Agonists Regulate the Expression of Stemness and Differentiation Genes in Brain Tumour Stem Cells
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International Journal of Molecular Sciences Article Phenotypic Subtyping and Re-Analysis of Existing Methylation Data from Autistic Probands in Simplex Families Reveal ASD Subtype-Associated Differentially Methylated Genes and Biological Functions Elizabeth C. Lee y and Valerie W. Hu * Department of Biochemistry and Molecular Medicine, The George Washington University, School of Medicine and Health Sciences, Washington, DC 20037, USA; [email protected] * Correspondence: [email protected]; Tel.: +1-202-994-8431 Current address: W. Harry Feinstone Department of Molecular Microbiology and Immunology, y Johns Hopkins Bloomberg School of Public Health, Baltimore, MD 21205, USA. Received: 25 August 2020; Accepted: 17 September 2020; Published: 19 September 2020 Abstract: Autism spectrum disorder (ASD) describes a group of neurodevelopmental disorders with core deficits in social communication and manifestation of restricted, repetitive, and stereotyped behaviors. Despite the core symptomatology, ASD is extremely heterogeneous with respect to the severity of symptoms and behaviors. This heterogeneity presents an inherent challenge to all large-scale genome-wide omics analyses. In the present study, we address this heterogeneity by stratifying ASD probands from simplex families according to the severity of behavioral scores on the Autism Diagnostic Interview-Revised diagnostic instrument, followed by re-analysis of existing DNA methylation data from individuals in three ASD subphenotypes in comparison to that of their respective unaffected siblings. We demonstrate that subphenotyping of cases enables the identification of over 1.6 times the number of statistically significant differentially methylated regions (DMR) and DMR-associated genes (DAGs) between cases and controls, compared to that identified when all cases are combined. Our analyses also reveal ASD-related neurological functions and comorbidities that are enriched among DAGs in each phenotypic subgroup but not in the combined case group. -
Revealing the Mechanism of Xist-Mediated Silencing
Revealing the Mechanism of Xist-mediated Silencing Thesis by Chun-Kan Chen In Partial Fulfillment of the Requirements for the degree of Doctor of Philosophy CALIFORNIA INSTITUTE OF TECHNOLOGY Pasadena, California 2018 Defended November 1, 2017 ii 2017 Chun-Kan Chen ORCID: 0000-0002-1194-9137 iii ACKNOWLEDGEMENTS First of all, I’d like to thank my great mentor, Dr. Mitch Guttman (California Institute of Technology, Pasadena, CA), who led me to become an independent researcher and gave me valuable advice that guided me to accomplish this thesis. He has always been supportive of my future plans and career goals. I really enjoyed every discussion we have had. We often generated some interesting ideas for projects during our discussions. I would also like to send my thanks to my lab mates, Amy Chow, Mario Blanco, and Erik Aznauryan, who helped me with many experiments to move the project forward. I’d like to acknowledge Dr. Kathrin Plath (University of California, Los Angeles, Los Angeles, CA) for the collaboration and his critical comments on this project. Also, I want to thank Jesse Engreitz and Patrick McDonel, who provided helpful comments and suggestions to the project. I want to thank my parents, brother, and parents-in-law who provided both instrumental and emotional support to assist me in completing my Ph.D. degree. I also want to thank my friends, Lily Chen, Pei-Ying Lin, Tzu-Yao Wang, and Wei Li, for giving me valuable social support during my years in graduate school. Last but not least, I would like to send my special thanks to my wife, Christine Juang, who has always been supportive. -
