghai, People's Republic of China.,Institute for Advanced Study, Tongji University, Shanghai, People's Republic of China
| | - Yiwei Yang
- Clinical and Translational Research Center of Shanghai First Maternity and Infant Hospital, Shanghai Key Laboratory of Signaling and Disease Research, Collaborative Innovation Center for Brain Science, School of Life Sciences and Technology, Tongji University, Shanghai, People's Republic of China
| | - Wen Chen
- Clinical and Translational Research Center of Shanghai First Maternity and Infant Hospital, Shanghai Key Laboratory of Signaling and Disease Research, Collaborative Innovation Center for Brain Science, School of Life Sciences and Technology, Tongji University, Shanghai, People's Republic of China
| | - Jiuhong Kang
- Clinical and Translational Research Center of Shanghai First Maternity and Infant Hospital, Shanghai Key Laboratory of Signaling and Disease Research, Collaborative Innovation Center for Brain Science, School of Life Sciences and Technology, Tongji University, Shanghai, People's Republic of China.,Tsingtao Advanced Research Institute, Tongji University, Qingdao, People's Republic of China
| | - Songcheng Zhu
- Clinical and Translational Research Center of Shanghai First Maternity and Infant Hospital, Shanghai Key Laboratory of Signaling and Disease Research, Collaborative Innovation Center for Brain Science, School of Life Sciences and Technology, Tongji University, Shanghai, People's Republic of China
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19
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Dynamic CpG methylation delineates subregions within super-enhancers selectively decommissioned at the exit from naive pluripotency. Nat Commun 2020; 11:1112. [PMID: 32111830 PMCID: PMC7048827 DOI: 10.1038/s41467-020-14916-7] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2019] [Accepted: 02/08/2020] [Indexed: 12/29/2022] Open
Abstract
Clusters of enhancers, referred as to super-enhancers (SEs), control the expression of cell identity genes. The organisation of these clusters, and how they are remodelled upon developmental transitions remain poorly understood. Here, we report the existence of two types of enhancer units within SEs typified by distinctive CpG methylation dynamics in embryonic stem cells (ESCs). We find that these units are either prone for decommissioning or remain constitutively active in epiblast stem cells (EpiSCs), as further established in the peri-implantation epiblast in vivo. Mechanistically, we show a pivotal role for ESRRB in regulating the activity of ESC-specific enhancer units and propose that the developmentally regulated silencing of ESRRB triggers the selective inactivation of these units within SEs. Our study provides insights into the molecular events that follow the loss of ESRRB binding, and offers a mechanism by which the naive pluripotency transcriptional programme can be partially reset upon embryo implantation.
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20
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Rodriguez D, Ramkairsingh M, Lin X, Kapoor A, Major P, Tang D. The Central Contributions of Breast Cancer Stem Cells in Developing Resistance to Endocrine Therapy in Estrogen Receptor (ER)-Positive Breast Cancer. Cancers (Basel) 2019; 11:cancers11071028. [PMID: 31336602 PMCID: PMC6678134 DOI: 10.3390/cancers11071028] [Citation(s) in RCA: 48] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2019] [Revised: 07/17/2019] [Accepted: 07/17/2019] [Indexed: 12/11/2022] Open
Abstract
Breast cancer stem cells (BCSC) play critical roles in the acquisition of resistance to endocrine therapy in estrogen receptor (ER)-positive (ER + ve) breast cancer (BC). The resistance results from complex alterations involving ER, growth factor receptors, NOTCH, Wnt/β-catenin, hedgehog, YAP/TAZ, and the tumor microenvironment. These mechanisms are likely converged on regulating BCSCs, which then drive the development of endocrine therapy resistance. In this regard, hormone therapies enrich BCSCs in ER + ve BCs under both pre-clinical and clinical settings along with upregulation of the core components of “stemness” transcriptional factors including SOX2, NANOG, and OCT4. SOX2 initiates a set of reactions involving SOX9, Wnt, FXY3D, and Src tyrosine kinase; these reactions stimulate BCSCs and contribute to endocrine resistance. The central contributions of BCSCs to endocrine resistance regulated by complex mechanisms offer a unified strategy to counter the resistance. ER + ve BCs constitute approximately 75% of BCs to which hormone therapy is the major therapeutic approach. Likewise, resistance to endocrine therapy remains the major challenge in the management of patients with ER + ve BC. In this review we will discuss evidence supporting a central role of BCSCs in developing endocrine resistance and outline the strategy of targeting BCSCs to reduce hormone therapy resistance.
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Affiliation(s)
- David Rodriguez
- Department of Medicine, McMaster University, Hamilton, ON L8S 4K1, Canada
- The Research Institute of St Joe's Hamilton, St Joseph's Hospital, Hamilton, ON L8N 4A6, Canada
- Urological Cancer Center for Research and Innovation (UCCRI), St Joseph's Hospital, Hamilton, ON L8N 4A6, Canada
- The Hamilton Center for Kidney Research, St. Joseph's Hospital, Hamilton, ON L8N 4A6, Canada
| | - Marc Ramkairsingh
- Department of Medicine, McMaster University, Hamilton, ON L8S 4K1, Canada
- The Research Institute of St Joe's Hamilton, St Joseph's Hospital, Hamilton, ON L8N 4A6, Canada
- Urological Cancer Center for Research and Innovation (UCCRI), St Joseph's Hospital, Hamilton, ON L8N 4A6, Canada
- The Hamilton Center for Kidney Research, St. Joseph's Hospital, Hamilton, ON L8N 4A6, Canada
| | - Xiaozeng Lin
- Department of Medicine, McMaster University, Hamilton, ON L8S 4K1, Canada
- The Research Institute of St Joe's Hamilton, St Joseph's Hospital, Hamilton, ON L8N 4A6, Canada
- Urological Cancer Center for Research and Innovation (UCCRI), St Joseph's Hospital, Hamilton, ON L8N 4A6, Canada
- The Hamilton Center for Kidney Research, St. Joseph's Hospital, Hamilton, ON L8N 4A6, Canada
| | - Anil Kapoor
- The Research Institute of St Joe's Hamilton, St Joseph's Hospital, Hamilton, ON L8N 4A6, Canada
- Urological Cancer Center for Research and Innovation (UCCRI), St Joseph's Hospital, Hamilton, ON L8N 4A6, Canada
- Department of Surgery, McMaster University, Hamilton, Hamilton, ON L8S 4K1, Canada
| | - Pierre Major
- Division of Medical Oncology, Department of Oncology, McMaster University, Hamilton, ON, L8V 5C2, Canada
| | - Damu Tang
- Department of Medicine, McMaster University, Hamilton, ON L8S 4K1, Canada.
- The Research Institute of St Joe's Hamilton, St Joseph's Hospital, Hamilton, ON L8N 4A6, Canada.
- Urological Cancer Center for Research and Innovation (UCCRI), St Joseph's Hospital, Hamilton, ON L8N 4A6, Canada.
- The Hamilton Center for Kidney Research, St. Joseph's Hospital, Hamilton, ON L8N 4A6, Canada.
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21
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Targeting steroid receptor co-activators to inhibit breast cancer stem cells. Oncoscience 2019; 5:281-282. [PMID: 30652114 PMCID: PMC6326735 DOI: 10.18632/oncoscience.469] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2018] [Accepted: 08/02/2018] [Indexed: 11/28/2022] Open
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22
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Whitworth DJ, Limnios IJ, Gauthier ME, Weeratunga P, Ovchinnikov DA, Baillie G, Grimmond SM, Graves JAM, Wolvetang EJ. Platypus Induced Pluripotent Stem Cells: The Unique Pluripotency Signature of a Monotreme. Stem Cells Dev 2019; 28:151-164. [PMID: 30417748 DOI: 10.1089/scd.2018.0179] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
The platypus (Ornithorhynchus anatinus) is an egg-laying monotreme mammal whose ancestors diverged ∼166 million years ago from the evolutionary pathway that eventually gave rise to both marsupial and eutherian mammals. Consequently, its genome is an extraordinary amalgam of both ancestral reptilian and derived mammalian features. To gain insight into the evolution of mammalian pluripotency, we have generated induced pluripotent stem cells from the platypus (piPSCs). Deep sequencing of the piPSC transcriptome revealed that piPSCs robustly express the core eutherian pluripotency factors POU5F1/OCT4, SOX2, and NANOG. Given the more extensive role of SOX3 over SOX2 in avian pluripotency, our data indicate that between 315 and 166 million years ago, primitive mammals replaced the role of SOX3 in the vertebrate pluripotency network with SOX2. DAX1/NR0B1 is not expressed in piPSCs and an analysis of the platypus DAX1 promoter revealed the absence of a proximal SOX2-binding DNA motif known to be critical for DAX1 expression in eutherian pluripotent stem cells, suggesting that the acquisition of SOX2 responsiveness by DAX1 has facilitated its recruitment into the pluripotency network of eutherians. Using the RNAseq data, we were also able to demonstrate that in both fibroblasts and piPSCs, the expression ratio of X chromosomes to autosomes (X1-5 X1-5:AA) is approximately equal to 1, indicating that there is no upregulation of X-linked genes. Finally, the RNAseq data also allowed us to explore the process of X-linked gene inactivation in the platypus, where we determined that for any given gene, there is no preference for silencing of the maternal or paternal allele; that is, within a population of cells, the silencing of X-linked genes is not imprinted.
