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Řasová K, Martinková P, Vařejková M, Miznerová B, Pavlíková M, Hlinovská J, Hlinovský D, Philippová Š, Novotný M, Pospíšilová K, Biedková P, Vojíková R, Havlík J, O'Leary VB, Černá M, Bartoš A, Philipp T. COMIRESTROKE—A clinical study protocol for monitoring clinical effect and molecular biological readouts of COMprehensive Intensive REhabilitation program after STROKE: A four-arm parallel-group randomized double blinded controlled trial with a longitudinal design. Front Neurol 2022; 13:954712. [DOI: 10.3389/fneur.2022.954712] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2022] [Accepted: 10/17/2022] [Indexed: 11/05/2022] Open
Abstract
IntroductionWhile the role of physiotherapy as part of a comprehensive inpatient rehabilitation is indisputable, clear evidence concerning the effectiveness of different rehabilitation managements [interdisciplinary implementing the International Classification of Functioning, disability and health (ICF) vs. multidisciplinary model] and physiotherapy categories (neuroproprioceptive “facilitation, inhibition” vs. motor/skill acquisitions using technologies) are still lacking. In this study, four kinds of comprehensive inpatient rehabilitation with different management and content of physical therapy will be compared. Moreover, focus will be placed on the identification of novel biological molecules reflective of effective rehabilitation. Long non-coding RNAs (lncRNAs) are transcripts (>200 bps) of limited coding potential, which have recently been recognized as key factors in neuronal signaling pathways in ischemic stroke and as such, may provide a valuable readout of patient recovery and neuroprotection during therapeutic progression.Methods and analysisAdults after the first ischemic stroke in an early sub-acute phase with motor disability will be randomly assigned to one of four groups and undergo a 3 weeks comprehensive inpatient rehabilitation of different types: interdisciplinary team work using ICF model as a guide; multidisciplinary teamwork implementing neuroproprioceptive “facilitation and inhibition” physiotherapy; multidisciplinary teamwork implementing technology-based physiotherapy; and standard multidisciplinary teamwork. Primary (the Goal Attainment Scale, the Patient-Reported Outcomes Measurement Information System, and the World Health Organization Disability Assessment Schedule) and secondary (motor, cognitive, psychological, speech and swallowing functions, functional independence) outcomes will be measured. A blood sample will be obtained upon consent (20 mls; representing pre-rehabilitation molecular) before and after the inpatient program. Primary outcomes will be followed up again 3 and 12 months after the end of the program. The overarching aim of this study is to determine the effectiveness of various rehabilitation managements and physiotherapeutic categories implemented by patients post ischemic stroke via analysis of primary, secondary and long non-coding RNA readouts. This clinical trial will offer an innovative approach not previously tested and will provide new complex analysis along with public assessable molecular biological evidence of various rehabilitation methodology for the alleviation of the effects of ischemic stroke.Clinical trial registrationNCT05323916, https://clinicaltrials.gov/ct2/show/NCT05323916.
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Sun H, Zeng J, Miao Z, Lei KC, Huang C, Hu L, Su SM, Chan UI, Miao K, Zhang X, Zhang A, Guo S, Chen S, Meng Y, Deng M, Hao W, Lei H, Lin Y, Yang Z, Tang D, Wong KH, Zhang XD, Xu X, Deng CX. Dissecting the heterogeneity and tumorigenesis of BRCA1 deficient mammary tumors via single cell RNA sequencing. Am J Cancer Res 2021; 11:9967-9987. [PMID: 34815798 PMCID: PMC8581428 DOI: 10.7150/thno.63995] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2021] [Accepted: 10/08/2021] [Indexed: 12/21/2022] Open
Abstract
Background: BRCA1 plays critical roles in mammary gland development and mammary tumorigenesis. And loss of BRCA1 induces mammary tumors in a stochastic manner. These tumors present great heterogeneity at both intertumor and intratumor levels. Methods: To comprehensively elucidate the heterogeneity of BRCA1 deficient mammary tumors and the underlying mechanisms for tumor initiation and progression, we conducted bulk and single cell RNA sequencing (scRNA-seq) on both mammary gland cells and mammary tumor cells isolated from Brca1 knockout mice. Results: We found the BRCA1 deficient tumors could be classified into four subtypes with distinct molecular features and different sensitivities to anti-cancer drugs at the intertumor level. Whereas within the tumors, heterogeneous subgroups were classified mainly due to the different activities of cell proliferation, DNA damage response/repair and epithelial-to-mesenchymal transition (EMT). Besides, we reconstructed the BRCA1 related mammary tumorigenesis to uncover the transcriptomes alterations during this process via pseudo-temporal analysis of the scRNA-seq data. Furthermore, from candidate markers for BRCA1 mutant tumors, we discovered and validated one oncogene Mrc2, whose loss could reduce mammary tumor growth in vitro and in vivo. Conclusion: Our study provides a useful resource for better understanding of mammary tumorigenesis induced by BRCA1 deficiency.
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3
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A Novel cis Regulatory Element Regulates Human XIST in a CTCF-Dependent Manner. Mol Cell Biol 2021; 41:e0038220. [PMID: 34060915 DOI: 10.1128/mcb.00382-20] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
The long noncoding RNA XIST is the master regulator for the process of X chromosome inactivation (XCI) in mammalian females. Here, we report the existence of a hitherto-uncharacterized cis regulatory element (cRE) within the first exon of human XIST, which determines the transcriptional status of XIST during the initiation and maintenance phases of XCI. In the initiation phase, pluripotency factors bind to this cRE and keep XIST repressed. In the maintenance phase of XCI, the cRE is enriched for CTCF, which activates XIST transcription. By employing a CRISPR-dCas9-KRAB-based interference strategy, we demonstrate that binding of CTCF to the newly identified cRE is critical for regulating XIST in a YY1-dependent manner. Collectively, our study uncovers the combinatorial effect of multiple transcriptional regulators influencing XIST expression during the initiation and maintenance phases of XCI.
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4
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Sharp JA, Perea-Resa C, Wang W, Blower MD. Cell division requires RNA eviction from condensing chromosomes. J Cell Biol 2021; 219:211450. [PMID: 33053167 PMCID: PMC7549315 DOI: 10.1083/jcb.201910148] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2019] [Revised: 08/21/2020] [Accepted: 08/31/2020] [Indexed: 12/28/2022] Open
Abstract
During mitosis, the genome is transformed from a decondensed, transcriptionally active state to a highly condensed, transcriptionally inactive state. Mitotic chromosome reorganization is marked by the general attenuation of transcription on chromosome arms, yet how the cell regulates nuclear and chromatin-associated RNAs after chromosome condensation and nuclear envelope breakdown is unknown. SAF-A/hnRNPU is an abundant nuclear protein with RNA-to-DNA tethering activity, coordinated by two spatially distinct nucleic acid–binding domains. Here we show that RNA is evicted from prophase chromosomes through Aurora-B–dependent phosphorylation of the SAF-A DNA-binding domain; failure to execute this pathway leads to accumulation of SAF-A–RNA complexes on mitotic chromosomes, defects in metaphase chromosome alignment, and elevated rates of chromosome missegregation in anaphase. This work reveals a role for Aurora-B in removing chromatin-associated RNAs during prophase and demonstrates that Aurora-B–dependent relocalization of SAF-A during cell division contributes to the fidelity of chromosome segregation.
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Affiliation(s)
- Judith A Sharp
- Department of Molecular Biology, Massachusetts General Hospital, Boston, MA.,Department of Genetics, Harvard Medical School, Boston, MA
| | - Carlos Perea-Resa
- Department of Molecular Biology, Massachusetts General Hospital, Boston, MA.,Department of Genetics, Harvard Medical School, Boston, MA
| | - Wei Wang
- Department of Molecular Biology, Massachusetts General Hospital, Boston, MA.,Department of Genetics, Harvard Medical School, Boston, MA
| | - Michael D Blower
- Department of Molecular Biology, Massachusetts General Hospital, Boston, MA.,Department of Genetics, Harvard Medical School, Boston, MA
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5
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Hekman RM, Hume AJ, Goel RK, Abo KM, Huang J, Blum BC, Werder RB, Suder EL, Paul I, Phanse S, Youssef A, Alysandratos KD, Padhorny D, Ojha S, Mora-Martin A, Kretov D, Ash PEA, Verma M, Zhao J, Patten JJ, Villacorta-Martin C, Bolzan D, Perea-Resa C, Bullitt E, Hinds A, Tilston-Lunel A, Varelas X, Farhangmehr S, Braunschweig U, Kwan JH, McComb M, Basu A, Saeed M, Perissi V, Burks EJ, Layne MD, Connor JH, Davey R, Cheng JX, Wolozin BL, Blencowe BJ, Wuchty S, Lyons SM, Kozakov D, Cifuentes D, Blower M, Kotton DN, Wilson AA, Mühlberger E, Emili A. Actionable Cytopathogenic Host Responses of Human Alveolar Type 2 Cells to SARS-CoV-2. Mol Cell 2020; 80:1104-1122.e9. [PMID: 33259812 PMCID: PMC7674017 DOI: 10.1016/j.molcel.2020.11.028] [Citation(s) in RCA: 63] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2020] [Revised: 10/16/2020] [Accepted: 11/11/2020] [Indexed: 12/11/2022]
Abstract
Human transmission of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), causative pathogen of the COVID-19 pandemic, exerts a massive health and socioeconomic crisis. The virus infects alveolar epithelial type 2 cells (AT2s), leading to lung injury and impaired gas exchange, but the mechanisms driving infection and pathology are unclear. We performed a quantitative phosphoproteomic survey of induced pluripotent stem cell-derived AT2s (iAT2s) infected with SARS-CoV-2 at air-liquid interface (ALI). Time course analysis revealed rapid remodeling of diverse host systems, including signaling, RNA processing, translation, metabolism, nuclear integrity, protein trafficking, and cytoskeletal-microtubule organization, leading to cell cycle arrest, genotoxic stress, and innate immunity. Comparison to analogous data from transformed cell lines revealed respiratory-specific processes hijacked by SARS-CoV-2, highlighting potential novel therapeutic avenues that were validated by a high hit rate in a targeted small molecule screen in our iAT2 ALI system.