Molecular Genetic Delineation of 2Q37.3 Deletion in Autism and Osteodystrophy: Report of a Case and of New Markers for Deletion Screening by PCR
UC Irvine UC Irvine Previously Published Works Title Molecular genetic delineation of 2q37.3 deletion in autism and osteodystrophy: report of a case and of new markers for deletion screening by PCR. Permalink https://escholarship.org/uc/item/83f0x61r Journal Cytogenetics and cell genetics, 94(1-2) ISSN 0301-0171 Authors Smith, M Escamilla, JR Filipek, P et al. Publication Date 2001 DOI 10.1159/000048775 License https://creativecommons.org/licenses/by/4.0/ 4.0 Peer reviewed eScholarship.org Powered by the California Digital Library University of California Original Article Cytogenet Cell Genet 94:15–22 (2001) Molecular genetic delineation of 2q37.3 deletion in autism and osteodystrophy: report of a case and of new markers for deletion screening by PCR M. Smith, J.R. Escamilla, P. Filipek, M.E. Bocian, C. Modahl, P. Flodman, and M.A. Spence Department of Pediatrics, University of California, Irvine CA (USA) Abstract. We recently studied a patient who meets criteria us to determine the parental origin of the deletion in our for autistic disorder and has a 2q37 deletion. Molecular cyto- patient. DNA from 8–13 unrelated individuals was used to genetic studies were carried out using DNA isolated from 22 determine heterozygosity estimates for these markers. We re- different 2q37 mapped BACs to more precisely define the view four genes deleted in our patient – genes whose known extent of the chromosome deletion. We also analyzed 2q37 functions and sites of expression in the brain and/or bone make mapped polymorphic markers. In addition DNA sequences of them candidates for involvement in autism and/or the osteo- BACs in the deletion region were scanned to identify microsa- dystrophy observed in patients with 2q37.3 deletions. -
Association of BRCA1 with the Inactive X Chromosome and XIST RNA
FirstCite Published online e-publishing Association of BRCA1 with the inactive X chromosome and XIST RNA Shridar Ganesan1, Daniel P. Silver1, Ronny Drapkin1, Roger Greenberg1, Jean Feunteun2 and David M. Livingston1* 1The Dana-Farber Cancer Institute and Harvard Medical School, 1 Jimmy Fund Way, Boston, MA 02115, USA 2Laboratoire de Genetique et Transfert de Gene, Institut Gustav-Roussy, Villejuif 94805, France Breast cancer, early onset 1 (BRCA1) encodes a nuclear protein that participates in breast and ovarian cancer suppression. The molecular basis for the gender and tissue specificity of the BRCA1 cancer syn- drome is unknown. Recently, we observed that a fraction of BRCA1 in female cells is localized on the inactive X chromosome (Xi). Chromatin immunoprecipitation (ChIP) experiments have demonstrated that BRCA1 physically associates with Xi-specific transcript (XIST) RNA, a non-coding RNA known to coat Xi and to participate in the initiation of its inactivation during early embryogenesis. Cells lacking wild- type BRCA1 show abnormalities in Xi, including lack of proper XIST RNA localization. Reintroduction of wild-type, but not mutant, BRCA1 can correct this defect in XIST localization in these cells. Depletion of BRCA1 in female diploid cells led to a defect in proper XIST localization on Xi and in the development of normal Xi heterchromatic superstructure. Moreover, depletion of BRCA1 led to an increased likelihood of re-expression of a green fluorescent protein (GFP) reporter gene embedded on Xi. Taken together, these findings are consistent with a model in which BRCA1 function contributes to the maintenance of proper Xi heterochromatin superstructure. Although the data imply a novel gender-specific consequence of BRCA1 loss, the relevance of the BRCA1/Xi function to the tumour suppressor activity of BRCA1 remains unclear and needs to be tested. -