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Affiliation(s)
- Deanne J Whitworth
- 1 School of Veterinary Science, University of Queensland, Gatton, Australia.,2 Australian Institute for Bioengineering and Nanotechnology, University of Queensland, St Lucia, Australia
| | - Ioannis J Limnios
- 2 Australian Institute for Bioengineering and Nanotechnology, University of Queensland, St Lucia, Australia.,3 Research School of Biology, Australian National University, Acton, Australia.,4 Clem Jones Centre for Regenerative Medicine, Faculty of Health Sciences and Medicine, Bond University, Gold Coast, Queensland, Australia
| | | | | | - Dmitry A Ovchinnikov
- 2 Australian Institute for Bioengineering and Nanotechnology, University of Queensland, St Lucia, Australia
| | - Gregory Baillie
- 5 Institute for Molecular Bioscience, University of Queensland, St Lucia, Australia
| | - Sean M Grimmond
- 5 Institute for Molecular Bioscience, University of Queensland, St Lucia, Australia
| | | | - Ernst J Wolvetang
- 2 Australian Institute for Bioengineering and Nanotechnology, University of Queensland, St Lucia, Australia
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23
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Machado MS, Rosa FD, Lira MC, Urtreger AJ, Rubio MF, Costas MA. The inflammatory cytokine TNF contributes with RAC3-induced malignant transformation. EXCLI JOURNAL 2018; 17:1030-1042. [PMID: 30585274 PMCID: PMC6298201 DOI: 10.17179/excli2018-1759] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/26/2018] [Accepted: 10/16/2018] [Indexed: 12/16/2022]
Abstract
RAC3 is a coactivator of steroid receptors and NF-κB. It is usually overexpressed in several tumors, contributes to maintain cancer stem cells and also to induce them when is overexpressed in non-tumoral cells. In this work, we investigated whether the inflammatory cytokine TNF may contribute to the transforming effects of RAC3 overexpression in the non-tumoral HEK293 cell line. The study model included the HEK293 tumoral transformed cell line constitutively overexpressing RAC3 by stable transfection and control non-tumoral cells transfected with an empty vector. The HeLa and T47D tumoral cells that naturally overexpress RAC3 were used as positive control. We found that TNF potentiated RAC3-induced mesenchymal transition, involving an increased E-Cadherin downregulation, Vimentin and SNAIL upregulation and enhanced migratory behavior. Moreover, concerning the molecular mechanisms by which TNF potentiates the RAC3 transforming action, they involve the IKK activation, which in addition induced the β-Catenin transactivation. Our results demonstrate that although RAC3 overexpression could be a signal strong enough to induce cancer stem cells, the inflammatory microenvironment may be playing a key role contributing to the migratory and invasive phenotype required for metastasis and cancer persistence.
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Affiliation(s)
- Mileni Soares Machado
- Laboratorio de Biología Molecular y Apoptosis, Instituto de Investigaciones Médicas Alfredo Lanari, IDIM-CONICET, Facultad de Medicina, Universidad de Buenos Aires, Combatientes de Malvinas 3150, C1427ARO Buenos Aires, Argentina
| | - Francisco D Rosa
- Laboratorio de Biología Molecular y Apoptosis, Instituto de Investigaciones Médicas Alfredo Lanari, IDIM-CONICET, Facultad de Medicina, Universidad de Buenos Aires, Combatientes de Malvinas 3150, C1427ARO Buenos Aires, Argentina
| | - María C Lira
- Laboratorio de Biología Molecular y Apoptosis, Instituto de Investigaciones Médicas Alfredo Lanari, IDIM-CONICET, Facultad de Medicina, Universidad de Buenos Aires, Combatientes de Malvinas 3150, C1427ARO Buenos Aires, Argentina
| | - Alejandro J Urtreger
- Universidad de Buenos Aires, Instituto de Oncología Ángel H. Roffo, Área Investigación, Av. San Martín 5481, C1417DTB Buenos Aires, Argentina.,Member of the Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET)
| | - María F Rubio
- Laboratorio de Biología Molecular y Apoptosis, Instituto de Investigaciones Médicas Alfredo Lanari, IDIM-CONICET, Facultad de Medicina, Universidad de Buenos Aires, Combatientes de Malvinas 3150, C1427ARO Buenos Aires, Argentina.,Member of the Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET)
| | - Mónica A Costas
- Laboratorio de Biología Molecular y Apoptosis, Instituto de Investigaciones Médicas Alfredo Lanari, IDIM-CONICET, Facultad de Medicina, Universidad de Buenos Aires, Combatientes de Malvinas 3150, C1427ARO Buenos Aires, Argentina.,Member of the Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET)
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24
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Weeratunga P, Shahsavari A, Ovchinnikov DA, Wolvetang EJ, Whitworth DJ. Induced Pluripotent Stem Cells from a Marsupial, the Tasmanian Devil (Sarcophilus harrisii): Insight into the Evolution of Mammalian Pluripotency. Stem Cells Dev 2018; 27:112-122. [PMID: 29161957 DOI: 10.1089/scd.2017.0224] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
We demonstrate the generation of Tasmanian devil (Sarcophilus harrisii) induced pluripotent stem cells (DeviPSCs) from dermal fibroblasts by lentiviral delivery of human transcription factors. DeviPSCs display characteristic pluripotent stem cell colony morphology, with individual cells having a high nuclear-to-cytoplasmic ratio and alkaline phosphatase activity. DeviPSCs are leukemia inhibitory factor dependent and have reactivated endogenous octamer-binding transcription factor 4 [OCT4, POU domain, class 5, transcription factor 1 (POU5F1)], POU2 [POU domain, class 5, transcription factor 3 (POU5F3)], sex determining region Y-box 2 (SOX2), Nanog homeobox (NANOG) and dosage-sensitive sex reversal, adrenal hypoplasia congenita critical region on the X chromosome, gene 1 (DAX1) genes, retained a normal karyotype, and concurrently silenced exogenous human transgenes. Notably, co-expression of both OCT4 and POU2 suggests that they are representative of cells of the epiblast, the marsupial equivalent of the inner cell mass. DeviPSCs readily form embryoid bodies and in vitro teratomas containing derivatives of all three embryonic germ layers. To date, DeviPSCs have been stably maintained for more than 45 passages. Our DeviPSCs provide an invaluable resource for studies into marsupial pluripotency and development, and they may also serve as an important tool in efforts to combat the threat of devil facial tumor disease.
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Affiliation(s)
- Prasanna Weeratunga
- 1 School of Veterinary Science, University of Queensland , Gatton, Australia
| | - Arash Shahsavari
- 1 School of Veterinary Science, University of Queensland , Gatton, Australia
| | - Dmitry A Ovchinnikov
- 2 Australian Institute for Bioengineering and Nanotechnology, University of Queensland , St. Lucia, Australia
| | - Ernst J Wolvetang
- 2 Australian Institute for Bioengineering and Nanotechnology, University of Queensland , St. Lucia, Australia
| | - Deanne J Whitworth
- 1 School of Veterinary Science, University of Queensland , Gatton, Australia .,2 Australian Institute for Bioengineering and Nanotechnology, University of Queensland , St. Lucia, Australia
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25
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Percharde M, Lin CJ, Yin Y, Guan J, Peixoto GA, Bulut-Karslioglu A, Biechele S, Huang B, Shen X, Ramalho-Santos M. A LINE1-Nucleolin Partnership Regulates Early Development and ESC Identity. Cell 2018; 174:391-405.e19. [PMID: 29937225 PMCID: PMC6046266 DOI: 10.1016/j.cell.2018.05.043] [Citation(s) in RCA: 302] [Impact Index Per Article: 50.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2017] [Revised: 03/20/2018] [Accepted: 05/17/2018] [Indexed: 01/07/2023]
Abstract
Transposable elements represent nearly half of mammalian genomes and are generally described as parasites, or "junk DNA." The LINE1 retrotransposon is the most abundant class and is thought to be deleterious for cells, yet it is paradoxically highly expressed during early development. Here, we report that LINE1 plays essential roles in mouse embryonic stem cells (ESCs) and pre-implantation embryos. In ESCs, LINE1 acts as a nuclear RNA scaffold that recruits Nucleolin and Kap1/Trim28 to repress Dux, the master activator of a transcriptional program specific to the 2-cell embryo. In parallel, LINE1 RNA mediates binding of Nucleolin and Kap1 to rDNA, promoting rRNA synthesis and ESC self-renewal. In embryos, LINE1 RNA is required for Dux silencing, synthesis of rRNA, and exit from the 2-cell stage. The results reveal an essential partnership between LINE1 RNA, Nucleolin, Kap1, and peri-nucleolar chromatin in the regulation of transcription, developmental potency, and ESC self-renewal.
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Affiliation(s)
- Michelle Percharde
- Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, Center for Reproductive Sciences, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Chih-Jen Lin
- The University of Edinburgh, MRC Centre for Reproductive Health, Queen's Medical Research Institute, 47 Little France Crescent, Edinburgh, EH16 4TJ, Scotland, UK
| | - Yafei Yin
- Tsinghua-Peking Center for Life Sciences, School of Medicine, Tsinghua University, Beijing 100084, China
| | - Juan Guan
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Gabriel A Peixoto
- Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, Center for Reproductive Sciences, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Aydan Bulut-Karslioglu
- Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, Center for Reproductive Sciences, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Steffen Biechele
- Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, Center for Reproductive Sciences, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Bo Huang
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA 94143, USA; Chan Zuckerberg Biohub, San Francisco, CA 94158, USA
| | - Xiaohua Shen
- Tsinghua-Peking Center for Life Sciences, School of Medicine, Tsinghua University, Beijing 100084, China
| | - Miguel Ramalho-Santos
- Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, Center for Reproductive Sciences, University of California, San Francisco, San Francisco, CA 94143, USA.
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26
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Liu Z, Tjian R. Visualizing transcription factor dynamics in living cells. J Cell Biol 2018; 217:1181-1191. [PMID: 29378780 PMCID: PMC5881510 DOI: 10.1083/jcb.201710038] [Citation(s) in RCA: 118] [Impact Index Per Article: 19.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2017] [Revised: 01/03/2018] [Accepted: 01/16/2018] [Indexed: 12/16/2022] Open
Abstract
The assembly of sequence-specific enhancer-binding transcription factors (TFs) at cis-regulatory elements in the genome has long been regarded as the fundamental mechanism driving cell type-specific gene expression. However, despite extensive biochemical, genetic, and genomic studies in the past three decades, our understanding of molecular mechanisms underlying enhancer-mediated gene regulation remains incomplete. Recent advances in imaging technologies now enable direct visualization of TF-driven regulatory events and transcriptional activities at the single-cell, single-molecule level. The ability to observe the remarkably dynamic behavior of individual TFs in live cells at high spatiotemporal resolution has begun to provide novel mechanistic insights and promises new advances in deciphering causal-functional relationships of TF targeting, genome organization, and gene activation. In this review, we review current transcription imaging techniques and summarize converging results from various lines of research that may instigate a revision of models to describe key features of eukaryotic gene regulation.