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Affiliation(s)
- Ryan M Hekman
- Center for Network Systems Biology, Boston University, Boston, MA, USA; Department of Biochemistry, Boston University School of Medicine, Boston, MA, USA
| | - Adam J Hume
- Department of Microbiology, Boston University School of Medicine, Boston, MA, USA; National Emerging Infectious Diseases Laboratories, Boston University, Boston, MA, USA
| | - Raghuveera Kumar Goel
- Center for Network Systems Biology, Boston University, Boston, MA, USA; Department of Biochemistry, Boston University School of Medicine, Boston, MA, USA
| | - Kristine M Abo
- Center for Regenerative Medicine of Boston University and Boston Medical Center, Boston, MA, USA; The Pulmonary Center, Department of Medicine, Boston University School of Medicine, Boston, MA, USA
| | - Jessie Huang
- Center for Regenerative Medicine of Boston University and Boston Medical Center, Boston, MA, USA; The Pulmonary Center, Department of Medicine, Boston University School of Medicine, Boston, MA, USA
| | - Benjamin C Blum
- Center for Network Systems Biology, Boston University, Boston, MA, USA; Department of Biochemistry, Boston University School of Medicine, Boston, MA, USA
| | - Rhiannon B Werder
- Center for Regenerative Medicine of Boston University and Boston Medical Center, Boston, MA, USA; The Pulmonary Center, Department of Medicine, Boston University School of Medicine, Boston, MA, USA
| | - Ellen L Suder
- Department of Microbiology, Boston University School of Medicine, Boston, MA, USA; National Emerging Infectious Diseases Laboratories, Boston University, Boston, MA, USA
| | - Indranil Paul
- Center for Network Systems Biology, Boston University, Boston, MA, USA; Department of Biochemistry, Boston University School of Medicine, Boston, MA, USA
| | - Sadhna Phanse
- Center for Network Systems Biology, Boston University, Boston, MA, USA
| | - Ahmed Youssef
- Center for Network Systems Biology, Boston University, Boston, MA, USA; Department of Biochemistry, Boston University School of Medicine, Boston, MA, USA; Bioinformatics Program, Boston University, Boston, MA, USA
| | - Konstantinos D Alysandratos
- Center for Regenerative Medicine of Boston University and Boston Medical Center, Boston, MA, USA; The Pulmonary Center, Department of Medicine, Boston University School of Medicine, Boston, MA, USA
| | - Dzmitry Padhorny
- Department of Applied Mathematics and Statistics, Stony Brook University, Stony Brook, NY, USA; Laufer Center for Physical and Quantitative Biology, Stony Brook University, Stony Brook, NY, USA
| | - Sandeep Ojha
- Department of Biochemistry, Boston University School of Medicine, Boston, MA, USA
| | | | - Dmitry Kretov
- Department of Biochemistry, Boston University School of Medicine, Boston, MA, USA
| | - Peter E A Ash
- Department of Pharmacology, Boston University School of Medicine, Boston, MA, USA
| | - Mamta Verma
- Department of Pharmacology, Boston University School of Medicine, Boston, MA, USA
| | - Jian Zhao
- Department of Electrical and Computer Engineering, Boston University, Boston, MA, USA
| | - J J Patten
- Department of Microbiology, Boston University School of Medicine, Boston, MA, USA; National Emerging Infectious Diseases Laboratories, Boston University, Boston, MA, USA
| | - Carlos Villacorta-Martin
- Center for Regenerative Medicine of Boston University and Boston Medical Center, Boston, MA, USA
| | - Dante Bolzan
- Department of Computer Science, University of Miami, Miami, FL, USA
| | - Carlos Perea-Resa
- Department of Molecular Biology, Harvard Medical School, Boston, MA, USA
| | - Esther Bullitt
- Department of Physiology and Biophysics, Boston University, Boston, MA, USA
| | - Anne Hinds
- The Pulmonary Center, Department of Medicine, Boston University School of Medicine, Boston, MA, USA
| | - Andrew Tilston-Lunel
- Department of Biochemistry, Boston University School of Medicine, Boston, MA, USA
| | - Xaralabos Varelas
- Department of Biochemistry, Boston University School of Medicine, Boston, MA, USA
| | - Shaghayegh Farhangmehr
- Donnelly Centre, University of Toronto, Toronto, ON, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
| | | | - Julian H Kwan
- Center for Network Systems Biology, Boston University, Boston, MA, USA; Department of Biochemistry, Boston University School of Medicine, Boston, MA, USA
| | - Mark McComb
- Center for Network Systems Biology, Boston University, Boston, MA, USA; Department of Biochemistry, Boston University School of Medicine, Boston, MA, USA; Center for Biomedical Mass Spectrometry, Boston University School of Medicine, Boston, MA, USA
| | - Avik Basu
- Center for Network Systems Biology, Boston University, Boston, MA, USA; Department of Biochemistry, Boston University School of Medicine, Boston, MA, USA
| | - Mohsan Saeed
- Department of Biochemistry, Boston University School of Medicine, Boston, MA, USA; National Emerging Infectious Diseases Laboratories, Boston University, Boston, MA, USA
| | - Valentina Perissi
- Department of Biochemistry, Boston University School of Medicine, Boston, MA, USA
| | - Eric J Burks
- Department of Pathology and Laboratory Medicine, Boston University School of Medicine, Boston, MA, USA
| | - Matthew D Layne
- Department of Biochemistry, Boston University School of Medicine, Boston, MA, USA
| | - John H Connor
- Department of Microbiology, Boston University School of Medicine, Boston, MA, USA; National Emerging Infectious Diseases Laboratories, Boston University, Boston, MA, USA
| | - Robert Davey
- Department of Microbiology, Boston University School of Medicine, Boston, MA, USA; National Emerging Infectious Diseases Laboratories, Boston University, Boston, MA, USA
| | - Ji-Xin Cheng
- Department of Biomedical Engineering, Boston University, Boston, MA, USA
| | - Benjamin L Wolozin
- Department of Pharmacology, Boston University School of Medicine, Boston, MA, USA
| | - Benjamin J Blencowe
- Donnelly Centre, University of Toronto, Toronto, ON, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
| | - Stefan Wuchty
- Department of Computer Science, University of Miami, Miami, FL, USA; Department of Biology, University of Miami, Miami, FL, USA; Miami Institute of Data Science and Computing, Miami, FL, USA
| | - Shawn M Lyons
- Department of Biochemistry, Boston University School of Medicine, Boston, MA, USA
| | - Dima Kozakov
- Department of Applied Mathematics and Statistics, Stony Brook University, Stony Brook, NY, USA; Laufer Center for Physical and Quantitative Biology, Stony Brook University, Stony Brook, NY, USA
| | - Daniel Cifuentes
- Department of Biochemistry, Boston University School of Medicine, Boston, MA, USA
| | - Michael Blower
- Department of Biochemistry, Boston University School of Medicine, Boston, MA, USA; Department of Molecular Biology, Harvard Medical School, Boston, MA, USA
| | - Darrell N Kotton
- Center for Regenerative Medicine of Boston University and Boston Medical Center, Boston, MA, USA; The Pulmonary Center, Department of Medicine, Boston University School of Medicine, Boston, MA, USA.
| | - Andrew A Wilson
- Center for Regenerative Medicine of Boston University and Boston Medical Center, Boston, MA, USA; The Pulmonary Center, Department of Medicine, Boston University School of Medicine, Boston, MA, USA.
| | - Elke Mühlberger
- Department of Microbiology, Boston University School of Medicine, Boston, MA, USA; National Emerging Infectious Diseases Laboratories, Boston University, Boston, MA, USA.
| | - Andrew Emili
- Center for Network Systems Biology, Boston University, Boston, MA, USA; Department of Biochemistry, Boston University School of Medicine, Boston, MA, USA; Department of Biology, Boston University, Boston, MA, USA.
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6
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Abstract
Long non-coding RNA (lncRNA) Xist has emerged as a key modulator in dosage compensation by randomly inactivating one of the X chromosomes in mammals during embryonic development. Dysregulation of X chromosome inactivation (XCI) due to deletion of Xist has been proven to induce hematologic cancer in mice. However, this phenomenon is not consistent in humans as growing evidence suggests Xist can suppress or promote cancer growth in different organs of the human body. In this review, we discuss recent advances of XCI in human embryonic stem cells and provide an explanation for the seemingly contradictory roles of Xist in development of human cancer.
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Affiliation(s)
- Yung-Kang Chen
- School of Medicine, Taipei Medical University, Taipei, Taiwan.,Department of General Medicine, Taipei Veterans General Hospital, Taipei, Taiwan
| | - Yun Yen
- Graduate Institute of Medical Informatics, Taipei Medical University, Taipei, Taiwan. .,TMU Research Center of Cancer Translational Medicine, Taipei Medical University, 250 Wuxing Street, Taipei City, 110, Taiwan. .,Taipei Municipal Wanfang Hospital, Taipei Medical University, Taipei, Taiwan. .,Program for Cancer Molecular Biology and Drug Discovery, College of Medical Science and Technology, Taipei Medical University, Taipei, Taiwan.
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7
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Initiation of X Chromosome Inactivation during Bovine Embryo Development. Cells 2020; 9:cells9041016. [PMID: 32325818 PMCID: PMC7226380 DOI: 10.3390/cells9041016] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2020] [Revised: 04/13/2020] [Accepted: 04/16/2020] [Indexed: 02/06/2023] Open
Abstract
X-chromosome inactivation (XCI) is a developmental process that aims to equalize the dosage of X-linked gene products between XY males and XX females in eutherian mammals. In female mouse embryos, paternal XCI is initiated at the 4-cell stage; however, the X chromosome is reactivated in the inner cell mass cells of blastocysts, and random XCI is subsequently initiated in epiblast cells. However, recent findings show that the patterns of XCI are not conserved among mammals. In this study, we used quantitative RT-PCR and RNA in situ hybridization combined with immunofluorescence to investigate the pattern of XCI during bovine embryo development. Expression of XIST (X-inactive specific transcript) RNA was significantly upregulated at the morula stage. For the first time, we demonstrate that XIST accumulation in bovine embryos starts in nuclei of female morulae, but its colocalization with histone H3 lysine 27 trimethylation was first detected in day 7 blastocysts. Both in the inner cell mass and in putative epiblast precursors, we observed a proportion of cells with XIST RNA and H3K27me3 colocalization. Surprisingly, the onset of XCI did not lead to a global downregulation of X-linked genes, even in day 9 blastocysts. Together, our findings confirm that diverse patterns of XCI initiation exist among developing mammalian embryos.
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8
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Perea-Resa C, Bury L, Cheeseman IM, Blower MD. Cohesin Removal Reprograms Gene Expression upon Mitotic Entry. Mol Cell 2020; 78:127-140.e7. [PMID: 32035037 PMCID: PMC7178822 DOI: 10.1016/j.molcel.2020.01.023] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2019] [Revised: 11/18/2019] [Accepted: 01/16/2020] [Indexed: 01/02/2023]
Abstract
As cells enter mitosis, the genome is restructured to facilitate chromosome segregation, accompanied by dramatic changes in gene expression. However, the mechanisms that underlie mitotic transcriptional regulation are unclear. In contrast to transcribed genes, centromere regions retain transcriptionally active RNA polymerase II (Pol II) in mitosis. Here, we demonstrate that chromatin-bound cohesin is necessary to retain elongating Pol II at centromeres. We find that WAPL-mediated removal of cohesin from chromosome arms during prophase is required for the dissociation of Pol II and nascent transcripts, and failure of this process dramatically alters mitotic gene expression. Removal of cohesin/Pol II from chromosome arms in prophase is important for accurate chromosome segregation and normal activation of gene expression in G1. We propose that prophase cohesin removal is a key step in reprogramming gene expression as cells transition from G2 through mitosis to G1.
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Affiliation(s)
- Carlos Perea-Resa
- Department of Molecular Biology, Massachusetts General Hospital, Boston, MA 02114, USA; Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Leah Bury
- Whitehead Institute for Biomedical Research, 455 Main St., Cambridge, MA 02142, USA; Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02142, USA
| | - Iain M Cheeseman
- Whitehead Institute for Biomedical Research, 455 Main St., Cambridge, MA 02142, USA; Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02142, USA
| | - Michael D Blower
- Department of Molecular Biology, Massachusetts General Hospital, Boston, MA 02114, USA; Department of Genetics, Harvard Medical School, Boston, MA 02115, USA.
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9
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Choudhari R, Sedano MJ, Harrison AL, Subramani R, Lin KY, Ramos EI, Lakshmanaswamy R, Gadad SS. Long noncoding RNAs in cancer: From discovery to therapeutic targets. Adv Clin Chem 2019; 95:105-147. [PMID: 32122521 DOI: 10.1016/bs.acc.2019.08.003] [Citation(s) in RCA: 81] [Impact Index Per Article: 16.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Long noncoding RNAs (lncRNAs) have recently gained considerable attention as key players in biological regulation; however, the mechanisms by which lncRNAs govern various disease processes remain mysterious and are just beginning to be understood. The ease of next-generation sequencing technologies has led to an explosion of genomic information, especially for the lncRNA class of noncoding RNAs. LncRNAs exhibit the characteristics of mRNAs, such as polyadenylation, 5' methyl capping, RNA polymerase II-dependent transcription, and splicing. These transcripts comprise more than 200 nucleotides (nt) and are not translated into proteins. Directed interrogation of annotated lncRNAs from RNA-Seq datasets has revealed dramatic differences in their expression, largely driven by alterations in transcription, the cell cycle, and RNA metabolism. The fact that lncRNAs are expressed cell- and tissue-specifically makes them excellent biomarkers for ongoing biological events. Notably, lncRNAs are differentially expressed in several cancers and show a distinct association with clinical outcomes. Novel methods and strategies are being developed to study lncRNA function and will provide researchers with the tools and opportunities to develop lncRNA-based therapeutics for cancer.
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Affiliation(s)
- Ramesh Choudhari
- Center of Emphasis in Cancer, Department of Molecular and Translational Medicine, Paul L. Foster School of Medicine, Texas Tech University Health Sciences Center El Paso, El Paso, TX, United States
| | - Melina J Sedano
- Center of Emphasis in Cancer, Department of Molecular and Translational Medicine, Paul L. Foster School of Medicine, Texas Tech University Health Sciences Center El Paso, El Paso, TX, United States
| | - Alana L Harrison
- Center of Emphasis in Cancer, Department of Molecular and Translational Medicine, Paul L. Foster School of Medicine, Texas Tech University Health Sciences Center El Paso, El Paso, TX, United States
| | - Ramadevi Subramani
- Center of Emphasis in Cancer, Department of Molecular and Translational Medicine, Paul L. Foster School of Medicine, Texas Tech University Health Sciences Center El Paso, El Paso, TX, United States; Graduate School of Biomedical Sciences, Texas Tech University Health Sciences Center El Paso, El Paso, TX, United States
| | - Ken Y Lin
- The Department of Obstetrics & Gynecology and Women's Health, Albert Einstein College of Medicine, Bronx, NY, United States
| | - Enrique I Ramos
- Center of Emphasis in Cancer, Department of Molecular and Translational Medicine, Paul L. Foster School of Medicine, Texas Tech University Health Sciences Center El Paso, El Paso, TX, United States
| | - Rajkumar Lakshmanaswamy
- Center of Emphasis in Cancer, Department of Molecular and Translational Medicine, Paul L. Foster School of Medicine, Texas Tech University Health Sciences Center El Paso, El Paso, TX, United States; Graduate School of Biomedical Sciences, Texas Tech University Health Sciences Center El Paso, El Paso, TX, United States
| | - Shrikanth S Gadad
- Center of Emphasis in Cancer, Department of Molecular and Translational Medicine, Paul L. Foster School of Medicine, Texas Tech University Health Sciences Center El Paso, El Paso, TX, United States; Graduate School of Biomedical Sciences, Texas Tech University Health Sciences Center El Paso, El Paso, TX, United States; Cecil H. and Ida Green Center for Reproductive Biology Sciences and Division of Basic Reproductive Biology Research, Department of Obstetrics and Gynecology, University of Texas Southwestern Medical Center, Dallas, TX, United States.