Long Non‑Coding Rnas XIST and MALAT1 Hijack the PD‑L1 Regulatory Signaling Pathway in Breast Cancer Subtypes
ONCOLOGY LETTERS 22: 593, 2021 Long non‑coding RNAs XIST and MALAT1 hijack the PD‑L1 regulatory signaling pathway in breast cancer subtypes AMANY SAMIR1, REDA ABDEL TAWAB2 and HEND M. EL TAYEBI1 1Molecular Pharmacology Research Group, Department of Pharmacology and Toxicology, German University in Cairo, Cairo 11835; 2Department of General Surgery, Ain Shams University, Cairo 11772, Egypt Received July 18, 2020; Accepted January 14, 2021 DOI: 10.3892/ol.2021.12854 Abstract. Long non‑coding RNAs (lncRNAs) have attracted presence of lncRNAs. Therefore, the results of the present widespread attention as potential biological and patho‑ study indicated that although miR‑182‑5p exhibited an onco‑ logical regulators. lncRNAs are involved in several biological genic effect, XIST exerted a dominant effect on the regulation processes in cancer. Triple negative breast cancer (TNBC) is of the PD‑L1 signaling pathway via the inhibition of the onco‑ characterized by strong heterogeneity and aggressiveness. At genic function of MALAT1. present, the implication of microRNAs (miRs) and lncRNAs in immunotherapy has been poorly studied. Nevertheless, Introduction the blockade of immune checkpoints, particularly that of the programmed cell‑death protein‑1/programmed cell‑death In the context of tumor biology, the six hallmarks of cancer ligand‑1 (PD‑L1) axis, is considered as a principle approach in have been proposed to be associated with progressively breast cancer (BC) therapy. The present study aimed to inves‑ growing tumors and to be responsible for the complexity of tigate the interaction between immune‑modulatory upstream neoplastic diseases, and these are limitless replicative poten‑ signaling pathways of the PD‑L1 transcript that could enhance tial, evading apoptosis, self‑sufficiency in growth signals, personalized targeted therapy. -
Non-Coding RNA: X-Chromosome Inactivation Unravelled
RESEARCH HIGHLIGHTS Nature Reviews Molecular Cell Biology | AOP, published online 8 May 2015; doi:10.1038/nrm3998 NON-CODING RNA X-chromosome inactivation unravelled The long non-coding RNA (lncRNA) specific and reproducible set of ten suggesting that SAFA acts to localize Xist (X inactive-specific transcript) is proteins that directly interact with Xist to genomic DNA. Depleting required for the transcriptional silenc- Xist. Of these proteins, knocking Xist binds to SHARP led to the retention of Pol II ing of one X chromosome in each cell, down the genes encoding scaffold SHARP to at Xist-coated X chromosomes, in a process known as X-chromosome attachment factor A (SAFA; also recruit SMRT indicating that SHARP might be inactivation (XCI) that occurs during known as HNRNPU), SMRT- and required for initiating transcriptional mammalian female development. HDAC1-associated repressor protein and activate silencing following Xist localization, Owing to technical limitations, little (SHARP; also known as SPEN or HDAC3 … possibly by recruiting the transcrip- is known about the mechanism of MSX2-interacting protein) and resulting in tional co-repressors SMRT and transcriptional silencing during XCI. lamin-B receptor (LBR) largely abol- HDAC3. Indeed, depleting SMRT McHugh et al. now describe using ished the silencing of XCI‑affected gene silencing or HDAC3 (but not other HDACs) RNA antisense purification followed genes in the male ES cells as well as in abrogated Xist-dependent gene by quantitative mass spectrometry differentiating female ES cells. These silencing. Another feature of XCI (RAP–MS) — a novel approach for three proteins are therefore required is the recruitment of the Polycomb identifying proteins that directly for Xist-mediated gene silencing. -