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Affiliation(s)
- Zhe Liu
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA
| | - Robert Tjian
- Department of Molecular and Cell Biology, Li Ka Shing Center for Biomedical and Health Sciences, California Institute for Regenerative Medicine Center of Excellence, University of California, Berkeley, Berkeley, CA
- Howard Hughes Medical Institute, Berkeley, CA
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27
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Truong TH, Hu H, Temiz NA, Hagen KM, Girard BJ, Brady NJ, Schwertfeger KL, Lange CA, Ostrander JH. Cancer Stem Cell Phenotypes in ER + Breast Cancer Models Are Promoted by PELP1/AIB1 Complexes. Mol Cancer Res 2018; 16:707-719. [PMID: 29348189 PMCID: PMC5882512 DOI: 10.1158/1541-7786.mcr-17-0598] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2017] [Revised: 12/13/2017] [Accepted: 01/11/2018] [Indexed: 02/06/2023]
Abstract
Proline, glutamic acid, leucine-rich protein 1 (PELP1) is overexpressed in approximately 80% of invasive breast tumors. PELP1 dynamically shuttles between the nucleus and cytoplasm, but is primarily nuclear in normal breast tissue. However, altered localization of PELP1 to the cytoplasm is an oncogenic event that promotes breast cancer initiation and progression. Herein, interacting partners unique to cytoplasmic PELP1 and the mechanisms by which these interactions promote oncogenic PELP1 signaling were sought. AIB1 (amplified in breast cancer 1; also known as SRC-3 or NCOA3) was identified as a novel binding partner of cytoplasmic PELP1 in both estrogen receptor-positive (ER+) and ER-negative cell lines. Cytoplasmic PELP1 expression elevated basal phosphorylation levels (i.e., activation) of AIB1 at Thr24, enhanced ALDH+ tumorsphere formation, and upregulated specific target genes independently of hormone stimulation. Direct manipulation of AIB1 levels using shRNA abrogated cytoplasmic PELP1-induced tumorsphere formation and downregulated cytoplasmic PELP1-specific target genes. SI-2, an AIB1 inhibitor, limited the PELP1/AIB1 interaction and decreased cytoplasmic PELP1-induced tumorsphere formation. Similar results were observed in a murine-derived MMTV-AIB1 tumor cell line. Furthermore, in vivo syngeneic tumor studies revealed that PELP1 knockdown resulted in increased survival of tumor-bearing mice as compared with mice injected with control cells.Implications: These data demonstrate that cytoplasmic PELP1/AIB1-containing complexes function to promote advanced cancer phenotypes, including outgrowth of stem-like cells, associated with estrogen-independent breast cancer progression. Mol Cancer Res; 16(4); 707-19. ©2018 AACR.
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Affiliation(s)
- Thu H Truong
- Department of Medicine, Division of Hematology, Oncology, and Transplantation, Masonic Cancer Center, University of Minnesota, Minneapolis, Minnesota
| | - Hsiangyu Hu
- Department of Medicine, Division of Hematology, Oncology, and Transplantation, Masonic Cancer Center, University of Minnesota, Minneapolis, Minnesota
| | - Nuri A Temiz
- Masonic Cancer Center, Institute for Health Informatics, University of Minnesota, Minneapolis, Minnesota
| | - Kyla M Hagen
- Department of Medicine, Division of Hematology, Oncology, and Transplantation, Masonic Cancer Center, University of Minnesota, Minneapolis, Minnesota
| | - Brian J Girard
- Department of Medicine, Division of Hematology, Oncology, and Transplantation, Masonic Cancer Center, University of Minnesota, Minneapolis, Minnesota
| | - Nicholas J Brady
- Department of Medicine, Division of Hematology, Oncology, and Transplantation, Masonic Cancer Center, University of Minnesota, Minneapolis, Minnesota
| | - Kathryn L Schwertfeger
- Department of Laboratory Medicine and Pathology, Masonic Cancer Center, University of Minnesota, Minneapolis, Minnesota
| | - Carol A Lange
- Department of Medicine, Division of Hematology, Oncology, and Transplantation, Masonic Cancer Center, University of Minnesota, Minneapolis, Minnesota.
- Department of Pharmacology, Masonic Cancer Center, University of Minnesota, Minneapolis, Minnesota
| | - Julie H Ostrander
- Department of Medicine, Division of Hematology, Oncology, and Transplantation, Masonic Cancer Center, University of Minnesota, Minneapolis, Minnesota.
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28
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Heckler MM, Zeleke TZ, Divekar SD, Fernandez AI, Tiek DM, Woodrick J, Farzanegan A, Roy R, Üren A, Mueller SC, Riggins RB. Antimitotic activity of DY131 and the estrogen-related receptor beta 2 (ERRβ2) splice variant in breast cancer. Oncotarget 2018; 7:47201-47220. [PMID: 27363015 PMCID: PMC5216935 DOI: 10.18632/oncotarget.9719] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2015] [Accepted: 05/19/2016] [Indexed: 01/09/2023] Open
Abstract
Breast cancer remains a leading cause of cancer-related death in women, and triple negative breast cancer (TNBC) lacks clinically actionable therapeutic targets. Death in mitosis is a tumor suppressive mechanism that occurs in cancer cells experiencing a defective M phase. The orphan estrogen-related receptor beta (ERRβ) is a key reprogramming factor in murine embryonic and induced pluripotent stem cells. In primates, ERRβ is alternatively spliced to produce several receptor isoforms. In cellular models of glioblastoma, short form (ERRβsf) and beta2 (ERRβ2) splice variants differentially regulate cell cycle progression in response to the synthetic agonist DY131, with ERRβ2 driving arrest in G2/M.The goals of the present study are to determine the cellular function(s) of ligand-activated ERRβ splice variants in breast cancer and evaluate the potential of DY131 to serve as an antimitotic agent, particularly in TNBC. DY131 inhibits growth in a diverse panel of breast cancer cell lines, causing cell death that involves the p38 stress kinase pathway and a bimodal cell cycle arrest. ERRβ2 facilitates the block in G2/M, and DY131 delays progression from prophase to anaphase. Finally, ERRβ2 localizes to centrosomes and DY131 causes mitotic spindle defects. Targeting ERRβ2 may therefore be a promising therapeutic strategy in breast cancer.
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Affiliation(s)
- Mary M Heckler
- Department of Oncology, Lombardi Comprehensive Cancer Center, Georgetown University Medical Center, Washington, DC 20057, USA
| | - Tizita Zewde Zeleke
- Department of Oncology, Lombardi Comprehensive Cancer Center, Georgetown University Medical Center, Washington, DC 20057, USA
| | - Shailaja D Divekar
- Department of Oncology, Lombardi Comprehensive Cancer Center, Georgetown University Medical Center, Washington, DC 20057, USA
| | - Aileen I Fernandez
- Department of Oncology, Lombardi Comprehensive Cancer Center, Georgetown University Medical Center, Washington, DC 20057, USA
| | - Deanna M Tiek
- Department of Oncology, Lombardi Comprehensive Cancer Center, Georgetown University Medical Center, Washington, DC 20057, USA
| | - Jordan Woodrick
- Department of Oncology, Lombardi Comprehensive Cancer Center, Georgetown University Medical Center, Washington, DC 20057, USA
| | - Alexander Farzanegan
- Department of Oncology, Lombardi Comprehensive Cancer Center, Georgetown University Medical Center, Washington, DC 20057, USA
| | - Rabindra Roy
- Department of Oncology, Lombardi Comprehensive Cancer Center, Georgetown University Medical Center, Washington, DC 20057, USA
| | - Aykut Üren
- Department of Oncology, Lombardi Comprehensive Cancer Center, Georgetown University Medical Center, Washington, DC 20057, USA
| | - Susette C Mueller
- Department of Oncology, Lombardi Comprehensive Cancer Center, Georgetown University Medical Center, Washington, DC 20057, USA
| | - Rebecca B Riggins
- Department of Oncology, Lombardi Comprehensive Cancer Center, Georgetown University Medical Center, Washington, DC 20057, USA
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29
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Panelo LC, Machado MS, Rubio MF, Jaworski F, Alvarado CV, Paz LA, Urtreger AJ, Vazquez E, Costas MA. High RAC3 expression levels are required for induction and maintaining of cancer cell stemness. Oncotarget 2018; 9:5848-5860. [PMID: 29464039 PMCID: PMC5814179 DOI: 10.18632/oncotarget.23635] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2017] [Accepted: 12/04/2017] [Indexed: 01/10/2023] Open
Abstract
RAC3 is a transcription coactivator, usually overexpressed in several tumors and required to maintain the pluripotency in normal stem cells. In this work we studied the association between RAC3 overexpression on cancer cell stemness and the capacity of this protein to induce cancer stem properties in non tumoral cells. We performed in vitro and in vivo experiments using two strategies: by overexpressing RAC3 in the non tumoral cell line HEK293 and by silencing RAC3 in the human colorectal epithelial cell line HCT116 by transfection. Furthermore, we analysed public repository microarrays data from human colorectal tumors in different developmental stages. We found that RAC3 overexpression was mainly associated to CD133+ side-population of colon cancer cells and also to early and advanced stages of colon cancer, involving increased expression of mesenchymal and stem markers. In turn, RAC3 silencing induced diminished tumoral properties and cancer stem cells as determined by Hoechst efflux, tumorspheres and clonogenic growth, which correlated with decreased Nanog and OCT4 expression. In non tumoral cells, RAC3 overexpression induced tumoral transformation; mesenchymal phenotype and stem markers expression. Moreover, these transformed cells generated tumors in vivo. Our results demonstrate that RAC3 is required for maintaining and induction of cancer cell stemness.