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10
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Semmler L, Reiter-Brennan C, Klein A. BRCA1 and Breast Cancer: a Review of the Underlying Mechanisms Resulting in the Tissue-Specific Tumorigenesis in Mutation Carriers. J Breast Cancer 2019; 22:1-14. [PMID: 30941229 PMCID: PMC6438831 DOI: 10.4048/jbc.2019.22.e6] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2018] [Accepted: 12/30/2018] [Indexed: 12/24/2022] Open
Abstract
Since the first cloning of BRCA1 in 1994, many of its cellular interactions have been elucidated. However, its highly specific role in tumorigenesis in the breast tissue—carriers of BRCA1 mutations are predisposed to life-time risks of up to 80%—relative to many other tissues that remain unaffected, has not yet been fully enlightened. In this article, we have applied a universal model of tissue-specificity of cancer genes to BRCA1 and present a systematic review of proposed concepts classified into 4 categories. Firstly, tissue-specific differences in levels of BRCA1 expression and secondly differences in expression of proteins with redundant functions are outlined. Thirdly, cell-type specific interactions of BRCA1 are presented: its regulation of aromatase, its interaction with Progesterone- and receptor activator of nuclear factor-κB ligand-signaling that controls proliferation of luminal progenitor cells, and its influence on cell differentiation via modulation of the key regulators jagged 1-NOTCH and snail family transcriptional repressor 2. Fourthly, factors specific to the cell-type as well as the environment of the breast tissue are elucidated: distinct frequency of losses of heterozygosity, interaction with X inactivation specific transcript RNA, estrogen-dependent induction of genotoxic metabolites and nuclear factor (erythroid-derived 2)-like 2, and regulation of sirtuin 1. In conclusion, the impact of these concepts on the formation of hormone-sensitive and -insensitive breast tumors is outlined.
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Affiliation(s)
- Lukas Semmler
- Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Institute of Biochemistry, Berlin, Germany
| | - Cara Reiter-Brennan
- Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Institute of Biochemistry, Berlin, Germany
| | - Andreas Klein
- Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Institute of Biochemistry, Berlin, Germany
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11
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Zeng H, Wang J, Chen T, Zhang K, Chen J, Wang L, Li H, Tuluhong D, Li J, Wang S. Downregulation of long non-coding RNA Opa interacting protein 5-antisense RNA 1 inhibits breast cancer progression by targeting sex-determining region Y-box 2 by microRNA-129-5p upregulation. Cancer Sci 2018; 110:289-302. [PMID: 30443959 PMCID: PMC6317922 DOI: 10.1111/cas.13879] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2018] [Revised: 11/09/2018] [Accepted: 11/13/2018] [Indexed: 12/28/2022] Open
Abstract
Several studies have shown an important role for long non‐coding RNA (lncRNA) in breast cancer progression. The present study investigated the role of lncRNA Opa interacting protein 5‐antisense RNA 1 (OIP5‐AS1) in the progression of breast cancer. OIP5‐AS1 was significantly upregulated in breast cancer tissues and in breast cancer cell lines, and OIP5‐AS1 downregulation inhibited the malignant behavior of breast cancer in vitro and in vivo. For in‐depth exploration of the mechanism of OIP5‐AS1 in breast cancer, we found that expression of microRNA‐129‐5p(miR‐129‐5p), which was found to bind sites in the sequence of OIP5‐AS1, in breast cancer tissues was negatively correlated with OIP5‐AS1. Also, luciferase assays indicated that OIP5‐AS1 acted as a miR‐129‐5p sponge, resulting in upregulated expression of the sex‐determining region Y‐box 2 (SOX2) transcription factor. Our study showed that OIP5‐AS1 plays a critical role in promoting breast cancer progression and that OIP5‐AS1 downregulation targets SOX2 by miR‐129‐5p upregulation.
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Affiliation(s)
- Huijuan Zeng
- Department of General Surgery, Jinling Hospital, Medical School of Nanjing University, Nanjing, China
| | - Jingjie Wang
- Department of General Surgery, Jinling Hospital, Medical School of Nanjing University, Nanjing, China
| | - Tao Chen
- Department of General Surgery, Jinling Hospital, Medical School of Nanjing University, Nanjing, China
| | - Kai Zhang
- Department of Medical Oncology, Jinling Hospital, Medical School of Nanjing University, Nanjing, China
| | - Jing Chen
- Department of Medical Oncology, Jinling Hospital, Medical School of Nanjing University, Nanjing, China
| | - Lulu Wang
- Department of General Surgery, Jinling Hospital, Medical School of Nanjing University, Nanjing, China
| | - Hanjun Li
- Department of General Surgery, Jinling Hospital, Medical School of Nanjing University, Nanjing, China
| | - Dilihumaer Tuluhong
- Department of General Surgery, Jinling Hospital, Medical School of Nanjing University, Nanjing, China
| | - Jieshou Li
- Department of General Surgery, Jinling Hospital, Medical School of Nanjing University, Nanjing, China
| | - Shaohua Wang
- Department of General Surgery, Jinling Hospital, Medical School of Nanjing University, Nanjing, China
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12
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Lin XQ, Huang ZM, Chen X, Wu F, Wu W. XIST Induced by JPX Suppresses Hepatocellular Carcinoma by Sponging miR-155-5p. Yonsei Med J 2018; 59:816-826. [PMID: 30091314 PMCID: PMC6082978 DOI: 10.3349/ymj.2018.59.7.816] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/19/2018] [Revised: 06/15/2018] [Accepted: 06/28/2018] [Indexed: 02/06/2023] Open
Abstract
PURPOSE The influence of X-inactive specific transcript (XIST) and X-chromosome inactivation associated long non-coding RNAs (lncRNAs) just proximal to XIST (JPX) on hepatocellular carcinoma (HCC) remains controversial in light of previous reports, which the present study aimed to verify. MATERIALS AND METHODS The DIANA lncRNA-microRNA (miRNA) interaction database was used to explore miRNA interactions with JPX or XIST. JPX, XIST, and miR-155-5p expression levels in paired HCC specimens and adjacent normal tissue were analyzed by RT-qPCR. Interaction between XIST and miR-155-5p was verified by dual luciferase reporter assay. Expression levels of miR-155-5p and its known target genes, SOX6 and PTEN, were verified by RT-qPCR and Western blot in HepG2 cells with or without XIST knock-in. The potential suppressive role of XIST and JPX on HCC was verified by cell functional assays and tumor formation assay using a xenograft model. RESULTS JPX and XIST expression was significantly decreased in HCC pathologic specimens, compared to adjacent tissue, which correlated with HCC progression and increased miR-155-5p expression. Dual luciferase reporter assay revealed XIST as a direct target of miR-155-5p. XIST knock-in significantly reduced miR-155-5p expression level and increased that of SOX6 and PTEN, while significantly inhibiting HepG2 cell growth in vitro, which was partially reversed by miR-155-5p mimic transfection. JPX knock-in significantly increased XIST expression and inhibited HepG2 cell growth in vitro or tumor formation in vivo in a XIST dependent manner. CONCLUSION JPX and XIST play a suppressive role in HCC. JPX increases expression levels of XIST in HCC cells, which suppresses HCC development by sponging the cancer promoting miR-155-5p.
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Affiliation(s)
- Xiu Qing Lin
- Department of Gastroenterology, First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
| | - Zhi Ming Huang
- Department of Gastroenterology, First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
| | - Xin Chen
- Department of Gastroenterology, First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
| | - Fang Wu
- Department of Gastroenterology, First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
| | - Wei Wu
- Department of Gastroenterology, First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China.
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13
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Yang Z, Jiang X, Jiang X, Zhao H. X-inactive-specific transcript: A long noncoding RNA with complex roles in human cancers. Gene 2018; 679:28-35. [PMID: 30171939 DOI: 10.1016/j.gene.2018.08.071] [Citation(s) in RCA: 51] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2018] [Revised: 08/20/2018] [Accepted: 08/27/2018] [Indexed: 12/13/2022]
Abstract
The X-inactive-specific transcript (XIST/Xist) is one of the first long non-coding RNAs discovered in mammals and plays an essential role in X chromosome inactivation. XIST is dysregulated and acts as an oncogene or a tumor suppressor in different human malignancies. XIST is implicated in many aspects of carcinogenesis including tumor initiation, invasion, metastasis, apoptosis, cell cycle, stemness, autophagy, and drug resistance. This review focuses on research progress on the roles of XIST in tumor development. The multiple pathological functions of XIST in various cancers are systematically reviewed to elucidate the molecular basis of its biological roles and to provide new directions for future research.
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Affiliation(s)
- Zhi Yang
- Department of General Surgery, The Fourth Affiliated Hospital of China Medical University, Shenyang, China
| | - Xiaodi Jiang
- Department of Infectious Diseases, Shengjing Hospital of China Medical University, Shenyang, China
| | - Xiaofeng Jiang
- Department of General Surgery, The Fourth Affiliated Hospital of China Medical University, Shenyang, China.
| | - Haiying Zhao
- Department of General Surgery, The Fourth Affiliated Hospital of China Medical University, Shenyang, China.
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14
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Abstract
Long non-coding RNAs (lncRNAs) refer to functional cellular RNAs molecules longer than 200 nucleotides in length. Unlike microRNAs, which have been widely studied, little is known about the enigmatic role of lncRNAs. However, lncRNAs have motivated extensively attention in the past few years and are emerging as potentially important regulators in pathological processes, including in cancer. We now understand that lncRNAs play role in cancer through their interactions with DNA, protein, and RNA in many instances. Moreover, accumulating evidence has recognized that large classes of lncRNAs are functional for ovarian cancer. Nevertheless, the biological phenomena and molecular mechanisms of lncRNAs in ovarian cancer remain to be better identified. In this review, we outline the dysregulated expression of lncRNAs and their potential clinical implications in ovarian cancer, with a particular emphasis on discussing the well characterized mechanisms underlying lncRNAs in ovarian cancer.
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Affiliation(s)
- Lei Zhan
- Department of gynecology and obstetrics, The Second Affiliated Hospital of Anhui Medical University, Hefei, 230601 China
| | - Jun Li
- School of Pharmacy, Anhui Key Laboratory of Bioactivity of Natural Products, Anhui Medical University, Hefei, 230032 China
| | - Bing Wei
- Department of gynecology and obstetrics, The Second Affiliated Hospital of Anhui Medical University, Hefei, 230601 China
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15
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Richard JLC, Eichhorn PJA. Deciphering the roles of lncRNAs in breast development and disease. Oncotarget 2018; 9:20179-20212. [PMID: 29732012 PMCID: PMC5929455 DOI: 10.18632/oncotarget.24591] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2017] [Accepted: 02/21/2018] [Indexed: 02/06/2023] Open
Abstract
Breast cancer is the second leading cause of cancer related deaths in women. It is therefore important to understand the mechanisms underlying breast cancer development as well as raises the need for enhanced, non-invasive strategies for novel prognostic and diagnostic methods. The emergence of long non-coding RNAs (lncRNAs) as potential key players in neoplastic disease has received considerable attention over the past few years. This relatively new class of molecular regulators has been shown from ongoing research to act as critical players for key biological processes. Deregulated expression levels of lncRNAs have been observed in a number of cancers including breast cancer. Furthermore, lncRNAs have been linked to breast cancer initiation, progression, metastases and to limit sensitivity to certain targeted therapeutics. In this review we provide an update on the lncRNAs associated with breast cancer and mammary gland development and illustrate the versatility of such lncRNAs in gene control, differentiation and development both in normal physiological conditions and in diseased states. We also highlight the therapeutic and diagnostic potential of lncRNAs in cancer.
