Nuclear Receptor Coregulators in Cancer Biology Bert W
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Longitudinal Study of Leukocyte DNA Methylation and Biomarkers for Cancer Risk in Older Adults
bioRxiv preprint doi: https://doi.org/10.1101/597666; this version posted April 3, 2019. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC-ND 4.0 International license. 1 Longitudinal Study of Leukocyte DNA Methylation and 2 Biomarkers for Cancer Risk in Older Adults 3 Alexandra H. Bartlett1, Jane W Liang1, Jose Vladimir Sandoval-Sierra1, Jay H 4 Fowke 1, Eleanor M Simonsick2, Karen C Johnson1, Khyobeni Mozhui1* 5 1Department of Preventive Medicine, University of Tennessee Health Science 6 Center, Memphis, Tennessee, USA 7 2Intramural Research Program, National Institute on Aging, Baltimore Maryland, 8 USA 9 AHB: [email protected]; JWL: [email protected]; JVSS: 10 [email protected]; JHF: [email protected]; EMS: [email protected]; 11 KCJ: [email protected]; KM: [email protected] 12 *Corresponding author: Khyobeni Mozhui 13 14 15 16 17 18 1 bioRxiv preprint doi: https://doi.org/10.1101/597666; this version posted April 3, 2019. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC-ND 4.0 International license. 19 Abstract 20 Background: Changes in DNA methylation over the course of life may provide 21 an indicator of risk for cancer. We explored longitudinal changes in CpG 22 methylation from blood leukocytes, and likelihood of a future cancer diagnosis. -
PAX5 Expression in Acute Leukemias: Higher B-Lineage Specificity Than Cd79a and Selective Association with T(8;21)-Acute Myelogenous Leukemia
[CANCER RESEARCH 64, 7399–7404, October 15, 2004] PAX5 Expression in Acute Leukemias: Higher B-Lineage Specificity Than CD79a and Selective Association with t(8;21)-Acute Myelogenous Leukemia Enrico Tiacci,1 Stefano Pileri,2 Annette Orleth,1 Roberta Pacini,1 Alessia Tabarrini,1 Federica Frenguelli,1 Arcangelo Liso,3 Daniela Diverio,4 Francesco Lo-Coco,5 and Brunangelo Falini1 1Institutes of Hematology and Internal Medicine, University of Perugia, Perugia, Italy; 2Unit of Hematopathology, University of Bologne, Bologne, Italy; 3Section of Hematology, University of Foggia, Foggia, Italy; 4Department of Cellular Biotechnologies and Hematology, University La Sapienza of Rome, Rome, Italy; and 5Department of Biopathology, University Tor Vergata of Rome, Rome, Italy ABSTRACT (13, 16). PAX5 expression also occurs in the adult testis and in the mesencephalon and spinal cord during embryogenesis (17), suggesting an The transcription factor PAX5 plays a key role in the commitment of important role in the development of these tissues. hematopoietic precursors to the B-cell lineage, but its expression in acute Rearrangement of the PAX5 gene through reciprocal chromosomal leukemias has not been thoroughly investigated. Hereby, we analyzed routine biopsies from 360 acute leukemias of lymphoid (ALLs) and mye- translocations has been described in different types of B-cell malig- loid (AMLs) origin with a specific anti-PAX5 monoclonal antibody. Blasts nancies (18–23), and, more recently, PAX5 has also been shown to be from 150 B-cell ALLs showed strong PAX5 nuclear expression, paralleling targeted by aberrant hypermutation in Ͼ50% of diffuse large B-cell that of CD79a in the cytoplasm. Conversely, PAX5 was not detected in 50 lymphomas (24). -
Further Delineation of Chromosomal Consensus Regions in Primary
Leukemia (2007) 21, 2463–2469 & 2007 Nature Publishing Group All rights reserved 0887-6924/07 $30.00 www.nature.com/leu ORIGINAL ARTICLE Further delineation of chromosomal consensus regions in primary mediastinal B-cell lymphomas: an analysis of 37 tumor samples using high-resolution genomic profiling (array-CGH) S Wessendorf1,6, TFE Barth2,6, A Viardot1, A Mueller3, HA Kestler3, H Kohlhammer1, P Lichter4, M Bentz5,HDo¨hner1,PMo¨ller2 and C Schwaenen1 1Klinik fu¨r Innere Medizin III, Zentrum fu¨r Innere Medizin der Universita¨t Ulm, Ulm, Germany; 2Institut fu¨r Pathologie, Universita¨t Ulm, Ulm, Germany; 3Forschungsdozentur Bioinformatik, Universita¨t Ulm, Ulm, Germany; 4Abt. Molekulare Genetik, Deutsches Krebsforschungszentrum, Heidelberg, Germany and 5Sta¨dtisches Klinikum Karlsruhe, Karlsruhe, Germany Primary mediastinal B-cell