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Affiliation(s)
- Laura C Panelo
- Laboratorio de Biología Moleculary Apoptosis, Instituto de Investigaciones Médicas Alfredo Lanari, IDIM-CONICET, Facultad de Medicina, Universidad de Buenos Aires, C1427ARO Buenos Aires, Argentina
| | - Mileni Soares Machado
- Laboratorio de Biología Moleculary Apoptosis, Instituto de Investigaciones Médicas Alfredo Lanari, IDIM-CONICET, Facultad de Medicina, Universidad de Buenos Aires, C1427ARO Buenos Aires, Argentina
| | - María F Rubio
- Laboratorio de Biología Moleculary Apoptosis, Instituto de Investigaciones Médicas Alfredo Lanari, IDIM-CONICET, Facultad de Medicina, Universidad de Buenos Aires, C1427ARO Buenos Aires, Argentina.,Laboratorio de Inflamación y Cancer, IQUIBICEN-CONICET, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, C1428EGA Buenos Aires, Argentina.,Argentine National Research Council (CONICET), C1425FQB Godoy Cruz (CABA), República Argentina
| | - Felipe Jaworski
- Laboratorio de Inflamación y Cancer, IQUIBICEN-CONICET, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, C1428EGA Buenos Aires, Argentina
| | - Cecilia V Alvarado
- Laboratorio de Biología Moleculary Apoptosis, Instituto de Investigaciones Médicas Alfredo Lanari, IDIM-CONICET, Facultad de Medicina, Universidad de Buenos Aires, C1427ARO Buenos Aires, Argentina
| | - Leonardo A Paz
- Laboratorio de Anatomía Patológica, Instituto de Investigaciones Médicas Alfredo Lanari, Facultad de Medicina, Universidad de Buenos Aires, C1427ARO Buenos Aires, Argentina
| | - Alejandro J Urtreger
- Laboratorio de Anatomía Patológica, Instituto de Investigaciones Médicas Alfredo Lanari, Facultad de Medicina, Universidad de Buenos Aires, C1427ARO Buenos Aires, Argentina.,Universidad de Buenos Aires, Instituto de Oncología "Angel H Roffo", Area de Investigación, C1417DTB Buenos Aires, Argentina.,Argentine National Research Council (CONICET), C1425FQB Godoy Cruz (CABA), República Argentina
| | - Elba Vazquez
- Laboratorio de Inflamación y Cancer, IQUIBICEN-CONICET, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, C1428EGA Buenos Aires, Argentina.,Argentine National Research Council (CONICET), C1425FQB Godoy Cruz (CABA), República Argentina
| | - Mónica A Costas
- Laboratorio de Biología Moleculary Apoptosis, Instituto de Investigaciones Médicas Alfredo Lanari, IDIM-CONICET, Facultad de Medicina, Universidad de Buenos Aires, C1427ARO Buenos Aires, Argentina.,Argentine National Research Council (CONICET), C1425FQB Godoy Cruz (CABA), República Argentina
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30
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miR-25/93 mediates hypoxia-induced immunosuppression by repressing cGAS. Nat Cell Biol 2017; 19:1286-1296. [PMID: 28920955 PMCID: PMC5658024 DOI: 10.1038/ncb3615] [Citation(s) in RCA: 90] [Impact Index Per Article: 12.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2017] [Accepted: 08/17/2017] [Indexed: 02/07/2023]
Abstract
The mechanisms by which hypoxic tumors evade immunological pressure and anti-tumor immunity remain elusive. Here, we report that two hypoxia-responsive microRNAs, miR25 and miR93, are important for establishing an immunosuppressive tumor microenvironment by down-regulating expression of the DNA-sensor cGAS. Mechanistically, miR25/93 targets NCOA3, an epigenetic factor that maintains basal levels of cGAS expression, leading to repression of cGAS upon hypoxia. This allows hypoxic tumor cells to escape immunological responses induced by damage-associated molecular pattern molecules (DAMPs), specifically the release of mtDNA. Moreover, restoring cGAS expression results in an anti-tumor immune response. Clinically, decreased levels of cGAS are associated with poor prognosis for patients with breast cancer harboring high levels of miR25/93. Together, these data suggest that inactivation of the cGAS pathway plays a critical role in tumor progression, and reveals a direct link between hypoxia-responsive miRNAs and adaptive immune responses to the hypoxic tumor microenvironment, thus unveiling potential new therapeutic strategies.
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31
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Festuccia N, Owens N, Navarro P. Esrrb, an estrogen-related receptor involved in early development, pluripotency, and reprogramming. FEBS Lett 2017; 592:852-877. [DOI: 10.1002/1873-3468.12826] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2017] [Revised: 08/11/2017] [Accepted: 08/19/2017] [Indexed: 12/12/2022]
Affiliation(s)
- Nicola Festuccia
- Epigenetics of Stem Cells; Department of Developmental and Stem Cell Biology; Institut Pasteur; CNRS UMR3738; Paris France
| | - Nick Owens
- Epigenetics of Stem Cells; Department of Developmental and Stem Cell Biology; Institut Pasteur; CNRS UMR3738; Paris France
| | - Pablo Navarro
- Epigenetics of Stem Cells; Department of Developmental and Stem Cell Biology; Institut Pasteur; CNRS UMR3738; Paris France
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32
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Yang F, Ren Y, Li H, Wang H. ESRRB plays a crucial role in the promotion of porcine cell reprograming. J Cell Physiol 2017. [PMID: 28636277 DOI: 10.1002/jcp.26063] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
The estrogen-related receptor b (ESRRB) is an orphan nuclear receptor and targets many genes involved in self-renewal and pluripotency. In mouse ES cells, overexpression of ESRRB can maintain LIF-independent self-renewal in the absence of Nanog. However, the fundamental features of porcine ESRRB remain elusive. In this study, we revealed the expression profiles of ESRRB in both porcine pluripotent stem cells and early stage embryos and dissected the functional domains of ESRRB protein to prove that ESRRB is a key transcription factor that enhanced porcine pluripotent gene activation. Addition of ESRRB into the cocktail of core pluripotent factors Oct4, Sox2, Klf4, and c-Myc (OSKM + E) could significantly enhance the reprograming efficiency and the formation of alkaline phosphatase positive colonies. Conversely, knockdown of ESRRB in piPSCs significantly reduced the expression level of pluripotent genes, minimized the alkaline phosphatase activity, and initiated the porcine induced pluripotent stem cell differentiation. Therefore, porcine ESRRB is a crucial transcription factor to improve the self-renewal of piPSCs.
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Affiliation(s)
- Fan Yang
- Department of Animal Biotechnology, College of Veterinary Medicine, Northwest A&F University, Yangling, Shaanxi, China
| | - Yahui Ren
- Department of Animal Biotechnology, College of Veterinary Medicine, Northwest A&F University, Yangling, Shaanxi, China
| | - Huan Li
- Department of Animal Biotechnology, College of Veterinary Medicine, Northwest A&F University, Yangling, Shaanxi, China
| | - Huayan Wang
- Department of Animal Biotechnology, College of Veterinary Medicine, Northwest A&F University, Yangling, Shaanxi, China
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33
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Rohira AD, Yan F, Wang L, Wang J, Zhou S, Lu A, Yu Y, Xu J, Lonard DM, O'Malley BW. Targeting SRC Coactivators Blocks the Tumor-Initiating Capacity of Cancer Stem-like Cells. Cancer Res 2017; 77:4293-4304. [PMID: 28611048 DOI: 10.1158/0008-5472.can-16-2982] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2016] [Revised: 04/20/2017] [Accepted: 06/08/2017] [Indexed: 01/06/2023]
Abstract
Tumor-initiating cells (TIC) represent cancer stem-like cell (CSC) subpopulations within tumors that are thought to give rise to recurrent cancer after therapy. Identifying key regulators of TIC/CSC maintenance is essential for the development of therapeutics designed to limit recurrence. The steroid receptor coactivator 3 (SRC-3) is overexpressed in a wide range of cancers, driving tumor initiation, cell proliferation, and metastasis. Here we report that SRC-3 supports the TIC/CSC state and induces an epithelial-to-mesenchymal transition (EMT) by driving expression of the master EMT regulators and stem cell markers. We also show that inhibition of SRC-3 and SRC-1 with SI-2, a second-generation SRC-3/SRC-1 small-molecule inhibitor, targets the CSC/TIC population both in vitro and in vivo Collectively, these results identify SRC coactivators as regulators of stem-like capacity in cancer cells and that these coactivators can serve as potential therapeutic targets to prevent the recurrence of cancer. Cancer Res; 77(16); 4293-304. ©2017 AACR.
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Affiliation(s)
- Aarti D Rohira
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, Texas
| | - Fei Yan
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, Texas
| | - Lei Wang
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, Texas
| | - Jin Wang
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, Texas.,Department of Pharmacology, Baylor College of Medicine, Houston, Texas.,Center for Drug Discovery, Baylor College of Medicine, Houston, Texas
| | - Suoling Zhou
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, Texas
| | - Andrew Lu
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, Texas
| | - Yang Yu
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, Texas
| | - Jianming Xu
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, Texas
| | - David M Lonard
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, Texas
| | - Bert W O'Malley
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, Texas.
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Frieda KL, Linton JM, Hormoz S, Choi J, Chow KHK, Singer ZS, Budde MW, Elowitz MB, Cai L. Synthetic recording and in situ readout of lineage information in single cells. Nature 2017; 541:107-111. [PMID: 27869821 PMCID: PMC6487260 DOI: 10.1038/nature20777] [Citation(s) in RCA: 263] [Impact Index Per Article: 37.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2016] [Accepted: 11/11/2016] [Indexed: 12/13/2022]
Abstract
Reconstructing the lineage relationships and dynamic event histories of individual cells within their native spatial context is a long-standing challenge in biology. Many biological processes of interest occur in optically opaque or physically inaccessible contexts, necessitating approaches other than direct imaging. Here we describe a synthetic system that enables cells to record lineage information and event histories in the genome in a format that can be subsequently read out of single cells in situ. This system, termed memory by engineered mutagenesis with optical in situ readout (MEMOIR), is based on a set of barcoded recording elements termed scratchpads. The state of a given scratchpad can be irreversibly altered by CRISPR/Cas9-based targeted mutagenesis, and later read out in single cells through multiplexed single-molecule RNA fluorescence hybridization (smFISH). Using MEMOIR as a proof of principle, we engineered mouse embryonic stem cells to contain multiple scratchpads and other recording components. In these cells, scratchpads were altered in a progressive and stochastic fashion as the cells proliferated. Analysis of the final states of scratchpads in single cells in situ enabled reconstruction of lineage information from cell colonies. Combining analysis of endogenous gene expression with lineage reconstruction in the same cells further allowed inference of the dynamic rates at which embryonic stem cells switch between two gene expression states. Finally, using simulations, we show how parallel MEMOIR systems operating in the same cell could enable recording and readout of dynamic cellular event histories. MEMOIR thus provides a versatile platform for information recording and in situ, single-cell readout across diverse biological systems.