Reprogramming Capacity of Nanog Is Functionally Conserved in Vertebrates and Resides in a Unique Homeodomain Thorold W
Reprogramming capacity of Nanog is functionally conserved in vertebrates and resides in a unique homeodomain Thorold W. Theunissen, Yael Costa, Aliaksandra Radzisheuskaya, A., Anouk L. van Oosten, Fabrice Lavial, Bertrand Pain, L. Filipe C. Castro Castro, José C. R. Silva, J. C. R. To cite this version: Thorold W. Theunissen, Yael Costa, Aliaksandra Radzisheuskaya, A., Anouk L. van Oosten, Fabrice Lavial, et al.. Reprogramming capacity of Nanog is functionally conserved in vertebrates and resides in a unique homeodomain. Development (Cambridge, England), Company of Biologists, 2011, 138 (22), pp.4853-4865. 10.1242/dev.068775. hal-02644461 HAL Id: hal-02644461 https://hal.inrae.fr/hal-02644461 Submitted on 28 May 2020 HAL is a multi-disciplinary open access L’archive ouverte pluridisciplinaire HAL, est archive for the deposit and dissemination of sci- destinée au dépôt et à la diffusion de documents entific research documents, whether they are pub- scientifiques de niveau recherche, publiés ou non, lished or not. The documents may come from émanant des établissements d’enseignement et de teaching and research institutions in France or recherche français ou étrangers, des laboratoires abroad, or from public or private research centers. publics ou privés. Distributed under a Creative Commons Attribution - NonCommercial - ShareAlike| 4.0 International License DEVELOPMENT AND STEM CELLS RESEARCH ARTICLE 4853 Development 138, 4853-4865 (2011) doi:10.1242/dev.068775 © 2011. Published by The Company of Biologists Ltd Reprogramming capacity of Nanog is functionally conserved in vertebrates and resides in a unique homeodomain Thorold W. Theunissen1, Yael Costa1, Aliaksandra Radzisheuskaya1, Anouk L. van Oosten1, Fabrice Lavial2, Bertrand Pain3, L. -
Thoughts About SLC16A2, TSIX and XIST Gene Like Sites in the Human Genome and a Potential Role in Cellular Chromosome Counting Martina Rinčić1, Ivan Y
Rinčić et al. Molecular Cytogenetics (2016) 9:56 DOI 10.1186/s13039-016-0271-7 HYPOTHESIS Open Access Thoughts about SLC16A2, TSIX and XIST gene like sites in the human genome and a potential role in cellular chromosome counting Martina Rinčić1, Ivan Y. Iourov2,3,4 and Thomas Liehr5* Abstract Background: Chromosome counting is a process in which cells determine somehow their intrinsic chromosome number(s). The best-studied cellular mechanism that involves chromosome counting is ‘chromosome-kissing’ and X-chromosome inactivation (XCI) mechanism. It is necessary for the well-known dosage compensation between the genders in mammals to balance the number of active X-chromosomes (Xa) with regard to diploid set of autosomes. At the onset of XCI, two X-chromosomes are coming in close proximity and pair physically by a specific segment denominated X-pairing region (Xpr) that involves the SLC16A2 gene. Results: An Ensembl BLAST search for human and mouse SLC16A2/Slc16a2 homologues revealed, that highly similar sequences can be found at almost each chromosome in the corresponding genomes. Additionally, a BLAST search for SLC16A2/TSIX/XIST (genes responsible for XCI) reveled that “SLC16A2/TSIX/XIST like sequences” cover equally all chromosomes, too. With respect to this we provide following hypotheses. Hypotheses: If a single genomic region containing the SLC16A2 gene on X-chromosome is responsible for maintaining “balanced” active copy numbers, it is possible that similar sequences or gene/s have the same function on other chromosomes (autosomes). SLC16A2 like sequences on autosomes could encompass evolutionary older, but functionally active key regions for chromosome counting in early embryogenesis. -