lymphoma (PMBL) is an aggressive the expression of BSAP, BOB1, OCT2, PAX5 and PU1 was extranodal B-cell non-Hodgkin’s lymphoma with specific clin- added to the spectrum typical of PMBL features.9 ical, histopathological and genomic features. To characterize Genetically, a pattern of highly recurrent karyotype alterations further the genotype of PMBL, we analyzed 37 tumor samples and PMBL cell lines Med-B1 and Karpas1106P using array- with the hallmark of chromosomal gains of the subtelomeric based comparative genomic hybridization (matrix- or array- region of chromosome 9 supported the concept of a unique CGH) to a 2.8k genomic microarray. Due to a higher genomic disease entity that distinguishes PMBL from other B-cell non- resolution, we identified altered chromosomal regions in much Hodgkin’s lymphomas.10,11 Together with less specific gains on higher frequencies compared with standard CGH: for example, 2p15 and frequent mutations of the SOCS1 gene, a notable þ 9p24 (68%), þ 2p15 (51%), þ 7q22 (32%), þ 9q34 (32%), genomic similarity to classical Hodgkin’s lymphoma was þ 11q23 (18%), þ 12q (30%) and þ 18q21 (24%). -
Longitudinal Study of Leukocyte DNA Methylation and Biomarkers for Cancer Risk in Older Adults Alexandra H
Bartlett et al. Biomarker Research (2019) 7:10 https://doi.org/10.1186/s40364-019-0161-3 RESEARCH Open Access Longitudinal study of leukocyte DNA methylation and biomarkers for cancer risk in older adults Alexandra H. Bartlett1, Jane W. Liang1, Jose Vladimir Sandoval-Sierra1, Jay H. Fowke1, Eleanor M. Simonsick2, Karen C. Johnson1 and Khyobeni Mozhui1* Abstract Background: Changes in DNA methylation over the course of life may provide an indicator of risk for cancer. We explored longitudinal changes in CpG methylation from blood leukocytes, and likelihood of future cancer diagnosis. Methods: Peripheral blood samples were obtained at baseline and at follow-up visit from 20 participants in the Health, Aging and Body Composition prospective cohort study. Genome-wide CpG methylation was assayed using the Illumina Infinium Human MethylationEPIC (HM850K) microarray. Results: Global patterns in DNA methylation from CpG-based analyses showed extensive changes in cell composition over time in participants who developed cancer. By visit year 6, the proportion of CD8+ T-cells decreased (p-value = 0. 02), while granulocytes cell levels increased (p-value = 0.04) among participants diagnosed with cancer compared to those who remained cancer-free (cancer-free vs. cancer-present: 0.03 ± 0.02 vs. 0.003 ± 0.005 for CD8+ T-cells; 0.52 ± 0. 14 vs. 0.66 ± 0.09 for granulocytes). Epigenome-wide analysis identified three CpGs with suggestive p-values ≤10− 5 for differential methylation between cancer-free and cancer-present groups, including a CpG located in MTA3, agene linked with metastasis. At a lenient statistical threshold (p-value ≤3×10− 5), the top 10 cancer-associated CpGs included a site near RPTOR that is involved in the mTOR pathway, and the candidate tumor suppressor genes REC8, KCNQ1,andZSWIM5. -
Genomic Profiling of Adult Acute Lymphoblastic Leukemia by Single
SUPPLEMENTARY APPENDIX Genomic profiling of adult acute lymphoblastic leukemia by single nucleotide polymorphism oligonucleotide microarray and comparison to pediatric acute lymphoblastic leukemia Ryoko Okamoto,1 Seishi Ogawa,2 Daniel Nowak,1 Norihiko Kawamata,1 Tadayuki Akagi,1,3 Motohiro Kato,2 Masashi Sanada,2 Tamara Weiss,4 Claudia Haferlach,4 Martin Dugas,5 Christian Ruckert,5 Torsten Haferlach,4 and H. Phillip Koeffler1,6 1Division of Hematology and Oncology, Cedars-Sinai Medical Center, UCLA School of Medicine, Los Angeles, CA, USA; 2Cancer Genomics Project, Graduate School of Medicine, University of Tokyo, Tokyo, Japan; 3Department of Stem Cell Biology, Graduate School of Medical Science, Kanazawa University 4MLL Munich Leukemia Laboratory, Munich, Germany; 5Department of Medical Informatics and Biomathematics, University of Münster, Münster, Germany; 6Cancer Science Institute of Singapore, National University of Singapore, Singapore Citation: Okamoto R, Ogawa S, Nowak D, Kawamata N, Akagi T, Kato M, Sanada M, Weiss T, Haferlach C, Dugas M, Ruckert C, Haferlach T, and Koeffler HP. Genomic profiling of adult acute lymphoblastic leukemia by single nucleotide polymorphism oligonu- cleotide microarray and comparison to pediatric acute lymphoblastic leukemia. Haematologica 2010;95(9):1481-1488. doi:10.3324/haematol.2009.011114 Online Supplementary Data ed by PCR of genomic DNA and subsequent direct sequencing of SNP in a region of CNN-LOH in an ALL sample versus the corresponding Design and Methods matched normal sample (Online Supplementary -