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Affiliation(s)
- Kirsten L Frieda
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, California 91125, USA
| | - James M Linton
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, California 91125, USA
| | - Sahand Hormoz
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, California 91125, USA
| | - Joonhyuk Choi
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California 91125, USA
| | - Ke-Huan K Chow
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, California 91125, USA
| | - Zakary S Singer
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, California 91125, USA
| | - Mark W Budde
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, California 91125, USA
| | - Michael B Elowitz
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, California 91125, USA
- Howard Hughes Medical Institute, California Institute of Technology, Pasadena, California 91125, USA
| | - Long Cai
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California 91125, USA
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35
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Kim T, Hwang D, Lee D, Kim JH, Kim SY, Lim DS. MRTF potentiates TEAD-YAP transcriptional activity causing metastasis. EMBO J 2016; 36:520-535. [PMID: 28028053 DOI: 10.15252/embj.201695137] [Citation(s) in RCA: 77] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2016] [Revised: 11/25/2016] [Accepted: 11/28/2016] [Indexed: 12/12/2022] Open
Abstract
Yes-associated protein (YAP) and myocardin-related transcription factor (MRTF) play similar roles and exhibit significant crosstalk in directing transcriptional responses to chemical and physical extracellular cues. The mechanism underlying this crosstalk, however, remains unclear. Here, we show MRTF family proteins bind YAP via a conserved PPXY motif that interacts with the YAP WW domain. This interaction allows MRTF to recruit NcoA3 to the TEAD-YAP transcriptional complex and potentiate its transcriptional activity. We show this interaction of MRTF and YAP is critical for LPA-induced cancer cell invasion in vitro and breast cancer metastasis to the lung in vivo We also demonstrate the significance of MRTF-YAP binding in regulation of YAP activity upon acute actin cytoskeletal damage. Acute actin disruption induces nucleo-cytoplasmic shuttling of MRTF, and this process underlies the LATS-independent regulation of YAP activity. Our results provide clear evidence of crosstalk between MRTF and YAP independent of the LATS kinases that normally act upstream of YAP signaling. Our results also suggest a mechanism by which extracellular stimuli can coordinate physiological events downstream of YAP.
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Affiliation(s)
- Tackhoon Kim
- National Creative Research Initiatives Center for Cell Division and Differentiation, Department of Biological Sciences, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, Korea
| | - Daehee Hwang
- National Creative Research Initiatives Center for Cell Division and Differentiation, Department of Biological Sciences, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, Korea
| | - Dahye Lee
- National Creative Research Initiatives Center for Cell Division and Differentiation, Department of Biological Sciences, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, Korea
| | - Jeong-Hwan Kim
- Medical Genomics Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, Korea
| | - Seon-Young Kim
- Medical Genomics Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, Korea
| | - Dae-Sik Lim
- National Creative Research Initiatives Center for Cell Division and Differentiation, Department of Biological Sciences, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, Korea
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36
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Zhang L, Wong J, Vanacker JM. The estrogen-related receptors (ERRs): potential targets against bone loss. Cell Mol Life Sci 2016; 73:3781-7. [PMID: 27514376 PMCID: PMC11108346 DOI: 10.1007/s00018-016-2328-5] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2016] [Accepted: 08/04/2016] [Indexed: 01/20/2023]
Abstract
Bone loss and the resulting skeletal fragility is induced by several pathological or natural conditions, the most prominent of which being aging as well as the decreased levels of circulating estrogens in post-menopause females. To date, most treatments against bone loss aim at preventing excess bone resorption. We here summarize data indicating that the estrogen-related receptors (ERRs) α and γ prevent bone formation. Inhibiting these receptors may thus constitute an anabolic approach by increasing bone formation.
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Affiliation(s)
- Ling Zhang
- Institut de Génomique Fonctionnelle de Lyon, CNRS UMR5242, Université de Lyon, Université Lyon I, Ecole Normale Supérieure de Lyon, Lyon, France
- Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences, School of Life Sciences, East China Normal University, Shanghai, 200241, China
| | - Jiemin Wong
- Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences, School of Life Sciences, East China Normal University, Shanghai, 200241, China
| | - Jean-Marc Vanacker
- Institut de Génomique Fonctionnelle de Lyon, CNRS UMR5242, Université de Lyon, Université Lyon I, Ecole Normale Supérieure de Lyon, Lyon, France.
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37
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Uranishi K, Akagi T, Koide H, Yokota T. Esrrb directly binds to Gata6 promoter and regulates its expression with Dax1 and Ncoa3. Biochem Biophys Res Commun 2016; 478:1720-5. [PMID: 27601327 DOI: 10.1016/j.bbrc.2016.09.011] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2016] [Accepted: 09/02/2016] [Indexed: 11/27/2022]
Abstract
Estrogen-related receptor beta (Esrrb) is expressed in embryonic stem (ES) cells and is involved in self-renewal ability and pluripotency. Previously, we found that Dax1 is associated with Esrrb and represses its transcriptional activity. Further, the disruption of the Dax1-Esrrb interaction increases the expression of the extra-embryonic endoderm marker Gata6 in ES cells. Here, we investigated the influences of Esrrb and Dax1 on Gata6 expression. Esrrb overexpression in ES cells induced endogenous Gata6 mRNA and Gata6 promoter activity. In addition, the Gata6 promoter was found to contain the Esrrb recognition motifs ERRE1 and ERRE2, and the latter was the responsive element of Esrrb. Associations between ERRE2 and Esrrb were then confirmed by biotin DNA pulldown and chromatin immunoprecipitation assays. Subsequently, we showed that Esrrb activity at the Gata6 promoter was repressed by Dax1, and although Dax1 did not bind to ERRE2, it was associated with Esrrb, which directly binds to ERRE2. In addition, the transcriptional activity of Esrrb was enhanced by nuclear receptor co-activator 3 (Ncoa3), which has recently been shown to be a binding partner of Esrrb. Finally, we showed that Dax1 was associated with Ncoa3 and repressed its transcriptional activity. Taken together, the present study indicates that the Gata6 promoter is activated by Esrrb in association with Ncoa3, and Dax1 inhibited activities of Esrrb and Ncoa3, resulting maintenance of the undifferentiated status of ES cells.
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Affiliation(s)
- Kousuke Uranishi
- Department of Stem Cell Biology, Faculty of Medicine, Institute of Medical, Pharmaceutical and Health Sciences, Kanazawa University, Japan
| | - Tadayuki Akagi
- Department of Stem Cell Biology, Faculty of Medicine, Institute of Medical, Pharmaceutical and Health Sciences, Kanazawa University, Japan.
| | - Hiroshi Koide
- Department of Stem Cell Biology, Faculty of Medicine, Institute of Medical, Pharmaceutical and Health Sciences, Kanazawa University, Japan
| | - Takashi Yokota
- Department of Stem Cell Biology, Faculty of Medicine, Institute of Medical, Pharmaceutical and Health Sciences, Kanazawa University, Japan.
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38
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Divekar SD, Tiek DM, Fernandez A, Riggins RB. Estrogen-related receptor β (ERRβ) - renaissance receptor or receptor renaissance? NUCLEAR RECEPTOR SIGNALING 2016; 14:e002. [PMID: 27507929 PMCID: PMC4978380 DOI: 10.1621/nrs.14002] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/05/2015] [Accepted: 03/25/2016] [Indexed: 01/11/2023]
Abstract
Estrogen-related receptors (ERRs) are founding members of the orphan nuclear receptor (ONR) subgroup of the nuclear receptor superfamily. Twenty-seven years of study have yet to identify cognate ligands for the ERRs, though they have firmly placed ERRα and ERRγ at the intersection of cellular metabolism and oncogenesis. The pace of discovery for novel functions of ERRβ, however, has until recently been somewhat slower than that of its family members. ERRβ has also been largely ignored in summaries and perspectives of the ONR literature. Here, we provide an overview of established and emerging knowledge of ERRβ in mouse, man, and other species, highlighting unique aspects of ERRβ biology that set it apart from the other two estrogen-related receptors, with a focus on the impact of alternative splicing on the structure and function of this receptor.
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Affiliation(s)
- Shailaja D Divekar
- Department of Oncology, Lombardi Comprehensive Cancer Center, Georgetown University Medical Center, Washington, DC (SDD, DMT, AF, RBR)
| | - Deanna M Tiek
- Department of Oncology, Lombardi Comprehensive Cancer Center, Georgetown University Medical Center, Washington, DC (SDD, DMT, AF, RBR)
| | - Aileen Fernandez
- Department of Oncology, Lombardi Comprehensive Cancer Center, Georgetown University Medical Center, Washington, DC (SDD, DMT, AF, RBR)
| | - Rebecca B Riggins
- Department of Oncology, Lombardi Comprehensive Cancer Center, Georgetown University Medical Center, Washington, DC (SDD, DMT, AF, RBR)
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39
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Yang F, Du X, Wang Y, Wang C, Huang C, Xiao Q, Bai X, Wang H. Characterization and functional analysis of porcine estrogen-related receptors and their alternative splicing variants. J Anim Sci 2016; 93:4258-66. [PMID: 26440325 DOI: 10.2527/jas.2015-9188] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
Abstract
Estrogen-related receptors (ESRR) are orphan nuclear hormone receptors with unidentified ligands; they play important roles in tissue regulation and development and maintenance of pluripotent cell identity. The splicer variant, genomic organization, and physiological roles of ESRR have been elucidated in the human and the mouse. However, in livestock, they remain elusive. In this study, we cloned porcine ESRR family members , , and . Two alternative splicing variants, and , and a novel were identified. To determine the domain function, we constructed vectors with sequential deletions of the ESRRB coding sequence. The functional analysis showed that the C domain of ESRR plays a core role in promoting the activation of estrogen response elements that are found in all kinds of ESRR-targeting genes, whereas the E domain is not essential for transcription regulation of ESRR unless a specific and identified ligand is applied.