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Review Xatzipsalti Maria et al. Congenital Hypopituitarism: Various Genes, … Horm Metab Res 2018; 00: 00–00 Congenital Hypopituitarism: Various Genes, Various Phenotypes Authors Maria Xatzipsalti1, 2, Antonis Voutetakis1, Lela Stamoyannou2, George P. Chrousos1, Christina Kanaka-Gantenbein1 Affiliations ABSTRacT 1 Division of Endocrinology, Diabetes and Metabolism, The ontogenesis and development of the pituitary gland is a First Department of Pediatrics, Medical School, National highly complex process that depends on a cascade of transcrip- and Kapodistrian University of Athens, “Aghia Sofia” tion factors and signaling molecules. Spontaneous mutations Children's Hospital, Athens, Greece and transgenic murine models have demonstrated a role for 2 First Department of Pediatrics, “Aglaia Kyriakou” many of these factors, including HESX1, PROP1, PIT1, LHX3, Children's Hospital, Athens, Greece LHX4, SOX2, SOX3, OTX2, PAX6, FGFR1, SHH, GLI2, and FGF8 in the etiology of congenital hypopituitarism. Genetic muta- Key words tions in any of these factors can lead to congenital hypopitui- pituitary, combined pituitary hormone deficiency, congenital tarism, which is characterized by the deficiency in one or more hypopituitarism, transcription factors, syndromic hypopitui- pituitary hormones. The phenotype can be highly variable, tarism, non-syndromic hypopituitarism consisting of isolated hypopituitarism or more complex disor- ders. The same phenotype can be attributed to different gene received 27.03.2018 mutations; while a given gene mutation can -
FOS Rescues Neuronal Differentiation of Sox2-Deleted Neural Stem Cells by Genome-Wide Regulation of Common SOX2 and AP1(FOS-JUN) Target Genes
cells Article FOS Rescues Neuronal Differentiation of Sox2-Deleted Neural Stem Cells by Genome-Wide Regulation of Common SOX2 and AP1(FOS-JUN) Target Genes Miriam Pagin 1,† , Mattias Pernebrink 2,3,†, Mattia Pitasi 1, Federica Malighetti 1, Chew-Yee Ngan 4, Sergio Ottolenghi 1, Giulio Pavesi 5, Claudio Cantù 2,3,* and Silvia K. Nicolis 1,* 1 Department of Biotechnology and Biosciences, University of Milano-Bicocca, Piazza della Scienza 2, 20126 Milano, Italy; [email protected] (M.P.); [email protected] (M.P.); [email protected] (F.M.); [email protected] (S.O.) 2 Wallenberg Centre for Molecular Medicine, Linköping University, SE-581 83 Linköping, Sweden; [email protected] 3 Department of Biomedical and Clinical Sciences, Division of Molecular Medicine and Virology, Faculty of Medicine and Health Sciences, Linköping University, SE-581 83 Linköping, Sweden 4 The Jackson Laboratory for Genomic Medicine, Farmington, CT 06032, USA; [email protected] 5 Department of Biosciences, University of Milano, Via Celoria 26, 20134 Milano, Italy; [email protected] * Correspondence: [email protected] (C.C.); [email protected] (S.K.N.) † Joint first authors. Abstract: The transcription factor SOX2 is important for brain development and for neural stem Citation: Pagin, M.; Pernebrink, M.; cells (NSC) maintenance. Sox2-deleted (Sox2-del) NSC from neonatal mouse brain are lost after Pitasi, M.; Malighetti, F.; Ngan, C.-Y.; few passages in culture. Two highly expressed genes, Fos and Socs3, are strongly downregulated in Ottolenghi, S.; Pavesi, G.; Cantù, C.; Sox2-del NSC; we previously showed that Fos or Socs3 overexpression by lentiviral transduction fully Nicolis, S.K. -