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Affiliation(s)
- John Lalith Charles Richard
- Cancer Science Institute of Singapore, National University of Singapore, 117599, Singapore
- Department of Pharmacology, Yong Loo Lin School of Medicine, National University of Singapore, 117597, Singapore
- Current Address: Genome Institute of Singapore, Agency for Science Technology and Research, 138672, Singapore
| | - Pieter Johan Adam Eichhorn
- Cancer Science Institute of Singapore, National University of Singapore, 117599, Singapore
- Department of Pharmacology, Yong Loo Lin School of Medicine, National University of Singapore, 117597, Singapore
- School of Pharmacy, Curtin University, Perth, 6845, Australia
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16
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Wang J, Ye C, Xiong H, Shen Y, Lu Y, Zhou J, Wang L. Dysregulation of long non-coding RNA in breast cancer: an overview of mechanism and clinical implication. Oncotarget 2018; 8:5508-5522. [PMID: 27732939 PMCID: PMC5354927 DOI: 10.18632/oncotarget.12537] [Citation(s) in RCA: 65] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2016] [Accepted: 10/03/2016] [Indexed: 01/16/2023] Open
Abstract
Long non-coding RNAs (lncRNAs), which occupy nearly 98% of genome, have crucial roles in cancer development, including breast cancer. Breast cancer is a disease with high incidence. Despite of recent progress in understanding the molecular mechanisms and combined therapy strategies, the functions and mechanisms of lncRNAs in breast cancer remains unclear. This review presents the currently basic knowledge and research approaches of lncRNAs. We also highlight the latest advances of seven classic lncRNAs and three novel lncRNAs in breast cancer, elucidating their mechanisms and possible therapeutic targets. Additionally, association between lncRNA and specific molecular subtype of breast cancer is reported. Lastly, we briefly delineate the potential roles of lncRNAs in clinical applications as biomarkers and treatment targets.
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Affiliation(s)
- Ji Wang
- Department of Surgical Oncology, Sir Run Run Shaw Hospital, Zhejiang University, Hangzhou, Zhejiang, China.,Biomedical Research Center and Key Laboratory of Biotherapy of Zhejiang Province, Hangzhou, Zhejiang, China
| | - Chenyang Ye
- Cancer Institute (Key Laboratory of Cancer Prevention & Intervention, National Ministry of Education), Second Affiliated Hospital, Zhejiang University, Hangzhou, Zhejiang, China
| | - Hanchu Xiong
- Department of Surgical Oncology, Sir Run Run Shaw Hospital, Zhejiang University, Hangzhou, Zhejiang, China.,Biomedical Research Center and Key Laboratory of Biotherapy of Zhejiang Province, Hangzhou, Zhejiang, China
| | - Yong Shen
- Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Yi Lu
- Department of Surgical Oncology, Sir Run Run Shaw Hospital, Zhejiang University, Hangzhou, Zhejiang, China.,Biomedical Research Center and Key Laboratory of Biotherapy of Zhejiang Province, Hangzhou, Zhejiang, China
| | - Jichun Zhou
- Department of Surgical Oncology, Sir Run Run Shaw Hospital, Zhejiang University, Hangzhou, Zhejiang, China.,Biomedical Research Center and Key Laboratory of Biotherapy of Zhejiang Province, Hangzhou, Zhejiang, China
| | - Linbo Wang
- Department of Surgical Oncology, Sir Run Run Shaw Hospital, Zhejiang University, Hangzhou, Zhejiang, China.,Biomedical Research Center and Key Laboratory of Biotherapy of Zhejiang Province, Hangzhou, Zhejiang, China
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17
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Wang ZY, Hu M, Dai MH, Xiong J, Zhang S, Wu HJ, Zhang SS, Gong ZJ. Upregulation of the long non-coding RNA AFAP1-AS1 affects the proliferation, invasion and survival of tongue squamous cell carcinoma via the Wnt/β-catenin signaling pathway. Mol Cancer 2018; 17:3. [PMID: 29310682 PMCID: PMC5757289 DOI: 10.1186/s12943-017-0752-2] [Citation(s) in RCA: 50] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2017] [Accepted: 12/26/2017] [Indexed: 02/08/2023] Open
Abstract
Background Long non-coding RNA (lncRNA) actin filament associated protein 1 antisense RNA1 (AFAP1-AS1) is oriented in an antisense direction to the protein-coding gene AFAP1 in the opposite strand. Previous studies showed that lncRNA AFAP1-AS1 was upregulated and acted as an oncogene in a variety of tumors. However, the expression and biological functions of lncRNA AFAP1-AS1 in tongue squamous cell carcinoma (TSCC) are still unknown. Methods The expression level of AFAP1-AS1 was measured in 103 pairs of human TSCC tissues and corresponding adjacent normal tongue mucous tissues. The correlation between AFAP1-AS1 and the clinicopathological features was evaluated using the chi-square test. The effects of AFAP1-AS1 on TSCC cells were determined via a CCK-8 assay, clone formation assay, flow cytometry, wound healing assay and transwell assay. Furthermore, the effect of AFAP1-AS1 knockdown on the activation of the Wnt/β-catenin signaling pathway was investigated. Finally, CAL-27 cells with AFAP1-AS1 knockdown were subcutaneously injected into nude mice to evaluate the effect of AFAP1-AS1 on tumor growth in vivo. Results In this study, we found that lncRNA AFAP1-AS1 was increased in TSCC tissues and that patients with high AFAP1-AS1 expression had a shorter overall survival. Short hairpin RNA (shRNA)-mediated AFAP1-AS1 knockdown significantly decreased the proliferation of TSCC cells. Furthermore, AFAP1-AS1 silencing partly inhibited cell migration and invasion. Inhibition of AFAP1-AS1 decreased the activity of the Wnt/β-catenin pathway and suppressed the expression of EMT-related genes (SLUG, SNAIL1, VIM, CADN, ZEB1, ZEB2, SMAD2 and TWIST1) in TSCC cells. In addition, CAL-27 cells with AFAP1-AS1 knockdown were injected into nude mice to investigate the effect of AFAP1-AS1 on tumorigenesis in vivo. Downregulation of AFAP1-AS1 suppressed tumor growth and inhibited the expression of EMT-related genes (SLUG, SNIAL1, VIM, ZEB1, NANOG, SMAD2, NESTIN and SOX2) in vivo. Conclusions Taken together, our findings present a road map for targeting the newly identified lncRNA AFAP1-AS1 to suppress TSCC progression, and these results elucidate a novel potential therapeutic strategy for TSCC.
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Affiliation(s)
- Ze-You Wang
- Department of Laboratory Medicine, The Second Xiangya Hospital, Central South University, Changsha, Hunan, 410011, China
| | - Min Hu
- Department of Laboratory Medicine, The Second Xiangya Hospital, Central South University, Changsha, Hunan, 410011, China
| | - Min-Hui Dai
- Department of Ophthalmology, Xiangya Hospital, Central South University, Changsha, Hunan, 410008, China
| | - Jing Xiong
- Department of Ophthalmology, Xiangya Hospital, Central South University, Changsha, Hunan, 410008, China
| | - Shuai Zhang
- Department of Clinical Medicine, Fujian Medical University, Fuzhou, Fujian, 350100, China.,Department of Oral and Maxillofacial Surgery, The Second Xiangya Hospital, Central South University, Changsha, Hunan, 410011, China
| | - Han-Jiang Wu
- Department of Oral and Maxillofacial Surgery, The Second Xiangya Hospital, Central South University, Changsha, Hunan, 410011, China
| | - Shan-Shan Zhang
- Department of Oral and Maxillofacial Surgery, The Second Xiangya Hospital, Central South University, Changsha, Hunan, 410011, China. .,Department of Stomatology, Xiangya Hospital, Central South University, Changsha, Hunan, 410008, China.
| | - Zhao-Jian Gong
- Department of Oral and Maxillofacial Surgery, The Second Xiangya Hospital, Central South University, Changsha, Hunan, 410011, China.
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18
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McNulty SM, Sullivan LL, Sullivan BA. Human Centromeres Produce Chromosome-Specific and Array-Specific Alpha Satellite Transcripts that Are Complexed with CENP-A and CENP-C. Dev Cell 2017; 42:226-240.e6. [PMID: 28787590 DOI: 10.1016/j.devcel.2017.07.001] [Citation(s) in RCA: 132] [Impact Index Per Article: 18.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2017] [Revised: 05/24/2017] [Accepted: 07/03/2017] [Indexed: 11/28/2022]
Abstract
Human centromeres are defined by alpha satellite DNA arrays that are distinct and chromosome specific. Most human chromosomes contain multiple alpha satellite arrays that are competent for centromere assembly. Here, we show that human centromeres are defined by chromosome-specific RNAs linked to underlying organization of distinct alpha satellite arrays. Active and inactive arrays on the same chromosome produce discrete sets of transcripts in cis. Non-coding RNAs produced from active arrays are complexed with CENP-A and CENP-C, while inactive-array transcripts associate with CENP-B and are generally less stable. Loss of CENP-A does not affect transcript abundance or stability. However, depletion of array-specific RNAs reduces CENP-A and CENP-C at the targeted centromere via faulty CENP-A loading, arresting cells before mitosis. This work shows that each human alpha satellite array produces a unique set of non-coding transcripts, and RNAs present at active centromeres are necessary for kinetochore assembly and cell-cycle progression.
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Affiliation(s)
- Shannon M McNulty
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, NC 27710, USA
| | - Lori L Sullivan
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, NC 27710, USA
| | - Beth A Sullivan
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, NC 27710, USA; Division of Human Genetics, Duke University Medical Center, Durham, NC 27710, USA.
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19
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Zhang R, Xia T. Long non-coding RNA XIST regulates PDCD4 expression by interacting with miR-21-5p and inhibits osteosarcoma cell growth and metastasis. Int J Oncol 2017; 51:1460-1470. [PMID: 29048648 PMCID: PMC5643066 DOI: 10.3892/ijo.2017.4127] [Citation(s) in RCA: 72] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2017] [Accepted: 08/09/2017] [Indexed: 12/11/2022] Open
Abstract
lncRNA-X-inactive specific transcript (lncRNA XIST) has been demonstrated to be a tumor suppressor involved in the pathogenesis and development of various cancers. However, the function of XIST and its working mechanism in osteosarcoma (OS) remain enigmatic. Firstly, we determined the expression of XIST in OS tissues and cell lines by quantitative reverse transcription-PCR (qRT-PCR) and explored whether aberrant XIST expression was associated with recurrence and short overall survival. Furthermore, the effects of XIST on osteosarcoma cells were studied by lentivirus mediated overexpression approach in vitro and in vivo. Detection of a set of epithelial-mesenchymal transition (EMT) markers was performed to explore whether XIST is involved in EMT. Finally, we investigated the regulatory mechanism of XIST acting as a competitive endogenous RNA (ceRNA) of miR-21-5p in OS progression and metastasis. lncRNA XIST was significantly downregulated in osteosarcoma tissues and osteosarcoma cells, and associated with recurrence and short overall survival in OS patients. XIST overexpression remarkably inhibited the proliferation of OS cells as well as the xenograft tumor formation in vivo. Both cell invasion and migration were inhibited by XIST overexpression via suppressing the EMT process. These results indicated that XIST functioned as a tumor suppressor in OS. Moreover, we found that miR-21-5p interacted with XIST by directly targeting the miRNA-binding site in the XIST sequence, and qRT-PCR results showed XIST and miR-21-5p could affect each other's expression, respectively. The following assays verified that the tumor suppressor, PDCD4 was a functional target of miR-21-5p in OS cells. Finally, we affirmed that XIST regulated PDCD4 expression by competitively binding to miR-21-5p. XIST inhibited cell proliferation and cell mobility by competitively binding to miR-21-5p and upregulating PDCD4 in OS. Our study demonstrated that lncRNA-XIST, which acts as a miRNA sponge, impedes miR-21-5p to maintain the expression of PDCD4, which contributes to the progression of OS. Our findings suggest that the newly identified XIST/miR-21-5p/PDCD4 axis could be a potential biomarker or therapeutic target for OS.
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Affiliation(s)
- Rui Zhang
- Department of Orthopaedics, South Campus, Ren Ji Hospital, School of Medicine, Shanghai Jiaotong University, Shanghai 201112, P.R. China
| | - Tian Xia
- Shanghai Mierxuan Biotechnology Co., Ltd., Shanghai 200233, P.R. China
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20
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Robert Finestra T, Gribnau J. X chromosome inactivation: silencing, topology and reactivation. Curr Opin Cell Biol 2017; 46:54-61. [PMID: 28236732 DOI: 10.1016/j.ceb.2017.01.007] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2016] [Revised: 01/19/2017] [Accepted: 01/30/2017] [Indexed: 01/22/2023]
Abstract
To ensure X-linked gene dosage compensation between females (XX) and males (XY), one X chromosome undergoes X chromosome inactivation (XCI) in female cells. This process is tightly regulated throughout development by many different factors, with Xist as a key regulator, encoding a long non-coding RNA, involved in establishment of several layers of repressive epigenetic modifications. Several recent studies on XCI focusing on identification and characterization of Xist RNA-protein interactors, revealed new factors involved in gene silencing, genome topology and nuclear membrane attachment, amongst others. Also, new insights in higher order chromatin organization have been presented, revealing differences between the topological organization of active and inactive X chromosomes (Xa and Xi), with associated differences in gene expression. Finally, further evidence indicates that the inactive state of the Xi can be (partially) reversed, and that this X chromosome reactivation (XCR) might be associated with disease.