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40
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Kumar V, Rayan NA, Muratani M, Lim S, Elanggovan B, Xin L, Lu T, Makhija H, Poschmann J, Lufkin T, Ng HH, Prabhakar S. Comprehensive benchmarking reveals H2BK20 acetylation as a distinctive signature of cell-state-specific enhancers and promoters. Genome Res 2016; 26:612-23. [PMID: 26957309 PMCID: PMC4864461 DOI: 10.1101/gr.201038.115] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2015] [Accepted: 03/07/2016] [Indexed: 12/12/2022]
Abstract
Although over 35 different histone acetylation marks have been described, the overwhelming majority of regulatory genomics studies focus exclusively on H3K27ac and H3K9ac. In order to identify novel epigenomic traits of regulatory elements, we constructed a benchmark set of validated enhancers by performing 140 enhancer assays in human T cells. We tested 40 chromatin signatures on this unbiased enhancer set and identified H2BK20ac, a little-studied histone modification, as the most predictive mark of active enhancers. Notably, we detected a novel class of functionally distinct enhancers enriched in H2BK20ac but lacking H3K27ac, which was present in all examined cell lines and also in embryonic forebrain tissue. H2BK20ac was also unique in highlighting cell-type-specific promoters. In contrast, other acetylation marks were present in all active promoters, regardless of cell-type specificity. In stimulated microglial cells, H2BK20ac was more correlated with cell-state-specific expression changes than H3K27ac, with TGF-beta signaling decoupling the two acetylation marks at a subset of regulatory elements. In summary, our study reveals a previously unknown connection between histone acetylation and cell-type-specific gene regulation and indicates that H2BK20ac profiling can be used to uncover new dimensions of gene regulation.
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Affiliation(s)
- Vibhor Kumar
- Computational and Systems Biology, Genome Institute of Singapore, Singapore 138672, Singapore
| | - Nirmala Arul Rayan
- Computational and Systems Biology, Genome Institute of Singapore, Singapore 138672, Singapore
| | - Masafumi Muratani
- Department of Genome Biology, Faculty of Medicine, University of Tsukuba, Ibaraki, 305-8575, Japan; Stem Cell and Developmental Biology, Genome Institute of Singapore, Singapore 138672, Singapore
| | - Stefan Lim
- Computational and Systems Biology, Genome Institute of Singapore, Singapore 138672, Singapore
| | - Bavani Elanggovan
- Computational and Systems Biology, Genome Institute of Singapore, Singapore 138672, Singapore
| | - Lixia Xin
- Computational and Systems Biology, Genome Institute of Singapore, Singapore 138672, Singapore
| | - Tess Lu
- Computational and Systems Biology, Genome Institute of Singapore, Singapore 138672, Singapore
| | - Harshyaa Makhija
- Computational and Systems Biology, Genome Institute of Singapore, Singapore 138672, Singapore
| | - Jeremie Poschmann
- Computational and Systems Biology, Genome Institute of Singapore, Singapore 138672, Singapore
| | - Thomas Lufkin
- Stem Cell and Developmental Biology, Genome Institute of Singapore, Singapore 138672, Singapore; Department of Biology, Clarkson University, Potsdam, New York 13699, USA
| | - Huck Hui Ng
- Stem Cell and Developmental Biology, Genome Institute of Singapore, Singapore 138672, Singapore; Department of Biological Sciences, National University of Singapore, Singapore 117543, Singapore
| | - Shyam Prabhakar
- Computational and Systems Biology, Genome Institute of Singapore, Singapore 138672, Singapore
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41
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Mantsoki A, Devailly G, Joshi A. Gene expression variability in mammalian embryonic stem cells using single cell RNA-seq data. Comput Biol Chem 2016; 63:52-61. [PMID: 26951854 PMCID: PMC5012374 DOI: 10.1016/j.compbiolchem.2016.02.004] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2016] [Accepted: 02/01/2016] [Indexed: 01/05/2023]
Abstract
BACKGROUND Gene expression heterogeneity contributes to development as well as disease progression. Due to technological limitations, most studies to date have focused on differences in mean expression across experimental conditions, rather than differences in gene expression variance. The advent of single cell RNA sequencing has now made it feasible to study gene expression heterogeneity and to characterise genes based on their coefficient of variation. METHODS We collected single cell gene expression profiles for 32 human and 39 mouse embryonic stem cells and studied correlation between diverse characteristics such as network connectivity and coefficient of variation (CV) across single cells. We further systematically characterised properties unique to High CV genes. RESULTS Highly expressed genes tended to have a low CV and were enriched for cell cycle genes. In contrast, High CV genes were co-expressed with other High CV genes, were enriched for bivalent (H3K4me3 and H3K27me3) marked promoters and showed enrichment for response to DNA damage and DNA repair. CONCLUSIONS Taken together, this analysis demonstrates the divergent characteristics of genes based on their CV. High CV genes tend to form co-expression clusters and they explain bivalency at least in part.
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Affiliation(s)
- Anna Mantsoki
- The Roslin institute, University of Edinburgh, Easter bush campus, Midlothian EH25 9RG, UK.
| | - Guillaume Devailly
- The Roslin institute, University of Edinburgh, Easter bush campus, Midlothian EH25 9RG, UK.
| | - Anagha Joshi
- The Roslin institute, University of Edinburgh, Easter bush campus, Midlothian EH25 9RG, UK.
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42
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Fang L, Zhang J, Zhang H, Yang X, Jin X, Zhang L, Skalnik DG, Jin Y, Zhang Y, Huang X, Li J, Wong J. H3K4 Methyltransferase Set1a Is A Key Oct4 Coactivator Essential for Generation of Oct4 Positive Inner Cell Mass. Stem Cells 2016; 34:565-80. [PMID: 26785054 DOI: 10.1002/stem.2250] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2015] [Accepted: 10/01/2015] [Indexed: 11/09/2022]
Abstract
Limited core transcription factors and transcriptional cofactors have been shown to govern embryonic stem cell (ESC) transcriptional circuitry and pluripotency, but the molecular interactions between the core transcription factors and cofactors remains ill defined. Here, we analyzed the protein-protein interactions between Oct4, Sox2, Klf4, and Myc (abbreviated as OSKM) and a large panel of cofactors. The data reveal both specific and common interactions between OSKM and cofactors. We found that among the SET1/MLL family H3K4 methyltransferases, Set1a specifically interacts with Oct4 and this interaction is independent of Wdr5. Set1a is recruited to and required for H3K4 methylation at the Oct4 target gene promoters and transcriptional activation of Oct4 target genes in ESCs, and consistently Set1a is required for ESC maintenance and induced pluripotent stem cell generation. Gene expression profiling and chromatin immunoprecipitation-seq analyses demonstrate the broad involvement of Set1a in Oct4 transcription circuitry and strong enrichment at TSS sites. Gene knockout study demonstrates that Set1a is not only required for mouse early embryonic development but also for the generation of Oct4-positive inner cell mass. Together our study provides valuable information on the molecular interactions between OSKM and cofactors and molecular mechanisms for the functional importance of Set1a in ESCs and early development.
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Affiliation(s)
- Lan Fang
- Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai, China
| | - Jun Zhang
- MOE Key Laboratory of Model Animals for Disease Study, Model Animal Research Center of Nanjing University and National Resource Center for Mutant Mice, Nanjing, China.,School of Life Science and Technology, ShanghaiTech University, Shanghai, China
| | - Hui Zhang
- Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai, China
| | - Xiaoqin Yang
- Shanghai Key Laboratory of Signaling and Disease Research, School of Life Science and Technology, Tongji University, Shanghai, China
| | - Xueling Jin
- Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai, China
| | - Ling Zhang
- Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai, China
| | - David G Skalnik
- Biology Department, School of Science, Indiana University-Purdue University Indianapolis, Indianapolis, Indiana, USA
| | - Ying Jin
- Department of Molecular Development, Shanghai JiaoTong University School of Medicine, Shanghai, China
| | - Yong Zhang
- Shanghai Key Laboratory of Signaling and Disease Research, School of Life Science and Technology, Tongji University, Shanghai, China
| | - Xingxu Huang
- MOE Key Laboratory of Model Animals for Disease Study, Model Animal Research Center of Nanjing University and National Resource Center for Mutant Mice, Nanjing, China.,School of Life Science and Technology, ShanghaiTech University, Shanghai, China
| | - Jiwen Li
- Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai, China
| | - Jiemin Wong
- Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai, China.,Collaborative Innovation Center for Cancer Medicine, Sun Yat-Sen University Cancer Center, Guangzhou, China
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43
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Lu Y, Li J, Cheng J, Lubahn DB. Messenger RNA profile analysis deciphers new Esrrb responsive genes in prostate cancer cells. BMC Mol Biol 2015; 16:21. [PMID: 26627478 PMCID: PMC4667504 DOI: 10.1186/s12867-015-0049-1] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2015] [Accepted: 11/13/2015] [Indexed: 11/25/2022] Open
Abstract
Background Orphan nuclear receptor estrogen related receptor β (Esrrb or ERRβ) is well known in stem cells and early embryonic development. However, little is known about its function in cancer. Method We investigated the mRNA profile alterations induced by Esrrb expression and its synthetic ligand DY131 in human prostate cancer DU145 cells via RNA-Seq analysis. Results We distinguished 67 mRNAs differentially expressed by Esrrb alone. Although DY131 alone did not change any gene, treatment of DY131 in the presence of Esrrb altered 1161 mRNAs. These observations indicated Esrrb had both ligand-independent and ligand-dependent activity. When Esrrb was expressed, DY131 treatment further regulated 15 Esrrb-altered mRNAs. DY131 acted as an antagonist for 11 of 15 mRNAs (wdr52, f13a1, pxdn, spns2, loc100506599, tagln, loc441454, tkel1, sema3f, zcwpw2, sdc2) and as an agonist for 4 of the 15 mRNAs (rarres3, oasl, padi2, ddx60). Gene ontology analyses showed altered genes are related to transcription and translation regulation, cell proliferation and apoptosis regulation, and cellular metabolism. Conclusion Our results characterized mRNA profiles in DU145 prostate cancer cells driven by Esrrb expression and Esrrb ligand DY131, and provided multiple markers to characterize Esrrb’s function in Esrrb research. Electronic supplementary material The online version of this article (doi:10.1186/s12867-015-0049-1) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Yuan Lu
- Department of Biochemistry, University of Missouri, Columbia, MO, 65211, USA. .,MU Center for Botanical Interaction Studies, University of Missouri, Columbia, MO, 65211, USA. .,Xiphophorus Genetic Stock Center, Texas State University, San Marcos, TX, 78666, USA.