Figure S1. Basic Information of RNA-Seq Results. (A) Bar Plot of Reads Component for Each Sample
Figure S1. Basic information of RNA-seq results. (A) Bar plot of reads component for each sample. (B) Dot plot shows the principal component analysis (PCA) of each sample. (C) Venn diagram of DEGs for three time points, the overlap part of the circles represents common differentially expressed genes between combinations. Figure S2. Scatter plot of DEGs for each time point. The X and Y axes represent the logarithmic value of gene expression. Red represents up-regulated DEG, blue represents down-regulated DEG, and gray represents non-DEG. Table S1. Primers used for quantitative real-time PCR analysis of DEGs. Gene Primer Sequence Forward 5’-CTACGAGTGGATGGTCAAGAGC-3’ FOXO1 Reverse 5’-CCAGTTCCTTCATTCTGCACACG-3’ Forward 5’-GACGTCCGGCATCAGAGAAA-3’ IRS2 Reverse 5’-TCCACGGCTAATCGTCACAG-3’ Forward 5’-CACAACCAGGACCTCACACC-3’ IRS1 Reverse 5’-CTTGGCACGATAGAGAGCGT-3’ Forward 5’-AGGATACCACTCCCAACAGACCT-3’ IL6 Reverse 5’-CAAGTGCATCATCGTTGTTCATAC-3’ Forward 5’-TCACGTTGTACGCAGCTACC-3’ CCL5 Reverse 5’-CAGTCCTCTTACAGCCTTTGG-3’ Forward 5’-CTGTGCAGCCGCAGTGCCTACC-3’ BMP7 Reverse 5’-ATCCCTCCCCACCCCACCATCT-3’ Forward 5’-CTCTCCCCCTCGACTTCTGA-3’ BCL2 Reverse 5’-AGTCACGCGGAACACTTGAT-3’ Forward 5’-CTGTCGAACACAGTGGTACCTG-3’ FGF7 Reverse 5’-CCAACTGCCACTGTCCTGATTTC-3’ Forward 5’-GGGAGCCAAAAGGGTCATCA-3’ GAPDH Reverse 5’-CGTGGACTGTGGTCATGAGT-3’ Supplementary material: Differentially expressed genes log2(SADS-CoV_12h/ Qvalue (SADS-CoV _12h/ Gene Symbol Control_12h) Control_12h) PTGER4 -1.03693 6.79E-04 TMEM72 -3.08132 3.66E-04 IFIT2 -1.02918 2.11E-07 FRAT2 -1.09282 4.66E-05 -
Mouse Thalamic Differentiation: Gli-Dependent Pattern and Gli-Independent Prepattern
ORIGINAL RESEARCH ARTICLE published: 22 February 2012 doi: 10.3389/fnins.2012.00027 Mouse thalamic differentiation: Gli-dependent pattern and Gli-independent prepattern Roberta Haddad-Tóvolli 1, Michael Heide 1, Xunlei Zhou 1, Sandra Blaess 2 and Gonzalo Alvarez-Bolado1* 1 Department of Neuroanatomy, Institute of Anatomy and Cell Biology, University of Heidelberg, Heidelberg, Germany 2 Institute of Reconstructive Neurobiology, Life and Brain Center, University of Bonn, Bonn, Germany Edited by: Sonic hedgehog (Shh) signaling is essential for thalamic development.The Gli transcription Steffen Scholpp, Karlsruhe Institute of factors act downstream of Shh – while Gli2 is the major activator (GliA), Gli3 acts primarily Technology, Germany as a repressor (GliR). The thalamus is remarkable among dorsal structures because of its Reviewed by: Tomomi Shimogori, RIKEN Brain proximity to the mid-diencephalic organizer, a unique dorsal Shh source. This lends com- Science Institute, Japan plexity to the interactions between Shh, Gli2, and Gli3, suggesting the presence of a dorsal David J. Price, University of Gli activator which elsewhere is found only ventrally, and making the dissection of thala- Edinburgh, UK mic Gli functions particularly interesting. A current model based on mutant phenotypes in *Correspondence: telencephalon and midbrain postulates a degree of reciprocal antagonism of Shh and Gli3 Gonzalo Alvarez-Bolado, Department of Neuroanatomy, Institute of in dorsal brain regions. To approach the role of Gli factors in thalamic specification we first Anatomy and Cell Biology, University analyzed mice deficient in Gli2 or Gli3.InGli2 mutants, the thalamus is small and poorly of Heidelberg, Im Neuenheimer Feld differentiated with the exception of the medial and intralaminar nuclei which, in contrast, 307, 69120 Heidelberg, Germany.