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Affiliation(s)
- Teresa Robert Finestra
- Department of Developmental Biology, Erasmus MC, Wytemaweg 80, Rotterdam CN 3015, The Netherlands
| | - Joost Gribnau
- Department of Developmental Biology, Erasmus MC, Wytemaweg 80, Rotterdam CN 3015, The Netherlands.
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21
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Sedic M, Kuperwasser C. BRCA1-hapoinsufficiency: Unraveling the molecular and cellular basis for tissue-specific cancer. Cell Cycle 2016; 15:621-7. [PMID: 26822887 DOI: 10.1080/15384101.2016.1141841] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Over the past 20 years tremendous progress has been made in understanding the function of BRCA1 gene products. Yet one question still remains: why is mutation of BRCA1 typically associated with preferential development of breast and ovarian cancers and not tumors in other tissues? Here we discuss recent evidence documenting the effect of BRCA1-haploinsufficiency in different cells and tissues and synthesize a model for how mutations in a single BRCA1 allele in human cells might preferentially confer increased cancer risk in breast epithelial cells.
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Affiliation(s)
- Maja Sedic
- a Department of Developmental , Chemical, and Molecular Biology, Sackler School of Graduate Biomedical Sciences, Tufts University School of Medicine , Boston , MA , USA.,b Raymond and Beverly Sackler Convergence Laboratory, Tufts University School of Medicine , Boston , MA , USA.,c Molecular Oncology Research Institute, Tufts Medical Center , Boston , MA , USA
| | - Charlotte Kuperwasser
- a Department of Developmental , Chemical, and Molecular Biology, Sackler School of Graduate Biomedical Sciences, Tufts University School of Medicine , Boston , MA , USA.,b Raymond and Beverly Sackler Convergence Laboratory, Tufts University School of Medicine , Boston , MA , USA.,c Molecular Oncology Research Institute, Tufts Medical Center , Boston , MA , USA
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22
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Tripathi R, Soni A, Varadwaj PK. Integrated analysis of dysregulated lncRNA expression in breast cancer cell identified by RNA-seq study. Noncoding RNA Res 2016; 1:35-42. [PMID: 30159409 PMCID: PMC6096410 DOI: 10.1016/j.ncrna.2016.09.002] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2016] [Revised: 09/13/2016] [Accepted: 09/21/2016] [Indexed: 12/03/2022] Open
Abstract
Among all the sequencing techniques, RNA sequencing (RNA-seq) has galloped with pace adopting the profiling of transcriptomic data in almost every biological analytics area like gene regulation study, development biology and clinical research. Recently the discovery of differentially expressed genes across different conditions has outshone the barrier of genetic & epigenetic regulations. The present work identified and analyzed differentially expressed novel long non-coding RNAs (lncRNAs) for breast cancer. A complex computational pipeline was adopted for the study which includes analysis of 18498 differentially expressed genes with 4114 up-regulated and 3475 down-regulated transcripts. The overexpression of lnc-MTAP (CDKN2B-AS1), lnc-PCP4 (DSCAM-S1), and lnc-FAM (H19) in breast cells suggests that these lncRNAs may have significant role to play in breast cancer. These results validated the relevance of the dysregulation pattern in cancer cells due to the presence of lncRNAs. The study further opens a new scope for experimental analysis to confirm the aberrant expression pattern of these lncRNAs which may act as potential bio-markers for the diagnosis and early detection of breast cancer.
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Affiliation(s)
- Rashmi Tripathi
- Department of Bioinformatics, Indian Institute of Information Technology, Allahabad, U.P, India
| | - Apoorva Soni
- Department of Molecular and Cellular Engineering, Sam Higginbottom Institute of Agriculture, Technology and Sciences, Allahabad, U.P, India
| | - Pritish Kumar Varadwaj
- Department of Bioinformatics, Indian Institute of Information Technology, Allahabad, U.P, India
- Corresponding author.
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23
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New concepts on BARD1: Regulator of BRCA pathways and beyond. Int J Biochem Cell Biol 2016; 72:1-17. [DOI: 10.1016/j.biocel.2015.12.008] [Citation(s) in RCA: 60] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2015] [Revised: 12/15/2015] [Accepted: 12/16/2015] [Indexed: 01/09/2023]
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24
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Schouten PC, Vollebergh MA, Opdam M, Jonkers M, Loden M, Wesseling J, Hauptmann M, Linn SC. High XIST and Low 53BP1 Expression Predict Poor Outcome after High-Dose Alkylating Chemotherapy in Patients with a BRCA1-like Breast Cancer. Mol Cancer Ther 2015; 15:190-8. [DOI: 10.1158/1535-7163.mct-15-0470] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2015] [Accepted: 11/06/2015] [Indexed: 11/16/2022]
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25
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Francia S. Non-Coding RNA: Sequence-Specific Guide for Chromatin Modification and DNA Damage Signaling. Front Genet 2015; 6:320. [PMID: 26617633 PMCID: PMC4643122 DOI: 10.3389/fgene.2015.00320] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2015] [Accepted: 10/09/2015] [Indexed: 12/19/2022] Open
Abstract
Chromatin conformation shapes the environment in which our genome is transcribed into RNA. Transcription is a source of DNA damage, thus it often occurs concomitantly to DNA damage signaling. Growing amounts of evidence suggest that different types of RNAs can, independently from their protein-coding properties, directly affect chromatin conformation, transcription and splicing, as well as promote the activation of the DNA damage response (DDR) and DNA repair. Therefore, transcription paradoxically functions to both threaten and safeguard genome integrity. On the other hand, DNA damage signaling is known to modulate chromatin to suppress transcription of the surrounding genetic unit. It is thus intriguing to understand how transcription can modulate DDR signaling while, in turn, DDR signaling represses transcription of chromatin around the DNA lesion. An unexpected player in this field is the RNA interference (RNAi) machinery, which play roles in transcription, splicing and chromatin modulation in several organisms. Non-coding RNAs (ncRNAs) and several protein factors involved in the RNAi pathway are well known master regulators of chromatin while only recent reports show their involvement in DDR. Here, we discuss the experimental evidence supporting the idea that ncRNAs act at the genomic loci from which they are transcribed to modulate chromatin, DDR signaling and DNA repair.
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Affiliation(s)
- Sofia Francia
- IFOM - FIRC Institute of Molecular Oncology Milan, Italy ; Istituto di Genetica Molecolare, Consiglio Nazionale delle Ricerche Pavia, Italy
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Kang J, Lee HJ, Kim J, Lee JJ, Maeng LS. Dysregulation of X chromosome inactivation in high grade ovarian serous adenocarcinoma. PLoS One 2015; 10:e0118927. [PMID: 25742136 PMCID: PMC4351149 DOI: 10.1371/journal.pone.0118927] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2014] [Accepted: 01/07/2015] [Indexed: 01/31/2023] Open
Abstract
BACKGROUND One of the two copies of the X chromosome is randomly inactivated in females as a means of dosage compensation. Loss of X chromosome inactivation (XCI) is observed in breast and ovarian cancers, and is frequent in basal-like subtype and BRCA1 mutation-associated breast cancers. We investigated the clinical implications of the loss of XCI in ovarian cancer and the association between the loss of XCI and BRCA1 dysfunction. MATERIALS AND METHODS We used open source data generated by The Cancer Genome Atlas (TCGA) Genome Data Analysis Centers. Ward's hierarchical clustering method was used to classify the methylation status of the X chromosome. RESULTS We grouped 584 high grade serous ovarian adenocarcinomas (HG-SOA) according to methylation status, loss of heterozygosity and deletion or gain of X chromosome into the following five groups: preserved inactivated X chromosome (Xi) group (n = 175), partial reactivation of Xi group (n = 100), p arm deletion of Xi group (n = 35), q arm deletion of Xi group (n = 44), and two copies of active X group (n = 230). We found four genes (XAGE3, ZNF711, MAGEA4, and ZDHHC15) that were up-regulated by loss of XCI. HG-SOA with loss of XCI showed aggressive behavior (overall survival of partial reactivation of Xi group: HR 1.7, 95% CI 1.1-2.5, two copies of active X group: HR 1.4, 95% CI 1.0-1.9). Mutation and hypermethylation of BRCA1 were not frequent in HG-SOA with loss of XCI. CONCLUSIONS Loss of XCI is common in HG-SOA and is associated with poor clinical outcome. The role of BRCA1 in loss of XCI might be limited. XCI induced aberrant expression of cancer-testis antigens, which may have a role in tumor aggressiveness.
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Affiliation(s)
- Jun Kang
- Department of Hospital Pathology, Inchun St. Mary’s hospital, College of Medicine, The Catholic University of Korea, Inchun, Republic of Korea
- * E-mail:
| | - Hee Jin Lee
- Department of Pathology, University of Ulsan College of Medicine, Asan Medical Center, Seoul, Republic of Korea
| | - Jiyoung Kim
- Department of Hospital Pathology, Inchun St. Mary’s hospital, College of Medicine, The Catholic University of Korea, Inchun, Republic of Korea
| | - Jae Jun Lee
- Department of Hospital Pathology, Inchun St. Mary’s hospital, College of Medicine, The Catholic University of Korea, Inchun, Republic of Korea
| | - Lee-so Maeng
- Department of Hospital Pathology, Inchun St. Mary’s hospital, College of Medicine, The Catholic University of Korea, Inchun, Republic of Korea
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Chaligné R, Popova T, Mendoza-Parra MA, Saleem MAM, Gentien D, Ban K, Piolot T, Leroy O, Mariani O, Gronemeyer H, Vincent-Salomon A, Stern MH, Heard E. The inactive X chromosome is epigenetically unstable and transcriptionally labile in breast cancer. Genome Res 2015; 25:488-503. [PMID: 25653311 PMCID: PMC4381521 DOI: 10.1101/gr.185926.114] [Citation(s) in RCA: 85] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2014] [Accepted: 01/28/2015] [Indexed: 12/19/2022]
Abstract
Disappearance of the Barr body is considered a hallmark of cancer, although whether this corresponds to genetic loss or to epigenetic instability and transcriptional reactivation is unclear. Here we show that breast tumors and cell lines frequently display major epigenetic instability of the inactive X chromosome, with highly abnormal 3D nuclear organization and global perturbations of heterochromatin, including gain of euchromatic marks and aberrant distributions of repressive marks such as H3K27me3 and promoter DNA methylation. Genome-wide profiling of chromatin and transcription reveal modified epigenomic landscapes in cancer cells and a significant degree of aberrant gene activity from the inactive X chromosome, including several genes involved in cancer promotion. We demonstrate that many of these genes are aberrantly reactivated in primary breast tumors, and we further demonstrate that epigenetic instability of the inactive X can lead to perturbed dosage of X-linked factors. Taken together, our study provides the first integrated analysis of the inactive X chromosome in the context of breast cancer and establishes that epigenetic erosion of the inactive X can lead to the disappearance of the Barr body in breast cancer cells. This work offers new insights and opens up the possibility of exploiting the inactive X chromosome as an epigenetic biomarker at the molecular and cytological levels in cancer.