| | - Jilong Li
- MU Center for Botanical Interaction Studies, University of Missouri, Columbia, MO, 65211, USA. .,Computer Science Department, University of Missouri, Columbia, MO, 65211, USA. .,Informatics Institute, University of Missouri, Columbia, MO, 65211, USA.
| | - Jianlin Cheng
- MU Center for Botanical Interaction Studies, University of Missouri, Columbia, MO, 65211, USA. .,Computer Science Department, University of Missouri, Columbia, MO, 65211, USA. .,Informatics Institute, University of Missouri, Columbia, MO, 65211, USA.
| | - Dennis B Lubahn
- Department of Biochemistry, University of Missouri, Columbia, MO, 65211, USA. .,MU Center for Botanical Interaction Studies, University of Missouri, Columbia, MO, 65211, USA.
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44
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Rraklli V, Södersten E, Nyman U, Hagey DW, Holmberg J. Elevated levels of ZAC1 disrupt neurogenesis and promote rapid in vivo reprogramming. Stem Cell Res 2015; 16:1-9. [PMID: 26610203 DOI: 10.1016/j.scr.2015.11.002] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/26/2015] [Revised: 10/27/2015] [Accepted: 11/09/2015] [Indexed: 01/26/2023] Open
Abstract
The zinc finger transcription factor Zac1 is expressed in dividing progenitors of the nervous system with expression levels negatively controlled by genomic imprinting. To explore the consequences of elevated ZAC1 levels during neurogenesis we overexpressed it in the developing CNS. Increased levels of ZAC1 rapidly promoted upregulation of CDK inhibitors P57 and P27 followed by cell cycle exit. Surprisingly this was accompanied by stalled neuronal differentiation. Genome wide expression analysis of cortical cells overexpressing Zac1 revealed a decrease in neuronal gene expression and an increased expression of imprinted genes, factors regulating mesoderm formation as well as features of differentiated muscle. In addition, we observed a rapid induction of several genes regulating pluripotency. Taken together, our data suggests that expression levels of Zac1 need to be kept under strict control to avoid premature cell cycle exit, disrupted neurogenesis and aberrant expression of non-neuronal genes including pluripotency associated factors.
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Affiliation(s)
- Vilma Rraklli
- Department of Cell and Molecular Biology, Ludwig Institute for Cancer Research, Karolinska Institutet, Nobels väg 3, 171 77, Stockholm, Sweden
| | - Erik Södersten
- Department of Cell and Molecular Biology, Ludwig Institute for Cancer Research, Karolinska Institutet, Nobels väg 3, 171 77, Stockholm, Sweden
| | - Ulrika Nyman
- Department of Cell and Molecular Biology, Ludwig Institute for Cancer Research, Karolinska Institutet, Nobels väg 3, 171 77, Stockholm, Sweden
| | - Daniel W Hagey
- Department of Cell and Molecular Biology, Ludwig Institute for Cancer Research, Karolinska Institutet, Nobels väg 3, 171 77, Stockholm, Sweden
| | - Johan Holmberg
- Department of Cell and Molecular Biology, Ludwig Institute for Cancer Research, Karolinska Institutet, Nobels väg 3, 171 77, Stockholm, Sweden.
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45
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Fernández Larrosa PN, Ruíz Grecco M, Mengual Gómez D, Alvarado CV, Panelo LC, Rubio MF, Alonso DF, Gómez DE, Costas MA. RAC3 more than a nuclear receptor coactivator: a key inhibitor of senescence that is downregulated in aging. Cell Death Dis 2015; 6:e1902. [PMID: 26469953 PMCID: PMC4632280 DOI: 10.1038/cddis.2015.218] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2014] [Revised: 06/24/2015] [Accepted: 07/01/2015] [Indexed: 11/10/2022]
Abstract
Receptor-associated coactivator 3 (RAC3) is a nuclear receptor coactivator usually overexpressed in tumors that exerts oncogenic functions in the cytoplasm and the nucleus. Although as part of its oncogenic actions it was previously identified as an inhibitor of apoptosis and autophagy, its expression is required in order to preserve the pluripotency and embryonic stem cell self-renewal. In this work we investigated its role in cellular senescence. We found that RAC3 overexpression in the nontumoral HEK293 cells inhibits the premature senescence induced by hydrogen peroxide or rapamycin. The mechanism involves not only the inhibition of autophagy early induced by these stimuli in the pathway to senescence, but also the increase in levels and nuclear localization of both the cell cycle suppressors p53/p21 and the longevity promoters FOXO1A, FOXO3A and SIRT1. Furthermore, we found that RAC3 overexpression is required in order to maintain the telomerase activity. In tumoral HeLa cells its activity was inhibited by depletion of RAC3 inducing replicative senescence. Moreover, we demonstrated that in vivo, levels of RAC3 are downregulated in the liver from aged as compared with young rats, whereas the levels of p21 are increased, correlating with the expected senescent cell contents in aged tissues. A similar downregulation of RAC3 was observed in the premature and replicative senescence of human fetal WI-38 cells and premature senescence of hepatocyte HepG2 cell line. Taken together, all these results demonstrate that RAC3 is an inhibitor of senescence whose downregulation in aged individuals could be probably a tumor suppressor mechanism, avoiding the clonal expansion of risky old cells having damaged DNA.
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Affiliation(s)
- P N Fernández Larrosa
- Laboratorio de Biología Molecular y Apoptosis, Instituto de Investigaciones Médicas Alfredo Lanari, IDIM-CONICET, Facultad de Medicina, Universidad de Buenos Aires, Combatientes de Malvinas 3150, Buenos Aires C1427ARO, Argentina
| | - M Ruíz Grecco
- Laboratorio de Biología Molecular y Apoptosis, Instituto de Investigaciones Médicas Alfredo Lanari, IDIM-CONICET, Facultad de Medicina, Universidad de Buenos Aires, Combatientes de Malvinas 3150, Buenos Aires C1427ARO, Argentina
| | - D Mengual Gómez
- Laboratorio de Oncología Molecular, Universidad Nacional de Quilmes, R. Sáenz Peña 352, Bernal, Buenos Aires B1876BXD Argentina
| | - C V Alvarado
- Laboratorio de Biología Molecular y Apoptosis, Instituto de Investigaciones Médicas Alfredo Lanari, IDIM-CONICET, Facultad de Medicina, Universidad de Buenos Aires, Combatientes de Malvinas 3150, Buenos Aires C1427ARO, Argentina
| | - L C Panelo
- Laboratorio de Biología Molecular y Apoptosis, Instituto de Investigaciones Médicas Alfredo Lanari, IDIM-CONICET, Facultad de Medicina, Universidad de Buenos Aires, Combatientes de Malvinas 3150, Buenos Aires C1427ARO, Argentina
| | - M F Rubio
- Laboratorio de Biología Molecular y Apoptosis, Instituto de Investigaciones Médicas Alfredo Lanari, IDIM-CONICET, Facultad de Medicina, Universidad de Buenos Aires, Combatientes de Malvinas 3150, Buenos Aires C1427ARO, Argentina
| | - D F Alonso
- Laboratorio de Oncología Molecular, Universidad Nacional de Quilmes, R. Sáenz Peña 352, Bernal, Buenos Aires B1876BXD Argentina
| | - D E Gómez
- Laboratorio de Oncología Molecular, Universidad Nacional de Quilmes, R. Sáenz Peña 352, Bernal, Buenos Aires B1876BXD Argentina
| | - M A Costas
- Laboratorio de Biología Molecular y Apoptosis, Instituto de Investigaciones Médicas Alfredo Lanari, IDIM-CONICET, Facultad de Medicina, Universidad de Buenos Aires, Combatientes de Malvinas 3150, Buenos Aires C1427ARO, Argentina
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46
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Regulation of Nucleosome Architecture and Factor Binding Revealed by Nuclease Footprinting of the ESC Genome. Cell Rep 2015; 13:61-69. [PMID: 26411677 DOI: 10.1016/j.celrep.2015.08.071] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2015] [Revised: 08/01/2015] [Accepted: 08/25/2015] [Indexed: 12/15/2022] Open
Abstract
Functional interactions between gene regulatory factors and chromatin architecture have been difficult to directly assess. Here, we use micrococcal nuclease (MNase) footprinting to probe the functions of two chromatin-remodeling complexes. By simultaneously quantifying alterations in small MNase footprints over the binding sites of 30 regulatory factors in mouse embryonic stem cells (ESCs), we provide evidence that esBAF and Mbd3/NuRD modulate the binding of several regulatory proteins. In addition, we find that nucleosome occupancy is reduced at specific loci in favor of subnucleosomes upon depletion of esBAF, including sites of histone H2A.Z localization. Consistent with these data, we demonstrate that esBAF is required for normal H2A.Z localization in ESCs, suggesting esBAF either stabilizes H2A.Z-containing nucleosomes or promotes subnucleosome to nucleosome conversion by facilitating H2A.Z deposition. Therefore, integrative examination of MNase footprints reveals insights into nucleosome dynamics and functional interactions between chromatin structure and key gene-regulatory factors.