A Computational Approach for Defining a Signature of Β-Cell Golgi Stress in Diabetes Mellitus
Page 1 of 781 Diabetes A Computational Approach for Defining a Signature of β-Cell Golgi Stress in Diabetes Mellitus Robert N. Bone1,6,7, Olufunmilola Oyebamiji2, Sayali Talware2, Sharmila Selvaraj2, Preethi Krishnan3,6, Farooq Syed1,6,7, Huanmei Wu2, Carmella Evans-Molina 1,3,4,5,6,7,8* Departments of 1Pediatrics, 3Medicine, 4Anatomy, Cell Biology & Physiology, 5Biochemistry & Molecular Biology, the 6Center for Diabetes & Metabolic Diseases, and the 7Herman B. Wells Center for Pediatric Research, Indiana University School of Medicine, Indianapolis, IN 46202; 2Department of BioHealth Informatics, Indiana University-Purdue University Indianapolis, Indianapolis, IN, 46202; 8Roudebush VA Medical Center, Indianapolis, IN 46202. *Corresponding Author(s): Carmella Evans-Molina, MD, PhD ([email protected]) Indiana University School of Medicine, 635 Barnhill Drive, MS 2031A, Indianapolis, IN 46202, Telephone: (317) 274-4145, Fax (317) 274-4107 Running Title: Golgi Stress Response in Diabetes Word Count: 4358 Number of Figures: 6 Keywords: Golgi apparatus stress, Islets, β cell, Type 1 diabetes, Type 2 diabetes 1 Diabetes Publish Ahead of Print, published online August 20, 2020 Diabetes Page 2 of 781 ABSTRACT The Golgi apparatus (GA) is an important site of insulin processing and granule maturation, but whether GA organelle dysfunction and GA stress are present in the diabetic β-cell has not been tested. We utilized an informatics-based approach to develop a transcriptional signature of β-cell GA stress using existing RNA sequencing and microarray datasets generated using human islets from donors with diabetes and islets where type 1(T1D) and type 2 diabetes (T2D) had been modeled ex vivo. To narrow our results to GA-specific genes, we applied a filter set of 1,030 genes accepted as GA associated. -
A PAX5-OCT4-PRDM1 Developmental Switch Specifies Human Primordial Germ Cells
A PAX5-OCT4-PRDM1 Developmental Switch Specifies Human Primordial Germ Cells Fang Fang1,2, Benjamin Angulo1,2, Ninuo Xia1,2, Meena Sukhwani3, Zhengyuan Wang4, Charles C Carey5, Aurélien Mazurie5, Jun Cui1,2, Royce Wilkinson5, Blake Wiedenheft5, Naoko Irie6, M. Azim Surani6, Kyle E Orwig3, Renee A Reijo Pera1,2 1Department of Cell Biology and Neurosciences, Montana State University, Bozeman, MT 59717, USA 2Department of Chemistry and Biochemistry, Montana State University, Bozeman, MT 59717, USA 3Department of Obstetrics, Gynecology and Reproductive Sciences, University of Pittsburgh, School of Medicine; Magee Women’s Research Institute, Pittsburgh, PA, 15213, USA 4Genomic Medicine Division, Hematology Branch, NHLBI/NIH, MD 20850, USA 5Department of Microbiology and Immunology, Montana State University, Bozeman, MT 59717, USA. 6Wellcome Trust Cancer Research UK Gurdon Institute, Tennis Court Road, University of Cambridge, Cambridge CB2 1QN, UK. Correspondence should be addressed to F.F. (e-mail: [email protected]) 1 Abstract Dysregulation of genetic pathways during human germ cell development leads to infertility. Here, we analyzed bona fide human primordial germ cells (hPGCs) to probe the developmental genetics of human germ cell specification and differentiation. We examined distribution of OCT4 occupancy in hPGCs relative to human embryonic stem cells (hESCs). We demonstrate that development, from pluripotent stem cells to germ cells, is driven by switching partners with OCT4 from SOX2 to PAX5 and PRDM1. Gain- and loss-of-function studies revealed that PAX5 encodes a critical regulator of hPGC development. Moreover, analysis of epistasis indicates that PAX5 acts upstream of OCT4 and PRDM1. The PAX5-OCT4-PRDM1 proteins form a core transcriptional network that activates germline and represses somatic programs during human germ cell differentiation. -