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Affiliation(s)
- Ronan Chaligné
- Centre de Recherche, Institut Curie, 75248 Paris Cedex 05, France; Centre National de la Recherche Scientifique, Unité Mixte de Recherche 3215, Institut Curie, 75248 Paris Cedex 05, France; Institut National de la Santé et de la Recherche Médicale U934, Institut Curie, 75248 Paris Cedex 05, France; Equipe Labellisée Ligue Contre le Cancer, UMR3215, 75248 Paris Cedex 05, France
| | - Tatiana Popova
- Centre de Recherche, Institut Curie, 75248 Paris Cedex 05, France; Institut National de la Santé et de la Recherche Médicale U830, Institut Curie, 75248 Paris Cedex 05, France
| | - Marco-Antonio Mendoza-Parra
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Equipe Labellisée Ligue Contre le Cancer, Centre National de la Recherche Scientifique UMR 7104, Institut National de la Santé et de la Recherche Médicale U964, University of Strasbourg, 67404 Illkirch Cedex, France
| | - Mohamed-Ashick M Saleem
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Equipe Labellisée Ligue Contre le Cancer, Centre National de la Recherche Scientifique UMR 7104, Institut National de la Santé et de la Recherche Médicale U964, University of Strasbourg, 67404 Illkirch Cedex, France
| | - David Gentien
- Centre de Recherche, Institut Curie, 75248 Paris Cedex 05, France; Department of Tumor Biology, Institut Curie, 75248 Paris Cedex 05, France
| | - Kristen Ban
- Centre de Recherche, Institut Curie, 75248 Paris Cedex 05, France; Centre National de la Recherche Scientifique, Unité Mixte de Recherche 3215, Institut Curie, 75248 Paris Cedex 05, France; Institut National de la Santé et de la Recherche Médicale U934, Institut Curie, 75248 Paris Cedex 05, France; Equipe Labellisée Ligue Contre le Cancer, UMR3215, 75248 Paris Cedex 05, France
| | - Tristan Piolot
- Centre de Recherche, Institut Curie, 75248 Paris Cedex 05, France; Plate-forme d'Imagerie Cellulaire et Tissulaire at BDD (Pict@BDD), Institut Curie, 75248 Paris Cedex 05, France
| | - Olivier Leroy
- Centre de Recherche, Institut Curie, 75248 Paris Cedex 05, France; Plate-forme d'Imagerie Cellulaire et Tissulaire at BDD (Pict@BDD), Institut Curie, 75248 Paris Cedex 05, France
| | - Odette Mariani
- Department of Tumor Biology, Institut Curie, 75248 Paris Cedex 05, France
| | - Hinrich Gronemeyer
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Equipe Labellisée Ligue Contre le Cancer, Centre National de la Recherche Scientifique UMR 7104, Institut National de la Santé et de la Recherche Médicale U964, University of Strasbourg, 67404 Illkirch Cedex, France;
| | - Anne Vincent-Salomon
- Centre de Recherche, Institut Curie, 75248 Paris Cedex 05, France; Equipe Labellisée Ligue Contre le Cancer, UMR3215, 75248 Paris Cedex 05, France; Institut National de la Santé et de la Recherche Médicale U830, Institut Curie, 75248 Paris Cedex 05, France; Department of Tumor Biology, Institut Curie, 75248 Paris Cedex 05, France;
| | - Marc-Henri Stern
- Centre de Recherche, Institut Curie, 75248 Paris Cedex 05, France; Institut National de la Santé et de la Recherche Médicale U830, Institut Curie, 75248 Paris Cedex 05, France; Department of Tumor Biology, Institut Curie, 75248 Paris Cedex 05, France;
| | - Edith Heard
- Centre de Recherche, Institut Curie, 75248 Paris Cedex 05, France; Centre National de la Recherche Scientifique, Unité Mixte de Recherche 3215, Institut Curie, 75248 Paris Cedex 05, France; Institut National de la Santé et de la Recherche Médicale U934, Institut Curie, 75248 Paris Cedex 05, France; Equipe Labellisée Ligue Contre le Cancer, UMR3215, 75248 Paris Cedex 05, France;
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Salvador MA, Wicinski J, Cabaud O, Toiron Y, Finetti P, Josselin E, Lelièvre H, Kraus-Berthier L, Depil S, Bertucci F, Collette Y, Birnbaum D, Charafe-Jauffret E, Ginestier C. The histone deacetylase inhibitor abexinostat induces cancer stem cells differentiation in breast cancer with low Xist expression. Clin Cancer Res 2013; 19:6520-31. [PMID: 24141629 DOI: 10.1158/1078-0432.ccr-13-0877] [Citation(s) in RCA: 105] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
PURPOSE Cancer stem cells (CSC) are the tumorigenic cell population that has been shown to sustain tumor growth and to resist conventional therapies. The purpose of this study was to evaluate the potential of histone deacetylase inhibitors (HDACi) as anti-CSC therapies. EXPERIMENTAL DESIGN We evaluated the effect of the HDACi compound abexinostat on CSCs from 16 breast cancer cell lines (BCL) using ALDEFLUOR assay and tumorsphere formation. We performed gene expression profiling to identify biomarkers predicting drug response to abexinostat. Then, we used patient-derived xenograft (PDX) to confirm, in vivo, abexinostat treatment effect on breast CSCs according to the identified biomarkers. RESULTS We identified two drug-response profiles to abexinostat in BCLs. Abexinostat induced CSC differentiation in low-dose sensitive BCLs, whereas it did not have any effect on the CSC population from high-dose sensitive BCLs. Using gene expression profiling, we identified the long noncoding RNA Xist (X-inactive specific transcript) as a biomarker predicting BCL response to HDACi. We validated that low Xist expression predicts drug response in PDXs associated with a significant reduction of the breast CSC population. CONCLUSIONS Our study opens promising perspectives for the use of HDACi as a differentiation therapy targeting the breast CSCs and identified a biomarker to select patients with breast cancer susceptible to responding to this treatment.
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Affiliation(s)
- Marion A Salvador
- Authors' Affiliations: Institut national de la santé et de la recherche medicale (INSERM), CRCM, U1068, Laboratoire d'Oncologie Moléculaire; Département de Biopathologie, Institut Paoli-Calmettes; Aix Marseille Université, F-13007; CNRS, CRCM, 7258; INSERM, CRCM, U1068, TrGET, Marseille; and Institut de Recherches Internationales Servier, Paris, France
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Ríos-Arrabal S, Artacho-Cordón F, León J, Román-Marinetto E, del Mar Salinas-Asensio M, Calvente I, Núñez MI. Involvement of free radicals in breast cancer. SPRINGERPLUS 2013; 2:404. [PMID: 24024092 PMCID: PMC3765596 DOI: 10.1186/2193-1801-2-404] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/14/2013] [Accepted: 08/22/2013] [Indexed: 12/14/2022]
Abstract
Researchers have recently shown an increased interest in free radicals and their role in the tumor microenvironment. Free radicals are molecules with high instability and reactivity due to the presence of an odd number of electrons in the outermost orbit of their atoms. Free radicals include reactive oxygen and nitrogen species, which are key players in the initiation and progression of tumor cells and enhance their metastatic potential. In fact, they are now considered a hallmark of cancer. However, both reactive species may contribute to improve the outcomes of radiotherapy in cancer patients. Besides, high levels of reactive oxygen species may be indicators of genotoxic damage in non-irradiated normal tissues. The purpose of this article is to review recent research on free radicals and carcinogenesis in order to understand the pathways that contribute to tumor malignancy. This review outlines the involvement of free radicals in relevant cellular events, including their effects on genetic instability through (growth factors and tumor suppressor genes, their enhancement of mitogenic signals, and their participation in cell remodeling, proliferation, senescence, apoptosis, and autophagy processes; the possible relationship between free radicals and inflammation is also explored. This knowledge is crucial for evaluating the relevance of free radicals as therapeutic targets in cancer.
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Affiliation(s)
- Sandra Ríos-Arrabal
- />Departamento de Radiología y Medicina Física, Universidad de Granada, Av. Madrid s/n, 18012 Granada, Spain
| | - Francisco Artacho-Cordón
- />Departamento de Radiología y Medicina Física, Universidad de Granada, Av. Madrid s/n, 18012 Granada, Spain
- />Instituto de Investigación Biosanitaria de Granada, Granada, Spain
| | - Josefa León
- />Ciber de Enfermedades Hepáticas y Digestivas CIBERehd, Granada, Spain
| | - Elisa Román-Marinetto
- />Departamento de Radiología y Medicina Física, Universidad de Granada, Av. Madrid s/n, 18012 Granada, Spain
| | | | - Irene Calvente
- />Departamento de Radiología y Medicina Física, Universidad de Granada, Av. Madrid s/n, 18012 Granada, Spain
| | - Maria Isabel Núñez
- />Departamento de Radiología y Medicina Física, Universidad de Granada, Av. Madrid s/n, 18012 Granada, Spain
- />Instituto de Investigación Biosanitaria de Granada, Granada, Spain
- />Instituto de Biopatología y Medicina Regenerativa (IBIMER), Universidad de Granada, Av. Conocimiento, s/n, 18100 Armilla Granada, Spain
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30
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The histone chaperone Spt6 coordinates histone H3K27 demethylation and myogenesis. EMBO J 2013; 32:1075-86. [PMID: 23503590 DOI: 10.1038/emboj.2013.54] [Citation(s) in RCA: 57] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2013] [Accepted: 02/13/2013] [Indexed: 12/15/2022] Open
Abstract
Histone chaperones affect chromatin structure and gene expression through interaction with histones and RNA polymerase II (PolII). Here, we report that the histone chaperone Spt6 counteracts H3K27me3, an epigenetic mark deposited by the Polycomb Repressive Complex 2 (PRC2) and associated with transcriptional repression. By regulating proper engagement and function of the H3K27 demethylase KDM6A (UTX), Spt6 effectively promotes H3K27 demethylation, muscle gene expression, and cell differentiation. ChIP-Seq experiments reveal an extensive genome-wide overlap of Spt6, PolII, and KDM6A at transcribed regions that are devoid of H3K27me3. Mammalian cells and zebrafish embryos with reduced Spt6 display increased H3K27me3 and diminished expression of the master regulator MyoD, resulting in myogenic differentiation defects. As a confirmation for an antagonistic relationship between Spt6 and H3K27me3, inhibition of PRC2 permits MyoD re-expression in myogenic cells with reduced Spt6. Our data indicate that, through cooperation with PolII and KDM6A, Spt6 orchestrates removal of H3K27me3, thus controlling developmental gene expression and cell differentiation.
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31
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Manoukian S, Verderio P, Tabano S, Colapietro P, Pizzamiglio S, Grati FR, Calvello M, Peissel B, Burn J, Pensotti V, Allemani C, Sirchia SM, Radice P, Miozzo M. X chromosome inactivation pattern in BRCA gene mutation carriers. Eur J Cancer 2013; 49:1136-41. [PMID: 23146957 DOI: 10.1016/j.ejca.2012.10.013] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2012] [Revised: 09/12/2012] [Accepted: 10/08/2012] [Indexed: 10/27/2022]
Abstract
An association of preferential X chromosome inactivation (XCI) with BRCA gene status and breast/ovarian cancer risk has been reported. We evaluated XCI in a large group of BRCA mutation carriers compared to non-carriers and investigated associations between preferential XCI (⩾90:10) and age, mutated gene, cancer development and chemotherapy. XCI was analysed by human androgen receptor (HUMARA) assay and pyrosequencing in 437 BRCA1 or BRCA2 mutation carriers and 445 age-matched controls. The distribution of XCI patterns in the two groups was compared by logistic regression analysis. The association between preferential XCI and selected variables was investigated in both univariate and multivariate fashion. In univariate analyses preferential XCI was not significantly associated with the probability of being a BRCA mutation carrier, nor with cancer status, whereas chemotherapeutic regime and age both showed a significant association. In multivariate analysis only age maintained significance (odds ratio, 1.056; 95% confidence interval, 1.016-1.096). Our findings do not support the usefulness of XCI analysis for the identification of BRCA mutation carriers and cancer risk assessment. The increasing preferential XCI frequency with ageing and the association with chemotherapy justify extending the investigation to other categories of female cancer patients to identify possible X-linked loci implicated in cell survival.
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Affiliation(s)
- Siranoush Manoukian
- Unit of Medical Genetics, Department of Preventive and Predictive Medicine, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
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The WSTF-ISWI chromatin remodeling complex transiently associates with the human inactive X chromosome during late S-phase prior to BRCA1 and γ-H2AX. PLoS One 2012; 7:e50023. [PMID: 23166813 PMCID: PMC3498190 DOI: 10.1371/journal.pone.0050023] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2012] [Accepted: 10/16/2012] [Indexed: 01/08/2023] Open
Abstract
Replicating the genome prior to each somatic cell division not only requires precise duplication of the genetic information, but also accurately reestablishing the epigenetic signatures that instruct how the genetic material is to be interpreted in the daughter cells. The mammalian inactive X chromosome (Xi), which is faithfully inherited in a silent state in each daughter cell, provides an excellent model of epigenetic regulation. While much is known about the early stages of X chromosome inactivation, much less is understood with regards to retaining the Xi chromatin through somatic cell division. Here we report that the WSTF-ISWI chromatin remodeling complex (WICH) associates with the Xi during late S-phase as the Xi DNA is replicated. Elevated levels of WICH at the Xi is restricted to late S-phase and appears before BRCA1 and γ-H2A.X. The sequential appearance of WICH and BRCA1/γ-H2A.X implicate each as performing important but distinct roles in the maturation and maintenance of heterochromatin at the Xi.
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Abstract
The discovery of numerous noncoding RNA (ncRNA) transcripts in species from yeast to mammals has dramatically altered our understanding of cell biology, especially the biology of diseases such as cancer. In humans, the identification of abundant long ncRNA (lncRNA) >200 bp has catalyzed their characterization as critical components of cancer biology. Recently, roles for lncRNAs as drivers of tumor suppressive and oncogenic functions have appeared in prevalent cancer types, such as breast and prostate cancer. In this review, we highlight the emerging impact of ncRNAs in cancer research, with a particular focus on the mechanisms and functions of lncRNAs.