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Twigger AJ, Hepworth AR, Lai CT, Chetwynd E, Stuebe AM, Blancafort P, Hartmann PE, Geddes DT, Kakulas F. Gene expression in breastmilk cells is associated with maternal and infant characteristics. Sci Rep 2015; 5:12933. [PMID: 26255679 PMCID: PMC4542700 DOI: 10.1038/srep12933] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2015] [Accepted: 07/15/2015] [Indexed: 01/11/2023] Open
Abstract
Breastmilk is a rich source of cells with a heterogeneous composition comprising early-stage stem cells, progenitors and more differentiated cells. The gene expression profiles of these cells and their associations with characteristics of the breastfeeding mother and infant are poorly understood. This study investigated factors associated with the cellular dynamics of breastmilk and explored variations amongst women. Genes representing different breastmilk cell populations including mammary epithelial and myoepithelial cells, progenitors, and multi-lineage stem cells showed great variation in expression. Stem cell markers ESRRB and CK5, myoepithelial marker CK14, and lactocyte marker α-lactalbumin were amongst the genes most highly expressed across all samples tested. Genes exerting similar functions, such as either stem cell regulation or milk production, were found to be closely associated. Infant gestational age at delivery and changes in maternal bra cup size between pre-pregnancy and postpartum lactation were associated with expression of genes controlling stemness as well as milk synthesis. Additional correlations were found between genes and dyad characteristics, which may explain abnormalities related to low breastmilk supply or preterm birth. Our findings highlight the heterogeneity of breastmilk cell content and its changes associated with characteristics of the breastfeeding dyad that may reflect changing infant needs.
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Affiliation(s)
- Alecia-Jane Twigger
- School of Chemistry and Biochemistry, Faculty of Science, The University of Western Australia, 35 Stirling Highway, Crawley WA 6009, Australia
| | - Anna R Hepworth
- School of Chemistry and Biochemistry, Faculty of Science, The University of Western Australia, 35 Stirling Highway, Crawley WA 6009, Australia
| | - Ching Tat Lai
- School of Chemistry and Biochemistry, Faculty of Science, The University of Western Australia, 35 Stirling Highway, Crawley WA 6009, Australia
| | - Ellen Chetwynd
- Department of Obstetrics and Gynecology, Division of Maternal-Fetal Medicine, School of Medicine, University of North Carolina, 3010 Old Clinic Building, CB 7615, Chapel Hill, NC 27599, USA
| | - Alison M Stuebe
- Department of Obstetrics and Gynecology, Division of Maternal-Fetal Medicine, School of Medicine, University of North Carolina, 3010 Old Clinic Building, CB 7615, Chapel Hill, NC 27599, USA
| | - Pilar Blancafort
- 1] Department of Pharmacology, School of Medicine, University of North Carolina, 120 Mason Farm Road, Chapel Hill, NC 27599, USA [2] Cancer Epigenetics group, the Harry Perkins Institute of Medical Research, and School of Anatomy, Physiology and human Biology, The University of Western Australia, 35 Stirling Highway, Crawley WA 6009, Australia
| | - Peter E Hartmann
- School of Chemistry and Biochemistry, Faculty of Science, The University of Western Australia, 35 Stirling Highway, Crawley WA 6009, Australia
| | - Donna T Geddes
- School of Chemistry and Biochemistry, Faculty of Science, The University of Western Australia, 35 Stirling Highway, Crawley WA 6009, Australia
| | - Foteini Kakulas
- School of Chemistry and Biochemistry, Faculty of Science, The University of Western Australia, 35 Stirling Highway, Crawley WA 6009, Australia
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48
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Latos PA, Goncalves A, Oxley D, Mohammed H, Turro E, Hemberger M. Fgf and Esrrb integrate epigenetic and transcriptional networks that regulate self-renewal of trophoblast stem cells. Nat Commun 2015. [PMID: 26206133 DOI: 10.1038/ncomms8776] [Citation(s) in RCA: 78] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
Esrrb (oestrogen-related receptor beta) is a transcription factor implicated in embryonic stem (ES) cell self-renewal, yet its knockout causes intrauterine lethality due to defects in trophoblast development. Here we show that in trophoblast stem (TS) cells, Esrrb is a downstream target of fibroblast growth factor (Fgf) signalling and is critical to drive TS cell self-renewal. In contrast to its occupancy of pluripotency-associated loci in ES cells, Esrrb sustains the stemness of TS cells by direct binding and regulation of TS cell-specific transcription factors including Elf5 and Eomes. To elucidate the mechanisms whereby Esrrb controls the expression of its targets, we characterized its TS cell-specific interactome using mass spectrometry. Unlike in ES cells, Esrrb interacts in TS cells with the histone demethylase Lsd1 and with the RNA Polymerase II-associated Integrator complex. Our findings provide new insights into both the general and context-dependent wiring of transcription factor networks in stem cells by master transcription factors.
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Affiliation(s)
- Paulina A Latos
- 1] Epigenetics Programme, The Babraham Institute, Babraham Research Campus, Cambridge CB22 3AT, UK [2] Centre for Trophoblast Research, University of Cambridge, Downing Street, Cambridge CB2 3EG, UK
| | | | - David Oxley
- Proteomics Group, The Babraham Institute, Babraham Research Campus, Cambridge CB22 3AT, UK
| | - Hisham Mohammed
- Epigenetics Programme, The Babraham Institute, Babraham Research Campus, Cambridge CB22 3AT, UK
| | - Ernest Turro
- 1] Department of Haematology, University of Cambridge, NHS Blood and Transplant, Long Road, Cambridge CB2 0PT, UK [2] Medical Research Council Biostatistics Unit, Cambridge Institute of Public Health, Robinson Way, Forvie Site, Cambridge CB2 0SR, UK
| | - Myriam Hemberger
- 1] Epigenetics Programme, The Babraham Institute, Babraham Research Campus, Cambridge CB22 3AT, UK [2] Centre for Trophoblast Research, University of Cambridge, Downing Street, Cambridge CB2 3EG, UK
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Netrin-1 regulates somatic cell reprogramming and pluripotency maintenance. Nat Commun 2015; 6:7398. [PMID: 26154507 PMCID: PMC4510695 DOI: 10.1038/ncomms8398] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2015] [Accepted: 05/05/2015] [Indexed: 01/14/2023] Open
Abstract
The generation of induced pluripotent stem (iPS) cells holds great promise in regenerative medicine. The use of the transcription factors Oct4, Sox2, Klf4 and c-Myc for reprogramming is extensively documented, but comparatively little is known about soluble molecules promoting reprogramming. Here we identify the secreted cue Netrin-1 and its receptor DCC, described for their respective survival/death functions in normal and oncogenic contexts, as reprogramming modulators. In various somatic cells, we found that reprogramming is accompanied by a transient transcriptional repression of Netrin-1 mediated by an Mbd3/Mta1/Chd4-containing NuRD complex. Mechanistically, Netrin-1 imbalance induces apoptosis mediated by the receptor DCC in a p53-independent manner. Correction of the Netrin-1/DCC equilibrium constrains apoptosis and improves reprogramming efficiency. Our work also sheds light on Netrin-1's function in protecting embryonic stem cells from apoptosis mediated by its receptor UNC5b, and shows that the treatment with recombinant Netrin-1 improves the generation of mouse and human iPS cells. Reprogramming holds great promise for regenerative medicine but the molecular mechanisms governing the generation of induced pluripotent stem cells remain unclear. Here, the authors reveal functions for the axonal guidance cue Netrin-1 in constraining apoptosis at the early stage of reprogramming and in established pluripotent cells.
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50
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Constitutive activities of estrogen-related receptors: Transcriptional regulation of metabolism by the ERR pathways in health and disease. Biochim Biophys Acta Mol Basis Dis 2015; 1852:1912-27. [PMID: 26115970 DOI: 10.1016/j.bbadis.2015.06.016] [Citation(s) in RCA: 128] [Impact Index Per Article: 14.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2015] [Revised: 06/15/2015] [Accepted: 06/17/2015] [Indexed: 12/17/2022]
Abstract
The estrogen-related receptors (ERRs) comprise a small group of orphan nuclear receptor transcription factors. The ERRα and ERRγ isoforms play a central role in the regulation of metabolic genes and cellular energy metabolism. Although less is known about ERRβ, recent studies have revealed the importance of this isoform in the maintenance of embryonic stem cell pluripotency. Thus, ERRs are essential to many biological processes. The development of several ERR knockout and overexpression models and the application of advanced functional genomics have allowed rapid advancement of our understanding of the physiology regulated by ERR pathways. Moreover, it has enabled us to begin to delineate the distinct programs regulated by ERRα and ERRγ that have overlapping effects on metabolism and growth. The current review primarily focuses on the physiologic roles of ERR isoforms related to their metabolic regulation; therefore, the ERRα and ERRγ are discussed in the greatest detail. We emphasize findings from gain- and loss-of-function models developed to characterize ERR control of skeletal muscle, heart and musculoskeletal physiology. These models have revealed that coordinating metabolic capacity with energy demand is essential for seemingly disparate processes such as muscle differentiation and hypertrophy, innate immune function, thermogenesis, and bone remodeling. Furthermore, the models have revealed that ERRα- and ERRγ-deficiency in mice accelerates progression of pathologic processes and implicates ERRs as etiologic factors in disease. We highlight the human diseases in which ERRs and their downstream metabolic pathways are perturbed, including heart failure and diabetes. While no natural ligand has been identified for any of the ERR isoforms, the potential for using synthetic small molecules to modulate their activity has been demonstrated. Based on our current understanding of their transcriptional mechanisms and physiologic relevance, the ERRs have emerged as potential therapeutic targets for treatment of osteoporosis, muscle atrophy, insulin resistance and heart failure in humans.
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