Benefits of Cancerplex
CancerPlexSM is a comprehensive genetic assessment of a patient’s tumor that guides oncologists towards effective treatment options. What is CancerPlex? CancerPlex is a next generation DNA sequencing test for solid SM tumors. The specific coding regions of over 400 known cancer Potential outcomes from CancerPlex genes are simultaneously determined using a small amount of Identification of variants associated with response or resis- DNA extracted from tumor samples, including formalin-fixed, tance to an FDA-approved therapy for the patient’s disease. paraffin-embedded (FFPE) tissue and cell blocks from fine-needle aspirates or effusions. This analysis is performed in a single assay, Identification of variants associated with response or resis- simplifying and streamlining the test ordering process, and eliminat- tance to a therapy associated with another clinical indication. ing time consuming serial testing. Clinically actionable information unique to each patient’s tumor is consolidated into a simple report. Identification of variants associated with a therapy(s) in CancerPlex reveals missense changes, insertions and deletions, clinical development. and previously described rearrangements of ALK, RET, and ROS. Benefits of CancerPlex: CancerPlex genes were selected because of their importance in tumor The average turn-around-time for CancerPlex is under 10 biology. Analyzing more genes increases the chance of discovering business days, dramatically shortening the waiting period for actionable findings that lead to more choices for treatment. Our initial the start of treatment. results indicate that CancerPlex analysis identifies actionable findings up to 20% more frequently than previously published studies. CancerPlex ordering is simple: KEW provides all necessary shipping materials, can facilitate tissue retrieval and return with Since knowledge of tumor biology changes rapidly, CancerPlex pathologists, and manages 3rd party payment for the test. -
Cellular and Molecular Signatures in the Disease Tissue of Early
Cellular and Molecular Signatures in the Disease Tissue of Early Rheumatoid Arthritis Stratify Clinical Response to csDMARD-Therapy and Predict Radiographic Progression Frances Humby1,* Myles Lewis1,* Nandhini Ramamoorthi2, Jason Hackney3, Michael Barnes1, Michele Bombardieri1, Francesca Setiadi2, Stephen Kelly1, Fabiola Bene1, Maria di Cicco1, Sudeh Riahi1, Vidalba Rocher-Ros1, Nora Ng1, Ilias Lazorou1, Rebecca E. Hands1, Desiree van der Heijde4, Robert Landewé5, Annette van der Helm-van Mil4, Alberto Cauli6, Iain B. McInnes7, Christopher D. Buckley8, Ernest Choy9, Peter Taylor10, Michael J. Townsend2 & Costantino Pitzalis1 1Centre for Experimental Medicine and Rheumatology, William Harvey Research Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, Charterhouse Square, London EC1M 6BQ, UK. Departments of 2Biomarker Discovery OMNI, 3Bioinformatics and Computational Biology, Genentech Research and Early Development, South San Francisco, California 94080 USA 4Department of Rheumatology, Leiden University Medical Center, The Netherlands 5Department of Clinical Immunology & Rheumatology, Amsterdam Rheumatology & Immunology Center, Amsterdam, The Netherlands 6Rheumatology Unit, Department of Medical Sciences, Policlinico of the University of Cagliari, Cagliari, Italy 7Institute of Infection, Immunity and Inflammation, University of Glasgow, Glasgow G12 8TA, UK 8Rheumatology Research Group, Institute of Inflammation and Ageing (IIA), University of Birmingham, Birmingham B15 2WB, UK 9Institute of -
Contribution of Enhancer-Driven and Master-Regulator Genes to Autoimmune Disease Revealed Using Functionally Informed SNP-To-Gene Linking Strategies Kushal K