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Affiliation(s)
- John R Prensner
- Michigan Center for Translational Pathology, Department of Pathology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
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Peri S, de Cicco RL, Santucci-Pereira J, Slifker M, Ross EA, Russo IH, Russo PA, Arslan AA, Belitskaya-Lévy I, Zeleniuch-Jacquotte A, Bordas P, Lenner P, Åhman J, Afanasyeva Y, Johansson R, Sheriff F, Hallmans G, Toniolo P, Russo J. Defining the genomic signature of the parous breast. BMC Med Genomics 2012; 5:46. [PMID: 23057841 PMCID: PMC3487939 DOI: 10.1186/1755-8794-5-46] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2012] [Accepted: 09/19/2012] [Indexed: 11/10/2022] Open
Abstract
Background It is accepted that a woman's lifetime risk of developing breast cancer after menopause is reduced by early full term pregnancy and multiparity. This phenomenon is thought to be associated with the development and differentiation of the breast during pregnancy. Methods In order to understand the underlying molecular mechanisms of pregnancy induced breast cancer protection, we profiled and compared the transcriptomes of normal breast tissue biopsies from 71 parous (P) and 42 nulliparous (NP) healthy postmenopausal women using Affymetrix Human Genome U133 Plus 2.0 arrays. To validate the results, we performed real time PCR and immunohistochemistry. Results We identified 305 differentially expressed probesets (208 distinct genes). Of these, 267 probesets were up- and 38 down-regulated in parous breast samples; bioinformatics analysis using gene ontology enrichment revealed that up-regulated genes in the parous breast represented biological processes involving differentiation and development, anchoring of epithelial cells to the basement membrane, hemidesmosome and cell-substrate junction assembly, mRNA and RNA metabolic processes and RNA splicing machinery. The down-regulated genes represented biological processes that comprised cell proliferation, regulation of IGF-like growth factor receptor signaling, somatic stem cell maintenance, muscle cell differentiation and apoptosis. Conclusions This study suggests that the differentiation of the breast imprints a genomic signature that is centered in the mRNA processing reactome. These findings indicate that pregnancy may induce a safeguard mechanism at post-transcriptional level that maintains the fidelity of the transcriptional process.
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Affiliation(s)
- Suraj Peri
- Breast Cancer Research Laboratory, Fox Chase Cancer Center, Philadelphia, PA 19111, USA
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Heterochromatin instability in cancer: from the Barr body to satellites and the nuclear periphery. Semin Cancer Biol 2012; 23:99-108. [PMID: 22722067 DOI: 10.1016/j.semcancer.2012.06.008] [Citation(s) in RCA: 80] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2012] [Revised: 05/25/2012] [Accepted: 06/11/2012] [Indexed: 12/31/2022]
Abstract
In recent years it has been recognized that the development of cancer involves a series of not only genetic but epigenetic changes across the genome. At the same time, connections between epigenetic regulation, chromatin packaging, and overall nuclear architecture are increasingly appreciated. The cell-type specific organization of heterochromatin, established upon cell differentiation, is responsible for maintaining much of the genome in a repressed state, within a highly compartmentalized nucleus. This review focuses on recent evidence that in cancer the normal packaging and higher organization of heterochromatin is often compromised. Gross changes in nuclear morphology have long been a criterion for pathologic diagnosis of many cancers, but the specific nuclear components impacted, the mechanisms involved, and the implications for cancer progression have barely begun to emerge. We discuss recent findings regarding distinct heterochromatin types, including the inactive X chromosome, constitutive heterochromatin of peri/centric satellites, and the peripheral heterochromatic compartment (PHC). A theme developed here is that the higher-order organization of satellites and the peripheral heterochromatic compartment may be tightly linked, and that compromise of this organization may promote broad epigenomic imbalance in cancer. Recent studies into the potential role(s) of the breast cancer tumor suppressor, BRCA1, in maintaining heterochromatin will be highlighted. Many questions remain about this new area of cancer epigenetics, which is likely more important in cancer development and progression than widely appreciated. We propose that broad, stochastic compromise in heterochromatin maintenance would create a diversity of expression profiles, and thus a rich opportunity for one or more cells to emerge with a selective growth advantage and potential for neoplasia.
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Rottenberg S, Vollebergh MA, de Hoon B, de Ronde J, Schouten PC, Kersbergen A, Zander SAL, Pajic M, Jaspers JE, Jonkers M, Lodén M, Sol W, van der Burg E, Wesseling J, Gillet JP, Gottesman MM, Gribnau J, Wessels L, Linn SC, Jonkers J, Borst P. Impact of intertumoral heterogeneity on predicting chemotherapy response of BRCA1-deficient mammary tumors. Cancer Res 2012; 72:2350-61. [PMID: 22396490 DOI: 10.1158/0008-5472.can-11-4201] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
The lack of markers to predict chemotherapy responses in patients poses a major handicap in cancer treatment. We searched for gene expression patterns that correlate with docetaxel or cisplatin response in a mouse model for breast cancer associated with BRCA1 deficiency. Array-based expression profiling did not identify a single marker gene predicting docetaxel response, despite an increase in Abcb1 (P-glycoprotein) expression that was sufficient to explain resistance in several poor responders. Intertumoral heterogeneity explained the inability to identify a predictive gene expression signature for docetaxel. To address this problem, we used a novel algorithm designed to detect differential gene expression in a subgroup of the poor responders that could identify tumors with increased Abcb1 transcript levels. In contrast, standard analytical tools, such as significance analysis of microarrays, detected a marker only if it correlated with response in a substantial fraction of tumors. For example, low expression of the Xist gene correlated with cisplatin hypersensitivity in most tumors, and it also predicted long recurrence-free survival of HER2-negative, stage III breast cancer patients treated with intensive platinum-based chemotherapy. Our findings may prove useful for selecting patients with high-risk breast cancer who could benefit from platinum-based therapy.
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Affiliation(s)
- Sven Rottenberg
- Division of Molecular Biology, The Netherlands Cancer Institute, Amsterdam, The Netherlands.
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Hysolli E, Jung YW, Tanaka Y, Kim KY, Park IH. The lesser known story of X chromosome reactivation: a closer look into the reprogramming of the inactive X chromosome. Cell Cycle 2012; 11:229-35. [PMID: 22234239 DOI: 10.4161/cc.11.2.18998] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Abstract
X-chromosome inactivation (XCI) is an important mechanism employed by mammalian XX female cells to level X-linked gene expression with that of male XY cells. XCI occurs early in development as the pluripotent cells of the inner cell mass (ICM) in blastocysts successively differentiate into cells of all three germ layers. X-chromosome reactivation (XCR), the reversal of XCI, is critical for germ cell formation as a mechanism to diversify the X-chromosome gene pool. Here we review the characterization of XCR, and further explore its natural occurrence during development and the in vitro models of cellular reprogramming. We also review the key regulators involved in XCI for their role in suppressing the active histone marks and the genes in the active chromosome for their inhibition of X inactivation signals.
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Affiliation(s)
- Eriona Hysolli
- Department of Genetics, Yale Stem Cell Center, Yale School of Medicine, New Haven, CT, USA
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Abstract
BACKGROUND X inactive-specific transcript (XIST) RNA is involved in X chromosome silencing in female cells and allows X chromosome equilibration with males. X inactive-specific transcript expression has been found to be dysregulated in a variety of human cancers when compared to normal cells; meanwhile, the inactivated X chromosome has been noted to be conspicuously absent in human cancer specimens, whereas X chromosome duplications are widely noted. The specific pathways whereby changes in X chromosome status and XIST expression occur in cancer remain incompletely described. Nevertheless, a role for XIST in BRCA1-mediated epigenetic activity has been proposed. METHODS Here we review the data regarding XIST expression and X chromosome status in a variety of female, male, and non-sex-related human cancers. CONCLUSIONS It is not yet known whether X chromosome duplication, XIST dysregulation, and over-expression of X-linked genes represent important factors in tumorgenesis or are simply a consequence of overall epigenetic instability in these cancers.
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Hasegawa Y, Brockdorff N, Kawano S, Tsutui K, Tsutui K, Nakagawa S. The Matrix Protein hnRNP U Is Required for Chromosomal Localization of Xist RNA. Dev Cell 2010; 19:469-76. [DOI: 10.1016/j.devcel.2010.08.006] [Citation(s) in RCA: 279] [Impact Index Per Article: 19.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2010] [Revised: 05/06/2010] [Accepted: 06/28/2010] [Indexed: 01/12/2023]
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Buonomo SBC. Heterochromatin DNA replication and Rif1. Exp Cell Res 2010; 316:1907-13. [PMID: 20347809 DOI: 10.1016/j.yexcr.2010.03.015] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2010] [Revised: 03/16/2010] [Accepted: 03/17/2010] [Indexed: 10/19/2022]
Abstract
Constitutive heterochromatin is essential for chromosome maintenance in all eukaryotes. However, the repetitive nature of the underlying DNA, the presence of very stable protein-DNA complexes and the highly compacted nature of this type of chromatin represent a challenge for the DNA replication machinery. Data collected from different model organisms suggest that at least some of the components of the DNA replication checkpoint could be essential for ensuring the completion of DNA replication in the context of heterochromatin. I review and discuss the literature that directly or indirectly contributes to the formulation of this hypothesis. In particular, I focus my attention on Rif1, a newly discovered member of the DNA replication checkpoint. Recent data generated in mammalian cells highlight the spatial and temporal relation between Rif1, pericentromeric heterochromatin and S-phase. I review these recent and the previous data coming from studies performed in yeast in order to highlight the possible evolutionary conserved links and propose a molecular model for Rif1 role in heterochromatin replication.
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Affiliation(s)
- S B C Buonomo
- EMBL Mouse Biology Unit, Via Ramarini 32, Monteorotondo, Rome, Italy.
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Linn SC, Van 't Veer LJ. Clinical relevance of the triple-negative breast cancer concept: genetic basis and clinical utility of the concept. Eur J Cancer 2010; 45 Suppl 1:11-26. [PMID: 19775601 DOI: 10.1016/s0959-8049(09)70012-7] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
The beginning of microarray technology in the 1990s and the sequencing of the human genome in 2000 paved the way for the seminal paper of the Stanford group on the molecular portraits of human breast tumours in the same year. They described four distinct breast cancer subtypes, which they called 'luminal', 'basal', 'HER2-positive', and 'normal breast-like', based on unique gene expression patterns. This paper caused a paradigm shift. Breast cancer was no longer hormone receptor-positive or -negative, but rather luminal, basal or HER2-positive. Since then, numerous papers have appeared, trying to further characterise these subtypes on the DNA, RNA and protein level. Other groups have focussed on the epidemiology, prognosis and outcome after therapy of breast cancer patients according to these molecular subtypes. A promising prognostic marker within the subgroup of basal-like breast cancer is an up-regulated immune response, which is associated with favourable outcome. In addition, the majority of basal-like breast cancers harbour traits of a DNA damage repair defect. This feature can be exploited by the use of DNA damaging agents, and first exciting clinical results of the combination of carboplatin, gemcitabine and a poly (ADP-ribose) polymerase 1 (PARP-1) inhibitor have recently been reported. In this review, the molecular characterisation of triple-negative breast cancer, a proxy for basal-like breast cancer, is described and findings have been put into clinical context.
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Affiliation(s)
- Sabine C Linn
- Division of Medical Oncology, Netherlands Cancer Institute, Amsterdam, The Netherlands
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Barakat TS, Gribnau J. X chromosome inactivation and embryonic stem cells. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2010; 695:132-54. [PMID: 21222204 DOI: 10.1007/978-1-4419-7037-4_10] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
X chromosome inactivation (XCI) is a process required to equalize the dosage of X-encoded genes between female and male cells. XCI is initiated very early during female embryonic development or upon differentiation of female embryonic stem (ES) cells and results in inactivation of one X chromosome in every female somatic cell. The regulation of XCI involves factors that also play a crucial role in ES cell maintenance and differentiation and the XCI process therefore provides a beautiful paradigm to study ES cell biology. In this chapter we describe the important cis and trans acting regulators of XCI and introduce the models that have been postulated to explain initiation of XCI in female cells only. We also discuss the proteins involved in the establishment of the inactive X chromosome and describe the different chromatin modifications associated with the inactivation process. Finally, we describe the potential of mouse and human ES and induced pluripotent stem (iPS) cells as model systems to study the XCI process.
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Affiliation(s)
- Tahsin Stefan Barakat
- Department of Reproduction and Development, University Medical Center, Room Ee 09-71, Erasmus MC, 3015 GE, Rotterdam, Netherlands
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Hall LL, Byron M, Pageau G, Lawrence JB. AURKB-mediated effects on chromatin regulate binding versus release of XIST RNA to the inactive chromosome. ACTA ACUST UNITED AC 2009; 186:491-507. [PMID: 19704020 PMCID: PMC2733744 DOI: 10.1083/jcb.200811143] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
How XIST RNA strictly localizes across the inactive X chromosome is unknown; however, prophase release of human XIST RNA provides a clue. Tests of inhibitors that mimic mitotic chromatin modifications implicated an indirect role of PP1 (protein phosphatase 1), potentially via its interphase repression of Aurora B kinase (AURKB), which phosphorylates H3 and chromosomal proteins at prophase. RNA interference to AURKB causes mitotic retention of XIST RNA, unlike other mitotic or broad kinase inhibitors. Thus, AURKB plays an unexpected role in regulating RNA binding to heterochromatin, independent of mechanics of mitosis. H3 phosphorylation (H3ph) was shown to precede XIST RNA release, whereas results exclude H1ph involvement. Of numerous Xi chromatin (chromosomal protein) hallmarks, ubiquitination closely follows XIST RNA retention or release. Surprisingly, H3S10ph staining (but not H3S28ph) is excluded from Xi and is potentially linked to ubiquitination. Results suggest a model of multiple distinct anchor points for XIST RNA. This study advances understanding of RNA chromosome binding and the roles of AURKB and demonstrates a novel approach to manipulate and study XIST RNA.
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Affiliation(s)
- Lisa L Hall
- Department of Cell Biology, University of Massachusetts Medical School, Worcester, MA 01655, USA.
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BRCA1 interacts with Smad3 and regulates Smad3-mediated TGF-beta signaling during oxidative stress responses. PLoS One 2009; 4:e7091. [PMID: 19768112 PMCID: PMC2740868 DOI: 10.1371/journal.pone.0007091] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2009] [Accepted: 08/25/2009] [Indexed: 11/29/2022] Open
Abstract
Background BRCA1 is a key regulatory protein participating in cell cycle checkpoint and DNA damage repair networks. BRCA1 plays important roles in protecting numerous cellular processes in response to cell damaging signals. Transforming growth factor-beta (TGF-β) is a potent regulator of growth, apoptosis and invasiveness of tumor cells. TFG-β activates Smad signaling via its two cell surface receptors, the TbetaRII and ALK5/TbetaRI, leading to Smad-mediated transcriptional regulation. Methodology/Principal Findings Here, we report an important role of BRCA1 in modulating TGF-β signaling during oxidative stress responses. Wild-type (WT) BRCA1, but not mutated BRCA1 failed to activate TGF-β mediated transactivation of the TGF-β responsive reporter, p3TP-Lux. Further, WT-BRCA1, but not mutated BRCA1 increased the expression of Smad3 protein in a dose-dependent manner, while silencing of WT-BRCA1 by siRNA decreased Smad3 and Smad4 interaction induced by TGF-β in MCF-7 breast cancer cells. BRCA1 interacted with Smad3 upon TGF-β1 stimulation in MCF-7 cells and this interaction was mediated via the domain of 298–436aa of BRCA1 and Smad3 domain of 207–426aa. In addition, H2O2 increased the colocalization and the interaction of Smad3 with WT-BRCA1. Interestingly, TGF-β1 induced Smad3 and Smad4 interaction was increased in the presence of H2O2 in cells expressing WT-BRCA1, while the TGF-β1 induced interaction between Smad3 and Smad4 was decreased upon H2O2 treatment in a dose-dependent manner in HCC1937 breast cancer cells, deficient for endogenous BRCA1. This interaction between Smad3 and Smad4 was increased in reconstituted HCC1937 cells expressing WT-BRCA1 (HCC1937/BRCA1). Further, loss of BRCA1 resulted in H2O2 induced nuclear export of phosphor-Smad3 protein to the cytoplasm, resulting decreased of Smad3 and Smad4 interaction induced by TGF-β and in significant decrease in Smad3 and Smad4 transcriptional activities. Conclusions/Significance These results strongly suggest that loss or reduction of BRCA1 alters TGF-β growth inhibiting activity via Smad3 during oxidative stress responses.
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Sirchia SM, Tabano S, Monti L, Recalcati MP, Gariboldi M, Grati FR, Porta G, Finelli P, Radice P, Miozzo M. Misbehaviour of XIST RNA in breast cancer cells. PLoS One 2009; 4:e5559. [PMID: 19440381 PMCID: PMC2679222 DOI: 10.1371/journal.pone.0005559] [Citation(s) in RCA: 63] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2009] [Accepted: 04/14/2009] [Indexed: 11/18/2022] Open
Abstract
A role of X chromosome inactivation process in the development of breast cancer have been suggested. In particular, the relationship between the breast cancer predisposing gene BRCA1 and XIST, the main mediator of X chromosome inactivation, has been intensely investigated, but still remains controversial. We investigated this topic by assessing XIST behaviour in different groups of breast carcinomas and in a panel of breast cancer cell lines both BRCA1 mutant and wild type. In addition, we evaluated the occurrence of broader defects of heterochromatin in relation to BRCA1 status in breast cancer cells. We provide evidence that in breast cancer cells BRCA1 is involved in XIST regulation on the active X chromosome, but not in its localization as previously suggested, and that XIST can be unusually expressed by an active X and can decorate it. This indicates that the detection of XIST cloud in cancer cell is not synonymous of the presence of an inactive X chromosome. Moreover, we show that global heterochromatin defects observed in breast tumor cells are independent of BRCA1 status. Our observations sheds light on a possible previously uncharacterized mechanism of breast carcinogenesis mediated by XIST misbehaviour, particularly in BRCA1-related cancers. Moreover, the significant higher levels of XIST-RNA detected in BRCA1-associated respect to sporadic basal-like cancers, opens the possibility to use XIST expression as a marker to discriminate between the two groups of tumors.
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Affiliation(s)
- Silvia M Sirchia
- Department of Medicine, Surgery and Dentistry, Medical Genetics Unit, Università degli Studi di Milano, Milano, Italy.
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Venkitaraman AR. Linking the Cellular Functions ofBRCAGenes to Cancer Pathogenesis and Treatment. ANNUAL REVIEW OF PATHOLOGY-MECHANISMS OF DISEASE 2009; 4:461-87. [DOI: 10.1146/annurev.pathol.3.121806.151422] [Citation(s) in RCA: 168] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Ashok R. Venkitaraman
- Department of Oncology, University of Cambridge, and the Medical Research Council Cancer Cell Unit, Hutchison/MRC Research Center, Cambridge CB2 0XZ, United Kingdom;
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Lose F, Duffy DL, Kay GF, Kedda MA, Spurdle AB. Skewed X chromosome inactivation and breast and ovarian cancer status: evidence for X-linked modifiers of BRCA1. J Natl Cancer Inst 2008; 100:1519-29. [PMID: 18957670 DOI: 10.1093/jnci/djn345] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
BACKGROUND X chromosome inactivation, which silences gene expression from one of the two X chromosomes in females, is usually random. Skewed X inactivation has been implicated in both the expression and the suppression of X-linked disease phenotypes and has been reported to occur more frequently in breast and ovarian cancer patients, including BRCA1 or BRCA2 mutation carriers, than in control subjects. METHODS We assessed the pattern of X chromosome inactivation using methylation-specific polymerase chain reaction amplification of the exon 1 microsatellite region of the X-linked androgen receptor (AR) gene in DNA from blood samples obtained from control subjects without a personal history of breast or ovarian cancer (n = 735), ovarian cancer patients (n = 313), familial breast cancer patients who did not carry mutations in BRCA1 or BRCA2 (n = 235), and affected and unaffected carriers of mutations in BRCA1 (n = 260) or BRCA2 (n = 63). We defined the pattern of X chromosome inactivation as skewed when the same X chromosome was active in at least 90% of cells. The association between skewed X inactivation and disease and/or BRCA mutation status was assessed by logistic regression analysis. The association between skewed X inactivation and age at cancer diagnosis was assessed by Cox proportional hazards regression analysis. All statistical tests were two-sided. RESULTS The age-adjusted frequency of skewed X inactivation was not statistically significantly higher in ovarian cancer or familial breast cancer case subjects compared with control subjects. Skewed X inactivation was higher in BRCA1 mutation carriers than in control subjects (odds ratio [OR] = 2.7, 95% confidence interval [CI] = 1.1 to 6.2; P = .02), particularly among unaffected women (OR = 6.1, 95% CI = 1.5 to 31.8; P = .005). Among BRCA1 mutation carriers, those with skewed X inactivation were older at diagnosis of breast or ovarian cancer than those without skewed X inactivation (hazard ratio [HR] of breast or ovarian cancer = 0.37, 95% CI = 0.14 to 0.95; P = .04). Among BRCA2 mutation carriers, skewed X inactivation also occurred more frequently in unaffected carriers than in those diagnosed with breast or ovarian cancer (OR = 5.2, 95% CI = 0.5 to 28.9; P = .08) and was associated with delayed age at onset (HR = 0.59, 95% CI = 0.37 to 0.94; P = .03). CONCLUSIONS Skewed X inactivation occurs at an increased frequency in BRCA1 (and possibly BRCA2) mutation carriers compared with control subjects and is associated with a statistically significant increase in age at diagnosis of breast and ovarian cancer.
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Affiliation(s)
- Felicity Lose
- Cancer and Cell Biology Division, Queensland Institute of Medical Research, Herston, Brisbane, Queensland, Australia
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48
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Erwin JA, Lee JT. New twists in X-chromosome inactivation. Curr Opin Cell Biol 2008; 20:349-55. [PMID: 18508252 DOI: 10.1016/j.ceb.2008.04.007] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2008] [Accepted: 04/21/2008] [Indexed: 10/22/2022]
Abstract
Dosage compensation, the mechanism by which organisms equalize the relative gene expression of dimorphic sex chromosomes, requires action of a diverse range of epigenetic mechanisms. The mammalian form, 'named X-chromosome inactivation' (XCI), involves silencing of one X chromosome in the female cell and regulation by genes that make noncoding RNAs (ncRNA). With large-scale genomic and transcriptome studies pointing to a crucial role for noncoding elements in organizing the epigenome, XCI emerges as a major paradigm and a focus of active research worldwide. With more surprising twists, recent advances point to the significance of RNA-directed chromatin change, chromosomal trans-interactions, nuclear organization, and evolutionary change. These findings have impacted our understanding of general gene regulation and are discussed herein.
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Affiliation(s)
- Jennifer A Erwin
- Howard Hughes Medical Institute, Department of Molecular Biology, Massachusetts General Hospital, Boston, MA, USA
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49
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Salstrom JL. X-inactivation and the dynamic maintenance of gene silencing. Mol Genet Metab 2007; 92:56-62. [PMID: 17604203 DOI: 10.1016/j.ymgme.2007.05.015] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/10/2007] [Revised: 05/23/2007] [Accepted: 05/23/2007] [Indexed: 01/25/2023]
Abstract
X-inactivation has long been a topic of fascination for educators, researchers, and clinicians alike. From complex patterns of inheritance to phenotypic variation among females with X-linked traits, a myriad of hypothesis and interpretations exist. Once thought to be random yet complete, X-inactivation has proven itself the poster child of the exception rather than the rule. Indeed, patterns of X-inactivation are all too often non-random, and many X-linked genes are capable of escaping X-inactivation. Similarly, X-inactivation is well-known for being stably maintained for life, but some previously inactivated X-linked genes reactivate with increasing age. Moreover, recent papers illustrate that X-inactivation can be challenged in other ways, thereby rendering the stability of X-inactivation compromised. This review describes factors involved in the maintenance of X-inactivation as we know it and discusses these emerging data that suggest a more dynamic model of the maintenance of X-inactivation may be in order.
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Affiliation(s)
- Jennifer L Salstrom
- Department of Human Genetics, David Geffen School of Medicine at UCLA, 6505 Gonda Center-Mail Code 708822, 695 Charles E Young Drive South, Los Angeles, CA 90095-708822, USA.
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Pageau GJ, Hall LL, Ganesan S, Livingston DM, Lawrence JB. The disappearing Barr body in breast and ovarian cancers. Nat Rev Cancer 2007; 7:628-33. [PMID: 17611545 DOI: 10.1038/nrc2172] [Citation(s) in RCA: 91] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Interest has recently reawakened in whether loss of the heterochromatic X chromosome (Barr body) is prevalent in certain breast and ovarian cancers, and new insights into the mechanisms involved have emerged. Mitotic segregation errors commonly explain the loss of the inactive X chromosome (Xi), but compromise of Xi heterochromatin in some cancers may signal broader deficits of nuclear heterochromatin. The debated link between BRCA1 and Xi might reflect a general relationship between BRCA1 and heterochromatin, which could connect BRCA1 to both epigenetic and genetic instability. We suggest that heterochromatic instability is a common but largely unexplored mechanism, leading to widespread genomic misregulation and the evolution of some cancers.
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Affiliation(s)
- Gayle J Pageau
- Department of Cell Biology, University of Massachusetts Medical School, Worcester, Massachusetts 01655, USA
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