bioRxiv preprint doi: https://doi.org/10.1101/2020.09.02.279059; this version posted March 31, 2021. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC-ND 4.0 International license. Contribution of enhancer-driven and master-regulator genes to autoimmune disease revealed using functionally informed SNP-to-gene linking strategies Kushal K. Dey1, Steven Gazal1, Bryce van de Geijn 1,3, Samuel Sungil Kim 1,4, Joseph Nasser5, Jesse M. Engreitz5, Alkes L. Price 1,2,5 1 Department of Epidemiology, Harvard T. H. Chan School of Public Health, Boston, MA, USA 2 Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA 3 Genentech, South San Francisco, CA 4 Department of Electrical Engineering and Computer Science, Massachusetts Institute of Technology, Cambridge, MA 5 Broad Institute of MIT and Harvard, Cambridge, MA, USA Abstract Gene regulation is known to play a fundamental role in human disease, but mechanisms of regulation vary greatly across genes. Here, we explore the con- tributions to disease of two types of genes: genes whose regulation is driven by enhancer regions as opposed to promoter regions (Enhancer-driven) and genes that regulate many other genes in trans (Master-regulator). We link these genes to SNPs using a comprehensive set of SNP-to-gene (S2G) strategies and apply stratified LD score regression to the resulting SNP annotations to draw three main conclusions about 11 autoimmune diseases and blood cell traits (average Ncase=13K across 6 autoimmune diseases, average N=443K across 5 blood cell traits). -
Intrinsically Disordered Meningioma-1 Stabilizes the BAF Complex to Cause AML
Article Intrinsically disordered Meningioma-1 stabilizes the BAF complex to cause AML Graphical abstract Authors Simone S. Riedel, Congcong Lu, Hongbo M. Xie, ..., Gerd A. Blobel, Benjamin A. Garcia, Kathrin M. Bernt Correspondence [email protected] In brief Meningioma-1 (MN1) translocations result in overexpression of MN1 through enhancer hijacking, or expression of an MN1 fusion protein. MN1 is an intrinsically disordered polyQ protein. MN1 overexpression is sufficient to cause malignant transformation via over- stabilization of the BAF complex at critical enhancers. Highlights d MN1 translocations in AML result in MN1 overexpression due to enhancer hijacking d MN1 interacts with the myeloid progenitor BAF complex d MN1 over-stabilizes the BAF complex at critical enhancers d Overexpression of the polyQ protein MN1 is sufficient to cause AML Riedel et al., 2021, Molecular Cell 81, 1–17 June 3, 2021 ª 2021 Elsevier Inc. https://doi.org/10.1016/j.molcel.2021.04.014 ll Please cite this article in press as: Riedel et al., Intrinsically disordered Meningioma-1 stabilizes the BAF complex to cause AML, Molecular Cell (2021), https://doi.org/10.1016/j.molcel.2021.04.014 ll Article Intrinsically disordered Meningioma-1 stabilizes the BAF complex to cause AML Simone S. Riedel,1 Congcong Lu,2 Hongbo M. Xie,3 Kevin Nestler,1 Marit W. Vermunt,4 Alexandra Lenard,1 Laura Bennett,5 Nancy A. Speck,5 Ichiro Hanamura,6 Julie A. Lessard,7 Gerd A. Blobel,4,8 Benjamin A. Garcia,2 and Kathrin M. Bernt1,8,9,* 1Division of Pediatric Oncology, Children’s Hospital -
UNIVERSITY of CALIFORNIA RIVERSIDE Investigations Into The
UNIVERSITY OF CALIFORNIA RIVERSIDE Investigations into the Role of TAF1-mediated Phosphorylation in Gene Regulation A Dissertation submitted in partial satisfaction of the requirements for the degree of Doctor of Philosophy in Cell, Molecular and Developmental Biology by Brian James Gadd December 2012 Dissertation Committee: Dr. Xuan Liu, Chairperson Dr. Frank Sauer Dr. Frances M. Sladek Copyright by Brian James Gadd 2012 The Dissertation of Brian James Gadd is approved Committee Chairperson University of California, Riverside Acknowledgments I am thankful to Dr. Liu for her patience and support over the last eight years. I am deeply indebted to my committee members, Dr. Frank Sauer and Dr. Frances Sladek for the insightful comments on my research and this dissertation. Thanks goes out to CMDB, especially Dr. Bachant, Dr. Springer and Kathy Redd for their support. Thanks to all the members of the Liu lab both past and present. A very special thanks to the members of the Sauer lab, including Silvia, Stephane, David, Matt, Stephen, Ninuo, Toby, Josh, Alice, Alex and Flora. You have made all the years here fly by and made them so enjoyable. From the Sladek lab I want to thank Eugene, John, Linh and Karthi. Special thanks go out to all the friends I’ve made over the years here. Chris, Amber, Stephane and David, thank you so much for feeding me, encouraging me and keeping me sane. Thanks to the brothers for all your encouragement and prayers. To any I haven’t mentioned by name, I promise I haven’t forgotten all you’ve done for me during my graduate years.